From db33f7727cd1dc284ee7a2a9ca3435fe3dae69d6 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Mon, 15 Apr 2024 16:22:40 +0300
Subject: [PATCH 001/239] Update "dhp-stats-update" workflow to use
 "spark"-actions, instead of "hive" ones. Note: Currently the code is set to
 only test the "Step1".

---
 .../dhp-stats-update/installProject.sh        |  18 +
 .../dhp-stats-update/runOozieWorkfow.sh       |  20 +
 .../graph/stats/oozie_app/scripts/step1.sql   |   4 +-
 .../graph/stats/oozie_app/scripts/step10.sql  |  24 +-
 .../graph/stats/oozie_app/scripts/step11.sql  |  18 +-
 .../graph/stats/oozie_app/scripts/step12.sql  |  34 +-
 .../graph/stats/oozie_app/scripts/step13.sql  |  34 +-
 .../graph/stats/oozie_app/scripts/step14.sql  |  30 +-
 .../graph/stats/oozie_app/scripts/step15.sql  |  26 +-
 .../stats/oozie_app/scripts/step15_5.sql      |  36 +-
 .../scripts/step16_1-definitions.sql          |  12 +-
 .../stats/oozie_app/scripts/step16_5.sql      |  20 +-
 .../graph/stats/oozie_app/scripts/step2.sql   |  38 +-
 .../scripts/step21-createObservatoryDB.sql    |  38 +-
 .../graph/stats/oozie_app/scripts/step3.sql   |  38 +-
 .../graph/stats/oozie_app/scripts/step4.sql   |  36 +-
 .../graph/stats/oozie_app/scripts/step5.sql   |  36 +-
 .../graph/stats/oozie_app/scripts/step6.sql   |  30 +-
 .../graph/stats/oozie_app/scripts/step7.sql   |  30 +-
 .../graph/stats/oozie_app/scripts/step8.sql   |  36 +-
 .../graph/stats/oozie_app/scripts/step9.sql   |   8 +-
 .../dhp/oa/graph/stats/oozie_app/workflow.xml | 443 +++++++++++++-----
 22 files changed, 627 insertions(+), 382 deletions(-)
 create mode 100755 dhp-workflows/dhp-stats-update/installProject.sh
 create mode 100755 dhp-workflows/dhp-stats-update/runOozieWorkfow.sh

diff --git a/dhp-workflows/dhp-stats-update/installProject.sh b/dhp-workflows/dhp-stats-update/installProject.sh
new file mode 100755
index 000000000..afd95578d
--- /dev/null
+++ b/dhp-workflows/dhp-stats-update/installProject.sh
@@ -0,0 +1,18 @@
+# Install the whole "dnet-hadoop" project.
+
+# Delete this module's previous build-files in order to avoid any conflicts.
+rm -rf target/ ||
+
+# Go to the root directory of this project.
+cd ../../
+
+# Select the build profile.
+DEFAULT_PROFILE=''  # It's the empty profile.
+NEWER_VERSIONS_PROFILE='-Pscala-2.12'
+CHOSEN_MAVEN_PROFILE=${DEFAULT_PROFILE}
+
+# Install the project.
+mvn clean install -U ${CHOSEN_MAVEN_PROFILE} -Dmaven.test.skip=true
+
+# We skip tests for all modules, since the take a big amount of time and some of them fail.
+# Any test added to this module, will be executed in the "runOozieWorkflow.sh" script.
diff --git a/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh b/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh
new file mode 100755
index 000000000..a4825a3ae
--- /dev/null
+++ b/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh
@@ -0,0 +1,20 @@
+# This script deploys and runs the oozie workflow on the cluster, defined in the "~/.dhp/application.properties" file.
+
+# Select the build profile.
+DEFAULT_PROFILE=''  # It's the empty profile.
+NEWER_VERSIONS_PROFILE='-Pscala-2.12'
+CHOSEN_MAVEN_PROFILE=${DEFAULT_PROFILE}
+
+# Build and deploy this module.
+mvn clean package -U ${CHOSEN_MAVEN_PROFILE} -Poozie-package,deploy,run \
+      -Dworkflow.source.dir=eu/dnetlib/dhp/oa/graph/stats
+
+# Show the Oozie-job-ID.
+echo -e "\n\nShowing the contents of \"extract-and-run-on-remote-host.log\":\n"
+cat ./target/extract-and-run-on-remote-host.log
+
+# Check oozie workflow status
+# oozie job -oozie http://iis-cdh5-test-m3:11000/oozie -info <workflow-ID>
+
+# Get the <job-ID> from the previous output and check the logs:
+# yarn logs -applicationId <job-ID>
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql
index 9697a1dc8..467a98872 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql
@@ -4,5 +4,5 @@
 --------------------------------------------------------------
 --------------------------------------------------------------
 
-DROP database IF EXISTS ${stats_db_name} CASCADE;
-CREATE database ${stats_db_name};
+DROP database IF EXISTS ${stats_db_name} CASCADE; /*EOS*/
+CREATE database ${stats_db_name}; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
index bbd7b3bbc..9088ce205 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
@@ -5,27 +5,27 @@
 ------------------------------------------------------------------------------------------------
 CREATE OR REPLACE VIEW ${stats_db_name}.fundref AS
 SELECT *
-FROM ${external_stats_db_name}.fundref;
+FROM ${external_stats_db_name}.fundref; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.country AS
 SELECT *
-FROM ${external_stats_db_name}.country;
+FROM ${external_stats_db_name}.country; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.countrygdp AS
 SELECT *
-FROM ${external_stats_db_name}.countrygdp;
+FROM ${external_stats_db_name}.countrygdp; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.roarmap AS
 SELECT *
-FROM ${external_stats_db_name}.roarmap;
+FROM ${external_stats_db_name}.roarmap; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.rndexpediture AS
 SELECT *
-FROM ${external_stats_db_name}.rndexpediture;
+FROM ${external_stats_db_name}.rndexpediture; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.licenses_normalized AS
 SELECT *
-FROM ${external_stats_db_name}.licenses_normalized;
+FROM ${external_stats_db_name}.licenses_normalized; /*EOS*/
 
 ------------------------------------------------------------------------------------------------
 ------------------------------------------------------------------------------------------------
@@ -33,23 +33,23 @@ FROM ${external_stats_db_name}.licenses_normalized;
 ------------------------------------------------------------------------------------------------
 ------------------------------------------------------------------------------------------------
 create or replace view ${stats_db_name}.usage_stats as
-select * from openaire_prod_usage_stats.usage_stats;
+select * from openaire_prod_usage_stats.usage_stats; /*EOS*/
 
 create or replace view ${stats_db_name}.downloads_stats as
-select * from openaire_prod_usage_stats.downloads_stats;
+select * from openaire_prod_usage_stats.downloads_stats; /*EOS*/
 
 create or replace view ${stats_db_name}.pageviews_stats as
-select * from openaire_prod_usage_stats.pageviews_stats;
+select * from openaire_prod_usage_stats.pageviews_stats; /*EOS*/
 
 create or replace view ${stats_db_name}.views_stats as
-select * from openaire_prod_usage_stats.views_stats;
+select * from openaire_prod_usage_stats.views_stats; /*EOS*/
 
 ------------------------------------------------------------------------------------------------
 ------------------------------------------------------------------------------------------------
 -- Creation date of the database
 ------------------------------------------------------------------------------------------------
 ------------------------------------------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.creation_date purge;
+DROP TABLE IF EXISTS ${stats_db_name}.creation_date purge; /*EOS*/
 
 create table ${stats_db_name}.creation_date STORED AS PARQUET as
-select date_format(current_date(), 'dd-MM-yyyy') as date;
+select date_format(current_date(), 'dd-MM-yyyy') as date; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
index 638fb0f7a..06600db19 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
@@ -10,7 +10,7 @@ SET harvested='true'
 WHERE datasource_tmp.id IN (SELECT DISTINCT d.id
                             FROM ${stats_db_name}.datasource_tmp d,
                                  ${stats_db_name}.result_datasources rd
-                            WHERE d.id = rd.datasource);
+                            WHERE d.id = rd.datasource); /*EOS*/
 
 -- Project temporary table update and final project table creation with final updates that can not be applied to ORC tables
 UPDATE ${stats_db_name}.project_tmp
@@ -19,8 +19,8 @@ WHERE project_tmp.id IN (SELECT pr.id
                          FROM ${stats_db_name}.project_results pr,
                               ${stats_db_name}.result r
                          WHERE pr.result = r.id
-                           AND r.type = 'publication');
-DROP TABLE IF EXISTS ${stats_db_name}.stored purge;
+                           AND r.type = 'publication'); /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.stored purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project stored as parquet as
 SELECT p.id,
@@ -63,7 +63,7 @@ FROM ${stats_db_name}.project_tmp p
                       AND r.type = 'publication'
                       AND datediff(to_date(r.date), to_date(pp.enddate)) > 0
                     GROUP BY pp.id) AS prr2
-                   ON prr2.id = p.id;
+                   ON prr2.id = p.id; /*EOS*/
 
 UPDATE ${stats_db_name}.publication_tmp
 SET delayed = 'yes'
@@ -73,7 +73,7 @@ WHERE publication_tmp.id IN (SELECT distinct r.id
                                   ${stats_db_name}.project_tmp p
                              WHERE r.id = pr.result
                                AND pr.id = p.id
-                               AND to_date(r.date) - to_date(p.enddate) > 0);
+                               AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
 
 UPDATE ${stats_db_name}.dataset_tmp
 SET delayed = 'yes'
@@ -83,7 +83,7 @@ WHERE dataset_tmp.id IN (SELECT distinct r.id
                               ${stats_db_name}.project_tmp p
                          WHERE r.id = pr.result
                            AND pr.id = p.id
-                           AND to_date(r.date) - to_date(p.enddate) > 0);
+                           AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
 
 UPDATE ${stats_db_name}.software_tmp
 SET delayed = 'yes'
@@ -93,7 +93,7 @@ WHERE software_tmp.id IN (SELECT distinct r.id
                                ${stats_db_name}.project_tmp p
                           WHERE r.id = pr.result
                             AND pr.id = p.id
-                            AND to_date(r.date) - to_date(p.enddate) > 0);
+                            AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
 
 UPDATE ${stats_db_name}.otherresearchproduct_tmp
 SET delayed = 'yes'
@@ -103,7 +103,7 @@ WHERE otherresearchproduct_tmp.id IN (SELECT distinct r.id
                                            ${stats_db_name}.project_tmp p
                                       WHERE r.id = pr.result
                                         AND pr.id = p.id
-                                        AND to_date(r.date) - to_date(p.enddate) > 0);
+                                        AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.project_results_publication AS
 SELECT result_projects.id          AS result,
@@ -116,4 +116,4 @@ FROM ${stats_db_name}.result_projects,
      ${stats_db_name}.project
 WHERE result_projects.id = result.id
   AND result.type = 'publication'
-  AND project.id = result_projects.project;
\ No newline at end of file
+  AND project.id = result_projects.project; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql
index 0a1904de7..ff95524be 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql
@@ -1,42 +1,42 @@
 ------------------------------------------------------------------------------------------------------
 -- Creating parquet tables from the updated temporary tables and removing unnecessary temporary tables
 ------------------------------------------------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.datasource purge;
+DROP TABLE IF EXISTS ${stats_db_name}.datasource purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource stored AS parquet AS
 SELECT *
-FROM ${stats_db_name}.datasource_tmp;
+FROM ${stats_db_name}.datasource_tmp; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication stored AS parquet AS
 SELECT *
-FROM ${stats_db_name}.publication_tmp;
+FROM ${stats_db_name}.publication_tmp; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset stored AS parquet AS
 SELECT *
-FROM ${stats_db_name}.dataset_tmp;
+FROM ${stats_db_name}.dataset_tmp; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software stored AS parquet AS
 SELECT *
-FROM ${stats_db_name}.software_tmp;
+FROM ${stats_db_name}.software_tmp; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct stored AS parquet AS
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_tmp;
+FROM ${stats_db_name}.otherresearchproduct_tmp; /*EOS*/
 
-DROP TABLE ${stats_db_name}.project_tmp;
-DROP TABLE ${stats_db_name}.datasource_tmp;
-DROP TABLE ${stats_db_name}.publication_tmp;
-DROP TABLE ${stats_db_name}.dataset_tmp;
-DROP TABLE ${stats_db_name}.software_tmp;
-DROP TABLE ${stats_db_name}.otherresearchproduct_tmp;
+DROP TABLE ${stats_db_name}.project_tmp; /*EOS*/
+DROP TABLE ${stats_db_name}.datasource_tmp; /*EOS*/
+DROP TABLE ${stats_db_name}.publication_tmp; /*EOS*/
+DROP TABLE ${stats_db_name}.dataset_tmp; /*EOS*/
+DROP TABLE ${stats_db_name}.software_tmp; /*EOS*/
+DROP TABLE ${stats_db_name}.otherresearchproduct_tmp; /*EOS*/
 
 ----------------------------------------------
 -- Re-creating views from final parquet tables
@@ -54,4 +54,4 @@ SELECT *, bestlicence AS access_mode
 FROM ${stats_db_name}.dataset
 UNION ALL
 SELECT *, bestlicence AS access_mode
-FROM ${stats_db_name}.otherresearchproduct;
+FROM ${stats_db_name}.otherresearchproduct; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
index 8c1dbdc4d..68a46ded3 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
@@ -5,7 +5,7 @@
 -- Sources related tables/views
 ------------------------------------------------------
 ------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.publication_sources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources STORED AS PARQUET as
 SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
@@ -16,9 +16,9 @@ LEFT OUTER JOIN
 (
     SELECT substr(d.id, 4) id 
     from ${openaire_db_name}.datasource d 
-    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_sources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources STORED AS PARQUET as
 SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
@@ -29,9 +29,9 @@ LEFT OUTER JOIN
 (
     SELECT substr(d.id, 4) id 
     from ${openaire_db_name}.datasource d 
-    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; /*EOS*/
     
-DROP TABLE IF EXISTS ${stats_db_name}.software_sources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources STORED AS PARQUET as
 SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
@@ -42,9 +42,9 @@ LEFT OUTER JOIN
 (
     SELECT substr(d.id, 4) id 
     from ${openaire_db_name}.datasource d 
-    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; /*EOS*/
     
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_sources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources STORED AS PARQUET as
 SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
@@ -55,7 +55,7 @@ LEFT OUTER JOIN
 (
     SELECT substr(d.id, 4) id 
     from ${openaire_db_name}.datasource d 
-    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on p.datasource = d.id; /*EOS*/
 
 CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_sources AS
 SELECT * FROM ${stats_db_name}.publication_sources
@@ -64,9 +64,9 @@ SELECT * FROM ${stats_db_name}.dataset_sources
 UNION ALL
 SELECT * FROM ${stats_db_name}.software_sources
 UNION ALL
-SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
+SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_orcid purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_orcid purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_orcid STORED AS PARQUET as
 select distinct res.id, upper(regexp_replace(res.orcid, 'http://orcid.org/' ,'')) as orcid
@@ -76,9 +76,9 @@ from (
     LATERAL VIEW explode(author) a as auth
     LATERAL VIEW explode(auth.pid) ap as auth_pid
     LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type
-    WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res;
+    WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_result purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_result purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_result stored as parquet as
 select substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype
@@ -91,9 +91,9 @@ where reltype='resultResult'
     and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE
     and r1.resulttype.classname != 'other'
     and r2.resulttype.classname != 'other'
-    and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE;
+    and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_citations_oc purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_citations_oc purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_citations_oc stored as parquet as
 select substr(target, 4) as id, count(distinct substr(source, 4)) as citations
@@ -108,9 +108,9 @@ where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:cr
     and r1.resulttype.classname != 'other'
     and r2.resulttype.classname != 'other'
     and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE
-group by substr(target, 4);
+group by substr(target, 4); /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_references_oc purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_references_oc purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_references_oc stored as parquet as
 select substr(source, 4) as id, count(distinct substr(target, 4)) as references
@@ -125,4 +125,4 @@ where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:cr
     and r1.resulttype.classname != 'other'
     and r2.resulttype.classname != 'other'
     and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE
-group by substr(source, 4);
\ No newline at end of file
+group by substr(source, 4); /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
index f50c13521..f61c70221 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
@@ -5,33 +5,33 @@
 -- Licences related tables/views
 ------------------------------------------------------
 ------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.publication_licenses purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, licenses.value as type
 from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses
-where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
+where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_licenses purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, licenses.value as type 
 from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses
-where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
+where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_licenses purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, licenses.value as type 
 from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses
-where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
+where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_licenses purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, licenses.value as type 
 from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses
-where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE;
+where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
 CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_licenses AS
 SELECT * FROM ${stats_db_name}.publication_licenses
@@ -40,15 +40,15 @@ SELECT * FROM ${stats_db_name}.dataset_licenses
 UNION ALL
 SELECT * FROM ${stats_db_name}.software_licenses
 UNION ALL
-SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses;
+SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.organization_pids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.organization_pids purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids STORED AS PARQUET AS
 select substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid 
-from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid;
+from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.organization_sources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.organization_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources STORED AS PARQUET as
 SELECT o.id, case when d.id is null then 'other' else o.datasource end as datasource 
@@ -58,10 +58,10 @@ FROM (
     LEFT OUTER JOIN (
         SELECT substr(d.id, 4) id 
         from ${openaire_db_name}.datasource d 
-        WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id;
+        WHERE d.datainfo.deletedbyinference=false and d.datainfo.invisible = FALSE) d on o.datasource = d.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_accessroute purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_accessroute purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_accessroute STORED AS PARQUET as
 select distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result
-lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute;
+lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
index ce6b6cc2f..7c618fd0f 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
@@ -6,7 +6,7 @@
 ------------------------------------------------------
 ------------------------------------------------------
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_refereed purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_refereed purge; /*EOS*/
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_refereed STORED AS PARQUET as
 with peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
@@ -22,9 +22,9 @@ from (
     union all
     select non_peer_reviewed.* from non_peer_reviewed
     left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
-    where peer_reviewed.id is null) pr;
+    where peer_reviewed.id is null) pr; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_refereed purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_refereed purge; /*EOS*/
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_refereed STORED AS PARQUET as
 with peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
@@ -40,9 +40,9 @@ from (
     union all
     select non_peer_reviewed.* from non_peer_reviewed
     left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
-    where peer_reviewed.id is null) pr;
+    where peer_reviewed.id is null) pr; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_refereed purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_refereed purge; /*EOS*/
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_refereed STORED AS PARQUET as
 with peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
@@ -58,9 +58,9 @@ from (
     union all
     select non_peer_reviewed.* from non_peer_reviewed
     left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
-    where peer_reviewed.id is null) pr;
+    where peer_reviewed.id is null) pr; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_refereed purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_refereed purge; /*EOS*/
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_refereed STORED AS PARQUET as
 with peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
@@ -76,7 +76,7 @@ from (
     union all
     select non_peer_reviewed.* from non_peer_reviewed
     left join peer_reviewed on peer_reviewed.id=non_peer_reviewed.id
-    where peer_reviewed.id is null) pr;
+    where peer_reviewed.id is null) pr; /*EOS*/
 
 CREATE VIEW IF NOT EXISTS ${stats_db_name}.result_refereed as
 select * from ${stats_db_name}.publication_refereed
@@ -85,17 +85,17 @@ select * from ${stats_db_name}.dataset_refereed
 union all
 select * from ${stats_db_name}.software_refereed
 union all
-select * from ${stats_db_name}.otherresearchproduct_refereed;
+select * from ${stats_db_name}.otherresearchproduct_refereed; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.indi_impact_measures purge;
+DROP TABLE IF EXISTS ${stats_db_name}.indi_impact_measures purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_impact_measures STORED AS PARQUET as
 select substr(id, 4) as id, measures_ids.id impactmetric, cast(measures_ids.unit.value[0] as double) score,
 cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] impact_class
 from ${openaire_db_name}.result lateral view explode(measures) measures as measures_ids
-where measures_ids.id!='views' and measures_ids.id!='downloads';
+where measures_ids.id!='views' and measures_ids.id!='downloads'; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_apc_affiliations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_apc_affiliations purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_apc_affiliations STORED AS PARQUET as
 select distinct substr(rel.target,4) id, substr(rel.source,4) organization, o.legalname.value name,
@@ -104,4 +104,4 @@ rel.properties[1].value apc_currency
 from ${openaire_db_name}.relation rel
 join ${openaire_db_name}.organization o on o.id=rel.source
 join ${openaire_db_name}.result r on r.id=rel.target
-where rel.subreltype = 'affiliation' and rel.datainfo.deletedbyinference = false and size(rel.properties)>0;
\ No newline at end of file
+where rel.subreltype = 'affiliation' and rel.datainfo.deletedbyinference = false and size(rel.properties)>0; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
index 6ed686a05..54743e046 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
@@ -1,25 +1,25 @@
 -------------------------------------------
 --- Extra tables, mostly used by indicators
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_projectcount purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_projectcount purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_projectcount STORED AS PARQUET as
 select r.id, count(distinct p.id) as count
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
 left outer join ${stats_db_name}.project p on p.id=rp.project
-group by r.id;
+group by r.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_fundercount purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_fundercount purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_fundercount STORED AS PARQUET as
 select r.id, count(distinct p.funder) as count
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
 left outer join ${stats_db_name}.project p on p.id=rp.project
-group by r.id;
+group by r.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_resultcount purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_resultcount purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.project_resultcount STORED AS PARQUET as
 with rcount as (
@@ -33,17 +33,17 @@ select rcount.pid, sum(case when rcount.type='publication' then rcount.count els
     sum(case when rcount.type='software' then rcount.count else 0 end) as software,
     sum(case when rcount.type='other' then rcount.count else 0 end) as other
 from rcount
-group by rcount.pid;
+group by rcount.pid; /*EOS*/
 
-create or replace view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture;
-create or replace view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure;
-create or replace view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents;
-create or replace view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
-create or replace view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
-create or replace view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
-create or replace view ${stats_db_name}.graduatedoctorates as select * from stats_ext.graduatedoctorates;
+create or replace view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture; /*EOS*/
+create or replace view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure; /*EOS*/
+create or replace view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents; /*EOS*/
+create or replace view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers; /*EOS*/
+create or replace view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft; /*EOS*/
+create or replace view ${stats_db_name}.hrrst as select * from stats_ext.hrrst; /*EOS*/
+create or replace view ${stats_db_name}.graduatedoctorates as select * from stats_ext.graduatedoctorates; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_instance purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_instance purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_instance stored as parquet as
 select distinct r.*
@@ -51,9 +51,9 @@ from (
          select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom,
                 substr(inst.hostedby.key, 4) as hostedby, inst.dateofacceptance.value as dateofacceptance, inst.license.value as license, p.qualifier.classname as pidtype, p.value as pid
          from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst lateral view outer explode(inst.pid) pids as p) r
-join ${stats_db_name}.result res on res.id=r.id;
+join ${stats_db_name}.result res on res.id=r.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_apc purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_apc purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_apc STORED AS PARQUET as
 select distinct r.id, r.amount, r.currency
@@ -61,6 +61,6 @@ from (
          select substr(r.id, 4) as id, cast(inst.processingchargeamount.value as float) as amount, inst.processingchargecurrency.value as currency
          from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst) r
 join ${stats_db_name}.result res on res.id=r.id
-where r.amount is not null;
+where r.amount is not null; /*EOS*/
 
-create or replace view ${stats_db_name}.issn_gold_oa_dataset as select * from ${external_stats_db_name}.issn_gold_oa_dataset;
\ No newline at end of file
+create or replace view ${stats_db_name}.issn_gold_oa_dataset as select * from ${external_stats_db_name}.issn_gold_oa_dataset; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
index b55af13d4..399381b12 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
@@ -3,26 +3,26 @@
 ----------------------------------------------------
 
 -- Peer reviewed:
-drop table if exists ${stats_db_name}.result_peerreviewed purge;
+drop table if exists ${stats_db_name}.result_peerreviewed purge; /*EOS*/
 
 create table IF NOT EXISTS ${stats_db_name}.result_peerreviewed STORED AS PARQUET as
 select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id
-left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id;
+left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; /*EOS*/
 
 -- Green OA:
-drop table if exists ${stats_db_name}.result_greenoa purge;
+drop table if exists ${stats_db_name}.result_greenoa purge; /*EOS*/
 
 create table IF NOT EXISTS ${stats_db_name}.result_greenoa STORED AS PARQUET as
 select r.id, case when green.green_oa=1 then true else false end as green
 from ${stats_db_name}.result r
-left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id;
+left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; /*EOS*/
 
 -- GOLD OA:
-drop table if exists ${stats_db_name}.result_gold purge;
+drop table if exists ${stats_db_name}.result_gold purge; /*EOS*/
 
 create table IF NOT EXISTS ${stats_db_name}.result_gold STORED AS PARQUET as
 select r.id, case when gold.is_gold=1 then true else false end as gold
 from ${stats_db_name}.result r
-         left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id;
\ No newline at end of file
+         left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
index 7faa91697..1b838ca1b 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
@@ -1,6 +1,6 @@
 -- replace the creation of the result view to include the boolean fields from the previous tables (green, gold,
 -- peer reviewed)
-drop table if exists ${stats_db_name}.result_tmp;
+drop table if exists ${stats_db_name}.result_tmp; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.result_tmp (
     id STRING,
@@ -20,37 +20,37 @@ CREATE TABLE ${stats_db_name}.result_tmp (
     peer_reviewed BOOLEAN,
     green BOOLEAN,
     gold BOOLEAN)
-clustered by (id) into 100 buckets stored as orc tblproperties('transactional'='true');
+clustered by (id) into 100 buckets stored as orc tblproperties('transactional'='true'); /*EOS*/
 
 insert into ${stats_db_name}.result_tmp
 select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
 FROM ${stats_db_name}.publication r
 LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
 LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id;
+LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
 
 insert into ${stats_db_name}.result_tmp
 select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
 FROM ${stats_db_name}.dataset r
 LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
 LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id;
+LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
 
 insert into ${stats_db_name}.result_tmp
 select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
 FROM ${stats_db_name}.software r
 LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
 LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id;
+LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
 
 insert into ${stats_db_name}.result_tmp
 select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
 FROM ${stats_db_name}.otherresearchproduct r
 LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
 LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id;
+LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
 
-drop table if exists ${stats_db_name}.result;
-drop view if exists ${stats_db_name}.result;
-create table ${stats_db_name}.result stored as parquet as select * from ${stats_db_name}.result_tmp;
-drop table ${stats_db_name}.result_tmp;
\ No newline at end of file
+drop table if exists ${stats_db_name}.result; /*EOS*/
+drop view if exists ${stats_db_name}.result; /*EOS*/
+create table ${stats_db_name}.result stored as parquet as select * from ${stats_db_name}.result_tmp; /*EOS*/
+drop table ${stats_db_name}.result_tmp; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
index 8e56f98fc..4aa90b1a2 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
@@ -5,7 +5,7 @@
 --------------------------------------------------------------
 
 -- Publication temporary table
-DROP TABLE IF EXISTS ${stats_db_name}.publication_tmp purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_tmp purge; /*EOS*/
 CREATE TABLE ${stats_db_name}.publication_tmp
 (
     id               STRING,
@@ -22,7 +22,7 @@ CREATE TABLE ${stats_db_name}.publication_tmp
     abstract         BOOLEAN,
     type             STRING
 )
-    clustered by (id) into 100 buckets stored as orc tblproperties ('transactional' = 'true');
+    clustered by (id) into 100 buckets stored as orc tblproperties ('transactional' = 'true'); /*EOS*/
 
 INSERT INTO ${stats_db_name}.publication_tmp
 SELECT substr(p.id, 4)                                            as id,
@@ -39,17 +39,17 @@ SELECT substr(p.id, 4)                                            as id,
        case when size(p.description) > 0 then true else false end as abstract,
        'publication'                                              as type
 from ${openaire_db_name}.publication p
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_classifications purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_classifications STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, instancetype.classname as type
 from ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.instance.instancetype) instances as instancetype
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_concepts purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_concepts STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, case
@@ -58,9 +58,9 @@ SELECT substr(p.id, 4) as id, case
     when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
 from ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.context) contexts as context
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_datasources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_datasources STORED AS PARQUET as
 SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
@@ -71,44 +71,44 @@ FROM (
          LEFT OUTER JOIN (
     SELECT substr(d.id, 4) id
     from ${openaire_db_name}.datasource d
-    WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_languages purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_languages STORED AS PARQUET AS
 select substr(p.id, 4) as id, p.language.classname as language
 FROM ${openaire_db_name}.publication p
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_oids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_oids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.originalid) oids AS ids
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_pids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_pids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid
 FROM ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.pid) pids AS ppid
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_topics purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_topics STORED AS PARQUET as
 select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic
 FROM ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.subject) subjects AS subject
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.publication_citations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.publication_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_citations STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.publication p
          lateral view explode(p.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
-  and p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
\ No newline at end of file
+  and p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
index 66620ac38..adcf23b7a 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
@@ -5,7 +5,7 @@ from ${stats_db_name}.result r
     select rl.id, sum(case when rl.type like 'CC%' then 1 else 0 end) as count
     from ${stats_db_name}.result_licenses rl
     group by rl.id
-) rln on rln.id=r.id;
+) rln on rln.id=r.id; /*EOS*/
 
 
 create table ${observatory_db_name}.result_affiliated_country stored as parquet as
@@ -35,7 +35,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name; /*EOS*/
 
 
 create table ${observatory_db_name}.result_affiliated_year stored as parquet as
@@ -65,7 +65,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year; /*EOS*/
 
 
 create table ${observatory_db_name}.result_affiliated_year_country stored as parquet as
@@ -95,7 +95,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name; /*EOS*/
 
 
 create table ${observatory_db_name}.result_affiliated_datasource stored as parquet as
@@ -127,7 +127,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_datasource_country stored as parquet as
 select
@@ -158,7 +158,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_organization stored as parquet as
 select
@@ -187,7 +187,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_organization_country stored as parquet as
 select
@@ -216,7 +216,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_funder stored as parquet as
 select
@@ -247,7 +247,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_funder_country stored as parquet as
 select
@@ -278,7 +278,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_country stored as parquet as
 select
@@ -309,7 +309,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_year stored as parquet as
 select
@@ -340,7 +340,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year; /*EOS*/
 
 
 create table ${observatory_db_name}.result_deposited_year_country stored as parquet as
@@ -372,7 +372,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_datasource stored as parquet as
 select
@@ -403,7 +403,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_datasource_country stored as parquet as
 select
@@ -434,7 +434,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_organization stored as parquet as
 select
@@ -465,7 +465,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_organization_country stored as parquet as
 select
@@ -496,7 +496,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_funder stored as parquet as
 select
@@ -529,7 +529,7 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_funder_country stored as parquet as
 select
@@ -562,4 +562,4 @@ from ${stats_db_name}.result r
          left outer join ${stats_db_name}.result_fundercount rfc on rfc.id=r.id
 group by r.green, r.gold, case when rl.type is not null then true else false end, case when pids.pid is not null then true else false end,
          case when r.access_mode in ('Open Access', 'Open Source') then true else false end, r.peer_reviewed, r.type, abstract,
-         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name;
+         cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
index 0384de4ec..1ff4beadb 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
@@ -5,7 +5,7 @@
 ------------------------------------------------------
 
 -- Dataset temporary table supporting updates
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_tmp purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_tmp purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_tmp
 (
@@ -23,7 +23,7 @@ CREATE TABLE ${stats_db_name}.dataset_tmp
     abstract         BOOLEAN,
     type             STRING
 )
-    clustered by (id) into 100 buckets stored AS orc tblproperties ('transactional' = 'true');
+    clustered by (id) into 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
 
 INSERT INTO ${stats_db_name}.dataset_tmp
 SELECT substr(d.id, 4)                                            AS id,
@@ -40,26 +40,26 @@ SELECT substr(d.id, 4)                                            AS id,
        CASE WHEN SIZE(d.description) > 0 THEN TRUE ELSE FALSE end AS abstract,
        'dataset'                                                  AS type
 FROM ${openaire_db_name}.dataset d
-WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false;
+WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_citations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_citations STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.dataset d
          LATERAL VIEW explode(d.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
-  and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false;
+  and d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_classifications purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_classifications STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_concepts purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_concepts STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, case
@@ -68,9 +68,9 @@ SELECT substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
 from ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.context) contexts as context
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_datasources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_datasources STORED AS PARQUET AS
 SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
@@ -82,35 +82,35 @@ FROM (
          LEFT OUTER JOIN (
     SELECT substr(d.id, 4) id
     FROM ${openaire_db_name}.datasource d
-    WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_languages purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_languages STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, p.language.classname AS language
 FROM ${openaire_db_name}.dataset p
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_oids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_oids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.originalid) oids AS ids
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_pids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_pids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.pid) pids AS ppid
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_topics purge;
+DROP TABLE IF EXISTS ${stats_db_name}.dataset_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_topics STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.subject) subjects AS subject
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
\ No newline at end of file
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
index d8f4d65e4..426d53773 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
@@ -5,7 +5,7 @@
 --------------------------------------------------------
 
 -- Software temporary table supporting updates
-DROP TABLE IF EXISTS ${stats_db_name}.software_tmp purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_tmp purge; /*EOS*/
 CREATE TABLE ${stats_db_name}.software_tmp
 (
     id               STRING,
@@ -22,7 +22,7 @@ CREATE TABLE ${stats_db_name}.software_tmp
     abstract         BOOLEAN,
     type             STRING
 )
-    clustered by (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true');
+    clustered by (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
 
 INSERT INTO ${stats_db_name}.software_tmp
 SELECT substr(s.id, 4)                                            as id,
@@ -39,24 +39,24 @@ SELECT substr(s.id, 4)                                            as id,
        CASE WHEN SIZE(s.description) > 0 THEN TRUE ELSE FALSE END AS abstract,
        'software'                                                 as type
 from ${openaire_db_name}.software s
-where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false;
+where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_citations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_citations STORED AS PARQUET AS
 SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.software s
          LATERAL VIEW explode(s.extrainfo) citations as citation
 where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
-  and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false;
+  and s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_classifications purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_classifications STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_concepts STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, case
@@ -65,9 +65,9 @@ SELECT substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.context) contexts AS context
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_datasources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_datasources STORED AS PARQUET AS
 SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource
@@ -79,35 +79,35 @@ FROM (
          LEFT OUTER JOIN (
     SELECT substr(d.id, 4) id
     FROM ${openaire_db_name}.datasource d
-    WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id;
+    WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d ON p.datasource = d.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_languages purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_languages STORED AS PARQUET AS
 select substr(p.id, 4) AS id, p.language.classname AS language
 FROM ${openaire_db_name}.software p
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_oids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_oids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.originalid) oids AS ids
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_pids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_pids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.pid) pids AS ppid
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.software_topics purge;
+DROP TABLE IF EXISTS ${stats_db_name}.software_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_topics STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.subject) subjects AS subject
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
\ No newline at end of file
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
index fae0fbb63..6b5adff9d 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
@@ -5,7 +5,7 @@
 --------------------------------------------------------------------------------
 
 -- Otherresearchproduct temporary table supporting updates
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_tmp purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_tmp purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp
 (
@@ -22,7 +22,7 @@ CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp
     source           STRING,
     abstract         BOOLEAN,
     type             STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true');
+) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
 
 INSERT INTO ${stats_db_name}.otherresearchproduct_tmp
 SELECT substr(o.id, 4)                                            AS id,
@@ -39,23 +39,23 @@ SELECT substr(o.id, 4)                                            AS id,
        CASE WHEN SIZE(o.description) > 0 THEN TRUE ELSE FALSE END AS abstract,
        'other'                                                    AS type
 FROM ${openaire_db_name}.otherresearchproduct o
-WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false;
+WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; /*EOS*/
 
 -- Otherresearchproduct_citations
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_citations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_citations STORED AS PARQUET AS
 SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
-  and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false;
+  and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_concepts purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, case
@@ -63,9 +63,9 @@ SELECT substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
                                   when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.context) contexts AS context
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_datasources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources STORED AS PARQUET AS
 SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
@@ -74,32 +74,32 @@ FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) A
       where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p
          LEFT OUTER JOIN(SELECT substr(d.id, 4) id
                          from ${openaire_db_name}.datasource d
-                         WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id;
+                         WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_languages purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_languages STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, p.language.classname AS language
 FROM ${openaire_db_name}.otherresearchproduct p
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_oids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_oids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_pids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_pids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_topics purge;
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_topics STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
\ No newline at end of file
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
index 165f77946..75ec7d69c 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
@@ -3,38 +3,38 @@
 -- Project table/view and Project related tables/views
 ------------------------------------------------------
 ------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.project_oids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_oids STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids
-where p.datainfo.deletedbyinference=false  and p.datainfo.invisible=false;
+where p.datainfo.deletedbyinference=false  and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_organizations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_organizations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS
 SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization
 from ${openaire_db_name}.relation r
 WHERE r.reltype = 'projectOrganization' and r.source like '40|%'
-  and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
+  and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_results purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_results purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS
 SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance
 FROM ${openaire_db_name}.relation r
 WHERE r.reltype = 'resultProject' and r.target like '40|%'
-  and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
+  and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_classification purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_classification purge; /*EOS*/
 
 create table ${stats_db_name}.project_classification STORED AS PARQUET as
 select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3
 from ${openaire_db_name}.project p
     lateral view explode(p.h2020classification) classifs as class
-where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false and class.h2020programme is not null;
+where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false and class.h2020programme is not null; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_tmp purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_tmp purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_tmp
 (
@@ -61,7 +61,7 @@ CREATE TABLE ${stats_db_name}.project_tmp
     totalcost       FLOAT,
     fundedamount    FLOAT,
     currency        STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true');
+) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
 
 INSERT INTO ${stats_db_name}.project_tmp
 SELECT substr(p.id, 4)                                                 AS id,
@@ -88,18 +88,18 @@ SELECT substr(p.id, 4)                                                 AS id,
        p.fundedamount                                                  AS fundedamount,
        p.currency.value                                                AS currency
 FROM ${openaire_db_name}.project p
-WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.funder purge;
+DROP TABLE IF EXISTS ${stats_db_name}.funder purge; /*EOS*/
 
 create table ${stats_db_name}.funder STORED AS PARQUET as
 select distinct xpath_string(fund, '//funder/id')        as id,
                 xpath_string(fund, '//funder/name')      as name,
                 xpath_string(fund, '//funder/shortname') as shortname,
                 xpath_string(fundingtree[0].value, '//funder/jurisdiction') as country
-from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund;
+from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fundingtree as fund; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_organization_contribution purge;
+DROP TABLE IF EXISTS ${stats_db_name}.project_organization_contribution purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_organization_contribution STORED AS PARQUET AS
 SELECT distinct substr(r.source, 4) AS project, substr(r.target, 4) AS organization,
@@ -107,4 +107,4 @@ properties[0].value contribution, properties[1].value currency
 from ${openaire_db_name}.relation r
 LATERAL VIEW explode (r.properties) properties
 where properties[0].key='contribution' and r.reltype = 'projectOrganization' and r.source like '40|%'
-and properties[0].value>0.0 and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
\ No newline at end of file
+and properties[0].value>0.0 and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index eb16a161e..2cc7c13c4 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -16,7 +16,7 @@ SELECT *, bestlicence AS access_mode
 FROM ${stats_db_name}.dataset_tmp
 UNION ALL
 SELECT *, bestlicence AS access_mode
-FROM ${stats_db_name}.otherresearchproduct_tmp;
+FROM ${stats_db_name}.otherresearchproduct_tmp; /*EOS*/
 
 -- Views on final tables
 CREATE OR REPLACE VIEW ${stats_db_name}.result_datasources AS
@@ -30,7 +30,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_datasources
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_datasources;
+FROM ${stats_db_name}.otherresearchproduct_datasources; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_citations AS
 SELECT *
@@ -43,7 +43,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_citations
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_citations;
+FROM ${stats_db_name}.otherresearchproduct_citations; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_classifications AS
 SELECT *
@@ -56,7 +56,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_classifications
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_classifications;
+FROM ${stats_db_name}.otherresearchproduct_classifications; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_concepts AS
 SELECT *
@@ -69,7 +69,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_concepts
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_concepts;
+FROM ${stats_db_name}.otherresearchproduct_concepts; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_languages AS
 SELECT *
@@ -82,7 +82,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_languages
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_languages;
+FROM ${stats_db_name}.otherresearchproduct_languages; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_oids AS
 SELECT *
@@ -95,7 +95,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_oids
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_oids;
+FROM ${stats_db_name}.otherresearchproduct_oids; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_pids AS
 SELECT *
@@ -108,7 +108,7 @@ SELECT *
 FROM ${stats_db_name}.dataset_pids
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_pids;
+FROM ${stats_db_name}.otherresearchproduct_pids; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.result_topics AS
 SELECT *
@@ -121,9 +121,9 @@ SELECT *
 FROM ${stats_db_name}.dataset_topics
 UNION ALL
 SELECT *
-FROM ${stats_db_name}.otherresearchproduct_topics;
+FROM ${stats_db_name}.otherresearchproduct_topics; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_fos purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_fos purge; /*EOS*/
 
 create table ${stats_db_name}.result_fos stored as parquet as
 with
@@ -133,22 +133,22 @@ with
 select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3
 from lvl1
  join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)
- join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4);
+ join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4); /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS
 SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
 FROM ${openaire_db_name}.relation r
 WHERE r.reltype = 'resultOrganization'
   and r.target like '50|%'
-  and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false;
+  and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.result_projects purge;
+DROP TABLE IF EXISTS ${stats_db_name}.result_projects purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS
 select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
 FROM ${stats_db_name}.result r
          JOIN ${stats_db_name}.project_results pr ON r.id = pr.result
-         JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id;
+         JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 07204db0c..3f40dbb21 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -5,7 +5,7 @@
 -- Datasource table/view and Datasource related tables/views
 ------------------------------------------------------------
 ------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp purge;
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_tmp
 (
@@ -22,7 +22,7 @@ CREATE TABLE ${stats_db_name}.datasource_tmp
     `compatibility`    STRING,
     issn_printed       STRING,
     issn_online        STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true');
+) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
 
 -- Insert statement that takes into account the piwik_id of the openAIRE graph
 INSERT INTO ${stats_db_name}.datasource_tmp
@@ -46,14 +46,14 @@ FROM ${openaire_db_name}.datasource d1
                LATERAL VIEW EXPLODE(originalid) temp AS originalidd
       WHERE originalidd like "piwik:%") AS d2
      ON d1.id = d2.id
-WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false;
+WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; /*EOS*/
 
 -- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table.
 -- Creating a temporary dual table that will be removed after the following insert
 
-CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1));
+CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1)); /*EOS*/
 
-INSERT INTO ${stats_db_name}.dual VALUES ('X');
+INSERT INTO ${stats_db_name}.dual VALUES ('X'); /*EOS*/
 
 INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`,
                                              `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`, `issn_printed`, `issn_online`)
@@ -71,42 +71,42 @@ SELECT 'other',
        null,
        null
 FROM ${stats_db_name}.dual
-WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository');
-DROP TABLE ${stats_db_name}.dual;
+WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); /*EOS*/
+DROP TABLE ${stats_db_name}.dual; /*EOS*/
 
-UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name = 'Unknown Repository';
-UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1';
+UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name = 'Unknown Repository'; /*EOS*/
+UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1'; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge;
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, langs.languages AS language
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages
-where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false;
+where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge;
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids
-where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false;
+where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge;
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS
 SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
 FROM ${openaire_db_name}.relation r
-WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false;
+WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; /*EOS*/
 
 -- datasource sources:
 -- where the datasource info have been collected from.
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge;
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS
 select substr(d.id, 4) as id, substr(cf.key, 4) as datasource
 from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf
-where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false;
+where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
 SELECT datasource AS id, id AS result
-FROM ${stats_db_name}.result_datasources;
+FROM ${stats_db_name}.result_datasources; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
index 19d301e27..afde8160e 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
@@ -3,7 +3,7 @@
 -- Organization table/view and Organization related tables/views
 ----------------------------------------------------------------
 ----------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.organization purge;
+DROP TABLE IF EXISTS ${stats_db_name}.organization purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization STORED AS PARQUET AS
 SELECT substr(o.id, 4)        as id,
@@ -11,12 +11,12 @@ SELECT substr(o.id, 4)        as id,
        o.legalshortname.value as legalshortname,
        o.country.classid      as country
 FROM ${openaire_db_name}.organization o
-WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible = FALSE;
+WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible = FALSE; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.organization_datasources AS
 SELECT organization AS id, id AS datasource
-FROM ${stats_db_name}.datasource_organizations;
+FROM ${stats_db_name}.datasource_organizations; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.organization_projects AS
 SELECT id AS project, organization as id
-FROM ${stats_db_name}.project_organizations;
\ No newline at end of file
+FROM ${stats_db_name}.project_organizations; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index 813fffcf9..1460477ae 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -154,180 +154,354 @@
     </kill>
 
     <action name="Step1">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step1.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
-        <ok to="Step2"/>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step1</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
+<!--        <ok to="Step2"/>-->
+        <ok to="End"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step2">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step2.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step2</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step3"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step3">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step3.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step3</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step4"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step4">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step4.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step4</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step5"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step5">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step5.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step5</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step6"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step6">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step6.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step6</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step7"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step7">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step7.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step7</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step8"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step8">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step8.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step8</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step9"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step9">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step9.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step9</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step10"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step10">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step10.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-            <param>external_stats_db_name=${external_stats_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step10</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step11"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step11">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step11.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-            <param>external_stats_db_name=${external_stats_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step11</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step12"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step12">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step12.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step12</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step13"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step13">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step13.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step13</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step14"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step14">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step14.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step14</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step15"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step15">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step15.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step15</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step15_5"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step15_5">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step15_5.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-            <param>external_stats_db_name=${external_stats_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step15_5</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Contexts"/>
         <error to="Kill"/>
     </action>
@@ -379,23 +553,45 @@
     </action>
 
     <action name="Step16_1-definitions">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step16_1-definitions.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step16_1-definitions</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step16_5"/>
         <error to="Kill"/>
     </action>
 
     <action name="Step16_5">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step16_5.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step16_5</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="Step19-finalize"/>
         <error to="Kill"/>
     </action>
@@ -461,12 +657,23 @@
     </action>
 
     <action name="step21-createObservatoryDB">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step21-createObservatoryDB.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>observatory_db_name=${observatory_db_name}</param>
-        </hive2>
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Step21-createObservatoryDB</name>
+            <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
+            <jar>dhp-stats-update-${projectVersion}.jar</jar>
+            <spark-opts>
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                ${sparkClusterOpts}
+                ${sparkResourceOpts}
+                ${sparkApplicationOpts}
+            </spark-opts>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+        </spark>
         <ok to="step21-createObservatoryDB-post"/>
         <error to="Kill"/>
     </action>

From 0b897f2f667a2bbbf9cb57af5ea4651c01a438c6 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Tue, 16 Apr 2024 18:17:54 +0300
Subject: [PATCH 002/239] Fix and add missing "DROP TABLE" statements, in
 "dhp-stats-update" sql-scripts.

---
 .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql   | 3 ++-
 .../stats/oozie_app/scripts/step16-createIndicatorsTables.sql | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql | 4 +++-
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 ++
 5 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
index 06600db19..f4d06587b 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
@@ -20,7 +20,8 @@ WHERE project_tmp.id IN (SELECT pr.id
                               ${stats_db_name}.result r
                          WHERE pr.result = r.id
                            AND r.type = 'publication'); /*EOS*/
-DROP TABLE IF EXISTS ${stats_db_name}.stored purge; /*EOS*/
+
+DROP TABLE IF EXISTS ${stats_db_name}.project purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project stored as parquet as
 SELECT p.id,
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
index 70cde6481..c2231d54c 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
@@ -965,6 +965,8 @@ select allresults.ri_initiative, result_findable.no_result_findable/allresults.n
 from allresults
          join result_findable on result_findable.ri_initiative=allresults.ri_initiative; /*EOS*/
 
+drop table if exists ${stats_db_name}.indi_pub_publicly_funded purge; /*EOS*/
+
 create table if not exists ${stats_db_name}.indi_pub_publicly_funded stored as parquet as
 with org_names_pids as
 (select org.id,name, pid from ${stats_db_name}.organization org
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
index 426d53773..0cffff052 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
@@ -58,6 +58,8 @@ FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
+DROP TABLE IF EXISTS ${stats_db_name}.software_concepts purge; /*EOS*/
+
 CREATE TABLE ${stats_db_name}.software_concepts STORED AS PARQUET AS
 SELECT substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
index 6b5adff9d..d742bcc2a 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
@@ -50,6 +50,8 @@ FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
   and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false; /*EOS*/
 
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_classifications purge; /*EOS*/
+
 CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications STORED AS PARQUET AS
 SELECT substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
@@ -72,7 +74,7 @@ SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS dataso
 FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource
       from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance
       where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p
-         LEFT OUTER JOIN(SELECT substr(d.id, 4) id
+         LEFT OUTER JOIN (SELECT substr(d.id, 4) id
                          from ${openaire_db_name}.datasource d
                          WHERE d.datainfo.deletedbyinference = false and d.datainfo.invisible=false) d on p.datasource = d.id; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 3f40dbb21..23fa743f9 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -51,6 +51,8 @@ WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; /*
 -- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table.
 -- Creating a temporary dual table that will be removed after the following insert
 
+DROP TABLE IF EXISTS ${stats_db_name}.dual purge; /*EOS*/
+
 CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1)); /*EOS*/
 
 INSERT INTO ${stats_db_name}.dual VALUES ('X'); /*EOS*/

From ca091c0f1e578d57467d9e1c496050420e6d8175 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 17 Apr 2024 14:03:59 +0300
Subject: [PATCH 003/239] dhp-stats-update: - Fix not passing some parameters
 to some Spark actions. - Allow the workflow to run up to Step7. The first 7
 steps seem to work out of the box.

---
 dhp-workflows/dhp-stats-update/runOozieWorkfow.sh     |  2 +-
 .../dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml | 11 +++++++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh b/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh
index a4825a3ae..2f2fc29d5 100755
--- a/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh
+++ b/dhp-workflows/dhp-stats-update/runOozieWorkfow.sh
@@ -17,4 +17,4 @@ cat ./target/extract-and-run-on-remote-host.log
 # oozie job -oozie http://iis-cdh5-test-m3:11000/oozie -info <workflow-ID>
 
 # Get the <job-ID> from the previous output and check the logs:
-# yarn logs -applicationId <job-ID>
+# yarn logs -applicationId application_<job-ID>
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index 1460477ae..c2c6f9822 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -171,8 +171,7 @@
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
         </spark>
-<!--        <ok to="Step2"/>-->
-        <ok to="End"/>
+        <ok to="Step2"/>
         <error to="Kill"/>
     </action>
 
@@ -304,7 +303,8 @@
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
         </spark>
-        <ok to="Step8"/>
+<!--        <ok to="Step8"/>-->
+        <ok to="End"/>
         <error to="Kill"/>
     </action>
 
@@ -369,6 +369,7 @@
             <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql</arg>
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
         <ok to="Step11"/>
         <error to="Kill"/>
@@ -391,6 +392,7 @@
             <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql</arg>
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
         <ok to="Step12"/>
         <error to="Kill"/>
@@ -501,6 +503,7 @@
             <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql</arg>
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
         <ok to="Contexts"/>
         <error to="Kill"/>
@@ -672,7 +675,7 @@
             <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql</arg>
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
-            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>--observatory_db_name</arg><arg>${observatory_db_name}</arg>
         </spark>
         <ok to="step21-createObservatoryDB-post"/>
         <error to="Kill"/>

From 6f2ebb2a52fa99735e92867ffdfbd701926f3dd8 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Thu, 18 Apr 2024 15:35:03 +0300
Subject: [PATCH 004/239] Revert Step8 and Step11 to use Hive again, since
 their "UPDATE" statements are not supported by Spark.

---
 .../graph/stats/oozie_app/scripts/step11.sql  | 18 +++----
 .../graph/stats/oozie_app/scripts/step8.sql   | 37 +++++++-------
 .../dhp/oa/graph/stats/oozie_app/workflow.xml | 49 ++++++++++++++-----
 3 files changed, 64 insertions(+), 40 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
index f4d06587b..207c1b124 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
@@ -10,7 +10,7 @@ SET harvested='true'
 WHERE datasource_tmp.id IN (SELECT DISTINCT d.id
                             FROM ${stats_db_name}.datasource_tmp d,
                                  ${stats_db_name}.result_datasources rd
-                            WHERE d.id = rd.datasource); /*EOS*/
+                            WHERE d.id = rd.datasource); -- /*EOS*/
 
 -- Project temporary table update and final project table creation with final updates that can not be applied to ORC tables
 UPDATE ${stats_db_name}.project_tmp
@@ -19,9 +19,9 @@ WHERE project_tmp.id IN (SELECT pr.id
                          FROM ${stats_db_name}.project_results pr,
                               ${stats_db_name}.result r
                          WHERE pr.result = r.id
-                           AND r.type = 'publication'); /*EOS*/
+                           AND r.type = 'publication'); -- /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.project purge; -- /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project stored as parquet as
 SELECT p.id,
@@ -64,7 +64,7 @@ FROM ${stats_db_name}.project_tmp p
                       AND r.type = 'publication'
                       AND datediff(to_date(r.date), to_date(pp.enddate)) > 0
                     GROUP BY pp.id) AS prr2
-                   ON prr2.id = p.id; /*EOS*/
+                   ON prr2.id = p.id; -- /*EOS*/
 
 UPDATE ${stats_db_name}.publication_tmp
 SET delayed = 'yes'
@@ -74,7 +74,7 @@ WHERE publication_tmp.id IN (SELECT distinct r.id
                                   ${stats_db_name}.project_tmp p
                              WHERE r.id = pr.result
                                AND pr.id = p.id
-                               AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
+                               AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
 
 UPDATE ${stats_db_name}.dataset_tmp
 SET delayed = 'yes'
@@ -84,7 +84,7 @@ WHERE dataset_tmp.id IN (SELECT distinct r.id
                               ${stats_db_name}.project_tmp p
                          WHERE r.id = pr.result
                            AND pr.id = p.id
-                           AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
+                           AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
 
 UPDATE ${stats_db_name}.software_tmp
 SET delayed = 'yes'
@@ -94,7 +94,7 @@ WHERE software_tmp.id IN (SELECT distinct r.id
                                ${stats_db_name}.project_tmp p
                           WHERE r.id = pr.result
                             AND pr.id = p.id
-                            AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
+                            AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
 
 UPDATE ${stats_db_name}.otherresearchproduct_tmp
 SET delayed = 'yes'
@@ -104,7 +104,7 @@ WHERE otherresearchproduct_tmp.id IN (SELECT distinct r.id
                                            ${stats_db_name}.project_tmp p
                                       WHERE r.id = pr.result
                                         AND pr.id = p.id
-                                        AND to_date(r.date) - to_date(p.enddate) > 0); /*EOS*/
+                                        AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.project_results_publication AS
 SELECT result_projects.id          AS result,
@@ -117,4 +117,4 @@ FROM ${stats_db_name}.result_projects,
      ${stats_db_name}.project
 WHERE result_projects.id = result.id
   AND result.type = 'publication'
-  AND project.id = result_projects.project; /*EOS*/
\ No newline at end of file
+  AND project.id = result_projects.project; -- /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 23fa743f9..07e19d68b 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -5,7 +5,7 @@
 -- Datasource table/view and Datasource related tables/views
 ------------------------------------------------------------
 ------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp purge; -- /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_tmp
 (
@@ -23,6 +23,7 @@ CREATE TABLE ${stats_db_name}.datasource_tmp
     issn_printed       STRING,
     issn_online        STRING
 ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
+) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -- /*EOS*/
 
 -- Insert statement that takes into account the piwik_id of the openAIRE graph
 INSERT INTO ${stats_db_name}.datasource_tmp
@@ -46,16 +47,16 @@ FROM ${openaire_db_name}.datasource d1
                LATERAL VIEW EXPLODE(originalid) temp AS originalidd
       WHERE originalidd like "piwik:%") AS d2
      ON d1.id = d2.id
-WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; /*EOS*/
+WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; -- /*EOS*/
 
 -- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table.
 -- Creating a temporary dual table that will be removed after the following insert
 
-DROP TABLE IF EXISTS ${stats_db_name}.dual purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.dual purge; -- /*EOS*/
 
-CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1)); /*EOS*/
+CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1)); -- /*EOS*/
 
-INSERT INTO ${stats_db_name}.dual VALUES ('X'); /*EOS*/
+INSERT INTO ${stats_db_name}.dual VALUES ('X'); -- /*EOS*/
 
 INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`,
                                              `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`, `issn_printed`, `issn_online`)
@@ -73,42 +74,42 @@ SELECT 'other',
        null,
        null
 FROM ${stats_db_name}.dual
-WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); /*EOS*/
-DROP TABLE ${stats_db_name}.dual; /*EOS*/
+WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); -- /*EOS*/
+DROP TABLE ${stats_db_name}.dual; -- /*EOS*/
 
-UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name = 'Unknown Repository'; /*EOS*/
-UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1'; /*EOS*/
+UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name = 'Unknown Repository'; -- /*EOS*/
+UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1'; -- /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; -- /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, langs.languages AS language
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages
-where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
+where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; -- /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; -- /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids
-where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
+where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; -- /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; -- /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS
 SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
 FROM ${openaire_db_name}.relation r
-WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; /*EOS*/
+WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; -- /*EOS*/
 
 -- datasource sources:
 -- where the datasource info have been collected from.
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; -- /*EOS*/
 
 create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS
 select substr(d.id, 4) as id, substr(cf.key, 4) as datasource
 from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf
-where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; /*EOS*/
+where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; -- /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
 SELECT datasource AS id, id AS result
-FROM ${stats_db_name}.result_datasources; /*EOS*/
+FROM ${stats_db_name}.result_datasources; -- /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index c2c6f9822..5c255a488 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -308,7 +308,7 @@
         <error to="Kill"/>
     </action>
 
-    <action name="Step8">
+<!--    <action name="Step8">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
@@ -316,18 +316,29 @@
             <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
             <jar>dhp-stats-update-${projectVersion}.jar</jar>
             <spark-opts>
-                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                &#45;&#45;conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
                 ${sparkClusterOpts}
                 ${sparkResourceOpts}
                 ${sparkApplicationOpts}
             </spark-opts>
-            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
-            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql</arg>
-            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
-            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>&#45;&#45;hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>&#45;&#45;sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql</arg>
+            <arg>&#45;&#45;stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>&#45;&#45;openaire_db_name</arg><arg>${openaire_db_name}</arg>
         </spark>
         <ok to="Step9"/>
         <error to="Kill"/>
+    </action>-->
+
+    <action name="Step8">
+        <hive2 xmlns="uri:oozie:hive2-action:0.1">
+            <jdbc-url>${hive_jdbc_url}</jdbc-url>
+            <script>scripts/step8.sql</script>
+            <param>stats_db_name=${stats_db_name}</param>
+            <param>openaire_db_name=${openaire_db_name}</param>
+        </hive2>
+        <ok to="Step9"/>
+        <error to="Kill"/>
     </action>
 
     <action name="Step9">
@@ -375,7 +386,7 @@
         <error to="Kill"/>
     </action>
 
-    <action name="Step11">
+<!--    <action name="Step11">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
@@ -383,19 +394,31 @@
             <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
             <jar>dhp-stats-update-${projectVersion}.jar</jar>
             <spark-opts>
-                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                &#45;&#45;conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
                 ${sparkClusterOpts}
                 ${sparkResourceOpts}
                 ${sparkApplicationOpts}
             </spark-opts>
-            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
-            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql</arg>
-            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
-            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
-            <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
+            <arg>&#45;&#45;hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>&#45;&#45;sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql</arg>
+            <arg>&#45;&#45;stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>&#45;&#45;openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>&#45;&#45;external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
         <ok to="Step12"/>
         <error to="Kill"/>
+    </action>-->
+
+    <action name="Step11">
+        <hive2 xmlns="uri:oozie:hive2-action:0.1">
+            <jdbc-url>${hive_jdbc_url}</jdbc-url>
+            <script>scripts/step11.sql</script>
+            <param>stats_db_name=${stats_db_name}</param>
+            <param>openaire_db_name=${openaire_db_name}</param>
+            <param>external_stats_db_name=${external_stats_db_name}</param>
+        </hive2>
+        <ok to="Step12"/>
+        <error to="Kill"/>
     </action>
 
     <action name="Step12">

From d46b78b65949a58447821e050ed0179a8173c404 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Thu, 18 Apr 2024 15:40:27 +0300
Subject: [PATCH 005/239] dhp-stats-update: - Set Steps 2-7 and 9 to limit the
 amount of files generated by Spark, from 8000, down to 100, to improve
 file-transfer and querying performance. - Allow the workflow to run up to
 Step10. The Step11 seems to have some issues even when using hive-action.

---
 .../oa/graph/stats/oozie_app/scripts/step2.sql   | 16 ++++++++--------
 .../oa/graph/stats/oozie_app/scripts/step3.sql   | 16 ++++++++--------
 .../oa/graph/stats/oozie_app/scripts/step4.sql   | 16 ++++++++--------
 .../oa/graph/stats/oozie_app/scripts/step5.sql   | 16 ++++++++--------
 .../oa/graph/stats/oozie_app/scripts/step6.sql   | 12 ++++++------
 .../oa/graph/stats/oozie_app/scripts/step7.sql   |  9 ++++-----
 .../oa/graph/stats/oozie_app/scripts/step9.sql   |  2 +-
 .../dhp/oa/graph/stats/oozie_app/workflow.xml    |  6 +++---
 8 files changed, 46 insertions(+), 47 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
index 4aa90b1a2..8ec663573 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
@@ -44,7 +44,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.publication_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_classifications STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, instancetype.classname as type
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, instancetype.classname as type
 from ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.instance.instancetype) instances as instancetype
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -52,7 +52,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.publication_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_concepts STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, case
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, case
     when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
     when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
     when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
@@ -63,7 +63,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.publication_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_datasources STORED AS PARQUET as
-SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource
+SELECT /*+ COALESCE(100) */ p.id, case when d.id is null then 'other' else p.datasource end as datasource
 FROM (
          SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) as datasource
          from ${openaire_db_name}.publication p lateral view explode(p.instance) instances as instance
@@ -76,14 +76,14 @@ FROM (
 DROP TABLE IF EXISTS ${stats_db_name}.publication_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_languages STORED AS PARQUET AS
-select substr(p.id, 4) as id, p.language.classname as language
+select /*+ COALESCE(100) */ substr(p.id, 4) as id, p.language.classname as language
 FROM ${openaire_db_name}.publication p
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.publication_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_oids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, oids.ids AS oid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.originalid) oids AS ids
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -91,7 +91,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.publication_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_pids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value as pid
 FROM ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.pid) pids AS ppid
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -99,7 +99,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.publication_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_topics STORED AS PARQUET as
-select substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic
+select /*+ COALESCE(100) */ substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS TYPE, subjects.subject.value AS topic
 FROM ${openaire_db_name}.publication p
          LATERAL VIEW explode(p.subject) subjects AS subject
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -107,7 +107,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.publication_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.publication_citations STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.publication p
          lateral view explode(p.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
index 1ff4beadb..ebedb5dc5 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
@@ -45,7 +45,7 @@ WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_citations STORED AS PARQUET AS
-SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
+SELECT /*+ COALESCE(100) */ substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.dataset d
          LATERAL VIEW explode(d.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
@@ -54,7 +54,7 @@ WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !=
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_classifications STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, instancetype.classname AS type
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -62,7 +62,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_concepts STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, case
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
                                   when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
@@ -73,7 +73,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_datasources STORED AS PARQUET AS
-SELECT p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
+SELECT /*+ COALESCE(100) */ p.id, case when d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
 FROM (
          SELECT substr(p.id, 4) as id, substr(instances.instance.hostedby.key, 4) AS datasource
          FROM ${openaire_db_name}.dataset p
@@ -87,14 +87,14 @@ FROM (
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_languages STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, p.language.classname AS language
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, p.language.classname AS language
 FROM ${openaire_db_name}.dataset p
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_oids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, oids.ids AS oid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.originalid) oids AS ids
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -102,7 +102,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_pids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.pid) pids AS ppid
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -110,7 +110,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.dataset_topics STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
 FROM ${openaire_db_name}.dataset p
          LATERAL VIEW explode(p.subject) subjects AS subject
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
index 0cffff052..4957d8d2f 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
@@ -44,7 +44,7 @@ where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.software_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_citations STORED AS PARQUET AS
-SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
+SELECT /*+ COALESCE(100) */ substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.software s
          LATERAL VIEW explode(s.extrainfo) citations as citation
 where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
@@ -53,7 +53,7 @@ where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !=
 DROP TABLE IF EXISTS ${stats_db_name}.software_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_classifications STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, instancetype.classname AS type
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -61,7 +61,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.software_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_concepts STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, case
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
                                   when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
@@ -72,7 +72,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.software_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_datasources STORED AS PARQUET AS
-SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource
+SELECT /*+ COALESCE(100) */ p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource end as datasource
 FROM (
          SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource
          FROM ${openaire_db_name}.software p
@@ -86,14 +86,14 @@ FROM (
 DROP TABLE IF EXISTS ${stats_db_name}.software_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_languages STORED AS PARQUET AS
-select substr(p.id, 4) AS id, p.language.classname AS language
+select /*+ COALESCE(100) */ substr(p.id, 4) AS id, p.language.classname AS language
 FROM ${openaire_db_name}.software p
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.software_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_oids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, oids.ids AS oid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.originalid) oids AS ids
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -101,7 +101,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.software_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_pids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.pid) pids AS ppid
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
@@ -109,7 +109,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.software_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.software_topics STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
 FROM ${openaire_db_name}.software p
          LATERAL VIEW explode(p.subject) subjects AS subject
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
index d742bcc2a..820ec4395 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
@@ -45,7 +45,7 @@ WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_citations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_citations STORED AS PARQUET AS
-SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
+SELECT /*+ COALESCE(100) */ substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
 FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
   and o.datainfo.deletedbyinference = false and o.datainfo.invisible=false; /*EOS*/
@@ -53,14 +53,14 @@ WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") !=
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_classifications purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_classifications STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, instancetype.classname AS type
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, instancetype.classname AS type
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.instancetype) instances AS instancetype
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_concepts purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_concepts STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, case
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, case
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+::.+$' then contexts.context.id
                                   when contexts.context.id RLIKE '^[^::]+::[^::]+$' then concat(contexts.context.id, '::other')
                                   when contexts.context.id RLIKE '^[^::]+$' then concat(contexts.context.id, '::other::other') END as concept
@@ -70,7 +70,7 @@ where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_datasources purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_datasources STORED AS PARQUET AS
-SELECT p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
+SELECT /*+ COALESCE(100) */ p.id, CASE WHEN d.id IS NULL THEN 'other' ELSE p.datasource END AS datasource
 FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) AS datasource
       from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.instance) instances as instance
       where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false) p
@@ -81,27 +81,27 @@ FROM (SELECT substr(p.id, 4) AS id, substr(instances.instance.hostedby.key, 4) A
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_languages STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, p.language.classname AS language
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, p.language.classname AS language
 FROM ${openaire_db_name}.otherresearchproduct p
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_oids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, oids.ids AS oid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.originalid) oids AS ids
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_pids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_pids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, ppid.qualifier.classname AS type, ppid.value AS pid
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.pid) pids AS ppid
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_topics purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.otherresearchproduct_topics STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
 FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject
 where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
index 75ec7d69c..d2688ec07 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
@@ -6,14 +6,14 @@
 DROP TABLE IF EXISTS ${stats_db_name}.project_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_oids STORED AS PARQUET AS
-SELECT substr(p.id, 4) AS id, oids.ids AS oid
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.project p LATERAL VIEW explode(p.originalid) oids AS ids
 where p.datainfo.deletedbyinference=false  and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.project_organizations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_organizations STORED AS PARQUET AS
-SELECT substr(r.source, 4) AS id, substr(r.target, 4) AS organization
+SELECT /*+ COALESCE(100) */ substr(r.source, 4) AS id, substr(r.target, 4) AS organization
 from ${openaire_db_name}.relation r
 WHERE r.reltype = 'projectOrganization' and r.source like '40|%'
   and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; /*EOS*/
@@ -21,7 +21,7 @@ WHERE r.reltype = 'projectOrganization' and r.source like '40|%'
 DROP TABLE IF EXISTS ${stats_db_name}.project_results purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_results STORED AS PARQUET AS
-SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance
+SELECT /*+ COALESCE(100) */ substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance
 FROM ${openaire_db_name}.relation r
 WHERE r.reltype = 'resultProject' and r.target like '40|%'
   and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; /*EOS*/
@@ -29,7 +29,7 @@ WHERE r.reltype = 'resultProject' and r.target like '40|%'
 DROP TABLE IF EXISTS ${stats_db_name}.project_classification purge; /*EOS*/
 
 create table ${stats_db_name}.project_classification STORED AS PARQUET as
-select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3
+select /*+ COALESCE(100) */ substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3
 from ${openaire_db_name}.project p
     lateral view explode(p.h2020classification) classifs as class
 where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false and class.h2020programme is not null; /*EOS*/
@@ -93,7 +93,7 @@ WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EO
 DROP TABLE IF EXISTS ${stats_db_name}.funder purge; /*EOS*/
 
 create table ${stats_db_name}.funder STORED AS PARQUET as
-select distinct xpath_string(fund, '//funder/id')        as id,
+select /*+ COALESCE(100) */ distinct xpath_string(fund, '//funder/id')        as id,
                 xpath_string(fund, '//funder/name')      as name,
                 xpath_string(fund, '//funder/shortname') as shortname,
                 xpath_string(fundingtree[0].value, '//funder/jurisdiction') as country
@@ -102,7 +102,7 @@ from ${openaire_db_name}.project p lateral view explode(p.fundingtree.value) fun
 DROP TABLE IF EXISTS ${stats_db_name}.project_organization_contribution purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.project_organization_contribution STORED AS PARQUET AS
-SELECT distinct substr(r.source, 4) AS project, substr(r.target, 4) AS organization,
+SELECT /*+ COALESCE(100) */ distinct substr(r.source, 4) AS project, substr(r.target, 4) AS organization,
 properties[0].value contribution, properties[1].value currency
 from ${openaire_db_name}.relation r
 LATERAL VIEW explode (r.properties) properties
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index 2cc7c13c4..f3ab52004 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -130,7 +130,7 @@ with
     lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'),
     lvl2 as (select id, topic from ${stats_db_name}.result_topics where topic like '____ %' and type='Fields of Science and Technology classification'),
     lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification')
-select lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3
+select /*+ COALESCE(100) */ lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3
 from lvl1
  join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)
  join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4); /*EOS*/
@@ -138,7 +138,7 @@ from lvl1
 DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS
-SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
+SELECT /*+ COALESCE(100) */ substr(r.target, 4) AS id, substr(r.source, 4) AS organization
 FROM ${openaire_db_name}.relation r
 WHERE r.reltype = 'resultOrganization'
   and r.target like '50|%'
@@ -147,8 +147,7 @@ WHERE r.reltype = 'resultOrganization'
 DROP TABLE IF EXISTS ${stats_db_name}.result_projects purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS
-select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
+select /*+ COALESCE(100) */ pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
 FROM ${stats_db_name}.result r
          JOIN ${stats_db_name}.project_results pr ON r.id = pr.result
-         JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; /*EOS*/
-
+         JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
index afde8160e..1d76b89a6 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
@@ -6,7 +6,7 @@
 DROP TABLE IF EXISTS ${stats_db_name}.organization purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization STORED AS PARQUET AS
-SELECT substr(o.id, 4)        as id,
+SELECT /*+ COALESCE(100) */ substr(o.id, 4)        as id,
        o.legalname.value      as name,
        o.legalshortname.value as legalshortname,
        o.country.classid      as country
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index 5c255a488..37d837e76 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -303,8 +303,7 @@
             <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
         </spark>
-<!--        <ok to="Step8"/>-->
-        <ok to="End"/>
+        <ok to="Step8"/>
         <error to="Kill"/>
     </action>
 
@@ -382,7 +381,8 @@
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
             <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
-        <ok to="Step11"/>
+<!--        <ok to="Step11"/>-->
+        <ok to="End"/>
         <error to="Kill"/>
     </action>
 

From 2616971e2bc23ee172ffc64e0a6730ed1356f9a8 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Thu, 18 Apr 2024 16:18:16 +0300
Subject: [PATCH 006/239] dhp-stats-update: remove leftover duplicate line

---
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql    | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 07e19d68b..90c3ebef6 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -22,7 +22,6 @@ CREATE TABLE ${stats_db_name}.datasource_tmp
     `compatibility`    STRING,
     issn_printed       STRING,
     issn_online        STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
 ) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -- /*EOS*/
 
 -- Insert statement that takes into account the piwik_id of the openAIRE graph

From ed052a3476bf5c8980412b0d1b8387491d761ab2 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 6 May 2024 16:08:33 +0200
Subject: [PATCH 007/239] job for the population of the oai database

---
 .../dhp/oa/oaipmh/IrishOaiExporterJob.java    | 156 ++++++++++++++++++
 .../dhp/oa/oaipmh/OaiRecordWrapper.java       |  50 ++++++
 2 files changed, 206 insertions(+)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
 create mode 100644 dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
new file mode 100644
index 000000000..9a608b6fa
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -0,0 +1,156 @@
+package eu.dnetlib.dhp.oa.oaipmh;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.time.LocalDateTime;
+import java.util.ArrayList;
+import java.util.Optional;
+import java.util.Properties;
+import java.util.zip.GZIPOutputStream;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoder;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.dom4j.Document;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Node;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.oa.provision.XmlConverterJob;
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
+
+public class IrishOaiExporterJob {
+
+	private static final Logger log = LoggerFactory.getLogger(IrishOaiExporterJob.class);
+
+	protected static final int NUM_CONNECTIONS = 20;
+
+	public static void main(final String[] args) throws Exception {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+				IOUtils
+						.toString(XmlConverterJob.class
+								.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
+		parser.parseArgument(args);
+
+		final Boolean isSparkSessionManaged = Optional
+				.ofNullable(parser.get("isSparkSessionManaged"))
+				.map(Boolean::valueOf)
+				.orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		final String dbUrl = parser.get("dbUrl");
+		final String dbTable = parser.get("dbTable");
+		final String dbUser = parser.get("dbUser");
+		final String dbPwd = parser.get("dbPwd");
+		final int numConnections = Optional
+				.ofNullable(parser.get("numConnections"))
+				.map(Integer::valueOf)
+				.orElse(NUM_CONNECTIONS);
+
+		log.info("inputPath:     '{}'", inputPath);
+		log.info("dbUrl:         '{}'", dbUrl);
+		log.info("dbUser:        '{}'", dbUser);
+		log.info("table:         '{}'", dbTable);
+		log.info("dbPwd:         '{}'", "xxx");
+		log.info("numPartitions: '{}'", numConnections);
+
+		final Properties connectionProperties = new Properties();
+		connectionProperties.put("user", dbUser);
+		connectionProperties.put("password", dbPwd);
+
+		final SparkConf conf = new SparkConf();
+		conf.registerKryoClasses(new Class[] {
+				SerializableSolrInputDocument.class
+		});
+
+		final Encoder<TupleWrapper> encoderTuple = Encoders.bean(TupleWrapper.class);
+		final Encoder<OaiRecordWrapper> encoderOaiRecord = Encoders.bean(OaiRecordWrapper.class);
+
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
+
+			final Dataset<OaiRecordWrapper> docs = spark
+					.read()
+					.schema(encoderTuple.schema())
+					.json(inputPath)
+					.as(encoderTuple)
+					.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
+					.map((MapFunction<String, OaiRecordWrapper>) IrishOaiExporterJob::asIrishOaiResult, encoderOaiRecord)
+					.filter((FilterFunction<OaiRecordWrapper>) obj -> (obj != null) && StringUtils.isNotBlank(obj.getId()));
+
+			docs.repartition(numConnections)
+					.write()
+					.mode(SaveMode.Overwrite)
+					.jdbc(dbUrl, dbTable, connectionProperties);
+
+		});
+	}
+
+	private static OaiRecordWrapper asIrishOaiResult(final String xml) {
+		try {
+			final Document doc = DocumentHelper.parseText(xml);
+			final OaiRecordWrapper r = new OaiRecordWrapper();
+
+			if (isValid(doc)) {
+				r.setId(doc.valueOf("//*[local-name()='objIdentifier']").trim());
+				r.setBody(gzip(xml));
+				r.setDate(LocalDateTime.now());
+				r.setSets(new ArrayList<>());
+			}
+			return r;
+		} catch (final Exception e) {
+			log.error("Error parsing record: " + xml, e);
+			throw new RuntimeException("Error parsing record: " + xml, e);
+		}
+	}
+
+	private static boolean isValid(final Document doc) {
+
+		final Node n = doc.selectSingleNode("//*[local-name()='entity']/*[local-name()='result']");
+
+		if (n != null) {
+			for (final Object o : n.selectNodes(".//*[local-name()='datainfo']/*[local-name()='deletedbyinference']")) {
+				if ("true".equals(((Node) o).getText().trim())) { return false; }
+			}
+
+			for (final Object o : n.selectNodes("./*[local-name()='country']")) {
+				if ("IE".equals(((Node) o).valueOf("@classid").trim())) { return true; }
+			}
+
+			for (final Object o : n.selectNodes(".//*[local-name()='rel']")) {
+				final String relType = ((Node) o).valueOf("./[local-name() = 'to']/@type").trim();
+				final String relCountry = ((Node) o).valueOf("./*[local-name() = 'country']/@classid").trim();
+				if ("organization".equals(relType) && "IE".equals(relCountry)) { return true; }
+			}
+		}
+		return false;
+
+	}
+
+	private static byte[] gzip(final String str) {
+		if (StringUtils.isBlank(str)) { return null; }
+
+		try {
+			final ByteArrayOutputStream obj = new ByteArrayOutputStream();
+			final GZIPOutputStream gzip = new GZIPOutputStream(obj);
+			gzip.write(str.getBytes("UTF-8"));
+			gzip.flush();
+			gzip.close();
+			return obj.toByteArray();
+		} catch (final IOException e) {
+			throw new RuntimeException("error in gzip", e);
+		}
+	}
+}
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java
new file mode 100644
index 000000000..4c2766754
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java
@@ -0,0 +1,50 @@
+package eu.dnetlib.dhp.oa.oaipmh;
+
+import java.io.Serializable;
+import java.time.LocalDateTime;
+import java.util.List;
+
+public class OaiRecordWrapper implements Serializable {
+
+	private static final long serialVersionUID = 8997046455575004880L;
+
+	private String id;
+	private byte[] body;
+	private LocalDateTime date;
+	private List<String> sets;
+
+	public OaiRecordWrapper() {}
+
+	public String getId() {
+		return this.id;
+	}
+
+	public void setId(final String id) {
+		this.id = id;
+	}
+
+	public byte[] getBody() {
+		return this.body;
+	}
+
+	public void setBody(final byte[] body) {
+		this.body = body;
+	}
+
+	public LocalDateTime getDate() {
+		return this.date;
+	}
+
+	public void setDate(final LocalDateTime date) {
+		this.date = date;
+	}
+
+	public List<String> getSets() {
+		return this.sets;
+	}
+
+	public void setSets(final List<String> sets) {
+		this.sets = sets;
+	}
+
+}

From aa40e53c19acf6c8007b7819bea3e65ba642e057 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Tue, 7 May 2024 08:01:19 +0200
Subject: [PATCH 008/239] oai exporter parameters

---
 .../input_params_irish_oai_exporter.json      | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json

diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json
new file mode 100644
index 000000000..99a12927b
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json
@@ -0,0 +1,38 @@
+[
+  {
+    "paramName": "i",
+    "paramLongName": "inputPath",
+    "paramDescription": "The path of the input records on HDFS",
+    "paramRequired": true
+  },
+  {
+    "paramName": "nc",
+    "paramLongName": "numConnections",
+    "paramDescription": "number of connections to the postgres db (for the write operation)",
+    "paramRequired": false
+  },
+  {
+    "paramName": "du",
+    "paramLongName": "dbUrl",
+    "paramDescription": "the url of the database",
+    "paramRequired": true
+  },
+  {
+    "paramName": "dusr",
+    "paramLongName": "dbUser",
+    "paramDescription": "the user of the database",
+    "paramRequired": true
+  },
+  {
+    "paramName": "t",
+    "paramLongName": "dbTable",
+    "paramDescription": "the name of the table in the database",
+    "paramRequired": true
+  },
+  {
+    "paramName": "dpwd",
+    "paramLongName": "dbPwd",
+    "paramDescription": "the password for the user of the database",
+    "paramRequired": true
+  }		
+]

From 70bf6ac41561d487109a04ef60b0659a8785d989 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Tue, 7 May 2024 09:36:26 +0200
Subject: [PATCH 009/239] oai exporter tests

---
 .../dhp/oa/oaipmh/IrishOaiExporterJob.java    | 11 ++-
 .../oa/oaipmh/IrishOaiExporterJobTest.java    | 93 +++++++++++++++++++
 .../eu/dnetlib/dhp/oa/oaipmh/record_IE.xml    | 89 ++++++++++++++++++
 .../dhp/oa/oaipmh/record_IE_deleted.xml       | 89 ++++++++++++++++++
 .../eu/dnetlib/dhp/oa/oaipmh/record_IT.xml    | 66 +++++++++++++
 5 files changed, 344 insertions(+), 4 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE.xml
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE_deleted.xml
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IT.xml

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
index 9a608b6fa..e2ae890e5 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -98,7 +98,7 @@ public class IrishOaiExporterJob {
 		});
 	}
 
-	private static OaiRecordWrapper asIrishOaiResult(final String xml) {
+	protected static OaiRecordWrapper asIrishOaiResult(final String xml) {
 		try {
 			final Document doc = DocumentHelper.parseText(xml);
 			final OaiRecordWrapper r = new OaiRecordWrapper();
@@ -116,21 +116,24 @@ public class IrishOaiExporterJob {
 		}
 	}
 
-	private static boolean isValid(final Document doc) {
+	protected static boolean isValid(final Document doc) {
 
 		final Node n = doc.selectSingleNode("//*[local-name()='entity']/*[local-name()='result']");
 
 		if (n != null) {
+
 			for (final Object o : n.selectNodes(".//*[local-name()='datainfo']/*[local-name()='deletedbyinference']")) {
 				if ("true".equals(((Node) o).getText().trim())) { return false; }
 			}
 
+			// verify the main country of the result
 			for (final Object o : n.selectNodes("./*[local-name()='country']")) {
 				if ("IE".equals(((Node) o).valueOf("@classid").trim())) { return true; }
 			}
 
+			// verify the countries of the related organizations
 			for (final Object o : n.selectNodes(".//*[local-name()='rel']")) {
-				final String relType = ((Node) o).valueOf("./[local-name() = 'to']/@type").trim();
+				final String relType = ((Node) o).valueOf("./*[local-name() = 'to']/@type").trim();
 				final String relCountry = ((Node) o).valueOf("./*[local-name() = 'country']/@classid").trim();
 				if ("organization".equals(relType) && "IE".equals(relCountry)) { return true; }
 			}
@@ -139,7 +142,7 @@ public class IrishOaiExporterJob {
 
 	}
 
-	private static byte[] gzip(final String str) {
+	protected static byte[] gzip(final String str) {
 		if (StringUtils.isBlank(str)) { return null; }
 
 		try {
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
new file mode 100644
index 000000000..6140b0907
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
@@ -0,0 +1,93 @@
+package eu.dnetlib.dhp.oa.oaipmh;
+
+import static org.junit.Assert.assertNull;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.zip.GZIPInputStream;
+
+import org.apache.commons.io.IOUtils;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.io.SAXReader;
+import org.junit.jupiter.api.Test;
+
+class IrishOaiExporterJobTest {
+
+	@Test
+	void testAsIrishOaiResult() throws Exception {
+		final String xml = IOUtils.toString(getClass().getResourceAsStream("record_IE.xml"));
+		final OaiRecordWrapper res = IrishOaiExporterJob.asIrishOaiResult(xml);
+		assertNotNull(res.getId());
+		assertNotNull(res.getBody());
+		assertNotNull(res.getSets());
+		assertNotNull(res.getDate());
+		assertEquals("dedup_wf_002::532be02f990b479a1da46d71f1a4c3f0", res.getId());
+		assertTrue(res.getBody().length > 0);
+		assertTrue(res.getSets().isEmpty());
+	}
+
+	@Test
+	void testIsValid_IE() throws DocumentException {
+		final Document doc = new SAXReader().read(getClass().getResourceAsStream("record_IE.xml"));
+		assertTrue(IrishOaiExporterJob.isValid(doc));
+	}
+
+	@Test
+	void testIsValid_invalid_country() throws DocumentException {
+		final Document doc = new SAXReader().read(getClass().getResourceAsStream("record_IT.xml"));
+		assertFalse(IrishOaiExporterJob.isValid(doc));
+	}
+
+	@Test
+	void testIsValid_deleted() throws DocumentException {
+		final Document doc = new SAXReader().read(getClass().getResourceAsStream("record_IE_deleted.xml"));
+		assertFalse(IrishOaiExporterJob.isValid(doc));
+	}
+
+	@Test
+	void testGzip_simple() {
+		final String message = "<test />";
+		final byte[] bytes = IrishOaiExporterJob.gzip(message);
+		assertNotNull(bytes);
+		assertTrue(bytes.length > 0);
+		assertEquals(message, decompress(bytes));
+	}
+
+	@Test
+	void testGzip_empty() {
+		assertNull(IrishOaiExporterJob.gzip(""));
+		assertNull(IrishOaiExporterJob.gzip(null));
+	}
+
+	private static String decompress(final byte[] compressed) {
+		final StringBuilder outStr = new StringBuilder();
+		if ((compressed == null) || (compressed.length == 0)) { return null; }
+		try {
+			if (isCompressed(compressed)) {
+				final GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(compressed));
+				final BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(gis, "UTF-8"));
+
+				String line;
+				while ((line = bufferedReader.readLine()) != null) {
+					outStr.append(line);
+				}
+			} else {
+				outStr.append(compressed);
+			}
+			return outStr.toString();
+		} catch (final IOException e) {
+			throw new RuntimeException("error in gunzip", e);
+		}
+	}
+
+	private static boolean isCompressed(final byte[] compressed) {
+		return (compressed[0] == (byte) GZIPInputStream.GZIP_MAGIC) && (compressed[1] == (byte) (GZIPInputStream.GZIP_MAGIC >> 8));
+	}
+}
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE.xml
new file mode 100644
index 000000000..01b7334f8
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/oaipmh/record_IE.xml
@@ -0,0 +1,89 @@
+<record rank="null">
+    <result>
+        <header>
+            <objIdentifier>dedup_wf_002::532be02f990b479a1da46d71f1a4c3f0</objIdentifier>
+            <dateOfCollection>2023-03-31T18:37:45.599Z</dateOfCollection>
+            <dateOfTransformation>2023-03-31T18:45:52.701Z</dateOfTransformation>
+        </header>
+        <metadata>
+            <entity schemaLocation="http://namespace.openaire.eu/oaf https://www.openaire.eu/schema/1.0/oaf-1.0.xsd">
+                <result>
+                    <collectedfrom name="Waterford Institute of Technology - Open Access Repository" id="opendoar____::50c1f44e426560f3f2cdcb3e19e39903" />
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+                            <instancetype classid="0013" classname="Part of book or chapter of book" schemeid="dnet:publication_resource" schemename="dnet:publication_resource" />
+                            <pid classid="handle" classname="Handle" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">2158/608965</pid>
+                            <alternateidentifier classid="urn" classname="urn" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:crosswalk:repository" trust="0.9">http://hdl.handle.net/2158/608965</alternateidentifier>
+                            <refereed classid="0002" classname="nonPeerReviewed" schemeid="dnet:review_levels" schemename="dnet:review_levels" />
+                            <webresource>
+                                <url>https://hdl.handle.net/2158/608965</url>
+                            </webresource>
+                        </instance>
+                    </children>
+                </result>
+            </entity>
+        </metadata>
+    </result>
+</record>
\ No newline at end of file

From e234848af8b0a313a0c8b3988d2ceb4f425edc78 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Wed, 8 May 2024 10:00:53 +0200
Subject: [PATCH 010/239] oaf record: xpath for root

---
 .../main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
index e2ae890e5..fff5d015d 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -105,7 +105,7 @@ public class IrishOaiExporterJob {
 
 			if (isValid(doc)) {
 				r.setId(doc.valueOf("//*[local-name()='objIdentifier']").trim());
-				r.setBody(gzip(xml));
+				r.setBody(gzip(doc.selectSingleNode("//*[local-name()='entity']").asXML()));
 				r.setDate(LocalDateTime.now());
 				r.setSets(new ArrayList<>());
 			}

From c9a327bc5094f48c08f4d7d0b3274378d8d8c63f Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Wed, 8 May 2024 11:34:08 +0200
Subject: [PATCH 011/239] refactoring of gzip method

---
 .../dhp/oa/oaipmh/IrishOaiExporterJob.java    | 14 +++++------
 .../oa/oaipmh/IrishOaiExporterJobTest.java    | 24 +++++--------------
 2 files changed, 13 insertions(+), 25 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
index fff5d015d..b59f0ae73 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -4,6 +4,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
+import java.nio.charset.Charset;
 import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Optional;
@@ -145,15 +146,14 @@ public class IrishOaiExporterJob {
 	protected static byte[] gzip(final String str) {
 		if (StringUtils.isBlank(str)) { return null; }
 
-		try {
-			final ByteArrayOutputStream obj = new ByteArrayOutputStream();
-			final GZIPOutputStream gzip = new GZIPOutputStream(obj);
-			gzip.write(str.getBytes("UTF-8"));
-			gzip.flush();
-			gzip.close();
-			return obj.toByteArray();
+		try (final ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
+			try (final GZIPOutputStream gzip = new GZIPOutputStream(baos)) {
+				IOUtils.write(str.getBytes(Charset.defaultCharset()), gzip);
+			}
+			return baos.toByteArray();
 		} catch (final IOException e) {
 			throw new RuntimeException("error in gzip", e);
 		}
 	}
+
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
index 6140b0907..e33c701c5 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
@@ -6,10 +6,9 @@ import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
-import java.io.InputStreamReader;
+import java.nio.charset.Charset;
 import java.util.zip.GZIPInputStream;
 
 import org.apache.commons.io.IOUtils;
@@ -57,7 +56,7 @@ class IrishOaiExporterJobTest {
 		final byte[] bytes = IrishOaiExporterJob.gzip(message);
 		assertNotNull(bytes);
 		assertTrue(bytes.length > 0);
-		assertEquals(message, decompress(bytes));
+		assertEquals(message, gunzip(bytes));
 	}
 
 	@Test
@@ -66,22 +65,11 @@ class IrishOaiExporterJobTest {
 		assertNull(IrishOaiExporterJob.gzip(null));
 	}
 
-	private static String decompress(final byte[] compressed) {
-		final StringBuilder outStr = new StringBuilder();
+	public static String gunzip(final byte[] compressed) {
 		if ((compressed == null) || (compressed.length == 0)) { return null; }
-		try {
-			if (isCompressed(compressed)) {
-				final GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(compressed));
-				final BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(gis, "UTF-8"));
-
-				String line;
-				while ((line = bufferedReader.readLine()) != null) {
-					outStr.append(line);
-				}
-			} else {
-				outStr.append(compressed);
-			}
-			return outStr.toString();
+		if (!isCompressed(compressed)) { return new String(compressed); }
+		try (final GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(compressed))) {
+			return IOUtils.toString(gis, Charset.defaultCharset());
 		} catch (final IOException e) {
 			throw new RuntimeException("error in gunzip", e);
 		}

From 2b3b5fe9a172bb1fafb4815a5c52aa9fcaff6644 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Wed, 15 May 2024 14:13:16 +0200
Subject: [PATCH 012/239] oai finalization and test

---
 .../dhp/oa/oaipmh/IrishOaiExporterJob.java    | 26 ++++-
 .../dhp/oa/oaipmh/OaiRecordWrapper.java       | 11 ++-
 .../input_params_irish_oai_exporter.json      |  6 --
 .../eu/dnetlib/dhp/oa/oaipmh/oai-finalize.sql | 12 +++
 .../dhp/oa/oaipmh/DbSerializationTest.java    | 97 +++++++++++++++++++
 .../oa/oaipmh/IrishOaiExporterJobTest.java    | 14 ++-
 6 files changed, 146 insertions(+), 20 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oai-finalize.sql
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
index b59f0ae73..433baf272 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.oa.oaipmh;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
@@ -5,6 +6,9 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.nio.charset.Charset;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.Statement;
 import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Optional;
@@ -37,6 +41,8 @@ public class IrishOaiExporterJob {
 
 	protected static final int NUM_CONNECTIONS = 20;
 
+	public static final String TMP_OAI_TABLE = "temp_oai_data";
+
 	public static void main(final String[] args) throws Exception {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -53,7 +59,6 @@ public class IrishOaiExporterJob {
 
 		final String inputPath = parser.get("inputPath");
 		final String dbUrl = parser.get("dbUrl");
-		final String dbTable = parser.get("dbTable");
 		final String dbUser = parser.get("dbUser");
 		final String dbPwd = parser.get("dbPwd");
 		final int numConnections = Optional
@@ -64,7 +69,6 @@ public class IrishOaiExporterJob {
 		log.info("inputPath:     '{}'", inputPath);
 		log.info("dbUrl:         '{}'", dbUrl);
 		log.info("dbUser:        '{}'", dbUser);
-		log.info("table:         '{}'", dbTable);
 		log.info("dbPwd:         '{}'", "xxx");
 		log.info("numPartitions: '{}'", numConnections);
 
@@ -80,6 +84,7 @@ public class IrishOaiExporterJob {
 		final Encoder<TupleWrapper> encoderTuple = Encoders.bean(TupleWrapper.class);
 		final Encoder<OaiRecordWrapper> encoderOaiRecord = Encoders.bean(OaiRecordWrapper.class);
 
+		log.info("Creating temporary table...");
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 
 			final Dataset<OaiRecordWrapper> docs = spark
@@ -91,12 +96,23 @@ public class IrishOaiExporterJob {
 					.map((MapFunction<String, OaiRecordWrapper>) IrishOaiExporterJob::asIrishOaiResult, encoderOaiRecord)
 					.filter((FilterFunction<OaiRecordWrapper>) obj -> (obj != null) && StringUtils.isNotBlank(obj.getId()));
 
-			docs.repartition(numConnections)
+			docs
+					.repartition(numConnections)
 					.write()
 					.mode(SaveMode.Overwrite)
-					.jdbc(dbUrl, dbTable, connectionProperties);
+					.jdbc(dbUrl, TMP_OAI_TABLE, connectionProperties);
 
 		});
+		log.info("Temporary table created.");
+
+		log.info("Updating OAI records...");
+		try (final Connection con = DriverManager.getConnection(dbUrl, dbUser, dbPwd)) {
+			try (final Statement st = con.createStatement()) {
+				final String query = IOUtils.toString(IrishOaiExporterJob.class.getResourceAsStream("oai-finalize.sql"));
+				st.execute(query);
+			}
+		}
+		log.info("DONE.");
 	}
 
 	protected static OaiRecordWrapper asIrishOaiResult(final String xml) {
@@ -107,7 +123,7 @@ public class IrishOaiExporterJob {
 			if (isValid(doc)) {
 				r.setId(doc.valueOf("//*[local-name()='objIdentifier']").trim());
 				r.setBody(gzip(doc.selectSingleNode("//*[local-name()='entity']").asXML()));
-				r.setDate(LocalDateTime.now());
+				r.setDate(LocalDateTime.now().toString());
 				r.setSets(new ArrayList<>());
 			}
 			return r;
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java
index 4c2766754..2fdf32c96 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/OaiRecordWrapper.java
@@ -1,7 +1,7 @@
+
 package eu.dnetlib.dhp.oa.oaipmh;
 
 import java.io.Serializable;
-import java.time.LocalDateTime;
 import java.util.List;
 
 public class OaiRecordWrapper implements Serializable {
@@ -10,10 +10,11 @@ public class OaiRecordWrapper implements Serializable {
 
 	private String id;
 	private byte[] body;
-	private LocalDateTime date;
+	private String date;
 	private List<String> sets;
 
-	public OaiRecordWrapper() {}
+	public OaiRecordWrapper() {
+	}
 
 	public String getId() {
 		return this.id;
@@ -31,11 +32,11 @@ public class OaiRecordWrapper implements Serializable {
 		this.body = body;
 	}
 
-	public LocalDateTime getDate() {
+	public String getDate() {
 		return this.date;
 	}
 
-	public void setDate(final LocalDateTime date) {
+	public void setDate(final String date) {
 		this.date = date;
 	}
 
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json
index 99a12927b..86b2bb0d3 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json
@@ -23,12 +23,6 @@
     "paramDescription": "the user of the database",
     "paramRequired": true
   },
-  {
-    "paramName": "t",
-    "paramLongName": "dbTable",
-    "paramDescription": "the name of the table in the database",
-    "paramRequired": true
-  },
   {
     "paramName": "dpwd",
     "paramLongName": "dbPwd",
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oai-finalize.sql b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oai-finalize.sql
new file mode 100644
index 000000000..1ec0dfee0
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oai-finalize.sql
@@ -0,0 +1,12 @@
+BEGIN; 
+	
+DELETE FROM oai_data; 
+
+INSERT INTO oai_data(id, body, date, sets) SELECT 
+	id, 
+	body, 
+	date::timestamp, 
+	sets 
+FROM temp_oai_data;
+
+COMMIT;
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java
new file mode 100644
index 000000000..f33708f86
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java
@@ -0,0 +1,97 @@
+
+package eu.dnetlib.dhp.oa.oaipmh;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.sql.Connection;
+import java.sql.DriverManager;
+import java.sql.Statement;
+import java.time.LocalDateTime;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+
+@Disabled
+public class DbSerializationTest {
+
+	private static SparkSession spark;
+
+	public static final String dbUrl = "jdbc:postgresql://localhost:5432/db_test";
+	public static final String dbUser = null;
+	public static final String dbPwd = null;
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+
+		final SparkConf conf = new SparkConf();
+		conf.setAppName("TEST");
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+
+		spark = SparkSession
+				.builder()
+				.appName("TEST")
+				.config(conf)
+				.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		spark.stop();
+	}
+
+	@Test
+	public void testDatabaseSerialization() throws Exception {
+		final Properties connectionProperties = new Properties();
+		if (dbUser != null) {
+			connectionProperties.put("user", dbUser);
+		}
+		if (dbPwd != null) {
+			connectionProperties.put("password", dbPwd);
+		}
+
+		runWithSparkSession(new SparkConf(), false, spark -> {
+
+			final List<OaiRecordWrapper> list = new ArrayList<>();
+
+			for (int i = 0; i < 10; i++) {
+				final OaiRecordWrapper r = new OaiRecordWrapper();
+				r.setId("record_" + i);
+				r.setBody("jsahdjkahdjahdajad".getBytes());
+				r.setDate(LocalDateTime.now().toString());
+				r.setSets(Arrays.asList());
+				list.add(r);
+			}
+
+			final Dataset<OaiRecordWrapper> docs = spark.createDataset(list, Encoders.bean(OaiRecordWrapper.class));
+
+			docs
+					.write()
+					.mode(SaveMode.Overwrite)
+					.jdbc(dbUrl, IrishOaiExporterJob.TMP_OAI_TABLE, connectionProperties);
+
+		});
+
+		try (final Connection con = DriverManager.getConnection(dbUrl, dbUser, dbPwd)) {
+			try (final Statement st = con.createStatement()) {
+				final String query = IOUtils.toString(getClass().getResourceAsStream("oai-finalize.sql"));
+				st.execute(query);
+			}
+		}
+
+	}
+
+}
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
index e33c701c5..57a32e246 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.oa.oaipmh;
 
 import static org.junit.Assert.assertNull;
@@ -17,7 +18,7 @@ import org.dom4j.DocumentException;
 import org.dom4j.io.SAXReader;
 import org.junit.jupiter.api.Test;
 
-class IrishOaiExporterJobTest {
+public class IrishOaiExporterJobTest {
 
 	@Test
 	void testAsIrishOaiResult() throws Exception {
@@ -66,8 +67,12 @@ class IrishOaiExporterJobTest {
 	}
 
 	public static String gunzip(final byte[] compressed) {
-		if ((compressed == null) || (compressed.length == 0)) { return null; }
-		if (!isCompressed(compressed)) { return new String(compressed); }
+		if ((compressed == null) || (compressed.length == 0)) {
+			return null;
+		}
+		if (!isCompressed(compressed)) {
+			return new String(compressed);
+		}
 		try (final GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream(compressed))) {
 			return IOUtils.toString(gis, Charset.defaultCharset());
 		} catch (final IOException e) {
@@ -76,6 +81,7 @@ class IrishOaiExporterJobTest {
 	}
 
 	private static boolean isCompressed(final byte[] compressed) {
-		return (compressed[0] == (byte) GZIPInputStream.GZIP_MAGIC) && (compressed[1] == (byte) (GZIPInputStream.GZIP_MAGIC >> 8));
+		return (compressed[0] == (byte) GZIPInputStream.GZIP_MAGIC)
+			&& (compressed[1] == (byte) (GZIPInputStream.GZIP_MAGIC >> 8));
 	}
 }

From 888637773cfc4d076d27d5fc83bd1b5008f521c2 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Mon, 27 May 2024 12:34:49 +0300
Subject: [PATCH 013/239] Add missing "/*EOS*/" comments.

---
 .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql   | 2 +-
 .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql   | 2 +-
 .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql | 2 +-
 .../oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql | 2 +-
 .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql | 2 +-
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql | 4 ++--
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
index 9a9a507e3..8cab942e6 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
@@ -1,4 +1,4 @@
-set mapred.job.queue.name=analytics;
+set mapred.job.queue.name=analytics; /*EOS*/
 ------------------------------------------------------
 ------------------------------------------------------
 -- Additional relations
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
index 989b92268..1f3027b7d 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
@@ -1,4 +1,4 @@
-set mapred.job.queue.name=analytics;
+set mapred.job.queue.name=analytics; /*EOS*/
 
 ------------------------------------------------------
 ------------------------------------------------------
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
index be5d42f96..d18cf569f 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
@@ -1,4 +1,4 @@
-set mapred.job.queue.name=analytics;
+set mapred.job.queue.name=analytics; /*EOS*/
 
 -------------------------------------------
 --- Extra tables, mostly used by indicators
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
index dd830a24d..0da4394c8 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
@@ -1,4 +1,4 @@
-set mapred.job.queue.name=analytics;
+set mapred.job.queue.name=analytics; /*EOS*/
 
 ----------------------------------------------------
 -- Shortcuts for various definitions in stats db ---
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
index e723ec8b1..416298e4c 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
@@ -1,4 +1,4 @@
-set mapred.job.queue.name=analytics;
+set mapred.job.queue.name=analytics; /*EOS*/
 
 -- replace the creation of the result view to include the boolean fields from the previous tables (green, gold,
 -- peer reviewed)
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
index 59213c4d5..f0e5ce091 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
@@ -1,4 +1,4 @@
-set mapred.job.queue.name=analytics;
+set mapred.job.queue.name=analytics; /*EOS*/
 
 --------------------------------------------------------------
 --------------------------------------------------------------
@@ -113,4 +113,4 @@ SELECT /*+ COALESCE(100) */ substr(p.id, 4) AS id, xpath_string(citation.value,
 FROM ${openaire_db_name}.publication p
          lateral view explode(p.extrainfo) citations AS citation
 WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
-  and p.datainfo.deletedbyinference = false and p.datainfo.invisible=false;
+  and p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/

From a644a6f4fef8a1d2dfdc21c9edaa463a24855d77 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 29 May 2024 12:10:11 +0300
Subject: [PATCH 014/239] Catch Spark-sql errors and show a log with the
 statement that failed.

---
 .../main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java    | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java
index 027bf0735..01d1b9f6a 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oozie/RunSQLSparkJob.java
@@ -65,7 +65,13 @@ public class RunSQLSparkJob {
 				for (String statement : sql.split(";\\s*/\\*\\s*EOS\\s*\\*/\\s*")) {
 					log.info("executing: {}", statement);
 					long startTime = System.currentTimeMillis();
-					spark.sql(statement).show();
+					try {
+						spark.sql(statement).show();
+					} catch (Exception e) {
+						log.error("Error executing statement: {}", statement, e);
+						System.err.println("Error executing statement: " + statement + "\n" + e);
+						throw e;
+					}
 					log
 						.info(
 							"executed in {}",

From 81090ad593b1bb1572c033989c86e79f795670e6 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 5 Jun 2024 10:03:33 +0200
Subject: [PATCH 015/239] [IE OAIPHM] added oozie workflow, minor changes, code
 formatting

---
 .../dhp/oa/oaipmh/IrishOaiExporterJob.java    |  68 ++++++-----
 .../dhp/oa/oaipmh/oozie_app/workflow.xml      | 106 ++++++++++++++++++
 .../dhp/oa/oaipmh/DbSerializationTest.java    |  14 +--
 .../oa/oaipmh/IrishOaiExporterJobTest.java    |   3 +-
 4 files changed, 155 insertions(+), 36 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oozie_app/workflow.xml

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
index 433baf272..57f180fa0 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -46,15 +46,16 @@ public class IrishOaiExporterJob {
 	public static void main(final String[] args) throws Exception {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-				IOUtils
-						.toString(XmlConverterJob.class
-								.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
+			IOUtils
+				.toString(
+					XmlConverterJob.class
+						.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
 		parser.parseArgument(args);
 
 		final Boolean isSparkSessionManaged = Optional
-				.ofNullable(parser.get("isSparkSessionManaged"))
-				.map(Boolean::valueOf)
-				.orElse(Boolean.TRUE);
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
 		final String inputPath = parser.get("inputPath");
@@ -62,9 +63,9 @@ public class IrishOaiExporterJob {
 		final String dbUser = parser.get("dbUser");
 		final String dbPwd = parser.get("dbPwd");
 		final int numConnections = Optional
-				.ofNullable(parser.get("numConnections"))
-				.map(Integer::valueOf)
-				.orElse(NUM_CONNECTIONS);
+			.ofNullable(parser.get("numConnections"))
+			.map(Integer::valueOf)
+			.orElse(NUM_CONNECTIONS);
 
 		log.info("inputPath:     '{}'", inputPath);
 		log.info("dbUrl:         '{}'", dbUrl);
@@ -78,29 +79,31 @@ public class IrishOaiExporterJob {
 
 		final SparkConf conf = new SparkConf();
 		conf.registerKryoClasses(new Class[] {
-				SerializableSolrInputDocument.class
+			SerializableSolrInputDocument.class
 		});
 
 		final Encoder<TupleWrapper> encoderTuple = Encoders.bean(TupleWrapper.class);
 		final Encoder<OaiRecordWrapper> encoderOaiRecord = Encoders.bean(OaiRecordWrapper.class);
 
+		final String date = LocalDateTime.now().toString();
+
 		log.info("Creating temporary table...");
 		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
 
 			final Dataset<OaiRecordWrapper> docs = spark
-					.read()
-					.schema(encoderTuple.schema())
-					.json(inputPath)
-					.as(encoderTuple)
-					.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
-					.map((MapFunction<String, OaiRecordWrapper>) IrishOaiExporterJob::asIrishOaiResult, encoderOaiRecord)
-					.filter((FilterFunction<OaiRecordWrapper>) obj -> (obj != null) && StringUtils.isNotBlank(obj.getId()));
+				.read()
+				.schema(encoderTuple.schema())
+				.json(inputPath)
+				.as(encoderTuple)
+				.map((MapFunction<TupleWrapper, String>) TupleWrapper::getXml, Encoders.STRING())
+				.map((MapFunction<String, OaiRecordWrapper>) r -> asIrishOaiResult(r, date), encoderOaiRecord)
+				.filter((FilterFunction<OaiRecordWrapper>) obj -> (obj != null) && StringUtils.isNotBlank(obj.getId()));
 
 			docs
-					.repartition(numConnections)
-					.write()
-					.mode(SaveMode.Overwrite)
-					.jdbc(dbUrl, TMP_OAI_TABLE, connectionProperties);
+				.repartition(numConnections)
+				.write()
+				.mode(SaveMode.Overwrite)
+				.jdbc(dbUrl, TMP_OAI_TABLE, connectionProperties);
 
 		});
 		log.info("Temporary table created.");
@@ -108,14 +111,15 @@ public class IrishOaiExporterJob {
 		log.info("Updating OAI records...");
 		try (final Connection con = DriverManager.getConnection(dbUrl, dbUser, dbPwd)) {
 			try (final Statement st = con.createStatement()) {
-				final String query = IOUtils.toString(IrishOaiExporterJob.class.getResourceAsStream("oai-finalize.sql"));
+				final String query = IOUtils
+					.toString(IrishOaiExporterJob.class.getResourceAsStream("oai-finalize.sql"));
 				st.execute(query);
 			}
 		}
 		log.info("DONE.");
 	}
 
-	protected static OaiRecordWrapper asIrishOaiResult(final String xml) {
+	protected static OaiRecordWrapper asIrishOaiResult(final String xml, final String date) {
 		try {
 			final Document doc = DocumentHelper.parseText(xml);
 			final OaiRecordWrapper r = new OaiRecordWrapper();
@@ -123,7 +127,7 @@ public class IrishOaiExporterJob {
 			if (isValid(doc)) {
 				r.setId(doc.valueOf("//*[local-name()='objIdentifier']").trim());
 				r.setBody(gzip(doc.selectSingleNode("//*[local-name()='entity']").asXML()));
-				r.setDate(LocalDateTime.now().toString());
+				r.setDate(date);
 				r.setSets(new ArrayList<>());
 			}
 			return r;
@@ -140,19 +144,25 @@ public class IrishOaiExporterJob {
 		if (n != null) {
 
 			for (final Object o : n.selectNodes(".//*[local-name()='datainfo']/*[local-name()='deletedbyinference']")) {
-				if ("true".equals(((Node) o).getText().trim())) { return false; }
+				if ("true".equals(((Node) o).getText().trim())) {
+					return false;
+				}
 			}
 
 			// verify the main country of the result
 			for (final Object o : n.selectNodes("./*[local-name()='country']")) {
-				if ("IE".equals(((Node) o).valueOf("@classid").trim())) { return true; }
+				if ("IE".equals(((Node) o).valueOf("@classid").trim())) {
+					return true;
+				}
 			}
 
 			// verify the countries of the related organizations
 			for (final Object o : n.selectNodes(".//*[local-name()='rel']")) {
 				final String relType = ((Node) o).valueOf("./*[local-name() = 'to']/@type").trim();
 				final String relCountry = ((Node) o).valueOf("./*[local-name() = 'country']/@classid").trim();
-				if ("organization".equals(relType) && "IE".equals(relCountry)) { return true; }
+				if ("organization".equals(relType) && "IE".equals(relCountry)) {
+					return true;
+				}
 			}
 		}
 		return false;
@@ -160,7 +170,9 @@ public class IrishOaiExporterJob {
 	}
 
 	protected static byte[] gzip(final String str) {
-		if (StringUtils.isBlank(str)) { return null; }
+		if (StringUtils.isBlank(str)) {
+			return null;
+		}
 
 		try (final ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
 			try (final GZIPOutputStream gzip = new GZIPOutputStream(baos)) {
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oozie_app/workflow.xml
new file mode 100644
index 000000000..c4caad91e
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/oaipmh/oozie_app/workflow.xml
@@ -0,0 +1,106 @@
+<workflow-app name="irish-oaipmh-provision" xmlns="uri:oozie:workflow:0.5">
+
+    <parameters>
+        <property>
+            <name>inputPath</name>
+            <description>The path of the input records on HDFS</description>
+        </property>
+        <property>
+            <name>numConnections</name>
+            <description>number of connections to the postgres db (for the write operation)</description>
+        </property>
+        <property>
+            <name>dbUrl</name>
+            <description>the url of the database</description>
+        </property>
+        <property>
+            <name>dbUser</name>
+            <description>the user of the database</description>
+        </property>
+        <property>
+            <name>dbPwd</name>
+            <description>the password for the user of the database</description>
+        </property>
+
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="oaiphm_provision"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="irish_oaiphm_provision">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Irish OAI-PHM provision</name>
+            <class>eu.dnetlib.dhp.oa.oaipmh.IrishOaiExporterJob</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=8000
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--numConnections</arg><arg>${numConnections}</arg>
+            <arg>--dbUrl</arg><arg>${dbUrl}</arg>
+            <arg>--dbUser</arg><arg>${dbUser}</arg>
+            <arg>--dbPwd</arg><arg>${dbPwd}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java
index f33708f86..d487fda94 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/DbSerializationTest.java
@@ -42,10 +42,10 @@ public class DbSerializationTest {
 		conf.set("spark.driver.host", "localhost");
 
 		spark = SparkSession
-				.builder()
-				.appName("TEST")
-				.config(conf)
-				.getOrCreate();
+			.builder()
+			.appName("TEST")
+			.config(conf)
+			.getOrCreate();
 	}
 
 	@AfterAll
@@ -79,9 +79,9 @@ public class DbSerializationTest {
 			final Dataset<OaiRecordWrapper> docs = spark.createDataset(list, Encoders.bean(OaiRecordWrapper.class));
 
 			docs
-					.write()
-					.mode(SaveMode.Overwrite)
-					.jdbc(dbUrl, IrishOaiExporterJob.TMP_OAI_TABLE, connectionProperties);
+				.write()
+				.mode(SaveMode.Overwrite)
+				.jdbc(dbUrl, IrishOaiExporterJob.TMP_OAI_TABLE, connectionProperties);
 
 		});
 
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
index 57a32e246..c16f75e1d 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJobTest.java
@@ -10,6 +10,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.nio.charset.Charset;
+import java.time.LocalDateTime;
 import java.util.zip.GZIPInputStream;
 
 import org.apache.commons.io.IOUtils;
@@ -23,7 +24,7 @@ public class IrishOaiExporterJobTest {
 	@Test
 	void testAsIrishOaiResult() throws Exception {
 		final String xml = IOUtils.toString(getClass().getResourceAsStream("record_IE.xml"));
-		final OaiRecordWrapper res = IrishOaiExporterJob.asIrishOaiResult(xml);
+		final OaiRecordWrapper res = IrishOaiExporterJob.asIrishOaiResult(xml, LocalDateTime.now().toString());
 		assertNotNull(res.getId());
 		assertNotNull(res.getBody());
 		assertNotNull(res.getSets());

From 73bd1938a5a8dfead4035f50fded1108cf45a281 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 5 Jun 2024 12:17:35 +0200
Subject: [PATCH 016/239] [graph2hive] use sparkExecutorMemory to define also
 the memoryOverhead

---
 .../dhp/oa/graph/hive/oozie_app/workflow.xml  | 30 ++++++++++++++-----
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
index 4468382be..eec67fc5c 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
@@ -116,17 +116,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=10000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/publication</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>8000</arg>
+            <arg>--numPartitions</arg><arg>10000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -143,17 +145,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=4000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>4000</arg>
+            <arg>--numPartitions</arg><arg>8000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -170,11 +174,13 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
@@ -197,17 +203,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/software</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>300</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -224,17 +232,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=200
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/datasource</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>100</arg>
+            <arg>--numPartitions</arg><arg>200</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -251,17 +261,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/organization</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>400</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -278,17 +290,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/project</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>100</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>
@@ -305,17 +319,19 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/relation</arg>
             <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
             <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
             <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
-            <arg>--numPartitions</arg><arg>10000</arg>
+            <arg>--numPartitions</arg><arg>15000</arg>
         </spark>
         <ok to="join_import"/>
         <error to="Kill"/>

From f70dc76b61a2597ed1a62d90a5f8394cf8710f19 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 6 Jun 2024 10:43:10 +0200
Subject: [PATCH 017/239] minor

---
 .../oaf/utils/ResultTypeComparator.java       | 87 -------------------
 .../dhp/oa/oaipmh/IrishOaiExporterJob.java    |  3 +-
 2 files changed, 1 insertion(+), 89 deletions(-)
 delete mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java
deleted file mode 100644
index e10b281b8..000000000
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ResultTypeComparator.java
+++ /dev/null
@@ -1,87 +0,0 @@
-
-package eu.dnetlib.dhp.schema.oaf.utils;
-
-import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
-
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Result;
-
-public class ResultTypeComparator implements Comparator<Result> {
-
-	public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
-
-	@Override
-	public int compare(Result left, Result right) {
-
-		if (left == null && right == null)
-			return 0;
-		if (left == null)
-			return 1;
-		if (right == null)
-			return -1;
-
-		HashSet<String> lCf = getCollectedFromIds(left);
-		HashSet<String> rCf = getCollectedFromIds(right);
-
-		if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
-			return -1;
-		}
-		if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
-			return 1;
-		}
-
-		if (left.getResulttype() == null || left.getResulttype().getClassid() == null) {
-			if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
-				return 0;
-			}
-			return 1;
-		} else if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
-			return -1;
-		}
-
-		String lClass = left.getResulttype().getClassid();
-		String rClass = right.getResulttype().getClassid();
-
-		if (!lClass.equals(rClass)) {
-			if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
-				return 1;
-
-			if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
-				return 1;
-
-			if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
-				return 1;
-
-			if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
-				return 1;
-		}
-
-		// Else (but unlikely), lexicographical ordering will do.
-		return lClass.compareTo(rClass);
-	}
-
-	protected HashSet<String> getCollectedFromIds(Result left) {
-		return Optional
-			.ofNullable(left.getCollectedfrom())
-			.map(
-				cf -> cf
-					.stream()
-					.map(KeyValue::getKey)
-					.collect(Collectors.toCollection(HashSet::new)))
-			.orElse(new HashSet<>());
-	}
-}
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
index 57f180fa0..3d69370af 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/oaipmh/IrishOaiExporterJob.java
@@ -31,7 +31,6 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.oa.provision.XmlConverterJob;
 import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
 
@@ -48,7 +47,7 @@ public class IrishOaiExporterJob {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
-					XmlConverterJob.class
+					IrishOaiExporterJob.class
 						.getResourceAsStream("/eu/dnetlib/dhp/oa/oaipmh/input_params_irish_oai_exporter.json")));
 		parser.parseArgument(args);
 

From ce2364743a445e42c434c910852dc26a1b75a7a8 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 6 Jun 2024 10:43:43 +0200
Subject: [PATCH 018/239] applying changes from PR#442: Fix for missing
 collectedfrom after dedup

---
 .../oaf/utils/MergeEntitiesComparator.java    | 104 ++++++++++++++++++
 .../dhp/schema/oaf/utils/MergeUtils.java      |  53 +++++----
 .../dhp/oa/dedup/DatasetMergerTest.java       | 103 +++++++++++++++++
 .../dhp/oa/dedup/EntityMergerTest.java        |  10 +-
 .../dnetlib/dhp/dedup/json/dataset_merge.json |   2 +
 5 files changed, 239 insertions(+), 33 deletions(-)
 create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
 create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java
 create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/dataset_merge.json

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
new file mode 100644
index 000000000..5792fc10f
--- /dev/null
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
@@ -0,0 +1,104 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
+
+import java.util.*;
+import java.util.stream.Collectors;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class MergeEntitiesComparator implements Comparator<Oaf> {
+	static final List<String> PID_AUTHORITIES = Arrays
+		.asList(
+			ModelConstants.ARXIV_ID,
+			ModelConstants.PUBMED_CENTRAL_ID,
+			ModelConstants.EUROPE_PUBMED_CENTRAL_ID,
+			ModelConstants.DATACITE_ID,
+			ModelConstants.CROSSREF_ID);
+
+	static final List<String> RESULT_TYPES = Arrays
+		.asList(
+			ModelConstants.ORP_RESULTTYPE_CLASSID,
+			ModelConstants.SOFTWARE_RESULTTYPE_CLASSID,
+			ModelConstants.DATASET_RESULTTYPE_CLASSID,
+			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
+
+	public static final Comparator<Oaf> INSTANCE = new MergeEntitiesComparator();
+
+	@Override
+	public int compare(Oaf left, Oaf right) {
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return -1;
+		if (right == null)
+			return 1;
+
+		int res = 0;
+
+		// pid authority
+		int cfp1 = left
+			.getCollectedfrom()
+			.stream()
+			.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+			.max(Integer::compare)
+			.orElse(-1);
+		int cfp2 = right
+			.getCollectedfrom()
+			.stream()
+			.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+			.max(Integer::compare)
+			.orElse(-1);
+
+		if (cfp1 >= 0 && cfp1 > cfp2) {
+			return 1;
+		} else if (cfp2 >= 0 && cfp2 > cfp1) {
+			return -1;
+		}
+
+		// trust
+		if (left.getDataInfo() != null && right.getDataInfo() != null) {
+			res = left.getDataInfo().getTrust().compareTo(right.getDataInfo().getTrust());
+		}
+
+		// result type
+		if (res == 0) {
+			if (left instanceof Result && right instanceof Result) {
+				Result r1 = (Result) left;
+				Result r2 = (Result) right;
+
+				if (r1.getResulttype() == null || r1.getResulttype().getClassid() == null) {
+					if (r2.getResulttype() != null && r2.getResulttype().getClassid() != null) {
+						return -1;
+					}
+				} else if (r2.getResulttype() == null || r2.getResulttype().getClassid() == null) {
+					return 1;
+				}
+
+				int rt1 = RESULT_TYPES.indexOf(r1.getResulttype().getClassid());
+				int rt2 = RESULT_TYPES.indexOf(r2.getResulttype().getClassid());
+
+				if (rt1 >= 0 && rt1 > rt2) {
+					return 1;
+				} else if (rt2 >= 0 && rt2 > rt1) {
+					return -1;
+				}
+			}
+		}
+
+		// id
+		if (res == 0) {
+			if (left instanceof OafEntity && right instanceof OafEntity) {
+				res = ((OafEntity) left).getId().compareTo(((OafEntity) right).getId());
+			}
+		}
+
+		return res;
+	}
+
+}
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index 28db94766..f1221add3 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -40,27 +40,12 @@ public class MergeUtils {
 
 	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
 		boolean checkDelegateAuthority) {
-		TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
-			int res = 0;
 
-			if (o1.getDataInfo() != null && o2.getDataInfo() != null) {
-				res = o1.getDataInfo().getTrust().compareTo(o2.getDataInfo().getTrust());
-			}
+		ArrayList<T> sortedEntities = new ArrayList<>();
+		oafEntityIterator.forEachRemaining(sortedEntities::add);
+		sortedEntities.sort(MergeEntitiesComparator.INSTANCE.reversed());
 
-			if (res == 0) {
-				if (o1 instanceof Result && o2 instanceof Result) {
-					return ResultTypeComparator.INSTANCE.compare((Result) o1, (Result) o2);
-				}
-			}
-
-			return res;
-		});
-
-		while (oafEntityIterator.hasNext()) {
-			sortedEntities.add(oafEntityIterator.next());
-		}
-
-		Iterator<T> it = sortedEntities.descendingIterator();
+		Iterator<T> it = sortedEntities.iterator();
 		T merged = it.next();
 
 		while (it.hasNext()) {
@@ -143,7 +128,7 @@ public class MergeUtils {
 	 * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
 	 * such version.
 	 * <p>
-	 * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
+	 * Otherwise, it considers a resulttype priority order implemented in {@link MergeEntitiesComparator}
 	 * and proceeds with the canonical property merging.
 	 *
 	 * @param left
@@ -161,8 +146,9 @@ public class MergeUtils {
 		if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
 			return right;
 		}
+
 		// TODO: raise trust to have preferred fields from one or the other??
-		if (new ResultTypeComparator().compare(left, right) < 0) {
+		if (MergeEntitiesComparator.INSTANCE.compare(left, right) > 0) {
 			return mergeResultFields(left, right);
 		} else {
 			return mergeResultFields(right, left);
@@ -225,9 +211,9 @@ public class MergeUtils {
 
 	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
 		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
-		if (left == null) {
-			return right;
-		} else if (right == null) {
+		if (left == null || left.isEmpty()) {
+			return right != null ? right : new ArrayList<>();
+		} else if (right == null || right.isEmpty()) {
 			return left;
 		}
 
@@ -405,7 +391,7 @@ public class MergeUtils {
 		}
 
 		// should be an instance attribute, get the first non-null value
-		merge.setLanguage(coalesce(merge.getLanguage(), enrich.getLanguage()));
+		merge.setLanguage(coalesceQualifier(merge.getLanguage(), enrich.getLanguage()));
 
 		// distinct countries, do not manage datainfo
 		merge.setCountry(mergeQualifiers(merge.getCountry(), enrich.getCountry(), trust));
@@ -575,6 +561,13 @@ public class MergeUtils {
 		return m != null ? m : e;
 	}
 
+	private static Qualifier coalesceQualifier(Qualifier m, Qualifier e) {
+		if (m == null || m.getClassid() == null || StringUtils.isBlank(m.getClassid())) {
+			return e;
+		}
+		return m;
+	}
+
 	private static List<Author> mergeAuthors(List<Author> author, List<Author> author1, int trust) {
 		List<List<Author>> authors = new ArrayList<>();
 		if (author != null) {
@@ -587,6 +580,10 @@ public class MergeUtils {
 	}
 
 	private static String instanceKeyExtractor(Instance i) {
+		// three levels of concatenating:
+		// 1. ::
+		// 2. @@
+		// 3. ||
 		return String
 			.join(
 				"::",
@@ -594,10 +591,10 @@ public class MergeUtils {
 				kvKeyExtractor(i.getCollectedfrom()),
 				qualifierKeyExtractor(i.getAccessright()),
 				qualifierKeyExtractor(i.getInstancetype()),
-				Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
+				Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
 				Optional
 					.ofNullable(i.getPid())
-					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
 					.orElse(null));
 	}
 
@@ -706,7 +703,7 @@ public class MergeUtils {
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
 			.ofNullable(sp)
-			.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
+			.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
 			.orElse(null);
 	}
 
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java
new file mode 100644
index 000000000..726814c43
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java
@@ -0,0 +1,103 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.codehaus.jackson.map.ObjectMapper;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+import scala.Tuple2;
+
+class DatasetMergerTest implements Serializable {
+
+	private List<Tuple2<String, Dataset>> datasets;
+
+	private String testEntityBasePath;
+	private DataInfo dataInfo;
+	private final String dedupId = "50|doi_________::3d18564ef27ebe9ef3bd8b4dec67e148";
+	private Dataset dataset_top;
+
+	@BeforeEach
+	public void setUp() throws Exception {
+		testEntityBasePath = Paths
+			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
+			.toFile()
+			.getAbsolutePath();
+
+		datasets = readSample(testEntityBasePath + "/dataset_merge.json", Dataset.class);
+
+		dataset_top = getTopPub(datasets);
+
+		dataInfo = setDI();
+	}
+
+	@Test
+	void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
+		Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
+
+		// verify id
+		assertEquals(dedupId, pub_merged.getId());
+		assertEquals(2, pub_merged.getInstance().size());
+	}
+
+	public DataInfo setDI() {
+		DataInfo dataInfo = new DataInfo();
+		dataInfo.setTrust("0.9");
+		dataInfo.setDeletedbyinference(false);
+		dataInfo.setInferenceprovenance("testing");
+		dataInfo.setInferred(true);
+		return dataInfo;
+	}
+
+	public Dataset getTopPub(List<Tuple2<String, Dataset>> publications) {
+
+		Double maxTrust = 0.0;
+		Dataset maxPub = new Dataset();
+		for (Tuple2<String, Dataset> publication : publications) {
+			Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
+			if (pubTrust > maxTrust) {
+				maxTrust = pubTrust;
+				maxPub = publication._2();
+			}
+		}
+		return maxPub;
+	}
+
+	public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
+		List<Tuple2<String, T>> res = new ArrayList<>();
+		BufferedReader reader;
+		try {
+			reader = new BufferedReader(new FileReader(path));
+			String line = reader.readLine();
+			while (line != null) {
+				res
+					.add(
+						new Tuple2<>(
+							MapDocumentUtil.getJPathString("$.id", line),
+							new ObjectMapper().readValue(line, clazz)));
+				// read next line
+				line = reader.readLine();
+			}
+			reader.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		return res;
+	}
+
+}
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
index 4a5a3bd1b..995407edb 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java
@@ -93,14 +93,14 @@ class EntityMergerTest implements Serializable {
 		assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
 		assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
 		assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
-		assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
-		assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());
-		assertEquals(pub_top.getPublisher(), pub_merged.getPublisher());
-		assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate());
+		assertEquals(pub_top.getResulttype().getClassid(), pub_merged.getResulttype().getClassid());
+		assertEquals(pub_top.getLanguage().getClassid(), pub_merged.getLanguage().getClassid());
+		assertEquals("Elsevier BV", pub_merged.getPublisher().getValue());
+		assertEquals(pub_top.getEmbargoenddate().getValue(), pub_merged.getEmbargoenddate().getValue());
 		assertEquals(pub_top.getResourcetype().getClassid(), "");
 		assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation());
 		assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance());
-		assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
+		// assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
 		assertEquals(3, pub_merged.getInstance().size());
 		assertEquals(2, pub_merged.getCountry().size());
 		assertEquals(0, pub_merged.getSubject().size());
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/dataset_merge.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/dataset_merge.json
new file mode 100644
index 000000000..86d1a8133
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/dataset_merge.json
@@ -0,0 +1,2 @@
+{"publisher": {"value": "DANS Data Station Archaeology"}, "dateofcollection": "2024-04-30T12:49:55+0000", "dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": true}, "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "language": {"classid": "und", "classname": "Undetermined", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "author": [{"affiliation": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "(Geonius)"}], "fullname": "S.A.H. Augustin", "pid": [], "rank": 1}, {"affiliation": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "(Geonius)"}], "fullname": "J.J.G. Geraeds", "pid": [], "rank": 2}], "resourcetype": {"classid": "UNKNOWN", "classname": "Unknown", "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource"}, "originalId": ["50|datacite____::3d18564ef27ebe9ef3bd8b4dec67e148", "10.17026/ar/vt9ya1"], "description": [{"value": "In opdracht van Gemeente Beesel heeft Geonius Archeologie in maart 2023 een Inventariserend Veldonderzoek door middel van Proefsleuven (IVO-P) uitgevoerd voor het plangebied Heijackerstraat te Beesel in de gemeente Beesel. Aanleiding voor het uitvoeren van het archeologisch onderzoek vormt de aanvraag van een omgevingsvergunning voor bouw van 20 nieuwe woningen. Uit het vooronderzoek is gebleken dat het plangebied in een dalvakteterras ligt rondom opgestoven landduinen langsheen de Maas. De bodem bestaat volgens de bodemkaart uit vorstvaaggronden. Het plangebied is in het verleden voor zover kon worden vastgesteld in gebruik geweest als bouwland en is niet bebouwd geweest. Het IVO-O heeft uitgewezen dat de bodemopbouw deels intact is, al lijken in sommige boringen sporen van vergravingen of verstoringen te bevatten. Op grond van de resultaten van het vooronderzoek is een hoge verwachting opgesteld op het voorkomen van archeologische waarden uit het paleolithicum tot aan de vroege middeleeuwen. Voor de periode late middeleeuwen en nieuwe tijd is een lage verwachting opgesteld. Op grond van de resultaten van het vooronderzoek is een IVO-P uitgevoerd. Hierbij is een vindplaats aangetroffen bestaande uit drie subrecente greppels en een tweetal recente verstoringen. De vindplaats is als niet behoudenswaardig gewaardeerd. Aanbevolen is het plangebied vrij te geven voor de geplande ontwikkeling."}], "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Archeologisch onderzoek IVO-P plangebied Heijackerstraat te Beesel"}], "pid": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17026/ar/vt9ya1"}], "id": "50|doi_________::3d18564ef27ebe9ef3bd8b4dec67e148", "instance": [{"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemeid": "dnet:review_levels", "schemename": "dnet:review_levels"}, "hostedby": {"key": "10|re3data_____::84e123776089ce3c7a33db98d9cd15a8", "value": "EASY"}, "url": ["https://dx.doi.org/10.17026/ar/vt9ya1"], "pid": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17026/ar/vt9ya1"}], "instanceTypeMapping": [{"originalType": "Dataset", "typeLabel": "dataset", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_ddb1"}], "dateofacceptance": {"value": "2024-01-01"}, "collectedfrom": {"key": "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254", "value": "Datacite"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0021", "classname": "Dataset", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "relevantdate": [{"qualifier": {"classid": "issued", "classname": "issued", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2024-01-01"}], "resulttype": {"classid": "dataset", "classname": "dataset", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "context": [], "collectedfrom": [{"key": "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254", "value": "Datacite"}], "dateoftransformation": "2024-04-30T12:49:55+0000", "subject": [], "dateofacceptance": {"value": "2024-01-01"}, "metaResourceType": {"classid": "Research Data", "classname": "Research Data", "schemeid": "openaire::meta_resource_types", "schemename": "openaire::meta_resource_types"}}
+{"geolocation": [{"box": "", "place": "", "point": ""}], "dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": true}, "resourcetype": {"classid": "dataset", "classname": "dataset", "schemeid": "dnet:dataCite_resource", "schemename": "dnet:dataCite_resource"}, "pid": [], "contributor": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "Geonius"}], "oaiprovenance": {"originDescription": {"metadataNamespace": "", "harvestDate": "2024-05-05T04:33:31Z", "baseURL": "https://easy.dans.knaw.nl/oai", "datestamp": "", "altered": true, "identifier": "oai:easy.dans.knaw.nl:easy-dataset:341200"}}, "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "relevantdate": [], "collectedfrom": [{"key": "10|re3data_____::730f562f9efe8a3b3742d2da510d4335", "value": "B2FIND"}], "id": "50|r3730f562f9e::ace629fb505b6b4343faca03edde1841", "subject": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Ancient Cultures"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Humanities"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemeid": "dnet:subject_classification_typologies", "schemename": "dnet:subject_classification_typologies"}, "value": "Archaeology"}], "lastupdatetimestamp": 1716803651625, "author": [{"surname": "Augustin", "name": "S. A. H.", "pid": [], "rank": 1, "affiliation": [], "fullname": "S.A.H. Augustin"}, {"surname": "Geraeds", "name": "J. J. G.", "pid": [], "rank": 2, "affiliation": [], "fullname": "J.J.G. Geraeds"}], "instance": [{"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemeid": "dnet:review_levels", "schemename": "dnet:review_levels"}, "hostedby": {"key": "10|re3data_____::84e123776089ce3c7a33db98d9cd15a8", "value": "DANS-EASY"}, "url": ["http://dx.doi.org/https://doi.org/10.17026/AR/VT9YA1"], "pid": [], "instanceTypeMapping": [{"originalType": "Dataset", "typeLabel": "dataset", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_ddb1"}], "alternateIdentifier": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17026/ar/vt9ya1"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17026/ar/vt9ya1"}, {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.17026/ar/vt9ya1"}], "dateofacceptance": {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "2024-01-01"}, "collectedfrom": {"key": "10|re3data_____::730f562f9efe8a3b3742d2da510d4335", "value": "B2FIND"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0021", "classname": "Dataset", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2024-05-10T00:02:09+0000", "metaResourceType": {"classid": "Research Data", "classname": "Research Data", "schemeid": "openaire::meta_resource_types", "schemename": "openaire::meta_resource_types"}, "dateoftransformation": "2024-05-26T00:23:54.028Z", "description": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "In opdracht van Gemeente Beesel heeft Geonius Archeologie in maart 2023 een Inventariserend Veldonderzoek door middel van Proefsleuven (IVO-P) uitgevoerd voor het plangebied Heijackerstraat te Beesel in de gemeente Beesel. Aanleiding voor het uitvoeren van het archeologisch onderzoek vormt de aanvraag van een omgevingsvergunning voor bouw van 20 nieuwe woningen. Uit het vooronderzoek is gebleken dat het plangebied in een dalvakteterras ligt rondom opgestoven landduinen langsheen de Maas. De bodem bestaat volgens de bodemkaart uit vorstvaaggronden. Het plangebied is in het verleden voor zover kon worden vastgesteld in gebruik geweest als bouwland en is niet bebouwd geweest. Het IVO-O heeft uitgewezen dat de bodemopbouw deels intact is, al lijken in sommige boringen sporen van vergravingen of verstoringen te bevatten. Op grond van de resultaten van het vooronderzoek is een hoge verwachting opgesteld op het voorkomen van archeologische waarden uit het paleolithicum tot aan de vroege middeleeuwen. Voor de periode late middeleeuwen en nieuwe tijd is een lage verwachting opgesteld. Op grond van de resultaten van het vooronderzoek is een IVO-P uitgevoerd. Hierbij is een vindplaats aangetroffen bestaande uit drie subrecente greppels en een tweetal recente verstoringen. De vindplaats is als niet behoudenswaardig gewaardeerd. Aanbevolen is het plangebied vrij te geven voor de geplande ontwikkeling."}], "format": [], "coverage": [], "externalReference": [], "publisher": {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "Data Archiving and Networked Services (DANS)"}, "context": [], "eoscifguidelines": [], "language": {"classid": "und", "classname": "Undetermined", "schemeid": "dnet:languages", "schemename": "dnet:languages"}, "resulttype": {"classid": "dataset", "classname": "dataset", "schemeid": "dnet:result_typologies", "schemename": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["oai:easy.dans.knaw.nl:easy-dataset:341200", "50|r3730f562f9e::ace629fb505b6b4343faca03edde1841"], "source": [], "dateofacceptance": {"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "value": "2024-01-01"}, "title": [{"dataInfo": {"invisible": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "trust": "0.9", "inferred": false, "deletedbyinference": false}, "qualifier": {"classid": "main title", "classname": "main title", "schemeid": "dnet:dataCite_title", "schemename": "dnet:dataCite_title"}, "value": "Archeologisch onderzoek IVO-P plangebied Heijackerstraat te Beesel"}]}
\ No newline at end of file

From 92c3abd5a4e969cc47313b851f2f93f5c7dcfc87 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 29 May 2024 14:36:49 +0200
Subject: [PATCH 019/239] [graph cleaning] use sparkExecutorMemory to define
 also the memoryOverhead

---
 .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml  | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
index f6bf053cd..4188cb018 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
@@ -156,6 +156,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -190,6 +191,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -224,6 +226,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -258,6 +261,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -292,6 +296,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -326,6 +331,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -360,6 +366,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -394,6 +401,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}

From 1477406ecc06eafcc704c55e2a317a74e13fcf62 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Wed, 5 Jun 2024 16:20:40 +0200
Subject: [PATCH 020/239] [bulkTag] fixed issue that made project disappear in
 graph_10_enriched

---
 .../src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
index 9e1acc7b2..354741690 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
@@ -172,7 +172,7 @@ public class SparkBulkTagJob {
 			.option("compression", "gzip")
 			.json(outputPath + "project");
 
-		readPath(spark, outputPath + "project", Datasource.class)
+		readPath(spark, outputPath + "project", Project.class)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")

From ec79405cc9e4cbdadeb983be3b01408c259bc751 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 7 Jun 2024 11:30:31 +0200
Subject: [PATCH 021/239] [graph raw] set organization type from openorgs

---
 .../dhp/oa/graph/raw/MigrateDbEntitiesApplication.java     | 1 +
 .../dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql | 7 +++++--
 pom.xml                                                    | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
index da6885db3..c9a32cde6 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
@@ -398,6 +398,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 			o.setEcsmevalidated(field(Boolean.toString(rs.getBoolean("ecsmevalidated")), info));
 			o.setEcnutscode(field(Boolean.toString(rs.getBoolean("ecnutscode")), info));
 			o.setCountry(prepareQualifierSplitting(rs.getString("country")));
+			o.setOrganizationType(Organization.OrganizationType.valueOf(rs.getString("typology")));
 			o.setDataInfo(info);
 			o.setLastupdatetimestamp(lastUpdateTimestamp);
 
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql
index 0ec303939..16ad9e265 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForProvision.sql
@@ -28,7 +28,8 @@ SELECT
     (array_remove(array_cat(ARRAY[o.ec_internationalorganization], array_agg(od.ec_internationalorganization)), NULL))[1]              AS ecinternationalorganization,
     (array_remove(array_cat(ARRAY[o.ec_enterprise], array_agg(od.ec_enterprise)), NULL))[1]                      AS ecenterprise,
     (array_remove(array_cat(ARRAY[o.ec_smevalidated], array_agg(od.ec_smevalidated)), NULL))[1]                    AS ecsmevalidated,
-    (array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1]                       AS ecnutscode
+    (array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1]                       AS ecnutscode,
+    org_types.name                                                                                              AS typology
 FROM organizations o
 	LEFT OUTER JOIN acronyms a    ON (a.id = o.id)
 	LEFT OUTER JOIN urls u        ON (u.id = o.id)
@@ -37,6 +38,7 @@ FROM organizations o
 	LEFT OUTER JOIN oa_duplicates d ON (o.id = d.local_id AND d.reltype != 'is_different')
     LEFT OUTER JOIN organizations od ON (d.oa_original_id = od.id)
     LEFT OUTER JOIN other_ids idup  ON (od.id = idup.id)
+    LEFT OUTER JOIN org_types ON (org_types.val = o.type)
 WHERE
     o.status = 'approved' OR o.status = 'suggested'
 GROUP BY
@@ -44,4 +46,5 @@ GROUP BY
 	o.name,
 	o.creation_date,
 	o.modification_date,
-	o.country;
\ No newline at end of file
+	o.country,
+	org_types.name;
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index cc8d509f7..9e554204d 100644
--- a/pom.xml
+++ b/pom.xml
@@ -960,7 +960,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.2]</dhp-schemas.version>
+        <dhp-schemas.version>[6.1.3-SNAPSHOT]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From c7265724182b7747540e69eaec2732799dca2d0f Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Fri, 7 Jun 2024 12:03:26 +0200
Subject: [PATCH 022/239] changed some parameters in OSF test

---
 .../dhp/collection/plugin/rest/OsfPreprintCollectorTest.java  | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
index 0e64f8bab..a1b723e33 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
@@ -36,8 +36,8 @@ public class OsfPreprintCollectorTest {
 	private final String resultTotalXpath = "/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']";
 
 	private final String resumptionParam = "page";
-	private final String resumptionType = "page";
-	private final String resumptionXpath = "/*/*[local-name()='links']/*[local-name()='next']";
+	private final String resumptionType = "scan";
+	private final String resumptionXpath = "substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')";
 
 	private final String resultSizeParam = "page[size]";
 	private final String resultSizeValue = "100";

From 3776327a8cc3e725af8af49255598681eac83d1f Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 10 Jun 2024 15:22:33 +0200
Subject: [PATCH 023/239] hostedby patching to work with the updated Crossref
 contents, resolved conflict

---
 .../SparkApplyHostedByMapToResult.scala       | 39 ++++++++++++-------
 1 file changed, 25 insertions(+), 14 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala
index a900fc241..db7edf53e 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala
@@ -25,27 +25,38 @@ object SparkApplyHostedByMapToResult {
           val i = p.getInstance().asScala
           if (i.size == 1) {
             val inst: Instance = i.head
-            inst.getHostedby.setKey(ei.getHostedById)
-            inst.getHostedby.setValue(ei.getName)
-            if (ei.getOpenAccess) {
-              inst.setAccessright(
-                OafMapperUtils.accessRight(
-                  ModelConstants.ACCESS_RIGHT_OPEN,
-                  "Open Access",
-                  ModelConstants.DNET_ACCESS_MODES,
-                  ModelConstants.DNET_ACCESS_MODES
-                )
-              )
-              inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)
-              p.setBestaccessright(OafMapperUtils.createBestAccessRights(p.getInstance()));
-            }
+            patchInstance(p, ei, inst)
 
+          } else {
+            val cf = i.map(ii => ii.getCollectedfrom.getValue)
+            if (cf.contains("Crossref")) {
+              i.foreach(ii => {
+                patchInstance(p, ei, ii)
+              })
+            }
           }
         }
         p
       })(Encoders.bean(classOf[Publication]))
   }
 
+  private def patchInstance(p: Publication, ei: EntityInfo, inst: Instance): Unit = {
+    inst.getHostedby.setKey(ei.getHostedById)
+    inst.getHostedby.setValue(ei.getName)
+    if (ei.getOpenAccess) {
+      inst.setAccessright(
+        OafMapperUtils.accessRight(
+          ModelConstants.ACCESS_RIGHT_OPEN,
+          "Open Access",
+          ModelConstants.DNET_ACCESS_MODES,
+          ModelConstants.DNET_ACCESS_MODES
+        )
+      )
+      inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)
+      p.setBestaccessright(OafMapperUtils.createBestAccessRights(p.getInstance()));
+    }
+  }
+
   def main(args: Array[String]): Unit = {
 
     val logger: Logger = LoggerFactory.getLogger(getClass)

From b0eba210c068219580cfa78c17aa23f2e1e170f8 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 10 Jun 2024 16:15:07 +0200
Subject: [PATCH 024/239] [actionset promotion] use sparkExecutorMemory to
 define also the memoryOverhead

---
 dhp-shade-package/dependency-reduced-pom.xml  | 113 ++++++++++++++++++
 .../wf/dataset/oozie_app/workflow.xml         |   2 +
 .../wf/datasource/oozie_app/workflow.xml      |   1 +
 .../wf/main/oozie_app/workflow.xml            |   1 +
 .../wf/organization/oozie_app/workflow.xml    |   1 +
 .../oozie_app/workflow.xml                    |   4 +-
 .../wf/project/oozie_app/workflow.xml         |   1 +
 .../wf/publication/oozie_app/workflow.xml     |   6 +-
 .../wf/relation/oozie_app/workflow.xml        |   3 +-
 .../wf/software/oozie_app/workflow.xml        |   4 +-
 10 files changed, 131 insertions(+), 5 deletions(-)
 create mode 100644 dhp-shade-package/dependency-reduced-pom.xml

diff --git a/dhp-shade-package/dependency-reduced-pom.xml b/dhp-shade-package/dependency-reduced-pom.xml
new file mode 100644
index 000000000..04843072f
--- /dev/null
+++ b/dhp-shade-package/dependency-reduced-pom.xml
@@ -0,0 +1,113 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+  <parent>
+    <artifactId>dhp</artifactId>
+    <groupId>eu.dnetlib.dhp</groupId>
+    <version>1.2.5-SNAPSHOT</version>
+  </parent>
+  <modelVersion>4.0.0</modelVersion>
+  <artifactId>dhp-shade-package</artifactId>
+  <description>This module create a jar of all module dependencies</description>
+  <build>
+    <plugins>
+      <plugin>
+        <artifactId>maven-shade-plugin</artifactId>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>shade</goal>
+            </goals>
+            <configuration>
+              <transformers>
+                <transformer>
+                  <mainClass>eu.dnetlib.dhp.oa.dedup.SparkCreateSimRels</mainClass>
+                </transformer>
+                <transformer />
+                <transformer>
+                  <resource>META-INF/cxf/bus-extensions.txt</resource>
+                </transformer>
+              </transformers>
+              <filters>
+                <filter>
+                  <artifact>*:*</artifact>
+                  <excludes>
+                    <exclude>META-INF/maven/**</exclude>
+                    <exclude>META-INF/*.SF</exclude>
+                    <exclude>META-INF/*.DSA</exclude>
+                    <exclude>META-INF/*.RSA</exclude>
+                  </excludes>
+                </filter>
+              </filters>
+              <relocations>
+                <relocation>
+                  <pattern>com</pattern>
+                  <shadedPattern>repackaged.com.google.common</shadedPattern>
+                  <includes>
+                    <include>com.google.common.**</include>
+                  </includes>
+                </relocation>
+              </relocations>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+  <dependencies>
+    <dependency>
+      <groupId>org.projectlombok</groupId>
+      <artifactId>lombok</artifactId>
+      <version>1.18.28</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter</artifactId>
+      <version>5.6.1</version>
+      <scope>test</scope>
+      <exclusions>
+        <exclusion>
+          <artifactId>junit-jupiter-api</artifactId>
+          <groupId>org.junit.jupiter</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>junit-jupiter-params</artifactId>
+          <groupId>org.junit.jupiter</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>junit-jupiter-engine</artifactId>
+          <groupId>org.junit.jupiter</groupId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-core</artifactId>
+      <version>3.3.3</version>
+      <scope>test</scope>
+      <exclusions>
+        <exclusion>
+          <artifactId>byte-buddy</artifactId>
+          <groupId>net.bytebuddy</groupId>
+        </exclusion>
+        <exclusion>
+          <artifactId>byte-buddy-agent</artifactId>
+          <groupId>net.bytebuddy</groupId>
+        </exclusion>
+      </exclusions>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-junit-jupiter</artifactId>
+      <version>3.3.3</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+  <distributionManagement>
+    <site>
+      <id>DHPSite</id>
+      <url>${dhp.site.stage.path}/dhp-common</url>
+    </site>
+  </distributionManagement>
+</project>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
index 5401b45ca..b1bc1d6e1 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/dataset/oozie_app/workflow.xml
@@ -103,6 +103,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -156,6 +157,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml
index f9bd66ae3..9a84f4708 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/datasource/oozie_app/workflow.xml
@@ -95,6 +95,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
index 393f04e89..65ddd402b 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
@@ -125,6 +125,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml
index ebfdeee31..0d73b498d 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/organization/oozie_app/workflow.xml
@@ -95,6 +95,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
index 02399ed9b..ca8362c9b 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/otherresearchproduct/oozie_app/workflow.xml
@@ -103,6 +103,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -155,11 +156,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=2560
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/otherresearchproduct</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml
index 57c2357b4..37310da79 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/project/oozie_app/workflow.xml
@@ -95,6 +95,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
index 92b114776..a4b0b237c 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml
@@ -103,11 +103,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7000
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@@ -156,11 +157,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7000
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml
index e9e5f0b45..f72847ba8 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml
@@ -95,11 +95,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=10000
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
index 1d36ddf94..dbe8a63c1 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/software/oozie_app/workflow.xml
@@ -103,6 +103,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -155,11 +156,12 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=2560
+                --conf spark.sql.shuffle.partitions=4000
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/software</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>

From 85c1eae7e0da86e25aa2da74d90ac82ecf150e27 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Mon, 10 Jun 2024 19:03:30 +0200
Subject: [PATCH 025/239] Fixes for pagination strategy looping at end of
 download

---
 .../collection/plugin/rest/RestIterator.java  | 58 +++++++++++++------
 1 file changed, 40 insertions(+), 18 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
index 2518fd92f..9037a454e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
@@ -12,6 +12,8 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Queue;
 import java.util.concurrent.PriorityBlockingQueue;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 
 import javax.xml.transform.OutputKeys;
 import javax.xml.transform.Transformer;
@@ -19,16 +21,10 @@ import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerFactory;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathExpression;
-import javax.xml.xpath.XPathExpressionException;
-import javax.xml.xpath.XPathFactory;
+import javax.xml.xpath.*;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.http.HttpHeaders;
-import org.apache.http.entity.ContentType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.w3c.dom.Node;
@@ -51,7 +47,6 @@ import eu.dnetlib.dhp.common.collection.HttpClientParams;
  *
  */
 public class RestIterator implements Iterator<String> {
-
 	private static final Logger log = LoggerFactory.getLogger(RestIterator.class);
 	public static final String UTF_8 = "UTF-8";
 	private static final int MAX_ATTEMPTS = 5;
@@ -60,11 +55,15 @@ public class RestIterator implements Iterator<String> {
 
 	private final String AUTHBASIC = "basic";
 
+	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG
+		+ ">";
+
 	private final String baseUrl;
 	private final String resumptionType;
 	private final String resumptionParam;
 	private final String resultFormatValue;
-	private String queryParams;
+	private String queryParams = "";
 	private final int resultSizeValue;
 	private int resumptionInt = 0; // integer resumption token (first record to harvest)
 	private int resultTotal = -1;
@@ -158,7 +157,12 @@ public class RestIterator implements Iterator<String> {
 	}
 
 	private void initQueue() {
-		this.query = this.baseUrl + "?" + this.queryParams + this.querySize + this.queryFormat;
+		if (queryParams.equals("") && querySize.equals("") && queryFormat.equals("")) {
+			query = baseUrl;
+		} else {
+			query = baseUrl + "?" + queryParams + querySize + queryFormat;
+		}
+
 		log.info("REST calls starting with {}", this.query);
 	}
 
@@ -219,9 +223,8 @@ public class RestIterator implements Iterator<String> {
 
 		try {
 			String resultJson;
-			String resultXml = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+			String resultXml = XML_HEADER;
 			String nextQuery = "";
-			final String emptyXml = resultXml + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
 			Node resultNode = null;
 			NodeList nodeList = null;
 			String qUrlArgument = "";
@@ -236,6 +239,21 @@ public class RestIterator implements Iterator<String> {
 				}
 			}
 
+			// find pagination page start number in queryParam and remove before start the first query
+			if ((resumptionType.toLowerCase().equals("pagination") || resumptionType.toLowerCase().equals("page"))
+				&& (query.contains("paginationStart="))) {
+
+				final Matcher m = Pattern.compile("paginationStart=([0-9]+)").matcher(query);
+				m.find(); // guaranteed to be true for this regex
+
+				String[] pageVal = m.group(0).split("=");
+				pagination = Integer.parseInt(pageVal[1]);
+
+				// remove page start number from queryParams
+				query = query.replaceFirst("&?paginationStart=[0-9]+", "");
+
+			}
+
 			try {
 				log.info("requesting URL [{}]", query);
 
@@ -261,7 +279,7 @@ public class RestIterator implements Iterator<String> {
 					this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
 				}
 
-				if (!(emptyXml).equalsIgnoreCase(resultXml)) {
+				if (!isEmptyXml(resultXml)) {
 					resultNode = (Node) this.xpath
 						.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
 					nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
@@ -270,8 +288,7 @@ public class RestIterator implements Iterator<String> {
 						final StringWriter sw = new StringWriter();
 						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
 						final String toEnqueue = sw.toString();
-						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue)
-							|| emptyXml.equalsIgnoreCase(toEnqueue)) {
+						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
 							log
 								.warn(
 									"The following record resulted in empty item for the feeding queue: {}", resultXml);
@@ -299,6 +316,7 @@ public class RestIterator implements Iterator<String> {
 							throw new CollectorException("Mode: discover, Param 'resultSizeValue' is less than 2");
 						}
 						qUrlArgument = qUrl.getQuery();
+
 						final String[] arrayQUrlArgument = qUrlArgument.split("&");
 						for (final String arrayUrlArgStr : arrayQUrlArgument) {
 							if (arrayUrlArgStr.startsWith(this.resumptionParam)) {
@@ -312,7 +330,7 @@ public class RestIterator implements Iterator<String> {
 							}
 						}
 
-						if (((emptyXml).equalsIgnoreCase(resultXml))
+						if (isEmptyXml(resultXml)
 							|| ((nodeList != null) && (nodeList.getLength() < this.resultSizeValue))) {
 							// resumptionStr = "";
 							if (nodeList != null) {
@@ -331,13 +349,13 @@ public class RestIterator implements Iterator<String> {
 
 					case "pagination":
 					case "page": // pagination, iterate over page numbers
-						this.pagination += 1;
-						if (nodeList != null) {
+						if (nodeList != null && nodeList.getLength() > 0) {
 							this.discoverResultSize += nodeList.getLength();
 						} else {
 							this.resultTotal = this.discoverResultSize;
 							this.pagination = this.discoverResultSize;
 						}
+						this.pagination += 1;
 						this.resumptionInt = this.pagination;
 						this.resumptionStr = Integer.toString(this.resumptionInt);
 						break;
@@ -415,6 +433,10 @@ public class RestIterator implements Iterator<String> {
 
 	}
 
+	private boolean isEmptyXml(String s) {
+		return EMPTY_XML.equalsIgnoreCase(s);
+	}
+
 	private boolean isInteger(final String s) {
 		boolean isValidInteger = false;
 		try {

From 9da006e98ceb53a120be36b5529f90ec765639b6 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 11 Jun 2024 10:28:32 +0200
Subject: [PATCH 026/239] [SDGFoSActionSet]remove datainfo for the result. It
 is not needed (qualifier.classid = UPDATE) useless since subject do not go at
 the level of the instance

---
 .../PrepareFOSSparkJob.java                        | 14 +-------------
 .../PrepareSDGSparkJob.java                        | 14 +-------------
 2 files changed, 2 insertions(+), 26 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
index c248423d4..ec957a208 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
@@ -115,19 +115,7 @@ public class PrepareFOSSparkJob implements Serializable {
 			.forEach(
 				l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
 		r.setSubject(sbjs);
-		r
-			.setDataInfo(
-				OafMapperUtils
-					.dataInfo(
-						false, null, true,
-						false,
-						OafMapperUtils
-							.qualifier(
-								ModelConstants.PROVENANCE_ENRICH,
-								null,
-								ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						null));
+
 		return r;
 	}
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
index bfdf14234..a88607986 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
@@ -81,19 +81,7 @@ public class PrepareSDGSparkJob implements Serializable {
 						s -> sbjs
 							.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
 				r.setSubject(sbjs);
-				r
-					.setDataInfo(
-						OafMapperUtils
-							.dataInfo(
-								false, null, true,
-								false,
-								OafMapperUtils
-									.qualifier(
-										ModelConstants.PROVENANCE_ENRICH,
-										null,
-										ModelConstants.DNET_PROVENANCE_ACTIONS,
-										ModelConstants.DNET_PROVENANCE_ACTIONS),
-								null));
+
 				return r;
 			}, Encoders.bean(Result.class))
 			.write()

From a8d68c9d294518734d9e6ac724ab40d9e4ff5d3d Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 11 Jun 2024 12:40:50 +0200
Subject: [PATCH 027/239] avoid NPEs

---
 .../oaf/utils/MergeEntitiesComparator.java    | 30 ++++++++++---------
 1 file changed, 16 insertions(+), 14 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
index 5792fc10f..ff6c2689a 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
@@ -1,13 +1,9 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
-import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
-
 import java.util.*;
-import java.util.stream.Collectors;
 
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Result;
@@ -42,17 +38,23 @@ public class MergeEntitiesComparator implements Comparator<Oaf> {
 		int res = 0;
 
 		// pid authority
-		int cfp1 = left
-			.getCollectedfrom()
-			.stream()
-			.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
-			.max(Integer::compare)
+		int cfp1 = Optional
+			.ofNullable(left.getCollectedfrom())
+			.map(
+				cf -> cf
+					.stream()
+					.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+					.max(Integer::compare)
+					.orElse(-1))
 			.orElse(-1);
-		int cfp2 = right
-			.getCollectedfrom()
-			.stream()
-			.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
-			.max(Integer::compare)
+		int cfp2 = Optional
+			.ofNullable(right.getCollectedfrom())
+			.map(
+				cf -> cf
+					.stream()
+					.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+					.max(Integer::compare)
+					.orElse(-1))
 			.orElse(-1);
 
 		if (cfp1 >= 0 && cfp1 > cfp2) {

From 11fe3a4fe0af870ee519de5dd546d2d28483c4a4 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 11 Jun 2024 14:21:01 +0200
Subject: [PATCH 028/239] [graph resolution] use sparkExecutorMemory to define
 also the memoryOverhead

---
 .../eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml
index 74e792f07..916a9f2b1 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml
@@ -45,6 +45,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.shuffle.partitions=15000
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -79,6 +80,7 @@
                 --executor-memory=${sparkExecutorMemory}
                 --executor-cores=${sparkExecutorCores}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.shuffle.partitions=10000
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}

From 4f2a61e10fc5b6983f6f637120eef0c67f38f73d Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Wed, 29 May 2024 23:05:20 +0200
Subject: [PATCH 029/239] Change the selection criteria for the pivot record of
 a group so that by best pid type becomes the first criteria. This will have
 the effect to slowly converge to records having DOI pid

---
 .../main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
index f73ff92ec..0ff40f6f8 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java
@@ -203,8 +203,8 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 			WindowSpec w = Window
 				.partitionBy("groupId")
 				.orderBy(
-					col("lastUsage").desc_nulls_last(),
 					col("pidType").asc_nulls_last(),
+					col("lastUsage").desc_nulls_last(),
 					col("collectedfrom").desc_nulls_last(),
 					col("date").asc_nulls_last(),
 					col("id").asc_nulls_last());

From d90cb099b8deababf4428626fd9e7f164fbe2ae1 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Tue, 11 Jun 2024 20:23:44 +0200
Subject: [PATCH 030/239] Fix for paginationStart parameter management

---
 .../eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
index 9037a454e..caef266d7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
@@ -249,7 +249,8 @@ public class RestIterator implements Iterator<String> {
 				String[] pageVal = m.group(0).split("=");
 				pagination = Integer.parseInt(pageVal[1]);
 
-				// remove page start number from queryParams
+				// remove page start number from query and queryParams
+				queryParams = queryParams.replaceFirst("&?paginationStart=[0-9]+", "");
 				query = query.replaceFirst("&?paginationStart=[0-9]+", "");
 
 			}

From 9bf2bda1c6916ea45675a71e9c115c83182371bd Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Wed, 12 Jun 2024 13:28:51 +0200
Subject: [PATCH 031/239] Fix: next returned a null value at end of stream

---
 .../collection/plugin/rest/RestIterator.java  | 30 +++++++++++--------
 1 file changed, 17 insertions(+), 13 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
index caef266d7..0895d5f43 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java
@@ -176,19 +176,6 @@ public class RestIterator implements Iterator<String> {
 	 */
 	@Override
 	public boolean hasNext() {
-		if (this.recordQueue.isEmpty() && this.query.isEmpty()) {
-			disconnect();
-			return false;
-		}
-		return true;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * @see java.util.Iterator#next()
-	 */
-	@Override
-	public String next() {
 		synchronized (this.recordQueue) {
 			while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
 				try {
@@ -198,6 +185,23 @@ public class RestIterator implements Iterator<String> {
 					throw new RuntimeException(e);
 				}
 			}
+
+			if (!this.recordQueue.isEmpty()) {
+				return true;
+			}
+
+			disconnect();
+			return false;
+		}
+	}
+
+	/*
+	 * (non-Javadoc)
+	 * @see java.util.Iterator#next()
+	 */
+	@Override
+	public String next() {
+		synchronized (this.recordQueue) {
 			return this.recordQueue.poll();
 		}
 	}

From d942a1101bfb60b536f56e39ab9a7a00925ac6f3 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Fri, 14 Jun 2024 12:14:38 +0300
Subject: [PATCH 032/239] Miscellaneous updates to the copying operation to
 Impala Cluster: - Show some counts and the elapsed time for various
 sub-tasks. - Code polishing.

---
 .../oozie_app/copyDataToImpalaCluster.sh      | 35 +++++++++++--------
 .../oozie_app/copyDataToImpalaCluster.sh      | 35 +++++++++++--------
 .../oozie_app/copyDataToImpalaCluster.sh      | 35 +++++++++++--------
 .../oozie_app/copyDataToImpalaCluster.sh      | 35 +++++++++++--------
 4 files changed, 80 insertions(+), 60 deletions(-)

diff --git a/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
index ca0f7a643..55deada40 100644
--- a/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
@@ -55,20 +55,20 @@ function print_elapsed_time()
   hours=$((elapsed_time / 3600))
   minutes=$(((elapsed_time % 3600) / 60))
   seconds=$((elapsed_time % 60))
-  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+  printf "%02d:%02d:%02d" $hours $minutes $seconds
 }
 
 
 function copydb() {
   db=$1
-  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
+  start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
-    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
+    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
     rm -f error.log
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
@@ -78,6 +78,7 @@ function copydb() {
   fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
+  start_file_transfer_time=$(date +%s)
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
   # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
@@ -93,7 +94,7 @@ function copydb() {
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
   if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
-    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
+    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster, after: $(print_elapsed_time start_file_transfer_time)\n"
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
@@ -118,6 +119,7 @@ function copydb() {
   fi
 
   echo -e "\nCreating schema for db: '${db}'\n"
+  start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
@@ -128,7 +130,8 @@ function copydb() {
   all_create_view_statements=()
   num_tables=0
 
-  entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
+  entities_on_ocean=(`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`)  # Get the tables and views without any potential the "WARN" logs.
+  echo -e "\nGoing to create ${#entities_on_ocean[@]} entities for db '${db}'..\n"
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
     create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
@@ -152,8 +155,9 @@ function copydb() {
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            rm -f error.log
             exit 6
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
         fi
       fi
     fi
@@ -208,8 +212,11 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
+  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
+
+  start_compute_stats_time=$(date +%s)
   echo -e "\nComputing stats for tables..\n"
-  entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
@@ -221,20 +228,18 @@ function copydb() {
     fi
   done
 
+  echo -e "\nFinished computing stats for tables, after: $(print_elapsed_time start_compute_stats_time)\n"
+  rm -f error.log # Cleanup the temp log-file.
+
   # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
-  if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
-    echo -e "\nAll entities have been copied to Impala cluster.\n"
+  if [[ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]]; then
+    echo -e "\nAll entities have been copied to Impala cluster.\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
   else
-    echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
-    rm -f error.log
+    echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 8
     fi
   fi
-
-  rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n"
-  print_elapsed_time start_db_time
 }
 
 
diff --git a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
index ca0f7a643..55deada40 100644
--- a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
@@ -55,20 +55,20 @@ function print_elapsed_time()
   hours=$((elapsed_time / 3600))
   minutes=$(((elapsed_time % 3600) / 60))
   seconds=$((elapsed_time % 60))
-  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+  printf "%02d:%02d:%02d" $hours $minutes $seconds
 }
 
 
 function copydb() {
   db=$1
-  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
+  start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
-    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
+    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
     rm -f error.log
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
@@ -78,6 +78,7 @@ function copydb() {
   fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
+  start_file_transfer_time=$(date +%s)
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
   # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
@@ -93,7 +94,7 @@ function copydb() {
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
   if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
-    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
+    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster, after: $(print_elapsed_time start_file_transfer_time)\n"
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
@@ -118,6 +119,7 @@ function copydb() {
   fi
 
   echo -e "\nCreating schema for db: '${db}'\n"
+  start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
@@ -128,7 +130,8 @@ function copydb() {
   all_create_view_statements=()
   num_tables=0
 
-  entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
+  entities_on_ocean=(`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`)  # Get the tables and views without any potential the "WARN" logs.
+  echo -e "\nGoing to create ${#entities_on_ocean[@]} entities for db '${db}'..\n"
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
     create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
@@ -152,8 +155,9 @@ function copydb() {
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            rm -f error.log
             exit 6
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
         fi
       fi
     fi
@@ -208,8 +212,11 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
+  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
+
+  start_compute_stats_time=$(date +%s)
   echo -e "\nComputing stats for tables..\n"
-  entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
@@ -221,20 +228,18 @@ function copydb() {
     fi
   done
 
+  echo -e "\nFinished computing stats for tables, after: $(print_elapsed_time start_compute_stats_time)\n"
+  rm -f error.log # Cleanup the temp log-file.
+
   # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
-  if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
-    echo -e "\nAll entities have been copied to Impala cluster.\n"
+  if [[ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]]; then
+    echo -e "\nAll entities have been copied to Impala cluster.\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
   else
-    echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
-    rm -f error.log
+    echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 8
     fi
   fi
-
-  rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n"
-  print_elapsed_time start_db_time
 }
 
 
diff --git a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
index dd2203eef..43498abd2 100644
--- a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
@@ -55,20 +55,20 @@ function print_elapsed_time()
   hours=$((elapsed_time / 3600))
   minutes=$(((elapsed_time % 3600) / 60))
   seconds=$((elapsed_time % 60))
-  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+  printf "%02d:%02d:%02d" $hours $minutes $seconds
 }
 
 
 function copydb() {
   db=$1
-  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
+  start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
-    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
+    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
     rm -f error.log
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
@@ -78,6 +78,7 @@ function copydb() {
   fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
+  start_file_transfer_time=$(date +%s)
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
   # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
@@ -93,7 +94,7 @@ function copydb() {
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
   if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
-    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
+    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster, after: $(print_elapsed_time start_file_transfer_time)\n"
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
@@ -118,6 +119,7 @@ function copydb() {
   fi
 
   echo -e "\nCreating schema for db: '${db}'\n"
+  start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
@@ -128,7 +130,8 @@ function copydb() {
   all_create_view_statements=()
   num_tables=0
 
-  entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
+  entities_on_ocean=(`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`)  # Get the tables and views without any potential the "WARN" logs.
+  echo -e "\nGoing to create ${#entities_on_ocean[@]} entities for db '${db}'..\n"
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
     create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
@@ -152,8 +155,9 @@ function copydb() {
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            rm -f error.log
             exit 6
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
         fi
       fi
     fi
@@ -208,8 +212,11 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
+  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
+
+  start_compute_stats_time=$(date +%s)
   echo -e "\nComputing stats for tables..\n"
-  entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
@@ -221,20 +228,18 @@ function copydb() {
     fi
   done
 
+  echo -e "\nFinished computing stats for tables, after: $(print_elapsed_time start_compute_stats_time)\n"
+  rm -f error.log # Cleanup the temp log-file.
+
   # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
-  if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
-    echo -e "\nAll entities have been copied to Impala cluster.\n"
+  if [[ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]]; then
+    echo -e "\nAll entities have been copied to Impala cluster.\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
   else
-    echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
-    rm -f error.log
+    echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 8
     fi
   fi
-
-  rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n"
-  print_elapsed_time start_db_time
 }
 
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
index 918775f49..1d5842d06 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
@@ -57,20 +57,20 @@ function print_elapsed_time()
   hours=$((elapsed_time / 3600))
   minutes=$(((elapsed_time % 3600) / 60))
   seconds=$((elapsed_time % 60))
-  printf "\nElapsed time: %02d:%02d:%02d\n\n" $hours $minutes $seconds
+  printf "%02d:%02d:%02d" $hours $minutes $seconds
 }
 
 
 function copydb() {
   db=$1
-  start_db_time=$(date +%s)
   echo -e "\nStart processing db: '${db}'..\n"
+  start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
-    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE! EXITING...\n\n"
+    echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
     rm -f error.log
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 2
@@ -80,6 +80,7 @@ function copydb() {
   fi
 
   echo -e "\n\nCopying files of '${db}', from Ocean to Impala cluster..\n"
+  start_file_transfer_time=$(date +%s)
   # Using max-bandwidth of: 70 * 150 Mb/s = 10.5 Gb/s
   # Using max memory of: 70 * 6144 = 430 Gb
   # Using 1MB as a buffer-size.
@@ -95,7 +96,7 @@ function copydb() {
                 ${OCEAN_HDFS_NODE}/user/hive/warehouse/${db}.db ${IMPALA_HDFS_DB_BASE_PATH}
 
   if [ $? -eq 0 ]; then # Check the exit status of the "hadoop distcp" command.
-    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster.\n"
+    echo -e "\nSuccessfully copied the files of '${db}' from Ocean to Impala cluster, after: $(print_elapsed_time start_file_transfer_time)\n"
   else
     echo -e "\n\nERROR: FAILED TO TRANSFER THE FILES OF '${db}', WITH 'hadoop distcp'. GOT EXIT STATUS: $?\n\n"
     rm -f error.log
@@ -120,6 +121,7 @@ function copydb() {
   fi
 
   echo -e "\nCreating schema for db: '${db}'\n"
+  start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
   impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
@@ -130,7 +132,8 @@ function copydb() {
   all_create_view_statements=()
   num_tables=0
 
-  entities_on_ocean=`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`  # Get the tables and views without any potential the "WARN" logs.
+  entities_on_ocean=(`hive -e "show tables in ${db};" | sed 's/WARN:.*//g'`)  # Get the tables and views without any potential the "WARN" logs.
+  echo -e "\nGoing to create ${#entities_on_ocean[@]} entities for db '${db}'..\n"
   for i in ${entities_on_ocean[@]}; do # Use un-quoted values, as the elements are single-words.
     # Check if this is a view by showing the create-statement where it should print "create view" for a view, not the "create table". Unfortunately, there is no "show views" command.
     create_entity_statement=`hive --database ${db} -e "show create table ${i};"`  # We need to use the "--database", instead of including it inside the query, in order to return the statements with the '`' chars being in the right place to be used by impala-shell. However, we need to add the db-name in the "CREATE VIEW view_name" statement.
@@ -154,8 +157,9 @@ function copydb() {
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+            rm -f error.log
             exit 6
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
         fi
       fi
     fi
@@ -210,8 +214,11 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
+  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
+
+  start_compute_stats_time=$(date +%s)
   echo -e "\nComputing stats for tables..\n"
-  entities_on_impala=`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`
   for i in ${entities_on_impala[@]}; do # Use un-quoted values, as the elemetns are single-words.
     # Taking the create table statement from the Ocean cluster, just to check if its a view, as the output is easier than using impala-shell from Impala cluster.
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
@@ -223,20 +230,18 @@ function copydb() {
     fi
   done
 
+  echo -e "\nFinished computing stats for tables, after: $(print_elapsed_time start_compute_stats_time)\n"
+  rm -f error.log # Cleanup the temp log-file.
+
   # Check if the entities in both clusters are the same, down to the exact names, not just the counts. (they are sorted in the same way both in hive and impala)
-  if [ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]; then
-    echo -e "\nAll entities have been copied to Impala cluster.\n"
+  if [[ "${entities_on_impala[@]}" == "${entities_on_ocean[@]}" ]]; then
+    echo -e "\nAll entities have been copied to Impala cluster.\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
   else
-    echo -e "\n\nERROR: 1 OR MORE ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n"
-    rm -f error.log
+    echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
       exit 8
     fi
   fi
-
-  rm -f error.log
-  echo -e "\n\nFinished processing db: ${db}\n"
-  print_elapsed_time start_db_time
 }
 
 STATS_DB=$1

From 38636942c7af3f400f01618a6667f07fa29268d0 Mon Sep 17 00:00:00 2001
From: Antonis Lempesis <antleb@di.uoa.gr>
Date: Fri, 14 Jun 2024 15:11:19 +0300
Subject: [PATCH 033/239] filtering out deletedbyinference and invinsible
 results from accessroute

---
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
index 7bad34e86..dafec9a6f 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
@@ -65,4 +65,5 @@ DROP TABLE IF EXISTS ${stats_db_name}.result_accessroute purge;
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_accessroute STORED AS PARQUET as
 select distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result
-lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute;
+    lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute
+WHERE datainfo.deletedbyinference=false and datainfo.invisible = FALSE;

From 3095047e5e6cf1cba744264296f5e01f96bfb4b4 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Tue, 18 Jun 2024 14:40:41 +0300
Subject: [PATCH 034/239] Miscellaneous updates to the copying operation to
 Impala Cluster: - Fix not breaking out of the VIEWS-infinite-loop when the
 "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" is set to "false". - Exit the script
 when no HDFS-active-node was found, independently of the
 "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR". - Fix view_name-recognition in a
 log-message, by using the more advanced "Perl-Compatible Regular Expressions"
 in "grep". - Add error-handling for "compute stats" errors.

---
 .../oozie_app/copyDataToImpalaCluster.sh      | 24 ++++++++++++-------
 .../oozie_app/copyDataToImpalaCluster.sh      | 24 ++++++++++++-------
 .../oozie_app/copyDataToImpalaCluster.sh      | 24 ++++++++++++-------
 .../oozie_app/copyDataToImpalaCluster.sh      | 24 ++++++++++++-------
 4 files changed, 64 insertions(+), 32 deletions(-)

diff --git a/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
index 55deada40..978cf4a9a 100644
--- a/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
@@ -32,9 +32,7 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
-    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 1
-    fi
+    exit 1  # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -148,7 +146,7 @@ function copydb() {
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
             exit 5
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -188,7 +186,7 @@ function copydb() {
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
         ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
           all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
@@ -200,9 +198,11 @@ function copydb() {
     # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
-      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
+      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
       if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
         exit 7
+      else
+        break # Break form the inf-loop of views and continue by computing stats for the tables.
       fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
@@ -224,7 +224,15 @@ function copydb() {
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
+      if [ -n "$log_errors" ]; then
+        echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
+        if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+          rm -f error.log
+          exit 8
+        fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
+      fi
     fi
   done
 
@@ -237,7 +245,7 @@ function copydb() {
   else
     echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 8
+      exit 9
     fi
   fi
 }
diff --git a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
index 55deada40..978cf4a9a 100644
--- a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
@@ -32,9 +32,7 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
-    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 1
-    fi
+    exit 1  # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -148,7 +146,7 @@ function copydb() {
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
             exit 5
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -188,7 +186,7 @@ function copydb() {
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
         ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
           all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
@@ -200,9 +198,11 @@ function copydb() {
     # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
-      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
+      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
       if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
         exit 7
+      else
+        break # Break form the inf-loop of views and continue by computing stats for the tables.
       fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
@@ -224,7 +224,15 @@ function copydb() {
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
+      if [ -n "$log_errors" ]; then
+        echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
+        if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+          rm -f error.log
+          exit 8
+        fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
+      fi
     fi
   done
 
@@ -237,7 +245,7 @@ function copydb() {
   else
     echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 8
+      exit 9
     fi
   fi
 }
diff --git a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
index 43498abd2..55ae3114e 100644
--- a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
@@ -32,9 +32,7 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
-    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 1
-    fi
+    exit 1  # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -148,7 +146,7 @@ function copydb() {
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
             exit 5
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -188,7 +186,7 @@ function copydb() {
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
         ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
           all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
@@ -200,9 +198,11 @@ function copydb() {
     # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
-      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
+      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
       if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
         exit 7
+      else
+        break # Break form the inf-loop of views and continue by computing stats for the tables.
       fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
@@ -224,7 +224,15 @@ function copydb() {
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
+      if [ -n "$log_errors" ]; then
+        echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
+        if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+          rm -f error.log
+          exit 8
+        fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
+      fi
     fi
   done
 
@@ -237,7 +245,7 @@ function copydb() {
   else
     echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 8
+      exit 9
     fi
   fi
 }
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
index 1d5842d06..07a8a4534 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
@@ -30,9 +30,7 @@ while [ $COUNTER -lt 3 ]; do
 done
 if [ -z "$IMPALA_HDFS_NODE" ]; then
     echo -e "\n\nERROR: PROBLEM WHEN SETTING THE HDFS-NODE FOR IMPALA CLUSTER! | AFTER ${COUNTER} RETRIES.\n\n"
-    if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 1
-    fi
+    exit 1  # This is fatal and we have to exit independently of the "SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR" config, as none of the DBs will be able to get transferred.
 fi
 echo -e "Active IMPALA HDFS Node: ${IMPALA_HDFS_NODE} , after ${COUNTER} retries.\n\n"
 
@@ -150,7 +148,7 @@ function copydb() {
           echo -e "\nERROR: THE TABLE \"${i}\" HAD NO FILES TO GET THE SCHEMA FROM! IT'S EMPTY!\n\n"
           if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
             exit 5
-          fi
+          fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
         impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
@@ -190,7 +188,7 @@ function copydb() {
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
-        echo -e "\nView '$(cat error.log | grep -Eo "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
+        echo -e "\nView '$(cat error.log | grep -Po "Query: CREATE VIEW ([^\s]+)" | sed 's/Query: CREATE VIEW //g')' failed to be created, possibly because it depends on another view.\n"
         ((new_num_of_views_to_retry++)) # Increment it here, instead of acquiring the array's size in the end, as that doesn't work for some reason.
       else
           all_create_view_statements=("${all_create_view_statements[@]/$create_view_statement}")  # Remove the current successful statement from the list.
@@ -202,9 +200,11 @@ function copydb() {
     # Although the above command reduces the "active" elements to just the few to-be-retried, it does not manage to make the array return the its true size through the "${#all_create_view_statements[@]}" statement. So we use counters.
 
     if [[ $new_num_of_views_to_retry -eq $previous_num_of_views_to_retry ]]; then
-      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! EXITING..\n\n"
+      echo -e "\n\nERROR: THE NUMBER OF VIEWS TO RETRY HAS NOT BEEN REDUCED! THE SCRIPT IS LIKELY GOING TO AN INFINITE-LOOP! BREAKING-OUT..\n\n"
       if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
         exit 7
+      else
+        break # Break form the inf-loop of views and continue by computing stats for the tables.
       fi
     elif [[ $new_num_of_views_to_retry -gt 0 ]]; then
       echo -e "\nTo be retried \"create_view_statements\" (${new_num_of_views_to_retry}):\n\n${all_create_view_statements[@]}\n"
@@ -226,7 +226,15 @@ function copydb() {
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
       impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}";
+      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
+      if [ -n "$log_errors" ]; then
+        echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
+        if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
+          rm -f error.log
+          exit 8
+        fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
+      fi
     fi
   done
 
@@ -239,7 +247,7 @@ function copydb() {
   else
     echo -e "\n\nERROR: $((${#entities_on_ocean[@]} - ${#entities_on_impala[@]})) ENTITIES OF DB '${db}' FAILED TO BE COPIED TO IMPALA CLUSTER!\n\n\nFinished processing db: '${db}', after: $(print_elapsed_time start_db_time)\n"
     if [[ SHOULD_EXIT_WHOLE_SCRIPT_UPON_ERROR -eq 1 ]]; then
-      exit 8
+      exit 9
     fi
   fi
 }

From ac270f795b998e6774da8ff4a6d4d729816f2c10 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Wed, 19 Jun 2024 11:11:52 +0200
Subject: [PATCH 035/239] [IrishFunderList]make changed according to 9635
 comment 14, 15 and 16

---
 .../dhp/collection/crossref/irish_funder.json | 25 +++----------------
 1 file changed, 4 insertions(+), 21 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
index e4f491e5c..9482904c5 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
@@ -58,7 +58,7 @@
     "uri": "http://dx.doi.org/10.13039/100010414",
     "name": "Health Research Board",
     "synonym": [
-      "501100001590"
+      "501100001590", "501100023273"
     ]
   },
   {
@@ -85,12 +85,6 @@
     "name": "Irish College of General Practitioners",
     "synonym": []
   },
-  {
-    "id": "100012734",
-    "uri": "http://dx.doi.org/10.13039/100012734",
-    "name": "Department for Culture, Heritage and the Gaeltacht, Ireland",
-    "synonym": []
-  },
   {
     "id": "100012754",
     "uri": "http://dx.doi.org/10.13039/100012754",
@@ -233,7 +227,7 @@
     "id": "100018064",
     "uri": "http://dx.doi.org/10.13039/100018064",
     "name": "Department of Tourism, Culture, Arts, Gaeltacht, Sport and Media",
-    "synonym": []
+    "synonym": ["100012734"]
   },
   {
     "id": "100018172",
@@ -319,12 +313,7 @@
     "name": "Centre for Ageing Research and Development in Ireland",
     "synonym": []
   },
-  {
-    "id": "501100001583",
-    "uri": "http://dx.doi.org/10.13039/501100001583",
-    "name": "Cystinosis Foundation Ireland",
-    "synonym": []
-  },
+
   {
     "id": "501100001584",
     "uri": "http://dx.doi.org/10.13039/501100001584",
@@ -605,7 +594,7 @@
     "id": "501100009315",
     "uri": "http://dx.doi.org/10.13039/501100009315",
     "name": "Cystinosis Ireland",
-    "synonym": []
+    "synonym": ["501100001583"]
   },
   {
     "id": "501100010808",
@@ -763,12 +752,6 @@
     "name": "Institute of Technology, Tralee",
     "synonym": []
   },
-  {
-    "id": "501100023273",
-    "uri": "http://dx.doi.org/10.13039/501100023273",
-    "name": "HRB Clinical Research Facility Galway",
-    "synonym": []
-  },
   {
     "id": "501100023378",
     "uri": "http://dx.doi.org/10.13039/501100023378",

From d35edac212181c32037f20dc2a3e59e7458f9eb0 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 20 Jun 2024 12:28:28 +0200
Subject: [PATCH 036/239] [IrishFunderList]make changed according to 9635
 comment 20, 21, 22 and 23

---
 .../dhp/collection/crossref/irish_funder.json | 30 ++-----------------
 1 file changed, 3 insertions(+), 27 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
index 9482904c5..e50dc2dee 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
@@ -85,18 +85,6 @@
     "name": "Irish College of General Practitioners",
     "synonym": []
   },
-  {
-    "id": "100012754",
-    "uri": "http://dx.doi.org/10.13039/100012754",
-    "name": "Horizon Pharma",
-    "synonym": []
-  },
-  {
-    "id": "100012891",
-    "uri": "http://dx.doi.org/10.13039/100012891",
-    "name": "Medical Research Charities Group",
-    "synonym": []
-  },
   {
     "id": "100012919",
     "uri": "http://dx.doi.org/10.13039/100012919",
@@ -275,13 +263,13 @@
     "id": "100019637",
     "uri": "http://dx.doi.org/10.13039/100019637",
     "name": "Horizon Therapeutics",
-    "synonym": []
+    "synonym": ["100012754"]
   },
   {
     "id": "100020174",
     "uri": "http://dx.doi.org/10.13039/100020174",
     "name": "Health Research Charities Ireland",
-    "synonym": []
+    "synonym": ["100012891"]
   },
   {
     "id": "100020202",
@@ -510,7 +498,7 @@
     "id": "501100003037",
     "uri": "http://dx.doi.org/10.13039/501100003037",
     "name": "Elan",
-    "synonym": []
+    "synonym": ["501100021694"]
   },
   {
     "id": "501100003496",
@@ -584,12 +572,6 @@
     "name": "Technological University Dublin",
     "synonym": []
   },
-  {
-    "id": "501100009269",
-    "uri": "http://dx.doi.org/10.13039/501100009269",
-    "name": "Programme of Competitive Forestry Research for Development",
-    "synonym": []
-  },
   {
     "id": "501100009315",
     "uri": "http://dx.doi.org/10.13039/501100009315",
@@ -716,12 +698,6 @@
     "name": "Insight SFI Research Centre for Data Analytics",
     "synonym": []
   },
-  {
-    "id": "501100021694",
-    "uri": "http://dx.doi.org/10.13039/501100021694",
-    "name": "Elan Pharma International",
-    "synonym": []
-  },
   {
     "id": "501100021838",
     "uri": "http://dx.doi.org/10.13039/501100021838",

From 66cd28f70a94536e38ff6368b65c88b9b2d3bbfc Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Thu, 20 Jun 2024 14:33:46 +0300
Subject: [PATCH 037/239] - Fix not using the "export HADOOP_USER_NAME"
 statement in "createPDFsAggregated.sh", which caused permission-issues when
 creating tables with Impala. - Remove unused "--user" parameter in
 "impala-shell" calls. - Code polishing.

---
 .../oozie_app/copyDataToImpalaCluster.sh      | 14 +++++-----
 .../oozie_app/copyDataToImpalaCluster.sh      | 14 +++++-----
 .../oozie_app/copyDataToImpalaCluster.sh      | 14 +++++-----
 .../oozie_app/copyDataToImpalaCluster.sh      | 19 ++++++-------
 .../stats/oozie_app/createPDFsAggregated.sh   | 28 +++++++++++--------
 5 files changed, 46 insertions(+), 43 deletions(-)

diff --git a/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
index 978cf4a9a..09ea1b393 100644
--- a/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-hist-snaps/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-hist-snaps/oozie_app/copyDataToImpalaCluster.sh
@@ -63,7 +63,7 @@ function copydb() {
   start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+  impala-shell -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
@@ -120,7 +120,7 @@ function copydb() {
   start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
+  impala-shell -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
@@ -148,7 +148,7 @@ function copydb() {
             exit 5
           fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
-        impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
+        impala-shell -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
@@ -182,7 +182,7 @@ function copydb() {
     new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+      impala-shell -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
@@ -212,7 +212,7 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  entities_on_impala=(`impala-shell -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
   echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
 
   start_compute_stats_time=$(date +%s)
@@ -222,9 +222,9 @@ function copydb() {
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      impala-shell -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      impala-shell -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
       log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
       if [ -n "$log_errors" ]; then
         echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
diff --git a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
index 978cf4a9a..09ea1b393 100644
--- a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/copyDataToImpalaCluster.sh
@@ -63,7 +63,7 @@ function copydb() {
   start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+  impala-shell -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
@@ -120,7 +120,7 @@ function copydb() {
   start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
+  impala-shell -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
@@ -148,7 +148,7 @@ function copydb() {
             exit 5
           fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
-        impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
+        impala-shell -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
@@ -182,7 +182,7 @@ function copydb() {
     new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+      impala-shell -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
@@ -212,7 +212,7 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  entities_on_impala=(`impala-shell -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
   echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
 
   start_compute_stats_time=$(date +%s)
@@ -222,9 +222,9 @@ function copydb() {
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      impala-shell -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      impala-shell -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
       log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
       if [ -n "$log_errors" ]; then
         echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
diff --git a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
index 55ae3114e..d75412df8 100644
--- a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/copyDataToImpalaCluster.sh
@@ -63,7 +63,7 @@ function copydb() {
   start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+  impala-shell -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
@@ -120,7 +120,7 @@ function copydb() {
   start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
+  impala-shell -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
@@ -148,7 +148,7 @@ function copydb() {
             exit 5
           fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
-        impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
+        impala-shell -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
@@ -182,7 +182,7 @@ function copydb() {
     new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+      impala-shell -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
@@ -212,7 +212,7 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  entities_on_impala=(`impala-shell -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
   echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
 
   start_compute_stats_time=$(date +%s)
@@ -222,9 +222,9 @@ function copydb() {
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      impala-shell -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      impala-shell -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
       log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
       if [ -n "$log_errors" ]; then
         echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
index 07a8a4534..96c61d91a 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/copyDataToImpalaCluster.sh
@@ -65,7 +65,7 @@ function copydb() {
   start_db_time=$(date +%s)
 
   # Delete the old DB from Impala cluster (if exists).
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+  impala-shell -i ${IMPALA_HOSTNAME} -q "drop database if exists ${db} cascade" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
   log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
   if [ -n "$log_errors" ]; then
     echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN DROPPING THE OLD DATABASE FROM IMPALA CLUSTER! EXITING...\n\n"
@@ -122,7 +122,7 @@ function copydb() {
   start_create_schema_time=$(date +%s)
 
   # create the new database (with the same name)
-  impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create database ${db}"
+  impala-shell -i ${IMPALA_HOSTNAME} -q "create database ${db}"
 
   # Because "Hive" and "Impala" do not have compatible schemas, we cannot use the "show create table <name>" output from hive to create the exact same table in impala.
   # So, we have to find at least one parquet file (check if it's there) from the table in the ocean cluster for impala to use it to extract the table-schema itself from that file.
@@ -150,7 +150,7 @@ function copydb() {
             exit 5
           fi  # This error is not FATAL, do we do not return from this function, in normal circumstances.
       else
-        impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
+        impala-shell -i ${IMPALA_HOSTNAME} -q "create table ${db}.${i} like parquet '${CURRENT_PRQ_FILE}' stored as parquet;" |& tee error.log
         log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
         if [ -n "$log_errors" ]; then
           echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN CREATING TABLE '${i}'!\n\n"
@@ -184,7 +184,7 @@ function copydb() {
     new_num_of_views_to_retry=0
 
     for create_view_statement in "${all_create_view_statements[@]}"; do # Here we use double quotes, as the elements are phrases, instead of single-words.
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
+      impala-shell -i ${IMPALA_HOSTNAME} -q "${create_view_statement}" |& tee error.log # impala-shell prints all logs in stderr, so wee need to capture them and put them in a file, in order to perform "grep" on them later
       specific_errors=`cat error.log | grep -E "FAILED: ParseException line 1:13 missing TABLE at 'view'|ERROR: AnalysisException: Could not resolve table reference:"`
       if [ -n "$specific_errors" ]; then
         echo -e "\nspecific_errors: ${specific_errors}\n"
@@ -214,7 +214,7 @@ function copydb() {
     previous_num_of_views_to_retry=$new_num_of_views_to_retry
   done
 
-  entities_on_impala=(`impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
+  entities_on_impala=(`impala-shell -i ${IMPALA_HOSTNAME} --delimited -q "show tables in ${db}"`)
   echo -e "\nThe schema of db '${db}', along with ${#entities_on_impala[@]} entities have been created, on Impala cluster, after: $(print_elapsed_time start_create_schema_time)\n"
 
   start_compute_stats_time=$(date +%s)
@@ -224,9 +224,9 @@ function copydb() {
     create_view_statement=`hive -e "show create table ${db}.${i};" | grep "CREATE VIEW"`  # This grep works here, as we do not want to match multiple-lines.
     if [ -z "$create_view_statement" ]; then  # If it's a table, then go load the data to it.
       # Invalidate metadata of this DB's tables, in order for Impala to be aware of all parquet files put inside the tables' directories, previously, by "hadoop distcp".
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
+      impala-shell -i ${IMPALA_HOSTNAME} -q "INVALIDATE METADATA ${db}.${i}"
       sleep 1
-      impala-shell --user ${HADOOP_USER_NAME} -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
+      impala-shell -i ${IMPALA_HOSTNAME} -q "compute stats ${db}.${i}" |& tee error.log
       log_errors=`cat error.log | grep -E "WARN|ERROR|FAILED"`
       if [ -n "$log_errors" ]; then
         echo -e "\n\nERROR: THERE WAS A PROBLEM WHEN COMPUTING STATS FOR TABLE '${i}'!\n\n"
@@ -271,8 +271,7 @@ copydb $MONITOR_DB'_institutions'
 copydb $MONITOR_DB'_ris_tail'
 
 contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other"
-for i in ${contexts}
-do
-  tmp=`echo "$i"  | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
+for i in ${contexts}; do
+  tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
   copydb ${MONITOR_DB}'_'${tmp}
 done
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh
index 46631a0c2..9eec0bb20 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/createPDFsAggregated.sh
@@ -6,21 +6,26 @@ then
     ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder}
 fi
 
+export HADOOP_USER_NAME=$3
+
+IMPALA_HOSTNAME='impala-cluster-dn1.openaire.eu'
+
 function createPDFsAggregated() {
   db=$1
 
-impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} -q "drop table if exists indi_is_result_accessible";
+  impala-shell -i ${IMPALA_HOSTNAME} -d ${db} -q "drop table if exists indi_is_result_accessible";
 
-impala-shell --user $HADOOP_USER_NAME -i impala-cluster-dn1.openaire.eu -d ${db} -q "create table indi_is_result_accessible stored as parquet as
+  impala-shell -i ${IMPALA_HOSTNAME} -d ${db} -q "create table indi_is_result_accessible stored as parquet as
     select distinct p.id, coalesce(is_result_accessible, 0) as is_result_accessible from result p
     left outer join
-    (select id, 1 as is_result_accessible from (select pl.* from result r
-    join pdfaggregation_i.publication p on r.id=p.id
-    join pdfaggregation_i.payload pl on pl.id=p.id
-    union all
-    select pl.* from result r
-    join pdfaggregation_i.publication p on r.id=p.dedupid
-    join pdfaggregation_i.payload pl on pl.id=p.id) foo) tmp on p.id=tmp.id";
+      (select id, 1 as is_result_accessible from (select pl.* from result r
+      join pdfaggregation_i.publication p on r.id=p.id
+      join pdfaggregation_i.payload pl on pl.id=p.id
+      union all
+      select pl.* from result r
+      join pdfaggregation_i.publication p on r.id=p.dedupid
+      join pdfaggregation_i.payload pl on pl.id=p.id) foo)
+      tmp on p.id=tmp.id";
 }
 
 STATS_DB=$1
@@ -35,8 +40,7 @@ createPDFsAggregated $MONITOR_DB'_institutions'
 createPDFsAggregated $MONITOR_DB'_ris_tail'
 
 contexts="knowmad::other dh-ch::other enermaps::other gotriple::other neanias-atmospheric::other rural-digital-europe::other covid-19::other aurora::other neanias-space::other north-america-studies::other north-american-studies::other eutopia::other"
-for i in ${contexts}
-do
-   tmp=`echo "$i"  | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
+for i in ${contexts}; do
+  tmp=`echo "$i" | sed 's/'-'/'_'/g' | sed 's/'::'/'_'/g'`
   createPDFsAggregated ${MONITOR_DB}'_'${tmp}
 done
\ No newline at end of file

From 9f6e16a03cb5f55f58902e97b05a041ff66abd4b Mon Sep 17 00:00:00 2001
From: Serafeim Chatzopoulos <s.chatzopoulos@gmail.com>
Date: Thu, 20 Jun 2024 16:03:15 +0300
Subject: [PATCH 038/239] Add support to cretate/update solr collection aliases

---
 .../dhp/oa/provision/ProvisionConstants.java  |  3 +
 .../oa/provision/SolrAdminApplication.java    | 55 +++++++++++++++++--
 .../provision/input_solradmin_parameters.json | 13 +++++
 .../dhp/oa/provision/oozie_app/workflow.xml   | 29 ++++++++++
 .../provision/SolrAdminApplicationTest.java   | 25 ++++++++-
 5 files changed, 118 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java
index 01d161b6b..81398016a 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/ProvisionConstants.java
@@ -14,4 +14,7 @@ public class ProvisionConstants {
 		return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
 	}
 
+	public static final String PUBLIC_ALIAS_NAME = "public";
+	public static final String SHADOW_ALIAS_NAME = "shadow";
+
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
index 0033978bf..459ca0b50 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
@@ -9,6 +9,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrResponse;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.client.solrj.impl.CloudSolrClient;
+import org.apache.solr.client.solrj.request.CollectionAdminRequest;
 import org.apache.solr.client.solrj.response.UpdateResponse;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -23,7 +24,7 @@ public class SolrAdminApplication implements Closeable {
 	private static final Logger log = LoggerFactory.getLogger(SolrAdminApplication.class);
 
 	enum Action {
-		DELETE_BY_QUERY, COMMIT
+		DELETE_BY_QUERY, COMMIT, UPDATE_ALIASES
 	}
 
 	private final CloudSolrClient solrClient;
@@ -62,8 +63,21 @@ public class SolrAdminApplication implements Closeable {
 		final String collection = ProvisionConstants.getCollectionName(format);
 		log.info("collection: {}", collection);
 
+		final String publicFormat = parser.get("publicFormat");
+		log.info("publicFormat: {}", publicFormat);
+
+		final String shadowFormat = parser.get("shadowFormat");
+		log.info("shadowFormat: {}", shadowFormat);
+
+		// get collection names from metadata format profiles names
+		final String publicCollection = ProvisionConstants.getCollectionName(publicFormat);
+		log.info("publicCollection: {}", publicCollection);
+
+		final String shadowCollection = ProvisionConstants.getCollectionName(shadowFormat);
+		log.info("shadowCollection: {}", shadowCollection);
+
 		try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) {
-			app.execute(action, collection, query, commit);
+			app.execute(action, collection, query, commit, publicCollection, shadowCollection);
 		}
 	}
 
@@ -73,21 +87,28 @@ public class SolrAdminApplication implements Closeable {
 	}
 
 	public SolrResponse commit(String collection) throws IOException, SolrServerException {
-		return execute(Action.COMMIT, collection, null, true);
+		return execute(Action.COMMIT, collection, null, true, null, null);
 	}
 
-	public SolrResponse execute(Action action, String collection, String query, boolean commit)
+	public SolrResponse execute(Action action, String collection, String query, boolean commit,
+		String publicCollection, String shadowCollection)
 		throws IOException, SolrServerException {
 		switch (action) {
 
 			case DELETE_BY_QUERY:
 				UpdateResponse rsp = solrClient.deleteByQuery(collection, query);
 				if (commit) {
-					solrClient.commit(collection);
+					return solrClient.commit(collection);
 				}
 				return rsp;
+
 			case COMMIT:
 				return solrClient.commit(collection);
+
+			case UPDATE_ALIASES:
+				this.updateAliases(publicCollection, shadowCollection);
+				return null;
+
 			default:
 				throw new IllegalArgumentException("action not managed: " + action);
 		}
@@ -98,4 +119,28 @@ public class SolrAdminApplication implements Closeable {
 		solrClient.close();
 	}
 
+	private void updateAliases(String publicCollection, String shadowCollection)
+		throws SolrServerException, IOException {
+
+		// delete current aliases
+		this.deleteAlias(ProvisionConstants.PUBLIC_ALIAS_NAME);
+		this.deleteAlias(ProvisionConstants.SHADOW_ALIAS_NAME);
+
+		// create aliases
+		this.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, publicCollection);
+		this.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, shadowCollection);
+
+	}
+
+	public SolrResponse deleteAlias(String aliasName) throws SolrServerException, IOException {
+		CollectionAdminRequest.DeleteAlias deleteAliasRequest = CollectionAdminRequest.deleteAlias(aliasName);
+		return deleteAliasRequest.process(solrClient);
+	}
+
+	public SolrResponse createAlias(String aliasName, String collection) throws IOException, SolrServerException {
+		CollectionAdminRequest.CreateAlias createAliasRequest = CollectionAdminRequest
+			.createAlias(aliasName, collection);
+		return createAliasRequest.process(solrClient);
+	}
+
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
index 23eca2f7b..6e3f21ef2 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
@@ -28,5 +28,18 @@
     "paramLongName": "commit",
     "paramDescription": "should the action be followed by a commit?",
     "paramRequired": false
+  },
+  {
+    "paramName": "pf",
+    "paramLongName": "publicFormat",
+    "paramDescription": "the name of the public metadata format profile - used to create an alias",
+    "paramRequired": false
+  },
+  {
+    "paramName": "sf",
+    "paramLongName": "shadowFormat",
+    "paramDescription": "the name of the shadow metadata format profile - used to create an alias",
+    "paramRequired": false
   }
+
 ]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
index a754c7a5d..02195c0aa 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
@@ -110,6 +110,14 @@
             <name>sparkNetworkTimeout</name>
             <description>configures spark.network.timeout</description>
         </property>
+        <property>
+            <name>publicFormat</name>
+            <description>the public metadata format - used to create the public collection alias</description>
+        </property>
+        <property>
+            <name>shadowFormat</name>
+            <description>the shadow metadata format - used to create the shadow collection alias</description>
+        </property>
     </parameters>
 
     <global>
@@ -133,6 +141,7 @@
             <case to="create_payloads">${wf:conf('resumeFrom') eq 'create_payloads'}</case>
             <case to="drop_solr_collection">${wf:conf('resumeFrom') eq 'drop_solr_collection'}</case>
             <case to="to_solr_index">${wf:conf('resumeFrom') eq 'to_solr_index'}</case>
+            <case to="update_solr_aliases">${wf:conf('resumeFrom') eq 'update_solr_aliases'}</case>
             <default to="prepare_relations"/>
         </switch>
     </decision>
@@ -721,5 +730,25 @@
         <error to="Kill"/>
     </action>
 
+    <!-- Action that updates the solr core aliases - out of order execution, only using the 'resume_from' param -->
+    <action name="update_solr_aliases">
+        <java>
+            <configuration>
+                <property>
+                    <name>oozie.launcher.mapreduce.user.classpath.first</name>
+                    <value>true</value>
+                </property>
+            </configuration>
+            <main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--format</arg><arg>${format}</arg>
+            <arg>--action</arg><arg>UPDATE_ALIASES</arg>
+            <arg>--publicFormat</arg><arg>${publicFormat}</arg>
+            <arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
+        </java>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
     <end name="End"/>
 </workflow-app>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
index 9d5bff3cf..43e4c9ed7 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
@@ -4,9 +4,9 @@ package eu.dnetlib.dhp.oa.provision;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+import org.apache.solr.client.solrj.response.CollectionAdminResponse;
 import org.apache.solr.client.solrj.response.SolrPingResponse;
 import org.apache.solr.client.solrj.response.UpdateResponse;
-import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
 class SolrAdminApplicationTest extends SolrTest {
@@ -24,7 +24,7 @@ class SolrAdminApplicationTest extends SolrTest {
 		SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
 
 		UpdateResponse rsp = (UpdateResponse) admin
-			.execute(SolrAdminApplication.Action.DELETE_BY_QUERY, DEFAULT_COLLECTION, "*:*", false);
+			.execute(SolrAdminApplication.Action.DELETE_BY_QUERY, DEFAULT_COLLECTION, "*:*", false, null, null);
 
 		assertEquals(0, rsp.getStatus());
 	}
@@ -39,4 +39,25 @@ class SolrAdminApplicationTest extends SolrTest {
 		assertEquals(0, rsp.getStatus());
 	}
 
+	@Test
+	void testAdminApplication_CREATE_ALIAS() throws Exception {
+
+		SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
+
+		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, DEFAULT_COLLECTION);
+		assertEquals(0, rsp.getStatus());
+
+	}
+
+	@Test
+	void testAdminApplication_DELETE_ALIAS() throws Exception {
+
+		SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
+
+		CollectionAdminResponse rsp = (CollectionAdminResponse) admin.deleteAlias(ProvisionConstants.PUBLIC_ALIAS_NAME);
+		assertEquals(0, rsp.getStatus());
+
+	}
+
 }

From 6055212f7706b26d2e95c52ebf90c638918ea110 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 25 Jun 2024 12:39:02 +0200
Subject: [PATCH 039/239] merged from the json_payload branch

---
 .../model/ProvisionModelSupport.java          |  83 +++++++++++++++---
 .../dhp/oa/provision/xml/part-00000.json.gz   | Bin 66906 -> 0 bytes
 2 files changed, 72 insertions(+), 11 deletions(-)
 delete mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000.json.gz

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index f46aebdcf..a8c9ceeb3 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -32,6 +32,7 @@ import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
+import eu.dnetlib.dhp.schema.solr.Measure;
 import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
@@ -76,6 +77,7 @@ public class ProvisionModelSupport {
 		r.setCollectedfrom(asProvenance(e.getCollectedfrom()));
 		r.setContext(asContext(e.getContext(), contextMapper));
 		r.setPid(asPid(e.getPid()));
+		r.setMeasures(mapMeasures(e.getMeasures()));
 
 		if (e instanceof eu.dnetlib.dhp.schema.oaf.Result) {
 			r.setResult(mapResult((eu.dnetlib.dhp.schema.oaf.Result) e));
@@ -106,6 +108,14 @@ public class ProvisionModelSupport {
 		final RelatedEntity re = rew.getTarget();
 		final RecordType relatedRecordType = RecordType.valueOf(re.getType());
 		final Relation relation = rew.getRelation();
+		final String relationProvenance = Optional
+			.ofNullable(relation.getDataInfo())
+			.map(
+				d -> Optional
+					.ofNullable(d.getProvenanceaction())
+					.map(Qualifier::getClassid)
+					.orElse(null))
+			.orElse(null);
 		rr
 			.setHeader(
 				RelatedRecordHeader
@@ -113,7 +123,9 @@ public class ProvisionModelSupport {
 						relation.getRelType(),
 						relation.getRelClass(),
 						StringUtils.substringAfter(relation.getTarget(), IdentifierFactory.ID_PREFIX_SEPARATOR),
-						relatedRecordType));
+						relatedRecordType,
+						relationProvenance,
+						Optional.ofNullable(relation.getDataInfo()).map(DataInfo::getTrust).orElse(null)));
 
 		rr.setAcronym(re.getAcronym());
 		rr.setCode(re.getCode());
@@ -131,11 +143,20 @@ public class ProvisionModelSupport {
 		rr.setOfficialname(re.getOfficialname());
 		rr.setOpenairecompatibility(mapCodeLabel(re.getOpenairecompatibility()));
 		rr.setPid(asPid(re.getPid()));
-		rr.setProjectTitle(rr.getProjectTitle());
+		rr.setWebsiteurl(re.getWebsiteurl());
+		rr.setProjectTitle(re.getProjectTitle());
 		rr.setPublisher(re.getPublisher());
 		rr.setResulttype(mapQualifier(re.getResulttype()));
 		rr.setTitle(Optional.ofNullable(re.getTitle()).map(StructuredProperty::getValue).orElse(null));
 
+		if (relation.getValidated() == null) {
+			relation.setValidated(false);
+		}
+		if (ModelConstants.OUTCOME.equals(relation.getSubRelType())
+			&& StringUtils.isNotBlank(relation.getValidationDate())) {
+			rr.setValidationDate(relation.getValidationDate());
+		}
+
 		return rr;
 	}
 
@@ -266,6 +287,7 @@ public class ProvisionModelSupport {
 		ds.setOfficialname(mapField(d.getOfficialname()));
 		ds.setDescription(mapField(d.getDescription()));
 		ds.setJournal(mapJournal(d.getJournal()));
+		ds.setWebsiteurl(mapField(d.getWebsiteurl()));
 		ds.setLogourl(mapField(d.getLogourl()));
 		ds.setAccessinfopackage(mapFieldList(d.getAccessinfopackage()));
 		ds.setCertificates(mapField(d.getCertificates()));
@@ -311,6 +333,7 @@ public class ProvisionModelSupport {
 		ds.setSubjects(asSubjectSP(d.getSubjects()));
 		ds.setSubmissionpolicyurl(d.getSubmissionpolicyurl());
 		ds.setThematic(d.getThematic());
+		ds.setContentpolicies(mapCodeLabel(d.getContentpolicies()));
 		ds.setVersioncontrol(d.getVersioncontrol());
 		ds.setVersioning(mapField(d.getVersioning()));
 
@@ -326,6 +349,7 @@ public class ProvisionModelSupport {
 		rs.setOtherTitles(getOtherTitles(r.getTitle()));
 		rs.setDescription(mapFieldList(r.getDescription()));
 		rs.setSubject(asSubject(r.getSubject()));
+		rs.setLanguage(asLanguage(r.getLanguage()));
 		rs.setPublicationdate(mapField(r.getDateofacceptance()));
 		rs.setPublisher(mapField(r.getPublisher()));
 		rs.setEmbargoenddate(mapField(r.getEmbargoenddate()));
@@ -341,14 +365,14 @@ public class ProvisionModelSupport {
 		rs.setCountry(asCountry(r.getCountry()));
 		rs.setEoscifguidelines(asEOSCIF(r.getEoscifguidelines()));
 
-		rs.setGreen(r.getIsGreen());
+		rs.setIsGreen(r.getIsGreen());
 		rs
 			.setOpenAccessColor(
 				Optional
 					.ofNullable(r.getOpenAccessColor())
 					.map(color -> OpenAccessColor.valueOf(color.toString()))
 					.orElse(null));
-		rs.setInDiamondJournal(r.getIsInDiamondJournal());
+		rs.setIsInDiamondJournal(r.getIsInDiamondJournal());
 		rs.setPubliclyFunded(r.getPubliclyFunded());
 		rs.setTransformativeAgreement(r.getTransformativeAgreement());
 
@@ -375,6 +399,13 @@ public class ProvisionModelSupport {
 		return rs;
 	}
 
+	private static Language asLanguage(Qualifier lang) {
+		return Optional
+			.ofNullable(lang)
+			.map(q -> Language.newInstance(q.getClassid(), q.getClassname()))
+			.orElse(null);
+	}
+
 	@Nullable
 	private static List<String> getOtherTitles(List<StructuredProperty> titleList) {
 		return Optional
@@ -422,7 +453,7 @@ public class ProvisionModelSupport {
 						Instance i = new Instance();
 						i.setCollectedfrom(asProvenance(instance.getCollectedfrom()));
 						i.setHostedby(asProvenance(instance.getHostedby()));
-						i.setFulltext(i.getFulltext());
+						i.setFulltext(instance.getFulltext());
 						i.setPid(asPid(instance.getPid()));
 						i.setAlternateIdentifier(asPid(instance.getAlternateIdentifier()));
 						i.setAccessright(mapAccessRight(instance.getAccessright()));
@@ -453,7 +484,8 @@ public class ProvisionModelSupport {
 	private static AccessRight mapAccessRight(eu.dnetlib.dhp.schema.oaf.AccessRight accessright) {
 		return AccessRight
 			.newInstance(
-				mapQualifier(accessright),
+				accessright.getClassid(),
+				accessright.getClassname(),
 				Optional
 					.ofNullable(accessright.getOpenAccessRoute())
 					.map(route -> OpenAccessRoute.valueOf(route.toString()))
@@ -508,7 +540,25 @@ public class ProvisionModelSupport {
 	}
 
 	private static Provenance asProvenance(KeyValue keyValue) {
-		return Optional.ofNullable(keyValue).map(cf -> Provenance.newInstance(cf.getKey(), cf.getValue())).orElse(null);
+		return Optional
+			.ofNullable(keyValue)
+			.map(
+				kv -> Provenance
+					.newInstance(
+						StringUtils.substringAfter(kv.getKey(), IdentifierFactory.ID_PREFIX_SEPARATOR),
+						kv.getValue()))
+			.orElse(null);
+	}
+
+	private static List<Measure> mapMeasures(List<eu.dnetlib.dhp.schema.oaf.Measure> measures) {
+		return Optional
+			.ofNullable(measures)
+			.map(
+				ml -> ml
+					.stream()
+					.map(m -> Measure.newInstance(m.getId(), mapCodeLabelKV(m.getUnit())))
+					.collect(Collectors.toList()))
+			.orElse(null);
 	}
 
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
@@ -581,7 +631,14 @@ public class ProvisionModelSupport {
 			.map(
 				pids -> pids
 					.stream()
-					.map(p -> Pid.newInstance(p.getQualifier().getClassname(), p.getValue()))
+					.filter(p -> Objects.nonNull(p.getQualifier()))
+					.filter(p -> Objects.nonNull(p.getQualifier().getClassid()))
+					.map(
+						p -> Pid
+							.newInstance(
+								p.getValue(),
+								p.getQualifier().getClassid(),
+								p.getQualifier().getClassname()))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}
@@ -607,7 +664,9 @@ public class ProvisionModelSupport {
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
 					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
-					.map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassname()))
+					.map(
+						s -> Subject
+							.newInstance(s.getValue(), s.getQualifier().getClassid(), s.getQualifier().getClassname()))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}
@@ -620,7 +679,9 @@ public class ProvisionModelSupport {
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
 					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
-					.map(s -> Subject.newInstance(s.getValue(), s.getQualifier().getClassname()))
+					.map(
+						s -> Subject
+							.newInstance(s.getValue(), s.getQualifier().getClassid(), s.getQualifier().getClassname()))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}
@@ -689,7 +750,7 @@ public class ProvisionModelSupport {
 	private static CodeLabel mapCodeLabel(KeyValue kv) {
 		return Optional
 			.ofNullable(kv)
-			.map(q -> CodeLabel.newInstance(kv.getKey(), kv.getValue()))
+			.map(k -> CodeLabel.newInstance(k.getKey(), k.getValue()))
 			.orElse(null);
 	}
 
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000.json.gz b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/part-00000.json.gz
deleted file mode 100644
index 8dfcea4fa86f1b6dff330b0f9d0bba873f5b0768..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001

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FzW}!ckwpLi


From 1c30eacac2ead489dc4ee1cba26ff79ca9a08b58 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 25 Jun 2024 15:27:38 +0200
Subject: [PATCH 040/239] updated index feeding procedure to exploit the
 collection aliases

---
 .../oa/provision/SolrAdminApplication.java    |  20 +-
 .../dhp/oa/provision/SolrRecordDumpJob.java   |  19 +-
 .../dhp/oa/provision/XmlIndexingJob.java      |  23 +-
 .../input_params_solr_record_dump.json        |   2 +-
 .../provision/input_params_update_index.json  |   4 +-
 .../provision/input_solradmin_parameters.json |   6 -
 .../dhp/oa/provision/oozie_app/workflow.xml   |  23 +-
 .../provision/SolrAdminApplicationTest.java   |  12 +-
 .../oa/provision/SolrConfigExploreTest.java   | 142 +++++++-
 .../dhp/oa/provision/SolrConfigTest.java      |  20 +-
 .../dhp/oa/provision/SolrExploreTest.java     |  52 ---
 .../eu/dnetlib/dhp/oa/provision/SolrTest.java |  31 +-
 .../dhp/oa/provision/XmlIndexingJobTest.java  |  70 +++-
 .../eu/dnetlib/dhp/oa/provision/fields.xml    |   7 +-
 .../conf/exploreTestConfig/managed-schema     | 339 ++++++++----------
 .../oa/provision/xml/xml_json_sample.json.gz  | Bin 0 -> 354497 bytes
 pom.xml                                       |   2 +-
 17 files changed, 402 insertions(+), 370 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/xml_json_sample.json.gz

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
index 459ca0b50..44426e8c5 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
@@ -40,9 +40,6 @@ public class SolrAdminApplication implements Closeable {
 		final String isLookupUrl = parser.get("isLookupUrl");
 		log.info("isLookupUrl: {}", isLookupUrl);
 
-		final String format = parser.get("format");
-		log.info("format: {}", format);
-
 		final Action action = Action.valueOf(parser.get("action"));
 		log.info("action: {}", action);
 
@@ -60,9 +57,6 @@ public class SolrAdminApplication implements Closeable {
 		final String zkHost = isLookup.getZkHost();
 		log.info("zkHost: {}", zkHost);
 
-		final String collection = ProvisionConstants.getCollectionName(format);
-		log.info("collection: {}", collection);
-
 		final String publicFormat = parser.get("publicFormat");
 		log.info("publicFormat: {}", publicFormat);
 
@@ -77,7 +71,7 @@ public class SolrAdminApplication implements Closeable {
 		log.info("shadowCollection: {}", shadowCollection);
 
 		try (SolrAdminApplication app = new SolrAdminApplication(zkHost)) {
-			app.execute(action, collection, query, commit, publicCollection, shadowCollection);
+			app.execute(action, query, commit, publicCollection, shadowCollection);
 		}
 	}
 
@@ -86,24 +80,24 @@ public class SolrAdminApplication implements Closeable {
 		this.solrClient = new CloudSolrClient.Builder(zk.getHosts(), zk.getChroot()).build();
 	}
 
-	public SolrResponse commit(String collection) throws IOException, SolrServerException {
-		return execute(Action.COMMIT, collection, null, true, null, null);
+	public SolrResponse commit(String shadowCollection) throws IOException, SolrServerException {
+		return execute(Action.COMMIT, null, true, null, shadowCollection);
 	}
 
-	public SolrResponse execute(Action action, String collection, String query, boolean commit,
+	public SolrResponse execute(Action action, String query, boolean commit,
 		String publicCollection, String shadowCollection)
 		throws IOException, SolrServerException {
 		switch (action) {
 
 			case DELETE_BY_QUERY:
-				UpdateResponse rsp = solrClient.deleteByQuery(collection, query);
+				UpdateResponse rsp = solrClient.deleteByQuery(shadowCollection, query);
 				if (commit) {
-					return solrClient.commit(collection);
+					return solrClient.commit(shadowCollection);
 				}
 				return rsp;
 
 			case COMMIT:
-				return solrClient.commit(collection);
+				return solrClient.commit(shadowCollection);
 
 			case UPDATE_ALIASES:
 				this.updateAliases(publicCollection, shadowCollection);
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java
index faa18851b..06a35eda5 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrRecordDumpJob.java
@@ -36,7 +36,7 @@ public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
 
 	private final String inputPath;
 
-	private final String format;
+	private final String shadowFormat;
 
 	private final String outputPath;
 
@@ -61,8 +61,8 @@ public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
 		final String inputPath = parser.get("inputPath");
 		log.info("inputPath: {}", inputPath);
 
-		final String format = parser.get("format");
-		log.info("format: {}", format);
+		final String shadowFormat = parser.get("shadowFormat");
+		log.info("shadowFormat: {}", shadowFormat);
 
 		final String outputPath = Optional
 			.ofNullable(parser.get("outputPath"))
@@ -95,27 +95,24 @@ public class SolrRecordDumpJob extends AbstractSolrRecordTransformJob {
 				final String isLookupUrl = parser.get("isLookupUrl");
 				log.info("isLookupUrl: {}", isLookupUrl);
 				final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
-				new SolrRecordDumpJob(spark, inputPath, format, outputPath).run(isLookup);
+				new SolrRecordDumpJob(spark, inputPath, shadowFormat, outputPath).run(isLookup);
 			});
 	}
 
-	public SolrRecordDumpJob(SparkSession spark, String inputPath, String format, String outputPath) {
+	public SolrRecordDumpJob(SparkSession spark, String inputPath, String shadowFormat, String outputPath) {
 		this.spark = spark;
 		this.inputPath = inputPath;
-		this.format = format;
+		this.shadowFormat = shadowFormat;
 		this.outputPath = outputPath;
 	}
 
 	public void run(ISLookupClient isLookup) throws ISLookUpException, TransformerException {
-		final String fields = isLookup.getLayoutSource(format);
+		final String fields = isLookup.getLayoutSource(shadowFormat);
 		log.info("fields: {}", fields);
 
 		final String xslt = isLookup.getLayoutTransformer();
 
-		final String dsId = isLookup.getDsId(format);
-		log.info("dsId: {}", dsId);
-
-		final String indexRecordXslt = getLayoutTransformer(format, fields, xslt);
+		final String indexRecordXslt = getLayoutTransformer(shadowFormat, fields, xslt);
 		log.info("indexRecordTransformer {}", indexRecordXslt);
 
 		final Encoder<TupleWrapper> encoder = Encoders.bean(TupleWrapper.class);
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
index 78154e0ab..386445057 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJob.java
@@ -40,6 +40,8 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 
 	private final String format;
 
+	private final String shadowCollection;
+
 	private final int batchSize;
 
 	private final SparkSession spark;
@@ -63,8 +65,11 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 		final String inputPath = parser.get("inputPath");
 		log.info("inputPath: {}", inputPath);
 
-		final String format = parser.get("format");
-		log.info("format: {}", format);
+		final String shadowFormat = parser.get("shadowFormat");
+		log.info("shadowFormat: {}", shadowFormat);
+
+		final String shadowCollection = ProvisionConstants.getCollectionName(shadowFormat);
+		log.info("shadowCollection: {}", shadowCollection);
 
 		final Integer batchSize = Optional
 			.ofNullable(parser.get("batchSize"))
@@ -85,15 +90,17 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 				final String isLookupUrl = parser.get("isLookupUrl");
 				log.info("isLookupUrl: {}", isLookupUrl);
 				final ISLookupClient isLookup = new ISLookupClient(ISLookupClientFactory.getLookUpService(isLookupUrl));
-				new XmlIndexingJob(spark, inputPath, format, batchSize)
+				new XmlIndexingJob(spark, inputPath, shadowFormat, shadowCollection, batchSize)
 					.run(isLookup);
 			});
 	}
 
-	public XmlIndexingJob(SparkSession spark, String inputPath, String format, Integer batchSize) {
+	public XmlIndexingJob(SparkSession spark, String inputPath, String format, String shadowCollection,
+		Integer batchSize) {
 		this.spark = spark;
 		this.inputPath = inputPath;
 		this.format = format;
+		this.shadowCollection = shadowCollection;
 		this.batchSize = batchSize;
 	}
 
@@ -103,12 +110,6 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 
 		final String xslt = isLookup.getLayoutTransformer();
 
-		final String dsId = isLookup.getDsId(format);
-		log.info("dsId: {}", dsId);
-
-		final String collection = ProvisionConstants.getCollectionName(format);
-		log.info("collection: {}", collection);
-
 		final String zkHost = isLookup.getZkHost();
 		log.info("zkHost: {}", zkHost);
 
@@ -130,7 +131,7 @@ public class XmlIndexingJob extends AbstractSolrRecordTransformJob {
 			.javaRDD()
 			.map(
 				t -> new StreamingInputDocumentFactory().parseDocument(t.getXml(), t.getJson()));
-		DHPSolrSupport.indexDocs(zkHost, collection, batchSize, docs.rdd());
+		DHPSolrSupport.indexDocs(zkHost, shadowCollection, batchSize, docs.rdd());
 	}
 
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json
index 7e5734222..3c2c1e05d 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_solr_record_dump.json
@@ -13,7 +13,7 @@
   },
   {
     "paramName": "f",
-    "paramLongName": "format",
+    "paramLongName": "shadowFormat",
     "paramDescription": "MDFormat name found in the IS profile",
     "paramRequired": true
   },
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json
index 3396020e0..c8364bb28 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_params_update_index.json
@@ -13,8 +13,8 @@
   },
   {
     "paramName": "f",
-    "paramLongName": "format",
-    "paramDescription": "MDFormat name found in the IS profile",
+    "paramLongName": "shadowFormat",
+    "paramDescription": "MDFormat name found in the IS profile bound to the shadow index collection to feed",
     "paramRequired": true
   },
   {
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
index 6e3f21ef2..23a378857 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/input_solradmin_parameters.json
@@ -5,12 +5,6 @@
     "paramDescription": "the URL to the ISLookUp Service",
     "paramRequired": true
   },
-  {
-    "paramName": "f",
-    "paramLongName": "format",
-    "paramDescription": "metadata format profile name",
-    "paramRequired": true
-  },
   {
     "paramName": "a",
     "paramLongName": "action",
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
index 02195c0aa..6c58d2466 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
@@ -35,9 +35,13 @@
             <description>maximum number of relations allowed for a each entity grouping by target</description>
         </property>
         <property>
-            <name>format</name>
+            <name>shadowFormat</name>
             <description>metadata format name (DMF|TMF)</description>
         </property>
+        <property>
+            <name>publicFormat</name>
+            <description>the public metadata format - used to create the public collection alias</description>
+        </property>
         <property>
             <name>batchSize</name>
             <description>number of records to be included in each indexing request</description>
@@ -110,14 +114,6 @@
             <name>sparkNetworkTimeout</name>
             <description>configures spark.network.timeout</description>
         </property>
-        <property>
-            <name>publicFormat</name>
-            <description>the public metadata format - used to create the public collection alias</description>
-        </property>
-        <property>
-            <name>shadowFormat</name>
-            <description>the shadow metadata format - used to create the shadow collection alias</description>
-        </property>
     </parameters>
 
     <global>
@@ -650,8 +646,8 @@
             </configuration>
             <main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--format</arg><arg>${format}</arg>
             <arg>--action</arg><arg>DELETE_BY_QUERY</arg>
+            <arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
             <arg>--query</arg><arg>${solrDeletionQuery}</arg>
             <arg>--commit</arg><arg>true</arg>
         </java>
@@ -681,7 +677,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${workingDir}/xml_json</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--format</arg><arg>${format}</arg>
+            <arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
             <arg>--batchSize</arg><arg>${batchSize}</arg>
         </spark>
         <ok to="commit_solr_collection"/>
@@ -698,7 +694,7 @@
             </configuration>
             <main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--format</arg><arg>${format}</arg>
+            <arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
             <arg>--action</arg><arg>COMMIT</arg>
         </java>
         <ok to="End"/>
@@ -723,7 +719,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${workingDir}/xml_json</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--format</arg><arg>${format}</arg>
+            <arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
             <arg>--outputPath</arg><arg>${workingDir}/solr_documents</arg>
         </spark>
         <ok to="End"/>
@@ -741,7 +737,6 @@
             </configuration>
             <main-class>eu.dnetlib.dhp.oa.provision.SolrAdminApplication</main-class>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--format</arg><arg>${format}</arg>
             <arg>--action</arg><arg>UPDATE_ALIASES</arg>
             <arg>--publicFormat</arg><arg>${publicFormat}</arg>
             <arg>--shadowFormat</arg><arg>${shadowFormat}</arg>
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
index 43e4c9ed7..3834f530e 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplicationTest.java
@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.provision;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+import org.apache.solr.client.solrj.request.SolrPing;
 import org.apache.solr.client.solrj.response.CollectionAdminResponse;
 import org.apache.solr.client.solrj.response.SolrPingResponse;
 import org.apache.solr.client.solrj.response.UpdateResponse;
@@ -13,7 +14,10 @@ class SolrAdminApplicationTest extends SolrTest {
 
 	@Test
 	void testPing() throws Exception {
-		SolrPingResponse pingResponse = miniCluster.getSolrClient().ping();
+		final SolrPing ping = new SolrPing();
+		ping.getParams().set("collection", ProvisionConstants.SHADOW_ALIAS_NAME);
+		SolrPingResponse pingResponse = ping.process(miniCluster.getSolrClient());
+
 		log.info("pingResponse: '{}'", pingResponse.getStatus());
 		assertEquals(0, pingResponse.getStatus());
 	}
@@ -24,7 +28,7 @@ class SolrAdminApplicationTest extends SolrTest {
 		SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
 
 		UpdateResponse rsp = (UpdateResponse) admin
-			.execute(SolrAdminApplication.Action.DELETE_BY_QUERY, DEFAULT_COLLECTION, "*:*", false, null, null);
+			.execute(SolrAdminApplication.Action.DELETE_BY_QUERY, "*:*", false, null, SHADOW_COLLECTION);
 
 		assertEquals(0, rsp.getStatus());
 	}
@@ -34,7 +38,7 @@ class SolrAdminApplicationTest extends SolrTest {
 
 		SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
 
-		UpdateResponse rsp = (UpdateResponse) admin.commit(DEFAULT_COLLECTION);
+		UpdateResponse rsp = (UpdateResponse) admin.commit(SHADOW_COLLECTION);
 
 		assertEquals(0, rsp.getStatus());
 	}
@@ -45,7 +49,7 @@ class SolrAdminApplicationTest extends SolrTest {
 		SolrAdminApplication admin = new SolrAdminApplication(miniCluster.getSolrClient().getZkHost());
 
 		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
-			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, DEFAULT_COLLECTION);
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, SHADOW_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 
 	}
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
index 424262eef..41eac2a30 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
@@ -1,29 +1,59 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
+import java.io.File;
 import java.io.IOException;
 import java.net.URI;
+import java.nio.file.Path;
 
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
+import org.apache.solr.client.solrj.embedded.JettyConfig;
+import org.apache.solr.client.solrj.impl.CloudSolrClient;
+import org.apache.solr.client.solrj.request.CollectionAdminRequest;
+import org.apache.solr.client.solrj.request.ConfigSetAdminRequest;
+import org.apache.solr.client.solrj.request.QueryRequest;
+import org.apache.solr.client.solrj.response.CollectionAdminResponse;
 import org.apache.solr.client.solrj.response.QueryResponse;
+import org.apache.solr.cloud.MiniSolrCloudCluster;
 import org.apache.solr.common.SolrDocument;
+import org.apache.solr.common.params.CollectionParams;
 import org.apache.solr.common.params.CommonParams;
+import org.apache.solr.common.params.CoreAdminParams;
+import org.apache.solr.common.params.ModifiableSolrParams;
+import org.apache.solr.common.util.NamedList;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
+import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
 
-import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 @ExtendWith(MockitoExtension.class)
-public class SolrConfigExploreTest extends SolrExploreTest {
+public class SolrConfigExploreTest {
+
+	protected static final Logger log = LoggerFactory.getLogger(SolrConfigExploreTest.class);
+
+	protected static final String SHADOW_FORMAT = "c1";
+	protected static final String SHADOW_COLLECTION = SHADOW_FORMAT + "-index-openaire";
+	protected static final String PUBLIC_FORMAT = "c2";
+	protected static final String PUBLIC_COLLECTION = PUBLIC_FORMAT + "-index-openaire";
+
+	protected static final String CONFIG_NAME = "testConfig";
+
+	protected static SolrAdminApplication admin;
 
 	protected static SparkSession spark;
 
@@ -35,15 +65,17 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 	@Mock
 	private ISLookupClient isLookupClient;
 
+	@TempDir
+	public static Path workingDir;
+
+	protected static MiniSolrCloudCluster miniCluster;
+
 	@BeforeEach
 	public void prepareMocks() throws ISLookUpException, IOException {
 		isLookupClient.setIsLookup(isLookUpService);
 
 		int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort();
 
-		Mockito
-			.when(isLookupClient.getDsId(Mockito.anyString()))
-			.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
 		Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort));
 		Mockito
 			.when(isLookupClient.getLayoutSource(Mockito.anyString()))
@@ -54,12 +86,12 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 	}
 
 	@BeforeAll
-	public static void before() {
+	public static void setup() throws Exception {
 
 		SparkConf conf = new SparkConf();
 		conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
 		conf.registerKryoClasses(new Class[] {
-			SerializableSolrInputDocument.class
+				SerializableSolrInputDocument.class
 		});
 
 		conf.setMaster("local[1]");
@@ -69,16 +101,76 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
 
 		spark = SparkSession
-			.builder()
-			.appName(XmlIndexingJobTest.class.getSimpleName())
-			.config(conf)
-			.getOrCreate();
+				.builder()
+				.appName(SolrConfigExploreTest.class.getSimpleName())
+				.config(conf)
+				.getOrCreate();
+
+		// random unassigned HTTP port
+		final int jettyPort = 0;
+		final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build();
+
+		log.info(String.format("working directory: %s", workingDir.toString()));
+		System.setProperty("solr.log.dir", workingDir.resolve("logs").toString());
+
+		// create a MiniSolrCloudCluster instance
+		miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig);
+
+		// Upload Solr configuration directory to ZooKeeper
+		String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig";
+		File configDir = new File(solrZKConfigDir);
+
+		miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME);
+
+		// override settings in the solrconfig include
+		System.setProperty("solr.tests.maxBufferedDocs", "100000");
+		System.setProperty("solr.tests.maxIndexingThreads", "-1");
+		System.setProperty("solr.tests.ramBufferSizeMB", "100");
+
+		// use non-test classes so RandomizedRunner isn't necessary
+		System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler");
+		System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory");
+		System.setProperty("solr.lock.type", "single");
+
+		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
+		log
+				.info(
+						CollectionAdminRequest.ClusterStatus
+								.getClusterStatus()
+								.process(miniCluster.getSolrClient())
+								.toString());
+
+		NamedList<Object> res = createCollection(
+				miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
+		res.forEach(o -> log.info(o.toString()));
+
+		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
+
+		res = createCollection(
+				miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+		res.forEach(o -> log.info(o.toString()));
+
+		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
+		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
+				.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+		assertEquals(0, rsp.getStatus());
+		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
+		assertEquals(0, rsp.getStatus());
+
+		log
+				.info(
+						CollectionAdminRequest.ClusterStatus
+								.getClusterStatus()
+								.process(miniCluster.getSolrClient())
+								.toString());
 
 	}
 
 	@AfterAll
-	public static void tearDown() {
+	public static void tearDown() throws Exception {
 		spark.stop();
+		miniCluster.shutdown();
+		FileUtils.deleteDirectory(workingDir.toFile());
 	}
 
 	@Test
@@ -86,8 +178,9 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 
 		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
 
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
+		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
+			.run(isLookupClient);
+		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -101,14 +194,13 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 			query.add(CommonParams.Q, q);
 			query.set("debugQuery", "on");
 
-			log.info("Submit query to Solr with params: {}", query.toString());
-			QueryResponse rsp = miniCluster.getSolrClient().query(query);
+			log.info("Submit query to Solr with params: {}", query);
+			QueryResponse rsp = miniCluster.getSolrClient().query(ProvisionConstants.SHADOW_ALIAS_NAME, query);
 //            System.out.println(rsp.getHighlighting());
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-				System.out
-					.println(
+				log.info(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -122,4 +214,18 @@ public class SolrConfigExploreTest extends SolrExploreTest {
 			}
 		}
 	}
+
+	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
+														int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
+		ModifiableSolrParams modParams = new ModifiableSolrParams();
+		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
+		modParams.set("name", name);
+		modParams.set("numShards", numShards);
+		modParams.set("replicationFactor", replicationFactor);
+		modParams.set("collection.configName", configName);
+		modParams.set("maxShardsPerNode", maxShardsPerNode);
+		QueryRequest request = new QueryRequest(modParams);
+		request.setPath("/admin/collections");
+		return client.request(request);
+	}
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
index 625b6d131..2c62389c6 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
@@ -2,24 +2,15 @@
 package eu.dnetlib.dhp.oa.provision;
 
 import java.io.IOException;
-import java.io.StringReader;
 import java.net.URI;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.io.Text;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
-import org.apache.solr.common.SolrInputField;
 import org.apache.solr.common.params.CommonParams;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaPairRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
-import org.dom4j.io.SAXReader;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
@@ -50,9 +41,6 @@ public class SolrConfigTest extends SolrTest {
 
 		int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort();
 
-		Mockito
-			.when(isLookupClient.getDsId(Mockito.anyString()))
-			.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
 		Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort));
 		Mockito
 			.when(isLookupClient.getLayoutSource(Mockito.anyString()))
@@ -95,9 +83,9 @@ public class SolrConfigTest extends SolrTest {
 
 		String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml";
 
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize)
+		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
+		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -109,8 +97,8 @@ public class SolrConfigTest extends SolrTest {
 			SolrQuery query = new SolrQuery();
 			query.add(CommonParams.Q, q);
 
-			log.info("Submit query to Solr with params: {}", query.toString());
-			QueryResponse rsp = miniCluster.getSolrClient().query(query);
+			log.info("Submit query to Solr with params: {}", query);
+			QueryResponse rsp = miniCluster.getSolrClient().query(ProvisionConstants.SHADOW_ALIAS_NAME, query);
 
 			for (SolrDocument doc : rsp.getResults()) {
 				System.out
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java
index 34a9465a7..5b5e42fbd 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java
@@ -34,58 +34,6 @@ public abstract class SolrExploreTest {
 	@TempDir
 	public static Path workingDir;
 
-	@BeforeAll
-	public static void setup() throws Exception {
-
-		// random unassigned HTTP port
-		final int jettyPort = 0;
-		final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build();
-
-		log.info(String.format("working directory: %s", workingDir.toString()));
-		System.setProperty("solr.log.dir", workingDir.resolve("logs").toString());
-
-		// create a MiniSolrCloudCluster instance
-		miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig);
-
-		// Upload Solr configuration directory to ZooKeeper
-		String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig";
-		File configDir = new File(solrZKConfigDir);
-
-		miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME);
-
-		// override settings in the solrconfig include
-		System.setProperty("solr.tests.maxBufferedDocs", "100000");
-		System.setProperty("solr.tests.maxIndexingThreads", "-1");
-		System.setProperty("solr.tests.ramBufferSizeMB", "100");
-
-		// use non-test classes so RandomizedRunner isn't necessary
-		System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler");
-		System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory");
-		System.setProperty("solr.lock.type", "single");
-
-		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
-		log
-			.info(
-				CollectionAdminRequest.ClusterStatus
-					.getClusterStatus()
-					.process(miniCluster.getSolrClient())
-					.toString());
-
-		NamedList<Object> res = createCollection(
-			miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME);
-		res.forEach(o -> log.info(o.toString()));
-
-		miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION);
-
-		log
-			.info(
-				CollectionAdminRequest.ClusterStatus
-					.getClusterStatus()
-					.process(miniCluster.getSolrClient())
-					.toString());
-
-	}
-
 	@AfterAll
 	public static void shutDown() throws Exception {
 		miniCluster.shutdown();
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java
index 79527b891..2caf09799 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrTest.java
@@ -1,6 +1,8 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 import java.io.File;
 import java.nio.file.Path;
 
@@ -10,6 +12,7 @@ import org.apache.solr.client.solrj.impl.CloudSolrClient;
 import org.apache.solr.client.solrj.request.CollectionAdminRequest;
 import org.apache.solr.client.solrj.request.ConfigSetAdminRequest;
 import org.apache.solr.client.solrj.request.QueryRequest;
+import org.apache.solr.client.solrj.response.CollectionAdminResponse;
 import org.apache.solr.cloud.MiniSolrCloudCluster;
 import org.apache.solr.common.params.CollectionParams;
 import org.apache.solr.common.params.CoreAdminParams;
@@ -21,14 +24,21 @@ import org.junit.jupiter.api.io.TempDir;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import sun.security.provider.SHA;
+
 public abstract class SolrTest {
 
 	protected static final Logger log = LoggerFactory.getLogger(SolrTest.class);
 
-	protected static final String FORMAT = "test";
-	protected static final String DEFAULT_COLLECTION = FORMAT + "-index-openaire";
+	protected static final String SHADOW_FORMAT = "c1";
+	protected static final String SHADOW_COLLECTION = SHADOW_FORMAT + "-index-openaire";
+	protected static final String PUBLIC_FORMAT = "c2";
+	protected static final String PUBLIC_COLLECTION = PUBLIC_FORMAT + "-index-openaire";
+
 	protected static final String CONFIG_NAME = "testConfig";
 
+	protected static SolrAdminApplication admin;
+
 	protected static MiniSolrCloudCluster miniCluster;
 
 	@TempDir
@@ -72,10 +82,21 @@ public abstract class SolrTest {
 					.toString());
 
 		NamedList<Object> res = createCollection(
-			miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
-		miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION);
+		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
+
+		res = createCollection(
+			miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+		res.forEach(o -> log.info(o.toString()));
+
+		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
+		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+		assertEquals(0, rsp.getStatus());
+		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
+		assertEquals(0, rsp.getStatus());
 
 		log
 			.info(
@@ -83,12 +104,12 @@ public abstract class SolrTest {
 					.getClusterStatus()
 					.process(miniCluster.getSolrClient())
 					.toString());
-
 	}
 
 	@AfterAll
 	public static void shutDown() throws Exception {
 		miniCluster.shutdown();
+		admin.close();
 		FileUtils.deleteDirectory(workingDir.toFile());
 	}
 
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java
index 522c34ef1..8149c2526 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlIndexingJobTest.java
@@ -10,6 +10,7 @@ import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
+import org.apache.solr.client.solrj.SolrResponse;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.params.CommonParams;
 import org.apache.spark.SparkConf;
@@ -50,9 +51,6 @@ public class XmlIndexingJobTest extends SolrTest {
 
 		int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort();
 
-		Mockito
-			.when(isLookupClient.getDsId(Mockito.anyString()))
-			.thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl");
 		Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort));
 		Mockito
 			.when(isLookupClient.getLayoutSource(Mockito.anyString()))
@@ -103,46 +101,72 @@ public class XmlIndexingJobTest extends SolrTest {
 
 		long nRecord = records.count();
 
-		new XmlIndexingJob(spark, inputPath, FORMAT, batchSize).run(isLookupClient);
+		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
+			.run(isLookupClient);
 
-		assertEquals(0, miniCluster.getSolrClient().commit().getStatus());
+		assertEquals(0, miniCluster.getSolrClient().commit(SHADOW_COLLECTION).getStatus());
 
-		QueryResponse rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "*:*"));
+		QueryResponse rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
+				new SolrQuery().add(CommonParams.Q, "*:*"));
 
 		assertEquals(
 			nRecord, rsp.getResults().getNumFound(),
 			"the number of indexed records should be equal to the number of input records");
 
-		rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isgreen:true"));
+		rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
+				new SolrQuery().add(CommonParams.Q, "isgreen:true"));
 		assertEquals(
-			0, rsp.getResults().getNumFound(),
+			4, rsp.getResults().getNumFound(),
 			"the number of indexed records having isgreen = true");
 
-		rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze"));
+		rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
+				new SolrQuery().add(CommonParams.Q, "openaccesscolor:bronze"));
 		assertEquals(
-			0, rsp.getResults().getNumFound(),
+			2, rsp.getResults().getNumFound(),
 			"the number of indexed records having openaccesscolor = bronze");
 
-		rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true"));
+		rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
+				new SolrQuery().add(CommonParams.Q, "isindiamondjournal:true"));
 		assertEquals(
 			0, rsp.getResults().getNumFound(),
 			"the number of indexed records having isindiamondjournal = true");
 
-		rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "publiclyfunded:true"));
+		rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
+				new SolrQuery().add(CommonParams.Q, "publiclyfunded:true"));
 		assertEquals(
 			0, rsp.getResults().getNumFound(),
 			"the number of indexed records having publiclyfunded = true");
 
-		rsp = miniCluster.getSolrClient().query(new SolrQuery().add(CommonParams.Q, "peerreviewed:true"));
+		rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
+				new SolrQuery().add(CommonParams.Q, "peerreviewed:true"));
 		assertEquals(
-			0, rsp.getResults().getNumFound(),
+			35, rsp.getResults().getNumFound(),
 			"the number of indexed records having peerreviewed = true");
 
 		rsp = miniCluster
 			.getSolrClient()
 			.query(
+				ProvisionConstants.SHADOW_ALIAS_NAME,
 				new SolrQuery()
-					.add(CommonParams.Q, "objidentifier:\"iddesignpres::ae77e56e84ad058d9e7f19fa2f7325db\"")
+					.add(CommonParams.Q, "objidentifier:\"57a035e5b1ae::236d6d8c1e03368b5ae72acfeeb11bbc\"")
 					.add(CommonParams.FL, "__json"));
 		assertEquals(
 			1, rsp.getResults().getNumFound(),
@@ -158,6 +182,22 @@ public class XmlIndexingJobTest extends SolrTest {
 
 		log.info((String) json.get());
 
+		admin
+			.execute(
+				SolrAdminApplication.Action.UPDATE_ALIASES, null, false,
+				SHADOW_COLLECTION, PUBLIC_COLLECTION);
+
+		rsp = miniCluster
+			.getSolrClient()
+			.query(
+				ProvisionConstants.PUBLIC_ALIAS_NAME,
+				new SolrQuery()
+					.add(CommonParams.Q, "objidentifier:\"57a035e5b1ae::236d6d8c1e03368b5ae72acfeeb11bbc\"")
+					.add(CommonParams.FL, "__json"));
+
+		assertEquals(
+			1, rsp.getResults().getNumFound(),
+			"the number of indexed records having the given identifier, found in the public collection");
 	}
 
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml
index ba3fa83df..8567acf85 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/fields.xml
@@ -68,15 +68,12 @@
         <FIELD copy="true" indexable="false" name="externalreflabel" result="false" stat="false" tokenizable="true" xpath="distinct-values(//*[local-name()='entity']/*//children/externalreference/label)"/>
         <FIELD copy="true" indexable="true" name="resultidentifier" result="false" stat="false" type="string_ci" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/children/instance/webresource/*[local-name()='url'])"/>
         <FIELD copy="true" indexable="false" name="resultsource" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/source)"/>
-
         <FIELD indexable="true" multivalued="false" name="isgreen" result="false" stat="false" type="boolean" value="//*[local-name()='entity']/*[local-name()='result']/isgreen"/>
         <FIELD indexable="true" multivalued="false" name="openaccesscolor" result="false" stat="false" tokenizable="false" value="//*[local-name()='entity']/*[local-name()='result']/openaccesscolor"/>
         <FIELD indexable="true" multivalued="false" name="isindiamondjournal" result="false" stat="false" type="boolean" value="//*[local-name()='entity']/*[local-name()='result']/isindiamondjournal"/>
         <FIELD indexable="true" multivalued="false" name="publiclyfunded" result="false" stat="false" type="boolean" value="//*[local-name()='entity']/*[local-name()='result']/publiclyfunded"/>
-
         <FIELD indexable="true" multivalued="false" name="peerreviewed" result="false" stat="false" type="boolean" value="some $refereed in //*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='refereed']/@classid satisfies ($refereed = '0001')"/>
-
-
+        <FIELD indexable="true" multivalued="false" name="haslicense" result="false" stat="false" type="boolean" value="some $license in //*[local-name()='entity']/*[local-name()='result']/children/instance/*[local-name()='license']/text() satisfies (string-length($license) &gt; 0)"/>
         <FIELD indexable="true" name="eoscifguidelines" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name() = 'result']/eoscifguidelines/@code)"/><!-- FOS and SDGs non tokenizable for faceted search-->
         <FIELD indexable="true" name="fos" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/subject[@classid='FOS'])"/>
         <FIELD indexable="true" name="foslabel" result="false" stat="false" tokenizable="false" value="concat(./text(), '||', replace(./text(), '^\d+\s', ''))" xpath="//*[local-name()='entity']/*[local-name()='result']/subject[@classid='FOS']"/>
@@ -93,6 +90,7 @@
         <FIELD indexable="true" name="relorganizationid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='organization'])"/>
         <FIELD copy="true" indexable="true" name="relorganizationname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/legalname)"/>
         <FIELD copy="true" indexable="true" name="relorganizationshortname" result="false" stat="false" xpath="distinct-values(//*[local-name()='entity']/*//rel[./to/@type='organization']/legalshortname)"/>
+        <FIELD indexable="true" name="relorganization" result="false" stat="false" tokenizable="false" value="distinct-values(concat(./to, '||', ./legalname))" xpath="//*[local-name()='entity']/*//rel[./to/@type='organization']"/>
         <FIELD indexable="true" name="relresultid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to[@type='publication' or @type='dataset' or @type='software' or @type='otherresearchproduct'])"/>
         <FIELD indexable="true" name="relresulttype" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to/@type)"/>
         <FIELD indexable="true" name="relclass" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*//rel/to/@class)"/>
@@ -122,6 +120,7 @@
         <FIELD indexable="true" name="categoryid" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/category/@id)"/>
         <FIELD indexable="true" name="conceptname" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*[local-name()='result']/context/category//concept/@label)"/><!-- new index field for country info from different xpaths for any type of entity -->
         <FIELD indexable="true" name="country" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/country/@classid | //*[local-name()='entity']/*//rel[./to/@type='organization']/country/@classid | //*[local-name()='entity']//funder/@jurisdiction)"/>
+        <FIELD indexable="true" name="countrynojurisdiction" result="false" stat="false" tokenizable="false" xpath="distinct-values(//*[local-name()='entity']/*/country/@classid | //*[local-name()='entity']/*//rel[./to/@type='organization']/country/@classid)"/>
         <FIELD indexable="false" name="oafentity" result="true" stat="false" tokenizable="false" xpath="//*[local-name() = 'entity']"/><!-- impact indicators -->
         <FIELD copy="false" indexable="true" multivalued="false" name="influence" result="false" stat="false" type="pfloat" xpath="//measure[@id='influence']/@score/number()"/>
         <FIELD copy="false" indexable="true" multivalued="false" name="influence_class" result="false" stat="false" type="string" xpath="//measure[@id='influence']/@class/string()"/>
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema
index 9720d3f37..d4e1cbede 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema
@@ -194,228 +194,173 @@
   <fieldType name="tints" class="solr.TrieIntField" positionIncrementGap="0" docValues="true" multiValued="true" precisionStep="8"/>
   <fieldType name="tlong" class="solr.TrieLongField" positionIncrementGap="0" docValues="true" precisionStep="8"/>
   <fieldType name="tlongs" class="solr.TrieLongField" positionIncrementGap="0" docValues="true" multiValued="true" precisionStep="8"/>
-
-  <!-- Indexed fields -->
   <field name="__all" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="__deleted" type="boolean" default="false" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="false"/>
-  <field name="__dsid" type="string" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="true"/>
-  <field name="__dsversion" type="pdate" omitNorms="true" omitTermFreqAndPositions="true" indexed="true" stored="true"/>
   <field name="__indexrecordidentifier" type="string" multiValued="false" indexed="true" required="true" stored="true"/>
-  <field name="__result" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
   <field name="__json" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
+  <field name="__result" type="string" docValues="false" multiValued="false" indexed="false" stored="true"/>
   <field name="_root_" type="string" docValues="false" indexed="true" stored="false"/>
   <field name="_version_" type="long" multiValued="false" indexed="true" stored="true"/>
-  <field name="authorid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
-  <field name="authoridtype" type="string_ci" multiValued="true" indexed="true" stored="false"/>
-  <field name="categoryid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="categoryname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="collectedfrom" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="collectedfromdatasourceid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="collectedfromname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="community" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="communityid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="communityname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="conceptid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="conceptname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="contextid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="contextname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="contexttype" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="country" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourcecompatibilityid" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="datasourcecompatibilityname" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="datasourceenglishname" type="text_common" multiValued="true" indexed="true" stored="false"/>
+  <field name="authorid" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="categoryid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="citation_count" type="pint" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="citation_count_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="collectedfromdatasourceid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="collectedfromname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="community" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="communityid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="conceptname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="contextid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="contextname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="country" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="countrynojurisdiction" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourcecompatibilityid" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="datasourcecompatibilityname" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="datasourceenglishname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourcejurisdiction" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourceodcontenttypes" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourceoddescription" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourceodlanguages" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourceodsubjects" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourceofficialname" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourcesubject" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourceodcontenttypes" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourceoddescription" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourceodlanguages" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourceodsubjects" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourceofficialname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourcesubject" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="datasourcethematic" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
-  <field name="datasourcetypename" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="datasourcetypeuiid" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="datasourcetypeuiname" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="dateofcollection" type="pdate" multiValued="false" indexed="true" stored="false"/>
-  <field name="deletedbyinference" type="string" multiValued="true" indexed="true" stored="false"/>
+  <field name="datasourcetypename" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="datasourcetypeuiid" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="datasourcetypeuiname" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="dateofcollection" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="deletedbyinference" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="eoscdatasourcetype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="eoscifguidelines" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="eosctype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
-  <field name="externalrefclass" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="externalrefid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="externalreflabel" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="externalrefsite" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="funder" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="funderid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="funderjurisdiction" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundername" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="funderoriginalname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundershortname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel0_description" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel0_id" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel0_name" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel1_description" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel1_id" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel1_name" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel2_description" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel2_id" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="fundinglevel2_name" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="inferenceprovenance" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="inferred" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="instancetypename" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="oafentity" type="string" multiValued="true" indexed="false" stored="false"/>
-  <field name="oaftype" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="objidentifier" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationalternativenames" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationcountryname" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="organizationdupid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecenterprise" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecinternationalorganization" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecinternationalorganizationeurinterests" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationeclegalbody" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationeclegalperson" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecnonprofit" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecnutscode" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecresearchorganization" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationecsmevalidated" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationlegalname" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
-  <field name="organizationlegalshortname" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
-  <field name="originalid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
-  <field name="pid" type="string_ci" multiValued="true" indexed="true" stored="false"/>
-  <field name="pidclassid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="pidclassname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="projectacronym" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
-  <field name="projectcallidentifier" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectcode" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
-  <field name="projectcode_nt" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="projectcontracttypename" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectduration" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectecarticle29_3" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectecsc39" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectenddate" type="pdate" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectendyear" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectkeywords" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="projectoamandatepublications" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectstartdate" type="pdate" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectstartyear" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="projectsubject" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="projecttitle" type="ngramtext" multiValued="true" indexed="true" stored="false"/>
-  <field name="provenanceactionclassid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relclass" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relcollectedfromid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relcollectedfromname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relcontracttypeid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relcontracttypename" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="reldatasourcecompatibilityid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfunder" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfunderid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfunderjurisdiction" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundername" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundershortname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundinglevel0_id" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundinglevel0_name" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundinglevel1_id" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundinglevel1_name" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundinglevel2_id" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relfundinglevel2_name" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relinferenceprovenance" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relinferred" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relorganizationcountryid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relorganizationcountryname" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="relorganizationid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relorganizationname" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="relorganizationshortname" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="relproject" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relprojectcode" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relprojectid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relprojectname" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relprojecttitle" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="relprovenanceactionclassid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relresultid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="relresulttype" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="reltrust" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultacceptanceyear" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="resultaccessright" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultauthor" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultauthor_nt" type="string_ci" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultbestaccessright" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="resultdateofacceptance" type="pdate" multiValued="false" indexed="true" stored="false"/>
-  <field name="resultdescription" type="text_en" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultdupid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultembargoenddate" type="pdate" multiValued="false" indexed="true" stored="false"/>
-  <field name="resultembargoendyear" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="resulthostingdatasource" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resulthostingdatasourceid" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resulthostingdatasourcename" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultidentifier" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultlanguagename" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="resultlicense" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultpublisher" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultsource" type="text_common" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultsubject" type="text_en" multiValued="true" indexed="true" stored="false"/>
-  <field name="resultsubjectclass" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="resulttitle" type="text_en" multiValued="true" indexed="true" stored="false"/>
-  <field name="resulttypeid" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="resulttypename" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="semrelid" type="string" multiValued="true" indexed="true" stored="false"/>
+  <field name="externalreflabel" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fos" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="foslabel" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="funder" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="funderid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundershortname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel0_description" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel0_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel0_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel1_description" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel1_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel1_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel2_description" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel2_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="fundinglevel2_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="haslicense" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="impulse" type="pint" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="impulse_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="influence" type="pfloat" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="influence_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="instancetypename" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="isgreen" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="isindiamondjournal" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="oafentity" type="string" docValues="false" multiValued="true" indexed="false" stored="false"/>
+  <field name="oaftype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="objidentifier" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="openaccesscolor" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="orcidtypevalue" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="organizationalternativenames" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="organizationdupid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="organizationlegalname" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="organizationlegalshortname" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="originalid" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="peerreviewed" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="pid" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="pidclassid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="popularity" type="pfloat" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="popularity_alt" type="pfloat" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="popularity_alt_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="popularity_class" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectacronym" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="projectcallidentifier" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectcode" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="projectcode_nt" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="projectduration" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectecsc39" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectenddate" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectendyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectkeywords" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="projectoamandatepublications" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectstartdate" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projectstartyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="projecttitle" type="ngramtext" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="projecttitle_alternative" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="provenanceactionclassid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="publiclyfunded" type="boolean" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="relclass" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relcontracttypename" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="reldatasourcecompatibilityid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfunder" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfunderid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundershortname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundinglevel0_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundinglevel0_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundinglevel1_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundinglevel1_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundinglevel2_id" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relfundinglevel2_name" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relorganizationcountryid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relorganizationcountryname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relorganizationid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relorganizationname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relorganizationshortname" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relproject" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relprojectcode" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relprojectid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relprojectname" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relprojecttitle" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relresultid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="relresulttype" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultacceptanceyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="resultauthor" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultbestaccessright" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="resultdateofacceptance" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="resultdescription" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultdupid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultembargoenddate" type="date" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="resultembargoendyear" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="resulthostingdatasource" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resulthostingdatasourceid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultidentifier" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultlanguagename" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="resultpublisher" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultsource" type="text_common" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resultsubject" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resulttitle" type="text_en" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="resulttypeid" type="string" docValues="false" multiValued="false" indexed="true" stored="false"/>
+  <field name="sdg" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="semrelid" type="string" docValues="false" multiValued="true" indexed="true" stored="false"/>
+  <field name="status" type="string_ci" docValues="false" multiValued="true" indexed="true" stored="false"/>
   <field name="text" type="text_common" indexed="false" stored="false"/>
-  <field name="trust" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="versioning" type="string" multiValued="true" indexed="true" stored="false"/>
-  <field name="isgreen" type="boolean" multiValued="false" indexed="true" stored="false"/>
-  <field name="openaccesscolor" type="string" multiValued="false" indexed="true" stored="false"/>
-  <field name="isindiamondjournal" type="boolean" multiValued="false" indexed="true" stored="false"/>
-  <field name="publiclyfunded" type="boolean" multiValued="false" indexed="true" stored="false"/>
-  <field name="peerreviewed" type="boolean" multiValued="false" indexed="true" stored="false"/>
-
-  <!-- Copy field definitions follow: -->
-
-  <!-- Data source -->
   <copyField source="datasourceenglishname" dest="__all"/>
   <copyField source="datasourceoddescription" dest="__all"/>
+  <copyField source="datasourceodsubjects" dest="__all"/>
   <copyField source="datasourceofficialname" dest="__all"/>
   <copyField source="datasourcesubject" dest="__all"/>
-
-  <!-- Organization -->
+  <copyField source="externalreflabel" dest="__all"/>
+  <copyField source="fundinglevel0_description" dest="__all"/>
+  <copyField source="fundinglevel1_description" dest="__all"/>
+  <copyField source="fundinglevel2_description" dest="__all"/>
   <copyField source="organizationalternativenames" dest="__all"/>
-  <copyField source="organizationecenterprise" dest="__all"/>
-  <copyField source="organizationecinternationalorganization" dest="__all"/>
-  <copyField source="organizationecinternationalorganizationeurinterests" dest="__all"/>
-  <copyField source="organizationeclegalbody" dest="__all"/>
-  <copyField source="organizationeclegalperson" dest="__all"/>
-  <copyField source="organizationecnonprofit" dest="__all"/>
-  <copyField source="organizationecnutscode" dest="__all"/>
-  <copyField source="organizationecresearchorganization" dest="__all"/>
-  <copyField source="organizationecsmevalidated" dest="__all"/>
   <copyField source="organizationlegalname" dest="__all"/>
   <copyField source="organizationlegalshortname" dest="__all"/>
-
-  <!-- Project -->
   <copyField source="projectacronym" dest="__all"/>
   <copyField source="projectcode" dest="__all"/>
   <copyField source="projectkeywords" dest="__all"/>
   <copyField source="projecttitle" dest="__all"/>
-
-  <!-- Result -->
-  <copyField source="resultpublisher" dest="__all"/>
-  <copyField source="resultsource" dest="__all"/>
-  <copyField source="resultidentifier" dest="__all"/>
-  <copyField source="resultauthor" dest="__all"/>
-  <copyField source="resulttitle" dest="__all"/>
-  <copyField source="resultdescription" dest="__all"/>
-  <copyField source="resultsubject" dest="__all"/>
-  <copyField source="resultacceptanceyear" dest="__all"/>
-
-  <!-- Other -->
-  <copyField source="externalreflabel" dest="__all"/>
-
-  <copyField source="fundinglevel0_description" dest="__all"/>
-  <copyField source="fundinglevel1_description" dest="__all"/>
-  <copyField source="fundinglevel2_description" dest="__all"/>
-
+  <copyField source="projecttitle_alternative" dest="__all"/>
   <copyField source="relcontracttypename" dest="__all"/>
   <copyField source="relorganizationcountryname" dest="__all"/>
   <copyField source="relorganizationname" dest="__all"/>
   <copyField source="relorganizationshortname" dest="__all"/>
-  <copyField source="relprojecttitle" dest="__all"/>
   <copyField source="relprojectname" dest="__all"/>
-
+  <copyField source="relprojecttitle" dest="__all"/>
+  <copyField source="resultacceptanceyear" dest="__all"/>
+  <copyField source="resultauthor" dest="__all"/>
+  <copyField source="resultdescription" dest="__all"/>
+  <copyField source="resultidentifier" dest="__all"/>
+  <copyField source="resultpublisher" dest="__all"/>
+  <copyField source="resultsource" dest="__all"/>
+  <copyField source="resulttitle" dest="__all"/>
 </schema>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/xml_json_sample.json.gz b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/xml/xml_json_sample.json.gz
new file mode 100644
index 0000000000000000000000000000000000000000..81e4a1c3afb50979b571bcf857a3a809b147a03d
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HVj3|3gLW9K

literal 0
HcmV?d00001

diff --git a/pom.xml b/pom.xml
index 9e554204d..42afbd372 100644
--- a/pom.xml
+++ b/pom.xml
@@ -960,7 +960,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.3-SNAPSHOT]</dhp-schemas.version>
+        <dhp-schemas.version>[6.1.3]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From 1ccf01cdb8f1334c04f0537a25386c15e2770d0c Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 28 Jun 2024 12:38:07 +0200
Subject: [PATCH 041/239] Using the updated Solr JSON payload model classes

---
 .../model/ProvisionModelSupport.java          | 20 +++++++++++++++++--
 pom.xml                                       |  2 +-
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index a8c9ceeb3..b450b95be 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,6 +5,7 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -375,7 +376,7 @@ public class ProvisionModelSupport {
 		rs.setIsInDiamondJournal(r.getIsInDiamondJournal());
 		rs.setPubliclyFunded(r.getPubliclyFunded());
 		rs.setTransformativeAgreement(r.getTransformativeAgreement());
-
+		rs.setExternalReference(mapExternalReference(r.getExternalReference()));
 		rs.setInstance(mapInstances(r.getInstance()));
 
 		if (r instanceof Publication) {
@@ -561,6 +562,21 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
+	private static List<ExternalReference> mapExternalReference(List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+		return Optional.ofNullable(externalReference)
+				.map(ext -> ext.stream()
+						.map(e -> ExternalReference.newInstance(
+								e.getSitename(),
+								e.getLabel(),
+								e.getAlternateLabel(),
+								e.getUrl(),
+								mapCodeLabel(e.getQualifier()),
+								e.getRefidentifier(),
+								e.getQuery()))
+						.collect(Collectors.toList()))
+				.orElse(Lists.newArrayList());
+	}
+
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
 		ContextMapper contextMapper) {
 
@@ -579,7 +595,7 @@ public class ProvisionModelSupport {
 		}
 
 		return Optional
-			.ofNullable(contexts)
+			.of(contexts)
 			.map(
 				ctx -> ctx
 					.stream()
diff --git a/pom.xml b/pom.xml
index 42afbd372..a5bc6cedd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -960,7 +960,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.3]</dhp-schemas.version>
+        <dhp-schemas.version>[6.1.4-SNAPSHOT]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From 1bc8c5d1735a43e392299089fa8b61de5204dc33 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 28 Jun 2024 14:21:12 +0200
Subject: [PATCH 042/239] [graph provision] fixed serialization of the
 instancetypes

---
 .../oa/provision/utils/XmlRecordFactory.java  | 21 ++++++++++++-------
 .../provision/IndexRecordTransformerTest.java | 17 ++++++++++-----
 2 files changed, 26 insertions(+), 12 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index ec322dbd4..3d89b1e34 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -1315,7 +1315,7 @@ public class XmlRecordFactory implements Serializable {
 								instance
 									.getCollectedfrom()
 									.stream()
-									.filter(cf -> kvNotBlank(cf))
+									.filter(XmlRecordFactory::kvNotBlank)
 									.map(cf -> XmlSerializationUtils.mapKeyValue("collectedfrom", cf))
 									.collect(Collectors.toList()));
 					}
@@ -1326,7 +1326,7 @@ public class XmlRecordFactory implements Serializable {
 								instance
 									.getHostedby()
 									.stream()
-									.filter(hb -> kvNotBlank(hb))
+									.filter(XmlRecordFactory::kvNotBlank)
 									.map(hb -> XmlSerializationUtils.mapKeyValue("hostedby", hb))
 									.collect(Collectors.toList()));
 					}
@@ -1336,7 +1336,7 @@ public class XmlRecordFactory implements Serializable {
 								instance
 									.getDateofacceptance()
 									.stream()
-									.filter(d -> isNotBlank(d))
+									.filter(StringUtils::isNotBlank)
 									.map(d -> XmlSerializationUtils.asXmlElement("dateofacceptance", d))
 									.collect(Collectors.toList()));
 					}
@@ -1346,7 +1346,7 @@ public class XmlRecordFactory implements Serializable {
 								instance
 									.getInstancetype()
 									.stream()
-									.filter(t -> !StringUtils.isNotBlank(t.getClassid()))
+									.filter(t -> StringUtils.isNotBlank(t.getClassid()))
 									.map(t -> XmlSerializationUtils.mapQualifier("instancetype", t))
 									.collect(Collectors.toList()));
 					}
@@ -1356,7 +1356,7 @@ public class XmlRecordFactory implements Serializable {
 								instance
 									.getDistributionlocation()
 									.stream()
-									.filter(d -> isNotBlank(d))
+									.filter(StringUtils::isNotBlank)
 									.map(d -> XmlSerializationUtils.asXmlElement("distributionlocation", d))
 									.collect(Collectors.toList()));
 					}
@@ -1409,7 +1409,7 @@ public class XmlRecordFactory implements Serializable {
 								instance
 									.getLicense()
 									.stream()
-									.filter(d -> isNotBlank(d))
+									.filter(StringUtils::isNotBlank)
 									.map(d -> XmlSerializationUtils.asXmlElement("license", d))
 									.collect(Collectors.toList()));
 					}
@@ -1540,11 +1540,16 @@ public class XmlRecordFactory implements Serializable {
 					.min(new RefereedComparator())
 					.orElse(XmlInstance.UNKNOWN_REVIEW_LEVEL));
 
+		Map<String, Qualifier> instanceTypes = Maps.newHashMap();
+
 		instances.forEach(p -> {
 			final Instance i = p.getRight();
 			instance.getCollectedfrom().add(i.getCollectedfrom());
 			instance.getHostedby().add(i.getHostedby());
-			instance.getInstancetype().add(i.getInstancetype());
+
+			if (Optional.ofNullable(i.getInstancetype()).map(Qualifier::getClassid).isPresent()) {
+				instanceTypes.putIfAbsent(i.getInstancetype().getClassid(), i.getInstancetype());
+			}
 			instance
 				.setProcessingchargeamount(
 					Optional.ofNullable(i.getProcessingchargeamount()).map(apc -> apc.getValue()).orElse(null));
@@ -1571,6 +1576,8 @@ public class XmlRecordFactory implements Serializable {
 				.ifPresent(instance::setFulltext);
 		});
 
+		instance.getInstancetype().addAll(instanceTypes.values());
+
 		if (instance.getHostedby().size() > 1
 			&& instance.getHostedby().stream().anyMatch(hb -> ModelConstants.UNKNOWN_REPOSITORY.equals(hb))) {
 			instance.getHostedby().remove(ModelConstants.UNKNOWN_REPOSITORY);
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java
index 718b43f03..923a68352 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java
@@ -5,6 +5,7 @@ import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
 
 import java.io.IOException;
+import java.io.StringReader;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.Arrays;
@@ -16,6 +17,9 @@ import javax.xml.transform.TransformerException;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.util.ClientUtils;
 import org.apache.solr.common.SolrInputDocument;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.io.SAXReader;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -34,7 +38,6 @@ import eu.dnetlib.dhp.utils.saxon.SaxonTransformerFactory;
 
 /**
  * This test can be used to produce a record that can be manually fed to Solr in XML format.
- *
  * The input is a JoinedEntity, i.e. a json representation of an OpenAIRE entity that embeds all the linked entities.
  */
 public class IndexRecordTransformerTest {
@@ -54,7 +57,7 @@ public class IndexRecordTransformerTest {
 	}
 
 	@Test
-	public void testPublicationRecordTransformation() throws IOException, TransformerException {
+	public void testPublicationRecordTransformation() throws IOException, TransformerException, DocumentException {
 
 		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
 			PayloadConverterJob.schemaLocation);
@@ -71,11 +74,15 @@ public class IndexRecordTransformerTest {
 						new RelatedEntityWrapper(rel,
 							CreateRelatedEntitiesJob_phase1.asRelatedEntity(pj, Project.class))));
 
-		final String record = xmlRecordFactory.build(je);
+		final String xmlRecord = xmlRecordFactory.build(je);
 
-		assertNotNull(record);
+		assertNotNull(xmlRecord);
 
-		testRecordTransformation(record);
+		Document doc = new SAXReader().read(new StringReader(xmlRecord));
+
+		assertEquals("Article", doc.valueOf("//children/instance/instancetype/@classname"));
+
+		testRecordTransformation(xmlRecord);
 	}
 
 	@Test

From 14539f9c8bb554204e96246a94fa6f78aa721971 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 28 Jun 2024 14:52:43 +0200
Subject: [PATCH 043/239] [graph provision] publicFormat worfklow parameter
 defined as optional

---
 .../eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml        | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
index 6c58d2466..15d3b6300 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
@@ -38,10 +38,6 @@
             <name>shadowFormat</name>
             <description>metadata format name (DMF|TMF)</description>
         </property>
-        <property>
-            <name>publicFormat</name>
-            <description>the public metadata format - used to create the public collection alias</description>
-        </property>
         <property>
             <name>batchSize</name>
             <description>number of records to be included in each indexing request</description>

From a10e8d9f05b32d59ec5b9feda1ca0d7e5e12ba70 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Fri, 28 Jun 2024 16:46:52 +0200
Subject: [PATCH 044/239] implementation of countryMatch and addition of
 workflow parameters

---
 .../eu/dnetlib/pace/tree/CountryMatch.java    | 47 +++++++++++++++++++
 .../pace/comparators/ComparatorTest.java      | 19 ++++++++
 .../openorgs/oozie_app/config-default.xml     |  8 ++++
 .../oa/dedup/openorgs/oozie_app/workflow.xml  |  2 +
 .../dnetlib/dhp/dedup/conf/org.curr.conf.json |  2 +-
 5 files changed, 77 insertions(+), 1 deletion(-)
 create mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
new file mode 100644
index 000000000..9cf616356
--- /dev/null
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
@@ -0,0 +1,47 @@
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("countryMatch")
+public class CountryMatch extends AbstractStringComparator {
+
+    public CountryMatch(Map<String, String> params) {
+        super(params, new com.wcohen.ss.JaroWinkler());
+    }
+
+    public CountryMatch(final double weight) {
+        super(weight, new com.wcohen.ss.JaroWinkler());
+    }
+
+    protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
+        super(weight, ssalgo);
+    }
+
+    @Override
+    public double distance(final String a, final String b, final Config conf) {
+        if (a.isEmpty() || b.isEmpty()) {
+            return -1.0; // return -1 if a field is missing
+        }
+        if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
+            return -1.0; // return -1 if a country is UNKNOWN
+        }
+
+        return a.equals(b) ? 1.0 : 0;
+    }
+
+    @Override
+    public double getWeight() {
+        return super.weight;
+    }
+
+    @Override
+    protected double normalize(final double d) {
+        return d;
+    }
+}
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index b37e16cf5..8e72f4efc 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -336,4 +336,23 @@ public class ComparatorTest extends AbstractPaceTest {
 		System.out.println("compare = " + compare);
 	}
 
+	@Test
+	public void countryMatch() {
+
+		CountryMatch countryMatch = new CountryMatch(params);
+
+		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
+		assertEquals(-1.0, result);
+
+		result = countryMatch.distance("CHILE", "UNKNOWN", conf);
+		assertEquals(-1.0, result);
+
+		result = countryMatch.distance("CHILE", "ITALY", conf);
+		assertEquals(0.0, result);
+
+		result = countryMatch.distance("CHILE", "CHILE", conf);
+		assertEquals(1.0, result);
+
+	}
+
 }
diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml
index 2e0ed9aee..6d375f03f 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/config-default.xml
@@ -15,4 +15,12 @@
         <name>oozie.action.sharelib.for.spark</name>
         <value>spark2</value>
     </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>pivotHistoryDatabase</name>
+        <value>&#x200B;</value>
+    </property>
 </configuration>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml
index 6947019e8..7c633facc 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/openorgs/oozie_app/workflow.xml
@@ -198,6 +198,8 @@
             <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
             <arg>--actionSetId</arg><arg>${actionSetId}</arg>
             <arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+            <arg>--pivotHistoryDatabase</arg><arg>${pivotHistoryDatabase}</arg>
         </spark>
         <ok to="PrepareOrgRels"/>
         <error to="Kill"/>
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json
index 726f2b899..917c9426b 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json
@@ -49,7 +49,7 @@
           },
           {
             "field": "country",
-            "comparator": "exactMatch",
+            "comparator": "countryMatch",
             "weight": 1,
             "countIfUndefined": "true",
             "params": {}

From 67ff783e650d3b42894dae334b6643778effc9b5 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Sat, 29 Jun 2024 17:13:01 +0200
Subject: [PATCH 045/239] [Person]First implementation to include Person entity
 in the graph

---
 .../actionmanager/personentity/Coauthors.java |  19 +
 .../actionmanager/personentity/Couples.java   |  40 +++
 .../personentity/ExtractPerson.java           | 331 ++++++++++++++++++
 .../actionmanager/personentity/WorkList.java  |  23 ++
 .../CreateActionSetFromWebEntries.java        |  12 +-
 .../dhp/collection/orcid/model/Author.java    |   3 +
 .../dhp/collection/orcid/model/ORCIDItem.java |   3 +
 .../dhp/collection/orcid/model/Work.java      |   2 +
 .../personentity/as_parameters.json           |  26 ++
 .../actionmanager/person/CreatePersonAS.java  | 114 ++++++
 .../actionmanager/person/WorkJson/part-00000  |  10 +
 pom.xml                                       |  19 +
 12 files changed, 599 insertions(+), 3 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/person/WorkJson/part-00000

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
new file mode 100644
index 000000000..a755c875f
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
@@ -0,0 +1,19 @@
+package eu.dnetlib.dhp.actionmanager.personentity;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+
+
+public class Coauthors implements Serializable {
+    private ArrayList<Relation> coauthors;
+
+    public ArrayList<Relation> getCoauthors() {
+        return coauthors;
+    }
+
+    public void setCoauthors(ArrayList<Relation> coauthors) {
+        this.coauthors = coauthors;
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java
new file mode 100644
index 000000000..65670b22e
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java
@@ -0,0 +1,40 @@
+package eu.dnetlib.dhp.actionmanager.personentity;
+
+import eu.dnetlib.dhp.schema.oaf.Person;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import scala.Tuple2;
+
+
+import java.io.Serializable;
+
+public class Couples implements Serializable {
+    Person p ;
+    Relation r;
+
+    public Couples() {
+
+    }
+
+    public Person getP() {
+        return p;
+    }
+
+    public void setP(Person p) {
+        this.p = p;
+    }
+
+    public Relation getR() {
+        return r;
+    }
+
+    public void setR(Relation r) {
+        this.r = r;
+    }
+
+    public static <Tuples> Couples newInstance(Tuple2<Person, Relation> couple){
+        Couples c = new Couples();
+        c.p = couple._1();
+        c.r = couple._2();
+        return c;
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
new file mode 100644
index 000000000..0bbda0343
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -0,0 +1,331 @@
+package eu.dnetlib.dhp.actionmanager.personentity;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.Constants;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.collection.orcid.model.Author;
+import eu.dnetlib.dhp.collection.orcid.model.Employment;
+import eu.dnetlib.dhp.collection.orcid.model.Work;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Person;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.Pid;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import eu.dnetlib.dhp.utils.DHPUtils;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.*;
+import org.apache.spark.sql.*;
+import org.jetbrains.annotations.NotNull;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.spark_project.jetty.util.StringUtil;
+import scala.Tuple2;
+import static org.apache.spark.sql.functions.*;
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.*;
+import java.util.stream.Collectors;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+public class ExtractPerson implements Serializable {
+    private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+    private static final String OPENAIRE_PREFIX = "openaire____";
+    private static final String SEPARATOR = "::";
+    private static final String orcidKey = "10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
+
+    private static final String DOI_PREFIX = "50|doi_________::";
+
+    private static final String PMID_PREFIX = "50|pmid________::";
+    private static final String ARXIV_PREFIX = "50|arXiv_______::";
+
+    private static final String PMCID_PREFIX = "50|pmcid_______::";
+    private static final String ROR_PREFIX = "20|ror_________::";
+    private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
+    public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
+    public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
+
+
+    public static void main(final String[] args) throws IOException, ParseException {
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+                IOUtils
+                        .toString(
+                                Objects
+                                        .requireNonNull(
+                                                ExtractPerson.class
+                                                        .getResourceAsStream(
+                                                                "/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json"))));
+
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        final String inputPath = parser.get("inputPath");
+        log.info("inputPath {}", inputPath);
+
+        final String outputPath = parser.get("outputPath");
+        log.info("outputPath {}", outputPath);
+
+        final String workingDir = parser.get("workingDir");
+        log.info("workingDir {}", workingDir);
+
+        SparkConf conf = new SparkConf();
+        runWithSparkSession(
+                conf,
+                isSparkSessionManaged,
+                spark -> createActionSet(spark, inputPath, outputPath, workingDir));
+
+    }
+
+    private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
+
+        Dataset<Author> authors = spark
+                .read()
+                .parquet(inputPath + "Authors").as(Encoders.bean(Author.class));
+
+        Dataset<Work> works = spark
+                .read()
+                .parquet(inputPath + "Works")
+                .as(Encoders.bean(Work.class))
+                .filter((FilterFunction<Work>) w -> Optional.ofNullable(w.getPids()).isPresent() &&
+                        w.getPids().stream().anyMatch(p->p.getSchema().equalsIgnoreCase("doi") ||
+                                p.getSchema().equalsIgnoreCase("pmc") ||
+                                p.getSchema().equalsIgnoreCase("pmid") ||
+                                p.getSchema().equalsIgnoreCase("arxiv")));
+
+        Dataset<Employment> employmentDataset = spark
+                .read()
+                .parquet(inputPath + "Employments")
+                .as(Encoders.bean(Employment.class));
+
+
+        Dataset<Author> peopleToMap = authors.joinWith(works, authors.col("orcid").equalTo(works.col("orcid")))
+                .map((MapFunction<Tuple2<Author, Work>, Author>) t2 -> t2._1(), Encoders.bean(Author.class))
+                .groupByKey((MapFunction<Author, String>) a -> a.getOrcid(), Encoders.STRING())
+                .mapGroups((MapGroupsFunction<String, Author, Author>) (k, it) -> it.next(), Encoders.bean(Author.class));
+
+
+        Dataset<Employment> employment = employmentDataset.joinWith(peopleToMap, employmentDataset.col("orcid").equalTo(peopleToMap.col("orcid")))
+                .map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
+
+        peopleToMap.show(false);
+
+        Dataset<Person> people;
+        people = peopleToMap.map((MapFunction<Author, Person>) op -> {
+            Person person = new Person();
+            person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
+            person.setBiography(Optional.ofNullable(op.getBiography())
+
+                    .orElse(""));
+            KeyValue kv = OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS);
+            kv.setDataInfo(null);
+            person.setCollectedfrom(Arrays.asList(kv));
+            person.setAlternativeNames(Optional.ofNullable(op.getOtherNames())
+
+                    .orElse(new ArrayList<>()));
+            person.setFamilyName(Optional.ofNullable(op.getFamilyName())
+
+                    .orElse(""));
+            person.setGivenName(Optional.ofNullable(op.getGivenName())
+
+                    .orElse(""));
+            person.setPid(Optional.ofNullable(op.getOtherPids())
+                    .map(v -> v.stream().map(p -> Pid.newInstance(p.getSchema(), p.getValue())).collect(Collectors.toList()))
+                    .orElse(new ArrayList<>())
+            );
+            person.getPid().add(Pid.newInstance(ModelConstants.ORCID, op.getOrcid()));
+            person.setDateofcollection(op.getLastModifiedDate());
+            person.setOriginalId(Arrays.asList(op.getOrcid()));
+            return person;
+        }, Encoders.bean(Person.class));
+
+
+        people.show(false);
+
+
+        Dataset<Relation> authorship;
+        authorship = works
+                .flatMap((FlatMapFunction<Work, Relation>) ExtractPerson::getAuthorshipRelationIterator
+                        , Encoders.bean(Relation.class));
+
+
+        authorship.show(false);
+
+
+        Dataset<Relation> coauthorship = works
+                .flatMap((FlatMapFunction<Work, Tuple2<String, String>>) w -> {
+                    List<Tuple2<String, String>> lista = new ArrayList<>();
+                    w.getPids().stream().forEach(p -> {
+                        if (p.getSchema().equalsIgnoreCase("doi") || p.getSchema().equalsIgnoreCase("pmc") || p.getSchema().equalsIgnoreCase("pmid") || p.getSchema().equalsIgnoreCase("arxiv"))
+                            lista.add(new Tuple2<>(p.getValue(), w.getOrcid()));
+                    });
+                    return lista.iterator();
+                }, Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
+                .groupByKey((MapFunction<Tuple2<String, String>, String>) Tuple2::_1, Encoders.STRING())
+                .mapGroups((MapGroupsFunction<String, Tuple2<String, String>, Coauthors>) (k, it) ->
+                        extractCoAuthors(it), Encoders.bean(Coauthors.class))
+                .flatMap((FlatMapFunction<Coauthors, Relation>) c -> c.getCoauthors().iterator(), Encoders.bean(Relation.class))
+                .groupByKey((MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
+                .mapGroups((MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class));
+
+        coauthorship.show(false);
+        Dataset<Relation> affiliation = employment
+                .filter((FilterFunction<Employment>) e -> Optional.ofNullable(e.getAffiliationId()).isPresent())
+                .filter((FilterFunction<Employment>) e -> e.getAffiliationId().getSchema().equalsIgnoreCase("ror"))
+                .map((MapFunction<Employment, Relation>) ExtractPerson::getAffiliationRelation
+                        , Encoders.bean(Relation.class));
+
+        affiliation.show(false);
+
+        people.toJavaRDD()
+                .map(p -> new AtomicAction(p.getClass(), p))
+                .union(authorship.toJavaRDD().map(r-> new AtomicAction(r.getClass(),r)))
+                .union(coauthorship.toJavaRDD().map(r-> new AtomicAction(r.getClass(),r)))
+                .union(affiliation.toJavaRDD().map(r->new AtomicAction(r.getClass(),r)))
+                .mapToPair(
+                        aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+                                new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+                .saveAsHadoopFile(
+                        outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);//, GzipCodec.class);
+    }
+
+    private static Coauthors extractCoAuthors(Iterator<Tuple2<String, String>> it) {
+        Coauthors coauth = new Coauthors();
+        ArrayList<Relation> ret = new ArrayList<>();
+        List<String> coauthors = new ArrayList<>();
+        while(it.hasNext())
+            coauthors.add(it.next()._2());
+        for (int i = 0; i < coauthors.size() -1; i++ )
+            for(int j = i + 1; j < coauthors.size(); j++)
+                ret.addAll(getCoAuthorshipRelations(coauthors.get(i), coauthors.get(j)));
+
+        coauth.setCoauthors(ret);
+
+        return coauth;
+    }
+
+    private static Relation getAffiliationRelation(Employment row) {
+        String source =  PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
+        String target =  ROR_PREFIX
+                + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
+        List<KeyValue> properties = new ArrayList<>() ;
+
+        Relation relation =
+         OafMapperUtils.getRelation(source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE, ModelConstants.ORG_PERSON_PARTICIPATES ,
+                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+                OafMapperUtils.dataInfo(false, null, false, false,
+                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
+                null);
+
+        if(Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())){
+            KeyValue kv = new KeyValue();
+            kv.setKey("startDate");
+            kv.setValue(row.getStartDate());
+            properties.add(kv);
+        }
+        if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
+            KeyValue kv = new KeyValue();
+            kv.setKey("endDate");
+            kv.setValue(row.getEndDate());
+            properties.add(kv);
+        }
+
+        if (properties.size() > 0)
+            relation.setProperties(properties);
+        return relation;
+
+
+    }
+
+    private static Collection<? extends Relation> getCoAuthorshipRelations(String orcid1, String orcid2) {
+        String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
+        String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
+
+        return Arrays.asList(OafMapperUtils.getRelation(source, target,ModelConstants.PERSON_PERSON_RELTYPE,
+                ModelConstants.PERSON_PERSON_SUBRELTYPE,
+                ModelConstants.PERSON_PERSON_HASCOAUTHORED,
+                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+                OafMapperUtils.dataInfo(false, null, false, false,
+                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
+                null),
+                OafMapperUtils.getRelation(target, source,ModelConstants.PERSON_PERSON_RELTYPE,
+                        ModelConstants.PERSON_PERSON_SUBRELTYPE,
+                        ModelConstants.PERSON_PERSON_HASCOAUTHORED,
+                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+                OafMapperUtils.dataInfo(false, null, false, false,
+                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
+                null));
+
+    }
+
+    private static @NotNull Iterator<Relation> getAuthorshipRelationIterator(Work w) {
+
+        if(Optional.ofNullable(w.getPids()).isPresent())
+                return w.getPids()
+                        .stream()
+                                .map(pid -> getRelation(w.getOrcid(), pid))
+                                .filter(Objects::nonNull).collect(Collectors.toList()).iterator();
+        List<Relation> ret = new ArrayList<>();
+        return ret.iterator();
+    }
+
+
+    private static Relation getRelation(String orcid, eu.dnetlib.dhp.collection.orcid.model.Pid pid){
+        String target ;
+        String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
+        switch (pid.getSchema()){
+                case "doi":
+                    target = DOI_PREFIX
+                            + IdentifierFactory
+                            .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), pid.getValue()));
+                    break;
+                case "pmid":
+                    target = PMID_PREFIX
+                            + IdentifierFactory
+                            .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pid.getValue()));
+                    break;
+                case "arxiv":
+                    target = ARXIV_PREFIX
+                            + IdentifierFactory
+                            .md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), pid.getValue()));
+                    break;
+                case "pmcid":
+                    target = PMCID_PREFIX
+                            + IdentifierFactory
+                            .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), pid.getValue()));
+                    break;
+
+                default:
+                    return null;
+            }
+
+
+        return OafMapperUtils.getRelation(source, target,ModelConstants.RESULT_PERSON_RELTYPE,
+                ModelConstants.RESULT_PERSON_SUBRELTYPE,
+                ModelConstants.RESULT_PERSON_HASAUTHORED,
+                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+                OafMapperUtils.dataInfo(false, null, false, false,
+                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
+                null);
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java
new file mode 100644
index 000000000..71d2b491a
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java
@@ -0,0 +1,23 @@
+package eu.dnetlib.dhp.actionmanager.personentity;
+
+import eu.dnetlib.dhp.collection.orcid.model.Work;
+import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+
+public class WorkList implements Serializable {
+    private ArrayList<Work> workArrayList;
+
+    public ArrayList<Work> getWorkArrayList() {
+        return workArrayList;
+    }
+
+    public void setWorkArrayList(ArrayList<Work> workArrayList) {
+        this.workArrayList = workArrayList;
+    }
+
+    public WorkList() {
+        workArrayList = new ArrayList<>();
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index 27970f2c3..263179d6f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -104,8 +104,8 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				final String ror = ROR_PREFIX
 					+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
 				ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
-				ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
-				ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
+//				ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
+//				ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
 
 				return ret
 					.iterator();
@@ -139,11 +139,17 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				"institution", functions
 					.explode(
 						functions.col("institutions")))
+
 			.selectExpr(
-				"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
+				"id", "doi", "institution.ror as ror",
 				"institution.country_code as country_code", "publication_year")
 			.distinct();
 
+//			.selectExpr(
+//				"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
+//				"institution.country_code as country_code", "publication_year")
+//			.distinct();
+
 	}
 
 	private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java
index df87e4333..a1545ebfe 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Author.java
@@ -20,6 +20,9 @@ public class Author extends ORCIDItem {
 
 	private String lastModifiedDate;
 
+	public Author() {
+	}
+
 	public String getBiography() {
 		return biography;
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java
index 6bc47bc26..419823cb1 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/ORCIDItem.java
@@ -11,4 +11,7 @@ public class ORCIDItem {
 	public void setOrcid(String orcid) {
 		this.orcid = orcid;
 	}
+
+	public ORCIDItem() {
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java
index 670170323..a8683aaaf 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/model/Work.java
@@ -32,4 +32,6 @@ public class Work extends ORCIDItem {
 		pids.add(pid);
 	}
 
+	public Work() {
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
new file mode 100644
index 000000000..3310f16e4
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
@@ -0,0 +1,26 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+    "paramName": "wd",
+    "paramLongName": "workingDir",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  }
+]
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
new file mode 100644
index 000000000..a4d56ba2e
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
@@ -0,0 +1,114 @@
+
+package eu.dnetlib.dhp.actionmanager.person;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
+import eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson;
+import eu.dnetlib.dhp.collection.orcid.model.Author;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class CreatePersonAS {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(CreatePersonAS.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(CreatePersonAS.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CreatePersonAS.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.codegen.wholeStage","false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(CreatePersonAS.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testAuthors() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/person/")
+			.getPath();
+
+//		spark
+//				.read()
+//				.parquet(inputPath + "Authors")
+//				.as(Encoders.bean(Author.class))
+//						.filter((FilterFunction<Author>) a -> Optional.ofNullable(a.getOtherNames()).isPresent() &&
+//								Optional.ofNullable(a.getBiography()).isPresent())
+//								.write()
+//										.mode(SaveMode.Overwrite)
+//												.parquet(workingDir.toString() + "AuthorsSubset");
+
+
+		ExtractPerson
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet1",
+						"-workingDir",
+						workingDir.toString() + "/working"
+				});
+
+
+
+	}
+
+
+	}
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/person/WorkJson/part-00000 b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/person/WorkJson/part-00000
new file mode 100644
index 000000000..636595d49
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/person/WorkJson/part-00000
@@ -0,0 +1,10 @@
+{"orcid":"0000-0001-6291-9619","title":"A Visible Light Driven Photoelectrochemical Chloramphenicol Aptasensor Based on a Gold Nanoparticle-Functionalized 3D Flower-like MoS<sub>2</sub>/TiO<sub>2</sub> Heterostructure","pids":[{"value":"10.1021/acs.langmuir.1c02956","schema":"doi"},{"value":"2-s2.0-85124885368","schema":"eid"},{"value":"15205827 07437463","schema":"issn"}]}
+{"orcid":"0000-0002-3210-3034","title":"A Visible Light Driven Photoelectrochemical Chloramphenicol Aptasensor Based on a Gold Nanoparticle-Functionalized 3D Flower-like MoS<sub>2</sub>/TiO<sub>2</sub> Heterostructure","pids":[{"value":"10.1021/acs.langmuir.1c02956","schema":"doi"},{"value":"2-s2.0-85124885368","schema":"eid"},{"value":"15205827 07437463","schema":"issn"}]}
+{"orcid":"0000-0001-6291-9619","title":"Study of High-Transverse-Momentum Higgs Boson Production in Association with a Vector Boson in the <math display=\"inline\"><mrow><mi>q</mi><mi>q</mi><mi>b</mi><mi>b</mi></mrow></math> Final State with the ATLAS Detector","pids":[{"value":"2736741","schema":"other-id"},{"value":"10.1103/PhysRevLett.132.131802","schema":"doi"},{"value":"2312.07605","schema":"arxiv"}]}
+{"orcid":"0000-0002-3210-3034","title":"Study of High-Transverse-Momentum Higgs Boson Production in Association with a Vector Boson in the <math display=\"inline\"><mrow><mi>q</mi><mi>q</mi><mi>b</mi><mi>b</mi></mrow></math> Final State with the ATLAS Detector","pids":[{"value":"2736741","schema":"other-id"},{"value":"10.1103/PhysRevLett.132.131802","schema":"doi"},{"value":"2312.07605","schema":"arxiv"}]}
+{"orcid":"0000-0002-9030-7609","title":"Search for supersymmetry in a final state containing two photons and missing transverse momentum in √s = 13 TeV pp collisions at the LHC using the ATLAS detector","pids":[{"value":"10.1140/epjc/s10052-016-4344-x","schema":"doi"},{"value":"2-s2.0-84988710988","schema":"eid"},{"value":"14346052 14346044","schema":"issn"}]}
+{"orcid":"0000-0003-2552-9691","title":"Search for supersymmetry in a final state containing two photons and missing transverse momentum in $\\sqrt{s}$ = 13 TeV $pp$ collisions at the LHC using the ATLAS detector","pids":[{"value":"1473744","schema":"other-id"},{"value":"10.1140/epjc/s10052-016-4344-x","schema":"doi"},{"value":"1606.09150","schema":"arxiv"}]}
+{"orcid":"0000-0003-0305-8980","title":"Search for supersymmetry in a final state containing two photons and missing transverse momentum in √s = 13 TeV pp collisions at the LHC using the ATLAS detector","pids":[{"value":"10.1140/epjc/s10052-016-4344-x","schema":"doi"},{"value":"2-s2.0-84988710988","schema":"eid"}]}
+{"orcid":"0000-0002-9030-7609","title":"Measurement of the energy response of the ATLAS calorimeter to charged pions from $W^{\\pm }\\rightarrow \\tau ^{\\pm }(\\rightarrow \\pi ^{\\pm }\\nu _{\\tau })\\nu _{\\tau }$ events in Run 2 data","pids":[{"value":"1909507","schema":"other-id"},{"value":"10.1140/epjc/s10052-022-10117-2","schema":"doi"},{"value":"2108.09043","schema":"arxiv"}]}
+{"orcid":"0000-0003-2629-4046","title":"Measurement of the energy response of the ATLAS calorimeter to charged pions from $W^{\\pm }\\rightarrow \\tau ^{\\pm }(\\rightarrow \\pi ^{\\pm }\\nu _{\\tau })\\nu _{\\tau }$ events in Run 2 data","pids":[{"value":"1909507","schema":"other-id"},{"value":"10.1140/epjc/s10052-022-10117-2","schema":"doi"},{"value":"2108.09043","schema":"arxiv"}]}
+{"orcid":"0000-0001-8582-8912","title":"Measurement of the energy response of the ATLAS calorimeter to charged pions from $W^{\\pm }\\rightarrow \\tau ^{\\pm }(\\rightarrow \\pi ^{\\pm }\\nu _{\\tau })\\nu _{\\tau }$ events in Run 2 data","pids":[{"value":"1909507","schema":"other-id"},{"value":"10.1140/epjc/s10052-022-10117-2","schema":"doi"},{"value":"2108.09043","schema":"arxiv"}]}
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 9e554204d..c8d7a980a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -994,6 +994,25 @@
 
     <!-- Build with scala 12 and Spark 3.4 -->
     <profiles>
+        <!-- Activate ARM-compatible snappy dependency on new Silicon Macs -->
+        <profile>
+            <id>arm-silicon-mac</id>
+            <activation>
+                <os>
+                    <arch>aarch64</arch>
+                    <family>mac</family>
+                </os>
+            </activation>
+            <dependencyManagement>
+                <dependencies>
+                    <dependency>
+                        <groupId>org.xerial.snappy</groupId>
+                        <artifactId>snappy-java</artifactId>
+                        <version>1.1.8.4</version>
+                    </dependency>
+                </dependencies>
+            </dependencyManagement>
+        </profile>
         <profile>
             <id>spark-34</id>
             <properties>

From 236b64d8305a93cea73630c89b14d3784b923ae7 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Sat, 29 Jun 2024 18:29:20 +0200
Subject: [PATCH 046/239] [AffiliationIngestion]Extended the ingestion of
 affiliation from open aire to include also links derived from Web Crawl.
 Extended the test. Inserted in Constatns the id and name of the webcrawl
 datasource to be used here and also in the ingestion of links from web crawl

---
 .../eu/dnetlib/dhp/actionmanager/Constants.java   |  3 +++
 .../PrepareAffiliationRelations.java              | 15 ++++++++++++---
 .../webcrawl/CreateActionSetFromWebEntries.java   | 10 ++++++----
 .../input_actionset_parameter.json                |  8 +++++++-
 .../bipaffiliations/oozie_app/workflow.xml        |  6 +++++-
 .../PrepareAffiliationRelationsTest.java          |  7 ++++---
 .../actionmanager/bipaffiliations/doi_to_ror.json |  4 +++-
 7 files changed, 40 insertions(+), 13 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
index 006d3af76..73b4b77cb 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
@@ -42,6 +42,9 @@ public class Constants {
 	public static final String NULL = "NULL";
 	public static final String NA = "N/A";
 
+	public static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
+	public static final String WEB_CRAWL_NAME = "Web Crawl";
+
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	private Constants() {
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index c10eb5c8c..b0b757005 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -41,9 +41,9 @@ public class PrepareAffiliationRelations implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 	private static final String ID_PREFIX = "50|doi_________::";
-	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
-	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
-	public static final String BIP_INFERENCE_PROVENANCE = "bip:affiliation:crossref";
+	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:openaireinference";
+	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by OpenAIRE";
+	public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
 
 	public static <I extends Result> void main(String[] args) throws Exception {
 
@@ -71,6 +71,9 @@ public class PrepareAffiliationRelations implements Serializable {
 		final String dataciteInputPath = parser.get("dataciteInputPath");
 		log.info("dataciteInputPath: {}", dataciteInputPath);
 
+		final String webcrawlInputPath = parser.get("webCrawlInputPath");
+		log.info("webcrawlInputPath: {}", webcrawlInputPath);
+
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
@@ -102,10 +105,16 @@ public class PrepareAffiliationRelations implements Serializable {
 				JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
 					spark, dataciteInputPath, collectedFromDatacite);
 
+				List<KeyValue> collectedFromWebCrawl = OafMapperUtils
+						.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
+				JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
+						spark, webcrawlInputPath, collectedFromWebCrawl);
+
 				crossrefRelations
 					.union(pubmedRelations)
 					.union(openAPCRelations)
 					.union(dataciteRelations)
+						.union(webCrawlRelations)
 					.saveAsHadoopFile(
 						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index 27970f2c3..f4b0cbc6f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -1,12 +1,15 @@
 
 package eu.dnetlib.dhp.actionmanager.webcrawl;
 
+
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.actionmanager.Constants;
+import io.netty.util.Constant;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.GzipCodec;
@@ -44,8 +47,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 	private static final String PMID_PREFIX = "50|pmid________::";
 
 	private static final String PMCID_PREFIX = "50|pmc_________::";
-	private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
-	private static final String WEB_CRAWL_NAME = "Web Crawl";
+
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(String[] args) throws Exception {
@@ -214,7 +216,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 						ModelConstants.IS_AUTHOR_INSTITUTION_OF,
 						Arrays
 							.asList(
-								OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
+								OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
 						OafMapperUtils
 							.dataInfo(
 								false, null, false, false,
@@ -233,7 +235,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 						ModelConstants.HAS_AUTHOR_INSTITUTION,
 						Arrays
 							.asList(
-								OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
+								OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
 						OafMapperUtils
 							.dataInfo(
 								false, null, false, false,
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
index 9671129f7..4d85cf26b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
@@ -28,7 +28,13 @@
     "paramLongName": "dataciteInputPath",
     "paramDescription": "the path to get the input data from Datacite",
     "paramRequired": true
-  },
+  },{
+  "paramName": "wip",
+  "paramLongName": "webCrawlInputPath",
+  "paramDescription": "the path to get the input data from Web Crawl",
+  "paramRequired": true
+}
+,
   {
     "paramName": "o",
     "paramLongName": "outputPath",
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
index e8e6a7c33..2e89c07fd 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
@@ -17,6 +17,10 @@
             <name>dataciteInputPath</name>
             <description>the path where to find the inferred affiliation relations from Datacite</description>
         </property>
+        <property>
+            <name>webCrawlInputPath</name>
+            <description>the path where to find the inferred affiliation relations from webCrawl</description>
+        </property>
         <property>
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
@@ -112,7 +116,7 @@
             <arg>--pubmedInputPath</arg><arg>${pubmedInputPath}</arg>
             <arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
             <arg>--dataciteInputPath</arg><arg>${dataciteInputPath}</arg>
-
+            <arg>--webCrawlInputPath</arg><arg>${webCrawlInputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
index bceb9d754..bb0188e43 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
@@ -88,6 +88,7 @@ public class PrepareAffiliationRelationsTest {
 					"-pubmedInputPath", crossrefAffiliationRelationPath,
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
+						"-webCrawlInputPath", crossrefAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -104,7 +105,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(80, tmp.count());
+		assertEquals(120, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -115,7 +116,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				40, execVerification
+				60, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -123,7 +124,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				40, execVerification
+				60, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
index 985a8d14b..08dc3f7eb 100644
--- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
@@ -4,4 +4,6 @@
 {"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
 {"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
 {"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]}
-{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
\ No newline at end of file
+{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
+{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]}
+{"DOI": "10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]}
\ No newline at end of file

From 9cbe966b4adcc497798af69f1a01c47aab3b5926 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Sat, 29 Jun 2024 18:35:49 +0200
Subject: [PATCH 047/239] [AffiliationIngestion]refactoring

---
 .../bipaffiliations/PrepareAffiliationRelations.java        | 6 +++---
 .../webcrawl/CreateActionSetFromWebEntries.java             | 5 ++---
 .../bipaffiliations/PrepareAffiliationRelationsTest.java    | 2 +-
 3 files changed, 6 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index b0b757005..8f911e980 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -106,15 +106,15 @@ public class PrepareAffiliationRelations implements Serializable {
 					spark, dataciteInputPath, collectedFromDatacite);
 
 				List<KeyValue> collectedFromWebCrawl = OafMapperUtils
-						.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
+					.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
 				JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-						spark, webcrawlInputPath, collectedFromWebCrawl);
+					spark, webcrawlInputPath, collectedFromWebCrawl);
 
 				crossrefRelations
 					.union(pubmedRelations)
 					.union(openAPCRelations)
 					.union(dataciteRelations)
-						.union(webCrawlRelations)
+					.union(webCrawlRelations)
 					.saveAsHadoopFile(
 						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index f4b0cbc6f..533b90cd8 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -1,15 +1,12 @@
 
 package eu.dnetlib.dhp.actionmanager.webcrawl;
 
-
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.actionmanager.Constants;
-import io.netty.util.Constant;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.GzipCodec;
@@ -24,6 +21,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.actionmanager.Constants;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -32,6 +30,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import io.netty.util.Constant;
 import scala.Tuple2;
 
 /**
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
index bb0188e43..bffe41ac7 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
@@ -88,7 +88,7 @@ public class PrepareAffiliationRelationsTest {
 					"-pubmedInputPath", crossrefAffiliationRelationPath,
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
-						"-webCrawlInputPath", crossrefAffiliationRelationPath,
+					"-webCrawlInputPath", crossrefAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 

From a2b708bb71b1f8a81f3d2ef369eb80638ade7808 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Sat, 29 Jun 2024 18:36:47 +0200
Subject: [PATCH 048/239] [AffiliationIngestion]refactoring

---
 .../model/ProvisionModelSupport.java          | 20 ++++---
 .../oa/provision/SolrConfigExploreTest.java   | 56 ++++++++++---------
 .../dhp/oa/provision/SolrConfigTest.java      |  3 +-
 3 files changed, 44 insertions(+), 35 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index b450b95be..abcf4992f 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -31,6 +30,7 @@ import eu.dnetlib.dhp.schema.solr.Context;
 import eu.dnetlib.dhp.schema.solr.Country;
 import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
 import eu.dnetlib.dhp.schema.solr.Measure;
@@ -562,10 +562,16 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
-	private static List<ExternalReference> mapExternalReference(List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
-		return Optional.ofNullable(externalReference)
-				.map(ext -> ext.stream()
-						.map(e -> ExternalReference.newInstance(
+	private static List<ExternalReference> mapExternalReference(
+		List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+		return Optional
+			.ofNullable(externalReference)
+			.map(
+				ext -> ext
+					.stream()
+					.map(
+						e -> ExternalReference
+							.newInstance(
 								e.getSitename(),
 								e.getLabel(),
 								e.getAlternateLabel(),
@@ -573,8 +579,8 @@ public class ProvisionModelSupport {
 								mapCodeLabel(e.getQualifier()),
 								e.getRefidentifier(),
 								e.getQuery()))
-						.collect(Collectors.toList()))
-				.orElse(Lists.newArrayList());
+					.collect(Collectors.toList()))
+			.orElse(Lists.newArrayList());
 	}
 
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
index 41eac2a30..90aef5adc 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
@@ -1,12 +1,13 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Path;
 
-import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -32,14 +33,13 @@ import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
-
-import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 @ExtendWith(MockitoExtension.class)
 public class SolrConfigExploreTest {
@@ -91,7 +91,7 @@ public class SolrConfigExploreTest {
 		SparkConf conf = new SparkConf();
 		conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
 		conf.registerKryoClasses(new Class[] {
-				SerializableSolrInputDocument.class
+			SerializableSolrInputDocument.class
 		});
 
 		conf.setMaster("local[1]");
@@ -101,10 +101,10 @@ public class SolrConfigExploreTest {
 		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
 
 		spark = SparkSession
-				.builder()
-				.appName(SolrConfigExploreTest.class.getSimpleName())
-				.config(conf)
-				.getOrCreate();
+			.builder()
+			.appName(SolrConfigExploreTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
 
 		// random unassigned HTTP port
 		final int jettyPort = 0;
@@ -134,35 +134,35 @@ public class SolrConfigExploreTest {
 
 		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
 		log
-				.info(
-						CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
-								.process(miniCluster.getSolrClient())
-								.toString());
+			.info(
+				CollectionAdminRequest.ClusterStatus
+					.getClusterStatus()
+					.process(miniCluster.getSolrClient())
+					.toString());
 
 		NamedList<Object> res = createCollection(
-				miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
 
 		res = createCollection(
-				miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
 		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
-				.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 
 		log
-				.info(
-						CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
-								.process(miniCluster.getSolrClient())
-								.toString());
+			.info(
+				CollectionAdminRequest.ClusterStatus
+					.getClusterStatus()
+					.process(miniCluster.getSolrClient())
+					.toString());
 
 	}
 
@@ -180,7 +180,8 @@ public class SolrConfigExploreTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -200,7 +201,8 @@ public class SolrConfigExploreTest {
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-				log.info(
+				log
+					.info(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -216,7 +218,7 @@ public class SolrConfigExploreTest {
 	}
 
 	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
-														int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
+		int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
 		ModifiableSolrParams modParams = new ModifiableSolrParams();
 		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
 		modParams.set("name", name);
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
index 2c62389c6..c04fa1cc6 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
@@ -85,7 +85,8 @@ public class SolrConfigTest extends SolrTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",

From 7d3292551b976a5b07f7e283ec95d0bc4015e8e7 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 2 Jul 2024 15:43:11 +0200
Subject: [PATCH 049/239] ignore dates containing 'null's

---
 .../java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java   | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index f1221add3..7606a4d2f 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -655,6 +655,13 @@ public class MergeUtils {
 			return d1;
 		}
 
+		if (StringUtils.contains(d1.getValue(), "null")) {
+			return d2;
+		}
+		if (StringUtils.contains(d2.getValue(), "null")) {
+			return d1;
+		}
+
 		return Stream
 			.of(d1, d2)
 			.min(

From 54e11b6a4352862b762b5127fe38a5cea28092c0 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 3 Jul 2024 13:03:15 +0300
Subject: [PATCH 050/239] Improve performance and efficiency by rewriting the
 creation process of "publication", "project", "dataset", "datasource",
 "software", "otherresearchproduct" and "result" tables, to be performed in a
 single query, for each one.

---
 .../graph/stats/oozie_app/scripts/step11.sql  | 102 ----------------
 .../graph/stats/oozie_app/scripts/step12.sql  |  40 +-----
 .../stats/oozie_app/scripts/step16_5.sql      |  74 ++++--------
 .../graph/stats/oozie_app/scripts/step2.sql   |  68 +++++------
 .../graph/stats/oozie_app/scripts/step3.sql   |  65 +++++-----
 .../graph/stats/oozie_app/scripts/step4.sql   |  68 +++++------
 .../graph/stats/oozie_app/scripts/step5.sql   |  66 +++++-----
 .../graph/stats/oozie_app/scripts/step6.sql   | 114 ++++++++++--------
 .../graph/stats/oozie_app/scripts/step7.sql   |  10 +-
 .../graph/stats/oozie_app/scripts/step8.sql   |  99 +++++----------
 10 files changed, 248 insertions(+), 458 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
index 207c1b124..7597f1429 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
@@ -4,108 +4,6 @@
 ----------------------------------------------------------------
 ----------------------------------------------------------------
 
---Datasource temporary table updates
-UPDATE ${stats_db_name}.datasource_tmp
-SET harvested='true'
-WHERE datasource_tmp.id IN (SELECT DISTINCT d.id
-                            FROM ${stats_db_name}.datasource_tmp d,
-                                 ${stats_db_name}.result_datasources rd
-                            WHERE d.id = rd.datasource); -- /*EOS*/
-
--- Project temporary table update and final project table creation with final updates that can not be applied to ORC tables
-UPDATE ${stats_db_name}.project_tmp
-SET haspubs='yes'
-WHERE project_tmp.id IN (SELECT pr.id
-                         FROM ${stats_db_name}.project_results pr,
-                              ${stats_db_name}.result r
-                         WHERE pr.result = r.id
-                           AND r.type = 'publication'); -- /*EOS*/
-
-DROP TABLE IF EXISTS ${stats_db_name}.project purge; -- /*EOS*/
-
-CREATE TABLE ${stats_db_name}.project stored as parquet as
-SELECT p.id,
-       p.acronym,
-       p.title,
-       p.funder,
-       p.funding_lvl0,
-       p.funding_lvl1,
-       p.funding_lvl2,
-       p.ec39,
-       p.type,
-       p.startdate,
-       p.enddate,
-       p.start_year,
-       p.end_year,
-       p.duration,
-       CASE WHEN prr1.id IS NULL THEN 'no' ELSE 'yes' END            AS haspubs,
-       CASE WHEN prr1.id IS NULL THEN 0 ELSE prr1.np END             AS numpubs,
-       CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.daysForlastPub END AS daysforlastpub,
-       CASE WHEN prr2.id IS NULL THEN 0 ELSE prr2.dp END             AS delayedpubs,
-       p.callidentifier,
-       p.code,
-       p.totalcost,
-       p.fundedamount,
-       p.currency
-FROM ${stats_db_name}.project_tmp p
-         LEFT JOIN (SELECT pr.id, count(distinct pr.result) AS np
-                    FROM ${stats_db_name}.project_results pr
-                             INNER JOIN ${stats_db_name}.result r ON pr.result = r.id
-                    WHERE r.type = 'publication'
-                    GROUP BY pr.id) AS prr1 on prr1.id = p.id
-         LEFT JOIN (SELECT pp.id,
-                           max(datediff(to_date(r.date), to_date(pp.enddate))) AS daysForlastPub,
-                           count(distinct r.id)                                AS dp
-                    FROM ${stats_db_name}.project_tmp pp,
-                         ${stats_db_name}.project_results pr,
-                         ${stats_db_name}.result r
-                    WHERE pp.id = pr.id
-                      AND pr.result = r.id
-                      AND r.type = 'publication'
-                      AND datediff(to_date(r.date), to_date(pp.enddate)) > 0
-                    GROUP BY pp.id) AS prr2
-                   ON prr2.id = p.id; -- /*EOS*/
-
-UPDATE ${stats_db_name}.publication_tmp
-SET delayed = 'yes'
-WHERE publication_tmp.id IN (SELECT distinct r.id
-                             FROM ${stats_db_name}.result r,
-                                  ${stats_db_name}.project_results pr,
-                                  ${stats_db_name}.project_tmp p
-                             WHERE r.id = pr.result
-                               AND pr.id = p.id
-                               AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
-
-UPDATE ${stats_db_name}.dataset_tmp
-SET delayed = 'yes'
-WHERE dataset_tmp.id IN (SELECT distinct r.id
-                         FROM ${stats_db_name}.result r,
-                              ${stats_db_name}.project_results pr,
-                              ${stats_db_name}.project_tmp p
-                         WHERE r.id = pr.result
-                           AND pr.id = p.id
-                           AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
-
-UPDATE ${stats_db_name}.software_tmp
-SET delayed = 'yes'
-WHERE software_tmp.id IN (SELECT distinct r.id
-                          FROM ${stats_db_name}.result r,
-                               ${stats_db_name}.project_results pr,
-                               ${stats_db_name}.project_tmp p
-                          WHERE r.id = pr.result
-                            AND pr.id = p.id
-                            AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
-
-UPDATE ${stats_db_name}.otherresearchproduct_tmp
-SET delayed = 'yes'
-WHERE otherresearchproduct_tmp.id IN (SELECT distinct r.id
-                                      FROM ${stats_db_name}.result r,
-                                           ${stats_db_name}.project_results pr,
-                                           ${stats_db_name}.project_tmp p
-                                      WHERE r.id = pr.result
-                                        AND pr.id = p.id
-                                        AND to_date(r.date) - to_date(p.enddate) > 0); -- /*EOS*/
-
 CREATE OR REPLACE VIEW ${stats_db_name}.project_results_publication AS
 SELECT result_projects.id          AS result,
        result_projects.project     AS project_results,
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql
index ff95524be..4f0b45fed 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step12.sql
@@ -1,42 +1,4 @@
-------------------------------------------------------------------------------------------------------
--- Creating parquet tables from the updated temporary tables and removing unnecessary temporary tables
-------------------------------------------------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.datasource purge; /*EOS*/
-
-CREATE TABLE ${stats_db_name}.datasource stored AS parquet AS
-SELECT *
-FROM ${stats_db_name}.datasource_tmp; /*EOS*/
-
-DROP TABLE IF EXISTS ${stats_db_name}.publication purge; /*EOS*/
-
-CREATE TABLE ${stats_db_name}.publication stored AS parquet AS
-SELECT *
-FROM ${stats_db_name}.publication_tmp; /*EOS*/
-
-DROP TABLE IF EXISTS ${stats_db_name}.dataset purge; /*EOS*/
-
-CREATE TABLE ${stats_db_name}.dataset stored AS parquet AS
-SELECT *
-FROM ${stats_db_name}.dataset_tmp; /*EOS*/
-
-DROP TABLE IF EXISTS ${stats_db_name}.software purge; /*EOS*/
-
-CREATE TABLE ${stats_db_name}.software stored AS parquet AS
-SELECT *
-FROM ${stats_db_name}.software_tmp; /*EOS*/
-
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct purge; /*EOS*/
-
-CREATE TABLE ${stats_db_name}.otherresearchproduct stored AS parquet AS
-SELECT *
-FROM ${stats_db_name}.otherresearchproduct_tmp; /*EOS*/
-
-DROP TABLE ${stats_db_name}.project_tmp; /*EOS*/
-DROP TABLE ${stats_db_name}.datasource_tmp; /*EOS*/
-DROP TABLE ${stats_db_name}.publication_tmp; /*EOS*/
-DROP TABLE ${stats_db_name}.dataset_tmp; /*EOS*/
-DROP TABLE ${stats_db_name}.software_tmp; /*EOS*/
-DROP TABLE ${stats_db_name}.otherresearchproduct_tmp; /*EOS*/
+set mapred.job.queue.name=analytics; /*EOS*/
 
 ----------------------------------------------
 -- Re-creating views from final parquet tables
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
index 416298e4c..a2be22603 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_5.sql
@@ -1,58 +1,26 @@
 set mapred.job.queue.name=analytics; /*EOS*/
 
--- replace the creation of the result view to include the boolean fields from the previous tables (green, gold,
+-- replace the creation of the result view with a table, which will include the boolean fields from the previous tables (green, gold,
 -- peer reviewed)
-drop table if exists ${stats_db_name}.result_tmp; /*EOS*/
 
-CREATE TABLE ${stats_db_name}.result_tmp (
-    id STRING,
-    title STRING,
-    publisher STRING,
-    journal STRING,
-    `date` STRING,
-    `year` INT,
-    bestlicence STRING,
-    access_mode STRING,
-    embargo_end_date STRING,
-    delayed BOOLEAN,
-    authors INT,
-    source STRING,
-    abstract BOOLEAN,
-    type STRING ,
-    peer_reviewed BOOLEAN,
-    green BOOLEAN,
-    gold BOOLEAN)
-clustered by (id) into 100 buckets stored as orc tblproperties('transactional'='true'); /*EOS*/
-
-insert into ${stats_db_name}.result_tmp
-select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
-FROM ${stats_db_name}.publication r
-LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
-
-insert into ${stats_db_name}.result_tmp
-select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
-FROM ${stats_db_name}.dataset r
-LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
-
-insert into ${stats_db_name}.result_tmp
-select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
-FROM ${stats_db_name}.software r
-LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
-
-insert into ${stats_db_name}.result_tmp
-select r.id, r.title, r.publisher, r.journal, r.`date`, date_format(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
-FROM ${stats_db_name}.otherresearchproduct r
-LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
-LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
-
-drop table if exists ${stats_db_name}.result; /*EOS*/
 drop view if exists ${stats_db_name}.result; /*EOS*/
-create table ${stats_db_name}.result stored as parquet as select * from ${stats_db_name}.result_tmp; /*EOS*/
-drop table ${stats_db_name}.result_tmp; /*EOS*/
\ No newline at end of file
+drop table if exists ${stats_db_name}.result; /*EOS*/
+
+CREATE TABLE ${stats_db_name}.result stored as parquet as
+SELECT /*+ COALESCE(100) */ r.id, r.title, r.publisher, r.journal, r.`date`, DATE_FORMAT(r.`date`, 'yyyy'), r.bestlicence, r.bestlicence, r.embargo_end_date, r.delayed, r.authors, r.source, r.abstract, r.type, pr.peer_reviewed, green.green, gold.gold
+FROM (
+    (SELECT id, title, p.publisher, journal, `date`, DATE_FORMAT(`date`, 'yyyy'), bestlicence, bestlicence, embargo_end_date, delayed, authors, source, abstract, type
+        FROM ${stats_db_name}.publication)
+    UNION ALL
+    (SELECT id, title, p.publisher, journal, `date`, DATE_FORMAT(`date`, 'yyyy'), bestlicence, bestlicence, embargo_end_date, delayed, authors, source, abstract, type
+        FROM ${stats_db_name}.dataset)
+    UNION ALL
+    (select id, title, p.publisher, journal, `date`, DATE_FORMAT(`date`, 'yyyy'), bestlicence, bestlicence, embargo_end_date, delayed, authors, source, abstract, type
+        FROM ${stats_db_name}.software)
+    UNION ALL
+    (select id, title, p.publisher, journal, `date`, DATE_FORMAT(`date`, 'yyyy'), bestlicence, bestlicence, embargo_end_date, delayed, authors, source, abstract, type
+        FROM ${stats_db_name}.otherresearchproduct)
+    ) r
+LEFT OUTER JOIN ${stats_db_name}.result_peerreviewed pr on pr.id=r.id
+LEFT OUTER JOIN ${stats_db_name}.result_greenoa green on green.id=r.id
+LEFT OUTER JOIN ${stats_db_name}.result_gold gold on gold.id=r.id; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
index f0e5ce091..0abec2358 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step2.sql
@@ -7,41 +7,41 @@ set mapred.job.queue.name=analytics; /*EOS*/
 --------------------------------------------------------------
 
 -- Publication temporary table
-DROP TABLE IF EXISTS ${stats_db_name}.publication_tmp purge; /*EOS*/
-CREATE TABLE ${stats_db_name}.publication_tmp
-(
-    id               STRING,
-    title            STRING,
-    publisher        STRING,
-    journal          STRING,
-    date             STRING,
-    year             STRING,
-    bestlicence      STRING,
-    embargo_end_date STRING,
-    delayed          BOOLEAN,
-    authors          INT,
-    source           STRING,
-    abstract         BOOLEAN,
-    type             STRING
-)
-    clustered by (id) into 100 buckets stored as orc tblproperties ('transactional' = 'true'); /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.publication purge; /*EOS*/
+
+CREATE TABLE ${stats_db_name}.publication stored as parquet as
+with pub_pr as (
+    select pub.id as pub_id, case when (to_date(pub.dateofacceptance.value) > to_date( pj.enddate.value)) then true else false end as delayed
+    from ${openaire_db_name}.publication pub
+             join ${openaire_db_name}.relation rel
+                  on reltype = 'resultProject' and relclass = 'isProducedBy' and rel.source=pub.id
+                      and rel.datainfo.deletedbyinference = false and rel.datainfo.invisible = false
+             join ${openaire_db_name}.project pj on pj.id=rel.target and pj.datainfo.deletedbyinference = false and pj.datainfo.invisible = false
+    where pub.datainfo.deletedbyinference = false and pub.datainfo.invisible = false
+),
+ pub_delayed as (
+     select pub_id, max(delayed) as delayed
+     from pub_pr
+     group by pub_id
+ )
+select /*+ COALESCE(100) */
+    substr(pub.id, 4)                                                     as id,
+    pub.title[0].value                                                    as title,
+    pub.publisher.value                                                   as publisher,
+    pub.journal.name                                                      as journal,
+    pub.dateofacceptance.value                                            as date,
+    date_format(pub.dateofacceptance.value, 'yyyy')                       as year,
+    pub.bestaccessright.classname                                         as bestlicence,
+    pub.embargoenddate.value                                              as embargo_end_date,
+    coalesce(pub_delayed.delayed, false)                                  as delayed, -- It's delayed, when the publication was published after the end of at least one of its projects.
+    size(pub.author)                                                      as authors,
+    concat_ws('\u003B', pub.source.value)                                 as source,
+    case when size(pub.description) > 0 then true else false end          as abstract,
+    'publication'                                                         as type
+from ${openaire_db_name}.publication pub
+    left outer join pub_delayed on pub.id=pub_delayed.pub_id
+where pub.datainfo.deletedbyinference = false and pub.datainfo.invisible = false; /*EOS*/
 
-INSERT INTO ${stats_db_name}.publication_tmp
-SELECT substr(p.id, 4)                                            as id,
-       p.title[0].value                                           as title,
-       p.publisher.value                                          as publisher,
-       p.journal.name                                             as journal,
-       p.dateofacceptance.value                                   as date,
-       date_format(p.dateofacceptance.value, 'yyyy')              as year,
-       p.bestaccessright.classname                                as bestlicence,
-       p.embargoenddate.value                                     as embargo_end_date,
-       false                                                      as delayed,
-       size(p.author)                                             as authors,
-       concat_ws('\u003B', p.source.value)                        as source,
-       case when size(p.description) > 0 then true else false end as abstract,
-       'publication'                                              as type
-from ${openaire_db_name}.publication p
-where p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.publication_classifications purge; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
index ebedb5dc5..8f203fc83 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
@@ -5,42 +5,41 @@
 ------------------------------------------------------
 
 -- Dataset temporary table supporting updates
-DROP TABLE IF EXISTS ${stats_db_name}.dataset_tmp purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.dataset purge; /*EOS*/
 
-CREATE TABLE ${stats_db_name}.dataset_tmp
-(
-    id               STRING,
-    title            STRING,
-    publisher        STRING,
-    journal          STRING,
-    date             STRING,
-    year             STRING,
-    bestlicence      STRING,
-    embargo_end_date STRING,
-    delayed          BOOLEAN,
-    authors          INT,
-    source           STRING,
-    abstract         BOOLEAN,
-    type             STRING
+CREATE TABLE ${stats_db_name}.dataset stored as parquet as
+with datast_pr as (
+    select datast.id as datast_id, case when (to_date(datast.dateofacceptance.value) > to_date( pj.enddate.value)) then true else false end as delayed
+    from ${openaire_db_name}.dataset datast
+        join ${openaire_db_name}.relation rel
+            on reltype = 'resultProject' and relclass = 'isProducedBy' and rel.source=datast.id
+                and rel.datainfo.deletedbyinference = false and rel.datainfo.invisible = false
+    join ${openaire_db_name}.project pj on pj.id=rel.target and pj.datainfo.deletedbyinference = false and pj.datainfo.invisible = false
+    where datast.datainfo.deletedbyinference = false and datast.datainfo.invisible = false
+),
+datast_delayed as (
+    select datast_id, max(delayed) as delayed
+    from datast_pr
+    group by datast_id
 )
-    clustered by (id) into 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
+select /*+ COALESCE(100) */
+    substr(datast.id, 4)                                                  as id,
+    datast.title[0].value                                                 as title,
+    datast.publisher.value                                                as publisher,
+    cast(null as string)                                                  as journal,
+    datast.dateofacceptance.value                                         as date,
+    date_format(datast.dateofacceptance.value, 'yyyy')                    as year,
+    datast.bestaccessright.classname                                      as bestlicence,
+    datast.embargoenddate.value                                           as embargo_end_date,
+    coalesce(datast_delayed.delayed, false)                               as delayed, -- It's delayed, when the dataset was published after the end of the project.
+    size(datast.author)                                                   as authors,
+    concat_ws('\u003B', datast.source.value)                              as source,
+    case when size(datast.description) > 0 then true else false end       as abstract,
+    'dataset'                                                             as type
+from ${openaire_db_name}.dataset datast
+    left outer join datast_delayed on datast.id=datast_delayed.datast_id
+where datast.datainfo.deletedbyinference = false and datast.datainfo.invisible = false; /*EOS*/
 
-INSERT INTO ${stats_db_name}.dataset_tmp
-SELECT substr(d.id, 4)                                            AS id,
-       d.title[0].value                                           AS title,
-       d.publisher.value                                          AS publisher,
-       cast(null AS string)                                       AS journal,
-       d.dateofacceptance.value                                   as date,
-       date_format(d.dateofacceptance.value, 'yyyy')              AS year,
-       d.bestaccessright.classname                                AS bestlicence,
-       d.embargoenddate.value                                     AS embargo_end_date,
-       false                                                      AS delayed,
-       size(d.author)                                             AS authors,
-       concat_ws('\u003B', d.source.value)                        AS source,
-       CASE WHEN SIZE(d.description) > 0 THEN TRUE ELSE FALSE end AS abstract,
-       'dataset'                                                  AS type
-FROM ${openaire_db_name}.dataset d
-WHERE d.datainfo.deletedbyinference = FALSE and d.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_citations purge; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
index 4957d8d2f..5e4c9f420 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
@@ -5,41 +5,41 @@
 --------------------------------------------------------
 
 -- Software temporary table supporting updates
-DROP TABLE IF EXISTS ${stats_db_name}.software_tmp purge; /*EOS*/
-CREATE TABLE ${stats_db_name}.software_tmp
-(
-    id               STRING,
-    title            STRING,
-    publisher        STRING,
-    journal          STRING,
-    date             STRING,
-    year             STRING,
-    bestlicence      STRING,
-    embargo_end_date STRING,
-    delayed          BOOLEAN,
-    authors          INT,
-    source           STRING,
-    abstract         BOOLEAN,
-    type             STRING
-)
-    clustered by (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.software purge; /*EOS*/
+
+CREATE TABLE ${stats_db_name}.software stored as parquet as
+with soft_pr as (
+    select soft.id as soft_id, case when (to_date(soft.dateofacceptance.value) > to_date( pj.enddate.value)) then true else false end as delayed
+    from ${openaire_db_name}.software soft
+        join ${openaire_db_name}.relation rel
+            on reltype = 'resultProject' and relclass = 'isProducedBy' and rel.source=soft.id
+                and rel.datainfo.deletedbyinference = false and rel.datainfo.invisible = false
+        join ${openaire_db_name}.project pj on pj.id=rel.target and pj.datainfo.deletedbyinference = false and pj.datainfo.invisible = false
+    where soft.datainfo.deletedbyinference = false and soft.datainfo.invisible = false
+),
+soft_delayed as (
+    select soft_id, max(delayed) as delayed
+    from soft_pr
+    group by soft_id
+)
+select /*+ COALESCE(100) */
+    substr(soft.id, 4)                                                       as id,
+    soft.title[0].value                                                      as title,
+    soft.publisher.value                                                     as publisher,
+    cast(null as string)                                                     as journal,
+    soft.dateofacceptance.value                                              as date,
+    date_format(soft.dateofacceptance.value, 'yyyy')                         as year,
+    soft.bestaccessright.classname                                           as bestlicence,
+    soft.embargoenddate.value                                                as embargo_end_date,
+    coalesce(soft_delayed.delayed, false)                                    as delayed, -- It's delayed, when the software was published after the end of the project.
+    size(soft.author)                                                        as authors,
+    concat_ws('\u003B', soft.source.value)                                   as source,
+    case when size(soft.description) > 0 then true else false end            as abstract,
+    'software'                                                               as type
+from ${openaire_db_name}.software soft
+         left outer join soft_delayed on soft.id=soft_delayed.soft_id
+where soft.datainfo.deletedbyinference = false and soft.datainfo.invisible = false; /*EOS*/
 
-INSERT INTO ${stats_db_name}.software_tmp
-SELECT substr(s.id, 4)                                            as id,
-       s.title[0].value                                           AS title,
-       s.publisher.value                                          AS publisher,
-       CAST(NULL AS string)                                       AS journal,
-       s.dateofacceptance.value                                   AS DATE,
-       date_format(s.dateofacceptance.value, 'yyyy')              AS YEAR,
-       s.bestaccessright.classname                                AS bestlicence,
-       s.embargoenddate.value                                     AS embargo_end_date,
-       FALSE                                                      AS delayed,
-       SIZE(s.author)                                             AS authors,
-       concat_ws('\u003B', s.source.value)                        AS source,
-       CASE WHEN SIZE(s.description) > 0 THEN TRUE ELSE FALSE END AS abstract,
-       'software'                                                 as type
-from ${openaire_db_name}.software s
-where s.datainfo.deletedbyinference = false and s.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.software_citations purge; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
index 820ec4395..3134ba316 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
@@ -5,41 +5,41 @@
 --------------------------------------------------------------------------------
 
 -- Otherresearchproduct temporary table supporting updates
-DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_tmp purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct purge; /*EOS*/
 
-CREATE TABLE ${stats_db_name}.otherresearchproduct_tmp
-(
-    id               STRING,
-    title            STRING,
-    publisher        STRING,
-    journal          STRING,
-    date             STRING,
-    year             STRING,
-    bestlicence      STRING,
-    embargo_end_date STRING,
-    delayed          BOOLEAN,
-    authors          INT,
-    source           STRING,
-    abstract         BOOLEAN,
-    type             STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
+CREATE TABLE ${stats_db_name}.otherresearchproduct stored as parquet as
+with other_pr as (
+    select other.id as other_id, case when (to_date(other.dateofacceptance.value) > to_date( pj.enddate.value)) then true else false end as delayed
+    from ${openaire_db_name}.otherresearchproduct other
+    join ${openaire_db_name}.relation rel
+        on reltype = 'resultProject' and relclass = 'isProducedBy' and rel.source=other.id
+            and rel.datainfo.deletedbyinference = false and rel.datainfo.invisible = false
+    join ${openaire_db_name}.project pj on pj.id=rel.target and pj.datainfo.deletedbyinference = false and pj.datainfo.invisible = false
+    where other.datainfo.deletedbyinference = false and other.datainfo.invisible = false
+),
+other_delayed as (
+    select other_id, max(delayed) as delayed
+    from other_pr
+    group by other_id
+)
+select /*+ COALESCE(100) */
+    substr(other.id, 4)                                            as id,
+    other.title[0].value                                           as title,
+    other.publisher.value                                          as publisher,
+    cast(null as string)                                           as journal,
+    other.dateofacceptance.value                                   as date,
+    date_format(other.dateofacceptance.value, 'yyyy')              as year,
+    other.bestaccessright.classname                                as bestlicence,
+    other.embargoenddate.value                                     as embargo_end_date,
+    false                                                          as delayed,
+    size(other.author)                                             as authors,
+    concat_ws('\u003B', other.source.value)                        as source,
+    case when size(other.description) > 0 then true else false end as abstract,
+    'other'                                                        as type
+from ${openaire_db_name}.otherresearchproduct other
+    left outer join other_delayed on other.id=other_delayed.other_id
+where other.datainfo.deletedbyinference = false and other.datainfo.invisible = false; /*EOS*/
 
-INSERT INTO ${stats_db_name}.otherresearchproduct_tmp
-SELECT substr(o.id, 4)                                            AS id,
-       o.title[0].value                                           AS title,
-       o.publisher.value                                          AS publisher,
-       CAST(NULL AS string)                                       AS journal,
-       o.dateofacceptance.value                                   AS DATE,
-       date_format(o.dateofacceptance.value, 'yyyy')              AS year,
-       o.bestaccessright.classname                                AS bestlicence,
-       o.embargoenddate.value                                     as embargo_end_date,
-       FALSE                                                      AS delayed,
-       SIZE(o.author)                                             AS authors,
-       concat_ws('\u003B', o.source.value)                        AS source,
-       CASE WHEN SIZE(o.description) > 0 THEN TRUE ELSE FALSE END AS abstract,
-       'other'                                                    AS type
-FROM ${openaire_db_name}.otherresearchproduct o
-WHERE o.datainfo.deletedbyinference = FALSE and o.datainfo.invisible=false; /*EOS*/
 
 -- Otherresearchproduct_citations
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_citations purge; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
index d2688ec07..de6b803ab 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
@@ -34,61 +34,69 @@ from ${openaire_db_name}.project p
     lateral view explode(p.h2020classification) classifs as class
 where p.datainfo.deletedbyinference=false and p.datainfo.invisible=false and class.h2020programme is not null; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.project_tmp purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.project purge; /*EOS*/
 
-CREATE TABLE ${stats_db_name}.project_tmp
-(
-    id             STRING,
-    acronym        STRING,
-    title          STRING,
-    funder         STRING,
-    funding_lvl0   STRING,
-    funding_lvl1   STRING,
-    funding_lvl2   STRING,
-    ec39           STRING,
-    type           STRING,
-    startdate      STRING,
-    enddate        STRING,
-    start_year     INT,
-    end_year       INT,
-    duration       INT,
-    haspubs        STRING,
-    numpubs        INT,
-    daysforlastpub INT,
-    delayedpubs    INT,
-    callidentifier STRING,
-    code           STRING,
-    totalcost       FLOAT,
-    fundedamount    FLOAT,
-    currency        STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); /*EOS*/
+CREATE TABLE ${stats_db_name}.project stored as parquet as
+with pr_pub as (
+    select pr.id as pr_id, pub.id as pub_id,
+        (case when datediff(pub.dt_dateofacceptance, pr.dt_enddate) > 0 then true else false end) as delayed,
+        max(datediff(pub.dt_dateofacceptance, pr.dt_enddate)) as daysForlastPub
+    from (select id, to_date(dateofacceptance.value) as dt_dateofacceptance from ${openaire_db_name}.publication
+        where datainfo.deletedbyinference = false and datainfo.invisible = false) pub
+    join ${openaire_db_name}.relation rel
+        on rel.reltype = 'resultProject' and rel.relclass = 'isProducedBy' and rel.source=pub.id
+            and rel.datainfo.deletedbyinference = false and rel.datainfo.invisible = false
+    join (select id, to_date(enddate.value) as dt_enddate from ${openaire_db_name}.project
+            where datainfo.deletedbyinference = false and datainfo.invisible = false) pr
+        on pr.id=rel.target
+    group by pr.id, pub.id, pub.dt_dateofacceptance, pr.dt_enddate
+),
+num_pubs_pr as (
+    select pr_id, count( distinct pub_id) as num_pubs
+    from pr_pub
+    group by pr_id
+),
+pub_delayed as (
+    select pr_id, pub_id, max(delayed) as delayed
+    from pr_pub
+    group by pr_id, pub_id
+),
+num_pub_delayed as (
+    select pr_id, count(distinct pub_id) as num_delayed
+    from pub_delayed
+    where delayed
+    group by pr_id
+)
+select /*+ COALESCE(100) */
+    substr(p.id, 4)                                                             as id,
+    p.acronym.value                                                             as acronym,
+    p.title.value                                                               as title,
+    xpath_string(p.fundingtree[0].value, '//funder/name')                       as funder,
+    xpath_string(p.fundingtree[0].value, '//funding_level_0/name')              as funding_lvl0,
+    xpath_string(p.fundingtree[0].value, '//funding_level_1/name')              as funding_lvl1,
+    xpath_string(p.fundingtree[0].value, '//funding_level_2/name')              as funding_lvl2,
+    p.ecsc39.value                                                              as ec39,
+    p.contracttype.classname                                                    as type,
+    p.startdate.value                                                           as startdate,
+    p.enddate.value                                                             as enddate,
+    year(p.startdate.value)                                                     as start_year,
+    year(p.enddate.value)                                                       as end_year,
+    cast(months_between(p.enddate.value, p.startdate.value) as int)             as duration,
+    case when pr_pub.pub_id is null then 'no' else 'yes' end                    as haspubs,
+    num_pubs_pr.num_pubs                                                        as numpubs,
+    pr_pub.daysForlastPub                                                       as daysForlastPub,
+    npd.num_delayed                                                             as delayedpubs,
+    p.callidentifier.value                                                      as callidentifier,
+    p.code.value                                                                as code,
+    p.totalcost                                                                 as totalcost,
+    p.fundedamount                                                              as fundedamount,
+    p.currency.value                                                            as currency
+from ${openaire_db_name}.project p
+left outer join pr_pub on pr_pub.pr_id = p.id
+left outer join num_pubs_pr on num_pubs_pr.pr_id = p.id
+left outer join num_pub_delayed npd on npd.pr_id=p.id
+where p.datainfo.deletedbyinference = false and p.datainfo.invisible = false; /*EOS*/
 
-INSERT INTO ${stats_db_name}.project_tmp
-SELECT substr(p.id, 4)                                                 AS id,
-       p.acronym.value                                                 AS acronym,
-       p.title.value                                                   AS title,
-       xpath_string(p.fundingtree[0].value, '//funder/name')           AS funder,
-       xpath_string(p.fundingtree[0].value, '//funding_level_0/name')  AS funding_lvl0,
-       xpath_string(p.fundingtree[0].value, '//funding_level_1/name')  AS funding_lvl1,
-       xpath_string(p.fundingtree[0].value, '//funding_level_2/name')  AS funding_lvl2,
-       p.ecsc39.value                                                  AS ec39,
-       p.contracttype.classname                                        AS type,
-       p.startdate.value                                               AS startdate,
-       p.enddate.value                                                 AS enddate,
-       year(p.startdate.value)                                         AS start_year,
-       year(p.enddate.value)                                           AS end_year,
-       CAST(MONTHS_BETWEEN(p.enddate.value, p.startdate.value) AS INT) AS duration,
-       'no'                                                            AS haspubs,
-       0                                                               AS numpubs,
-       0                                                               AS daysforlastpub,
-       0                                                               AS delayedpubs,
-       p.callidentifier.value                                          AS callidentifier,
-       p.code.value                                                    AS code,
-       p.totalcost                                                     AS totalcost,
-       p.fundedamount                                                  AS fundedamount,
-       p.currency.value                                                AS currency
-FROM ${openaire_db_name}.project p
-WHERE p.datainfo.deletedbyinference = false and p.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.funder purge; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index 7a23991fe..2283e6291 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -7,16 +7,16 @@
 -- Views on temporary tables that should be re-created in the end
 CREATE OR REPLACE VIEW ${stats_db_name}.result as
 SELECT *, bestlicence AS access_mode
-FROM ${stats_db_name}.publication_tmp
+FROM ${stats_db_name}.publication
 UNION ALL
 SELECT *, bestlicence AS access_mode
-FROM ${stats_db_name}.software_tmp
+FROM ${stats_db_name}.software
 UNION ALL
 SELECT *, bestlicence AS access_mode
-FROM ${stats_db_name}.dataset_tmp
+FROM ${stats_db_name}.dataset
 UNION ALL
 SELECT *, bestlicence AS access_mode
-FROM ${stats_db_name}.otherresearchproduct_tmp; /*EOS*/
+FROM ${stats_db_name}.otherresearchproduct; /*EOS*/
 
 -- Views on final tables
 CREATE OR REPLACE VIEW ${stats_db_name}.result_datasources AS
@@ -153,4 +153,4 @@ CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS
 select /*+ COALESCE(100) */ pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
 FROM ${stats_db_name}.result r
          JOIN ${stats_db_name}.project_results pr ON r.id = pr.result
-         JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id; /*EOS*/
\ No newline at end of file
+         JOIN ${stats_db_name}.project p ON p.id = pr.id; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 90c3ebef6..b280dc946 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -5,81 +5,36 @@
 -- Datasource table/view and Datasource related tables/views
 ------------------------------------------------------------
 ------------------------------------------------------------
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_tmp purge; -- /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource purge; /*EOS*/
 
-CREATE TABLE ${stats_db_name}.datasource_tmp
-(
-    `id`               string,
-    `name`             STRING,
-    `type`             STRING,
-    `dateofvalidation` STRING,
-    `yearofvalidation` string,
-    `harvested`        BOOLEAN,
-    `piwik_id`         INT,
-    `latitude`         STRING,
-    `longitude`        STRING,
-    `websiteurl`       STRING,
-    `compatibility`    STRING,
-    issn_printed       STRING,
-    issn_online        STRING
-) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true'); -- /*EOS*/
+CREATE TABLE ${stats_db_name}.datasource stored as parquet as
+with piwik_datasource as (
+    select id, split(originalidd, '\\:')[1] as piwik_id
+    from ${openaire_db_name}.datasource
+             lateral view explode(originalid) temp as originalidd
+    where originalidd like "piwik:%"
+)
+select /*+ COALESCE(100) */
+       substr(dtrce.id, 4)                                                                                                 as id,
+       case when dtrce.officialname.value='Unknown Repository' then 'Other' else dtrce.officialname.value end              as name,
+       dtrce.datasourcetype.classname                                                                                      as type,
+       dtrce.dateofvalidation.value                                                                                        as dateofvalidation,
+       case when dtrce.dateofvalidation.value='-1' then null else date_format(dtrce.dateofvalidation.value, 'yyyy') end    as yearofvalidation,
+       case when res.d_id is null then false else true end                                                                 as harvested,
+       case when piwik_d.piwik_id is null then 0 else piwik_d.piwik_id end                                                 as piwik_id,
+       dtrce.latitude.value                                                                                                as latitude,
+       dtrce.longitude.value                                                                                               as longitude,
+       dtrce.websiteurl.value                                                                                              as websiteurl,
+       dtrce.openairecompatibility.classid                                                                                 as compatibility,
+       dtrce.journal.issnprinted                                                                                           as issn_printed,
+       dtrce.journal.issnonline                                                                                            as issn_online
+from ${openaire_db_name}.datasource dtrce
+         left outer join (select inst.hostedby.key as d_id from ${openaire_db_name}.result lateral view outer explode (instance) insts as inst) res on res.d_id=dtrce.id
+         left outer join piwik_datasource piwik_d on piwik_d.id=dtrce.id
+where dtrce.datainfo.deletedbyinference = false and dtrce.datainfo.invisible = false; /*EOS*/
 
--- Insert statement that takes into account the piwik_id of the openAIRE graph
-INSERT INTO ${stats_db_name}.datasource_tmp
-SELECT substr(d1.id, 4)                                          AS id,
-       officialname.value                                        AS name,
-       datasourcetype.classname                                  AS type,
-       dateofvalidation.value                                    AS dateofvalidation,
-       date_format(d1.dateofvalidation.value, 'yyyy')            AS yearofvalidation,
-       FALSE                                                     AS harvested,
-       CASE WHEN d2.piwik_id IS NULL THEN 0 ELSE d2.piwik_id END AS piwik_id,
-       d1.latitude.value                                         AS latitude,
-       d1.longitude.value                                        AS longitude,
-       d1.websiteurl.value                                       AS websiteurl,
-       d1.openairecompatibility.classid                          AS compatibility,
-       d1.journal.issnprinted                                    AS issn_printed,
-       d1.journal.issnonline                                    AS issn_online
-FROM ${openaire_db_name}.datasource d1
-         LEFT OUTER JOIN
-     (SELECT id, split(originalidd, '\\:')[1] as piwik_id
-      FROM ${openaire_db_name}.datasource
-               LATERAL VIEW EXPLODE(originalid) temp AS originalidd
-      WHERE originalidd like "piwik:%") AS d2
-     ON d1.id = d2.id
-WHERE d1.datainfo.deletedbyinference = FALSE and d1.datainfo.invisible=false; -- /*EOS*/
 
--- Updating temporary table with everything that is not based on results -> This is done with the following "dual" table.
--- Creating a temporary dual table that will be removed after the following insert
-
-DROP TABLE IF EXISTS ${stats_db_name}.dual purge; -- /*EOS*/
-
-CREATE TABLE ${stats_db_name}.dual ( dummy CHAR(1)); -- /*EOS*/
-
-INSERT INTO ${stats_db_name}.dual VALUES ('X'); -- /*EOS*/
-
-INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`,
-                                             `piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`, `issn_printed`, `issn_online`)
-SELECT 'other',
-       'Other',
-       'Repository',
-       NULL,
-       NULL,
-       false,
-       0,
-       NULL,
-       NULL,
-       NULL,
-       'unknown',
-       null,
-       null
-FROM ${stats_db_name}.dual
-WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository'); -- /*EOS*/
-DROP TABLE ${stats_db_name}.dual; -- /*EOS*/
-
-UPDATE ${stats_db_name}.datasource_tmp SET name='Other' WHERE name = 'Unknown Repository'; -- /*EOS*/
-UPDATE ${stats_db_name}.datasource_tmp SET yearofvalidation=null WHERE yearofvalidation = '-1'; -- /*EOS*/
-
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; -- /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, langs.languages AS language

From bb12d0b4df50919fea19d5a4d25dcb39718fdfb1 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 3 Jul 2024 16:26:39 +0200
Subject: [PATCH 051/239] removed legacy actionmanager dependencies

---
 dhp-workflows/dhp-actionmanager/pom.xml       |    4 +-
 .../dnetlib/dhp/actionmanager/ISClient.java   |   29 +-
 dhp-workflows/dhp-swh/pom.xml                 |   43 -
 pom.xml                                       | 2029 ++++++++---------
 4 files changed, 937 insertions(+), 1168 deletions(-)

diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml
index ce13502b6..1ef55a060 100644
--- a/dhp-workflows/dhp-actionmanager/pom.xml
+++ b/dhp-workflows/dhp-actionmanager/pom.xml
@@ -50,11 +50,12 @@
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
-
+<!--
         <dependency>
             <groupId>eu.dnetlib</groupId>
             <artifactId>dnet-actionmanager-api</artifactId>
         </dependency>
+
         <dependency>
             <groupId>eu.dnetlib</groupId>
             <artifactId>dnet-actionmanager-common</artifactId>
@@ -93,6 +94,7 @@
                 </exclusion>
             </exclusions>
         </dependency>
+-->
 
     </dependencies>
 </project>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
index 088e618c7..24d50029c 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
+++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
@@ -4,7 +4,6 @@ package eu.dnetlib.dhp.actionmanager;
 import java.io.Serializable;
 import java.io.StringReader;
 import java.util.List;
-import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -22,13 +21,14 @@ import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 
-import eu.dnetlib.actionmanager.rmi.ActionManagerException;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 public class ISClient implements Serializable {
 
+	private static final long serialVersionUID = 4632443200867340872L;
+
 	private static final Logger log = LoggerFactory.getLogger(ISClient.class);
 
 	private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
@@ -65,7 +65,7 @@ public class ISClient implements Serializable {
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
 				.orElseThrow(() -> new IllegalStateException("empty set list"));
-		} catch (ActionManagerException | ISLookUpException e) {
+		} catch (ISLookUpException e) {
 			throw new IllegalStateException("unable to query ActionSets info from the IS");
 		}
 	}
@@ -89,31 +89,18 @@ public class ISClient implements Serializable {
 		return Joiner.on("/").join(basePath, t.getMiddle(), t.getRight());
 	}
 
-	private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
+	private String getBasePathHDFS(ISLookUpService isLookup) throws ISLookUpException {
 		return queryServiceProperty(isLookup, "basePath");
 	}
 
 	private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
-		throws ActionManagerException {
+		throws ISLookUpException {
 		final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
 			+ propertyName
 			+ "']/@value/string()";
 		log.debug("quering for service property: {}", q);
-		try {
-			final List<String> value = isLookup.quickSearchProfile(q);
-			return Iterables.getOnlyElement(value);
-		} catch (ISLookUpException e) {
-			String msg = "Error accessing service profile, using query: " + q;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		} catch (NoSuchElementException e) {
-			String msg = "missing service property: " + propertyName;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		} catch (IllegalArgumentException e) {
-			String msg = "found more than one service property: " + propertyName;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		}
+
+		final List<String> value = isLookup.quickSearchProfile(q);
+		return Iterables.getOnlyElement(value);
 	}
 }
diff --git a/dhp-workflows/dhp-swh/pom.xml b/dhp-workflows/dhp-swh/pom.xml
index 80fff4587..ef9049b20 100644
--- a/dhp-workflows/dhp-swh/pom.xml
+++ b/dhp-workflows/dhp-swh/pom.xml
@@ -51,49 +51,6 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-common</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>eu.dnetlib</groupId>
-                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon-dom</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>jgrapht</groupId>
-                    <artifactId>jgrapht</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>net.sf.ehcache</groupId>
-                    <artifactId>ehcache</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.springframework</groupId>
-                    <artifactId>spring-test</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.*</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>apache</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
diff --git a/pom.xml b/pom.xml
index a5bc6cedd..47b7d5f38 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,1107 +1,930 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
-    <modelVersion>4.0.0</modelVersion>
-    <groupId>eu.dnetlib.dhp</groupId>
-    <artifactId>dhp</artifactId>
-    <version>1.2.5-SNAPSHOT</version>
-    <packaging>pom</packaging>
-
-    <licenses>
-        <license>
-            <name>GNU Affero General Public License v3.0 or later</name>
-            <url>https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText</url>
-            <distribution>repo</distribution>
-            <comments>This program is free software: you can redistribute it and/or modify it under the terms of the
-                GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the
-                License, or (at your option) any later version.
-            </comments>
-        </license>
-    </licenses>
-
-    <modules>
-        <module>dhp-build</module>
-        <module>dhp-pace-core</module>
-        <module>dhp-common</module>
-        <module>dhp-workflows</module>
-        <module>dhp-shade-package</module>
-    </modules>
-
-    <issueManagement>
-        <system>Redmine</system>
-        <url>https://support.openaire.eu/projects/openaire</url>
-    </issueManagement>
-
-    <ciManagement>
-        <system>jenkins</system>
-        <url>https://jenkins-dnet.d4science.org/</url>
-    </ciManagement>
-
-    <scm>
-        <connection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</connection>
-        <developerConnection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</developerConnection>
-        <url>https://code-repo.d4science.org/D-Net/dnet-hadoop/</url>
-        <tag>HEAD</tag>
-    </scm>
-
-    <description>This module is the root descriptor for the dnet-hadoop project</description>
-
-    <pluginRepositories>
-    </pluginRepositories>
-
-    <repositories>
-
-        <repository>
-            <id>Openaire-third-parties-snaphot</id>
-            <name>Openaire third parties Snapshot</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/Openaire-third-parties-snaphot/</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-            <snapshots>
-                <enabled>true</enabled>
-            </snapshots>
-        </repository>
-
-        <repository>
-            <id>dnet45-releases</id>
-            <name>D-Net 45 releases</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
-            <layout>default</layout>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-            <releases>
-                <enabled>true</enabled>
-            </releases>
-        </repository>
-        <repository>
-            <id>dnet45-snapshots</id>
-            <name>D-Net 45 snapshots</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
-            <layout>default</layout>
-            <snapshots>
-                <enabled>true</enabled>
-            </snapshots>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-        </repository>
-        <repository>
-            <id>dnet45-bootstrap-snapshot</id>
-            <name>D-Net 45 Bootstrap Snapshot</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-snapshot/</url>
-            <releases>
-                <enabled>false</enabled>
-            </releases>
-            <snapshots>
-                <enabled>true</enabled>
-            </snapshots>
-            <layout>default</layout>
-        </repository>
-        <repository>
-            <id>dnet45-bootstrap-release</id>
-            <name>D-Net 45 Bootstrap Release</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-release/</url>
-            <releases>
-                <enabled>true</enabled>
-            </releases>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-            <layout>default</layout>
-        </repository>
-        <repository>
-            <id>cloudera</id>
-            <name>Cloudera Repository</name>
-            <url>https://repository.cloudera.com/artifactory/cloudera-repos</url>
-            <releases>
-                <enabled>true</enabled>
-            </releases>
-            <snapshots>
-                <enabled>false</enabled>
-            </snapshots>
-        </repository>
-        <repository>
-            <id>dnet-deps</id>
-            <name>dnet-dependencies</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
-            <layout>default</layout>
-        </repository>
-        <repository>
-            <id>maven-restlet</id>
-            <name>Restlet repository</name>
-            <url>https://maven.restlet.talend.com</url>
-        </repository>
-        <repository>
-            <id>conjars</id>
-            <name>conjars</name>
-            <url>https://conjars.wensel.net/repo/</url>
-        </repository>
-    </repositories>
-
-    <dependencies>
-        <!-- Quick FIX not to remove lombok everywhere -->
-        <dependency>
-            <groupId>org.projectlombok</groupId>
-            <artifactId>lombok</artifactId>
-            <version>1.18.28</version>
-            <scope>provided</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.junit.jupiter</groupId>
-            <artifactId>junit-jupiter</artifactId>
-            <version>${junit-jupiter.version}</version>
-            <scope>test</scope>
-        </dependency>
-
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-core</artifactId>
-            <version>${mockito-core.version}</version>
-            <scope>test</scope>
-        </dependency>
-
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-junit-jupiter</artifactId>
-            <version>${mockito-core.version}</version>
-            <scope>test</scope>
-        </dependency>
-
-    </dependencies>
-
-    <dependencyManagement>
-        <dependencies>
-            <dependency>
-                <groupId>eu.dnetlib.dhp</groupId>
-                <artifactId>dhp-schemas</artifactId>
-                <version>${dhp-schemas.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.hadoop</groupId>
-                <artifactId>hadoop-hdfs</artifactId>
-                <version>${dhp.hadoop.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.hadoop</groupId>
-                <artifactId>hadoop-common</artifactId>
-                <version>${dhp.hadoop.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.hadoop</groupId>
-                <artifactId>hadoop-client</artifactId>
-                <version>${dhp.hadoop.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.hadoop</groupId>
-                <artifactId>hadoop-distcp</artifactId>
-                <version>${dhp.hadoop.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.spark</groupId>
-                <artifactId>spark-core_${scala.binary.version}</artifactId>
-                <version>${dhp.spark.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.spark</groupId>
-                <artifactId>spark-sql_${scala.binary.version}</artifactId>
-                <version>${dhp.spark.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.spark</groupId>
-                <artifactId>spark-graphx_${scala.binary.version}</artifactId>
-                <version>${dhp.spark.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.spark</groupId>
-                <artifactId>spark-hive_${scala.binary.version}</artifactId>
-                <version>${dhp.spark.version}</version>
-                <scope>test</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>org.slf4j</groupId>
-                <artifactId>slf4j-api</artifactId>
-                <version>${org.slf4j.version}</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>org.slf4j</groupId>
-                <artifactId>slf4j-log4j12</artifactId>
-                <version>${org.slf4j.version}</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>org.slf4j</groupId>
-                <artifactId>jcl-over-slf4j</artifactId>
-                <version>${org.slf4j.version}</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-slf4j2-impl</artifactId>
-                <version>${log4j.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-api</artifactId>
-                <version>${log4j.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-core</artifactId>
-                <version>${log4j.version}</version>
-            </dependency>
-            <dependency>
-                <!-- API bridge between log4j 1 and 2 -->
-                <groupId>org.apache.logging.log4j</groupId>
-                <artifactId>log4j-1.2-api</artifactId>
-                <version>${log4j.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.commons</groupId>
-                <artifactId>commons-lang3</artifactId>
-                <version>${dhp.commons.lang.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.commons</groupId>
-                <artifactId>commons-beanutils</artifactId>
-                <version>${commons-beanutils.version}</version>
-            </dependency>
-
-
-            <dependency>
-                <groupId>commons-validator</groupId>
-                <artifactId>commons-validator</artifactId>
-                <version>${commons-validator.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.github.sisyphsu</groupId>
-                <artifactId>dateparser</artifactId>
-                <version>${dateparser.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>me.xuender</groupId>
-                <artifactId>unidecode</artifactId>
-                <version>${unidecode.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.google.guava</groupId>
-                <artifactId>guava</artifactId>
-                <version>${dhp.guava.version}</version>
-            </dependency>
-
-
-            <dependency>
-                <groupId>commons-codec</groupId>
-                <artifactId>commons-codec</artifactId>
-                <version>${commons-codec.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>commons-io</groupId>
-                <artifactId>commons-io</artifactId>
-                <version>${commons-io.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>commons-cli</groupId>
-                <artifactId>commons-cli</artifactId>
-                <version>1.2</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>net.sf.saxon</groupId>
-                <artifactId>Saxon-HE</artifactId>
-                <version>9.9.1-6</version>
-            </dependency>
-
-            <dependency>
-                <groupId>dom4j</groupId>
-                <artifactId>dom4j</artifactId>
-                <version>1.6.1</version>
-            </dependency>
-
-            <dependency>
-                <groupId>xml-apis</groupId>
-                <artifactId>xml-apis</artifactId>
-                <version>1.4.01</version>
-            </dependency>
-
-            <dependency>
-                <groupId>jaxen</groupId>
-                <artifactId>jaxen</artifactId>
-                <version>1.1.6</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.mycila.xmltool</groupId>
-                <artifactId>xmltool</artifactId>
-                <version>3.3</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.solr</groupId>
-                <artifactId>solr-solrj</artifactId>
-                <version>${solr.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <artifactId>*</artifactId>
-                        <groupId>*</groupId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-            <dependency>
-                <groupId>com.lucidworks.spark</groupId>
-                <artifactId>spark-solr</artifactId>
-                <version>${sparksolr.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <artifactId>*</artifactId>
-                        <groupId>*</groupId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.solr</groupId>
-                <artifactId>solr-test-framework</artifactId>
-                <version>${solr.version}</version>
-                <scope>test</scope>
-            </dependency>
-            <dependency>
-                <groupId>io.dropwizard.metrics</groupId>
-                <artifactId>metrics-core</artifactId>
-                <version>3.2.6</version>
-                <scope>test</scope>
-            </dependency>
-
-
-            <dependency>
-                <groupId>org.apache.httpcomponents</groupId>
-                <artifactId>httpclient</artifactId>
-                <version>${org.apache.httpcomponents.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.httpcomponents</groupId>
-                <artifactId>httpmime</artifactId>
-                <version>${org.apache.httpcomponents.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>org.noggit</groupId>
-                <artifactId>noggit</artifactId>
-                <version>0.8</version>
-            </dependency>
-            <dependency>
-                <groupId>org.apache.zookeeper</groupId>
-                <artifactId>zookeeper</artifactId>
-                <version>${zookeeper.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>net.schmizz</groupId>
-                <artifactId>sshj</artifactId>
-                <version>0.10.0</version>
-                <scope>test</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-core</artifactId>
-                <version>${dhp.jackson.version}</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-annotations</artifactId>
-                <version>${dhp.jackson.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-databind</artifactId>
-                <version>${dhp.jackson.version}</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>dnet-actionmanager-common</artifactId>
-                <version>${dnet-actionmanager-common.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>org.apache.hadoop</groupId>
-                        <artifactId>hadoop-common</artifactId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>dnet-actionmanager-api</artifactId>
-                <version>${dnet-actionmanager-api.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>eu.dnetlib</groupId>
-                        <artifactId>cnr-misc-utils</artifactId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>cnr-rmi-api</artifactId>
-                <version>${cnr-rmi-api.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>eu.dnetlib.dhp</groupId>
-                <artifactId>dnet-openaire-broker-common</artifactId>
-                <version>${dnet-openaire-broker-common.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.cxf</groupId>
-                <artifactId>cxf-rt-transports-http</artifactId>
-                <version>3.1.5</version>
-            </dependency>
-
-            <dependency>
-                <groupId>javax.persistence</groupId>
-                <artifactId>javax.persistence-api</artifactId>
-                <version>2.2</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>com.jayway.jsonpath</groupId>
-                <artifactId>json-path</artifactId>
-                <version>2.4.0</version>
-            </dependency>
-            <dependency>
-                <groupId>com.arakelian</groupId>
-                <artifactId>java-jq</artifactId>
-                <version>0.10.1</version>
-            </dependency>
-            <dependency>
-                <groupId>edu.cmu</groupId>
-                <artifactId>secondstring</artifactId>
-                <version>1.0.0</version>
-            </dependency>
-            <dependency>
-                <groupId>org.mongodb</groupId>
-                <artifactId>mongo-java-driver</artifactId>
-                <version>${mongodb.driver.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>io.fares.junit.mongodb</groupId>
-                <artifactId>mongodb-junit-test</artifactId>
-                <version>1.1.0</version>
-            </dependency>
-            <dependency>
-                <groupId>org.postgresql</groupId>
-                <artifactId>postgresql</artifactId>
-                <version>42.2.10</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.antlr</groupId>
-                <artifactId>stringtemplate</artifactId>
-                <version>3.2.1</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.antlr</groupId>
-                <artifactId>ST4</artifactId>
-                <version>4.3.4</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.ximpleware</groupId>
-                <artifactId>vtd-xml</artifactId>
-                <version>${vtd.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.elasticsearch</groupId>
-                <artifactId>elasticsearch-hadoop</artifactId>
-                <version>7.6.0</version>
-            </dependency>
-
-
-            <dependency>
-                <groupId>org.apache.oozie</groupId>
-                <artifactId>oozie-client</artifactId>
-                <version>${dhp.oozie.version}</version>
-                <scope>provided</scope>
-                <exclusions>
-                    <!-- conflicts -->
-                    <exclusion>
-                        <artifactId>slf4j-simple</artifactId>
-                        <groupId>org.slf4j</groupId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-
-
-            <dependency>
-                <groupId>com.squareup.okhttp3</groupId>
-                <artifactId>okhttp</artifactId>
-                <version>${okhttp.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.commons</groupId>
-                <artifactId>commons-compress</artifactId>
-                <version>${common.compress.version}</version>
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-            <dependency>
-                <groupId>org.apache.commons</groupId>
-                <artifactId>commons-csv</artifactId>
-                <version>${common.csv.version}</version>
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-            <dependency>
-                <groupId>org.apache.poi</groupId>
-                <artifactId>poi-ooxml</artifactId>
-                <version>${apache.poi.version}</version>
-            </dependency>
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-                <groupId>org.json</groupId>
-                <artifactId>json</artifactId>
-                <version>20180813</version>
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-            <dependency>
-                <groupId>org.json4s</groupId>
-                <artifactId>json4s-jackson_${scala.binary.version}</artifactId>
-                <version>${json4s.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.github.victools</groupId>
-                <artifactId>jsonschema-generator</artifactId>
-                <version>${jsonschemagenerator.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.commons</groupId>
-                <artifactId>commons-text</artifactId>
-                <version>${common.text.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.opencsv</groupId>
-                <artifactId>opencsv</artifactId>
-                <version>5.5</version>
-            </dependency>
-            <dependency>
-                <groupId>io.github.classgraph</groupId>
-                <artifactId>classgraph</artifactId>
-                <version>4.8.71</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.fasterxml.jackson.dataformat</groupId>
-                <artifactId>jackson-dataformat-xml</artifactId>
-                <version>${jackson.version}</version>
-                <scope>provided</scope>
-            </dependency>
-            <dependency>
-                <groupId>com.fasterxml.jackson.module</groupId>
-                <artifactId>jackson-module-jsonSchema</artifactId>
-                <version>${jackson.version}</version>
-                <scope>provided</scope>
-            </dependency>
-
-            <dependency>
-                <groupId>org.apache.commons</groupId>
-                <artifactId>commons-math3</artifactId>
-                <version>3.6.1</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.google.code.gson</groupId>
-                <artifactId>gson</artifactId>
-                <version>${google.gson.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>commons-collections</groupId>
-                <artifactId>commons-collections</artifactId>
-                <version>${commons.collections.version}</version>
-            </dependency>
-            <dependency>
-                <groupId>commons-logging</groupId>
-                <artifactId>commons-logging</artifactId>
-                <version>${commons.logging.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.reflections</groupId>
-                <artifactId>reflections</artifactId>
-                <version>${reflections.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.scala-lang</groupId>
-                <artifactId>scala-library</artifactId>
-                <version>${scala.version}</version>
-            </dependency>
-
-            <dependency>
-                <groupId>com.ibm.icu</groupId>
-                <artifactId>icu4j</artifactId>
-                <version>70.1</version>
-            </dependency>
-
-            <dependency>
-                <groupId>org.javassist</groupId>
-                <artifactId>javassist</artifactId>
-                <version>${javassist.version}</version>
-            </dependency>
-        </dependencies>
-    </dependencyManagement>
-
-    <build>
-        <directory>target</directory>
-        <outputDirectory>target/classes</outputDirectory>
-        <finalName>${project.artifactId}-${project.version}</finalName>
-        <testOutputDirectory>target/test-classes</testOutputDirectory>
-        <pluginManagement>
-            <plugins>
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-plugin-plugin</artifactId>
-                    <version>3.3</version>
-                </plugin>
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-project-info-reports-plugin</artifactId>
-                    <version>3.0.0</version>
-                </plugin>
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-site-plugin</artifactId>
-                    <version>3.9.1</version>
-                    <configuration>
-                        <skip>${dhp.site.skip}</skip>
-                    </configuration>
-                </plugin>
-
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-compiler-plugin</artifactId>
-                    <version>${maven.compiler.plugin.version}</version>
-                    <configuration>
-                        <source>1.8</source>
-                        <target>1.8</target>
-                        <encoding>${project.build.sourceEncoding}</encoding>
-                    </configuration>
-                </plugin>
-
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-jar-plugin</artifactId>
-                    <version>3.0.2</version>
-                </plugin>
-
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-source-plugin</artifactId>
-                    <version>3.0.1</version>
-                    <executions>
-                        <execution>
-                            <id>attach-sources</id>
-                            <phase>verify</phase>
-                            <goals>
-                                <goal>jar-no-fork</goal>
-                            </goals>
-                        </execution>
-                    </executions>
-                </plugin>
-
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-surefire-plugin</artifactId>
-                    <version>3.0.0-M4</version>
-                    <configuration>
-                        <redirectTestOutputToFile>true</redirectTestOutputToFile>
-                        <trimStackTrace>false</trimStackTrace>
-                    </configuration>
-                </plugin>
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-javadoc-plugin</artifactId>
-                    <version>3.2.0</version>
-                    <configuration>
-                        <detectLinks>true</detectLinks>
-                        <doclint>none</doclint>
-                    </configuration>
-                </plugin>
-                <plugin>
-                    <groupId>org.apache.maven.plugins</groupId>
-                    <artifactId>maven-dependency-plugin</artifactId>
-                    <version>3.6.0</version>
-                </plugin>
-
-                <plugin>
-                    <groupId>net.revelc.code.formatter</groupId>
-                    <artifactId>formatter-maven-plugin</artifactId>
-                    <version>2.11.0</version>
-                    <dependencies>
-                        <dependency>
-                            <groupId>eu.dnetlib.dhp</groupId>
-                            <artifactId>dhp-code-style</artifactId>
-                            <version>${project.version}</version>
-                        </dependency>
-                    </dependencies>
-                </plugin>
-                <plugin>
-                    <groupId>org.antipathy</groupId>
-                    <artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
-                    <version>1.0.1640073709.733712b</version>
-                    <dependencies>
-                        <dependency>
-                            <groupId>eu.dnetlib.dhp</groupId>
-                            <artifactId>dhp-code-style</artifactId>
-                            <version>${project.version}</version>
-                        </dependency>
-                    </dependencies>
-                </plugin>
-            </plugins>
-        </pluginManagement>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-site-plugin</artifactId>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-project-info-reports-plugin</artifactId>
-            </plugin>
-            <plugin>
-                <groupId>net.revelc.code.formatter</groupId>
-                <artifactId>formatter-maven-plugin</artifactId>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>format</goal>
-                        </goals>
-                        <configuration>
-                            <configFile>eclipse/formatter_dnet.xml</configFile>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>net.revelc.code</groupId>
-                <artifactId>impsort-maven-plugin</artifactId>
-                <version>1.6.2</version>
-                <configuration>
-                    <groups>java.,javax.,org.,com.</groups>
-                    <staticGroups>java,*</staticGroups>
-                    <excludes>
-                        <exclude>**/thrift/*.java</exclude>
-                    </excludes>
-                </configuration>
-                <executions>
-                    <execution>
-                        <id>sort-imports</id>
-                        <goals>
-                            <goal>sort</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.antipathy</groupId>
-                <artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
-                <configuration>
-                    <configLocation>
-                        https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf
-                    </configLocation>
-                    <skipTestSources>false</skipTestSources>
-                    <skipSources>false</skipSources>
-                    <sourceDirectories>
-                        <param>${project.basedir}/src/main/scala</param>
-                    </sourceDirectories>
-                    <testSourceDirectories>
-                        <param>${project.basedir}/src/test/scala</param>
-                    </testSourceDirectories>
-                    <validateOnly>false</validateOnly>
-                    <onlyChangedFiles>false</onlyChangedFiles>
-                    <branch>: git rev-parse --abbrev-ref HEAD</branch>
-                    <useSpecifiedRepositories>false</useSpecifiedRepositories>
-                </configuration>
-                <executions>
-                    <execution>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>format</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-release-plugin</artifactId>
-                <version>2.5.3</version>
-            </plugin>
-            <plugin>
-                <groupId>org.jacoco</groupId>
-                <artifactId>jacoco-maven-plugin</artifactId>
-                <version>0.8.10</version>
-                <configuration>
-                    <excludes>
-                        <exclude>**/schemas/*</exclude>
-                        <exclude>**/com/cloudera/**/*</exclude>
-                        <exclude>**/org/apache/avro/io/**/*</exclude>
-                    </excludes>
-                </configuration>
-                <executions>
-                    <execution>
-                        <id>default-prepare-agent</id>
-                        <goals>
-                            <goal>prepare-agent</goal>
-                        </goals>
-                    </execution>
-                    <execution>
-                        <id>default-report</id>
-                        <phase>prepare-package</phase>
-                        <goals>
-                            <goal>report</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
-        </plugins>
-
-        <extensions>
-            <extension>
-                <groupId>org.apache.maven.wagon</groupId>
-                <artifactId>wagon-ssh</artifactId>
-                <version>2.10</version>
-            </extension>
-        </extensions>
-    </build>
-    <distributionManagement>
-        <snapshotRepository>
-            <id>dnet45-snapshots</id>
-            <name>DNet45 Snapshots</name>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
-            <layout>default</layout>
-        </snapshotRepository>
-        <repository>
-            <id>dnet45-releases</id>
-            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
-        </repository>
-        <site>
-            <id>DHPSite</id>
-            <url>${dhp.site.stage.path}/</url>
-        </site>
-    </distributionManagement>
-    <reporting>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-javadoc-plugin</artifactId>
-                <configuration>
-                    <detectLinks>true</detectLinks>
-                    <doclint>none</doclint>
-                </configuration>
-            </plugin>
-        </plugins>
-    </reporting>
-
-    <properties>
-        <dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
-        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-        <maven.compiler.source>1.8</maven.compiler.source>
-        <maven.compiler.target>1.8</maven.compiler.target>
-
-        <!-- scala version -->
-        <scala.version>2.11.12</scala.version>
-        <scala.binary.version>2.11</scala.binary.version>
-
-        <!-- plugin versions -->
-        <maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
-        <maven.failsave.plugin.version>2.22.2</maven.failsave.plugin.version>
-        <properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
-        <net.alchim31.maven.version>4.0.1</net.alchim31.maven.version>
-
-        <!-- dependency versions -->
-        <apache.poi.version>4.1.2</apache.poi.version>
-        <cnr-rmi-api.version>[2.6.1]</cnr-rmi-api.version>
-        <common.compress.version>1.20</common.compress.version>
-        <common.csv.version>1.8</common.csv.version>
-        <common.text.version>1.8</common.text.version>
-        <commons-beanutils.version>1.9.4</commons-beanutils.version>
-        <commons-codec.version>1.9</commons-codec.version>
-        <commons.collections.version>3.2.1</commons.collections.version>
-        <commons-io.version>2.4</commons-io.version>
-        <commons.logging.version>1.1.3</commons.logging.version>
-        <commons-validator.version>1.7</commons-validator.version>
-        <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.4-SNAPSHOT]</dhp-schemas.version>
-        <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
-        <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
-        <dhp.guava.version>11.0.2</dhp.guava.version>
-        <dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
-        <dhp.jackson.version>2.9.6</dhp.jackson.version>
-        <dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
-        <dhp.site.skip>true</dhp.site.skip>
-        <dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
-        <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
-        <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
-        <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
-        <google.gson.version>2.2.2</google.gson.version>
-        <log4j.version>1.2.17</log4j.version>
-        <javassist.version>3.19.0-GA</javassist.version>
-        <json4s.version>3.5.3</json4s.version>
-        <jsonschemagenerator.version>4.13.0</jsonschemagenerator.version>
-        <junit-jupiter.version>5.6.1</junit-jupiter.version>
-        <mockito-core.version>3.3.3</mockito-core.version>
-        <mongodb.driver.version>3.4.2</mongodb.driver.version>
-        <okhttp.version>4.7.2</okhttp.version>
-        <org.apache.httpcomponents.version>4.5.3</org.apache.httpcomponents.version>
-        <org.slf4j.version>1.7.25</org.slf4j.version>
-        <reflections.version>0.9.10</reflections.version>
-        <scala-xml.version>1.3.0</scala-xml.version>
-        <solr.version>7.5.0</solr.version>
-        <sparksolr.version>3.6.0</sparksolr.version>
-        <unidecode.version>0.0.7</unidecode.version>
-        <vtd.version>[2.12,3.0)</vtd.version>
-        <zookeeper.version>3.4.6</zookeeper.version>
-    </properties>
-
-    <!-- Build with scala 12 and Spark 3.4 -->
-    <profiles>
-        <profile>
-            <id>spark-34</id>
-            <properties>
-                <scala.binary.version>2.12</scala.binary.version>
-                <scala.version>2.12.18</scala.version>
-                <scala-xml.version>1.3.0</scala-xml.version>
-
-                <!-- plugin versions -->
-                <net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
-
-                <!-- dependencies -->
-                <common.compress.version>1.22</common.compress.version>
-                <common.csv.version>1.8</common.csv.version>
-                <common.text.version>1.10.0</common.text.version>
-                <commons-beanutils.version>1.9.4</commons-beanutils.version>
-                <commons-codec.version>1.15</commons-codec.version>
-                <commons.collections.version>3.2.2</commons.collections.version>
-                <commons-io.version>2.11.0</commons-io.version>
-                <commons.logging.version>1.1.3</commons.logging.version>
-                <commons-validator.version>1.7</commons-validator.version>
-
-                <dhp.guava.version>14.0.1</dhp.guava.version>
-                <solr.version>8.11.0</solr.version>
-                <sparksolr.version>4.0.4</sparksolr.version>
-                <dhp.spark.version>3.4.2.openaire</dhp.spark.version>
-                <dhp.jackson.version>2.14.2</dhp.jackson.version>
-                <dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
-                <log4j.version>2.19.0</log4j.version>
-                <json4s.version>3.7.0-M11</json4s.version>
-                <javassist.version>3.25.0-GA</javassist.version>
-                <okhttp.version>4.10.0</okhttp.version>
-                <org.slf4j.version>2.0.6</org.slf4j.version>
-                <reflections.version>0.10.2</reflections.version>
-                <zookeeper.version>3.6.3</zookeeper.version>
-            </properties>
-        </profile>
-
-        <profile>
-            <id>spark-35</id>
-            <properties>
-                <scala.binary.version>2.12</scala.binary.version>
-                <scala.version>2.12.18</scala.version>
-                <scala-xml.version>1.3.0</scala-xml.version>
-
-                <!-- plugin versions -->
-                <net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
-
-                <!-- dependencies -->
-                <common.compress.version>1.23.0</common.compress.version>
-                <common.csv.version>1.8</common.csv.version>
-                <common.text.version>1.10.0</common.text.version>
-                <commons-beanutils.version>1.9.4</commons-beanutils.version>
-                <commons-codec.version>1.16.0</commons-codec.version>
-                <commons.collections.version>3.2.2</commons.collections.version>
-                <commons-io.version>2.13.0</commons-io.version>
-                <commons.logging.version>1.1.3</commons.logging.version>
-                <commons-validator.version>1.7</commons-validator.version>
-
-                <dhp.guava.version>14.0.1</dhp.guava.version>
-                <solr.version>8.11.0</solr.version>
-                <sparksolr.version>4.0.4</sparksolr.version>
-                <dhp.spark.version>3.5.1.openaire-SNAPSHOT</dhp.spark.version>
-                <dhp.jackson.version>2.15.2</dhp.jackson.version>
-                <dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
-                <log4j.version>2.20.0</log4j.version>
-                <json4s.version>3.7.0-M11</json4s.version>
-                <javassist.version>3.25.0-GA</javassist.version>
-                <okhttp.version>4.10.0</okhttp.version>
-                <org.slf4j.version>2.0.7</org.slf4j.version>
-                <reflections.version>0.10.2</reflections.version>
-                <zookeeper.version>3.6.3</zookeeper.version>
-            </properties>
-        </profile>
-
-        <profile>
-            <id>java11</id>
-            <activation>
-                <jdk>[11</jdk>
-            </activation>
-            <build>
-                <pluginManagement>
-                    <plugins>
-                        <plugin>
-                            <groupId>org.apache.maven.plugins</groupId>
-                            <artifactId>maven-surefire-plugin</artifactId>
-                            <version>3.0.0-M4</version>
-                            <configuration>
-                                <!-- only for java 11+ to run spark in tests -->
-                                <argLine>--add-opens=java.base/java.lang=ALL-UNNAMED
-                                    --add-opens=java.base/java.lang.invoke=ALL-UNNAMED
-                                    --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
-                                    --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED
-                                    --add-opens=java.base/java.nio=ALL-UNNAMED
-                                    --add-opens=java.base/java.util=ALL-UNNAMED
-                                    --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
-                                    --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED
-                                    --add-opens=java.base/sun.nio.ch=ALL-UNNAMED
-                                    --add-opens=java.base/sun.nio.cs=ALL-UNNAMED
-                                    --add-opens=java.base/sun.security.action=ALL-UNNAMED
-                                    --add-opens=java.base/sun.util.calendar=ALL-UNNAMED
-                                </argLine>
-                                <redirectTestOutputToFile>true</redirectTestOutputToFile>
-                                <trimStackTrace>false</trimStackTrace>
-                            </configuration>
-                        </plugin>
-                    </plugins>
-                </pluginManagement>
-            </build>
-        </profile>
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>eu.dnetlib.dhp</groupId>
+	<artifactId>dhp</artifactId>
+	<version>1.2.5-SNAPSHOT</version>
+	<packaging>pom</packaging>
+
+	<licenses>
+		<license>
+			<name>GNU Affero General Public License v3.0 or later</name>
+			<url>https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText</url>
+			<distribution>repo</distribution>
+			<comments>This program is free software: you can redistribute it and/or modify it under the terms of the
+				GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the
+				License, or (at your option) any later version.</comments>
+		</license>
+	</licenses>
+
+	<modules>
+		<module>dhp-build</module>
+		<module>dhp-pace-core</module>
+		<module>dhp-common</module>
+		<module>dhp-workflows</module>
+	</modules>
+
+	<issueManagement>
+		<system>Redmine</system>
+		<url>https://support.openaire.eu/projects/openaire</url>
+	</issueManagement>
+
+	<ciManagement>
+		<system>jenkins</system>
+		<url>https://jenkins-dnet.d4science.org/</url>
+	</ciManagement>
+
+	<scm>
+		<connection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</connection>
+		<developerConnection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</developerConnection>
+		<url>https://code-repo.d4science.org/D-Net/dnet-hadoop/</url>
+		<tag>HEAD</tag>
+	</scm>
+
+	<description>This module is the root descriptor for the dnet-hadoop project</description>
+
+	<pluginRepositories>
+	</pluginRepositories>
+
+	<repositories>
+		<repository>
+			<id>dnet45-releases</id>
+			<name>D-Net 45 releases</name>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
+			<layout>default</layout>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+			<releases>
+				<enabled>true</enabled>
+			</releases>
+		</repository>
+		<repository>
+			<id>dnet45-snapshots</id>
+			<name>D-Net 45 snapshots</name>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
+			<layout>default</layout>
+			<snapshots>
+				<enabled>true</enabled>
+			</snapshots>
+			<releases>
+				<enabled>false</enabled>
+			</releases>
+		</repository>
+		<repository>
+			<id>dnet45-bootstrap-snapshot</id>
+			<name>D-Net 45 Bootstrap Snapshot</name>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-snapshot/</url>
+			<releases>
+				<enabled>false</enabled>
+			</releases>
+			<snapshots>
+				<enabled>true</enabled>
+			</snapshots>
+			<layout>default</layout>
+		</repository>
+		<repository>
+			<id>dnet45-bootstrap-release</id>
+			<name>D-Net 45 Bootstrap Release</name>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-release/</url>
+			<releases>
+				<enabled>true</enabled>
+			</releases>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+			<layout>default</layout>
+		</repository>
+		<repository>
+			<id>cloudera</id>
+			<name>Cloudera Repository</name>
+			<url>https://repository.cloudera.com/artifactory/cloudera-repos</url>
+			<releases>
+				<enabled>true</enabled>
+			</releases>
+			<snapshots>
+				<enabled>false</enabled>
+			</snapshots>
+		</repository>
+		<repository>
+			<id>dnet-deps</id>
+			<name>dnet-dependencies</name>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
+			<layout>default</layout>
+		</repository>
+		<repository>
+			<id>maven-restlet</id>
+			<name>Restlet repository</name>
+			<url>https://maven.restlet.talend.com</url>
+		</repository>
+		<repository>
+			<id>conjars</id>
+			<name>conjars</name>
+			<url>https://conjars.wensel.net/repo/</url>
+		</repository>
+	</repositories>
+
+	<dependencies>
+		<dependency>
+			<groupId>org.junit.jupiter</groupId>
+			<artifactId>junit-jupiter</artifactId>
+			<version>${junit-jupiter.version}</version>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>org.mockito</groupId>
+			<artifactId>mockito-core</artifactId>
+			<version>${mockito-core.version}</version>
+			<scope>test</scope>
+		</dependency>
+
+		<dependency>
+			<groupId>org.mockito</groupId>
+			<artifactId>mockito-junit-jupiter</artifactId>
+			<version>${mockito-core.version}</version>
+			<scope>test</scope>
+		</dependency>
+
+	</dependencies>
+
+	<dependencyManagement>
+		<dependencies>
+			<dependency>
+				<groupId>eu.dnetlib.dhp</groupId>
+				<artifactId>${dhp-schemas.artifact}</artifactId>
+				<version>${dhp-schemas.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.hadoop</groupId>
+				<artifactId>hadoop-hdfs</artifactId>
+				<version>${dhp.hadoop.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.hadoop</groupId>
+				<artifactId>hadoop-common</artifactId>
+				<version>${dhp.hadoop.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.hadoop</groupId>
+				<artifactId>hadoop-client</artifactId>
+				<version>${dhp.hadoop.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.hadoop</groupId>
+				<artifactId>hadoop-distcp</artifactId>
+				<version>${dhp.hadoop.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.spark</groupId>
+				<artifactId>spark-core_${scala.binary.version}</artifactId>
+				<version>${dhp.spark.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.spark</groupId>
+				<artifactId>spark-sql_${scala.binary.version}</artifactId>
+				<version>${dhp.spark.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.spark</groupId>
+				<artifactId>spark-graphx_${scala.binary.version}</artifactId>
+				<version>${dhp.spark.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.spark</groupId>
+				<artifactId>spark-hive_${scala.binary.version}</artifactId>
+				<version>${dhp.spark.version}</version>
+				<scope>test</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>org.slf4j</groupId>
+				<artifactId>jcl-over-slf4j</artifactId>
+				<version>1.7.25</version>
+				<scope>provided</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>org.apache.commons</groupId>
+				<artifactId>commons-lang3</artifactId>
+				<version>${dhp.commons.lang.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>commons-validator</groupId>
+				<artifactId>commons-validator</artifactId>
+				<version>1.7</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.github.sisyphsu</groupId>
+				<artifactId>dateparser</artifactId>
+				<version>1.0.7</version>
+			</dependency>
+
+			<dependency>
+				<groupId>me.xuender</groupId>
+				<artifactId>unidecode</artifactId>
+				<version>0.0.7</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.google.guava</groupId>
+				<artifactId>guava</artifactId>
+				<version>${dhp.guava.version}</version>
+			</dependency>
+
+
+			<dependency>
+				<groupId>commons-codec</groupId>
+				<artifactId>commons-codec</artifactId>
+				<version>1.9</version>
+			</dependency>
+
+			<dependency>
+				<groupId>commons-io</groupId>
+				<artifactId>commons-io</artifactId>
+				<version>2.4</version>
+			</dependency>
+
+			<dependency>
+				<groupId>commons-cli</groupId>
+				<artifactId>commons-cli</artifactId>
+				<version>1.2</version>
+				<scope>provided</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>net.sf.saxon</groupId>
+				<artifactId>Saxon-HE</artifactId>
+				<version>9.9.1-6</version>
+			</dependency>
+
+			<dependency>
+				<groupId>dom4j</groupId>
+				<artifactId>dom4j</artifactId>
+				<version>1.6.1</version>
+			</dependency>
+
+			<dependency>
+				<groupId>xml-apis</groupId>
+				<artifactId>xml-apis</artifactId>
+				<version>1.4.01</version>
+			</dependency>
+
+			<dependency>
+				<groupId>jaxen</groupId>
+				<artifactId>jaxen</artifactId>
+				<version>1.1.6</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.mycila.xmltool</groupId>
+				<artifactId>xmltool</artifactId>
+				<version>3.3</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.apache.solr</groupId>
+				<artifactId>solr-solrj</artifactId>
+				<version>${solr.version}</version>
+				<exclusions>
+					<exclusion>
+						<artifactId>*</artifactId>
+						<groupId>*</groupId>
+					</exclusion>
+				</exclusions>
+			</dependency>
+			<dependency>
+				<groupId>com.lucidworks.spark</groupId>
+				<artifactId>spark-solr</artifactId>
+				<version>${sparksolr.version}</version>
+				<exclusions>
+					<exclusion>
+						<artifactId>*</artifactId>
+						<groupId>*</groupId>
+					</exclusion>
+				</exclusions>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.solr</groupId>
+				<artifactId>solr-test-framework</artifactId>
+				<version>${solr.version}</version>
+				<scope>test</scope>
+			</dependency>
+			<dependency>
+				<groupId>io.dropwizard.metrics</groupId>
+				<artifactId>metrics-core</artifactId>
+				<version>3.2.6</version>
+				<scope>test</scope>
+			</dependency>
+
+
+			<dependency>
+				<groupId>org.apache.httpcomponents</groupId>
+				<artifactId>httpclient</artifactId>
+				<version>${org.apache.httpcomponents.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.httpcomponents</groupId>
+				<artifactId>httpmime</artifactId>
+				<version>${org.apache.httpcomponents.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>org.noggit</groupId>
+				<artifactId>noggit</artifactId>
+				<version>0.8</version>
+			</dependency>
+			<dependency>
+				<groupId>org.apache.zookeeper</groupId>
+				<artifactId>zookeeper</artifactId>
+				<version>3.4.11</version>
+			</dependency>
+
+			<dependency>
+				<groupId>net.schmizz</groupId>
+				<artifactId>sshj</artifactId>
+				<version>0.10.0</version>
+				<scope>test</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>com.fasterxml.jackson.core</groupId>
+				<artifactId>jackson-core</artifactId>
+				<version>${dhp.jackson.version}</version>
+				<scope>provided</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>com.fasterxml.jackson.core</groupId>
+				<artifactId>jackson-annotations</artifactId>
+				<version>${dhp.jackson.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>com.fasterxml.jackson.core</groupId>
+				<artifactId>jackson-databind</artifactId>
+				<version>${dhp.jackson.version}</version>
+				<scope>provided</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>eu.dnetlib</groupId>
+				<artifactId>cnr-rmi-api</artifactId>
+				<version>${cnr-rmi-api.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>eu.dnetlib.dhp</groupId>
+				<artifactId>dnet-openaire-broker-common</artifactId>
+				<version>${dnet-openaire-broker-common.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.apache.cxf</groupId>
+				<artifactId>cxf-rt-transports-http</artifactId>
+				<version>3.1.5</version>
+			</dependency>
+			<dependency>
+				<groupId>javax.persistence</groupId>
+				<artifactId>javax.persistence-api</artifactId>
+				<version>2.2</version>
+				<scope>provided</scope>
+			</dependency>
+
+			<dependency>
+				<groupId>com.jayway.jsonpath</groupId>
+				<artifactId>json-path</artifactId>
+				<version>2.4.0</version>
+			</dependency>
+			<dependency>
+				<groupId>com.arakelian</groupId>
+				<artifactId>java-jq</artifactId>
+				<version>0.10.1</version>
+			</dependency>
+			<dependency>
+				<groupId>edu.cmu</groupId>
+				<artifactId>secondstring</artifactId>
+				<version>1.0.0</version>
+			</dependency>
+			<dependency>
+				<groupId>org.mongodb</groupId>
+				<artifactId>mongo-java-driver</artifactId>
+				<version>${mongodb.driver.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>io.fares.junit.mongodb</groupId>
+				<artifactId>mongodb-junit-test</artifactId>
+				<version>1.1.0</version>
+			</dependency>
+			<dependency>
+				<groupId>org.postgresql</groupId>
+				<artifactId>postgresql</artifactId>
+				<version>42.2.10</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.antlr</groupId>
+				<artifactId>stringtemplate</artifactId>
+				<version>3.2.1</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.antlr</groupId>
+				<artifactId>ST4</artifactId>
+				<version>4.3.4</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.ximpleware</groupId>
+				<artifactId>vtd-xml</artifactId>
+				<version>${vtd.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.elasticsearch</groupId>
+				<artifactId>elasticsearch-hadoop</artifactId>
+				<version>7.6.0</version>
+			</dependency>
+
+
+			<dependency>
+				<groupId>org.apache.oozie</groupId>
+				<artifactId>oozie-client</artifactId>
+				<version>${dhp.oozie.version}</version>
+				<scope>provided</scope>
+				<exclusions>
+					<!-- conflicts -->
+					<exclusion>
+						<artifactId>slf4j-simple</artifactId>
+						<groupId>org.slf4j</groupId>
+					</exclusion>
+				</exclusions>
+			</dependency>
+
+
+			<dependency>
+				<groupId>com.squareup.okhttp3</groupId>
+				<artifactId>okhttp</artifactId>
+				<version>${okhttp.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.apache.commons</groupId>
+				<artifactId>commons-compress</artifactId>
+				<version>${common.compress.version}</version>
+			</dependency>
+
+			<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
+			<dependency>
+				<groupId>org.apache.commons</groupId>
+				<artifactId>commons-csv</artifactId>
+				<version>${common.csv.version}</version>
+			</dependency>
+
+
+			<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
+			<dependency>
+				<groupId>org.apache.poi</groupId>
+				<artifactId>poi-ooxml</artifactId>
+				<version>${apache.poi.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.json</groupId>
+				<artifactId>json</artifactId>
+				<version>20180813</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.json4s</groupId>
+				<artifactId>json4s-jackson_${scala.binary.version}</artifactId>
+				<version>${json4s.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.github.victools</groupId>
+				<artifactId>jsonschema-generator</artifactId>
+				<version>${jsonschemagenerator.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.apache.commons</groupId>
+				<artifactId>commons-text</artifactId>
+				<version>${common.text.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.opencsv</groupId>
+				<artifactId>opencsv</artifactId>
+				<version>5.5</version>
+			</dependency>
+			<dependency>
+				<groupId>io.github.classgraph</groupId>
+				<artifactId>classgraph</artifactId>
+				<version>4.8.71</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.fasterxml.jackson.dataformat</groupId>
+				<artifactId>jackson-dataformat-xml</artifactId>
+				<version>${jackson.version}</version>
+				<scope>provided</scope>
+			</dependency>
+			<dependency>
+				<groupId>com.fasterxml.jackson.module</groupId>
+				<artifactId>jackson-module-jsonSchema</artifactId>
+				<version>${jackson.version}</version>
+				<scope>provided</scope>
+			</dependency>
+
+
+			<dependency>
+				<groupId>org.apache.commons</groupId>
+				<artifactId>commons-math3</artifactId>
+				<version>3.6.1</version>
+			</dependency>
+
+
+			<dependency>
+				<groupId>com.google.code.gson</groupId>
+				<artifactId>gson</artifactId>
+				<version>${google.gson.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>commons-collections</groupId>
+				<artifactId>commons-collections</artifactId>
+				<version>${commons.collections.version}</version>
+			</dependency>
+			<dependency>
+				<groupId>commons-logging</groupId>
+				<artifactId>commons-logging</artifactId>
+				<version>${commons.logging.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.reflections</groupId>
+				<artifactId>reflections</artifactId>
+				<version>0.9.10</version>
+			</dependency>
+
+			<dependency>
+				<groupId>org.scala-lang</groupId>
+				<artifactId>scala-library</artifactId>
+				<version>${scala.version}</version>
+			</dependency>
+
+			<dependency>
+				<groupId>com.ibm.icu</groupId>
+				<artifactId>icu4j</artifactId>
+				<version>70.1</version>
+			</dependency>
+		</dependencies>
+	</dependencyManagement>
+
+	<build>
+		<directory>target</directory>
+		<outputDirectory>target/classes</outputDirectory>
+		<finalName>${project.artifactId}-${project.version}</finalName>
+		<testOutputDirectory>target/test-classes</testOutputDirectory>
+		<pluginManagement>
+			<plugins>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-plugin-plugin</artifactId>
+					<version>3.3</version>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-project-info-reports-plugin</artifactId>
+					<version>3.0.0</version>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-site-plugin</artifactId>
+					<version>3.9.1</version>
+					<configuration>
+						<skip>${dhp.site.skip}</skip>
+					</configuration>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-compiler-plugin</artifactId>
+					<version>${maven.compiler.plugin.version}</version>
+					<configuration>
+						<source>1.8</source>
+						<target>1.8</target>
+						<encoding>${project.build.sourceEncoding}</encoding>
+					</configuration>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-jar-plugin</artifactId>
+					<version>3.0.2</version>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-source-plugin</artifactId>
+					<version>3.0.1</version>
+					<executions>
+						<execution>
+							<id>attach-sources</id>
+							<phase>verify</phase>
+							<goals>
+								<goal>jar-no-fork</goal>
+							</goals>
+						</execution>
+					</executions>
+				</plugin>
+
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-surefire-plugin</artifactId>
+					<version>3.0.0-M4</version>
+					<configuration>
+						<redirectTestOutputToFile>true</redirectTestOutputToFile>
+					</configuration>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-javadoc-plugin</artifactId>
+					<version>3.2.0</version>
+					<configuration>
+						<detectLinks>true</detectLinks>
+						<doclint>none</doclint>
+					</configuration>
+				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-dependency-plugin</artifactId>
+					<version>3.6.0</version>
+				</plugin>
+
+				<plugin>
+					<groupId>net.revelc.code.formatter</groupId>
+					<artifactId>formatter-maven-plugin</artifactId>
+					<version>2.11.0</version>
+					<dependencies>
+						<dependency>
+							<groupId>eu.dnetlib.dhp</groupId>
+							<artifactId>dhp-code-style</artifactId>
+							<version>${project.version}</version>
+						</dependency>
+					</dependencies>
+				</plugin>
+				<plugin>
+					<groupId>org.antipathy</groupId>
+					<artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
+					<version>1.0.1640073709.733712b</version>
+					<dependencies>
+						<dependency>
+							<groupId>eu.dnetlib.dhp</groupId>
+							<artifactId>dhp-code-style</artifactId>
+							<version>${project.version}</version>
+						</dependency>
+					</dependencies>
+				</plugin>
+			</plugins>
+		</pluginManagement>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-site-plugin</artifactId>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-project-info-reports-plugin</artifactId>
+			</plugin>
+			<plugin>
+				<groupId>net.revelc.code.formatter</groupId>
+				<artifactId>formatter-maven-plugin</artifactId>
+				<executions>
+					<execution>
+						<goals>
+							<goal>format</goal>
+						</goals>
+						<configuration>
+							<configFile>eclipse/formatter_dnet.xml</configFile>
+						</configuration>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>net.revelc.code</groupId>
+				<artifactId>impsort-maven-plugin</artifactId>
+				<version>1.4.1</version>
+				<configuration>
+					<groups>java.,javax.,org.,com.</groups>
+					<staticGroups>java,*</staticGroups>
+					<excludes>
+						<exclude>**/thrift/*.java</exclude>
+					</excludes>
+				</configuration>
+				<executions>
+					<execution>
+						<id>sort-imports</id>
+						<goals>
+							<goal>sort</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.antipathy</groupId>
+				<artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
+				<configuration>
+					<configLocation>https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf</configLocation>
+					<skipTestSources>false</skipTestSources>
+					<skipSources>false</skipSources>
+					<sourceDirectories>
+						<param>${project.basedir}/src/main/scala</param>
+					</sourceDirectories>
+					<testSourceDirectories>
+						<param>${project.basedir}/src/test/scala</param>
+					</testSourceDirectories>
+					<validateOnly>false</validateOnly>
+					<onlyChangedFiles>false</onlyChangedFiles>
+					<branch>: git rev-parse --abbrev-ref HEAD</branch>
+					<useSpecifiedRepositories>false</useSpecifiedRepositories>
+				</configuration>
+				<executions>
+					<execution>
+						<phase>validate</phase>
+						<goals>
+							<goal>format</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-release-plugin</artifactId>
+				<version>2.5.3</version>
+			</plugin>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<version>0.7.9</version>
+				<configuration>
+					<excludes>
+						<exclude>**/schemas/*</exclude>
+						<exclude>**/com/cloudera/**/*</exclude>
+						<exclude>**/org/apache/avro/io/**/*</exclude>
+					</excludes>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>default-report</id>
+						<phase>prepare-package</phase>
+						<goals>
+							<goal>report</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+
+		</plugins>
+
+		<extensions>
+			<extension>
+				<groupId>org.apache.maven.wagon</groupId>
+				<artifactId>wagon-ssh</artifactId>
+				<version>2.10</version>
+			</extension>
+		</extensions>
+	</build>
+	<distributionManagement>
+		<snapshotRepository>
+			<id>dnet45-snapshots</id>
+			<name>DNet45 Snapshots</name>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
+			<layout>default</layout>
+		</snapshotRepository>
+		<repository>
+			<id>dnet45-releases</id>
+			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
+		</repository>
+		<site>
+			<id>DHPSite</id>
+			<url>${dhp.site.stage.path}/</url>
+		</site>
+	</distributionManagement>
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-javadoc-plugin</artifactId>
+				<configuration>
+					<detectLinks>true</detectLinks>
+					<doclint>none</doclint>
+				</configuration>
+			</plugin>
+		</plugins>
+	</reporting>
+
+	<properties>
+		<dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
+		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+		<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
+		<maven.compiler.source>1.8</maven.compiler.source>
+		<maven.compiler.target>1.8</maven.compiler.target>
+		<maven.failsave.plugin.version>2.22.2</maven.failsave.plugin.version>
+		<properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
+		<dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
+		<dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
+		<dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
+		<dhp-schemas.artifact>dhp-schemas</dhp-schemas.artifact>
+		<sparksolr.version>3.6.0</sparksolr.version>
+		<dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
+		<dhp.jackson.version>2.9.6</dhp.jackson.version>
+		<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
+		<dhp.site.skip>true</dhp.site.skip>
+		<dhp.guava.version>11.0.2</dhp.guava.version>
+		<scala.version>2.11.12</scala.version>
+		<scala.binary.version>2.11</scala.binary.version>
+		<scala-xml.version>1.3.0</scala-xml.version>
+		<junit-jupiter.version>5.6.1</junit-jupiter.version>
+		<mockito-core.version>3.3.3</mockito-core.version>
+		<mongodb.driver.version>3.4.2</mongodb.driver.version>
+		<vtd.version>[2.12,3.0)</vtd.version>
+		<dhp-schemas.version>[6.1.3]</dhp-schemas.version>
+		<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
+		<cnr-rmi-api.version>[2.6.1]</cnr-rmi-api.version>
+		<solr.version>7.5.0</solr.version>
+		<okhttp.version>4.7.2</okhttp.version>
+		<common.compress.version>1.20</common.compress.version>
+		<json4s.version>3.5.3</json4s.version>
+		<jsonschemagenerator.version>4.13.0</jsonschemagenerator.version>
+		<common.csv.version>1.8</common.csv.version>
+		<apache.poi.version>4.1.2</apache.poi.version>
+		<common.text.version>1.8</common.text.version>
+		<org.apache.httpcomponents.version>4.5.3</org.apache.httpcomponents.version>
+		<net.alchim31.maven.version>4.0.1</net.alchim31.maven.version>
+		<google.gson.version>2.2.2</google.gson.version>
+		<commons.logging.version>1.1.3</commons.logging.version>
+		<commons.collections.version>3.2.1</commons.collections.version>
+	</properties>
+
+	<!-- Build with scala 12 and Spark 3.4 -->
+	<profiles>
+		<profile>
+			<id>scala-2.12</id>
+			<properties>
+				<scala.binary.version>2.12</scala.binary.version>
+				<scala.version>2.12.18</scala.version>
+				<!-- scala-xml.version>2.1.0</scala-xml.version -->
+
+
+				<sparksolr.version>4.0.2</sparksolr.version>
+				<dhp.spark.version>3.4.1</dhp.spark.version>
+				<dhp.jackson.version>2.14.2</dhp.jackson.version>
+				<dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
+				<json4s.version>3.7.0-M11</json4s.version>
+				<net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
+
+				<!--
+				<dhp-schemas.artifact>dhp-schemas_${scala.binary.version}</dhp-schemas.artifact>
+				<dhp-schemas.version>3.17.2-SNAPSHOT</dhp-schemas.version>
+				 -->
+			</properties>
+		</profile>
+
+		<!-- Activate ARM-compatible snappy dependency on new Silicon Macs -->
+		<profile>
+			<id>arm-silicon-mac</id>
+			<activation>
+				<os>
+					<arch>aarch64</arch>
+					<family>mac</family>
+				</os>
+			</activation>
+			<dependencyManagement>
+				<dependencies>
+					<dependency>
+						<groupId>org.xerial.snappy</groupId>
+						<artifactId>snappy-java</artifactId>
+						<version>1.1.8.4</version>
+					</dependency>
+				</dependencies>
+			</dependencyManagement>
+		</profile>
 	</profiles>
 </project>
\ No newline at end of file

From aa4d7d5e20370435e7863a16526a113aa80bcb6f Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 3 Jul 2024 19:14:25 +0300
Subject: [PATCH 052/239] Prioritize the rest of the stats-queries over other
 tasks on the cluster, by putting them in the "analytics" queue.

---
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql  | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql  | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql  | 2 ++
 .../oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 2 ++
 .../graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql | 2 ++
 .../stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql      | 2 ++
 .../stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql | 2 ++
 .../stats/oozie_app/scripts/step20-createMonitorDB_funded.sql   | 2 ++
 .../oozie_app/scripts/step20-createMonitorDB_institutions.sql   | 2 ++
 .../stats/oozie_app/scripts/step21-createObservatoryDB.sql      | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql   | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql   | 2 ++
 18 files changed, 36 insertions(+)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql
index 467a98872..4551d6282 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step1.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 --------------------------------------------------------------
 --------------------------------------------------------------
 -- Stats database creation
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
index 9088ce205..48d8961ff 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step10.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ------------------------------------------------------------------------------------------------
 ------------------------------------------------------------------------------------------------
 -- Tables/views from external tables/views (Fundref, Country, CountyGDP, roarmap, rndexpediture)
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
index 7597f1429..e98a778db 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ----------------------------------------------------------------
 ----------------------------------------------------------------
 -- Post processing - Updates on main tables
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
index 68a46ded3..20784bce9 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ------------------------------------------------------
 ------------------------------------------------------
 -- Additional relations
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
index 4abb6bdbc..4940bb96d 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 create view if not exists TARGET.category as select * from SOURCE.category;
 create view if not exists TARGET.concept as select * from SOURCE.concept;
 create view if not exists TARGET.context as select * from SOURCE.context;
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
index a8392b226..7e31408bc 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql
index 4469782f0..9dab79222 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql
@@ -1,5 +1,7 @@
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
+set mapred.job.queue.name=analytics; /*EOS*/
+
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql
index a28206d56..c6ef15d45 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql
@@ -1,5 +1,7 @@
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
+set mapred.job.queue.name=analytics; /*EOS*/
+
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql
index ce6475c22..8e3db49ff 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql
@@ -1,5 +1,7 @@
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
+set mapred.job.queue.name=analytics; /*EOS*/
+
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
index 62c68c625..286ffe427 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
@@ -1,5 +1,7 @@
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
+set mapred.job.queue.name=analytics; /*EOS*/
+
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
index adcf23b7a..1a7f34e96 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 create table ${observatory_db_name}.result_cc_licence stored as parquet as
 select r.id, coalesce(rln.count, 0) > 0 as cc_licence
 from ${stats_db_name}.result r
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
index 8f203fc83..0e1e02b12 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step3.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ------------------------------------------------------
 ------------------------------------------------------
 -- Dataset table/view and Dataset related tables/views
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
index 5e4c9f420..0ccb17fcc 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step4.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 --------------------------------------------------------
 --------------------------------------------------------
 -- Software table/view and Software related tables/views
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
index 3134ba316..cd7834d84 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step5.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 --------------------------------------------------------------------------------
 --------------------------------------------------------------------------------
 -- Otherresearchproduct table/view and Otherresearchproduct related tables/views
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
index de6b803ab..d261c96e2 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step6.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ------------------------------------------------------
 ------------------------------------------------------
 -- Project table/view and Project related tables/views
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index 2283e6291..6cab86a41 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ----------------------------------------------------
 ----------------------------------------------------
 -- Result table/view and Result related tables/views
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index b280dc946..d0b6abad9 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 -- noinspection SqlNoDataSourceInspectionForFile
 
 ------------------------------------------------------------
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
index 1d76b89a6..f504a5c12 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step9.sql
@@ -1,3 +1,5 @@
+set mapred.job.queue.name=analytics; /*EOS*/
+
 ----------------------------------------------------------------
 ----------------------------------------------------------------
 -- Organization table/view and Organization related tables/views

From 7ce051d7668c6d8081a512d4c623d701891ecc7b Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 3 Jul 2024 19:49:19 +0300
Subject: [PATCH 053/239] - Update the remaining hive-actions to spark-actions.
 - Update the version of shell-actions. - Fix missing "/*EOS*/" indicators.

---
 .../graph/stats/oozie_app/scripts/step11.sql  |  2 +-
 .../graph/stats/oozie_app/scripts/step14.sql  |  2 +-
 .../graph/stats/oozie_app/scripts/step7.sql   |  6 +-
 .../graph/stats/oozie_app/scripts/step8.sql   | 16 ++---
 .../dhp/oa/graph/stats/oozie_app/workflow.xml | 70 ++++++-------------
 5 files changed, 36 insertions(+), 60 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
index e98a778db..48373af9b 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql
@@ -17,4 +17,4 @@ FROM ${stats_db_name}.result_projects,
      ${stats_db_name}.project
 WHERE result_projects.id = result.id
   AND result.type = 'publication'
-  AND project.id = result_projects.project; -- /*EOS*/
\ No newline at end of file
+  AND project.id = result_projects.project; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
index 163e92415..9bbf94480 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
@@ -66,4 +66,4 @@ DROP TABLE IF EXISTS ${stats_db_name}.result_accessroute purge; /*EOS*/
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_accessroute STORED AS PARQUET as
 select distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result
     lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute
-WHERE datainfo.deletedbyinference=false and datainfo.invisible = FALSE;
+WHERE datainfo.deletedbyinference=false and datainfo.invisible = FALSE; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index 6cab86a41..1323adf80 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -135,9 +135,9 @@ with
     lvl4 as (select id, topic from ${stats_db_name}.result_topics where topic like '________ %' and type='Fields of Science and Technology classification')
 select /*+ COALESCE(100) */ lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3, lvl4.topic as lvl4
 from lvl1
- join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)
- join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4)
- join lvl4 on lvl4.id=lvl1.id and substr(lvl4.topic, 1, 6)=substr(lvl3.topic, 1, 6);
+    join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)
+    join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4)
+    join lvl4 on lvl4.id=lvl1.id and substr(lvl4.topic, 1, 6)=substr(lvl3.topic, 1, 6); /*EOS*/
 
 
 DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index d0b6abad9..b15efac4a 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -41,31 +41,31 @@ DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; /*EOS*/
 CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, langs.languages AS language
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages
-where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; -- /*EOS*/
+where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; -- /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS
 SELECT substr(d.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids
-where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; -- /*EOS*/
+where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
 
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; -- /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS
 SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
 FROM ${openaire_db_name}.relation r
-WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; -- /*EOS*/
+WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; /*EOS*/
 
 -- datasource sources:
 -- where the datasource info have been collected from.
-DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; -- /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS
 select substr(d.id, 4) as id, substr(cf.key, 4) as datasource
 from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf
-where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; -- /*EOS*/
+where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
 SELECT datasource AS id, id AS result
-FROM ${stats_db_name}.result_datasources; -- /*EOS*/
+FROM ${stats_db_name}.result_datasources; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index d6fc864c3..8422af4c9 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -307,7 +307,7 @@
         <error to="Kill"/>
     </action>
 
-<!--    <action name="Step8">
+    <action name="Step8">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
@@ -315,29 +315,18 @@
             <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
             <jar>dhp-stats-update-${projectVersion}.jar</jar>
             <spark-opts>
-                &#45;&#45;conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
                 ${sparkClusterOpts}
                 ${sparkResourceOpts}
                 ${sparkApplicationOpts}
             </spark-opts>
-            <arg>&#45;&#45;hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
-            <arg>&#45;&#45;sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql</arg>
-            <arg>&#45;&#45;stats_db_name</arg><arg>${stats_db_name}</arg>
-            <arg>&#45;&#45;openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
         </spark>
         <ok to="Step9"/>
         <error to="Kill"/>
-    </action>-->
-
-    <action name="Step8">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step8.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-        </hive2>
-        <ok to="Step9"/>
-        <error to="Kill"/>
     </action>
 
     <action name="Step9">
@@ -381,12 +370,11 @@
             <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
             <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
-<!--        <ok to="Step11"/>-->
-        <ok to="End"/>
+        <ok to="Step11"/>
         <error to="Kill"/>
     </action>
 
-<!--    <action name="Step11">
+    <action name="Step11">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
@@ -394,31 +382,19 @@
             <class>eu.dnetlib.dhp.oozie.RunSQLSparkJob</class>
             <jar>dhp-stats-update-${projectVersion}.jar</jar>
             <spark-opts>
-                &#45;&#45;conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
                 ${sparkClusterOpts}
                 ${sparkResourceOpts}
                 ${sparkApplicationOpts}
             </spark-opts>
-            <arg>&#45;&#45;hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
-            <arg>&#45;&#45;sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql</arg>
-            <arg>&#45;&#45;stats_db_name</arg><arg>${stats_db_name}</arg>
-            <arg>&#45;&#45;openaire_db_name</arg><arg>${openaire_db_name}</arg>
-            <arg>&#45;&#45;external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--sql</arg><arg>eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step11.sql</arg>
+            <arg>--stats_db_name</arg><arg>${stats_db_name}</arg>
+            <arg>--openaire_db_name</arg><arg>${openaire_db_name}</arg>
+            <arg>--external_stats_db_name</arg><arg>${external_stats_db_name}</arg>
         </spark>
         <ok to="Step12"/>
         <error to="Kill"/>
-    </action>-->
-
-    <action name="Step11">
-        <hive2 xmlns="uri:oozie:hive2-action:0.1">
-            <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/step11.sql</script>
-            <param>stats_db_name=${stats_db_name}</param>
-            <param>openaire_db_name=${openaire_db_name}</param>
-            <param>external_stats_db_name=${external_stats_db_name}</param>
-        </hive2>
-        <ok to="Step12"/>
-        <error to="Kill"/>
     </action>
 
     <action name="Step12">
@@ -533,7 +509,7 @@
     </action>
 
     <action name="Contexts">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>contexts.sh</exec>
@@ -624,7 +600,7 @@
     </action>
 
     <action name="Step19-finalize">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>finalizedb.sh</exec>
@@ -637,7 +613,7 @@
     </action>
 
     <action name="step20-createMonitorDB">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>monitor.sh</exec>
@@ -670,7 +646,7 @@
     <!--    </action>-->
 
     <action name="step21-createObservatoryDB-pre">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>observatory-pre.sh</exec>
@@ -706,7 +682,7 @@
     </action>
 
     <action name="step21-createObservatoryDB-post">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>observatory-post.sh</exec>
@@ -719,7 +695,7 @@
     </action>
 
     <action name="step22-copyDataToImpalaCluster">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>copyDataToImpalaCluster.sh</exec>
@@ -738,7 +714,7 @@
     </action>
 
     <action name="step22a-createPDFsAggregated">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>createPDFsAggregated.sh</exec>
@@ -754,7 +730,7 @@
     </action>
 
     <action name="step23-finalizeImpalaCluster">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>finalizeImpalaCluster.sh</exec>
@@ -773,7 +749,7 @@
     </action>
 
     <action name="Step24-updateCache">
-        <shell xmlns="uri:oozie:shell-action:0.1">
+        <shell xmlns="uri:oozie:shell-action:0.3">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <exec>updateCache.sh</exec>

From 7b7dd32ad5e4eb08d995ae04dc909b87eed01875 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 3 Jul 2024 19:53:24 +0300
Subject: [PATCH 054/239] - Fix placement of some "set
 mapred.job.queue.name=analytics" statements and remove their unused "/*EOS*/"
 indicator. - Add stacktrace-info to failed actions.

---
 .../stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql    | 4 ++--
 .../oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql     | 4 ++--
 .../stats/oozie_app/scripts/step20-createMonitorDB_funded.sql | 4 ++--
 .../oozie_app/scripts/step20-createMonitorDB_institutions.sql | 4 ++--
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 2 ++
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql | 2 +-
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml      | 3 ++-
 7 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql
index 9dab79222..0f3dc1d4f 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs.sql
@@ -1,7 +1,7 @@
+set mapred.job.queue.name=analytics;
+
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
-set mapred.job.queue.name=analytics; /*EOS*/
-
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql
index c6ef15d45..2a082c2cd 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_RIs_tail.sql
@@ -1,7 +1,7 @@
+set mapred.job.queue.name=analytics;
+
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
-set mapred.job.queue.name=analytics; /*EOS*/
-
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql
index 8e3db49ff..759843d68 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_funded.sql
@@ -1,7 +1,7 @@
+set mapred.job.queue.name=analytics;
+
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
-set mapred.job.queue.name=analytics; /*EOS*/
-
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
index 286ffe427..118ccddac 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
@@ -1,7 +1,7 @@
+set mapred.job.queue.name=analytics;
+
 drop database if exists TARGET cascade;
 create database if not exists TARGET;
-set mapred.job.queue.name=analytics; /*EOS*/
-
 
 create table TARGET.result stored as parquet as
     select distinct * from (
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index 1323adf80..0717d7897 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -139,6 +139,8 @@ from lvl1
     join lvl3 on lvl3.id=lvl1.id and substr(lvl3.topic, 1, 4)=substr(lvl2.topic, 1, 4)
     join lvl4 on lvl4.id=lvl1.id and substr(lvl4.topic, 1, 6)=substr(lvl3.topic, 1, 6); /*EOS*/
 
+DROP TABLE ${stats_db_name}.result_fos_base_tmp purge; /*EOS*/
+
 
 DROP TABLE IF EXISTS ${stats_db_name}.result_organization purge; /*EOS*/
 
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index b15efac4a..9a3995a8f 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -67,5 +67,5 @@ from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfro
 where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
-SELECT datasource AS id, id AS result
+SELECT /*+ COALESCE(100) */ datasource AS id, id AS result
 FROM ${stats_db_name}.result_datasources; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index 8422af4c9..d08cf8f59 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -150,7 +150,8 @@
     </decision>
 
     <kill name="Kill">
-        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}
+            ${wf:actionData(wf:lastErrorNode())['stackTrace']}]</message>
     </kill>
 
     <action name="Step1">

From ce0aee21cce147911d8e3cdc7c5d3c6606cfb012 Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 3 Jul 2024 20:15:33 +0300
Subject: [PATCH 055/239] Improve performance of transferring the stats-DBs to
 another cluster and querying the DBs' tables, by ordering Spark to create up
 to 100 files per table, instead of thousands.

---
 .../graph/stats/oozie_app/scripts/step13.sql  |  16 +-
 .../graph/stats/oozie_app/scripts/step14.sql  |  17 +-
 .../graph/stats/oozie_app/scripts/step15.sql  |  12 +-
 .../stats/oozie_app/scripts/step15_5.sql      |  10 +-
 .../scripts/step16-createIndicatorsTables.sql | 182 +++++++++---------
 .../scripts/step16_1-definitions.sql          |   6 +-
 .../scripts/step21-createObservatoryDB.sql    |  38 ++--
 .../graph/stats/oozie_app/scripts/step8.sql   |  10 +-
 8 files changed, 145 insertions(+), 146 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
index 20784bce9..a590c190e 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql
@@ -10,7 +10,7 @@ set mapred.job.queue.name=analytics; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.publication_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_sources STORED AS PARQUET as
-SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
+SELECT /*+ COALESCE(100) */ p.id, case when d.id is null then 'other' else p.datasource end as datasource
 FROM (
     SELECT  substr(p.id, 4) as id, substr(datasource, 4) as datasource 
 from ${openaire_db_name}.publication p lateral view explode(p.collectedfrom.key) c as datasource) p 
@@ -23,7 +23,7 @@ LEFT OUTER JOIN
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_sources STORED AS PARQUET as
-SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
+SELECT /*+ COALESCE(100) */ p.id, case when d.id is null then 'other' else p.datasource end as datasource
 FROM (
     SELECT  substr(p.id, 4) as id, substr(datasource, 4) as datasource 
 from ${openaire_db_name}.dataset p lateral view explode(p.collectedfrom.key) c as datasource) p 
@@ -36,7 +36,7 @@ LEFT OUTER JOIN
 DROP TABLE IF EXISTS ${stats_db_name}.software_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_sources STORED AS PARQUET as
-SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
+SELECT /*+ COALESCE(100) */ p.id, case when d.id is null then 'other' else p.datasource end as datasource
 FROM (
     SELECT  substr(p.id, 4) as id, substr(datasource, 4) as datasource 
 from ${openaire_db_name}.software p lateral view explode(p.collectedfrom.key) c as datasource) p 
@@ -49,7 +49,7 @@ LEFT OUTER JOIN
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_sources STORED AS PARQUET as
-SELECT p.id, case when d.id is null then 'other' else p.datasource end as datasource 
+SELECT /*+ COALESCE(100) */ p.id, case when d.id is null then 'other' else p.datasource end as datasource
 FROM (
     SELECT  substr(p.id, 4) as id, substr(datasource, 4) as datasource 
 from ${openaire_db_name}.otherresearchproduct p lateral view explode(p.collectedfrom.key) c as datasource) p 
@@ -71,7 +71,7 @@ SELECT * FROM ${stats_db_name}.otherresearchproduct_sources; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.result_orcid purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_orcid STORED AS PARQUET as
-select distinct res.id, upper(regexp_replace(res.orcid, 'http://orcid.org/' ,'')) as orcid
+select /*+ COALESCE(100) */ distinct res.id, upper(regexp_replace(res.orcid, 'http://orcid.org/' ,'')) as orcid
 from (
     SELECT substr(res.id, 4) as id, auth_pid.value as orcid
     FROM ${openaire_db_name}.result res
@@ -83,7 +83,7 @@ from (
 DROP TABLE IF EXISTS ${stats_db_name}.result_result purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_result stored as parquet as
-select substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype
+select /*+ COALESCE(100) */ substr(rel.source, 4) as source, substr(rel.target, 4) as target, relclass, subreltype
 from ${openaire_db_name}.relation rel
 join ${openaire_db_name}.result r1 on rel.source=r1.id
 join ${openaire_db_name}.result r2 on r2.id=rel.target
@@ -98,7 +98,7 @@ where reltype='resultResult'
 DROP TABLE IF EXISTS ${stats_db_name}.result_citations_oc purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_citations_oc stored as parquet as
-select substr(target, 4) as id, count(distinct substr(source, 4)) as citations
+select /*+ COALESCE(100) */ substr(target, 4) as id, count(distinct substr(source, 4)) as citations
 from ${openaire_db_name}.relation rel
 join ${openaire_db_name}.result r1 on rel.source=r1.id
 join ${openaire_db_name}.result r2 on r2.id=rel.target
@@ -115,7 +115,7 @@ group by substr(target, 4); /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.result_references_oc purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_references_oc stored as parquet as
-select substr(source, 4) as id, count(distinct substr(target, 4)) as references
+select /*+ COALESCE(100) */ substr(source, 4) as id, count(distinct substr(target, 4)) as references
 from ${openaire_db_name}.relation rel
          join ${openaire_db_name}.result r1 on rel.source=r1.id
          join ${openaire_db_name}.result r2 on r2.id=rel.target
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
index 9bbf94480..9e71b88f5 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step14.sql
@@ -1,4 +1,5 @@
 set mapred.job.queue.name=analytics; /*EOS*/
+
 ------------------------------------------------------
 ------------------------------------------------------
 -- Additional relations
@@ -9,28 +10,28 @@ set mapred.job.queue.name=analytics; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.publication_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.publication_licenses STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, licenses.value as type
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, licenses.value as type
 from ${openaire_db_name}.publication p LATERAL VIEW explode(p.instance.license) instances as licenses
 where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.dataset_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.dataset_licenses STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, licenses.value as type 
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, licenses.value as type
 from ${openaire_db_name}.dataset p LATERAL VIEW explode(p.instance.license) instances as licenses
 where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.software_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.software_licenses STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, licenses.value as type 
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, licenses.value as type
 from ${openaire_db_name}.software p LATERAL VIEW explode(p.instance.license) instances as licenses
 where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.otherresearchproduct_licenses purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.otherresearchproduct_licenses STORED AS PARQUET AS
-SELECT substr(p.id, 4) as id, licenses.value as type 
+SELECT /*+ COALESCE(100) */ substr(p.id, 4) as id, licenses.value as type
 from ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.instance.license) instances as licenses
 where licenses.value is not null and licenses.value != '' and p.datainfo.deletedbyinference=false and p.datainfo.invisible = FALSE; /*EOS*/
 
@@ -46,15 +47,15 @@ SELECT * FROM ${stats_db_name}.otherresearchproduct_licenses; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.organization_pids purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_pids STORED AS PARQUET AS
-select substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid 
+select /*+ COALESCE(100) */ substr(o.id, 4) as id, ppid.qualifier.classname as type, ppid.value as pid
 from ${openaire_db_name}.organization o lateral view explode(o.pid) pids as ppid; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.organization_sources purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.organization_sources STORED AS PARQUET as
-SELECT o.id, case when d.id is null then 'other' else o.datasource end as datasource 
+SELECT /*+ COALESCE(100) */ o.id, case when d.id is null then 'other' else o.datasource end as datasource
 FROM (
-    SELECT  substr(o.id, 4) as id, substr(instances.instance.key, 4) as datasource 
+    SELECT substr(o.id, 4) as id, substr(instances.instance.key, 4) as datasource
     from ${openaire_db_name}.organization o lateral view explode(o.collectedfrom) instances as instance) o 
     LEFT OUTER JOIN (
         SELECT substr(d.id, 4) id 
@@ -64,6 +65,6 @@ FROM (
 DROP TABLE IF EXISTS ${stats_db_name}.result_accessroute purge; /*EOS*/
 
 CREATE TABLE IF NOT EXISTS ${stats_db_name}.result_accessroute STORED AS PARQUET as
-select distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result
+select /*+ COALESCE(100) */ distinct substr(id,4) as id, accessroute from ${openaire_db_name}.result
     lateral view explode (instance.accessright.openaccessroute) openaccessroute as accessroute
 WHERE datainfo.deletedbyinference=false and datainfo.invisible = FALSE; /*EOS*/
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
index 1f3027b7d..08609afff 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15.sql
@@ -18,7 +18,7 @@ non_peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
     from ${openaire_db_name}.publication r lateral view explode(r.instance) instances as inst
     where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
-select distinct *
+select /*+ COALESCE(100) */ distinct *
 from (
     select peer_reviewed.* from peer_reviewed
     union all
@@ -36,7 +36,7 @@ non_peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
     from ${openaire_db_name}.dataset r lateral view explode(r.instance) instances as inst
     where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
-select distinct *
+select /*+ COALESCE(100) */ distinct *
 from (
     select peer_reviewed.* from peer_reviewed
     union all
@@ -54,7 +54,7 @@ non_peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
     from ${openaire_db_name}.software r lateral view explode(r.instance) instances as inst
     where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
-select distinct *
+select /*+ COALESCE(100) */ distinct *
 from (
     select peer_reviewed.* from peer_reviewed
     union all
@@ -72,7 +72,7 @@ non_peer_reviewed as (
     select distinct substr(r.id, 4) as id, inst.refereed.classname as refereed
     from ${openaire_db_name}.otherresearchproduct r lateral view explode(r.instance) instances as inst
     where r.datainfo.deletedbyinference=false and r.datainfo.invisible = FALSE and inst.refereed.classname='nonPeerReviewed')
-select distinct *
+select /*+ COALESCE(100) */ distinct *
 from (
     select peer_reviewed.* from peer_reviewed
     union all
@@ -92,7 +92,7 @@ select * from ${stats_db_name}.otherresearchproduct_refereed; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.indi_impact_measures purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_impact_measures STORED AS PARQUET as
-select substr(id, 4) as id, measures_ids.id impactmetric, cast(measures_ids.unit.value[0] as double) score,
+select /*+ COALESCE(100) */ substr(id, 4) as id, measures_ids.id impactmetric, cast(measures_ids.unit.value[0] as double) score,
 cast(measures_ids.unit.value[0] as decimal(6,3)) score_dec, measures_ids.unit.value[1] impact_class
 from ${openaire_db_name}.result lateral view explode(measures) measures as measures_ids
 where measures_ids.id!='views' and measures_ids.id!='downloads'; /*EOS*/
@@ -100,7 +100,7 @@ where measures_ids.id!='views' and measures_ids.id!='downloads'; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.result_apc_affiliations purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_apc_affiliations STORED AS PARQUET as
-select distinct substr(rel.target,4) id, substr(rel.source,4) organization, o.legalname.value name,
+select /*+ COALESCE(100) */ distinct substr(rel.target,4) id, substr(rel.source,4) organization, o.legalname.value name,
 cast(rel.properties[0].value as double) apc_amount,
 rel.properties[1].value apc_currency
 from ${openaire_db_name}.relation rel
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
index d18cf569f..d61b4d2ef 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql
@@ -6,7 +6,7 @@ set mapred.job.queue.name=analytics; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.result_projectcount purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_projectcount STORED AS PARQUET as
-select r.id, count(distinct p.id) as count
+select /*+ COALESCE(100) */ r.id, count(distinct p.id) as count
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
 left outer join ${stats_db_name}.project p on p.id=rp.project
@@ -15,7 +15,7 @@ group by r.id; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.result_fundercount purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_fundercount STORED AS PARQUET as
-select r.id, count(distinct p.funder) as count
+select /*+ COALESCE(100) */ r.id, count(distinct p.funder) as count
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.result_projects rp on rp.id=r.id
 left outer join ${stats_db_name}.project p on p.id=rp.project
@@ -30,7 +30,7 @@ with rcount as (
     left outer join ${stats_db_name}.result_projects rp on rp.project=p.id
     left outer join ${stats_db_name}.result r on r.id=rp.id
     group by r.type, p.id )
-select rcount.pid, sum(case when rcount.type='publication' then rcount.count else 0 end) as publications,
+select /*+ COALESCE(100) */ rcount.pid, sum(case when rcount.type='publication' then rcount.count else 0 end) as publications,
     sum(case when rcount.type='dataset' then rcount.count else 0 end) as datasets,
     sum(case when rcount.type='software' then rcount.count else 0 end) as software,
     sum(case when rcount.type='other' then rcount.count else 0 end) as other
@@ -48,7 +48,7 @@ create or replace view ${stats_db_name}.graduatedoctorates as select * from stat
 DROP TABLE IF EXISTS ${stats_db_name}.result_instance purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_instance stored as parquet as
-select distinct r.*
+select /*+ COALESCE(100) */ distinct r.*
 from (
          select substr(r.id, 4) as id, inst.accessright.classname as accessright, inst.accessright.openaccessroute as accessright_uw, substr(inst.collectedfrom.key, 4) as collectedfrom,
                 substr(inst.hostedby.key, 4) as hostedby, inst.dateofacceptance.value as dateofacceptance, inst.license.value as license, p.qualifier.classname as pidtype, p.value as pid
@@ -58,7 +58,7 @@ join ${stats_db_name}.result res on res.id=r.id; /*EOS*/
 DROP TABLE IF EXISTS ${stats_db_name}.result_apc purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.result_apc STORED AS PARQUET as
-select distinct r.id, r.amount, r.currency
+select /*+ COALESCE(100) */ distinct r.id, r.amount, r.currency
 from (
          select substr(r.id, 4) as id, cast(inst.processingchargeamount.value as float) as amount, inst.processingchargecurrency.value as currency
          from ${openaire_db_name}.result r lateral view explode(r.instance) instances as inst) r
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
index 562487474..6e7f00b53 100755
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql
@@ -1,7 +1,7 @@
 -- Sprint 1 ----
 drop table if exists ${stats_db_name}.indi_pub_green_oa purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_green_oa stored as parquet as
-select distinct p.id, coalesce(green_oa, 0) as green_oa
+select /*+ COALESCE(100) */ distinct p.id, coalesce(green_oa, 0) as green_oa
 from ${stats_db_name}.publication p
 left outer join (
     select p.id, 1 as green_oa
@@ -12,7 +12,7 @@ left outer join (
 
 drop table if exists ${stats_db_name}.indi_pub_grey_lit purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_grey_lit stored as parquet as
-select distinct p.id, coalesce(grey_lit, 0) as grey_lit
+select /*+ COALESCE(100) */ distinct p.id, coalesce(grey_lit, 0) as grey_lit
 from ${stats_db_name}.publication p
 left outer join (
     select p.id, 1 as grey_lit
@@ -23,7 +23,7 @@ left outer join (
 
 drop table if exists ${stats_db_name}.indi_pub_doi_from_crossref purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_doi_from_crossref stored as parquet as
-select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref
+select /*+ COALESCE(100) */ distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref
 from ${stats_db_name}.publication p
 left outer join (
     select ri.id, 1 as doi_from_crossref from ${stats_db_name}.result_instance ri
@@ -33,7 +33,7 @@ left outer join (
 -- Sprint 2 ----
 drop table if exists ${stats_db_name}.indi_result_has_cc_licence purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_result_has_cc_licence stored as parquet as
-select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
+select /*+ COALESCE(100) */ distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
 from ${stats_db_name}.result r
 left outer join (
     select r.id, license.type as lic from ${stats_db_name}.result r
@@ -42,7 +42,7 @@ left outer join (
 
 drop table if exists ${stats_db_name}.indi_result_has_cc_licence_url purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_result_has_cc_licence_url stored as parquet as
-select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url
+select /*+ COALESCE(100) */ distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url
 from ${stats_db_name}.result r
 left outer join (
     select r.id, lower(parse_url(license.type, "HOST")) as lic_host
@@ -52,12 +52,12 @@ left outer join (
 
 drop table if exists ${stats_db_name}.indi_pub_has_abstract purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_has_abstract stored as parquet as
-select distinct publication.id, cast(coalesce(abstract, true) as int) has_abstract
+select /*+ COALESCE(100) */ distinct publication.id, cast(coalesce(abstract, true) as int) has_abstract
 from ${stats_db_name}.publication; /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_result_with_orcid purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_result_with_orcid stored as parquet as
-select distinct r.id, coalesce(has_orcid, 0) as has_orcid
+select /*+ COALESCE(100) */ distinct r.id, coalesce(has_orcid, 0) as has_orcid
 from ${stats_db_name}.result r
 left outer join (
     select id, 1 as has_orcid from ${stats_db_name}.result_orcid) tmp on r.id= tmp.id; /*EOS*/
@@ -66,7 +66,7 @@ left outer join (
 ---- Sprint 3 ----
 drop table if exists ${stats_db_name}.indi_funded_result_with_fundref purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_funded_result_with_fundref stored as parquet as
-select distinct r.result as id, coalesce(fundref, 0) as fundref
+select /*+ COALESCE(100) */ distinct r.result as id, coalesce(fundref, 0) as fundref
 from ${stats_db_name}.project_results r
 left outer join (
     select distinct result, 1 as fundref from ${stats_db_name}.project_results where provenance='Harvested') tmp on r.result= tmp.result; /*EOS*/
@@ -77,7 +77,7 @@ create table if not exists ${stats_db_name}.indi_result_org_collab stored as par
         SELECT ro.organization organization, ro.id, o.name
         from ${stats_db_name}.result_organization ro
         join ${stats_db_name}.organization o on o.id=ro.organization where o.name is not null)
-    select o1.organization org1, o1.name org1name1, o2.organization org2, o2.name org2name2, count(o1.id) as collaborations
+    select /*+ COALESCE(100) */ o1.organization org1, o1.name org1name1, o2.organization org2, o2.name org2name2, count(o1.id) as collaborations
     from tmp as o1
     join tmp as o2 where o1.id=o2.id and o1.organization!=o2.organization and o1.name!=o2.name
     group by o1.organization, o2.organization, o1.name, o2.name; /*EOS*/
@@ -89,7 +89,7 @@ create table if not exists ${stats_db_name}.indi_result_org_country_collab store
         from ${stats_db_name}.result_organization ro
         join ${stats_db_name}.organization o on o.id=ro.organization
         where country <> 'UNKNOWN'  and o.name is not null)
-    select o1.organization org1,o1.name org1name1, o2.country country2, count(o1.id) as collaborations
+    select /*+ COALESCE(100) */ o1.organization org1,o1.name org1name1, o2.country country2, count(o1.id) as collaborations
     from tmp as o1 join tmp as o2 on o1.id=o2.id
     where o1.id=o2.id and o1.country!=o2.country
     group by o1.organization, o1.id, o1.name, o2.country; /*EOS*/
@@ -100,7 +100,7 @@ create table if not exists ${stats_db_name}.indi_project_collab_org stored as pa
         select o.id organization, o.name, ro.project as project
         from ${stats_db_name}.organization o
         join ${stats_db_name}.organization_projects ro on o.id=ro.id  where o.name is not null)
-    select o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations
+    select /*+ COALESCE(100) */ o1.organization org1,o1.name orgname1, o2.organization org2, o2.name orgname2, count(distinct o1.project) as collaborations
     from tmp as o1
     join tmp as o2 on o1.project=o2.project
     where o1.organization<>o2.organization and o1.name<>o2.name
@@ -112,7 +112,7 @@ create table if not exists ${stats_db_name}.indi_project_collab_org_country stor
         select o.id organization, o.name, o.country , ro.project as project
         from ${stats_db_name}.organization o
         join ${stats_db_name}.organization_projects ro on o.id=ro.id and o.country <> 'UNKNOWN' and o.name is not null)
-    select o1.organization org1,o1.name org1name, o2.country country2, count(distinct o1.project) as collaborations
+    select /*+ COALESCE(100) */ o1.organization org1,o1.name org1name, o2.country country2, count(distinct o1.project) as collaborations
     from tmp as o1
     join tmp as o2 on o1.project=o2.project
     where o1.organization<>o2.organization and o1.country<>o2.country
@@ -124,7 +124,7 @@ create table if not exists ${stats_db_name}.indi_funder_country_collab stored as
         join ${stats_db_name}.organization o on o.id=op.id
         join ${stats_db_name}.project p on p.id=op.project
         where country <> 'UNKNOWN')
-    select f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations
+    select /*+ COALESCE(100) */ f1.funder, f1.country as country1, f2.country as country2, count(distinct f1.project) as collaborations
     from tmp as f1
     join tmp as f2 on f1.project=f2.project
     where f1.country<>f2.country
@@ -136,7 +136,7 @@ create table if not exists ${stats_db_name}.indi_result_country_collab stored as
         select distinct country, ro.id as result  from ${stats_db_name}.organization o
         join ${stats_db_name}.result_organization ro on o.id=ro.organization
         where country <> 'UNKNOWN' and o.name is not null)
-    select o1.country country1, o2.country country2, count(o1.result) as collaborations
+    select /*+ COALESCE(100) */ o1.country country1, o2.country country2, count(o1.result) as collaborations
     from tmp as o1
     join tmp as o2 on o1.result=o2.result
     where o1.country<>o2.country
@@ -146,7 +146,7 @@ create table if not exists ${stats_db_name}.indi_result_country_collab stored as
 ---- Sprint 4 ----
 drop table if exists ${stats_db_name}.indi_pub_diamond purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet as
-    select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
+    select /*+ COALESCE(100) */ distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal
     from ${stats_db_name}.publication_datasources pd
     left outer join (
         select pd.id, 1 as in_diamond_journal
@@ -157,7 +157,7 @@ create table if not exists ${stats_db_name}.indi_pub_diamond stored as parquet a
 
 drop table if exists ${stats_db_name}.indi_pub_in_transformative purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_in_transformative stored as parquet as
-    select distinct pd.id, coalesce(is_transformative, 0) as is_transformative
+    select /*+ COALESCE(100) */ distinct pd.id, coalesce(is_transformative, 0) as is_transformative
     from ${stats_db_name}.publication pd
     left outer join (
         select  pd.id, 1 as is_transformative
@@ -168,7 +168,7 @@ create table if not exists ${stats_db_name}.indi_pub_in_transformative stored as
 
 drop table if exists ${stats_db_name}.indi_pub_closed_other_open purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_closed_other_open stored as parquet as
-    select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open
+    select /*+ COALESCE(100) */ distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open
     from ${stats_db_name}.result_instance ri
     left outer join (
         select ri.id, 1 as pub_closed_other_open
@@ -182,14 +182,14 @@ create table if not exists ${stats_db_name}.indi_pub_closed_other_open stored as
 ---- Sprint 5 ----
 drop table if exists ${stats_db_name}.indi_result_no_of_copies purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_result_no_of_copies stored as parquet as
-    select id, count(id) as number_of_copies
+    select /*+ COALESCE(100) */ id, count(id) as number_of_copies
     from ${stats_db_name}.result_instance
     group by id; /*EOS*/
 
 ---- Sprint 6 ----
 drop table if exists ${stats_db_name}.indi_pub_downloads purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_downloads stored as parquet as
-    SELECT result_id, sum(downloads) no_downloads
+    SELECT /*+ COALESCE(100) */ result_id, sum(downloads) no_downloads
     from openaire_prod_usage_stats.usage_stats
     join ${stats_db_name}.publication on result_id=id
     where downloads>0
@@ -197,7 +197,7 @@ create table if not exists ${stats_db_name}.indi_pub_downloads stored as parquet
 
 drop table if exists ${stats_db_name}.indi_pub_downloads_datasource purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_downloads_datasource stored as parquet as
-    SELECT result_id, repository_id, sum(downloads) no_downloads
+    SELECT /*+ COALESCE(100) */ result_id, repository_id, sum(downloads) no_downloads
     from openaire_prod_usage_stats.usage_stats
     join ${stats_db_name}.publication on result_id=id
     where downloads>0
@@ -205,14 +205,14 @@ create table if not exists ${stats_db_name}.indi_pub_downloads_datasource stored
 
 drop table if exists ${stats_db_name}.indi_pub_downloads_year purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_downloads_year stored as parquet as
-    SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, sum(downloads) no_downloads
+    SELECT /*+ COALESCE(100) */ result_id, cast(substring(us.`date`, 1,4) as int) as `year`, sum(downloads) no_downloads
     from openaire_prod_usage_stats.usage_stats us
     join ${stats_db_name}.publication on result_id=id where downloads>0
     GROUP BY result_id, substring(us.`date`, 1,4); /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_pub_downloads_datasource_year purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_downloads_datasource_year stored as parquet as
-    SELECT result_id, cast(substring(us.`date`, 1,4) as int) as `year`, repository_id, sum(downloads) no_downloads
+    SELECT /*+ COALESCE(100) */ result_id, cast(substring(us.`date`, 1,4) as int) as `year`, repository_id, sum(downloads) no_downloads
     from openaire_prod_usage_stats.usage_stats us
     join ${stats_db_name}.publication on result_id=id
     where downloads>0
@@ -241,7 +241,7 @@ create table if not exists ${stats_db_name}.indi_pub_gold_oa stored as parquet a
             UNION ALL
             select id, issn_online as issn from ${stats_db_name}.datasource d left semi join gold_oa on gold_oa.issn=d.issn_online) foo
     )
-    SELECT DISTINCT pd.id, coalesce(is_gold, 0) as is_gold
+    SELECT /*+ COALESCE(100) */ DISTINCT pd.id, coalesce(is_gold, 0) as is_gold
     FROM ${stats_db_name}.publication pd
     left outer join (
             select pd.id, 1 as is_gold
@@ -272,7 +272,7 @@ create table if not exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc stored as
         FROM ${stats_db_name}.datasource
         WHERE issn_online IS NOT NULL ) as issn
         WHERE LENGTH(issn) > 7)
-    SELECT DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa
+    SELECT /*+ COALESCE(100) */ DISTINCT pd.id, coalesce(is_hybrid_oa, 0) as is_hybrid_oa
     FROM ${stats_db_name}.publication_datasources pd
     LEFT OUTER JOIN (
         SELECT pd.id, 1 as is_hybrid_oa from ${stats_db_name}.publication_datasources pd
@@ -284,7 +284,7 @@ create table if not exists ${stats_db_name}.indi_pub_hybrid_oa_with_cc stored as
 
 drop table if exists ${stats_db_name}.indi_pub_hybrid purge; /*EOS*/
 create table if not exists ${stats_db_name}.indi_pub_hybrid stored as parquet as
-select distinct p.id, coalesce(is_hybrid, 0) is_hybrid
+select /*+ COALESCE(100) */ distinct p.id, coalesce(is_hybrid, 0) is_hybrid
 from ${stats_db_name}.publication p
 left outer join (
     select p.id, 1 as is_hybrid
@@ -313,7 +313,7 @@ create table if not exists ${stats_db_name}.indi_org_fairness stored as parquet
         where  cast(year as int)>2003
         group by ro.organization)
 --return results_fair/all_results
-    select allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
+    select /*+ COALESCE(100) */ allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
     from allresults
     join result_fair on result_fair.organization=allresults.organization; /*EOS*/
 
@@ -336,7 +336,7 @@ select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name
 drop table if exists ${stats_db_name}.indi_org_fairness_pub_pr purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_fairness_pub_pr stored as parquet as
-select ar.organization, rf.no_result_fair/ar.no_allresults org_fairness
+select /*+ COALESCE(100) */ ar.organization, rf.no_result_fair/ar.no_allresults org_fairness
 from allresults ar
          join result_fair rf on rf.organization=ar.organization; /*EOS*/
 
@@ -357,7 +357,7 @@ CREATE TEMPORARY VIEW allresults as select year, ro.organization, count(distinct
 drop table if exists ${stats_db_name}.indi_org_fairness_pub_year purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_fairness_pub_year stored as parquet as
-select cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
+select /*+ COALESCE(100) */ cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
 from allresults
          join result_fair on result_fair.organization=allresults.organization and result_fair.year=allresults.year; /*EOS*/
 
@@ -381,7 +381,7 @@ CREATE TEMPORARY VIEW allresults as
 drop table if exists ${stats_db_name}.indi_org_fairness_pub purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_fairness_pub stored as parquet as
-select ar.organization, rf.no_result_fair/ar.no_allresults org_fairness
+select /*+ COALESCE(100) */ ar.organization, rf.no_result_fair/ar.no_allresults org_fairness
 from allresults ar join result_fair rf
 on rf.organization=ar.organization; /*EOS*/
 
@@ -404,7 +404,7 @@ CREATE TEMPORARY VIEW allresults as
 drop table if exists ${stats_db_name}.indi_org_fairness_year purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_fairness_year stored as parquet as
-    select cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
+    select /*+ COALESCE(100) */ cast(allresults.year as int) year, allresults.organization, result_fair.no_result_fair/allresults.no_allresults org_fairness
     from allresults
     join result_fair on result_fair.organization=allresults.organization and cast(result_fair.year as int)=cast(allresults.year as int); /*EOS*/
 
@@ -427,7 +427,7 @@ CREATE TEMPORARY VIEW allresults as
 drop table if exists ${stats_db_name}.indi_org_findable_year purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_findable_year stored as parquet as
-select cast(allresults.year as int) year, allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable
+select /*+ COALESCE(100) */ cast(allresults.year as int) year, allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable
 from allresults
          join result_with_pid on result_with_pid.organization=allresults.organization and cast(result_with_pid.year as int)=cast(allresults.year as int); /*EOS*/
 
@@ -450,7 +450,7 @@ select ro.organization, count(distinct ro.id) no_allresults from ${stats_db_name
 drop table if exists ${stats_db_name}.indi_org_findable purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_findable stored as parquet as
-select allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable
+select /*+ COALESCE(100) */ allresults.organization, result_with_pid.no_result_with_pid/allresults.no_allresults org_findable
 from allresults
          join result_with_pid on result_with_pid.organization=allresults.organization; /*EOS*/
 
@@ -516,7 +516,7 @@ select software_oa.organization, software_oa.no_oasoftware/allsoftware.no_allsof
 drop table if exists ${stats_db_name}.indi_org_openess purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_openess stored as parquet as
-select allpubsshare.organization,
+select /*+ COALESCE(100) */ allpubsshare.organization,
        (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end)
            +(case when d is null then 0 else 1 end))
            org_openess FROM allpubsshare
@@ -593,7 +593,7 @@ select allsoftware.year, software_oa.organization, software_oa.no_oasoftware/all
 drop table if exists ${stats_db_name}.indi_org_openess_year purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_org_openess_year stored as parquet as
-select cast(allpubsshare.year as int) year, allpubsshare.organization,
+select /*+ COALESCE(100) */ cast(allpubsshare.year as int) year, allpubsshare.organization,
        (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end)
            +(case when d is null then 0 else 1 end))
            org_openess FROM allpubsshare
@@ -617,7 +617,7 @@ DROP VIEW allsoftwaresshare; /*EOS*/
 drop table if exists ${stats_db_name}.indi_pub_has_preprint purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_pub_has_preprint stored as parquet as
-select distinct p.id, coalesce(has_preprint, 0) as has_preprint
+select /*+ COALESCE(100) */ distinct p.id, coalesce(has_preprint, 0) as has_preprint
 from ${stats_db_name}.publication_classifications p
          left outer join (
     select p.id, 1 as has_preprint
@@ -627,7 +627,7 @@ from ${stats_db_name}.publication_classifications p
 drop table if exists ${stats_db_name}.indi_pub_in_subscribed purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_pub_in_subscribed stored as parquet as
-select distinct p.id, coalesce(is_subscription, 0) as is_subscription
+select /*+ COALESCE(100) */ distinct p.id, coalesce(is_subscription, 0) as is_subscription
 from ${stats_db_name}.publication p
          left outer join(
     select  p.id, 1 as is_subscription from ${stats_db_name}.publication p
@@ -640,7 +640,7 @@ from ${stats_db_name}.publication p
 drop table if exists ${stats_db_name}.indi_result_with_pid purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_result_with_pid stored as parquet as
-select distinct p.id, coalesce(result_with_pid, 0) as result_with_pid
+select /*+ COALESCE(100) */ distinct p.id, coalesce(result_with_pid, 0) as result_with_pid
 from ${stats_db_name}.result p
          left outer join (
     select p.id, 1 as result_with_pid
@@ -654,7 +654,7 @@ group by rf.id; /*EOS*/
 drop table if exists ${stats_db_name}.indi_pub_interdisciplinarity purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_pub_interdisciplinarity stored as parquet as
-select distinct p.id as id, coalesce(is_interdisciplinary, 0)
+select /*+ COALESCE(100) */ distinct p.id as id, coalesce(is_interdisciplinary, 0)
 as is_interdisciplinary
 from pub_fos_totals p
 left outer join (
@@ -666,7 +666,7 @@ drop view pub_fos_totals; /*EOS*/
 drop table if exists ${stats_db_name}.indi_pub_bronze_oa purge; /*EOS*/
 
 create table ${stats_db_name}.indi_pub_bronze_oa stored as parquet as
-select distinct p.id,coalesce(is_bronze_oa,0) is_bronze_oa
+select /*+ COALESCE(100) */ distinct p.id,coalesce(is_bronze_oa,0) is_bronze_oa
 from ${stats_db_name}.publication p
 left outer join (
     select p.id, 1 as is_bronze_oa
@@ -689,7 +689,7 @@ where p.end_year is NOT NULL and r.year is not null; /*EOS*/
 drop table if exists ${stats_db_name}.indi_is_project_result_after purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_is_project_result_after stored as parquet as
-select pry.project_id, pry.acronym, pry.result_id,
+select /*+ COALESCE(100) */ pry.project_id, pry.acronym, pry.result_id,
 coalesce(is_project_result_after, 0) as is_project_result_after
 from project_year_result_year pry
 left outer join (select pry.project_id, pry.acronym, pry.result_id, 1 as is_project_result_after
@@ -701,7 +701,7 @@ drop view project_year_result_year; /*EOS*/
 drop table if exists ${stats_db_name}.indi_is_funder_plan_s purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_is_funder_plan_s stored as parquet as
-select distinct f.id, f.name, coalesce(is_funder_plan_s, 0) as is_funder_plan_s
+select /*+ COALESCE(100) */ distinct f.id, f.name, coalesce(is_funder_plan_s, 0) as is_funder_plan_s
 from ${stats_db_name}.funder f
          left outer join (select id, name, 1 as is_funder_plan_s from ${stats_db_name}.funder
          join stats_ext.plan_s_short on c_o_alition_s_organisation_funder=name) tmp
@@ -722,7 +722,7 @@ create table if not exists ${stats_db_name}.indi_funder_fairness stored as parqu
     join ${stats_db_name}.project p on p.id=rp.project
     where  cast(year as int)>2003
     group by p.funder)
-select allresults.funder, result_fair.no_result_fair/allresults.no_allresults funder_fairness
+select /*+ COALESCE(100) */ allresults.funder, result_fair.no_result_fair/allresults.no_allresults funder_fairness
 from allresults
          join result_fair on result_fair.funder=allresults.funder; /*EOS*/
 
@@ -745,7 +745,7 @@ allresults as
     join ${stats_db_name}.result r on r.id=rc.id
     where  cast(year as int)>2003
     group by rc.ri_initiative)
-select allresults.ri_initiative, result_fair.no_result_fair/allresults.no_allresults ris_fairness
+select /*+ COALESCE(100) */ allresults.ri_initiative, result_fair.no_result_fair/allresults.no_allresults ris_fairness
 from allresults
          join result_fair on result_fair.ri_initiative=allresults.ri_initiative; /*EOS*/
 
@@ -817,16 +817,14 @@ select software_oa.funder, software_oa.no_oasoftware/allsoftware.no_allsoftware
 drop table if exists ${stats_db_name}.indi_funder_openess purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_funder_openess stored as parquet as
-select allpubsshare.funder,
-       (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end)
-           +(case when d is null then 0 else 1 end))
-           funder_openess FROM allpubsshare
-                                left outer join (select funder,d from
-    alldatasetssshare) tmp1
-                                                on tmp1.funder=allpubsshare.funder
-                                left outer join (select funder,s from
-    allsoftwaresshare) tmp2
-                                                on tmp2.funder=allpubsshare.funder; /*EOS*/
+select /*+ COALESCE(100) */ allpubsshare.funder,
+   (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end)
+       +(case when d is null then 0 else 1 end)) funder_openess
+FROM allpubsshare
+    left outer join (select funder,d from alldatasetssshare) tmp1
+        on tmp1.funder=allpubsshare.funder
+    left outer join (select funder,s from allsoftwaresshare) tmp2
+        on tmp2.funder=allpubsshare.funder; /*EOS*/
 
 DROP VIEW pubs_oa; /*EOS*/
 DROP VIEW datasets_oa; /*EOS*/
@@ -905,7 +903,7 @@ select software_oa.ri_initiative, software_oa.no_oasoftware/allsoftware.no_allso
 drop table if exists ${stats_db_name}.indi_ris_openess purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_ris_openess stored as parquet as
-select allpubsshare.ri_initiative,
+select /*+ COALESCE(100) */ allpubsshare.ri_initiative,
        (p+if(isnull(s),0,s)+if(isnull(d),0,d))/(1+(case when s is null then 0 else 1 end)
            +(case when d is null then 0 else 1 end))
 	ris_openess FROM allpubsshare
@@ -943,7 +941,7 @@ with result_findable as
     join ${stats_db_name}.project p on p.id=rp.project
     where  cast(year as int)>2003
     group by p.funder)
-select allresults.funder, result_findable.no_result_findable/allresults.no_allresults funder_findable
+select /*+ COALESCE(100) */ allresults.funder, result_findable.no_result_findable/allresults.no_allresults funder_findable
 from allresults
          join result_findable on result_findable.funder=allresults.funder; /*EOS*/
 
@@ -952,22 +950,22 @@ drop table if exists ${stats_db_name}.indi_ris_findable purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_ris_findable stored as parquet as
 with result_contexts as
-(select distinct rc.id, context.name ri_initiative from ${stats_db_name}.result_concepts rc
-join ${stats_db_name}.concept on concept.id=rc.concept
-join ${stats_db_name}.category on category.id=concept.category
-join ${stats_db_name}.context on context.id=category.context),
-result_findable as
-        (select rc.ri_initiative ri_initiative, count(distinct rc.id) no_result_findable from result_contexts rc
-    join ${stats_db_name}.result r on r.id=rc.id
-    join ${stats_db_name}.result_pids rp on rp.id=r.id
-    where cast(r.year as int)>2003
-    group by rc.ri_initiative),
-allresults as
-(select rc.ri_initiative ri_initiative, count(distinct rc.id) no_allresults from result_contexts rc
-    join ${stats_db_name}.result r on r.id=rc.id
-    where  cast(r.year as int)>2003
-    group by rc.ri_initiative)
-select allresults.ri_initiative, result_findable.no_result_findable/allresults.no_allresults ris_findable
+    (select distinct rc.id, context.name ri_initiative from ${stats_db_name}.result_concepts rc
+    join ${stats_db_name}.concept on concept.id=rc.concept
+    join ${stats_db_name}.category on category.id=concept.category
+    join ${stats_db_name}.context on context.id=category.context),
+    result_findable as
+            (select rc.ri_initiative ri_initiative, count(distinct rc.id) no_result_findable from result_contexts rc
+        join ${stats_db_name}.result r on r.id=rc.id
+        join ${stats_db_name}.result_pids rp on rp.id=r.id
+        where cast(r.year as int)>2003
+        group by rc.ri_initiative),
+    allresults as
+    (select rc.ri_initiative ri_initiative, count(distinct rc.id) no_allresults from result_contexts rc
+        join ${stats_db_name}.result r on r.id=rc.id
+        where  cast(r.year as int)>2003
+        group by rc.ri_initiative)
+select /*+ COALESCE(100) */ allresults.ri_initiative, result_findable.no_result_findable/allresults.no_allresults ris_findable
 from allresults
          join result_findable on result_findable.ri_initiative=allresults.ri_initiative; /*EOS*/
 
@@ -975,20 +973,20 @@ drop table if exists ${stats_db_name}.indi_pub_publicly_funded purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.indi_pub_publicly_funded stored as parquet as
 with org_names_pids as
-(select org.id,name, pid from ${stats_db_name}.organization org
-join ${stats_db_name}.organization_pids op on org.id=op.id),
-publicly_funded_orgs as
-(select distinct name from
-(select pf.name from stats_ext.insitutions_for_publicly_funded pf
-join ${stats_db_name}.fundref f on f.name=pf.name where f.type='government'
-union all
-select pf.name from stats_ext.insitutions_for_publicly_funded pf
-join ${stats_db_name}.project p on p.funder=pf.name
-union all
-select op.name from stats_ext.insitutions_for_publicly_funded pf
-join org_names_pids op on (op.name=pf.name or op.pid=pf.ror)
-and pf.publicly_funded='yes') foo)
-select distinct p.id, coalesce(publicly_funded, 0) as publicly_funded
+    (select org.id,name, pid from ${stats_db_name}.organization org
+    join ${stats_db_name}.organization_pids op on org.id=op.id),
+    publicly_funded_orgs as
+    (select distinct name from
+    (select pf.name from stats_ext.insitutions_for_publicly_funded pf
+    join ${stats_db_name}.fundref f on f.name=pf.name where f.type='government'
+    union all
+    select pf.name from stats_ext.insitutions_for_publicly_funded pf
+    join ${stats_db_name}.project p on p.funder=pf.name
+    union all
+    select op.name from stats_ext.insitutions_for_publicly_funded pf
+    join org_names_pids op on (op.name=pf.name or op.pid=pf.ror)
+    and pf.publicly_funded='yes') foo)
+select /*+ COALESCE(100) */ distinct p.id, coalesce(publicly_funded, 0) as publicly_funded
 from ${stats_db_name}.publication p
 left outer join (
 select distinct ro.id, 1 as publicly_funded from ${stats_db_name}.result_organization ro
@@ -997,7 +995,7 @@ join publicly_funded_orgs pfo on o.name=pfo.name) tmp on p.id=tmp.id; /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_pub_green_with_license purge; /*EOS*/
 create table ${stats_db_name}.indi_pub_green_with_license stored as parquet as
-select distinct p.id, coalesce(green_with_license, 0) as green_with_license
+select /*+ COALESCE(100) */ distinct p.id, coalesce(green_with_license, 0) as green_with_license
 from ${stats_db_name}.publication p
 left outer join (
     select distinct p.id, 1 as green_with_license from ${stats_db_name}.publication p
@@ -1008,7 +1006,7 @@ left outer join (
 drop table if exists ${stats_db_name}.result_country purge; /*EOS*/
 
 create table ${stats_db_name}.result_country stored as parquet as
-select distinct id, country
+select /*+ COALESCE(100) */ distinct id, country
 from (
     select ro.id, o.country
     from ${stats_db_name}.result_organization ro
@@ -1023,7 +1021,7 @@ where rc.country is not null; /*EOS*/
 
 drop table if exists ${stats_db_name}.indi_result_oa_with_license purge; /*EOS*/
 create table ${stats_db_name}.indi_result_oa_with_license stored as parquet as
-select distinct r.id, coalesce(oa_with_license,0) as oa_with_license
+select /*+ COALESCE(100) */ distinct r.id, coalesce(oa_with_license,0) as oa_with_license
 from ${stats_db_name}.result r
 left outer join (select distinct r.id, 1 as oa_with_license from ${stats_db_name}.result r
 join ${stats_db_name}.result_licenses rl on rl.id=r.id where r.bestlicence='Open Access') tmp on r.id=tmp.id; /*EOS*/
@@ -1031,9 +1029,9 @@ join ${stats_db_name}.result_licenses rl on rl.id=r.id where r.bestlicence='Open
 drop table if exists ${stats_db_name}.indi_result_oa_without_license purge; /*EOS*/
 create table ${stats_db_name}.indi_result_oa_without_license stored as parquet as
 with without_license as
-(select distinct id from ${stats_db_name}.indi_result_oa_with_license
-where oa_with_license=0)
-select distinct r.id, coalesce(oa_without_license,0) as oa_without_license
+    (select distinct id from ${stats_db_name}.indi_result_oa_with_license
+    where oa_with_license=0)
+select /*+ COALESCE(100) */ distinct r.id, coalesce(oa_without_license,0) as oa_without_license
 from ${stats_db_name}.result r
 left outer join (select distinct r.id, 1 as oa_without_license
 from ${stats_db_name}.result r
@@ -1044,7 +1042,7 @@ drop table if exists ${stats_db_name}.indi_result_under_transformative purge; /*
 create table ${stats_db_name}.indi_result_under_transformative stored as parquet as
 with transformative_dois as (
     select distinct doi from stats_ext.transformative_facts)
-select distinct r.id, coalesce(under_transformative,0) as under_transformative
+select /*+ COALESCE(100) */ distinct r.id, coalesce(under_transformative,0) as under_transformative
 from ${stats_db_name}.result r
 left outer join (
     select distinct rp.id, 1 as under_transformative
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
index 0da4394c8..80256e2df 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16_1-definitions.sql
@@ -8,7 +8,7 @@ set mapred.job.queue.name=analytics; /*EOS*/
 drop table if exists ${stats_db_name}.result_peerreviewed purge; /*EOS*/
 
 create table IF NOT EXISTS ${stats_db_name}.result_peerreviewed STORED AS PARQUET as
-select r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed
+select /*+ COALESCE(100) */ r.id as id, case when doi.doi_from_crossref=1 and grey.grey_lit=0 then true else false end as peer_reviewed
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.indi_pub_doi_from_crossref doi on doi.id=r.id
 left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; /*EOS*/
@@ -17,7 +17,7 @@ left outer join ${stats_db_name}.indi_pub_grey_lit grey on grey.id=r.id; /*EOS*/
 drop table if exists ${stats_db_name}.result_greenoa purge; /*EOS*/
 
 create table IF NOT EXISTS ${stats_db_name}.result_greenoa STORED AS PARQUET as
-select r.id, case when green.green_oa=1 then true else false end as green
+select /*+ COALESCE(100) */ r.id, case when green.green_oa=1 then true else false end as green
 from ${stats_db_name}.result r
 left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; /*EOS*/
 
@@ -25,6 +25,6 @@ left outer join ${stats_db_name}.indi_pub_green_oa green on green.id=r.id; /*EOS
 drop table if exists ${stats_db_name}.result_gold purge; /*EOS*/
 
 create table IF NOT EXISTS ${stats_db_name}.result_gold STORED AS PARQUET as
-select r.id, case when gold.is_gold=1 then true else false end as gold
+select /*+ COALESCE(100) */ r.id, case when gold.is_gold=1 then true else false end as gold
 from ${stats_db_name}.result r
          left outer join ${stats_db_name}.indi_pub_gold_oa gold on gold.id=r.id; /*EOS*/
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
index 1a7f34e96..85d90eaf1 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step21-createObservatoryDB.sql
@@ -1,7 +1,7 @@
 set mapred.job.queue.name=analytics; /*EOS*/
 
 create table ${observatory_db_name}.result_cc_licence stored as parquet as
-select r.id, coalesce(rln.count, 0) > 0 as cc_licence
+select /*+ COALESCE(100) */ r.id, coalesce(rln.count, 0) > 0 as cc_licence
 from ${stats_db_name}.result r
          left outer join (
     select rl.id, sum(case when rl.type like 'CC%' then 1 else 0 end) as count
@@ -11,7 +11,7 @@ from ${stats_db_name}.result r
 
 
 create table ${observatory_db_name}.result_affiliated_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -41,7 +41,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
 
 
 create table ${observatory_db_name}.result_affiliated_year stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -71,7 +71,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
 
 
 create table ${observatory_db_name}.result_affiliated_year_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -101,7 +101,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
 
 
 create table ${observatory_db_name}.result_affiliated_datasource stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -132,7 +132,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_datasource_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -163,7 +163,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_organization stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -192,7 +192,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_organization_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -221,7 +221,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_funder stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -252,7 +252,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder; /*EOS*/
 
 create table ${observatory_db_name}.result_affiliated_funder_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -283,7 +283,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -314,7 +314,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_year stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -346,7 +346,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
 
 
 create table ${observatory_db_name}.result_deposited_year_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -377,7 +377,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, r.year, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_datasource stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -408,7 +408,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_datasource_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -439,7 +439,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, d.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_organization stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -470,7 +470,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_organization_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -501,7 +501,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, o.name, c.code, c.name; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_funder stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
@@ -534,7 +534,7 @@ group by r.green, r.gold, case when rl.type is not null then true else false end
          cc_licence, r.authors > 1, rpc.count > 1, rfc.count > 1, p.funder; /*EOS*/
 
 create table ${observatory_db_name}.result_deposited_funder_country stored as parquet as
-select
+select /*+ COALESCE(100) */
     count(distinct r.id) as total,
     r.green,
     r.gold,
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 9a3995a8f..98225af14 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -39,21 +39,21 @@ where dtrce.datainfo.deletedbyinference = false and dtrce.datainfo.invisible = f
 DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_languages STORED AS PARQUET AS
-SELECT substr(d.id, 4) AS id, langs.languages AS language
+SELECT /*+ COALESCE(100) */ substr(d.id, 4) AS id, langs.languages AS language
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.odlanguages.value) langs AS languages
 where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.datasource_oids purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_oids STORED AS PARQUET AS
-SELECT substr(d.id, 4) AS id, oids.ids AS oid
+SELECT /*+ COALESCE(100) */ substr(d.id, 4) AS id, oids.ids AS oid
 FROM ${openaire_db_name}.datasource d LATERAL VIEW explode(d.originalid) oids AS ids
 where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.datasource_organizations purge; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS
-SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization
+SELECT /*+ COALESCE(100) */ substr(r.target, 4) AS id, substr(r.source, 4) AS organization
 FROM ${openaire_db_name}.relation r
 WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.source like '20|%' and r.datainfo.invisible=false; /*EOS*/
 
@@ -62,10 +62,10 @@ WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = f
 DROP TABLE IF EXISTS ${stats_db_name}.datasource_sources purge; /*EOS*/
 
 create table if not exists ${stats_db_name}.datasource_sources STORED AS PARQUET AS
-select substr(d.id, 4) as id, substr(cf.key, 4) as datasource
+select /*+ COALESCE(100) */ substr(d.id, 4) as id, substr(cf.key, 4) as datasource
 from ${openaire_db_name}.datasource d lateral view explode(d.collectedfrom) cfrom as cf
 where d.datainfo.deletedbyinference = false and d.datainfo.invisible=false; /*EOS*/
 
 CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
-SELECT /*+ COALESCE(100) */ datasource AS id, id AS result
+SELECT datasource AS id, id AS result
 FROM ${stats_db_name}.result_datasources; /*EOS*/

From e9686365a21dbcf4fe14e9c8ea211d4db62fe39d Mon Sep 17 00:00:00 2001
From: LSmyrnaios <lsmyrnaios@gmail.com>
Date: Wed, 3 Jul 2024 20:24:36 +0300
Subject: [PATCH 056/239] Improve performance of creating the "result_fos"
 table, by using a temp-table to cache data, which is requested multiple
 times.

---
 .../dhp/oa/graph/stats/oozie_app/scripts/step7.sql | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
index 0717d7897..bffd59ef1 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql
@@ -125,14 +125,20 @@ UNION ALL
 SELECT *
 FROM ${stats_db_name}.otherresearchproduct_topics; /*EOS*/
 
+
+DROP TABLE IF EXISTS ${stats_db_name}.result_fos_base_tmp purge; /*EOS*/
+
+create table ${stats_db_name}.result_fos_base_tmp stored as parquet as
+select /*+ COALESCE(100) */ id, topic from ${stats_db_name}.result_topics where type='Fields of Science and Technology classification'; /*EOS*/
+
 DROP TABLE IF EXISTS ${stats_db_name}.result_fos purge; /*EOS*/
 
 create table ${stats_db_name}.result_fos stored as parquet as
 with
-    lvl1 as (select id, topic from ${stats_db_name}.result_topics where topic like '__ %' and type='Fields of Science and Technology classification'),
-    lvl2 as (select id, topic from ${stats_db_name}.result_topics where topic like '____ %' and type='Fields of Science and Technology classification'),
-    lvl3 as (select id, topic from ${stats_db_name}.result_topics where topic like '______ %' and type='Fields of Science and Technology classification'),
-    lvl4 as (select id, topic from ${stats_db_name}.result_topics where topic like '________ %' and type='Fields of Science and Technology classification')
+    lvl1 as (select * from ${stats_db_name}.result_fos_base_tmp where topic like '__ %'),
+    lvl2 as (select * from ${stats_db_name}.result_fos_base_tmp where topic like '____ %'),
+    lvl3 as (select * from ${stats_db_name}.result_fos_base_tmp where topic like '______ %'),
+    lvl4 as (select * from ${stats_db_name}.result_fos_base_tmp where topic like '________ %')
 select /*+ COALESCE(100) */ lvl1.id, lvl1.topic as lvl1, lvl2.topic as lvl2, lvl3.topic as lvl3, lvl4.topic as lvl4
 from lvl1
     join lvl2 on lvl1.id=lvl2.id and substr(lvl2.topic, 1, 2)=substr(lvl1.topic, 1, 2)

From 1180d78b712c8dd308eb38d9a2fd1928239eb71d Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 4 Jul 2024 09:41:12 +0200
Subject: [PATCH 057/239] make entity level pids unique by pidType:pidValue

---
 .../main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index 7606a4d2f..74fd13ae7 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -328,7 +328,7 @@ public class MergeUtils {
 		final T merged = mergeOafFields(original, enrich, trust);
 
 		merged.setOriginalId(unionDistinctListOfString(merged.getOriginalId(), enrich.getOriginalId()));
-		merged.setPid(unionDistinctLists(merged.getPid(), enrich.getPid(), trust));
+		merged.setPid(mergeLists(merged.getPid(), enrich.getPid(), trust, MergeUtils::spKeyExtractor, (p1, p2) -> p1));
 		merged.setDateofcollection(LocalDateTime.now().toString());
 		merged
 			.setDateoftransformation(

From ddd20e7f8edb69e5493e8c5af80d9931da08c582 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 4 Jul 2024 12:08:46 +0200
Subject: [PATCH 058/239] [Person]first implementation of the action set to
 include Person entity in the graph starting from the orcid data

---
 .../actionmanager/personentity/Coauthors.java |  18 +-
 .../actionmanager/personentity/Couples.java   |  50 +-
 .../personentity/ExtractPerson.java           | 621 ++++++++++--------
 .../actionmanager/personentity/WorkList.java  |  28 +-
 .../personentity/as_parameters.json           |  13 +-
 .../actionmanager/personentity/job.properties |   2 +
 .../personentity/oozie_app/config-default.xml |  30 +
 .../personentity/oozie_app/workflow.xml       | 111 ++++
 .../actionmanager/person/CreatePersonAS.java  | 150 ++++-
 9 files changed, 683 insertions(+), 340 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/config-default.xml
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
index a755c875f..f550178d7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
@@ -1,19 +1,19 @@
-package eu.dnetlib.dhp.actionmanager.personentity;
 
-import eu.dnetlib.dhp.schema.oaf.Relation;
+package eu.dnetlib.dhp.actionmanager.personentity;
 
 import java.io.Serializable;
 import java.util.ArrayList;
 
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class Coauthors implements Serializable {
-    private ArrayList<Relation> coauthors;
+	private ArrayList<Relation> coauthors;
 
-    public ArrayList<Relation> getCoauthors() {
-        return coauthors;
-    }
+	public ArrayList<Relation> getCoauthors() {
+		return coauthors;
+	}
 
-    public void setCoauthors(ArrayList<Relation> coauthors) {
-        this.coauthors = coauthors;
-    }
+	public void setCoauthors(ArrayList<Relation> coauthors) {
+		this.coauthors = coauthors;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java
index 65670b22e..d052b52b6 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Couples.java
@@ -1,40 +1,40 @@
+
 package eu.dnetlib.dhp.actionmanager.personentity;
 
+import java.io.Serializable;
+
 import eu.dnetlib.dhp.schema.oaf.Person;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import scala.Tuple2;
 
-
-import java.io.Serializable;
-
 public class Couples implements Serializable {
-    Person p ;
-    Relation r;
+	Person p;
+	Relation r;
 
-    public Couples() {
+	public Couples() {
 
-    }
+	}
 
-    public Person getP() {
-        return p;
-    }
+	public Person getP() {
+		return p;
+	}
 
-    public void setP(Person p) {
-        this.p = p;
-    }
+	public void setP(Person p) {
+		this.p = p;
+	}
 
-    public Relation getR() {
-        return r;
-    }
+	public Relation getR() {
+		return r;
+	}
 
-    public void setR(Relation r) {
-        this.r = r;
-    }
+	public void setR(Relation r) {
+		this.r = r;
+	}
 
-    public static <Tuples> Couples newInstance(Tuple2<Person, Relation> couple){
-        Couples c = new Couples();
-        c.p = couple._1();
-        c.r = couple._2();
-        return c;
-    }
+	public static <Tuples> Couples newInstance(Tuple2<Person, Relation> couple) {
+		Couples c = new Couples();
+		c.p = couple._1();
+		c.r = couple._2();
+		return c;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 0bbda0343..b7d5f4367 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -1,27 +1,18 @@
+
 package eu.dnetlib.dhp.actionmanager.personentity;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static org.apache.spark.sql.functions.*;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.*;
+import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.actionmanager.Constants;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.collection.orcid.model.Author;
-import eu.dnetlib.dhp.collection.orcid.model.Employment;
-import eu.dnetlib.dhp.collection.orcid.model.Work;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Person;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.schema.oaf.Pid;
-import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
-import eu.dnetlib.dhp.schema.oaf.utils.PidType;
-import eu.dnetlib.dhp.utils.DHPUtils;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
@@ -31,301 +22,399 @@ import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.spark_project.jetty.util.StringUtil;
-import scala.Tuple2;
-import static org.apache.spark.sql.functions.*;
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.*;
-import java.util.stream.Collectors;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.Constants;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.collection.orcid.model.Author;
+import eu.dnetlib.dhp.collection.orcid.model.Employment;
+import eu.dnetlib.dhp.collection.orcid.model.Work;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Person;
+import eu.dnetlib.dhp.schema.oaf.Pid;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import eu.dnetlib.dhp.utils.DHPUtils;
+import scala.Tuple2;
 
 public class ExtractPerson implements Serializable {
-    private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
+	private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
 
-    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-    private static final String OPENAIRE_PREFIX = "openaire____";
-    private static final String SEPARATOR = "::";
-    private static final String orcidKey = "10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private static final String OPENAIRE_PREFIX = "openaire____";
+	private static final String SEPARATOR = "::";
+	private static final String orcidKey = "10|" + OPENAIRE_PREFIX + SEPARATOR
+		+ DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
 
-    private static final String DOI_PREFIX = "50|doi_________::";
+	private static final String DOI_PREFIX = "50|doi_________::";
 
-    private static final String PMID_PREFIX = "50|pmid________::";
-    private static final String ARXIV_PREFIX = "50|arXiv_______::";
+	private static final String PMID_PREFIX = "50|pmid________::";
+	private static final String ARXIV_PREFIX = "50|arXiv_______::";
 
-    private static final String PMCID_PREFIX = "50|pmcid_______::";
-    private static final String ROR_PREFIX = "20|ror_________::";
-    private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
-    public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
-    public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
+	private static final String PMCID_PREFIX = "50|pmcid_______::";
+	private static final String ROR_PREFIX = "20|ror_________::";
+	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
+	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
+	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
 
+	public static void main(final String[] args) throws IOException, ParseException {
 
-    public static void main(final String[] args) throws IOException, ParseException {
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							ExtractPerson.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json"))));
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-                IOUtils
-                        .toString(
-                                Objects
-                                        .requireNonNull(
-                                                ExtractPerson.class
-                                                        .getResourceAsStream(
-                                                                "/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json"))));
+		parser.parseArgument(args);
 
-        parser.parseArgument(args);
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
 
-        Boolean isSparkSessionManaged = Optional
-                .ofNullable(parser.get("isSparkSessionManaged"))
-                .map(Boolean::valueOf)
-                .orElse(Boolean.TRUE);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}", inputPath);
 
-        final String inputPath = parser.get("inputPath");
-        log.info("inputPath {}", inputPath);
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
 
-        final String outputPath = parser.get("outputPath");
-        log.info("outputPath {}", outputPath);
+		final String workingDir = parser.get("workingDir");
+		log.info("workingDir {}", workingDir);
 
-        final String workingDir = parser.get("workingDir");
-        log.info("workingDir {}", workingDir);
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+				createActionSet(spark, inputPath, outputPath, workingDir);
+			});
 
-        SparkConf conf = new SparkConf();
-        runWithSparkSession(
-                conf,
-                isSparkSessionManaged,
-                spark -> createActionSet(spark, inputPath, outputPath, workingDir));
+	}
 
-    }
+	private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
 
-    private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
+		Dataset<Author> authors = spark
+			.read()
+			.parquet(inputPath + "Authors")
+			.as(Encoders.bean(Author.class));
 
-        Dataset<Author> authors = spark
-                .read()
-                .parquet(inputPath + "Authors").as(Encoders.bean(Author.class));
+		Dataset<Work> works = spark
+			.read()
+			.parquet(inputPath + "Works")
+			.as(Encoders.bean(Work.class))
+			.filter(
+				(FilterFunction<Work>) w -> Optional.ofNullable(w.getPids()).isPresent() &&
+					w
+						.getPids()
+						.stream()
+						.anyMatch(
+							p -> p.getSchema().equalsIgnoreCase("doi") ||
+								p.getSchema().equalsIgnoreCase("pmc") ||
+								p.getSchema().equalsIgnoreCase("pmid") ||
+								p.getSchema().equalsIgnoreCase("arxiv")));
 
-        Dataset<Work> works = spark
-                .read()
-                .parquet(inputPath + "Works")
-                .as(Encoders.bean(Work.class))
-                .filter((FilterFunction<Work>) w -> Optional.ofNullable(w.getPids()).isPresent() &&
-                        w.getPids().stream().anyMatch(p->p.getSchema().equalsIgnoreCase("doi") ||
-                                p.getSchema().equalsIgnoreCase("pmc") ||
-                                p.getSchema().equalsIgnoreCase("pmid") ||
-                                p.getSchema().equalsIgnoreCase("arxiv")));
+		Dataset<Employment> employmentDataset = spark
+			.read()
+			.parquet(inputPath + "Employments")
+			.as(Encoders.bean(Employment.class));
 
-        Dataset<Employment> employmentDataset = spark
-                .read()
-                .parquet(inputPath + "Employments")
-                .as(Encoders.bean(Employment.class));
+		Dataset<Author> peopleToMap = authors
+			.joinWith(works, authors.col("orcid").equalTo(works.col("orcid")))
+			.map((MapFunction<Tuple2<Author, Work>, Author>) t2 -> t2._1(), Encoders.bean(Author.class))
+			.groupByKey((MapFunction<Author, String>) a -> a.getOrcid(), Encoders.STRING())
+			.mapGroups((MapGroupsFunction<String, Author, Author>) (k, it) -> it.next(), Encoders.bean(Author.class));
 
+		Dataset<Employment> employment = employmentDataset
+			.joinWith(peopleToMap, employmentDataset.col("orcid").equalTo(peopleToMap.col("orcid")))
+			.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
 
-        Dataset<Author> peopleToMap = authors.joinWith(works, authors.col("orcid").equalTo(works.col("orcid")))
-                .map((MapFunction<Tuple2<Author, Work>, Author>) t2 -> t2._1(), Encoders.bean(Author.class))
-                .groupByKey((MapFunction<Author, String>) a -> a.getOrcid(), Encoders.STRING())
-                .mapGroups((MapGroupsFunction<String, Author, Author>) (k, it) -> it.next(), Encoders.bean(Author.class));
+		Dataset<Person> people;
+		peopleToMap.map((MapFunction<Author, Person>) op -> {
+			Person person = new Person();
+			person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
+			person
+				.setBiography(
+					Optional
+						.ofNullable(op.getBiography())
 
+						.orElse(""));
+			KeyValue kv = OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS);
+			kv.setDataInfo(null);
+			person.setCollectedfrom(Arrays.asList(kv));
+			person
+				.setAlternativeNames(
+					Optional
+						.ofNullable(op.getOtherNames())
 
-        Dataset<Employment> employment = employmentDataset.joinWith(peopleToMap, employmentDataset.col("orcid").equalTo(peopleToMap.col("orcid")))
-                .map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
+						.orElse(new ArrayList<>()));
+			person
+				.setFamilyName(
+					Optional
+						.ofNullable(op.getFamilyName())
 
-        peopleToMap.show(false);
+						.orElse(""));
+			person
+				.setGivenName(
+					Optional
+						.ofNullable(op.getGivenName())
 
-        Dataset<Person> people;
-        people = peopleToMap.map((MapFunction<Author, Person>) op -> {
-            Person person = new Person();
-            person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
-            person.setBiography(Optional.ofNullable(op.getBiography())
+						.orElse(""));
+			person
+				.setPid(
+					Optional
+						.ofNullable(op.getOtherPids())
+						.map(
+							v -> v
+								.stream()
+								.map(p -> Pid.newInstance(p.getSchema(), p.getValue()))
+								.collect(Collectors.toList()))
+						.orElse(new ArrayList<>()));
+			person.getPid().add(Pid.newInstance(ModelConstants.ORCID, op.getOrcid()));
+			person.setDateofcollection(op.getLastModifiedDate());
+			person.setOriginalId(Arrays.asList(op.getOrcid()));
+			return person;
+		}, Encoders.bean(Person.class))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(workingDir + "/people");
 
-                    .orElse(""));
-            KeyValue kv = OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS);
-            kv.setDataInfo(null);
-            person.setCollectedfrom(Arrays.asList(kv));
-            person.setAlternativeNames(Optional.ofNullable(op.getOtherNames())
+		works
+			.flatMap(
+				(FlatMapFunction<Work, Relation>) ExtractPerson::getAuthorshipRelationIterator,
+				Encoders.bean(Relation.class))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(workingDir + "/authorship");
 
-                    .orElse(new ArrayList<>()));
-            person.setFamilyName(Optional.ofNullable(op.getFamilyName())
+		works
+			.flatMap((FlatMapFunction<Work, Tuple2<String, String>>) w -> {
+				List<Tuple2<String, String>> lista = new ArrayList<>();
+				w.getPids().stream().forEach(p -> {
+					if (p.getSchema().equalsIgnoreCase("doi") || p.getSchema().equalsIgnoreCase("pmc")
+						|| p.getSchema().equalsIgnoreCase("pmid") || p.getSchema().equalsIgnoreCase("arxiv"))
+						lista.add(new Tuple2<>(p.getValue(), w.getOrcid()));
+				});
+				return lista.iterator();
+			}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
+			.groupByKey((MapFunction<Tuple2<String, String>, String>) Tuple2::_1, Encoders.STRING())
+			.mapGroups(
+				(MapGroupsFunction<String, Tuple2<String, String>, Coauthors>) (k, it) -> extractCoAuthors(it),
+				Encoders.bean(Coauthors.class))
+			.flatMap(
+				(FlatMapFunction<Coauthors, Relation>) c -> c.getCoauthors().iterator(), Encoders.bean(Relation.class))
+			.groupByKey((MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
+			.mapGroups(
+				(MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(workingDir + "/coauthorship");
 
-                    .orElse(""));
-            person.setGivenName(Optional.ofNullable(op.getGivenName())
+		employment
+			.filter((FilterFunction<Employment>) e -> Optional.ofNullable(e.getAffiliationId()).isPresent())
+			.filter((FilterFunction<Employment>) e -> e.getAffiliationId().getSchema().equalsIgnoreCase("ror"))
+			.map(
+				(MapFunction<Employment, Relation>) ExtractPerson::getAffiliationRelation,
+				Encoders.bean(Relation.class))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Overwrite)
+			.json(workingDir + "/affiliation");
 
-                    .orElse(""));
-            person.setPid(Optional.ofNullable(op.getOtherPids())
-                    .map(v -> v.stream().map(p -> Pid.newInstance(p.getSchema(), p.getValue())).collect(Collectors.toList()))
-                    .orElse(new ArrayList<>())
-            );
-            person.getPid().add(Pid.newInstance(ModelConstants.ORCID, op.getOrcid()));
-            person.setDateofcollection(op.getLastModifiedDate());
-            person.setOriginalId(Arrays.asList(op.getOrcid()));
-            return person;
-        }, Encoders.bean(Person.class));
+		spark
+			.read()
+			.json(workingDir + "/people")
+			.as(Encoders.bean(Person.class))
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p))
+			.union(
+				getRelations(spark, workingDir + "/authorship").toJavaRDD().map(r -> new AtomicAction(r.getClass(), r)))
+			.union(
+				getRelations(spark, workingDir + "/coauthorship")
+					.toJavaRDD()
+					.map(r -> new AtomicAction(r.getClass(), r)))
+			.union(
+				getRelations(spark, workingDir + "/affiliation")
+					.toJavaRDD()
+					.map(r -> new AtomicAction(r.getClass(), r)))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+	}
 
+	private static Dataset<Relation> getRelations(SparkSession spark, String path) {
+		return spark.read().json(path).as(Encoders.bean(Relation.class));
+	}
 
-        people.show(false);
+	private static Coauthors extractCoAuthors(Iterator<Tuple2<String, String>> it) {
+		Coauthors coauth = new Coauthors();
+		ArrayList<Relation> ret = new ArrayList<>();
+		List<String> coauthors = new ArrayList<>();
+		while (it.hasNext())
+			coauthors.add(it.next()._2());
+		for (int i = 0; i < coauthors.size() - 1; i++)
+			for (int j = i + 1; j < coauthors.size(); j++)
+				ret.addAll(getCoAuthorshipRelations(coauthors.get(i), coauthors.get(j)));
 
+		coauth.setCoauthors(ret);
 
-        Dataset<Relation> authorship;
-        authorship = works
-                .flatMap((FlatMapFunction<Work, Relation>) ExtractPerson::getAuthorshipRelationIterator
-                        , Encoders.bean(Relation.class));
+		return coauth;
+	}
 
+	private static Relation getAffiliationRelation(Employment row) {
+		String source = PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
+		String target = ROR_PREFIX
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
+		List<KeyValue> properties = new ArrayList<>();
 
-        authorship.show(false);
+		Relation relation = OafMapperUtils
+			.getRelation(
+				source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE,
+				ModelConstants.ORG_PERSON_PARTICIPATES,
+				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS,
+								ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.91"),
+				null);
 
+		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
+			KeyValue kv = new KeyValue();
+			kv.setKey("startDate");
+			kv.setValue(row.getStartDate());
+			properties.add(kv);
+		}
+		if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
+			KeyValue kv = new KeyValue();
+			kv.setKey("endDate");
+			kv.setValue(row.getEndDate());
+			properties.add(kv);
+		}
 
-        Dataset<Relation> coauthorship = works
-                .flatMap((FlatMapFunction<Work, Tuple2<String, String>>) w -> {
-                    List<Tuple2<String, String>> lista = new ArrayList<>();
-                    w.getPids().stream().forEach(p -> {
-                        if (p.getSchema().equalsIgnoreCase("doi") || p.getSchema().equalsIgnoreCase("pmc") || p.getSchema().equalsIgnoreCase("pmid") || p.getSchema().equalsIgnoreCase("arxiv"))
-                            lista.add(new Tuple2<>(p.getValue(), w.getOrcid()));
-                    });
-                    return lista.iterator();
-                }, Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
-                .groupByKey((MapFunction<Tuple2<String, String>, String>) Tuple2::_1, Encoders.STRING())
-                .mapGroups((MapGroupsFunction<String, Tuple2<String, String>, Coauthors>) (k, it) ->
-                        extractCoAuthors(it), Encoders.bean(Coauthors.class))
-                .flatMap((FlatMapFunction<Coauthors, Relation>) c -> c.getCoauthors().iterator(), Encoders.bean(Relation.class))
-                .groupByKey((MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
-                .mapGroups((MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class));
+		if (properties.size() > 0)
+			relation.setProperties(properties);
+		return relation;
 
-        coauthorship.show(false);
-        Dataset<Relation> affiliation = employment
-                .filter((FilterFunction<Employment>) e -> Optional.ofNullable(e.getAffiliationId()).isPresent())
-                .filter((FilterFunction<Employment>) e -> e.getAffiliationId().getSchema().equalsIgnoreCase("ror"))
-                .map((MapFunction<Employment, Relation>) ExtractPerson::getAffiliationRelation
-                        , Encoders.bean(Relation.class));
+	}
 
-        affiliation.show(false);
+	private static Collection<? extends Relation> getCoAuthorshipRelations(String orcid1, String orcid2) {
+		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid1);
+		String target = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid2);
 
-        people.toJavaRDD()
-                .map(p -> new AtomicAction(p.getClass(), p))
-                .union(authorship.toJavaRDD().map(r-> new AtomicAction(r.getClass(),r)))
-                .union(coauthorship.toJavaRDD().map(r-> new AtomicAction(r.getClass(),r)))
-                .union(affiliation.toJavaRDD().map(r->new AtomicAction(r.getClass(),r)))
-                .mapToPair(
-                        aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-                                new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-                .saveAsHadoopFile(
-                        outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);//, GzipCodec.class);
-    }
+		return Arrays
+			.asList(
+				OafMapperUtils
+					.getRelation(
+						source, target, ModelConstants.PERSON_PERSON_RELTYPE,
+						ModelConstants.PERSON_PERSON_SUBRELTYPE,
+						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
+						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+						OafMapperUtils
+							.dataInfo(
+								false, null, false, false,
+								OafMapperUtils
+									.qualifier(
+										ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
+										ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+								"0.91"),
+						null),
+				OafMapperUtils
+					.getRelation(
+						target, source, ModelConstants.PERSON_PERSON_RELTYPE,
+						ModelConstants.PERSON_PERSON_SUBRELTYPE,
+						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
+						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+						OafMapperUtils
+							.dataInfo(
+								false, null, false, false,
+								OafMapperUtils
+									.qualifier(
+										ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
+										ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+								"0.91"),
+						null));
 
-    private static Coauthors extractCoAuthors(Iterator<Tuple2<String, String>> it) {
-        Coauthors coauth = new Coauthors();
-        ArrayList<Relation> ret = new ArrayList<>();
-        List<String> coauthors = new ArrayList<>();
-        while(it.hasNext())
-            coauthors.add(it.next()._2());
-        for (int i = 0; i < coauthors.size() -1; i++ )
-            for(int j = i + 1; j < coauthors.size(); j++)
-                ret.addAll(getCoAuthorshipRelations(coauthors.get(i), coauthors.get(j)));
+	}
 
-        coauth.setCoauthors(ret);
+	private static @NotNull Iterator<Relation> getAuthorshipRelationIterator(Work w) {
 
-        return coauth;
-    }
+		if (Optional.ofNullable(w.getPids()).isPresent())
+			return w
+				.getPids()
+				.stream()
+				.map(pid -> getRelation(w.getOrcid(), pid))
+				.filter(Objects::nonNull)
+				.collect(Collectors.toList())
+				.iterator();
+		List<Relation> ret = new ArrayList<>();
+		return ret.iterator();
+	}
 
-    private static Relation getAffiliationRelation(Employment row) {
-        String source =  PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
-        String target =  ROR_PREFIX
-                + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
-        List<KeyValue> properties = new ArrayList<>() ;
+	private static Relation getRelation(String orcid, eu.dnetlib.dhp.collection.orcid.model.Pid pid) {
+		String target;
+		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
+		switch (pid.getSchema()) {
+			case "doi":
+				target = DOI_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), pid.getValue()));
+				break;
+			case "pmid":
+				target = PMID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pid.getValue()));
+				break;
+			case "arxiv":
+				target = ARXIV_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), pid.getValue()));
+				break;
+			case "pmcid":
+				target = PMCID_PREFIX
+					+ IdentifierFactory
+						.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), pid.getValue()));
+				break;
 
-        Relation relation =
-         OafMapperUtils.getRelation(source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE, ModelConstants.ORG_PERSON_PARTICIPATES ,
-                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-                OafMapperUtils.dataInfo(false, null, false, false,
-                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
-                null);
+			default:
+				return null;
+		}
 
-        if(Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())){
-            KeyValue kv = new KeyValue();
-            kv.setKey("startDate");
-            kv.setValue(row.getStartDate());
-            properties.add(kv);
-        }
-        if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
-            KeyValue kv = new KeyValue();
-            kv.setKey("endDate");
-            kv.setValue(row.getEndDate());
-            properties.add(kv);
-        }
-
-        if (properties.size() > 0)
-            relation.setProperties(properties);
-        return relation;
-
-
-    }
-
-    private static Collection<? extends Relation> getCoAuthorshipRelations(String orcid1, String orcid2) {
-        String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
-        String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
-
-        return Arrays.asList(OafMapperUtils.getRelation(source, target,ModelConstants.PERSON_PERSON_RELTYPE,
-                ModelConstants.PERSON_PERSON_SUBRELTYPE,
-                ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-                OafMapperUtils.dataInfo(false, null, false, false,
-                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
-                null),
-                OafMapperUtils.getRelation(target, source,ModelConstants.PERSON_PERSON_RELTYPE,
-                        ModelConstants.PERSON_PERSON_SUBRELTYPE,
-                        ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-                OafMapperUtils.dataInfo(false, null, false, false,
-                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
-                null));
-
-    }
-
-    private static @NotNull Iterator<Relation> getAuthorshipRelationIterator(Work w) {
-
-        if(Optional.ofNullable(w.getPids()).isPresent())
-                return w.getPids()
-                        .stream()
-                                .map(pid -> getRelation(w.getOrcid(), pid))
-                                .filter(Objects::nonNull).collect(Collectors.toList()).iterator();
-        List<Relation> ret = new ArrayList<>();
-        return ret.iterator();
-    }
-
-
-    private static Relation getRelation(String orcid, eu.dnetlib.dhp.collection.orcid.model.Pid pid){
-        String target ;
-        String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
-        switch (pid.getSchema()){
-                case "doi":
-                    target = DOI_PREFIX
-                            + IdentifierFactory
-                            .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), pid.getValue()));
-                    break;
-                case "pmid":
-                    target = PMID_PREFIX
-                            + IdentifierFactory
-                            .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pid.getValue()));
-                    break;
-                case "arxiv":
-                    target = ARXIV_PREFIX
-                            + IdentifierFactory
-                            .md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), pid.getValue()));
-                    break;
-                case "pmcid":
-                    target = PMCID_PREFIX
-                            + IdentifierFactory
-                            .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), pid.getValue()));
-                    break;
-
-                default:
-                    return null;
-            }
-
-
-        return OafMapperUtils.getRelation(source, target,ModelConstants.RESULT_PERSON_RELTYPE,
-                ModelConstants.RESULT_PERSON_SUBRELTYPE,
-                ModelConstants.RESULT_PERSON_HASAUTHORED,
-                Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-                OafMapperUtils.dataInfo(false, null, false, false,
-                        OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
-                null);
-    }
+		return OafMapperUtils
+			.getRelation(
+				source, target, ModelConstants.RESULT_PERSON_RELTYPE,
+				ModelConstants.RESULT_PERSON_SUBRELTYPE,
+				ModelConstants.RESULT_PERSON_HASAUTHORED,
+				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS,
+								ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.91"),
+				null);
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java
index 71d2b491a..92842bfcf 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/WorkList.java
@@ -1,23 +1,25 @@
-package eu.dnetlib.dhp.actionmanager.personentity;
 
-import eu.dnetlib.dhp.collection.orcid.model.Work;
-import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
+package eu.dnetlib.dhp.actionmanager.personentity;
 
 import java.io.Serializable;
 import java.util.ArrayList;
 
+import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
+
+import eu.dnetlib.dhp.collection.orcid.model.Work;
+
 public class WorkList implements Serializable {
-    private ArrayList<Work> workArrayList;
+	private ArrayList<Work> workArrayList;
 
-    public ArrayList<Work> getWorkArrayList() {
-        return workArrayList;
-    }
+	public ArrayList<Work> getWorkArrayList() {
+		return workArrayList;
+	}
 
-    public void setWorkArrayList(ArrayList<Work> workArrayList) {
-        this.workArrayList = workArrayList;
-    }
+	public void setWorkArrayList(ArrayList<Work> workArrayList) {
+		this.workArrayList = workArrayList;
+	}
 
-    public WorkList() {
-        workArrayList = new ArrayList<>();
-    }
+	public WorkList() {
+		workArrayList = new ArrayList<>();
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
index 3310f16e4..5175552e7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
@@ -16,11 +16,10 @@
     "paramLongName": "isSparkSessionManaged",
     "paramDescription": "the hdfs name node",
     "paramRequired": false
-  },
-  {
-    "paramName": "wd",
-    "paramLongName": "workingDir",
-    "paramDescription": "the hdfs name node",
-    "paramRequired": false
-  }
+  }, {
+  "paramName": "wd",
+  "paramLongName": "workingDir",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
+}
 ]
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
new file mode 100644
index 000000000..d2269718c
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
@@ -0,0 +1,2 @@
+inputPath=/data/orcid_2023/tables/
+outputPath=/user/miriam.baglioni/peopleAS
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/config-default.xml
new file mode 100644
index 000000000..d262cb6e0
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/config-default.xml
@@ -0,0 +1,30 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml
new file mode 100644
index 000000000..166e7bb9c
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml
@@ -0,0 +1,111 @@
+<workflow-app name="PersonEntity" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+
+        <property>
+            <name>inputPath</name>
+            <description>inputPath</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="deleteoutputpath"/>
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+    <action name="deleteoutputpath">
+        <fs>
+            <delete path="${outputPath}"/>
+            <mkdir path="${outputPath}"/>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="atomicactions"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="atomicactions">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the ActionSet for Person entity and relevant relations</name>
+            <class>eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=4
+                --executor-memory=4G
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=5G
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=15000
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
index a4d56ba2e..2e7b21010 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
@@ -1,15 +1,13 @@
 
 package eu.dnetlib.dhp.actionmanager.person;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
-import eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson;
-import eu.dnetlib.dhp.collection.orcid.model.Author;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.Optional;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.spark.SparkConf;
@@ -27,12 +25,18 @@ import org.junit.jupiter.api.Test;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.IOException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.util.Optional;
+import com.fasterxml.jackson.databind.ObjectMapper;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
+import eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson;
+import eu.dnetlib.dhp.collection.orcid.model.Author;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Person;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class CreatePersonAS {
 
@@ -57,7 +61,7 @@ public class CreatePersonAS {
 		conf.set("spark.driver.host", "localhost");
 		conf.set("hive.metastore.local", "true");
 		conf.set("spark.ui.enabled", "false");
-		conf.set("spark.sql.codegen.wholeStage","false");
+		conf.set("spark.sql.codegen.wholeStage", "false");
 		conf.set("spark.sql.warehouse.dir", workingDir.toString());
 		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
 
@@ -92,7 +96,6 @@ public class CreatePersonAS {
 //										.mode(SaveMode.Overwrite)
 //												.parquet(workingDir.toString() + "AuthorsSubset");
 
-
 		ExtractPerson
 			.main(
 				new String[] {
@@ -102,13 +105,120 @@ public class CreatePersonAS {
 					inputPath,
 					"-outputPath",
 					workingDir.toString() + "/actionSet1",
-						"-workingDir",
-						workingDir.toString() + "/working"
+					"-workingDir",
+					workingDir.toString() + "/working"
 				});
 
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
 
+		JavaRDD<Relation> relations = sc
+			.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
+			.filter(v -> "eu.dnetlib.dhp.schema.oaf.Relation".equalsIgnoreCase(v._1().toString()))
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+//
+		JavaRDD<Person> people = sc
+			.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
+			.filter(v -> "eu.dnetlib.dhp.schema.oaf.Person".equalsIgnoreCase(v._1().toString()))
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Person) aa.getPayload()));
+//
+		Assertions.assertEquals(7, people.count());
+		Assertions
+			.assertEquals(
+				"Paulo",
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getGivenName());
+		Assertions
+			.assertEquals(
+				"Tavares",
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getFamilyName());
+		Assertions
+			.assertEquals(
+				4,
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getAlternativeNames()
+					.size());
+		Assertions
+			.assertEquals(
+				4,
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getPid()
+					.size());
+		Assertions
+			.assertTrue(
+				people
+					.filter(
+						p -> p.getPid().stream().anyMatch(id -> id.getValue().equalsIgnoreCase("0000-0002-3210-3034")))
+					.first()
+					.getPid()
+					.stream()
+					.anyMatch(
+						p -> p.getSchema().equalsIgnoreCase("Scopus Author ID")
+							&& p.getValue().equalsIgnoreCase("15119405200")));
+
+		Assertions
+			.assertEquals(
+				16,
+				relations
+					.filter(r -> r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED))
+					.count());
+		Assertions
+			.assertEquals(
+				14,
+				relations
+					.filter(r -> r.getRelClass().equalsIgnoreCase(ModelConstants.PERSON_PERSON_HASCOAUTHORED))
+					.count());
+		Assertions
+			.assertEquals(
+				3,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED))
+					.count());
+		Assertions
+			.assertEquals(
+				2,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED)
+							&& r.getTarget().startsWith("50|doi"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.RESULT_PERSON_HASAUTHORED)
+							&& r.getTarget().startsWith("50|arXiv"))
+					.count());
+
+		Assertions
+			.assertEquals(
+				1,
+				relations
+					.filter(
+						r -> r.getSource().equalsIgnoreCase("30|orcid_______::" + DHPUtils.md5("0000-0001-6291-9619"))
+							&& r.getRelClass().equalsIgnoreCase(ModelConstants.PERSON_PERSON_HASCOAUTHORED))
+					.count());
+		Assertions.assertEquals(33, relations.count());
 
 	}
 
-
-	}
+}

From 814e650e12c15f3a74449b0c79f70193e12327f7 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 4 Jul 2024 12:24:28 +0200
Subject: [PATCH 059/239] [Irish Tender]changed the irish.json file according
 to comments #26, #29, and #34 for 9635

---
 .../dhp/collection/crossref/irish_funder.json | 46 +++----------------
 1 file changed, 7 insertions(+), 39 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
index e50dc2dee..a49e4e300 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/crossref/irish_funder.json
@@ -1,10 +1,5 @@
 [
-  {
-    "id": "100007630",
-    "uri": "http://dx.doi.org/10.13039/100007630",
-    "name": "College of Engineering and Informatics, National University of Ireland, Galway",
-    "synonym": []
-  },
+
   {
     "id": "100007731",
     "uri": "http://dx.doi.org/10.13039/100007731",
@@ -432,13 +427,13 @@
     "id": "501100001634",
     "uri": "http://dx.doi.org/10.13039/501100001634",
     "name": "University of Galway",
-    "synonym": []
+    "synonym": ["501100019905", "100007630", "501100020570", "501100023852"]
   },
   {
     "id": "501100001635",
     "uri": "http://dx.doi.org/10.13039/501100001635",
     "name": "University of Limerick",
-    "synonym": []
+    "synonym": ["501100014531"]
   },
   {
     "id": "501100001636",
@@ -468,7 +463,7 @@
     "id": "501100002736",
     "uri": "http://dx.doi.org/10.13039/501100002736",
     "name": "Covidien",
-    "synonym": []
+    "synonym": ["501100003956"]
   },
   {
     "id": "501100002755",
@@ -518,12 +513,6 @@
     "name": "Irish Institute of Clinical Neuroscience",
     "synonym": []
   },
-  {
-    "id": "501100003956",
-    "uri": "http://dx.doi.org/10.13039/501100003956",
-    "name": "Aspect Medical Systems",
-    "synonym": []
-  },
   {
     "id": "501100004162",
     "uri": "http://dx.doi.org/10.13039/501100004162",
@@ -644,12 +633,7 @@
     "name": "Irish Centre for High-End Computing",
     "synonym": []
   },
-  {
-    "id": "501100019905",
-    "uri": "http://dx.doi.org/10.13039/501100019905",
-    "name": "Galway University Foundation",
-    "synonym": []
-  },
+
   {
     "id": "501100020036",
     "uri": "http://dx.doi.org/10.13039/501100020036",
@@ -824,12 +808,7 @@
     "name": "Energy Policy Research Centre, Economic and Social Research Institute",
     "synonym": []
   },
-  {
-    "id": "501100014531",
-    "uri": "http://dx.doi.org/10.13039/501100014531",
-    "name": "Physical Education and Sport Sciences Department, University of Limerick",
-    "synonym": []
-  },
+
   {
     "id": "501100014745",
     "uri": "http://dx.doi.org/10.13039/501100014745",
@@ -842,22 +821,11 @@
     "name": "ADAPT - Centre for Digital Content Technology",
     "synonym": []
   },
-  {
-    "id": "501100020570",
-    "uri": "http://dx.doi.org/10.13039/501100020570",
-    "name": "College of Medicine, Nursing and Health Sciences, National University of Ireland, Galway",
-    "synonym": []
-  },
+
   {
     "id": "501100020871",
     "uri": "http://dx.doi.org/10.13039/501100020871",
     "name": "Bernal Institute, University of Limerick",
     "synonym": []
-  },
-  {
-    "id": "501100023852",
-    "uri": "http://dx.doi.org/10.13039/501100023852",
-    "name": "Moore Institute for Research in the Humanities and Social Studies, University of Galway",
-    "synonym": []
   }
 ]
\ No newline at end of file

From c4658350613a3d124a3119a73efff7e33d8df443 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 9 Jul 2024 12:29:55 +0200
Subject: [PATCH 060/239] [Person]new implementation for the extraction of the
 coAuthorship relations

---
 .../personentity/CoAuthorshipIterator.java    | 80 +++++++++++++++++++
 .../actionmanager/personentity/Coauthors.java |  7 +-
 .../personentity/ExtractPerson.java           | 37 ++++++---
 3 files changed, 108 insertions(+), 16 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
new file mode 100644
index 000000000..76e4c4851
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
@@ -0,0 +1,80 @@
+
+package eu.dnetlib.dhp.actionmanager.personentity;
+
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.Person;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.utils.DHPUtils;
+
+public class CoAuthorshipIterator implements Iterator<Relation> {
+	private int firstIndex;
+	private int secondIndex;
+	private boolean firstRelation;
+	private List<String> authors;
+	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______::";
+	private static final String OPENAIRE_PREFIX = "openaire____";
+	private static final String SEPARATOR = "::";
+	private static final String ORCID_KEY = "10|" + OPENAIRE_PREFIX + SEPARATOR
+		+ DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
+	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
+	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
+
+	@Override
+	public boolean hasNext() {
+		return firstIndex < authors.size() - 1;
+	}
+
+	@Override
+	public Relation next() {
+		Relation rel = null;
+		if (firstRelation) {
+			rel = getRelation(authors.get(firstIndex), authors.get(secondIndex));
+			firstRelation = Boolean.FALSE;
+		} else {
+			rel = getRelation(authors.get(secondIndex), authors.get(firstIndex));
+			firstRelation = Boolean.TRUE;
+			secondIndex += 1;
+			if (secondIndex >= authors.size()) {
+				firstIndex += 1;
+				secondIndex = firstIndex + 1;
+			}
+		}
+
+		return rel;
+	}
+
+	public CoAuthorshipIterator(List<String> authors) {
+		this.authors = authors;
+		this.firstIndex = 0;
+		this.secondIndex = 1;
+		this.firstRelation = Boolean.TRUE;
+
+	}
+
+	private Relation getRelation(String orcid1, String orcid2) {
+		String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
+		String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
+		return OafMapperUtils
+			.getRelation(
+				source, target, ModelConstants.PERSON_PERSON_RELTYPE,
+				ModelConstants.PERSON_PERSON_SUBRELTYPE,
+				ModelConstants.PERSON_PERSON_HASCOAUTHORED,
+				Arrays.asList(OafMapperUtils.keyValue(ORCID_KEY, ModelConstants.ORCID_DS)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						"0.91"),
+				null);
+	}
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
index f550178d7..17f46d5c7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
@@ -3,17 +3,18 @@ package eu.dnetlib.dhp.actionmanager.personentity;
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.List;
 
 import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class Coauthors implements Serializable {
-	private ArrayList<Relation> coauthors;
+	private List<String> coauthors;
 
-	public ArrayList<Relation> getCoauthors() {
+	public List<String> getCoauthors() {
 		return coauthors;
 	}
 
-	public void setCoauthors(ArrayList<Relation> coauthors) {
+	public void setCoauthors(List<String> coauthors) {
 		this.coauthors = coauthors;
 	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index b7d5f4367..064fb41a1 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -26,6 +26,7 @@ import org.spark_project.jetty.util.StringUtil;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.actionmanager.Constants;
+import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.collection.orcid.model.Author;
 import eu.dnetlib.dhp.collection.orcid.model.Employment;
@@ -202,7 +203,7 @@ public class ExtractPerson implements Serializable {
 			.mode(SaveMode.Overwrite)
 			.json(workingDir + "/authorship");
 
-		works
+		Dataset<Relation> coauthorship = works
 			.flatMap((FlatMapFunction<Work, Tuple2<String, String>>) w -> {
 				List<Tuple2<String, String>> lista = new ArrayList<>();
 				w.getPids().stream().forEach(p -> {
@@ -217,10 +218,13 @@ public class ExtractPerson implements Serializable {
 				(MapGroupsFunction<String, Tuple2<String, String>, Coauthors>) (k, it) -> extractCoAuthors(it),
 				Encoders.bean(Coauthors.class))
 			.flatMap(
-				(FlatMapFunction<Coauthors, Relation>) c -> c.getCoauthors().iterator(), Encoders.bean(Relation.class))
+				(FlatMapFunction<Coauthors, Relation>) c -> new CoAuthorshipIterator(c.getCoauthors()),
+				Encoders.bean(Relation.class))
 			.groupByKey((MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
 			.mapGroups(
-				(MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class))
+				(MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class));
+
+		coauthorship
 			.write()
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
@@ -237,10 +241,16 @@ public class ExtractPerson implements Serializable {
 			.mode(SaveMode.Overwrite)
 			.json(workingDir + "/affiliation");
 
-		spark
+		people = spark
 			.read()
-			.json(workingDir + "/people")
-			.as(Encoders.bean(Person.class))
+			.textFile(workingDir + "/people")
+			.map(
+				(MapFunction<String, Person>) value -> OBJECT_MAPPER
+					.readValue(value, Person.class),
+				Encoders.bean(Person.class));
+
+		people.show(false);
+		people
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
 			.union(
@@ -261,20 +271,21 @@ public class ExtractPerson implements Serializable {
 	}
 
 	private static Dataset<Relation> getRelations(SparkSession spark, String path) {
-		return spark.read().json(path).as(Encoders.bean(Relation.class));
+		return spark
+			.read()
+			.textFile(path)
+			.map(
+				(MapFunction<String, Relation>) value -> OBJECT_MAPPER
+					.readValue(value, Relation.class),
+				Encoders.bean(Relation.class));// spark.read().json(path).as(Encoders.bean(Relation.class));
 	}
 
 	private static Coauthors extractCoAuthors(Iterator<Tuple2<String, String>> it) {
 		Coauthors coauth = new Coauthors();
-		ArrayList<Relation> ret = new ArrayList<>();
 		List<String> coauthors = new ArrayList<>();
 		while (it.hasNext())
 			coauthors.add(it.next()._2());
-		for (int i = 0; i < coauthors.size() - 1; i++)
-			for (int j = i + 1; j < coauthors.size(); j++)
-				ret.addAll(getCoAuthorshipRelations(coauthors.get(i), coauthors.get(j)));
-
-		coauth.setCoauthors(ret);
+		coauth.setCoauthors(coauthors);
 
 		return coauth;
 	}

From 2a36ccb997c0ba5ebdca757c1d88ab3cfc7f7249 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Tue, 9 Jul 2024 16:58:10 +0200
Subject: [PATCH 061/239] optimization of normalization stage in openorgs
 workflow, implementation of new comparators replacing older versions,
 openorgs configuration update, addition of inference flag in model
 definition, new test classes

---
 ...ustering.java => LegalnameClustering.java} |  31 ++-
 .../pace/common/AbstractPaceFunctions.java    |  94 +++++++
 .../java/eu/dnetlib/pace/model/FieldDef.java  |  20 ++
 .../eu/dnetlib/pace/model/SparkModel.scala    |  22 ++
 .../java/eu/dnetlib/pace/tree/CityMatch.java  |  48 ----
 .../java/eu/dnetlib/pace/tree/CodeMatch.java  |  51 ++++
 .../eu/dnetlib/pace/tree/CountryMatch.java    |  61 +++--
 .../pace/tree/JaroWinklerLegalname.java       |  59 +++++
 .../pace/tree/JaroWinklerNormalizedName.java  |  74 ------
 .../eu/dnetlib/pace/tree/KeywordMatch.java    |  50 ----
 .../pace/tree/support/TreeNodeDef.java        |   2 +-
 .../pace/tree/support/TreeNodeStats.java      |  36 ++-
 .../pace/tree/support/TreeProcessor.java      |  11 +-
 .../eu/dnetlib/pace/config/country_map.csv    | 239 ++++++++++++++++++
 .../clustering/ClusteringFunctionTest.java    |  38 +--
 .../dnetlib/pace/common/PaceFunctionTest.java |  43 ++++
 .../pace/comparators/ComparatorTest.java      |  70 ++---
 .../dhp/oa/dedup/DecisionTreeTest.java        |  83 ++++++
 .../dnetlib/dhp/oa/dedup/SparkDedupTest.java  |  14 +-
 .../dhp/oa/dedup/SparkOpenorgsDedupTest.java  |   9 +-
 .../dhp/oa/dedup/jpath/JsonPathTest.java      |  25 ++
 .../dnetlib/dhp/dedup/conf/org.curr.conf.json | 187 +++-----------
 .../oa/dedup/jpath/organization_example1.json |   1 +
 23 files changed, 807 insertions(+), 461 deletions(-)
 rename dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/{KeywordsClustering.java => LegalnameClustering.java} (54%)
 delete mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CityMatch.java
 create mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java
 create mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerLegalname.java
 delete mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java
 delete mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/KeywordMatch.java
 create mode 100644 dhp-pace-core/src/main/resources/eu/dnetlib/pace/config/country_map.csv
 create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java
 create mode 100644 dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/organization_example1.json

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/LegalnameClustering.java
similarity index 54%
rename from dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java
rename to dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/LegalnameClustering.java
index fdd8d1fb1..8a76a4bc3 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/KeywordsClustering.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/LegalnameClustering.java
@@ -2,31 +2,41 @@
 package eu.dnetlib.pace.clustering;
 
 import java.util.*;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
 import eu.dnetlib.pace.config.Config;
 
-@ClusteringClass("keywordsclustering")
-public class KeywordsClustering extends AbstractClusteringFunction {
+@ClusteringClass("legalnameclustering")
+public class LegalnameClustering extends AbstractClusteringFunction {
 
-	public KeywordsClustering(Map<String, Object> params) {
+	private static final Pattern CITY_CODE_PATTERN = Pattern.compile("city::\\d+");
+	private static final Pattern KEYWORD_CODE_PATTERN = Pattern.compile("key::\\d+");
+
+	public LegalnameClustering(Map<String, Object> params) {
 		super(params);
 	}
 
+	public Set<String> getRegexList(String input, Pattern codeRegex) {
+		Matcher matcher = codeRegex.matcher(input);
+		Set<String> cities = new HashSet<>();
+		while (matcher.find()) {
+			cities.add(matcher.group());
+		}
+		return cities;
+	}
+
 	@Override
 	protected Collection<String> doApply(final Config conf, String s) {
 
-		// takes city codes and keywords codes without duplicates
-		Set<String> keywords = getKeywords(s, conf.translationMap(), paramOrDefault("windowSize", 4));
-		Set<String> cities = getCities(s, paramOrDefault("windowSize", 4));
-
 		// list of combination to return as result
 		final Collection<String> combinations = new LinkedHashSet<String>();
 
-		for (String keyword : keywordsToCodes(keywords, conf.translationMap())) {
-			for (String city : citiesToCodes(cities)) {
+		for (String keyword : getRegexList(s, KEYWORD_CODE_PATTERN)) {
+			for (String city : getRegexList(s, CITY_CODE_PATTERN)) {
 				combinations.add(keyword + "-" + city);
 				if (combinations.size() >= paramOrDefault("max", 2)) {
 					return combinations;
@@ -42,9 +52,6 @@ public class KeywordsClustering extends AbstractClusteringFunction {
 		return fields
 			.stream()
 			.filter(f -> !f.isEmpty())
-			.map(KeywordsClustering::cleanup)
-			.map(KeywordsClustering::normalize)
-			.map(s -> filterAllStopWords(s))
 			.map(s -> doApply(conf, s))
 			.map(c -> filterBlacklisted(c, ngramBlacklist))
 			.flatMap(c -> c.stream())
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
index b055077d8..6ef550c50 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
@@ -27,6 +27,14 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 	private static Map<String, String> cityMap = AbstractPaceFunctions
 		.loadMapFromClasspath("/eu/dnetlib/pace/config/city_map.csv");
 
+	// keywords map to be used when translating the keyword names into codes
+	private static Map<String, String> keywordMap = AbstractPaceFunctions
+		.loadMapFromClasspath("/eu/dnetlib/pace/config/translation_map.csv");
+
+	// country map to be used when inferring the country from the city name
+	private static Map<String, String> countryMap = AbstractPaceFunctions
+		.loadCountryMapFromClasspath("/eu/dnetlib/pace/config/country_map.csv");
+
 	// list of stopwords in different languages
 	protected static Set<String> stopwords_gr = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_gr.txt");
 	protected static Set<String> stopwords_en = loadFromClasspath("/eu/dnetlib/pace/config/stopwords_en.txt");
@@ -74,6 +82,64 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return s12;
 	}
 
+	public static String countryInference(final String original, String inferFrom) {
+		if (!original.equalsIgnoreCase("unknown"))
+			return original;
+
+		inferFrom = cleanup(inferFrom);
+		inferFrom = normalize(inferFrom);
+		inferFrom = filterAllStopWords(inferFrom);
+		Set<String> cities = getCities(inferFrom, 4);
+		return citiesToCountry(cities).stream().findFirst().orElse("UNKNOWN");
+	}
+
+	public static String cityInference(String original) {
+		original = cleanup(original);
+		original = normalize(original);
+		original = filterAllStopWords(original);
+
+		Set<String> cities = getCities(original, 4);
+
+		for (String city : cities) {
+			original = original.replaceAll(city, cityMap.get(city));
+		}
+
+		return original;
+	}
+
+	public static String keywordInference(String original) {
+		original = cleanup(original);
+		original = normalize(original);
+		original = filterAllStopWords(original);
+
+		Set<String> keywords = getKeywords(original, keywordMap, 4);
+
+		for (String keyword : keywords) {
+			original = original.replaceAll(keyword, keywordMap.get(keyword));
+		}
+
+		return original;
+	}
+
+	public static String cityKeywordInference(String original) {
+		original = cleanup(original);
+		original = normalize(original);
+		original = filterAllStopWords(original);
+
+		Set<String> keywords = getKeywords(original, keywordMap, 4);
+		Set<String> cities = getCities(original, 4);
+
+		for (String keyword : keywords) {
+			original = original.replaceAll(keyword, keywordMap.get(keyword));
+		}
+
+		for (String city : cities) {
+			original = original.replaceAll(city, cityMap.get(city));
+		}
+
+		return original;
+	}
+
 	protected static String fixXML(final String a) {
 
 		return a
@@ -208,6 +274,30 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return m;
 	}
 
+	public static Map<String, String> loadCountryMapFromClasspath(final String classpath) {
+
+		Transliterator transliterator = Transliterator.getInstance("Any-Eng");
+
+		final Map<String, String> m = new HashMap<>();
+		try {
+			for (final String s : IOUtils
+				.readLines(AbstractPaceFunctions.class.getResourceAsStream(classpath), StandardCharsets.UTF_8)) {
+				// string is like this: country_code;city1;city2;city3
+				String[] line = s.split(";");
+				String value = line[0];
+				for (int i = 1; i < line.length; i++) {
+					String city = fixAliases(transliterator.transliterate(line[i].toLowerCase()));
+					String code = cityMap.get(city);
+					m.put(code, value);
+				}
+			}
+		} catch (final Throwable e) {
+			return new HashMap<>();
+		}
+		return m;
+
+	}
+
 	public static String removeKeywords(String s, Set<String> keywords) {
 
 		s = " " + s + " ";
@@ -237,6 +327,10 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		return toCodes(keywords, cityMap);
 	}
 
+	public static Set<String> citiesToCountry(Set<String> cities) {
+		return toCodes(toCodes(cities, cityMap), countryMap);
+	}
+
 	protected static String firstLC(final String s) {
 		return StringUtils.substring(s, 0, 1).toLowerCase();
 	}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
index 7ad9b7445..b0dc11656 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
@@ -47,9 +47,21 @@ public class FieldDef implements Serializable {
 
 	private String clean;
 
+	private String infer;
+
+	private String inferenceFrom;
+
 	public FieldDef() {
 	}
 
+	public String getInferenceFrom() {
+		return inferenceFrom;
+	}
+
+	public void setInferenceFrom(final String inferenceFrom) {
+		this.inferenceFrom = inferenceFrom;
+	}
+
 	public String getName() {
 		return name;
 	}
@@ -126,6 +138,14 @@ public class FieldDef implements Serializable {
 		this.clean = clean;
 	}
 
+	public String getInfer() {
+		return infer;
+	}
+
+	public void setInfer(String infer) {
+		this.infer = infer;
+	}
+
 	@Override
 	public String toString() {
 		try {
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
index e6a1c4ccc..c6db62339 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
@@ -123,9 +123,19 @@ case class SparkModel(conf: DedupConfig) {
               case _ => res(index)
             }
           }
+
+          if (StringUtils.isNotBlank(fdef.getInfer)) {
+            val inferFrom : String = if (StringUtils.isNotBlank(fdef.getInferenceFrom)) fdef.getInferenceFrom else fdef.getPath
+            res(index) = res(index) match {
+              case x: Seq[String] => x.map(inference(_, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer))
+              case _ => inference(res(index).toString, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer)
+            }
+          }
+
         }
 
         res
+
     }
 
     new GenericRowWithSchema(values, schema)
@@ -146,5 +156,17 @@ case class SparkModel(conf: DedupConfig) {
     res
   }
 
+  def inference(value: String, inferfrom: String, infertype: String) : String = {
+    val res = infertype match {
+      case "country" => AbstractPaceFunctions.countryInference(value, inferfrom)
+      case "city" => AbstractPaceFunctions.cityInference(value)
+      case "keyword" => AbstractPaceFunctions.keywordInference(value)
+      case "city_keyword" => AbstractPaceFunctions.cityKeywordInference(value)
+      case _ => value
+    }
+
+    res
+  }
+
 }
 
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CityMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CityMatch.java
deleted file mode 100644
index 1d898ad83..000000000
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CityMatch.java
+++ /dev/null
@@ -1,48 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("cityMatch")
-public class CityMatch extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	public CityMatch(Map<String, String> params) {
-		super(params);
-		this.params = params;
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-
-		String ca = cleanup(a);
-		String cb = cleanup(b);
-
-		ca = normalize(ca);
-		cb = normalize(cb);
-
-		ca = filterAllStopWords(ca);
-		cb = filterAllStopWords(cb);
-
-		Set<String> cities1 = getCities(ca, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> cities2 = getCities(cb, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		Set<String> codes1 = citiesToCodes(cities1);
-		Set<String> codes2 = citiesToCodes(cities2);
-
-		// if no cities are detected, the comparator gives 1.0
-		if (codes1.isEmpty() && codes2.isEmpty())
-			return 1.0;
-		else {
-			if (codes1.isEmpty() ^ codes2.isEmpty())
-				return -1; // undefined if one of the two has no cities
-			return commonElementsPercentage(codes1, codes2);
-		}
-	}
-}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java
new file mode 100644
index 000000000..25a12bcdf
--- /dev/null
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java
@@ -0,0 +1,51 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("codeMatch")
+public class CodeMatch extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	private Pattern CODE_REGEX;
+
+	public CodeMatch(Map<String, String> params) {
+		super(params);
+		this.params = params;
+		this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]::\\d+"));
+	}
+
+	public Set<String> getRegexList(String input) {
+		Matcher matcher = this.CODE_REGEX.matcher(input);
+		Set<String> cities = new HashSet<>();
+		while (matcher.find()) {
+			cities.add(matcher.group());
+		}
+		return cities;
+	}
+
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+
+		Set<String> codes1 = getRegexList(a);
+		Set<String> codes2 = getRegexList(b);
+
+		// if no codes are detected, the comparator gives 1.0
+		if (codes1.isEmpty() && codes2.isEmpty())
+			return 1.0;
+		else {
+			if (codes1.isEmpty() ^ codes2.isEmpty())
+				return -1; // undefined if one of the two has no codes
+			return commonElementsPercentage(codes1, codes2);
+		}
+	}
+}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
index 9cf616356..96a87c455 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
@@ -1,6 +1,8 @@
+
 package eu.dnetlib.pace.tree;
 
 import java.util.Map;
+import java.util.Set;
 
 import com.wcohen.ss.AbstractStringDistance;
 
@@ -11,37 +13,42 @@ import eu.dnetlib.pace.tree.support.ComparatorClass;
 @ComparatorClass("countryMatch")
 public class CountryMatch extends AbstractStringComparator {
 
-    public CountryMatch(Map<String, String> params) {
-        super(params, new com.wcohen.ss.JaroWinkler());
-    }
+	private Map<String, String> params;
 
-    public CountryMatch(final double weight) {
-        super(weight, new com.wcohen.ss.JaroWinkler());
-    }
+	public CountryMatch(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		this.params = params;
+	}
 
-    protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
-        super(weight, ssalgo);
-    }
+	public CountryMatch(final double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
 
-    @Override
-    public double distance(final String a, final String b, final Config conf) {
-        if (a.isEmpty() || b.isEmpty()) {
-            return -1.0; // return -1 if a field is missing
-        }
-        if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
-            return -1.0; // return -1 if a country is UNKNOWN
-        }
+	protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
 
-        return a.equals(b) ? 1.0 : 0;
-    }
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
 
-    @Override
-    public double getWeight() {
-        return super.weight;
-    }
+		if (a.isEmpty() || b.isEmpty()) {
+			return -1.0; // return -1 if a field is missing
+		}
+		if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
+			return -1.0; // return -1 if a country is UNKNOWN
+		}
+
+		return a.equals(b) ? 1.0 : 0;
+	}
+
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
+
+	@Override
+	protected double normalize(final double d) {
+		return d;
+	}
 
-    @Override
-    protected double normalize(final double d) {
-        return d;
-    }
 }
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerLegalname.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerLegalname.java
new file mode 100644
index 000000000..e4a48c459
--- /dev/null
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerLegalname.java
@@ -0,0 +1,59 @@
+
+package eu.dnetlib.pace.tree;
+
+import java.util.Map;
+import java.util.Set;
+
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
+@ComparatorClass("jaroWinklerLegalname")
+public class JaroWinklerLegalname extends AbstractStringComparator {
+
+	private Map<String, String> params;
+
+	private final String CITY_CODE_REGEX = "city::\\d+";
+	private final String KEYWORD_CODE_REGEX = "key::\\d+";
+
+	public JaroWinklerLegalname(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		this.params = params;
+	}
+
+	public JaroWinklerLegalname(double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
+
+	protected JaroWinklerLegalname(double weight, AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
+
+	@Override
+	public double distance(String a, String b, final Config conf) {
+
+		String ca = a.replaceAll(CITY_CODE_REGEX, "").replaceAll(KEYWORD_CODE_REGEX, " ");
+		String cb = b.replaceAll(CITY_CODE_REGEX, "").replaceAll(KEYWORD_CODE_REGEX, " ");
+
+		ca = ca.replaceAll("[ ]{2,}", " ");
+		cb = cb.replaceAll("[ ]{2,}", " ");
+
+		if (ca.isEmpty() && cb.isEmpty())
+			return 1.0;
+		else
+			return normalize(ssalgo.score(ca, cb));
+	}
+
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
+
+	@Override
+	protected double normalize(double d) {
+		return d;
+	}
+
+}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java
deleted file mode 100644
index 576b9281d..000000000
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JaroWinklerNormalizedName.java
+++ /dev/null
@@ -1,74 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import com.wcohen.ss.AbstractStringDistance;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("jaroWinklerNormalizedName")
-public class JaroWinklerNormalizedName extends AbstractStringComparator {
-
-	private Map<String, String> params;
-
-	public JaroWinklerNormalizedName(Map<String, String> params) {
-		super(params, new com.wcohen.ss.JaroWinkler());
-		this.params = params;
-	}
-
-	public JaroWinklerNormalizedName(double weight) {
-		super(weight, new com.wcohen.ss.JaroWinkler());
-	}
-
-	protected JaroWinklerNormalizedName(double weight, AbstractStringDistance ssalgo) {
-		super(weight, ssalgo);
-	}
-
-	@Override
-	public double distance(String a, String b, final Config conf) {
-		String ca = cleanup(a);
-		String cb = cleanup(b);
-
-		ca = normalize(ca);
-		cb = normalize(cb);
-
-		ca = filterAllStopWords(ca);
-		cb = filterAllStopWords(cb);
-
-		Set<String> keywords1 = getKeywords(
-			ca, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> keywords2 = getKeywords(
-			cb, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		Set<String> cities1 = getCities(ca, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> cities2 = getCities(cb, Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		ca = removeKeywords(ca, keywords1);
-		ca = removeKeywords(ca, cities1);
-		cb = removeKeywords(cb, keywords2);
-		cb = removeKeywords(cb, cities2);
-
-		ca = ca.replaceAll("[ ]{2,}", " ");
-		cb = cb.replaceAll("[ ]{2,}", " ");
-
-		if (ca.isEmpty() && cb.isEmpty())
-			return 1.0;
-		else
-			return normalize(ssalgo.score(ca, cb));
-	}
-
-	@Override
-	public double getWeight() {
-		return super.weight;
-	}
-
-	@Override
-	protected double normalize(double d) {
-		return d;
-	}
-
-}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/KeywordMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/KeywordMatch.java
deleted file mode 100644
index 53acb4dc8..000000000
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/KeywordMatch.java
+++ /dev/null
@@ -1,50 +0,0 @@
-
-package eu.dnetlib.pace.tree;
-
-import java.util.Map;
-import java.util.Set;
-
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-
-@ComparatorClass("keywordMatch")
-public class KeywordMatch extends AbstractStringComparator {
-
-	Map<String, String> params;
-
-	public KeywordMatch(Map<String, String> params) {
-		super(params);
-		this.params = params;
-	}
-
-	@Override
-	public double distance(final String a, final String b, final Config conf) {
-
-		String ca = cleanup(a);
-		String cb = cleanup(b);
-
-		ca = normalize(ca);
-		cb = normalize(cb);
-
-		ca = filterAllStopWords(ca);
-		cb = filterAllStopWords(cb);
-
-		Set<String> keywords1 = getKeywords(
-			ca, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-		Set<String> keywords2 = getKeywords(
-			cb, conf.translationMap(), Integer.parseInt(params.getOrDefault("windowSize", "4")));
-
-		Set<String> codes1 = toCodes(keywords1, conf.translationMap());
-		Set<String> codes2 = toCodes(keywords2, conf.translationMap());
-
-		// if no cities are detected, the comparator gives 1.0
-		if (codes1.isEmpty() && codes2.isEmpty())
-			return 1.0;
-		else {
-			if (codes1.isEmpty() ^ codes2.isEmpty())
-				return -1.0; // undefined if one of the two has no keywords
-			return commonElementsPercentage(codes1, codes2);
-		}
-	}
-}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
index 0973fdf1e..0ff03f5e1 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
@@ -48,7 +48,7 @@ public class TreeNodeDef implements Serializable {
 	// function for the evaluation of the node
 	public TreeNodeStats evaluate(Row doc1, Row doc2, Config conf) {
 
-		TreeNodeStats stats = new TreeNodeStats();
+		TreeNodeStats stats = new TreeNodeStats(ignoreUndefined);
 
 		// for each field in the node, it computes the
 		for (FieldConf fieldConf : fields) {
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
index 2b96048b4..a210c06b2 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
@@ -9,8 +9,11 @@ public class TreeNodeStats implements Serializable {
 
 	private Map<String, FieldStats> results; // this is an accumulator for the results of the node
 
-	public TreeNodeStats() {
+	private final boolean ignoreUndefined;
+
+	public TreeNodeStats(boolean ignoreUndefined) {
 		this.results = new HashMap<>();
+		this.ignoreUndefined = ignoreUndefined;
 	}
 
 	public Map<String, FieldStats> getResults() {
@@ -22,7 +25,10 @@ public class TreeNodeStats implements Serializable {
 	}
 
 	public int fieldsCount() {
-		return this.results.size();
+		if(ignoreUndefined)
+			return this.results.size();
+		else
+			return this.results.size() - undefinedCount();	//do not count undefined
 	}
 
 	public int undefinedCount() {
@@ -78,11 +84,25 @@ public class TreeNodeStats implements Serializable {
 		double min = 100.0; // random high value
 		for (FieldStats fs : this.results.values()) {
 			if (fs.getResult() < min) {
-				if (fs.getResult() >= 0.0 || (fs.getResult() == -1 && fs.isCountIfUndefined()))
+				if (fs.getResult() == -1) {
+					if (fs.isCountIfUndefined()) {
+						min = 0.0;
+					}
+					else {
+						min = -1;
+					}
+				}
+				else {
 					min = fs.getResult();
+				}
 			}
 		}
-		return min;
+		if (ignoreUndefined) {
+			return min==-1.0? 0.0 : min;
+		}
+		else {
+			return min;
+		}
 	}
 
 	// if at least one is true, return 1.0
@@ -91,7 +111,11 @@ public class TreeNodeStats implements Serializable {
 			if (fieldStats.getResult() >= fieldStats.getThreshold())
 				return 1.0;
 		}
-		return 0.0;
+		if (!ignoreUndefined && undefinedCount()>0){
+			return -1.0;
+		} else {
+			return 0.0;
+		}
 	}
 
 	// if at least one is false, return 0.0
@@ -100,7 +124,7 @@ public class TreeNodeStats implements Serializable {
 
 			if (fieldStats.getResult() == -1) {
 				if (fieldStats.isCountIfUndefined())
-					return 0.0;
+					return ignoreUndefined? 0.0 : -1.0;
 			} else {
 				if (fieldStats.getResult() < fieldStats.getThreshold())
 					return 0.0;
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
index 263504dbb..8ae5aa591 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
@@ -43,18 +43,17 @@ public class TreeProcessor {
 
 			TreeNodeStats stats = currentNode.evaluate(doc1, doc2, config);
 			treeStats.addNodeStats(nextNodeName, stats);
-
-			// if ignoreUndefined=false the miss is considered as undefined
-			if (!currentNode.isIgnoreUndefined() && stats.undefinedCount() > 0) {
+			
+			double finalScore = stats.getFinalScore(currentNode.getAggregation());
+			if(finalScore == -1.0)
 				nextNodeName = currentNode.getUndefined();
-			}
-			// if ignoreUndefined=true the miss is ignored and the score computed anyway
-			else if (stats.getFinalScore(currentNode.getAggregation()) >= currentNode.getThreshold()) {
+			else if (finalScore >= currentNode.getThreshold()) {
 				nextNodeName = currentNode.getPositive();
 			} else {
 				nextNodeName = currentNode.getNegative();
 			}
 
+
 		} while (MatchType.parse(nextNodeName) == MatchType.UNDEFINED);
 
 		treeStats.setResult(MatchType.parse(nextNodeName));
diff --git a/dhp-pace-core/src/main/resources/eu/dnetlib/pace/config/country_map.csv b/dhp-pace-core/src/main/resources/eu/dnetlib/pace/config/country_map.csv
new file mode 100644
index 000000000..01e49979c
--- /dev/null
+++ b/dhp-pace-core/src/main/resources/eu/dnetlib/pace/config/country_map.csv
@@ -0,0 +1,239 @@
+JP;Sapporo;Kobe;Okayama;Maebashi;Nagoya;Yamaguchi;Sendai;Nagano;Saga;Otsu;Niigata;Akita;Fukui;Matsue;Yamagata;Wakayama;Nagasaki;Kumamoto;Shizuoka;Osaka;Chiba;Hiroshima;Yawatahama-shi;Gifu;Takamatsu;Naha;Fukushima;Yokohama;Kagoshima;Kyoto;Aomori;Kanazawa;Miyazaki;Tsu;Tokyo;Toyama;Kochi;Tokushima;Hirado;Fukuoka;Mito;Japan;Utsunomiya;Nara;Kofu;Kozakai-cho;Saitama;Oita;Matsuyama;Morioka
+ID;Tahuna;Amuntai;Karanganyar;Pangkalpinang;Makassar;Ranai;Sampit;Melonguane;Kotabumi;Jember;Banjar;Tanjungpandan;Tembagapura;Kisaran;Pangururan;Rangkasbitung;Bandar Lampung;Buntok;Tarutung;Makale;Saumlaki;Larantuka;Raba;Palangkaraya;Airmadidi;Ruteng;Indonesia;Padang;Sanana;Jambi;Bagan Si Api-api;Rantau Prapat;Watampone;Tambolaka;Bandung;Meulaboh;Cilacap;Serui;Denpasar;Manggar;Bengkalis;Piru;Parigi;Pekanbaru;Bengkulu;Tenggarong;Maumere;Majalengka;Soreang;Menggala;Palu;Sumenep;Sumber;Surabaya;Kandangan;Kupang;Betun;Kendari;Tanjungpinang;Mataram;Waingapu;Maba;Ambon;Ciamis;Rantepao;Atambua;Manado;Pelabuhanratu;Nabire;Banyuwangi;Ransiki;Bintuni;Lubuk Sikaping;Ende;Tanjung Selor;Cibinong;Kefamenanu;Wamena;Fakfak;Praya;Dompu;Tobelo;Sumbawa Besar;Raha;Biak;Gunungsitoli;Kuala Kapuas;Tuban;Bangkinang;Yogyakarta;Amahai;Pariaman;Pontianak;Merauke;Putussibau;Leramatang;Sofifi;Kolonodale;Singaraja;Cianjur;Jakarta;Jepara;Tomohon;Medan;Poso;Namlea;Kuningan;Taliwang;Pamekasan;Kuala Pembuang;Purwokerto;Bangkalan;Kaimana;Batang;Muara Teweh;Sorong;Ungaran;Barabai;Waikabubak;Prabumulih;Masamba;Samarinda;Semarang;Puruk Cahu;Pageralam;Barru;Rappang;Martapura;Sentani;Painan;Indramayu;Banjarmasin;Cimerak;Karawang;Tamiang Layang;Bungku;Pinrang;Jayapura;Bebandem;Manokwari;Majene;Ampana;Purwakarta;Palembang;Slateng Dua;Garut;Subang;Sungailiat;Lahat;Mamuju;Soe;Pati;Tentena;Singaparna;Kalabahi;Luwuk;Tarogong;Banda Aceh;Saparua;Teminabuan;Gorontalo;Serang
+IN;Ahmedabad;Shimla;Calicut;Jammu;Raipur;Chennai;New Delhi;Itanagar;Dehra Dun;Kolkata;Chandigarh;Jaipur;Thiruvananthapuram;Panchkula;India;Hyderabad;Bhopal;Bhubaneshwar;Kohima;Bangalore;Amaravati;Port Blair;Lucknow;Shillong;Aizawl;Dispur;Kavaratti;Mumbai;Daman;Gangtok;Imphal;Delhi;Srinagar;Agartala;Patna;Panaji;Ghandinagar;Ranchi;Puducherry;Madurai
+CN;Changsha;Guangzhou;Fuqing;Dongyang;Yushan;Qingping;Leiyang;Hongshui;Shanhu;Meishan;Suileng;Gyegu;Quyang;Encheng;Weinan;Xushan;Tongliao;Qinzhou;Tengyue;Taiyuan;Tacheng;Tangdong;Puxi;Shuangcheng;Wencheng;Dexing;Beijing;Taohuajiang;Dongping;Jinhua;Wuzhong;Golmud;Boli;Yi Xian;Medog;Yatou;Chaozhou;Zalantun;Xigaze;Anqing;Wangqing;Zhijiang;Linkou;Zhamog;Zhugang;Fuding;Mishan;Jinbi;Longjiang;Neijiang;Yiwu;Fangchenggang;Bayan Hot;Beian;Yuquan;Urumqi;Mianyang;Luocheng;Jinshi;Xinpu;Huishi;Yilong;Hengzhou;Huanggang;Yichun;Tuodian;Zuitou;Xining;Jinan;Jinzhong;Zhongcheng;Lu'an;Dongxing;Yinggen;Fuyuan;Dadukou;Anlu;Weichanglu;Qingquan;Tangdukou;Dongta;Qingdao;Gaoyou;Dalain Hob;Yunzhong;Xiedian;Wuchang;Changde;Minzhu;Yicheng;Jiamusi;Qamdo;Loufan;Zhujiacun;Gutao;Shangzhi;Dianbu;Shacheng;Zhuji;Guigang;Qingan;Ji'an;Huazangsi;Leping;Changling;Dashiqiao;Mazhang;Tailai;Baishan;Jiangmen;Altay;Kaiyuan;Chang'an;Beihai;Suohe;Shenyang;Zhangye;Sanming;Guankou;Ma'erkang;Nanchang;Karakax;Rongcheng;Ningbo;Kaiyun;Linxi;Heshan;Xinyu;Kaifeng Chengguanzhen;Liujiaxia;Guang'an;Mengmeng;Tieli;Chengjiao;Lianzhou;Jian'ou;Yangjiang;Leizhou;Xianyang;Yian;Jianshe;Kunming;Deyang;Liuhe;Yangshe;Xiaping;Dongtai;Huquan;Fujin;Siyang;Yisuhe;Yanqi;Kaiwen;Lingshou;Hechi;Taixing;Jiancheng;Qinggang;Xireg;Yutan;Xinzhou;Laojiezi;Xiayang;Yancheng;Liaocheng;Ningde;Heihe;Gaizhou;Xibeijie;Helixi;Taicheng;Uchturpan;Jiaoxiyakou;Chongqing;Jiayuguan;Yanjiang;Nenjiang;Suonan;Xianshuigu;Yakou;Gexianzhuang;Qiqihar;Lanyi;Shangtianba;Laiyuan;Tianchang;Meizhou;Huichang;Haikou;Zequ;Shuanghe;Shijiazhuang;Mizhou;Luanzhou;Yunfu;Mali;Zanhuang;Hoh Ereg;Xishan;Fucheng;Huaiyang;Qionghu;Wuxi;Anguo;Xinhualu;Nehe;Xinxing;Weifen;Tekes;Longquan;Kuaidamao;Rizhao;Zhangzhou;Zhaozhou;Tongshan;Yongbei;Lecheng;Jinshan;Zhenzhou;Huili Chengguanzhen;Xiangyang;Muping;Baoding;Changzhou;Qianzhou;Huilong;Kaji;Dingzhou;Langzhong;Ailan 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Shi;Yushu;Wuhu;Zhongba;Taizhou;Shulan;Longyan;Cili;Lushar;Gaozhou;Hengshui;Songyang;Jinchang;Helong;Shenzhou;Kuytun;Ganzhou;Luohe;Nilka;Puyang;Dali;Guilin;Qapqal;Nanping;Luancheng;Korla;Yingkou;Chengjiao Chengguanzhen;Dongguan;Zhengjiatun;Xihuachi;Xi'an;Harbin;Gar;Leshou;Baiquan;Yaofeng;Quanzhou;Lianran;Guma;Aksu;Xinhua;Gaobeidian;Shangpa;Shihezi;Lianshan;Aheqi;Yiyang;Wuxue;Hezhou;Mingxing;Jizhou;Wenchang;Baocheng;Chuimatan;Haicheng;Liancheng;Jinghong;Shaowu;Heyuan;Ma'anshan;Foshan;Qingyuan;Huzhou;Toli;Zunhua;Xiping;Turpan;Maoming;Huizhou;Hekou;Hefei;Chongzuo;Yanghe;Lechang;Guangming;Yibin;Wancheng;Hongliuwan;Yinchuan;Zhaodong;Lianhe;Kangbao;Qagan Us;Gaoping;Simao;Xichang;Lin'an;Jishi;Huangzhai;Suihua;Xiluodu;Hailin;Zhanjiang;Qincheng;Xiamen;Kashgar;Qiaotou;Nanning;Shantou;Fusui;Gaocheng;Zhanggu;Chuqung;Liuzhou;Shuangyashan;Jingping;Longhua;Shanwei;Shazhou;Lanzhou;Rucheng;Jinhe;Yunxian Chengguanzhen
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+BR;Lagoa do Mato;Sousa;Neopolis;Pirai do Norte;Limoeiro do Norte;Anastacio;Frecheirinha;Varjota;Rio Tinto;Palmeira dos Indios;Cha Grande;Balsas;Araioses;Aracati;Remigio;Floriano;Ico;Guamare;Itiquira;Pedras de Fogo;Ipiau;Conceicao de Jacuipe;Jucas;Cha da Alegria;Itapecuru Mirim;Acopiara;Goianinha;Pao de Acucar;Manaquiri;Paramoti;Colina;Jucurutu;Rio Formoso;Coari;Rio Real;Sao Felix;Aragoiania;Ararenda;Itapiranga;Baiao;Patu;Amapa;Itubera;Atalaia;Passagem Franca;Uropa;Caem;Carnaubal;Gurupi;Alta Floresta;Sao Tome;Jaru;Guajara-Mirim;Primavera;Macajuba;Dianopolis;Queimadas;Madalena;Fonte Boa;Morro Agudo;Morada Nova;Pastos Bons;Goias;Tapiramuta;Acarau;Atalaia do Norte;Cristinapolis;Aratuba;Sao Francisco;Mazagao;Viseu;Aracaju;Feira de Santana;Penedo;Cuite;Parnarama;Boqueirao;Barreira;Conceicao das Alagoas;Juazeirinho;Colorado do Oeste;Brazil;Canguaretama;Lucena;Sapeacu;Feijo;Sao Francisco do Maranhao;Ielmo Marinho;Barra;Santa Quiteria do Maranhao;Guaraci;Castanhal;Grajau;Edeia;Passira;Pimenta Bueno;Nazare da Mata;Acari;Escada;Codajas;Itagi;Beneditinos;Palmacia;Japura;Tracuateua;Ji-Parana;Jaragua;Formosa do Rio Preto;Sao Joao Batista;Santa Luzia do Itanhy;Soledade;Florania;Tuntum;Ibiraci;Altos;Cupira;Lagoa dos Gatos;Luis Correia;Uarini;Lagoa da Confusao;Florianopolis;Alhandra;Baixa Grande;Anguera;Araxa;Mineiros;Pocao de Pedras;Penalva;Joaquim Gomes;Nova Olinda;Mansidao;Governador Dix-Sept Rosado;Simoes Filho;Tucuma;Arari;Varzedo;Sao Pedro do Piaui;Joao Camara;Natividade;Lavras da Mangabeira;Alcantaras;Santana do Cariri;Jaguaretama;Brasnorte;Barao do Grajau;Aragarcas;Itainopolis;Santa Isabel do Para;Carauari;Nina Rodrigues;Nossa Senhora dos Milagres;Sao Miguel das Matas;Aratuipe;Baturite;Colares;Pianco;Messias;Pires Ferreira;Moreno;Campo Maior;Ibateguara;Tapaua;Capao da Canoa;Augustinopolis;Manoel Vitorino;Palhano;Cacu;Torres;Aguas Belas;Ibipetuba;Paulino Neves;Ubata;Tibau do Sul;Capanema;Itumbiara;Palmares;Olimpia;Quixada;Frutal;Tome-Acu;Cururupu;Vitoria;Xapuri;Paripiranga;Paragominas;Juripiranga;Wagner;Marapanim;Rio de Janeiro;Meruoca;Sao Francisco do Conde;Itapipoca;Capim;Sao Jose da Coroa Grande;Canutama;Serra Branca;Colonia Leopoldina;Riachao das Neves;Calcoene;Matoes;Madre de Deus;Santa Ines;Candido Mendes;Valente;Umbauba;Joao Pessoa;Craibas;Urucurituba;Buriti Alegre;Orobo;Goiania;Jaboatao dos Guararapes;Vargem Grande;Sao Bento;Autazes;Coelho Neto;Mauriti;Parnaiba;Crateus;Mata de Sao Joao;Guara;Alto Santo;Mocajuba;Quipapa;Campo Novo do Parecis;Maragogipe;Iraucuba;Indiaroba;Sacramento;Coracao de Maria;Nova Crixas;Arara;Barauna;Formoso do Araguaia;Puxinana;Saubara;Serra Preta;Pedro Velho;Morro do Chapeu;Lagoa do Ouro;Barra de Santa Rosa;Manacapuru;Tiangua;Anori;Sao Miguel do Guapore;Ipojuca;Caninde;Uniao dos Palmares;Jandaira;Sao Vicente Ferrer;Barreirinha;Capitao Poco;Pauini;Alianca;Russas;Maranguape;Baia da Traicao;Aracoiaba;Itamaraca;Gudofredo 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Parecis;Umarizal;Maraba;Coroata;Rio Preto da Eva;Passa e Fica;Conceicao do Almeida;Ibirataia;Sao Luis do Quitunde;Tocantinopolis;Tonantins;Boa Vista;Novo Airao;Itapissuma;Cumaru;Alagoa Grande;Miranorte;Guaira;Itapororoca;Tupanatinga;Monte Alegre;Barretos;Mundo Novo;Tejucuoca;Patrocinio Paulista;Macapa;Presidente Vargas;Currais Novos;Croata;Anapurus;Nilo Pecanha;Senador Jose Porfirio;Ipiranga do Piaui;Porto de Pedras;Paco do Lumiar;Chapada dos Guimaraes;Itamarati;Santo Antonio;Gloria do Goita;Santo Antonio do Ica;Vila do Conde;Jericoacoara;Serrolandia;Sao Joaquim da Barra;Poranga;Centralina;Euclides da Cunha;Braganca;Sao Caetano de Odivelas;Ibicuitinga;Pocone;Bananeiras;Axixa do Tocantins;Cruzeiro do Sul;Sao Sebastiao do Uatuma;Amarante;Caldeirao Grande;Barreirinhas;Costa Marques;Santa Teresinha (2);Brejo do Cruz;Catende;Diamantino;Codo;Esperanca;Maxaranguape;Guiratinga;Pontalina;Nova Brasilandia d'Oeste;Aquidaba;Macaiba;Jaguaribara;Ribeiropolis;Belo 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Goias;Catu;Anajas;Camamu;Limoeiro;Sao Miguel do Araguaia;Carmo do Rio Verde;Caucaia;Sao Joao;Terra Santa;Pio XII;Passos;Campo Formoso;Nossa Senhora do Livramento;Valenca;Careiro da Varzea;Goianapolis;Colinas do Tocantins;Acarape;Barroquinha;Jardim do Serido;Augusto Correa;Guapo;Porto Acre;Tres Cachoeiras;Caridade;Brejo Santo;Alagoa Nova;Sorriso;Matriz de Camarajibe;Canapolis;Maceio;Camarajibe;Fortim;Aracas;Maruim;Delta;Soure;Terra Alta;Colider;Demerval Lobao;Porangatu;Itau de Minas;Belterra;Ipaporanga;Palmeirais;Japaratinga;Sao Sebastiao do Passe;Itaporanga;Porto Franco;Manicore;Salvaterra;Pindobacu;Coremas;Guimaraes;Abaiara;Ceara-Mirim;Rio do Fogo;Seringueiras;Tamandare;Antenor Navarro;Loreto;Campo do Brito;Marau;Jitauna;Montes Altos;Sirinhaem;Missao Velha;Pereiro;Ruy Barbosa;Paraipaba;Porto Alegre do Norte;Caraubas;Touros;Sao Paulo de Olivenca;Wanderlandia;Nazaria;Palmas;Pinheiro;Massaranduba;Ipaumirim;Porto Valter;Sao Domingos do Maranhao;Jutai;Anajatuba;Labrea;Aramari;Carneiros;Confresa;Utinga;Humaita;Cascavel;Buriti dos Lopes;Cocal;Planura;Carutapera;Porto Grande;Aurora;Santo Amaro;Cajari;Chapadinha;Melgaco;Curuca;Dario Meira;Matinha;Amatura;Luis Gomes;Itarema;Anicuns;Eusebio;Massape;Vila Rica;Afonso Bezerra;Monsenhor Gil;Rolim de Moura;Santa Maria do Para;Fronteiras;Itabaianinha;Macaparana;Barreiros;Paraibano;Vitoria de Santo Antao;Timon;Apuiares;Serrinha;Magalhaes de Almeida;Jacareacanga;Acailandia;Viana;Moncao;Peri-Mirim;Curua;Mata Roma;Sao Joaquim do Monte;Mirador;Sao Jose da Tapera;Xexeu;Tartarugalzinho;Dias d'Avila;Capitao de Campos;Guarabira;Banabuiu;Belem;Nossa Senhora Aparecida;Uruburetama;Jacunda;Colinas;Maracacume;Agrestina;Icatu;Pacoti;Sao Benedito;Maracas;Buenos Aires;Sao Jose de Ribamar;Jaicos;Salinas da Margarida;Conceicao do Coite;Valinhos;Lucas do Rio Verde;Sao Luis de Montes Belos;Vera Cruz;Dom Pedro;Oros;Jardim de Piranhas;Martinopole;Nisia Floresta;Marechal Deodoro;Sao Sebastiao de Lagoa de Roca;Ocara;Brasil Novo;Campo Redondo;Santana do Ipanema;Ibiapina;Santa Teresinha;Cedral;Nova Ipixuna;Regeneracao;Groairas;Almeirim;Graca;Goiatuba;Mamanguape;Cortes;Paraiso do Tocantins;Boa Viagem;Taperoa;Benjamin Constant;Baia Formosa;Brasilia;Jaqueira;Parnamirim;Quirinopolis;Tefe;Mirinzal;Ourem;Caapiranga;Itapitanga;Farias Brito;Miguelopolis;Olho d'Agua das Flores;Cacimba de Dentro;Nobres;Conceicao da Feira;Itaitinga;Itaquitinga;Pirpirituba;Conceicao do Araguaia;Jose de Freitas;Barbalha;Cacimbinhas;Maribondo;Pau d'Alho;Juazeiro do Norte;Itapaci;Santa Luzia;Corrente;Capinopolis;Marcolandia;Jaguaquara;Aquiraz;Poco Branco;Quixeramobim;Mirante da Serra;Caico;Condado;Simao Dias;Paracuru;Redencao;Aquidauana;Santana do Acarau;Poxoreo;Rubiataba;Monsenhor Tabosa;Itatuba;Laje;Bonito;Macau;Pocinhos;Carius;Cabedelo;Chupinguaia;Capim Grosso;Alto do Rodrigues;Urbano Santos;Caririacu;Terra Boa;Araua;Icapui;Ourilandia do Norte;Piquet Carneiro;Uniao;Grossos;Buriti Bravo;Eirunepe;Sao Miguel do Guama;Sao Luis;Alexandria;Manuel Urbano;Alto Garcas;Alagoinhas;Upanema;Miguel Alves;Sao Pedro da Agua Branca;Carpina;Santa Helena de Goias;Fortaleza dos Nogueiras;Chaves;Montanhas;Jaguaripe;Amarante do Maranhao;Nova Ubirata;Saire;Igarape-Acu;Santo Antonio dos Lopes;Rosario do Catete;Potengi;Juina;Sao Jose do Campestre;Teresina;Santa Terezinha de Goias;Sao Goncalo do Amarante;Nova Veneza;Saloa;Joaquim Nabuco;Pedra Preta;Itacoatiara;Jaguaruana;Sao Miguel;Sao Felix do Araguaia;Solonopole;Aripuana;Guaraciaba do Norte;Sao Paulo do Potengi;Crixas;Iraci;Valenca do Piaui;Maracana;Sao Geraldo do Araguaia;Tabuleiro do Norte;Candeias;Fortuna;Tarauaca;Ubajara;Piranhas;Parintins;Cidelandia;Cantanhede;Tutoia;Tabatinga;Beruri;Porto Velho;Novo Lino;Fagundes;Major Isidoro;Sao Benedito do Rio Preto;Poco das Trincheiras;Quixabeira;Caetes;Goianesia;Sao Jose da Laje;Sobral;Vilhena;Morros;Igarapava;Itaiba;Brasileia;Nordestina;Ares;Santa Maria das Barreiras;Rio Largo;Correntes;Inhuma;Passo de Camarajibe;Salvador;Brejao;Brejo
+KR;Cheongju;Sejong;Daegu;Pocheon;Andong;Jeju;Hongseong;Gimpo;Muan;Jeonju;Changwon;Heunghae;Haeryong;Busan;Daejeon;Gangneung;Korea, South;Bucheon;Mokpo;Chuncheon;Goyang;Paju;Suncheon;Guryongpo;Suwon;Incheon;Boryeong;Sokcho;Naju;Yangsan;Gwangyang;Gwangju;Pohang;Seoul;Ulsan;Yeosu
+MX;La Resolana;Nacajuca;Colotlan;Emiliano Zapata;Tlacolula de Matamoros;Coyotepec;Rioverde;Xicotencatl;Amatitan;Chiconcuac;Rafael Delgado;Coacoatzintla;Cuautla;Choix;Ciudad Mante;Tacambaro de Codallos;Quiroga;Carlos A. Carrillo;Ciudad Altamirano;Benito Juarez;Acatic;La Huerta;Tuxtla;Cocotitlan;Acatzingo;Aguascalientes;Tanhuato de Guerrero;Texcatepec;Cardenas;San Jose del Cabo;Moloacan;Ciudad Madero;Juan Aldama;Cuquio;La Trinitaria;Rayon;Ojinaga;Jalapa;Jalpa de Mendez;Perote;Union de San Antonio;Zacatelco;Huandacareo;Ayutla de los Libres;Ixtlahuaca;Candelaria;Santa Ana Jilotzingo;Paraiso;Polotitlan de la Ilustracion;Morelia;Orizaba;Camargo;Acambaro;Santo Domingo Tehuantepec;Tecoanapa;San Pedro Mixtepec;San Andres Timilpan;Jose Maria Morelos;Chiapa de Corzo;Poza Rica de Hidalgo;Temamatla;Tlajomulco de Zuniga;Guadalajara;Candelaria Loxicha;Puerto Penasco;Silao;Chalco;Cuajinicuilapa;Salvatierra;Churumuco de Morelos;San Pedro Garza Garcia;Soledad de Graciano Sanchez;Santiago;Turicato;Escarcega;Chilapa de Alvarez;Zapotlan del Rey;La Huacana;Mexico City;Tamuin;Las Rosas;Capulhuac;Huauchinango;Petatlan;Navolato;Zontecomatlan de Lopez y Fuentes;Sultepec;Teotitlan;Pajapan;Cuencame de Ceniceros;San Francisco del Rincon;Tampamolon Corona;San Julian;Chimalhuacan;Macuspana;Jilotlan de los Dolores;Mineral del Monte;Tecamachalco;Empalme;Tixkokob;Nautla;Guanajuato;Salamanca;Motozintla;Ascension;Citlaltepec;Platon Sanchez;Heroica Nogales;Zapotlan de Juarez;El Pueblito;Teopisca;Atlatlahucan;Cerritos;Valle Hermoso;Coyuca de Catalan;Sonoita;Puebla;Cuernavaca;San Felipe del Progreso;Ixtaczoquitlan;Uriangato;Cochoapa el Grande;Santa Isabel Cholula;Salinas de Hidalgo;Ciudad de Atlixco;Valle de Bravo;Cunduacan;Yuriria;Santa Maria Huatulco;Abasolo;Ixtlahuacan del Rio;Cananea;Vicente Guerrero;Tlacolulan;Altepexi;Tapachula;Nanchital de Lazaro Cardenas del Rio;Ensenada;Ciudad Serdan;Tlalpujahua de Rayon;Jimenez;Tlalnepantla;Tonala;Chiconquiaco;Filomeno Mata;Magdalena de Kino;Coquimatlan;Reynosa;Ciudad Guzman;Acapetahua;Garcia;La Paz;Texistepec;Ocotlan de Morelos;Cosio;Ocuilan de Arteaga;Chilcuautla;San Andres Tuxtla;Doctor Mora;Magdalena;Tecolotlan;Arriaga;Felipe Carrillo Puerto;Nuevo Casas Grandes;San Pedro Pochutla;Tolcayuca;Juchitan de Zaragoza;Tamazunchale;Tejupilco;San Felipe;Valle Nacional;Tala;Villahermosa;San Luis Potosi;Tizimin;Huasca de Ocampo;Nacozari de Garcia;Santa Cruz Atizapan;Ciudad Guadalupe Victoria;Tehuacan;Altamira;Tlapa de Comonfort;Tecate;Tepetzintla;Jiutepec;Ocosingo;Mazapil;Jiquipilas;Encarnacion de Diaz;Etchojoa;San Pablo Huixtepec;Huejucar;Naucalpan de Juarez;Suchiapa;La Cruz;Saucillo;Yecuatla;Chicoloapan;Tres Valles;Delicias;Oteapan;Mazatlan Villa de Flores;Amatlan de los Reyes;Pinotepa;Zapotiltic;Jonuta;Jocotepec;Charcas;El Espinal;Jesus Maria;San Ignacio Cerro Gordo;Venustiano Carranza;Soledad Atzompa;El Rosario;Hecelchakan;Huejotzingo;Soledad de Doblado;Ayutla;Jaltenco;Tepotzotlan;Yahualica de Gonzalez Gallo;Celaya;Putla Villa de Guerrero;Erongaricuaro;Ciudad Santa Catarina;Tomatlan;Villa Corona;Torreon;San Juan del Rio del Centauro del Norte;San Buenaventura;Pantelho;Atoyac de Alvarez;Tlacotepec;Cozumel;Xico;Monclova;Apizaco;Coatepec;Mecatlan;Uman;Castillo de Teayo;Zimatlan de Alvarez;Ciudad Cuauhtemoc;Acambay;Guasave;San Pedro Jicayan;Tixtla de Guerrero;Espita;Jocotitlan;Ignacio de la Llave;Tepic;Joquicingo;Valparaiso;Campeche;Muna;Playa del Carmen;San Juan del Rio;Xalapa;Mazatan;Sabinas;Santiago Suchilquitongo;Guamuchil;Mineral de Angangueo;Temascalapa;Paso del Macho;Nochistlan de Mejia;Ixhuatlan de Madero;Cuautepec de Hinojosa;Hidalgotitlan;Tecamac;Meoqui;Ometepec;Zumpango del Rio;Champoton;Asuncion Nochixtlan;Texcoco;Ozuluama de Mascarenas;Acanceh;Halacho;Hueyotlipan;Tecali;Rincon de Romos;Mazatlan;Villa Luvianos;Cacahoatan;Tezontepec;San Nicolas de los Ranchos;Tatahuicapan;Lagos de Moreno;Colima;Soyalo;Isla Mujeres;Ixtapaluca;Galeana;Ciudad Benito Juarez;Yecapixtla;Durango;Huamantla;Ezequiel Montes;Juarez;Acatlan;San Pedro Huamelula;Actopan;Tepalcatepec;Villaflores;Monterrey;Playas de Rosarito;Tetela de Ocampo;Tepetlixpa;Texcaltitlan;Jamapa;Almoloya de Alquisiras;Zacualpan;Kanasin;Ozumba;San Blas;Queretaro;Degollado;Jaral del Progreso;Tecuala;Tzintzuntzan;Juventino Rosas;Ciudad Apodaca;Balancan;San Jose Villa de Allende;Ixhuatlancillo;Valle de Santiago;Santa Maria Jacatepec;Ayapango;Nuevo Laredo;Cotija de la Paz;Senguio;Mariano Escobedo;Tapalpa;Zacatecas;Cuitzeo del Porvenir;Frontera;Cerro Azul;Totolapan;Ciudad Miguel Aleman;Santa Maria Chilchotla;Tantoyuca;Union de Tula;San Fernando;Pahuatlan de Valle;Apaseo el Alto;San Jose del Rincon Centro;Toluca;Zapotlanejo;Cosamaloapan;Cadereyta Jimenez;Amatan;Huehuetoca;Chichihualco;Ramos Arizpe;Ocoyoacac;Santiago Tulantepec;Lerma;Ilamatlan;La Independencia;San Carlos Yautepec;Jiquilpan de Juarez;Ciudad de Allende;Panuco;San Miguel de Allende;Chanal;Zacatepec;Soyaniquilpan;Mexicaltzingo;Pachuca;Tamiahua;Ciudad Melchor Muzquiz;Heroica Guaymas;Soteapan;Simojovel de Allende;Guachochi;Naolinco de Victoria;Talpa de Allende;Fortin de las Flores;Coatepec Harinas;Tequila;Tepatitlan de Morelos;Calimaya;Cuilapan de Guerrero;Boca del Rio;Ciudad Hidalgo;Jaltipan de Morelos;Navojoa;Ciudad Lerdo;Atenco;Pijijiapan;Tenancingo;Tehuipango;Ciudad Acuna;Santa Ana Maya;San Pablo Villa de Mitla;Agua Prieta;Huatabampo;Calvillo;Huixcolotla;Ahualulco de Mercado;Almoloya;Tototlan;Cuatro Cienegas de Carranza;San Rafael;General Panfilo Natera;Veracruz;Ameca;Coatzacoalcos;Acaxochitlan;Gomez Palacio;Dolores Hidalgo Cuna de la Independencia Nacional;Tlalixcoyan;Jalacingo;Ocozocoautla de Espinosa;Acala;Manlio Fabio Altamirano;Tenango del Aire;Los Reyes de Juarez;Zaragoza;Santa Maria Xadani;Ixmiquilpan;Juchipila;Nuevo San Juan Parangaricutiro;Pihuamo;Compostela;Mazamitla;Pabellon de Arteaga;Pesqueria;Salinas Victoria;Tlahualilo de Zaragoza;Tlaxcala;Santiago Tuxtla;Etzatlan;Matamoros;Santa Maria Colotepec;Ecatzingo;Ursulo Galvan;Huehuetla;Parras de la Fuente;Manzanillo;Chavinda;Amatepec;Ciudad Constitucion;Piedras Negras;Tulum;Escuintla;Tijuana;Villa Aldama;Cosautlan;Acapulco de Juarez;Zinapecuaro;Alamo;Fresnillo;Tierra Colorada;Iguala de la Independencia;Coroneo;Alamos;San Mateo Atenco;Tulancingo;Guadalupe;Escuinapa;Cueramaro;Aldama;Huatusco;Mexicali;Huanimaro;Tuxpan;Monte Escobedo;Tlalnelhuayocan;San Luis Rio Colorado;Jose Cardel;Temascalcingo;Santiago Papasquiaro;Cuauhtemoc;Huixquilucan;Malinalco;Ciudad Rio Bravo;Zumpango;Chilon;Temoaya;Tezoyuca;Jamay;Comapa;Cuichapa;Comala;Teocuitatlan de Corona;Pichucalco;Amacuzac;Jerez de Garcia Salinas;Tlaquepaque;Santa Rosalia;Tepatlaxco;Tuxpam de Rodriguez Cano;Hueyapan de Ocampo;Atlautla;Chihuahua;Tepoztlan;Ciudad Sabinas Hidalgo;Chilpancingo;Parral;Villanueva;Papantla de Olarte;Ejutla de Crespo;Zempoala;Heroica Caborca;Mexico;Villa Purificacion;Cheran;Hunucma;Las Margaritas;Taxco de Alarcon;Villa de Zaachila;Angel R. Cabada;Cuetzalan;Ciudad General Escobedo;Nava;Tlachichilco;Melchor Ocampo;El Salto;Santa Maria del Tule;San Cristobal;Mecayapan;Maxcanu;Cuapiaxtla de Madero;Miacatlan;Tapilula;Comitan;Tempoal de Sanchez;Altamirano;Zacatlan;Comalapa;Zozocolco de Hidalgo;Merida;Puente Nacional;Ixhuatlan del Sureste;Los Mochis;Chapala;Tepetlan;Linares;Juchique de Ferrer;Amatenango del Valle;Santa Barbara;Puerto Vallarta;Zacoalco de Torres;San Gregorio Atzompa;Tlalmanalco;Villagran;Misantla;San Salvador;Tecoman;Tultepec;Coalcoman de Vazquez Pallares;Calpulalpan;Xalatlaco;Almoloya del Rio;Miahuatlan;Teoloyucan;Tlayacapan;San Pedro;Teapa;Playa Vicente;Mascota;Jalpan;Apan;Leon de los Aldama;Huaquechula;Villa Victoria;Las Vigas de Ramirez;Loreto;Santa Ana Chiautempan;Axochiapan;Cihuatlan;San Jose de Gracia;Bochil;Apaxco de Ocampo;Tlaltetela;Yajalon;Huixtla;Irapuato;Cienega de Flores;Nezahualcoyotl;Hostotipaquillo;Singuilucan;Chinampa de Gorostiza;Santa Maria Jalapa del Marques;Zongolica;San Juan Cancuc;San Jose Tenango;Santiago Tianguistenco;San Bartolo Tutotepec;Zihuatanejo;Ojuelos de Jalisco;San Martin de las Piramides;Tultitlan de Mariano Escobedo;Cintalapa de Figueroa;Tenosique;China;Ciudad de Huajuapam de Leon;Sayula de Aleman;Minatitlan;Tequixquiac;Villa Hidalgo;Mixtla de Altamirano;Doctor Arroyo;Tataltepec de Valdes;Sahuayo de Morelos;Progreso;Ciudad Obregon;Miahuatlan de Porfirio Diaz;Tizayuca;Santiago Ixcuintla;Cuautitlan Izcalli;Ciudad de Huitzuco;Reforma;Apaseo el Grande;San Francisco de los Romo;Isla;El Fuerte;Temascaltepec de Gonzalez;El Oro de Hidalgo;Sayula;Villa Donato Guerra;Patzcuaro;Uruapan;San Juan de los Lagos;Tetela del Volcan;Tepeapulco;Chalma;Culiacan;Cortazar;Tecolutla;Alvarado;San Juan Evangelista;Chapa de Mota;Jamiltepec;Ahumada;Cancun;Ixtlahuacan de los Membrillos;Tezoatlan de Segura y Luna;Pantepec;Francisco I. Madero;Vista Hermosa de Negrete;Oxchuc;Metepec;Tlacoachistlahuaca;Hermosillo;Castanos;Matehuala;Canatlan;Ixtapan de la Sal;Amecameca de Juarez;Naranjos;Ciudad Lopez Mateos;Pueblo Nuevo;Berriozabal;Zinacantepec;San Juanito de Escobedo;Maravatio de Ocampo;Ayotoxco de Guerrero;Villa Juarez;Ocotlan;Tecpan de Galeana;Amatenango de la Frontera;Chocaman;Comalcalco;Ciudad Manuel Doblado;Xochistlahuaca;Montemorelos;Tzitzio;Contla;Cruz Grande;Juanacatlan;Jilotepec;Allende;Axapusco;Huejuquilla el Alto;San Blas Atempa;Zacualpan de Amilpas;Tepechitlan;Totutla;Santa Ana Nextlalpan;San Martin Texmelucan de Labastida;La Piedad;Jaltenango;Nicolas Romero;Tezonapa;Atotonilco el Alto;Gonzalez;Tlalixtac de Cabrera;Cuautitlan;Cazones de Herrera;Santo Tomas de los Platanos;Villa Union;Pajacuaran;Epazoyucan;San Nicolas de los Garza;Penamiller;Ciudad del Carmen;Heroica Ciudad de Tlaxiaco;Heroica Matamoros;Autlan de Navarro;Tepetlaoxtoc;El Arenal;Tlapacoyan;Martinez de la Torre;Santa Maria Tonameca;Cadereyta;La Barca;Cordoba;Tenango de Doria;Madera;Otumba;Juan Rodriguez Clara;Tampico;Oaxaca;Huitzilan;Chetumal;Grajales;Benemerito;San Luis de la Paz;Penjamo;Sombrerete;Zapopan;Nuevo Ideal;Villa del Carbon;Tequisquiapan;Ciudad Valles;Temixco;Rio Grande;La Magdalena Tlaltelulco;Villa de Alvarez;Lerdo de Tejada;Villa Corzo;Tlaltenango de Sanchez Roman;Ciudad Tula;Saltillo;Catemaco;Chenalho;Ciudad Victoria;Santiago Tangamandapio;Pinal de Amoles;Nogales;Santa Clara del Cobre;Ecatepec;Acayucan;Paso de Ovejas;Juchitepec;Tila;Coacalco;Calkini;Santa Ana;Mapastepec;Palenque;Purisima de Bustos
+EG;Az Zaqaziq;Kafr ash Shaykh;Al Fayyum;Suhaj;Qina;At Tur;Damanhur;Suez;Asyut;Al Minya;Matruh;Rafah;Aswan;Egypt;Al Kharjah;Ash Shaykh Zuwayd;Luxor;Port Said;Bani Suwayf;Ismailia;Al Mansurah;Damietta;Al Ghardaqah;Banha;Alexandria;Shibin al Kawm;Bi'r al `Abd;Al `Arish;Cairo;Giza;Tanta
+BD;Rajshahi;Sylhet;Naogaon;Rangpur;Barishal;Dhaka;Khulna;Mymensingh;Chattogram;Gaibandha;Bangladesh
+TH;Chaiyo;Phrai Bueng;Loei;Pa Mok;Phrae;Roi Et;Rattaphum;Phak Hai;Nong Khai;Kamphaeng Phet;Bang Sao Thong;Phuket;Phon Charoen;Sai Buri;Chiang Klang;Chum Phae;Mae Hong Son;Lop Buri;Prachuap Khiri Khan;Phra Phutthabat;Sattahip;Chachoengsao;Bang Phae;Pak Thong Chai;Phra Pradaeng;Chumphon;Thong Pha Phum;Bang Phlat;Mae Sot;Uthai Thani;Salaya;Bang Kruai;Chiang Rai;Bueng Kan;Thung Song;Ranong;Si Sa Ket;Singhanakhon;Akat Amnuai;Nong Bua Lamphu;Bua Yai;Sai Mai;Surat Thani;Yala;Tha Bo;Don Sak;Si Wilai;Det Udom;Rong Kwang;Sing Buri;Nakhon Si Thammarat;Samut Songkhram;Tha Chang;Doi Saket;Wang Sombun;Wang Nam Yen;Bueng Khong Long;Narathiwat;Ban Phai;Kanchanaburi;Maha Sarakham;Saraburi;Ban Na San;Chom Thong;Nakhon Phanom;Thoen;Lamphun;Pak Chong;Kalasin;Ban Bueng;Thung Sai;Sa Kaeo;Bang Bua Thong;Thap Khlo;Phayao;Songkhla;Hat Yai;Huai Yot;Chon Buri;Pak Phanang;Phangnga;Phimai;Warin Chamrap;Kanchanadit;Takua Pa;Phichit;Non Sung;Kaset Wisai;Tha Yang;Phitsanulok;Sakon Nakhon;Nakhon Ratchasima;Klaeng;Doi Lo;Ubon Ratchathani;Pa Sang;Buri Ram;Kantharalak;Tha Mai;Khlong Luang;Mae Ai;Photharam;Tak Bai;Sawankhalok;Rayong;Krathum Baen;Chaiyaphum;Phanat Nikhom;Nong Ki;San Kamphaeng;Suphan Buri;Fao Rai;Chai Prakan;Pran Buri;Tak;Aranyaprathet;Khon Kaen;Taphan Hin;Na Klang;Lam Luk Ka;Khao Yoi;Ang Thong;Ban Chang;Si Satchanalai;Bangkok;Bang Khla;Sadao;Nonthaburi;Phra Nakhon Si Ayutthaya;Wiang Haeng;Sai Ngam;Ko Samui;Bang Racham;Betong;Mukdahan;Dok Kham Tai;Phra Samut Chedi;Pua;Chiang Mai;Tha Luang;Udon Thani;Kosum Phisai;Lampang;Samut Prakan;Wichian Buri;Thap Than;Ban Laem;Trat;Chok Chai;Bang Ban;Nam Som;Wang Saphung;Sikhio;Kathu;Pong Nam Ron;Kantang;Si Racha;Kaeng Khro;Trang;Chanthaburi;Wiang Sa;Nong Khae;Mae Wang;Mae Rim;Pathum Thani;Kranuan;Song Phi Nong;Tha Muang;Nong Bua;Prakhon Chai;Suwannaphum;Satuek;Nakhon Nayok;Nan;Samut Sakhon;Ratchaburi;Nakhon Pathom;Pattani;Cha-am;Ban Pong;Lom Sak;Sukhothai;Nakhon Thai;Phetchabun;Mae Sai;Yasothon;Hua Hin;Khlung;Su-ngai Kolok;Sung Noen;Amnat Charoen;Kaeng Khoi;Pak Kret;Nakhon Sawan;Phetchaburi;Sam Phran;Ban Dung;Den Chai;Satun;Kuchinarai;Nong Wua So;Na Wa;Nang Rong;Phai Sali;Prachin Buri;Phon;Sam Ko;Kut Chap;Yang Talat;Chai Nat;Kamalasai;Phatthalung;Krabi;Surin;Lang Suan;Phibun Mangsahan;Nong Kung Si;Kui Buri;Takhli;Na Yung;Uttaradit;Thailand
+RU;Magas;Pavlovskiy Posad;Kem;Baksan;Barnaul;Dzerzhinsk;Primorsko-Akhtarsk;Tuapse;Bezhetsk;Mozhaysk;Rybinsk;Gulkevichi;Shatura;Ardon;Akhtubinsk;Izhevsk;Kirovo-Chepetsk;Taldom;Zhukovo;Argun;Apatity;Magadan;Nytva;Zelenogradsk;Derbent;Gorno-Altaysk;Budennovsk;Kostroma;Saint Petersburg;Baltiysk;Novoselitskoye;Khimki;Peschanokopskoye;Maykop;Yeysk;Konstantinovsk;Krasnyy Sulin;Kargopol;Starodub;Kudymkar;Sharya;Tutayev;Stavropol;Kotelniki;Kokhma;Ivanovo;Petropavlovsk-Kamchatskiy;Elkhotovo;Slavyansk-na-Kubani;Zheleznogorsk;Kashin;Vyazma;Astrakhan;Gryazi;Kimovsk;Krasnyy Yar;Komsomol'sk-na-Amure;Uzlovaya;Novopavlovsk;Seltso;Boksitogorsk;Shakhunya;Tomsk;Kondopoga;Vyksa;Kineshma;Kirishi;Kimry;Zhukovskiy;Kochubeyevskoye;Pervomaysk;Sergach;Lyudinovo;Vyatskiye Polyany;Nalchik;Khasavyurt;Ulan-Ude;Shuya;Gvardeysk;Nizhniy Novgorod;Slobodskoy;Gatchina;Akhty;Sergiyev Posad;Zelenokumsk;Rybnoye;Chaplygin;Tyumen;Mirnyy;Bogorodsk;Krasnoyarsk;Kemerovo;Udomlya;Chudovo;Alagir;Zadonsk;Kirov;Novodvinsk;Yaransk;Tver;Privolzhsk;Lytkarino;Nikel;Vladimir;Tula;Ramenskoye;Dankov;Kozelsk;Kalyazin;Abakan;Rasskazovo;Galich;Kuvshinovo;Volokolamsk;Svetlyy;Ostrov;Dylym;Kameshkovo;Belaya Glina;Pochinok;Losino-Petrovskiy;Nar'yan-Mar;Kungur;Yur'yev-Pol'skiy;Uchkeken;Kstovo;Sasovo;Ostashkov;Gudermes;Uglich;Saratov;Valday;Sarapul;Solnechnogorsk;Labinsk;Pitkyaranta;Mozdok;Belorechensk;Pestovo;Kozmodemyansk;Ipatovo;Shchigry;Belaya Kholunitsa;Pionerskiy;Prokhladnyy;Uren;Lebedyan;Chekhov;Kandalaksha;Lyubertsy;Oboyan;Vyazniki;Rylsk;Borovsk;Anapa;Gavrilov-Yam;Unecha;Belgorod;Bologoye;Saransk;Urzhum;Syktyvkar;Kizlyar;Kursavka;Ikryanoye;Aleksandrovskoye;Krasnogorsk;Stupino;Terek;Cheboksary;Digora;Voronezh;Novosibirsk;Mytishchi;Smolensk;Salekhard;Lukoyanov;Volosovo;Kotelnich;Salsk;Danilov;Furmanov;Sobinka;Kislovodsk;Temryuk;Beslan;Azov;Zhukovka;Anadyr;Aksay;Polyarnyy;Blagoveshchensk;Podporozhye;Pskov;Kizilyurt;Nelidovo;Yaroslavl;Podolsk;Belomorsk;Orel;Noginsk;Korenovsk;Reutov;Volgorechensk;Rzhev;Teykovo;Yuzha;Semenov;Krasnogvardeyskoye;Suzdal;Tikhvin;Priozersk;Dubovskoye;Tambov;Kaliningrad;Korolev;Mozhga;Kovdor;Pokrovskoye;Aleksin;Elektrostal;Semikarakorsk;Lodeynoye Pole;Kursk;Bryansk;Khanty-Mansiysk;Volodarsk;Fokino;Yartsevo;Segezha;Domodedovo;Kingisepp;Kolomna;Fryazino;Millerovo;Stroitel;Serpukhov;Slantsy;Moscow;Yoshkar-Ola;Levashi;Naro-Fominsk;Suoyarvi;Nazran;Ulyanovsk;Tikhoretsk;Odintsovo;Tsimlyansk;Botlikh;Kasimov;Pyatigorsk;Torzhok;Luga;Ertil;Bronnitsy;Apsheronsk;Vyshniy Volochek;Pavlovsk;Krymsk;Chernyakhovsk;Nartkala;Makhachkala;Klintsy;Dubna;Babayurt;Yelets;Novoaleksandrovsk;Malaya Vishera;Yefremov;Rudnya;Velsk;Izobil'nyy;Novozybkov;Orenburg;Pochep;Yessentuki;Sudogda;Narimanov;Ust'-Dzheguta;Skopin;Yekaterinburg;Sortavala;Zvenigovo;Ryazhsk;Kamyzyak;Korablino;Kola;Velikiy Novgorod;Manturovo;Konakovo;Shchekino;Onega;Yasnogorsk;Kulebaki;Melenki;Rodniki;Novomoskovsk;Yegoryevsk;Chaltyr;Soltsy;Ryazan;Vologda;Dmitrov;Kamensk-Shakhtinskiy;Lgov;Timashevsk;Neftekumsk;Mezen;Kambarka;Belev;Lyskovo;Tyrnyauz;Samara;Kazan;Volkhov;Levokumskoye;Pavlovo;Kovrov;Balashikha;Omutninsk;Murmansk;Belaya Kalitva;Kirovsk;Vladikavkaz;Zheleznovodsk;Vsevolozhsk;Petrozavodsk;Zavyalovo;Shali;Zernograd;Divnoye;Cherkessk;Dolgoprudnyy;Khabarovsk;Mayskiy;Pudozh;Nevel;Zavolzhsk;Chita;Kashira;Gusev;Velikiye Luki;Krasnoznamensk;Zuyevka;Pereslavl'-Zalesskiy;Irkutsk;Tarusa;Gus'-Khrustal'nyy;Chernogolovka;Istra;Groznyy;Lipetsk;Safonovo;Gorodets;Dorogobuzh;Omsk;Murom;Medvezhyegorsk;Rossosh;Kirzhach;Yuzhno-Sakhalinsk;Borovichi;Arzgir;Vichuga;Mtsensk;Blagodarnyy;Kotlas;Urus-Martan;Kurchaloy;Mikhaylov;Adygeysk;Orekhovo-Zuyevo;Karachev;Suvorov;Gagarin;Shchelkovo;Surazh;Proletarsk;Klin;Kaluga;Guryevsk;Severodvinsk;Gorokhovets;Elista;Karachayevsk;Arzamas;Kireyevsk;Penza;Pushkino;Severomorsk;Sernovodsk;Svetlogorsk;Abinsk;Luza;Perevoz;Porkhov;Kasumkent;Neman;Votkinsk;Nevinnomyssk;Neya;Nyandoma;Sukhinichi;Volgograd;Lobnya;Malgobek;Kirs;Birobidzhan;Petushki;Buynaksk;Pechory;Achkhoy-Martan;Yelnya;Morozovsk;Rostov;Lermontov;Kolchugino;Karabulak;Obninsk;Staraya Russa;Kyzyl;Kurchatov;Sarov;Perm;Vidnoye;Navashino;Toropets;Nolinsk;Livny;Usman;Kurgan;Svetlograd;Georgiyevsk;Voskresensk;Krasnodar;Vladivostok;Volzhsk;Opochka;Aleksandrov;Roslavl;Vyborg;Venev;Ufa;Chelyabinsk;Donskoy;Russia;Buy;Mineral'nyye Vody;Chkalovsk;Plavsk;Tosno;Koryazhma;Glazov;Arkhangelsk;Sovetsk;Nerekhta;Kostomuksha;Bogoroditsk;Kharabali;Kondrovo;Yakutsk;Likhoslavl;Dzerzhinskiy;Ruza;Maloyaroslavets;Kurganinsk
+AR;Colon;Famailla;Carhue;Las Flores;San Justo;Pigue;Ranchos;General Jose de San Martin;General Juan Madariaga;Esteban Echeverria;Santiago del Estero;Obera;Chamical;Azul;La Quiaca;Jesus Maria;Berisso;Rio Cuarto;Pilar;General Villegas;El Calafate;Villa Angela;Benito Juarez;San Ramon de la Nueva Oran;San Isidro;Zarate;Quimili;Chacabuco;Bernardo de Irigoyen;San Rafael;Apostoles;Abra Pampa;Bragado;Joaquin V. Gonzalez;Junin de los Andes;Chascomus;Las Heras;Rauch;Gualeguay;Necochea;Concepcion del Uruguay;General Acha;La Leonesa;Gobernador Virasora;San Bernardo;Aguilares;Merlo;Gastre;General Las Heras;Coronel Dorrego;Tres Arroyos;Baradero;Campo Largo;Villa Berthet;Alto Rio Senguer;Anatuya;Santa Rosa de Rio Primero;Mar del Plata;Lomas de Zamora;Esquel;Moron;Malargue;General Rodriguez;Empedrado;Capitan Sarmiento;Villa La Angostura;Esperanza;Tandil;Termas de Rio Hondo;Daireaux;Rosario del Tala;Carmen de Areco;Banda del Rio Sali;Monte Quemado;San Miguel de Tucuman;Reconquista;Diamante;Cerrillos;Formosa;Tostado;Lincoln;General Martin Miguel de Guemes;Nueve de Julio;Andalgala;Berazategui;General Pinedo;Goya;San Juan;Pehuajo;Canuelas;Maipu;Canada de Gomez;Ushuaia;La Cruz;San Luis;Buenos Aires;Jose Maria Ezeiza;General San Martin;Rosario;Resistencia;Monte Caseros;Sierra Colorada;Rodeo;Concepcion;Quitilipi;Balcarce;Las Brenas;Chepes;Puerto Madryn;Miramar;Las Rosas;Comodoro Rivadavia;General Alvear;Puan;Castelli;Nogoya;La Rioja;Federal;Ramallo;Libertador General San Martin;Villa Ojo de Agua;Jose C. Paz;Tornquist;Saladas;Viedma;Santa Fe;Rivadavia;General Conesa;San Julian;Bell Ville;Capilla del Senor;Laboulaye;General Belgrano;Ingeniero Guillermo N. Juarez;Victoria;Guernica;Perito Moreno;Arrecifes;Carmen de Patagones;Caucete;Gualeguaychu;Caseros;San Martin de los Andes;Machagai;Villa Maria;Lanus;Monteros;Belen de Escobar;Hurlingham;Palpala;Villa Paranacito;Campana;Villa del Rosario;Gobernador Gregores;Chimbas;Lujan de Cuyo;Zapala;Frias;Argentina;Lobos;Pergamino;General Viamonte;Posadas;Catamarca;Concordia;Villa Mercedes;San Jose de Jachal;San Roque;Parana;Henderson;Adolfo Gonzales Chaves;Chilecito;Carlos Casares;Santa Rosa;Godoy Cruz;Puerto Tirol;Charata;Rio Gallegos;Villa Constitucion;Federacion;Clorinda;San Vicente;Casilda;Tinogasta;Victorica;Ensenada;Alta Gracia;Rosario de Lerma;Rafaela;San Antonio de Areco;Neuquen;La Banda;Dean Funes;Belen;Cosquin;Villaguay;San Andres de Giles;Presidencia Roque Saenz Pena;Avellaneda;Oliva;Choele Choel;Sauce;San Jose de Feliciano;General Pico;Puerto Rico;San Cristobal;Puerto Deseado;La Plata;Villa Krause;Chumbicha;Mburucuya;Villa Union;San Fernando;Chivilcoy;La Carlota;Marcos Juarez;Marcos Paz;Susques;La Paz;Bahia Blanca;Olavarria;Mercedes;San Francisco;Cruz del Eje;Leandro N. Alem;Vera;Los Polvorines;Corzuela;Pinamar;Tafi Viejo;Veinticinco de Mayo;Ituzaingo;Villa Aberastain;Mendoza;Ayacucho;Cafayate;Rosario de la Frontera;Santa Sylvina;General Roca;San Martin;San Isidro de Lules;Cordoba;Sarmiento;Magdalena;Telsen;Tartagal;Villa Gesell;Coronda;Loberia;San Nicolas de los Arroyos;Lujan;Junin;Comandante Fontana;Tres Isletas;Corrientes;Presidencia de la Plaza;San Salvador;Yerba Buena;San Salvador de Jujuy;Dolores;San Antonio Oeste;San Luis del Palmar;Navarro;Humahuaca;Santa Lucia;Eldorado;San Javier;Pirane;Pampa del Infierno;Salta;Bella Vista;Rinconada;Paso de los Libres;Rio Grande;San Carlos de Bariloche;San Pedro;Tunuyan;Trenque Lauquen;Curuzu Cuatia;Roque Perez;Las Lajas;Florencio Varela;Quilmes;Rawson;Brandsen;Punta Alta;Santa Maria;Coronel Suarez;Chos Malal;Santo Tome;San Antonio de los Cobres;Trancas
+NG;Kaduna;Somolu;Auchi;Umuahia;Ede;Abeokuta;Aba;Dutse;Yenagoa;Ilobu;Owo;Damboa;Igboho;Asaba;Chibok;Baure;Zango;Nguru;Ipokia;Nsukka;Biu;Ikot Ekpene;Ibadan;Offa;Kaura Namoda;Orlu;Wukari;Minna;Lokoja;Otukpo;Agege;Jalingo;Lafia;Malumfashi;Isanlu;Ikom;Birnin Kebbi;Epe;Hong;Ugep;Abakaliki;Sokoto;Bama;Mubi;Calabar;Potiskum;Kontagora;Ondo;Kukawa;Sapele;Akure;Apapa;Ile-Ife;Numan;Enugu;Nnewi;Azare;Ikot Abasi;Okene;Iwo;Awka;Makurdi;Zaria;Kano;Funtua;Owerri;Shagamu;Nigeria;Kisi;Gashua;Benin City;Gusau;Osogbo;Bauchi;Gwoza;Ogbomoso;Katsina;Idah;Ilesa;Iseyin;Kuje;Warri;Abuja;Ipetumodu;Osisioma;Maiduguri;Jos;Keffi;Gombe;Lagos;Uyo;Ado-Ekiti;Mushin;Abaji;Burutu;Yola;Mai'Adua;Oyo;Ikeja;Port Harcourt;Saki;Kumo;Ikare;Ilorin;Gwagwalada;Damaturu;Onitsha;Ijebu-Ode;Bida
+TR;Alasehir;Harran;Andirin;Selcuk;Kocaeli;Golcuk;Iznik;Duzici;Kepsut;Salihli;Kavaklidere;Gebze;Yatagan;Askale;Turgutlu;Sulakyurt;Alanya;Karapinar;Civril;Bolvadin;Karamursel;Koprukoy;Didim;Sivas;Battalgazi;Karkamis;Sungurlu;Sinanpasa;Tosya;Eruh;Ardesen;Gemerek;Cicekdagi;Soke;Selcuklu;Konak;Sorgun;Ayvalik;Arhavi;Konya;Koycegiz;Karakocan;Sariveliler;Yigilca;Pamukova;Bodrum;Devrek;Turkeli;Ciftlik;Kars;Ankara;Erfelek;Kelkit;Yesilova;Guneysu;Hassa;Hazro;Ozalp;Malkara;Sarkisla;Pendik;Arifiye;Caycuma;Egirdir;Catalpinar;Ceyhan;Kapakli;Catak;Kavak;Gorele;Pazar;Golbasi;Gumushane;Yenimahalle;Of;Beydag;Muradiye;Cesme;Siirt;Cerkezkoy;Unye;Nazilli;Taskopru;Tonya;Erbaa;Kilis;Bitlis;Ceylanpinar;Solhan;Armutlu;Nilufer;Bafra;Kovancilar;Yomra;Aralik;Cayeli;Avanos;Terme;Niksar;Adana;Gomec;Mudanya;Menderes;Simav;Golmarmara;Mazidagi;Taslicay;Istanbul;Kirkagac;Akdagmadeni;Erzin;Buldan;Akhisar;Bilecik;Cobanlar;Baykan;Oltu;Gole;Saraykent;Kumlu;Havsa;Mardin;Aksaray;Kadinhani;Cat;Akkus;Mezitli;Toprakkale;Dursunbey;Osmangazi;Antalya;Ulubey;Huyuk;Gevas;Cankiri;Ayancik;Sebin Karahisar;Susuz;Kayseri;Yakacik;Sultandagi;Gumusova;Safranbolu;Ferizli;Meric;Tunceli;Altinova;Buyukcekmece;Cungus;Dargecit;Kucukkuyu;Espiye;Cubuk;Ortakoy;Vize;Sarkikaraagac;Acigol;Hayrabolu;Golyaka;Sabanozu;Kecioren;Kesan;Uzumlu;Ula;Harbiye;Sultanhani;Suruc;Elmadag;Bayramic;Oguzeli;Ilic;Alacati;Diyadin;Gerze;Yaprakli;Kozan;Polatli;Digor;Bahcesaray;Urla;Mut;Kastamonu;Resadiye;Akyurt;Kizilcahamam;Derinkuyu;Siran;Cal;Saruhanli;Sarioglan;Malatya;Menemen;Gumushacikoy;Kiraz;Isparta;Ahmetli;Besni;Haskoy;Cildir;Can;Cumra;Dortyol;Datca;Golpazari;Soma;Sarayonu;Hinis;Divrigi;Varto;Arapgir;Adakli;Osmancik;Acipayam;Adalar;Kulu;Sivrihisar;Muratli;Dereli;Turkey;Sogut;Carsamba;Tekkekoy;Akcaabat;Yildizeli;Suhut;Bozdogan;Arsuz;Cifteler;Kahramanmaras;Van;Manavgat;Demre;Marmaris;Gordes;Cekerek;Kangal;Denizli;Hidirbey;Samsun;Yakakent;Bergama;Midyat;Korkut;Sariyer;Gonen;Sutculer;Nizip;Tasucu;Karatas;Yumurtalik;Asarcik;Serinhisar;Duzkoy;Camardi;Incirliova;Alapli;Tatvan;Kaynarca;Kirsehir;Osmaneli;Eregli;Cavdir;Karaburun;Tekirdag;Goksun;Yenipazar;Afsin;Sincan;Hani;Manisa;Hatay;Pinarbasi;Dicle;Pazarcik;Beypazari;Alpu;Kocasinan;Umurlu;Sason;Kagizman;Siverek;Sanliurfa;Arakli;Marmara Ereglisi;Kinik;Ortaklar;Eskisehir;Ahlat;Honaz;Yahyali;Tire;Amasra;Sariz;Dogubayazit;Camoluk;Susehri;Ulukisla;Elbistan;Ciftlikkoy;Sarkoy;Mamak;Nigde;Balikesir;Ezine;Karayazi;Guneysinir;Tasova;Bayburt;Gulsehir;Cayiralan;Corlu;Erdemli;Banaz;Kale;Incesu;Talas;Tortum;Eynesil;Dosemealti;Golkoy;Karaman;Bozkurt;Kutahya;Senkaya;Urgup;Belen;Canakkale;Tavas;Kosk;Mersin;Domanic;Kilimli;Kozluk;Genc;Tirebolu;Foca;Lice;Yavuzeli;Bingol;Ermenek;Mecitozu;Zonguldak;Korkuteli;Caldiran;Semdinli;Corum;Silivri;Kulp;Yalova;Serik;Amasya;Gaziantep;Refahiye;Ihsaniye;Uludere;Ayvacik;Gerede;Ivrindi;Kocakoy;Kozlu;Sultanhisar;Sile;Hisarcik;Kursunlu;Sinop;Birecik;Borcka;Sogutlu;Yuksekova;Ispir;Korfez;Cinar;Balya;Araban;Luleburgaz;Meram;Akseki;Gurgentepe;Savsat;Gemlik;Samandag;Aydin;Fatsa;Lapseki;Erdek;Tufanbeyli;Gokcebey;Yozgat;Emirgazi;Bismil;Doganhisar;Zile;Celtik;Pozanti;Ortaca;Adiyaman;Aliaga;Akyazi;Aktepe;Kayapinar;Agri;Dogansehir;Burhaniye;Sakarya;Rize;Salpazari;Caglayancerit;Tokat;Akcakoca;Erzurum;Gaziemir;Palu;Diyarbakir;Reyhanli;Bulancak;Sarikamis;Karpuzlu;Ondokuzmayis;Gazipasa;Bucak;Gallipoli;Anamur;Surmene;Keskin;Ipsala;Pervari;Imamoglu;Selim;Yahsihan;Kemalpasa;Cizre;Hakkari;Hacilar;Trabzon;Camas;Dikili;Halfeti;Bartin;Yaglidere;Cinarcik;Hendek;Narman;Seyitgazi;Sur;Yenisehir;Alaca;Bursa;Kadirli;Turkoglu;Buyukorhan;Vezirkopru;Bayat;Kucukcekmece;Inegol;Cayirova;Aybasti;Hizan;Karabuk;Egil;Kurtalan;Taskent;Mugla;Bor;Artvin;Kumru;Igdir;Kabatas;Mus;Yerkoy;Viransehir;Nurdagi;Sarikaya;Tuzluca;Senirkent;Yildirim;Dalaman;Tut;Zara;Savur;Eleskirt;Karaisali;Gulagac;Aglasun;Iskenderun;Cihanbeyli;Bornova;Sivrice;Guclukonak;Tomarza;Nevsehir;Turhal;Yuregir;Suluova;Patnos;Catalca;Karasu;Fethiye;Batman;Bahce;Cide;Aydincik;Derik;Sereflikochisar;Usak;Edirne;Arpacay;Cerkes;Vakfikebir;Silifke;Torbali;Gorukle;Milas;Cumayeri;Omerli;Susurluk;Gurun;Giresun;Findikli;Piraziz;Sirnak;Kusadasi;Saimbeyli;Alacam;Tekman;Eceabat;Saricam;Ordu;Kocarli;Kirikkale;Babaeski;Elmali;Manyas;Bolu;Yesilhisar;Nurhak;Aslanapa;Sindirgi;Kas;Sarigol;Bayindir;Cankaya;Cermik;Horasan;Baglar;Akcakale;Arsin;Serinyol;Mucur;Bozkir;Bandirma;Baskil;Uzundere;Kirikhan;Germencik;Sirvan;Bala;Goynucek;Selendi;Aladag;Afyonkarahisar;Develi;Gursu;Cay;Cine;Beysehir;Biga;Koyulhisar;Karacabey;Demirozu;Edremit;Tarsus;Emet;Akyaka;Silvan;Altinozu;Kalecik;Besiri;Cayirli;Carsibasi;Emirdag;Osmaniye;Yunak;Altindag;Davutlar;Kose;Hilvan;Nusaybin;Yalvac;Arac;Bogazliyan;Feke;Sapanca;Bozuyuk;Geyve;Caykara;Yayladagi;Cameli;Orhaneli;Aksehir;Mesudiye;Orhangazi;Buharkent;Caybasi;Silopi;Idil;Pasinler;Havran;Kula;Karahalli;Alucra;Karakopru;Bulanik;Mutki;Seyhan;Islahiye;Baskale;Sefaatli;Altinyayla;Altintas;Altunhisar;Aksu;Kesap;Karliova;Saray;Ayas;Gediz;Yenice;Golhisar;Torul;Sivasli;Saraykoy;Duzce;Odemis;Kahta;Adilcevaz;Nallihan;Esme;Bigadic;Yazihan;Basmakci;Ulus;Beykoz;Yusufeli;Savastepe;Izmir;Ilgin;Karsiyaka;Aricak;Seferhisar;Seydisehir;Kocaali;Ekinozu;Mustafakemalpasa;Gurpinar;Almus;Pazaryeri;Uzunkopru;Gokceada;Besikduzu;Ergani;Burdur;Guney;Karapurcek;Yesilli;Ercis;Derince;Havza;Karacasu;Kumluca;Demirci;Altinekin;Etimesgut;Inebolu;Tefenni;Haymana;Koprubasi;Bozyazi;Kartal;Yesilyurt;Evren;Melikgazi;Merzifon;Boyabat;Buca;Persembe;Kandira;Iskilip;Sumbas;Karacoban;Ikizce;Hadim;Kiziltepe;Guroymak;Korgan;Darende;Bunyan;Bozova;Elazig;Kirklareli;Macka;Puturge;Hopa;Kuyucak;Akcadag;Kaman;Keles;Ardahan;Duragan;Finike;Tavsanli;Cilimli;Malazgirt;Erzincan;Cukurca;Kaynasli;Camliyayla;Gulnar
+PK;Tando Muhammad Khan;Jacobabad;Chilas;Peshawar;Turbat;Jamshoro;Gujrat;Gujranwala;Sahiwal;Khanewal;New Mirpur;Pishin;Umarkot;Jhelum;Ziarat;Timargara;Dera Allahyar;Jhang City;Uthal;Kohat;Saidu Sharif;Kalat;Vihari;Thatta;Badin;Gakuch;Quetta;Muzaffargarh;Sialkot City;Bhakkar;Khushab;Shekhupura;Bannu;Lahore;Swabi;Hyderabad City;Mardan;Kotli;Khairpur Mir's;Karak;Lodhran;Panjgur;Gwadar;Gilgit;Dera Ghazi Khan;Haripur;Bahawalnagar;Okara;Faisalabad;Bahawalpur;Batgram;Hangu;Chiniot;Abbottabad;Karachi;Ghotki;Sanghar;Mirpur Khas;Sargodha;Bagh;Naushahro Firoz;Pakpattan;Kharan;Tando Allahyar;Pakistan;Dadu;Mandi Bahauddin;Sukkur;Nowshera;Tank;Nawabshah;Chitral;Hafizabad;Zhob;Rawalpindi;Islamabad;Charsadda;Larkana;Toba Tek Singh;Kasur;Mianwali;Multan;Chakwal;Mansehra;Dera Ismail Khan
+VN;Thanh Phu;Son La;Hung Yen;Tay Ninh;Thai Binh;Con Dao;Buon Ma Thuot;Cam Ranh;An Chau;Nha Trang;Phu Tho;My Tho;Dong Ha;A Yun Pa;Ha Giang;Ho Chi Minh City;Hoa Binh;Bac Kan;Ky Anh;Da Nang;Kien Giang;Nga Bay;Haiphong;Soc Trang;Tam Ky;Kien Luong;Dong Hoi;Huong Tra;Tuy Hoa;Duc Pho;Cho Moi;Pleiku;Cao Bang;Di Linh;Bien Hoa;Phan Rang-Thap Cham;Long My;Thu Duc;Vung Tau;Thu Dau Mot;An Phu;Yen Bai;Thanh Hoa;Cho Lach;Phu Quoc;Phan Thiet;Trang Bang;Phuc Yen;Lang Son;Vi Thanh;Di An;Long Xuyen;Hanoi;Rach Gia;An Nhon;Tan Chau;Sa Pa;Quang Ngai;Hai Duong;Gia Nghia;Phu Ly;Kon Tum;Dong Xoai;Duyen Hai;Ba Don;Long Thanh;Viet Tri;Ha Long;Ca Mau;Ha Tinh;Bac Giang;Buon Trap;Mong Cai;Thai Nguyen;Vinh;Ninh Hoa;Bo;Tan Phu;Nam Dinh;Long Khanh;Kinh Mon;Quy Nhon;Binh Minh;Son Tay;Bac Ninh;Thi Tran Ngai Giao;Vinh Yen;Vietnam;Huong Canh;Hue;Tam Diep;Dien Bien Phu;Cam Pha;Vinh Chau;Ben Tre;Chon Thanh;Ha Tien;Bao Loc;Lai Chau;Lao Cai;Song Cau;Can Tho;Tan Uyen;Khe Sanh;Tan An;Tuyen Quang;Cao Lanh;Quang Yen;Tra Vinh;Bac Lieu;Vinh Long;Ninh Binh;Hoa Thanh;Sa Dec;Hang Tram;Da Lat
+IR;Bastak;Ahram;Qarah Zia' od Din;Lordegan;Quchan;Kavar;Rasak;Kalardasht;Bandar `Abbas;Shirvan;Bandar-e Gaz;Asadabad;Sabzevar;Ramsar;Komijan;Showt;Fannuj;Ravar;Semirom;`Aliabad-e Katul;Qazvin;Qarchak;Shahin Dezh;Zarrin Shahr;Zaboli;Boshruyeh;Heris;Torbat-e Heydariyeh;Ahvaz;Dalgan;Bojnurd;Ardal;Dehloran;Kermanshah;Aligudarz;Neqab;Sonqor;Neyriz;Bahar;Dehaqan;Kaleybar;Bam;Ashtian;Zehak;Arsanjan;Khash;Osku;Piranshahr;Garmsar;Meshgin Shahr;Namin;Robat Karim;Sari;Estahban;Pakdasht;Azarshahr;Basht;Khorramshahr;Mehran;Shahr-e Kord;Abhar;Razan;Poldasht;`Anbarabad;Gerash;Charam;Rabor;Rafsanjan;Zahedan;Kahnuj;Nazarabad;Sa`adat Shahr;Sarableh;Borujerd;Bajestan;Bafq;Landeh;Ilam;Sarakhs;Miandasht;Fereydunshahr;Hamadan;Ramshir;Zanjan;Nowshahr;Varamin;Suran;Mirjaveh;Babolsar;Qorveh;Khomeyn;Tabas;Tabriz;Semnan;Saqqez;Azadshahr;Anar;Qa'en;Birjand;Shahin Shahr;Khalkhal;Hendijan;Shahr-e Herat;Borujen;Tiran;Qom;Paveh;Aleshtar;Jam;Torqabeh;Galugah;Kherameh;Bandar-e Bushehr;Sarbisheh;Ashkhaneh;Saravan;Joghtay;Khorramdarreh;Seyah Cheshmeh;Do Gonbadan;Ahar;Dowlatabad;Eslamshahr;Taft;Yazd;Mashhad;Dehgolan;Farashband;Sarpol-e Zahab;Bukan;Marvdasht;Baneh;Sorkheh;Damavand;Nehbandan;Torbat-e Jam;Darreh Shahr;Sepidan;Ferdows;Kalaleh;Bandar-e Torkaman;Kuhbanan;Bandar-e `Asaluyeh;Kuhdasht;Kangan;Malekan;Farsan;Sarayan;Kashmar;Nikshahr;Ardestan;Jiroft;Shiraz;Mobarakeh;Galikesh;Astaneh-ye Ashrafiyeh;Fariman;Harsin;Germi;Najafabad;Eqlid;Hashtrud;Maragheh;Omidiyeh;Sowme`eh Sara;Marand;Gotvand;Golpayegan;Andimeshk;Ardabil;Shushtar;Taybad;Ravansar;Delijan;Dargaz;Hoveyzeh;Oshnaviyeh;Bardaskan;Fasa;Maraveh Tappeh;Langarud;Aran Bidgol;Kabudarahang;Bileh Savar;Amlash;Susangerd;Feyzabad;Gomishan;Alvand;Khorramabad;Javanrud;Hamidiyeh;Amol;Ben;Mahallat;Damghan;Khvansar;Takab;Fardis;Azna;Esfarayen;Tuyserkan;Jolfa;Karaj;Meybod;Kerman;Shabestar;Siahkal;Bandar-e Khamir;Shahreza;Shush;Fuman;Bijar;Shahr-e Qods;Arak;Sanandaj;Likak;Esfahan;Hashtpar;Ramhormoz;Ashkezar;Dorud;Zarand;`Ajab Shir;Zabol;Takestan;Kut-e `Abdollah;Jask;Masjed Soleyman;Khowrmuj;Eshtehard;Abarkuh;Yasuj;Qasr-e Shirin;Babol;Shahr-e Babak;Neyshabur;Gonabad;Sahneh;Manujan;Khomeyni Shahr;Sardasht;Dezful;Tonekabon;Salmas;Sarvestan;Rasht;Khowy;Rudsar;Malard;Naqadeh;Gilan-e Gharb;Safashahr;Hashtgerd;Kazerun;Orumiyeh;Eyvan;Natanz;Kashan;Mahdishahr;Khonj;Gonbad-e Kavus;Iran;Divandarreh;Shahriar;Bardsir;Konarak;Qeshm;Eslamabad-e Gharb;Arakvaz-e Malekshahi;Bandar-e Mahshahr;Poldokhtar;Qasr-e Qand;Surak;Bandar-e Deylam;Rezvanshahr;Lamerd;Khvaf;Garmeh;Jahrom;Malayer;Tafresh;Jajarm;Mianeh;Bandar-e Lengeh;Shahrud;Dehdasht;Qal`eh Ganj;Sarab;Nahavand;Bandar-e Genaveh;Minudasht;Haftkel;Baft;Mohammadabad;Shazand;Bonab;Fereydun Kenar;Deyr;Behshahr;Tehran;Marivan;Bandar-e Anzali;Behbahan;Sirjan;Famenin;Ardakan;Saveh;Chabahar;Gorgan;Neka;Borazjan;Shadegan;Abyek;Iranshahr;Bagh-e Malek;Falavarjan
+CD;Gemena;Inongo;Mbandaka;Kindu;Goma;Isiro;Mbuji-Mayi;Lusambo;Kabinda;Gbadolite;Matadi;Kananga;Bandundu;Lisala;Buta;Kenge;Kisangani;Bunia;Kamina;Kolwezi;Kalemie;Congo (Kinshasa);Tshikapa;Boende;Lubumbashi;Bukavu;Kinshasa
+GB;London
+FR;Apt;Evreux;Nanterre;Lorient;Fougeres;Vierzon;Arcachon;Chambery;Mantes-la-Jolie;Briancon;Evry;Cholet;Chateau-Gontier;Luneville;Soissons;Parthenay;Avignon;Sarlat-la-Caneda;Saint-Brieuc;Clermont-Ferrand;Paris;Bordeaux;Besancon;Toulon;Arles;Thionville;Grenoble;Albi;Tours;Issoudun;Colmar;Lens;Torcy;Avranches;Ales;Toul;Draguignan;Sarcelles;Boulogne-Billancourt;Nogent-sur-Marne;Bourg-en-Bresse;Pau;Riom;Abbeville;Marseille;Rennes;Bergerac;Cherbourg;Vannes;Tarbes;Montargis;Grasse;Beauvais;Vendome;Cognac;Vienne;Senlis;Metz;Tulle;Bonneville;Foix;Epernay;Meaux;Amiens;Cergy;Caen;Laon;Perpignan;Vesoul;Cahors;Angouleme;Castres;Chalons-en-Champagne;Palaiseau;Aurillac;Dax;Antony;Orleans;Compiegne;Douai;Montauban;Carpentras;Figeac;Limoges;Mulhouse;Bourges;Digne-les-Bains;Strasbourg;Lille;Dijon;Epinal;Rambouillet;Le Mans;Chateauroux;Rodez;Marmande;Blois;Pontarlier;Troyes;La Fleche;Fontainebleau;Bernay;Creteil;Chartres;Saint-Julien-en-Genevois;Bressuire;Alencon;Issoire;Nantes;Nancy;Belfort;Castelsarrasin;Provins;Le Havre;La Roche-sur-Yon;Gap;Cosne sur Loire;Saint-Denis;Boulogne-sur-Mer;Autun;Toulouse;Mayenne;Auxerre;Mont-de-Marsan;Sedan;Saint-Omer;Nevers;Bethune;Perigueux;Les Sables-d'Olonne;Angers;Roanne;Chateaudun;Saint-Quentin;Bayeux;Mende;Laval;Lannion;Montbrison;Saint-Dizier;Verdun;Pamiers;Chatellerault;Oloron-Sainte-Marie;Saint-Gaudens;Vitry-le-Francois;Clermont;Etampes;France;Chalon-sur-Saone;Dole;Villefranche-sur-Saone;Dinan;Chateaubriant;Valence;Limoux;Saint-Lo;Melun;Valenciennes;Bayonne;Thonon-les-Bains;Millau;Chaumont;Chateau-Thierry;Poitiers;Thiers;Le Raincy;Lyon;Sarreguemines;Carcassonne;Saint-Etienne;Aix-en-Provence;Bobigny;Saint-Nazaire;Rochefort;Libourne;Auch;Lons-le-Saunier;Pontivy;Villefranche-de-Rouergue;Istres;Cambrai;Sarrebourg;Le Puy-en-Velay;Molsheim;Dieppe;Sens;Villeneuve-sur-Lot;Vire;Pithiviers;Beziers;Brive-la-Gaillarde;Saint-Die-des-Vosges;Dunkerque;Charleville-Mezieres;Forbach;Albertville;Nice;Ussel;Nogent-le-Rotrou;Brignoles;Saverne;Moulins;Nimes;Annecy;L'Hay-les-Roses;La Rochelle;Bar-le-Duc;Gex;Saumur;Saintes;Argenteuil;Belley;Calais;Montbeliard;Saint-Claude;Lisieux;Redon;Narbonne;Beaune;Fontenay-le-Comte;Reims;Muret;Haguenau;Morlaix;Montlucon;Selestat;Gueret;Brest;Niort;Privas;Versailles;Tournon-sur-Rhone;Rouen;Saint-Germain-en-Laye;Arras;Quimper;Saint-Amand-Montrond;Macon;Agen;Vichy;Dreux;Ajaccio;Argentan;Montpellier;Saint-Malo
+PE;Cusco;Chachapoyas;Puno;Trujillo;Abancay;Ayacucho;Pucallpa;Chiclayo;Pampas;Cerro de Pasco;Iquitos;Ica;Huacho;Arequipa;Piura;Huancavelica;Peru;Callao;Tacna;Puerto Maldonado;Huancayo;Huanuco;Tumbes;Moyobamba;Moquegua;Lima;Cajamarca;Contamana;Huaraz
+AO;Sumbe;Ndalatando;Malanje;Benguela;Ondjiva;Luanda;Angola;Caxito;Huambo;Uige;Cabinda;Dundo;Luena;Mocamedes;Mbanza Kongo;Lubango;Saurimo;Menongue;Cuito
+MY;Labuan;Putrajaya;Kota Bharu;Kuantan;George Town;Kuala Terengganu;Malaysia;Kota Kinabalu;Kangar;Alor Setar;Shah Alam;Johor Bahru;Kuching;Kuala Lumpur;Ipoh;Melaka;Seremban;Tumpat
+ZA;Polokwane;Bhisho;Cape Town;Nelspruit;Pretoria;Mahikeng;Pietermaritzburg;Bloemfontein;South Africa;Johannesburg;Kimberley
+CO;Yarumal;Cucuta;Neiva;Cajica;Arboledas;Puerto Berrio;Ipiales;Padilla;Pradera;Ospina;Cienaga;Cicuco;Darien;Chia;El Carmen de Bolivar;Mitu;Muzo;Cachira;Piedecuesta;San Jose del Fragua;Tauramena;Morroa;Jerico;Puerto Boyaca;Candelaria;Itagui;San Carlos de Guaroa;El Dovio;San Jose del Guaviare;Popayan;Mistrato;Vistahermosa;Garagoa;Cartago;La Apartada;Manaure;Zarzal;Marquetalia;Combita;Medellin;Tumaco;San Bernardo del Viento;San Zenon;San Jeronimo;Ituango;Ansermanuevo;Chima;Socota;Cartagena;Totoro;Curiti;Sopetran;Moniquira;Tarqui;Abejorral;Genova;Bosconia;Samaniego;Puerto Libertador;Agustin Codazzi;Istmina;Nemocon;Santa Rosa de Cabal;Balboa;Guatica;Tame;Curumani;Fundacion;Sonson;Santo Domingo;Monteria;La Jagua de Ibirico;El Paujil;Angostura;El Carmen;Pacora;Los Cordobas;Aracataca;Buesaco;Susa;Tocaima;Puerto Gaitan;El Retorno;Puerto Lopez;La Argentina;Espinal;Guarne;Toledo;Pereira;Pelaya;Mosquera;Arjona;San Jacinto;San Vicente;Apia;Carmen de Apicala;Guamal;Tocancipa;Mocoa;San Estanislao;El Banco;Maicao;Villagarzon;Sabanalarga;Salgar;Iscuande;Pasca;Leticia;San Juan de Uraba;Cajamarca;Cotorra;Pueblo Bello;Jambalo;Monitos;El Copey;Inirida;Carmen de Viboral;Tuchin;Nobsa;Anori;Pacho;El Cairo;Chinu;Sibate;Juan de Acosta;El Tarra;Guaitarilla;Jurado;Cimitarra;Valdivia;Ponedera;Villahermosa;Pie de Pato;Guadalajara de Buga;San Antonio del Tequendama;Unguia;Sesquile;La Palma;Rionegro;Obando;Morales;Palestina;El Reten;Piamonte;San Juan de Arama;La Cruz;Puerto Concordia;La Plata;Fortul;San Lorenzo;Caparrapi;Acandi;Norosi;Chivolo;Cerete;Ovejas;Montecristo;Momil;Soacha;Caldono;Aipe;Samaca;Rovira;Caicedonia;Tierralta;Arauquita;Bolivar;Palmito;Maria la Baja;Pupiales;Aquitania;Viterbo;Dagua;Guateque;Malaga;San Bernardo;Sabanagrande;La Tebaida;Tado;Pasto;Andalucia;Toribio;Puerto Santander;Zambrano;Entrerrios;Condoto;Sincelejo;Floridablanca;Potosi;Zapatoca;Sampues;Yotoco;San Marcos;Tena;Manzanares;Villapinzon;Cunday;Apartado;Melgar;Roldanillo;Puerto Wilches;Fusagasuga;Guaduas;Tubara;Belen de Umbria;El Carmen de Chucuri;Tuta;Coyaima;Plato;Distraccion;Guayabal;San Sebastian de Buenavista;Tenjo;Santander de Quilichao;Coconuco;Gamarra;Villa de San Diego de Ubate;San Carlos;Baranoa;Saldana;Purisima de la Concepcion;Saravena;Suaita;Zipaquira;Choconta;Chigorodo;Iles;Sogamoso;Armenia;San Benito Abad;Natagaima;Viota;San Martin de Loba;Gachancipa;Pueblo Rico;Santa Genoveva de Docordo;Restrepo;Suarez;Pijino del Carmen;Sucre;Mani;Piendamo;Facatativa;Santuario;Silvia;El Playon;Santo Tomas;Los Patios;Tiquisio;Los Santos;Monterrey;La Montanita;Chachagui;Caqueza;Algarrobo;Caldas;Neira;San Gil;Puerto Lleras;Pizarro;Trinidad;Betania;Barbacoas;Honda;El Carmen de Atrato;La Estrella;Chinacota;Puerto Colombia;El Doncello;Turbana;Suesca;San Pablo;Colombia;Quinchia;Solano;Toca;Barrancabermeja;Paipa;Betulia;La Macarena;Tibu;San Fernando;Suaza;El Cerrito;Nuqui;San Luis de Since;Urumita;Sevilla;San Juan del Cesar;Majagual;Achi;Caucasia;Choachi;La Ceja;San Martin;San Juan Nepomuceno;Donmatias;Purificacion;Gigante;Simijaca;Cisneros;La Virginia;Aguazul;Tesalia;Narino;El Tambo;Supia;Mogotes;Puerto Salgar;Riofrio;Galeras;Santa Marta;Clemencia;Sabana de Torres;Guasca;Agua de Dios;Oiba;Teorama;Cumbal;Castilla La Nueva;Necocli;Florida;Villeta;Caloto;Rio de Oro;Velez;La Gloria;San Jacinto del Cauca;Bello;Bucaramanga;Palmar de Varela;Aguadas;La Mesa;El Tablon;Chitaga;Bocas de Satinga;Puerto Narino;Villa Rica;Covenas;Barbosa;San Rafael;Fresno;Simiti;Mahates;Argelia;Puerto Carreno;Orocue;Villa de Leyva;Santa Rosa de Viterbo;Segovia;Yacuanquer;Cienaga de Oro;San Onofre;Amalfi;Frontino;El Pinon;La Esperanza;El Bordo;Taminango;San Pedro de Uraba;Puerto Nare;Hatillo de Loba;Zaragoza;Ginebra;El Aguila;La Victoria;Santa Catalina;Granada;Montelibano;San Alberto;Fuente de Oro;Nunchia;Fonseca;Ubala;San Antonio;Filadelfia;Palocabildo;Bogota;Puerto Escondido;Guacheta;Carepa;Funza;Valencia;Sardinata;Flandes;Sotomayor;Consaca;Calamar;Tibana;Lerida;Tausa;Ibague;Arauca;Bojaca;Guadalupe;Mutis;Marsella;Turbo;Socorro;Timbiqui;Rioblanco;Sibundoy;Ricaurte;Carlosama;Yumbo;La Calera;Isnos;Dosquebradas;San Sebastian;Timbio;Yondo;Tamesis;Iquira;Malambo;Acacias;Lejanias;Puerto Triunfo;Trujillo;Pamplona;Miranda;Planadas;San Pelayo;Acevedo;Aguachica;San Juan de Betulia;Guatape;Becerril;Santiago de Tolu;Retiro;Tibasosa;Cartagena del Chaira;Turbaco;Algeciras;Rosas;Giron;Usiacuri;El Zulia;San Roque;Yopal;Carmen de Carupa;Villanueva;Arbelaez;San Sebastian de Mariquita;El Colegio;Guaranda;Magangue;Puerto Tejada;Aranzazu;La Dorada;Amaga;Mercaderes;Campamento;Envigado;El Roble;Puerto Rico;Villavicencio;Margarita;Copacabana;Circasia;Puente Nacional;Sandona;Yali;Puerto Asis;Tabio;Linares;Astrea;Santa Barbara de Pinto;Santa Barbara;Raquira;Junin;Vijes;El Paso;Puerto Leguizamo;Convencion;Timana;El Rosal;Santa Lucia;Chiquinquira;Abrego;Altos del Rosario;Talaigua Nuevo;La Union;Canasgordas;Palermo;Valledupar;Guacari;Sopo;Caceres;San Pedro;Alcala;Siachoque;Pivijay;Charala;Arboletes;Nueva Granada;Chita;Tunja;Sahagun;Uribia;El Dificil;La Sierra;Coello;Riosucio;Hatonuevo;Planeta Rica;Cumaral;Salamina;Tuquerres;Ocana;Garzon;Manati;Risaralda;San Andres de Sotavento;Anolaima;Toro;Ayapel;Paz de Ariporo;El Bagre;San Vicente de Chucuri;Suan;Girardota;Galapa;Palmira;Umbita;Campoalegre;Pensilvania;Buenaventura;San Agustin;Chinchina;Cumaribo;Albania;Dibulla;Madrid;San Diego;Subachoque;Taraza;Fredonia;Cogua;Chiriguana;Repelon;Landazuri;Briceno;Pital;Guachucal;Yolombo;Cali;Arroyohondo;Buenos Aires;Fomeque;Alvarado;Rivera;Sitionuevo;Belalcazar;Anapoima;San Jose;Barranco de Loba;Marinilla;Santa Rosa del Sur;Jardin;Saboya;Pitalito;Villamaria;Buenavista;La Florida;Ortega;Orito;Vegachi;Mutata;Cocorna;Anzoategui;Ebejico;Lenguazaque;Ciudad Bolivar;Urrao;La Primavera;Yacopi;Chaparral;Barranquilla;Pueblo Nuevo;Riohacha;Corinto;San Antero;La Vega;Yaguara;Sabaneta;Quibdo;Santa Rosa de Osos;San Vicente del Caguan;Inza;Silvania;La Belleza;Regidor;Villa del Rosario;Bugalagrande;San Calixto;Ramiriqui;Quimbaya;Filandia;Andes;Concordia;Falan;Teruel;Medina;Santa Rosa;Caimito;Montenegro;Hacari;Tolu Viejo;Tenerife;Canalete;Nechi;Pailitas;Puerto Caicedo;Duitama;Jamundi;Anserma;Gacheta;Venecia;Lorica;Soledad;Guapi;Gonzalez;Cajibio;Bellavista;Angelopolis;Campo de la Cruz;Tello;Pesca;Dabeiba;Libano;Almaguer;Puebloviejo;Cachipay;Lloro;Santa Fe de Antioquia;Remedios;Belen de los Andaquies;Chimichagua;Guachaves;Oporapa;Ataco;Cordoba;Venadillo;Manizales;Barrancas;Titiribi;Los Palmitos;Calarca;Tamalameque;Samana;Sasaima;El Charco;Saladoblanco;Pinillos;Polonuevo;Bagado;Guamo;Mesetas;Corozal;Luruaco;Icononzo;Cota;Tulua;Paispamba;San Andres;Florencia;Girardot;Santa Ana;Puerto Guzman;Ventaquemada;Solita;Une
+TZ;Chake Chake;Zanzibar;Arusha;Bukoba;Vwawa;Mahonda;Bariadi;Shinyanga;Tanzania;Morogoro;Moshi;Mbeya;Mkokotoni;Lindi;Singida;Njombe;Kigoma;Koani;Iringa;Wete;Mpanda;Geita;Mtwara;Mwanza;Kibaha;Dar es Salaam;Sumbawanga;Dodoma;Musoma;Songea;Tabora;Babati;Tanga
+SD;Sudan;Singa;Khartoum;Wad Medani;Ed Daein;Rabak;El Obeid;Port Sudan;Kadugli;Ed Damer;El Fasher;Gedaref;Dongola;Nyala;Kassala;El Geneina;Ed Damazin;Zalingei;El Fula
+HK;Hong Kong
+SA;Medina;Saudi Arabia;Jazan;Al Qurayyat;Abha;Buraydah;Mecca;Riyadh;Sakaka;Al Bahah;Ha'il;Al Wajh;Arar;Ad Dammam;Tabuk;Najran
+CL;Cochrane;Pozo Almonte;Osorno;Coquimbo;Cauquenes;Puerto Montt;Puente Alto;Linares;Valparaiso;San Antonio;Chillan;Arica;Iquique;Antofagasta;La Serena;Los Andes;Angol;Chile;Melipilla;Talagante;Lebu;Valdivia;Santiago;La Ligua;Castro;San Felipe;Colina;Calama;Concepcion;Pichilemu;Copiapo;Illapel;San Bernardo;Curico;La Union;Rancagua;Punta Arenas;Los Angeles;Chanaral;Puerto Williams;Coyhaique;Talca;Ovalle;Temuco;Quillota;Tocopilla;Quilpue;Vallenar;Puerto Aysen;Puerto Natales;San Fernando
+ES;Merida;Castellon de la Plana;Barcelona;Bilbao;Granada;Guadalajara;Salamanca;Cuenca;Santander;Sevilla;Valladolid;Pamplona;A Coruna;Huelva;Ciudad Real;Lugo;Cordoba;Vitoria-Gasteiz;Girona;Santa Cruz;Pontevedra;Logrono;Badajoz;Jaen;Valencia;Tarragona;Avila;Santiago de Compostela;Cadiz;Oviedo;Palencia;Teruel;Toledo;Lleida;Malaga;Zamora;Albacete;Murcia;Almeria;Ourense;Donostia;Burgos;Caceres;Segovia;Huesca;Soria;Leon;Spain;Zaragoza;Madrid;Alicante;Las Palmas;Palma
+IQ;Erbil;Al Kut;Jamjamal;Ar Rutbah;`Aynkawah;Sawran;Al Kufah;Halabjah;Ba`qubah;Ash Shamiyah;Kifri;Anah;Kuysinjaq;Sayyid Sadiq;Ash Shaykhan;Al Hillah;Karbala';Al Hayy;Kirkuk;Al Hindiyah;Qaladizay;Rawah;Makhmur;Baghdad;Abi al Khasib;Al Basrah;Al Hamzah;Samarra';Al Qa'im;Al `Aziziyah;Al Musayyib;Az Zubayr;Iraq;Saymayl;As Suwayrah;Al Fallujah;Mosul;Kalar;Al Faw;Al Hamdaniyah;Shaqlawah;Ar Ramadi;Al `Amarah;Hit;Tall `Afar;Al Jabayish;Tuz Khurmatu;Al Qurnah;An Nasiriyah;Ash Shatrah;`Aqrah;Zakhu;As Samawah;Rawanduz;Al Hashimiyah;Sinjar;Batufah;Al `Amadiyah;An Najaf;An Nu`maniyah;Abu Ghurayb;Dahuk;Balad;Bayji;Khanaqin;Raniyah;As Sulaymaniyah;Al Miqdadiyah;Hadithah;Tikrit;Ad Diwaniyah;Ar Rumaythah
+SG;Singapore
+CM;Ebolowa;Bafoussam;Buea;Ngaoundere;Cameroon;Bertoua;Garoua;Maroua;Yaounde;Douala;Bamenda
+CA;Ottawa;Quebec City;Halifax;Toronto;Victoria;Regina;Iqaluit;Edmonton;Fredericton;Winnipeg;Yellowknife;St. John's;Whitehorse;Canada;Charlottetown
+KE;Kisumu;Lodwar;Iten;Kapenguria;Kajiado;Kerugoya;Murang'a;Kenya;Maralal;Wote;Narok;Bungoma;Meru;Migori;Wajir;Homa Bay;Mandera;Embu;Nyamira;Kitale;Kiambu;Ol Kalou;Mombasa;Kitui;Eldoret;Hola;Rumuruti;Marsabit;Kisii;Nakuru;Lamu;Nairobi;Busia;Garissa;Kapsabet;Kwale;Kericho;Kabarnet;Mwatate;Sotik Post;Kakamega;Siaya;Isiolo;Machakos;Nyeri
+MM;Hpa-An;Pathein;Loikaw;Monywa;Burma;Myitkyina;Dawei;Magway;Sittwe;Mandalay;Mawlamyine;Rangoon;Taunggyi;Hakha;Nay Pyi Taw;Bago
+US;Salem;Sacramento;Helena;Jackson;Harrisburg;Albany;Little Rock;Lincoln;Hartford;Honolulu;Augusta;Boston;Jefferson City;Columbus;Cheyenne;Charleston;Baton Rouge;Bismarck;Concord;Springfield;Des Moines;St. Paul;Pierre;Boise;Atlanta;Dover;Annapolis;Nashville;Providence;Juneau;Denver;Phoenix;Austin;Richmond;Oklahoma City;Montgomery;Lansing;Frankfort;Montpelier;Tallahassee;Carson City;Salt Lake City;Olympia;Topeka;United States;Santa Fe;Madison;Columbia;Washington;Trenton;Indianapolis;Raleigh
+AU;Perth;Hobart;Canberra;Brisbane;Adelaide;Australia;Melbourne;Darwin;Sydney
+CI;Duekoue;Adzope;Dimbokro;Minignan;Yamoussoukro;Aboisso;Dabakala;Soubre;Sinfra;Toumodi;Gagnoa;Seguela;San-Pedro;Abengourou;Grand-Bassam;Daoukro;Dabou;Bouna;Man;Kong;Daloa;Ferkessedougou;Côte d’Ivoire;Korhogo;Agboville;Biankouma;Sassandra;Bondoukou;Boundiali;Touba;Abidjan;Bangolo;Oume;Bouafle;Mankono;Divo;Bingerville;Jacqueville;Odienne;Katiola;Bongouanou;Guiglo;Grand-Lahou;Sipilou;Bouake
+DE;;Meschede;Freiburg im Breisgau;Ansbach;Aichach;Tauberbischofsheim;Landshut;Lauterbach;Sigmaringen;Sommerda;Chemnitz;Kunzelsau;Stadthagen;Greiz;Kleve;Gottingen;Recklinghausen;Parchim;Esslingen;Ratzeburg;Husum;Wolfenbuttel;Hagen;Lorrach;Peine;Hanau;Helmstedt;Cuxhaven;Lichtenfels;Villingen-Schwenningen;Gorlitz;Hassfurt;Mannheim;Germany;Stade;Osterode;Bad Ems;Augsburg;Heidelberg;Siegen;Halle;Bad Kissingen;Luneburg;Pfarrkirchen;Forst (Lausitz);Wittmund;Bad Schwalbach;Neunkirchen;Prenzlau;Neuwied;Kempten;Jena;Hannover;Ravensburg;Detmold;Bad Neuenahr-Ahrweiler;Euskirchen;Aurich;Bad Segeberg;Celle;Bad Salzungen;Hamburg;Schwabisch Hall;Schwelm;Eisenberg;Leer;Gunzburg;Baden-Baden;Emmendingen;Ulm;Limburg;Erlangen;Stralsund;Bayreuth;Wurzburg;Schwandorf;Salzgitter;Munster;Regensburg;Bad Tolz;Bottrop;Ludwigsburg;Haldensleben;Saarbrucken;Pinneberg;Altenburg;Passau;Kronach;Eisenach;Furth;Tirschenreuth;Heilbronn;Cottbus;Biberach;Gelsenkirchen;Bergisch Gladbach;Kaufbeuren;Tubingen;Saarlouis;Merzig;Plon;Balingen;Meppen;Minden;Kassel;Gera;Eberswalde;Straubing;Sonthofen;Bautzen;Germersheim;Frankenthal;Worms;Meiningen;Reutlingen;Erfurt;Pirmasens;Dusseldorf;Nuremberg;Bitburg;Donauworth;Karlsruhe;Miesbach;Herford;Memmingen;Delmenhorst;Neumunster;Greifswald;Duren;Duisburg;Unna;Vechta;Sondershausen;Hamm;Kelheim;Aschaffenburg;Neu-Ulm;Stuttgart;Oldenburg;Dingolfing;Monchengladbach;Zweibrucken;Schleswig;Nordhorn;Wilhelmshaven;Lauf;Potsdam;Senftenberg;Darmstadt;Kiel;Neubrandenburg;Wiesbaden;Waldshut-Tiengen;Mettmann;Torgau;Solingen;Salzwedel;Apolda;Traunstein;Uelzen;Altotting;Bad Homburg;Kulmbach;Bernburg;Hildburghausen;Gummersbach;Lubeck;Bad Kreuznach;Frankfurt;Bamberg;Weissenburg;Remscheid;Luchow;Saalfeld;Borken;Bremen;Weimar;Dresden;Brake;Arnstadt;Gotha;Neumarkt;Montabaur;Jever;Bad Oldesloe;Ebersberg;Speyer;Heinsberg;Perleberg;Freudenstadt;Diepholz;Neuss;Essen;Burg;Trier;Luckenwalde;Schleiz;Magdeburg;Frankfurt (Oder);Boblingen;Berlin;Siegburg;Wetzlar;Ingolstadt;Rathenow;Rottweil;Pfaffenhofen;Calw;Merseburg;Cham;Waiblingen;Bad Hersfeld;Eschwege;Hof;Herne;Neustadt;Wesel;Mainz;Amberg;Eichstatt;Hameln;Sankt Wendel;Neuburg;Fulda;Soest;Ludwigshafen;Wunsiedel;Northeim;Paderborn;Bad Neustadt;Leipzig;Bad Reichenhall;Marktoberdorf;Giessen;Pforzheim;Annaberg-Buchholz;Viersen;Bad Fallingbostel;Homburg;Neuruppin;Heppenheim;Eutin;Gross-Gerau;Rendsburg;Goslar;Coburg;Korbach;Landsberg;Gutersloh;Meissen;Pirna;Braunschweig;Wolfsburg;Schwerin;Wismar;Plauen;Kaiserslautern;Offenburg;Bochum;Forchheim;Naumburg;Stendal;Heidenheim;Bonn;Kitzingen;Munich;Krefeld;Bielefeld;Mulheim;Mosbach;Sangerhausen;Steinfurt;Cloppenburg;Regen;Aachen;Landau;Coesfeld;Miltenberg;Mindelheim;Weilheim;Hoxter;Bergheim;Verden;Koblenz;Leverkusen;Emden;Alzey;Friedberg;Halberstadt;Ingelheim;Bad Durkheim;Heilbad Heiligenstadt;Oranienburg;Muhlhausen;Goppingen;Lubben (Spreewald);Muhldorf;Brandenburg;Furstenfeldbruck;Freiberg;Osterholz-Scharmbeck;Zwickau;Dillingen;Wittlich;Warendorf;Heide;Gifhorn;Hofheim;Winsen;Dortmund;Erbach;Freising;Deggendorf;Holzminden;Hildesheim;Aalen;Osnabruck;Itzehoe;Dachau;Marburg;Schwabach;Wuppertal;Tuttlingen;Sonneberg;Rosenheim;Rastatt;Suhl;Herzberg;Nordhausen;Olpe;Gustrow;Starnberg;Erding;Oberhausen;Ludenscheid;Flensburg;Westerstede
+AF;Tarin Kot;Qalat;Panjab;Ghazni;Mama Khel;Imam Sahib;Sangin;Maimanah;Bazarak;Lashkar Gah;Fayroz Koh;Ghoriyan;Maidan Shahr;Bagrami;Qal`ah-ye Now;Farah;Qarqin;Asadabad;Mazar-e Sharif;Baghlan;Nili;Faizabad;Karukh;Baraki Barak;Taywarah;Sar-e Pul;Sharan;Khulm;Zaranj;Kuhsan;Pul-e `Alam;Charikar;Bamyan;Taluqan;Gardez;Kunduz;Afghanistan;Andkhoy;Khanabad;Balkh;Khost;Kabul;Shibirghan;Aqchah;Herat;Jalalabad;Pul-e Khumri;Mahmud-e Raqi;Mehtar Lam;Parun;Kandahar;Aibak
+ML;Nioro;Koulikoro;Kolondieba;Bandiagara;Yelimane;Baroueli;Menaka;Sikasso;Kidal;Kadiolo;Mali;Bamako;Dire;Kangaba;Gourma Rharous;Tominian;Djenne;Gao;Youwarou;Kayes;Douentza;Ansongo;Yorosso;San;Banamba;Tenenkou;Bourem;Bafoulabe;Kita;Koro;Niono;Bougouni;Timbuktu;Koutiala;Nara;Mopti;Goundam;Kati;Segou;Tessalit;Bankass;Diema
+JO;Ar Ramtha;Al Juwayyidah;Az Zarqa';Ma`an;Muthallath al Azraq;Al `Aqabah;Jordan;As Salt;Busayra;`Ajlun;Al Hisn;Al Jizah;Ash Shunah ash Shamaliyah;Dayr Abu Sa`id;Irbid;Amman;Jarash;Ar Rusayfah;Al Karak;Al Fuhays;Sahab;Madaba;Al Mazar ash Shamali;Al Mafraq;At Tafilah
+MA;Guelmim;Marrakech;Beni Mellal;Agadir;Tangier;Morocco;Oujda-Angad;Tifariti;Errachidia;Casablanca;Fes;Rabat
+GH;Kumasi;Techiman;Cape Coast;Damongo;Accra;Sunyani;Ho;Bolgatanga;Dambai;Wa;Ghana;Sekondi;Tamale;Koforidua;Goaso;Nalerigu;Sefwi Wiawso
+DZ;El Golea;Mila;Tindouf;Chlef;Bordj Bou Arreridj;Relizane;El Oued;Tlemcen;Khenchela;El Tarf;Oum el Bouaghi;Boumerdes;Skikda;Tizi Ouzou;Guelma;Sidi Bel Abbes;Bordj Mokhtar;El Bayadh;Algeria;I-n-Salah;Bechar;Ouled Djellal;Ain Temouchent;Mostaganem;Laghouat;El Meghaier;Adrar;Setif;Algiers;Blida;Jijel;Mascara;Oran;Ghardaia;Touggourt;Ouargla;Tissemsilt;Naama;Djanet;Djelfa;In Guezzam;Saida;M'Sila;Bouira;Souk Ahras;Annaba;Tamanrasset;Beni Abbes;Ain Defla;Biskra;Tebessa;Constantine;Tiaret;Illizi;Medea;Bejaia;Tipasa;Batna;Timimoun
+AE;United Arab Emirates;Ra's al Khaymah;Sharjah;Dubai;Abu Dhabi;Umm al Qaywayn;Al Fujayrah;`Ajman
+GR;Kaisariani;Salamina;Drama;Giannitsa;Larisa;Tyrnavos;Palaio Faliro;Alimos;Chios;Katerini;Nea Ionia;Kiato;Kalymnos;Agios Dimitrios;Pefki;Greece;Ano Liosia;Spata;Zacharo;Irakleia;Mesolongi;Karpenisi;Kos;Voula;Kalamaria;Patra;Serres;Aliartos;Nea Filadelfeia;Chalandri;Kilkis;Koufalia;Rethymno;Didymoteicho;Aigaleo;Ptolemaida;Argos;Kifisia;Psychiko;Panorama;Edessa;Nea Moudania;Acharnes;Vyronas;Lamia;Rafina;Veroia;Thessaloniki;Ioannina;Ierapetra;Korinthos;Kavala;Agrinio;Chaidari;Thermi;Kerkyra;Polygyros;Agios Nikolaos;Piraeus;Moschato;Alexandroupoli;Kranidi;Gazi;Korydallos;Agia Varvara;Aigio;Ermoupoli;Amaliada;Elefsina;Skydra;Naousa;Agia Paraskevi;Ano Syros;Aspropyrgos;Sindos;Livadeia;Farsala;Peraia;Xanthi;Nea Smyrni;Stavroupoli;Paiania;Mandra;Metamorfosi;Gerakas;Arta;Sparti;Komotini;Argostoli;Tripoli;Peristeri;Sykies;Zografos;Nikaia;Athens;Evosmos;Siteia;Petroupoli;Agioi Anargyroi;Nafpaktos;Mytilini;Dafni;Florina;Argos Orestiko;Kastoria;Perama;Karditsa;Kozani;Volos;Alexandreia;Kalamata;Kallithea;Vrilissia;Irakleio;Koropi;Orestiada;Argyroupoli;Oraiokastro;Marousi;Rodos;Zakynthos;Pyrgos;Galatsi;Amfilochia;Ilioupoli;Thebes;Xylokastro;Trikala;Ilion;Loutraki;Megara;Chrysoupoli;Chania;Nafplio;Grevena;Cholargos;Lagkadas;Ampelokipoi;Melissia;Glyfada;Messini;Kalyvia Thorikou;Lefkada;Keratsini;Preveza;Chalkida
+ET;Harar;Ethiopia;Jijiga;Semera;Mekele;Awasa;Asosa;Dire Dawa;Bahir Dar;Addis Ababa;Gambela;Bonga
+TW;Taibao;Taitung;Keelung;Zhubei;Banqiao;Changhua;Tainan;Taoyuan District;Pingtung;Douliu;Taipei;Hualien;Jincheng;Magong;Taichung;Yilan;Hsinchu;Nantou;Nangan;Taiwan;Chiayi;Kaohsiung;Miaoli
+GT;Pochuta;San Jose El Idolo;San Carlos Alzatate;Concepcion Tutuapa;San Pedro Carcha;Quezaltepeque;San Juan Chamelco;Comitancillo;San Cristobal Totonicapan;Uspantan;El Asintal;Cabrican;Coatepeque;Sacapulas;Tiquisate;Casillas;Patzicia;San Miguel Ixtahuacan;Magdalena Milpas Altas;Santa Catarina Ixtahuacan;Livingston;Rabinal;Jacaltenango;San Juan Cotzal;Teculutan;Huite;Salama;Santa Maria Chiquimula;Santa Catarina Mita;Pasaco;Concepcion Chiquirichapa;San Pedro Sacatepequez;Raxruha;Tacana;Champerico;San Luis Jilotepeque;San Miguel Panan;El Progreso;Huitan;San Vicente Pacaya;San Lucas Sacatepequez;San Jose Ojetenam;Pastores;La Maquina;San Rafael Petzal;Santo Domingo Xenacoj;Santiago Chimaltenango;Quetzaltenango;Jocotan;Santa Ana Huista;Chuarrancho;Jalapa;Yupiltepeque;Concepcion Las Minas;Santo Tomas La Union;Tucuru;San Sebastian Coatan;San Jose Acatempa;Ciudad Vieja;Guanagazapa;Parramos;San Juan Sacatepequez;La Esperanza;Santa Lucia Cotzumalguapa;Santa Cruz Mulua;San Marcos;Tectitan;Zaragoza;San Juan Ixcoy;Mixco;San Juan Bautista;Almolonga;San Sebastian Huehuetenango;San Antonio La Paz;San Bartolome Milpas Altas;San Pedro Pinula;San Juan La Laguna;Chimaltenango;San Gaspar Ixchil;Pueblo Nuevo Vinas;Zacualpa;Coban;San Andres Sajcabaja;Chicacao;Canilla;Nuevo San Carlos;Santa Lucia La Reforma;Cubulco;Santa Clara La Laguna;San Pedro Ayampuc;Santo Domingo Suchitepequez;Santa Cruz del Quiche;San Pedro Jocopilas;Salcaja;Palestina de los Altos;Patulul;Agua Blanca;Ciudad Melchor de Mencos;Concepcion Huista;Cuyotenango;Solola;Poptun;Playa Grande;San Andres Itzapa;Santa Cruz Naranjo;Huehuetenango;San Luis;San Rafael La Independencia;Colotenango;Chichicastenango;El Chal;Escuintla;Ixchiguan;Santa Catarina Pinula;La Blanca;Moyuta;La Gomera;Momostenango;Jocotenango;Villa Canales;Chajul;San Jorge;Esquipulas Palo Gordo;El Chol;San Francisco El Alto;Tecpan Guatemala;Conguaco;Nahuala;Nenton;Cuilapa;San Agustin Acasaguastlan;Alotenango;Samayac;Santa Cruz Verapaz;Chinautla;Cuilco;Santa Lucia Milpas Altas;El Tumbador;Sumpango;Santa Eulalia;Tamahu;Taxisco;Purulha;San Jose Poaquil;San Sebastian;San Jose Pinula;San Antonio Suchitepequez;Cantel;Amatitlan;Joyabaj;Soloma;San Andres Xecul;Chiquimulilla;Comapa;Antigua Guatemala;Chisec;Sipacapa;Fraijanes;Gualan;Pajapita;San Cristobal Cucho;Malacatan;Pachalum;San Pablo Jocopilas;Cajola;Flores;Santa Lucia Utatlan;Totonicapan;San Martin Jilotepeque;Fray Bartolome de Las Casas;Asuncion Mita;Santa Rosa de Lima;San Raimundo;Zapotitlan;Usumatlan;Barberena;Guazacapan;San Lucas Toliman;Petapa;Palin;San Juan Atitan;Palencia;Esquipulas;San Rafael Pie de la Cuesta;Morazan;San Bartolo;Ixtahuacan;Todos Santos Cuchumatan;Acatenango;Senahu;Zunilito;Guatemala;San Mateo Ixtatan;San Pedro La Laguna;Rio Bravo;Olintepeque;Atescatempa;Tajumulco;San Francisco la Union;Ciudad Tecun Uman;San Pablo;Ostuncalco;Santiago Atitlan;El Palmar;San Francisco Zapotitlan;Patzun;San Antonio Palopo;Chiantla;Panzos;Jalpatagua;Panajachel;San Martin Zapotitlan;El Quetzal;Masagua;Santa Maria de Jesus;Lanquin;San Antonio Huista;Sanarate;San Miguel Duenas;El Estor;San Manuel Chaparron;Sibilia;San Francisco;San Martin Sacatepequez;Chinique;San Antonio Sacatepequez;San Andres Villa Seca;San Bernardino;Villa Nueva;Mataquescuintla;Santa Barbara;Jerez;Iztapa;Puerto Barrios;Siquinala;Santa Maria Ixhuatan;Cabanas;San Antonio Aguas Calientes;Flores Costa Cuca;Sibinal;Chicaman;Estanzuela;Chiche;Zunil;Dolores;San Felipe;Sayaxche;Chiquimula;Retalhuleu;Jutiapa;La Libertad;Tactic;San Pedro Necta;San Miguel Acatan;El Tejar;Nueva Concepcion;San Miguel Siguila;San Antonio Ilotenango;La Union;San Jose La Arada;Yepocapa;San Bartolome Jocotenango;Aguacatan;San Juan Ermita;Sansare;San Juan Tecuaco;Zacapa;San Carlos Sija;Monjas;Malacatancito;Santa Cruz Balanya;Olopa;Quesada;San Rafael Las Flores;Guastatoya;Guatemala City;Colomba;Camotan;Santiago Sacatepequez;Morales;San Miguel Chicaj;Mazatenango;Santa Apolonia;Santa Ana;Ocos;Cunen;Nueva Santa Rosa;Los Amates;La Democracia;San Cristobal Verapaz
+KW;Kuwait City
+HU;Mezotur;Balatonfured;Mateszalka;Karcag;Zalaegerszeg;Oroszlany;Nyirbator;Siklos;Hajduszoboszlo;Monor;Bicske;Sarkad;Varpalota;Hatvan;Balassagyarmat;Sopron;Nyiregyhaza;Kiskunfelegyhaza;Baja;Pecs;Gyomaendrod;Pilisvorosvar;Szarvas;Szekesfehervar;Szombathely;Tata;Gyongyos;Hodmezovasarhely;Sarbogard;Salgotarjan;Nagykallo;Dabas;Budakeszi;Gyal;Mor;Heves;Kiskunmajsa;Sarospatak;Gardony;Vecses;Celldomolk;Nagykata;Godollo;Dunaujvaros;Sarvar;Tatabanya;Tiszavasvari;Tapolca;Szekszard;Barcs;Kazincbarcika;Hajdunanas;Hungary;Erd;Tolna;Komlo;Komarom;Mohacs;Kiskoros;Esztergom;Bekes;Bekescsaba;Debrecen;Kecskemet;Oroshaza;Balmazujvaros;Batonyterenye;Balatonalmadi;Mosonmagyarovar;Dunakeszi;Rackeve;Marcali;Puspokladany;Bonyhad;Mako;Siofok;Edeleny;Szeged;Veszprem;Hajduboszormeny;Gyula;Ajka;Cegled;Eger;Tiszakecske;Kisvarda;Szentes;Jaszbereny;Mezokovesd;Hajduhadhaz;Csongrad;Papa;Szolnok;Kaposvar;Tiszaujvaros;Kormend;Satoraljaujhely;Szigetvar;Paszto;Nagykanizsa;Szentendre;Tiszafured;Ozd;Paks;Budapest;Torokszentmiklos;Gyor;Miskolc;Kalocsa;Kapuvar;Koszeg;Nagykoros;Dombovar;Keszthely;Nagyatad;Vac;Berettyoujfalu;Kiskunhalas;Csorna;Szigetszentmiklos
+YE;Lahij;Raydah;Az Zaydiyah;Al Mukalla;Zinjibar;Hajjah;Aden;At Tawahi;Zabid;Yemen;Al Ma`alla';Dhamar;Bayt al Faqih;Bajil;Al Mahwit;Al Hudaydah;Mocha;Ash Shaykh `Uthman;Al Bayda';Say'un;Tarim;Rada`;Ash Shihr;`Amran;Ad Dali`;Ma`bar;Khamir;Hadibu;Al Mansurah;Ataq;Ta`izz;Yarim;Sa`dah;Jiblah;Al Ghayzah;Marib;Al Jabin;Ja`ar;Ibb;Sanaa;Al Hazm
+UZ;Chortoq;Marhamat;Termiz;Dang`ara;Yangiariq;Toyloq Qishlog'i;Jondor Shaharchasi;Nukus;Galaosiyo Shahri;Andijon;Jizzax;Buloqboshi;Shahrixon;Yozyovon;Usmat Shaharchasi;Samarkand;Paxtaobod;Paxtakor Shahri;Qanliko`l;Gurlan;Oqtosh Shahri;Do'stlik Shahri;Gagarin Shahri;Qorako`l Shahri;Jomboy Shahri;Oltiariq;Uchquduq Shahri;Toshloq;Payariq Shahri;Kuyganyor;G'oliblar Qishlog'i;Baliqchi;Bukhara;Asaka;Xonqa;Poytug`;Quvasoy;Yangirabot;Juma Shahri;Yangi Mirishkor;Ishtixon Shahri;Vodil;Qo`rg`ontepa;Loyish Shaharchasi;Beshkent Shahri;G'ijduvon Shahri;Qarshi;Xo`jayli Shahri;Uchqurghon Shahri;Taxtako`pir;Qorovul;Vobkent Shahri;Romitan Shahri;Zomin Shaharchasi;Beshariq;G'allaorol Shahri;Namangan;Payshamba Shahri;Kattaqo'rg'on Shahri;Shofirkon Shahri;Hazorasp;Xo`jaobod;Shovot;Qo'shko'pir;Kegeyli Shahar;Farg`ona;Kogon Shahri;Kosonsoy;Uchtepa Qishlog'i;Nurobod Shahri;Yaypan;Urgut Shahri;Tashkent;Uzbekistan;Qorao`zak;Chimboy Shahri;Qorashina;G`uzor;Navoiy;Xiva;Qo`ng`irot Shahri;Quva;Bulung'ur Shahri;Rishton;Haqqulobod;Guliston;Ziyodin Shaharchasi;Bog'ot;Zarbdor Shaharchasi;Urganch
+UA;Skvyra;Sevastopol;Henichesk;Zaporizhzhia;Chortkiv;Krasnohrad;Izmail;Ochakiv;Artsyz;Rozdilna;Horlivka;Svitlovodsk;Bershad;Bakhmut;Kalanchak;Bakhchysarai;Smila;Bilohirsk;Novhorod-Siverskyi;Tiachiv;Bila Tserkva;Kobeliaky;Znamianka;Rakhiv;Kiliia;Nikopol;Shyroke;Lviv;Novomyrhorod;Olevsk;Kalmiuske;Chaplynka;Dolyna;Skadovsk;Izium;Kryvyi Rih;Novohrad-Volynskyi;Storozhynets;Tarashcha;Hlobyne;Pokrovsk;Radomyshl;Tulchyn;Kovel;Tokmak;Dubno;Berehove;Uman;Rokytne;Novoazovsk;Piatykhatky;Zolotonosha;Lutsk;Nova Odesa;Tysmenytsia;Bohodukhiv;Kamianka-Dniprovska;Bilhorod-Dnistrovskyi;Vynohradiv;Kalynivka;Okhtyrka;Simferopol;Poltava;Nemyriv;Khmilnyk;Dolynska;Khotyn;Berezivka;Melitopol;Mykolaiv;Bilozerka;Sokyriany;Sumy;Myronivka;Alchevsk;Pervomaisk;Vyshhorod;Reshetylivka;Kosiv;Reni;Bobrynets;Kurman;Berdychiv;Makiivka;Kramatorsk;Khmelnytskyi;Sievierodonetsk;Yampil;Polohy;Zhytomyr;Shakhtarsk;Oleksandriia;Svatove;Berdiansk;Kamianets-Podilskyi;Drohobych;Marhanets;Ukraine;Chuhuiv;Yuzhnoukrainsk;Volnovakha;Kaharlyk;Bilovodsk;Fastiv;Mizhhiria;Dnipro;Kalush;Horodyshche;Chyhyryn;Tlumach;Zolochiv;Yakymivka;Zhmerynka;Lubny;Novoukrainka;Brovary;Berezhany;Hlyboka;Pohrebyshche;Mukacheve;Vesele;Kherson;Zalishchyky;Chervonohrad;Yavoriv;Novyi Buh;Kamin-Kashyrskyi;Snihurivka;Koriukivka;Prymorsk;Mariupol;Liubashivka;Dovzhansk;Enerhodar;Cherkasy;Boryspil;Synelnykove;Sarny;Balta;Nyzhnohirskyi;Novomoskovsk;Chornomorske;Pustomyty;Stryi;Zhydachiv;Kharkiv;Bar;Odesa;Khust;Zvenyhorodka;Saky;Koziatyn;Kyiv;Chernivtsi;Obukhiv;Kupiansk;Starobilsk;Horodenka;Kolomyia;Romny;Sniatyn;Novotroitske;Kerch;Myrhorod;Kozova;Lokhvytsya;Haivoron;Bolhrad;Podilsk;Voznesensk;Oleshky;Illintsi;Konotop;Yevpatoriia;Bucha;Kryzhopil;Pryluky;Luhansk;Mala Vyska;Rivne;Tatarbunary;Kremenchuk;Ivano-Frankivsk;Kropyvnytskyi;Korosten;Khorol;Verkhnodniprovsk;Yany Kapu;Chernihiv;Nizhyn;Apostolove;Bashtanka;Ovidiopol;Kakhovka;Nadvirna;Kamianske;Shostka;Pavlohrad;Vasylivka;Irshava;Donetsk;Tetiiv;Hola Prystan;Kremenets;Biliaivka;Mykhailivka;Uzhhorod;Varash;Ternivka;Dzhankoi;Makariv;Ternopil;Vinnytsia;Perevalsk;Mohyliv-Podilskyi;Sambir;Haisyn;Lozova
+BO;Potosi;La Paz;Santa Cruz;Cochabamba;Bolivia;Tarija;Sucre;Cobija;Trinidad;Oruro
+KP;Sariwon;Kanggye;Wonsan;Sariwon-si;Pyongyang;Ch'ongjin;Rajin;Korea, North;Hyesan;Hoeryong;Namsan;Sinuiju;Kaesong;Haeju;P'yongsong-si;Hamhung
+IT;Trani;Trento;Trieste;Nuoro;Crotone;Vercelli;Florence;Belluno;Genoa;Brindisi;Viterbo;Pavia;Catanzaro;Pesaro;Latina;Como;Caltanissetta;Frosinone;Matera;Rovigo;Gorizia;Pistoia;Ferrara;Avellino;Tempio Pausania;Vicenza;Cagliari;Catania;Forli;Lucca;L'Aquila;Reggio di Calabria;Campobasso;Agrigento;Arezzo;Foggia;Bolzano;Bologna;Naples;Perugia;Massa;Trapani;Mantova;Potenza;Andria;Bergamo;Pescara;Rieti;Lodi;Reggio Emilia;Caserta;Siena;Taranto;Alessandria;Terni;Sondrio;Rimini;Novara;Varese;Italy;La Spezia;Ascoli Piceno;Prato;Messina;Cremona;Padova;Lecce;Brescia;Teramo;Chieti;Villacidro;Livorno;Ragusa;Grosseto;Ancona;Turin;Biella;Lecco;Vibo Valentia;Monza;Fermo;Salerno;Aosta;Savona;Udine;Ravenna;Tortoli;Benevento;Enna;Bari;Macerata;Pordenone;Rome;Modena;Barletta;Verona;Milan;Oristano;Siracusa;Imperia;Sassari;Pisa;Iglesias;Palermo;Olbia;Cosenza;Carbonia;Treviso;Venice;Parma;Cuneo;Piacenza;Verbania;Asti
+EC;Loja;Cuenca;Macas;Tulcan;Latacunga;Guayaquil;Azogues;Santa Elena;Santo Domingo de los Colorados;Zamora;Puerto Baquerizo Moreno;Guaranda;Puyo;Machala;Nueva Loja;Riobamba;Ibarra;Babahoyo;Quito;Esmeraldas;Tena;Ambato;Puerto Francisco de Orellana;Portoviejo;Ecuador
+SO;Boosaaso;Xuddur;Mogadishu;Baidoa;Buurhakaba;Kismaayo;Qoryooley;Gaalkacyo;Bu'aale;Afgooye;Hobyo;Jawhar;Dhuusamarreeb;Garbahaarrey;Marka;Laascaanood;Hargeysa;Somalia;Boorama;Beledweyne;Ceerigaabo;Garoowe;Burco
+SY;Nubl;Ar Rastan;Khan Shaykhun;Darayya;Darat `Izzah;Aleppo;Tall Abyad;Jisr ash Shughur;Jaramana;Hamah;As Suwayda';Suran;Al Qamishli;Sahnaya;Tallkalakh;Al Mayadin;`Afrin;Ash Shaykh Badr;Damascus;Dayr az Zawr;Muhradah;Tall Rif`at;Armanaz;Dayr Hafir;Izra;Harasta;Babila;Maskanah;Ghabaghib;Salkhad;Homs;`Ayn al `Arab;Al Qunaytirah;Ar Raqqah;Busra ash Sham;Kafr Takharim;Syria;Binnish;Al Qutayfah;As Suqaylibiyah;Hish;Yabrud;Al Hajar al Aswad;Jablah;Al `Asharah;Ash Shaddadah;Taftanaz;As Sanamayn;Jarabulus;Tartus;Nawa;Muh Hasan;As Safirah;At Tall;Sarmin;Khirbat Ghazalah;Manbij;Tallbisah;Tadmur;Ath Thawrah;Madaya;Masyaf;Baniyas;Ma`arrat an Nu`man;Tasil;Al Musayfirah;Jindayris;Qadsayya;An Nabk;Ar Ruhaybah;Hajin;Idlib;Ra's al `Ayn;Harim;Kafr Batna;Kafr Nubl;As Sukhnah;Al Qardahah;Dhiban;Al Malikiyah;Shahba;Ad Duraykish;I`zaz;Shin;Al Atarib;Albu Kamal;Mari`;Al Qusayr;Jasim;Kafr Zayta;Safita;Ma`arratmisrin;Salqin;`Amuda;Duma;Al Kiswah;Al Hasakah;Tall Salhab;Al Muzayrib;Latakia;As Salamiyah;Qatana;Qal`at al Madiq;Al Qaryatayn;Dar`a;Dayr `Atiyah;Az Zabadani;Jayrud;Saraqib;Tadif;Saydnaya;Al Ghizlaniyah;Ad Darbasiyah;Mahin
+ZM;Lusaka;Choma;Chinsali;Zambia;Ndola;Kasama;Chipata;Mansa;Kabwe;Mongu;Solwezi
+BF;Yako;Boromo;Diapaga;Bobo-Dioulasso;Reo;Ziniare;Manga;Gayeri;Kombissiri;Kaya;Boulsa;Batie;Tougan;Koupela;Burkina Faso;Dedougou;Dano;Djibo;Po;Ouahigouya;Bousse;Hounde;Titao;Banfora;Nouna;Zorgo;Pama;Kokologo;Diebougou;Gorom-Gorom;Gourcy;Leo;Aribinda;Bogande;Fada Ngourma;Toma;Sapone;Ouargaye;Sebba;Koudougou;Tenkodogo;Dori;Ouagadougou;Korsimoro;Tanghin-Dassouri;Gaoua;Sapouy;Orodara;Salanso;Kongoussi
+LB;Joubb Jannine;Batroun;Amioun;Bcharre;Beirut;Tripoli;Bent Jbail;El Hermel;Nabatiye;Zgharta;Halba;Baalbek;Lebanon;Zahle;Jounie;Tyre;Aaley;Sidon;Baabda;Jbail
+RO;Piatra Neamt;Focsani;Bucharest;Vaslui;Cluj-Napoca;Zalau;Craiova;Resita;Galati;Iasi;Satu Mare;Calarasi;Botosani;Ploiesti;Drobeta-Turnu Severin;Baia Mare;Oradea;Giurgiu;Slatina;Romania;Braila;Buzau;Timisoara;Hunedoara;Constanta;Slobozia;Targu Jiu;Sfantu-Gheorghe;Bistrita;Brasov;Miercurea-Ciuc;Suceava;Arad;Alexandria;Tulcea;Targoviste;Targu-Mures;Bacau;Sibiu;Alba Iulia;Pitesti;Ramnicu Valcea
+LK;Trincomalee;Anuradhapura;Sri Jayewardenepura Kotte;Ratnapura;Colombo;Sri Lanka;Badulla;Galle;Jaffna;Kandy;Kurunegala
+AZ;Agsu;Saatli;Goygol;Qax;Gadabay;Lerik;Babak;Bilasuvar;Naxcivan;Haciqabul;Ordubad;Samux;Agdam;Sarur;Imisli;Barda;Naftalan;Baku;Ucar;Neftcala;Heydarabad;Samkir;Yevlax;Qusar;Azerbaijan;Susa;Astara;Sabirabad;Zaqatala;Quba;Goycay;Ismayilli;Tovuz;Siyazan;Agstafa;Zardab;Oguz;Goranboy;Cabrayil;Xocali;Qubadli;Davaci;Yardimli;Agcabadi;Sumqayit;Tartar;Culfa;Agdas;Lacin;Sahbuz;Qazax;Saki;Lankaran;Mingacevir;Xocavand;Daskasan;Masalli;Xizi;Xacmaz;Salyan;Kalbacar;Qivraq;Ganca;Fuzuli;Xirdalan;Kurdamir;Beylaqan;Calilabad;Qobustan;Qabala;Balakan
+MG;Morondava;Fenoarivo Atsinanana;Maevatanana;Manakara;Antsohihy;Mahajanga;Tsiroanomandidy;Farafangana;Antsiranana;Antananarivo;Maintirano;Tolanaro;Ambatondrazaka;Ambovombe;Antsirabe;Sambava;Ambositra;Fianarantsoa;Toliara;Ihosy;Toamasina;Miarinarivo;Madagascar
+VE;Machiques;Colon;Rubio;Aragua de Barcelona;Caracas;Guanare;Tariba;Escuque;Puerto Piritu;La Guaira;Barquisimeto;Motatan;El Limon;Ocumare del Tuy;San Antonio de Los Altos;Ciudad Guayana;El Tocuyo;Cabimas;Caucagua;La Colonia Tovar;Baruta;El Consejo;Ciudad Piar;Maiquetia;Montalban;Chichiriviche;Guatire;San Diego;Guacara;La Victoria;Valera;Quibor;Ejido;Turmero;Altagracia de Orituco;San Jose de Aerocuar;Calabozo;Anaco;Cabudare;Cumana;San Carlos;Valencia;Valle de La Pascua;Cantaura;Caraballeda;Monte Carmelo;Petare;El Callao;San Carlos del Zulia;Tocuyito;Piritu;Palo Negro;Punto Fijo;Guanta;Maturin;Lecherias;El Socorro;Bocono;Las Mercedes;Ciudad Bolivar;Villa de Cura;Guasipati;Yaritagua;Barcelona;Carupano;Puerto La Cruz;Chaguaramas;Trujillo;Onoto;Uracoa;Sabaneta;Chivacoa;El Tigre;Charallave;Puerto Cabello;Guasdualito;Los Teques;Santa Cruz;Coro;Tucupita;Higuerote;San Jose de Guaribe;Caripito;La Asuncion;Maracay;Rio Caribe;Maracaibo;Acarigua;Clarines;Barbacoas;Tucacas;Juangriego;Puerto Ayacucho;El Palmar;Ciudad Ojeda;Venezuela;San Antonio del Tachira;Urena;Isla Raton;Porlamar;San Cristobal;Pampan;Carache;San Fernando;Aguasay;Carvajal;Barinas;Merida;La Grita;Santa Maria de Ipire;Carora;Guigue;Santa Barbara;Araure;Upata;Santa Cruz de Los Taques;El Valle del Espiritu Santo;La Esmeralda;Guarenas;Socopo;Catia La Mar;Cagua;Cocorote;Los Guayos;San Felipe;Ospino;Sarare;Santa Rita;Pampatar;Santa Lucia;Puerto Cumarebo;San Juan de los Morros;Pampanito;Achaguas;Santa Teresa del Tuy;Sanare;Nirgua;Cojedes;San Pedro de Coche;Santa Ana;Cua;Zaraza;Tinaquillo;San Mateo
+AT;Zell am See;Feldbach;Austria;Imst;Amstetten;Weiz;Bregenz;Neunkirchen;Vocklabruck;Lienz;Bludenz;Deutschlandsberg;Zwettl;Krems an der Donau;Salzburg;Leoben;Dornbirn;Innsbruck;Baden;Klosterneuburg;Judenburg;Eisenstadt;Korneuburg;Sankt Johann im Pongau;Bruck an der Mur;Ganserndorf;Steyr;Gmunden;Vienna;Volkermarkt;Wolfsberg;Feldkirchen;Schwaz;Mistelbach;Voitsberg;Spittal an der Drau;Linz;Hallein;Modling;Sankt Polten;Braunau am Inn;Wiener Neustadt;Kufstein;Klagenfurt;Sankt Veit an der Glan;Ried im Innkreis;Villach;Graz;Wels;Hollabrunn;Leibnitz
+ZW;Chinhoyi;Harare;Marondera;Lupane;Mutare;Gweru;Gwanda;Zimbabwe;Bulawayo;Masvingo;Bindura
+KH;Sisophon;Tbeng Meanchey;Kampong Speu;Kampong Cham;Kampong Chhnang;Stung Treng;Prey Veng;Svay Rieng;Kampong Trach;Koh Kong;Takeo;Battambang;Sihanoukville;Sen Monorom;Kratie;Kampot;Pailin;Phnom Penh;Lumphat;Suong;Kampong Thom;Cambodia;Krong Kep;Siem Reap;Samraong;Ta Khmau;Banlung;Pursat
+SE;Vanersborg;Kavlinge;Skelleftea;Balsta;Timra;Ronneby;Ornskoldsvik;Gavle;Orebro;Gislaved;Ulricehamn;Ystad;Oxelosund;Mjolby;Uddevalla;Harnosand;Ljungby;Arboga;Soderhamn;Sala;Taby;Staffanstorp;Hassleholm;Stockholm;Karlskrona;Enkoping;Sandviken;Karlstad;Molndal;Jonkoping;Mariestad;Tranas;Vasteras;Malmo;Hagfors;Vaxjo;Hallstahammar;Katrineholm;Motala;Uppsala;Eskilstuna;Nynashamn;Hoor;Falun;Skara;Stenungsund;Kalmar;Vetlanda;Bollnas;Hudiksvall;Kungsangen;Vallentuna;Vasterhaninge;Kumla;Kiruna;Koping;Kinna;Skovde;Vimmerby;Ostersund;Upplands Vasby;Sundsvall;Skoghall;Lomma;Lerum;Sunne;Kungsbacka;Lidkoping;Boden;Habo;Molnlycke;Tibro;Tumba;Gothenburg;Borlange;Kristianstad;Fagersta;Falkoping;Linkoping;Alingsas;Varberg;Arvika;Karlskoga;Ekero;Trelleborg;Strangnas;Amal;Akersberga;Sater;Norrtalje;Marsta;Helsingborg;Saffle;Gagnef;Lidingo;Eslov;Svedala;Sodertalje;Orkelljunga;Nykoping;Nybro;Sjobo;Astorp;Angelholm;Halmstad;Lycksele;Oskarshamn;Eksjo;Pitea;Kungalv;Lulea;Norrkoping;Ludvika;Sweden;Filipstad;Solleftea;Umea;Visby;Kristinehamn;Nassjo;Boras;Avesta;Lindesberg;Trollhattan;Gustavsberg;Arlov;Finspang;Hoganas;Almhult;Landskrona;Mora;Vastervik
+CU;Ciro Redondo;Colon;Jobabo;Santa Cruz del Sur;Vinales;Jaruco;Ranchuelo;Manati;Palma Soriano;Cardenas;Sagua de Tanamo;Los Arabos;Perico;Limonar;Guira de Melena;Palmira;Minas;Buey Arriba;Jesus Menendez;Jaguey Grande;Majagua;Aguada de Pasajeros;Nueva Gerona;Sancti Spiritus;Campechuela;Candelaria;Guisa;Moron;Najasa;Marti;Guaimaro;Imias;Cacocum;Baguanos;Jovellanos;Bayamo;Manzanillo;Guanajay;San Luis;Pilon;Havana;Cabaiguan;Quemado de Guines;Carlos Manuel de Cespedes;Media Luna;Guantanamo;Bejucal;Madruga;Taguasco;San Jose de las Lajas;San German;Minas de Matahambre;Guines;Yaguajay;Moa;Cuba;Santa Clara;Chambas;Puerto Padre;Esmeralda;Placetas;San Antonio del Sur;Santo Domingo;Nueva Paz;Batabano;Bolivia;Union de Reyes;Lajas;Artemisa;Trinidad;San Nicolas;La Sierpe;Corralillo;Caimito;Camaguey;Santa Cruz del Norte;Jatibonico;Rio Cauto;Sagua la Grande;Colombia;Venezuela;Bartolome Maso;Yara;Quivican;San Cristobal;Consolacion del Sur;Vertientes;Fomento;Remedios;Sibanicu;Manicaragua;Bahia Honda;Mayari;Baracoa;Melena del Sur;Banes;Primero de Enero;Gibara;Contramaestre;Los Palacios;Jiguani;Cayo Mambi;Las Tunas;Alquizar;Cienfuegos;Matanzas;Cruces;Jimaguayu;Rodas;Cifuentes;Pedro Betancourt;Santa Lucia;Caibarien;Santiago de Cuba;Holguin;Ciego de Avila;San Juan y Martinez;Mariel;Cumanayagua;San Antonio de los Banos;La Palma;Antilla;Amancio;Bauta;Pinar del Rio;Camajuani;Calimete;Encrucijada;Florencia;Niquero;Florida
+BY;Baranavichy;Rechytsa;Maladzyechna;Bykhaw;Belarus;Babruysk;Mahilyow;Krychaw;Ivanava;Hantsavichy;Mazyr;Yelsk;Rahachow;Chavusy;Ashmyany;Vyetka;Ivatsevichy;Vawkavysk;Minsk;Pruzhany;Svyetlahorsk;Vilyeyka;Khoyniki;Kobryn;Masty;Zhytkavichy;Klimavichy;Hrodna;Zhlobin;Smarhon;Lyuban;Polatsk;Drahichyn;Pinsk;Pastavy;Slonim;Brest;Orsha;Byalynichy;Talachyn;Homyel';Chachersk;Kalinkavichy;Salihorsk;Mstsislaw;Vitsyebsk;Horki;Horad Zhodzina;Lyakhavichy;Shklow;Haradok;Shchuchyn;Hlybokaye;Kastsyukovichy;Braslaw;Kapyl;Malaryta;Valozhyn;Lyelchytsy;Horad Smalyavichy;Staryya Darohi;Dobrush;Luninyets;Nyasvizh;Astravyets;Buda-Kashalyova;Asipovichy;Pyetrykaw;Lahoysk;Slutsk;Horad Barysaw;Klyetsk;Zhabinka;Byaroza
+NL;Winterswijk;Rucphen;Den Helder;Valkenswaard;Oldenzaal;Haren;Kapelle;Bedum;Roermond;Putten;Stein;Sliedrecht;Oosterhout;Houten;Montfoort;Malden;Ede;Brielle;Urk;Wierden;Waalre;Burgum;Bergen op Zoom;Papendrecht;Nijmegen;Arnhem;Heerde;Rijen;Neerijnen;Schiedam;Hulst;Oosterwolde;Purmerend;Beek;Bodegraven;Harlingen;Tiel;Middelburg;Lelystad;Huizen;Alkmaar;Middelharnis;Nijverdal;Zwolle;Pijnacker;Tholen;Hengelo;Aalsmeer;Steenbergen;Franeker;Raamsdonksveer;Doesburg;Apeldoorn;Almere;Beuningen;Brummen;Oirschot;Utrecht;Someren;Tilburg;Hardinxveld-Giessendam;Winsum;Sneek;Goes;Deventer;Hoogeveen;Heeze;Zevenaar;Sittard;Uden;Brunssum;Amstelveen;Katwijk;Wijk bij Duurstede;Appingedam;Spijkenisse;Drachten;Elburg;Bladel;Epe;Venray;Wijchen;Beverwijk;Aalten;Groesbeek;Oss;Zutphen;Oisterwijk;Tubbergen;Vlaardingen;Grave;Simpelveld;Hendrik-Ido-Ambacht;Dordrecht;Heemstede;Breda;Cuijk;Rhenen;Hilversum;Sassenheim;Haaksbergen;Doorn;Boxtel;IJmuiden;Waddinxveen;Joure;Delfzijl;Landgraaf;Lochem;Son en Breugel;Geldermalsen;Wolvega;Deurne;Asten;Zandvoort;Gennep;Uitgeest;Terneuzen;Heerlen;Heerhugowaard;IJsselstein;Meerssen;Staphorst;Enkhuizen;Noordwijkerhout;Boekel;Laren;Heerenveen;Rotterdam;Nieuwegein;Leek;Capelle aan den IJssel;Noordwijk;Woerden;Woudrichem;Strijen;Leiden;Oldebroek;Oostzaan;Nuth;Werkendam;Boskoop;Maastricht;Heemskerk;Blaricum;Schagen;Hellevoetsluis;Woudenberg;Horst;Amersfoort;Zundert;Soest;Eemnes;'s-Hertogenbosch;Ermelo;Haarlem;Hillegom;Scherpenzeel;Beilen;Almelo;Best;Zaandam;Duiven;Baarn;Veenendaal;Emmeloord;Amsterdam;Alblasserdam;Voorschoten;Helmond;Bussum;The Hague;Zierikzee;Waalwijk;Bergeijk;Bergen;Volendam;Nederweert;Kampen;Netherlands;Nuenen;Barneveld;Kaatsheuvel;Leeuwarden;Doetinchem;Wassenaar;Landsmeer;Goirle;Haaren;Dongen;Coevorden;Leusden;Veldhoven;Heiloo;Vianen;Monnickendam;Gemert;Zoetermeer;Weert;Emmen;Beek en Donk;Veghel;Harderwijk;Maarssen;Zeewolde;Hoogezand;Denekamp;Uithoorn;Zaltbommel;Hoofddorp;Boxmeer;Opmeer;Oudenbosch;Roelofarendsveen;Veendam;Nunspeet;Kerkrade;Lopik;Krimpen aan den IJssel;Sint-Michielsgestel;Zuidhorn;Dalfsen;Bergambacht;Heesch;Lisse;Leidschendam;Oud-Beijerland;Rijswijk;Eijsden;Vlissingen;Venlo;Leiderdorp;Lemmer;Hoorn;Gouda;Diemen;Schoonhoven;Zeist;Castricum;Meppel;Maassluis;Etten-Leur;Oegstgeest;Bilthoven;Vught;Borne;Sint Anthonis;Stadskanaal;Geldrop;Delft;Zoeterwoude;Eindhoven;Wageningen;Ommen;Made;Naaldwijk;Raalte;Barendrecht;Hilvarenbeek;Sint-Oedenrode;Westervoort;Schinnen;Dronten;Gorinchem;Assen;Losser;Dokkum;Hattem;Voerendaal;Groningen;Oudewater;Roosendaal;Nijkerk;Culemborg;Ridderkerk;Eersel;Enschede;Alphen aan den Rijn;Weesp;Hardenberg;Vaals;Druten;Zwijndrecht
+KZ;Taraz;Beyneu;Shiyeli;Qaratau;Shakhtinsk;Ekibastuz;Qashyr;Alga;Aqtobe;Novoishimskiy;Kazakhstan;Shalqar;Turkistan;Taldyqorghan;Qapshaghay;Qarabalyq;Balqash;Khromtau;Soran;Ertis;Kishkenekol;Qazyqurt;Zhitiqara;Zaysan;Kegen;Pavlodar;Oktyabr'sk;Almaty;Qyzylorda;Makhambet;Petropavl;Qaraghandy;Bulaevo;Osakarovka;Bayanauyl;Zhosaly;Saumalkol;Bayghanin;Aral;Shetpe;Sarykemer;Kentau;Atbasar;Esil;Oral;Atyrau;Zhetisay;Aqsu;Semey;Mangghystau;Esik;Qostanay;Qulsary;Inderbor;Borovskoy;Ayagoz;Shymkent;Temirtau;Astana;Aksay;Ushtobe;Bauyrzhan Momyshuly;Qazaly;Shchuchinsk;Oskemen;Zhangatas;Stepnogorsk;Qarabulaq;Fort-Shevchenko;Satbayev;Aqkol;Talghar;Abay;Derzhavinsk;Shemonaikha;Qulan;Qarqaraly;Rudnyy;Taiynsha;Qaskeleng;Uryzhar;Tekeli;Zyryanovsk;Uzynaghash;Lengir;Zhezqazghan;Torghay;Qarazhal;Makinsk;Atasu;Shongzhy;Ereymentau;Aqtau;Shu;Kokshetau;Sarqan;Zharkent;Arys;Balpyq Bi;Sholaqqorghan;Qusmuryn;Shar;Maqat;Sharbaqty;Arqalyq;Chapaev;Usharal;Ridder;Zhanibek
+MW;Kasungu;Dowa;Karonga;Ntcheu;Nkhata Bay;Salima;Ntchisi;Lilongwe;Mangochi;Dedza;Phalombe;Nkhotakota;Mchinji;Nsanje;Machinga;Blantyre;Mzimba;Neno;Mwanza;Chitipa;Mulanje;Thyolo;Rumphi;Zomba;Chikwawa;Chiradzulu;Balaka;Malawi
+PL;Bedzin;Gdansk;Pulawy;Wejherowo;Mielec;Glogow;Nysa;Zabkowice Slaskie;Bartoszyce;Wolomin;Walbrzych;Swiecie;Olawa;Otwock;Legionowo;Drawsko Pomorskie;Kamien Pomorski;Garwolin;Zywiec;Miedzychod;Grodzisk Mazowiecki;Zabrze;Rypin;Nowy Targ;Boleslawiec;Swiedbodzin;Siedlce;Gryfino;Klobuck;Przasnysz;Busko-Zdroj;Slupsk;Myslowice;Lidzbark Warminski;Koscian;Tychy;Sieradz;Gizycko;Sandomierz;Ostrzeszow;Siemiatycze;Czluchow;Krosno Odrzanskie;Elk;Klodzko;Lublin;Miedzyrzecz;Zuromin;Wolsztyn;Olesnica;Olesno;Lubin;Strzelce Krajenskie;Lask;Puck;Sroda Wielkopolska;Nisko;Dabrowa Tarnowska;Jedrzejow;Stargard Szczecinski;Szczytno;Kalisz;Kedzierzyn-Kozle;Wschowa;Chrzanow;Ruda Slaska;Radomsko;Swidwin;Wyszkow;Wieliczka;Chelm;Sztum;Parczew;Sokolow Podlaski;Krapkowice;Slupca;Ostroleka;Radom;Rybnik;Zakopane;Czarnkow;Ropczyce;Milicz;Aleksandrow Kujawski;Olsztyn;Legnica;Pinczow;Lowicz;Trzebnica;Sierpc;Skarzysko-Kamienna;Mikolow;Augustow;Polkowice;Jaworzno;Znin;Debica;Naklo nad Notecia;Sochaczew;Poland;Sepolno Krajenskie;Lobez;Zyrardow;Gorzow Wielkopolski;Zawiercie;Glubczyce;Kwidzyn;Pyrzyce;Wielun;Suwalki;Leczna;Wabrzezno;Hrubieszow;Nidzica;Wegorzewo;Nowy Tomysl;Warsaw;Rzeszow;Chorzow;Wloclawek;Police;Wagrowiec;Nowe Miasto Lubawskie;Nowy Sacz;Grojec;Zamosc;Tomaszow Mazowiecki;Tomaszow Lubelski;Nowy Dwor Mazowiecki;Janow Lubelski;Kolbuszowa;Mragowo;Sopot;Bielsko-Biala;Zagan;Slubice;Chojnice;Swinoujscie;Tarnobrzeg;Brzeziny;Wieruszow;Luban;Ciechanow;Tczew;Kamienna Gora;Hajnowka;Belchatow;Krotoszyn;Bytow;Mysliborz;Tarnowskie Gory;Gorlice;Plock;Krosno;Bialogard;Inowroclaw;Walcz;Gryfice;Dabrowa Gornicza;Kartuzy;Pruszkow;Pila;Strzelce Opolskie;Grajewo;Poznan;Torun;Koszalin;Chodziez;Raciborz;Lancut;Minsk Mazowiecki;Konskie;Kolo;Limanowa;Swietochlowice;Jawor;Pabianice;Grudziadz;Kutno;Strzelin;Nowa Sol;Prudnik;Grodzisk Wielkopolski;Zambrow;Mogilno;Wlodawa;Kozienice;Mlawa;Piaseczno;Gora;Cieszyn;Zgorzelec;Lubartow;Zory;Bilgoraj;Piekary Slaskie;Opoczno;Turek;Kolobrzeg;Brzeg;Namyslow;Miechow;Oswiecim;Gostyn;Konin;Dzialdowo;Kolno;Gliwice;Bytom;Jaroslaw;Olecko;Ostrowiec Swietokrzyski;Brzesko;Zary;Sucha Beskidzka;Bierun;Lomza;Zlotow;Myszkow;Gdynia;Ozarow Mazowiecki;Swidnik;Staszow;Przeworsk;Ustrzyki Dolne;Lubaczow;Starachowice;Choszczno;Zielona Gora;Rawicz;Srem;Zgierz;Makow Mazowiecki;Olkusz;Ketrzyn;Bochnia;Brodnica;Przemysl;Bydgoszcz;Leszno;Lipno;Wroclaw;Jelenia Gora;Chelmno;Lebork;Lukow;Ostroda;Oborniki;Szczecinek;Krasnik;Ilawa;Ryki;Opole;Pisz;Ostrow Mazowiecka;Golub-Dobrzyn;Lodz;Slawno;Kielce;Sokolka;Goleniow;Wolow;Tuchola;Szydlowiec;Krakow;Pruszcz Gdanski;Piotrkow Trybunalski;Pszczyna;Kepno;Stalowa Wola;Swidnica;Lubliniec;Wloszczowa;Bielsk Podlaski;Siemianowice Slaskie;Pleszew;Jaslo;Elblag;Rawa Mazowiecka;Szczecin;Lezajsk;Pultusk;Krasnystaw;Sulecin;Sosnowiec;Malbork;Wodzislaw Slaski;Goldap;Sanok;Gostynin;Czestochowa;Biala Podlaska;Starogard Gdanski;Myslenice;Wegrow;Zlotoryja;Plonsk;Bialystok;Zdunska Wola;Dzierzoniow;Radzyn Podlaski;Braniewo;Skierniewice;Monki;Tarnow;Wrzesnia;Szamotuly;Kluczbork;Leczyca;Wadowice;Koscierzyna;Ostrow Wielkopolski;Katowice;Wysokie Mazowieckie;Jastrzebie-Zdroj;Sroda Slaska;Nowy Dwor Gdanski;Jarocin;Gniezno
+PR;San Juan
+CG;Owando;Djambala;Brazzaville;Madingou;Dolisie;Loango;Kinkala;Congo (Brazzaville);Sibiti;Impfondo;Ouesso;Pointe-Noire;Ewo
+UY;Montevideo;Mercedes;Treinta y Tres;Rocha;Maldonado;Canelones;Durazno;Rivera;Uruguay;Melo;Tacuarembo;San Jose;Minas;Paysandu;Salto;Fray Bentos;Colonia del Sacramento;Florida;Artigas
+HN;La Paz;La Ceiba;Yuscaran;Trujillo;San Pedro Sula;Honduras;Santa Barbara;Ciudad Choluteca;Juticalpa;Tegucigalpa;Puerto Lempira;Santa Rosa de Copan;Roatan;La Esperanza;Nueva Ocotepeque;Comayagua;Gracias;Nacaome;Yoro
+UG;Nakasongola;Rukungiri;Kiryandongo;Lwengo;Kasanda;Ntoroko;Lyantonde;Otuke;Gulu;Namutumba;Kotido;Kanungu;Kyenjojo;Soroti;Bukwo;Nabilatuk;Luuka Town;Mitoma;Adjumani;Bundibugyo;Rubirizi;Kabale;Sironko;Busia;Pader;Moyo;Nsiika;Mukono;Kasaali;Maracha;Kiboga;Bulisa;Kalungu;Lira;Kalangala;Kamwenge;Kyankwanzi;Agago;Ntara;Lamwo;Tororo;Luwero;Busesa;Mpigi;Uganda;Bulambuli;Mityana;Kumi;Kibingo;Alebtong;Ngora;Kayunga;Amolatar;Nwoya;Kagadi;Kibiito;Napak;Kiruhura;Serere;Masaka;Pakwach;Kalaki;Kyegegwa;Rubanda;Abim;Manafwa;Amuria;Mbale;Mayuge;Buikwe;Bukomansimbi;Kapchorwa;Jinja;Wakiso;Zombo;Nakapiripirit;Arua;Koboko;Mbarara;Kakumiro;Buyende;Amudat;Yumbe;Kampala;Ibanda;Kanoni;Mubende;Kisoro;Rakai;Binyin;Apac;Butaleja;Iganga;Palenga;Kinoni;Oyam;Katakwi;Butebo;Hoima;Kitamilo;Fort Portal;Kaliro;Kitgum;Gombe;Butalangu;Nebbi;Kibuku;Bugiri;Bushenyi;Mparo;Namayingo;Dokolo;Amuru;Moroto;Kasese;Bududa;Kole;Ntungamo;Sembabule;Isingiro;Kamuli;Kaberamaido;Bupoto;Masindi;Bukedea;Pallisa;Kaabong
+GN;Faranah;Kindia;Gueckedou;Fria;Pita;Kissidougou;Koundara;Macenta;Guinea;Gaoual;Mali;Tougue;Mamou;Forecariah;Dinguiraye;Dalaba;Boke;Conakry;Kouroussa;N'Zerekore;Yomou;Boffa;Kerouane;Telimele;Siguiri;Dabola;Beyla;Kankan;Labe
+BG;Sofia;Stara Zagora;Montana;Tutrakan;Veliko Tarnovo;Kyustendil;Blagoevgrad;Bulgaria;Dospat;Sliven;Gabrovo;Rakitovo;Burgas;Knezha;Kavarna;Pazardzhik;Zlatograd;Smolyan;Pernik;Kozloduy;Velingrad;Pleven;Vidin;Sozopol;Lovech;Silistra;Panagyurishte;Haskovo;Razgrad;Plovdiv;Peshtera;Balchik;Berkovitsa;Shumen;Yambol;Lom;Svishtov;Varna;Kardzhali;Ruse;Dobrich;Pomorie;Nesebar;Targovishte;Vratsa
+CR;San Jose;Costa Rica;Heredia;Liberia;Puntarenas;Alajuela;Cartago;Puerto Limon
+RW;Kigali;Byumba;Rwanda;Nyanza;Kibuye;Rwamagana
+PA;Colon;Penonome;Chepo;Jaque;Sabanitas;Las Tablas;Puerto Armuelles;Sieyik;Union Choco;Puerto Pilon;Bocas del Toro;Alcalde Diaz;Buabidi;Pacora;Arraijan;Santiago;Ancon;Bajo Boquete;Kusapin;Tocumen;Cativa;Aguadulce;Nuevo Arraijan;Chilibre;Puerto Caimito;Chitre;Changuinola;Gaigirgordub;David;Panama;La Chorrera;La Palma;Almirante;Panama City;El Coco;San Miguelito
+SN;Thies;Diourbel;Kolda;Fatick;Ziguinchor;Dakar;Kaolack;Matam;Sedhiou;Saint-Louis;Louga;Tambacounda;Senegal;Kedougou;Kaffrine
+OM;`Ibri;Muscat;Hayma';Oman;Sur;Ibra';Salalah;Ar Rustaq;Suhar;Khasab;Nizwa;Al Buraymi;Al Mazyunah
+MN;Uliastay;Ulaangom;Baruun-Urt;Mandalgovi;Ulaan-Uul;Ondorhaan;Dzuunmod;Suhbaatar;Hovd;Bayanhongor;Bulgan;Altay;Hoshoot;Mongolia;Choyr;Saynshand;Choybalsan;Tsetserleg;Arvayheer;Erdenet;Dalanzadgad;Darhan;Olgiy;Dalandzadgad;Harhorin;Moron;Ulaanbaatar
+IL;Beersheba;Tel Aviv-Yafo;Nazareth;Jerusalem;Haifa;Israel;Ramla
+DK;Taastrup;Frederiksvaerk;Ikast;Thisted;Skive;Copenhagen;Esbjerg;Hjorring;Slagelse;Vejle;Vordingborg;Kalundborg;Svendborg;Hedensted;Kolding;Nykobing Mors;Frederikshavn;Holstebro;Silkeborg;Horsholm;Nykobing Falster;Ringsted;Denmark;Holbaek;Herning;Haslev;Hobro;Grenaa;Bronderslev;Koge;Odense;Aarhus;Stovring;Skanderborg;Nyborg;Odder;Varde;Vejen;Horsens;Sonderborg;Naestved;Frederikssund;Helsingor;Soro;Fredericia;Viborg;Randers;Ringkobing;Helsinge;Dragor;Solrod Strand;Ronne;Aabenraa;Struer;Roskilde;Middelfart;Aalborg;Aars;Hillerod;Haderslev;Farum
+FI;Hamina;Imatra;Laukaa;Espoo;Savonlinna;Tuusula;Jarvenpaa;Kempele;Kerava;Sipoo;Kontiolahti;Loimaa;Ii;Kirkkonummi;Alavus;Forssa;Lempaala;Laitila;Karkkila;Masku;Liperi;Ylojarvi;Kitee;Eura;Kajaani;Raahe;Somero;Kuusamo;Jyvaskyla;Joensuu;Tornio;Loviisa;Ylivieska;Jamsa;Sodankyla;Hameenkyro;Kalajoki;Sotkamo;Kurikka;Hanko;Helsinki;Orivesi;Orimattila;Eurajoki;Muhos;Kauniainen;Korsholm;Kangasala;Salo;Kankaanpaa;Nokia;Kuopio;Rauma;Turku;Keuruu;Vaasa;Siilinjarvi;Huittinen;Mantsala;Lieksa;Nivala;Pieksamaki;Lappeenranta;Kaarina;Janakkala;Mariehamn;Raisio;Lahti;Alajarvi;Ulvila;Lapua;Kotka;Porvoo;Kokkola;Leppavirta;Hollola;Paimio;Saarijarvi;Mikkeli;Naantali;Jakobstad;Pargas;Iisalmi;Kauhava;Hausjarvi;Kemijarvi;Sastamala;Heinola;Vantaa;Pirkkala;Uusikaupunki;Kemi;Tampere;Kouvola;Hameenlinna;Valkeakoski;Kauhajoki;Narpes;Riihimaki;Varkaus;Rovaniemi;Lapinlahti;Hyvinkaa;Finland;Muurame;Seinajoki;Lohja;Lieto;Raseborg;Pori;Liminka;Ilmajoki;Aanekoski;Oulu
+CZ;Plzen;Liberec;Usti nad Labem;Brno;Pardubice;Hradec Kralove;Prague;Jihlava;Zlin;Ostrava;Czechia;Karlovy Vary;Olomouc;Ceske Budejovice
+NZ;Stratford;Auckland;Whangarei;Greymouth;Wellington;Dunedin;Napier;New Zealand;Palmerston North;Hamilton;Gisborne;Richmond;Blenheim;Waitangi;Nelson;Invercargill;Christchurch;Whakatane
+DO;Monte Plata;San Francisco de Macoris;Salcedo;La Vega;Bani;Jimani;Santo Domingo;La Romana;Sabaneta;San Juan;Nagua;El Seibo;Monte Cristi;Santiago;Samana;Pedernales;Bonao;Moca;Azua;San Jose de Ocoa;Higuey;Comendador;Puerto Plata;San Pedro de Macoris;Hato Mayor;Santo Domingo Este;Neiba;San Cristobal;Dajabon;Dominican Republic;Barahona;Mao;Cotui
+PT;Santiago do Cacem;Mirandela;Albergaria-a-Velha;Olhao;Guarda;Rio Maior;Elvas;Caldas da Rainha;Tondela;Lourinha;Alcobaca;Vouzela;Sines;Silves;Beja;Melgaco;Lousa;Coimbra;Fafe;Aljustrel;Batalha;Peso da Regua;Baiao;Ponte de Lima;Montemor-o-Novo;Serta;Alcanena;Tavira;Gouveia;Portimao;Ponta Delgada;Portalegre;Torres Vedras;Macedo de Cavaleiros;Tomar;Celorico de Basto;Vagos;Gondomar;Ovar;Vila Real;Vendas Novas;Viseu;Miranda do Corvo;Moncao;Ansiao;Esposende;Mangualde;Satao;Vila Real de Santo Antonio;Montalegre;Montijo;Lousada;Vila Verde;Cabeceiras de Basto;Tabua;Vila Nova de Gaia;Castelo Branco;Moura;Alcochete;Idanha-a-Nova;Evora;Vila do Conde;Ponte da Barca;Fundao;Castro Daire;Braganca;Cadaval;Odivelas;Amarante;Moimenta da Beira;Agueda;Viana do Castelo;Mealhada;Pombal;Sao Joao da Madeira;Pacos de Ferreira;Almeirim;Loule;Povoa de Varzim;Barreiro;Seixal;Reguengos de Monsaraz;Trofa;Santarem;Salvaterra de Magos;Vila Pouca de Aguiar;Mortagua;Arruda dos Vinhos;Condeixa-a-Nova;Montemor-o-Velho;Sobral de Monte Agraco;Ourem;Benavente;Oliveira de Azemeis;Entroncamento;Sao Pedro do Sul;Abrantes;Bombarral;Chamusca;Odemira;Maia;Sesimbra;Obidos;Oliveira do Hospital;Porto;Valongo;Mafra;Vieira do Minho;Vinhais;Santo Tirso;Ponte de Sor;Povoa de Lanhoso;Cinfaes;Espinho;Vila Nova de Cerveira;Torres Novas;Loures;Arganil;Arcos de Valdevez;Nazare;Grandola;Paredes de Coura;Figueira da Foz;Barcelos;Mira;Alijo;Pinhel;Anadia;Portugal;Resende;Aveiro;Lagoa;Estremoz;Funchal;Arouca;Leiria;Braga;Ilhavo;Trancoso;Chaves;Azambuja;Lisbon;Moita;Sintra;Alcacer do Sal;Valenca;Oliveira do Bairro;Marinha Grande;Murtosa;Porto de Mos;Torre de Moncorvo;Lagos;Paredes;Sabugal;Amares;Penafiel;Matosinhos;Feira;Penacova;Almada;Seia;Felgueiras;Peniche;Setubal;Vila Franca de Xira;Amadora;Soure;Palmela;Serpa;Cantanhede;Oeiras;Estarreja;Coruche;Guimaraes;Sao Bras de Alportel;Cascais;Lamego;Sever do Vouga;Nelas;Cartaxo;Marco de Canavezes;Famalicao;Oliveira de Frades;Faro;Albufeira;Ferreira do Zezere;Alenquer;Vale de Cambra;Covilha;Santa Comba Dao
+IE;Limerick;Dun Dealgan;Nenagh;Tralee;Waterford;Port Laoise;Ennis;Tallaght;Tullamore;Castlebar;Monaghan;Ros Comain;Lifford;Dunleary;Swords;Naas;Wexford;Carrick on Shannon;Galway;Wicklow;Carlow;Kilkenny;Ireland;Cork;An Cabhan;Sligo;Clonmel;Dublin;Mullingar;Longford;Trim
+BE;Roeselare;Waremme;Wavre;Sint-Niklaas;Maaseik;Mons;Ostend;Marche-en-Famenne;Mouscron;Bruges;Soignies;Aalst;Namur;Ath;Virton;Veurne;Diksmuide;Belgium;Enghien;Eeklo;Philippeville;Gent;Charleroi;Tielt;Oudenaarde;Turnhout;Brussels;Bastogne;Hannut;Kortrijk;Hasselt;Liege;Arlon;Verviers;Thuin;Vilvoorde;Antwerp;Tournai;Tongeren;Nivelles;Mechelen;Ieper;Dendermonde;Huy;Dinant
+RS;Presevo;Gadzin Han;Knic;Priboj;Kragujevac;Zrenjanin;Kikinda;Blace;Bajina Basta;Kovacica;Vladicin Han;Senta;Ljubovija;Bojnik;Smederevska Palanka;Nova Varos;Stara Pazova;Kanjiza;Srbobran;Mali Idos;Sabac;Niska Banja;Sremski Karlovci;Pozarevac;Lazarevac;Serbia;Kostolac;Valjevo;Novi Becej;Crna Trava;Vrbas;Razanj;Bela Crkva;Ada;Bosilegrad;Arilje;Rekovac;Indija;Jagodina;Backa Topola;Novi Pazar;Vrnjacka Banja;Bujanovac;Vladimirci;Malo Crnice;Coka;Krupanj;Dimitrovgrad;Becej;Vrsac;Golubac;Pirot;Sid;Surcin;Nova Crnja;Negotin;Merosina;Cacak;Novi Sad;Kraljevo;Nis;Sjenica;Zabalj;Lajkovac;Kula;Lucani;Koceljeva;Vranje;Arandelovac;Plandiste;Kovin;Belgrade;Varvarin;Cuprija;Medveda;Veliko Gradiste;Mali Zvornik;Titel;Sokobanja;Pancevo;Lapovo;Zitorada;Velika Plana;Pozega;Novi Knezevac;Uzice;Petrovac na Mlavi;Trstenik;Bor;Doljevac;Vlasotince;Leskovac;Bela Palanka;Kursumlija;Ljig;Irig;Svilajnac;Sremska Mitrovica;Ruma;Zagubica;Zabari;Prokuplje;Zajecar;Bogatic;Boljevac;Krusevac;Topola;Majdanpek;Babusnica;Backa Palanka;Svrljig;Osecina;Gornji Milanovac;Brus;Petrovaradin;Ivanjica;Aleksinac;Aleksandrovac;Raska;Loznica;Cicevac;Prijepolje;Smederevo;Zemun;Mionica;Zitiste;Kucevo;Cajetina;Despotovac;Beocin;Batocina;Paracin;Kladovo;Ub;Subotica;Trgoviste;Backi Petrovac;Temerin;Bac;Sombor;Apatin;Knjazevac;Secanj;Lebane;Tutin;Kosjeric;Pecinci;Opovo;Mladenovac;Odzaci;Raca;Alibunar;Surdulica
+QA;Ash Shihaniyah;Ar Rayyan;Madinat ash Shamal;Umm Salal `Ali;Al Wakrah;Doha;Az Za`ayin;Qatar;Al Khawr
+LY;Tobruk;Libya;Al Jawf;Nalut;Ghat;Al Marj;Zuwarah;Al `Aziziyah;Tripoli;Al Bayda';Surt;Sabha;Hun;Murzuq;Awbari;Gharyan;Idri;Misratah;Benghazi;Ajdabiya;Az Zawiyah;Darnah
+BI;Bubanza;Bururi;Ngozi;Kayanza;Karuzi;Gitega;Makamba;Cibitoke;Isale;Ruyigi;Burundi;Rumonge;Kirundo;Muyinga;Muramvya;Rutana;Bujumbura;Cankuzo
+MZ;Tete;Beira;Maputo;Quelimane;Chimoio;Pemba;Lichinga;Mozambique;Inhambane;Nampula;Xai-Xai
+KG;Kulundu;Belovodskoe;Kerben;Kyrgyzstan;Kayyngdy;Kara-Balta;Kochkor;Kemin;Gulcho;Bishkek;Massy;Batken;Naryn;Aravan;Karakol;Baetov;Chuy;Kara-Suu;Jalal-Abad;Kara-Bak;Isfana;Buzhum;Toktogul;Kant;Talas;Eski-Nookat;Kazarman;Ala-Buka;At-Bashy;Teploklyuchenka;Ivanovka;Pokrovka;Osh;Bazar-Korgon;Kyzyl-Adyr;Kyzyl-Suu;Suzak;Bokonbaev;Uch-Korgon;Cholpon-Ata;Tup;Sokuluk;Lebedinovka;Kara-Kulja
+GE;Khashuri;Kutaisi;Rustavi;Senaki;Zugdidi;Ozurgeti;Marneuli;Sokhumi;Chiatura;Poti;Zestaponi;Akhaltsikhe;Telavi;Sagarejo;Kaspi;Gori;Batumi;Ambrolauri;Tbilisi;Kobuleti;Mtskheta;Georgia;Samtredia
+TD;Doba;Pala;Bongor;Faya;Mongo;Amdjarass;Goz-Beida;Moundou;Sarh;Moussoro;Chad;Massenya;Koumra;Bol;Abeche;N'Djamena;Ati;Biltine;Massakory;Bardai;Am-Timan;Fada;Lai;Mao
+MR;Tidjikja;Nema;Kaedi;Dar Naim;Aleg;Mauritania;Tevragh Zeina;Rosso;Nouadhibou;Kiffa;Zouerate;Selibaby;Aioun;Atar;Akjoujt;Nouakchott;Arafat
+AM;Ijevan;Artashat;Ashtarak;Gavarr;Armavir;Gyumri;Yerevan;Armenia;Yeghegnadzor;Hrazdan;Vanadzor;Kapan
+NO;Skien;Rorvik;Mandal;Os;Porsgrunn;As;Svolvaer;Volda;Randaberg;Namsos;Rygge;Stavanger;Fredrikstad;Bryne;Voss;Hammerfest;Kristiansand;Oslo;Trondheim;Stord;Sandnes;Narvik;Kopervik;Kongsberg;Drammen;Tonsberg;Stjordal;Moss;Brumunddal;Lyngdal;Harstad;Mosjoen;Bodo;Egersund;Nittedal;Finnsnes;Ski;Alesund;Sandvika;Askim;Bergen;Alta;Kongsvinger;Arendal;Sarpsborg;Tromso;Hamar;Stange;Verdal;Lorenskog;Fauske;Haugesund;Sogndal;Kristiansund;Notodden;Grimstad;Lier;Orsta;Farsund;Gjovik;Kirkenes;Nesoddtangen;Forde;Molde;Asker;Elverum;Halden;Sogne;Vadso;Nannestad;Honefoss;Kleppe;Kragero;Vennesla;Lillehammer;Norway;Levanger;Floro;Eidsvoll;Royken;Steinkjer;Mo i Rana
+NI;Altagracia;San Lorenzo;Palacaguina;El Almendro;San Isidro;Greytown;Managua;Ocotal;Tisma;Quezalguaque;Nueva Guinea;Bonanza;Nandaime;Masaya;San Ramon;Santa Rosa del Penon;Jalapa;Siuna;Chichigalpa;Rivas;Prinzapolka;Muy Muy;Potosi;El Ayote;Mulukuku;Rancho Grande;San Marcos;Ticuantepe;San Juan de Rio Coco;San Dionisio;Granada;Quilali;Bilwi;Condega;San Rafael del Sur;Esteli;Somotillo;Juigalpa;La Trinidad;Niquinohomo;San Carlos;Villa Sandino;Ciudad Sandino;El Jicaro;Matagalpa;Jinotepe;Jinotega;Tola;Moyogalpa;Muelle de los Bueyes;Waspan;San Miguelito;Pueblo Nuevo;Matiguas;El Tortuguero;Corinto;San Francisco Libre;Santo Domingo;Rio Blanco;Telica;Sebaco;Villa El Carmen;Totogalpa;El Viejo;Esquipulas;Villanueva;Acoyapa;Terrabona;El Realejo;Masatepe;El Cua;El Rama;El Crucero;Belen;San Jose de Bocay;Murra;Kukrahill;Tipitapa;Wiwili;El Jicaral;Camoapa;San Fernando;Comalapa;San Lucas;San Sebastian de Yali;San Rafael del Norte;Bocana de Paiwas;San Juan de Limay;Nagarote;Nicaragua;Rosita;Teustepe;Boaco;El Sauce;Telpaneca;Posoltega;Achuapa;Yalaguina;Ciudad Dario;La Concepcion;Mateare;La Libertad;La Paz Centro;Nindiri;La Cruz de Rio Grande;Somoto;Chinandega;Leon;Diriomo;Bluefields;Nandasmo;San Juan del Sur;Diriamba
+TM;Ashgabat;Mary;Anew;Turkmenistan;Balkanabat;Turkmenabat;Dasoguz
+NE;Dosso;Maradi;Gaya;Nguigmi;Arlit;Tillaberi;Niger;Tahoua;Niamey;Diffa;Madaoua;Birnin Konni;Agadez;Guidan Roumdji;Goure;Zinder
+LR;Robertsport;Monrovia;Harper;Gbarnga;Cestos City;Voinjama;Tubmanburg;Liberia;Zwedru;Sanniquellie;Bopolu;Barclayville;Kakata;Buchanan;Greenville;Fish Town;Bensonville
+HT;Jacmel;Haiti;Port-au-Prince;Cap-Haitien;Gonaives;Miragoane;Hinche;Jeremie;Fort Liberte;Les Cayes;Port-de-Paix
+ER;Keren;Massawa;Eritrea;Barentu;Assab;Mendefera;Asmara
+SL;Freetown;Bo;Sierra Leone;Kenema;Makeni;Port Loko
+LA;Salavan;Savannakhet;Louang Namtha;Xam Nua;Ban Houayxay;Pakxe;Laos;Xekong;Xaignabouli;Phon-Hong;Phongsali;Thakhek;Pakxan;Muang Sing;Phonsavan;Attapu;Anouvong;Xai;Vientiane;Louangphabang
+LV;Aizkraukle;Liepaja;Kuldiga;Riga;Valmiera;Marupe;Preili;Ogre;Madona;Saulkrasti;Livani;Tukums;Aluksne;Varaklani;Adazi;Saldus;Dobele;Latvia;Rezekne;Valka;Balvi;Kraslava;Kekava;Ludza;Salaspils;Limbazi;Cesis;Ropazi;Sigulda;Daugavpils;Talsi;Olaine;Jurmala;Gulbene;Smiltene;Jekabpils;Ventspils;Bauska;Ulbroka;Jelgava
+CF;Bria;Bimbo;Mbaiki;Bangassou;Bouar;Mobaye;Bossangoa;Berberati;Bangui;Kaga Bandoro;Sibut;Obo;Birao;Nola;Central African Republic;Bozoum;Ndele;Bambari
+TJ;Istaravshan;Buston;Shahrinav;Somoniyon;Norak;Vakhsh;Hulbuk;Tursunzoda;Fayzobod;Hisor;Vanj;Konibodom;Danghara;Vahdat;Ayni;Dushanbe;Jilikul;Levakant;Khovaling;Moskva;Khorugh;Ghafurov;Obikiik;Abdurahmoni Jomi;Roghun;Shahritus;Dusti;Mu'minobod;Bokhtar;Shurobod;Ghonchi;Shahriston;Panj;Tajikistan;Yovon;Farkhor;Panjakent;Khujand;Isfara;Rasht;Kulob
+NP;Godawari;Biratnagar;Pokhara;Janakpur;Butwal;Bhairahawa;Birendranagar;Kathmandu;Nepal;Hetauda
+GA;Koulamoutou;Oyem;Makokou;Lambarene;Port-Gentil;Franceville;Gabon;Tchibanga;Mouila;Libreville
+HR;Viskovo;Varazdin;Belisce;Pozega;Solin;Slavonski Brod;Pula;Labin;Vrbovec;Kastav;Cepin;Pazin;Metkovic;Podstrana;Kutina;Duga Resa;Novska;Crikvenica;Rovinj;Sisak;Gospic;Popovaca;Imotski;Trogir;Nova Gradiska;Garesnica;Umag;Koprivnica;Ivanec;Zadar;Slatina;Valpovo;Sibenik;Jastrebarsko;Zupanja;Daruvar;Bjelovar;Novi Marof;Vodice;Sveti Ivan Zelina;Dubrovnik;Porec;Sinj;Ivanic-Grad;Brdovec;Dakovo;Knin;Croatia;Ogulin;Cakovec;Pleternica;Zagreb;Osijek;Nasice;Virovitica;Krizevci;Opatija;Matulji;Rijeka;Nedelisce;Velika Gorica;Samobor;Vinkovci;Krapina;Zapresic;Omis;Split;Zabok;Dugo Selo;Vukovar;Makarska;Benkovac;Petrinja
+LT;Taurage;Pagegiai;Kaunas;Kedainiai;Radviliskis;Birstonas;Visaginas;Silute;Zarasai;Salcininkai;Joniskis;Elektrenai;Ignalina;Plunge;Prienai;Sakiai;Skuodas;Naujoji Akmene;Kazlu Ruda;Vilkaviskis;Svencionys;Kaisiadorys;Klaipeda;Lazdijai;Mazeikiai;Rokiskis;Kelme;Marijampole;Silale;Druskininkai;Utena;Anyksciai;Varena;Pakruojis;Vilnius;Lithuania;Raseiniai;Alytus;Ukmerge;Trakai;Siauliai;Kupiskis;Telsiai;Rietavas;Jurbarkas;Birzai;Kalvarija;Nida;Panevezys;Moletai;Pasvalys;Palanga;Jonava;Sirvintos;Kretinga
+MD;Telenesti;Comrat;Criuleni;Nisporeni;Moldova;Cocieri;Drochia;Briceni;Soldanesti;Calarasi;Floresti;Causeni;Hincesti;Soroca;Balti;Edinet;Basarabeasca;Glodeni;Chisinau;Cantemir;Falesti;Stefan Voda;Taraclia;Donduseni;Riscani;Ialoveni;Anenii Noi;Leova;Singerei;Cimislia;Bender;Tiraspol;Orhei;Ungheni;Rezina;Straseni;Ocnita;Cahul
+PG;Kundiawa;Port Moresby;Wewak;Alotau;Madang;Buka;Wabag;Vanimo;Tari;Lorengau;Kimbe;Goroka;Papua New Guinea;Daru;Popondetta;Kurumul;Kokopo;Lae;Kavieng;Mendi;Kerema;Mount Hagen
+BJ;Ouidah;Kandi;Savalou;Parakou;Abomey;Djougou;Natitingou;Porto-Novo;Sakete;Lokossa;Benin;Dogbo;Cotonou
+BH;Manama
+EE;Kohtla-Jarve;Narva;Johvi;Paide;Rakvere;Tartu;Tallinn;Kardla;Viljandi;Parnu;Keila;Sillamae;Polva;Estonia;Jogeva;Rapla;Valga;Haapsalu;Kuressaare;Maardu;Voru
+DJ;Dikhil;Djibouti;Ali Sabieh;Obock;Arta;Tadjourah
+TN;Kasserine;Monastir;Kairouan;Sidi Bouzid;Gafsa;Sousse;Ben Arous;Beja;Tataouine;Manouba;El Kef;Medenine;Zaghouan;Jendouba;Kebili;Gabes;Ariana;Tunis;Bizerte;Tozeur;Sfax;Tunisia;Siliana;Mahdia;Nabeul
+XG;Gaza
+JM;Falmouth;Lucea;Port Antonio;Morant Bay;Kingston;Spanish Town;Jamaica;Port Maria;Savanna-la-Mar;Mandeville;May Pen;Half Way Tree;Black River;Saint Ann's Bay;Montego Bay
+MK;Zelenikovo;Brvenica;Vrapciste;Makedonska Kamenica;Novo Selo;Bogovinje;Cucer-Sandevo;Rosoman;Kicevo;Kocani;Gostivar;Lipkovo;Vasilevo;Stip;Petrovec;Jegunovce;Konce;Pehcevo;Ilinden;Gradsko;North Macedonia;Bogdanci;Plasnica;Lozovo;Star Dojran;Kratovo;Centar Zupa;Radovis;Debar;Kumanovo;Ohrid;Vevcani;Sopiste;Rankovce;Sveti Nikole;Veles;Tearce;Vinica;Makedonski Brod;Probistip;Kavadarci;Zrnovci;Rostusa;Prilep;Aracinovo;Berovo;Zelino;Bosilovo;Struga;Mogila;Studenicani;Novaci;Strumica;Tetovo;Belcista;Bitola;Demir Kapija;Resen;Gevgelija;Dolneni;Krusevo;Valandovo;Skopje;Kriva Palanka;Demir Hisar;Staro Nagoricane;Delcevo;Krivogastani;Negotino;Karbinci;Oblesevo
+GW;Cacheu;Guinea-Bissau;Quinhamel;Bissau;Buba;Gabu;Farim;Catio;Bolama;Bafata
+MT;Victoria;Lija;Safi;Valletta;Ghasri;Gzira;Ghaxaq;Ghajnsielem;Mellieha;Tarxien;Xewkija;Imtarfa;Mosta;San Giljan;Siggiewi;Iklin;Qormi;Qrendi;Ta' Xbiex;Santa Lucija;Imsida;Gharb;Nadur;Birzebbuga;Xaghra;Marsaskala;Saint Paul's Bay;Imdina;Gudja;Sliema;Swieqi;Marsaxlokk;Attard;San Gwann;Floriana;Birkirkara;Fontana;Imqabba;Vittoriosa;Senglea;Marsa;Qala;Munxar;Dingli;Balzan;Cospicua;Fgura;Luqa;Zurrieq;San Lawrenz;Zabbar;Imgarr;Rabat;Pieta;Kalkara;Gharghur;Naxxar;Sannat;Malta;Hamrun;Kercem;Zebbug;Kirkop;Zejtun;Pembroke;Xghajra;Santa Venera;Paola
+PY;Caazapa;Fuerte Olimpo;Filadelfia;Villa Hayes;Pilar;San Pedro de Ycuamandiyu;Aregua;Caacupe;Ciudad del Este;Pedro Juan Caballero;Concepcion;Asuncion;Encarnacion;Paraguari;Villarrica;Paraguay;San Juan Bautista;Salto del Guaira;Coronel Oviedo
+SK;Hlohovec;Poprad;Nove Zamky;Dunajska Streda;Presov;Senica;Ziar nad Hronom;Sabinov;Malacky;Rimavska Sobota;Detva;Vel'ky Krtis;Michalovce;Humenne;Piest'any;Trebisov;Bratislava;Kysucke Nove Mesto;Pezinok;Zvolen;Liptovsky Mikulas;Senec;Partizanske;Zilina;Svidnik;Puchov;Vranov nad Topl'ou;Zlate Moravce;Trencin;Ruzomberok;Banska Stiavnica;Bardejov;Dolny Kubin;Nitra;Lucenec;Revuca;Slovakia;Topol'cany;Spisska Nova Ves;Galanta;Snina;Skalica;Cadca;Nove Mesto nad Vahom;Prievidza;Povazska Bystrica;Banska Bystrica;Levoca;Stropkov;Kosice;Bytca;Levice;Brezno;Trnava;Sal'a;Kezmarok;Tvrdosin;Banovce nad Bebravou;Myjava;Martin;Roznava;Stara L'ubovna
+SS;Wau;South Sudan;Bor;Malakal;Rumbek;Aweil;Juba;Kuacjok;Yambio;Torit;Bentiu
+CH;Aarau;Altdorf;Rheinfelden;Kussnacht;Switzerland;Einsiedeln;Solothurn;Rapperswil-Jona;Brig-Glis;Herisau;Rorschach;Yverdon-les-Bains;Geneva;Sankt Gallen;Schaffhausen;Wil;Hinwil;Chur;La Chaux-de-Fonds;Bern;Weinfelden;Lachen;Pfaffikon;Bremgarten;Glarus;Frauenfeld;Renens;Winterthur;Basel;Sion;Schwyz;Thun;Lausanne;Uster;Stans;Appenzell;Kreuzlingen;Altstatten;Davos;Sursee;Bellinzona;Zug;Lucerne;Neuchatel;Fribourg;Langnau;Liestal;Delemont;Sarnen;Zurich
+NA;Otjiwarongo;Windhoek;Keetmanshoop;Oshakati;Eenhana;Gobabis;Outapi;Nkurenkuru;Omuthiya;Katima Mulilo;Opuwo;Rundu;Namibia;Mariental;Swakopmund
+BA;Gradacac;Zepce;Banja Luka;Celic;Donji Vakuf;Kladanj;Doboj;Ilijas;Gacko;Zivinice;Jajce;Gracanica;Bileca;Odzak;Gradiska;Vares;Bugojno;Cazin;Tesanj;Lopare;Brcko;Vitez;Kljuc;Sarajevo;Posusje;Bihac;Tuzla;Vogosca;Banovici;Rogatica;Srebrenik;Prijedor;Visoko;Kiseljak;Bijeljina;Srbac;Fojnica;Olovo;Stolac;Bratunac;Sapna;Srebrenica;Vlasenica;Pale;Bosanska Krupa;Mostar;Lukavac;Maglaj;Breza;Capljina;Siroki Brijeg;Busovaca;Gorazde;Gornji Vakuf;Trebinje;Jablanica;Bosnia and Herzegovina;Travnik;Citluk;Livno;Novi Travnik;Orasje;Milici;Zenica;Zvornik;Sanski Most;Hadzici;Ilidza;Foca;Ljubuski;Derventa;Brod;Novi Grad
+AL;Shkoder;Peshkopi;Albania;Lezhe;Vlore;Berat;Durres;Kukes;Korce;Elbasan;Gjirokaster;Fier;Tirana
+GM;Mansa Konko;Basse Santa Su;Brikama;Kanifing;Kerewan;Gambia, The;Janjanbureh;Banjul
+LS;Thaba-Tseka;Qacha's Nek;Mohale's Hoek;Mafeteng;Teyateyaneng;Quthing;Mokhotlong;Butha-Buthe;Lesotho;Leribe;Maseru
+CY;Famagusta;Kyrenia;Cyprus;Larnaca;Limassol;Paphos;Nicosia
+SV;Zacatecoluca;Sonsonate;Sensuntepeque;La Union;El Salvador;Ahuachapan;Santa Tecla;Chalatenango;San Francisco;San Vicente;San Miguel;Usulutan;Santa Ana;San Salvador;Cojutepeque
+RE;Saint-Denis
+GQ;Pale;Luba;Djibloho;Evinayong;Mongomo;Ebebiyin;Malabo;Equatorial Guinea;Bata
+SI;Ljubljana;Vojnik;Piran;Slovenska Bistrica;Sredisce ob Dravi;Dobrovnik;Skofljica;Vransko;Race;Kamnik;Dragomer;Naklo;Starse;Trzin;Brezice;Sempeter pri Gorici;Nazarje;Kocevje;Prevalje;Grad;Lasko;Zgornja Hajdina;Radece;Ig;Gornja Radgona;Bohinjska Bistrica;Slovenske Konjice;Benedikt;Vrhnika;Podlehnik;Sveta Trojica v Slovenskih Goricah;Gornji Petrovci;Smarjeske Toplice;Trbovlje;Kidricevo;Polzela;Moravce;Velike Lasce;Cerkno;Kuzma;Cerklje na Gorenjskem;Markovci;Lukovica;Jesenice;Nova Gorica;Odranci;Recica;Destrnik;Apace;Salovci;Bistrica ob Sotli;Gorenja Vas;Kozje;Podcetrtek;Braslovce;Vitomarci;Hodos;Velenje;Beltinci;Trzic;Ravne na Koroskem;Mirna Pec;Mirna;Cirkulane;Vipava;Selnica ob Dravi;Majsperk;Videm pri Ptuju;Mislinja;Nova Vas;Verzej;Jursinci;Sencur;Bled;Ilirska Bistrica;Straza;Sevnica;Ziri;Maribor;Kranjska Gora;Sentrupert;Medvode;Ankaran;Spodnje Hoce;Komen;Dravograd;Zelezniki;Puconci;Izola;Krizevci;Crnomelj;Cerknica;Rogasovci;Trebnje;Metlika;Borovnica;Kranj;Gornji Grad;Kostanjevica na Krki;Vitanje;Prebold;Semic;Zagorje;Sodrazica;Sostanj;Crna na Koroskem;Zgornja Kungota;Videm;Brezovica;Ajdovscina;Radenci;Radlje ob Dravi;Lovrenc na Pohorju;Logatec;Muta;Sentjur;Luce;Kobilje;Turnisce;Skofja Loka;Solcava;Sentilj;Postojna;Mezica;Poljcane;Ljubno;Store;Zgornje Gorje;Zalec;Velika Polana;Pesnica;Dobrna;Novo Mesto;Ormoz;Vuzenica;Slovenia;Osilnica;Celje;Zgornje Jezersko;Tabor;Ljutomer;Skocjan;Smartno;Ribnica;Komenda;Oplotnica;Rogatec;Dol;Trnovska Vas;Krsko;Domzale;Zetale;Jurovski Dol;Podvelka;Ptuj;Sezana;Kostel;Kobarid;Tolmin;Smarje;Ruse;Zavrc;Miklavz na Dravskem Polju;Slovenj Gradec;Litija;Rogaska Slatina;Razkrizje;Miren;Horjul;Dobrova;Preddvor;Murska Sobota;Bovec;Mokronog;Tisina;Menges;Zrece;Kanal;Divaca;Gorisnica;Cankova;Crensovci;Zuzemberk;Stari Trg;Koper;Dolenjske Toplice;Ivancna Gorica;Spodnji Duplek;Vodice;Hrastnik;Tomaz pri Ormozu;Dobrovo;Hrib-Loski Potok;Lenart v Slovenskih Goricah;Cerkvenjak;Sveta Ana;Sveti Jurij;Dornava;Makole;Moravske-Toplice;Mozirje;Sentjernej;Lendava;Dobje;Pivka;Grosuplje;Idrija;Radovljica
+BS;Nassau
+MQ;Fort-de-France
+BW;Selibe Phikwe;Kasane;Kanye;Masunga;Maun;Jwaneng;Serowe;Lobatse;Gaborone;Tshabong;Francistown;Botswana;Mochudi;Sowa Town;Molepolole;Ghanzi;Ramotswa
+SR;Groningen;Onverwacht;Totness;Lelydorp;Albina;Nieuw Nickerie;Brokopondo;Paramaribo;Nieuw Amsterdam;Suriname
+TL;Viqueque;Same;Manatuto;Lospalos;Baucau;Aileu;Timor-Leste;Maliana;Pante Macassar;Dili;Ainaro;Gleno;Suai;Liquica
+XK;Kamenice;Peje;Lipjan;Istog;Podujeve;Pristina;Junik;Ranillug;Mitrovice;Gjilan;Shtime;Hani i Elezit;Ferizaj;Zubin Potok;Kosovo;Rahovec;Kllokot;Partesh;Gracanice;Mamushe;Kline;Decan;Fushe Kosove;Malisheve;Suhareke;Shterpce;Dragash;Prizren;Viti;Obiliq;Kacanik;Gjakove;Leposaviq;Zvecan;Vushtrri;Novoberde;Gllogovc;Skenderaj
+GY;Vreed-en-Hoop;New Amsterdam;Lethem;Mahdia;Fort Wellington;Linden;Georgetown;Guyana;Mabaruma;Bartica
+FJ;Suva
+NC;We;Noumea;Kone;New Caledonia
+ME;Savnik;Cetinje;Zabljak;Golubovci;Ulcinj;Rozaje;Herceg Novi;Pluzine;Danilovgrad;Plav;Pljevlja;Petnjica;Tivat;Andrijevica;Gusinje;Niksic;Montenegro;Budva;Bijelo Polje;Bar;Kolasin;Tuzi;Podgorica;Kotor;Mojkovac;Berane
+CW;Willemstad
+MU;Port Louis
+IS;Reykjavik
+MV;Viligili;Foammulah;Dhihdhoo;Hithadhoo;Felidhoo;Kudahuvadhoo;Rasdhoo;Eydhafushi;Veymandoo;Funadhoo;Thinadhoo;Fonadhoo;Mahibadhoo;Male;Muli;Nilandhoo;Thulusdhoo;Kulhudhuffushi;Manadhoo;Maldives;Ungoofaaru;Naifaru
+LU;Capellen;Vianden;Echternach;Luxembourg;Grevenmacher;Remich;Mersch;Redange-sur-Attert;Clervaux;Esch-sur-Alzette;Dudelange;Wiltz;Diekirch;Differdange
+PF;Papeete
+BT;Daga;Samdrup Jongkhar;Lhuentse;Wangdue Phodrang;Samtse;Zhemgang;Bhutan;Tsirang;Thimphu;Sarpang;Mongar;Trongsa;Tsimasham;Paro;Jakar;Pemagatshel;Haa;Trashigang;Trashi Yangtse;Gasa;Punakha
+TG;Atakpame;Sokode;Kara;Togo;Dapaong;Lome
+SZ;Eswatini;Mbabane;Nhlangano;Lobamba;Manzini;Siteki
+BB;Bridgetown
+TT;Couva;Tunapuna;Scarborough;Rio Claro;Point Fortin;Port of Spain;Aranguez;Trinidad and Tobago;Siparia;Debe;Arima;San Fernando;Diego Martin;Princes Town;Chaguanas;Sangre Grande
+SB;Honiara;Buala;Taro;Tigoa;Tulagi;Kirakira;Solomon Islands;Gizo;Auki;Lata
+YT;Mamoudzou
+CV;Espargos;Assomada;Calheta de Sao Miguel;Cidade Velha;Sao Filipe;Tarrafal;Praia;Pombas;Porto Ingles;Porto Novo;Mindelo;Cova Figueira;Joao Teves;Ponta do Sol;Pedra Badejo;Ribeira Brava;Sal Rei;Igreja;Picos;Ribeira Grande;Sao Domingos;Cabo Verde;Nova Sintra
+LC;Castries
+ST;Sao Tome and Principe;Santo Antonio;Sao Tome;Neves;Santana;Guadalupe;Trindade;Sao Joao dos Angolares
+GF;Saint-Laurent-du-Maroni;Saint-Georges;Kourou;Sinnamary;Cayenne;Roura;French Guiana;Iracoubo
+BZ;Corozal;San Ignacio;Belize City;Punta Gorda;Belmopan;Orange Walk;Belize;Dangriga
+BN;Brunei;Bangar;Tutong;Kuala Belait;Bandar Seri Begawan
+VU;Isangel;Lakatoro;Luganville;Saratamata;Vanuatu;Port-Vila;Sola
+WS;Samoa;Saleaula;Safotulafai;Safotu;Lufilufi;Samamea;Satupa`itea;Apia;Vailoa;Mulifanua;Afega;Asau;Leulumoega
+MC;Monaco
+AW;Oranjestad
+GI;Gibraltar
+JE;Saint Helier
+MH;Majuro
+KM;Mutsamudu;Fomboni;Moroni;Comoros
+KI;Tarawa
+IM;Douglas
+KY;George Town
+SC;Victoria
+TO;Nuku`alofa
+AD;La Massana;Canillo;Ordino;Andorra;Escaldes-Engordany;Encamp;Andorra la Vella;Sant Julia de Loria
+AG;Saint John's
+GG;Saint Peter Port
+GL;Qaqortoq;Nuuk;Sisimiut;Ilulissat;Aasiaat;Greenland
+DM;Roseau
+VC;Kingstown
+FM;Kolonia;Colonia;Tofol;Palikir;Micronesia, Federated States of;Weno
+FO;Sorvagur;Kunoy;Oyrarbakki;Skalavik;Fuglafjordhur;Toftir;Kirkja;Skopun;Kvivik;Sandur;Saltangara;Tvoroyri;Skuvoy;Hov;Vestmanna;Famjin;Torshavn;Husavik;Hvalba;Sandavagur;Klaksvik;Vagur;Hvannasund;Strendur;Sumba;Faroe Islands;Porkeri;Nordhragota;Vidhareidhi;Eidhi
+KN;Basseterre
+VG;Road Town
+AS;Pago Pago
+SM;Faetano;Serravalle;Borgo Maggiore;Fiorentino;San Marino;Domagnano;Montegiardino;Acquaviva;Chiesanuova
+BQ;Oranjestad;The Bottom;Bonaire, Sint Eustatius, and Saba;Kralendijk
+TV;Funafuti
+LI;Balzers;Triesenberg;Ruggell;Schellenberg;Mauren;Triesen;Vaduz;Planken;Schaan;Eschen;Liechtenstein;Gamprin
+MF;Marigot
+PM;Saint-Pierre
+GD;Saint George's
+CK;Avarua
+TC;Grand Turk
+AI;The Valley
+MP;Capitol Hill
+BL;Gustavia
+FK;Stanley
+SX;Philipsburg
+XR;Longyearbyen
+CX;Flying Fish Cove
+GU;Hagta
+WF;Leava;Wallis and Futuna;Mata-Utu
+BM;Hamilton
+VA;Vatican City
+NR;Yaren
+SH;Edinburgh of the Seven Seas;Saint Helena, Ascension, and Tristan da Cunha;Jamestown;Georgetown
+NU;Alofi
+MS;Montserrat;Brades;Plymouth
+NF;Kingston
+GP;Basse-Terre
+PW;Ngerulmud
+PN;Adamstown
+GS;King Edward Point
+VI;Charlotte Amalie
\ No newline at end of file
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
index 80e349a3f..1f1827ab3 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
@@ -3,6 +3,7 @@ package eu.dnetlib.pace.clustering;
 
 import java.util.Map;
 
+import com.mongodb.connection.Cluster;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
@@ -177,41 +178,16 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void testKeywordsClustering() {
+	public void legalnameClustering() {
 
-		final ClusteringFunction cf = new KeywordsClustering(params);
-		final String s = "Polytechnic University of Turin";
+		final ClusteringFunction cf = new LegalnameClustering(params);
+		String s = "key::1 key::2 city::1";
 		System.out.println(s);
 		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 
-		final String s1 = "POLITECNICO DI TORINO";
-		System.out.println(s1);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s1)));
-
-		final String s2 = "Universita farmaceutica culturale di milano bergamo";
-		System.out.println("s2 = " + s2);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s2)));
-
-		final String s3 = "universita universita milano milano";
-		System.out.println("s3 = " + s3);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s3)));
-
-		final String s4 = "Politechniki Warszawskiej (Warsaw University of Technology)";
-		System.out.println("s4 = " + s4);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s4)));
-
-		final String s5 = "İstanbul Ticarət Universiteti";
-		System.out.println("s5 = " + s5);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s5)));
-
-		final String s6 = "National and Kapodistrian University of Athens";
-		System.out.println("s6 = " + s6);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s6)));
-
-		final String s7 = "Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών";
-		System.out.println("s7 = " + s7);
-		System.out.println(cf.apply(conf, Lists.newArrayList(s7)));
-
+		s = "key::1 key::2 city::1 city::2";
+		System.out.println(s);
+		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 	}
 
 	@Test
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java
index 7fd81d975..4ec120f4a 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java
@@ -54,4 +54,47 @@ public class PaceFunctionTest extends AbstractPaceFunctions {
 		System.out.println("Fixed aliases  : " + fixAliases(TEST_STRING));
 	}
 
+	@Test
+	public void countryInferenceTest() {
+		assertEquals("IT", countryInference("UNKNOWN", "Università di Bologna"));
+		assertEquals("UK", countryInference("UK", "Università di Bologna"));
+		assertEquals("IT", countryInference("UNKNOWN", "Universiteé de Naples"));
+		assertEquals("UNKNOWN", countryInference("UNKNOWN", "Università del Lavoro"));
+	}
+
+	@Test
+	public void cityInferenceTest() {
+		assertEquals("universita city::3181928", cityInference("Università di Bologna"));
+		assertEquals("university city::3170647", cityInference("University of Pisa"));
+		assertEquals("universita", cityInference("Università del lavoro"));
+		assertEquals("universita city::3173331 city::3169522", cityInference("Università di Modena e Reggio Emilia"));
+	}
+
+	@Test
+	public void keywordInferenceTest() {
+		assertEquals("key::41 turin", keywordInference("Polytechnic University of Turin"));
+		assertEquals("key::41 torino", keywordInference("POLITECNICO DI TORINO"));
+		assertEquals(
+			"key::1 key::60 key::81 milano bergamo",
+			keywordInference("Universita farmaceutica culturale di milano bergamo"));
+		assertEquals("key::1 key::1 milano milano", keywordInference("universita universita milano milano"));
+		assertEquals(
+			"key::10 kapodistriako panepistemio athenon",
+			keywordInference("Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών"));
+	}
+
+	@Test
+	public void cityKeywordInferenceTest() {
+		assertEquals("key::41 city::3165524", cityKeywordInference("Polytechnic University of Turin"));
+		assertEquals("key::41 city::3165524", cityKeywordInference("POLITECNICO DI TORINO"));
+		assertEquals(
+			"key::1 key::60 key::81 city::3173435 city::3182164",
+			cityKeywordInference("Universita farmaceutica culturale di milano bergamo"));
+		assertEquals(
+			"key::1 key::1 city::3173435 city::3173435", cityKeywordInference("universita universita milano milano"));
+		assertEquals(
+			"key::10 kapodistriako panepistemio city::264371",
+			cityKeywordInference("Εθνικό και Καποδιστριακό Πανεπιστήμιο Αθηνών"));
+	}
+
 }
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index 8e72f4efc..fe0dca7f1 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -35,6 +35,7 @@ public class ComparatorTest extends AbstractPaceTest {
 		params.put("name_th", "0.95");
 		params.put("jpath_value", "$.value");
 		params.put("jpath_classid", "$.qualifier.classid");
+		params.put("codeRegex", "key::\\d+");
 	}
 
 	@Test
@@ -44,52 +45,23 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void cityMatchTest() {
-		final CityMatch cityMatch = new CityMatch(params);
+	public void codeMatchTest() {
+		CodeMatch codeMatch = new CodeMatch(params);
 
-		// both names with no cities
-		assertEquals(1.0, cityMatch.distance("Università", "Centro di ricerca", conf));
+		// both names with no codes
+		assertEquals(1.0, codeMatch.distance("testing1", "testing2", conf));
 
-		// one of the two names with no cities
-		assertEquals(-1.0, cityMatch.distance("Università di Bologna", "Centro di ricerca", conf));
+		// one of the two names with no codes
+		assertEquals(-1.0, codeMatch.distance("testing1 key::1", "testing", conf));
 
-		// both names with cities (same)
-		assertEquals(1.0, cityMatch.distance("Universita di Bologna", "Biblioteca di Bologna", conf));
+		// both names with codes (same)
+		assertEquals(1.0, codeMatch.distance("testing1 key::1", "testing2 key::1", conf));
 
-		// both names with cities (different)
-		assertEquals(0.0, cityMatch.distance("Universita di Bologna", "Universita di Torino", conf));
-		assertEquals(0.0, cityMatch.distance("Franklin College", "Concordia College", conf));
+		// both names with codes (different)
+		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", conf));
 
-		// particular cases
-		assertEquals(1.0, cityMatch.distance("Free University of Bozen-Bolzano", "Università di Bolzano", conf));
-		assertEquals(
-			1.0,
-			cityMatch
-				.distance(
-					"Politechniki Warszawskiej (Warsaw University of Technology)", "Warsaw University of Technology",
-					conf));
-
-		// failing becasuse 'Allen' is a transliterrated greek stopword
-		// assertEquals(-1.0, cityMatch.distance("Allen (United States)", "United States Military Academy", conf));
-		assertEquals(-1.0, cityMatch.distance("Washington (United States)", "United States Military Academy", conf));
-	}
-
-	@Test
-	public void keywordMatchTest() {
-		params.put("threshold", "0.5");
-
-		final KeywordMatch keywordMatch = new KeywordMatch(params);
-
-		assertEquals(
-			0.5, keywordMatch.distance("Biblioteca dell'Universita di Bologna", "Università di Bologna", conf));
-		assertEquals(1.0, keywordMatch.distance("Universita degli studi di Pisa", "Universita di Pisa", conf));
-		assertEquals(1.0, keywordMatch.distance("Polytechnic University of Turin", "POLITECNICO DI TORINO", conf));
-		assertEquals(1.0, keywordMatch.distance("Istanbul Commerce University", "İstanbul Ticarət Universiteti", conf));
-		assertEquals(1.0, keywordMatch.distance("Franklin College", "Concordia College", conf));
-		assertEquals(2.0 / 3.0, keywordMatch.distance("University of Georgia", "Georgia State University", conf));
-		assertEquals(0.5, keywordMatch.distance("University College London", "University of London", conf));
-		assertEquals(0.5, keywordMatch.distance("Washington State University", "University of Washington", conf));
-		assertEquals(-1.0, keywordMatch.distance("Allen (United States)", "United States Military Academy", conf));
+		// both names with codes (1 same, 1 different)
+		assertEquals(0.5,codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
 
 	}
 
@@ -155,15 +127,15 @@ public class ComparatorTest extends AbstractPaceTest {
 	}
 
 	@Test
-	public void jaroWinklerNormalizedNameTest() {
+	public void jaroWinklerLegalnameTest() {
 
-		final JaroWinklerNormalizedName jaroWinklerNormalizedName = new JaroWinklerNormalizedName(params);
+		final JaroWinklerLegalname jaroWinklerLegalname = new JaroWinklerLegalname(params);
 
-		double result = jaroWinklerNormalizedName
-			.distance("AT&T (United States)", "United States Military Academy", conf);
+		double result = jaroWinklerLegalname
+			.distance("AT&T (United States)", "United States key::2 key::1", conf);
 		System.out.println("result = " + result);
 
-		result = jaroWinklerNormalizedName.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
+		result = jaroWinklerLegalname.distance("NOAA - Servicio Meteorol\\u00f3gico Nacional", "NOAA - NWS", conf);
 		System.out.println("result = " + result);
 
 	}
@@ -344,13 +316,13 @@ public class ComparatorTest extends AbstractPaceTest {
 		double result = countryMatch.distance("UNKNOWN", "UNKNOWN", conf);
 		assertEquals(-1.0, result);
 
-		result = countryMatch.distance("CHILE", "UNKNOWN", conf);
+		result = countryMatch.distance("CL", "UNKNOWN", conf);
 		assertEquals(-1.0, result);
 
-		result = countryMatch.distance("CHILE", "ITALY", conf);
+		result = countryMatch.distance("CL", "IT", conf);
 		assertEquals(0.0, result);
 
-		result = countryMatch.distance("CHILE", "CHILE", conf);
+		result = countryMatch.distance("CL", "CL", conf);
 		assertEquals(1.0, result);
 
 	}
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java
new file mode 100644
index 000000000..28f2bfc66
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java
@@ -0,0 +1,83 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import java.io.IOException;
+
+import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
+import eu.dnetlib.pace.tree.support.TreeProcessor;
+import eu.dnetlib.pace.tree.support.TreeStats;
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.sql.Row;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+import org.junit.platform.commons.util.StringUtils;
+
+import eu.dnetlib.pace.config.DedupConfig;
+import eu.dnetlib.pace.model.SparkModel;
+
+class DecisionTreeTest {
+
+    @Test
+    void testJPath() throws IOException {
+
+        DedupConfig conf = DedupConfig
+                .load(IOUtils.toString(getClass().getResourceAsStream("dedup_conf_organization.json")));
+
+        final String org = IOUtils.toString(getClass().getResourceAsStream("organization.json"));
+
+        Row row = SparkModel.apply(conf).rowFromJson(org);
+
+        System.out.println("row = " + row);
+        Assertions.assertNotNull(row);
+        Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
+
+        System.out.println("row = " + row.getAs("countrytitle"));
+    }
+
+    @Test
+    void jsonToModelTest() throws IOException{
+        DedupConfig conf = DedupConfig
+                .load(IOUtils
+                        .toString(
+                                SparkOpenorgsDedupTest.class
+                                        .getResourceAsStream(
+                                                "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+
+        final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
+
+        Row row = SparkModel.apply(conf).rowFromJson(org);
+        // to check that the same parsing returns the same row
+        Row row1 = SparkModel.apply(conf).rowFromJson(org);
+
+        Assertions.assertEquals(row, row1);
+        System.out.println("row = " + row);
+        Assertions.assertNotNull(row);
+        Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
+    }
+
+    @Test
+    void organizationDecisionTreeTest() throws Exception {
+        DedupConfig conf = DedupConfig
+                .load(IOUtils
+                        .toString(
+                                SparkOpenorgsDedupTest.class
+                                        .getResourceAsStream(
+                                                "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+
+        final String org1 = "{\"eclegalbody\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecresearchorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"SUSF - Universit\\\\u00e9 internationale de floride\"}, \"pid\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"qualifier\": {\"classid\": \"grid\", \"classname\": \"grid\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"grid.65456.34\"}], \"websiteurl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"http://www.fiu.edu/\"}, \"ecnutscode\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"logourl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"collectedfrom\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"GRID - Global Research Identifier Database\", \"key\": \"10|openaire____::ff4a008470319a22d9cf3d14af485977\"}], \"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"UNKNOWN\", \"classname\": \"UNKNOWN\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}, \"inferred\": true, \"inferenceprovenance\": \"dedup-similarity-organization-simple\", \"invisible\": false, \"trust\": \"0.89\"}, \"alternativeNames\": [], \"echighereducation\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"id\": \"20|grid________::f22e08fb7bd544b4355f99bef2c43ad5\", \"eclegalperson\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"lastupdatetimestamp\": 1566902405602, \"ecinternationalorganizationeurinterests\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"dateofcollection\": \"\", \"dateoftransformation\": \"\", \"ecnonprofit\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecenterprise\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecinternationalorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalshortname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"FIU\"}, \"country\": {\"classid\": \"US\", \"classname\": \"United States\", \"schemename\": \"dnet:countries\", \"schemeid\": \"dnet:countries\"}, \"extraInfo\": [], \"originalId\": [], \"ecsmevalidated\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}}";
+        final String org2 = "{\"eclegalbody\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecresearchorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"SUSF - Universidad Internacional de Florida\"}, \"pid\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"qualifier\": {\"classid\": \"grid\", \"classname\": \"grid\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"grid.65456.34\"}], \"websiteurl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"http://www.fiu.edu/\"}, \"ecnutscode\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"logourl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"collectedfrom\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"GRID - Global Research Identifier Database\", \"key\": \"10|openaire____::ff4a008470319a22d9cf3d14af485977\"}], \"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"UNKNOWN\", \"classname\": \"UNKNOWN\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}, \"inferred\": true, \"inferenceprovenance\": \"dedup-similarity-organization-simple\", \"invisible\": false, \"trust\": \"0.89\"}, \"alternativeNames\": [], \"echighereducation\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"id\": \"20|grid________::2b261e9d8c2a63abbfd5826918c23b6d\", \"eclegalperson\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"lastupdatetimestamp\": 1566902405602, \"ecinternationalorganizationeurinterests\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"dateofcollection\": \"\", \"dateoftransformation\": \"\", \"ecnonprofit\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecenterprise\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecinternationalorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalshortname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"FIU\"}, \"country\": {\"classid\": \"US\", \"classname\": \"United States\", \"schemename\": \"dnet:countries\", \"schemeid\": \"dnet:countries\"}, \"extraInfo\": [], \"originalId\": [], \"ecsmevalidated\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}}";
+
+        Row row1 = SparkModel.apply(conf).rowFromJson(org1);
+        Row row2 = SparkModel.apply(conf).rowFromJson(org2);
+
+        System.out.println("row1 = " + row1);
+        System.out.println("row2 = " + row2);
+        TreeProcessor tree = new TreeProcessor(conf);
+
+        boolean result = tree.compare(row1, row2);
+
+        System.out.println("result = " + result);
+
+    }
+
+}
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
index c80c98bb7..3bfd861f8 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
@@ -190,7 +190,7 @@ public class SparkDedupTest implements Serializable {
 		System.out.println("orp_simrel = " + orp_simrel);
 
 		if (CHECK_CARDINALITIES) {
-			assertEquals(751, orgs_simrel);
+			assertEquals(742, orgs_simrel);
 			assertEquals(566, pubs_simrel);
 			assertEquals(113, sw_simrel);
 			assertEquals(148, ds_simrel);
@@ -251,7 +251,7 @@ public class SparkDedupTest implements Serializable {
 
 		// entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
 		if (CHECK_CARDINALITIES) {
-			assertEquals(751, orgs_simrel);
+			assertEquals(742, orgs_simrel);
 			assertEquals(566, pubs_simrel);
 			assertEquals(148, ds_simrel);
 			assertEquals(280, orp_simrel);
@@ -442,7 +442,7 @@ public class SparkDedupTest implements Serializable {
 		final List<Relation> merges = pubs
 			.filter("source == '50|arXiv_dedup_::c93aeb433eb90ed7a86e29be00791b7c'")
 			.collectAsList();
-		assertEquals(3, merges.size());
+		assertEquals(1, merges.size());
 		Set<String> dups = Sets
 			.newHashSet(
 				"50|doi_________::3b1d0d8e8f930826665df9d6b82fbb73",
@@ -451,7 +451,7 @@ public class SparkDedupTest implements Serializable {
 		merges.forEach(r -> {
 			assertEquals(ModelConstants.RESULT_RESULT, r.getRelType());
 			assertEquals(ModelConstants.DEDUP, r.getSubRelType());
-			assertEquals(ModelConstants.MERGES, r.getRelClass());
+			assertEquals(ModelConstants.IS_MERGED_IN, r.getRelClass());
 			assertTrue(dups.contains(r.getTarget()));
 		});
 
@@ -561,7 +561,7 @@ public class SparkDedupTest implements Serializable {
 		System.out.println("orp_mergerel = " + orp_mergerel);
 
 		if (CHECK_CARDINALITIES) {
-			assertEquals(1268, orgs_mergerel);
+			assertEquals(1278, orgs_mergerel);
 			assertEquals(1156, pubs.count());
 			assertEquals(292, sw_mergerel);
 			assertEquals(476, ds_mergerel);
@@ -618,7 +618,7 @@ public class SparkDedupTest implements Serializable {
 		System.out.println("orp_deduprecord = " + orp_deduprecord);
 
 		if (CHECK_CARDINALITIES) {
-			assertEquals(86, orgs_deduprecord);
+			assertEquals(78, orgs_deduprecord);
 			assertEquals(96, pubs.count());
 			assertEquals(47, sw_deduprecord);
 			assertEquals(97, ds_deduprecord);
@@ -761,7 +761,7 @@ public class SparkDedupTest implements Serializable {
 
 		if (CHECK_CARDINALITIES) {
 			assertEquals(930, publications);
-			assertEquals(839, organizations);
+			assertEquals(831, organizations);
 			assertEquals(100, projects);
 			assertEquals(100, datasource);
 			assertEquals(196, softwares);
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java
index 6f2a6904b..b2b5d824b 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsDedupTest.java
@@ -22,8 +22,11 @@ import java.util.Properties;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
@@ -143,7 +146,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		assertEquals(86, orgs_simrel);
+		assertEquals(92, orgs_simrel);
 	}
 
 	@Test
@@ -172,7 +175,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "organization"))
 			.count();
 
-		assertEquals(122, orgs_simrel);
+		assertEquals(128, orgs_simrel);
 	}
 
 	@Test
@@ -207,7 +210,7 @@ public class SparkOpenorgsDedupTest implements Serializable {
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
 			.count();
-		assertEquals(132, orgs_mergerel);
+		assertEquals(128, orgs_mergerel);
 
 		// verify that a DiffRel is in the mergerels (to be sure that the job supposed to remove them has something to
 		// do)
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
index 705c2cc84..40a73c9b3 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup.jpath;
 
 import java.io.IOException;
 
+import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.junit.jupiter.api.Assertions;
@@ -24,6 +25,30 @@ class JsonPathTest {
 
 		Row row = SparkModel.apply(conf).rowFromJson(org);
 
+		System.out.println("row = " + row);
+		Assertions.assertNotNull(row);
+		Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
+
+		System.out.println("row = " + row.getAs("countrytitle"));
+	}
+
+	@Test
+	void jsonToModelTest() throws IOException{
+		DedupConfig conf = DedupConfig
+				.load(IOUtils
+						.toString(
+								SparkOpenorgsDedupTest.class
+										.getResourceAsStream(
+												"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+
+		final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
+
+		Row row = SparkModel.apply(conf).rowFromJson(org);
+		// to check that the same parsing returns the same row
+		Row row1 = SparkModel.apply(conf).rowFromJson(org);
+
+		Assertions.assertEquals(row, row1);
+		System.out.println("row = " + row);
 		Assertions.assertNotNull(row);
 		Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
 	}
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json
index 917c9426b..f00f6198e 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json
@@ -4,8 +4,8 @@
     "dedupRun" : "001",
     "entityType" : "organization",
     "subEntityValue": "organization",
-    "orderField" : "legalname",
-    "queueMaxSize" : "2000",
+    "orderField" : "original_legalname",
+    "queueMaxSize" : "100000",
     "groupMaxSize" : "50",
     "slidingWindowSize" : "200",
     "idPath":"$.id",
@@ -15,10 +15,10 @@
   },
   "pace" : {
     "clustering" : [
-      { "name" : "sortedngrampairs", "fields" : [ "legalname" ], "params" : { "max" : 2, "ngramLen" : "3"} },
-      { "name" : "suffixprefix", "fields" : [ "legalname" ], "params" : { "max" : 1, "len" : "3" } },
+      { "name" : "sortedngrampairs", "fields" : [ "original_legalname" ], "params" : { "max" : 2, "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "original_legalname" ], "params" : { "max" : 1, "len" : "3" } },
       { "name" : "urlclustering", "fields" : [ "websiteurl" ], "params" : { } },
-      { "name" : "keywordsclustering", "fields" : [ "legalname" ], "params" : { "max": 2, "windowSize": 4} }
+      { "name" : "legalnameclustering", "fields" : [ "legalname" ], "params" : { "max": 2} }
     ],
     "decisionTree" : {
       "start": {
@@ -29,16 +29,23 @@
             "weight": 1,
             "countIfUndefined": "false",
             "params": {}
+          },
+          {
+            "field": "rorid",
+            "comparator": "exactMatch",
+            "weight": 1,
+            "countIfUndefined": "false",
+            "params": {}
           }
         ],
         "threshold": 1,
-        "aggregation": "AVG",
+        "aggregation": "OR",
         "positive": "MATCH",
         "negative": "NO_MATCH",
-        "undefined": "layer2",
+        "undefined": "necessaryConditions",
         "ignoreUndefined": "false"
       },
-      "layer2": {
+      "necessaryConditions": {
         "fields": [
           {
             "field": "websiteurl",
@@ -55,14 +62,14 @@
             "params": {}
           },
           {
-            "field": "legalname",
+            "field": "original_legalname",
             "comparator": "numbersMatch",
             "weight": 1,
             "countIfUndefined": "true",
             "params": {}
           },
           {
-            "field": "legalname",
+            "field": "original_legalname",
             "comparator": "romansMatch",
             "weight": 1,
             "countIfUndefined": "true",
@@ -71,68 +78,64 @@
         ],
         "threshold": 1,
         "aggregation": "AND",
-        "positive": "layer3",
+        "positive": "cityCheck",
         "negative": "NO_MATCH",
-        "undefined": "layer3",
+        "undefined": "cityCheck",
         "ignoreUndefined": "true"
       },
-      "layer3": {
+      "cityCheck": {
         "fields": [
           {
             "field": "legalname",
-            "comparator": "cityMatch",
+            "comparator": "codeMatch",
             "weight": 1.0,
             "countIfUndefined": "true",
             "params": {
-              "windowSize": "4"
+              "codeRegex": "city::\\d+"
             }
           }
         ],
         "threshold": 0.1,
         "aggregation": "AVG",
-        "positive": "layer4",
+        "positive": "keywordCheck",
         "negative": "NO_MATCH",
         "undefined": "NO_MATCH",
         "ignoreUndefined": "true"
       },
-      "layer4": {
+      "keywordCheck": {
         "fields": [
           {
             "field": "legalname",
-            "comparator": "keywordMatch",
+            "comparator": "codeMatch",
             "weight": 1.0,
             "countIfUndefined": "true",
             "params": {
-              "windowSize": "4"
+              "codeRegex": "key::\\d+"
             }
           }
         ],
         "threshold": 0.7,
         "aggregation": "AVG",
-        "positive": "layer5",
+        "positive": "nameCheck",
         "negative": "NO_MATCH",
-        "undefined": "layer5",
+        "undefined": "nameCheck",
         "ignoreUndefined": "true"
       },
-      "layer5": {
+      "nameCheck": {
         "fields": [
           {
             "field": "legalname",
-            "comparator": "jaroWinklerNormalizedName",
+            "comparator": "jaroWinklerLegalname",
             "weight": 0.9,
             "countIfUndefined": "true",
-            "params": {
-              "windowSize": "4"
-            }
+            "params": {}
           },
           {
             "field": "legalshortname",
-            "comparator": "jaroWinklerNormalizedName",
+            "comparator": "jaroWinklerLegalname",
             "weight": 0.1,
             "countIfUndefined": "false",
-            "params": {
-              "windowSize": 4
-            }
+            "params": {}
           }
         ],
         "threshold": 0.9,
@@ -144,126 +147,16 @@
       }
     },
     "model" : [
-      { "name" : "country", "type" : "String", "path" : "$.country.classid"},
-      { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value"},
-      { "name" : "legalname", "type" : "String", "path" : "$.legalname.value" },
+      { "name" : "country", "type" : "String", "path" : "$.country.classid", "infer" : "country", "inferenceFrom" : "$.legalname.value"},
+      { "name" : "legalshortname", "type" : "String", "path" : "$.legalshortname.value", "infer" : "city_keyword"},
+      { "name" : "original_legalname", "type" : "String", "path" : "$.legalname.value" },
+      { "name" : "legalname", "type" : "String", "path" : "$.legalname.value", "infer" : "city_keyword"},
       { "name" : "websiteurl", "type" : "URL", "path" : "$.websiteurl.value" },
       { "name" : "gridid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='grid')].value"},
+      { "name" : "rorid", "type" : "String", "path" : "$.pid[?(@.qualifier.classid =='ROR')].value"},
       { "name" : "originalId", "type" : "String", "path" : "$.id" }
     ],
-    "blacklists" : {
-      "legalname" : []
-    },
-    "synonyms": {
-      "key::1": ["university","università", "universitas", "università studi","universitario","universitaria","université", "universite", "universitaire","universitaires","universidad","universitade","Universität","universitaet","Uniwersytet","университет","universiteit","πανεπιστήμιο","universitesi","universiteti", "universiti"],
-      "key::2": ["studies","studi","études","estudios","estudos","Studien","studia","исследования","studies","σπουδές"],
-      "key::3": ["advanced","superiore","supérieur","supérieure","supérieurs","supérieures","avancado","avancados","fortgeschrittene","fortgeschritten","zaawansowany","передовой","gevorderd","gevorderde","προχωρημένος","προχωρημένη","προχωρημένο","προχωρημένες","προχωρημένα","wyzsza"],
-      "key::4": ["institute","istituto","institut","instituto","instituto","Institut","instytut","институт","instituut","ινστιτούτο"],
-      "key::5": ["hospital","ospedale","hôpital","hospital","hospital","Krankenhaus","szpital","больница","ziekenhuis","νοσοκομείο"],
-      "key::6": ["research","ricerca","recherche","investigacion","pesquisa","Forschung","badania","исследования","onderzoek","έρευνα","erevna","erevnas"],
-      "key::7": ["college","collegio","colegio","faculdade","Hochschule","Szkoła Wyższa","Высшая школа","κολλέγιο"],
-      "key::8": ["foundation","fondazione","fondation","fundación","fundação","Stiftung","Fundacja","фонд","stichting","ίδρυμα","idryma"],
-      "key::9": ["center","centro","centre","centro","centro","zentrum","centrum","центр","centrum","κέντρο"],
-      "key::10": ["national","nazionale","national","nationale","nationaux","nationales","nacional","nacional","national","krajowy","национальный","nationaal","nationale","εθνικό"],
-      "key::11": ["association","associazione","association","asociación","associação","Verein","verband","stowarzyszenie","ассоциация","associatie"],
-      "key::12": ["society","societa","société","sociedad","sociedade","gesellschaft","społeczeństwo","общество","maatschappij","κοινωνία"],
-      "key::13": ["international","internazionale","international","internacional","internacional","international","międzynarodowy","Международный","internationaal","internationale","διεθνής","διεθνή","διεθνές"],
-      "key::14": ["community","comunita","communauté","comunidad","comunidade","Gemeinschaft","społeczność","сообщество","gemeenschap","κοινότητα"],
-      "key::15": ["school","scuola","école","escuela","escola","schule","Szkoła","школа","school","σχολείο"],
-      "key::16": ["education","educazione","éducation","educacion","Educação","Bildung","Edukacja","образование","opleiding","εκπαίδευση"],
-      "key::17": ["academy","accademia","académie","academia","academia","Akademie","akademie","академия","academie","ακαδημία"],
-      "key::18": ["public","pubblico","public","publique","publics","publiques","publico","publico","Öffentlichkeit","publiczny","публичный","publiek","publieke","δημόσιος","δημόσια","δημόσιο"],
-      "key::19": ["museum","museo","musée","mueso","museu","museum","muzeum","музей","museum","μουσείο"],
-      "key::20": ["group","gruppo","groupe","grupo","grupo","gruppe","grupa","группа","groep","ομάδα","όμιλος"],
-      "key::21": ["department","dipartimento","département","departamento","departamento","abteilung","departament","отдел","afdeling","τμήμα"],
-      "key::22": ["council","consiglio","conseil","Consejo","conselho","gesellschaft","rada","совет","raad","συμβούλιο"],
-      "key::23": ["library","biblioteca","bibliothèque","biblioteca","biblioteca","Bibliothek","biblioteka","библиотека","bibliotheek","βιβλιοθήκη"],
-      "key::24": ["ministry","ministero","ministère","ministerio","ministério","Ministerium","ministerstwo","министерство","ministerie","υπουργείο"],
-      "key::25": ["services","servizi","services","servicios","Serviços","Dienstleistungen","usługi","услуги","diensten","υπηρεσίες"],
-      "key::26": ["central","centrale","central","centrale","centrales","central","central","zentral","centralny","цетральный","centraal","κεντρικός","κεντρική","κεντρικό","κεντρικά"],
-      "key::27": ["general","generale","général","générale","généraux","générales","general","geral","general","Allgemeines","general","общий","algemeen","algemene","γενικός","γενική","γενικό","γενικά"],
-      "key::28": ["applied","applicati","appliqué","appliquée","appliqués","appliquées","aplicado","aplicada","angewendet","stosowany","прикладной","toegepast","toegepaste","εφαρμοσμένος","εφαρμοσμένη","εφαρμοσμένο","εφαρμοσμένα"],
-      "key::29": ["european","europee","europea","européen","européenne","européens","européennes","europeo","europeu","europäisch","europejski","европейский","Europees","Europese","ευρωπαϊκός","ευρωπαϊκή","ευρωπαϊκό","ευρωπαϊκά"],
-      "key::30": ["agency","agenzia","agence","agencia","agencia","agentur","agencja","агенция","agentschap","πρακτορείο"],
-      "key::31": ["laboratory","laboratorio","laboratoire","laboratorio","laboratorio","labor","laboratorium","лаборатория","laboratorium","εργαστήριο"],
-      "key::32": ["industry","industria","industrie","индустрия","industrie","βιομηχανία"],
-      "key::33": ["industrial","industriale","industriel","industrielle","industriels","industrielles","индустриальный","industrieel","βιομηχανικός","βιομηχανική","βιομηχανικό","βιομηχανικά","βιομηχανικές"],
-      "key::34": ["consortium","consorzio","consortium","консорциум","consortium","κοινοπραξία"],
-      "key::35": ["organization","organizzazione","organisation","organización","organização","organizacja","организация","organisatie","οργανισμός"],
-      "key::36": ["authority","autorità","autorité","авторитет","autoriteit"],
-      "key::37": ["federation","federazione","fédération","федерация","federatie","ομοσπονδία"],
-      "key::38": ["observatory","osservatorio","observatoire","обсерватория","observatorium","αστεροσκοπείο"],
-      "key::39": ["bureau","ufficio","bureau","офис","bureau","γραφείο"],
-      "key::40": ["company","impresa","compagnie","société","компания","bedrijf","εταιρία"],
-      "key::41": ["polytechnic","politecnico","polytechnique","политехника","polytechnisch","πολυτεχνείο","universita politecnica","polytechnic university","universidad politecnica","universitat politecnica","politechnika","politechniki","university technology","university science technology"],
-      "key::42": ["coalition","coalizione","coalition","коалиция","coalitie","συνασπισμός"],
-      "key::43": ["initiative","iniziativa","initiative","инициатива","initiatief","πρωτοβουλία"],
-      "key::44": ["academic","accademico","académique","universitaire","акадеческий academisch","ακαδημαϊκός","ακαδημαϊκή","ακαδημαϊκό","ακαδημαϊκές","ακαδημαϊκοί"],
-      "key::45": ["institution","istituzione","institution","институциональный","instelling","ινστιτούτο"],
-      "key::46": ["division","divisione","division","отделение","divisie","τμήμα"],
-      "key::47": ["committee","comitato","comité","комитет","commissie","επιτροπή"],
-      "key::48": ["promotion","promozione","продвижение","proothisis","forderung"],
-      "key::49": ["medical","medicine","clinical","medicina","clinici","médico","medicina","clínica","médico","medicina","clínica","medizinisch","Medizin","klinisch","medisch","geneeskunde","klinisch","ιατρικός","ιατρική","ιατρικό","ιατρικά","κλινικός","κλινική","κλινικό","κλινικά","tıbbi","tıp","klinik","orvosi","orvostudomány","klinikai","zdravniški","medicinski","klinični","meditsiini","kliinik","kliiniline"],
-      "key::50": ["technology","technological","tecnologia","tecnologie","tecnología","tecnológico","tecnologia","tecnológico","Technologie","technologisch","technologie","technologisch","τεχνολογία","τεχνολογικός","τεχνολογική","τεχνολογικό","teknoloji","teknolojik","technológia","technológiai","tehnologija","tehnološki","tehnoloogia","tehnoloogiline","technologii","technical","texniki","teknik"],
-      "key::51": ["science","scientific","scienza","scientifiche","scienze","ciencia","científico","ciência","científico","Wissenschaft","wissenschaftlich","wetenschap","wetenschappelijk","επιστήμη","επιστημονικός","επιστημονική","επιστημονικό","επιστημονικά","bilim","bilimsel","tudomány","tudományos","znanost","znanstveni","teadus","teaduslik",""],
-      "key::52": ["engineering","ingegneria","ingeniería","engenharia","Ingenieurwissenschaft","ingenieurswetenschappen","bouwkunde","μηχανικός","μηχανική","μηχανικό","mühendislik","mérnöki","Inženirstvo","inseneeria","inseneri",""],
-      "key::53": ["management","gestione","gestionale","gestionali","gestión","administración","gestão","administração","Verwaltung","management","διαχείριση","yönetim","menedzsment","vodstvo","upravljanje","management","juhtkond","juhtimine","haldus",""],
-      "key::54": ["energy","energia","energía","energia","Energie","energie","ενέργεια","enerji","energia","energija","energia",""],
-      "key::55": ["agricultural","agriculture","agricoltura","agricole","agrícola","agricultura","agrícola","agricultura","landwirtschaftlich","Landwirtschaft","landbouwkundig","landbouw","αγροτικός","αγροτική","αγροτικό","γεωργικός","γεωργική","γεωργικό","γεωργία","tarımsal","tarım","mezőgazdasági","mezőgazdaság","poljedelski","poljedelstvo","põllumajandus","põllumajanduslik",""],
-      "key::56": ["information","informazione","información","informação","Information","informatie","πληροφορία","bilgi","információ","informacija","informatsioon","informatycznych",""],
-      "key::57": ["social","sociali","social","social","Sozial","sociaal","maatschappelijk","κοινωνικός","κοινωνική","κοινωνικό","κοινωνικά","sosyal","szociális","družbeni","sotsiaal","sotsiaalne",""],
-      "key::58": ["environmental","ambiente","medioambiental","ambiente","medioambiente","meioambiente","Umwelt","milieu","milieuwetenschap","milieukunde","περιβαλλοντικός","περιβαλλοντική","περιβαλλοντικό","περιβαλλοντικά","çevre","környezeti","okoliški","keskonna",""],
-      "key::59": ["business","economia","economiche","economica","negocio","empresa","negócio","Unternehmen","bedrijf","bedrijfskunde","επιχείρηση","iş","üzleti","posel","ettevõte/äri",""],
-      "key::60": ["pharmaceuticals","pharmacy","farmacia","farmaceutica","farmacéutica","farmacia","farmacêutica","farmácia","Pharmazeutika","Arzneimittelkunde","farmaceutica","geneesmiddelen","apotheek","φαρμακευτικός","φαρμακευτική","φαρμακευτικό","φαρμακευτικά","φαρμακείο","ilaç","eczane","gyógyszerészeti","gyógyszertár","farmacevtika","lekarništvo","farmaatsia","farmatseutiline",""],
-      "key::61": ["healthcare","health services","salute","atenciónmédica","cuidadodelasalud","cuidadoscomasaúde","Gesundheitswesen","gezondheidszorg","ιατροφαρμακευτικήπερίθαλψη","sağlıkhizmeti","egészségügy","zdravstvo","tervishoid","tervishoiu",""],
-      "key::62": ["history","storia","historia","história","Geschichte","geschiedenis","geschiedkunde","ιστορία","tarih","történelem","zgodovina","ajalugu",""],
-      "key::63": ["materials","materiali","materia","materiales","materiais","materialen","υλικά","τεκμήρια","malzemeler","anyagok","materiali","materjalid","vahendid",""],
-      "key::64": ["economics","economia","economiche","economica","economía","economia","Wirtschaft","economie","οικονομικά","οικονομικέςεπιστήμες","ekonomi","közgazdaságtan","gospodarstvo","ekonomija","majanduslik","majandus",""],
-      "key::65": ["therapeutics","terapeutica","terapéutica","terapêutica","therapie","θεραπευτική","tedavibilimi","gyógykezelés","terapevtika","terapeutiline","ravi",""],
-      "key::66": ["oncology","oncologia","oncologico","oncología","oncologia","Onkologie","oncologie","ογκολογία","onkoloji","onkológia","onkologija","onkoloogia",""],
-      "key::67": ["natural","naturali","naturale","natural","natural","natürlich","natuurlijk","φυσικός","φυσική","φυσικό","φυσικά","doğal","természetes","naraven","loodus",""],
-      "key::68": ["educational","educazione","pedagogia","educacional","educativo","educacional","pädagogisch","educatief","εκπαιδευτικός","εκπαιδευτική","εκπαιδευτικό","εκπαιδευτικά","eğitimsel","oktatási","izobraževalen","haridus","hariduslik",""],
-      "key::69": ["biomedical","biomedica","biomédico","biomédico","biomedizinisch","biomedisch","βιοιατρικός","βιοιατρική","βιοιατρικό","βιοιατρικά","biyomedikal","orvosbiológiai","biomedicinski","biomeditsiiniline",""],
-      "key::70": ["veterinary","veterinaria","veterinarie","veterinaria","veterinária","tierärtzlich","veterinair","veeartsenijlkunde","κτηνιατρικός","κτηνιατρική","κτηνιατρικό","κτηνιατρικά","veteriner","állatorvosi","veterinar","veterinarski","veterinaaria",""],
-      "key::71": ["chemistry","chimica","química","química","Chemie","chemie","scheikunde","χημεία","kimya","kémia","kemija","keemia",""],
-      "key::72": ["security","sicurezza","seguridad","segurança","Sicherheit","veiligheid","ασφάλεια","güvenlik","biztonsági","varnost","turvalisus","julgeolek",""],
-      "key::73": ["biotechnology","biotecnologia","biotecnologie","biotecnología","biotecnologia","Biotechnologie","biotechnologie","βιοτεχνολογία","biyoteknoloji","biotechnológia","biotehnologija","biotehnoloogia",""],
-      "key::74": ["military","militare","militari","militar","militar","Militär","militair","leger","στρατιωτικός","στρατιωτική","στρατιωτικό","στρατιωτικά","askeri","katonai","vojaški","vojni","militaar","wojskowa",""],
-      "key::75": ["theological","teologia","teologico","teológico","tecnológica","theologisch","theologisch","θεολογικός","θεολογική","θεολογικό","θεολογικά","teolojik","technológiai","teološki","teoloogia","usuteadus","teoloogiline",""],
-      "key::76": ["electronics","elettronica","electrónica","eletrônicos","Elektronik","elektronica","ηλεκτρονική","elektronik","elektronika","elektronika","elektroonika",""],
-      "key::77": ["forestry","forestale","forestali","silvicultura","forestal","floresta","Forstwirtschaft","bosbouw","δασοκομία","δασολογία","ormancılık","erdészet","gozdarstvo","metsandus",""],
-      "key::78": ["maritime","marittima","marittime","marittimo","marítimo","marítimo","maritiem","ναυτικός","ναυτική","ναυτικό","ναυτικά","ναυτιλιακός","ναυτιλιακή","ναυτιλιακό","ναυτιλιακά","θαλάσσιος","θαλάσσια","θαλάσσιο","denizcilik","tengeri","morski","mere","merendus",""],
-      "key::79": ["sports","sport","deportes","esportes","Sport","sport","sportwetenschappen","άθληση","γυμναστικήδραστηριότητα","spor","sport","šport","sport","spordi",""],
-      "key::80": ["surgery","chirurgia","chirurgiche","cirugía","cirurgia","Chirurgie","chirurgie","heelkunde","εγχείρηση","επέμβαση","χειρουργικήεπέμβαση","cerrahi","sebészet","kirurgija","kirurgia",""],
-      "key::81": ["cultural","culturale","culturali","cultura","cultural","cultural","kulturell","cultureel","πολιτιστικός","πολιτιστική","πολιτιστικό","πολιτισμικός","πολιτισμική","πολιτισμικό","kültürel","kultúrális","kulturni","kultuuri","kultuuriline",""],
-      "key::82": ["computerscience","informatica","ordenador","computadora","informática","computación","cienciasdelacomputación","ciênciadacomputação","Computer","computer","υπολογιστής","ηλεκτρονικόςυπολογιστής","bilgisayar","számítógép","računalnik","arvuti",""],
-      "key::83": ["finance","financial","finanza","finanziarie","finanza","financiero","finanças","financeiro","Finanzen","finanziell","financiën","financieel","χρηματοοικονομικά","χρηματοδότηση","finanse","finansal","pénzügy","pénzügyi","finance","finančni","finants","finantsiline",""],
-      "key::84": ["communication","comunicazione","comuniciación","comunicação","Kommunikation","communication","επικοινωνία","iletişim","kommunikáció","komuniciranje","kommunikatsioon",""],
-      "key::85": ["justice","giustizia","justicia","justiça","Recht","Justiz","justitie","gerechtigheid","δικαιοσύνη","υπουργείοδικαιοσύνης","δίκαιο","adalet","igazságügy","pravo","õigus",""],
-      "key::86": ["aerospace","aerospaziale","aerospaziali","aeroespacio","aeroespaço","Luftfahrt","luchtvaart","ruimtevaart","αεροπορικός","αεροπορική","αεροπορικό","αεροναυπηγικός","αεροναυπηγική","αεροναυπηγικό","αεροναυπηγικά","havacılıkveuzay","légtér","zrakoplovstvo","atmosfäär","kosmos",""],
-      "key::87": ["dermatology","dermatologia","dermatología","dermatologia","Dermatologie","dermatologie","δρματολογία","dermatoloji","bőrgyógyászat","dermatológia","dermatologija","dermatoloogia",""],
-      "key::88": ["architecture","architettura","arquitectura","arquitetura","Architektur","architectuur","αρχιτεκτονική","mimarlık","építészet","arhitektura","arhitektuur",""],
-      "key::89": ["mathematics","matematica","matematiche","matemáticas","matemáticas","Mathematik","wiskunde","mathematica","μαθηματικά","matematik","matematika","matematika","matemaatika",""],
-      "key::90": ["language","lingue","linguistica","linguistiche","lenguaje","idioma","língua","idioma","Sprache","taal","taalkunde","γλώσσα","dil","nyelv","jezik","keel",""],
-      "key::91": ["neuroscience","neuroscienza","neurociencia","neurociência","Neurowissenschaft","neurowetenschappen","νευροεπιστήμη","nörobilim","idegtudomány","nevroznanost","neuroteadused",""],
-      "key::92": ["automation","automazione","automatización","automação","Automatisierung","automatisering","αυτοματοποίηση","otomasyon","automatizálás","avtomatizacija","automatiseeritud",""],
-      "key::93": ["pediatric","pediatria","pediatriche","pediatrico","pediátrico","pediatría","pediátrico","pediatria","pädiatrisch","pediatrische","παιδιατρική","pediatrik","gyermekgyógyászat","pediatrija","pediaatria",""],
-      "key::94": ["photonics","fotonica","fotoniche","fotónica","fotônica","Photonik","fotonica","φωτονική","fotonik","fotonika","fotonika","fotoonika",""],
-      "key::95": ["mechanics", "mechanical", "meccanica","meccaniche","mecánica","mecânica","Mechanik","Maschinenbau","mechanica","werktuigkunde","μηχανικής","mekanik","gépészet","mehanika","mehaanika",""],
-      "key::96": ["psychiatrics","psichiatria","psichiatrica","psichiatriche","psiquiatría","psiquiatria","Psychiatrie","psychiatrie","ψυχιατρική","psikiyatrik","pszihiátria","psihiatrija","psühhaatria",""],
-      "key::97": ["psychology","fisiologia","psicología","psicologia","Psychologie","psychologie","ψυχολογία","psikoloji","pszihológia","psihologija","psühholoogia",""],
-      "key::98": ["automotive","industriaautomobilistica","industriadelautomóvil","automotriz","industriaautomotriz","automotivo","Automobilindustrie","autoindustrie","αυτοκίνητος","αυτοκίνητη","αυτοκίνητο","αυτοκινούμενος","αυτοκινούμενη","αυτοκινούμενο","αυτοκινητιστικός","αυτοκινητιστική","αυτοκινητιστικό","otomotiv","autóipari","samogiben","avtomobilskaindustrija","auto-",""],
-      "key::99": ["neurology","neurologia","neurologiche","neurología","neurologia","Neurologie","neurologie","zenuwleer","νευρολογία","nöroloji","neurológia","ideggyógyászat","nevrologija","neuroloogia",""],
-      "key::100": ["geology","geologia","geologiche","geología","geologia","Geologie","geologie","aardkunde","γεωλογία","jeoloji","geológia","földtudomány","geologija","geoloogia",""],
-      "key::101": ["microbiology","microbiologia","micro-biologia","microbiologiche","microbiología","microbiologia","Mikrobiologie","microbiologie","μικροβιολογία","mikrobiyoloji","mikrobiológia","mikrobiologija","mikrobioloogia",""],
-      "key::102": ["informatics","informatica","informática","informática","informatica",""],
-      "key::103": ["forschungsgemeinschaft","comunita ricerca","research community","research foundation","research association"],
-      "key::104": ["commerce","ticaret","ticarət","commercio","trade","handel","comercio"],
-      "key::105" : ["state", "stato", "etade", "estado", "statale", "etat", "zustand", "estado"],
-      "key::106" : ["seminary", "seminario", "seminaire", "seminar"],
-      "key::107" : ["agricultural forestry", "af", "a f"],
-      "key::108" : ["agricultural mechanical", "am", "a m"],
-      "key::109" : ["catholic", "catholique", "katholische", "catolica", "cattolica", "catolico"]
-    }
+    "blacklists" : {},
+    "synonyms": {}
   }
 }
\ No newline at end of file
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/organization_example1.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/organization_example1.json
new file mode 100644
index 000000000..52fb304a9
--- /dev/null
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/oa/dedup/jpath/organization_example1.json
@@ -0,0 +1 @@
+{"collectedfrom":[{"key":"10|openaire____::0362fcdb3076765d9c0041ad331553e8","value":"OpenOrgs Database","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1617006357185,"id":"20|openorgsmesh::8536807f92ca146e6f0990b07d712406","originalId":["openorgsmesh::0000098375-0dcc2286c99400f0ac63d0db84a57759"],"pid":[{"value":"0000 0004 1757 1758","qualifier":{"classid":"ISNI","classname":"International Standard Name Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"263329","qualifier":{"classid":"OrgRef","classname":"OrgRef","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"501100005969","qualifier":{"classid":"FundRef","classname":"FundRef","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"grid.6292.f","qualifier":{"classid":"GRID","classname":"GRID","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"https://ror.org/01111rn36","qualifier":{"classid":"ROR","classname":"ROR","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Q131262","qualifier":{"classid":"Wikidata","classname":"Wikidata","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofcollection":"2021-03-17","dateoftransformation":"2021-03-17","extraInfo":[],"oaiprovenance":null,"legalshortname":{"value":"Università di Bologna","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"legalname":{"value":"Università di Bologna","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"alternativeNames":[],"websiteurl":{"value":"http://www.unibo.it/en/homepage","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"logourl":null,"eclegalbody":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"eclegalperson":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecnonprofit":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecresearchorganization":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"echighereducation":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecinternationalorganizationeurinterests":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecinternationalorganization":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecenterprise":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecsmevalidated":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"ecnutscode":{"value":"false","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.880","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"country":{"classid":"IT","classname":"Italy","schemeid":"dnet:countries","schemename":"dnet:countries"}}
\ No newline at end of file

From 5cdba9172bb68c4f842efaddebc644e9cdef1b21 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Wed, 10 Jul 2024 14:53:13 +0200
Subject: [PATCH 062/239] implementeation of the new collector plugin:
 research_fi

---
 .../researchfi/ResearchFiCollectorPlugin.java |  72 +++++++++++
 .../plugin/researchfi/ResearchFiIterator.java | 115 ++++++++++++++++++
 .../ResearchFiCollectorPluginTest.java        |  55 +++++++++
 3 files changed, 242 insertions(+)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java
new file mode 100644
index 000000000..c5961c598
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java
@@ -0,0 +1,72 @@
+package eu.dnetlib.dhp.collection.plugin.researchfi;
+
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.http.NameValuePair;
+import org.apache.http.client.entity.UrlEncodedFormEntity;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.apache.http.message.BasicNameValuePair;
+import org.json.JSONObject;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class ResearchFiCollectorPlugin implements CollectorPlugin {
+
+	private static final Logger log = LoggerFactory.getLogger(ResearchFiCollectorPlugin.class);
+
+	@Override
+	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report)
+			throws CollectorException {
+
+		final String authUrl = api.getParams().get("auth_url");
+		final String clientId = api.getParams().get("auth_client_id");
+		final String clientSecret = api.getParams().get("auth_client_secret");
+
+		final String authToken = authenticate(authUrl, clientId, clientSecret);
+
+		final Iterator<String> iter = new ResearchFiIterator(api.getBaseUrl(), authToken);
+
+		return StreamSupport.stream(Spliterators.spliteratorUnknownSize(iter, Spliterator.ORDERED), false);
+	}
+
+	private String authenticate(final String authUrl, final String clientId, final String clientSecret) throws CollectorException {
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			final HttpPost req = new HttpPost(authUrl);
+			final List<NameValuePair> params = new ArrayList<>();
+			params.add(new BasicNameValuePair("grant_type", "client_credentials"));
+			params.add(new BasicNameValuePair("client_id", clientId));
+			params.add(new BasicNameValuePair("client_secret", clientSecret));
+
+			req.setEntity(new UrlEncodedFormEntity(params, "UTF-8"));
+
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				final String content = IOUtils.toString(response.getEntity().getContent());
+				final JSONObject obj = new JSONObject(content);
+				final String token = obj.getString("access_token");
+				if (StringUtils.isNotBlank(token)) { return token; }
+			}
+		} catch (final Throwable e) {
+			log.warn("Error obtaining access token", e);
+			throw new CollectorException("Error obtaining access token", e);
+		}
+		throw new CollectorException("Access token is missing");
+
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
new file mode 100644
index 000000000..38a3cece8
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
@@ -0,0 +1,115 @@
+package eu.dnetlib.dhp.collection.plugin.researchfi;
+
+import java.util.Iterator;
+import java.util.Queue;
+import java.util.concurrent.PriorityBlockingQueue;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.apache.http.Header;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClients;
+import org.json.JSONArray;
+
+import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class ResearchFiIterator implements Iterator<String> {
+
+	private static final Log log = LogFactory.getLog(ResearchFiIterator.class);
+
+	private static final int PAGE_SIZE = 100;
+
+	private final String baseUrl;
+	private final String authToken;
+	private int currPage;
+	private int nPages;
+
+	private final Queue<String> queue = new PriorityBlockingQueue<>();
+
+	public ResearchFiIterator(final String baseUrl, final String authToken) {
+		this.baseUrl = baseUrl;
+		this.authToken = authToken;
+		this.currPage = 0;
+		this.nPages = 0;
+	}
+
+	private void verifyStarted() {
+		if (this.currPage == 0) {
+			try {
+				nextCall();
+			} catch (final CollectorException e) {
+				throw new IllegalStateException(e);
+			}
+		}
+	}
+
+	@Override
+	public boolean hasNext() {
+		synchronized (this.queue) {
+			verifyStarted();
+			return !this.queue.isEmpty();
+		}
+	}
+
+	@Override
+	public String next() {
+		synchronized (this.queue) {
+			verifyStarted();
+			final String res = this.queue.poll();
+			while (this.queue.isEmpty() && (this.currPage < this.nPages)) {
+				try {
+					nextCall();
+				} catch (final CollectorException e) {
+					throw new IllegalStateException(e);
+				}
+			}
+			return res;
+		}
+	}
+
+	private void nextCall() throws CollectorException {
+
+		this.currPage += 1;
+
+		try (final CloseableHttpClient client = HttpClients.createDefault()) {
+			final String url;
+			if (!this.baseUrl.contains("?")) {
+				url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
+			} else if (!this.baseUrl.contains("PageSize=")) {
+				url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
+			} else {
+				url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage);
+			}
+			log.info("Calling url: " + url);
+
+			final HttpGet req = new HttpGet(url);
+			req.addHeader("Authorization", "Bearer " + this.authToken);
+			try (final CloseableHttpResponse response = client.execute(req)) {
+				for (final Header header : response.getAllHeaders()) {
+					log.debug("HEADER: " + header.getName() + " = " + header.getValue());
+					if ("x-page-count".equals(header.getName())) {
+						final int totalPages = NumberUtils.toInt(header.getValue());
+						if (this.nPages != totalPages) {
+							this.nPages = NumberUtils.toInt(header.getValue());
+							log.info("Total pages: " + totalPages);
+						}
+					}
+				}
+
+				final String content = IOUtils.toString(response.getEntity().getContent());
+				final JSONArray jsonArray = new JSONArray(content);
+
+				jsonArray.forEach(obj -> this.queue.add(JsonUtils.convertToXML(obj.toString())));
+			}
+		} catch (final Throwable e) {
+			log.warn("Error obtaining access token", e);
+			throw new CollectorException("Error obtaining access token", e);
+		}
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java
new file mode 100644
index 000000000..47c77796b
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java
@@ -0,0 +1,55 @@
+package eu.dnetlib.dhp.collection.plugin.researchfi;
+
+import java.util.HashSet;
+import java.util.Set;
+import java.util.concurrent.atomic.AtomicLong;
+
+import org.dom4j.DocumentException;
+import org.dom4j.DocumentHelper;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class ResearchFiCollectorPluginTest {
+
+	private final ResearchFiCollectorPlugin plugin = new ResearchFiCollectorPlugin();
+
+	@Test
+	@Disabled
+	void testCollect() throws CollectorException {
+		final ApiDescriptor api = new ApiDescriptor();
+		api.setBaseUrl("https://research.fi/api/rest/v1/funding-decisions?FunderName=AKA&FundingStartYearFrom=2022");
+		api.setProtocol("research_fi");
+		api.getParams().put("auth_url", "https://researchfi-auth.2.rahtiapp.fi/realms/publicapi/protocol/openid-connect/token");
+		api.getParams().put("auth_client_id", "");
+		api.getParams().put("auth_client_secret", "");
+
+		final AtomicLong count = new AtomicLong(0);
+		final Set<String> ids = new HashSet<>();
+
+		this.plugin.collect(api, new AggregatorReport()).forEach(s -> {
+
+			if (count.getAndIncrement() == 0) {
+				System.out.println("First: " + s);
+			}
+
+			try {
+				final String id = DocumentHelper.parseText(s).valueOf("/recordWrap/funderProjectNumber");
+				if (ids.contains(id)) {
+					System.out.println("Id already present: " + id);
+				}
+				ids.add(id);
+			} catch (final DocumentException e) {
+				throw new RuntimeException(e);
+			}
+		});
+
+		System.out.println("Total records: " + count);
+		System.out.println("Total identifiers: " + ids.size());
+
+	}
+
+}

From bbe52584f7b2d301408d73a69ee5ff63f20581cc Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Thu, 11 Jul 2024 15:14:34 +0200
Subject: [PATCH 063/239] log message

---
 .../plugin/researchfi/ResearchFiIterator.java | 23 ++++++++++---------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
index 38a3cece8..e08823c46 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
@@ -76,16 +76,17 @@ public class ResearchFiIterator implements Iterator<String> {
 
 		this.currPage += 1;
 
+		final String url;
+		if (!this.baseUrl.contains("?")) {
+			url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
+		} else if (!this.baseUrl.contains("PageSize=")) {
+			url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
+		} else {
+			url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage);
+		}
+		log.info("Calling url: " + url);
+
 		try (final CloseableHttpClient client = HttpClients.createDefault()) {
-			final String url;
-			if (!this.baseUrl.contains("?")) {
-				url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
-			} else if (!this.baseUrl.contains("PageSize=")) {
-				url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
-			} else {
-				url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage);
-			}
-			log.info("Calling url: " + url);
 
 			final HttpGet req = new HttpGet(url);
 			req.addHeader("Authorization", "Bearer " + this.authToken);
@@ -107,8 +108,8 @@ public class ResearchFiIterator implements Iterator<String> {
 				jsonArray.forEach(obj -> this.queue.add(JsonUtils.convertToXML(obj.toString())));
 			}
 		} catch (final Throwable e) {
-			log.warn("Error obtaining access token", e);
-			throw new CollectorException("Error obtaining access token", e);
+			log.warn("Error calling url: " + url, e);
+			throw new CollectorException("Error calling url: " + url, e);
 		}
 	}
 

From f9ed2ae33c95159072a913f2b235e7b0876ae63f Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 11 Jul 2024 15:24:29 +0200
Subject: [PATCH 064/239] [metadata collection] added the possibility to
 specify the JAVA_HOME and the JAVA_OPTS parameters

---
 .../dhp/collection/oozie_app/workflow.xml     | 21 ++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
index 0678eed11..9df88b4b6 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
@@ -48,12 +48,31 @@
             <description>Used to configure the heap size for the map JVM process. Should be 80% of mapreduce.map.memory.mb.</description>
         </property>
 
+        <property>
+            <name>JAVA_HOME</name>
+            <value>/srv/java/openjdk-17</value>
+            <description>Used to configure the Java home location for oozie.launcher.mapreduce.map.env</description>
+        </property>
 
     </parameters>
 
     <global>
         <job-tracker>${jobTracker}</job-tracker>
         <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapreduce.map.env</name>
+                <value>JAVA_HOME=${JAVA_HOME}</value>
+            </property>
+        </configuration>
     </global>
 
     <start to="collection_mode"/>
@@ -99,7 +118,7 @@
     <action name="CollectionWorker">
         <java>
             <main-class>eu.dnetlib.dhp.collection.CollectorWorkerApplication</main-class>
-            <java-opts>${collection_java_xmx}</java-opts>
+            <java-opts>${JAVA_OPTS} ${collection_java_xmx}</java-opts>
             <arg>--apidescriptor</arg><arg>${apiDescription}</arg>
             <arg>--namenode</arg><arg>${nameNode}</arg>
             <arg>--workflowId</arg><arg>${workflowId}</arg>

From 61d1fa9b9fe84850c5c21de6bc8027773df81368 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 12 Jul 2024 10:25:51 +0200
Subject: [PATCH 065/239] [metadata collection] added
 -Dcom.sun.security.enableAIAcaIssuers=true as a default for metadata
 collection

---
 .../eu/dnetlib/dhp/collection/oozie_app/workflow.xml        | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
index 9df88b4b6..f1364b63c 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/oozie_app/workflow.xml
@@ -54,6 +54,12 @@
             <description>Used to configure the Java home location for oozie.launcher.mapreduce.map.env</description>
         </property>
 
+        <property>
+            <name>JAVA_OPTS</name>
+                <value>-Dcom.sun.security.enableAIAcaIssuers=true</value>
+            <description>Used to configure the JAVA_OPTS parameter</description>
+        </property>
+
     </parameters>
 
     <global>

From e17edb25817e184f8bfbc4f2c21b73684ffd5f4b Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 12 Jul 2024 10:27:24 +0200
Subject: [PATCH 066/239] [broker] fine tuned the workflow memory settings

---
 .../oa/generate_all/oozie_app/workflow.xml    | 45 +++++++++++++------
 1 file changed, 31 insertions(+), 14 deletions(-)

diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
index bc6778f52..3e709117c 100644
--- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
@@ -7,7 +7,7 @@
         </property>
         <property>
             <name>outputDir</name>
-            <description>the path where the the generated data will be stored</description>
+            <description>the path where the generated data will be stored</description>
         </property>
 		<property>
             <name>datasourceIdWhitelist</name>
@@ -185,11 +185,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=5000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -209,11 +210,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -234,11 +236,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -258,11 +261,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=5000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -282,11 +286,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=10000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -306,11 +311,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -332,11 +338,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -356,11 +363,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -380,11 +388,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -404,11 +413,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -428,11 +438,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -452,11 +463,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--graphPath</arg><arg>${graphInputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
@@ -476,11 +488,12 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
+                --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
             <arg>--outputDir</arg><arg>${outputDir}</arg>
@@ -503,6 +516,7 @@
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} 
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@@ -535,6 +549,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -562,6 +577,7 @@
                 --executor-cores=${sparkExecutorCores}
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
@@ -585,6 +601,7 @@
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
                 --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
                 --conf spark.dynamicAllocation.maxExecutors=${sparkMaxExecutorsForIndexing} 
                 --conf spark.extraListeners=${spark2ExtraListeners}
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}

From f99fb2104007aab8aeee9d5491c66d4148a781a5 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Fri, 12 Jul 2024 15:29:45 +0200
Subject: [PATCH 067/239] tests

---
 .../simple/EnrichMissingAuthorOrcidTest.java  | 64 +++++++++++++++++++
 .../broker/oa/util/ConversionUtilsTest.java   | 50 +++++++++++++--
 2 files changed, 110 insertions(+), 4 deletions(-)
 create mode 100644 dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java

diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java
new file mode 100644
index 000000000..e61299800
--- /dev/null
+++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java
@@ -0,0 +1,64 @@
+package eu.dnetlib.dhp.broker.oa.matchers.simple;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.List;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.broker.objects.OaBrokerAuthor;
+import eu.dnetlib.broker.objects.OaBrokerMainEntity;
+
+class EnrichMissingAuthorOrcidTest {
+
+	final EnrichMissingAuthorOrcid matcher = new EnrichMissingAuthorOrcid();
+
+	@BeforeEach
+	void setUp() throws Exception {}
+
+	@Test
+	void testFindDifferences_1() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+	@Test
+	void testFindDifferences_2() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+
+		source.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
+		target.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
+
+		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
+		assertEquals(1, list.size());
+	}
+
+	@Test
+	void testFindDifferences_3() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+
+		source.getCreators().add(new OaBrokerAuthor("Claudio Atzori", null));
+		target.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
+
+		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+	@Test
+	void testFindDifferences_4() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		source.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
+		target.getCreators().add(new OaBrokerAuthor("Claudio Atzori", "0000-0001-9613-6639"));
+
+		final List<OaBrokerAuthor> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+}
diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java
index fc630df05..ee1bfed05 100644
--- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java
+++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java
@@ -2,27 +2,31 @@
 package eu.dnetlib.dhp.broker.oa.util;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNull;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import eu.dnetlib.broker.objects.OaBrokerMainEntity;
 import eu.dnetlib.broker.objects.OaBrokerTypedValue;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Author;
 import eu.dnetlib.dhp.schema.oaf.Instance;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
-class ConversionUtilsTest {
+public class ConversionUtilsTest {
 
 	@BeforeEach
-	void setUp() throws Exception {
-	}
+	public void setUp() throws Exception {}
 
 	@Test
-	void testAllResultPids() {
+	public void testAllResultPids() {
 		final Qualifier qf = new Qualifier();
 		qf.setClassid("test");
 		qf.setClassname("test");
@@ -91,4 +95,42 @@ class ConversionUtilsTest {
 		assertEquals(6, list.size());
 	}
 
+	public void testOafResultToBrokerResult() {
+
+		final Author a1 = createAuthor("Michele Artini", "0000-0002-4406-428X");
+		final Author a2 = createAuthor("Claudio Atzori", "http://orcid.org/0000-0001-9613-6639");
+		final Author a3 = createAuthor("Alessia Bardi", null);
+
+		final Result r = new Result();
+		r.setAuthor(Arrays.asList(a1, a2, a3));
+
+		final OaBrokerMainEntity br = ConversionUtils.oafResultToBrokerResult(r);
+
+		assertEquals(3, br.getCreators().size());
+		assertEquals("0000-0002-4406-428X", br.getCreators().get(0).getOrcid());
+		assertEquals("0000-0001-9613-6639", br.getCreators().get(1).getOrcid());
+		assertNull(br.getCreators().get(2).getOrcid());
+	}
+
+	private Author createAuthor(final String name, final String orcid) {
+
+		final Author a = new Author();
+		a.setFullname("Michele Artini");
+
+		if (orcid != null) {
+			final Qualifier q = new Qualifier();
+			q.setClassid(ModelConstants.ORCID);
+			q.setClassname(ModelConstants.ORCID);
+			q.setSchemeid("dnet:pids");
+			q.setSchemename("dnet:pids");
+
+			final StructuredProperty pid = new StructuredProperty();
+			pid.setQualifier(q);
+			pid.setValue(orcid);
+
+			a.setPid(Arrays.asList(pid));
+		}
+		return a;
+	}
+
 }

From 7fa3d512000250e2d549bac581a964d06930d4a5 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 12 Jul 2024 17:09:01 +0200
Subject: [PATCH 068/239] renamed class, updated criteria to consider the
 ORCIDs used in the matchers

---
 ...mpleEntititiesJob.java => PrepareSimpleEntitiesJob.java} | 6 +++---
 .../java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java | 3 +--
 .../dhp/broker/oa/generate_all/oozie_app/workflow.xml       | 2 +-
 3 files changed, 5 insertions(+), 6 deletions(-)
 rename dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/{PrepareSimpleEntititiesJob.java => PrepareSimpleEntitiesJob.java} (96%)

diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntitiesJob.java
similarity index 96%
rename from dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java
rename to dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntitiesJob.java
index 4cb3ecfd9..30e50931b 100644
--- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntititiesJob.java
+++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareSimpleEntitiesJob.java
@@ -26,15 +26,15 @@ import eu.dnetlib.dhp.schema.oaf.Publication;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.Software;
 
-public class PrepareSimpleEntititiesJob {
+public class PrepareSimpleEntitiesJob {
 
-	private static final Logger log = LoggerFactory.getLogger(PrepareSimpleEntititiesJob.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareSimpleEntitiesJob.class);
 
 	public static void main(final String[] args) throws Exception {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
-					PrepareSimpleEntititiesJob.class
+					PrepareSimpleEntitiesJob.class
 						.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/common_params.json")));
 		parser.parseArgument(args);
 
diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
index 4bf4d3341..237c21db8 100644
--- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
+++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
@@ -160,8 +160,7 @@ public class ConversionUtils {
 			.stream()
 			.filter(Objects::nonNull)
 			.filter(pid -> pid.getQualifier() != null)
-			.filter(pid -> pid.getQualifier().getClassid() != null)
-			.filter(pid -> pid.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID))
+			.filter(pid -> StringUtils.startsWithIgnoreCase(pid.getQualifier().getClassid(), ModelConstants.ORCID))
 			.map(StructuredProperty::getValue)
 			.map(ConversionUtils::cleanOrcid)
 			.filter(StringUtils::isNotBlank)
diff --git a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
index 3e709117c..f5409617b 100644
--- a/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/generate_all/oozie_app/workflow.xml
@@ -179,7 +179,7 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>PrepareSimpleEntititiesJob</name>
-            <class>eu.dnetlib.dhp.broker.oa.PrepareSimpleEntititiesJob</class>
+            <class>eu.dnetlib.dhp.broker.oa.PrepareSimpleEntitiesJob</class>
             <jar>dhp-broker-events-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-cores=${sparkExecutorCores}

From 6f6e85ddf445842d775f715b6d1ae7f14d37919d Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 15 Jul 2024 09:32:04 +0200
Subject: [PATCH 069/239] code formatting

---
 .../oa/matchers/simple/EnrichMissingAuthorOrcidTest.java      | 4 +++-
 .../eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java    | 3 ++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java
index e61299800..2a378ddd6 100644
--- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java
+++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.broker.oa.matchers.simple;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -16,7 +17,8 @@ class EnrichMissingAuthorOrcidTest {
 	final EnrichMissingAuthorOrcid matcher = new EnrichMissingAuthorOrcid();
 
 	@BeforeEach
-	void setUp() throws Exception {}
+	void setUp() throws Exception {
+	}
 
 	@Test
 	void testFindDifferences_1() {
diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java
index ee1bfed05..4c7891576 100644
--- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java
+++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java
@@ -23,7 +23,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 public class ConversionUtilsTest {
 
 	@BeforeEach
-	public void setUp() throws Exception {}
+	public void setUp() throws Exception {
+	}
 
 	@Test
 	public void testAllResultPids() {

From 1fb44198fb5fc732f8ff592cfc6e22722c8bf45c Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 15 Jul 2024 15:24:18 +0200
Subject: [PATCH 070/239] renamed workflow to better reflect its purpose

---
 .../eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
index 605c86ac9..697e30a09 100644
--- a/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-stats-promote/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml
@@ -1,4 +1,4 @@
-<workflow-app name="Graph Stats" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="Promote Graph Stats" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>stats_db_name</name>

From 38f8ed27fd7f53549637f9062c8028fe63e42437 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 15 Jul 2024 16:30:43 +0200
Subject: [PATCH 071/239] [graph provision] log the Solr admin application
 operations for alias deletion and creation

---
 .../java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java  | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
index 44426e8c5..2bf7d3fbb 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
@@ -128,12 +128,14 @@ public class SolrAdminApplication implements Closeable {
 
 	public SolrResponse deleteAlias(String aliasName) throws SolrServerException, IOException {
 		CollectionAdminRequest.DeleteAlias deleteAliasRequest = CollectionAdminRequest.deleteAlias(aliasName);
+		log.info("deleting alias: {}", aliasName);
 		return deleteAliasRequest.process(solrClient);
 	}
 
 	public SolrResponse createAlias(String aliasName, String collection) throws IOException, SolrServerException {
 		CollectionAdminRequest.CreateAlias createAliasRequest = CollectionAdminRequest
 			.createAlias(aliasName, collection);
+		log.info("creating alias: {} for collection: {}", aliasName, collection);
 		return createAliasRequest.process(solrClient);
 	}
 

From 5aa7847ea626be914f719464b69cf6e1b111e0f1 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 16 Jul 2024 10:38:50 +0200
Subject: [PATCH 072/239] consider the transformative agreement text when
 merging results

---
 .../main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index 74fd13ae7..ea402ecbf 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -464,6 +464,10 @@ public class MergeUtils {
 		merge.setIsInDiamondJournal(booleanOR(merge.getIsInDiamondJournal(), enrich.getIsInDiamondJournal()));
 		merge.setPubliclyFunded(booleanOR(merge.getPubliclyFunded(), enrich.getPubliclyFunded()));
 
+		if (StringUtils.isBlank(merge.getTransformativeAgreement())) {
+			merge.setTransformativeAgreement(enrich.getTransformativeAgreement());
+		}
+
 		return merge;
 	}
 

From beb93cdfe9563ae01102e6d105a82ef03a80fff1 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 16 Jul 2024 11:43:48 +0200
Subject: [PATCH 073/239] [graph provision] expand the context info for each
 entity type

---
 .../model/ProvisionModelSupport.java          | 20 ++++---
 .../oa/provision/utils/XmlRecordFactory.java  | 19 +++----
 .../oa/provision/SolrConfigExploreTest.java   | 56 ++++++++++---------
 .../dhp/oa/provision/SolrConfigTest.java      |  3 +-
 .../oa/provision/XmlRecordFactoryTest.java    | 41 +++++++++++++-
 .../dnetlib/dhp/oa/provision/project_aka.json |  1 +
 6 files changed, 91 insertions(+), 49 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index b450b95be..abcf4992f 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -31,6 +30,7 @@ import eu.dnetlib.dhp.schema.solr.Context;
 import eu.dnetlib.dhp.schema.solr.Country;
 import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
 import eu.dnetlib.dhp.schema.solr.Measure;
@@ -562,10 +562,16 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
-	private static List<ExternalReference> mapExternalReference(List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
-		return Optional.ofNullable(externalReference)
-				.map(ext -> ext.stream()
-						.map(e -> ExternalReference.newInstance(
+	private static List<ExternalReference> mapExternalReference(
+		List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+		return Optional
+			.ofNullable(externalReference)
+			.map(
+				ext -> ext
+					.stream()
+					.map(
+						e -> ExternalReference
+							.newInstance(
 								e.getSitename(),
 								e.getLabel(),
 								e.getAlternateLabel(),
@@ -573,8 +579,8 @@ public class ProvisionModelSupport {
 								mapCodeLabel(e.getQualifier()),
 								e.getRefidentifier(),
 								e.getQuery()))
-						.collect(Collectors.toList()))
-				.orElse(Lists.newArrayList());
+					.collect(Collectors.toList()))
+			.orElse(Lists.newArrayList());
 	}
 
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index 3d89b1e34..899dad221 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -219,6 +219,13 @@ public class XmlRecordFactory implements Serializable {
 		if (entity.getMeasures() != null) {
 			metadata.addAll(measuresAsXml(entity.getMeasures()));
 		}
+		if (entity.getContext() != null) {
+			contexts.addAll(entity.getContext().stream().map(Context::getId).collect(Collectors.toList()));
+			/* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */
+			if (contexts.contains("dh-ch::subcommunity::2")) {
+				contexts.add("clarin");
+			}
+		}
 
 		if (ModelSupport.isResult(type)) {
 			final Result r = (Result) entity;
@@ -245,14 +252,6 @@ public class XmlRecordFactory implements Serializable {
 							.collect(Collectors.toList()));
 			}
 
-			if (r.getContext() != null) {
-				contexts.addAll(r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList()));
-				/* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */
-				if (contexts.contains("dh-ch::subcommunity::2")) {
-					contexts.add("clarin");
-				}
-			}
-
 			if (r.getTitle() != null) {
 				metadata
 					.addAll(
@@ -1603,9 +1602,7 @@ public class XmlRecordFactory implements Serializable {
 	private List<String> buildContexts(final String type, final Set<String> contexts) {
 		final List<String> res = Lists.newArrayList();
 
-		if (contextMapper != null
-			&& !contextMapper.isEmpty()
-			&& MainEntityType.result.toString().equals(type)) {
+		if (contextMapper != null && !contextMapper.isEmpty()) {
 
 			XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");
 
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
index 41eac2a30..90aef5adc 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
@@ -1,12 +1,13 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Path;
 
-import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -32,14 +33,13 @@ import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
-
-import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 @ExtendWith(MockitoExtension.class)
 public class SolrConfigExploreTest {
@@ -91,7 +91,7 @@ public class SolrConfigExploreTest {
 		SparkConf conf = new SparkConf();
 		conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
 		conf.registerKryoClasses(new Class[] {
-				SerializableSolrInputDocument.class
+			SerializableSolrInputDocument.class
 		});
 
 		conf.setMaster("local[1]");
@@ -101,10 +101,10 @@ public class SolrConfigExploreTest {
 		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
 
 		spark = SparkSession
-				.builder()
-				.appName(SolrConfigExploreTest.class.getSimpleName())
-				.config(conf)
-				.getOrCreate();
+			.builder()
+			.appName(SolrConfigExploreTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
 
 		// random unassigned HTTP port
 		final int jettyPort = 0;
@@ -134,35 +134,35 @@ public class SolrConfigExploreTest {
 
 		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
 		log
-				.info(
-						CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
-								.process(miniCluster.getSolrClient())
-								.toString());
+			.info(
+				CollectionAdminRequest.ClusterStatus
+					.getClusterStatus()
+					.process(miniCluster.getSolrClient())
+					.toString());
 
 		NamedList<Object> res = createCollection(
-				miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
 
 		res = createCollection(
-				miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
 		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
-				.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 
 		log
-				.info(
-						CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
-								.process(miniCluster.getSolrClient())
-								.toString());
+			.info(
+				CollectionAdminRequest.ClusterStatus
+					.getClusterStatus()
+					.process(miniCluster.getSolrClient())
+					.toString());
 
 	}
 
@@ -180,7 +180,8 @@ public class SolrConfigExploreTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -200,7 +201,8 @@ public class SolrConfigExploreTest {
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-				log.info(
+				log
+					.info(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -216,7 +218,7 @@ public class SolrConfigExploreTest {
 	}
 
 	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
-														int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
+		int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
 		ModifiableSolrParams modParams = new ModifiableSolrParams();
 		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
 		modParams.set("name", name);
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
index 2c62389c6..c04fa1cc6 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
@@ -85,7 +85,8 @@ public class SolrConfigTest extends SolrTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
index d617991a1..ab4301f9a 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
@@ -1,8 +1,7 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.*;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -22,6 +21,7 @@ import com.google.common.collect.Lists;
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
+import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -51,7 +51,7 @@ public class XmlRecordFactoryTest {
 
 		assertNotNull(doc);
 
-		// System.out.println(doc.asXML());
+		System.out.println(doc.asXML());
 
 		assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
 		assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
@@ -267,4 +267,39 @@ public class XmlRecordFactoryTest {
 
 	}
 
+	@Test
+	public void test_AKA_project() throws DocumentException, IOException {
+		final ContextMapper contextMapper = new ContextMapper();
+
+		contextMapper
+			.put("dh-ch", new ContextDef("dh-ch", "Digital Humanities and Cultural Heritage", "context", "community"));
+		contextMapper.put("dh-ch::projects", new ContextDef("dh-ch::projects", "DH-CH Projects", "category", ""));
+		contextMapper
+			.put("dh-ch::projects::2", new ContextDef("dh-ch::projects::2", "ARIADNE", "concept", "community"));
+
+		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
+			PayloadConverterJob.schemaLocation);
+
+		final Project p = OBJECT_MAPPER
+			.readValue(
+				IOUtils.toString(getClass().getResourceAsStream("project_aka.json")),
+				Project.class);
+
+		assertNotNull(p.getContext());
+		assertEquals(1, p.getContext().size());
+		assertEquals("dh-ch::projects::2", p.getContext().get(0).getId());
+
+		final String xml = xmlRecordFactory.build(new JoinedEntity(p));
+
+		assertNotNull(xml);
+
+		final Document doc = new SAXReader().read(new StringReader(xml));
+
+		assertNotNull(doc);
+
+		assertEquals("dh-ch", doc.valueOf("//context/@id"));
+		assertEquals("dh-ch::projects", doc.valueOf("//context/category/@id"));
+		assertEquals("dh-ch::projects::2", doc.valueOf("//context/category/concept/@id"));
+	}
+
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json
new file mode 100644
index 000000000..18bd5adf4
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json
@@ -0,0 +1 @@
+{"context" : [{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"bulktagging:community:subject","classname":"Bulk Tagging for Communities","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"}],"id":"dh-ch::projects::2"}], "callidentifier":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Virkapäätöksiin liittyvä yleiskustannusosuus KY"},"code":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"204684"},"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"currency":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"EUR"},"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"dateofcollection":"2019-01-25","dateoftransformation":"2022-02-08","duration":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0"},"ecarticle29_3":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"ecsc39":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"enddate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2002-12-31"},"extraInfo":[],"fundedamount":3230.0,"fundingtree":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"<fundingtree><funder>\n         <id>aka_________::AKA</id>\n         <shortname>AKA</shortname>\n         <name>Academy of Finland</name>\n         <originalname>Academy of Finland</originalname>\n         <jurisdiction>FI</jurisdiction>\n      </funder></fundingtree>"}],"id":"40|aka_________::00f0012ac67a2f826f2e98dbdfd6b058","jsonextrainfo":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"{}"},"lastupdatetimestamp":1719997513126,"oamandatepublications":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"optional1":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"3,230 €"},"originalId":["aka_________::204684"],"pid":[],"startdate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2002-12-01"},"subjects":[],"title":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Tutkijan virkaan liittyvä yleiskustannusosuus suorituspaikalle"},"totalcost":0.0}
\ No newline at end of file

From 9d279101446a71236fe3edb53c5e51946aa2c2fd Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 16 Jul 2024 13:48:48 +0200
Subject: [PATCH 074/239] [BulkTag]added tagging for the organization relevant
 for the community. Added test. Changed the tagging variables.

---
 .../eu/dnetlib/pace/tree/CountryMatch.java    |  55 ++++----
 .../dnetlib/dhp/bulktag/SparkBulkTagJob.java  |  45 +++---
 .../bulktag/community/TaggingConstants.java   |   6 +
 .../dnetlib/dhp/bulktag/BulkTagJobTest.java   | 132 ++++++++++++++++++
 .../update_datasource/organization            |   4 +
 .../publication/update_datasource/project     |   4 +
 .../model/ProvisionModelSupport.java          |  20 ++-
 .../oa/provision/SolrConfigExploreTest.java   |  56 ++++----
 .../dhp/oa/provision/SolrConfigTest.java      |   3 +-
 9 files changed, 243 insertions(+), 82 deletions(-)
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/organization

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
index 9cf616356..c02381983 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.pace.tree;
 
 import java.util.Map;
@@ -11,37 +12,37 @@ import eu.dnetlib.pace.tree.support.ComparatorClass;
 @ComparatorClass("countryMatch")
 public class CountryMatch extends AbstractStringComparator {
 
-    public CountryMatch(Map<String, String> params) {
-        super(params, new com.wcohen.ss.JaroWinkler());
-    }
+	public CountryMatch(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+	}
 
-    public CountryMatch(final double weight) {
-        super(weight, new com.wcohen.ss.JaroWinkler());
-    }
+	public CountryMatch(final double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
 
-    protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
-        super(weight, ssalgo);
-    }
+	protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
 
-    @Override
-    public double distance(final String a, final String b, final Config conf) {
-        if (a.isEmpty() || b.isEmpty()) {
-            return -1.0; // return -1 if a field is missing
-        }
-        if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
-            return -1.0; // return -1 if a country is UNKNOWN
-        }
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+		if (a.isEmpty() || b.isEmpty()) {
+			return -1.0; // return -1 if a field is missing
+		}
+		if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
+			return -1.0; // return -1 if a country is UNKNOWN
+		}
 
-        return a.equals(b) ? 1.0 : 0;
-    }
+		return a.equals(b) ? 1.0 : 0;
+	}
 
-    @Override
-    public double getWeight() {
-        return super.weight;
-    }
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
 
-    @Override
-    protected double normalize(final double d) {
-        return d;
-    }
+	@Override
+	protected double normalize(final double d) {
+		return d;
+	}
 }
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
index 354741690..e9a45be40 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java
@@ -33,10 +33,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.bulktag.community.*;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Context;
-import eu.dnetlib.dhp.schema.oaf.Datasource;
-import eu.dnetlib.dhp.schema.oaf.Project;
-import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
@@ -114,27 +111,35 @@ public class SparkBulkTagJob {
 				extendCommunityConfigurationForEOSC(spark, inputPath, cc);
 				execBulkTag(
 					spark, inputPath, outputPath, protoMap, cc);
+				execEntityTag(
+					spark, inputPath + "organization", outputPath + "organization",
+					Utils.getCommunityOrganization(baseURL), Organization.class, TaggingConstants.CLASS_ID_ORGANIZATION,
+					TaggingConstants.CLASS_NAME_BULKTAG_ORGANIZATION);
+				execEntityTag(
+					spark, inputPath + "project", outputPath + "project", Utils.getCommunityProjects(baseURL),
+					Project.class, TaggingConstants.CLASS_ID_PROJECT, TaggingConstants.CLASS_NAME_BULKTAG_PROJECT);
 				execDatasourceTag(spark, inputPath, outputPath, Utils.getDatasourceCommunities(baseURL));
-				execProjectTag(spark, inputPath, outputPath, Utils.getCommunityProjects(baseURL));
+
 			});
 	}
 
-	private static void execProjectTag(SparkSession spark, String inputPath, String outputPath,
-		CommunityEntityMap communityProjects) {
-		Dataset<Project> projects = readPath(spark, inputPath + "project", Project.class);
+	private static <E extends OafEntity> void execEntityTag(SparkSession spark, String inputPath, String outputPath,
+		CommunityEntityMap communityEntity, Class<E> entityClass,
+		String classID, String calssName) {
+		Dataset<E> entity = readPath(spark, inputPath, entityClass);
 		Dataset<EntityCommunities> pc = spark
 			.createDataset(
-				communityProjects
+				communityEntity
 					.keySet()
 					.stream()
-					.map(k -> EntityCommunities.newInstance(k, communityProjects.get(k)))
+					.map(k -> EntityCommunities.newInstance(k, communityEntity.get(k)))
 					.collect(Collectors.toList()),
 				Encoders.bean(EntityCommunities.class));
 
-		projects
-			.joinWith(pc, projects.col("id").equalTo(pc.col("entityId")), "left")
-			.map((MapFunction<Tuple2<Project, EntityCommunities>, Project>) t2 -> {
-				Project ds = t2._1();
+		entity
+			.joinWith(pc, entity.col("id").equalTo(pc.col("entityId")), "left")
+			.map((MapFunction<Tuple2<E, EntityCommunities>, E>) t2 -> {
+				E ds = t2._1();
 				if (t2._2() != null) {
 					List<String> context = Optional
 						.ofNullable(ds.getContext())
@@ -156,8 +161,8 @@ public class SparkBulkTagJob {
 													false, TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false,
 													OafMapperUtils
 														.qualifier(
-															TaggingConstants.CLASS_ID_DATASOURCE,
-															TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE,
+															classID,
+															calssName,
 															ModelConstants.DNET_PROVENANCE_ACTIONS,
 															ModelConstants.DNET_PROVENANCE_ACTIONS),
 													"1")));
@@ -166,17 +171,17 @@ public class SparkBulkTagJob {
 					});
 				}
 				return ds;
-			}, Encoders.bean(Project.class))
+			}, Encoders.bean(entityClass))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(outputPath + "project");
+			.json(outputPath);
 
-		readPath(spark, outputPath + "project", Project.class)
+		readPath(spark, outputPath, entityClass)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(inputPath + "project");
+			.json(inputPath);
 	}
 
 	private static void execDatasourceTag(SparkSession spark, String inputPath, String outputPath,
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java
index aea21f8e5..6e6f12cfb 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java
@@ -13,6 +13,9 @@ public class TaggingConstants {
 	public static final String CLASS_ID_CZENODO = "community:zenodocommunity";
 	public static final String CLASS_ID_ADVANCED_CONSTRAINT = "community:advconstraint";
 
+	public static final String CLASS_ID_PROJECT = "community:project";
+	public static final String CLASS_ID_ORGANIZATION = "community:organization";
+
 	public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/";
 
 	public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject";
@@ -20,5 +23,8 @@ public class TaggingConstants {
 	public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo";
 	public static final String CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT = "Bulktagging for Community - Advanced Constraints";
 
+	public static final String CLASS_NAME_BULKTAG_PROJECT = "Bulktagging for Community - Project";
+	public static final String CLASS_NAME_BULKTAG_ORGANIZATION = "Bulktagging for Community - Organization";
+
 	public static final String TAGGING_TRUST = "0.8";
 }
diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
index a5280a3b3..f49774574 100644
--- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
+++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java
@@ -465,6 +465,138 @@ public class BulkTagJobTest {
 
 	}
 
+	@Test
+	void organizationTag() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
+			.getPath();
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
+		SparkBulkTagJob
+			.main(
+				new String[] {
+
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath", sourcePath,
+					"-taggingConf", taggingConf,
+
+					"-outputPath", workingDir.toString() + "/",
+					"-baseURL", "https://services.openaire.eu/openaire/community/",
+
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap",
+					"-nameNode", "local"
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Organization> tmp = sc
+			.textFile(workingDir.toString() + "/organization")
+			.map(item -> OBJECT_MAPPER.readValue(item, Organization.class));
+
+		Assertions.assertEquals(4, tmp.count());
+		org.apache.spark.sql.Dataset<Organization> verificationDataset = spark
+			.createDataset(tmp.rdd(), Encoders.bean(Organization.class));
+
+		verificationDataset.createOrReplaceTempView("organization");
+
+		String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+			+ "from organization "
+			+ "lateral view explode(context) c as MyT "
+			+ "lateral view explode(MyT.datainfo) d as MyD "
+			+ "where MyD.inferenceprovenance = 'bulktagging'";
+
+		org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
+
+		idExplodeCommunity.show(false);
+
+		Assertions.assertEquals(3, idExplodeCommunity.count());
+		Assertions
+			.assertEquals(
+				3, idExplodeCommunity.filter("provenance = 'community:organization'").count());
+		Assertions
+			.assertEquals(
+				3,
+				idExplodeCommunity
+					.filter("name = 'Bulktagging for Community - Organization'")
+					.count());
+
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'netherlands'").count());
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'beopen'").count());
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
+
+	}
+
+	@Test
+	void projectTag() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
+			.getPath();
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
+		SparkBulkTagJob
+			.main(
+				new String[] {
+
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath", sourcePath,
+					"-taggingConf", taggingConf,
+
+					"-outputPath", workingDir.toString() + "/",
+					"-baseURL", "https://services.openaire.eu/openaire/community/",
+
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap",
+					"-nameNode", "local"
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Project> tmp = sc
+			.textFile(workingDir.toString() + "/project")
+			.map(item -> OBJECT_MAPPER.readValue(item, Project.class));
+
+		Assertions.assertEquals(4, tmp.count());
+		org.apache.spark.sql.Dataset<Project> verificationDataset = spark
+			.createDataset(tmp.rdd(), Encoders.bean(Project.class));
+
+		verificationDataset.createOrReplaceTempView("project");
+
+		String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+			+ "from project "
+			+ "lateral view explode(context) c as MyT "
+			+ "lateral view explode(MyT.datainfo) d as MyD "
+			+ "where MyD.inferenceprovenance = 'bulktagging'";
+
+		org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
+
+		idExplodeCommunity.show(false);
+
+		Assertions.assertEquals(4, idExplodeCommunity.count());
+		Assertions
+			.assertEquals(
+				4, idExplodeCommunity.filter("provenance = 'community:project'").count());
+		Assertions
+			.assertEquals(
+				4,
+				idExplodeCommunity
+					.filter("name = 'Bulktagging for Community - Project'")
+					.count());
+
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'enermaps'").count());
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'clarin'").count());
+		Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'dh-ch'").count());
+
+	}
+
 	@Test
 	void bulktagByZenodoCommunityTest() throws Exception {
 		final String sourcePath = getClass()
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/organization b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/organization
new file mode 100644
index 000000000..cf7a2f90e
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/organization
@@ -0,0 +1,4 @@
+{"alternativeNames":[],"collectedfrom":[{"key":"10|openaire____::457528c43fabd74e212db2ed61101075","value":"Agence Nationale de la Recherche"}],"country":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:countries","schemename":"dnet:countries"},"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"dateofcollection":"2021-02-15","dateoftransformation":"2024-03-29","ecenterprise":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"echighereducation":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecinternationalorganization":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecinternationalorganizationeurinterests":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"eclegalbody":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"eclegalperson":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecnonprofit":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecnutscode":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecresearchorganization":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecsmevalidated":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"extraInfo":[],"id":"20|openorgs____::2b9422d5f5bac4aae99b24e61586d3d3","lastupdatetimestamp":1719997513126,"legalname":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"Laboratoire de Physique Statistique, UMR 8550 - Ecole Normale Supérieure"},"organizationType":"Unknown","originalId":["anr_________::9fdd505a0c45c6ad239c7c1406145820"],"pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"qualifier":{"classid":"RNSR","classname":"RNSR","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"RNSR:199812878L"}]}
+{"alternativeNames":[],"collectedfrom":[{"key":"10|openaire____::457528c43fabd74e212db2ed61101075","value":"Agence Nationale de la Recherche"}],"country":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:countries","schemename":"dnet:countries"},"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"dateofcollection":"2021-02-15","dateoftransformation":"2023-12-04","ecenterprise":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"echighereducation":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecinternationalorganization":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecinternationalorganizationeurinterests":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"eclegalbody":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"eclegalperson":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecnonprofit":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecnutscode":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecresearchorganization":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecsmevalidated":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"extraInfo":[],"id":"20|openorgs____::00010e003d3ce9c05e038cadfb6d4f03","lastupdatetimestamp":1719997513126,"legalname":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"National Institute for Agricultural and Food Research and Technology"},"organizationType":"Unknown","originalId":["anr_________::16ba9bdd7a02f3e5f38a9c6a0ca24be6"],"pid":[]}
+{"alternativeNames":[],"collectedfrom":[{"key":"10|openaire____::457528c43fabd74e212db2ed61101075","value":"Agence Nationale de la Recherche"}],"country":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:countries","schemename":"dnet:countries"},"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"dateofcollection":"2021-02-15","dateoftransformation":"2022-10-11","ecenterprise":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"echighereducation":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecinternationalorganization":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecinternationalorganizationeurinterests":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"eclegalbody":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"eclegalperson":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecnonprofit":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecnutscode":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecresearchorganization":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"ecsmevalidated":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"false"},"extraInfo":[],"id":"20|openorgs____::ad863df6deda1619a25e7fad4a534891","lastupdatetimestamp":1719997513126,"legalname":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.810"},"value":"INSTITUT DE VEILLE SANITAIRE"},"organizationType":"Unknown","originalId":["anr_________::27a60b3e005f647d173309729e4c62ae"],"pid":[]}
+{"alternativeNames":[],"collectedfrom":[{"key":"10|openaire____::b30dac7baac631f3da7c2bb18dd9891f","value":"CORDA - COmmon Research DAta 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\ No newline at end of file
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/project b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/project
index e69de29bb..2b9628ea1 100644
--- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/project
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/project
@@ -0,0 +1,4 @@
+{"code":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"unidentified"},"collectedfrom":[{"key":"10|openaire____::718b1e0b0206401b66e8d87f68876121","value":"Stroke Association"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"dateofcollection":"2024-04-20","dateoftransformation":"2024-04-20","duration":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0"},"ecarticle29_3":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"ecsc39":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"extraInfo":[],"fundedamount":0.0,"fundingtree":[],"id":"40|ukri________::6937e06c766521c0629d8a6ca20ca345","jsonextrainfo":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"{}"},"lastupdatetimestamp":1719997513126,"oamandatepublications":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"optional1":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"uk_funders_import"},"originalId":["501100000364::unidentified"],"pid":[],"subjects":[],"title":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"unidentified"},"totalcost":0.0}
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        <id>aka_________::AKA</id>\n         <shortname>AKA</shortname>\n         <name>Academy of Finland</name>\n         <originalname>Academy of Finland</originalname>\n         <jurisdiction>FI</jurisdiction>\n      </funder></fundingtree>"}],"id":"40|corda_______::ef782b2d85676aa3e5a907427feb18c4","jsonextrainfo":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"{}"},"lastupdatetimestamp":1719997513126,"measures":[{"id":"numOfInfluentialResults","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"19"}]},{"id":"numOfPopularResults","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"19"}]},{"id":"totalImpulse","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"486"}]},{"id":"totalCitationCount","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"840"}]},{"id":"downloads","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:usage_counts","classname":"measure:usage_counts","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"count","value":"17"}]},{"id":"views","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:usage_counts","classname":"measure:usage_counts","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"count","value":"9"}]}],"oamandatepublications":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"optional1":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"471,335 €"},"originalId":["aka_________::276480"],"pid":[],"startdate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2014-09-01"},"subjects":[],"title":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Yeast hybrid vigour: elucidation of mechanisms governing competitive advantage and sub-genome compatibility after interspecific hybridization"},"totalcost":0.0}
+{"callidentifier":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Subsidy for organising of international conferences KY"},"code":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"107956"},"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"currency":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"EUR"},"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"dateofcollection":"2019-01-25","dateoftransformation":"2022-02-08","duration":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0"},"ecarticle29_3":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"ecsc39":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"enddate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2005-12-31"},"extraInfo":[],"fundedamount":2000.0,"fundingtree":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"<fundingtree><funder>\n         <id>aka_________::AKA</id>\n         <shortname>AKA</shortname>\n         <name>Academy of Finland</name>\n         <originalname>Academy of Finland</originalname>\n         <jurisdiction>FI</jurisdiction>\n      </funder></fundingtree>"}],"id":"40|aka_________::017ddc7873b184db49337b2472cdc83f","jsonextrainfo":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"{}"},"lastupdatetimestamp":1719997513126,"oamandatepublications":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"optional1":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2,000 €"},"originalId":["aka_________::107956"],"pid":[],"startdate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2005-01-01"},"subjects":[],"title":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"NODALIDA 2005  15th Nordic Conference on Computational Linguistics, 19.-22.5.2005"},"totalcost":0.0}
+{"callidentifier":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Biofuture 2025, second stage LT"},"code":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"307624"},"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"currency":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"EUR"},"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"dateofcollection":"2024-07-05T18:46:23.059","dateoftransformation":"2022-02-08","duration":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0"},"ecarticle29_3":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"ecsc39":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"enddate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2020-12-31"},"extraInfo":[],"fundedamount":331277.0,"fundingtree":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"<fundingtree><funder>\n         <id>aka_________::AKA</id>\n         <shortname>AKA</shortname>\n         <name>Academy of Finland</name>\n         <originalname>Academy of Finland</originalname>\n         <jurisdiction>FI</jurisdiction>\n      </funder></fundingtree>"}],"id":"40|snsf________::911db67dc5eebd24d7787d69d4974ca4","jsonextrainfo":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"{}"},"lastupdatetimestamp":1719997513126,"measures":[{"id":"numOfInfluentialResults","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"8"}]},{"id":"numOfPopularResults","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"8"}]},{"id":"totalImpulse","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"28"}]},{"id":"totalCitationCount","unit":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"update","inferred":true,"invisible":false,"provenanceaction":{"classid":"measure:bip","classname":"measure:bip","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":""},"key":"score","value":"30"}]}],"oamandatepublications":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"optional1":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"331,277 €"},"originalId":["aka_________::307624"],"pid":[],"startdate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2017-01-01"},"subjects":[],"title":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Overcoming technology barriers with tailored catalysts: Design of molecularly functionalized heterogeneous catalysts for selective reductions of biomass-derived materials / Consortium: FunCat"},"totalcost":0.0}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index b450b95be..abcf4992f 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -31,6 +30,7 @@ import eu.dnetlib.dhp.schema.solr.Context;
 import eu.dnetlib.dhp.schema.solr.Country;
 import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
 import eu.dnetlib.dhp.schema.solr.Measure;
@@ -562,10 +562,16 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
-	private static List<ExternalReference> mapExternalReference(List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
-		return Optional.ofNullable(externalReference)
-				.map(ext -> ext.stream()
-						.map(e -> ExternalReference.newInstance(
+	private static List<ExternalReference> mapExternalReference(
+		List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+		return Optional
+			.ofNullable(externalReference)
+			.map(
+				ext -> ext
+					.stream()
+					.map(
+						e -> ExternalReference
+							.newInstance(
 								e.getSitename(),
 								e.getLabel(),
 								e.getAlternateLabel(),
@@ -573,8 +579,8 @@ public class ProvisionModelSupport {
 								mapCodeLabel(e.getQualifier()),
 								e.getRefidentifier(),
 								e.getQuery()))
-						.collect(Collectors.toList()))
-				.orElse(Lists.newArrayList());
+					.collect(Collectors.toList()))
+			.orElse(Lists.newArrayList());
 	}
 
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
index 41eac2a30..90aef5adc 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
@@ -1,12 +1,13 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Path;
 
-import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -32,14 +33,13 @@ import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
-
-import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 @ExtendWith(MockitoExtension.class)
 public class SolrConfigExploreTest {
@@ -91,7 +91,7 @@ public class SolrConfigExploreTest {
 		SparkConf conf = new SparkConf();
 		conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
 		conf.registerKryoClasses(new Class[] {
-				SerializableSolrInputDocument.class
+			SerializableSolrInputDocument.class
 		});
 
 		conf.setMaster("local[1]");
@@ -101,10 +101,10 @@ public class SolrConfigExploreTest {
 		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
 
 		spark = SparkSession
-				.builder()
-				.appName(SolrConfigExploreTest.class.getSimpleName())
-				.config(conf)
-				.getOrCreate();
+			.builder()
+			.appName(SolrConfigExploreTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
 
 		// random unassigned HTTP port
 		final int jettyPort = 0;
@@ -134,35 +134,35 @@ public class SolrConfigExploreTest {
 
 		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
 		log
-				.info(
-						CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
-								.process(miniCluster.getSolrClient())
-								.toString());
+			.info(
+				CollectionAdminRequest.ClusterStatus
+					.getClusterStatus()
+					.process(miniCluster.getSolrClient())
+					.toString());
 
 		NamedList<Object> res = createCollection(
-				miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
 
 		res = createCollection(
-				miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
 		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
-				.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 
 		log
-				.info(
-						CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
-								.process(miniCluster.getSolrClient())
-								.toString());
+			.info(
+				CollectionAdminRequest.ClusterStatus
+					.getClusterStatus()
+					.process(miniCluster.getSolrClient())
+					.toString());
 
 	}
 
@@ -180,7 +180,8 @@ public class SolrConfigExploreTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -200,7 +201,8 @@ public class SolrConfigExploreTest {
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-				log.info(
+				log
+					.info(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -216,7 +218,7 @@ public class SolrConfigExploreTest {
 	}
 
 	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
-														int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
+		int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
 		ModifiableSolrParams modParams = new ModifiableSolrParams();
 		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
 		modParams.set("name", name);
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
index 2c62389c6..c04fa1cc6 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
@@ -85,7 +85,8 @@ public class SolrConfigTest extends SolrTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",

From 9246bdec1ce5d34495370c1652103a3d8aa3c4bf Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 16 Jul 2024 14:07:37 +0200
Subject: [PATCH 075/239] [WebCrawlAffiliation]remove from the creation of the
 action set the relations for pmc and pmid. Only doi are allowed

---
 .../eu/dnetlib/dhp/actionmanager/Constants.java   |  3 +++
 .../webcrawl/CreateActionSetFromWebEntries.java   | 15 ++++++++-------
 2 files changed, 11 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
index 006d3af76..73b4b77cb 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
@@ -42,6 +42,9 @@ public class Constants {
 	public static final String NULL = "NULL";
 	public static final String NA = "N/A";
 
+	public static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
+	public static final String WEB_CRAWL_NAME = "Web Crawl";
+
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	private Constants() {
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index 27970f2c3..f2a73889f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -21,6 +21,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.actionmanager.Constants;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -29,6 +30,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import io.netty.util.Constant;
 import scala.Tuple2;
 
 /**
@@ -44,8 +46,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 	private static final String PMID_PREFIX = "50|pmid________::";
 
 	private static final String PMCID_PREFIX = "50|pmc_________::";
-	private static final String WEB_CRAWL_ID = "10|openaire____::fb98a192f6a055ba495ef414c330834b";
-	private static final String WEB_CRAWL_NAME = "Web Crawl";
+
 	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(String[] args) throws Exception {
@@ -104,8 +105,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				final String ror = ROR_PREFIX
 					+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
 				ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
-				ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
-				ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
+
 
 				return ret
 					.iterator();
@@ -139,8 +139,9 @@ public class CreateActionSetFromWebEntries implements Serializable {
 				"institution", functions
 					.explode(
 						functions.col("institutions")))
+
 			.selectExpr(
-				"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
+				"id", "doi", "institution.ror as ror",
 				"institution.country_code as country_code", "publication_year")
 			.distinct();
 
@@ -214,7 +215,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 						ModelConstants.IS_AUTHOR_INSTITUTION_OF,
 						Arrays
 							.asList(
-								OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
+								OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
 						OafMapperUtils
 							.dataInfo(
 								false, null, false, false,
@@ -233,7 +234,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 						ModelConstants.HAS_AUTHOR_INSTITUTION,
 						Arrays
 							.asList(
-								OafMapperUtils.keyValue(WEB_CRAWL_ID, WEB_CRAWL_NAME)),
+								OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
 						OafMapperUtils
 							.dataInfo(
 								false, null, false, false,

From d96215cb9b6c03198f723bf9f60261b283cb127a Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 16 Jul 2024 18:17:32 +0200
Subject: [PATCH 076/239] [UnpayWall]added othe : in the identifier
 construction

---
 .../scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index c4aa64fd4..27eaa61b5 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -93,7 +93,7 @@ case object Crossref2Oaf {
 
     val cf = new KeyValue
     cf.setValue("UnpayWall")
-    cf.setKey(s"10|openaire____:${DHPUtils.md5("UnpayWall".toLowerCase)}")
+    cf.setKey(s"10|openaire____::${DHPUtils.md5("UnpayWall".toLowerCase)}")
     cf
 
   }

From f17e1243ba4974942d2ce5062d85b90305320b70 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 17 Jul 2024 10:23:50 +0200
Subject: [PATCH 077/239] reverted changed contens under dhp-graph-provision

---
 .../oa/provision/SolrAdminApplication.java    |  2 +
 .../model/ProvisionModelSupport.java          | 20 +++----
 .../oa/provision/SolrConfigExploreTest.java   | 54 +++++++++----------
 .../dhp/oa/provision/SolrConfigTest.java      |  3 +-
 4 files changed, 36 insertions(+), 43 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
index 44426e8c5..2bf7d3fbb 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/SolrAdminApplication.java
@@ -128,12 +128,14 @@ public class SolrAdminApplication implements Closeable {
 
 	public SolrResponse deleteAlias(String aliasName) throws SolrServerException, IOException {
 		CollectionAdminRequest.DeleteAlias deleteAliasRequest = CollectionAdminRequest.deleteAlias(aliasName);
+		log.info("deleting alias: {}", aliasName);
 		return deleteAliasRequest.process(solrClient);
 	}
 
 	public SolrResponse createAlias(String aliasName, String collection) throws IOException, SolrServerException {
 		CollectionAdminRequest.CreateAlias createAliasRequest = CollectionAdminRequest
 			.createAlias(aliasName, collection);
+		log.info("creating alias: {} for collection: {}", aliasName, collection);
 		return createAliasRequest.process(solrClient);
 	}
 
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index abcf4992f..b450b95be 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,6 +5,7 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -30,7 +31,6 @@ import eu.dnetlib.dhp.schema.solr.Context;
 import eu.dnetlib.dhp.schema.solr.Country;
 import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
-import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
 import eu.dnetlib.dhp.schema.solr.Measure;
@@ -562,16 +562,10 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
-	private static List<ExternalReference> mapExternalReference(
-		List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
-		return Optional
-			.ofNullable(externalReference)
-			.map(
-				ext -> ext
-					.stream()
-					.map(
-						e -> ExternalReference
-							.newInstance(
+	private static List<ExternalReference> mapExternalReference(List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+		return Optional.ofNullable(externalReference)
+				.map(ext -> ext.stream()
+						.map(e -> ExternalReference.newInstance(
 								e.getSitename(),
 								e.getLabel(),
 								e.getAlternateLabel(),
@@ -579,8 +573,8 @@ public class ProvisionModelSupport {
 								mapCodeLabel(e.getQualifier()),
 								e.getRefidentifier(),
 								e.getQuery()))
-					.collect(Collectors.toList()))
-			.orElse(Lists.newArrayList());
+						.collect(Collectors.toList()))
+				.orElse(Lists.newArrayList());
 	}
 
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
index 90aef5adc..41eac2a30 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java
@@ -1,13 +1,12 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Path;
 
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -33,13 +32,14 @@ import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 @ExtendWith(MockitoExtension.class)
 public class SolrConfigExploreTest {
@@ -91,7 +91,7 @@ public class SolrConfigExploreTest {
 		SparkConf conf = new SparkConf();
 		conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
 		conf.registerKryoClasses(new Class[] {
-			SerializableSolrInputDocument.class
+				SerializableSolrInputDocument.class
 		});
 
 		conf.setMaster("local[1]");
@@ -101,10 +101,10 @@ public class SolrConfigExploreTest {
 		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
 
 		spark = SparkSession
-			.builder()
-			.appName(SolrConfigExploreTest.class.getSimpleName())
-			.config(conf)
-			.getOrCreate();
+				.builder()
+				.appName(SolrConfigExploreTest.class.getSimpleName())
+				.config(conf)
+				.getOrCreate();
 
 		// random unassigned HTTP port
 		final int jettyPort = 0;
@@ -134,35 +134,35 @@ public class SolrConfigExploreTest {
 
 		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
 		log
-			.info(
-				CollectionAdminRequest.ClusterStatus
-					.getClusterStatus()
-					.process(miniCluster.getSolrClient())
-					.toString());
+				.info(
+						CollectionAdminRequest.ClusterStatus
+								.getClusterStatus()
+								.process(miniCluster.getSolrClient())
+								.toString());
 
 		NamedList<Object> res = createCollection(
-			miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
+				miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
 
 		res = createCollection(
-			miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+				miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
 		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
-			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+				.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 
 		log
-			.info(
-				CollectionAdminRequest.ClusterStatus
-					.getClusterStatus()
-					.process(miniCluster.getSolrClient())
-					.toString());
+				.info(
+						CollectionAdminRequest.ClusterStatus
+								.getClusterStatus()
+								.process(miniCluster.getSolrClient())
+								.toString());
 
 	}
 
@@ -180,8 +180,7 @@ public class SolrConfigExploreTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions
-			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -201,8 +200,7 @@ public class SolrConfigExploreTest {
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-				log
-					.info(
+				log.info(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -218,7 +216,7 @@ public class SolrConfigExploreTest {
 	}
 
 	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
-		int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
+														int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
 		ModifiableSolrParams modParams = new ModifiableSolrParams();
 		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
 		modParams.set("name", name);
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
index c04fa1cc6..2c62389c6 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java
@@ -85,8 +85,7 @@ public class SolrConfigTest extends SolrTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions
-			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",

From 78b5e4bb6f44be063fdbf9a49ac966fb4b17353f Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 17 Jul 2024 10:48:20 +0200
Subject: [PATCH 078/239] reverted changed contens under dhp-graph-provision

---
 .../oa/provision/utils/XmlRecordFactory.java  | 19 ++++-----
 .../oa/provision/XmlRecordFactoryTest.java    | 41 +++++++++++++++++--
 .../dnetlib/dhp/oa/provision/project_aka.json |  1 +
 3 files changed, 47 insertions(+), 14 deletions(-)
 create mode 100644 dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index 3d89b1e34..899dad221 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -219,6 +219,13 @@ public class XmlRecordFactory implements Serializable {
 		if (entity.getMeasures() != null) {
 			metadata.addAll(measuresAsXml(entity.getMeasures()));
 		}
+		if (entity.getContext() != null) {
+			contexts.addAll(entity.getContext().stream().map(Context::getId).collect(Collectors.toList()));
+			/* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */
+			if (contexts.contains("dh-ch::subcommunity::2")) {
+				contexts.add("clarin");
+			}
+		}
 
 		if (ModelSupport.isResult(type)) {
 			final Result r = (Result) entity;
@@ -245,14 +252,6 @@ public class XmlRecordFactory implements Serializable {
 							.collect(Collectors.toList()));
 			}
 
-			if (r.getContext() != null) {
-				contexts.addAll(r.getContext().stream().map(c -> c.getId()).collect(Collectors.toList()));
-				/* FIXME: Workaround for CLARIN mining issue: #3670#note-29 */
-				if (contexts.contains("dh-ch::subcommunity::2")) {
-					contexts.add("clarin");
-				}
-			}
-
 			if (r.getTitle() != null) {
 				metadata
 					.addAll(
@@ -1603,9 +1602,7 @@ public class XmlRecordFactory implements Serializable {
 	private List<String> buildContexts(final String type, final Set<String> contexts) {
 		final List<String> res = Lists.newArrayList();
 
-		if (contextMapper != null
-			&& !contextMapper.isEmpty()
-			&& MainEntityType.result.toString().equals(type)) {
+		if (contextMapper != null && !contextMapper.isEmpty()) {
 
 			XMLTag document = XMLDoc.newDocument(true).addRoot("contextRoot");
 
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
index d617991a1..ab4301f9a 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
@@ -1,8 +1,7 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.*;
 
 import java.io.IOException;
 import java.io.StringReader;
@@ -22,6 +21,7 @@ import com.google.common.collect.Lists;
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
+import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -51,7 +51,7 @@ public class XmlRecordFactoryTest {
 
 		assertNotNull(doc);
 
-		// System.out.println(doc.asXML());
+		System.out.println(doc.asXML());
 
 		assertEquals("0000-0001-9613-6638", doc.valueOf("//creator[@rank = '1']/@orcid"));
 		assertEquals("0000-0001-9613-6639", doc.valueOf("//creator[@rank = '1']/@orcid_pending"));
@@ -267,4 +267,39 @@ public class XmlRecordFactoryTest {
 
 	}
 
+	@Test
+	public void test_AKA_project() throws DocumentException, IOException {
+		final ContextMapper contextMapper = new ContextMapper();
+
+		contextMapper
+			.put("dh-ch", new ContextDef("dh-ch", "Digital Humanities and Cultural Heritage", "context", "community"));
+		contextMapper.put("dh-ch::projects", new ContextDef("dh-ch::projects", "DH-CH Projects", "category", ""));
+		contextMapper
+			.put("dh-ch::projects::2", new ContextDef("dh-ch::projects::2", "ARIADNE", "concept", "community"));
+
+		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
+			PayloadConverterJob.schemaLocation);
+
+		final Project p = OBJECT_MAPPER
+			.readValue(
+				IOUtils.toString(getClass().getResourceAsStream("project_aka.json")),
+				Project.class);
+
+		assertNotNull(p.getContext());
+		assertEquals(1, p.getContext().size());
+		assertEquals("dh-ch::projects::2", p.getContext().get(0).getId());
+
+		final String xml = xmlRecordFactory.build(new JoinedEntity(p));
+
+		assertNotNull(xml);
+
+		final Document doc = new SAXReader().read(new StringReader(xml));
+
+		assertNotNull(doc);
+
+		assertEquals("dh-ch", doc.valueOf("//context/@id"));
+		assertEquals("dh-ch::projects", doc.valueOf("//context/category/@id"));
+		assertEquals("dh-ch::projects::2", doc.valueOf("//context/category/concept/@id"));
+	}
+
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json
new file mode 100644
index 000000000..18bd5adf4
--- /dev/null
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/project_aka.json
@@ -0,0 +1 @@
+{"context" : [{"dataInfo":[{"deletedbyinference":false,"inferenceprovenance":"bulktagging","inferred":true,"invisible":false,"provenanceaction":{"classid":"bulktagging:community:subject","classname":"Bulk Tagging for Communities","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"}],"id":"dh-ch::projects::2"}], "callidentifier":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Virkapäätöksiin liittyvä yleiskustannusosuus KY"},"code":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"204684"},"collectedfrom":[{"key":"10|openaire____::6ac933301a3933c8a22ceebea7000326","value":"Academy of Finland"}],"currency":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"EUR"},"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"dateofcollection":"2019-01-25","dateoftransformation":"2022-02-08","duration":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0"},"ecarticle29_3":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"ecsc39":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"enddate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2002-12-31"},"extraInfo":[],"fundedamount":3230.0,"fundingtree":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"<fundingtree><funder>\n         <id>aka_________::AKA</id>\n         <shortname>AKA</shortname>\n         <name>Academy of Finland</name>\n         <originalname>Academy of Finland</originalname>\n         <jurisdiction>FI</jurisdiction>\n      </funder></fundingtree>"}],"id":"40|aka_________::00f0012ac67a2f826f2e98dbdfd6b058","jsonextrainfo":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"{}"},"lastupdatetimestamp":1719997513126,"oamandatepublications":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"false"},"optional1":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"3,230 €"},"originalId":["aka_________::204684"],"pid":[],"startdate":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"2002-12-01"},"subjects":[],"title":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Tutkijan virkaan liittyvä yleiskustannusosuus suorituspaikalle"},"totalcost":0.0}
\ No newline at end of file

From 6c98d692159f992c5018b3cc0a29381468b4a296 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 17 Jul 2024 11:09:37 +0200
Subject: [PATCH 079/239] reverted changed contens under dhp-pace-core

---
 .../src/main/java/eu/dnetlib/pace/tree/CountryMatch.java    | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
index c02381983..96a87c455 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java
@@ -2,6 +2,7 @@
 package eu.dnetlib.pace.tree;
 
 import java.util.Map;
+import java.util.Set;
 
 import com.wcohen.ss.AbstractStringDistance;
 
@@ -12,8 +13,11 @@ import eu.dnetlib.pace.tree.support.ComparatorClass;
 @ComparatorClass("countryMatch")
 public class CountryMatch extends AbstractStringComparator {
 
+	private Map<String, String> params;
+
 	public CountryMatch(Map<String, String> params) {
 		super(params, new com.wcohen.ss.JaroWinkler());
+		this.params = params;
 	}
 
 	public CountryMatch(final double weight) {
@@ -26,6 +30,7 @@ public class CountryMatch extends AbstractStringComparator {
 
 	@Override
 	public double distance(final String a, final String b, final Config conf) {
+
 		if (a.isEmpty() || b.isEmpty()) {
 			return -1.0; // return -1 if a field is missing
 		}
@@ -45,4 +50,5 @@ public class CountryMatch extends AbstractStringComparator {
 	protected double normalize(final double d) {
 		return d;
 	}
+
 }

From db9c54c944d704f3e775093cda4f4b0b5574b970 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 17 Jul 2024 11:27:43 +0200
Subject: [PATCH 080/239] Revert "removed legacy actionmanager dependencies"

This reverts commit bb12d0b4df50919fea19d5a4d25dcb39718fdfb1.
---
 dhp-workflows/dhp-actionmanager/pom.xml       |    4 +-
 .../dnetlib/dhp/actionmanager/ISClient.java   |   29 +-
 dhp-workflows/dhp-swh/pom.xml                 |   43 +
 pom.xml                                       | 2029 +++++++++--------
 4 files changed, 1168 insertions(+), 937 deletions(-)

diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml
index 1ef55a060..ce13502b6 100644
--- a/dhp-workflows/dhp-actionmanager/pom.xml
+++ b/dhp-workflows/dhp-actionmanager/pom.xml
@@ -50,12 +50,11 @@
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
-<!--
+
         <dependency>
             <groupId>eu.dnetlib</groupId>
             <artifactId>dnet-actionmanager-api</artifactId>
         </dependency>
-
         <dependency>
             <groupId>eu.dnetlib</groupId>
             <artifactId>dnet-actionmanager-common</artifactId>
@@ -94,7 +93,6 @@
                 </exclusion>
             </exclusions>
         </dependency>
--->
 
     </dependencies>
 </project>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
index 24d50029c..088e618c7 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
+++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager;
 import java.io.Serializable;
 import java.io.StringReader;
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -21,14 +22,13 @@ import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 
+import eu.dnetlib.actionmanager.rmi.ActionManagerException;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 public class ISClient implements Serializable {
 
-	private static final long serialVersionUID = 4632443200867340872L;
-
 	private static final Logger log = LoggerFactory.getLogger(ISClient.class);
 
 	private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
@@ -65,7 +65,7 @@ public class ISClient implements Serializable {
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
 				.orElseThrow(() -> new IllegalStateException("empty set list"));
-		} catch (ISLookUpException e) {
+		} catch (ActionManagerException | ISLookUpException e) {
 			throw new IllegalStateException("unable to query ActionSets info from the IS");
 		}
 	}
@@ -89,18 +89,31 @@ public class ISClient implements Serializable {
 		return Joiner.on("/").join(basePath, t.getMiddle(), t.getRight());
 	}
 
-	private String getBasePathHDFS(ISLookUpService isLookup) throws ISLookUpException {
+	private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
 		return queryServiceProperty(isLookup, "basePath");
 	}
 
 	private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
-		throws ISLookUpException {
+		throws ActionManagerException {
 		final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
 			+ propertyName
 			+ "']/@value/string()";
 		log.debug("quering for service property: {}", q);
-
-		final List<String> value = isLookup.quickSearchProfile(q);
-		return Iterables.getOnlyElement(value);
+		try {
+			final List<String> value = isLookup.quickSearchProfile(q);
+			return Iterables.getOnlyElement(value);
+		} catch (ISLookUpException e) {
+			String msg = "Error accessing service profile, using query: " + q;
+			log.error(msg, e);
+			throw new ActionManagerException(msg, e);
+		} catch (NoSuchElementException e) {
+			String msg = "missing service property: " + propertyName;
+			log.error(msg, e);
+			throw new ActionManagerException(msg, e);
+		} catch (IllegalArgumentException e) {
+			String msg = "found more than one service property: " + propertyName;
+			log.error(msg, e);
+			throw new ActionManagerException(msg, e);
+		}
 	}
 }
diff --git a/dhp-workflows/dhp-swh/pom.xml b/dhp-workflows/dhp-swh/pom.xml
index ef9049b20..80fff4587 100644
--- a/dhp-workflows/dhp-swh/pom.xml
+++ b/dhp-workflows/dhp-swh/pom.xml
@@ -51,6 +51,49 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>eu.dnetlib</groupId>
+            <artifactId>dnet-actionmanager-common</artifactId>
+            <exclusions>
+                <exclusion>
+                    <groupId>eu.dnetlib</groupId>
+                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>saxonica</groupId>
+                    <artifactId>saxon-dom</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>jgrapht</groupId>
+                    <artifactId>jgrapht</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>net.sf.ehcache</groupId>
+                    <artifactId>ehcache</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.springframework</groupId>
+                    <artifactId>spring-test</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.apache.*</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>apache</groupId>
+                    <artifactId>*</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
diff --git a/pom.xml b/pom.xml
index 47b7d5f38..a5bc6cedd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,930 +1,1107 @@
 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
 
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>eu.dnetlib.dhp</groupId>
-	<artifactId>dhp</artifactId>
-	<version>1.2.5-SNAPSHOT</version>
-	<packaging>pom</packaging>
-
-	<licenses>
-		<license>
-			<name>GNU Affero General Public License v3.0 or later</name>
-			<url>https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText</url>
-			<distribution>repo</distribution>
-			<comments>This program is free software: you can redistribute it and/or modify it under the terms of the
-				GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the
-				License, or (at your option) any later version.</comments>
-		</license>
-	</licenses>
-
-	<modules>
-		<module>dhp-build</module>
-		<module>dhp-pace-core</module>
-		<module>dhp-common</module>
-		<module>dhp-workflows</module>
-	</modules>
-
-	<issueManagement>
-		<system>Redmine</system>
-		<url>https://support.openaire.eu/projects/openaire</url>
-	</issueManagement>
-
-	<ciManagement>
-		<system>jenkins</system>
-		<url>https://jenkins-dnet.d4science.org/</url>
-	</ciManagement>
-
-	<scm>
-		<connection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</connection>
-		<developerConnection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</developerConnection>
-		<url>https://code-repo.d4science.org/D-Net/dnet-hadoop/</url>
-		<tag>HEAD</tag>
-	</scm>
-
-	<description>This module is the root descriptor for the dnet-hadoop project</description>
-
-	<pluginRepositories>
-	</pluginRepositories>
-
-	<repositories>
-		<repository>
-			<id>dnet45-releases</id>
-			<name>D-Net 45 releases</name>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
-			<layout>default</layout>
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-			<releases>
-				<enabled>true</enabled>
-			</releases>
-		</repository>
-		<repository>
-			<id>dnet45-snapshots</id>
-			<name>D-Net 45 snapshots</name>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
-			<layout>default</layout>
-			<snapshots>
-				<enabled>true</enabled>
-			</snapshots>
-			<releases>
-				<enabled>false</enabled>
-			</releases>
-		</repository>
-		<repository>
-			<id>dnet45-bootstrap-snapshot</id>
-			<name>D-Net 45 Bootstrap Snapshot</name>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-snapshot/</url>
-			<releases>
-				<enabled>false</enabled>
-			</releases>
-			<snapshots>
-				<enabled>true</enabled>
-			</snapshots>
-			<layout>default</layout>
-		</repository>
-		<repository>
-			<id>dnet45-bootstrap-release</id>
-			<name>D-Net 45 Bootstrap Release</name>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-release/</url>
-			<releases>
-				<enabled>true</enabled>
-			</releases>
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-			<layout>default</layout>
-		</repository>
-		<repository>
-			<id>cloudera</id>
-			<name>Cloudera Repository</name>
-			<url>https://repository.cloudera.com/artifactory/cloudera-repos</url>
-			<releases>
-				<enabled>true</enabled>
-			</releases>
-			<snapshots>
-				<enabled>false</enabled>
-			</snapshots>
-		</repository>
-		<repository>
-			<id>dnet-deps</id>
-			<name>dnet-dependencies</name>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
-			<layout>default</layout>
-		</repository>
-		<repository>
-			<id>maven-restlet</id>
-			<name>Restlet repository</name>
-			<url>https://maven.restlet.talend.com</url>
-		</repository>
-		<repository>
-			<id>conjars</id>
-			<name>conjars</name>
-			<url>https://conjars.wensel.net/repo/</url>
-		</repository>
-	</repositories>
-
-	<dependencies>
-		<dependency>
-			<groupId>org.junit.jupiter</groupId>
-			<artifactId>junit-jupiter</artifactId>
-			<version>${junit-jupiter.version}</version>
-			<scope>test</scope>
-		</dependency>
-
-		<dependency>
-			<groupId>org.mockito</groupId>
-			<artifactId>mockito-core</artifactId>
-			<version>${mockito-core.version}</version>
-			<scope>test</scope>
-		</dependency>
-
-		<dependency>
-			<groupId>org.mockito</groupId>
-			<artifactId>mockito-junit-jupiter</artifactId>
-			<version>${mockito-core.version}</version>
-			<scope>test</scope>
-		</dependency>
-
-	</dependencies>
-
-	<dependencyManagement>
-		<dependencies>
-			<dependency>
-				<groupId>eu.dnetlib.dhp</groupId>
-				<artifactId>${dhp-schemas.artifact}</artifactId>
-				<version>${dhp-schemas.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.hadoop</groupId>
-				<artifactId>hadoop-hdfs</artifactId>
-				<version>${dhp.hadoop.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.hadoop</groupId>
-				<artifactId>hadoop-common</artifactId>
-				<version>${dhp.hadoop.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.hadoop</groupId>
-				<artifactId>hadoop-client</artifactId>
-				<version>${dhp.hadoop.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.hadoop</groupId>
-				<artifactId>hadoop-distcp</artifactId>
-				<version>${dhp.hadoop.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.spark</groupId>
-				<artifactId>spark-core_${scala.binary.version}</artifactId>
-				<version>${dhp.spark.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.spark</groupId>
-				<artifactId>spark-sql_${scala.binary.version}</artifactId>
-				<version>${dhp.spark.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.spark</groupId>
-				<artifactId>spark-graphx_${scala.binary.version}</artifactId>
-				<version>${dhp.spark.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.spark</groupId>
-				<artifactId>spark-hive_${scala.binary.version}</artifactId>
-				<version>${dhp.spark.version}</version>
-				<scope>test</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>org.slf4j</groupId>
-				<artifactId>jcl-over-slf4j</artifactId>
-				<version>1.7.25</version>
-				<scope>provided</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>org.apache.commons</groupId>
-				<artifactId>commons-lang3</artifactId>
-				<version>${dhp.commons.lang.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>commons-validator</groupId>
-				<artifactId>commons-validator</artifactId>
-				<version>1.7</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.github.sisyphsu</groupId>
-				<artifactId>dateparser</artifactId>
-				<version>1.0.7</version>
-			</dependency>
-
-			<dependency>
-				<groupId>me.xuender</groupId>
-				<artifactId>unidecode</artifactId>
-				<version>0.0.7</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.google.guava</groupId>
-				<artifactId>guava</artifactId>
-				<version>${dhp.guava.version}</version>
-			</dependency>
-
-
-			<dependency>
-				<groupId>commons-codec</groupId>
-				<artifactId>commons-codec</artifactId>
-				<version>1.9</version>
-			</dependency>
-
-			<dependency>
-				<groupId>commons-io</groupId>
-				<artifactId>commons-io</artifactId>
-				<version>2.4</version>
-			</dependency>
-
-			<dependency>
-				<groupId>commons-cli</groupId>
-				<artifactId>commons-cli</artifactId>
-				<version>1.2</version>
-				<scope>provided</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>net.sf.saxon</groupId>
-				<artifactId>Saxon-HE</artifactId>
-				<version>9.9.1-6</version>
-			</dependency>
-
-			<dependency>
-				<groupId>dom4j</groupId>
-				<artifactId>dom4j</artifactId>
-				<version>1.6.1</version>
-			</dependency>
-
-			<dependency>
-				<groupId>xml-apis</groupId>
-				<artifactId>xml-apis</artifactId>
-				<version>1.4.01</version>
-			</dependency>
-
-			<dependency>
-				<groupId>jaxen</groupId>
-				<artifactId>jaxen</artifactId>
-				<version>1.1.6</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.mycila.xmltool</groupId>
-				<artifactId>xmltool</artifactId>
-				<version>3.3</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.apache.solr</groupId>
-				<artifactId>solr-solrj</artifactId>
-				<version>${solr.version}</version>
-				<exclusions>
-					<exclusion>
-						<artifactId>*</artifactId>
-						<groupId>*</groupId>
-					</exclusion>
-				</exclusions>
-			</dependency>
-			<dependency>
-				<groupId>com.lucidworks.spark</groupId>
-				<artifactId>spark-solr</artifactId>
-				<version>${sparksolr.version}</version>
-				<exclusions>
-					<exclusion>
-						<artifactId>*</artifactId>
-						<groupId>*</groupId>
-					</exclusion>
-				</exclusions>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.solr</groupId>
-				<artifactId>solr-test-framework</artifactId>
-				<version>${solr.version}</version>
-				<scope>test</scope>
-			</dependency>
-			<dependency>
-				<groupId>io.dropwizard.metrics</groupId>
-				<artifactId>metrics-core</artifactId>
-				<version>3.2.6</version>
-				<scope>test</scope>
-			</dependency>
-
-
-			<dependency>
-				<groupId>org.apache.httpcomponents</groupId>
-				<artifactId>httpclient</artifactId>
-				<version>${org.apache.httpcomponents.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.httpcomponents</groupId>
-				<artifactId>httpmime</artifactId>
-				<version>${org.apache.httpcomponents.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>org.noggit</groupId>
-				<artifactId>noggit</artifactId>
-				<version>0.8</version>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.zookeeper</groupId>
-				<artifactId>zookeeper</artifactId>
-				<version>3.4.11</version>
-			</dependency>
-
-			<dependency>
-				<groupId>net.schmizz</groupId>
-				<artifactId>sshj</artifactId>
-				<version>0.10.0</version>
-				<scope>test</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>com.fasterxml.jackson.core</groupId>
-				<artifactId>jackson-core</artifactId>
-				<version>${dhp.jackson.version}</version>
-				<scope>provided</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>com.fasterxml.jackson.core</groupId>
-				<artifactId>jackson-annotations</artifactId>
-				<version>${dhp.jackson.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>com.fasterxml.jackson.core</groupId>
-				<artifactId>jackson-databind</artifactId>
-				<version>${dhp.jackson.version}</version>
-				<scope>provided</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>eu.dnetlib</groupId>
-				<artifactId>cnr-rmi-api</artifactId>
-				<version>${cnr-rmi-api.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>eu.dnetlib.dhp</groupId>
-				<artifactId>dnet-openaire-broker-common</artifactId>
-				<version>${dnet-openaire-broker-common.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.apache.cxf</groupId>
-				<artifactId>cxf-rt-transports-http</artifactId>
-				<version>3.1.5</version>
-			</dependency>
-			<dependency>
-				<groupId>javax.persistence</groupId>
-				<artifactId>javax.persistence-api</artifactId>
-				<version>2.2</version>
-				<scope>provided</scope>
-			</dependency>
-
-			<dependency>
-				<groupId>com.jayway.jsonpath</groupId>
-				<artifactId>json-path</artifactId>
-				<version>2.4.0</version>
-			</dependency>
-			<dependency>
-				<groupId>com.arakelian</groupId>
-				<artifactId>java-jq</artifactId>
-				<version>0.10.1</version>
-			</dependency>
-			<dependency>
-				<groupId>edu.cmu</groupId>
-				<artifactId>secondstring</artifactId>
-				<version>1.0.0</version>
-			</dependency>
-			<dependency>
-				<groupId>org.mongodb</groupId>
-				<artifactId>mongo-java-driver</artifactId>
-				<version>${mongodb.driver.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>io.fares.junit.mongodb</groupId>
-				<artifactId>mongodb-junit-test</artifactId>
-				<version>1.1.0</version>
-			</dependency>
-			<dependency>
-				<groupId>org.postgresql</groupId>
-				<artifactId>postgresql</artifactId>
-				<version>42.2.10</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.antlr</groupId>
-				<artifactId>stringtemplate</artifactId>
-				<version>3.2.1</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.antlr</groupId>
-				<artifactId>ST4</artifactId>
-				<version>4.3.4</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.ximpleware</groupId>
-				<artifactId>vtd-xml</artifactId>
-				<version>${vtd.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.elasticsearch</groupId>
-				<artifactId>elasticsearch-hadoop</artifactId>
-				<version>7.6.0</version>
-			</dependency>
-
-
-			<dependency>
-				<groupId>org.apache.oozie</groupId>
-				<artifactId>oozie-client</artifactId>
-				<version>${dhp.oozie.version}</version>
-				<scope>provided</scope>
-				<exclusions>
-					<!-- conflicts -->
-					<exclusion>
-						<artifactId>slf4j-simple</artifactId>
-						<groupId>org.slf4j</groupId>
-					</exclusion>
-				</exclusions>
-			</dependency>
-
-
-			<dependency>
-				<groupId>com.squareup.okhttp3</groupId>
-				<artifactId>okhttp</artifactId>
-				<version>${okhttp.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.apache.commons</groupId>
-				<artifactId>commons-compress</artifactId>
-				<version>${common.compress.version}</version>
-			</dependency>
-
-			<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
-			<dependency>
-				<groupId>org.apache.commons</groupId>
-				<artifactId>commons-csv</artifactId>
-				<version>${common.csv.version}</version>
-			</dependency>
-
-
-			<!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
-			<dependency>
-				<groupId>org.apache.poi</groupId>
-				<artifactId>poi-ooxml</artifactId>
-				<version>${apache.poi.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.json</groupId>
-				<artifactId>json</artifactId>
-				<version>20180813</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.json4s</groupId>
-				<artifactId>json4s-jackson_${scala.binary.version}</artifactId>
-				<version>${json4s.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.github.victools</groupId>
-				<artifactId>jsonschema-generator</artifactId>
-				<version>${jsonschemagenerator.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.apache.commons</groupId>
-				<artifactId>commons-text</artifactId>
-				<version>${common.text.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.opencsv</groupId>
-				<artifactId>opencsv</artifactId>
-				<version>5.5</version>
-			</dependency>
-			<dependency>
-				<groupId>io.github.classgraph</groupId>
-				<artifactId>classgraph</artifactId>
-				<version>4.8.71</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.fasterxml.jackson.dataformat</groupId>
-				<artifactId>jackson-dataformat-xml</artifactId>
-				<version>${jackson.version}</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>com.fasterxml.jackson.module</groupId>
-				<artifactId>jackson-module-jsonSchema</artifactId>
-				<version>${jackson.version}</version>
-				<scope>provided</scope>
-			</dependency>
-
-
-			<dependency>
-				<groupId>org.apache.commons</groupId>
-				<artifactId>commons-math3</artifactId>
-				<version>3.6.1</version>
-			</dependency>
-
-
-			<dependency>
-				<groupId>com.google.code.gson</groupId>
-				<artifactId>gson</artifactId>
-				<version>${google.gson.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>commons-collections</groupId>
-				<artifactId>commons-collections</artifactId>
-				<version>${commons.collections.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>commons-logging</groupId>
-				<artifactId>commons-logging</artifactId>
-				<version>${commons.logging.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.reflections</groupId>
-				<artifactId>reflections</artifactId>
-				<version>0.9.10</version>
-			</dependency>
-
-			<dependency>
-				<groupId>org.scala-lang</groupId>
-				<artifactId>scala-library</artifactId>
-				<version>${scala.version}</version>
-			</dependency>
-
-			<dependency>
-				<groupId>com.ibm.icu</groupId>
-				<artifactId>icu4j</artifactId>
-				<version>70.1</version>
-			</dependency>
-		</dependencies>
-	</dependencyManagement>
-
-	<build>
-		<directory>target</directory>
-		<outputDirectory>target/classes</outputDirectory>
-		<finalName>${project.artifactId}-${project.version}</finalName>
-		<testOutputDirectory>target/test-classes</testOutputDirectory>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-plugin-plugin</artifactId>
-					<version>3.3</version>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-project-info-reports-plugin</artifactId>
-					<version>3.0.0</version>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-site-plugin</artifactId>
-					<version>3.9.1</version>
-					<configuration>
-						<skip>${dhp.site.skip}</skip>
-					</configuration>
-				</plugin>
-
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<version>${maven.compiler.plugin.version}</version>
-					<configuration>
-						<source>1.8</source>
-						<target>1.8</target>
-						<encoding>${project.build.sourceEncoding}</encoding>
-					</configuration>
-				</plugin>
-
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-jar-plugin</artifactId>
-					<version>3.0.2</version>
-				</plugin>
-
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-source-plugin</artifactId>
-					<version>3.0.1</version>
-					<executions>
-						<execution>
-							<id>attach-sources</id>
-							<phase>verify</phase>
-							<goals>
-								<goal>jar-no-fork</goal>
-							</goals>
-						</execution>
-					</executions>
-				</plugin>
-
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-surefire-plugin</artifactId>
-					<version>3.0.0-M4</version>
-					<configuration>
-						<redirectTestOutputToFile>true</redirectTestOutputToFile>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-javadoc-plugin</artifactId>
-					<version>3.2.0</version>
-					<configuration>
-						<detectLinks>true</detectLinks>
-						<doclint>none</doclint>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-dependency-plugin</artifactId>
-					<version>3.6.0</version>
-				</plugin>
-
-				<plugin>
-					<groupId>net.revelc.code.formatter</groupId>
-					<artifactId>formatter-maven-plugin</artifactId>
-					<version>2.11.0</version>
-					<dependencies>
-						<dependency>
-							<groupId>eu.dnetlib.dhp</groupId>
-							<artifactId>dhp-code-style</artifactId>
-							<version>${project.version}</version>
-						</dependency>
-					</dependencies>
-				</plugin>
-				<plugin>
-					<groupId>org.antipathy</groupId>
-					<artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
-					<version>1.0.1640073709.733712b</version>
-					<dependencies>
-						<dependency>
-							<groupId>eu.dnetlib.dhp</groupId>
-							<artifactId>dhp-code-style</artifactId>
-							<version>${project.version}</version>
-						</dependency>
-					</dependencies>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-site-plugin</artifactId>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-project-info-reports-plugin</artifactId>
-			</plugin>
-			<plugin>
-				<groupId>net.revelc.code.formatter</groupId>
-				<artifactId>formatter-maven-plugin</artifactId>
-				<executions>
-					<execution>
-						<goals>
-							<goal>format</goal>
-						</goals>
-						<configuration>
-							<configFile>eclipse/formatter_dnet.xml</configFile>
-						</configuration>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>net.revelc.code</groupId>
-				<artifactId>impsort-maven-plugin</artifactId>
-				<version>1.4.1</version>
-				<configuration>
-					<groups>java.,javax.,org.,com.</groups>
-					<staticGroups>java,*</staticGroups>
-					<excludes>
-						<exclude>**/thrift/*.java</exclude>
-					</excludes>
-				</configuration>
-				<executions>
-					<execution>
-						<id>sort-imports</id>
-						<goals>
-							<goal>sort</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.antipathy</groupId>
-				<artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
-				<configuration>
-					<configLocation>https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf</configLocation>
-					<skipTestSources>false</skipTestSources>
-					<skipSources>false</skipSources>
-					<sourceDirectories>
-						<param>${project.basedir}/src/main/scala</param>
-					</sourceDirectories>
-					<testSourceDirectories>
-						<param>${project.basedir}/src/test/scala</param>
-					</testSourceDirectories>
-					<validateOnly>false</validateOnly>
-					<onlyChangedFiles>false</onlyChangedFiles>
-					<branch>: git rev-parse --abbrev-ref HEAD</branch>
-					<useSpecifiedRepositories>false</useSpecifiedRepositories>
-				</configuration>
-				<executions>
-					<execution>
-						<phase>validate</phase>
-						<goals>
-							<goal>format</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-release-plugin</artifactId>
-				<version>2.5.3</version>
-			</plugin>
-			<plugin>
-				<groupId>org.jacoco</groupId>
-				<artifactId>jacoco-maven-plugin</artifactId>
-				<version>0.7.9</version>
-				<configuration>
-					<excludes>
-						<exclude>**/schemas/*</exclude>
-						<exclude>**/com/cloudera/**/*</exclude>
-						<exclude>**/org/apache/avro/io/**/*</exclude>
-					</excludes>
-				</configuration>
-				<executions>
-					<execution>
-						<id>default-prepare-agent</id>
-						<goals>
-							<goal>prepare-agent</goal>
-						</goals>
-					</execution>
-					<execution>
-						<id>default-report</id>
-						<phase>prepare-package</phase>
-						<goals>
-							<goal>report</goal>
-						</goals>
-					</execution>
-				</executions>
-			</plugin>
-
-		</plugins>
-
-		<extensions>
-			<extension>
-				<groupId>org.apache.maven.wagon</groupId>
-				<artifactId>wagon-ssh</artifactId>
-				<version>2.10</version>
-			</extension>
-		</extensions>
-	</build>
-	<distributionManagement>
-		<snapshotRepository>
-			<id>dnet45-snapshots</id>
-			<name>DNet45 Snapshots</name>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
-			<layout>default</layout>
-		</snapshotRepository>
-		<repository>
-			<id>dnet45-releases</id>
-			<url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
-		</repository>
-		<site>
-			<id>DHPSite</id>
-			<url>${dhp.site.stage.path}/</url>
-		</site>
-	</distributionManagement>
-	<reporting>
-		<plugins>
-			<plugin>
-				<groupId>org.apache.maven.plugins</groupId>
-				<artifactId>maven-javadoc-plugin</artifactId>
-				<configuration>
-					<detectLinks>true</detectLinks>
-					<doclint>none</doclint>
-				</configuration>
-			</plugin>
-		</plugins>
-	</reporting>
-
-	<properties>
-		<dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
-		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-		<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
-		<maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
-		<maven.compiler.source>1.8</maven.compiler.source>
-		<maven.compiler.target>1.8</maven.compiler.target>
-		<maven.failsave.plugin.version>2.22.2</maven.failsave.plugin.version>
-		<properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
-		<dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
-		<dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
-		<dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
-		<dhp-schemas.artifact>dhp-schemas</dhp-schemas.artifact>
-		<sparksolr.version>3.6.0</sparksolr.version>
-		<dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
-		<dhp.jackson.version>2.9.6</dhp.jackson.version>
-		<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
-		<dhp.site.skip>true</dhp.site.skip>
-		<dhp.guava.version>11.0.2</dhp.guava.version>
-		<scala.version>2.11.12</scala.version>
-		<scala.binary.version>2.11</scala.binary.version>
-		<scala-xml.version>1.3.0</scala-xml.version>
-		<junit-jupiter.version>5.6.1</junit-jupiter.version>
-		<mockito-core.version>3.3.3</mockito-core.version>
-		<mongodb.driver.version>3.4.2</mongodb.driver.version>
-		<vtd.version>[2.12,3.0)</vtd.version>
-		<dhp-schemas.version>[6.1.3]</dhp-schemas.version>
-		<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
-		<cnr-rmi-api.version>[2.6.1]</cnr-rmi-api.version>
-		<solr.version>7.5.0</solr.version>
-		<okhttp.version>4.7.2</okhttp.version>
-		<common.compress.version>1.20</common.compress.version>
-		<json4s.version>3.5.3</json4s.version>
-		<jsonschemagenerator.version>4.13.0</jsonschemagenerator.version>
-		<common.csv.version>1.8</common.csv.version>
-		<apache.poi.version>4.1.2</apache.poi.version>
-		<common.text.version>1.8</common.text.version>
-		<org.apache.httpcomponents.version>4.5.3</org.apache.httpcomponents.version>
-		<net.alchim31.maven.version>4.0.1</net.alchim31.maven.version>
-		<google.gson.version>2.2.2</google.gson.version>
-		<commons.logging.version>1.1.3</commons.logging.version>
-		<commons.collections.version>3.2.1</commons.collections.version>
-	</properties>
-
-	<!-- Build with scala 12 and Spark 3.4 -->
-	<profiles>
-		<profile>
-			<id>scala-2.12</id>
-			<properties>
-				<scala.binary.version>2.12</scala.binary.version>
-				<scala.version>2.12.18</scala.version>
-				<!-- scala-xml.version>2.1.0</scala-xml.version -->
-
-
-				<sparksolr.version>4.0.2</sparksolr.version>
-				<dhp.spark.version>3.4.1</dhp.spark.version>
-				<dhp.jackson.version>2.14.2</dhp.jackson.version>
-				<dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
-				<json4s.version>3.7.0-M11</json4s.version>
-				<net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
-
-				<!--
-				<dhp-schemas.artifact>dhp-schemas_${scala.binary.version}</dhp-schemas.artifact>
-				<dhp-schemas.version>3.17.2-SNAPSHOT</dhp-schemas.version>
-				 -->
-			</properties>
-		</profile>
-
-		<!-- Activate ARM-compatible snappy dependency on new Silicon Macs -->
-		<profile>
-			<id>arm-silicon-mac</id>
-			<activation>
-				<os>
-					<arch>aarch64</arch>
-					<family>mac</family>
-				</os>
-			</activation>
-			<dependencyManagement>
-				<dependencies>
-					<dependency>
-						<groupId>org.xerial.snappy</groupId>
-						<artifactId>snappy-java</artifactId>
-						<version>1.1.8.4</version>
-					</dependency>
-				</dependencies>
-			</dependencyManagement>
-		</profile>
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>eu.dnetlib.dhp</groupId>
+    <artifactId>dhp</artifactId>
+    <version>1.2.5-SNAPSHOT</version>
+    <packaging>pom</packaging>
+
+    <licenses>
+        <license>
+            <name>GNU Affero General Public License v3.0 or later</name>
+            <url>https://spdx.org/licenses/AGPL-3.0-or-later.html#licenseText</url>
+            <distribution>repo</distribution>
+            <comments>This program is free software: you can redistribute it and/or modify it under the terms of the
+                GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the
+                License, or (at your option) any later version.
+            </comments>
+        </license>
+    </licenses>
+
+    <modules>
+        <module>dhp-build</module>
+        <module>dhp-pace-core</module>
+        <module>dhp-common</module>
+        <module>dhp-workflows</module>
+        <module>dhp-shade-package</module>
+    </modules>
+
+    <issueManagement>
+        <system>Redmine</system>
+        <url>https://support.openaire.eu/projects/openaire</url>
+    </issueManagement>
+
+    <ciManagement>
+        <system>jenkins</system>
+        <url>https://jenkins-dnet.d4science.org/</url>
+    </ciManagement>
+
+    <scm>
+        <connection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</connection>
+        <developerConnection>scm:git:gitea@code-repo.d4science.org:D-Net/dnet-hadoop.git</developerConnection>
+        <url>https://code-repo.d4science.org/D-Net/dnet-hadoop/</url>
+        <tag>HEAD</tag>
+    </scm>
+
+    <description>This module is the root descriptor for the dnet-hadoop project</description>
+
+    <pluginRepositories>
+    </pluginRepositories>
+
+    <repositories>
+
+        <repository>
+            <id>Openaire-third-parties-snaphot</id>
+            <name>Openaire third parties Snapshot</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/Openaire-third-parties-snaphot/</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+        </repository>
+
+        <repository>
+            <id>dnet45-releases</id>
+            <name>D-Net 45 releases</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
+            <layout>default</layout>
+            <snapshots>
+                <enabled>false</enabled>
+            </snapshots>
+            <releases>
+                <enabled>true</enabled>
+            </releases>
+        </repository>
+        <repository>
+            <id>dnet45-snapshots</id>
+            <name>D-Net 45 snapshots</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
+            <layout>default</layout>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+        </repository>
+        <repository>
+            <id>dnet45-bootstrap-snapshot</id>
+            <name>D-Net 45 Bootstrap Snapshot</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-snapshot/</url>
+            <releases>
+                <enabled>false</enabled>
+            </releases>
+            <snapshots>
+                <enabled>true</enabled>
+            </snapshots>
+            <layout>default</layout>
+        </repository>
+        <repository>
+            <id>dnet45-bootstrap-release</id>
+            <name>D-Net 45 Bootstrap Release</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-bootstrap-release/</url>
+            <releases>
+                <enabled>true</enabled>
+            </releases>
+            <snapshots>
+                <enabled>false</enabled>
+            </snapshots>
+            <layout>default</layout>
+        </repository>
+        <repository>
+            <id>cloudera</id>
+            <name>Cloudera Repository</name>
+            <url>https://repository.cloudera.com/artifactory/cloudera-repos</url>
+            <releases>
+                <enabled>true</enabled>
+            </releases>
+            <snapshots>
+                <enabled>false</enabled>
+            </snapshots>
+        </repository>
+        <repository>
+            <id>dnet-deps</id>
+            <name>dnet-dependencies</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
+            <layout>default</layout>
+        </repository>
+        <repository>
+            <id>maven-restlet</id>
+            <name>Restlet repository</name>
+            <url>https://maven.restlet.talend.com</url>
+        </repository>
+        <repository>
+            <id>conjars</id>
+            <name>conjars</name>
+            <url>https://conjars.wensel.net/repo/</url>
+        </repository>
+    </repositories>
+
+    <dependencies>
+        <!-- Quick FIX not to remove lombok everywhere -->
+        <dependency>
+            <groupId>org.projectlombok</groupId>
+            <artifactId>lombok</artifactId>
+            <version>1.18.28</version>
+            <scope>provided</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>${junit-jupiter.version}</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
+            <version>${mockito-core.version}</version>
+            <scope>test</scope>
+        </dependency>
+
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-junit-jupiter</artifactId>
+            <version>${mockito-core.version}</version>
+            <scope>test</scope>
+        </dependency>
+
+    </dependencies>
+
+    <dependencyManagement>
+        <dependencies>
+            <dependency>
+                <groupId>eu.dnetlib.dhp</groupId>
+                <artifactId>dhp-schemas</artifactId>
+                <version>${dhp-schemas.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.hadoop</groupId>
+                <artifactId>hadoop-hdfs</artifactId>
+                <version>${dhp.hadoop.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.hadoop</groupId>
+                <artifactId>hadoop-common</artifactId>
+                <version>${dhp.hadoop.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.hadoop</groupId>
+                <artifactId>hadoop-client</artifactId>
+                <version>${dhp.hadoop.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.hadoop</groupId>
+                <artifactId>hadoop-distcp</artifactId>
+                <version>${dhp.hadoop.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.spark</groupId>
+                <artifactId>spark-core_${scala.binary.version}</artifactId>
+                <version>${dhp.spark.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.spark</groupId>
+                <artifactId>spark-sql_${scala.binary.version}</artifactId>
+                <version>${dhp.spark.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.spark</groupId>
+                <artifactId>spark-graphx_${scala.binary.version}</artifactId>
+                <version>${dhp.spark.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.spark</groupId>
+                <artifactId>spark-hive_${scala.binary.version}</artifactId>
+                <version>${dhp.spark.version}</version>
+                <scope>test</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>slf4j-api</artifactId>
+                <version>${org.slf4j.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>slf4j-log4j12</artifactId>
+                <version>${org.slf4j.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.slf4j</groupId>
+                <artifactId>jcl-over-slf4j</artifactId>
+                <version>${org.slf4j.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-slf4j2-impl</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-api</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-core</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+            <dependency>
+                <!-- API bridge between log4j 1 and 2 -->
+                <groupId>org.apache.logging.log4j</groupId>
+                <artifactId>log4j-1.2-api</artifactId>
+                <version>${log4j.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-lang3</artifactId>
+                <version>${dhp.commons.lang.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-beanutils</artifactId>
+                <version>${commons-beanutils.version}</version>
+            </dependency>
+
+
+            <dependency>
+                <groupId>commons-validator</groupId>
+                <artifactId>commons-validator</artifactId>
+                <version>${commons-validator.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.github.sisyphsu</groupId>
+                <artifactId>dateparser</artifactId>
+                <version>${dateparser.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>me.xuender</groupId>
+                <artifactId>unidecode</artifactId>
+                <version>${unidecode.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.google.guava</groupId>
+                <artifactId>guava</artifactId>
+                <version>${dhp.guava.version}</version>
+            </dependency>
+
+
+            <dependency>
+                <groupId>commons-codec</groupId>
+                <artifactId>commons-codec</artifactId>
+                <version>${commons-codec.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>commons-io</groupId>
+                <artifactId>commons-io</artifactId>
+                <version>${commons-io.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>commons-cli</groupId>
+                <artifactId>commons-cli</artifactId>
+                <version>1.2</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>net.sf.saxon</groupId>
+                <artifactId>Saxon-HE</artifactId>
+                <version>9.9.1-6</version>
+            </dependency>
+
+            <dependency>
+                <groupId>dom4j</groupId>
+                <artifactId>dom4j</artifactId>
+                <version>1.6.1</version>
+            </dependency>
+
+            <dependency>
+                <groupId>xml-apis</groupId>
+                <artifactId>xml-apis</artifactId>
+                <version>1.4.01</version>
+            </dependency>
+
+            <dependency>
+                <groupId>jaxen</groupId>
+                <artifactId>jaxen</artifactId>
+                <version>1.1.6</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.mycila.xmltool</groupId>
+                <artifactId>xmltool</artifactId>
+                <version>3.3</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.solr</groupId>
+                <artifactId>solr-solrj</artifactId>
+                <version>${solr.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <artifactId>*</artifactId>
+                        <groupId>*</groupId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+            <dependency>
+                <groupId>com.lucidworks.spark</groupId>
+                <artifactId>spark-solr</artifactId>
+                <version>${sparksolr.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <artifactId>*</artifactId>
+                        <groupId>*</groupId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.solr</groupId>
+                <artifactId>solr-test-framework</artifactId>
+                <version>${solr.version}</version>
+                <scope>test</scope>
+            </dependency>
+            <dependency>
+                <groupId>io.dropwizard.metrics</groupId>
+                <artifactId>metrics-core</artifactId>
+                <version>3.2.6</version>
+                <scope>test</scope>
+            </dependency>
+
+
+            <dependency>
+                <groupId>org.apache.httpcomponents</groupId>
+                <artifactId>httpclient</artifactId>
+                <version>${org.apache.httpcomponents.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.httpcomponents</groupId>
+                <artifactId>httpmime</artifactId>
+                <version>${org.apache.httpcomponents.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.noggit</groupId>
+                <artifactId>noggit</artifactId>
+                <version>0.8</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.zookeeper</groupId>
+                <artifactId>zookeeper</artifactId>
+                <version>${zookeeper.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>net.schmizz</groupId>
+                <artifactId>sshj</artifactId>
+                <version>0.10.0</version>
+                <scope>test</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-core</artifactId>
+                <version>${dhp.jackson.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-annotations</artifactId>
+                <version>${dhp.jackson.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.core</groupId>
+                <artifactId>jackson-databind</artifactId>
+                <version>${dhp.jackson.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>eu.dnetlib</groupId>
+                <artifactId>dnet-actionmanager-common</artifactId>
+                <version>${dnet-actionmanager-common.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>org.apache.hadoop</groupId>
+                        <artifactId>hadoop-common</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+            <dependency>
+                <groupId>eu.dnetlib</groupId>
+                <artifactId>dnet-actionmanager-api</artifactId>
+                <version>${dnet-actionmanager-api.version}</version>
+                <exclusions>
+                    <exclusion>
+                        <groupId>eu.dnetlib</groupId>
+                        <artifactId>cnr-misc-utils</artifactId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+
+            <dependency>
+                <groupId>eu.dnetlib</groupId>
+                <artifactId>cnr-rmi-api</artifactId>
+                <version>${cnr-rmi-api.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>eu.dnetlib.dhp</groupId>
+                <artifactId>dnet-openaire-broker-common</artifactId>
+                <version>${dnet-openaire-broker-common.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.cxf</groupId>
+                <artifactId>cxf-rt-transports-http</artifactId>
+                <version>3.1.5</version>
+            </dependency>
+
+            <dependency>
+                <groupId>javax.persistence</groupId>
+                <artifactId>javax.persistence-api</artifactId>
+                <version>2.2</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>com.jayway.jsonpath</groupId>
+                <artifactId>json-path</artifactId>
+                <version>2.4.0</version>
+            </dependency>
+            <dependency>
+                <groupId>com.arakelian</groupId>
+                <artifactId>java-jq</artifactId>
+                <version>0.10.1</version>
+            </dependency>
+            <dependency>
+                <groupId>edu.cmu</groupId>
+                <artifactId>secondstring</artifactId>
+                <version>1.0.0</version>
+            </dependency>
+            <dependency>
+                <groupId>org.mongodb</groupId>
+                <artifactId>mongo-java-driver</artifactId>
+                <version>${mongodb.driver.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>io.fares.junit.mongodb</groupId>
+                <artifactId>mongodb-junit-test</artifactId>
+                <version>1.1.0</version>
+            </dependency>
+            <dependency>
+                <groupId>org.postgresql</groupId>
+                <artifactId>postgresql</artifactId>
+                <version>42.2.10</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.antlr</groupId>
+                <artifactId>stringtemplate</artifactId>
+                <version>3.2.1</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.antlr</groupId>
+                <artifactId>ST4</artifactId>
+                <version>4.3.4</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.ximpleware</groupId>
+                <artifactId>vtd-xml</artifactId>
+                <version>${vtd.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.elasticsearch</groupId>
+                <artifactId>elasticsearch-hadoop</artifactId>
+                <version>7.6.0</version>
+            </dependency>
+
+
+            <dependency>
+                <groupId>org.apache.oozie</groupId>
+                <artifactId>oozie-client</artifactId>
+                <version>${dhp.oozie.version}</version>
+                <scope>provided</scope>
+                <exclusions>
+                    <!-- conflicts -->
+                    <exclusion>
+                        <artifactId>slf4j-simple</artifactId>
+                        <groupId>org.slf4j</groupId>
+                    </exclusion>
+                </exclusions>
+            </dependency>
+
+
+            <dependency>
+                <groupId>com.squareup.okhttp3</groupId>
+                <artifactId>okhttp</artifactId>
+                <version>${okhttp.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-compress</artifactId>
+                <version>${common.compress.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-csv</artifactId>
+                <version>${common.csv.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>org.apache.poi</groupId>
+                <artifactId>poi-ooxml</artifactId>
+                <version>${apache.poi.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.json</groupId>
+                <artifactId>json</artifactId>
+                <version>20180813</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.json4s</groupId>
+                <artifactId>json4s-jackson_${scala.binary.version}</artifactId>
+                <version>${json4s.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.github.victools</groupId>
+                <artifactId>jsonschema-generator</artifactId>
+                <version>${jsonschemagenerator.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-text</artifactId>
+                <version>${common.text.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.opencsv</groupId>
+                <artifactId>opencsv</artifactId>
+                <version>5.5</version>
+            </dependency>
+            <dependency>
+                <groupId>io.github.classgraph</groupId>
+                <artifactId>classgraph</artifactId>
+                <version>4.8.71</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.fasterxml.jackson.dataformat</groupId>
+                <artifactId>jackson-dataformat-xml</artifactId>
+                <version>${jackson.version}</version>
+                <scope>provided</scope>
+            </dependency>
+            <dependency>
+                <groupId>com.fasterxml.jackson.module</groupId>
+                <artifactId>jackson-module-jsonSchema</artifactId>
+                <version>${jackson.version}</version>
+                <scope>provided</scope>
+            </dependency>
+
+            <dependency>
+                <groupId>org.apache.commons</groupId>
+                <artifactId>commons-math3</artifactId>
+                <version>3.6.1</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.google.code.gson</groupId>
+                <artifactId>gson</artifactId>
+                <version>${google.gson.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>commons-collections</groupId>
+                <artifactId>commons-collections</artifactId>
+                <version>${commons.collections.version}</version>
+            </dependency>
+            <dependency>
+                <groupId>commons-logging</groupId>
+                <artifactId>commons-logging</artifactId>
+                <version>${commons.logging.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.reflections</groupId>
+                <artifactId>reflections</artifactId>
+                <version>${reflections.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.scala-lang</groupId>
+                <artifactId>scala-library</artifactId>
+                <version>${scala.version}</version>
+            </dependency>
+
+            <dependency>
+                <groupId>com.ibm.icu</groupId>
+                <artifactId>icu4j</artifactId>
+                <version>70.1</version>
+            </dependency>
+
+            <dependency>
+                <groupId>org.javassist</groupId>
+                <artifactId>javassist</artifactId>
+                <version>${javassist.version}</version>
+            </dependency>
+        </dependencies>
+    </dependencyManagement>
+
+    <build>
+        <directory>target</directory>
+        <outputDirectory>target/classes</outputDirectory>
+        <finalName>${project.artifactId}-${project.version}</finalName>
+        <testOutputDirectory>target/test-classes</testOutputDirectory>
+        <pluginManagement>
+            <plugins>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-plugin-plugin</artifactId>
+                    <version>3.3</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-project-info-reports-plugin</artifactId>
+                    <version>3.0.0</version>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-site-plugin</artifactId>
+                    <version>3.9.1</version>
+                    <configuration>
+                        <skip>${dhp.site.skip}</skip>
+                    </configuration>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-compiler-plugin</artifactId>
+                    <version>${maven.compiler.plugin.version}</version>
+                    <configuration>
+                        <source>1.8</source>
+                        <target>1.8</target>
+                        <encoding>${project.build.sourceEncoding}</encoding>
+                    </configuration>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-jar-plugin</artifactId>
+                    <version>3.0.2</version>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-source-plugin</artifactId>
+                    <version>3.0.1</version>
+                    <executions>
+                        <execution>
+                            <id>attach-sources</id>
+                            <phase>verify</phase>
+                            <goals>
+                                <goal>jar-no-fork</goal>
+                            </goals>
+                        </execution>
+                    </executions>
+                </plugin>
+
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-surefire-plugin</artifactId>
+                    <version>3.0.0-M4</version>
+                    <configuration>
+                        <redirectTestOutputToFile>true</redirectTestOutputToFile>
+                        <trimStackTrace>false</trimStackTrace>
+                    </configuration>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-javadoc-plugin</artifactId>
+                    <version>3.2.0</version>
+                    <configuration>
+                        <detectLinks>true</detectLinks>
+                        <doclint>none</doclint>
+                    </configuration>
+                </plugin>
+                <plugin>
+                    <groupId>org.apache.maven.plugins</groupId>
+                    <artifactId>maven-dependency-plugin</artifactId>
+                    <version>3.6.0</version>
+                </plugin>
+
+                <plugin>
+                    <groupId>net.revelc.code.formatter</groupId>
+                    <artifactId>formatter-maven-plugin</artifactId>
+                    <version>2.11.0</version>
+                    <dependencies>
+                        <dependency>
+                            <groupId>eu.dnetlib.dhp</groupId>
+                            <artifactId>dhp-code-style</artifactId>
+                            <version>${project.version}</version>
+                        </dependency>
+                    </dependencies>
+                </plugin>
+                <plugin>
+                    <groupId>org.antipathy</groupId>
+                    <artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
+                    <version>1.0.1640073709.733712b</version>
+                    <dependencies>
+                        <dependency>
+                            <groupId>eu.dnetlib.dhp</groupId>
+                            <artifactId>dhp-code-style</artifactId>
+                            <version>${project.version}</version>
+                        </dependency>
+                    </dependencies>
+                </plugin>
+            </plugins>
+        </pluginManagement>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-site-plugin</artifactId>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-project-info-reports-plugin</artifactId>
+            </plugin>
+            <plugin>
+                <groupId>net.revelc.code.formatter</groupId>
+                <artifactId>formatter-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <goals>
+                            <goal>format</goal>
+                        </goals>
+                        <configuration>
+                            <configFile>eclipse/formatter_dnet.xml</configFile>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>net.revelc.code</groupId>
+                <artifactId>impsort-maven-plugin</artifactId>
+                <version>1.6.2</version>
+                <configuration>
+                    <groups>java.,javax.,org.,com.</groups>
+                    <staticGroups>java,*</staticGroups>
+                    <excludes>
+                        <exclude>**/thrift/*.java</exclude>
+                    </excludes>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>sort-imports</id>
+                        <goals>
+                            <goal>sort</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.antipathy</groupId>
+                <artifactId>mvn-scalafmt_${scala.binary.version}</artifactId>
+                <configuration>
+                    <configLocation>
+                        https://code-repo.d4science.org/D-Net/dnet-hadoop/raw/branch/beta/dhp-build/dhp-code-style/src/main/resources/scalafmt/scalafmt.conf
+                    </configLocation>
+                    <skipTestSources>false</skipTestSources>
+                    <skipSources>false</skipSources>
+                    <sourceDirectories>
+                        <param>${project.basedir}/src/main/scala</param>
+                    </sourceDirectories>
+                    <testSourceDirectories>
+                        <param>${project.basedir}/src/test/scala</param>
+                    </testSourceDirectories>
+                    <validateOnly>false</validateOnly>
+                    <onlyChangedFiles>false</onlyChangedFiles>
+                    <branch>: git rev-parse --abbrev-ref HEAD</branch>
+                    <useSpecifiedRepositories>false</useSpecifiedRepositories>
+                </configuration>
+                <executions>
+                    <execution>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>format</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-release-plugin</artifactId>
+                <version>2.5.3</version>
+            </plugin>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>0.8.10</version>
+                <configuration>
+                    <excludes>
+                        <exclude>**/schemas/*</exclude>
+                        <exclude>**/com/cloudera/**/*</exclude>
+                        <exclude>**/org/apache/avro/io/**/*</exclude>
+                    </excludes>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>default-prepare-agent</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                    <execution>
+                        <id>default-report</id>
+                        <phase>prepare-package</phase>
+                        <goals>
+                            <goal>report</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+        </plugins>
+
+        <extensions>
+            <extension>
+                <groupId>org.apache.maven.wagon</groupId>
+                <artifactId>wagon-ssh</artifactId>
+                <version>2.10</version>
+            </extension>
+        </extensions>
+    </build>
+    <distributionManagement>
+        <snapshotRepository>
+            <id>dnet45-snapshots</id>
+            <name>DNet45 Snapshots</name>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-snapshots</url>
+            <layout>default</layout>
+        </snapshotRepository>
+        <repository>
+            <id>dnet45-releases</id>
+            <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
+        </repository>
+        <site>
+            <id>DHPSite</id>
+            <url>${dhp.site.stage.path}/</url>
+        </site>
+    </distributionManagement>
+    <reporting>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-javadoc-plugin</artifactId>
+                <configuration>
+                    <detectLinks>true</detectLinks>
+                    <doclint>none</doclint>
+                </configuration>
+            </plugin>
+        </plugins>
+    </reporting>
+
+    <properties>
+        <dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+
+        <!-- scala version -->
+        <scala.version>2.11.12</scala.version>
+        <scala.binary.version>2.11</scala.binary.version>
+
+        <!-- plugin versions -->
+        <maven.compiler.plugin.version>3.6.0</maven.compiler.plugin.version>
+        <maven.failsave.plugin.version>2.22.2</maven.failsave.plugin.version>
+        <properties.maven.plugin.version>2.0.1</properties.maven.plugin.version>
+        <net.alchim31.maven.version>4.0.1</net.alchim31.maven.version>
+
+        <!-- dependency versions -->
+        <apache.poi.version>4.1.2</apache.poi.version>
+        <cnr-rmi-api.version>[2.6.1]</cnr-rmi-api.version>
+        <common.compress.version>1.20</common.compress.version>
+        <common.csv.version>1.8</common.csv.version>
+        <common.text.version>1.8</common.text.version>
+        <commons-beanutils.version>1.9.4</commons-beanutils.version>
+        <commons-codec.version>1.9</commons-codec.version>
+        <commons.collections.version>3.2.1</commons.collections.version>
+        <commons-io.version>2.4</commons-io.version>
+        <commons.logging.version>1.1.3</commons.logging.version>
+        <commons-validator.version>1.7</commons-validator.version>
+        <dateparser.version>1.0.7</dateparser.version>
+        <dhp-schemas.version>[6.1.4-SNAPSHOT]</dhp-schemas.version>
+        <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
+        <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
+        <dhp.guava.version>11.0.2</dhp.guava.version>
+        <dhp.hadoop.version>2.6.0-${dhp.cdh.version}</dhp.hadoop.version>
+        <dhp.jackson.version>2.9.6</dhp.jackson.version>
+        <dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
+        <dhp.site.skip>true</dhp.site.skip>
+        <dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
+        <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
+        <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
+        <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
+        <google.gson.version>2.2.2</google.gson.version>
+        <log4j.version>1.2.17</log4j.version>
+        <javassist.version>3.19.0-GA</javassist.version>
+        <json4s.version>3.5.3</json4s.version>
+        <jsonschemagenerator.version>4.13.0</jsonschemagenerator.version>
+        <junit-jupiter.version>5.6.1</junit-jupiter.version>
+        <mockito-core.version>3.3.3</mockito-core.version>
+        <mongodb.driver.version>3.4.2</mongodb.driver.version>
+        <okhttp.version>4.7.2</okhttp.version>
+        <org.apache.httpcomponents.version>4.5.3</org.apache.httpcomponents.version>
+        <org.slf4j.version>1.7.25</org.slf4j.version>
+        <reflections.version>0.9.10</reflections.version>
+        <scala-xml.version>1.3.0</scala-xml.version>
+        <solr.version>7.5.0</solr.version>
+        <sparksolr.version>3.6.0</sparksolr.version>
+        <unidecode.version>0.0.7</unidecode.version>
+        <vtd.version>[2.12,3.0)</vtd.version>
+        <zookeeper.version>3.4.6</zookeeper.version>
+    </properties>
+
+    <!-- Build with scala 12 and Spark 3.4 -->
+    <profiles>
+        <profile>
+            <id>spark-34</id>
+            <properties>
+                <scala.binary.version>2.12</scala.binary.version>
+                <scala.version>2.12.18</scala.version>
+                <scala-xml.version>1.3.0</scala-xml.version>
+
+                <!-- plugin versions -->
+                <net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
+
+                <!-- dependencies -->
+                <common.compress.version>1.22</common.compress.version>
+                <common.csv.version>1.8</common.csv.version>
+                <common.text.version>1.10.0</common.text.version>
+                <commons-beanutils.version>1.9.4</commons-beanutils.version>
+                <commons-codec.version>1.15</commons-codec.version>
+                <commons.collections.version>3.2.2</commons.collections.version>
+                <commons-io.version>2.11.0</commons-io.version>
+                <commons.logging.version>1.1.3</commons.logging.version>
+                <commons-validator.version>1.7</commons-validator.version>
+
+                <dhp.guava.version>14.0.1</dhp.guava.version>
+                <solr.version>8.11.0</solr.version>
+                <sparksolr.version>4.0.4</sparksolr.version>
+                <dhp.spark.version>3.4.2.openaire</dhp.spark.version>
+                <dhp.jackson.version>2.14.2</dhp.jackson.version>
+                <dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
+                <log4j.version>2.19.0</log4j.version>
+                <json4s.version>3.7.0-M11</json4s.version>
+                <javassist.version>3.25.0-GA</javassist.version>
+                <okhttp.version>4.10.0</okhttp.version>
+                <org.slf4j.version>2.0.6</org.slf4j.version>
+                <reflections.version>0.10.2</reflections.version>
+                <zookeeper.version>3.6.3</zookeeper.version>
+            </properties>
+        </profile>
+
+        <profile>
+            <id>spark-35</id>
+            <properties>
+                <scala.binary.version>2.12</scala.binary.version>
+                <scala.version>2.12.18</scala.version>
+                <scala-xml.version>1.3.0</scala-xml.version>
+
+                <!-- plugin versions -->
+                <net.alchim31.maven.version>4.8.1</net.alchim31.maven.version>
+
+                <!-- dependencies -->
+                <common.compress.version>1.23.0</common.compress.version>
+                <common.csv.version>1.8</common.csv.version>
+                <common.text.version>1.10.0</common.text.version>
+                <commons-beanutils.version>1.9.4</commons-beanutils.version>
+                <commons-codec.version>1.16.0</commons-codec.version>
+                <commons.collections.version>3.2.2</commons.collections.version>
+                <commons-io.version>2.13.0</commons-io.version>
+                <commons.logging.version>1.1.3</commons.logging.version>
+                <commons-validator.version>1.7</commons-validator.version>
+
+                <dhp.guava.version>14.0.1</dhp.guava.version>
+                <solr.version>8.11.0</solr.version>
+                <sparksolr.version>4.0.4</sparksolr.version>
+                <dhp.spark.version>3.5.1.openaire-SNAPSHOT</dhp.spark.version>
+                <dhp.jackson.version>2.15.2</dhp.jackson.version>
+                <dhp.commons.lang.version>3.12.0</dhp.commons.lang.version>
+                <log4j.version>2.20.0</log4j.version>
+                <json4s.version>3.7.0-M11</json4s.version>
+                <javassist.version>3.25.0-GA</javassist.version>
+                <okhttp.version>4.10.0</okhttp.version>
+                <org.slf4j.version>2.0.7</org.slf4j.version>
+                <reflections.version>0.10.2</reflections.version>
+                <zookeeper.version>3.6.3</zookeeper.version>
+            </properties>
+        </profile>
+
+        <profile>
+            <id>java11</id>
+            <activation>
+                <jdk>[11</jdk>
+            </activation>
+            <build>
+                <pluginManagement>
+                    <plugins>
+                        <plugin>
+                            <groupId>org.apache.maven.plugins</groupId>
+                            <artifactId>maven-surefire-plugin</artifactId>
+                            <version>3.0.0-M4</version>
+                            <configuration>
+                                <!-- only for java 11+ to run spark in tests -->
+                                <argLine>--add-opens=java.base/java.lang=ALL-UNNAMED
+                                    --add-opens=java.base/java.lang.invoke=ALL-UNNAMED
+                                    --add-opens=java.base/java.lang.reflect=ALL-UNNAMED
+                                    --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED
+                                    --add-opens=java.base/java.nio=ALL-UNNAMED
+                                    --add-opens=java.base/java.util=ALL-UNNAMED
+                                    --add-opens=java.base/java.util.concurrent=ALL-UNNAMED
+                                    --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED
+                                    --add-opens=java.base/sun.nio.ch=ALL-UNNAMED
+                                    --add-opens=java.base/sun.nio.cs=ALL-UNNAMED
+                                    --add-opens=java.base/sun.security.action=ALL-UNNAMED
+                                    --add-opens=java.base/sun.util.calendar=ALL-UNNAMED
+                                </argLine>
+                                <redirectTestOutputToFile>true</redirectTestOutputToFile>
+                                <trimStackTrace>false</trimStackTrace>
+                            </configuration>
+                        </plugin>
+                    </plugins>
+                </pluginManagement>
+            </build>
+        </profile>
 	</profiles>
 </project>
\ No newline at end of file

From 83327239de91fe0e32902c48cc8cf52bc7eb6433 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 17 Jul 2024 11:58:48 +0200
Subject: [PATCH 081/239] fixed pom definitions, bumped dependency version for
 the dhp-schema module, removed unnecessary dependencies

---
 .../pace/tree/support/TreeNodeStats.java      |  19 ++--
 .../pace/tree/support/TreeProcessor.java      |   5 +-
 .../clustering/ClusteringFunctionTest.java    |   2 +-
 .../pace/comparators/ComparatorTest.java      |   2 +-
 dhp-workflows/dhp-actionmanager/pom.xml       |  43 --------
 .../dnetlib/dhp/actionmanager/ISClient.java   |  27 ++---
 .../CreateActionSetFromWebEntries.java        |   1 -
 .../researchfi/ResearchFiCollectorPlugin.java |  10 +-
 .../plugin/researchfi/ResearchFiIterator.java |   1 +
 .../ResearchFiCollectorPluginTest.java        |   5 +-
 .../dhp/oa/dedup/DecisionTreeTest.java        | 100 +++++++++---------
 .../dhp/oa/dedup/jpath/JsonPathTest.java      |  15 +--
 .../model/ProvisionModelSupport.java          |   1 +
 dhp-workflows/dhp-swh/pom.xml                 |  43 --------
 pom.xml                                       |  27 +----
 15 files changed, 91 insertions(+), 210 deletions(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
index a210c06b2..f6b210a8c 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
@@ -25,10 +25,10 @@ public class TreeNodeStats implements Serializable {
 	}
 
 	public int fieldsCount() {
-		if(ignoreUndefined)
+		if (ignoreUndefined)
 			return this.results.size();
 		else
-			return this.results.size() - undefinedCount();	//do not count undefined
+			return this.results.size() - undefinedCount(); // do not count undefined
 	}
 
 	public int undefinedCount() {
@@ -87,20 +87,17 @@ public class TreeNodeStats implements Serializable {
 				if (fs.getResult() == -1) {
 					if (fs.isCountIfUndefined()) {
 						min = 0.0;
-					}
-					else {
+					} else {
 						min = -1;
 					}
-				}
-				else {
+				} else {
 					min = fs.getResult();
 				}
 			}
 		}
 		if (ignoreUndefined) {
-			return min==-1.0? 0.0 : min;
-		}
-		else {
+			return min == -1.0 ? 0.0 : min;
+		} else {
 			return min;
 		}
 	}
@@ -111,7 +108,7 @@ public class TreeNodeStats implements Serializable {
 			if (fieldStats.getResult() >= fieldStats.getThreshold())
 				return 1.0;
 		}
-		if (!ignoreUndefined && undefinedCount()>0){
+		if (!ignoreUndefined && undefinedCount() > 0) {
 			return -1.0;
 		} else {
 			return 0.0;
@@ -124,7 +121,7 @@ public class TreeNodeStats implements Serializable {
 
 			if (fieldStats.getResult() == -1) {
 				if (fieldStats.isCountIfUndefined())
-					return ignoreUndefined? 0.0 : -1.0;
+					return ignoreUndefined ? 0.0 : -1.0;
 			} else {
 				if (fieldStats.getResult() < fieldStats.getThreshold())
 					return 0.0;
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
index 8ae5aa591..28b3a82af 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
@@ -43,9 +43,9 @@ public class TreeProcessor {
 
 			TreeNodeStats stats = currentNode.evaluate(doc1, doc2, config);
 			treeStats.addNodeStats(nextNodeName, stats);
-			
+
 			double finalScore = stats.getFinalScore(currentNode.getAggregation());
-			if(finalScore == -1.0)
+			if (finalScore == -1.0)
 				nextNodeName = currentNode.getUndefined();
 			else if (finalScore >= currentNode.getThreshold()) {
 				nextNodeName = currentNode.getPositive();
@@ -53,7 +53,6 @@ public class TreeProcessor {
 				nextNodeName = currentNode.getNegative();
 			}
 
-
 		} while (MatchType.parse(nextNodeName) == MatchType.UNDEFINED);
 
 		treeStats.setResult(MatchType.parse(nextNodeName));
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
index 1f1827ab3..e62f742f8 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
@@ -3,12 +3,12 @@ package eu.dnetlib.pace.clustering;
 
 import java.util.Map;
 
-import com.mongodb.connection.Cluster;
 import org.junit.jupiter.api.BeforeAll;
 import org.junit.jupiter.api.Test;
 
 import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
+import com.mongodb.connection.Cluster;
 
 import eu.dnetlib.pace.AbstractPaceTest;
 import eu.dnetlib.pace.common.AbstractPaceFunctions;
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index fe0dca7f1..c008902c4 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -61,7 +61,7 @@ public class ComparatorTest extends AbstractPaceTest {
 		assertEquals(0.0, codeMatch.distance("testing1 key::1", "testing2 key::2", conf));
 
 		// both names with codes (1 same, 1 different)
-		assertEquals(0.5,codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
+		assertEquals(0.5, codeMatch.distance("key::1 key::2 testing1", "key::1 testing", conf));
 
 	}
 
diff --git a/dhp-workflows/dhp-actionmanager/pom.xml b/dhp-workflows/dhp-actionmanager/pom.xml
index ce13502b6..e0bba29d2 100644
--- a/dhp-workflows/dhp-actionmanager/pom.xml
+++ b/dhp-workflows/dhp-actionmanager/pom.xml
@@ -51,48 +51,5 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-common</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>eu.dnetlib</groupId>
-                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon-dom</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>jgrapht</groupId>
-                    <artifactId>jgrapht</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>net.sf.ehcache</groupId>
-                    <artifactId>ehcache</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.springframework</groupId>
-                    <artifactId>spring-test</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.*</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>apache</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
     </dependencies>
 </project>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
index 088e618c7..7ae2901e3 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
+++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java
@@ -4,7 +4,6 @@ package eu.dnetlib.dhp.actionmanager;
 import java.io.Serializable;
 import java.io.StringReader;
 import java.util.List;
-import java.util.NoSuchElementException;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -22,7 +21,6 @@ import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Sets;
 
-import eu.dnetlib.actionmanager.rmi.ActionManagerException;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -65,7 +63,7 @@ public class ISClient implements Serializable {
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
 				.orElseThrow(() -> new IllegalStateException("empty set list"));
-		} catch (ActionManagerException | ISLookUpException e) {
+		} catch (ISLookUpException e) {
 			throw new IllegalStateException("unable to query ActionSets info from the IS");
 		}
 	}
@@ -89,31 +87,18 @@ public class ISClient implements Serializable {
 		return Joiner.on("/").join(basePath, t.getMiddle(), t.getRight());
 	}
 
-	private String getBasePathHDFS(ISLookUpService isLookup) throws ActionManagerException {
+	private String getBasePathHDFS(ISLookUpService isLookup) throws ISLookUpException {
 		return queryServiceProperty(isLookup, "basePath");
 	}
 
 	private String queryServiceProperty(ISLookUpService isLookup, final String propertyName)
-		throws ActionManagerException {
+		throws ISLookUpException {
 		final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
 			+ propertyName
 			+ "']/@value/string()";
 		log.debug("quering for service property: {}", q);
-		try {
-			final List<String> value = isLookup.quickSearchProfile(q);
-			return Iterables.getOnlyElement(value);
-		} catch (ISLookUpException e) {
-			String msg = "Error accessing service profile, using query: " + q;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		} catch (NoSuchElementException e) {
-			String msg = "missing service property: " + propertyName;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		} catch (IllegalArgumentException e) {
-			String msg = "found more than one service property: " + propertyName;
-			log.error(msg, e);
-			throw new ActionManagerException(msg, e);
-		}
+
+		final List<String> value = isLookup.quickSearchProfile(q);
+		return Iterables.getOnlyElement(value);
 	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index f2a73889f..07668f53b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -106,7 +106,6 @@ public class CreateActionSetFromWebEntries implements Serializable {
 					+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
 				ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
 
-
 				return ret
 					.iterator();
 			}, Encoders.bean(Relation.class))
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java
index c5961c598..2603ecab1 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPlugin.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.researchfi;
 
 import java.util.ArrayList;
@@ -32,7 +33,7 @@ public class ResearchFiCollectorPlugin implements CollectorPlugin {
 
 	@Override
 	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report)
-			throws CollectorException {
+		throws CollectorException {
 
 		final String authUrl = api.getParams().get("auth_url");
 		final String clientId = api.getParams().get("auth_client_id");
@@ -45,7 +46,8 @@ public class ResearchFiCollectorPlugin implements CollectorPlugin {
 		return StreamSupport.stream(Spliterators.spliteratorUnknownSize(iter, Spliterator.ORDERED), false);
 	}
 
-	private String authenticate(final String authUrl, final String clientId, final String clientSecret) throws CollectorException {
+	private String authenticate(final String authUrl, final String clientId, final String clientSecret)
+		throws CollectorException {
 		try (final CloseableHttpClient client = HttpClients.createDefault()) {
 			final HttpPost req = new HttpPost(authUrl);
 			final List<NameValuePair> params = new ArrayList<>();
@@ -59,7 +61,9 @@ public class ResearchFiCollectorPlugin implements CollectorPlugin {
 				final String content = IOUtils.toString(response.getEntity().getContent());
 				final JSONObject obj = new JSONObject(content);
 				final String token = obj.getString("access_token");
-				if (StringUtils.isNotBlank(token)) { return token; }
+				if (StringUtils.isNotBlank(token)) {
+					return token;
+				}
 			}
 		} catch (final Throwable e) {
 			log.warn("Error obtaining access token", e);
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
index e08823c46..269a89f71 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.researchfi;
 
 import java.util.Iterator;
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java
index 47c77796b..3f715c2eb 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiCollectorPluginTest.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.researchfi;
 
 import java.util.HashSet;
@@ -23,7 +24,9 @@ public class ResearchFiCollectorPluginTest {
 		final ApiDescriptor api = new ApiDescriptor();
 		api.setBaseUrl("https://research.fi/api/rest/v1/funding-decisions?FunderName=AKA&FundingStartYearFrom=2022");
 		api.setProtocol("research_fi");
-		api.getParams().put("auth_url", "https://researchfi-auth.2.rahtiapp.fi/realms/publicapi/protocol/openid-connect/token");
+		api
+			.getParams()
+			.put("auth_url", "https://researchfi-auth.2.rahtiapp.fi/realms/publicapi/protocol/openid-connect/token");
 		api.getParams().put("auth_client_id", "");
 		api.getParams().put("auth_client_secret", "");
 
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java
index 28f2bfc66..6acc65e05 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DecisionTreeTest.java
@@ -3,81 +3,83 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import java.io.IOException;
 
-import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
-import eu.dnetlib.pace.tree.support.TreeProcessor;
-import eu.dnetlib.pace.tree.support.TreeStats;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.platform.commons.util.StringUtils;
 
+import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import eu.dnetlib.pace.config.DedupConfig;
 import eu.dnetlib.pace.model.SparkModel;
+import eu.dnetlib.pace.tree.support.TreeProcessor;
+import eu.dnetlib.pace.tree.support.TreeStats;
 
 class DecisionTreeTest {
 
-    @Test
-    void testJPath() throws IOException {
+	@Test
+	void testJPath() throws IOException {
 
-        DedupConfig conf = DedupConfig
-                .load(IOUtils.toString(getClass().getResourceAsStream("dedup_conf_organization.json")));
+		DedupConfig conf = DedupConfig
+			.load(IOUtils.toString(getClass().getResourceAsStream("dedup_conf_organization.json")));
 
-        final String org = IOUtils.toString(getClass().getResourceAsStream("organization.json"));
+		final String org = IOUtils.toString(getClass().getResourceAsStream("organization.json"));
 
-        Row row = SparkModel.apply(conf).rowFromJson(org);
+		Row row = SparkModel.apply(conf).rowFromJson(org);
 
-        System.out.println("row = " + row);
-        Assertions.assertNotNull(row);
-        Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
+		System.out.println("row = " + row);
+		Assertions.assertNotNull(row);
+		Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
 
-        System.out.println("row = " + row.getAs("countrytitle"));
-    }
+		System.out.println("row = " + row.getAs("countrytitle"));
+	}
 
-    @Test
-    void jsonToModelTest() throws IOException{
-        DedupConfig conf = DedupConfig
-                .load(IOUtils
-                        .toString(
-                                SparkOpenorgsDedupTest.class
-                                        .getResourceAsStream(
-                                                "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+	@Test
+	void jsonToModelTest() throws IOException {
+		DedupConfig conf = DedupConfig
+			.load(
+				IOUtils
+					.toString(
+						SparkOpenorgsDedupTest.class
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
 
-        final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
+		final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
 
-        Row row = SparkModel.apply(conf).rowFromJson(org);
-        // to check that the same parsing returns the same row
-        Row row1 = SparkModel.apply(conf).rowFromJson(org);
+		Row row = SparkModel.apply(conf).rowFromJson(org);
+		// to check that the same parsing returns the same row
+		Row row1 = SparkModel.apply(conf).rowFromJson(org);
 
-        Assertions.assertEquals(row, row1);
-        System.out.println("row = " + row);
-        Assertions.assertNotNull(row);
-        Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
-    }
+		Assertions.assertEquals(row, row1);
+		System.out.println("row = " + row);
+		Assertions.assertNotNull(row);
+		Assertions.assertTrue(StringUtils.isNotBlank(row.getAs("identifier")));
+	}
 
-    @Test
-    void organizationDecisionTreeTest() throws Exception {
-        DedupConfig conf = DedupConfig
-                .load(IOUtils
-                        .toString(
-                                SparkOpenorgsDedupTest.class
-                                        .getResourceAsStream(
-                                                "/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+	@Test
+	void organizationDecisionTreeTest() throws Exception {
+		DedupConfig conf = DedupConfig
+			.load(
+				IOUtils
+					.toString(
+						SparkOpenorgsDedupTest.class
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
 
-        final String org1 = "{\"eclegalbody\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecresearchorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"SUSF - Universit\\\\u00e9 internationale de floride\"}, \"pid\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"qualifier\": {\"classid\": \"grid\", \"classname\": \"grid\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"grid.65456.34\"}], \"websiteurl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"http://www.fiu.edu/\"}, \"ecnutscode\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"logourl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"collectedfrom\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"GRID - Global Research Identifier Database\", \"key\": \"10|openaire____::ff4a008470319a22d9cf3d14af485977\"}], \"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"UNKNOWN\", \"classname\": \"UNKNOWN\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}, \"inferred\": true, \"inferenceprovenance\": \"dedup-similarity-organization-simple\", \"invisible\": false, \"trust\": \"0.89\"}, \"alternativeNames\": [], \"echighereducation\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"id\": \"20|grid________::f22e08fb7bd544b4355f99bef2c43ad5\", \"eclegalperson\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"lastupdatetimestamp\": 1566902405602, \"ecinternationalorganizationeurinterests\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"dateofcollection\": \"\", \"dateoftransformation\": \"\", \"ecnonprofit\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecenterprise\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecinternationalorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalshortname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"FIU\"}, \"country\": {\"classid\": \"US\", \"classname\": \"United States\", \"schemename\": \"dnet:countries\", \"schemeid\": \"dnet:countries\"}, \"extraInfo\": [], \"originalId\": [], \"ecsmevalidated\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}}";
-        final String org2 = "{\"eclegalbody\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecresearchorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"SUSF - Universidad Internacional de Florida\"}, \"pid\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"qualifier\": {\"classid\": \"grid\", \"classname\": \"grid\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"grid.65456.34\"}], \"websiteurl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"http://www.fiu.edu/\"}, \"ecnutscode\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"logourl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"collectedfrom\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"GRID - Global Research Identifier Database\", \"key\": \"10|openaire____::ff4a008470319a22d9cf3d14af485977\"}], \"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"UNKNOWN\", \"classname\": \"UNKNOWN\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}, \"inferred\": true, \"inferenceprovenance\": \"dedup-similarity-organization-simple\", \"invisible\": false, \"trust\": \"0.89\"}, \"alternativeNames\": [], \"echighereducation\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"id\": \"20|grid________::2b261e9d8c2a63abbfd5826918c23b6d\", \"eclegalperson\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"lastupdatetimestamp\": 1566902405602, \"ecinternationalorganizationeurinterests\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"dateofcollection\": \"\", \"dateoftransformation\": \"\", \"ecnonprofit\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecenterprise\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecinternationalorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalshortname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"FIU\"}, \"country\": {\"classid\": \"US\", \"classname\": \"United States\", \"schemename\": \"dnet:countries\", \"schemeid\": \"dnet:countries\"}, \"extraInfo\": [], \"originalId\": [], \"ecsmevalidated\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}}";
+		final String org1 = "{\"eclegalbody\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecresearchorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"SUSF - Universit\\\\u00e9 internationale de floride\"}, \"pid\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"qualifier\": {\"classid\": \"grid\", \"classname\": \"grid\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"grid.65456.34\"}], \"websiteurl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"http://www.fiu.edu/\"}, \"ecnutscode\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"logourl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"collectedfrom\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"GRID - Global Research Identifier Database\", \"key\": \"10|openaire____::ff4a008470319a22d9cf3d14af485977\"}], \"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"UNKNOWN\", \"classname\": \"UNKNOWN\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}, \"inferred\": true, \"inferenceprovenance\": \"dedup-similarity-organization-simple\", \"invisible\": false, \"trust\": \"0.89\"}, \"alternativeNames\": [], \"echighereducation\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"id\": \"20|grid________::f22e08fb7bd544b4355f99bef2c43ad5\", \"eclegalperson\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"lastupdatetimestamp\": 1566902405602, \"ecinternationalorganizationeurinterests\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"dateofcollection\": \"\", \"dateoftransformation\": \"\", \"ecnonprofit\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecenterprise\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecinternationalorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalshortname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"FIU\"}, \"country\": {\"classid\": \"US\", \"classname\": \"United States\", \"schemename\": \"dnet:countries\", \"schemeid\": \"dnet:countries\"}, \"extraInfo\": [], \"originalId\": [], \"ecsmevalidated\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}}";
+		final String org2 = "{\"eclegalbody\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecresearchorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"SUSF - Universidad Internacional de Florida\"}, \"pid\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"qualifier\": {\"classid\": \"grid\", \"classname\": \"grid\", \"schemename\": \"dnet:pid_types\", \"schemeid\": \"dnet:pid_types\"}, \"value\": \"grid.65456.34\"}], \"websiteurl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"http://www.fiu.edu/\"}, \"ecnutscode\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"logourl\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"collectedfrom\": [{\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"GRID - Global Research Identifier Database\", \"key\": \"10|openaire____::ff4a008470319a22d9cf3d14af485977\"}], \"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"UNKNOWN\", \"classname\": \"UNKNOWN\", \"schemename\": \"dnet:provenanceActions\", \"schemeid\": \"dnet:provenanceActions\"}, \"inferred\": true, \"inferenceprovenance\": \"dedup-similarity-organization-simple\", \"invisible\": false, \"trust\": \"0.89\"}, \"alternativeNames\": [], \"echighereducation\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"id\": \"20|grid________::2b261e9d8c2a63abbfd5826918c23b6d\", \"eclegalperson\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"lastupdatetimestamp\": 1566902405602, \"ecinternationalorganizationeurinterests\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"dateofcollection\": \"\", \"dateoftransformation\": \"\", \"ecnonprofit\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecenterprise\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"ecinternationalorganization\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}, \"legalshortname\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"FIU\"}, \"country\": {\"classid\": \"US\", \"classname\": \"United States\", \"schemename\": \"dnet:countries\", \"schemeid\": \"dnet:countries\"}, \"extraInfo\": [], \"originalId\": [], \"ecsmevalidated\": {\"dataInfo\": {\"deletedbyinference\": false, \"provenanceaction\": {\"classid\": \"\", \"classname\": \"\", \"schemename\": \"\", \"schemeid\": \"\"}, \"inferred\": false, \"inferenceprovenance\": \"\", \"invisible\": false, \"trust\": \"\"}, \"value\": \"\"}}";
 
-        Row row1 = SparkModel.apply(conf).rowFromJson(org1);
-        Row row2 = SparkModel.apply(conf).rowFromJson(org2);
+		Row row1 = SparkModel.apply(conf).rowFromJson(org1);
+		Row row2 = SparkModel.apply(conf).rowFromJson(org2);
 
-        System.out.println("row1 = " + row1);
-        System.out.println("row2 = " + row2);
-        TreeProcessor tree = new TreeProcessor(conf);
+		System.out.println("row1 = " + row1);
+		System.out.println("row2 = " + row2);
+		TreeProcessor tree = new TreeProcessor(conf);
 
-        boolean result = tree.compare(row1, row2);
+		boolean result = tree.compare(row1, row2);
 
-        System.out.println("result = " + result);
+		System.out.println("result = " + result);
 
-    }
+	}
 
 }
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
index 40a73c9b3..18c9ce18d 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/jpath/JsonPathTest.java
@@ -3,13 +3,13 @@ package eu.dnetlib.dhp.oa.dedup.jpath;
 
 import java.io.IOException;
 
-import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 import org.junit.platform.commons.util.StringUtils;
 
+import eu.dnetlib.dhp.oa.dedup.SparkOpenorgsDedupTest;
 import eu.dnetlib.pace.config.DedupConfig;
 import eu.dnetlib.pace.model.SparkModel;
 
@@ -33,13 +33,14 @@ class JsonPathTest {
 	}
 
 	@Test
-	void jsonToModelTest() throws IOException{
+	void jsonToModelTest() throws IOException {
 		DedupConfig conf = DedupConfig
-				.load(IOUtils
-						.toString(
-								SparkOpenorgsDedupTest.class
-										.getResourceAsStream(
-												"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
+			.load(
+				IOUtils
+					.toString(
+						SparkOpenorgsDedupTest.class
+							.getResourceAsStream(
+								"/eu/dnetlib/dhp/dedup/conf/org.curr.conf.json")));
 
 		final String org = IOUtils.toString(getClass().getResourceAsStream("organization_example1.json"));
 
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index abcf4992f..1a75deafc 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -37,6 +37,7 @@ import eu.dnetlib.dhp.schema.solr.Measure;
 import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
+import eu.dnetlib.dhp.schema.solr.Pid;
 import eu.dnetlib.dhp.schema.solr.Project;
 import eu.dnetlib.dhp.schema.solr.Result;
 import eu.dnetlib.dhp.schema.solr.Subject;
diff --git a/dhp-workflows/dhp-swh/pom.xml b/dhp-workflows/dhp-swh/pom.xml
index 80fff4587..ef9049b20 100644
--- a/dhp-workflows/dhp-swh/pom.xml
+++ b/dhp-workflows/dhp-swh/pom.xml
@@ -51,49 +51,6 @@
             <artifactId>hadoop-distcp</artifactId>
         </dependency>
 
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-api</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib</groupId>
-            <artifactId>dnet-actionmanager-common</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>eu.dnetlib</groupId>
-                    <artifactId>dnet-openaireplus-mapping-utils</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>saxonica</groupId>
-                    <artifactId>saxon-dom</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>jgrapht</groupId>
-                    <artifactId>jgrapht</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>net.sf.ehcache</groupId>
-                    <artifactId>ehcache</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.springframework</groupId>
-                    <artifactId>spring-test</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.apache.*</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>apache</groupId>
-                    <artifactId>*</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
diff --git a/pom.xml b/pom.xml
index a5bc6cedd..e3e57eb4c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -440,29 +440,6 @@
                 <scope>provided</scope>
             </dependency>
 
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>dnet-actionmanager-common</artifactId>
-                <version>${dnet-actionmanager-common.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>org.apache.hadoop</groupId>
-                        <artifactId>hadoop-common</artifactId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-            <dependency>
-                <groupId>eu.dnetlib</groupId>
-                <artifactId>dnet-actionmanager-api</artifactId>
-                <version>${dnet-actionmanager-api.version}</version>
-                <exclusions>
-                    <exclusion>
-                        <groupId>eu.dnetlib</groupId>
-                        <artifactId>cnr-misc-utils</artifactId>
-                    </exclusion>
-                </exclusions>
-            </dependency>
-
             <dependency>
                 <groupId>eu.dnetlib</groupId>
                 <artifactId>cnr-rmi-api</artifactId>
@@ -960,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[6.1.4-SNAPSHOT]</dhp-schemas.version>
+        <dhp-schemas.version>[7.0.0]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>
@@ -969,8 +946,6 @@
         <dhp.oozie.version>4.1.0-${dhp.cdh.version}</dhp.oozie.version>
         <dhp.site.skip>true</dhp.site.skip>
         <dhp.spark.version>2.4.0.cloudera2</dhp.spark.version>
-        <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
-        <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
         <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
         <google.gson.version>2.2.2</google.gson.version>
         <log4j.version>1.2.17</log4j.version>

From 79985ad197ef1cdc9ca2d0401301432a1b96e3f9 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Wed, 17 Jul 2024 18:30:24 +0200
Subject: [PATCH 082/239] [Crossref]added mapping for DFG versus the
 unidentified project
 [https://support.openaire.eu/issues/9926?next_issue_id=9924&prev_issue_id=9927#note-4]

---
 .../eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index 27eaa61b5..ebe72ae5b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -888,7 +888,11 @@ case object Crossref2Oaf {
               val targetId = getProjectId("cihr________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
-
+//              Added mapping for DFG
+            case "10.13039/501100001659" =>
+              val targetId = getProjectId("dfgf________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             case "10.13039/100020031" =>
               val targetId = getProjectId("tara________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)

From 4f4c73d65b59118f194a263fb53272bd39160f3f Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Mon, 22 Jul 2024 15:19:02 +0200
Subject: [PATCH 083/239] minor change: addition of missing parameter in sql
 query

---
 .../eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql         | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql
index 3451333c0..2a7cbb9fc 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql
@@ -25,7 +25,8 @@ SELECT
 		o.country || '@@@dnet:countries'                          AS country,
 		array[]::text[]                                           AS alternativenames,
 		'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction,
-		 array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid
+		 array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid,
+        'Unknown'                                                 AS typology
 FROM dsm_organizations o
 	LEFT OUTER JOIN dsm_services d ON (d.id = o.collectedfrom)
 	LEFT OUTER JOIN dsm_organizationpids p ON (p.organization = o.id)

From d27e9ea50f7650df75fc4eb7dee1723693b35a35 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Tue, 23 Jul 2024 09:56:27 +0200
Subject: [PATCH 084/239] added ODF invisible stores in raw_all workflow

---
 .../oa/graph/raw_all/oozie_app/workflow.xml   | 30 +++++++++++++++++--
 1 file changed, 28 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
index b74562284..ff927fe52 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
@@ -368,6 +368,32 @@
             <arg>--mdLayout</arg><arg>store</arg>
             <arg>--mdInterpretation</arg><arg>cleaned</arg>
         </spark>
+        <ok to="ImportODF_hdfs_invisible"/>
+        <error to="Kill"/>
+    </action>
+    
+    <action name="ImportODF_hdfs_invisible">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>ImportODF_hdfs_invisible</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.MigrateHdfsMdstoresApplication</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores ${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--hdfsPath</arg><arg>${contentPath}/odf_mdstore_hdfs_invisible</arg>
+            <arg>--mdstoreManagerUrl</arg><arg>${mdstoreManagerUrl}</arg>
+            <arg>--mdFormat</arg><arg>ODF</arg>
+            <arg>--mdLayout</arg><arg>store</arg>
+            <arg>--mdInterpretation</arg><arg>intersection</arg>
+        </spark>
         <ok to="reuse_oaf_hdfs"/>
         <error to="Kill"/>
     </action>
@@ -529,7 +555,7 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
-            <arg>--sourcePaths</arg><arg>${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_mdstore_hdfs,${contentPath}/odf_mdstore_hdfs,${contentPath}/mdstore/*/*</arg>
+            <arg>--sourcePaths</arg><arg>${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_mdstore_hdfs,${contentPath}/odf_mdstore_hdfs,${contentPath}/odf_mdstore_hdfs_invisible,${contentPath}/mdstore/*/*</arg>
             <arg>--invalidPath</arg><arg>${workingDir}/invalid_records</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
         </spark>
@@ -553,7 +579,7 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
-            <arg>--sourcePaths</arg><arg>${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_mdstore_hdfs,${contentPath}/odf_mdstore_hdfs,${contentPath}/mdstore/*/*</arg>
+            <arg>--sourcePaths</arg><arg>${contentPath}/db_openaire,${contentPath}/db_openorgs,${contentPath}/oaf_mdstore_hdfs,${contentPath}/odf_mdstore_hdfs,${contentPath}/odf_mdstore_hdfs_invisible,${contentPath}/mdstore/*/*</arg>
             <arg>--targetPath</arg><arg>${workingDir}/entities</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
             <arg>--shouldHashId</arg><arg>${shouldHashId}</arg>

From 9573bf576d540d30246bda2c1c7a7857f101b412 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 23 Jul 2024 12:47:57 +0200
Subject: [PATCH 085/239] [SDG]added code to ingest also the SDG without DOI

---
 .../PrepareSDGSparkJob.java                   |  96 ++++++++++----
 .../fosnodoi/CreateActionSetSparkJob.java     |   7 -
 .../sdgnodoi/CreateActionSetSparkJob.java     |  86 ++++++++++++
 .../actionmanager/sdgnodoi/as_parameters.json |  20 +++
 .../sdgnodoi/oozie_app/config-default.xml     |  30 +++++
 .../sdgnodoi/oozie_app/workflow.xml           | 125 ++++++++++++++++++
 6 files changed, 328 insertions(+), 36 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/as_parameters.json
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/config-default.xml
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/workflow.xml

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
index a88607986..012178c1e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
@@ -6,26 +6,23 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
+import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.*;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.Subject;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class PrepareSDGSparkJob implements Serializable {
@@ -52,42 +49,83 @@ public class PrepareSDGSparkJob implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		final Boolean distributeDOI = Optional
+			.ofNullable(parser.get("distributeDoi"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("distribute doi {}", distributeDOI);
+
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				doPrepare(
-					spark,
-					sourcePath,
+				if (distributeDOI)
+					doPrepare(
+						spark,
+						sourcePath,
+
+						outputPath);
+				else
+					doPrepareoaid(spark, sourcePath, outputPath);
 
-					outputPath);
 			});
 	}
 
-	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
-		Dataset<SDGDataModel> sdgDataset = readPath(spark, sourcePath, SDGDataModel.class);
+	private static void doPrepareoaid(SparkSession spark, String sourcePath, String outputPath) {
+		Dataset<Row> sdgDataset = spark
+			.read()
+			.format("csv")
+			.option("sep", DEFAULT_DELIMITER)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(sourcePath);
 
 		sdgDataset
-			.groupByKey((MapFunction<SDGDataModel, String>) r -> r.getDoi().toLowerCase(), Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, SDGDataModel, Result>) (k, it) -> {
-				Result r = new Result();
-				r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
-				SDGDataModel first = it.next();
-				List<Subject> sbjs = new ArrayList<>();
-				sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
-				it
-					.forEachRemaining(
-						s -> sbjs
-							.add(getSubject(s.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
-				r.setSubject(sbjs);
-
-				return r;
-			}, Encoders.bean(Result.class))
+			.groupByKey((MapFunction<Row, String>) v -> ((String) v.getAs("oaid")).toLowerCase(), Encoders.STRING())
+			.mapGroups(
+				(MapGroupsFunction<String, Row, Result>) (k,
+					it) -> getResult(
+						DHPUtils
+							.generateUnresolvedIdentifier(
+								ModelSupport.entityIdPrefix.get(Result.class.getSimpleName().toLowerCase()) + "|" + k,
+								DOI),
+						it),
+				Encoders.bean(Result.class))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
 			.json(outputPath + "/sdg");
 	}
 
+	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
+		Dataset<Row> sdgDataset = spark.read().csv(sourcePath);
+
+		sdgDataset
+			.groupByKey((MapFunction<Row, String>) r -> ((String) r.getAs("doi")).toLowerCase(), Encoders.STRING())
+			.mapGroups(
+				(MapGroupsFunction<String, Row, Result>) PrepareSDGSparkJob::getResult, Encoders.bean(Result.class))
+			.write()
+			.mode(SaveMode.Overwrite)
+			.option("compression", "gzip")
+			.json(outputPath + "/sdg");
+	}
+
+	private static @NotNull Result getResult(String id, Iterator<Row> it) {
+		Result r = new Result();
+		r.setId(id);
+		Row first = it.next();
+		List<Subject> sbjs = new ArrayList<>();
+		sbjs.add(getSubject(first.getAs("sdg"), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
+		it
+			.forEachRemaining(
+				s -> sbjs
+					.add(getSubject(s.getAs("sdg"), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID)));
+		r.setSubject(sbjs);
+
+		return r;
+	}
+
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java
index e86fccb84..fceed2008 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/fosnodoi/CreateActionSetSparkJob.java
@@ -13,9 +13,6 @@ import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaPairRDD;
-import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
@@ -24,13 +21,9 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.utils.*;
 import scala.Tuple2;
 
 public class CreateActionSetSparkJob implements Serializable {
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java
new file mode 100644
index 000000000..a2f8cfa39
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java
@@ -0,0 +1,86 @@
+
+package eu.dnetlib.dhp.actionmanager.sdgnodoi;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.IOException;
+import java.io.Serializable;
+import java.util.Objects;
+import java.util.Optional;
+
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import scala.Tuple2;
+
+public class CreateActionSetSparkJob implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static void main(final String[] args) throws IOException, ParseException {
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					Objects
+						.requireNonNull(
+							CreateActionSetSparkJob.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json"))));
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("sourcePath");
+		log.info("inputPath {}", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}", outputPath);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> createActionSet(spark, inputPath, outputPath));
+
+	}
+
+	private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
+		spark
+			.read()
+			.textFile(inputPath)
+			.map(
+				(MapFunction<String, Result>) value -> OBJECT_MAPPER.readValue(value, Result.class),
+				Encoders.bean(Result.class))
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/as_parameters.json
new file mode 100644
index 000000000..3f056edf7
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/as_parameters.json
@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "sp",
+    "paramLongName": "sourcePath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  }
+]
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/config-default.xml
new file mode 100644
index 000000000..d262cb6e0
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/config-default.xml
@@ -0,0 +1,30 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/workflow.xml
new file mode 100644
index 000000000..82144d0d6
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/sdgnodoi/oozie_app/workflow.xml
@@ -0,0 +1,125 @@
+
+<workflow-app name="SDG no doi" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sdgPath</name>
+            <description>the input path of the resources to be extended</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="prepareSDG"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="prepareSDG">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the results from FOS</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sdgPath}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
+            <arg>--distributeDoi</arg><arg>false</arg>
+        </spark>
+        <ok to="produceActionSet"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+    <action name="produceActionSet">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Save the action set grouping results with the same id</name>
+            <class>eu.dnetlib.dhp.actionmanager.sdgnodoi.CreateActionSetSparkJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/prepared/sdg</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>
\ No newline at end of file

From 7d2c0a3723f8abaf7fa23cbb5f729db70b8a9c72 Mon Sep 17 00:00:00 2001
From: Antonis Lempesis <antleb@di.uoa.gr>
Date: Tue, 23 Jul 2024 15:10:17 +0300
Subject: [PATCH 086/239] added new institutions

---
 .../scripts/updateMonitorDB_institutions.sql         | 12 +++++++++++-
 .../scripts/step20-createMonitorDB_institutions.sql  | 10 ++++++++--
 2 files changed, 19 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB_institutions.sql b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB_institutions.sql
index 5ab8c88b5..a3f29a9e3 100644
--- a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB_institutions.sql
+++ b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB_institutions.sql
@@ -61,7 +61,17 @@ create table TARGET.result stored as parquet as
              'openorgs____::8839b55dae0c84d56fd533f52d5d483a',  -- Leibniz Institute of Ecological Urban and Regional Development
              'openorgs____::526468206bca24c1c90da6a312295cf4',	-- Cyprus University of Technology
              'openorgs____::b5ca9d4340e26454e367e2908ef3872f',	-- Alma Mater Studiorum University of Bologna
-             'openorgs____::a6340e6ecf60f6bba163659df985b0f2'	-- TU Dresden
+             'openorgs____::a6340e6ecf60f6bba163659df985b0f2',	-- TU Dresden
+             'openorgs____::64badd35233ba2cd4946368ef2f4cf57',  -- University of Vienna
+             'openorgs____::7501d66d2297a963ebfb075c43fff88e',  -- Royal Institute of Technology
+             'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf',	-- Sorbonne University
+             'openorgs____::b316f25380d106aac402f5ae8653910d',  -- Centre for Research on Ecology and Forestry Applications
+             'openorgs____::45a2076eee3013e0e85625ce61bcd272',  -- Institut d'Investigació Sanitària Illes Balears
+             'openorgs____::00b20b0a743a96169e6cf135e6e2bd7c',  -- Universidad Publica De Navarra
+             'openorgs____::0f398605c2459294d125ff23473a97dc',  -- Aalto University
+             'openorgs____::25b1fa62c7fd8e409d3a83c07e04b2d4',  -- WHU-Otto Beisheim School of Management
+             'openorgs____::d6eec313417f11205db4e736a34c0db6',  -- KEMPELENOV INSTITUT INTELIGENTNYCH TECHNOLOGII
+             'openorgs____::c2dfb90e797a2dc52f0084c549289d0c'  -- National Research Institute for Agriculture, Food and Environment
         )))  foo;
 
 --ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
\ No newline at end of file
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
index 62c68c625..1326979d8 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB_institutions.sql
@@ -65,5 +65,11 @@ create table TARGET.result stored as parquet as
              'openorgs____::64badd35233ba2cd4946368ef2f4cf57',  -- University of Vienna
              'openorgs____::7501d66d2297a963ebfb075c43fff88e',  -- Royal Institute of Technology
              'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf',	-- Sorbonne University
-             'openorgs____::b316f25380d106aac402f5ae8653910d'   -- Centre for Research on Ecology and Forestry Applications
-        )))  foo;
\ No newline at end of file
+             'openorgs____::b316f25380d106aac402f5ae8653910d',  -- Centre for Research on Ecology and Forestry Applications
+             'openorgs____::45a2076eee3013e0e85625ce61bcd272',  -- Institut d'Investigació Sanitària Illes Balears
+             'openorgs____::00b20b0a743a96169e6cf135e6e2bd7c',  -- Universidad Publica De Navarra
+             'openorgs____::0f398605c2459294d125ff23473a97dc',  -- Aalto University
+             'openorgs____::25b1fa62c7fd8e409d3a83c07e04b2d4',  -- WHU-Otto Beisheim School of Management
+             'openorgs____::d6eec313417f11205db4e736a34c0db6',  -- KEMPELENOV INSTITUT INTELIGENTNYCH TECHNOLOGII
+             'openorgs____::c2dfb90e797a2dc52f0084c549289d0c'  -- National Research Institute for Agriculture, Food and Environment
+            )))  foo;
\ No newline at end of file

From d0590e0e4994834a3db618547735e0e080bb2b02 Mon Sep 17 00:00:00 2001
From: Antonis Lempesis <antleb@di.uoa.gr>
Date: Tue, 23 Jul 2024 15:17:15 +0300
Subject: [PATCH 087/239] added latest institutions

---
 .../oozie_app/scripts/updateMonitorDBAll.sql         | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDBAll.sql b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDBAll.sql
index 35ab42029..064b5425b 100644
--- a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDBAll.sql
+++ b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDBAll.sql
@@ -81,7 +81,17 @@ create table TARGET.result stored as parquet as
              'openorgs____::8839b55dae0c84d56fd533f52d5d483a',  -- Leibniz Institute of Ecological Urban and Regional Development
              'openorgs____::526468206bca24c1c90da6a312295cf4',	-- Cyprus University of Technology
              'openorgs____::b5ca9d4340e26454e367e2908ef3872f',	-- Alma Mater Studiorum University of Bologna
-             'openorgs____::a6340e6ecf60f6bba163659df985b0f2'	-- TU Dresden
+             'openorgs____::a6340e6ecf60f6bba163659df985b0f2',	-- TU Dresden
+             'openorgs____::64badd35233ba2cd4946368ef2f4cf57',  -- University of Vienna
+             'openorgs____::7501d66d2297a963ebfb075c43fff88e',  -- Royal Institute of Technology
+             'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf',	-- Sorbonne University
+             'openorgs____::b316f25380d106aac402f5ae8653910d',  -- Centre for Research on Ecology and Forestry Applications
+             'openorgs____::45a2076eee3013e0e85625ce61bcd272',  -- Institut d'Investigació Sanitària Illes Balears
+             'openorgs____::00b20b0a743a96169e6cf135e6e2bd7c',  -- Universidad Publica De Navarra
+             'openorgs____::0f398605c2459294d125ff23473a97dc',  -- Aalto University
+             'openorgs____::25b1fa62c7fd8e409d3a83c07e04b2d4',  -- WHU-Otto Beisheim School of Management
+             'openorgs____::d6eec313417f11205db4e736a34c0db6',  -- KEMPELENOV INSTITUT INTELIGENTNYCH TECHNOLOGII
+             'openorgs____::c2dfb90e797a2dc52f0084c549289d0c'  -- National Research Institute for Agriculture, Food and Environment
         ))) foo;
 
 --ANALYZE TABLE TARGET.result COMPUTE STATISTICS;

From 19806c2ae3267f0e1080b2afffba4c51b4fe07c7 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 23 Jul 2024 17:12:55 +0200
Subject: [PATCH 088/239] [SDG]fixed switch of methods

---
 .../PrepareSDGSparkJob.java                    | 18 +++++++++++++-----
 .../sdgnodoi/CreateActionSetSparkJob.java      |  7 ++++++-
 2 files changed, 19 insertions(+), 6 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
index 012178c1e..be22077c3 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
@@ -73,7 +73,7 @@ public class PrepareSDGSparkJob implements Serializable {
 			});
 	}
 
-	private static void doPrepareoaid(SparkSession spark, String sourcePath, String outputPath) {
+	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
 		Dataset<Row> sdgDataset = spark
 			.read()
 			.format("csv")
@@ -84,7 +84,7 @@ public class PrepareSDGSparkJob implements Serializable {
 			.load(sourcePath);
 
 		sdgDataset
-			.groupByKey((MapFunction<Row, String>) v -> ((String) v.getAs("oaid")).toLowerCase(), Encoders.STRING())
+			.groupByKey((MapFunction<Row, String>) v -> ((String) v.getAs("doi")).toLowerCase(), Encoders.STRING())
 			.mapGroups(
 				(MapGroupsFunction<String, Row, Result>) (k,
 					it) -> getResult(
@@ -100,11 +100,19 @@ public class PrepareSDGSparkJob implements Serializable {
 			.json(outputPath + "/sdg");
 	}
 
-	private static void doPrepare(SparkSession spark, String sourcePath, String outputPath) {
-		Dataset<Row> sdgDataset = spark.read().csv(sourcePath);
+	private static void doPrepareoaid(SparkSession spark, String sourcePath, String outputPath) {
+		Dataset<Row> sdgDataset = spark
+			.read()
+			.format("csv")
+			.option("sep", DEFAULT_DELIMITER)
+			.option("inferSchema", "true")
+			.option("header", "true")
+			.option("quotes", "\"")
+			.load(sourcePath);
+		;
 
 		sdgDataset
-			.groupByKey((MapFunction<Row, String>) r -> ((String) r.getAs("doi")).toLowerCase(), Encoders.STRING())
+			.groupByKey((MapFunction<Row, String>) r -> "50|" + ((String) r.getAs("oaid")), Encoders.STRING())
 			.mapGroups(
 				(MapGroupsFunction<String, Row, Result>) PrepareSDGSparkJob::getResult, Encoders.bean(Result.class))
 			.write()
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java
index a2f8cfa39..0bc3b524b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/sdgnodoi/CreateActionSetSparkJob.java
@@ -10,6 +10,7 @@ import java.util.Optional;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.fs.Hdfs;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -23,6 +24,7 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import scala.Tuple2;
@@ -63,7 +65,10 @@ public class CreateActionSetSparkJob implements Serializable {
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
-			spark -> createActionSet(spark, inputPath, outputPath));
+			spark -> {
+				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
+				createActionSet(spark, inputPath, outputPath);
+			});
 
 	}
 

From 6f1801d7d1f1b1470813479905a94f618385f3d6 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 23 Jul 2024 17:34:48 +0200
Subject: [PATCH 089/239] [webcrawl]-

---
 .../webcrawl/RemoveRelationFromActionSet.java | 244 ++++++++++++++++++
 1 file changed, 244 insertions(+)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
new file mode 100644
index 000000000..074311f1f
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
@@ -0,0 +1,244 @@
+package eu.dnetlib.dhp.actionmanager.webcrawl;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.actionmanager.Constants;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.types.StructType;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import scala.Tuple2;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Optional;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+public class RemoveRelationFromActionSet
+        implements Serializable {
+    private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
+    private static final String DOI_PREFIX = "50|doi_________::";
+
+
+    public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    public static void main(String[] args) throws Exception {
+        String jsonConfiguration = IOUtils
+                .toString(
+                        CreateActionSetFromWebEntries.class
+                                .getResourceAsStream(
+                                        "/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json"));
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+        parser.parseArgument(args);
+
+        Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        final String inputPath = parser.get("actionSetPath");
+        log.info("inputPath: {}", inputPath);
+
+        final String outputPath = parser.get("outputPath");
+        log.info("outputPath: {}", outputPath);
+
+        final String blackListInputPath = parser.get("blackListPath");
+        log.info("blackListInputPath: {}", blackListInputPath);
+
+        SparkConf conf = new SparkConf();
+
+        runWithSparkSession(
+                conf,
+                isSparkSessionManaged,
+                spark -> {
+
+                    removeFromActionSet(spark, inputPath, outputPath, blackListInputPath);
+
+                });
+    }
+
+    private static void removeFromActionSet(SparkSession spark, String inputPath, String outputPath, String blackListInputPath) {
+
+    }
+
+    public static void createActionSet(SparkSession spark, String inputPath,
+                                       String outputPath, String blackListInputPath) {
+
+        final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
+                .filter("country_code=='IE'")
+                .drop("publication_year");
+
+        final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
+
+        dataset
+                .join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
+                .filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
+                .drop("OpenAlexId")
+                .flatMap((FlatMapFunction<Row, Relation>) row -> {
+                    List<Relation> ret = new ArrayList<>();
+                    final String ror = ROR_PREFIX
+                            + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
+                    ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
+
+                    return ret
+                            .iterator();
+                }, Encoders.bean(Relation.class))
+                .toJavaRDD()
+                .map(p -> new AtomicAction(p.getClass(), p))
+                .mapToPair(
+                        aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+                                new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+                .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+
+    }
+
+    private static Dataset<Row> readWebCrawl(SparkSession spark, String inputPath) {
+        StructType webInfo = StructType
+                .fromDDL(
+                        "`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, "
+                                +
+                                "`authorships` ARRAY<STRUCT <`institutions`: ARRAY <STRUCT <`ror`: STRING, `country_code` :STRING>>>>");
+
+        return spark
+                .read()
+                .schema(webInfo)
+                .json(inputPath)
+                .withColumn(
+                        "authors", functions
+                                .explode(
+                                        functions.col("authorships")))
+                .selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions")
+                .withColumn(
+                        "institution", functions
+                                .explode(
+                                        functions.col("institutions")))
+
+                .selectExpr(
+                        "id", "doi", "institution.ror as ror",
+                        "institution.country_code as country_code", "publication_year")
+                .distinct();
+
+    }
+
+    private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
+
+        return spark
+                .read()
+                .option("header", true)
+                .csv(inputPath)
+                .select("OpenAlexId");
+    }
+
+    private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
+        if (pmcid == null)
+            return new ArrayList<>();
+
+        return createAffiliatioRelationPair(
+                PMCID_PREFIX
+                        + IdentifierFactory
+                        .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))),
+                ror);
+    }
+
+    private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
+        if (pmid == null)
+            return new ArrayList<>();
+
+        return createAffiliatioRelationPair(
+                PMID_PREFIX
+                        + IdentifierFactory
+                        .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
+                ror);
+    }
+
+    private static String removeResolver(String pidType, String pid) {
+        switch (pidType) {
+            case "PMID":
+                return pid.substring(33);
+            case "PMC":
+                return "PMC" + pid.substring(43);
+            case "DOI":
+                return pid.substring(16);
+        }
+
+        throw new RuntimeException();
+
+    }
+
+    private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {
+        if (doi == null)
+            return new ArrayList<>();
+
+        return createAffiliatioRelationPair(
+                DOI_PREFIX
+                        + IdentifierFactory
+                        .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI", doi))),
+                ror);
+
+    }
+
+    private static List<Relation> createAffiliatioRelationPair(String resultId, String orgId) {
+        ArrayList<Relation> newRelations = new ArrayList();
+
+        newRelations
+                .add(
+                        OafMapperUtils
+                                .getRelation(
+                                        orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
+                                        ModelConstants.IS_AUTHOR_INSTITUTION_OF,
+                                        Arrays
+                                                .asList(
+                                                        OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
+                                        OafMapperUtils
+                                                .dataInfo(
+                                                        false, null, false, false,
+                                                        OafMapperUtils
+                                                                .qualifier(
+                                                                        "sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
+                                                                        ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+                                                        "0.9"),
+                                        null));
+
+        newRelations
+                .add(
+                        OafMapperUtils
+                                .getRelation(
+                                        resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
+                                        ModelConstants.HAS_AUTHOR_INSTITUTION,
+                                        Arrays
+                                                .asList(
+                                                        OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
+                                        OafMapperUtils
+                                                .dataInfo(
+                                                        false, null, false, false,
+                                                        OafMapperUtils
+                                                                .qualifier(
+                                                                        "sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
+                                                                        ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+                                                        "0.9"),
+                                        null));
+
+        return newRelations;
+
+    }
+}

From 01958a3e07f141a223094e96210603893f4ea8b8 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 24 Jul 2024 10:00:10 +0200
Subject: [PATCH 090/239] [graph provision] addded filter to exclude records
 marked with datainfo.deletedbyinference = true

---
 .../eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
index d46ab1404..351526336 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
@@ -11,6 +11,7 @@ import java.util.Optional;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.SparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.util.LongAccumulator;
@@ -29,6 +30,8 @@ import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
 import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.solr.SolrRecord;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -115,6 +118,12 @@ public class PayloadConverterJob {
 			.read()
 			.load(toSeq(paths))
 			.as(Encoders.kryo(JoinedEntity.class))
+			.filter(
+				(FilterFunction<JoinedEntity>) je -> !Optional
+					.ofNullable(je.getEntity())
+					.map(Oaf::getDataInfo)
+					.map(DataInfo::getDeletedbyinference)
+					.orElse(false))
 			.map(
 				(MapFunction<JoinedEntity, Tuple2<String, SolrRecord>>) je -> new Tuple2<>(
 					recordFactory.build(je, validateXML),

From d771a883f933f6142d6cc3160f2135bdb2b22d55 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 25 Jul 2024 09:53:48 +0200
Subject: [PATCH 091/239] [dedup] updated sql query used to read organizations
 from the OpenOrgs DB to include their typology

---
 .../dhp/oa/graph/sql/queryOpenOrgsForOrgsDedup.sql   | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForOrgsDedup.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForOrgsDedup.sql
index d9e4b855d..933c26356 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForOrgsDedup.sql
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOpenOrgsForOrgsDedup.sql
@@ -25,12 +25,14 @@ SELECT
     		null                           AS ecinternationalorganization,
     		null                                           AS ecenterprise,
     		null                                        AS ecsmevalidated,
-    		null                                             AS ecnutscode
+    		null                                             AS ecnutscode,
+    org_types.name                                                                                              AS typology
 FROM organizations o
 	LEFT OUTER JOIN acronyms a    ON (a.id = o.id)
 	LEFT OUTER JOIN urls u        ON (u.id = o.id)
 	LEFT OUTER JOIN other_ids i   ON (i.id = o.id)
 	LEFT OUTER JOIN other_names n ON (n.id = o.id)
+    LEFT OUTER JOIN org_types ON (org_types.val = o.type)
 WHERE
     o.status = 'approved'
 GROUP BY
@@ -38,7 +40,8 @@ GROUP BY
 	o.name,
 	o.creation_date,
 	o.modification_date,
-	o.country
+	o.country,
+	org_types.name
 
 UNION ALL
 
@@ -69,13 +72,15 @@ SELECT
     (array_remove(array_cat(ARRAY[o.ec_internationalorganization], array_agg(od.ec_internationalorganization)), NULL))[1]              AS ecinternationalorganization,
     (array_remove(array_cat(ARRAY[o.ec_enterprise], array_agg(od.ec_enterprise)), NULL))[1]                      AS ecenterprise,
     (array_remove(array_cat(ARRAY[o.ec_smevalidated], array_agg(od.ec_smevalidated)), NULL))[1]                    AS ecsmevalidated,
-    (array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1]                       AS ecnutscode
+    (array_remove(array_cat(ARRAY[o.ec_nutscode], array_agg(od.ec_nutscode)), NULL))[1]                       AS ecnutscode,
+    org_types.name                                                                                              AS typology
 FROM other_names n
 	LEFT OUTER JOIN organizations o ON (n.id = o.id)
 	LEFT OUTER JOIN urls u          ON (u.id = o.id)
 	LEFT OUTER JOIN other_ids i     ON (i.id = o.id)
 	LEFT OUTER JOIN oa_duplicates d ON (o.id = d.local_id)
     LEFT OUTER JOIN organizations od ON (d.oa_original_id = od.id)
+    LEFT OUTER JOIN org_types ON (org_types.val = o.type)
 WHERE
     o.status = 'approved'
 GROUP BY
@@ -83,4 +88,5 @@ GROUP BY
 	o.creation_date,
 	o.modification_date,
 	o.country,
+	org_types.name,
 	n.name;
\ No newline at end of file

From fc60661ac5d676c8ec9475def8c3dd03cb617749 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 25 Jul 2024 12:25:14 +0200
Subject: [PATCH 092/239] [webcrawl] added code and test (code/resource) to
 verify the deletion of the relations related to results put in blacklist

---
 .../CreateActionSetFromWebEntries.java        |   4 +-
 .../webcrawl/RemoveRelationFromActionSet.java | 323 +++++++-----------
 .../dhp/actionmanager/webcrawl/job.properties |  14 +-
 .../webcrawl/oozie_app/workflow.xml           |  34 +-
 .../actionmanager/webcrawl/CreateASTest.java  |  23 +-
 .../webcrawl/RemoveFromASTest.java            | 108 ++++++
 .../webcrawl/blackListRemove/not_irish.csv    |   2 +
 7 files changed, 291 insertions(+), 217 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveFromASTest.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index 9828ad907..7607cfc76 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -8,7 +8,7 @@ import java.util.*;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
-import org.apache.hadoop.io.compress.GzipCodec;
+import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.FilterFunction;
@@ -112,7 +112,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 
 	}
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
index 074311f1f..33dfbacf1 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
@@ -1,244 +1,159 @@
+
 package eu.dnetlib.dhp.actionmanager.webcrawl;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.actionmanager.Constants;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
-import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static org.apache.spark.sql.functions.*;
+
+import java.io.File;
+import java.io.Serializable;
+import java.util.Arrays;
+import java.util.Optional;
+
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.io.filefilter.DirectoryFileFilter;
+import org.apache.commons.io.filefilter.FileFileFilter;
 import org.apache.hadoop.io.Text;
+import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
-import org.apache.spark.sql.types.StructType;
+import org.apache.spark.sql.types.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import scala.Tuple2;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Optional;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
 public class RemoveRelationFromActionSet
-        implements Serializable {
-    private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
-    private static final String DOI_PREFIX = "50|doi_________::";
+	implements Serializable {
+	private static final Logger log = LoggerFactory.getLogger(CreateActionSetFromWebEntries.class);
 
+	private static final ObjectMapper MAPPER = new ObjectMapper();
+	private static final StructType KV_SCHEMA = StructType$.MODULE$
+		.apply(
+			Arrays
+				.asList(
+					StructField$.MODULE$.apply("key", DataTypes.StringType, false, Metadata.empty()),
+					StructField$.MODULE$.apply("value", DataTypes.StringType, false, Metadata.empty())));
 
-    public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private static final StructType ATOMIC_ACTION_SCHEMA = StructType$.MODULE$
+		.apply(
+			Arrays
+				.asList(
+					StructField$.MODULE$.apply("clazz", DataTypes.StringType, false, Metadata.empty()),
+					StructField$.MODULE$
+						.apply(
+							"payload", DataTypes.StringType, false, Metadata.empty())));
 
-    public static void main(String[] args) throws Exception {
-        String jsonConfiguration = IOUtils
-                .toString(
-                        CreateActionSetFromWebEntries.class
-                                .getResourceAsStream(
-                                        "/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json"));
+	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-        parser.parseArgument(args);
+	public static void main(String[] args) throws Exception {
+		String jsonConfiguration = IOUtils
+			.toString(
+				CreateActionSetFromWebEntries.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/webcrawl/as_parameters.json"));
 
-        Boolean isSparkSessionManaged = Optional
-                .ofNullable(parser.get("isSparkSessionManaged"))
-                .map(Boolean::valueOf)
-                .orElse(Boolean.TRUE);
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		parser.parseArgument(args);
 
-        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
 
-        final String inputPath = parser.get("actionSetPath");
-        log.info("inputPath: {}", inputPath);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-        final String outputPath = parser.get("outputPath");
-        log.info("outputPath: {}", outputPath);
+		// the actionSet path
+		final String inputPath = parser.get("sourcePath");
+		log.info("inputPath: {}", inputPath);
 
-        final String blackListInputPath = parser.get("blackListPath");
-        log.info("blackListInputPath: {}", blackListInputPath);
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath: {}", outputPath);
 
-        SparkConf conf = new SparkConf();
+		final String blackListInputPath = parser.get("blackListPath");
+		log.info("blackListInputPath: {}", blackListInputPath);
 
-        runWithSparkSession(
-                conf,
-                isSparkSessionManaged,
-                spark -> {
+		SparkConf conf = new SparkConf();
 
-                    removeFromActionSet(spark, inputPath, outputPath, blackListInputPath);
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
 
-                });
-    }
+				removeFromActionSet(spark, inputPath, outputPath, blackListInputPath);
 
-    private static void removeFromActionSet(SparkSession spark, String inputPath, String outputPath, String blackListInputPath) {
+			});
+	}
 
-    }
+	private static void removeFromActionSet(SparkSession spark, String inputPath, String outputPath,
+		String blackListInputPath) {
+		// read the blacklist
+		Dataset<String> blackList = readBlackList(spark, blackListInputPath)
+			.map(
+				(MapFunction<Row, String>) r -> IdentifierFactory
+					.idFromPid("50", "doi", ((String) r.getAs("DOI / PMID")).substring(16), true),
+				Encoders.STRING());
 
-    public static void createActionSet(SparkSession spark, String inputPath,
-                                       String outputPath, String blackListInputPath) {
+		// read the old actionset and get the relations in the payload
+		JavaPairRDD<Text, Text> seq = JavaSparkContext
+			.fromSparkContext(spark.sparkContext())
+			.sequenceFile(inputPath, Text.class, Text.class);
 
-        final Dataset<Row> dataset = readWebCrawl(spark, inputPath)
-                .filter("country_code=='IE'")
-                .drop("publication_year");
+		JavaRDD<Row> rdd = seq
+			.map(x -> RowFactory.create(x._1().toString(), x._2().toString()));
 
-        final Dataset<Row> blackList = readBlackList(spark, blackListInputPath);
+		Dataset<Row> actionSet = spark
+			.createDataFrame(rdd, KV_SCHEMA)
+			.withColumn("atomic_action", from_json(col("value"), ATOMIC_ACTION_SCHEMA))
+			.select(expr("atomic_action.*"));
 
-        dataset
-                .join(blackList, dataset.col("id").equalTo(blackList.col("OpenAlexId")), "left")
-                .filter((FilterFunction<Row>) r -> r.getAs("OpenAlexId") == null)
-                .drop("OpenAlexId")
-                .flatMap((FlatMapFunction<Row, Relation>) row -> {
-                    List<Relation> ret = new ArrayList<>();
-                    final String ror = ROR_PREFIX
-                            + IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
-                    ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
+		Dataset<Relation> relation = actionSet
+			.map(
+				(MapFunction<Row, Relation>) r -> MAPPER.readValue((String) r.getAs("payload"), Relation.class),
+				Encoders.bean(Relation.class));
 
-                    return ret
-                            .iterator();
-                }, Encoders.bean(Relation.class))
-                .toJavaRDD()
-                .map(p -> new AtomicAction(p.getClass(), p))
-                .mapToPair(
-                        aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-                                new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-                .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
+		// select only the relation not matching any pid in the blacklist as source for the relation
+		Dataset<Relation> relNoSource = relation
+			.joinWith(blackList, relation.col("source").equalTo(blackList.col("value")), "left")
+			.filter((FilterFunction<Tuple2<Relation, String>>) t2 -> t2._2() == null)
+			.map((MapFunction<Tuple2<Relation, String>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class));
 
-    }
+		// select only the relation not matching any pid in the blacklist as target of the relation
+		relNoSource
+			.joinWith(blackList, relNoSource.col("target").equalTo(blackList.col("value")), "left")
+			.filter((FilterFunction<Tuple2<Relation, String>>) t2 -> t2._2() == null)
+			.map((MapFunction<Tuple2<Relation, String>, Relation>) t2 -> t2._1(), Encoders.bean(Relation.class))
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+		;
 
-    private static Dataset<Row> readWebCrawl(SparkSession spark, String inputPath) {
-        StructType webInfo = StructType
-                .fromDDL(
-                        "`id` STRING , `doi` STRING, `ids` STRUCT<`pmid` :STRING, `pmcid`: STRING >, `publication_year` STRING, "
-                                +
-                                "`authorships` ARRAY<STRUCT <`institutions`: ARRAY <STRUCT <`ror`: STRING, `country_code` :STRING>>>>");
+	}
 
-        return spark
-                .read()
-                .schema(webInfo)
-                .json(inputPath)
-                .withColumn(
-                        "authors", functions
-                                .explode(
-                                        functions.col("authorships")))
-                .selectExpr("id", "doi", "ids", "publication_year", "authors.institutions as institutions")
-                .withColumn(
-                        "institution", functions
-                                .explode(
-                                        functions.col("institutions")))
+	private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
 
-                .selectExpr(
-                        "id", "doi", "institution.ror as ror",
-                        "institution.country_code as country_code", "publication_year")
-                .distinct();
+		return spark
+			.read()
+			.option("header", true)
+			.csv(inputPath)
+			.select("DOI / PMID");
+	}
 
-    }
-
-    private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
-
-        return spark
-                .read()
-                .option("header", true)
-                .csv(inputPath)
-                .select("OpenAlexId");
-    }
-
-    private static List<Relation> createAffiliationRelationPairPMCID(String pmcid, String ror) {
-        if (pmcid == null)
-            return new ArrayList<>();
-
-        return createAffiliatioRelationPair(
-                PMCID_PREFIX
-                        + IdentifierFactory
-                        .md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), removeResolver("PMC", pmcid))),
-                ror);
-    }
-
-    private static List<Relation> createAffiliationRelationPairPMID(String pmid, String ror) {
-        if (pmid == null)
-            return new ArrayList<>();
-
-        return createAffiliatioRelationPair(
-                PMID_PREFIX
-                        + IdentifierFactory
-                        .md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), removeResolver("PMID", pmid))),
-                ror);
-    }
-
-    private static String removeResolver(String pidType, String pid) {
-        switch (pidType) {
-            case "PMID":
-                return pid.substring(33);
-            case "PMC":
-                return "PMC" + pid.substring(43);
-            case "DOI":
-                return pid.substring(16);
-        }
-
-        throw new RuntimeException();
-
-    }
-
-    private static List<Relation> createAffiliationRelationPairDOI(String doi, String ror) {
-        if (doi == null)
-            return new ArrayList<>();
-
-        return createAffiliatioRelationPair(
-                DOI_PREFIX
-                        + IdentifierFactory
-                        .md5(PidCleaner.normalizePidValue(PidType.doi.toString(), removeResolver("DOI", doi))),
-                ror);
-
-    }
-
-    private static List<Relation> createAffiliatioRelationPair(String resultId, String orgId) {
-        ArrayList<Relation> newRelations = new ArrayList();
-
-        newRelations
-                .add(
-                        OafMapperUtils
-                                .getRelation(
-                                        orgId, resultId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
-                                        ModelConstants.IS_AUTHOR_INSTITUTION_OF,
-                                        Arrays
-                                                .asList(
-                                                        OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
-                                        OafMapperUtils
-                                                .dataInfo(
-                                                        false, null, false, false,
-                                                        OafMapperUtils
-                                                                .qualifier(
-                                                                        "sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
-                                                                        ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-                                                        "0.9"),
-                                        null));
-
-        newRelations
-                .add(
-                        OafMapperUtils
-                                .getRelation(
-                                        resultId, orgId, ModelConstants.RESULT_ORGANIZATION, ModelConstants.AFFILIATION,
-                                        ModelConstants.HAS_AUTHOR_INSTITUTION,
-                                        Arrays
-                                                .asList(
-                                                        OafMapperUtils.keyValue(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME)),
-                                        OafMapperUtils
-                                                .dataInfo(
-                                                        false, null, false, false,
-                                                        OafMapperUtils
-                                                                .qualifier(
-                                                                        "sysimport:crasswalk:webcrawl", "Imported from Webcrawl",
-                                                                        ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-                                                        "0.9"),
-                                        null));
-
-        return newRelations;
-
-    }
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties
index d7bd709fc..641e72610 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/job.properties
@@ -1,3 +1,11 @@
-sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
-outputPath=/tmp/miriam/webcrawlComplete/
-blackListPath=/user/miriam.baglioni/openalex-blackList
+#PROPERTIES TO CREATE THE ACTION SET
+#sourcePath=/user/miriam.baglioni/openalex-snapshot/data/works/
+#outputPath=/tmp/miriam/webcrawlComplete/
+#blackListPath=/user/miriam.baglioni/openalex-blackList
+#resumeFrom=create
+
+#PROPERTIES TO REMOVE FROM THE ACTION SET
+sourcePath=/var/lib/dnet/actionManager_PROD/webcrawl/rawset_28247629-468b-478e-9a42-bc540877125d_1718121542061/
+outputPath=/tmp/miriam/webcrawlRemoved/
+blackListPath=/user/miriam.baglioni/oalexBlackListNormalized
+resumeFrom=remove
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml
index b9394c7e6..ccf34c557 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/webcrawl/oozie_app/workflow.xml
@@ -20,12 +20,19 @@
         </configuration>
     </global>
 
-    <start to="create_actionset"/>
+    <start to="resumeFrom"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <decision name="resumeFrom">
+        <switch>
+            <case to="create_actionset">${wf:conf('resumeFrom') eq 'create'}</case>
+            <default to="remove_from_actionset"/>
+        </switch>
+    </decision>
+
     <action name="create_actionset">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -50,5 +57,30 @@
         <ok to="End"/>
         <error to="Kill"/>
     </action>
+
+    <action name="remove_from_actionset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Removes some relations found to be wrong from the AS</name>
+            <class>eu.dnetlib.dhp.actionmanager.webcrawl.RemoveRelationFromActionSet</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+            <arg>--blackListPath</arg><arg>${blackListPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
     <end name="End"/>
 </workflow-app>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java
index e9291f93c..d23b7faa2 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateASTest.java
@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.actionmanager.webcrawl;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 import java.io.IOException;
 import java.nio.file.Files;
@@ -101,7 +102,10 @@ public class CreateASTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-		Assertions.assertEquals(58, tmp.count());
+		tmp.foreach(r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
+		tmp.foreach(r -> assertTrue(r.getSource().startsWith("20|ror") || r.getSource().startsWith("50|doi")));
+		tmp.foreach(r -> assertTrue(r.getTarget().startsWith("20|ror") || r.getTarget().startsWith("50|doi")));
+		Assertions.assertEquals(24, tmp.count());
 
 	}
 
@@ -112,7 +116,7 @@ public class CreateASTest {
 
 		String inputPath = getClass()
 			.getResource(
-				"/eu/dnetlib/dhp/actionmanager/webcrawl/")
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/input/")
 			.getPath();
 		String blackListPath = getClass()
 			.getResource(
@@ -194,7 +198,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				2, tmp
+				1, tmp
 					.filter(
 						r -> r
 							.getSource()
@@ -207,7 +211,7 @@ public class CreateASTest {
 
 		Assertions
 			.assertEquals(
-				2, tmp
+				1, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -228,13 +232,13 @@ public class CreateASTest {
 								"20|ror_________::" + IdentifierFactory
 									.md5(
 										PidCleaner
-											.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
+											.normalizePidValue("ROR", "https://ror.org/03265fv13")))
 							&& r.getSource().startsWith("50|doi"))
 					.count());
 
 		Assertions
 			.assertEquals(
-				1, tmp
+				0, tmp
 					.filter(
 						r -> r
 							.getTarget()
@@ -268,6 +272,10 @@ public class CreateASTest {
 			.getResource(
 				"/eu/dnetlib/dhp/actionmanager/webcrawl")
 			.getPath();
+		String blackListPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/blackList/")
+			.getPath();
 
 		CreateActionSetFromWebEntries
 			.main(
@@ -277,7 +285,8 @@ public class CreateASTest {
 					"-sourcePath",
 					inputPath,
 					"-outputPath",
-					workingDir.toString() + "/actionSet1"
+					workingDir.toString() + "/actionSet1",
+					"-blackListPath", blackListPath
 				});
 
 		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveFromASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveFromASTest.java
new file mode 100644
index 000000000..bc78804f2
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveFromASTest.java
@@ -0,0 +1,108 @@
+
+package eu.dnetlib.dhp.actionmanager.webcrawl;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+
+/**
+ * @author miriam.baglioni
+ * @Date 22/04/24
+ */
+public class RemoveFromASTest {
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(RemoveFromASTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(RemoveFromASTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(RemoveFromASTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(RemoveFromASTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testNumberofRelations() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/actionSet/")
+			.getPath();
+		String blackListPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/")
+			.getPath();
+
+		RemoveRelationFromActionSet
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-sourcePath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet1",
+					"-blackListPath", blackListPath
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		Assertions.assertEquals(22, tmp.count());
+
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv
new file mode 100644
index 000000000..009925839
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv
@@ -0,0 +1,2 @@
+DOI / PMID,OpenAlexId,Comments,
+https://doi.org/10.1098/rstl.1684.0023,https://openalex.org/W2124362779,,
\ No newline at end of file

From d4bf449e8c64ec1b46b6aa44764b4e8781fe55f0 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 25 Jul 2024 14:53:06 +0200
Subject: [PATCH 093/239] minor

---
 .../eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java     | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java
index da3915aee..a0692cb34 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/JoinedEntity.java
@@ -5,14 +5,12 @@ import java.io.Serializable;
 import java.util.LinkedList;
 import java.util.List;
 
-import com.fasterxml.jackson.annotation.JsonSubTypes;
-import com.fasterxml.jackson.annotation.JsonTypeInfo;
-
-import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class JoinedEntity implements Serializable {
 
+	private static final long serialVersionUID = -6337458773099581114L;
+
 	private OafEntity entity;
 
 	private List<RelatedEntityWrapper> links;

From 7cff281d3e39d153c0e90cd2dccd88fc836e7e5e Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 25 Jul 2024 15:16:42 +0200
Subject: [PATCH 094/239] [webcrawl] the blacklist is now in json and no more
 in csv after the normalization process

---
 .../webcrawl/RemoveRelationFromActionSet.java              | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
index 33dfbacf1..08d543218 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/RemoveRelationFromActionSet.java
@@ -105,7 +105,7 @@ public class RemoveRelationFromActionSet
 		Dataset<String> blackList = readBlackList(spark, blackListInputPath)
 			.map(
 				(MapFunction<Row, String>) r -> IdentifierFactory
-					.idFromPid("50", "doi", ((String) r.getAs("DOI / PMID")).substring(16), true),
+					.idFromPid("50", "doi", ((String) r.getAs("doi")).substring(16), true),
 				Encoders.STRING());
 
 		// read the old actionset and get the relations in the payload
@@ -151,9 +151,8 @@ public class RemoveRelationFromActionSet
 
 		return spark
 			.read()
-			.option("header", true)
-			.csv(inputPath)
-			.select("DOI / PMID");
+			.json(inputPath)
+			.select("doi");
 	}
 
 }

From c7f6669f1a8fc9596c76b242f041249c4c778b2c Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 25 Jul 2024 15:20:18 +0200
Subject: [PATCH 095/239] [webcrawl] the blacklist is now in json and no more
 in csv after the normalization process

---
 .../actionmanager/webcrawl/CreateActionSetFromWebEntries.java  | 3 +--
 .../dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv   | 2 --
 .../dhp/actionmanager/webcrawl/blackListRemove/not_irish.json  | 1 +
 3 files changed, 2 insertions(+), 4 deletions(-)
 delete mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.json

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
index 7607cfc76..b5aed6ea2 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/webcrawl/CreateActionSetFromWebEntries.java
@@ -148,8 +148,7 @@ public class CreateActionSetFromWebEntries implements Serializable {
 
 		return spark
 			.read()
-			.option("header", true)
-			.csv(inputPath)
+			.json(inputPath)
 			.select("OpenAlexId");
 	}
 
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv
deleted file mode 100644
index 009925839..000000000
--- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.csv
+++ /dev/null
@@ -1,2 +0,0 @@
-DOI / PMID,OpenAlexId,Comments,
-https://doi.org/10.1098/rstl.1684.0023,https://openalex.org/W2124362779,,
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.json
new file mode 100644
index 000000000..2c470c555
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/webcrawl/blackListRemove/not_irish.json
@@ -0,0 +1 @@
+{"doi":"https://doi.org/10.1098/rstl.1684.0023","OpenAlexId":"https://openalex.org/W2124362779"}
\ No newline at end of file

From 359b8ebda81abb5fd82fa26028b65dd0fa7bead0 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 25 Jul 2024 15:22:29 +0200
Subject: [PATCH 096/239] [graph provision] include only FoS L1..L2 in the
 record serialization

---
 .../model/ProvisionModelSupport.java          | 11 ++++++++
 .../oa/provision/utils/XmlRecordFactory.java  |  6 ++--
 .../utils/XmlSerializationUtils.java          |  4 ---
 .../oa/provision/XmlRecordFactoryTest.java    |  2 ++
 .../dnetlib/dhp/oa/provision/publication.json | 28 +++++++++++++++++--
 5 files changed, 40 insertions(+), 11 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 1a75deafc..277d0deb6 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -702,6 +702,7 @@ public class ProvisionModelSupport {
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
 					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
+					.filter(ProvisionModelSupport::filterFosL1L2)
 					.map(
 						s -> Subject
 							.newInstance(s.getValue(), s.getQualifier().getClassid(), s.getQualifier().getClassname()))
@@ -709,6 +710,16 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
+	public static boolean filterFosL1L2(StructuredProperty s) {
+		final String subjectType = Optional.ofNullable(s.getQualifier()).map(Qualifier::getClassid).orElse("");
+		if (ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(subjectType)) {
+			String code = StringUtils.substringBefore(s.getValue(), " ");
+			return code.matches("^\\d{2}$|^\\d{4}$");
+		}
+
+		return true;
+	}
+
 	private static Country asCountry(eu.dnetlib.dhp.schema.oaf.Qualifier country) {
 		return Optional
 			.ofNullable(country)
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index 899dad221..44004faf3 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -20,6 +20,7 @@ import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
+import eu.dnetlib.dhp.oa.provision.model.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -41,10 +42,6 @@ import com.google.common.collect.Sets;
 import com.mycila.xmltool.XMLDoc;
 import com.mycila.xmltool.XMLTag;
 
-import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
-import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
-import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
-import eu.dnetlib.dhp.oa.provision.model.XmlInstance;
 import eu.dnetlib.dhp.schema.common.*;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Result;
@@ -389,6 +386,7 @@ public class XmlRecordFactory implements Serializable {
 							.getSubject()
 							.stream()
 							.filter(Objects::nonNull)
+							.filter(ProvisionModelSupport::filterFosL1L2)
 							.map(s -> XmlSerializationUtils.mapStructuredProperty("subject", s))
 							.collect(Collectors.toList()));
 			}
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
index fbd647ae4..b4517002c 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
@@ -5,11 +5,7 @@ import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.removePrefix;
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
 
-import java.util.HashSet;
 import java.util.List;
-import java.util.Optional;
-import java.util.Set;
-import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
index ab4301f9a..dcd021db1 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
+++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
@@ -97,6 +97,8 @@ public class XmlRecordFactoryTest {
 		assertEquals("bronze", doc.valueOf("//*[local-name() = 'result']/openaccesscolor/text()"));
 		assertEquals("true", doc.valueOf("//*[local-name() = 'result']/isindiamondjournal/text()"));
 		assertEquals("true", doc.valueOf("//*[local-name() = 'result']/publiclyfunded/text()"));
+
+		assertEquals(15, doc.selectNodes("//*[local-name() = 'result']/*[local-name() = 'subject']").size());
 	}
 
 	@Test
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
index a89ec62d5..a073fbebd 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
@@ -1886,12 +1886,34 @@
         "trust": ""
       },
       "qualifier": {
-        "classid": "keyword",
-        "classname": "keyword",
+        "classid": "FOS",
+        "classname": "Fields of Science and Technology classification",
         "schemeid": "dnet:subject_classification_typologies",
         "schemename": "dnet:subject_classification_typologies"
       },
-      "value": "Thermal conductivity"
+      "value": "0101 mathematics"
+    },
+    {
+      "dataInfo": {
+        "deletedbyinference": false,
+        "inferenceprovenance": "",
+        "inferred": false,
+        "invisible": false,
+        "provenanceaction": {
+          "classid": "",
+          "classname": "",
+          "schemeid": "",
+          "schemename": ""
+        },
+        "trust": ""
+      },
+      "qualifier": {
+        "classid": "FOS",
+        "classname": "Fields of Science and Technology classification",
+        "schemeid": "dnet:subject_classification_typologies",
+        "schemename": "dnet:subject_classification_typologies"
+      },
+      "value": "010101 applied mathematics"
     }
   ],
   "title": [

From a81c555fe6bfa23b7c4108eac2d0415d78c8a630 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 25 Jul 2024 15:26:47 +0200
Subject: [PATCH 097/239] [graph provision] include only FoS L1..L2 in the
 record serialization

---
 .../dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 277d0deb6..4a2326453 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -687,6 +687,7 @@ public class ProvisionModelSupport {
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
 					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
+					.filter(ProvisionModelSupport::filterFosL1L2)
 					.map(
 						s -> Subject
 							.newInstance(s.getValue(), s.getQualifier().getClassid(), s.getQualifier().getClassname()))
@@ -702,7 +703,6 @@ public class ProvisionModelSupport {
 					.stream()
 					.filter(s -> Objects.nonNull(s.getQualifier()))
 					.filter(s -> Objects.nonNull(s.getQualifier().getClassname()))
-					.filter(ProvisionModelSupport::filterFosL1L2)
 					.map(
 						s -> Subject
 							.newInstance(s.getValue(), s.getQualifier().getClassid(), s.getQualifier().getClassname()))

From 75a11d0ba5a3ff9a362c7c160ace11d0965a57a5 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 25 Jul 2024 16:34:32 +0200
Subject: [PATCH 098/239] [dedup] avoid NPEs in the countryInference dedup
 utility

---
 .../dnetlib/pace/common/AbstractPaceFunctions.java   |  2 +-
 .../eu/dnetlib/pace/common/PaceFunctionTest.java     | 12 ++++++++++--
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
index 6ef550c50..12a54bade 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/common/AbstractPaceFunctions.java
@@ -90,7 +90,7 @@ public class AbstractPaceFunctions extends PaceCommonUtils {
 		inferFrom = normalize(inferFrom);
 		inferFrom = filterAllStopWords(inferFrom);
 		Set<String> cities = getCities(inferFrom, 4);
-		return citiesToCountry(cities).stream().findFirst().orElse("UNKNOWN");
+		return citiesToCountry(cities).stream().filter(Objects::nonNull).findFirst().orElse("UNKNOWN");
 	}
 
 	public static String cityInference(String original) {
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java
index 4ec120f4a..92f7bf6ff 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/common/PaceFunctionTest.java
@@ -1,8 +1,7 @@
 
 package eu.dnetlib.pace.common;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.*;
 
 import org.junit.jupiter.api.*;
 
@@ -54,8 +53,17 @@ public class PaceFunctionTest extends AbstractPaceFunctions {
 		System.out.println("Fixed aliases  : " + fixAliases(TEST_STRING));
 	}
 
+	@Test()
+	public void countryInferenceTest_NPE() {
+		assertThrows(
+			NullPointerException.class,
+			() -> countryInference("UNKNOWN", null),
+			"Expected countryInference() to throw an NPE");
+	}
+
 	@Test
 	public void countryInferenceTest() {
+		assertEquals("UNKNOWN", countryInference("UNKNOWN", ""));
 		assertEquals("IT", countryInference("UNKNOWN", "Università di Bologna"));
 		assertEquals("UK", countryInference("UK", "Università di Bologna"));
 		assertEquals("IT", countryInference("UNKNOWN", "Universiteé de Naples"));

From 64740475d0a8f0209165cb15fc7f44b125700a23 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 29 Jul 2024 11:51:42 +0200
Subject: [PATCH 099/239] depending on dhp-schemas:7.0.1

---
 .../personentity/ExtractPerson.java            | 18 ++++++++++++------
 .../actionmanager/person/CreatePersonAS.java   | 13 +------------
 pom.xml                                        |  2 +-
 3 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 064fb41a1..d381ed176 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -13,7 +13,6 @@ import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.BZip2Codec;
-import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.*;
@@ -25,8 +24,6 @@ import org.spark_project.jetty.util.StringUtil;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.Constants;
-import eu.dnetlib.dhp.actionmanager.transformativeagreement.model.TransformativeAgreementModel;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.collection.orcid.model.Author;
 import eu.dnetlib.dhp.collection.orcid.model.Employment;
@@ -37,7 +34,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Person;
-import eu.dnetlib.dhp.schema.oaf.Pid;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@@ -181,10 +177,20 @@ public class ExtractPerson implements Serializable {
 						.map(
 							v -> v
 								.stream()
-								.map(p -> Pid.newInstance(p.getSchema(), p.getValue()))
+								.map(
+									p -> OafMapperUtils
+										.structuredProperty(
+											p.getValue(), p.getSchema(), p.getSchema(), ModelConstants.DNET_PID_TYPES,
+											ModelConstants.DNET_PID_TYPES, null))
 								.collect(Collectors.toList()))
 						.orElse(new ArrayList<>()));
-			person.getPid().add(Pid.newInstance(ModelConstants.ORCID, op.getOrcid()));
+			person
+				.getPid()
+				.add(
+					OafMapperUtils
+						.structuredProperty(
+							op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME,
+							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null));
 			person.setDateofcollection(op.getLastModifiedDate());
 			person.setOriginalId(Arrays.asList(op.getOrcid()));
 			return person;
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
index 2e7b21010..b5333c2fb 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/person/CreatePersonAS.java
@@ -1,22 +1,15 @@
 
 package eu.dnetlib.dhp.actionmanager.person;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
-import java.util.Optional;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.Assertions;
@@ -27,15 +20,11 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
 import eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson;
-import eu.dnetlib.dhp.collection.orcid.model.Author;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Person;
 import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class CreatePersonAS {
@@ -167,7 +156,7 @@ public class CreatePersonAS {
 					.getPid()
 					.stream()
 					.anyMatch(
-						p -> p.getSchema().equalsIgnoreCase("Scopus Author ID")
+						p -> p.getQualifier().getSchemename().equalsIgnoreCase("Scopus Author ID")
 							&& p.getValue().equalsIgnoreCase("15119405200")));
 
 		Assertions
diff --git a/pom.xml b/pom.xml
index dc1dd7308..666ba2350 100644
--- a/pom.xml
+++ b/pom.xml
@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[7.0.0]</dhp-schemas.version>
+        <dhp-schemas.version>[7.0.1]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From 9486e21a44f9c8e13919e7d43f34983866e3874f Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 30 Jul 2024 14:25:31 +0200
Subject: [PATCH 100/239] copy or process the person records throughout the
 graph pipeline

---
 .../oaf/utils/GraphCleaningFunctions.java     |   2 +
 .../wf/main/oozie_app/import.txt              |   1 +
 .../wf/main/oozie_app/workflow.xml            |  16 +++
 .../wf/person/oozie_app/workflow.xml          | 130 ++++++++++++++++++
 .../dhp/blacklist/oozie_app/workflow.xml      |  10 ++
 .../oozie_app/workflow.xml                    |  12 ++
 .../dhp/enrich/orcid/oozie_app/workflow.xml   |   8 ++
 .../dhp/oa/graph/clean/oozie_app/workflow.xml |  36 +++++
 8 files changed, 215 insertions(+)
 create mode 100644 dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
index 2be4e8e0c..b9dc3253b 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@@ -363,6 +363,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 				// nothing to clean here
 			} else if (value instanceof Project) {
 				// nothing to clean here
+			} else if (value instanceof Person) {
+				// nothing to clean here
 			} else if (value instanceof Organization) {
 				Organization o = (Organization) value;
 				if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt
index dd8f5e14e..14409a42a 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/import.txt
@@ -7,3 +7,4 @@ promote_action_payload_for_project_table classpath eu/dnetlib/dhp/actionmanager/
 promote_action_payload_for_publication_table classpath eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app
 promote_action_payload_for_relation_table classpath eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app
 promote_action_payload_for_software_table classpath eu/dnetlib/dhp/actionmanager/wf/software/oozie_app
+promote_action_payload_for_person_table classpath eu/dnetlib/dhp/actionmanager/wf/person/oozie_app
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
index 65ddd402b..7ccfb342e 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
@@ -148,6 +148,7 @@
         <path start="PromoteActionPayloadForPublicationTable"/>
         <path start="PromoteActionPayloadForRelationTable"/>
         <path start="PromoteActionPayloadForSoftwareTable"/>
+        <path start="PromoteActionPayloadForPersonTable"/>
     </fork>
 
     <action name="PromoteActionPayloadForDatasetTable">
@@ -270,6 +271,21 @@
         <error to="Kill"/>
     </action>
 
+    <action name="PromoteActionPayloadForPersonTable">
+        <sub-workflow>
+            <app-path>${wf:appPath()}/promote_action_payload_for_person_table</app-path>
+            <propagate-configuration/>
+            <configuration>
+                <property>
+                    <name>inputActionPayloadRootPath</name>
+                    <value>${workingDir}/action_payload_by_type</value>
+                </property>
+            </configuration>
+        </sub-workflow>
+        <ok to="JoinPromote"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="JoinPromote" to="End"/>
 
     <end name="End"/>
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml
new file mode 100644
index 000000000..7c119b305
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml
@@ -0,0 +1,130 @@
+<workflow-app name="promote_action_payload_for_person_table" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>activePromotePersonActionPayload</name>
+            <description>when true will promote actions with eu.dnetlib.dhp.schema.oaf.Person payload</description>
+        </property>
+        <property>
+            <name>inputGraphRootPath</name>
+            <description>root location of input materialized graph</description>
+        </property>
+        <property>
+            <name>inputActionPayloadRootPath</name>
+            <description>root location of action payloads to promote</description>
+        </property>
+        <property>
+            <name>outputGraphRootPath</name>
+            <description>root location for output materialized graph</description>
+        </property>
+        <property>
+            <name>mergeAndGetStrategy</name>
+            <description>strategy for merging graph table objects with action payload instances, MERGE_FROM_AND_GET or SELECT_NEWER_AND_GET</description>
+        </property>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="DecisionPromotePersonActionPayload"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <decision name="DecisionPromotePersonActionPayload">
+        <switch>
+            <case to="PromotePersonActionPayloadForPersonTable">
+                ${(activePromotePersonActionPayload eq "true") and
+                (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'person')) eq "true") and
+                (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Person')) eq "true")}
+            </case>
+            <default to="SkipPromotePersonActionPayloadForPersonTable"/>
+        </switch>
+    </decision>
+
+    <action name="PromotePersonActionPayloadForPersonTable">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>PromotePersonActionPayloadForPersonTable</name>
+            <class>eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJob</class>
+            <jar>dhp-actionmanager-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+            </spark-opts>
+            <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/person</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--inputActionPayloadPath</arg><arg>${inputActionPayloadRootPath}/clazz=eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--actionPayloadClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--outputGraphTablePath</arg><arg>${outputGraphRootPath}/person</arg>
+            <arg>--mergeAndGetStrategy</arg><arg>${mergeAndGetStrategy}</arg>
+            <arg>--promoteActionStrategy</arg><arg>${promoteActionStrategy}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="SkipPromotePersonActionPayloadForPersonTable">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <prepare>
+                <delete path="${outputGraphRootPath}/person"/>
+            </prepare>
+            <arg>-pb</arg>
+            <arg>${inputGraphRootPath}/person</arg>
+            <arg>${outputGraphRootPath}/person</arg>
+        </distcp>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml
index dd7827da4..563a549f3 100644
--- a/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-blacklist/src/main/resources/eu/dnetlib/dhp/blacklist/oozie_app/workflow.xml
@@ -63,6 +63,7 @@
         <path start="copy_software"/>
         <path start="copy_datasource"/>
         <path start="copy_project"/>
+        <path start="copy_person"/>
         <path start="copy_organization"/>
     </fork>
 
@@ -120,6 +121,15 @@
         <error to="Kill"/>
     </action>
 
+    <action name="copy_person">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <arg>${nameNode}/${sourcePath}/person</arg>
+            <arg>${nameNode}/${outputPath}/person</arg>
+        </distcp>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="copy_datasource">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
             <arg>${nameNode}/${sourcePath}/datasource</arg>
diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml
index ba3633e07..8eaa79c53 100644
--- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml
@@ -34,6 +34,7 @@
         <path start="copy_organization"/>
         <path start="copy_projects"/>
         <path start="copy_datasources"/>
+        <path start="copy_persons"/>
     </fork>
 
     <action name="copy_relation">
@@ -80,6 +81,17 @@
         <error to="Kill"/>
     </action>
 
+    <action name="copy_persons">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/person</arg>
+            <arg>${nameNode}/${outputPath}/person</arg>
+        </distcp>
+        <ok to="copy_wait"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="copy_wait" to="fork_prepare_assoc_step1"/>
 
     <fork name="fork_prepare_assoc_step1">
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml
index 72fc9e338..4031da15a 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml
@@ -89,6 +89,14 @@
             <arg>${nameNode}/${graphPath}/project</arg>
             <arg>${nameNode}/${targetPath}/project</arg>
         </distcp>
+        <ok to="copy_person"/>
+        <error to="Kill"/>
+    </action>
+    <action name="copy_person">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <arg>${nameNode}/${graphPath}/person</arg>
+            <arg>${nameNode}/${targetPath}/person</arg>
+        </distcp>
         <ok to="copy_relation"/>
         <error to="Kill"/>
     </action>
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
index 4188cb018..2512fc5bc 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
@@ -142,6 +142,7 @@
         <path start="clean_datasource"/>
         <path start="clean_organization"/>
         <path start="clean_project"/>
+        <path start="clean_person"/>
         <path start="clean_relation"/>
     </fork>
 
@@ -390,6 +391,41 @@
         <error to="Kill"/>
     </action>
 
+    <action name="clean_person">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Clean person</name>
+            <class>eu.dnetlib.dhp.oa.graph.clean.CleanGraphSparkJob</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=2000
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${graphInputPath}/person</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/person</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
+            <arg>--contextId</arg><arg>${contextId}</arg>
+            <arg>--verifyParam</arg><arg>${verifyParam}</arg>
+            <arg>--country</arg><arg>${country}</arg>
+            <arg>--verifyCountryParam</arg><arg>${verifyCountryParam}</arg>
+            <arg>--hostedBy</arg><arg>${workingDir}/working/hostedby</arg>
+            <arg>--collectedfrom</arg><arg>${collectedfrom}</arg>
+            <arg>--masterDuplicatePath</arg><arg>${workingDir}/masterduplicate</arg>
+            <arg>--deepClean</arg><arg>${shouldClean}</arg>
+        </spark>
+        <ok to="wait_clean"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="clean_relation">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>

From 6bdb8643e6531ea0acf004f14a10a8baf55fa308 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 31 Jul 2024 11:02:22 +0200
Subject: [PATCH 101/239] ActionManager promote: allow to ingest person records
 in a graph that did not contain them, bumped dhp-schemas version

---
 .../PromoteActionPayloadForGraphTableJob.java | 21 ++++++++++++-------
 .../PromoteActionPayloadFunctions.java        |  2 +-
 .../wf/person/oozie_app/workflow.xml          |  1 -
 pom.xml                                       |  2 +-
 4 files changed, 16 insertions(+), 10 deletions(-)

diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
index 56cbda4d6..f72fd4269 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
+++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java
@@ -151,12 +151,17 @@ public class PromoteActionPayloadForGraphTableJob {
 		SparkSession spark, String path, Class<G> rowClazz) {
 		logger.info("Reading graph table from path: {}", path);
 
-		return spark
-			.read()
-			.textFile(path)
-			.map(
-				(MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz),
-				Encoders.bean(rowClazz));
+		if (HdfsSupport.exists(path, spark.sparkContext().hadoopConfiguration())) {
+			return spark
+				.read()
+				.textFile(path)
+				.map(
+					(MapFunction<String, G>) value -> OBJECT_MAPPER.readValue(value, rowClazz),
+					Encoders.bean(rowClazz));
+		} else {
+			logger.info("Found empty graph table from path: {}", path);
+			return spark.emptyDataset(Encoders.bean(rowClazz));
+		}
 	}
 
 	private static <A extends Oaf> Dataset<A> readActionPayload(
@@ -223,7 +228,7 @@ public class PromoteActionPayloadForGraphTableJob {
 				rowClazz,
 				actionPayloadClazz);
 
-		if (shouldGroupById) {
+		if (Boolean.TRUE.equals(shouldGroupById)) {
 			return PromoteActionPayloadFunctions
 				.groupGraphTableByIdAndMerge(
 					joinedAndMerged, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, rowClazz);
@@ -250,6 +255,8 @@ public class PromoteActionPayloadForGraphTableJob {
 				return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Relation());
 			case "eu.dnetlib.dhp.schema.oaf.Software":
 				return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Software());
+			case "eu.dnetlib.dhp.schema.oaf.Person":
+				return () -> clazz.cast(new eu.dnetlib.dhp.schema.oaf.Person());
 			default:
 				throw new RuntimeException("unknown class: " + clazz.getCanonicalName());
 		}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
index f0b094240..a3b975d0a 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
+++ b/dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctions.java
@@ -50,7 +50,7 @@ public class PromoteActionPayloadFunctions {
 		PromoteAction.Strategy promoteActionStrategy,
 		Class<G> rowClazz,
 		Class<A> actionPayloadClazz) {
-		if (!isSubClass(rowClazz, actionPayloadClazz)) {
+		if (Boolean.FALSE.equals(isSubClass(rowClazz, actionPayloadClazz))) {
 			throw new RuntimeException(
 				"action payload type must be the same or be a super type of table row type");
 		}
diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml
index 7c119b305..1bacd09f1 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/person/oozie_app/workflow.xml
@@ -77,7 +77,6 @@
         <switch>
             <case to="PromotePersonActionPayloadForPersonTable">
                 ${(activePromotePersonActionPayload eq "true") and
-                (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputGraphRootPath')),'/'),'person')) eq "true") and
                 (fs:exists(concat(concat(concat(concat(wf:conf('nameNode'),'/'),wf:conf('inputActionPayloadRootPath')),'/'),'clazz=eu.dnetlib.dhp.schema.oaf.Person')) eq "true")}
             </case>
             <default to="SkipPromotePersonActionPayloadForPersonTable"/>
diff --git a/pom.xml b/pom.xml
index 666ba2350..175cb9e7c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[7.0.1]</dhp-schemas.version>
+        <dhp-schemas.version>[7.0.2]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From 975d44cac7e9fa617c9b00070eba88edafc98c7d Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 2 Aug 2024 16:14:10 +0200
Subject: [PATCH 102/239] [graph provision] added person to the provision
 workflow

---
 .../model/ProvisionModelSupport.java          | 11 ++++
 .../dhp/oa/provision/oozie_app/workflow.xml   | 59 +++++++++++++++++++
 2 files changed, 70 insertions(+)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 1a75deafc..196faf9ca 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,6 +5,7 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.solr.Person;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -89,6 +90,8 @@ public class ProvisionModelSupport {
 			r.setOrganization(mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) e));
 		} else if (e instanceof eu.dnetlib.dhp.schema.oaf.Project) {
 			r.setProject(mapProject((eu.dnetlib.dhp.schema.oaf.Project) e, vocs));
+		} else if (e instanceof eu.dnetlib.dhp.schema.oaf.Person) {
+			r.setPerson(mapPerson((eu.dnetlib.dhp.schema.oaf.Person) e));
 		}
 		r
 			.setLinks(
@@ -185,6 +188,14 @@ public class ProvisionModelSupport {
 		return ps;
 	}
 
+	private static Person mapPerson(eu.dnetlib.dhp.schema.oaf.Person p) {
+		Person ps = new Person();
+		ps.setFamilyName(p.getFamilyName());
+		ps.setGivenName(p.getGivenName());
+		ps.setAlternativeNames(p.getAlternativeNames());
+		return ps;
+	}
+
 	private static Funding mapFunding(List<String> fundingtree, VocabularyGroup vocs) {
 		SAXReader reader = new SAXReader();
 		return Optional
diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
index 15d3b6300..879911ccc 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/oa/provision/oozie_app/workflow.xml
@@ -180,6 +180,7 @@
         <path start="join_relation_datasource"/>
         <path start="join_relation_organization"/>
         <path start="join_relation_project"/>
+        <path start="join_relation_person"/>
     </fork>
 
     <action name="join_relation_publication">
@@ -378,6 +379,34 @@
         <error to="Kill"/>
     </action>
 
+    <action name="join_relation_person">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Join[relation.target = person.id]</name>
+            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
+            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/person</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/join_partial/person</arg>
+        </spark>
+        <ok to="wait_joins"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="wait_joins" to="fork_join_all_entities"/>
 
     <fork name="fork_join_all_entities">
@@ -388,6 +417,7 @@
         <path start="join_datasource_relations"/>
         <path start="join_organization_relations"/>
         <path start="join_project_relations"/>
+        <path start="join_person_relations"/>
     </fork>
 
     <action name="join_publication_relations">
@@ -593,6 +623,35 @@
         <error to="Kill"/>
     </action>
 
+    <action name="join_person_relations">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Join[person.id = relatedEntity.source]</name>
+            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
+            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCoresForJoining}
+                --executor-memory=${sparkExecutorMemoryForJoining}
+                --driver-memory=${sparkDriverMemoryForJoining}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemoryForJoining}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.network.timeout=${sparkNetworkTimeout}
+            </spark-opts>
+            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/person</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/join_entities/person</arg>
+            <arg>--numPartitions</arg><arg>10000</arg>
+        </spark>
+        <ok to="wait_join_phase2"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="wait_join_phase2" to="create_payloads"/>
 
     <action name="create_payloads">

From 0bf76f2a3401c550dea7da6c1fd4c38ca3903527 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 5 Aug 2024 09:35:07 +0200
Subject: [PATCH 103/239] [graph provision] added person to the graph2hive
 workflow

---
 .../dhp/oa/graph/hive/oozie_app/workflow.xml  | 30 +++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
index eec67fc5c..872ef8a2d 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hive/oozie_app/workflow.xml
@@ -102,6 +102,7 @@
         <path start="import_datasource"/>
         <path start="import_organization"/>
         <path start="import_project"/>
+        <path start="import_person"/>
         <path start="import_relation"/>
     </fork>
 
@@ -308,6 +309,35 @@
         <error to="Kill"/>
     </action>
 
+    <action name="import_person">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Import table person</name>
+            <class>eu.dnetlib.dhp.oa.graph.hive.GraphHiveTableImporterJob</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.executor.memoryOverhead=${sparkExecutorMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+                --conf spark.sql.shuffle.partitions=1000
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/person</arg>
+            <arg>--hiveDbName</arg><arg>${hiveDbName}</arg>
+            <arg>--className</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--hiveMetastoreUris</arg><arg>${hiveMetastoreUris}</arg>
+            <arg>--numPartitions</arg><arg>1000</arg>
+        </spark>
+        <ok to="join_import"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="import_relation">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>

From 985ca15264dbe3e7a3407451b2c883c76d2d87dd Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 5 Aug 2024 12:10:40 +0200
Subject: [PATCH 104/239] [openaire-affiliation]removes matchings without DOI

---
 .../bipaffiliations/PrepareAffiliationRelations.java        | 3 ++-
 .../dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala  | 6 ++++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 8f911e980..633e53d46 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -129,7 +129,8 @@ public class PrepareAffiliationRelations implements Serializable {
 		Dataset<Row> df = spark
 			.read()
 			.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-			.json(inputPath);
+			.json(inputPath)
+				.where("DOI is not NULL");
 
 		// unroll nested arrays
 		df = df
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
index f3a5fe77c..4e5ad5365 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
@@ -31,5 +31,11 @@ class ORCIDAuthorMatchersTest {
     assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin"))
     // assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented
   }
+  @Test def testDocumentationNames(): Unit = {
+    assertTrue(matchOrderedTokenAndAbbreviations("James C. A. Miller-Jones", "James Antony Miller-Jones"))
+  }
 
+  @Test def testDocumentationNames2(): Unit = {
+    assertTrue(matchOrderedTokenAndAbbreviations("James C. A. Miller-Jones", "James Antony Miller Jones"))
+  }
 }

From 8e7ef79ce09d41d57d9d70f90875563bd2799e40 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 5 Aug 2024 12:13:48 +0200
Subject: [PATCH 105/239] [bip affiliations] considers only DOI based records

---
 .../bipaffiliations/PrepareAffiliationRelations.java           | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 8f911e980..98915bdc5 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -129,7 +129,8 @@ public class PrepareAffiliationRelations implements Serializable {
 		Dataset<Row> df = spark
 			.read()
 			.schema("`DOI` STRING, `Matchings` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-			.json(inputPath);
+			.json(inputPath)
+			.where("DOI is not null");
 
 		// unroll nested arrays
 		df = df

From e16616b9646b77622a1a035574f2e8a39932294d Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 5 Aug 2024 15:57:37 +0200
Subject: [PATCH 106/239] added dataInfo to person records

---
 .../personentity/ExtractPerson.java           | 52 +++++++------------
 1 file changed, 20 insertions(+), 32 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index d381ed176..7e82698f7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -32,6 +32,7 @@ import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Person;
 import eu.dnetlib.dhp.schema.oaf.Relation;
@@ -62,6 +63,20 @@ public class ExtractPerson implements Serializable {
 	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
 	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
 
+	public static final DataInfo DATAINFO = OafMapperUtils
+		.dataInfo(
+			false,
+			null,
+			false,
+			false,
+			OafMapperUtils
+				.qualifier(
+					ORCID_AUTHORS_CLASSID,
+					ORCID_AUTHORS_CLASSNAME,
+					ModelConstants.DNET_PROVENANCE_ACTIONS,
+					ModelConstants.DNET_PROVENANCE_ACTIONS),
+			"0.91");
+
 	public static void main(final String[] args) throws IOException, ParseException {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -193,6 +208,7 @@ public class ExtractPerson implements Serializable {
 							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null));
 			person.setDateofcollection(op.getLastModifiedDate());
 			person.setOriginalId(Arrays.asList(op.getOrcid()));
+			person.setDataInfo(DATAINFO);
 			return person;
 		}, Encoders.bean(Person.class))
 			.write()
@@ -307,14 +323,7 @@ public class ExtractPerson implements Serializable {
 				source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE,
 				ModelConstants.ORG_PERSON_PARTICIPATES,
 				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				OafMapperUtils
-					.dataInfo(
-						false, null, false, false,
-						OafMapperUtils
-							.qualifier(
-								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						"0.91"),
+				DATAINFO,
 				null);
 
 		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
@@ -348,14 +357,7 @@ public class ExtractPerson implements Serializable {
 						ModelConstants.PERSON_PERSON_SUBRELTYPE,
 						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
 						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						OafMapperUtils
-							.dataInfo(
-								false, null, false, false,
-								OafMapperUtils
-									.qualifier(
-										ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
-										ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-								"0.91"),
+						DATAINFO,
 						null),
 				OafMapperUtils
 					.getRelation(
@@ -363,14 +365,7 @@ public class ExtractPerson implements Serializable {
 						ModelConstants.PERSON_PERSON_SUBRELTYPE,
 						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
 						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						OafMapperUtils
-							.dataInfo(
-								false, null, false, false,
-								OafMapperUtils
-									.qualifier(
-										ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME,
-										ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
-								"0.91"),
+						DATAINFO,
 						null));
 
 	}
@@ -424,14 +419,7 @@ public class ExtractPerson implements Serializable {
 				ModelConstants.RESULT_PERSON_SUBRELTYPE,
 				ModelConstants.RESULT_PERSON_HASAUTHORED,
 				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				OafMapperUtils
-					.dataInfo(
-						false, null, false, false,
-						OafMapperUtils
-							.qualifier(
-								ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						"0.91"),
+				DATAINFO,
 				null);
 	}
 }

From 5a7ba772717c36a7f5ccbf442b427337e700a0b5 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 12 Aug 2024 18:01:15 +0200
Subject: [PATCH 107/239] [Person]fix issue in affiliation relation id
 construction for person (missing ::)

---
 .../dnetlib/dhp/actionmanager/personentity/ExtractPerson.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 7e82698f7..6f61d427d 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -313,7 +313,7 @@ public class ExtractPerson implements Serializable {
 	}
 
 	private static Relation getAffiliationRelation(Employment row) {
-		String source = PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
+		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(row.getOrcid());
 		String target = ROR_PREFIX
 			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
 		List<KeyValue> properties = new ArrayList<>();

From 89fcf4086c9562269b4020e2f7888a051b167ed6 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 12 Aug 2024 18:04:43 +0200
Subject: [PATCH 108/239] [Person]fix issue in affiliation relation id
 construction for person (missing ::)

---
 .../dnetlib/dhp/actionmanager/personentity/ExtractPerson.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index d381ed176..e63a50984 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -297,7 +297,7 @@ public class ExtractPerson implements Serializable {
 	}
 
 	private static Relation getAffiliationRelation(Employment row) {
-		String source = PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
+		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(row.getOrcid());
 		String target = ROR_PREFIX
 			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
 		List<KeyValue> properties = new ArrayList<>();

From 468f2aa5a58ca1aee198ea96b714060a9931b313 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 12 Aug 2024 18:10:46 +0200
Subject: [PATCH 109/239] [AffiliationAffRo]align beta with new affiliation
 from publisher webpage introduced in production. AffRo collectedfrom OpenAIRE
 to discriminate against WebCrawl

---
 .../PrepareAffiliationRelations.java          | 102 ++++++++++++------
 .../PrepareAffiliationRelationsTest.java      |  18 +++-
 2 files changed, 83 insertions(+), 37 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 98915bdc5..70ca1576c 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -44,6 +44,8 @@ public class PrepareAffiliationRelations implements Serializable {
 	public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:openaireinference";
 	public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by OpenAIRE";
 	public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
+	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
+	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
 
 	public static <I extends Result> void main(String[] args) throws Exception {
 
@@ -74,6 +76,9 @@ public class PrepareAffiliationRelations implements Serializable {
 		final String webcrawlInputPath = parser.get("webCrawlInputPath");
 		log.info("webcrawlInputPath: {}", webcrawlInputPath);
 
+		final String publisherInputPath = parser.get("publisherInputPath");
+		log.info("publisherInputPath: {}", publisherInputPath);
+
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
@@ -84,43 +89,68 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, outputPath);
-
-				List<KeyValue> collectedFromCrossref = OafMapperUtils
-					.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
-				JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
-					spark, crossrefInputPath, collectedFromCrossref);
-
-				List<KeyValue> collectedFromPubmed = OafMapperUtils
-					.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
-				JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-					spark, pubmedInputPath, collectedFromPubmed);
-
-				List<KeyValue> collectedFromOpenAPC = OafMapperUtils
-					.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
-				JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
-					spark, openapcInputPath, collectedFromOpenAPC);
-
-				List<KeyValue> collectedFromDatacite = OafMapperUtils
-					.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
-				JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
-					spark, dataciteInputPath, collectedFromDatacite);
-
-				List<KeyValue> collectedFromWebCrawl = OafMapperUtils
-					.listKeyValues(Constants.WEB_CRAWL_ID, Constants.WEB_CRAWL_NAME);
-				JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-					spark, webcrawlInputPath, collectedFromWebCrawl);
-
-				crossrefRelations
-					.union(pubmedRelations)
-					.union(openAPCRelations)
-					.union(dataciteRelations)
-					.union(webCrawlRelations)
-					.saveAsHadoopFile(
-						outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
-
+				createActionSet(
+					spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
+					publisherInputPath, outputPath);
 			});
 	}
 
+	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
+		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
+		String outputPath) {
+		List<KeyValue> collectedFromCrossref = OafMapperUtils
+			.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
+		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
+			spark, crossrefInputPath, collectedFromCrossref);
+
+		List<KeyValue> collectedFromPubmed = OafMapperUtils
+			.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
+		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
+			spark, pubmedInputPath, collectedFromPubmed);
+
+		List<KeyValue> collectedFromOpenAPC = OafMapperUtils
+			.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
+		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
+			spark, openapcInputPath, collectedFromOpenAPC);
+
+		List<KeyValue> collectedFromDatacite = OafMapperUtils
+			.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
+		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
+			spark, dataciteInputPath, collectedFromDatacite);
+
+		List<KeyValue> collectedFromWebCrawl = OafMapperUtils
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
+			spark, webcrawlInputPath, collectedFromWebCrawl);
+
+		List<KeyValue> collectedfromPublisher = OafMapperUtils
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
+			spark, publisherlInputPath, collectedfromPublisher);
+
+		crossrefRelations
+			.union(pubmedRelations)
+			.union(openAPCRelations)
+			.union(dataciteRelations)
+			.union(webCrawlRelations)
+			.union(publisherRelations)
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+	}
+
+	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
+		List<KeyValue> collectedfrom) {
+
+		Dataset<Row> df = spark
+			.read()
+			.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
+			.json(inputPath)
+			.where("DOI is not null");
+
+		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
+
+	}
+
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
 		String inputPath,
 		List<KeyValue> collectedfrom) {
@@ -132,6 +162,10 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
+		return getTextTextJavaPairRDD(collectedfrom, df);
+	}
+
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
 		// unroll nested arrays
 		df = df
 			.withColumn("matching", functions.explode(new Column("Matchings")))
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
index bffe41ac7..ac9977a7e 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
@@ -78,6 +78,10 @@ public class PrepareAffiliationRelationsTest {
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 			.getPath();
 
+		String publisherAffiliationRelationPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
+			.getPath();
+
 		String outputPath = workingDir.toString() + "/actionSet";
 
 		PrepareAffiliationRelations
@@ -89,6 +93,7 @@ public class PrepareAffiliationRelationsTest {
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-webCrawlInputPath", crossrefAffiliationRelationPath,
+					"-publisherInputPath", publisherAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -105,7 +110,7 @@ public class PrepareAffiliationRelationsTest {
 //            );
 //        }
 		// count the number of relations
-		assertEquals(120, tmp.count());
+		assertEquals(138, tmp.count());
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -116,7 +121,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				60, execVerification
+				69, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -124,7 +129,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				60, execVerification
+				69, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
@@ -145,5 +150,12 @@ public class PrepareAffiliationRelationsTest {
 					.get(0)
 					.getString(4));
 
+		final String publisherid = ID_PREFIX
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s00217-010-1268-9"));
+		final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/03265fv13");
+
+		Assertions
+			.assertEquals(
+				1, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
 	}
 }

From db03f853660767450ad1d283c1b841c849b0110a Mon Sep 17 00:00:00 2001
From: Serafeim Chatzopoulos <s.chatzopoulos@gmail.com>
Date: Wed, 4 Sep 2024 14:25:44 +0300
Subject: [PATCH 110/239] Remove steps for updating BIP! from the impact
 indicators workflow

---
 .../oozie_app/get_score_limits.sh             |  63 -------
 .../oozie_app/map_openaire_ids_to_dois.py     |  60 -------
 .../oozie_app/map_scores_to_dois.py           | 168 -----------------
 .../impact_indicators/oozie_app/workflow.xml  | 169 ++----------------
 4 files changed, 16 insertions(+), 444 deletions(-)
 delete mode 100644 dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/get_score_limits.sh
 delete mode 100644 dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_openaire_ids_to_dois.py
 delete mode 100755 dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_scores_to_dois.py

diff --git a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/get_score_limits.sh b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/get_score_limits.sh
deleted file mode 100644
index 6d4161d7f..000000000
--- a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/get_score_limits.sh
+++ /dev/null
@@ -1,63 +0,0 @@
-#/usr/bin/bash
-
-# Read log files from ranking scripts and create a two-line file  
-# with score limits for the various measures. To be used by Kleanthis
-
-attrank_file=$(ls *attrank*.log);
-pr_file=$(ls *pagerank*.log)
-ram_file=$(ls *ram*.log);
-cc_file=$(ls *cc*.log);
-impulse_file=$(ls *impulse*.log);
-
-echo
-echo "-----------------------------"
-echo "Attrank file:${attrank_file}";
-echo "PageRank file:${pr_file}";
-echo "RAM file:${ram_file}";
-echo "CC file:${cc_file}";
-echo "Impulse file:${impulse_file}";
-echo "-----------------------------"
-echo
-echo
-
-# output file will be called score_limits.csv
-echo -e "influence_top001\tinfluence_top01\tinfluence_top1\tinfluence_top10\tpopularity_top001\tpopularity_top01\tpopularity_top1\tpopularity_top10\timpulse_top001\timpulse_top01\timpulse_top1\timpulse_top10\tcc_top001\tcc_top01\tcc_top1\tcc_top10" > score_limits.csv
-# ---------------------------------------------------- #
-# Get respective score limits (we don't need RAM)
-inf_001=$(grep "^0.01%" ${pr_file} | cut -f 2);
-inf_01=$(grep "^0.1%" ${pr_file} | cut -f 2);
-inf_1=$(grep "^1%" ${pr_file} | cut -f 2);
-inf_10=$(grep "^10%" ${pr_file} | cut -f 2);
-echo "Influnence limits:"
-echo -e "${inf_001}\t${inf_01}\t${inf_1}\t${inf_10}";
-# ---------------------------------------------------- #
-pop_001=$(grep "^0.01%" ${attrank_file} | cut -f 2);
-pop_01=$(grep "^0.1%" ${attrank_file} | cut -f 2);
-pop_1=$(grep "^1%" ${attrank_file} | cut -f 2);
-pop_10=$(grep "^10%" ${attrank_file} | cut -f 2);
-echo "Popularity limits:";
-echo -e "${pop_001}\t${pop_01}\t${pop_1}\t${pop_10}";
-# ---------------------------------------------------- #
-imp_001=$(grep "^0.01%" ${impulse_file} | cut -f 2);
-imp_01=$(grep "^0.1%" ${impulse_file} | cut -f 2);
-imp_1=$(grep "^1%" ${impulse_file} | cut -f 2);
-imp_10=$(grep "^10%" ${impulse_file} | cut -f 2);
-echo "Popularity limits:";
-echo -e "${imp_001}\t${imp_01}\t${imp_1}\t${imp_10}";
-# ---------------------------------------------------- #
-cc_001=$(grep "^0.01%" ${cc_file} | cut -f 2);
-cc_01=$(grep "^0.1%" ${cc_file} | cut -f 2);
-cc_1=$(grep "^1%" ${cc_file} | cut -f 2);
-cc_10=$(grep "^10%" ${cc_file} | cut -f 2);
-echo "Popularity limits:";
-echo -e "${cc_001}\t${cc_01}\t${cc_1}\t${cc_10}";
-# ---------------------------------------------------- #
-
-echo -e "${inf_001}\t${inf_01}\t${inf_1}\t${inf_10}\t${pop_001}\t${pop_01}\t${pop_1}\t${pop_10}\t${imp_001}\t${imp_01}\t${imp_1}\t${imp_10}\t${cc_001}\t${cc_01}\t${cc_1}\t${cc_10}" >> score_limits.csv
-
-echo
-echo "score_limits.csv contents:"
-cat score_limits.csv
-
-echo;
-echo;
diff --git a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_openaire_ids_to_dois.py b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_openaire_ids_to_dois.py
deleted file mode 100644
index 7997eec82..000000000
--- a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_openaire_ids_to_dois.py
+++ /dev/null
@@ -1,60 +0,0 @@
-import json
-import sys
-from pyspark.sql import SparkSession
-from pyspark import SparkConf, SparkContext
-
-if len(sys.argv) != 3:
-    print("Usage: map_openaire_ids_to_dois.py <hdfs_src_dir> <hdfs_output_dir>")
-    sys.exit(-1)
-
-conf = SparkConf().setAppName('BIP!: Map OpenAIRE IDs to DOIs')
-sc = SparkContext(conf = conf)
-spark = SparkSession.builder.appName('BIP!: Map OpenAIRE IDs to DOIs').getOrCreate()
-sc.setLogLevel('OFF')
-
-src_dir = sys.argv[1]
-output = sys.argv[2]
-
-# src_dir = "/tmp/beta_provision/graph/21_graph_cleaned/"
-# output = '/tmp/openaireid_to_dois/'
-
-def transform(doc):
-    
-    # get publication year from 'doc.dateofacceptance.value'
-    dateofacceptance = doc.get('dateofacceptance', {}).get('value')
-
-    year = 0 
-    
-    if (dateofacceptance is not None):
-        year = dateofacceptance.split('-')[0]
-
-    # for each pid get 'pid.value' if 'pid.qualifier.classid' equals to 'doi'
-    dois = [ pid['value'] for pid in doc.get('pid', [])  if (pid.get('qualifier', {}).get('classid') == 'doi' and pid['value'] is not None)]
-
-    num_dois = len(dois)
-    
-    # exlcude openaire ids that do not correspond to DOIs
-    if (num_dois == 0): 
-        return None
-        
-    fields = [ doc['id'], str(num_dois), chr(0x02).join(dois), str(year) ]
-    
-    return '\t'.join([ v.encode('utf-8') for v in fields ])
-    
-docs = None
-
-for result_type in ["publication", "dataset", "software", "otherresearchproduct"]:
-    
-    tmp = sc.textFile(src_dir + result_type).map(json.loads)
-    
-    if (docs is None):
-        docs = tmp
-    else:
-        # append all result types in one RDD
-        docs = docs.union(tmp)
-
-docs = docs.filter(lambda d: d.get('dataInfo', {}).get('deletedbyinference') == False and d.get('dataInfo', {}).get('invisible') == False)
-
-docs = docs.map(transform).filter(lambda d: d is not None)
-
-docs.saveAsTextFile(output)
diff --git a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_scores_to_dois.py b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_scores_to_dois.py
deleted file mode 100755
index f6a8e9996..000000000
--- a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/map_scores_to_dois.py
+++ /dev/null
@@ -1,168 +0,0 @@
-#!/usr/bin/python
-# This program reads the openaire to doi mapping from the ${synonymFolder} of the workflow
-# and uses this mapping to create doi-based score files in the format required by BiP! DB.
-# This is done by reading each openaire-id based ranking file and joining the openaire based
-# score and classes to all the corresponding dois.
-#################################################################################################
-# Imports
-import sys
-
-# Sparksession lib to communicate with cluster via session object
-from pyspark.sql import SparkSession
-
-# Import sql types to define schemas
-from pyspark.sql.types import *
-
-# Import sql functions with shorthand alias
-import pyspark.sql.functions as F
-
-from pyspark.sql.functions import max
-# from pyspark.sql.functions import udf
-#################################################################################################
-#################################################################################################
-# Clean up directory name - no longer needed in final workflow version
-'''
-def clean_directory_name(dir_name):
-    # We have a name with the form *_bip_universe<digits>_* or *_graph_universe<digits>_* 
-    # and we need to keep the parts in *	
-
-    
-    dir_name_parts = dir_name.split('_')
-    dir_name_parts = [part for part in dir_name_parts if ('bip' not in part and 'graph' not in part and 'universe' not in part and 'from' not in part)]
-    
-    dir_name = dir_name.replace("openaire_id_graph", "openaire_ids")
-    clean_name = dir_name + ".txt.gz"
-
-    # clean_name = '_'.join(dir_name_parts)
-
-    # if '_ids' not in clean_name:
-    #     clean_name = clean_name.replace('id_', 'ids_')
-        	
-    # clean_name = clean_name.replace('.txt', '')
-    # clean_name = clean_name.replace('.gz', '')
-
-    # if 'openaire_ids_' in clean_name:
-    #     clean_name = clean_name.replace('openaire_ids_', '')
-        # clean_name = clean_name + '.txt.gz'
-    # else:
-        # clean_name = clean_name + '.txt.gz'
-	
-    return clean_name
-'''
-#################################################################################################
-if len(sys.argv) < 3:
-    print ("Usage: ./map_scores_to_dois.py <synonym_folder> <num_partitions> <score_file_1> <score_file_2> <...etc...>")
-    sys.exit(-1)
-
-# Read arguments
-synonyms_folder = sys.argv[1]
-num_partitions = int(sys.argv[2])
-input_file_list = [argument.replace("_openaire_id_graph", "").replace("_openaire_id_graph_", "") + "_openaire_ids.txt.gz" for argument in sys.argv[3:]]
-# input_file_list = [clean_directory_name(item) for item in input_file_list]
-
-# Prepare output specific variables
-output_file_list = [item.replace("_openaire_ids", "") for item in input_file_list]
-output_file_list = [item + ".txt.gz" if not item.endswith(".txt.gz") else item for item in output_file_list]
-
-# --- INFO MESSAGES --- #
-print ("\n\n----------------------------")
-print ("Mpping openaire ids to DOIs")
-print ("Reading input from: " + synonyms_folder)
-print ("Num partitions: " + str(num_partitions))
-print ("Input files:" + " -- ".join(input_file_list))
-print ("Output files: " + " -- ".join(output_file_list))
-print ("----------------------------\n\n")
-#######################################################################################
-# We weill define the following schemas:
-# --> the schema of the openaire - doi mapping file [string - int - doi_list] (the separator of the doi-list is a non printable character)
-# --> a schema for floating point ranking scores [string - float - string]  (the latter string is the class)
-# --> a schema for integer ranking scores [string - int - string]  (the latter string is the class)
-
-float_schema = StructType([
-	StructField('id', StringType(), False),
-	StructField('score', FloatType(), False),
-	StructField('class', StringType(), False)
-	])
-	
-int_schema = StructType([
-	StructField('id', StringType(), False),
-	StructField('score', IntegerType(), False),
-	StructField('class', StringType(), False)
-	])
-	
-# This schema concerns the output of the file
-# containing the number of references of each doi
-synonyms_schema = StructType([
-	StructField('id', StringType(), False),
-	StructField('num_synonyms', IntegerType(), False),
-    StructField('doi_list', StringType(), False),
-	])
-#######################################################################################
-# Start spark session
-spark = SparkSession.builder.appName('Map openaire scores to DOIs').getOrCreate()
-# Set Log Level for spark session
-spark.sparkContext.setLogLevel('WARN')
-#######################################################################################
-# MAIN Program
-
-# Read and repartition the synonym folder - also cache it since we will need to perform multiple joins
-synonym_df = spark.read.schema(synonyms_schema).option('delimiter', '\t').csv(synonyms_folder)
-synonym_df = synonym_df.select('id',  F.split(F.col('doi_list'), chr(0x02)).alias('doi_list'))
-synonym_df = synonym_df.select('id', F.explode('doi_list').alias('doi')).repartition(num_partitions, 'id').cache()
-
-# TESTING
-# print ("Synonyms: " + str(synonym_df.count()))
-# print ("DF looks like this:" )
-# synonym_df.show(1000, False)
-
-print ("\n\n-----------------------------")
-# Now we need to join the score files on the openaire-id with the synonyms and then keep
-# only doi - score - class and write this to the output
-for offset, input_file in enumerate(input_file_list):
-
-    print ("Mapping scores from " + input_file)
-
-    # Select correct schema
-    schema = int_schema
-    if "attrank" in input_file.lower() or "pr" in input_file.lower() or "ram" in input_file.lower():
-        schema = float_schema
-    
-    # Load file to dataframe
-    ranking_df = spark.read.schema(schema).option('delimiter', '\t').csv(input_file).repartition(num_partitions, 'id')
-
-    # Get max score
-    max_score = ranking_df.select(max('score').alias('max')).collect()[0]['max']
-    print ("Max Score for " + str(input_file) + " is " + str(max_score))
-   
-    # TESTING
-    # print ("Loaded df sample:")
-    # ranking_df.show(1000, False)
-
-    # Join scores to synonyms and keep required fields
-    doi_score_df = synonym_df.join(ranking_df, ['id']).select('doi', 'score', 'class').repartition(num_partitions, 'doi').cache()
-    # Write output
-    output_file = output_file_list[offset]
-    print ("Writing to: " + output_file)
-    doi_score_df.write.mode('overwrite').option('delimiter','\t').option('header',False).csv(output_file, compression='gzip')
-    
-    # Creata another file for the bip update process
-    ranking_df = ranking_df.select('id', 'score', F.lit(F.col('score')/max_score).alias('normalized_score'), 'class', F.col('class').alias('class_dup'))
-    doi_score_df = synonym_df.join(ranking_df, ['id']).select('doi', 'score', 'normalized_score', 'class', 'class_dup').repartition(num_partitions, 'doi').cache()
-    output_file = output_file.replace(".txt.gz", "_for_bip_update.txt.gz")
-    print ("Writing bip update to: " + output_file)
-    doi_score_df.write.mode('overwrite').option('delimiter','\t').option('header',False).csv(output_file, compression='gzip')
- 
-    
-    # Free memory?
-    ranking_df.unpersist(True)
-
-print ("-----------------------------")
-print ("\n\nFinished!\n\n")
-
-
-
-
-
-
-
-
diff --git a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
index 70f5f8d2a..108cf70b1 100644
--- a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
@@ -17,10 +17,6 @@
 				<name>openaireGraphInputPath</name>
 				<value>${nameNode}/${workingDir}/openaire_id_graph</value>
 			</property>
-			<property>
-				<name>synonymFolder</name>
-				<value>${nameNode}/${workingDir}/openaireid_to_dois/</value>
-			</property>
 			<property>
 				<name>checkpointDir</name>
 				<value>${nameNode}/${workingDir}/check/</value>
@@ -32,29 +28,34 @@
 		</configuration>
 	</global>
 
-	<!-- start using a decision node, so as to determine from which point onwards a job will continue -->
+	<!-- Start using a decision node, to determine from which point onwards a job will continue -->
 	<start to="entry-point-decision" />
 
 	<decision name="entry-point-decision">
 		<switch>
-			<!-- The default will be set as the normal start, a.k.a. get-doi-synonyms -->
-			<!-- If any different condition is set, go to the corresponding start -->
+
+			<!-- Start from creating the citation network (i.e., normal execution should start from here) -->
+			<case to="create-openaire-ranking-graph">${wf:conf('resume') eq "start"}</case>
+
+			<!-- Different citation-based impact indicators are computed -->
 			<case to="spark-cc">${wf:conf('resume') eq "cc"}</case>
 			<case to="spark-ram">${wf:conf('resume') eq "ram"}</case>
 			<case to="spark-impulse">${wf:conf('resume') eq "impulse"}</case>
 			<case to="spark-pagerank">${wf:conf('resume') eq "pagerank"}</case>
 			<case to="spark-attrank">${wf:conf('resume') eq "attrank"}</case>
-			<!-- <case to="iterative-rankings">${wf:conf('resume') eq "rankings-iterative"}</case> -->
-			<case to="get-file-names">${wf:conf('resume') eq "format-results"}</case>
-			<case to="map-openaire-to-doi">${wf:conf('resume') eq "map-ids"}</case>
-			<case to="map-scores-to-dois">${wf:conf('resume') eq "map-scores"}</case>
-			<case to="create-openaire-ranking-graph">${wf:conf('resume') eq "start"}</case>
 
-			<!-- Aggregation of impact scores on the project level		-->
+			<!-- Format the results appropriately before transforming them to action sets -->
+			<case to="get-file-names">${wf:conf('resume') eq "format-results"}</case>
+
+			<!-- Aggregation of impact scores on the project level -->
 			<case to="project-impact-indicators">${wf:conf('resume') eq "projects-impact"}</case>
+
+			<!-- Create action sets -->
 			<case to="create-actionset">${wf:conf('resume') eq "create-actionset"}</case>
 
+			<!-- The default will be set as the normal start, a.k.a. create-openaire-ranking-graph -->
 			<default to="create-openaire-ranking-graph" />
+
 		</switch>
 	</decision>
 
@@ -295,18 +296,11 @@
 			<capture-output/>
 		</shell>
 
-		<ok to="format-result-files" />
+		<ok to="format-json-files" />
 		<error to="filename-getting-error" />
 
 	</action>
 
-	<!-- Now we will run in parallel the formatting of ranking files for BiP! DB and openaire (json files) -->
-	<fork name="format-result-files">
-		<path start="format-bip-files"/>
-		<path start="format-json-files"/>
-	</fork>
-
-
 	<!-- Format json files -->
 	<!-- Two parts: a) format files b) make the file endings .json.gz -->
 	<action name="format-json-files">
@@ -345,139 +339,8 @@
 			<file>${wfAppPath}/format_ranking_results.py#format_ranking_results.py</file>
 		</spark>
 
-		<ok to="join-file-formatting" />
-		<error to="json-formatting-fail" />
-	</action>
-
-	<!-- This is the second line of parallel workflow execution where we create the BiP! DB files -->
-	<action name="format-bip-files">
-		<!-- This is required as a tag for spark jobs, regardless of programming language -->
-		<spark xmlns="uri:oozie:spark-action:0.2">
-
-			<!-- using configs from an example on openaire -->
-			<master>yarn-cluster</master>
-			<mode>cluster</mode>
-
-			<!-- This is the name of our job -->
-			<name>Format Ranking Results BiP! DB</name>
-			<!-- Script name goes here -->
-			<jar>format_ranking_results.py</jar>
-			<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
-
-			<spark-opts>
-				--executor-memory=${sparkNormalExecutorMemory}
-				--executor-cores=${sparkExecutorCores}
-				--driver-memory=${sparkNormalDriverMemory}
-				--conf spark.executor.memoryOverhead=${sparkNormalExecutorMemory}
-				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
-				--conf spark.extraListeners=${spark2ExtraListeners}
-				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-				--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-				--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-			</spark-opts>
-
-			<!-- Script arguments here -->
-			<arg>zenodo</arg>
-			<!-- Input files must be identified dynamically -->
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['pr_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['attrank_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['cc_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['impulse_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['ram_file']}</arg>
-			<!-- Num partitions -->
-			<arg>${sparkShufflePartitions}</arg>
-			<!-- Type of data to be produced [bip (dois) / openaire (openaire-ids) ] -->
-			<arg>openaire</arg>
-			<!-- This needs to point to the file on the hdfs i think -->
-			<file>${wfAppPath}/format_ranking_results.py#format_ranking_results.py</file>
-		</spark>
-
-		<ok to="join-file-formatting" />
-		<error to="bip-formatting-fail" />
-	</action>
-
-	<!-- Finish formatting jobs -->
-	<join name="join-file-formatting" to="map-openaire-to-doi"/>
-
-	<!-- maps openaire ids to DOIs -->
-	<action name="map-openaire-to-doi">
-		<spark xmlns="uri:oozie:spark-action:0.2">
-
-			<!-- Delete previously created doi synonym folder -->
-			<prepare>
-				<delete path="${synonymFolder}"/>
-			</prepare>
-
-			<master>yarn-cluster</master>
-			<mode>cluster</mode>
-			<name>Openaire-DOI synonym collection</name>
-			<jar>map_openaire_ids_to_dois.py</jar>
-
-			<spark-opts>
-				--executor-memory=${sparkHighExecutorMemory}
-				--executor-cores=${sparkExecutorCores}
-				--driver-memory=${sparkHighDriverMemory}
-				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
-				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
-				--conf spark.extraListeners=${spark2ExtraListeners}
-				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-				--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-				--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-			</spark-opts>
-
-			<!-- Script arguments here -->
-			<arg>${openaireDataInput}/</arg>
-			<!-- number of partitions to be used on joins -->
-			<arg>${synonymFolder}</arg>
-
-			<file>${wfAppPath}/map_openaire_ids_to_dois.py#map_openaire_ids_to_dois.py</file>
-		</spark>
-
-		<ok to="map-scores-to-dois" />
-		<error to="synonym-collection-fail" />
-
-	</action>
-
-	<!-- mapping openaire scores to DOIs -->
-	<action name="map-scores-to-dois">
-		<!-- This is required as a tag for spark jobs, regardless of programming language -->
-		<spark xmlns="uri:oozie:spark-action:0.2">
-
-			<!-- using configs from an example on openaire -->
-			<master>yarn-cluster</master>
-			<mode>cluster</mode>
-			<name>Mapping Openaire Scores to DOIs</name>
-			<jar>map_scores_to_dois.py</jar>
-
-			<spark-opts>
-				--executor-memory=${sparkHighExecutorMemory}
-				--executor-cores=${sparkExecutorCores}
-				--driver-memory=${sparkHighDriverMemory}
-				--conf spark.executor.memoryOverhead=${sparkHighExecutorMemory}
-				--conf spark.sql.shuffle.partitions=${sparkShufflePartitions}
-				--conf spark.extraListeners=${spark2ExtraListeners}
-				--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-				--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-				--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-			</spark-opts>
-
-			<!-- Script arguments here -->
-			<arg>${synonymFolder}</arg>
-			<!-- Number of partitions -->
-			<arg>${sparkShufflePartitions}</arg>
-			<!-- The remaining input are the ranking files fproduced for bip db-->
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['pr_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['attrank_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['cc_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['impulse_file']}</arg>
-			<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['ram_file']}</arg>
-
-			<file>${wfAppPath}/map_scores_to_dois.py#map_scores_to_dois.py</file>
-		</spark>
-
 		<ok to="project-impact-indicators" />
-		<error to="map-scores-fail" />
-
+		<error to="json-formatting-fail" />
 	</action>
 
 	<action name="project-impact-indicators">

From b043f8a96370cfdf593fb05c71b119d6175fe240 Mon Sep 17 00:00:00 2001
From: Serafeim Chatzopoulos <s.chatzopoulos@gmail.com>
Date: Wed, 4 Sep 2024 14:28:43 +0300
Subject: [PATCH 111/239] Remove redundant error messages from impact
 indicators workflow

---
 .../graph/impact_indicators/oozie_app/workflow.xml   | 12 ------------
 1 file changed, 12 deletions(-)

diff --git a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
index 108cf70b1..5d8669823 100644
--- a/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
@@ -457,18 +457,6 @@
 		<message>Error formatting json files, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
 	</kill>
 
-	<kill name="bip-formatting-fail">
-		<message>Error formatting BIP files, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-
-	<kill name="synonym-collection-fail">
-		<message>Synonym collection failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-
-	<kill name="map-scores-fail">
-		<message>Mapping scores to DOIs failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-
 	<kill name="actionset-delete-fail">
 		<message>Deleting output path for actionsets failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
 	</kill>

From b64c144abfad208e7c0c5137adce3f1fc555706f Mon Sep 17 00:00:00 2001
From: Antonis Lempesis <antleb@di.uoa.gr>
Date: Thu, 5 Sep 2024 16:00:09 +0300
Subject: [PATCH 112/239] added new institutions

---
 .../scripts/step20-createMonitorDBAll.sql          | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
index a8392b226..ca5b0bb90 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
@@ -81,11 +81,17 @@ create table TARGET.result stored as parquet as
              'openorgs____::8839b55dae0c84d56fd533f52d5d483a',   -- Leibniz Institute of Ecological Urban and Regional Development
              'openorgs____::526468206bca24c1c90da6a312295cf4',	-- Cyprus University of Technology
              'openorgs____::b5ca9d4340e26454e367e2908ef3872f',	-- Alma Mater Studiorum University of Bologna
-             'openorgs____::a6340e6ecf60f6bba163659df985b0f2',  -- TU Dresden
-             'openorgs____::64badd35233ba2cd4946368ef2f4cf57',  --	University of Vienna
+             'openorgs____::a6340e6ecf60f6bba163659df985b0f2',	-- TU Dresden
+             'openorgs____::64badd35233ba2cd4946368ef2f4cf57',  -- University of Vienna
              'openorgs____::7501d66d2297a963ebfb075c43fff88e',  -- Royal Institute of Technology
-             'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf',  -- Sorbonne University
-             'openorgs____::b316f25380d106aac402f5ae8653910d'  --	Centre for Research on Ecology and Forestry Applications
+             'openorgs____::d5eb679abdd31f70fcd4c8ba711148bf',	-- Sorbonne University
+             'openorgs____::b316f25380d106aac402f5ae8653910d',  -- Centre for Research on Ecology and Forestry Applications
+             'openorgs____::45a2076eee3013e0e85625ce61bcd272',  -- Institut d'Investigació Sanitària Illes Balears
+             'openorgs____::00b20b0a743a96169e6cf135e6e2bd7c',  -- Universidad Publica De Navarra
+             'openorgs____::0f398605c2459294d125ff23473a97dc',  -- Aalto University
+             'openorgs____::25b1fa62c7fd8e409d3a83c07e04b2d4',  -- WHU-Otto Beisheim School of Management
+             'openorgs____::d6eec313417f11205db4e736a34c0db6',  -- KEMPELENOV INSTITUT INTELIGENTNYCH TECHNOLOGII
+             'openorgs____::c2dfb90e797a2dc52f0084c549289d0c'  -- National Research Institute for Agriculture, Food and Environment
         ) )) foo;
 
 create view if not exists TARGET.category as select * from SOURCE.category;

From 37ad259296c686ce3adee1758a2dbbdab9f35ab9 Mon Sep 17 00:00:00 2001
From: Antonis Lempesis <antleb@di.uoa.gr>
Date: Thu, 5 Sep 2024 16:02:44 +0300
Subject: [PATCH 113/239] cleanup

---
 .../oozie_app/scripts/updateMonitorDB.sql     | 76 -------------------
 1 file changed, 76 deletions(-)

diff --git a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB.sql b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB.sql
index 321fba87a..ede8a18bf 100644
--- a/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB.sql
+++ b/dhp-workflows/dhp-stats-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor/oozie_app/scripts/updateMonitorDB.sql
@@ -1,79 +1,3 @@
---drop database if exists TARGET cascade;
---create database if not exists TARGET;
---
---create view if not exists TARGET.category as select * from SOURCE.category;
---create view if not exists TARGET.concept as select * from SOURCE.concept;
---create view if not exists TARGET.context as select * from SOURCE.context;
---create view if not exists TARGET.country as select * from SOURCE.country;
---create view if not exists TARGET.countrygdp as select * from SOURCE.countrygdp;
---create view if not exists TARGET.creation_date as select * from SOURCE.creation_date;
---create view if not exists TARGET.funder as select * from SOURCE.funder;
---create view if not exists TARGET.fundref as select * from SOURCE.fundref;
---create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture;
---create view if not exists TARGET.rndgdpexpenditure as select * from SOURCE.rndgdpexpenditure;
---create view if not exists TARGET.doctoratestudents as select * from SOURCE.doctoratestudents;
---create view if not exists TARGET.totalresearchers as select * from SOURCE.totalresearchers;
---create view if not exists TARGET.totalresearchersft as select * from SOURCE.totalresearchersft;
---create view if not exists TARGET.hrrst as select * from SOURCE.hrrst;
---
---create table TARGET.result stored as parquet as
---    select distinct * from (
---        select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id)
---        union all
---        select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id)
---        union all
---        select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
---             'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC"
---             'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council
---             'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ??
---             'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University
---             'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade
---             'openorgs____::0ae431b820e4c33db8967fbb2b919150', --University of Helsinki
---             'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho
---             'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid
---             'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen
---             'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens
---             -- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot
---             'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University
---             'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark
---             'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin
---             'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt
---             'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven
---             'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape
---             'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute
---             'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University
---             'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg
---             'openorgs____::6445d7758d3a40c4d997953b6632a368', --National Institute of Informatics (NII)
---             'openorgs____::b77c01aa15de3675da34277d48de2ec1', -- Valencia Catholic University Saint Vincent Martyr
---             'openorgs____::7fe2f66cdc43983c6b24816bfe9cf6a0', -- Unviersity of Warsaw
---             'openorgs____::15e7921fc50d9aa1229a82a84429419e', -- University Of Thessaly
---             'openorgs____::11f7919dadc8f8a7251af54bba60c956', -- Technical University of Crete
---             'openorgs____::84f0c5f5dbb6daf42748485924efde4b', -- University of Piraeus
---             'openorgs____::4ac562f0376fce3539504567649cb373', -- University of Patras
---             'openorgs____::3e8d1f8c3f6cd7f418b09f1f58b4873b', -- Aristotle University of Thessaloniki
---             'openorgs____::3fcef6e1c469c10f2a84b281372c9814', -- World Bank
---             'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech
---             'openorgs____::e15adb13c4dadd49de4d35c39b5da93a',  -- Nanyang Technological University
---             'openorgs____::4b34103bde246228fcd837f5f1bf4212',  -- Autonomous University of Barcelona
---             'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb',	-- McMaster University
---             'openorgs____::51c7fc556e46381734a25a6fbc3fd398',	-- University of Modena and Reggio Emilia
---             'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db',	-- Bilkent University
---             'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06',	-- Saints Cyril and Methodius University of Skopje
---             'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan
---             'openorgs____::b8b8ca674452579f3f593d9f5e557483',   -- University College Cork
---             'openorgs____::38d7097854736583dde879d12dacafca'	-- Brown University
---             'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech
---             'openorgs____::2530baca8a15936ba2e3297f2bce2e7e',	-- University of Cape Town
---             'openorgs____::d11f981828c485cd23d93f7f24f24db1',  -- Technological University Dublin
---             'openorgs____::5e6bf8962665cdd040341171e5c631d8',  -- Delft University of Technology
---             'openorgs____::846cb428d3f52a445f7275561a7beb5d',  -- University of Manitoba
---             'openorgs____::eb391317ed0dc684aa81ac16265de041',	-- Universitat Rovira i Virgili
---             'openorgs____::66aa9fc2fceb271423dfabcc38752dc0',  -- Lund University
---             'openorgs____::3cff625a4370d51e08624cc586138b2f'	-- IMT Atlantique
---        ) )) foo;
---
---ANALYZE TABLE TARGET.result COMPUTE STATISTICS;
-
 create view if not exists TARGET.category as select * from SOURCE.category;
 create view if not exists TARGET.concept as select * from SOURCE.concept;
 create view if not exists TARGET.context as select * from SOURCE.context;

From 07e6e7b4d6e3489a55d8dca917c65e28ead21275 Mon Sep 17 00:00:00 2001
From: Alessia <alessia.bardi@gmail.com>
Date: Mon, 16 Sep 2024 13:41:56 +0200
Subject: [PATCH 114/239] #9839: include claimed affiliation relationships

---
 .../raw/MigrateDbEntitiesApplication.java     | 22 ++++++++++++
 .../raw/MigrateDbEntitiesApplicationTest.java | 35 +++++++++++++++++++
 .../raw/claimsrel_resultset_affiliation.json  | 27 ++++++++++++++
 3 files changed, 84 insertions(+)
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_affiliation.json

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
index c9a32cde6..00505fedc 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
@@ -519,6 +519,28 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 						r1 = setRelationSemantic(r1, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO);
 						r2 = setRelationSemantic(r2, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO);
 						break;
+					case "resultOrganization_affiliation_isAuthorInstitutionOf":
+						if (!"organization".equals(sourceType)) {
+							throw new IllegalStateException(
+									String
+											.format(
+													"invalid claim, sourceId: %s, targetId: %s, semantics: %s", sourceId, targetId,
+													semantics));
+						}
+						r1 = setRelationSemantic(r1, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF);
+						r2 = setRelationSemantic(r2, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION);
+						break;
+					case "resultOrganization_affiliation_hasAuthorInstitution":
+						if (!"organization".equals(targetType)) {
+							throw new IllegalStateException(
+									String
+											.format(
+													"invalid claim, sourceId: %s, targetId: %s, semantics: %s", sourceId, targetId,
+													semantics));
+						}
+						r1 = setRelationSemantic(r1, RESULT_ORGANIZATION, AFFILIATION, HAS_AUTHOR_INSTITUTION);
+						r2 = setRelationSemantic(r2, RESULT_ORGANIZATION, AFFILIATION, IS_AUTHOR_INSTITUTION_OF);
+						break;
 					default:
 						throw new IllegalArgumentException("claim semantics not managed: " + semantics);
 				}
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
index 27304ec06..c4d1b6b58 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
@@ -16,6 +16,8 @@ import java.util.Objects;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.common.RelationInverse;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.junit.jupiter.api.BeforeEach;
@@ -364,6 +366,39 @@ class MigrateDbEntitiesApplicationTest {
 		assertValidId(r1.getCollectedfrom().get(0).getKey());
 		assertValidId(r2.getCollectedfrom().get(0).getKey());
 	}
+	@Test
+	void testProcessClaims_affiliation() throws Exception {
+		final List<TypedField> fields = prepareMocks("claimsrel_resultset_affiliation.json");
+
+		final List<Oaf> list = app.processClaims(rs);
+
+		assertEquals(2, list.size());
+		verifyMocks(fields);
+
+		assertTrue(list.get(0) instanceof Relation);
+		assertTrue(list.get(1) instanceof Relation);
+
+		final Relation r1 = (Relation) list.get(0);
+		final Relation r2 = (Relation) list.get(1);
+
+		assertValidId(r1.getSource());
+		assertValidId(r1.getTarget());
+		assertValidId(r2.getSource());
+		assertValidId(r2.getTarget());
+		assertNotNull(r1.getDataInfo());
+		assertNotNull(r2.getDataInfo());
+		assertNotNull(r1.getDataInfo().getTrust());
+		assertNotNull(r2.getDataInfo().getTrust());
+		assertEquals(r1.getSource(), r2.getTarget());
+		assertEquals(r2.getSource(), r1.getTarget());
+		assertTrue(StringUtils.isNotBlank(r1.getRelClass()));
+		assertTrue(StringUtils.isNotBlank(r2.getRelClass()));
+		assertTrue(StringUtils.isNotBlank(r1.getRelType()));
+		assertTrue(StringUtils.isNotBlank(r2.getRelType()));
+
+		assertValidId(r1.getCollectedfrom().get(0).getKey());
+		assertValidId(r2.getCollectedfrom().get(0).getKey());
+	}
 
 	private List<TypedField> prepareMocks(final String jsonFile) throws IOException, SQLException {
 		final String json = IOUtils.toString(getClass().getResourceAsStream(jsonFile));
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_affiliation.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_affiliation.json
new file mode 100644
index 000000000..07cc025d6
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/claimsrel_resultset_affiliation.json
@@ -0,0 +1,27 @@
+[
+	{
+		"field": "source_type",
+		"type": "string",
+		"value": "organization"
+	},
+	{
+		"field": "source_id",
+		"type": "string",
+		"value": "openorgs____::b5ca9d4340e26454e367e2908ef3872f"
+	},
+	{
+		"field": "target_type",
+		"type": "string",
+		"value": "software"
+	},
+	{
+		"field": "target_id",
+		"type": "string",
+		"value": "userclaim___::bde53826d07c8cf47c99222a375cd2e8"
+	},
+	{
+		"field": "semantics",
+		"type": "string",
+		"value": "resultOrganization_affiliation_isAuthorInstitutionOf"
+	}
+]
\ No newline at end of file

From 6df6b4583ebeecda8ff69cd370b8d39d5d8dd7b3 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Mon, 16 Sep 2024 14:04:59 +0200
Subject: [PATCH 115/239] blacklist filtering moved before the cleanup phase in
 order to have case sensitive regex

---
 .../NumAuthorsTitleSuffixPrefixChain.java     |   2 +-
 .../java/eu/dnetlib/pace/model/FieldDef.java  |  16 +++
 .../eu/dnetlib/pace/model/SparkDeduper.scala  |  40 +------
 .../eu/dnetlib/pace/model/SparkModel.scala    | 100 ++++++++++++------
 .../clustering/ClusteringFunctionTest.java    |  13 +++
 .../pace/comparators/ComparatorTest.java      |  12 +++
 .../dnetlib/dhp/oa/dedup/SparkBlockStats.java |   1 -
 .../dnetlib/dhp/dedup/conf/pub.curr.conf.json |   2 +-
 8 files changed, 111 insertions(+), 75 deletions(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NumAuthorsTitleSuffixPrefixChain.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NumAuthorsTitleSuffixPrefixChain.java
index f1d1e17b9..4e6d8231f 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NumAuthorsTitleSuffixPrefixChain.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/clustering/NumAuthorsTitleSuffixPrefixChain.java
@@ -38,7 +38,7 @@ public class NumAuthorsTitleSuffixPrefixChain extends AbstractClusteringFunction
 
 	@Override
 	protected Collection<String> doApply(Config conf, String s) {
-		return suffixPrefixChain(cleanup(s), param("mod"));
+		return suffixPrefixChain(cleanup(s), paramOrDefault("mod", 10));
 	}
 
 	private Collection<String> suffixPrefixChain(String s, int mod) {
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
index b0dc11656..2e329f690 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/FieldDef.java
@@ -54,6 +54,22 @@ public class FieldDef implements Serializable {
 	public FieldDef() {
 	}
 
+	public FieldDef clone() {
+		FieldDef fieldDef = new FieldDef();
+		fieldDef.setName(this.name);
+		fieldDef.setPath(this.path);
+		fieldDef.setType(this.type);
+		fieldDef.setOverrideMatch(this.overrideMatch);
+		fieldDef.setSize(this.size);
+		fieldDef.setLength(this.length);
+		fieldDef.setFilter(this.filter);
+		fieldDef.setSorted(this.sorted);
+		fieldDef.setClean(this.clean);
+		fieldDef.setInfer(this.infer);
+		fieldDef.setInferenceFrom(this.inferenceFrom);
+		return fieldDef;
+	}
+
 	public String getInferenceFrom() {
 		return inferenceFrom;
 	}
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkDeduper.scala b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkDeduper.scala
index bc702b9e2..a3eb3cba8 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkDeduper.scala
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkDeduper.scala
@@ -19,48 +19,10 @@ case class SparkDeduper(conf: DedupConfig) extends Serializable {
   val model: SparkModel = SparkModel(conf)
 
   val dedup: (Dataset[Row] => Dataset[Row]) = df => {
-    df.transform(filterAndCleanup)
-      .transform(generateClustersWithCollect)
+    df.transform(generateClustersWithCollect)
       .transform(processBlocks)
   }
 
-
-  val filterAndCleanup: (Dataset[Row] => Dataset[Row]) = df => {
-    val df_with_filters = conf.getPace.getModel.asScala.foldLeft(df)((res, fdef) => {
-      if (conf.blacklists.containsKey(fdef.getName)) {
-        res.withColumn(
-          fdef.getName + "_filtered",
-          filterColumnUDF(fdef).apply(new Column(fdef.getName))
-        )
-      } else {
-        res
-      }
-    })
-
-    df_with_filters
-  }
-
-  def filterColumnUDF(fdef: FieldDef): UserDefinedFunction = {
-    val blacklist: Predicate[String] = conf.blacklists().get(fdef.getName)
-
-    if (blacklist == null) {
-      throw new IllegalArgumentException("Column: " + fdef.getName + " does not have any filter")
-    } else {
-      fdef.getType match {
-        case Type.List | Type.JSON =>
-          udf[Array[String], Array[String]](values => {
-            values.filter((v: String) => !blacklist.test(v))
-          })
-
-        case _ =>
-          udf[String, String](v => {
-            if (blacklist.test(v)) ""
-            else v
-          })
-      }
-    }
-  }
-
   val generateClustersWithCollect: (Dataset[Row] => Dataset[Row]) = df_with_filters => {
     var df_with_clustering_keys: Dataset[Row] = null
 
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
index c6db62339..580a88b7e 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala
@@ -5,12 +5,12 @@ import eu.dnetlib.pace.common.AbstractPaceFunctions
 import eu.dnetlib.pace.config.{DedupConfig, Type}
 import eu.dnetlib.pace.util.{MapDocumentUtil, SparkCompatUtils}
 import org.apache.commons.lang3.StringUtils
-import org.apache.spark.sql.catalyst.encoders.RowEncoder
 import org.apache.spark.sql.catalyst.expressions.GenericRowWithSchema
 import org.apache.spark.sql.types.{DataTypes, Metadata, StructField, StructType}
 import org.apache.spark.sql.{Dataset, Row}
 
 import java.util.Locale
+import java.util.function.Predicate
 import java.util.regex.Pattern
 import scala.collection.JavaConverters._
 
@@ -29,8 +29,20 @@ case class SparkModel(conf: DedupConfig) {
     identifier.setName(identifierFieldName)
     identifier.setType(Type.String)
 
+    // create fields for blacklist
+    val filtered = conf.getPace.getModel.asScala.flatMap(fdef => {
+      if (conf.blacklists().containsKey(fdef.getName)) {
+        val fdef_filtered = fdef.clone()
+        fdef_filtered.setName(fdef.getName + "_filtered")
+        Seq(fdef, fdef_filtered)
+      }
+      else {
+        Seq(fdef)
+      }
+    })
+
     // Construct a Spark StructType representing the schema of the model
-    (Seq(identifier) ++ conf.getPace.getModel.asScala)
+    (Seq(identifier) ++ filtered)
       .foldLeft(
         new StructType()
       )((resType, fieldDef) => {
@@ -44,7 +56,6 @@ case class SparkModel(conf: DedupConfig) {
         })
       })
 
-
   }
 
   val identityFieldPosition: Int = schema.fieldIndex(identifierFieldName)
@@ -52,7 +63,8 @@ case class SparkModel(conf: DedupConfig) {
   val orderingFieldPosition: Int = schema.fieldIndex(orderingFieldName)
 
   val parseJsonDataset: (Dataset[String] => Dataset[Row]) = df => {
-    df.map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
+    df
+      .map(r => rowFromJson(r))(SparkCompatUtils.encoderFor(schema))
   }
 
   def rowFromJson(json: String): Row = {
@@ -64,41 +76,63 @@ case class SparkModel(conf: DedupConfig) {
 
     schema.fieldNames.zipWithIndex.foldLeft(values) {
       case ((res, (fname, index))) =>
-        val fdef = conf.getPace.getModelMap.get(fname)
+
+        val fdef = conf.getPace.getModelMap.get(fname.split("_filtered")(0))
 
         if (fdef != null) {
-          res(index) = fdef.getType match {
-            case Type.String | Type.Int =>
-              MapDocumentUtil.truncateValue(
-                MapDocumentUtil.getJPathString(fdef.getPath, documentContext),
-                fdef.getLength
-              )
+          if (!fname.contains("_filtered")) { //process fields with no blacklist
+            res(index) = fdef.getType match {
+              case Type.String | Type.Int =>
+                MapDocumentUtil.truncateValue(
+                  MapDocumentUtil.getJPathString(fdef.getPath, documentContext),
+                  fdef.getLength
+                )
 
-            case Type.URL =>
-              var uv = MapDocumentUtil.getJPathString(fdef.getPath, documentContext)
-              if (!URL_REGEX.matcher(uv).matches)
-                uv = ""
-              uv
+              case Type.URL =>
+                var uv = MapDocumentUtil.getJPathString(fdef.getPath, documentContext)
+                if (!URL_REGEX.matcher(uv).matches)
+                  uv = ""
+                uv
 
-            case Type.List | Type.JSON =>
-              MapDocumentUtil.truncateList(
-                MapDocumentUtil.getJPathList(fdef.getPath, documentContext, fdef.getType),
-                fdef.getSize
-              ).asScala
+              case Type.List | Type.JSON =>
+                MapDocumentUtil.truncateList(
+                  MapDocumentUtil.getJPathList(fdef.getPath, documentContext, fdef.getType),
+                  fdef.getSize
+                ).asScala
 
-            case Type.StringConcat =>
-              val jpaths = CONCAT_REGEX.split(fdef.getPath)
+              case Type.StringConcat =>
+                val jpaths = CONCAT_REGEX.split(fdef.getPath)
 
-              MapDocumentUtil.truncateValue(
-                jpaths
-                  .map(jpath => MapDocumentUtil.getJPathString(jpath, documentContext))
-                  .mkString(" "),
-                fdef.getLength
-              )
+                MapDocumentUtil.truncateValue(
+                  jpaths
+                    .map(jpath => MapDocumentUtil.getJPathString(jpath, documentContext))
+                    .mkString(" "),
+                  fdef.getLength
+                )
 
-            case Type.DoubleArray =>
-              MapDocumentUtil.getJPathArray(fdef.getPath, json)
+              case Type.DoubleArray =>
+                MapDocumentUtil.getJPathArray(fdef.getPath, json)
+            }
           }
+          else { //process fields with blacklist
+            val blacklist: Predicate[String] = conf.blacklists().get(fdef.getName)
+
+            res(index) = fdef.getType match {
+              case Type.List | Type.JSON =>
+                MapDocumentUtil.truncateList(
+                  MapDocumentUtil.getJPathList(fdef.getPath, documentContext, fdef.getType),
+                  fdef.getSize
+                ).asScala.filter((v: String) => !blacklist.test(v))
+
+              case _ =>
+                val value: String = MapDocumentUtil.truncateValue(
+                  MapDocumentUtil.getJPathString(fdef.getPath, documentContext),
+                  fdef.getLength
+                )
+                if (blacklist.test(value)) "" else value
+            }
+          }
+
 
           val filter = fdef.getFilter
 
@@ -125,13 +159,12 @@ case class SparkModel(conf: DedupConfig) {
           }
 
           if (StringUtils.isNotBlank(fdef.getInfer)) {
-            val inferFrom : String = if (StringUtils.isNotBlank(fdef.getInferenceFrom)) fdef.getInferenceFrom else fdef.getPath
+            val inferFrom: String = if (StringUtils.isNotBlank(fdef.getInferenceFrom)) fdef.getInferenceFrom else fdef.getPath
             res(index) = res(index) match {
               case x: Seq[String] => x.map(inference(_, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer))
               case _ => inference(res(index).toString, MapDocumentUtil.getJPathString(inferFrom, documentContext), fdef.getInfer)
             }
           }
-
         }
 
         res
@@ -139,6 +172,7 @@ case class SparkModel(conf: DedupConfig) {
     }
 
     new GenericRowWithSchema(values, schema)
+
   }
 
   def clean(value: String, cleantype: String) : String = {
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
index e62f742f8..236f17eca 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/clustering/ClusteringFunctionTest.java
@@ -227,4 +227,17 @@ public class ClusteringFunctionTest extends AbstractPaceTest {
 		System.out.println(cf.apply(conf, Lists.newArrayList(s)));
 	}
 
+	@Test
+	public void testNumAuthorsTitleSuffixPrefixChain() {
+
+		final ClusteringFunction cf = new NumAuthorsTitleSuffixPrefixChain(params);
+		params.put("mod", 10);
+
+		final String title = "PARP-2 Regulates SIRT1 Expression and Whole-Body Energy Expenditure";
+		final String num_authors = "10";
+		System.out.println("title = " + title);
+		System.out.println("num_authors = " + num_authors);
+		System.out.println(cf.apply(conf, Lists.newArrayList(num_authors, title)));
+	}
+
 }
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index c008902c4..d2e83e695 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -327,4 +327,16 @@ public class ComparatorTest extends AbstractPaceTest {
 
 	}
 
+	@Test
+	public void titleVersionMatchTest() {
+
+		TitleVersionMatch titleVersionMatch = new TitleVersionMatch(params);
+
+		double result = titleVersionMatch
+			.compare(
+				"parp 2 regulates sirt 1 expression and whole body energy expenditure",
+				"parp 2 regulates sirt 1 expression and whole body energy expenditure", conf);
+		assertEquals(1.0, result);
+	}
+
 }
diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkBlockStats.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkBlockStats.java
index 3e5215d42..612a1cb19 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkBlockStats.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkBlockStats.java
@@ -91,7 +91,6 @@ public class SparkBlockStats extends AbstractSparkAction {
 				.read()
 				.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
 				.transform(deduper.model().parseJsonDataset())
-				.transform(deduper.filterAndCleanup())
 				.transform(deduper.generateClustersWithCollect())
 				.filter(functions.size(new Column("block")).geq(1));
 
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json
index c3a769874..c5ff1c1fa 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json
@@ -96,7 +96,7 @@
         "aggregation": "MAX",
         "positive": "layer4",
         "negative": "NO_MATCH",
-        "undefined": "MATCH",
+        "undefined": "layer4",
         "ignoreUndefined": "true"
       },
       "layer4": {

From bb9cee4f40caed22e19b65b9ee7e8ca7e5d2848b Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 16 Sep 2024 14:16:56 +0200
Subject: [PATCH 116/239] implementation of gtr2Publications plugin

---
 .../dhp/collection/CollectorWorker.java       |  59 ++---
 .../collection/plugin/CollectorPlugin.java    |   2 +-
 .../gtr2/Gtr2PublicationsCollectorPlugin.java |  40 ++++
 .../plugin/gtr2/Gtr2PublicationsIterator.java | 210 ++++++++++++++++++
 .../oa/provision/utils/XmlRecordFactory.java  |   2 +-
 5 files changed, 283 insertions(+), 30 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
index 98caa1741..5021b7727 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
@@ -22,6 +22,7 @@ import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.base.BaseCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin;
+import eu.dnetlib.dhp.collection.plugin.gtr2.Gtr2PublicationsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
@@ -58,7 +59,7 @@ public class CollectorWorker extends ReportingJob {
 
 	public void collect() throws UnknownCollectorPluginException, CollectorException, IOException {
 
-		final String outputPath = mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
+		final String outputPath = this.mdStoreVersion.getHdfsPath() + SEQUENCE_FILE_NAME;
 		log.info("outputPath path is {}", outputPath);
 
 		final CollectorPlugin plugin = getCollectorPlugin();
@@ -68,36 +69,36 @@ public class CollectorWorker extends ReportingJob {
 
 		try (SequenceFile.Writer writer = SequenceFile
 			.createWriter(
-				fileSystem.getConf(),
-				SequenceFile.Writer.file(new Path(outputPath)),
-				SequenceFile.Writer.keyClass(IntWritable.class),
-				SequenceFile.Writer.valueClass(Text.class),
+				this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
+					.keyClass(IntWritable.class),
+				SequenceFile.Writer
+					.valueClass(Text.class),
 				SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
 			final IntWritable key = new IntWritable(counter.get());
 			final Text value = new Text();
 			plugin
-				.collect(api, report)
-				.forEach(
-					content -> {
-						key.set(counter.getAndIncrement());
-						value.set(content);
-						try {
-							writer.append(key, value);
-						} catch (Throwable e) {
-							throw new RuntimeException(e);
-						}
-					});
-		} catch (Throwable e) {
-			report.put(e.getClass().getName(), e.getMessage());
+				.collect(this.api, this.report)
+				.forEach(content -> {
+					key.set(counter.getAndIncrement());
+					value.set(content);
+					try {
+						writer.append(key, value);
+					} catch (final Throwable e) {
+						throw new RuntimeException(e);
+					}
+				});
+		} catch (final Throwable e) {
+			this.report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e);
 		} finally {
 			shutdown();
-			report.ongoing(counter.longValue(), counter.longValue());
+			this.report.ongoing(counter.longValue(), counter.longValue());
 		}
 	}
 
-	private void scheduleReport(AtomicInteger counter) {
+	private void scheduleReport(final AtomicInteger counter) {
 		schedule(new ReporterCallback() {
+
 			@Override
 			public Long getCurrent() {
 				return counter.longValue();
@@ -112,33 +113,35 @@ public class CollectorWorker extends ReportingJob {
 
 	private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
 
-		switch (CollectorPlugin.NAME.valueOf(api.getProtocol())) {
+		switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
 			case oai:
-				return new OaiCollectorPlugin(clientParams);
+				return new OaiCollectorPlugin(this.clientParams);
 			case rest_json2xml:
-				return new RestCollectorPlugin(clientParams);
+				return new RestCollectorPlugin(this.clientParams);
 			case file:
-				return new FileCollectorPlugin(fileSystem);
+				return new FileCollectorPlugin(this.fileSystem);
 			case fileGzip:
-				return new FileGZipCollectorPlugin(fileSystem);
+				return new FileGZipCollectorPlugin(this.fileSystem);
 			case baseDump:
 				return new BaseCollectorPlugin(this.fileSystem);
+			case gtr2Publications:
+				return new Gtr2PublicationsCollectorPlugin(this.clientParams);
 			case other:
 				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
-					.ofNullable(api.getParams().get("other_plugin_type"))
+					.ofNullable(this.api.getParams().get("other_plugin_type"))
 					.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
 					.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
 
 				switch (plugin) {
 					case mdstore_mongodb_dump:
-						return new MongoDbDumpCollectorPlugin(fileSystem);
+						return new MongoDbDumpCollectorPlugin(this.fileSystem);
 					case mdstore_mongodb:
 						return new MDStoreCollectorPlugin();
 					default:
 						throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
 				}
 			default:
-				throw new UnknownCollectorPluginException("protocol is not managed: " + api.getProtocol());
+				throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
 		}
 	}
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
index 97d2d2585..0bba8d764 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
@@ -11,7 +11,7 @@ public interface CollectorPlugin {
 
 	enum NAME {
 
-		oai, other, rest_json2xml, file, fileGzip, baseDump;
+		oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications;
 
 		public enum OTHER_NAME {
 			mdstore_mongodb_dump, mdstore_mongodb
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java
new file mode 100644
index 000000000..543bcbe5a
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java
@@ -0,0 +1,40 @@
+
+package eu.dnetlib.dhp.collection.plugin.gtr2;
+
+import java.util.Iterator;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+public class Gtr2PublicationsCollectorPlugin implements CollectorPlugin {
+
+	private final HttpClientParams clientParams;
+
+	public Gtr2PublicationsCollectorPlugin(final HttpClientParams clientParams) {
+		this.clientParams = clientParams;
+	}
+
+	@Override
+	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
+
+		final String baseUrl = api.getBaseUrl();
+		final String startPage = api.getParams().get("startPage");
+		final String endPage = api.getParams().get("endPage");
+		final String fromDate = api.getParams().get("fromDate");
+
+		if ((fromDate != null) && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate); }
+
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseUrl, fromDate, startPage, endPage, this.clientParams);
+		final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
+
+		return StreamSupport.stream(spliterator, false);
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
new file mode 100644
index 000000000..c3c4cbac0
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
@@ -0,0 +1,210 @@
+package eu.dnetlib.dhp.collection.plugin.gtr2;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Queue;
+import java.util.function.Function;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.math.NumberUtils;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Element;
+import org.joda.time.DateTime;
+import org.joda.time.format.DateTimeFormat;
+import org.joda.time.format.DateTimeFormatter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
+
+public class Gtr2PublicationsIterator implements Iterator<String> {
+
+	public static final int PAGE_SIZE = 20;
+
+	private static final Logger log = LoggerFactory.getLogger(Gtr2PublicationsIterator.class);
+
+	private final HttpConnector2 connector;
+	private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd");
+
+	private static final int MAX_ATTEMPTS = 10;
+
+	private final String baseUrl;
+	private int currPage;
+	private int endPage;
+	private boolean incremental = false;
+	private DateTime fromDate;
+
+	private final Map<String, String> cache = new HashMap<>();
+
+	private final Queue<String> queue = new LinkedList<>();
+
+	private String nextElement;
+
+	public Gtr2PublicationsIterator(final String baseUrl, final String fromDate, final String startPage, final String endPage,
+			final HttpClientParams clientParams)
+			throws CollectorException {
+
+		this.baseUrl = baseUrl;
+		this.currPage = NumberUtils.toInt(startPage, 1);
+		this.endPage = NumberUtils.toInt(endPage, Integer.MAX_VALUE);
+		this.incremental = StringUtils.isNotBlank(fromDate);
+		this.connector = new HttpConnector2(clientParams);
+
+		if (this.incremental) {
+			this.fromDate = parseDate(fromDate);
+		}
+
+		prepareNextElement();
+	}
+
+	@Override
+	public boolean hasNext() {
+		return this.nextElement != null;
+	}
+
+	@Override
+	public String next() {
+		try {
+			return this.nextElement;
+		} finally {
+			prepareNextElement();
+		}
+	}
+
+	@Override
+	public void remove() {
+		throw new UnsupportedOperationException();
+	}
+
+	private void prepareNextElement() {
+		while ((this.currPage <= this.endPage) && this.queue.isEmpty()) {
+			log.debug("FETCHING PAGE + " + this.currPage + "/" + this.endPage);
+			this.queue.addAll(fetchPage(this.currPage++));
+		}
+		this.nextElement = this.queue.poll();
+	}
+
+	private List<String> fetchPage(final int pageNumber) {
+
+		final List<String> res = new ArrayList<>();
+		try {
+			final Document doc = loadURL(cleanURL(this.baseUrl + "/outcomes/publications?p=" + pageNumber), 0);
+
+			if (this.endPage == Integer.MAX_VALUE) {
+				this.endPage = NumberUtils.toInt(doc.valueOf("/*/@*[local-name() = 'totalPages']"));
+			}
+
+			for (final Object po : doc.selectNodes("//*[local-name() = 'publication']")) {
+				final Element mainEntity = (Element) ((Element) po).detach();
+
+				if (filterIncremental(mainEntity)) {
+					res.add(expandMainEntity(mainEntity));
+				} else {
+					log.debug("Skipped entity");
+				}
+
+			}
+		} catch (final Throwable e) {
+			log.error("Exception fetching page " + pageNumber, e);
+			throw new RuntimeException("Exception fetching page " + pageNumber, e);
+		}
+
+		return res;
+	}
+
+	private void addLinkedEntities(final Element master, final String relType, final Element newRoot, final Function<Document, Element> mapper) {
+
+		for (final Object o : master.selectNodes(".//*[local-name()='link']")) {
+			final String rel = ((Element) o).valueOf("@*[local-name()='rel']");
+			final String href = ((Element) o).valueOf("@*[local-name()='href']");
+
+			if (relType.equals(rel) && StringUtils.isNotBlank(href)) {
+				final String cacheKey = relType + "#" + href;
+				if (this.cache.containsKey(cacheKey)) {
+					try {
+						log.debug(" * from cache (" + relType + "): " + href);
+						newRoot.add(DocumentHelper.parseText(this.cache.get(cacheKey)).getRootElement());
+					} catch (final DocumentException e) {
+						log.error("Error retrieving cache element: " + cacheKey, e);
+						throw new RuntimeException("Error retrieving cache element: " + cacheKey, e);
+					}
+				} else {
+					final Document doc = loadURL(cleanURL(href), 0);
+					final Element elem = mapper.apply(doc);
+					newRoot.add(elem);
+					this.cache.put(cacheKey, elem.asXML());
+				}
+
+			}
+		}
+	}
+
+	private boolean filterIncremental(final Element e) {
+		if (!this.incremental || isAfter(e.valueOf("@*[local-name() = 'created']"), this.fromDate)
+				|| isAfter(e.valueOf("@*[local-name() = 'updated']"), this.fromDate)) {
+			return true;
+		}
+		return false;
+	}
+
+	private String expandMainEntity(final Element mainEntity) {
+		final Element newRoot = DocumentHelper.createElement("doc");
+		newRoot.add(mainEntity);
+		addLinkedEntities(mainEntity, "PROJECT", newRoot, this::asProjectElement);
+		return DocumentHelper.createDocument(newRoot).asXML();
+	}
+
+	private Element asProjectElement(final Document doc) {
+		final Element newOrg = DocumentHelper.createElement("project");
+		newOrg.addElement("id").setText(doc.valueOf("/*/@*[local-name()='id']"));
+		newOrg.addElement("code").setText(doc.valueOf("//*[local-name()='identifier' and @*[local-name()='type'] = 'RCUK']"));
+		newOrg.addElement("title").setText(doc.valueOf("//*[local-name()='title']"));
+		return newOrg;
+	}
+
+	private static String cleanURL(final String url) {
+		String cleaned = url;
+		if (cleaned.contains("gtr.gtr")) {
+			cleaned = cleaned.replace("gtr.gtr", "gtr");
+		}
+		if (cleaned.startsWith("http://")) {
+			cleaned = cleaned.replaceFirst("http://", "https://");
+		}
+		return cleaned;
+	}
+
+	private Document loadURL(final String cleanUrl, final int attempt) {
+		try {
+			log.debug("  * Downloading Url: " + cleanUrl);
+			final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes("UTF-8");
+			return DocumentHelper.parseText(new String(bytes));
+		} catch (final Throwable e) {
+			log.error("Error dowloading url: " + cleanUrl + ", attempt = " + attempt, e);
+			if (attempt >= MAX_ATTEMPTS) { throw new RuntimeException("Error dowloading url: " + cleanUrl, e); }
+			try {
+				Thread.sleep(60000); // I wait for a minute
+			} catch (final InterruptedException e1) {
+				throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
+			}
+			return loadURL(cleanUrl, attempt + 1);
+		}
+	}
+
+	private DateTime parseDate(final String s) {
+		// I expect dates in the format 'yyyy-MM-dd'. See class
+		// eu.dnetlib.msro.workflows.nodes.collect.FindDateRangeForIncrementalHarvestingJobNode
+		return DateTime.parse(s.substring(0, s.indexOf("T")), simpleDateTimeFormatter);
+	}
+
+	private boolean isAfter(final String d, final DateTime fromDate) {
+		return parseDate(d).isAfter(fromDate);
+	}
+}
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index 44004faf3..3c8f5cef5 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -20,7 +20,6 @@ import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
-import eu.dnetlib.dhp.oa.provision.model.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -42,6 +41,7 @@ import com.google.common.collect.Sets;
 import com.mycila.xmltool.XMLDoc;
 import com.mycila.xmltool.XMLTag;
 
+import eu.dnetlib.dhp.oa.provision.model.*;
 import eu.dnetlib.dhp.schema.common.*;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Result;

From 99b7adda0c352e8439d3dc09d5b72a324875f58f Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 16 Sep 2024 15:13:44 +0200
Subject: [PATCH 117/239] gtr2 unit test

---
 .../gtr2/Gtr2PublicationsIteratorTest.java    | 101 ++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java

diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
new file mode 100644
index 000000000..737ef0dca
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
@@ -0,0 +1,101 @@
+package eu.dnetlib.dhp.collection.plugin.gtr2;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import java.util.Iterator;
+
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+class Gtr2PublicationsIteratorTest {
+
+	private static final String baseURL = "https://gtr.ukri.org/gtr/api";
+
+	private static final HttpClientParams clientParams = new HttpClientParams();
+
+	@Test
+	@Disabled
+	public void testOne() throws Exception {
+		System.out.println("one publication");
+
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, null, null, null, clientParams);
+
+		if (iterator.hasNext()) {
+			final String res = iterator.next();
+			assertNotNull(res);
+			System.out.println(res);
+		}
+	}
+
+	@Test
+	@Disabled
+	public void testPaging() throws Exception {
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, null, "2", "2", clientParams);
+
+		while (iterator.hasNext()) {
+			Thread.sleep(300);
+			final String res = iterator.next();
+			assertNotNull(res);
+			System.out.println(res);
+		}
+	}
+
+	@Test
+	@Disabled
+	public void testOnePage() throws Exception {
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, null, "12", "12", clientParams);
+		final int count = iterateAndCount(iterator);
+		assertEquals(21, count);
+	}
+
+	@Test
+	@Disabled
+	public void testIncrementalHarvestingNoRecords() throws Exception {
+		System.out.println("incremental Harvesting");
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2050-12-12", "11", "13", clientParams);
+		final int count = iterateAndCount(iterator);
+		assertEquals(1, count);
+	}
+
+	@Test
+	@Disabled
+	public void testIncrementalHarvesting() throws Exception {
+		System.out.println("incremental Harvesting");
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2016-11-30", "11", "11", clientParams);
+		final int count = iterateAndCount(iterator);
+		assertEquals(21, count);
+	}
+
+	@Test
+	@Disabled
+	public void testCompleteHarvesting() throws Exception {
+		System.out.println("testing complete harvesting");
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, null, null, null, clientParams);
+		// TryIndentXmlString indenter = new TryIndentXmlString();
+		// it.setEndAtPage(3);
+
+		while (iterator.hasNext()) {
+			final String res = iterator.next();
+			assertNotNull(res);
+			// System.out.println(res);
+			// Scanner keyboard = new Scanner(System.in);
+			// System.out.println("press enter for next record");
+			// keyboard.nextLine();
+
+		}
+	}
+
+	private int iterateAndCount(final Iterator<String> iterator) throws Exception {
+		int i = 0;
+		while (iterator.hasNext()) {
+			assertNotNull(iterator.next());
+			i++;
+		}
+		System.out.println("Got " + i + " publications");
+		return i;
+	}
+
+}

From a2fac78dcc77ca3647765f73c4cbe86f40614dc6 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Tue, 17 Sep 2024 10:16:28 +0200
Subject: [PATCH 118/239] fixed a problem in incremental harvesting

---
 .../collection/plugin/gtr2/Gtr2PublicationsIterator.java  | 6 ++----
 .../plugin/gtr2/Gtr2PublicationsIteratorTest.java         | 8 ++++----
 2 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
index c3c4cbac0..9b122bbe6 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
@@ -199,12 +199,10 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 	}
 
 	private DateTime parseDate(final String s) {
-		// I expect dates in the format 'yyyy-MM-dd'. See class
-		// eu.dnetlib.msro.workflows.nodes.collect.FindDateRangeForIncrementalHarvestingJobNode
-		return DateTime.parse(s.substring(0, s.indexOf("T")), simpleDateTimeFormatter);
+		return DateTime.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter);
 	}
 
 	private boolean isAfter(final String d, final DateTime fromDate) {
-		return parseDate(d).isAfter(fromDate);
+		return StringUtils.isNotBlank(d) && parseDate(d).isAfter(fromDate);
 	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
index 737ef0dca..f02feb0ef 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
@@ -48,16 +48,16 @@ class Gtr2PublicationsIteratorTest {
 	public void testOnePage() throws Exception {
 		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, null, "12", "12", clientParams);
 		final int count = iterateAndCount(iterator);
-		assertEquals(21, count);
+		assertEquals(20, count);
 	}
 
 	@Test
 	@Disabled
 	public void testIncrementalHarvestingNoRecords() throws Exception {
 		System.out.println("incremental Harvesting");
-		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2050-12-12", "11", "13", clientParams);
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2050-12-12T", "11", "13", clientParams);
 		final int count = iterateAndCount(iterator);
-		assertEquals(1, count);
+		assertEquals(0, count);
 	}
 
 	@Test
@@ -66,7 +66,7 @@ class Gtr2PublicationsIteratorTest {
 		System.out.println("incremental Harvesting");
 		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2016-11-30", "11", "11", clientParams);
 		final int count = iterateAndCount(iterator);
-		assertEquals(21, count);
+		assertEquals(20, count);
 	}
 
 	@Test

From bfd05cdab26e4d2ed0cca1e5c91dfbbb37d588e7 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 16 Sep 2024 16:16:23 +0200
Subject: [PATCH 119/239] run mergeResultsOfDifferentTypes only when
 checkDelegatedAuthority is true

---
 .../dhp/schema/oaf/utils/MergeUtils.java      |   3 +-
 .../PromoteResultWithMeasuresTest.java        | 210 ++++++++++++++++++
 .../measures/actionPayloads/part0000.json     |   3 +
 .../promote/measures/graph/part00000.json     |   1 +
 4 files changed, 216 insertions(+), 1 deletion(-)
 create mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java
 create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json
 create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index ea402ecbf..ac7694d18 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -30,6 +30,7 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class MergeUtils {
+
 	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
 		return mergeGroup(s, oafEntityIterator, true);
 	}
@@ -88,7 +89,7 @@ public class MergeUtils {
 	private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) {
 
 		if (sameClass(left, right, Result.class)) {
-			if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) {
+			if (checkDelegatedAuthority) {
 				return mergeResultsOfDifferentTypes((Result) left, (Result) right);
 			}
 
diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java
new file mode 100644
index 000000000..3eafe7115
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java
@@ -0,0 +1,210 @@
+/*
+ * Copyright (c) 2024.
+ * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
+ * SPDX-License-Identifier: AGPL-3.0-or-later
+ */
+
+package eu.dnetlib.dhp.actionmanager.promote;
+
+import static eu.dnetlib.dhp.common.FunctionalInterfaceSupport.*;
+import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
+import static org.apache.spark.sql.functions.*;
+import static org.junit.jupiter.api.Assertions.*;
+
+import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.List;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
+
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.*;
+
+public class PromoteResultWithMeasuresTest {
+
+	private static final Logger log = LoggerFactory.getLogger(PromoteResultWithMeasuresTest.class);
+
+	private static SparkSession spark;
+
+	private static Path tempDir;
+
+	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		tempDir = Files.createTempDirectory(PromoteResultWithMeasuresTest.class.getSimpleName());
+		log.info("using work dir {}", tempDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setMaster("local[*]");
+		conf.setAppName(PromoteResultWithMeasuresTest.class.getSimpleName());
+		conf.set("spark.driver.host", "localhost");
+
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+
+		conf.set("spark.sql.warehouse.dir", tempDir.toString());
+		conf.set("hive.metastore.warehouse.dir", tempDir.resolve("warehouse").toString());
+
+		spark = SparkSession.builder().config(conf).getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		spark.stop();
+		FileUtils.deleteDirectory(tempDir.toFile());
+	}
+
+	@Test
+	void testPromoteResultWithMeasures_job() throws Exception {
+
+		final String inputGraphTablePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/promote/measures/graph")
+			.getPath();
+
+		final String inputActionPayloadPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads")
+			.getPath();
+
+		final String actionPayloadsPath = tempDir.resolve("actionPayloads").toString();
+
+		spark
+			.read()
+			.text(inputActionPayloadPath)
+			.withColumn("payload", col("value"))
+			.select("payload")
+			.write()
+			.parquet(actionPayloadsPath);
+
+		final Path outputGraphTablePath = tempDir.resolve("outputGraphTablePath");
+
+		PromoteActionPayloadForGraphTableJob
+			.main(new String[] {
+				"--isSparkSessionManaged", Boolean.FALSE.toString(),
+				"--graphTableClassName", Publication.class.getCanonicalName(),
+				"--inputGraphTablePath", inputGraphTablePath,
+				"--inputActionPayloadPath", actionPayloadsPath,
+				"--actionPayloadClassName", Result.class.getCanonicalName(),
+				"--outputGraphTablePath", outputGraphTablePath.toString(),
+				"--mergeAndGetStrategy", MergeAndGet.Strategy.MERGE_FROM_AND_GET.toString(),
+				"--promoteActionStrategy", PromoteAction.Strategy.ENRICH.toString(),
+				"--shouldGroupById", "true"
+			});
+
+		assertFalse(isDirEmpty(outputGraphTablePath));
+
+		final Encoder<Publication> pubEncoder = Encoders.bean(Publication.class);
+		List<Publication> results = spark
+			.read()
+			.schema(pubEncoder.schema())
+			.json(outputGraphTablePath.toString())
+			.as(pubEncoder)
+			.collectAsList();
+
+		verify(results);
+	}
+
+	@Test
+	void testPromoteResultWithMeasures_internal() throws JsonProcessingException {
+
+		Dataset<Publication> rowDS = spark
+			.read()
+			.schema(Encoders.bean(Publication.class).schema())
+			.json("src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph")
+			.as(Encoders.bean(Publication.class));
+
+		Dataset<Result> actionPayloadDS = spark
+			.read()
+			.schema(Encoders.bean(Result.class).schema())
+			.json("src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads")
+			.as(Encoders.bean(Result.class));
+
+		final MergeAndGet.Strategy mergeFromAndGet = MergeAndGet.Strategy.MERGE_FROM_AND_GET;
+
+		final SerializableSupplier<Function<Publication, String>> rowIdFn = ModelSupport::idFn;
+		final SerializableSupplier<BiFunction<Publication, Result, Publication>> mergeAndGetFn = MergeAndGet
+			.functionFor(mergeFromAndGet);
+		final SerializableSupplier<Publication> zeroFn = () -> Publication.class
+			.cast(new eu.dnetlib.dhp.schema.oaf.Publication());
+		final SerializableSupplier<Function<Publication, Boolean>> isNotZeroFn = PromoteResultWithMeasuresTest::isNotZeroFnUsingIdOrSourceAndTarget;
+
+		Dataset<Publication> joinedResults = PromoteActionPayloadFunctions
+			.joinGraphTableWithActionPayloadAndMerge(
+				rowDS,
+				actionPayloadDS,
+				rowIdFn,
+				ModelSupport::idFn,
+				mergeAndGetFn,
+				PromoteAction.Strategy.ENRICH,
+				Publication.class,
+				Result.class);
+
+		SerializableSupplier<BiFunction<Publication, Publication, Publication>> mergeRowsAndGetFn = MergeAndGet
+			.functionFor(mergeFromAndGet);
+
+		Dataset<Publication> mergedResults = PromoteActionPayloadFunctions
+			.groupGraphTableByIdAndMerge(
+				joinedResults, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, Publication.class);
+
+		verify(mergedResults.collectAsList());
+	}
+
+	private static void verify(List<Publication> results) throws JsonProcessingException {
+		assertNotNull(results);
+		assertEquals(1, results.size());
+
+		Result r = results.get(0);
+
+		log.info(OBJECT_MAPPER.writeValueAsString(r));
+
+		assertNotNull(r.getMeasures());
+		assertFalse(r.getMeasures().isEmpty());
+		assertTrue(
+			r
+				.getMeasures()
+				.stream()
+				.map(Measure::getId)
+				.collect(Collectors.toCollection(HashSet::new))
+				.containsAll(
+					Lists
+						.newArrayList(
+							"downloads", "views", "influence", "popularity", "influence_alt", "popularity_alt",
+							"impulse")));
+	}
+
+	private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSourceAndTarget() {
+		return t -> {
+			if (isSubClass(t, Relation.class)) {
+				final Relation rel = (Relation) t;
+				return StringUtils.isNotBlank(rel.getSource()) && StringUtils.isNotBlank(rel.getTarget());
+			}
+			return StringUtils.isNotBlank(((OafEntity) t).getId());
+		};
+	}
+
+	private static boolean isDirEmpty(final Path directory) throws IOException {
+		try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(directory)) {
+			return !dirStream.iterator().hasNext();
+		}
+	}
+
+}
diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json
new file mode 100644
index 000000000..806bcf5c8
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json
@@ -0,0 +1,3 @@
+{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":[{"id":"downloads","unit":[{"key":"opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO","value":"125","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:usage_counts","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"views","unit":[{"key":"opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO","value":"35","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:usage_counts","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"transformativeAgreement":null,"isGreen":null,"isInDiamondJournal":null}
+{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":[{"id":"influence","unit":[{"key":"score","value":"3.1167566E-9","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity","unit":[{"key":"score","value":"7.335433E-9","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"influence_alt","unit":[{"key":"score","value":"4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity_alt","unit":[{"key":"score","value":"2.96","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"impulse","unit":[{"key":"score","value":"4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"transformativeAgreement":null,"isGreen":null,"isInDiamondJournal":null}
+{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":null,"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":"hybrid","publiclyFunded":false,"transformativeAgreement":null,"isGreen":true,"isInDiamondJournal":false}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json
new file mode 100644
index 000000000..9f03cebe4
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json
@@ -0,0 +1 @@
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"https://zenodo.org/communities/eu"}], "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "SPHINX"}, {"qualifier": {"classid": "subtitle", "classname": "subtitle", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "a system for metapath-based entity exploration in heterogeneous information networks"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "SPHINX: A System for Metapath-based Entity Exploration in Heterogeneous Information Networks"}, {"qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "sphinx a system for metapath based entity exploration in heterogeneous information networks"}]}
\ No newline at end of file

From 23e0ab3a7c301a9f1bf3e10beb1944e08cb14fcb Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 16 Sep 2024 16:16:23 +0200
Subject: [PATCH 120/239] run mergeResultsOfDifferentTypes only when
 checkDelegatedAuthority is true

---
 .../dhp/schema/oaf/utils/MergeUtils.java      |   3 +-
 .../PromoteResultWithMeasuresTest.java        | 210 ++++++++++++++++++
 .../measures/actionPayloads/part0000.json     |   3 +
 .../promote/measures/graph/part00000.json     |   1 +
 4 files changed, 216 insertions(+), 1 deletion(-)
 create mode 100644 dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java
 create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json
 create mode 100644 dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index ea402ecbf..ac7694d18 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -30,6 +30,7 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class MergeUtils {
+
 	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
 		return mergeGroup(s, oafEntityIterator, true);
 	}
@@ -88,7 +89,7 @@ public class MergeUtils {
 	private static Oaf mergeEntities(Oaf left, Oaf right, boolean checkDelegatedAuthority) {
 
 		if (sameClass(left, right, Result.class)) {
-			if (!left.getClass().equals(right.getClass()) || checkDelegatedAuthority) {
+			if (checkDelegatedAuthority) {
 				return mergeResultsOfDifferentTypes((Result) left, (Result) right);
 			}
 
diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java
new file mode 100644
index 000000000..3eafe7115
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteResultWithMeasuresTest.java
@@ -0,0 +1,210 @@
+/*
+ * Copyright (c) 2024.
+ * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
+ * SPDX-License-Identifier: AGPL-3.0-or-later
+ */
+
+package eu.dnetlib.dhp.actionmanager.promote;
+
+import static eu.dnetlib.dhp.common.FunctionalInterfaceSupport.*;
+import static eu.dnetlib.dhp.schema.common.ModelSupport.isSubClass;
+import static org.apache.spark.sql.functions.*;
+import static org.junit.jupiter.api.Assertions.*;
+
+import java.io.IOException;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.List;
+import java.util.function.BiFunction;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
+
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.*;
+
+public class PromoteResultWithMeasuresTest {
+
+	private static final Logger log = LoggerFactory.getLogger(PromoteResultWithMeasuresTest.class);
+
+	private static SparkSession spark;
+
+	private static Path tempDir;
+
+	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		tempDir = Files.createTempDirectory(PromoteResultWithMeasuresTest.class.getSimpleName());
+		log.info("using work dir {}", tempDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setMaster("local[*]");
+		conf.setAppName(PromoteResultWithMeasuresTest.class.getSimpleName());
+		conf.set("spark.driver.host", "localhost");
+
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+
+		conf.set("spark.sql.warehouse.dir", tempDir.toString());
+		conf.set("hive.metastore.warehouse.dir", tempDir.resolve("warehouse").toString());
+
+		spark = SparkSession.builder().config(conf).getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		spark.stop();
+		FileUtils.deleteDirectory(tempDir.toFile());
+	}
+
+	@Test
+	void testPromoteResultWithMeasures_job() throws Exception {
+
+		final String inputGraphTablePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/promote/measures/graph")
+			.getPath();
+
+		final String inputActionPayloadPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads")
+			.getPath();
+
+		final String actionPayloadsPath = tempDir.resolve("actionPayloads").toString();
+
+		spark
+			.read()
+			.text(inputActionPayloadPath)
+			.withColumn("payload", col("value"))
+			.select("payload")
+			.write()
+			.parquet(actionPayloadsPath);
+
+		final Path outputGraphTablePath = tempDir.resolve("outputGraphTablePath");
+
+		PromoteActionPayloadForGraphTableJob
+			.main(new String[] {
+				"--isSparkSessionManaged", Boolean.FALSE.toString(),
+				"--graphTableClassName", Publication.class.getCanonicalName(),
+				"--inputGraphTablePath", inputGraphTablePath,
+				"--inputActionPayloadPath", actionPayloadsPath,
+				"--actionPayloadClassName", Result.class.getCanonicalName(),
+				"--outputGraphTablePath", outputGraphTablePath.toString(),
+				"--mergeAndGetStrategy", MergeAndGet.Strategy.MERGE_FROM_AND_GET.toString(),
+				"--promoteActionStrategy", PromoteAction.Strategy.ENRICH.toString(),
+				"--shouldGroupById", "true"
+			});
+
+		assertFalse(isDirEmpty(outputGraphTablePath));
+
+		final Encoder<Publication> pubEncoder = Encoders.bean(Publication.class);
+		List<Publication> results = spark
+			.read()
+			.schema(pubEncoder.schema())
+			.json(outputGraphTablePath.toString())
+			.as(pubEncoder)
+			.collectAsList();
+
+		verify(results);
+	}
+
+	@Test
+	void testPromoteResultWithMeasures_internal() throws JsonProcessingException {
+
+		Dataset<Publication> rowDS = spark
+			.read()
+			.schema(Encoders.bean(Publication.class).schema())
+			.json("src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph")
+			.as(Encoders.bean(Publication.class));
+
+		Dataset<Result> actionPayloadDS = spark
+			.read()
+			.schema(Encoders.bean(Result.class).schema())
+			.json("src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads")
+			.as(Encoders.bean(Result.class));
+
+		final MergeAndGet.Strategy mergeFromAndGet = MergeAndGet.Strategy.MERGE_FROM_AND_GET;
+
+		final SerializableSupplier<Function<Publication, String>> rowIdFn = ModelSupport::idFn;
+		final SerializableSupplier<BiFunction<Publication, Result, Publication>> mergeAndGetFn = MergeAndGet
+			.functionFor(mergeFromAndGet);
+		final SerializableSupplier<Publication> zeroFn = () -> Publication.class
+			.cast(new eu.dnetlib.dhp.schema.oaf.Publication());
+		final SerializableSupplier<Function<Publication, Boolean>> isNotZeroFn = PromoteResultWithMeasuresTest::isNotZeroFnUsingIdOrSourceAndTarget;
+
+		Dataset<Publication> joinedResults = PromoteActionPayloadFunctions
+			.joinGraphTableWithActionPayloadAndMerge(
+				rowDS,
+				actionPayloadDS,
+				rowIdFn,
+				ModelSupport::idFn,
+				mergeAndGetFn,
+				PromoteAction.Strategy.ENRICH,
+				Publication.class,
+				Result.class);
+
+		SerializableSupplier<BiFunction<Publication, Publication, Publication>> mergeRowsAndGetFn = MergeAndGet
+			.functionFor(mergeFromAndGet);
+
+		Dataset<Publication> mergedResults = PromoteActionPayloadFunctions
+			.groupGraphTableByIdAndMerge(
+				joinedResults, rowIdFn, mergeRowsAndGetFn, zeroFn, isNotZeroFn, Publication.class);
+
+		verify(mergedResults.collectAsList());
+	}
+
+	private static void verify(List<Publication> results) throws JsonProcessingException {
+		assertNotNull(results);
+		assertEquals(1, results.size());
+
+		Result r = results.get(0);
+
+		log.info(OBJECT_MAPPER.writeValueAsString(r));
+
+		assertNotNull(r.getMeasures());
+		assertFalse(r.getMeasures().isEmpty());
+		assertTrue(
+			r
+				.getMeasures()
+				.stream()
+				.map(Measure::getId)
+				.collect(Collectors.toCollection(HashSet::new))
+				.containsAll(
+					Lists
+						.newArrayList(
+							"downloads", "views", "influence", "popularity", "influence_alt", "popularity_alt",
+							"impulse")));
+	}
+
+	private static <T extends Oaf> Function<T, Boolean> isNotZeroFnUsingIdOrSourceAndTarget() {
+		return t -> {
+			if (isSubClass(t, Relation.class)) {
+				final Relation rel = (Relation) t;
+				return StringUtils.isNotBlank(rel.getSource()) && StringUtils.isNotBlank(rel.getTarget());
+			}
+			return StringUtils.isNotBlank(((OafEntity) t).getId());
+		};
+	}
+
+	private static boolean isDirEmpty(final Path directory) throws IOException {
+		try (DirectoryStream<Path> dirStream = Files.newDirectoryStream(directory)) {
+			return !dirStream.iterator().hasNext();
+		}
+	}
+
+}
diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json
new file mode 100644
index 000000000..806bcf5c8
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/actionPayloads/part0000.json
@@ -0,0 +1,3 @@
+{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":[{"id":"downloads","unit":[{"key":"opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO","value":"125","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:usage_counts","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"views","unit":[{"key":"opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO","value":"35","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:usage_counts","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"transformativeAgreement":null,"isGreen":null,"isInDiamondJournal":null}
+{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":[{"id":"influence","unit":[{"key":"score","value":"3.1167566E-9","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity","unit":[{"key":"score","value":"7.335433E-9","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"influence_alt","unit":[{"key":"score","value":"4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"popularity_alt","unit":[{"key":"score","value":"2.96","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]},{"id":"impulse","unit":[{"key":"score","value":"4","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"key":"class","value":"C5","dataInfo":{"invisible":false,"inferred":true,"deletedbyinference":false,"trust":"","inferenceprovenance":"update","provenanceaction":{"classid":"measure:bip","classname":"Inferred by OpenAIRE","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}]}],"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":null,"publiclyFunded":null,"transformativeAgreement":null,"isGreen":null,"isInDiamondJournal":null}
+{"collectedfrom":null,"dataInfo":null,"lastupdatetimestamp":null,"id":"50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b","originalId":null,"pid":null,"dateofcollection":null,"dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":null,"context":null,"processingchargeamount":null,"processingchargecurrency":null,"author":null,"resulttype":null,"metaResourceType":null,"language":null,"country":null,"subject":null,"title":null,"relevantdate":null,"description":null,"dateofacceptance":null,"publisher":null,"embargoenddate":null,"source":null,"fulltext":null,"format":null,"contributor":null,"resourcetype":null,"coverage":null,"bestaccessright":null,"externalReference":null,"instance":null,"eoscifguidelines":null,"openAccessColor":"hybrid","publiclyFunded":false,"transformativeAgreement":null,"isGreen":true,"isInDiamondJournal":false}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json
new file mode 100644
index 000000000..9f03cebe4
--- /dev/null
+++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/measures/graph/part00000.json
@@ -0,0 +1 @@
+{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:dedup", "classname": "sysimport:dedup", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "dedup-result-decisiontree-v4", "invisible": false, "trust": "0.8"}, "resourcetype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "pid": [{"qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}, {"qualifier": {"classid": "mag_id", "classname": "Microsoft Academic Graph Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "3086187510"}], "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "created", "classname": "created", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2020-09-14"}, {"qualifier": {"classid": "published-online", "classname": "published-online", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2020-09-14"}, {"qualifier": {"classid": "published-print", "classname": "published-print", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2020-08-01"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "issued", "classname": "issued", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2020-09-02"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "updated", "classname": "updated", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2020-09-01"}], "contributor": [], "id": "50|doi_dedup___::02317b7093277ec8aa0311d5c6a25b9b", "description": [{"value": "<jats:p>We present SPHINX, a system for metapath-based entity exploration in Heterogeneous Information Networks (HINs). 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"schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}], "instanceTypeMapping": [{"originalType": "journal-article", "typeLabel": "research article", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_2df8fbb1"}, {"originalType": "http://purl.org/coar/resource_type/c_2df8fbb1", "typeLabel": "Article", "vocabularyName": "openaire::user_resource_types", "typeCode": "Article"}], "collectedfrom": {"value": "UnpayWall", "key": "10|openaire____:8ac8380272269217cb09a928c8caa993"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes", "openAccessRoute": "green"}, "instancetype": {"classid": "0001", "classname": "Article", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}, {"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"value": "Unknown Repository", "key": "10|openaire____::55045bd2a65019fd8e6741a755395c8c"}, "url": ["http://dx.doi.org/10.14778/3415478.3415507"], "pid": [], "instanceTypeMapping": [{"originalType": "CONFERENCE_PROCEEDING", "vocabularyName": "openaire::coar_resource_types_3_1"}], "distributionlocation": "", "alternateIdentifier": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}], "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "2020-01-01"}, "collectedfrom": {"value": "European Union Open Data Portal", "key": "10|re3data_____::c4b2081b224be6b3e79d0e5e5556f631"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0004", "classname": "Conference object", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}, {"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"value": "Unknown Repository", "key": "10|openaire____::55045bd2a65019fd8e6741a755395c8c"}, "url": ["http://dx.doi.org/10.14778/3415478.3415507"], "pid": [], "instanceTypeMapping": [{"originalType": "Conference proceedings", "typeLabel": "conference proceedings", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_f744"}], "distributionlocation": "", "alternateIdentifier": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}], "dateofacceptance": {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "2020-01-01"}, "collectedfrom": {"value": "European Union Open Data Portal", "key": "10|re3data_____::c4b2081b224be6b3e79d0e5e5556f631"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0038", "classname": "Other literature type", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}, {"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"value": "ZENODO", "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69"}, "license": {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "CC BY"}, "url": ["http://dx.doi.org/10.14778/3415478.3415507"], "pid": [], "instanceTypeMapping": [{"originalType": "ConferencePaper", "typeLabel": "conference paper", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_5794"}, {"originalType": "http://purl.org/coar/resource_type/c_5794", "typeLabel": "Article", "vocabularyName": "openaire::user_resource_types", "typeCode": "Article"}], "alternateIdentifier": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "oai", "classname": "Open Archives Initiative", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "oai:zenodo.org:4010307"}], "dateofacceptance": {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "2020-09-02"}, "collectedfrom": {"value": "ZENODO", "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0004", "classname": "Conference object", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}, {"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"dataInfo": {"invisible": false, "deletedbyinference": false}, "value": "Unknown Repository", "key": "10|openaire____::55045bd2a65019fd8e6741a755395c8c"}, "url": ["http://www.vldb.org/pvldb/vol13/p2913-chatzopoulos.pdf", "https://dblp.uni-trier.de/db/journals/pvldb/pvldb13.html#ChatzopoulosPZV20", "https://dl.acm.org/doi/10.14778/3415478.3415507", "https://doi.org/10.14778/3415478.3415507"], "pid": [{"qualifier": {"classid": "mag_id", "classname": "Microsoft Academic Graph Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "3086187510"}, {"qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.14778/3415478.3415507"}], "instanceTypeMapping": [{"originalType": "Conference", "typeLabel": "conference output", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_c94f"}], "collectedfrom": {"value": "Microsoft Academic Graph", "key": "10|openaire____::5f532a3fc4f1ea403f37070f59a7a53a"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}], "dateofcollection": "2024-09-05T16:53:05.687", "metaResourceType": {"classid": "Research Literature", "classname": "Research Literature", "schemename": "openaire::meta_resource_types", "schemeid": "openaire::meta_resource_types"}, "fulltext": [], "dateofacceptance": {"value": "2020-08-01"}, "format": [], "journal": {"issnPrinted": "2150-8097", "vol": "13", "sp": "2913", "ep": "2916", "name": "Proceedings of the VLDB Endowment"}, "subject": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "02 engineering and technology"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "0202 electrical engineering, electronic engineering, information engineering"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5467381477355957"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "020201 artificial intelligence & image processing"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.4532618224620819"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "020204 information systems"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "02020108 Machine learning/Social Info Processing"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "02020402 Cryptography/Information governance"}], "coverage": [], "externalReference": [], "publisher": {"value": "Association for Computing Machinery (ACM)"}, "eoscifguidelines": [], "language": {"classid": "und", "classname": "Undetermined", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "resulttype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["10.14778/3415478.3415507", "50|doiboost____|02317b7093277ec8aa0311d5c6a25b9b", "825041_1260870_PUBLI", "50|r3c4b2081b22::0d0cc9ff8949f9091272abb7a9e083f8", "50|r3c4b2081b22::02317b7093277ec8aa0311d5c6a25b9b", "oai:zenodo.org:4010307", "50|od______2659::de3dfee8ed6f2e53c85690531ab23028", "3086187510"], "source": [{"value": "Crossref"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "value": "International Conference on Very Large Data Bases (VLDB)"}], "context": [{"dataInfo": [{"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}], "id": "https://zenodo.org/communities/smartdatalake-project"}, {"dataInfo": [{"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}], "id": "https://zenodo.org/communities/eu"}], "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "SPHINX"}, {"qualifier": {"classid": "subtitle", "classname": "subtitle", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "a system for metapath-based entity exploration in heterogeneous information networks"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "sysimport:crosswalk", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.9"}, "qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "SPHINX: A System for Metapath-based Entity Exploration in Heterogeneous Information Networks"}, {"qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "sphinx a system for metapath based entity exploration in heterogeneous information networks"}]}
\ No newline at end of file

From dcf09811a26f93c7340f0b089aa456b88832e308 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Thu, 19 Sep 2024 12:42:45 +0200
Subject: [PATCH 121/239] partial implementation of osfPreprints plugin

---
 .../dhp/collection/CollectorWorker.java       |  88 +++----
 .../collection/plugin/CollectorPlugin.java    |   2 +-
 .../gtr2/Gtr2PublicationsCollectorPlugin.java |   7 +-
 .../plugin/gtr2/Gtr2PublicationsIterator.java |  21 +-
 .../osf/OsfPreprintsCollectorPlugin.java      |  54 ++++
 .../plugin/osf/OsfPreprintsIterator.java      | 232 ++++++++++++++++++
 .../gtr2/Gtr2PublicationsIteratorTest.java    |   4 +-
 7 files changed, 353 insertions(+), 55 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
index 5021b7727..67e07ba59 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
@@ -26,6 +26,7 @@ import eu.dnetlib.dhp.collection.plugin.gtr2.Gtr2PublicationsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
+import eu.dnetlib.dhp.collection.plugin.osf.OsfPreprintsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
@@ -45,11 +46,11 @@ public class CollectorWorker extends ReportingJob {
 	private final HttpClientParams clientParams;
 
 	public CollectorWorker(
-		final ApiDescriptor api,
-		final FileSystem fileSystem,
-		final MDStoreVersion mdStoreVersion,
-		final HttpClientParams clientParams,
-		final AggregatorReport report) {
+			final ApiDescriptor api,
+			final FileSystem fileSystem,
+			final MDStoreVersion mdStoreVersion,
+			final HttpClientParams clientParams,
+			final AggregatorReport report) {
 		super(report);
 		this.api = api;
 		this.fileSystem = fileSystem;
@@ -68,25 +69,22 @@ public class CollectorWorker extends ReportingJob {
 		scheduleReport(counter);
 
 		try (SequenceFile.Writer writer = SequenceFile
-			.createWriter(
-				this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
-					.keyClass(IntWritable.class),
-				SequenceFile.Writer
-					.valueClass(Text.class),
-				SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
+				.createWriter(this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
+						.keyClass(IntWritable.class), SequenceFile.Writer
+								.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
 			final IntWritable key = new IntWritable(counter.get());
 			final Text value = new Text();
 			plugin
-				.collect(this.api, this.report)
-				.forEach(content -> {
-					key.set(counter.getAndIncrement());
-					value.set(content);
-					try {
-						writer.append(key, value);
-					} catch (final Throwable e) {
-						throw new RuntimeException(e);
-					}
-				});
+					.collect(this.api, this.report)
+					.forEach(content -> {
+						key.set(counter.getAndIncrement());
+						value.set(content);
+						try {
+							writer.append(key, value);
+						} catch (final Throwable e) {
+							throw new RuntimeException(e);
+						}
+					});
 		} catch (final Throwable e) {
 			this.report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e);
@@ -114,34 +112,36 @@ public class CollectorWorker extends ReportingJob {
 	private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
 
 		switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
-			case oai:
-				return new OaiCollectorPlugin(this.clientParams);
-			case rest_json2xml:
-				return new RestCollectorPlugin(this.clientParams);
-			case file:
-				return new FileCollectorPlugin(this.fileSystem);
-			case fileGzip:
-				return new FileGZipCollectorPlugin(this.fileSystem);
-			case baseDump:
-				return new BaseCollectorPlugin(this.fileSystem);
-			case gtr2Publications:
-				return new Gtr2PublicationsCollectorPlugin(this.clientParams);
-			case other:
-				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
+		case oai:
+			return new OaiCollectorPlugin(this.clientParams);
+		case rest_json2xml:
+			return new RestCollectorPlugin(this.clientParams);
+		case file:
+			return new FileCollectorPlugin(this.fileSystem);
+		case fileGzip:
+			return new FileGZipCollectorPlugin(this.fileSystem);
+		case baseDump:
+			return new BaseCollectorPlugin(this.fileSystem);
+		case gtr2Publications:
+			return new Gtr2PublicationsCollectorPlugin(this.clientParams);
+		case osfPreprints:
+			return new OsfPreprintsCollectorPlugin(this.clientParams);
+		case other:
+			final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
 					.ofNullable(this.api.getParams().get("other_plugin_type"))
 					.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
 					.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
 
-				switch (plugin) {
-					case mdstore_mongodb_dump:
-						return new MongoDbDumpCollectorPlugin(this.fileSystem);
-					case mdstore_mongodb:
-						return new MDStoreCollectorPlugin();
-					default:
-						throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
-				}
+			switch (plugin) {
+			case mdstore_mongodb_dump:
+				return new MongoDbDumpCollectorPlugin(this.fileSystem);
+			case mdstore_mongodb:
+				return new MDStoreCollectorPlugin();
 			default:
-				throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
+				throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
+			}
+		default:
+			throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
 		}
 	}
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
index 0bba8d764..72e691579 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
@@ -11,7 +11,7 @@ public interface CollectorPlugin {
 
 	enum NAME {
 
-		oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications;
+		oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints;
 
 		public enum OTHER_NAME {
 			mdstore_mongodb_dump, mdstore_mongodb
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java
index 543bcbe5a..15fdd8280 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsCollectorPlugin.java
@@ -29,9 +29,12 @@ public class Gtr2PublicationsCollectorPlugin implements CollectorPlugin {
 		final String endPage = api.getParams().get("endPage");
 		final String fromDate = api.getParams().get("fromDate");
 
-		if ((fromDate != null) && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) { throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate); }
+		if ((fromDate != null) && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}")) {
+			throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate);
+		}
 
-		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseUrl, fromDate, startPage, endPage, this.clientParams);
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseUrl, fromDate, startPage, endPage,
+			this.clientParams);
 		final Spliterator<String> spliterator = Spliterators.spliteratorUnknownSize(iterator, Spliterator.ORDERED);
 
 		return StreamSupport.stream(spliterator, false);
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
index 9b122bbe6..5b8f48680 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.gtr2;
 
 import java.util.ArrayList;
@@ -48,9 +49,10 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 
 	private String nextElement;
 
-	public Gtr2PublicationsIterator(final String baseUrl, final String fromDate, final String startPage, final String endPage,
-			final HttpClientParams clientParams)
-			throws CollectorException {
+	public Gtr2PublicationsIterator(final String baseUrl, final String fromDate, final String startPage,
+		final String endPage,
+		final HttpClientParams clientParams)
+		throws CollectorException {
 
 		this.baseUrl = baseUrl;
 		this.currPage = NumberUtils.toInt(startPage, 1);
@@ -120,7 +122,8 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 		return res;
 	}
 
-	private void addLinkedEntities(final Element master, final String relType, final Element newRoot, final Function<Document, Element> mapper) {
+	private void addLinkedEntities(final Element master, final String relType, final Element newRoot,
+		final Function<Document, Element> mapper) {
 
 		for (final Object o : master.selectNodes(".//*[local-name()='link']")) {
 			final String rel = ((Element) o).valueOf("@*[local-name()='rel']");
@@ -149,7 +152,7 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 
 	private boolean filterIncremental(final Element e) {
 		if (!this.incremental || isAfter(e.valueOf("@*[local-name() = 'created']"), this.fromDate)
-				|| isAfter(e.valueOf("@*[local-name() = 'updated']"), this.fromDate)) {
+			|| isAfter(e.valueOf("@*[local-name() = 'updated']"), this.fromDate)) {
 			return true;
 		}
 		return false;
@@ -165,7 +168,9 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 	private Element asProjectElement(final Document doc) {
 		final Element newOrg = DocumentHelper.createElement("project");
 		newOrg.addElement("id").setText(doc.valueOf("/*/@*[local-name()='id']"));
-		newOrg.addElement("code").setText(doc.valueOf("//*[local-name()='identifier' and @*[local-name()='type'] = 'RCUK']"));
+		newOrg
+			.addElement("code")
+			.setText(doc.valueOf("//*[local-name()='identifier' and @*[local-name()='type'] = 'RCUK']"));
 		newOrg.addElement("title").setText(doc.valueOf("//*[local-name()='title']"));
 		return newOrg;
 	}
@@ -188,7 +193,9 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 			return DocumentHelper.parseText(new String(bytes));
 		} catch (final Throwable e) {
 			log.error("Error dowloading url: " + cleanUrl + ", attempt = " + attempt, e);
-			if (attempt >= MAX_ATTEMPTS) { throw new RuntimeException("Error dowloading url: " + cleanUrl, e); }
+			if (attempt >= MAX_ATTEMPTS) {
+				throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
+			}
 			try {
 				Thread.sleep(60000); // I wait for a minute
 			} catch (final InterruptedException e1) {
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
new file mode 100644
index 000000000..bd628efb8
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
@@ -0,0 +1,54 @@
+
+package eu.dnetlib.dhp.collection.plugin.osf;
+
+import java.util.Optional;
+import java.util.Spliterator;
+import java.util.Spliterators;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.math.NumberUtils;
+
+import com.google.gson.Gson;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+public class OsfPreprintsCollectorPlugin implements CollectorPlugin {
+
+	public static final int PAGE_SIZE_VALUE_DEFAULT = 100;
+
+	private final HttpClientParams clientParams;
+
+	public OsfPreprintsCollectorPlugin(final HttpClientParams clientParams) {
+		this.clientParams = clientParams;
+	}
+
+	@Override
+	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
+		final String baseUrl = api.getBaseUrl();
+
+		final Gson gson = new Gson();
+
+		final int pageSize = Optional
+				.ofNullable(api.getParams().get("pageSize"))
+				.filter(StringUtils::isNotBlank)
+				.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
+				.orElse(PAGE_SIZE_VALUE_DEFAULT);
+
+		if (StringUtils.isBlank(baseUrl)) { throw new CollectorException("Param 'baseUrl' is null or empty"); }
+
+		final OsfPreprintsIterator it = new OsfPreprintsIterator(baseUrl, pageSize, getClientParams());
+
+		return StreamSupport
+				.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
+	}
+
+	public HttpClientParams getClientParams() {
+		return this.clientParams;
+	}
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
new file mode 100644
index 000000000..72c056d32
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -0,0 +1,232 @@
+
+package eu.dnetlib.dhp.collection.plugin.osf;
+
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.nio.charset.StandardCharsets;
+import java.util.Iterator;
+import java.util.Queue;
+import java.util.concurrent.PriorityBlockingQueue;
+
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+import javax.xml.xpath.XPath;
+import javax.xml.xpath.XPathConstants;
+import javax.xml.xpath.XPathExpression;
+import javax.xml.xpath.XPathFactory;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+
+import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
+
+public class OsfPreprintsIterator implements Iterator<String> {
+
+	private static final Logger log = LoggerFactory.getLogger(OsfPreprintsIterator.class);
+	public static final String UTF_8 = "UTF-8";
+	private static final int MAX_ATTEMPTS = 5;
+
+	private final HttpClientParams clientParams;
+
+	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
+	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG
+			+ ">";
+
+	private final String baseUrl;
+	private final int pageSize;
+
+	private int resumptionInt = 0; // integer resumption token (first record to harvest)
+	private int resultTotal = -1;
+	private String resumptionStr = Integer.toString(this.resumptionInt); // string resumption token (first record to
+																		 // harvest
+	// or token scanned from results)
+	private InputStream resultStream;
+	private Transformer transformer;
+	private XPath xpath;
+	private String query;
+	private XPathExpression xprResultTotalPath;
+	private XPathExpression xprResumptionPath;
+	private XPathExpression xprEntity;
+	private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
+
+	public OsfPreprintsIterator(
+			final String baseUrl,
+			final int pageSize,
+			final HttpClientParams clientParams) {
+
+		this.clientParams = clientParams;
+		this.baseUrl = baseUrl;
+		this.pageSize = pageSize;
+
+		try {
+			final TransformerFactory factory = TransformerFactory.newInstance();
+			this.transformer = factory.newTransformer();
+			this.transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+			this.transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
+			this.xpath = XPathFactory.newInstance().newXPath();
+			this.xprResultTotalPath = this.xpath.compile("/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']");
+			this.xprResumptionPath = this.xpath.compile("substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')");
+			this.xprEntity = this.xpath.compile("/*/*[local-name()='data']");
+		} catch (final Exception e) {
+			throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
+		}
+
+		initQueue();
+	}
+
+	private void initQueue() {
+		this.query = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize;
+		log.info("REST calls starting with {}", this.query);
+	}
+
+	private void disconnect() {
+		// TODO close inputstream
+	}
+
+	/*
+	 * (non-Javadoc)
+	 *
+	 * @see java.util.Iterator#hasNext()
+	 */
+	@Override
+	public boolean hasNext() {
+		synchronized (this.recordQueue) {
+			while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
+				try {
+					this.query = downloadPage(this.query, 0);
+				} catch (final CollectorException e) {
+					log.debug("CollectorPlugin.next()-Exception: {}", e);
+					throw new RuntimeException(e);
+				}
+			}
+
+			if (!this.recordQueue.isEmpty()) { return true; }
+
+			disconnect();
+			return false;
+		}
+	}
+
+	/*
+	 * (non-Javadoc)
+	 *
+	 * @see java.util.Iterator#next()
+	 */
+	@Override
+	public String next() {
+		synchronized (this.recordQueue) {
+			return this.recordQueue.poll();
+		}
+	}
+
+	/*
+	 * download page and return nextQuery (with number of attempt)
+	 */
+	private String downloadPage(final String query, final int attempt) throws CollectorException {
+
+		if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, query:" + query); }
+
+		if (attempt > 0) {
+			final int delay = (attempt * 5000);
+			log.debug("Attempt {} with delay {}", attempt, delay);
+			try {
+				Thread.sleep(delay);
+			} catch (final InterruptedException e) {
+				new CollectorException(e);
+			}
+		}
+
+		try {
+			String resultJson;
+			String resultXml = XML_HEADER;
+			String nextQuery = "";
+			Node resultNode = null;
+			NodeList nodeList = null;
+
+			try {
+				log.info("requesting URL [{}]", query);
+
+				final URL qUrl = new URL(query);
+
+				final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
+				conn.setRequestMethod("GET");
+				this.resultStream = conn.getInputStream();
+
+				resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
+				resultXml = JsonUtils.convertToXML(resultJson);
+				this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
+
+				if (!isEmptyXml(resultXml)) {
+					resultNode = (Node) this.xpath
+							.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
+					nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
+					log.debug("nodeList.length: {}", nodeList.getLength());
+					for (int i = 0; i < nodeList.getLength(); i++) {
+						final StringWriter sw = new StringWriter();
+						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
+						final String toEnqueue = sw.toString();
+						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
+							log
+									.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
+						} else {
+							this.recordQueue.add(sw.toString());
+						}
+					}
+				} else {
+					log.warn("resultXml is equal with emptyXml");
+				}
+
+				this.resumptionInt += this.pageSize;
+
+				this.resumptionStr = this.xprResumptionPath.evaluate(resultNode);
+
+			} catch (final Exception e) {
+				log.error(e.getMessage(), e);
+				throw new IllegalStateException("collection failed: " + e.getMessage());
+			}
+
+			try {
+				if (this.resultTotal == -1) {
+					this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
+					log.info("resultTotal was -1 is now: " + this.resultTotal);
+				}
+			} catch (final Exception e) {
+				log.error(e.getMessage(), e);
+				throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
+			}
+			log.debug("resultTotal: " + this.resultTotal);
+			log.debug("resInt: " + this.resumptionInt);
+			if (this.resumptionInt <= this.resultTotal) {
+				nextQuery = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize + "&page="
+						+ this.resumptionStr;
+			} else {
+				nextQuery = "";
+				// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
+				// resumptionInt and prevent a NullPointer Exception at mdStore
+			}
+			log.debug("nextQueryUrl: " + nextQuery);
+			return nextQuery;
+		} catch (final Throwable e) {
+			log.warn(e.getMessage(), e);
+			return downloadPage(query, attempt + 1);
+		}
+
+	}
+
+	private boolean isEmptyXml(final String s) {
+		return EMPTY_XML.equalsIgnoreCase(s);
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
index f02feb0ef..117d7b94f 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIteratorTest.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.collection.plugin.gtr2;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -55,7 +56,8 @@ class Gtr2PublicationsIteratorTest {
 	@Disabled
 	public void testIncrementalHarvestingNoRecords() throws Exception {
 		System.out.println("incremental Harvesting");
-		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2050-12-12T", "11", "13", clientParams);
+		final Iterator<String> iterator = new Gtr2PublicationsIterator(baseURL, "2050-12-12T", "11", "13",
+			clientParams);
 		final int count = iterateAndCount(iterator);
 		assertEquals(0, count);
 	}

From 9073b1159d51d1f939163385173e5e934812880c Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Thu, 19 Sep 2024 13:58:53 +0200
Subject: [PATCH 122/239] partial implementation of osfPreprints plugin + tests

---
 .../plugin/osf/OsfPreprintsIterator.java      | 29 ++++---------
 .../OsfPreprintsCollectorPluginTest.java}     | 42 +++++--------------
 2 files changed, 18 insertions(+), 53 deletions(-)
 rename dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/{rest/OsfPreprintCollectorTest.java => osf/OsfPreprintsCollectorPluginTest.java} (52%)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index 72c056d32..a3b1dc237 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -3,8 +3,6 @@ package eu.dnetlib.dhp.collection.plugin.osf;
 
 import java.io.InputStream;
 import java.io.StringWriter;
-import java.net.HttpURLConnection;
-import java.net.URL;
 import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
 import java.util.Queue;
@@ -31,18 +29,18 @@ import org.xml.sax.InputSource;
 import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
 
 public class OsfPreprintsIterator implements Iterator<String> {
 
 	private static final Logger log = LoggerFactory.getLogger(OsfPreprintsIterator.class);
-	public static final String UTF_8 = "UTF-8";
+
 	private static final int MAX_ATTEMPTS = 5;
 
 	private final HttpClientParams clientParams;
 
 	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
-	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG
-			+ ">";
+	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
 
 	private final String baseUrl;
 	private final int pageSize;
@@ -91,10 +89,6 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		log.info("REST calls starting with {}", this.query);
 	}
 
-	private void disconnect() {
-		// TODO close inputstream
-	}
-
 	/*
 	 * (non-Javadoc)
 	 *
@@ -114,7 +108,6 @@ public class OsfPreprintsIterator implements Iterator<String> {
 
 			if (!this.recordQueue.isEmpty()) { return true; }
 
-			disconnect();
 			return false;
 		}
 	}
@@ -158,15 +151,12 @@ public class OsfPreprintsIterator implements Iterator<String> {
 			try {
 				log.info("requesting URL [{}]", query);
 
-				final URL qUrl = new URL(query);
+				final HttpConnector2 connector = new HttpConnector2(this.clientParams);
 
-				final HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
-				conn.setRequestMethod("GET");
-				this.resultStream = conn.getInputStream();
-
-				resultJson = IOUtils.toString(this.resultStream, StandardCharsets.UTF_8);
+				resultJson = connector.getInputSource(query);
 				resultXml = JsonUtils.convertToXML(resultJson);
-				this.resultStream = IOUtils.toInputStream(resultXml, UTF_8);
+
+				this.resultStream = IOUtils.toInputStream(resultXml, StandardCharsets.UTF_8);
 
 				if (!isEmptyXml(resultXml)) {
 					resultNode = (Node) this.xpath
@@ -178,8 +168,7 @@ public class OsfPreprintsIterator implements Iterator<String> {
 						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
 						final String toEnqueue = sw.toString();
 						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
-							log
-									.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
+							log.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
 						} else {
 							this.recordQueue.add(sw.toString());
 						}
@@ -213,8 +202,6 @@ public class OsfPreprintsIterator implements Iterator<String> {
 						+ this.resumptionStr;
 			} else {
 				nextQuery = "";
-				// if (resumptionType.toLowerCase().equals("deep-cursor")) { resumptionInt -= 1; } // correct the
-				// resumptionInt and prevent a NullPointer Exception at mdStore
 			}
 			log.debug("nextQueryUrl: " + nextQuery);
 			return nextQuery;
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
similarity index 52%
rename from dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
rename to dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index a1b723e33..f6ddb3aeb 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/rest/OsfPreprintCollectorTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection.plugin.rest;
+package eu.dnetlib.dhp.collection.plugin.osf;
 
 import java.util.HashMap;
 import java.util.concurrent.atomic.AtomicInteger;
@@ -18,9 +18,9 @@ import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
 
-public class OsfPreprintCollectorTest {
+public class OsfPreprintsCollectorPluginTest {
 
-	private static final Logger log = LoggerFactory.getLogger(OsfPreprintCollectorTest.class);
+	private static final Logger log = LoggerFactory.getLogger(OsfPreprintsCollectorPlugin.class);
 
 	private final String baseUrl = "https://api.osf.io/v2/preprints/";
 
@@ -29,50 +29,28 @@ public class OsfPreprintCollectorTest {
 	// private final String authToken = "";
 	// private final String resultOutputFormat = "";
 
-	private final String queryParams = "filter:is_published:d=true";
-
-	private final String entityXpath = "/*/*[local-name()='data']";
-
-	private final String resultTotalXpath = "/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']";
-
-	private final String resumptionParam = "page";
-	private final String resumptionType = "scan";
-	private final String resumptionXpath = "substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')";
-
-	private final String resultSizeParam = "page[size]";
-	private final String resultSizeValue = "100";
-
-	private final String resultFormatParam = "format";
-	private final String resultFormatValue = "json";
+	private final int pageSize = 100;
 
 	private final ApiDescriptor api = new ApiDescriptor();
-	private RestCollectorPlugin rcp;
+
+	private OsfPreprintsCollectorPlugin plugin;
 
 	@BeforeEach
 	public void setUp() {
 		final HashMap<String, String> params = new HashMap<>();
-		params.put("resumptionType", this.resumptionType);
-		params.put("resumptionParam", this.resumptionParam);
-		params.put("resumptionXpath", this.resumptionXpath);
-		params.put("resultTotalXpath", this.resultTotalXpath);
-		params.put("resultFormatParam", this.resultFormatParam);
-		params.put("resultFormatValue", this.resultFormatValue);
-		params.put("resultSizeParam", this.resultSizeParam);
-		params.put("resultSizeValue", this.resultSizeValue);
-		params.put("queryParams", this.queryParams);
-		params.put("entityXpath", this.entityXpath);
+		params.put("pageSize", "" + this.pageSize);
 
 		this.api.setBaseUrl(this.baseUrl);
 		this.api.setParams(params);
 
-		this.rcp = new RestCollectorPlugin(new HttpClientParams());
+		this.plugin = new OsfPreprintsCollectorPlugin(new HttpClientParams());
 	}
 
 	@Test
 	@Disabled
 	void test_limited() throws CollectorException {
 		final AtomicInteger i = new AtomicInteger(0);
-		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
+		final Stream<String> stream = this.plugin.collect(this.api, new AggregatorReport());
 
 		stream.limit(2000).forEach(s -> {
 			Assertions.assertTrue(s.length() > 0);
@@ -88,7 +66,7 @@ public class OsfPreprintCollectorTest {
 	@Disabled
 	void test_all() throws CollectorException {
 		final AtomicLong i = new AtomicLong(0);
-		final Stream<String> stream = this.rcp.collect(this.api, new AggregatorReport());
+		final Stream<String> stream = this.plugin.collect(this.api, new AggregatorReport());
 
 		stream.forEach(s -> {
 			Assertions.assertTrue(s.length() > 0);

From 52bb7af03b87c8d40f4b304b7920b59720ddceba Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Thu, 19 Sep 2024 14:59:05 +0200
Subject: [PATCH 123/239] use of dom4j

---
 .../osf/OsfPreprintsCollectorPlugin.java      |   4 -
 .../plugin/osf/OsfPreprintsIterator.java      | 151 ++++--------------
 .../osf/OsfPreprintsCollectorPluginTest.java  |   5 -
 3 files changed, 27 insertions(+), 133 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
index bd628efb8..fdc9df06f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
@@ -10,8 +10,6 @@ import java.util.stream.StreamSupport;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.math.NumberUtils;
 
-import com.google.gson.Gson;
-
 import eu.dnetlib.dhp.collection.ApiDescriptor;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
@@ -32,8 +30,6 @@ public class OsfPreprintsCollectorPlugin implements CollectorPlugin {
 	public Stream<String> collect(final ApiDescriptor api, final AggregatorReport report) throws CollectorException {
 		final String baseUrl = api.getBaseUrl();
 
-		final Gson gson = new Gson();
-
 		final int pageSize = Optional
 				.ofNullable(api.getParams().get("pageSize"))
 				.filter(StringUtils::isNotBlank)
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index a3b1dc237..311daf859 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -1,30 +1,15 @@
 
 package eu.dnetlib.dhp.collection.plugin.osf;
 
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.nio.charset.StandardCharsets;
 import java.util.Iterator;
 import java.util.Queue;
 import java.util.concurrent.PriorityBlockingQueue;
 
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.xpath.XPath;
-import javax.xml.xpath.XPathConstants;
-import javax.xml.xpath.XPathExpression;
-import javax.xml.xpath.XPathFactory;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
+import org.dom4j.Document;
+import org.dom4j.DocumentHelper;
+import org.dom4j.Element;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
 
 import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
 import eu.dnetlib.dhp.common.collection.CollectorException;
@@ -39,24 +24,11 @@ public class OsfPreprintsIterator implements Iterator<String> {
 
 	private final HttpClientParams clientParams;
 
-	private static final String XML_HEADER = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
-	private static final String EMPTY_XML = XML_HEADER + "<" + JsonUtils.XML_WRAP_TAG + "></" + JsonUtils.XML_WRAP_TAG + ">";
-
 	private final String baseUrl;
 	private final int pageSize;
 
-	private int resumptionInt = 0; // integer resumption token (first record to harvest)
-	private int resultTotal = -1;
-	private String resumptionStr = Integer.toString(this.resumptionInt); // string resumption token (first record to
-																		 // harvest
-	// or token scanned from results)
-	private InputStream resultStream;
-	private Transformer transformer;
-	private XPath xpath;
-	private String query;
-	private XPathExpression xprResultTotalPath;
-	private XPathExpression xprResumptionPath;
-	private XPathExpression xprEntity;
+	private String currentUrl;
+
 	private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
 
 	public OsfPreprintsIterator(
@@ -68,38 +40,20 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		this.baseUrl = baseUrl;
 		this.pageSize = pageSize;
 
-		try {
-			final TransformerFactory factory = TransformerFactory.newInstance();
-			this.transformer = factory.newTransformer();
-			this.transformer.setOutputProperty(OutputKeys.INDENT, "yes");
-			this.transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
-			this.xpath = XPathFactory.newInstance().newXPath();
-			this.xprResultTotalPath = this.xpath.compile("/*/*[local-name()='links']/*[local-name()='meta']/*[local-name()='total']");
-			this.xprResumptionPath = this.xpath.compile("substring-before(substring-after(/*/*[local-name()='links']/*[local-name()='next'], 'page='), '&')");
-			this.xprEntity = this.xpath.compile("/*/*[local-name()='data']");
-		} catch (final Exception e) {
-			throw new IllegalStateException("xml transformation init failed: " + e.getMessage());
-		}
-
 		initQueue();
 	}
 
 	private void initQueue() {
-		this.query = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize;
-		log.info("REST calls starting with {}", this.query);
+		this.currentUrl = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize;
+		log.info("REST calls starting with {}", this.currentUrl);
 	}
 
-	/*
-	 * (non-Javadoc)
-	 *
-	 * @see java.util.Iterator#hasNext()
-	 */
 	@Override
 	public boolean hasNext() {
 		synchronized (this.recordQueue) {
-			while (this.recordQueue.isEmpty() && !this.query.isEmpty()) {
+			while (this.recordQueue.isEmpty() && !this.currentUrl.isEmpty()) {
 				try {
-					this.query = downloadPage(this.query, 0);
+					this.currentUrl = downloadPage(this.currentUrl, 0);
 				} catch (final CollectorException e) {
 					log.debug("CollectorPlugin.next()-Exception: {}", e);
 					throw new RuntimeException(e);
@@ -112,11 +66,6 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		}
 	}
 
-	/*
-	 * (non-Javadoc)
-	 *
-	 * @see java.util.Iterator#next()
-	 */
 	@Override
 	public String next() {
 		synchronized (this.recordQueue) {
@@ -124,12 +73,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		}
 	}
 
-	/*
-	 * download page and return nextQuery (with number of attempt)
-	 */
-	private String downloadPage(final String query, final int attempt) throws CollectorException {
+	private String downloadPage(final String url, final int attempt) throws CollectorException {
 
-		if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, query:" + query); }
+		if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, url:" + url); }
 
 		if (attempt > 0) {
 			final int delay = (attempt * 5000);
@@ -142,78 +88,35 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		}
 
 		try {
-			String resultJson;
-			String resultXml = XML_HEADER;
-			String nextQuery = "";
-			Node resultNode = null;
-			NodeList nodeList = null;
+			log.info("requesting URL [{}]", url);
 
-			try {
-				log.info("requesting URL [{}]", query);
+			final HttpConnector2 connector = new HttpConnector2(this.clientParams);
 
-				final HttpConnector2 connector = new HttpConnector2(this.clientParams);
+			final String json = connector.getInputSource(url);
+			final String xml = JsonUtils.convertToXML(json);
 
-				resultJson = connector.getInputSource(query);
-				resultXml = JsonUtils.convertToXML(resultJson);
+			final Document doc = DocumentHelper.parseText(xml);
 
-				this.resultStream = IOUtils.toInputStream(resultXml, StandardCharsets.UTF_8);
+			for (final Object o : doc.selectNodes("/*/*[local-name()='data']")) {
+				final Element n = (Element) ((Element) o).detach();
 
-				if (!isEmptyXml(resultXml)) {
-					resultNode = (Node) this.xpath
-							.evaluate("/", new InputSource(this.resultStream), XPathConstants.NODE);
-					nodeList = (NodeList) this.xprEntity.evaluate(resultNode, XPathConstants.NODESET);
-					log.debug("nodeList.length: {}", nodeList.getLength());
-					for (int i = 0; i < nodeList.getLength(); i++) {
-						final StringWriter sw = new StringWriter();
-						this.transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
-						final String toEnqueue = sw.toString();
-						if ((toEnqueue == null) || StringUtils.isBlank(toEnqueue) || isEmptyXml(toEnqueue)) {
-							log.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
-						} else {
-							this.recordQueue.add(sw.toString());
-						}
-					}
-				} else {
-					log.warn("resultXml is equal with emptyXml");
+				for (final Object o1 : n.selectNodes(".//contributors//href")) {
+					// TODO ADD creators
+				}
+				for (final Object o1 : n.selectNodes(".//primary_file//href")) {
+					// TODO ADD fulltexts
 				}
 
-				this.resumptionInt += this.pageSize;
-
-				this.resumptionStr = this.xprResumptionPath.evaluate(resultNode);
-
-			} catch (final Exception e) {
-				log.error(e.getMessage(), e);
-				throw new IllegalStateException("collection failed: " + e.getMessage());
+				this.recordQueue.add(DocumentHelper.createDocument(n).asXML());
 			}
 
-			try {
-				if (this.resultTotal == -1) {
-					this.resultTotal = Integer.parseInt(this.xprResultTotalPath.evaluate(resultNode));
-					log.info("resultTotal was -1 is now: " + this.resultTotal);
-				}
-			} catch (final Exception e) {
-				log.error(e.getMessage(), e);
-				throw new IllegalStateException("downloadPage resultTotal couldn't parse: " + e.getMessage());
-			}
-			log.debug("resultTotal: " + this.resultTotal);
-			log.debug("resInt: " + this.resumptionInt);
-			if (this.resumptionInt <= this.resultTotal) {
-				nextQuery = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize + "&page="
-						+ this.resumptionStr;
-			} else {
-				nextQuery = "";
-			}
-			log.debug("nextQueryUrl: " + nextQuery);
-			return nextQuery;
+			return doc.valueOf("/*/*[local-name()='links']/*[local-name()='next']");
+
 		} catch (final Throwable e) {
 			log.warn(e.getMessage(), e);
-			return downloadPage(query, attempt + 1);
+			return downloadPage(url, attempt + 1);
 		}
 
 	}
 
-	private boolean isEmptyXml(final String s) {
-		return EMPTY_XML.equalsIgnoreCase(s);
-	}
-
 }
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index f6ddb3aeb..10b93ea76 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -24,11 +24,6 @@ public class OsfPreprintsCollectorPluginTest {
 
 	private final String baseUrl = "https://api.osf.io/v2/preprints/";
 
-	// private final String requestHeaderMap = "";
-	// private final String authMethod = "";
-	// private final String authToken = "";
-	// private final String resultOutputFormat = "";
-
 	private final int pageSize = 100;
 
 	private final ApiDescriptor api = new ApiDescriptor();

From 339d8124f26bbf8cc6a3c6398d5d32c5066bbb91 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Fri, 20 Sep 2024 08:44:05 +0200
Subject: [PATCH 124/239] osf plugin: links to contributors and primaty_file

---
 .../plugin/osf/OsfPreprintsIterator.java      | 55 +++++++++++--------
 .../osf/OsfPreprintsCollectorPluginTest.java  |  8 +++
 2 files changed, 41 insertions(+), 22 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index 311daf859..3bb2e2bdf 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -8,6 +8,7 @@ import java.util.concurrent.PriorityBlockingQueue;
 import org.dom4j.Document;
 import org.dom4j.DocumentHelper;
 import org.dom4j.Element;
+import org.dom4j.Node;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -53,7 +54,7 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		synchronized (this.recordQueue) {
 			while (this.recordQueue.isEmpty() && !this.currentUrl.isEmpty()) {
 				try {
-					this.currentUrl = downloadPage(this.currentUrl, 0);
+					this.currentUrl = downloadPage(this.currentUrl);
 				} catch (final CollectorException e) {
 					log.debug("CollectorPlugin.next()-Exception: {}", e);
 					throw new RuntimeException(e);
@@ -73,8 +74,36 @@ public class OsfPreprintsIterator implements Iterator<String> {
 		}
 	}
 
-	private String downloadPage(final String url, final int attempt) throws CollectorException {
+	private String downloadPage(final String url) throws CollectorException {
 
+		final Document doc = downloadUrl(url, 0);
+
+		for (final Object o : doc.selectNodes("/*/data")) {
+
+			final Element n = (Element) ((Element) o).detach();
+
+			final Element group = DocumentHelper.createElement("group");
+			group.addAttribute("id", n.valueOf(".//data/id"));
+
+			group.addElement("preprint").add(n);
+
+			for (final Object o1 : n.selectNodes(".//contributors//href")) {
+				final Document doc1 = downloadUrl(((Node) o1).getText(), 0);
+				group.addElement("contributors").add(doc1.getRootElement().detach());
+			}
+			for (final Object o1 : n.selectNodes(".//primary_file//href")) {
+				final Document doc1 = downloadUrl(((Node) o1).getText(), 0);
+				group.addElement("primary_file").add(doc1.getRootElement().detach());
+			}
+
+			this.recordQueue.add(DocumentHelper.createDocument(group).asXML());
+		}
+
+		return doc.valueOf("/*/links/next");
+
+	}
+
+	private Document downloadUrl(final String url, final int attempt) throws CollectorException {
 		if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, url:" + url); }
 
 		if (attempt > 0) {
@@ -95,28 +124,10 @@ public class OsfPreprintsIterator implements Iterator<String> {
 			final String json = connector.getInputSource(url);
 			final String xml = JsonUtils.convertToXML(json);
 
-			final Document doc = DocumentHelper.parseText(xml);
-
-			for (final Object o : doc.selectNodes("/*/*[local-name()='data']")) {
-				final Element n = (Element) ((Element) o).detach();
-
-				for (final Object o1 : n.selectNodes(".//contributors//href")) {
-					// TODO ADD creators
-				}
-				for (final Object o1 : n.selectNodes(".//primary_file//href")) {
-					// TODO ADD fulltexts
-				}
-
-				this.recordQueue.add(DocumentHelper.createDocument(n).asXML());
-			}
-
-			return doc.valueOf("/*/*[local-name()='links']/*[local-name()='next']");
-
+			return DocumentHelper.parseText(xml);
 		} catch (final Throwable e) {
 			log.warn(e.getMessage(), e);
-			return downloadPage(url, attempt + 1);
+			return downloadUrl(url, attempt + 1);
 		}
-
 	}
-
 }
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index 10b93ea76..708a26acd 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -43,6 +43,14 @@ public class OsfPreprintsCollectorPluginTest {
 
 	@Test
 	@Disabled
+	void test_one() throws CollectorException {
+		this.plugin.collect(this.api, new AggregatorReport())
+				.limit(1)
+				.forEach(log::info);
+	}
+
+	@Test
+	// @Disabled
 	void test_limited() throws CollectorException {
 		final AtomicInteger i = new AtomicInteger(0);
 		final Stream<String> stream = this.plugin.collect(this.api, new AggregatorReport());

From 5f86c93be6fbe137b417213d49e0dd426b6c7898 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 20 Sep 2024 12:20:00 +0200
Subject: [PATCH 125/239] [graph provision] person serialisation

---
 .../CreateRelatedEntitiesJob_phase1.java      |  8 +++
 .../model/ProvisionModelSupport.java          |  7 ++-
 .../dhp/oa/provision/model/RelatedEntity.java | 39 ++++++++++++-
 .../oa/provision/utils/XmlRecordFactory.java  | 57 ++++++++++++++++++-
 4 files changed, 107 insertions(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
index 63f3c2ead..3fc5893c6 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
@@ -231,6 +231,14 @@ public class CreateRelatedEntitiesJob_phase1 {
 				if (!f.isEmpty()) {
 					re.setFundingtree(f.stream().map(Field::getValue).collect(Collectors.toList()));
 				}
+				break;
+			case person:
+				final Person person = (Person) entity;
+
+				re.setGivenName(person.getGivenName());
+				re.setFamilyName(person.getFamilyName());
+				re.setAlternativeNames(person.getAlternativeNames());
+
 				break;
 		}
 		return re;
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 797e84315..de7932a8a 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.Person;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -38,6 +37,8 @@ import eu.dnetlib.dhp.schema.solr.Measure;
 import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
+import eu.dnetlib.dhp.schema.solr.Person;
+import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import eu.dnetlib.dhp.schema.solr.Pid;
 import eu.dnetlib.dhp.schema.solr.Project;
 import eu.dnetlib.dhp.schema.solr.Result;
@@ -193,6 +194,10 @@ public class ProvisionModelSupport {
 		ps.setFamilyName(p.getFamilyName());
 		ps.setGivenName(p.getGivenName());
 		ps.setAlternativeNames(p.getAlternativeNames());
+		ps.setBiography(p.getBiography());
+		ps.setConsent(p.getConsent());
+		// ps.setSubject(...));
+
 		return ps;
 	}
 
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java
index ee010910c..2a6332857 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/RelatedEntity.java
@@ -51,6 +51,11 @@ public class RelatedEntity implements Serializable {
 	private Qualifier contracttype;
 	private List<String> fundingtree;
 
+	// person
+	private String givenName;
+	private String familyName;
+	private List<String> alternativeNames;
+
 	public String getId() {
 		return id;
 	}
@@ -251,6 +256,30 @@ public class RelatedEntity implements Serializable {
 		this.fundingtree = fundingtree;
 	}
 
+	public String getGivenName() {
+		return givenName;
+	}
+
+	public void setGivenName(String givenName) {
+		this.givenName = givenName;
+	}
+
+	public String getFamilyName() {
+		return familyName;
+	}
+
+	public void setFamilyName(String familyName) {
+		this.familyName = familyName;
+	}
+
+	public List<String> getAlternativeNames() {
+		return alternativeNames;
+	}
+
+	public void setAlternativeNames(List<String> alternativeNames) {
+		this.alternativeNames = alternativeNames;
+	}
+
 	@Override
 	public boolean equals(Object o) {
 		if (this == o)
@@ -280,7 +309,10 @@ public class RelatedEntity implements Serializable {
 			&& Objects.equal(code, that.code)
 			&& Objects.equal(acronym, that.acronym)
 			&& Objects.equal(contracttype, that.contracttype)
-			&& Objects.equal(fundingtree, that.fundingtree);
+			&& Objects.equal(fundingtree, that.fundingtree)
+			&& Objects.equal(givenName, that.givenName)
+			&& Objects.equal(familyName, that.familyName)
+			&& Objects.equal(alternativeNames, that.alternativeNames);
 	}
 
 	@Override
@@ -309,6 +341,9 @@ public class RelatedEntity implements Serializable {
 				code,
 				acronym,
 				contracttype,
-				fundingtree);
+				fundingtree,
+				familyName,
+				givenName,
+				alternativeNames);
 	}
 }
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index 44004faf3..b1f419a7e 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -20,7 +20,6 @@ import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
-import eu.dnetlib.dhp.oa.provision.model.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -42,6 +41,7 @@ import com.google.common.collect.Sets;
 import com.mycila.xmltool.XMLDoc;
 import com.mycila.xmltool.XMLTag;
 
+import eu.dnetlib.dhp.oa.provision.model.*;
 import eu.dnetlib.dhp.schema.common.*;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Result;
@@ -1035,6 +1035,42 @@ public class XmlRecordFactory implements Serializable {
 								.collect(Collectors.toList()));
 				}
 
+				break;
+			case person:
+				final Person person = (Person) entity;
+
+				if (person.getGivenName() != null) {
+					metadata.add(XmlSerializationUtils.asXmlElement("givenname", person.getGivenName()));
+				}
+				if (person.getFamilyName() != null) {
+					metadata.add(XmlSerializationUtils.asXmlElement("familyname", person.getFamilyName()));
+				}
+				if (person.getAlternativeNames() != null) {
+					metadata.addAll(person.getAlternativeNames());
+				}
+				if (person.getBiography() != null) {
+					metadata.add(XmlSerializationUtils.asXmlElement("biography", person.getBiography()));
+				}
+				if (person.getSubject() != null) {
+					metadata
+						.addAll(
+							person
+								.getSubject()
+								.stream()
+								.map(pt -> {
+									List<Tuple2<String, String>> attrs = Lists.newArrayList();
+									attrs.add(new Tuple2<>("schema", pt.getSchema()));
+									attrs.add(new Tuple2<>("value", pt.getValue()));
+									attrs.add(new Tuple2<>("fromYear", String.valueOf(pt.getFromYear())));
+									attrs.add(new Tuple2<>("toYear", String.valueOf(pt.getToYear())));
+									return XmlSerializationUtils.asXmlElement("subject", attrs);
+								})
+								.collect(Collectors.toList()));
+				}
+				if (person.getConsent() != null) {
+					metadata.add(XmlSerializationUtils.asXmlElement("consent", String.valueOf(person.getConsent())));
+				}
+
 				break;
 			default:
 				throw new IllegalArgumentException("invalid entity type: " + type);
@@ -1240,6 +1276,25 @@ public class XmlRecordFactory implements Serializable {
 								.collect(Collectors.toList()));
 				}
 				break;
+
+			case person:
+
+				if (isNotBlank(re.getGivenName())) {
+					metadata.add(XmlSerializationUtils.asXmlElement("givenname", re.getGivenName()));
+				}
+				if (isNotBlank(re.getFamilyName())) {
+					metadata.add(XmlSerializationUtils.asXmlElement("familyname", re.getFamilyName()));
+				}
+				if (re.getAlternativeNames() != null && !re.getAlternativeNames().isEmpty()) {
+					metadata
+						.addAll(
+							re
+								.getAlternativeNames()
+								.stream()
+								.map(name -> XmlSerializationUtils.asXmlElement("alternativename", name))
+								.collect(Collectors.toList()));
+				}
+				break;
 			default:
 				throw new IllegalArgumentException("invalid target type: " + targetType);
 		}

From 6b0f7cc8b09f93ba6435682137d691fd58bfd75e Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 23 Sep 2024 10:16:53 +0200
Subject: [PATCH 126/239] skip urls with authentication

---
 .../plugin/osf/OsfPreprintsIterator.java      |  5 ++++
 .../osf/OsfPreprintsCollectorPluginTest.java  | 29 ++++++++++++++++++-
 2 files changed, 33 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index 3bb2e2bdf..9484297d0 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -125,8 +125,13 @@ public class OsfPreprintsIterator implements Iterator<String> {
 			final String xml = JsonUtils.convertToXML(json);
 
 			return DocumentHelper.parseText(xml);
+
 		} catch (final Throwable e) {
 			log.warn(e.getMessage(), e);
+			if ((e instanceof CollectorException) && e.getMessage().contains("401")) {
+				final Element root = DocumentHelper.createElement("error_401_authorization_required");
+				return DocumentHelper.createDocument(root);
+			}
 			return downloadUrl(url, attempt + 1);
 		}
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index 708a26acd..3d8d7a91f 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -1,11 +1,15 @@
 
 package eu.dnetlib.dhp.collection.plugin.osf;
 
+import static org.junit.jupiter.api.Assertions.assertTrue;
+import static org.junit.jupiter.api.Assertions.fail;
+
 import java.util.HashMap;
 import java.util.concurrent.atomic.AtomicInteger;
 import java.util.concurrent.atomic.AtomicLong;
 import java.util.stream.Stream;
 
+import org.dom4j.DocumentHelper;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
@@ -17,6 +21,7 @@ import eu.dnetlib.dhp.collection.ApiDescriptor;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
 
 public class OsfPreprintsCollectorPluginTest {
 
@@ -50,7 +55,7 @@ public class OsfPreprintsCollectorPluginTest {
 	}
 
 	@Test
-	// @Disabled
+	@Disabled
 	void test_limited() throws CollectorException {
 		final AtomicInteger i = new AtomicInteger(0);
 		final Stream<String> stream = this.plugin.collect(this.api, new AggregatorReport());
@@ -83,4 +88,26 @@ public class OsfPreprintsCollectorPluginTest {
 		Assertions.assertTrue(i.get() > 0);
 	}
 
+	@Test
+	// @Disabled
+	void test_authentication_required() {
+		final HttpConnector2 connector = new HttpConnector2();
+
+		try {
+			final String res = connector.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
+			System.out.println(res);
+			fail();
+		} catch (final Throwable e) {
+
+			System.out.println("**** ERROR: " + e.getMessage());
+
+			if ((e instanceof CollectorException) && e.getMessage().contains("401")) {
+				System.out.println(" XML: " + DocumentHelper.createDocument().getRootElement().detach());
+			}
+
+			assertTrue(e.getMessage().contains("401"));
+		}
+
+	}
+
 }

From 2d7a7a962da50cdc172cdc07ed0d5fb5df78a6f7 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 23 Sep 2024 10:19:36 +0200
Subject: [PATCH 127/239] unit test @Disabled

---
 .../collection/plugin/osf/OsfPreprintsCollectorPluginTest.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index 3d8d7a91f..efba0c72e 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -89,7 +89,7 @@ public class OsfPreprintsCollectorPluginTest {
 	}
 
 	@Test
-	// @Disabled
+	@Disabled
 	void test_authentication_required() {
 		final HttpConnector2 connector = new HttpConnector2();
 

From e0ff84baf0d8caf88965d13cd45a946a783f229d Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 23 Sep 2024 10:29:46 +0200
Subject: [PATCH 128/239] [graph provision] person serialisation, limit the
 number of authorships and coauthorships before expanding the payloads

---
 .../dhp/schema/oaf/utils/ModelHardLimits.java | 12 +++++++
 .../dhp/oa/provision/PayloadConverterJob.java | 33 +++++++++++++++++++
 .../oa/provision/utils/XmlRecordFactory.java  |  8 ++++-
 3 files changed, 52 insertions(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
index 36d138ba1..e4b184fa1 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
@@ -1,6 +1,12 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
+import java.util.Map;
+
+import com.google.common.collect.Maps;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+
 public class ModelHardLimits {
 
 	private ModelHardLimits() {
@@ -19,6 +25,12 @@ public class ModelHardLimits {
 	public static final int MAX_ABSTRACT_LENGTH = 150000;
 	public static final int MAX_RELATED_ABSTRACT_LENGTH = 500;
 	public static final int MAX_INSTANCES = 10;
+	public static final Map<String, Integer> MAX_RELATIONS_BY_RELCLASS = Maps.newHashMap();
+
+	static {
+		MAX_RELATIONS_BY_RELCLASS.put(ModelConstants.PERSON_PERSON_HASCOAUTHORED, 500);
+		MAX_RELATIONS_BY_RELCLASS.put(ModelConstants.RESULT_PERSON_HASAUTHORED, 500);
+	}
 
 	public static String getCollectionName(String format) {
 		return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
index 351526336..cb2d2e799 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
@@ -2,10 +2,12 @@
 package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits.MAX_RELATIONS_BY_RELCLASS;
 import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
 
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -15,11 +17,13 @@ import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.apache.spark.util.LongAccumulator;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.common.collect.Lists;
 import com.google.common.collect.Maps;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
@@ -27,11 +31,13 @@ import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
 import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
+import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
 import eu.dnetlib.dhp.oa.provision.model.TupleWrapper;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
 import eu.dnetlib.dhp.schema.solr.SolrRecord;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -124,6 +130,9 @@ public class PayloadConverterJob {
 					.map(Oaf::getDataInfo)
 					.map(DataInfo::getDeletedbyinference)
 					.orElse(false))
+			.map(
+				(MapFunction<JoinedEntity, JoinedEntity>) PayloadConverterJob::pruneRelatedEntities,
+				Encoders.kryo(JoinedEntity.class))
 			.map(
 				(MapFunction<JoinedEntity, Tuple2<String, SolrRecord>>) je -> new Tuple2<>(
 					recordFactory.build(je, validateXML),
@@ -139,6 +148,30 @@ public class PayloadConverterJob {
 			.json(outputPath);
 	}
 
+	/**
+	 This function iterates through the RelatedEntityWrapper(s) associated to the JoinedEntity and rules out
+	 those exceeding the maximum allowed frequency defined in eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits#MAX_RELATIONS_BY_RELCLASS
+	 */
+	private static JoinedEntity pruneRelatedEntities(JoinedEntity je) {
+		Map<String, Long> freqs = Maps.newHashMap();
+		List<RelatedEntityWrapper> rew = Lists.newArrayList();
+
+		if (je.getLinks() != null) {
+			je.getLinks().forEach(link -> {
+				final String relClass = link.getRelation().getRelClass();
+				Long count = freqs.putIfAbsent(relClass, 0L);
+				if (Objects.isNull(count) || (MAX_RELATIONS_BY_RELCLASS.containsKey(relClass)
+					&& count <= MAX_RELATIONS_BY_RELCLASS.get(relClass))) {
+					rew.add(link);
+					freqs.put(relClass, freqs.get(relClass) + 1);
+				}
+			});
+			je.setLinks(rew);
+		}
+
+		return je;
+	}
+
 	private static void removeOutputDir(final SparkSession spark, final String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
index b1f419a7e..97d2d3989 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
@@ -1046,7 +1046,13 @@ public class XmlRecordFactory implements Serializable {
 					metadata.add(XmlSerializationUtils.asXmlElement("familyname", person.getFamilyName()));
 				}
 				if (person.getAlternativeNames() != null) {
-					metadata.addAll(person.getAlternativeNames());
+					metadata
+						.addAll(
+							person
+								.getAlternativeNames()
+								.stream()
+								.map(altName -> XmlSerializationUtils.asXmlElement("alternativename", altName))
+								.collect(Collectors.toList()));
 				}
 				if (person.getBiography() != null) {
 					metadata.add(XmlSerializationUtils.asXmlElement("biography", person.getBiography()));

From dbea7a4072e8e0b75dd907d173a6cf067f4fa7d6 Mon Sep 17 00:00:00 2001
From: Antonis Lempesis <antleb@di.uoa.gr>
Date: Mon, 23 Sep 2024 14:57:11 +0300
Subject: [PATCH 129/239] removed duplicate line

---
 .../graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql  | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
index ca5b0bb90..447fe3fb9 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDBAll.sql
@@ -262,7 +262,6 @@ create table TARGET.indi_pub_interdisciplinarity stored as parquet as select * f
 
 create table TARGET.result_apc_affiliations stored as parquet as select * from SOURCE.result_apc_affiliations orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 create table TARGET.result_instance stored as parquet as select * from SOURCE.result_instance orig where exists (select 1 from TARGET.result r where r.id=orig.id);
-create table TARGET.result_orcid stored as parquet as select * from SOURCE.result_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 create table TARGET.indi_pub_publicly_funded stored as parquet as select * from SOURCE.indi_pub_publicly_funded orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 
 create table TARGET.indi_is_project_result_after stored as parquet as select * from SOURCE.indi_is_project_result_after orig where exists (select 1 from TARGET.result r where r.id=orig.result_id);

From fdbe629f49b96e345e9993de01450636b3e12acc Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 23 Sep 2024 13:01:45 +0200
Subject: [PATCH 130/239] removed the deletedByInference=true filter

---
 .../eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java  | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
index 5ff469cd0..236269ff3 100644
--- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
+++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
@@ -70,9 +70,8 @@ public class PrepareRelatedProjectsJob {
 
 			final Dataset<Relation> rels = ClusterUtils
 				.loadRelations(graphPath, spark)
-				.filter((FilterFunction<Relation>) r -> r.getDataInfo().getDeletedbyinference())
-				.filter((FilterFunction<Relation>) r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
-				.filter((FilterFunction<Relation>) r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))
+				.filter((FilterFunction<Relation>) r -> ModelConstants.RESULT_PROJECT.equals(r.getRelType()))
+				.filter((FilterFunction<Relation>) r -> !BrokerConstants.IS_MERGED_IN_CLASS.equals(r.getRelClass()))
 				.filter((FilterFunction<Relation>) r -> !ClusterUtils.isDedupRoot(r.getSource()))
 				.filter((FilterFunction<Relation>) r -> !ClusterUtils.isDedupRoot(r.getTarget()));
 

From 7f81673f3ced3fe0f373d041d5ff47ac092d09d6 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 23 Sep 2024 13:01:45 +0200
Subject: [PATCH 131/239] removed the deletedByInference=true filter

---
 .../eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java  | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
index 5ff469cd0..236269ff3 100644
--- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
+++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/PrepareRelatedProjectsJob.java
@@ -70,9 +70,8 @@ public class PrepareRelatedProjectsJob {
 
 			final Dataset<Relation> rels = ClusterUtils
 				.loadRelations(graphPath, spark)
-				.filter((FilterFunction<Relation>) r -> r.getDataInfo().getDeletedbyinference())
-				.filter((FilterFunction<Relation>) r -> r.getRelType().equals(ModelConstants.RESULT_PROJECT))
-				.filter((FilterFunction<Relation>) r -> !r.getRelClass().equals(BrokerConstants.IS_MERGED_IN_CLASS))
+				.filter((FilterFunction<Relation>) r -> ModelConstants.RESULT_PROJECT.equals(r.getRelType()))
+				.filter((FilterFunction<Relation>) r -> !BrokerConstants.IS_MERGED_IN_CLASS.equals(r.getRelClass()))
 				.filter((FilterFunction<Relation>) r -> !ClusterUtils.isDedupRoot(r.getSource()))
 				.filter((FilterFunction<Relation>) r -> !ClusterUtils.isDedupRoot(r.getTarget()));
 

From e941adbe2beb1fcb14bfba2288eb0fcd12d60d87 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 23 Sep 2024 09:47:29 +0200
Subject: [PATCH 132/239] fixed a bug with topic ENRICH/MORE/SUBJECT/ARXIV

---
 .../oa/matchers/simple/EnrichMoreSubject.java |  2 +-
 .../simple/EnrichMoreSubjectTest.java         | 60 +++++++++++++++++++
 2 files changed, 61 insertions(+), 1 deletion(-)
 create mode 100644 dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java

diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
index b62b509c7..390357f99 100644
--- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
+++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
@@ -53,7 +53,7 @@ public class EnrichMoreSubject extends UpdateMatcher<OaBrokerTypedValue> {
 			.collect(Collectors.toSet());
 
 		return source
-			.getPids()
+			.getSubjects()
 			.stream()
 			.filter(s -> !existingSubjects.contains(subjectAsString(s)))
 			.collect(Collectors.toList());
diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java
new file mode 100644
index 000000000..1fb35c0c9
--- /dev/null
+++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java
@@ -0,0 +1,60 @@
+
+package eu.dnetlib.dhp.broker.oa.matchers.simple;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.broker.objects.OaBrokerMainEntity;
+import eu.dnetlib.broker.objects.OaBrokerTypedValue;
+
+public class EnrichMoreSubjectTest {
+
+	final EnrichMoreSubject matcher = new EnrichMoreSubject();
+
+	@BeforeEach
+	void setUp() throws Exception {
+	}
+
+	@Test
+	void testFindDifferences_1() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+	@Test
+	void testFindDifferences_2() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		source.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertEquals(1, list.size());
+	}
+
+	@Test
+	void testFindDifferences_3() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		target.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+	@Test
+	void testFindDifferences_4() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		source.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		target.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+}

From 0e89d4a1cfc4c2fbe4db61299cda84718a62a49f Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Mon, 23 Sep 2024 09:47:29 +0200
Subject: [PATCH 133/239] fixed a bug with topic ENRICH/MORE/SUBJECT/ARXIV

---
 .../oa/matchers/simple/EnrichMoreSubject.java |  2 +-
 .../simple/EnrichMoreSubjectTest.java         | 60 +++++++++++++++++++
 2 files changed, 61 insertions(+), 1 deletion(-)
 create mode 100644 dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java

diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
index b62b509c7..390357f99 100644
--- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
+++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubject.java
@@ -53,7 +53,7 @@ public class EnrichMoreSubject extends UpdateMatcher<OaBrokerTypedValue> {
 			.collect(Collectors.toSet());
 
 		return source
-			.getPids()
+			.getSubjects()
 			.stream()
 			.filter(s -> !existingSubjects.contains(subjectAsString(s)))
 			.collect(Collectors.toList());
diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java
new file mode 100644
index 000000000..1fb35c0c9
--- /dev/null
+++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMoreSubjectTest.java
@@ -0,0 +1,60 @@
+
+package eu.dnetlib.dhp.broker.oa.matchers.simple;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.broker.objects.OaBrokerMainEntity;
+import eu.dnetlib.broker.objects.OaBrokerTypedValue;
+
+public class EnrichMoreSubjectTest {
+
+	final EnrichMoreSubject matcher = new EnrichMoreSubject();
+
+	@BeforeEach
+	void setUp() throws Exception {
+	}
+
+	@Test
+	void testFindDifferences_1() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+	@Test
+	void testFindDifferences_2() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		source.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertEquals(1, list.size());
+	}
+
+	@Test
+	void testFindDifferences_3() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		target.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+	@Test
+	void testFindDifferences_4() {
+		final OaBrokerMainEntity source = new OaBrokerMainEntity();
+		final OaBrokerMainEntity target = new OaBrokerMainEntity();
+		source.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		target.setSubjects(Arrays.asList(new OaBrokerTypedValue("arxiv", "subject_01")));
+		final List<OaBrokerTypedValue> list = this.matcher.findDifferences(source, target);
+		assertTrue(list.isEmpty());
+	}
+
+}

From d1cadc77c90bd3e6eca9b351b9dc4620cb915c2c Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 24 Sep 2024 10:57:20 +0200
Subject: [PATCH 134/239] [graph provision] person serialisation, limit the
 number of authorships and coauthorships before expanding the payloads

---
 .../dhp/schema/oaf/utils/ModelHardLimits.java        |  6 +++---
 .../dhp/oa/provision/PayloadConverterJob.java        | 12 +++++++-----
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
index e4b184fa1..68f60d4d9 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
@@ -25,11 +25,11 @@ public class ModelHardLimits {
 	public static final int MAX_ABSTRACT_LENGTH = 150000;
 	public static final int MAX_RELATED_ABSTRACT_LENGTH = 500;
 	public static final int MAX_INSTANCES = 10;
-	public static final Map<String, Integer> MAX_RELATIONS_BY_RELCLASS = Maps.newHashMap();
+	public static final Map<String, Long> MAX_RELATIONS_BY_RELCLASS = Maps.newHashMap();
 
 	static {
-		MAX_RELATIONS_BY_RELCLASS.put(ModelConstants.PERSON_PERSON_HASCOAUTHORED, 500);
-		MAX_RELATIONS_BY_RELCLASS.put(ModelConstants.RESULT_PERSON_HASAUTHORED, 500);
+		MAX_RELATIONS_BY_RELCLASS.put(ModelConstants.PERSON_PERSON_HASCOAUTHORED, 500L);
+		MAX_RELATIONS_BY_RELCLASS.put(ModelConstants.RESULT_PERSON_HASAUTHORED, 500L);
 	}
 
 	public static String getCollectionName(String format) {
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
index cb2d2e799..58838d047 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
@@ -149,8 +149,8 @@ public class PayloadConverterJob {
 	}
 
 	/**
-	 This function iterates through the RelatedEntityWrapper(s) associated to the JoinedEntity and rules out
-	 those exceeding the maximum allowed frequency defined in eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits#MAX_RELATIONS_BY_RELCLASS
+	 * This function iterates through the RelatedEntityWrapper(s) associated to the JoinedEntity and rules out
+	 * those exceeding the maximum allowed frequency defined in eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits#MAX_RELATIONS_BY_RELCLASS
 	 */
 	private static JoinedEntity pruneRelatedEntities(JoinedEntity je) {
 		Map<String, Long> freqs = Maps.newHashMap();
@@ -159,9 +159,11 @@ public class PayloadConverterJob {
 		if (je.getLinks() != null) {
 			je.getLinks().forEach(link -> {
 				final String relClass = link.getRelation().getRelClass();
-				Long count = freqs.putIfAbsent(relClass, 0L);
-				if (Objects.isNull(count) || (MAX_RELATIONS_BY_RELCLASS.containsKey(relClass)
-					&& count <= MAX_RELATIONS_BY_RELCLASS.get(relClass))) {
+
+				final Long count = freqs.getOrDefault(relClass, Long.MAX_VALUE);
+				final Long max = MAX_RELATIONS_BY_RELCLASS.getOrDefault(relClass, Long.MAX_VALUE);
+
+				if (count <= max) {
 					rew.add(link);
 					freqs.put(relClass, freqs.get(relClass) + 1);
 				}

From 4f0463d7796ea18e32e94af551d1a951ed574503 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 24 Sep 2024 14:54:34 +0200
Subject: [PATCH 135/239] [graph provision] person serialisation, limit the
 number of authorships and coauthorships before expanding the payloads

---
 .../java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
index 58838d047..2593ef6fe 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PayloadConverterJob.java
@@ -160,12 +160,12 @@ public class PayloadConverterJob {
 			je.getLinks().forEach(link -> {
 				final String relClass = link.getRelation().getRelClass();
 
-				final Long count = freqs.getOrDefault(relClass, Long.MAX_VALUE);
+				final Long count = freqs.getOrDefault(relClass, 0L);
 				final Long max = MAX_RELATIONS_BY_RELCLASS.getOrDefault(relClass, Long.MAX_VALUE);
 
 				if (count <= max) {
 					rew.add(link);
-					freqs.put(relClass, freqs.get(relClass) + 1);
+					freqs.put(relClass, freqs.getOrDefault(relClass, 0L) + 1);
 				}
 			});
 			je.setLinks(rew);

From b35d046fd2e0c7e498c507031f3f926619b89449 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Tue, 24 Sep 2024 15:18:54 +0200
Subject: [PATCH 136/239] fixed a bug with 'null' string

---
 .../plugin/osf/OsfPreprintsIterator.java       | 18 +++++++++++++-----
 .../osf/OsfPreprintsCollectorPluginTest.java   |  7 +++++++
 2 files changed, 20 insertions(+), 5 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index 9484297d0..292e1c322 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -5,6 +5,7 @@ import java.util.Iterator;
 import java.util.Queue;
 import java.util.concurrent.PriorityBlockingQueue;
 
+import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentHelper;
 import org.dom4j.Element;
@@ -46,13 +47,14 @@ public class OsfPreprintsIterator implements Iterator<String> {
 
 	private void initQueue() {
 		this.currentUrl = this.baseUrl + "?filter:is_published:d=true&format=json&page[size]=" + this.pageSize;
+
 		log.info("REST calls starting with {}", this.currentUrl);
 	}
 
 	@Override
 	public boolean hasNext() {
 		synchronized (this.recordQueue) {
-			while (this.recordQueue.isEmpty() && !this.currentUrl.isEmpty()) {
+			while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl) && this.currentUrl.startsWith("http")) {
 				try {
 					this.currentUrl = downloadPage(this.currentUrl);
 				} catch (final CollectorException e) {
@@ -88,12 +90,18 @@ public class OsfPreprintsIterator implements Iterator<String> {
 			group.addElement("preprint").add(n);
 
 			for (final Object o1 : n.selectNodes(".//contributors//href")) {
-				final Document doc1 = downloadUrl(((Node) o1).getText(), 0);
-				group.addElement("contributors").add(doc1.getRootElement().detach());
+				final String href = ((Node) o1).getText();
+				if (StringUtils.isNotBlank(href) && href.startsWith("http")) {
+					final Document doc1 = downloadUrl(href, 0);
+					group.addElement("contributors").add(doc1.getRootElement().detach());
+				}
 			}
 			for (final Object o1 : n.selectNodes(".//primary_file//href")) {
-				final Document doc1 = downloadUrl(((Node) o1).getText(), 0);
-				group.addElement("primary_file").add(doc1.getRootElement().detach());
+				final String href = ((Node) o1).getText();
+				if (StringUtils.isNotBlank(href) && href.startsWith("http")) {
+					final Document doc1 = downloadUrl(href, 0);
+					group.addElement("primary_file").add(doc1.getRootElement().detach());
+				}
 			}
 
 			this.recordQueue.add(DocumentHelper.createDocument(group).asXML());
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index efba0c72e..fe2274c89 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -18,6 +18,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
@@ -110,4 +111,10 @@ public class OsfPreprintsCollectorPluginTest {
 
 	}
 
+	@Test
+	void testXML() {
+		final String xml = JsonUtils.convertToXML("{'next':null}");
+		System.out.println(xml);
+	}
+
 }

From fa2532db303f66c7a1780c0720ccec51cfb10864 Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Wed, 25 Sep 2024 09:38:50 +0200
Subject: [PATCH 137/239] fixed a bug with id

---
 .../dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index 292e1c322..de18ef37f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -85,7 +85,7 @@ public class OsfPreprintsIterator implements Iterator<String> {
 			final Element n = (Element) ((Element) o).detach();
 
 			final Element group = DocumentHelper.createElement("group");
-			group.addAttribute("id", n.valueOf(".//data/id"));
+			group.addAttribute("id", n.valueOf("./id"));
 
 			group.addElement("preprint").add(n);
 

From 6a097abc89f539c4127529f2992063c31b9eed45 Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@gmail.com>
Date: Wed, 18 Sep 2024 17:16:53 +0200
Subject: [PATCH 138/239] as described on ticket #9525 1. Changed the mapping
 applied to Crossref records: anything that has a relationship "is-review-of"
 must be mapped as publication of type "Review". 2. Force the hostedby of
 Crossref records with DOI prefix 10.3410 and 10.12703 to the H1 Connect data
 source.

---
 .../dhp/collection/crossref/Crossref2Oaf.scala   | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index ebe72ae5b..3c1880fba 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -504,6 +504,22 @@ case object Crossref2Oaf {
       )
     }
 
+    val is_review = json \ "relation" \ "is-review-of" \ "id"
+
+    if (is_review != JNothing) {
+      instance.setInstancetype(
+        OafMapperUtils.qualifier(
+          "0015",
+          "peerReviewed",
+          ModelConstants.DNET_REVIEW_LEVELS,
+          ModelConstants.DNET_REVIEW_LEVELS
+        )
+      )
+    }
+
+    if(doi.startsWith("10.3410") || doi.startsWith("10.12703"))
+      instance.setHostedby(OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true),"H1Connect"))
+
     instance.setAccessright(
       decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue)
     )

From 535a7b99f1d12506283a67ece8dcbeac706c3fc4 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 5 Aug 2024 16:55:07 +0200
Subject: [PATCH 139/239] the metadata collection plugins using the
 HttpConnector2 class shall now retry instead of failing in case of
 UnknownHostException

---
 .../java/eu/dnetlib/dhp/common/collection/HttpConnector2.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
index 78bb99e79..d2e53f11a 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java
@@ -212,11 +212,11 @@ public class HttpConnector2 {
 					.format(
 						"Unexpected status code: %s errors: %s", urlConn.getResponseCode(),
 						MAPPER.writeValueAsString(report)));
-		} catch (MalformedURLException | UnknownHostException e) {
+		} catch (MalformedURLException e) {
 			log.error(e.getMessage(), e);
 			report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e.getMessage(), e);
-		} catch (SocketTimeoutException | SocketException e) {
+		} catch (SocketTimeoutException | SocketException | UnknownHostException e) {
 			log.error(e.getMessage(), e);
 			report.put(e.getClass().getName(), e.getMessage());
 			backoffAndSleep(getClientParams().getRetryDelay() * retryNumber * 1000);

From e354f9853a7675982973703ed1237ad4d9da6630 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 25 Sep 2024 15:27:02 +0200
Subject: [PATCH 140/239] [OpenCitations] move the extracted contents under a
 backup path to avoid needing to re-download it in case of errors

---
 .../actionmanager/opencitations/ReadCOCI.java |  8 +++++++-
 .../input_readcoci_parameters.json            | 19 +++++++++++++------
 .../opencitations/oozie_app/workflow.xml      |  1 +
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
index 479aea458..4b0bbf145 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
@@ -49,6 +49,9 @@ public class ReadCOCI implements Serializable {
 		final String workingPath = parser.get("inputPath");
 		log.info("workingPath {}", workingPath);
 
+		final String backupPath = parser.get("backupPath");
+		log.info("backupPath {}", backupPath);
+
 		SparkConf sconf = new SparkConf();
 
 		Configuration conf = new Configuration();
@@ -68,12 +71,14 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					fileSystem,
 					outputPath,
+					backupPath,
 					delimiter);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
 		String outputPath,
+		String backupPath,
 		String delimiter) throws IOException {
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
 			.listFiles(
@@ -107,7 +112,8 @@ public class ReadCOCI implements Serializable {
 				.mode(SaveMode.Append)
 				.option("compression", "gzip")
 				.json(outputPath);
-			fileSystem.rename(fileStatus.getPath(), new Path("/tmp/miriam/OC/DONE"));
+
+			fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
 		}
 
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
index a74ceb983..d1f495d67 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
@@ -24,12 +24,19 @@
     "paramLongName": "outputPath",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  },  {
-  "paramName": "nn",
-  "paramLongName": "hdfsNameNode",
-  "paramDescription": "the hdfs name node",
-  "paramRequired": true
-}
+  },
+  {
+    "paramName": "nn",
+    "paramLongName": "hdfsNameNode",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": true
+  },
+  {
+    "paramName": "bp",
+    "paramLongName": "backupPath",
+    "paramDescription": "the hdfs path to move the OC data after the extraction",
+    "paramRequired": true
+  }
 ]
 
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
index 566cf7d02..f170af96f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
@@ -129,6 +129,7 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
             <arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
+            <arg>--backupPath</arg><arg>${inputPath}/backup</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
         </spark>

From 6397141e56b83f6fd6c89cba93fdda3533d1140b Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 25 Sep 2024 15:27:32 +0200
Subject: [PATCH 141/239] code formatting

---
 .../dhp/collection/CollectorWorker.java       | 89 ++++++++++---------
 .../osf/OsfPreprintsCollectorPlugin.java      | 14 +--
 .../plugin/osf/OsfPreprintsIterator.java      | 17 ++--
 .../collection/crossref/Crossref2Oaf.scala    |  6 +-
 .../osf/OsfPreprintsCollectorPluginTest.java  | 10 ++-
 5 files changed, 75 insertions(+), 61 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
index 67e07ba59..f63bfcb48 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
@@ -46,11 +46,11 @@ public class CollectorWorker extends ReportingJob {
 	private final HttpClientParams clientParams;
 
 	public CollectorWorker(
-			final ApiDescriptor api,
-			final FileSystem fileSystem,
-			final MDStoreVersion mdStoreVersion,
-			final HttpClientParams clientParams,
-			final AggregatorReport report) {
+		final ApiDescriptor api,
+		final FileSystem fileSystem,
+		final MDStoreVersion mdStoreVersion,
+		final HttpClientParams clientParams,
+		final AggregatorReport report) {
 		super(report);
 		this.api = api;
 		this.fileSystem = fileSystem;
@@ -69,22 +69,25 @@ public class CollectorWorker extends ReportingJob {
 		scheduleReport(counter);
 
 		try (SequenceFile.Writer writer = SequenceFile
-				.createWriter(this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
-						.keyClass(IntWritable.class), SequenceFile.Writer
-								.valueClass(Text.class), SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
+			.createWriter(
+				this.fileSystem.getConf(), SequenceFile.Writer.file(new Path(outputPath)), SequenceFile.Writer
+					.keyClass(IntWritable.class),
+				SequenceFile.Writer
+					.valueClass(Text.class),
+				SequenceFile.Writer.compression(SequenceFile.CompressionType.BLOCK, new DeflateCodec()))) {
 			final IntWritable key = new IntWritable(counter.get());
 			final Text value = new Text();
 			plugin
-					.collect(this.api, this.report)
-					.forEach(content -> {
-						key.set(counter.getAndIncrement());
-						value.set(content);
-						try {
-							writer.append(key, value);
-						} catch (final Throwable e) {
-							throw new RuntimeException(e);
-						}
-					});
+				.collect(this.api, this.report)
+				.forEach(content -> {
+					key.set(counter.getAndIncrement());
+					value.set(content);
+					try {
+						writer.append(key, value);
+					} catch (final Throwable e) {
+						throw new RuntimeException(e);
+					}
+				});
 		} catch (final Throwable e) {
 			this.report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e);
@@ -112,36 +115,36 @@ public class CollectorWorker extends ReportingJob {
 	private CollectorPlugin getCollectorPlugin() throws UnknownCollectorPluginException {
 
 		switch (CollectorPlugin.NAME.valueOf(this.api.getProtocol())) {
-		case oai:
-			return new OaiCollectorPlugin(this.clientParams);
-		case rest_json2xml:
-			return new RestCollectorPlugin(this.clientParams);
-		case file:
-			return new FileCollectorPlugin(this.fileSystem);
-		case fileGzip:
-			return new FileGZipCollectorPlugin(this.fileSystem);
-		case baseDump:
-			return new BaseCollectorPlugin(this.fileSystem);
-		case gtr2Publications:
-			return new Gtr2PublicationsCollectorPlugin(this.clientParams);
-		case osfPreprints:
-			return new OsfPreprintsCollectorPlugin(this.clientParams);
-		case other:
-			final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
+			case oai:
+				return new OaiCollectorPlugin(this.clientParams);
+			case rest_json2xml:
+				return new RestCollectorPlugin(this.clientParams);
+			case file:
+				return new FileCollectorPlugin(this.fileSystem);
+			case fileGzip:
+				return new FileGZipCollectorPlugin(this.fileSystem);
+			case baseDump:
+				return new BaseCollectorPlugin(this.fileSystem);
+			case gtr2Publications:
+				return new Gtr2PublicationsCollectorPlugin(this.clientParams);
+			case osfPreprints:
+				return new OsfPreprintsCollectorPlugin(this.clientParams);
+			case other:
+				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
 					.ofNullable(this.api.getParams().get("other_plugin_type"))
 					.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
 					.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
 
-			switch (plugin) {
-			case mdstore_mongodb_dump:
-				return new MongoDbDumpCollectorPlugin(this.fileSystem);
-			case mdstore_mongodb:
-				return new MDStoreCollectorPlugin();
+				switch (plugin) {
+					case mdstore_mongodb_dump:
+						return new MongoDbDumpCollectorPlugin(this.fileSystem);
+					case mdstore_mongodb:
+						return new MDStoreCollectorPlugin();
+					default:
+						throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
+				}
 			default:
-				throw new UnknownCollectorPluginException("plugin is not managed: " + plugin);
-			}
-		default:
-			throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
+				throw new UnknownCollectorPluginException("protocol is not managed: " + this.api.getProtocol());
 		}
 	}
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
index fdc9df06f..b0787eb45 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPlugin.java
@@ -31,17 +31,19 @@ public class OsfPreprintsCollectorPlugin implements CollectorPlugin {
 		final String baseUrl = api.getBaseUrl();
 
 		final int pageSize = Optional
-				.ofNullable(api.getParams().get("pageSize"))
-				.filter(StringUtils::isNotBlank)
-				.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
-				.orElse(PAGE_SIZE_VALUE_DEFAULT);
+			.ofNullable(api.getParams().get("pageSize"))
+			.filter(StringUtils::isNotBlank)
+			.map(s -> NumberUtils.toInt(s, PAGE_SIZE_VALUE_DEFAULT))
+			.orElse(PAGE_SIZE_VALUE_DEFAULT);
 
-		if (StringUtils.isBlank(baseUrl)) { throw new CollectorException("Param 'baseUrl' is null or empty"); }
+		if (StringUtils.isBlank(baseUrl)) {
+			throw new CollectorException("Param 'baseUrl' is null or empty");
+		}
 
 		final OsfPreprintsIterator it = new OsfPreprintsIterator(baseUrl, pageSize, getClientParams());
 
 		return StreamSupport
-				.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
+			.stream(Spliterators.spliteratorUnknownSize(it, Spliterator.ORDERED), false);
 	}
 
 	public HttpClientParams getClientParams() {
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
index de18ef37f..76adba1a8 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsIterator.java
@@ -34,9 +34,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 	private final Queue<String> recordQueue = new PriorityBlockingQueue<>();
 
 	public OsfPreprintsIterator(
-			final String baseUrl,
-			final int pageSize,
-			final HttpClientParams clientParams) {
+		final String baseUrl,
+		final int pageSize,
+		final HttpClientParams clientParams) {
 
 		this.clientParams = clientParams;
 		this.baseUrl = baseUrl;
@@ -54,7 +54,8 @@ public class OsfPreprintsIterator implements Iterator<String> {
 	@Override
 	public boolean hasNext() {
 		synchronized (this.recordQueue) {
-			while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl) && this.currentUrl.startsWith("http")) {
+			while (this.recordQueue.isEmpty() && StringUtils.isNotBlank(this.currentUrl)
+				&& this.currentUrl.startsWith("http")) {
 				try {
 					this.currentUrl = downloadPage(this.currentUrl);
 				} catch (final CollectorException e) {
@@ -63,7 +64,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 				}
 			}
 
-			if (!this.recordQueue.isEmpty()) { return true; }
+			if (!this.recordQueue.isEmpty()) {
+				return true;
+			}
 
 			return false;
 		}
@@ -112,7 +115,9 @@ public class OsfPreprintsIterator implements Iterator<String> {
 	}
 
 	private Document downloadUrl(final String url, final int attempt) throws CollectorException {
-		if (attempt > MAX_ATTEMPTS) { throw new CollectorException("Max Number of attempts reached, url:" + url); }
+		if (attempt > MAX_ATTEMPTS) {
+			throw new CollectorException("Max Number of attempts reached, url:" + url);
+		}
 
 		if (attempt > 0) {
 			final int delay = (attempt * 5000);
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index 3c1880fba..4bd6bcc09 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -517,8 +517,10 @@ case object Crossref2Oaf {
       )
     }
 
-    if(doi.startsWith("10.3410") || doi.startsWith("10.12703"))
-      instance.setHostedby(OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true),"H1Connect"))
+    if (doi.startsWith("10.3410") || doi.startsWith("10.12703"))
+      instance.setHostedby(
+        OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true), "H1Connect")
+      )
 
     instance.setAccessright(
       decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue)
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
index fe2274c89..664b84d5a 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/osf/OsfPreprintsCollectorPluginTest.java
@@ -50,9 +50,10 @@ public class OsfPreprintsCollectorPluginTest {
 	@Test
 	@Disabled
 	void test_one() throws CollectorException {
-		this.plugin.collect(this.api, new AggregatorReport())
-				.limit(1)
-				.forEach(log::info);
+		this.plugin
+			.collect(this.api, new AggregatorReport())
+			.limit(1)
+			.forEach(log::info);
 	}
 
 	@Test
@@ -95,7 +96,8 @@ public class OsfPreprintsCollectorPluginTest {
 		final HttpConnector2 connector = new HttpConnector2();
 
 		try {
-			final String res = connector.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
+			final String res = connector
+				.getInputSource("https://api.osf.io/v2/preprints/ydtzx/contributors/?format=json");
 			System.out.println(res);
 			fail();
 		} catch (final Throwable e) {

From c45cae447aa8aa18ec1e8a4e130d2c190cc5ff70 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Sat, 24 Feb 2024 16:54:30 +0100
Subject: [PATCH 142/239] Fix: invert the "natural" order when ordering by id
 lexicographically

---
 .../dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
index ff6c2689a..5f212c242 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeEntitiesComparator.java
@@ -96,7 +96,7 @@ public class MergeEntitiesComparator implements Comparator<Oaf> {
 		// id
 		if (res == 0) {
 			if (left instanceof OafEntity && right instanceof OafEntity) {
-				res = ((OafEntity) left).getId().compareTo(((OafEntity) right).getId());
+				res = ((OafEntity) right).getId().compareTo(((OafEntity) left).getId());
 			}
 		}
 

From e430826e0032870ab24f579777d9bd6f52d21458 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 30 Sep 2024 15:10:10 +0200
Subject: [PATCH 143/239] [ImportOC] fix to move original folder instead of
 extracted ones

---
 .../opencitations/GetOpenCitationsRefs.java         |  8 ++++++--
 .../dhp/actionmanager/opencitations/ReadCOCI.java   |  7 +------
 .../opencitations/input_parameters.json             |  6 ++++++
 .../opencitations/input_readcoci_parameters.json    |  6 ------
 .../opencitations/oozie_app/workflow.xml            | 13 +------------
 5 files changed, 14 insertions(+), 26 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java
index be653aed2..6a779f6c4 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java
@@ -46,6 +46,9 @@ public class GetOpenCitationsRefs implements Serializable {
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
 
+		final String backupPath = parser.get("backupPath");
+		log.info("backupPath {}", backupPath);
+
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
@@ -53,11 +56,11 @@ public class GetOpenCitationsRefs implements Serializable {
 
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
-		ocr.doExtract(inputPath, outputPath, fileSystem);
+		ocr.doExtract(inputPath, outputPath, backupPath, fileSystem);
 
 	}
 
-	private void doExtract(String inputPath, String outputPath, FileSystem fileSystem)
+	private void doExtract(String inputPath, String outputPath, String backupPath, FileSystem fileSystem)
 		throws IOException {
 
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
@@ -89,6 +92,7 @@ public class GetOpenCitationsRefs implements Serializable {
 				}
 
 			}
+			fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
 		}
 
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
index 4b0bbf145..de45d50b2 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java
@@ -49,9 +49,6 @@ public class ReadCOCI implements Serializable {
 		final String workingPath = parser.get("inputPath");
 		log.info("workingPath {}", workingPath);
 
-		final String backupPath = parser.get("backupPath");
-		log.info("backupPath {}", backupPath);
-
 		SparkConf sconf = new SparkConf();
 
 		Configuration conf = new Configuration();
@@ -71,14 +68,12 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					fileSystem,
 					outputPath,
-					backupPath,
 					delimiter);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, FileSystem fileSystem,
 		String outputPath,
-		String backupPath,
 		String delimiter) throws IOException {
 		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
 			.listFiles(
@@ -113,7 +108,7 @@ public class ReadCOCI implements Serializable {
 				.option("compression", "gzip")
 				.json(outputPath);
 
-			fileSystem.rename(fileStatus.getPath(), new Path(backupPath));
+			fileSystem.delete(fileStatus.getPath());
 		}
 
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json
index f4b6e2d68..10225f367 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json
@@ -16,5 +16,11 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
+  },
+  {
+    "paramName": "bp",
+    "paramLongName": "backupPath",
+    "paramDescription": "the hdfs path to move the OC data after the extraction",
+    "paramRequired": true
   }
 ]
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
index d1f495d67..f3d72e063 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json
@@ -30,12 +30,6 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  },
-  {
-    "paramName": "bp",
-    "paramLongName": "backupPath",
-    "paramDescription": "the hdfs path to move the OC data after the extraction",
-    "paramRequired": true
   }
 ]
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
index f170af96f..bb6a0eb21 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml
@@ -94,17 +94,7 @@
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
             <arg>--inputPath</arg><arg>${inputPath}/Original</arg>
             <arg>--outputPath</arg><arg>${inputPath}/Extracted</arg>
-        </java>
-        <ok to="read"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="extract_correspondence">
-        <java>
-            <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
-            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
-            <arg>--inputPath</arg><arg>${inputPath}/correspondence</arg>
-            <arg>--outputPath</arg><arg>${inputPath}/correspondence_extracted</arg>
+            <arg>--backupPath</arg><arg>${inputPath}/backup</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -129,7 +119,6 @@
             </spark-opts>
             <arg>--inputPath</arg><arg>${inputPath}/Extracted</arg>
             <arg>--outputPath</arg><arg>${inputPath}/JSON</arg>
-            <arg>--backupPath</arg><arg>${inputPath}/backup</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
         </spark>

From f3c179658a8d978796e31d6095b947e44665b2ef Mon Sep 17 00:00:00 2001
From: antleb <antleb@di.uoa.gr>
Date: Mon, 30 Sep 2024 17:12:21 +0300
Subject: [PATCH 144/239] datasource table creation split in steps

---
 .../oozie_app/scripts/buildIrishMonitorDB.sql |  4 ++--
 .../graph/stats/oozie_app/scripts/step8.sql   | 24 ++++++++++++-------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/scripts/buildIrishMonitorDB.sql b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/scripts/buildIrishMonitorDB.sql
index 3f0922020..acad90f63 100644
--- a/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/scripts/buildIrishMonitorDB.sql
+++ b/dhp-workflows/dhp-stats-monitor-irish/src/main/resources/eu/dnetlib/dhp/oa/graph/stats-monitor-irish/oozie_app/scripts/buildIrishMonitorDB.sql
@@ -32,7 +32,7 @@ select distinct * from (
        from SOURCE.result r
                 join SOURCE.result_projects rp on rp.id=r.id
                 join SOURCE.project p on p.id=rp.project
-                join openaire_prod_stats_monitor_ie_20231226b.irish_funders irf on irf.funder=p.funder
+                join TARGET.irish_funders irf on irf.funder=p.funder
        union all
        select r.*
        from SOURCE.result r
@@ -238,4 +238,4 @@ create table TARGET.indi_pub_publicly_funded stored as parquet as select * from
 create table TARGET.indi_result_oa_with_license stored as parquet as select * from SOURCE.indi_result_oa_with_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 create table TARGET.indi_result_oa_without_license stored as parquet as select * from SOURCE.indi_result_oa_without_license orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 
-create table TARGET.indi_result_under_transformative stored as parquet as select * from SOURCE.indi_result_under_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
\ No newline at end of file
+create table TARGET.indi_result_under_transformative stored as parquet as select * from SOURCE.indi_result_under_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id);
diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
index 98225af14..7504eba18 100644
--- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
+++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql
@@ -8,14 +8,20 @@ set mapred.job.queue.name=analytics; /*EOS*/
 ------------------------------------------------------------
 ------------------------------------------------------------
 DROP TABLE IF EXISTS ${stats_db_name}.datasource purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.harested_datasources purge; /*EOS*/
+DROP TABLE IF EXISTS ${stats_db_name}.piwik_datasource purge; /*EOS*/
+
+create table ${stats_db_name}.harested_datasources stored as parquet as
+select distinct inst.hostedby.key as d_id
+from ${openaire_db_name}.result lateral view outer explode (instance) insts as inst; /*EOS*/
+
+create table ${stats_db_name}.piwik_datasource stored as parquet as
+select id, split(originalidd, '\\:')[1] as piwik_id
+from ${openaire_db_name}.datasource
+         lateral view explode(originalid) temp as originalidd
+where originalidd like "piwik:%"; /*EOS*/
 
 CREATE TABLE ${stats_db_name}.datasource stored as parquet as
-with piwik_datasource as (
-    select id, split(originalidd, '\\:')[1] as piwik_id
-    from ${openaire_db_name}.datasource
-             lateral view explode(originalid) temp as originalidd
-    where originalidd like "piwik:%"
-)
 select /*+ COALESCE(100) */
        substr(dtrce.id, 4)                                                                                                 as id,
        case when dtrce.officialname.value='Unknown Repository' then 'Other' else dtrce.officialname.value end              as name,
@@ -31,10 +37,12 @@ select /*+ COALESCE(100) */
        dtrce.journal.issnprinted                                                                                           as issn_printed,
        dtrce.journal.issnonline                                                                                            as issn_online
 from ${openaire_db_name}.datasource dtrce
-         left outer join (select inst.hostedby.key as d_id from ${openaire_db_name}.result lateral view outer explode (instance) insts as inst) res on res.d_id=dtrce.id
-         left outer join piwik_datasource piwik_d on piwik_d.id=dtrce.id
+left outer join ${stats_db_name}.harested_datasources res on res.d_id=dtrce.id
+left outer join ${stats_db_name}.piwik_datasource piwik_d on piwik_d.id=dtrce.id
 where dtrce.datainfo.deletedbyinference = false and dtrce.datainfo.invisible = false; /*EOS*/
 
+drop table ${stats_db_name}.harested_datasources; /*EOS*/
+drop table ${stats_db_name}.piwik_datasource; /*EOS*/
 
 DROP TABLE IF EXISTS ${stats_db_name}.datasource_languages purge; /*EOS*/
 

From 10696f2a442d8dd62ac32464b2d6853ea5fd31f8 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 1 Oct 2024 15:54:13 +0200
Subject: [PATCH 145/239] reverted procedure for creating the UsageCounts
 actionset

---
 .../actionmanager/usagestats/SparkAtomicActionUsageJob.java  | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
index 897153762..d6b52ad9b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
@@ -112,10 +112,7 @@ public class SparkAtomicActionUsageJob implements Serializable {
 			.joinWith(datasource, resultModel.col("datasourceId").equalTo(datasource.col("id")), "left")
 			.map((MapFunction<Tuple2<UsageStatsResultModel, Datasource>, UsageStatsResultModel>) t2 -> {
 				UsageStatsResultModel usrm = t2._1();
-				if (Optional.ofNullable(t2._2()).isPresent())
-					usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
-				else
-					usrm.setDatasourceId(usrm.getDatasourceId() + "||NO_MATCH_FOUND");
+				usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
 				return usrm;
 			}, Encoders.bean(UsageStatsResultModel.class))
 			.write()

From 191fc3a4618c85bccc4a20e42f5745ed9a8dc2c9 Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
Date: Tue, 2 Apr 2024 16:28:27 +0200
Subject: [PATCH 146/239] [UsageCount] add check in case the datasource is not
 matched against those present in the graph

(cherry picked from commit b42bdd5fb3f33f0d90770602ad4fea87af550751)
---
 .../usagestats/SparkAtomicActionUsageJob.java              | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
index d6b52ad9b..d74b55475 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
@@ -111,8 +111,11 @@ public class SparkAtomicActionUsageJob implements Serializable {
 		resultModel
 			.joinWith(datasource, resultModel.col("datasourceId").equalTo(datasource.col("id")), "left")
 			.map((MapFunction<Tuple2<UsageStatsResultModel, Datasource>, UsageStatsResultModel>) t2 -> {
-				UsageStatsResultModel usrm = t2._1();
-				usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
+				if(Optional.ofNullable(t2._2()).isPresent())
+					usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
+				else
+					usrm.setDatasourceId(usrm.getDatasourceId() + "||NO_MATCH_FOUND");
+				return usrm;
 				return usrm;
 			}, Encoders.bean(UsageStatsResultModel.class))
 			.write()

From 7e6d12fa77d336acbb66b60ff327950a39616169 Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
Date: Tue, 2 Apr 2024 16:56:37 +0200
Subject: [PATCH 147/239] [UsageCount] fixed error

(cherry picked from commit 9c9a9562ae31f21cfcc20fafd06455f86bd2492f)
---
 .../dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
index d74b55475..1d5b35cff 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
@@ -111,12 +111,12 @@ public class SparkAtomicActionUsageJob implements Serializable {
 		resultModel
 			.joinWith(datasource, resultModel.col("datasourceId").equalTo(datasource.col("id")), "left")
 			.map((MapFunction<Tuple2<UsageStatsResultModel, Datasource>, UsageStatsResultModel>) t2 -> {
+				UsageStatsResultModel usrm = t2._1();
 				if(Optional.ofNullable(t2._2()).isPresent())
 					usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
 				else
 					usrm.setDatasourceId(usrm.getDatasourceId() + "||NO_MATCH_FOUND");
 				return usrm;
-				return usrm;
 			}, Encoders.bean(UsageStatsResultModel.class))
 			.write()
 			.mode(SaveMode.Overwrite)

From e5df68772d4f9a766224557069c74a16544c2f6b Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 2 Oct 2024 09:35:21 +0200
Subject: [PATCH 148/239] [graph provision] fixed serialisation of the usage
 counts as measures in the XML records

---
 .../utils/XmlSerializationUtils.java          |  3 ++-
 .../dnetlib/dhp/oa/provision/publication.json | 20 +++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
index b4517002c..85cebcdb6 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java
@@ -175,7 +175,8 @@ public class XmlSerializationUtils {
 				.append("<")
 				.append(name)
 				.append(" ")
-				.append(attr(measure.getId(), kv.getValue()))
+				.append(attr("id", measure.getId()))
+				.append(attr("score", kv.getValue()))
 				.append(attr("datasource", kv.getKey()))
 				.append(" />");
 		}
diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
index a073fbebd..a8cd6dcf6 100644
--- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
+++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json
@@ -8,6 +8,26 @@
     }
   ],
   "measures": [
+    {
+      "id": "views",
+      "unit": [
+        {
+          "key": "opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO",
+          "value": "5",
+          "dataInfo": null
+        }
+      ]
+    },
+    {
+      "id": "downloads",
+      "unit": [
+        {
+          "key": "opendoar____::358aee4cc897452c00244351e4d91f69||ZENODO",
+          "value": "2",
+          "dataInfo": null
+        }
+      ]
+    },
     {
       "id": "influence",
       "unit": [

From d5867a19920d8acd232b263b5d4bb9a6a4d87de0 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 8 Oct 2024 14:58:28 +0200
Subject: [PATCH 149/239] merged #490

---
 .../oaf/HashableStructuredProperty.java       |  70 ++++++++++
 .../schema/oaf/utils/CleaningFunctions.java   |  30 ----
 .../dhp/schema/oaf/utils/DoiCleaningRule.java |  14 +-
 .../oaf/utils/GraphCleaningFunctions.java     |  18 ++-
 .../schema/oaf/utils/IdentifierFactory.java   |   4 +-
 .../dhp/schema/oaf/utils/MergeUtils.java      |   2 +-
 .../schema/oaf/utils/PidValueComparator.java  |   4 +-
 .../java/eu/dnetlib/dhp/utils/DHPUtils.java   |   3 +-
 .../oaf/utils/IdentifierFactoryTest.java      |   4 +-
 .../schema/oaf/utils/publication_doi3.json    |   2 +-
 .../schema/oaf/utils/publication_pmc2.json    |   2 +-
 .../PrepareAffiliationRelations.java          | 129 +++++++++++++++---
 .../input_actionset_parameter.json            |  12 +-
 .../collection/crossref/Crossref2Oaf.scala    |   4 +-
 .../PrepareAffiliationRelationsTest.java      |  67 ++++++---
 .../CreateOpenCitationsASTest.java            |  13 +-
 .../CreateTAActionSetTest.java                |  13 +-
 .../bipaffiliations/doi_to_ror.json           |  19 +--
 .../bipaffiliations/doi_to_ror_old.json       |   9 ++
 .../bipaffiliations/publichers_old/publisher  |   6 +
 .../bipaffiliations/publishers/publisher      |   6 +
 .../raw/AbstractMdRecordToOafMapper.java      |  35 ++---
 .../dhp/oa/graph/raw/OafToOafMapper.java      |   3 +-
 .../dhp/oa/graph/raw/OdfToOafMapper.java      |   6 +-
 .../graph/clean/CleanGraphSparkJobTest.java   |  16 +--
 .../clean/GraphCleaningFunctionsTest.java     |  12 +-
 .../raw/GenerateEntitiesApplicationTest.java  |   8 +-
 .../dnetlib/dhp/oa/graph/raw/MappersTest.java |  97 ++++++++-----
 .../clean/graph/publication/publication.json  |   2 +-
 .../eu/dnetlib/dhp/oa/graph/clean/result.json |  32 +----
 .../dhp/oa/graph/raw/odf_record_base.xml      | 129 ++++++++++++++++++
 .../raw/organizations_resultset_entry.json    |   5 +
 .../oa/graph/sample/person/person_10.json.gz  | Bin 0 -> 1233 bytes
 .../graph/scholix/ScholixGenerationTest.scala |   3 +-
 34 files changed, 540 insertions(+), 239 deletions(-)
 create mode 100644 dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/person/person_10.json.gz

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java
new file mode 100644
index 000000000..aa60b097a
--- /dev/null
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/HashableStructuredProperty.java
@@ -0,0 +1,70 @@
+/*
+ * Copyright (c) 2024.
+ * SPDX-FileCopyrightText: © 2023 Consiglio Nazionale delle Ricerche
+ * SPDX-License-Identifier: AGPL-3.0-or-later
+ */
+
+package eu.dnetlib.dhp.schema.oaf;
+
+import org.apache.commons.lang3.builder.EqualsBuilder;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
+
+public class HashableStructuredProperty extends StructuredProperty {
+
+	private static final long serialVersionUID = 8371670185221126045L;
+
+	public static HashableStructuredProperty newInstance(String value, Qualifier qualifier, DataInfo dataInfo) {
+		if (value == null) {
+			return null;
+		}
+		final HashableStructuredProperty sp = new HashableStructuredProperty();
+		sp.setValue(value);
+		sp.setQualifier(qualifier);
+		sp.setDataInfo(dataInfo);
+		return sp;
+	}
+
+	public static HashableStructuredProperty newInstance(StructuredProperty sp) {
+		HashableStructuredProperty hsp = new HashableStructuredProperty();
+		hsp.setQualifier(sp.getQualifier());
+		hsp.setValue(sp.getValue());
+		hsp.setQualifier(sp.getQualifier());
+		return hsp;
+	}
+
+	public static StructuredProperty toStructuredProperty(HashableStructuredProperty hsp) {
+		StructuredProperty sp = new StructuredProperty();
+		sp.setQualifier(hsp.getQualifier());
+		sp.setValue(hsp.getValue());
+		sp.setQualifier(hsp.getQualifier());
+		return sp;
+	}
+
+	@Override
+	public int hashCode() {
+		return new HashCodeBuilder(11, 91)
+			.append(getQualifier().getClassid())
+			.append(getQualifier().getSchemeid())
+			.append(getValue())
+			.hashCode();
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (obj == null) {
+			return false;
+		}
+		if (obj == this) {
+			return true;
+		}
+		if (obj.getClass() != getClass()) {
+			return false;
+		}
+		final HashableStructuredProperty rhs = (HashableStructuredProperty) obj;
+		return new EqualsBuilder()
+			.append(getQualifier().getClassid(), rhs.getQualifier().getClassid())
+			.append(getQualifier().getSchemeid(), rhs.getQualifier().getSchemeid())
+			.append(getValue(), rhs.getValue())
+			.isEquals();
+	}
+}
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java
index c0ef339bd..49b30897c 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java
@@ -43,34 +43,4 @@ public class CleaningFunctions {
 		return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
 	}
 
-	/**
-	 * Utility method that normalises PID values on a per-type basis.
-	 * @param pid the PID whose value will be normalised.
-	 * @return the PID containing the normalised value.
-	 */
-	public static StructuredProperty normalizePidValue(StructuredProperty pid) {
-		pid
-			.setValue(
-				normalizePidValue(
-					pid.getQualifier().getClassid(),
-					pid.getValue()));
-
-		return pid;
-	}
-
-	public static String normalizePidValue(String pidType, String pidValue) {
-		String value = Optional
-			.ofNullable(pidValue)
-			.map(String::trim)
-			.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
-
-		switch (pidType) {
-
-			// TODO add cleaning for more PID types as needed
-			case "doi":
-				return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
-		}
-		return value;
-	}
-
 }
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java
index 43fb0feda..cd8957764 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/DoiCleaningRule.java
@@ -6,18 +6,11 @@ import org.apache.commons.lang3.StringUtils;
 public class DoiCleaningRule {
 
 	public static String clean(final String doi) {
-		return doi
-			.toLowerCase()
-			.replaceAll("\\s", "")
-			.replaceAll("^doi:", "")
-			.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
-	}
-
-	public static String normalizeDoi(final String input) {
-		if (input == null)
+		if (doi == null)
 			return null;
-		final String replaced = input
+		final String replaced = doi
 			.replaceAll("\\n|\\r|\\t|\\s", "")
+			.replaceAll("^doi:", "")
 			.toLowerCase()
 			.replaceFirst(CleaningFunctions.DOI_PREFIX_REGEX, CleaningFunctions.DOI_PREFIX);
 		if (StringUtils.isEmpty(replaced))
@@ -32,7 +25,6 @@ public class DoiCleaningRule {
 			return null;
 
 		return ret;
-
 	}
 
 }
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
index 2be4e8e0c..dfa9c5ad0 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@@ -563,12 +563,24 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						Optional
 							.ofNullable(i.getPid())
 							.ifPresent(pid -> {
-								final Set<StructuredProperty> pids = Sets.newHashSet(pid);
+								final Set<HashableStructuredProperty> pids = pid
+									.stream()
+									.map(HashableStructuredProperty::newInstance)
+									.collect(Collectors.toCollection(HashSet::new));
 								Optional
 									.ofNullable(i.getAlternateIdentifier())
 									.ifPresent(altId -> {
-										final Set<StructuredProperty> altIds = Sets.newHashSet(altId);
-										i.setAlternateIdentifier(Lists.newArrayList(Sets.difference(altIds, pids)));
+										final Set<HashableStructuredProperty> altIds = altId
+											.stream()
+											.map(HashableStructuredProperty::newInstance)
+											.collect(Collectors.toCollection(HashSet::new));
+										i
+											.setAlternateIdentifier(
+												Sets
+													.difference(altIds, pids)
+													.stream()
+													.map(HashableStructuredProperty::toStructuredProperty)
+													.collect(Collectors.toList()));
 									});
 							});
 
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
index 1d61c87df..2c77c3b37 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
@@ -175,7 +175,7 @@ public class IdentifierFactory implements Serializable {
 			return entity
 				.getPid()
 				.stream()
-				.map(CleaningFunctions::normalizePidValue)
+				.map(PidCleaner::normalizePidValue)
 				.filter(CleaningFunctions::pidFilter)
 				.collect(
 					Collectors
@@ -207,7 +207,7 @@ public class IdentifierFactory implements Serializable {
 					// filter away PIDs provided by a DS that is not considered an authority for the
 					// given PID Type
 					.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
-					.map(CleaningFunctions::normalizePidValue)
+					.map(PidCleaner::normalizePidValue)
 					.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
 					.filter(CleaningFunctions::pidFilter))
 			.orElse(Stream.empty());
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index ac7694d18..e01813110 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -972,7 +972,7 @@ public class MergeUtils {
 	private static String extractKeyFromPid(final StructuredProperty pid) {
 		if (pid == null)
 			return null;
-		final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
+		final StructuredProperty normalizedPid = PidCleaner.normalizePidValue(pid);
 
 		return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
 	}
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java
index 0e2083590..1e591ce72 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidValueComparator.java
@@ -18,8 +18,8 @@ public class PidValueComparator implements Comparator<StructuredProperty> {
 		if (right == null)
 			return -1;
 
-		StructuredProperty l = CleaningFunctions.normalizePidValue(left);
-		StructuredProperty r = CleaningFunctions.normalizePidValue(right);
+		StructuredProperty l = PidCleaner.normalizePidValue(left);
+		StructuredProperty r = PidCleaner.normalizePidValue(right);
 
 		return Optional
 			.ofNullable(l.getValue())
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
index e10d0c500..77453e5f0 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java
@@ -28,6 +28,7 @@ import com.jayway.jsonpath.JsonPath;
 
 import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 import net.minidev.json.JSONArray;
 import scala.collection.JavaConverters;
 import scala.collection.Seq;
@@ -104,7 +105,7 @@ public class DHPUtils {
 
 	public static String generateUnresolvedIdentifier(final String pid, final String pidType) {
 
-		final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid);
+		final String cleanedPid = PidCleaner.normalizePidValue(pidType, pid);
 
 		return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim());
 	}
diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java
index bce4b76b5..9cc0698a4 100644
--- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java
+++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java
@@ -29,7 +29,7 @@ class IdentifierFactoryTest {
 			"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
 
 		verifyIdentifier(
-			"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
+			"publication_doi3.json", "50|pmc_________::e2a339e0e11bfbf55462e14a07f1b304", true);
 
 		verifyIdentifier(
 			"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
@@ -41,7 +41,7 @@ class IdentifierFactoryTest {
 			"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
 
 		verifyIdentifier(
-			"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
+			"publication_pmc2.json", "50|pmc_________::e2a339e0e11bfbf55462e14a07f1b304", true);
 
 		verifyIdentifier(
 			"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json
index b1ea01f60..303c023be 100644
--- a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json
+++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi3.json
@@ -29,7 +29,7 @@
         },
         {
           "qualifier": {"classid": "pmc"},
-          "value": "21459329"
+          "value": "PMC21459329"
         }
       ]
     }
diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json
index e7d49eebb..3b7b6590e 100644
--- a/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json
+++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_pmc2.json
@@ -13,7 +13,7 @@
         },
         {
           "qualifier":{"classid":"pmc"},
-          "value":"21459329"
+          "value":"PMC21459329"
         }
       ]
     }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 70ca1576c..028fa47dc 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -10,7 +10,6 @@ import java.util.List;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.BZip2Codec;
-import org.apache.hadoop.io.compress.GzipCodec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
@@ -29,6 +28,7 @@ import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.DoiCleaningRule;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
@@ -46,6 +46,8 @@ public class PrepareAffiliationRelations implements Serializable {
 	public static final String BIP_INFERENCE_PROVENANCE = "openaire:affiliation";
 	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
 	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
+	public static final String DOI_URL_PREFIX = "https://doi.org/";
+	public static final int DOI_URL_PREFIX_LENGTH = 16;
 
 	public static <I extends Result> void main(String[] args) throws Exception {
 
@@ -98,35 +100,26 @@ public class PrepareAffiliationRelations implements Serializable {
 	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
 		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
 		String outputPath) {
-		List<KeyValue> collectedFromCrossref = OafMapperUtils
-			.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
-		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
-			spark, crossrefInputPath, collectedFromCrossref);
+		List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+
+		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
+			spark, crossrefInputPath, collectedfromOpenAIRE);
 
-		List<KeyValue> collectedFromPubmed = OafMapperUtils
-			.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
 		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-			spark, pubmedInputPath, collectedFromPubmed);
+			spark, pubmedInputPath, collectedfromOpenAIRE);
 
-		List<KeyValue> collectedFromOpenAPC = OafMapperUtils
-			.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
-		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
-			spark, openapcInputPath, collectedFromOpenAPC);
+		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel(
+			spark, openapcInputPath, collectedfromOpenAIRE);
 
-		List<KeyValue> collectedFromDatacite = OafMapperUtils
-			.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
 		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
-			spark, dataciteInputPath, collectedFromDatacite);
+			spark, dataciteInputPath, collectedfromOpenAIRE);
 
-		List<KeyValue> collectedFromWebCrawl = OafMapperUtils
-			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-			spark, webcrawlInputPath, collectedFromWebCrawl);
+			spark, webcrawlInputPath, collectedfromOpenAIRE);
 
-		List<KeyValue> collectedfromPublisher = OafMapperUtils
-			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
-			spark, publisherlInputPath, collectedfromPublisher);
+			spark, publisherlInputPath, collectedfromOpenAIRE);
 
 		crossrefRelations
 			.union(pubmedRelations)
@@ -138,6 +131,21 @@ public class PrepareAffiliationRelations implements Serializable {
 				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 	}
 
+	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark,
+		String inputPath,
+		List<KeyValue> collectedfrom) {
+
+		Dataset<Row> df = spark
+			.read()
+			.schema(
+				"`DOI` STRING, `Organizations` ARRAY<STRUCT<`PID`:STRING, `Value`:STRING,`Confidence`:DOUBLE, `Status`:STRING>>")
+			.json(inputPath)
+			.where("DOI is not null");
+
+		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
+
+	}
+
 	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
 		List<KeyValue> collectedfrom) {
 
@@ -165,6 +173,20 @@ public class PrepareAffiliationRelations implements Serializable {
 		return getTextTextJavaPairRDD(collectedfrom, df);
 	}
 
+	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelationsNewModel(SparkSession spark,
+		String inputPath,
+		List<KeyValue> collectedfrom) {
+		// load and parse affiliation relations from HDFS
+		Dataset<Row> df = spark
+			.read()
+			.schema(
+				"`DOI` STRING, `Matchings` ARRAY<STRUCT<`PID`:STRING, `Value`:STRING,`Confidence`:DOUBLE, `Status`:STRING>>")
+			.json(inputPath)
+			.where("DOI is not null");
+
+		return getTextTextJavaPairRDDNew(collectedfrom, df);
+	}
+
 	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
 		// unroll nested arrays
 		df = df
@@ -181,7 +203,7 @@ public class PrepareAffiliationRelations implements Serializable {
 
 				// DOI to OpenAIRE id
 				final String paperId = ID_PREFIX
-					+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi")));
+					+ IdentifierFactory.md5(DoiCleaningRule.clean(removePrefix(row.getAs("doi"))));
 
 				// ROR id to OpenAIRE id
 				final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
@@ -213,6 +235,69 @@ public class PrepareAffiliationRelations implements Serializable {
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) {
+		// unroll nested arrays
+		df = df
+			.withColumn("matching", functions.explode(new Column("Matchings")))
+			.select(
+				new Column("DOI").as("doi"),
+				new Column("matching.PID").as("pidtype"),
+				new Column("matching.Value").as("pidvalue"),
+				new Column("matching.Confidence").as("confidence"),
+				new Column("matching.Status").as("status"))
+			.where("status = 'active'");
+
+		// prepare action sets for affiliation relations
+		return df
+			.toJavaRDD()
+			.flatMap((FlatMapFunction<Row, Relation>) row -> {
+
+				// DOI to OpenAIRE id
+				final String paperId = ID_PREFIX
+					+ IdentifierFactory.md5(DoiCleaningRule.clean(removePrefix(row.getAs("doi"))));
+
+				// Organization to OpenAIRE identifier
+				String affId = null;
+				if (row.getAs("pidtype").equals("ROR"))
+					// ROR id to OpenIARE id
+					affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("pidvalue"));
+				else
+					// getting the OpenOrgs identifier for the organization
+					affId = row.getAs("pidvalue");
+
+				Qualifier qualifier = OafMapperUtils
+					.qualifier(
+						BIP_AFFILIATIONS_CLASSID,
+						BIP_AFFILIATIONS_CLASSNAME,
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
+						ModelConstants.DNET_PROVENANCE_ACTIONS);
+
+				// format data info; setting `confidence` into relation's `trust`
+				DataInfo dataInfo = OafMapperUtils
+					.dataInfo(
+						false,
+						BIP_INFERENCE_PROVENANCE,
+						true,
+						false,
+						qualifier,
+						Double.toString(row.getAs("confidence")));
+
+				// return bi-directional relations
+				return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
+
+			})
+			.map(p -> new AtomicAction(Relation.class, p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
+	}
+
+	private static String removePrefix(String doi) {
+		if (doi.startsWith(DOI_URL_PREFIX))
+			return doi.substring(DOI_URL_PREFIX_LENGTH);
+		return doi;
+	}
+
 	private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,
 		DataInfo dataInfo) {
 		return Arrays
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
index 4d85cf26b..b3d1d742b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json
@@ -28,13 +28,19 @@
     "paramLongName": "dataciteInputPath",
     "paramDescription": "the path to get the input data from Datacite",
     "paramRequired": true
-  },{
+  },
+  {
   "paramName": "wip",
   "paramLongName": "webCrawlInputPath",
   "paramDescription": "the path to get the input data from Web Crawl",
   "paramRequired": true
-}
-,
+  },
+  {
+    "paramName": "pub",
+    "paramLongName": "publisherInputPath",
+    "paramDescription": "the path to get the input data from publishers",
+    "paramRequired": true
+  },
   {
     "paramName": "o",
     "paramLongName": "outputPath",
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index 4bd6bcc09..7c45234f6 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -332,7 +332,7 @@ case object Crossref2Oaf {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
 
     //MAPPING Crossref DOI into PID
-    val doi: String = DoiCleaningRule.normalizeDoi((json \ "DOI").extract[String])
+    val doi: String = DoiCleaningRule.clean((json \ "DOI").extract[String])
     result.setPid(
       List(
         structuredProperty(
@@ -673,7 +673,7 @@ case object Crossref2Oaf {
     val doi = input.getString(0)
     val rorId = input.getString(1)
 
-    val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.normalizeDoi(doi)}"
+    val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.clean(doi)}"
     val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
 
     val r: Relation = new Relation
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
index ac9977a7e..179cbecb5 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
@@ -28,8 +28,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 
 public class PrepareAffiliationRelationsTest {
 
@@ -39,8 +39,7 @@ public class PrepareAffiliationRelationsTest {
 
 	private static Path workingDir;
 	private static final String ID_PREFIX = "50|doi_________::";
-	private static final Logger log = LoggerFactory
-		.getLogger(PrepareAffiliationRelationsTest.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelationsTest.class);
 
 	@BeforeAll
 	public static void beforeAll() throws IOException {
@@ -74,26 +73,34 @@ public class PrepareAffiliationRelationsTest {
 	@Test
 	void testMatch() throws Exception {
 
-		String crossrefAffiliationRelationPath = getClass()
+		String crossrefAffiliationRelationPathNew = getClass()
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
 			.getPath();
 
+		String crossrefAffiliationRelationPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json")
+			.getPath();
+
 		String publisherAffiliationRelationPath = getClass()
 			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
 			.getPath();
 
+		String publisherAffiliationRelationOldPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old")
+			.getPath();
+
 		String outputPath = workingDir.toString() + "/actionSet";
 
 		PrepareAffiliationRelations
 			.main(
 				new String[] {
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-					"-crossrefInputPath", crossrefAffiliationRelationPath,
+					"-crossrefInputPath", crossrefAffiliationRelationPathNew,
 					"-pubmedInputPath", crossrefAffiliationRelationPath,
-					"-openapcInputPath", crossrefAffiliationRelationPath,
+					"-openapcInputPath", crossrefAffiliationRelationPathNew,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-webCrawlInputPath", crossrefAffiliationRelationPath,
-					"-publisherInputPath", publisherAffiliationRelationPath,
+					"-publisherInputPath", publisherAffiliationRelationOldPath,
 					"-outputPath", outputPath
 				});
 
@@ -104,13 +111,8 @@ public class PrepareAffiliationRelationsTest {
 			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
 			.map(aa -> ((Relation) aa.getPayload()));
 
-//        for (Relation r : tmp.collect()) {
-//            System.out.println(
-//                    r.getSource() + "\t" + r.getTarget() + "\t" + r.getRelType() + "\t" + r.getRelClass() + "\t" + r.getSubRelType() + "\t" + r.getValidationDate() + "\t" + r.getDataInfo().getTrust() + "\t" + r.getDataInfo().getInferred()
-//            );
-//        }
 		// count the number of relations
-		assertEquals(138, tmp.count());
+		assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 =
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -121,7 +123,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				69, execVerification
+				75, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -129,21 +131,21 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				69, execVerification
+				75, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
 					.size());
 
 		// check confidence value of a specific relation
-		String sourceDOI = "10.1061/(asce)0733-9399(2002)128:7(759)";
+		String sourceDOI = "10.1089/10872910260066679";
 
 		final String sourceOpenaireId = ID_PREFIX
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", sourceDOI));
 
 		Assertions
 			.assertEquals(
-				"0.7071067812", execVerification
+				"1.0", execVerification
 					.filter(
 						"source='" + sourceOpenaireId + "'")
 					.collectAsList()
@@ -151,11 +153,34 @@ public class PrepareAffiliationRelationsTest {
 					.getString(4));
 
 		final String publisherid = ID_PREFIX
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s00217-010-1268-9"));
-		final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/03265fv13");
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1089/10872910260066679"));
+		final String rorId = "20|ror_________::" + IdentifierFactory.md5("https://ror.org/05cf8a891");
 
 		Assertions
 			.assertEquals(
-				1, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
+				2, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
+
+		Assertions
+			.assertEquals(
+				1, execVerification
+					.filter(
+						"source = '" + ID_PREFIX
+							+ IdentifierFactory
+								.md5(PidCleaner.normalizePidValue("doi", "10.1007/s00217-010-1268-9"))
+							+ "' and target = '" + "20|ror_________::"
+							+ IdentifierFactory.md5("https://ror.org/03265fv13") + "'")
+					.count());
+
+		Assertions
+			.assertEquals(
+				3, execVerification
+					.filter(
+						"source = '" + ID_PREFIX
+							+ IdentifierFactory
+								.md5(PidCleaner.normalizePidValue("doi", "10.1007/3-540-47984-8_14"))
+							+ "' and target = '" + "20|ror_________::"
+							+ IdentifierFactory.md5("https://ror.org/00a0n9e72") + "'")
+					.count());
+
 	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java
index ed80ed5c5..b690b6228 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java
@@ -31,6 +31,7 @@ import eu.dnetlib.dhp.schema.oaf.Publication;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 
 public class CreateOpenCitationsASTest {
 
@@ -280,17 +281,17 @@ public class CreateOpenCitationsASTest {
 	@Test
 	void testRelationsSourceTargetCouple() throws Exception {
 		final String doi1 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
 		final String doi2 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
 		final String doi3 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
 		final String doi4 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
 		final String doi5 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
 		final String doi6 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
 
 		String inputPath = getClass()
 			.getResource(
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java
index 0ec34311f..592c6283a 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/transformativeagreement/CreateTAActionSetTest.java
@@ -28,6 +28,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 
 /**
  * @author miriam.baglioni
@@ -270,17 +271,17 @@ public class CreateTAActionSetTest {
 	@Test
 	void testRelationsSourceTargetCouple() throws Exception {
 		final String doi1 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
 		final String doi2 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
 		final String doi3 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
 		final String doi4 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
 		final String doi5 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
 		final String doi6 = "50|doi_________::"
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
+			+ IdentifierFactory.md5(PidCleaner.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
 
 		String inputPath = getClass()
 			.getResource(
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
index 08dc3f7eb..b5a711694 100644
--- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json
@@ -1,9 +1,10 @@
-{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":"https:\/\/ror.org\/03yxnpp24","Confidence":0.7071067812},{"RORid":"https:\/\/ror.org\/01teme464","Confidence":0.89}]}
-{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]}
-{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]}
-{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
-{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
-{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]}
-{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
-{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]}
-{"DOI": "10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]}
\ No newline at end of file
+{"DOI":"10.1021\/ac020069k","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/01f5ytq51","Status":"active","Confidence":1}]}
+{"DOI":"10.1161\/01.cir.0000013846.72805.7e","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/02pttbw34","Status":"active","Confidence":1}]}
+{"DOI":"10.1161\/hy02t2.102992","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/00qqv6244","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/00p991c53","Status":"active","Confidence":1}]}
+{"DOI":"10.1126\/science.1073633","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/03xez1567","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/006w34k90","Status":"active","Confidence":1}]}
+{"DOI":"10.1089\/10872910260066679","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/05cf8a891","Status":"active","Confidence":1}]}
+{"DOI":"10.1108\/02656719610116117","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/03mnm0t94","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/007tn5k56","Status":"active","Confidence":1}]}
+{"DOI":"10.1080\/01443610050111986","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/001x4vz59","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/01tmqtf75","Status":"active","Confidence":1}]}
+{"DOI":"10.1021\/cm020118+","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/02cf1je33","Confidence":1,"Status":"inactive"},{"PID":"ROR","Value":"https:\/\/ror.org\/01hvx5h04","Confidence":1,"Status":"active"}]}
+{"DOI":"10.1161\/hc1202.104524","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/040r8fr65","Status":"active","Confidence":1},{"PID":"ROR","Value":"https:\/\/ror.org\/04fctr677","Status":"active","Confidence":1}]}
+{"DOI":"10.1021\/ma011134f","Matchings":[{"PID":"ROR","Value":"https:\/\/ror.org\/04tj63d06","Status":"active","Confidence":1}]}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json
new file mode 100644
index 000000000..d7f004deb
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror_old.json
@@ -0,0 +1,9 @@
+{"DOI":"10.1061\/(asce)0733-9399(2002)128:7(759)","Matchings":[{"RORid":"https:\/\/ror.org\/03yxnpp24","Confidence":0.7071067812},{"RORid":"https:\/\/ror.org\/01teme464","Confidence":0.89}]}
+{"DOI":"10.1105\/tpc.8.3.343","Matchings":[{"RORid":"https:\/\/ror.org\/02k40bc56","Confidence":0.7071067812}]}
+{"DOI":"10.1161\/01.cir.0000013305.01850.37","Matchings":[{"RORid":"https:\/\/ror.org\/00qjgza05","Confidence":1}]}
+{"DOI":"10.1142\/s021821650200186x","Matchings":[{"RORid":"https:\/\/ror.org\/035xkbk20","Confidence":1},{"RORid":"https:\/\/ror.org\/05apxxy63","Confidence":1}]}
+{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(575)","Matchings":[{"RORid":"https:\/\/ror.org\/04j198w64","Confidence":0.82}]}
+{"DOI":"10.1061\/(asce)0733-9372(2002)128:7(588)","Matchings":[{"RORid":"https:\/\/ror.org\/03m8km719","Confidence":0.8660254038},{"RORid":"https:\/\/ror.org\/02aze4h65","Confidence":0.87}]}
+{"DOI":"10.1161\/hy0202.103001","Matchings":[{"RORid":"https:\/\/ror.org\/057xtrt18","Confidence":0.7071067812}]}
+{"DOI": "10.1080/13669877.2015.1042504", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/03265fv13"}]}
+{"DOI": "https://doi.org/10.1007/3-540-47984-8_14", "Matchings": [{"Confidence": 1.0, "RORid": "https://ror.org/00a0n9e72"}]}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher
new file mode 100644
index 000000000..851263933
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publichers_old/publisher
@@ -0,0 +1,6 @@
+{"DOI": "10.1007/s00217-010-1268-9", "Authors": [{"Name": {"Full": "Martin Zarnkow", "First": null, "Last": null}, "Raw_affiliations": ["TU M\u00fcnchen, Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Andrea Faltermaier", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Werner Back", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Technologie der Brauerei I"], "Organization_PIDs": []}, {"Name": {"Full": "Martina Gastl", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Elkek K. Arendt", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}
+{"DOI": "10.1007/BF01154707", "Authors": [{"Name": {"Full": "Buggy, M.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}, {"Name": {"Full": "Carew, A.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/00a0n9e72", "Confidence": 1}]}
+{"DOI": "10.1007/s10237-017-0974-7", "Authors": [{"Name": {"Full": "Donnacha J. McGrath", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Anja Lena Thiebes", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Christian G. Cornelissen", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Barry O\u2019Brien", "First": null, "Last": null}, "Raw_affiliations": ["Department for Internal Medicine \u2013 Section for Pneumology, Medical Faculty, RWTH Aachen University, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}, {"Name": {"Full": "Stefan Jockenhoevel", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Mark Bruzzi", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Peter E. McHugh", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03bea9k73", "Confidence": 1}, {"RORid": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 0.87}, {"RORid": "https://ror.org/04xfq0f34", "Confidence": 1}]}
+{"DOI": "10.1007/BF03168973", "Authors": [{"Name": {"Full": "Sheehan, G.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}, {"Name": {"Full": "Chew, N.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}], "Organizations": []}
+{"DOI": "10.1007/s00338-009-0480-1", "Authors": [{"Name": {"Full": "Gleason, D. F.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Danilowicz, B. S.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Nolan, C. J.", "First": null, "Last": null}, "Raw_affiliations": ["School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"], "Organization_PIDs": [{"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/04agmb972", "Confidence": 1}, {"RORid": "https://ror.org/05m7pjf47", "Confidence": 1}]}
+{"DOI": "10.1007/s10993-010-9187-y", "Authors": [{"Name": {"Full": "Martin Howard", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"RORid": "https://ror.org/03265fv13", "Confidence": 1}]}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher
new file mode 100644
index 000000000..426500e73
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers/publisher
@@ -0,0 +1,6 @@
+{"DOI": "10.1007/s00217-010-1268-9", "Authors": [{"Name": {"Full": "Martin Zarnkow", "First": null, "Last": null}, "Raw_affiliations": ["TU M\u00fcnchen, Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Andrea Faltermaier", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Werner Back", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Technologie der Brauerei I"], "Organization_PIDs": []}, {"Name": {"Full": "Martina Gastl", "First": null, "Last": null}, "Raw_affiliations": ["Lehrstuhl f\u00fcr Brau- und Getr\u00e4nketechnologie"], "Organization_PIDs": []}, {"Name": {"Full": "Elkek K. Arendt", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"Value": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/03265fv13", "Confidence": 1}]}
+{"DOI": "10.1007/BF01154707", "Authors": [{"Name": {"Full": "Buggy, M.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/00a0n9e72", "Confidence": 1}]}, {"Name": {"Full": "Carew, A.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Materials Science and Technology, University of Limerick, Limerick, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/00a0n9e72", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/00a0n9e72", "Confidence": 1}]}
+{"DOI": "10.1007/s10237-017-0974-7", "Authors": [{"Name": {"Full": "Donnacha J. McGrath", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Anja Lena Thiebes", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Christian G. Cornelissen", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Barry O\u2019Brien", "First": null, "Last": null}, "Raw_affiliations": ["Department for Internal Medicine \u2013 Section for Pneumology, Medical Faculty, RWTH Aachen University, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/04xfq0f34", "Confidence": 1}]}, {"Name": {"Full": "Stefan Jockenhoevel", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/03bea9k73", "Confidence": 1}]}, {"Name": {"Full": "Mark Bruzzi", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biohybrid and Medical Textiles (BioTex), AME-Helmholtz Institute for Biomedical Engineering, ITA-Institut f\u00fcr Textiltechnik, RWTH Aachen University and at AMIBM Maastricht University, Maastricht, The Netherlands, Aachen, Germany"], "Organization_PIDs": [{"Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}]}, {"Name": {"Full": "Peter E. McHugh", "First": null, "Last": null}, "Raw_affiliations": ["Biomechanics Research Centre (BMEC), Biomedical Engineering, College of Engineering and Informatics, NUI Galway, Galway, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/03bea9k73", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/03bea9k73", "Confidence": 1}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/02jz4aj89", "Confidence": 0.82}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/04xfq0f34", "Confidence": 0.87}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/04xfq0f34", "Confidence": 1}]}
+{"DOI": "10.1007/BF03168973", "Authors": [{"Name": {"Full": "Sheehan, G.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}, {"Name": {"Full": "Chew, N.", "First": null, "Last": null}, "Raw_affiliations": ["Dept of Infectious Diseases, Mater Misercordiae Hospital, Dublin 7"], "Organization_PIDs": []}], "Organizations": []}
+{"DOI": "10.1007/s00338-009-0480-1", "Authors": [{"Name": {"Full": "Gleason, D. F.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"Value": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Danilowicz, B. S.", "First": null, "Last": null}, "Raw_affiliations": ["Department of Biology, Georgia Southern University, Statesboro, USA"], "Organization_PIDs": [{"Value": "https://ror.org/04agmb972", "Confidence": 1}]}, {"Name": {"Full": "Nolan, C. J.", "First": null, "Last": null}, "Raw_affiliations": ["School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland"], "Organization_PIDs": [{"Value": "https://ror.org/05m7pjf47", "Confidence": 1}]}], "Organizations": [{"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/04agmb972", "Confidence": 1}, {"Provenance":"AffRo","PID":"ROR","Status":"active","Value": "https://ror.org/05m7pjf47", "Confidence": 1}]}
+{"DOI": "10.1007/s10993-010-9187-y", "Authors": [{"Name": {"Full": "Martin Howard", "First": null, "Last": null}, "Raw_affiliations": ["University College Cork"], "Organization_PIDs": [{"Value": "https://ror.org/03265fv13", "Confidence": 1}]}], "Organizations": [{"PID":"ROR","Status":"active","Value": "https://ror.org/03265fv13", "Confidence": 1}]}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
index c95d5442a..a85f47d99 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
@@ -55,29 +55,7 @@ import eu.dnetlib.dhp.common.Constants;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.AccessRight;
-import eu.dnetlib.dhp.schema.oaf.Author;
-import eu.dnetlib.dhp.schema.oaf.Context;
-import eu.dnetlib.dhp.schema.oaf.Country;
-import eu.dnetlib.dhp.schema.oaf.DataInfo;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import eu.dnetlib.dhp.schema.oaf.EoscIfGuidelines;
-import eu.dnetlib.dhp.schema.oaf.Field;
-import eu.dnetlib.dhp.schema.oaf.GeoLocation;
-import eu.dnetlib.dhp.schema.oaf.Instance;
-import eu.dnetlib.dhp.schema.oaf.InstanceTypeMapping;
-import eu.dnetlib.dhp.schema.oaf.Journal;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.Software;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-import eu.dnetlib.dhp.schema.oaf.Subject;
+import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 
@@ -667,22 +645,25 @@ public abstract class AbstractMdRecordToOafMapper {
 		return this.vocs.getTermAsQualifier(schemeId, classId);
 	}
 
-	protected List<StructuredProperty> prepareListStructPropsWithValidQualifier(
+	protected List<HashableStructuredProperty> prepareListStructPropsWithValidQualifier(
 		final Node node,
 		final String xpath,
 		final String xpathClassId,
 		final String schemeId,
 		final DataInfo info) {
-		final List<StructuredProperty> res = new ArrayList<>();
+		final Set<HashableStructuredProperty> res = new HashSet<>();
 
 		for (final Object o : node.selectNodes(xpath)) {
 			final Node n = (Node) o;
 			final String classId = n.valueOf(xpathClassId).trim();
 			if (this.vocs.termExists(schemeId, classId)) {
-				res.add(structuredProperty(n.getText(), this.vocs.getTermAsQualifier(schemeId, classId), info));
+				res
+					.add(
+						HashableStructuredProperty
+							.newInstance(n.getText(), this.vocs.getTermAsQualifier(schemeId, classId), info));
 			}
 		}
-		return res;
+		return Lists.newArrayList(res);
 	}
 
 	protected List<StructuredProperty> prepareListStructProps(
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
index eee518353..98da48f9e 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
@@ -25,6 +25,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 
 public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
@@ -380,7 +381,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 		return prepareListStructPropsWithValidQualifier(
 			doc, "//oaf:identifier", "@identifierType", DNET_PID_TYPES, info)
 				.stream()
-				.map(CleaningFunctions::normalizePidValue)
+				.map(PidCleaner::normalizePidValue)
 				.collect(Collectors.toList());
 	}
 
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
index 57e0d2955..41fc37cb1 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
@@ -24,6 +24,7 @@ import eu.dnetlib.dhp.schema.common.RelationInverse;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
 
 public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
@@ -504,7 +505,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
-		final Set<StructuredProperty> res = new HashSet<>();
+		final Set<HashableStructuredProperty> res = new HashSet<>();
 		res
 			.addAll(
 				prepareListStructPropsWithValidQualifier(
@@ -524,7 +525,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 		return res
 			.stream()
-			.map(CleaningFunctions::normalizePidValue)
+			.map(PidCleaner::normalizePidValue)
+			.filter(CleaningFunctions::pidFilter)
 			.collect(Collectors.toList());
 	}
 
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java
index 4ae3f82c2..23de57204 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJobTest.java
@@ -388,7 +388,7 @@ public class CleanGraphSparkJobTest {
 			.collect(Collectors.toList());
 
 		assertNotNull(fos_subjects);
-		assertEquals(2, fos_subjects.size());
+		assertEquals(3, fos_subjects.size());
 
 		assertTrue(
 			fos_subjects
@@ -396,18 +396,10 @@ public class CleanGraphSparkJobTest {
 				.anyMatch(
 					s -> "0101 mathematics".equals(s.getValue()) &
 						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) &
-						"sysimport:crosswalk:datasetarchive"
-							.equals(s.getDataInfo().getProvenanceaction().getClassid())));
+						"subject:fos".equals(s.getDataInfo().getProvenanceaction().getClassid())));
 
-		assertTrue(
-			fos_subjects
-				.stream()
-				.anyMatch(
-					s -> "0102 computer and information sciences".equals(s.getValue()) &
-						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())));
-
-		verify_keyword(p, "In Situ Hybridization");
-		verify_keyword(p, "Avicennia");
+		verify_keyword(p, "FOS: Mathematics");
+		verify_keyword(p, "FOS: Computer and information sciences");
 	}
 
 	@Test
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
index 8d10508a9..cdc052dfa 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
@@ -266,7 +266,7 @@ public class GraphCleaningFunctionsTest {
 			.collect(Collectors.toList());
 
 		assertNotNull(fos_subjects);
-		assertEquals(2, fos_subjects.size());
+		assertEquals(3, fos_subjects.size());
 
 		assertTrue(
 			fos_subjects
@@ -274,18 +274,18 @@ public class GraphCleaningFunctionsTest {
 				.anyMatch(
 					s -> "0101 mathematics".equals(s.getValue()) &
 						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) &
-						"sysimport:crosswalk:datasetarchive"
-							.equals(s.getDataInfo().getProvenanceaction().getClassid())));
+						"subject:fos".equals(s.getDataInfo().getProvenanceaction().getClassid())));
 
 		assertTrue(
 			fos_subjects
 				.stream()
 				.anyMatch(
 					s -> "0102 computer and information sciences".equals(s.getValue()) &
-						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())));
+						ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) &
+						"subject:fos".equals(s.getDataInfo().getProvenanceaction().getClassid())));
 
-		verify_keyword(p_cleaned, "In Situ Hybridization");
-		verify_keyword(p_cleaned, "Avicennia");
+		verify_keyword(p_cleaned, "FOS: Computer and information sciences");
+		verify_keyword(p_cleaned, "FOS: Mathematics");
 
 		// TODO add more assertions to verity the cleaned values
 		System.out.println(MAPPER.writeValueAsString(p_cleaned));
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
index 6ec2f1d51..612e1d0b6 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplicationTest.java
@@ -44,7 +44,7 @@ class GenerateEntitiesApplicationTest {
 	}
 
 	@Test
-	void testMergeResult() throws IOException, DocumentException {
+	void testMergeResult() throws IOException {
 		Result publication = getResult("oaf_record.xml", Publication.class);
 		Result dataset = getResult("odf_dataset.xml", Dataset.class);
 		Result software = getResult("odf_software.xml", Software.class);
@@ -69,15 +69,15 @@ class GenerateEntitiesApplicationTest {
 		verifyMerge(orp, software, Software.class, ModelConstants.SOFTWARE_RESULTTYPE_CLASSID);
 	}
 
-	protected <T extends Result> void verifyMerge(Result publication, Result dataset, Class<T> clazz,
+	protected <T extends Result> void verifyMerge(Result r1, Result r2, Class<T> clazz,
 		String resultType) {
-		final Result merge = (Result) MergeUtils.merge(publication, dataset);
+		final Result merge = MergeUtils.checkedMerge(r1, r2, true);
 		assertTrue(clazz.isAssignableFrom(merge.getClass()));
 		assertEquals(resultType, merge.getResulttype().getClassid());
 	}
 
 	protected <T extends Result> Result getResult(String xmlFileName, Class<T> clazz)
-		throws IOException, DocumentException {
+		throws IOException {
 		final String xml = IOUtils.toString(getClass().getResourceAsStream(xmlFileName));
 		return new OdfToOafMapper(vocs, false, true)
 			.processMdRecord(xml)
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
index 4fb8f86f7..228c6308c 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@@ -216,7 +216,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testPublication_PubMed() throws IOException, DocumentException {
+	void testPublication_PubMed() throws IOException {
 
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record_pubmed.xml")));
@@ -264,8 +264,17 @@ class MappersTest {
 
 		assertFalse(p.getSubject().isEmpty());
 		assertFalse(p.getPid().isEmpty());
-		assertEquals("PMC1517292", p.getPid().get(0).getValue());
-		assertEquals("pmc", p.getPid().get(0).getQualifier().getClassid());
+
+		assertTrue(p.getPid().stream().anyMatch(pi -> "pmc".equals(pi.getQualifier().getClassid())));
+		assertEquals(
+			"PMC1517292",
+			p
+				.getPid()
+				.stream()
+				.filter(pi -> "pmc".equals(pi.getQualifier().getClassid()))
+				.findFirst()
+				.get()
+				.getValue());
 
 		assertNotNull(p.getInstance());
 		assertFalse(p.getInstance().isEmpty());
@@ -292,7 +301,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testPublicationInvisible() throws IOException, DocumentException {
+	void testPublicationInvisible() throws IOException {
 
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_record.xml")));
 
@@ -307,6 +316,25 @@ class MappersTest {
 
 	}
 
+	@Test
+	void testPublicationInvisible_BASE() throws IOException {
+
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_record_base.xml")));
+
+		final List<Oaf> list = new OdfToOafMapper(vocs, true, true).processMdRecord(xml);
+
+		assertFalse(list.isEmpty());
+		assertTrue(list.get(0) instanceof Publication);
+
+		final Publication p = (Publication) list.get(0);
+
+		assertTrue(p.getDataInfo().getInvisible());
+
+		System.out.println(new ObjectMapper().writeValueAsString(p));
+
+	}
+
 	@Test
 	void testOdfFwfEBookLibrary() throws IOException {
 		final String xml = IOUtils
@@ -318,7 +346,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testDataset() throws IOException, DocumentException {
+	void testDataset() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_dataset.xml")));
 
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@@ -332,19 +360,19 @@ class MappersTest {
 		final Relation r1 = (Relation) list.get(1);
 		final Relation r2 = (Relation) list.get(2);
 
-		assertEquals(d.getId(), r1.getSource());
-		assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getTarget());
+		assertEquals(d.getId(), r1.getTarget());
+		assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getSource());
 		assertEquals(ModelConstants.RESULT_PROJECT, r1.getRelType());
 		assertEquals(ModelConstants.OUTCOME, r1.getSubRelType());
-		assertEquals(ModelConstants.IS_PRODUCED_BY, r1.getRelClass());
+		assertEquals(ModelConstants.PRODUCES, r1.getRelClass());
 		assertTrue(r1.getValidated());
 		assertEquals("2020-01-01", r1.getValidationDate());
 
-		assertEquals(d.getId(), r2.getTarget());
-		assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getSource());
+		assertEquals(d.getId(), r2.getSource());
+		assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getTarget());
 		assertEquals(ModelConstants.RESULT_PROJECT, r2.getRelType());
 		assertEquals(ModelConstants.OUTCOME, r2.getSubRelType());
-		assertEquals(ModelConstants.PRODUCES, r2.getRelClass());
+		assertEquals(ModelConstants.IS_PRODUCED_BY, r2.getRelClass());
 		assertTrue(r2.getValidated());
 		assertEquals("2020-01-01", r2.getValidationDate());
 
@@ -450,7 +478,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testOdfBielefeld() throws IOException, DocumentException {
+	void testOdfBielefeld() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_bielefeld.xml")));
 
@@ -501,7 +529,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testOpentrial() throws IOException, DocumentException {
+	void testOpentrial() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_opentrial.xml")));
 
@@ -741,7 +769,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testSoftware() throws IOException, DocumentException {
+	void testSoftware() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_software.xml")));
 
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@@ -763,22 +791,21 @@ class MappersTest {
 		final Relation r1 = (Relation) list.get(1);
 		final Relation r2 = (Relation) list.get(2);
 
-		assertEquals(s.getId(), r1.getSource());
-		assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getTarget());
+		assertEquals(s.getId(), r1.getTarget());
+		assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getSource());
 		assertEquals(ModelConstants.RESULT_RESULT, r1.getRelType());
 		assertEquals(ModelConstants.RELATIONSHIP, r1.getSubRelType());
-		assertEquals(ModelConstants.IS_REFERENCED_BY, r1.getRelClass());
+		assertEquals(ModelConstants.REFERENCES, r1.getRelClass());
 
-		assertEquals(s.getId(), r2.getTarget());
-		assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getSource());
+		assertEquals(s.getId(), r2.getSource());
+		assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getTarget());
 		assertEquals(ModelConstants.RESULT_RESULT, r2.getRelType());
 		assertEquals(ModelConstants.RELATIONSHIP, r2.getSubRelType());
-		assertEquals(ModelConstants.REFERENCES, r2.getRelClass());
-
+		assertEquals(ModelConstants.IS_REFERENCED_BY, r2.getRelClass());
 	}
 
 	@Test
-	void testClaimDedup() throws IOException, DocumentException {
+	void testClaimDedup() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_dedup.xml")));
 		final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
@@ -792,7 +819,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testNakala() throws IOException, DocumentException {
+	void testNakala() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_nakala.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -820,7 +847,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testEnermaps() throws IOException, DocumentException {
+	void testEnermaps() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("enermaps.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -845,7 +872,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testClaimFromCrossref() throws IOException, DocumentException {
+	void testClaimFromCrossref() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_claim_crossref.xml")));
 		final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
@@ -862,7 +889,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testODFRecord() throws IOException, DocumentException {
+	void testODFRecord() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_record.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 		System.out.println("***************");
@@ -882,7 +909,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testTextGrid() throws IOException, DocumentException {
+	void testTextGrid() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("textgrid.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -916,7 +943,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testBologna() throws IOException, DocumentException {
+	void testBologna() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf-bologna.xml")));
 		final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -933,7 +960,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testJairo() throws IOException, DocumentException {
+	void testJairo() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("oaf_jairo.xml")));
 		final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -971,7 +998,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testZenodo() throws IOException, DocumentException {
+	void testZenodo() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -1016,7 +1043,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testOdfFromHdfs() throws IOException, DocumentException {
+	void testOdfFromHdfs() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_from_hdfs.xml")));
 
@@ -1065,7 +1092,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testXMLEncodedURL() throws IOException, DocumentException {
+	void testXMLEncodedURL() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("encoded-url.xml")));
 		final List<Oaf> list = new OafToOafMapper(vocs, false, true).processMdRecord(xml);
 
@@ -1081,7 +1108,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testXMLEncodedURL_ODF() throws IOException, DocumentException {
+	void testXMLEncodedURL_ODF() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("encoded-url_odf.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
@@ -1245,7 +1272,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testRiunet() throws IOException, DocumentException {
+	void testRiunet() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("riunet.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 		System.out.println("***************");
@@ -1291,7 +1318,7 @@ class MappersTest {
 	}
 
 	@Test
-	void testIRISPub() throws IOException, DocumentException {
+	void testIRISPub() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("iris-odf.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 		System.out.println("***************");
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json
index e2a2b9449..2536934c5 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/graph/publication/publication.json
@@ -1,4 +1,4 @@
-{"id":"50|CSC_________::2250a70c903c6ac6e4c01438259e9375","author":[{"affiliation":[],"fullname":"Brien, Tom","name":"Tom","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID12","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"https://orcid.org/0000-0001-9613-6639"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"orcid","classname":"ORCID12","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"0000-0001-9613-6639"}],"rank":1,"surname":"Brien"},{"affiliation":[],"fullname":"Ade, Peter","name":"Peter","pid":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"xyz","classname":"XYZ","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"qwerty"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"","schemename":""},"value":"asdasd"}],"rank":2,"surname":"Ade"},{"affiliation":[],"fullname":"Barry, Peter S.","name":"Peter S.","pid":null,"rank":3,"surname":"Barry"},{"affiliation":[],"fullname":"Dunscombe, Chris J.","name":"Chris J.","pid":[],"rank":4,"surname":"Dunscombe"},{"affiliation":[],"fullname":"Leadley, David R.","name":"David R.","pid":[],"rank":5,"surname":"Leadley"},{"affiliation":[],"fullname":"Morozov, Dmitry V.","name":"Dmitry V.","pid":[],"rank":6,"surname":"Morozov"},{"affiliation":[],"fullname":"Myronov, Maksym","name":"Maksym","pid":[],"rank":7,"surname":"Myronov"},{"affiliation":[],"fullname":"Parker, Evan","name":"Evan","pid":[],"rank":8,"surname":"Parker"},{"affiliation":[],"fullname":"Prest, Martin J.","name":"Martin J.","pid":[],"rank":9,"surname":"Prest"},{"affiliation":[],"fullname":"Prunnila, Mika","name":"Mika","pid":[],"rank":10,"surname":"Prunnila"},{"affiliation":[],"fullname":"Sudiwala, Rashmi V.","name":"Rashmi V.","pid":[],"rank":11,"surname":"Sudiwala"},{"affiliation":[],"fullname":"Whall, Terry E.","name":"Terry E.","pid":[],"rank":12,"surname":"Whall"},{"affiliation":[],"fullname":" - ","name":"","pid":[],"rank":13,"surname":""},{"affiliation":[],"fullname":" :none","name":"","pid":[],"rank":14,"surname":""}],"bestaccessright":null,"publisher":{"value":null},"collectedfrom":[{"key":"10|CSC_________::a2b9ce8435390bcbfc05f3cae3948747","value":"VIRTA"}],"context":[],"contributor":[],"country":[{"classid":"DE","classname":"DE","schemeid":"dnet:countries","schemename":"dnet:countries"}],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"sysimport:crosswalk:datasetarchive","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"7 oct 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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
index 8ef642dd3..bf43016ba 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
@@ -794,28 +794,6 @@
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-        "schemeid": "dnet:subject_classification_typologies",
-        "schemename": "dnet:subject_classification_typologies"
-      },
-      "value": "0101 mathematics"
-    },
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@@ -831,8 +809,8 @@
         "trust": "0.9"
       },
       "qualifier": {
-        "classid": "keyword",
-        "classname": "keyword",
+        "classid": "FOS",
+        "classname": "Fields of Science and Technology classification",
         "schemeid": "dnet:subject_classification_typologies",
         "schemename": "dnet:subject_classification_typologies"
       },
@@ -910,8 +888,8 @@
         "inferred": false,
         "invisible": false,
         "provenanceaction": {
-          "classid": "sysimport:actionset",
-          "classname": "Harvested",
+          "classid": "subject:fos",
+          "classname": "subject:fos",
           "schemeid": "dnet:provenanceActions",
           "schemename": "dnet:provenanceActions"
         },
@@ -923,7 +901,7 @@
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         "schemename": "dnet:subject_classification_typologies"
       },
-      "value": "Avicennia"
+      "value": "0102 computer and information sciences"
     },
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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml
new file mode 100644
index 000000000..6ae4a7f80
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_record_base.xml
@@ -0,0 +1,129 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<record xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
+        xmlns:datacite="http://datacite.org/schema/kernel-4"
+        xmlns:dr="http://www.driver-repository.eu/namespace/dr"
+        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+        xmlns:oaf="http://namespace.openaire.eu/oaf"
+        xmlns:oai="http://www.openarchives.org/OAI/2.0/"
+        xmlns:dri="http://www.driver-repository.eu/namespace/dri"
+        xmlns:xs="http://www.w3.org/2001/XMLSchema"
+        xmlns:dc="http://purl.org/dc/elements/1.1/">
+    <header xmlns="http://www.openarchives.org/OAI/2.0/">
+        <dri:objIdentifier>base_oa_____::7ecf1ef502253efffe203ca9a22bb9f1</dri:objIdentifier>
+        <identifier>ftunivqespace:oai:espace.library.uq.edu.au:UQ:336902</identifier>
+        <datestamp>2020-12-22T10:30:27Z</datestamp>
+        <dr:dateOfTransformation>2024-09-10T17:21:36.972Z</dr:dateOfTransformation>
+    </header>
+    <metadata>
+        <datacite:resource>
+            <datacite:identifier identifierType="DOI">https://doi.org/10.1016/j.envint.2014.07.004</datacite:identifier>
+            <datacite:alternateIdentifiers>
+                <datacite:identifier alternateIdentifierType="url">https://espace.library.uq.edu.au/view/UQ:336902</datacite:identifier>
+                <datacite:identifier alternateIdentifierType="oai-original">ftunivqespace:oai:espace.library.uq.edu.au:UQ:336902</datacite:identifier>
+            </datacite:alternateIdentifiers>
+            <datacite:relatedIdentifiers/>
+            <datacite:resourceType>Article contribution</datacite:resourceType>
+            <datacite:titles>
+                <datacite:title>The role of environmental factors in the spatial distribution of Japanese encephalitis in mainland China</datacite:title>
+            </datacite:titles>
+            <datacite:creators>
+                <datacite:creator>
+                    <datacite:creatorName>Wang, Liya</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Hu, Wenbiao</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Soares Magalhaes, Ricardo J.</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Bi, Peng</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Ding, Fan</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Sun, Hailong</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Li, Shenlong</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Yin, Wenwu</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Wei, Lan</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Liu, Qiyong</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Haque, Ubydul</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Sun, Yansong</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Huang, Liuyu</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Tong, Shilu</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Clements, Archie C.A.</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Zhang, Wenyi</datacite:creatorName>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>Li, Chengyi</datacite:creatorName>
+                </datacite:creator>
+            </datacite:creators>
+            <datacite:contributors/>
+            <datacite:descriptions>
+                <datacite:description descriptionType="Abstract">Japanese encephalitis (JE) is the most common cause of viral encephalitis and an important public health concern in the Asia-Pacific region, particularly in China where 50% of global cases are notified. To explore the association between environmental factors and human JE cases and identify the high risk areas for JE transmission in China, we used annual notified data on JE cases at the center of administrative township and environmental variables with a pixel resolution of 1. km. ×. 1. km from 2005 to 2011 to construct models using ecological niche modeling (ENM) approaches based on maximum entropy. These models were then validated by overlaying reported human JE case localities from 2006 to 2012 onto each prediction map. ENMs had good discriminatory ability with the area under the curve (AUC) of the receiver operating curve (ROC) of 0.82-0.91, and low extrinsic omission rate of 5.44-7.42%. Resulting maps showed JE being presented extensively throughout southwestern and central China, with local spatial variations in probability influenced by minimum temperatures, human population density, mean temperatures, and elevation, with contribution of 17.94%-38.37%, 15.47%-21.82%, 3.86%-21.22%, and 12.05%-16.02%, respectively. Approximately 60% of JE cases occurred in predicted high risk areas, which covered less than 6% of areas in mainland China. Our findings will help inform optimal geographical allocation of the limited resources available for JE prevention and control in China, find hidden high-risk areas, and increase the effectiveness of public health interventions against JE transmission.</datacite:description>
+            </datacite:descriptions>
+            <datacite:subjects>
+                <datacite:subject>Japanese encephalitis</datacite:subject>
+                <datacite:subject>Ecological niche model</datacite:subject>
+                <datacite:subject>MaxEnt</datacite:subject>
+                <datacite:subject>China</datacite:subject>
+                <datacite:subject>2300 Environmental Science</datacite:subject>
+                <datacite:subject classificationCode="950" subjectScheme="ddc">950</datacite:subject>
+            </datacite:subjects>
+            <datacite:publisher>Pergamon Press</datacite:publisher>
+            <datacite:publicationYear>2014</datacite:publicationYear>
+            <datacite:formats/>
+            <datacite:language>eng</datacite:language>
+            <oaf:accessrights/>
+        </datacite:resource>
+        <dr:CobjCategory type="publication">0001</dr:CobjCategory>
+        <oaf:accessrights>UNKNOWN</oaf:accessrights>
+        <oaf:identifier identifierType="doi">10.1163/qwerty</oaf:identifier>
+        <oaf:identifier identifierType="doi">0.1163/18763308-90001038</oaf:identifier>
+        <oaf:identifier identifierType="doi">https://doi.org/10.1016/j.envint.2014.07.004</oaf:identifier>
+        <oaf:identifier identifierType="doi">https://doi.org/10.1080/09672567.2013.792375</oaf:identifier>
+        <oaf:identifier identifierType="doi">http://doi.org/10.1080/08673487.2012.812376</oaf:identifier>
+        <oaf:identifier identifierType="doi">http://dx.doi.org/10.1090/08673487.2012.812376</oaf:identifier>
+        <oaf:identifier identifierType="url">https://espace.library.uq.edu.au/view/UQ:336902</oaf:identifier>
+        <oaf:identifier identifierType="oai-original">ftunivqespace:oai:espace.library.uq.edu.au:UQ:336902</oaf:identifier>
+        <oaf:hostedBy name="The University of Queensland: UQ eSpace" id="opendoar____::575"/>
+        <oaf:collectedFrom name="Bielefeld Academic Search Engine (BASE)"
+                           id="openaire____::base_search"/>
+        <oaf:dateAccepted>2014-12-01</oaf:dateAccepted>
+        <oaf:relation relClass="hasAuthorInstitution"
+                      relType="resultOrganization"
+                      subRelType="affiliation"
+                      targetType="organization">ror_________::https://ror.org/00rqy9422</oaf:relation>
+        <oaf:datainfo>
+            <oaf:inferred>false</oaf:inferred>
+            <oaf:deletedbyinference>false</oaf:deletedbyinference>
+            <oaf:trust>0.89</oaf:trust>
+            <oaf:inferenceprovenance/>
+            <oaf:provenanceaction classid="sysimport:crosswalk:aggregator"
+                                  classname="sysimport:crosswalk:aggregator"
+                                  schemeid="dnet:provenanceActions"
+                                  schemename="dnet:provenanceActions"/>
+        </oaf:datainfo>
+    </metadata>
+</record>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json
index cac6e5a32..204ba6aeb 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/organizations_resultset_entry.json
@@ -130,5 +130,10 @@
 		"value": [
 			"Pippo", "Foo"
 		]
+	},
+	{
+		"field": "typology",
+		"type": "string",
+		"value": "Government"
 	}
 ]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/person/person_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/person/person_10.json.gz
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zi_n<ZhBxq(r9y%V<fOzz5X-!f5(Vjeg_z}z8(8by)I)%|&tDurImxeJGjDqHq^VL~
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z;Syd#CIoGsN#Do$8uw39a~g&nr;^~@D&rXok_l}%wbEJPS<scVOz+^n6j~LMNV<32
zUm?FQ_rEr7X4+6^VV*SuK)Zf-{ZGmkp-$Ox0IVtdse$Qj7yIkK+nBOxY>kJJ(0w@$
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z8Js2>8s1>3a~ygCM#7HPMj@pOCF%a%X|0eS_`eVQzhCm7wXy3%(`{U9JqCO3D5E5=
zIMa+`jj*f~1cPVNFvqn;o|;`{6nM74oQpk+fV;>K5%AeW!1rn7|Ji!|^Ue9`PWl^b
zxw64nY^Y_7i=eoxLIusVWoifgg`yN%8z%RT{ww6bye#hq`xdO7ml^zlTkQ<!K3@zF
v7Fp-wl7ge=xRV)2f4}%+6pW$p3jhZZL5P8*Pw&4mAEWC(69M!aS0DfYu|H(n

literal 0
HcmV?d00001

diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala
index 204fe9794..f01c117cb 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGenerationTest.scala
@@ -4,12 +4,13 @@ import eu.dnetlib.dhp.schema.sx.scholix.ScholixResource
 import eu.dnetlib.dhp.sx.graph.SparkCreateScholexplorerDump
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
-import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.{Disabled, Test}
 import org.objenesis.strategy.StdInstantiatorStrategy
 
 class ScholixGenerationTest {
 
   @Test
+  @Disabled
   def generateScholix(): Unit = {
 
     val spark: SparkSession = SparkSession.builder().master("local[*]").getOrCreate()

From 62ff84333468db2137c182ad9a1bb0bf1acae6b3 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 8 Oct 2024 16:22:54 +0200
Subject: [PATCH 150/239] adopting dhp-schemas:8.0.1 to support Auhtor's
 rawAffiliationString(s). Improved graph2hive implementation

---
 .../usagestats/SparkAtomicActionUsageJob.java |   2 +-
 .../DataciteToOAFTransformation.scala         |   3 +--
 .../dnetlib/doiboost/mag/MagDataModel.scala   |   4 ++--
 .../graph/hive/GraphHiveTableImporterJob.java |  15 +++++++--------
 .../dhp/oa/graph/raw/OdfToOafMapper.java      |   2 +-
 .../oa/graph/GraphHiveImporterJobTest.java    |  12 ++++--------
 .../dnetlib/dhp/oa/graph/raw/MappersTest.java |  10 +++++-----
 .../graph/sample/dataset/dataset_10.json.gz   | Bin 6736 -> 6744 bytes
 .../otherresearchproduct_10.json.gz           | Bin 8073 -> 8086 bytes
 .../oa/graph/sample/person/person_10.json.gz  | Bin 1233 -> 1235 bytes
 .../sample/publication/publication_10.json.gz | Bin 5143 -> 5155 bytes
 .../graph/sample/software/software_10.json.gz | Bin 6410 -> 6421 bytes
 pom.xml                                       |   2 +-
 13 files changed, 22 insertions(+), 28 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
index 1d5b35cff..897153762 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java
@@ -112,7 +112,7 @@ public class SparkAtomicActionUsageJob implements Serializable {
 			.joinWith(datasource, resultModel.col("datasourceId").equalTo(datasource.col("id")), "left")
 			.map((MapFunction<Tuple2<UsageStatsResultModel, Datasource>, UsageStatsResultModel>) t2 -> {
 				UsageStatsResultModel usrm = t2._1();
-				if(Optional.ofNullable(t2._2()).isPresent())
+				if (Optional.ofNullable(t2._2()).isPresent())
 					usrm.setDatasourceId(usrm.getDatasourceId() + "||" + t2._2().getOfficialname().getValue());
 				else
 					usrm.setDatasourceId(usrm.getDatasourceId() + "||NO_MATCH_FOUND");
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
index 7603715b9..9f448d48b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
@@ -407,10 +407,9 @@ object DataciteToOAFTransformation {
         )
       }
       if (c.affiliation.isDefined)
-        a.setAffiliation(
+        a.setRawAffiliationString(
           c.affiliation.get
             .filter(af => af.nonEmpty)
-            .map(af => OafMapperUtils.field(af, dataInfo))
             .asJava
         )
       a.setRank(idx + 1)
diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala
index 185381f8f..ba3c92794 100644
--- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala
+++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala
@@ -313,7 +313,7 @@ case object ConversionUtil {
       if (f.author.DisplayName.isDefined)
         a.setFullname(f.author.DisplayName.get)
       if (f.affiliation != null)
-        a.setAffiliation(List(asField(f.affiliation)).asJava)
+        a.setRawAffiliationString(List(f.affiliation).asJava)
       a.setPid(
         List(
           createSP(
@@ -386,7 +386,7 @@ case object ConversionUtil {
       a.setFullname(f.author.DisplayName.get)
 
       if (f.affiliation != null)
-        a.setAffiliation(List(asField(f.affiliation)).asJava)
+        a.setRawAffiliationString(List(f.affiliation).asJava)
 
       a.setPid(
         List(
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
index 76e1d57a1..73243dbc5 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
@@ -9,10 +9,7 @@ import java.util.Optional;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.*;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -25,8 +22,6 @@ public class GraphHiveTableImporterJob {
 
 	private static final Logger log = LoggerFactory.getLogger(GraphHiveTableImporterJob.class);
 
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
 	public static void main(String[] args) throws Exception {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -74,7 +69,12 @@ public class GraphHiveTableImporterJob {
 	private static <T extends Oaf> void loadGraphTable(SparkSession spark, String inputPath, String hiveDbName,
 		Class<T> clazz, int numPartitions) {
 
-		Dataset<String> dataset = spark.read().textFile(inputPath);
+		final Encoder<T> clazzEncoder = Encoders.bean(clazz);
+
+		Dataset<Row> dataset = spark
+				.read()
+				.schema(clazzEncoder.schema())
+				.json(inputPath);
 
 		if (numPartitions > 0) {
 			log.info("repartitioning {} to {} partitions", clazz.getSimpleName(), numPartitions);
@@ -82,7 +82,6 @@ public class GraphHiveTableImporterJob {
 		}
 
 		dataset
-			.map((MapFunction<String, T>) s -> OBJECT_MAPPER.readValue(s, clazz), Encoders.bean(clazz))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.saveAsTable(tableIdentifier(hiveDbName, clazz));
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
index 41fc37cb1..ad61304a0 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
@@ -94,7 +94,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 					author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
 				}
 
-				author.setAffiliation(prepareListFields(n, "./*[local-name()='affiliation']", info));
+				author.setRawAffiliationString(prepareListString(n, "./*[local-name()='affiliation']"));
 				author.setPid(preparePids(n, info));
 				author.setRank(pos++);
 				res.add(author);
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java
index afaac04ea..e059cbc86 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/GraphHiveImporterJobTest.java
@@ -73,14 +73,10 @@ public class GraphHiveImporterJobTest {
 		GraphHiveImporterJob
 			.main(
 				new String[] {
-					"-isSparkSessionManaged",
-					Boolean.FALSE.toString(),
-					"-inputPath",
-					getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(),
-					"-hiveMetastoreUris",
-					"",
-					"-hiveDbName",
-					dbName
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--inputPath", getClass().getResource("/eu/dnetlib/dhp/oa/graph/sample").getPath(),
+					"--hiveMetastoreUris", "",
+					"--hiveDbName", dbName
 				});
 
 		ModelSupport.oafTypes
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
index 228c6308c..2cf3ea0c0 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@@ -406,15 +406,15 @@ class MappersTest {
 		assertEquals("Baracchini", author.get().getSurname());
 		assertEquals("Theo", author.get().getName());
 
-		assertEquals(1, author.get().getAffiliation().size());
-		final Optional<Field<String>> opAff = author
+		assertEquals(1, author.get().getRawAffiliationString().size());
+		final Optional<String> opAff = author
 			.get()
-			.getAffiliation()
+			.getRawAffiliationString()
 			.stream()
 			.findFirst();
 		assertTrue(opAff.isPresent());
-		final Field<String> affiliation = opAff.get();
-		assertEquals("ISTI-CNR", affiliation.getValue());
+		final String affiliation = opAff.get();
+		assertEquals("ISTI-CNR", affiliation);
 
 		assertFalse(d.getSubject().isEmpty());
 		assertFalse(d.getInstance().isEmpty());
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/dataset/dataset_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/dataset/dataset_10.json.gz
index 0da3c4071ab705e39e22e33967e39de56f788855..e112002d698a006ee75cfa83e72253d58e8db456 100644
GIT binary patch
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index 20b6a4dba3f02516796283f817134026a083e7a3..b32268d6aea1d4dcf83691483c04d7531f234831 100644
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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/person/person_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/person/person_10.json.gz
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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/publication/publication_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/publication/publication_10.json.gz
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diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/software/software_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/software/software_10.json.gz
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zsTlf_d=gSQg+AyTY$Usp9WV8SreIrB%>rohw7C2Vb`5wG0*z`GC=P+S8B4_IA)QU<
z_DkXiO_mjbgRTu6*jTNN)!JC?Z#Gt|g9DostF<cE#%iBCOIO5dJ8s`~?~2v--5_wB
zfH|!1^n0D4J#ZY_$Gc9(Zm%1R8^0W@U0M7Y#%jIp$a7nr!Dm0#uG49Ed$-1FU3bTA
zf2l9Exl$}k%?&AZ;bgm7O6_xPlfUt}NbNDqC>q`CIu?_)ao-rN4QQ@7j%^==Ug=QH
zY>Mt^6W)ZBOExAaN5_96M~U7i<Di1!c|OPcV0ji>m(bH$OMac>-8*(yW)0zo8^TFo
z4Pk2tKLtbB?7TL~5Vk7U8p6+=rK=3#uGhWW5C-dYIHr9sY=<7}4?7Gj*?}{5`d!a+
zSh&g%URC@V8p0iS<n>!#r~COq%YE0q{m8QJPJ8f$4B?mbBE<umM3f(7m8Vw;HDE91
zeWVHeD#bII_Oc*l^NLFOTszz<W%oCKmucV$U0~E7Ua)9hx9O{dIw76A@i?IJK4=Au
zVD6lN-eW>F$=UVQWWkYe#{Tv9$&Ewum&!FBcV5{G3hEu~U;{R9Ea1!+9T$1V#^a7C
zJ3c&n`)!lFp=t`YaIJH-l$!H`rDEQA+@WL#*-T_?o}=fFGk>vDc}fjCZ}K<pdo<Z*
zdrHET?uIv7@Di7~&yD^LKtU>6z`yTydn~nWu~p0Mu+EDIZ0YKkaiX&-(5I_M((+=R
zyqH{HiS+s^yuQ*MjLr8nmLY3n$OULF*v?r!wSHFMCtkh<v96T|nZ#>mf((}m%Zbf^
z6CW(>rSw9smvqFB`uf~KNk#;={uzr1>|aw7QL>=dG)DaQIdAiQ0LH8$ePz1XSz3{F
zo|q>Y(s041B#z_gIw;9E6Tc^iO4}RnMS8cK*r3)XN|?Q~*ao#My7P&MjSXt81>LE=
zsGAhjvMSdGwVpdmR|T~OgMoKvP>c4c&%B^dgHD_J1J`4nVYeIhdbHE&c&qL#URnGZ
z2DQ5FQM=vhIiDZh>GXU3USsVi@yPcq``9Gk()tY``P0H(Bbcx8NK_|<0SrUdBun?U
z+`O@+$l9>D&QA$doGSqffW*%XU#74d20<iypawv%NwRhRa&P;qv#-b*nVCCytyg3-
zydpBB!NrK|1s9k*ASe3xUa3EQ{Uw&RDpu-`Rna}-ww#td^7)C0#Qi_lu8BifhyyKV
zxW1N{7E)vmfyPg;j}j1*6w2Vo*-gR~p|e>88ccsBt#ALJ{<OHcI3VLWDHJlg)@als
zTexrECVx11do*%E!knSEOW#wrOX;Q4@Ba}$iiY)!<Cov~z4I;2)U8v@pC<YXW}Yz6
z>ge?I=LG%)T?Rdvg4rh$25)DX!f(d)iT^ASnY3RuKS-vm5oY~f*6+0mVq^VY>+yS`
Yp=JGEPkZh>5x>{}19s*i?oIsw0IUmUV*mgE

diff --git a/pom.xml b/pom.xml
index 666ba2350..e1d99f25b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[7.0.1]</dhp-schemas.version>
+        <dhp-schemas.version>[8.0.1]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From 62c4c3ed29dcf395b2f18c5c6495f6502f011c65 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Wed, 9 Oct 2024 12:26:03 +0200
Subject: [PATCH 151/239] implementation of new comparators for organization
 and dataset disambiguation

---
 .../java/eu/dnetlib/pace/tree/CodeMatch.java  |  2 +-
 .../eu/dnetlib/pace/tree/JsonListMatch.java   | 43 +++++++++++++------
 .../pace/comparators/ComparatorTest.java      | 34 ++++++++++++---
 3 files changed, 60 insertions(+), 19 deletions(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java
index 25a12bcdf..5cd21adcd 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CodeMatch.java
@@ -21,7 +21,7 @@ public class CodeMatch extends AbstractStringComparator {
 	public CodeMatch(Map<String, String> params) {
 		super(params);
 		this.params = params;
-		this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]::\\d+"));
+		this.CODE_REGEX = Pattern.compile(params.getOrDefault("codeRegex", "[a-zA-Z]+::\\d+"));
 	}
 
 	public Set<String> getRegexList(String input) {
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
index 3897e37f8..e95d9206e 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
@@ -41,21 +41,38 @@ public class JsonListMatch extends AbstractListComparator {
 			return -1;
 		}
 
-		final Set<String> ca = sa.stream().map(this::toComparableString).collect(Collectors.toSet());
-		final Set<String> cb = sb.stream().map(this::toComparableString).collect(Collectors.toSet());
+		Set<String> ca = sa.stream().map(this::toComparableString).collect(Collectors.toSet());
+		Set<String> cb = sb.stream().map(this::toComparableString).collect(Collectors.toSet());
 
-		int incommon = Sets.intersection(ca, cb).size();
-		int simDiff = Sets.symmetricDifference(ca, cb).size();
+		switch (MODE) {
+			case "count":
+				return Sets.intersection(ca, cb).size();
 
-		if (incommon + simDiff == 0) {
-			return 0.0;
+			case "percentage":
+				int incommon = Sets.intersection(ca, cb).size();
+				int simDiff = Sets.symmetricDifference(ca, cb).size();
+				if (incommon + simDiff == 0) {
+					return 0.0;
+				}
+				return (double) incommon / (incommon + simDiff);
+
+			case "type":
+				Set<String> typesA = ca.stream().map(s -> s.split("::")[0]).collect(Collectors.toSet());
+				Set<String> typesB = cb.stream().map(s -> s.split("::")[0]).collect(Collectors.toSet());
+
+				Set<String> types = Sets.intersection(typesA, typesB);
+
+				if (types.isEmpty())  // if no common type, it is impossible to compare
+					return -1;
+
+				ca = ca.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet());
+				cb = cb.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet());
+
+				return (double) Sets.intersection(ca, cb).size() / types.size();
+
+			default:
+				return -1;
 		}
-
-		if (MODE.equals("percentage"))
-			return (double) incommon / (incommon + simDiff);
-		else
-			return incommon;
-
 	}
 
 	// converts every json into a comparable string basing on parameters
@@ -69,7 +86,7 @@ public class JsonListMatch extends AbstractListComparator {
 		// for each path in the param list
 		for (String key : params.keySet().stream().filter(k -> k.contains("jpath")).collect(Collectors.toList())) {
 			String path = params.get(key);
-			String value = MapDocumentUtil.getJPathString(path, documentContext);
+			String value = MapDocumentUtil.getJPathString(path, documentContext).toLowerCase();
 			if (value == null || value.isEmpty())
 				value = "";
 			st.append(value);
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index c008902c4..635f1fa44 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -65,6 +65,23 @@ public class ComparatorTest extends AbstractPaceTest {
 
 	}
 
+	@Test
+	public void datasetVersionCodeMatchTest() {
+
+		params.put("codeRegex", "(?=[\\w-]*[a-zA-Z])(?=[\\w-]*\\d)[\\w-]+");
+		CodeMatch codeMatch = new CodeMatch(params);
+
+		// names have different codes
+		assertEquals(0.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ir02", conf));
+
+		// names have same code
+		assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ev02a", conf));
+
+		// code is not in both names
+		assertEquals(-1, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998 ev02a", conf));
+		assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998", conf));
+	}
+
 	@Test
 	public void listContainsMatchTest() {
 
@@ -257,15 +274,15 @@ public class ComparatorTest extends AbstractPaceTest {
 		List<String> a = createFieldList(
 			Arrays
 				.asList(
-					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"doi\",\"classname\":\"Digital Object Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"10.1111/pbi.12655\"}"),
+					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}",
+						"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"),
 			"authors");
 		List<String> b = createFieldList(
 			Arrays
 				.asList(
-					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmc\",\"classname\":\"PubMed Central ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"PMC5399005\"}",
-					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"pmid\",\"classname\":\"PubMed ID\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"27775869\"}",
-					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"user:claim\",\"classname\":\"Linked by user\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"doi\",\"classname\":\"Digital Object Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"10.1111/pbi.12655\"}",
-					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"handle\",\"classname\":\"Handle\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"1854/LU-8523529\"}"),
+					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}",
+					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:crosswalk:repository\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_2\"}",
+					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":\"\",\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"user:claim\",\"classname\":\"Linked by user\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"isni\",\"classname\":\"ISNI Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"isni_1\"}"),
 			"authors");
 
 		double result = jsonListMatch.compare(a, b, conf);
@@ -277,6 +294,13 @@ public class ComparatorTest extends AbstractPaceTest {
 		result = jsonListMatch.compare(a, b, conf);
 
 		assertEquals(1.0, result);
+
+		params.put("mode", "type");
+		jsonListMatch = new JsonListMatch(params);
+		result = jsonListMatch.compare(a, b, conf);
+
+		assertEquals(0.5, result);
+
 	}
 
 	@Test

From 56b05cde0b621d91e9b974453d6fe28f7061561b Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Wed, 9 Oct 2024 23:00:13 +0200
Subject: [PATCH 152/239] Revert the changes for IgnoreUndefined management in
 tree evaluation

---
 .../pace/tree/support/TreeNodeDef.java        |  2 +-
 .../pace/tree/support/TreeNodeStats.java      | 33 ++++---------------
 .../pace/tree/support/TreeProcessor.java      |  8 +++--
 3 files changed, 12 insertions(+), 31 deletions(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
index 0ff03f5e1..0973fdf1e 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeDef.java
@@ -48,7 +48,7 @@ public class TreeNodeDef implements Serializable {
 	// function for the evaluation of the node
 	public TreeNodeStats evaluate(Row doc1, Row doc2, Config conf) {
 
-		TreeNodeStats stats = new TreeNodeStats(ignoreUndefined);
+		TreeNodeStats stats = new TreeNodeStats();
 
 		// for each field in the node, it computes the
 		for (FieldConf fieldConf : fields) {
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
index f6b210a8c..2b96048b4 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeNodeStats.java
@@ -9,11 +9,8 @@ public class TreeNodeStats implements Serializable {
 
 	private Map<String, FieldStats> results; // this is an accumulator for the results of the node
 
-	private final boolean ignoreUndefined;
-
-	public TreeNodeStats(boolean ignoreUndefined) {
+	public TreeNodeStats() {
 		this.results = new HashMap<>();
-		this.ignoreUndefined = ignoreUndefined;
 	}
 
 	public Map<String, FieldStats> getResults() {
@@ -25,10 +22,7 @@ public class TreeNodeStats implements Serializable {
 	}
 
 	public int fieldsCount() {
-		if (ignoreUndefined)
-			return this.results.size();
-		else
-			return this.results.size() - undefinedCount(); // do not count undefined
+		return this.results.size();
 	}
 
 	public int undefinedCount() {
@@ -84,22 +78,11 @@ public class TreeNodeStats implements Serializable {
 		double min = 100.0; // random high value
 		for (FieldStats fs : this.results.values()) {
 			if (fs.getResult() < min) {
-				if (fs.getResult() == -1) {
-					if (fs.isCountIfUndefined()) {
-						min = 0.0;
-					} else {
-						min = -1;
-					}
-				} else {
+				if (fs.getResult() >= 0.0 || (fs.getResult() == -1 && fs.isCountIfUndefined()))
 					min = fs.getResult();
-				}
 			}
 		}
-		if (ignoreUndefined) {
-			return min == -1.0 ? 0.0 : min;
-		} else {
-			return min;
-		}
+		return min;
 	}
 
 	// if at least one is true, return 1.0
@@ -108,11 +91,7 @@ public class TreeNodeStats implements Serializable {
 			if (fieldStats.getResult() >= fieldStats.getThreshold())
 				return 1.0;
 		}
-		if (!ignoreUndefined && undefinedCount() > 0) {
-			return -1.0;
-		} else {
-			return 0.0;
-		}
+		return 0.0;
 	}
 
 	// if at least one is false, return 0.0
@@ -121,7 +100,7 @@ public class TreeNodeStats implements Serializable {
 
 			if (fieldStats.getResult() == -1) {
 				if (fieldStats.isCountIfUndefined())
-					return ignoreUndefined ? 0.0 : -1.0;
+					return 0.0;
 			} else {
 				if (fieldStats.getResult() < fieldStats.getThreshold())
 					return 0.0;
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
index 28b3a82af..263504dbb 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/support/TreeProcessor.java
@@ -44,10 +44,12 @@ public class TreeProcessor {
 			TreeNodeStats stats = currentNode.evaluate(doc1, doc2, config);
 			treeStats.addNodeStats(nextNodeName, stats);
 
-			double finalScore = stats.getFinalScore(currentNode.getAggregation());
-			if (finalScore == -1.0)
+			// if ignoreUndefined=false the miss is considered as undefined
+			if (!currentNode.isIgnoreUndefined() && stats.undefinedCount() > 0) {
 				nextNodeName = currentNode.getUndefined();
-			else if (finalScore >= currentNode.getThreshold()) {
+			}
+			// if ignoreUndefined=true the miss is ignored and the score computed anyway
+			else if (stats.getFinalScore(currentNode.getAggregation()) >= currentNode.getThreshold()) {
 				nextNodeName = currentNode.getPositive();
 			} else {
 				nextNodeName = currentNode.getNegative();

From 5015ba10eba66ba12750ff348cea559062f68e7e Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Mon, 14 Oct 2024 10:23:42 +0200
Subject: [PATCH 153/239] addition of date comparator

---
 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
new file mode 100644
index 000000000..91b8d1c41
--- /dev/null
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
@@ -0,0 +1,2 @@
+package eu.dnetlib.pace.tree;public class DateRange {
+}

From eab623ddfa0b01137df729981ef99abe0c129215 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Mon, 14 Oct 2024 10:24:19 +0200
Subject: [PATCH 154/239] implementation of date matcher

---
 .../java/eu/dnetlib/pace/tree/DateRange.java  | 67 ++++++++++++++++++-
 .../pace/comparators/ComparatorTest.java      | 19 ++++++
 2 files changed, 85 insertions(+), 1 deletion(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
index 91b8d1c41..c913109a4 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
@@ -1,2 +1,67 @@
-package eu.dnetlib.pace.tree;public class DateRange {
+package eu.dnetlib.pace.tree;
+
+import com.wcohen.ss.AbstractStringDistance;
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+import org.joda.time.DateTime;
+
+import java.time.DateTimeException;
+import java.time.LocalDate;
+import java.time.Period;
+import java.time.format.DateTimeFormatter;
+import java.util.Locale;
+import java.util.Map;
+
+@ComparatorClass("dateRange")
+public class DateRange extends AbstractStringComparator {
+
+    int YEAR_RANGE;
+
+    public DateRange(Map<String, String> params) {
+        super(params, new com.wcohen.ss.JaroWinkler());
+        YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3"));
+    }
+
+    public DateRange(final double weight) {
+        super(weight, new com.wcohen.ss.JaroWinkler());
+    }
+
+    protected DateRange(final double weight, final AbstractStringDistance ssalgo) {
+        super(weight, ssalgo);
+    }
+
+    public static boolean isNumeric(String str) {
+        return str.matches("\\d+");  //match a number with optional '-' and decimal.
+    }
+
+    @Override
+    public double distance(final String a, final String b, final Config conf) {
+        if (a.isEmpty() || b.isEmpty()) {
+            return -1.0; // return -1 if a field is missing
+        }
+
+        try {
+            DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH);
+            LocalDate d1 = LocalDate.parse(a, formatter);
+            LocalDate d2 = LocalDate.parse(b, formatter);
+            Period period = Period.between(d1, d2);
+
+            return period.getYears() <= YEAR_RANGE? 1.0 : 0.0;
+        }
+        catch (DateTimeException e) {
+            return -1.0;
+        }
+
+    }
+
+    @Override
+    public double getWeight() {
+        return super.weight;
+    }
+
+    @Override
+    protected double normalize(final double d) {
+        return d;
+    }
 }
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index 635f1fa44..5e1484254 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -351,4 +351,23 @@ public class ComparatorTest extends AbstractPaceTest {
 
 	}
 
+	@Test
+	public void dateMatch() {
+
+		DateRange dateRange = new DateRange(params);
+
+		double result = dateRange.distance("2021-05-13", "2023-05-13", conf);
+		assertEquals(1.0, result);
+
+		result = dateRange.distance("2021-05-13", "2025-05-13", conf);
+		assertEquals(0.0, result);
+
+		result = dateRange.distance("", "2020-05-05", conf);
+		assertEquals(-1.0, result);
+
+		result = dateRange.distance("invalid date", "2021-05-02", conf);
+		assertEquals(-1.0, result);
+
+	}
+
 }

From 0e5dd14538fc8b2ba2bc08f3af93793e3b9e19b7 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 18 Oct 2024 16:22:21 +0200
Subject: [PATCH 155/239] [createASfromAffRo] adding the provenance datasource
 used to get the relation (no datasource can be webcrawl = publisher, rawaff
 means oalex)

---
 .../PrepareAffiliationRelations.java          | 47 ++++++++++---------
 .../PrepareAffiliationRelationsTest.java      | 16 +++----
 2 files changed, 34 insertions(+), 29 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 028fa47dc..61a018a41 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -104,22 +104,22 @@ public class PrepareAffiliationRelations implements Serializable {
 			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
 		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
-			spark, crossrefInputPath, collectedfromOpenAIRE);
+			spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::crossref");
 
 		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-			spark, pubmedInputPath, collectedfromOpenAIRE);
+			spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::pubmed");
 
 		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel(
-			spark, openapcInputPath, collectedfromOpenAIRE);
+			spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::openapc");
 
-		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
-			spark, dataciteInputPath, collectedfromOpenAIRE);
+		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelationsNewModel(
+			spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::datacite");
 
-		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-			spark, webcrawlInputPath, collectedfromOpenAIRE);
+		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelationsNewModel(
+			spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::rawaff");
 
-		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
-			spark, publisherlInputPath, collectedfromOpenAIRE);
+		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisherNewModel(
+			spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::webcrawl");
 
 		crossrefRelations
 			.union(pubmedRelations)
@@ -133,7 +133,8 @@ public class PrepareAffiliationRelations implements Serializable {
 
 	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisherNewModel(SparkSession spark,
 		String inputPath,
-		List<KeyValue> collectedfrom) {
+		List<KeyValue> collectedfrom,
+		String dataprovenance) {
 
 		Dataset<Row> df = spark
 			.read()
@@ -142,12 +143,13 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
-		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
+		return getTextTextJavaPairRDDNew(
+			collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"), dataprovenance);
 
 	}
 
 	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
-		List<KeyValue> collectedfrom) {
+		List<KeyValue> collectedfrom, String dataprovenance) {
 
 		Dataset<Row> df = spark
 			.read()
@@ -155,13 +157,14 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
-		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
+		return getTextTextJavaPairRDD(
+			collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"), dataprovenance);
 
 	}
 
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
 		String inputPath,
-		List<KeyValue> collectedfrom) {
+		List<KeyValue> collectedfrom, String dataprovenance) {
 
 		// load and parse affiliation relations from HDFS
 		Dataset<Row> df = spark
@@ -170,12 +173,12 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
-		return getTextTextJavaPairRDD(collectedfrom, df);
+		return getTextTextJavaPairRDD(collectedfrom, df, dataprovenance);
 	}
 
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelationsNewModel(SparkSession spark,
 		String inputPath,
-		List<KeyValue> collectedfrom) {
+		List<KeyValue> collectedfrom, String dataprovenance) {
 		// load and parse affiliation relations from HDFS
 		Dataset<Row> df = spark
 			.read()
@@ -184,10 +187,11 @@ public class PrepareAffiliationRelations implements Serializable {
 			.json(inputPath)
 			.where("DOI is not null");
 
-		return getTextTextJavaPairRDDNew(collectedfrom, df);
+		return getTextTextJavaPairRDDNew(collectedfrom, df, dataprovenance);
 	}
 
-	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df) {
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(List<KeyValue> collectedfrom, Dataset<Row> df,
+		String dataprovenance) {
 		// unroll nested arrays
 		df = df
 			.withColumn("matching", functions.explode(new Column("Matchings")))
@@ -219,7 +223,7 @@ public class PrepareAffiliationRelations implements Serializable {
 				DataInfo dataInfo = OafMapperUtils
 					.dataInfo(
 						false,
-						BIP_INFERENCE_PROVENANCE,
+						dataprovenance,
 						true,
 						false,
 						qualifier,
@@ -235,7 +239,8 @@ public class PrepareAffiliationRelations implements Serializable {
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df) {
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDDNew(List<KeyValue> collectedfrom, Dataset<Row> df,
+		String dataprovenance) {
 		// unroll nested arrays
 		df = df
 			.withColumn("matching", functions.explode(new Column("Matchings")))
@@ -276,7 +281,7 @@ public class PrepareAffiliationRelations implements Serializable {
 				DataInfo dataInfo = OafMapperUtils
 					.dataInfo(
 						false,
-						BIP_INFERENCE_PROVENANCE,
+						dataprovenance,
 						true,
 						false,
 						qualifier,
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
index 179cbecb5..c704bb99b 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
@@ -98,9 +98,9 @@ public class PrepareAffiliationRelationsTest {
 					"-crossrefInputPath", crossrefAffiliationRelationPathNew,
 					"-pubmedInputPath", crossrefAffiliationRelationPath,
 					"-openapcInputPath", crossrefAffiliationRelationPathNew,
-					"-dataciteInputPath", crossrefAffiliationRelationPath,
-					"-webCrawlInputPath", crossrefAffiliationRelationPath,
-					"-publisherInputPath", publisherAffiliationRelationOldPath,
+					"-dataciteInputPath", crossrefAffiliationRelationPathNew,
+					"-webCrawlInputPath", crossrefAffiliationRelationPathNew,
+					"-publisherInputPath", publisherAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 
@@ -112,7 +112,7 @@ public class PrepareAffiliationRelationsTest {
 			.map(aa -> ((Relation) aa.getPayload()));
 
 		// count the number of relations
-		assertEquals(150, tmp.count());// 18 + 24 *3 + 30 * 2 =
+		assertEquals(162, tmp.count());// 18 + 24  + 30 * 4 =
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
@@ -123,7 +123,7 @@ public class PrepareAffiliationRelationsTest {
 		// verify that we have equal number of bi-directional relations
 		Assertions
 			.assertEquals(
-				75, execVerification
+				81, execVerification
 					.filter(
 						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
@@ -131,7 +131,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				75, execVerification
+				81, execVerification
 					.filter(
 						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
@@ -158,7 +158,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				2, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
+				4, execVerification.filter("source = '" + publisherid + "' and target = '" + rorId + "'").count());
 
 		Assertions
 			.assertEquals(
@@ -173,7 +173,7 @@ public class PrepareAffiliationRelationsTest {
 
 		Assertions
 			.assertEquals(
-				3, execVerification
+				1, execVerification
 					.filter(
 						"source = '" + ID_PREFIX
 							+ IdentifierFactory

From 2b27afaec8d3a6bd7bdaf2ff83040f88c68660e2 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 18 Oct 2024 16:22:51 +0200
Subject: [PATCH 156/239] [createASfromAffRo] refactoring after compilation

---
 .../dhp/oa/graph/hive/GraphHiveTableImporterJob.java        | 6 +++---
 .../dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala  | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
index 73243dbc5..d4fec3f52 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
@@ -72,9 +72,9 @@ public class GraphHiveTableImporterJob {
 		final Encoder<T> clazzEncoder = Encoders.bean(clazz);
 
 		Dataset<Row> dataset = spark
-				.read()
-				.schema(clazzEncoder.schema())
-				.json(inputPath);
+			.read()
+			.schema(clazzEncoder.schema())
+			.json(inputPath);
 
 		if (numPartitions > 0) {
 			log.info("repartitioning {} to {} partitions", clazz.getSimpleName(), numPartitions);
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
index 4e5ad5365..eece56b74 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
@@ -31,6 +31,7 @@ class ORCIDAuthorMatchersTest {
     assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin"))
     // assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented
   }
+
   @Test def testDocumentationNames(): Unit = {
     assertTrue(matchOrderedTokenAndAbbreviations("James C. A. Miller-Jones", "James Antony Miller-Jones"))
   }

From ce4ee1189f4d83ff114c63ddb782621db7a939b2 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 21 Oct 2024 14:38:15 +0200
Subject: [PATCH 157/239] [personEntity] create entity for each profile in
 orcid even without works. Added validated true to each relation coming from
 orcid data

---
 .../personentity/CoAuthorshipIterator.java    |  5 ++-
 .../personentity/ExtractPerson.java           | 31 +++++++++----------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
index 76e4c4851..94ac7ab28 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
@@ -61,7 +61,8 @@ public class CoAuthorshipIterator implements Iterator<Relation> {
 	private Relation getRelation(String orcid1, String orcid2) {
 		String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
 		String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
-		return OafMapperUtils
+		Relation relation =
+		OafMapperUtils
 			.getRelation(
 				source, target, ModelConstants.PERSON_PERSON_RELTYPE,
 				ModelConstants.PERSON_PERSON_SUBRELTYPE,
@@ -76,5 +77,7 @@ public class CoAuthorshipIterator implements Iterator<Relation> {
 								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
 						"0.91"),
 				null);
+		relation.setValidated(true);
+		return relation;
 	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 6f61d427d..c29c04699 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -144,18 +144,13 @@ public class ExtractPerson implements Serializable {
 			.parquet(inputPath + "Employments")
 			.as(Encoders.bean(Employment.class));
 
-		Dataset<Author> peopleToMap = authors
-			.joinWith(works, authors.col("orcid").equalTo(works.col("orcid")))
-			.map((MapFunction<Tuple2<Author, Work>, Author>) t2 -> t2._1(), Encoders.bean(Author.class))
-			.groupByKey((MapFunction<Author, String>) a -> a.getOrcid(), Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, Author, Author>) (k, it) -> it.next(), Encoders.bean(Author.class));
-
 		Dataset<Employment> employment = employmentDataset
-			.joinWith(peopleToMap, employmentDataset.col("orcid").equalTo(peopleToMap.col("orcid")))
+			.joinWith(authors, employmentDataset.col("orcid").equalTo(authors.col("orcid")))
 			.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
 
+		//Mapping all the orcid profiles even if the profile has no visible works
 		Dataset<Person> people;
-		peopleToMap.map((MapFunction<Author, Person>) op -> {
+		authors.map((MapFunction<Author, Person>) op -> {
 			Person person = new Person();
 			person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
 			person
@@ -325,6 +320,7 @@ public class ExtractPerson implements Serializable {
 				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
 				DATAINFO,
 				null);
+		relation.setValidated(true);
 
 		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
 			KeyValue kv = new KeyValue();
@@ -412,14 +408,15 @@ public class ExtractPerson implements Serializable {
 			default:
 				return null;
 		}
-
-		return OafMapperUtils
-			.getRelation(
-				source, target, ModelConstants.RESULT_PERSON_RELTYPE,
-				ModelConstants.RESULT_PERSON_SUBRELTYPE,
-				ModelConstants.RESULT_PERSON_HASAUTHORED,
-				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				DATAINFO,
-				null);
+		Relation relation = OafMapperUtils
+				.getRelation(
+						source, target, ModelConstants.RESULT_PERSON_RELTYPE,
+						ModelConstants.RESULT_PERSON_SUBRELTYPE,
+						ModelConstants.RESULT_PERSON_HASAUTHORED,
+						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+						DATAINFO,
+						null);
+		relation.setValidated(true);
+		return relation;
 	}
 }

From 09a2c93fc7197e48a8f769a131908e22ed02a78c Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 21 Oct 2024 16:21:15 +0200
Subject: [PATCH 158/239] [personEntity] added relations with projects
 extracting the info from the database

---
 .../personentity/ExtractPerson.java           | 166 ++++++++++++++----
 1 file changed, 133 insertions(+), 33 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index c29c04699..960dfbe44 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -2,13 +2,18 @@
 package eu.dnetlib.dhp.actionmanager.personentity;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.*;
 
+import java.io.BufferedWriter;
 import java.io.IOException;
+import java.io.OutputStreamWriter;
 import java.io.Serializable;
+import java.nio.charset.StandardCharsets;
+import java.sql.ResultSet;
+import java.sql.SQLException;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.common.DbClient;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
@@ -22,6 +27,7 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.spark_project.jetty.util.StringUtil;
 
+
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
@@ -43,9 +49,14 @@ import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
 public class ExtractPerson implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
-
+	private static final String QUERY = "SELECT * FROM project_person WHERE pid_type = 'ORCID'";
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 	private static final String OPENAIRE_PREFIX = "openaire____";
 	private static final String SEPARATOR = "::";
@@ -62,6 +73,12 @@ public class ExtractPerson implements Serializable {
 	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
 	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
 	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
+	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
+	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
+
+	public static List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+
 
 	public static final DataInfo DATAINFO = OafMapperUtils
 		.dataInfo(
@@ -106,19 +123,130 @@ public class ExtractPerson implements Serializable {
 		final String workingDir = parser.get("workingDir");
 		log.info("workingDir {}", workingDir);
 
+		final String dbUrl = parser.get("postgresUrl");
+		final String dbUser = parser.get("postgresUser");
+		final String dbPassword = parser.get("postgresPassword");
+
+		final String hdfsNameNode = parser.get("hdfsNameNode");
+
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				createActionSet(spark, inputPath, outputPath, workingDir);
+				extractInfoForActionSetFromORCID(spark, inputPath, workingDir);
+				extractInfoForActionSetFromProjects(spark, inputPath, workingDir, dbUrl, dbUser, dbPassword, workingDir + "/project", hdfsNameNode);
+				createActionSet(spark, outputPath, workingDir);
 			});
 
 	}
 
-	private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
+	private static void extractInfoForActionSetFromProjects(SparkSession spark, String inputPath, String workingDir,
+															String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode) throws IOException {
 
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
+
+		FileSystem fileSystem = FileSystem.get(conf);
+		Path hdfsWritePath = new Path(hdfsPath);
+		FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
+		try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
+			try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
+				dbClient.processResults(QUERY, rs -> writeRelation(getRelationWithProject(rs), writer));
+			}
+
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+	}
+
+	public static Relation getRelationWithProject(ResultSet rs) {
+		try {
+			return getProjectRelation(rs.getString("project"), rs.getString("pid"),
+					rs.getString("role"));
+		} catch (final SQLException e) {
+			throw new RuntimeException(e);
+		}
+    }
+
+	private static Relation getProjectRelation(String project, String orcid, String role) {
+
+			String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
+			String target = project.substring(0,14)
+					+ IdentifierFactory.md5(project.substring(15));
+			List<KeyValue> properties = new ArrayList<>();
+
+			Relation relation = OafMapperUtils
+					.getRelation(
+							source, target, ModelConstants.PROJECT_PERSON_RELTYPE, ModelConstants.PROJECT_PERSON_SUBRELTYPE,
+							ModelConstants.PROJECT_PERSON_PARTICIPATES,
+							collectedfromOpenAIRE,
+							DATAINFO,
+							null);
+			relation.setValidated(true);
+
+			if (StringUtil.isNotBlank(role)) {
+				KeyValue kv = new KeyValue();
+				kv.setKey("role");
+				kv.setValue(role);
+				properties.add(kv);
+			}
+
+
+			if (!properties.isEmpty())
+				relation.setProperties(properties);
+			return relation;
+
+
+	}
+
+	protected static void writeRelation(final Relation relation, BufferedWriter writer) {
+		try {
+			writer.write(OBJECT_MAPPER.writeValueAsString(relation));
+			writer.newLine();
+		} catch (final IOException e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	private static void createActionSet(SparkSession spark,String outputPath, String workingDir) {
+
+		Dataset<Person> people;
+		people = spark
+			.read()
+			.textFile(workingDir + "/people")
+			.map(
+				(MapFunction<String, Person>) value -> OBJECT_MAPPER
+					.readValue(value, Person.class),
+				Encoders.bean(Person.class));
+		
+		people
+			.toJavaRDD()
+			.map(p -> new AtomicAction(p.getClass(), p))
+			.union(
+				getRelations(spark, workingDir + "/authorship").toJavaRDD().map(r -> new AtomicAction(r.getClass(), r)))
+			.union(
+				getRelations(spark, workingDir + "/coauthorship")
+					.toJavaRDD()
+					.map(r -> new AtomicAction(r.getClass(), r)))
+			.union(
+				getRelations(spark, workingDir + "/affiliation")
+					.toJavaRDD()
+					.map(r -> new AtomicAction(r.getClass(), r)))
+				.union(
+						getRelations(spark, workingDir + "/project")
+								.toJavaRDD()
+								.map(r -> new AtomicAction(r.getClass(), r)))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+	}
+
+	private static void extractInfoForActionSetFromORCID(SparkSession spark, String inputPath, String workingDir) {
 		Dataset<Author> authors = spark
 			.read()
 			.parquet(inputPath + "Authors")
@@ -149,7 +277,7 @@ public class ExtractPerson implements Serializable {
 			.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
 
 		//Mapping all the orcid profiles even if the profile has no visible works
-		Dataset<Person> people;
+
 		authors.map((MapFunction<Author, Person>) op -> {
 			Person person = new Person();
 			person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
@@ -257,34 +385,6 @@ public class ExtractPerson implements Serializable {
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
 			.json(workingDir + "/affiliation");
-
-		people = spark
-			.read()
-			.textFile(workingDir + "/people")
-			.map(
-				(MapFunction<String, Person>) value -> OBJECT_MAPPER
-					.readValue(value, Person.class),
-				Encoders.bean(Person.class));
-
-		people.show(false);
-		people
-			.toJavaRDD()
-			.map(p -> new AtomicAction(p.getClass(), p))
-			.union(
-				getRelations(spark, workingDir + "/authorship").toJavaRDD().map(r -> new AtomicAction(r.getClass(), r)))
-			.union(
-				getRelations(spark, workingDir + "/coauthorship")
-					.toJavaRDD()
-					.map(r -> new AtomicAction(r.getClass(), r)))
-			.union(
-				getRelations(spark, workingDir + "/affiliation")
-					.toJavaRDD()
-					.map(r -> new AtomicAction(r.getClass(), r)))
-			.mapToPair(
-				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(
-				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 	}
 
 	private static Dataset<Relation> getRelations(SparkSession spark, String path) {

From 821540f94a0ae055c74cd642ec6921465465e8ae Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 22 Oct 2024 10:13:30 +0200
Subject: [PATCH 159/239] [personEntity] updated the property file to include
 also the db parameters. The same for the wf definition. Refactoring for
 compilation

---
 .../personentity/CoAuthorshipIterator.java    |  3 +-
 .../personentity/ExtractPerson.java           | 99 +++++++++----------
 .../personentity/as_parameters.json           | 25 +++++
 .../actionmanager/personentity/job.properties |  5 +-
 .../personentity/oozie_app/workflow.xml       | 16 +++
 .../orcid/ORCIDAuthorMatchersTest.scala       |  1 +
 6 files changed, 95 insertions(+), 54 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
index 94ac7ab28..131f3f466 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
@@ -61,8 +61,7 @@ public class CoAuthorshipIterator implements Iterator<Relation> {
 	private Relation getRelation(String orcid1, String orcid2) {
 		String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
 		String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
-		Relation relation =
-		OafMapperUtils
+		Relation relation = OafMapperUtils
 			.getRelation(
 				source, target, ModelConstants.PERSON_PERSON_RELTYPE,
 				ModelConstants.PERSON_PERSON_SUBRELTYPE,
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 960dfbe44..fb0621b6e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -13,9 +13,12 @@ import java.sql.SQLException;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.common.DbClient;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -27,13 +30,13 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.spark_project.jetty.util.StringUtil;
 
-
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.collection.orcid.model.Author;
 import eu.dnetlib.dhp.collection.orcid.model.Employment;
 import eu.dnetlib.dhp.collection.orcid.model.Work;
+import eu.dnetlib.dhp.common.DbClient;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -49,11 +52,6 @@ import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FSDataOutputStream;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
 public class ExtractPerson implements Serializable {
 	private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
 	private static final String QUERY = "SELECT * FROM project_person WHERE pid_type = 'ORCID'";
@@ -77,8 +75,7 @@ public class ExtractPerson implements Serializable {
 	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
 
 	public static List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
-			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
-
+		.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
 	public static final DataInfo DATAINFO = OafMapperUtils
 		.dataInfo(
@@ -136,14 +133,15 @@ public class ExtractPerson implements Serializable {
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
 				extractInfoForActionSetFromORCID(spark, inputPath, workingDir);
-				extractInfoForActionSetFromProjects(spark, inputPath, workingDir, dbUrl, dbUser, dbPassword, workingDir + "/project", hdfsNameNode);
+				extractInfoForActionSetFromProjects(
+					spark, inputPath, workingDir, dbUrl, dbUser, dbPassword, workingDir + "/project", hdfsNameNode);
 				createActionSet(spark, outputPath, workingDir);
 			});
 
 	}
 
 	private static void extractInfoForActionSetFromProjects(SparkSession spark, String inputPath, String workingDir,
-															String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode) throws IOException {
+		String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode) throws IOException {
 
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
@@ -164,41 +162,40 @@ public class ExtractPerson implements Serializable {
 
 	public static Relation getRelationWithProject(ResultSet rs) {
 		try {
-			return getProjectRelation(rs.getString("project"), rs.getString("pid"),
-					rs.getString("role"));
+			return getProjectRelation(
+				rs.getString("project"), rs.getString("pid"),
+				rs.getString("role"));
 		} catch (final SQLException e) {
 			throw new RuntimeException(e);
 		}
-    }
+	}
 
 	private static Relation getProjectRelation(String project, String orcid, String role) {
 
-			String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
-			String target = project.substring(0,14)
-					+ IdentifierFactory.md5(project.substring(15));
-			List<KeyValue> properties = new ArrayList<>();
+		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
+		String target = project.substring(0, 14)
+			+ IdentifierFactory.md5(project.substring(15));
+		List<KeyValue> properties = new ArrayList<>();
 
-			Relation relation = OafMapperUtils
-					.getRelation(
-							source, target, ModelConstants.PROJECT_PERSON_RELTYPE, ModelConstants.PROJECT_PERSON_SUBRELTYPE,
-							ModelConstants.PROJECT_PERSON_PARTICIPATES,
-							collectedfromOpenAIRE,
-							DATAINFO,
-							null);
-			relation.setValidated(true);
+		Relation relation = OafMapperUtils
+			.getRelation(
+				source, target, ModelConstants.PROJECT_PERSON_RELTYPE, ModelConstants.PROJECT_PERSON_SUBRELTYPE,
+				ModelConstants.PROJECT_PERSON_PARTICIPATES,
+				collectedfromOpenAIRE,
+				DATAINFO,
+				null);
+		relation.setValidated(true);
 
-			if (StringUtil.isNotBlank(role)) {
-				KeyValue kv = new KeyValue();
-				kv.setKey("role");
-				kv.setValue(role);
-				properties.add(kv);
-			}
-
-
-			if (!properties.isEmpty())
-				relation.setProperties(properties);
-			return relation;
+		if (StringUtil.isNotBlank(role)) {
+			KeyValue kv = new KeyValue();
+			kv.setKey("role");
+			kv.setValue(role);
+			properties.add(kv);
+		}
 
+		if (!properties.isEmpty())
+			relation.setProperties(properties);
+		return relation;
 
 	}
 
@@ -211,7 +208,7 @@ public class ExtractPerson implements Serializable {
 		}
 	}
 
-	private static void createActionSet(SparkSession spark,String outputPath, String workingDir) {
+	private static void createActionSet(SparkSession spark, String outputPath, String workingDir) {
 
 		Dataset<Person> people;
 		people = spark
@@ -221,7 +218,7 @@ public class ExtractPerson implements Serializable {
 				(MapFunction<String, Person>) value -> OBJECT_MAPPER
 					.readValue(value, Person.class),
 				Encoders.bean(Person.class));
-		
+
 		people
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
@@ -235,10 +232,10 @@ public class ExtractPerson implements Serializable {
 				getRelations(spark, workingDir + "/affiliation")
 					.toJavaRDD()
 					.map(r -> new AtomicAction(r.getClass(), r)))
-				.union(
-						getRelations(spark, workingDir + "/project")
-								.toJavaRDD()
-								.map(r -> new AtomicAction(r.getClass(), r)))
+			.union(
+				getRelations(spark, workingDir + "/project")
+					.toJavaRDD()
+					.map(r -> new AtomicAction(r.getClass(), r)))
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
 					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
@@ -276,7 +273,7 @@ public class ExtractPerson implements Serializable {
 			.joinWith(authors, employmentDataset.col("orcid").equalTo(authors.col("orcid")))
 			.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
 
-		//Mapping all the orcid profiles even if the profile has no visible works
+		// Mapping all the orcid profiles even if the profile has no visible works
 
 		authors.map((MapFunction<Author, Person>) op -> {
 			Person person = new Person();
@@ -509,13 +506,13 @@ public class ExtractPerson implements Serializable {
 				return null;
 		}
 		Relation relation = OafMapperUtils
-				.getRelation(
-						source, target, ModelConstants.RESULT_PERSON_RELTYPE,
-						ModelConstants.RESULT_PERSON_SUBRELTYPE,
-						ModelConstants.RESULT_PERSON_HASAUTHORED,
-						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						DATAINFO,
-						null);
+			.getRelation(
+				source, target, ModelConstants.RESULT_PERSON_RELTYPE,
+				ModelConstants.RESULT_PERSON_SUBRELTYPE,
+				ModelConstants.RESULT_PERSON_HASAUTHORED,
+				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
+				DATAINFO,
+				null);
 		relation.setValidated(true);
 		return relation;
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
index 5175552e7..1894a6beb 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/as_parameters.json
@@ -21,5 +21,30 @@
   "paramLongName": "workingDir",
   "paramDescription": "the hdfs name node",
   "paramRequired": false
+},
+  {
+    "paramName": "pu",
+    "paramLongName": "postgresUrl",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+
+  {
+    "paramName": "ps",
+    "paramLongName": "postgresUser",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },
+  {
+  "paramName": "pp",
+  "paramLongName": "postgresPassword",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
+},{
+  "paramName": "nn",
+  "paramLongName": "hdfsNameNode",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
 }
+
 ]
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
index d2269718c..ac63d8a68 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
@@ -1,2 +1,5 @@
 inputPath=/data/orcid_2023/tables/
-outputPath=/user/miriam.baglioni/peopleAS
\ No newline at end of file
+outputPath=/user/miriam.baglioni/peopleAS
+postgresUrl=jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus
+postgresUser=dnet'
+postgresPassword=dnetPwd
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml
index 166e7bb9c..5b613a76a 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/oozie_app/workflow.xml
@@ -9,6 +9,18 @@
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
         </property>
+        <property>
+            <name>postgresUrl</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>postgresUser</name>
+            <description>the path where to store the actionset</description>
+        </property>
+        <property>
+            <name>postgresPassword</name>
+            <description>the path where to store the actionset</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -102,6 +114,10 @@
             <arg>--inputPath</arg><arg>${inputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
             <arg>--workingDir</arg><arg>${workingDir}</arg>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <arg>--postgresUrl</arg><arg>${postgresUrl}</arg>
+            <arg>--postgresUser</arg><arg>${postgresUser}</arg>
+            <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
index 4e5ad5365..eece56b74 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
@@ -31,6 +31,7 @@ class ORCIDAuthorMatchersTest {
     assertTrue(matchOrderedTokenAndAbbreviations("孙林 Sun Lin", "Sun Lin"))
     // assertTrue(AuthorsMatchRevised.compare("孙林 Sun Lin", "孙林")); // not yet implemented
   }
+
   @Test def testDocumentationNames(): Unit = {
     assertTrue(matchOrderedTokenAndAbbreviations("James C. A. Miller-Jones", "James Antony Miller-Jones"))
   }

From aac5eb34995b6cf736c5a8dbdc67d66891a89992 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 22 Oct 2024 11:54:16 +0200
Subject: [PATCH 160/239] [personEntity] changed the data info for the
 relations with projects. added missing parameters to the job.properties file

---
 .../personentity/ExtractPerson.java           | 51 ++++++++-----------
 .../actionmanager/personentity/job.properties |  2 +-
 2 files changed, 22 insertions(+), 31 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index fb0621b6e..7b04d4d52 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -71,13 +71,15 @@ public class ExtractPerson implements Serializable {
 	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
 	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
 	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
+	public static final String FUNDER_AUTHORS_CLASSID = "sysimport:crosswalk:funderdatabase";
+	public static final String FUNDER_AUTHORS_CLASSNAME = "Imported from Funder Database";
 	public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
 	public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
 
 	public static List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
 		.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
-	public static final DataInfo DATAINFO = OafMapperUtils
+	public static final DataInfo ORCIDDATAINFO = OafMapperUtils
 		.dataInfo(
 			false,
 			null,
@@ -91,6 +93,20 @@ public class ExtractPerson implements Serializable {
 					ModelConstants.DNET_PROVENANCE_ACTIONS),
 			"0.91");
 
+	public static final DataInfo FUNDERDATAINFO = OafMapperUtils
+			.dataInfo(
+					false,
+					null,
+					false,
+					false,
+					OafMapperUtils
+							.qualifier(
+									FUNDER_AUTHORS_CLASSID,
+									FUNDER_AUTHORS_CLASSNAME,
+									ModelConstants.DNET_PROVENANCE_ACTIONS,
+									ModelConstants.DNET_PROVENANCE_ACTIONS),
+					"0.91");
+
 	public static void main(final String[] args) throws IOException, ParseException {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -182,7 +198,7 @@ public class ExtractPerson implements Serializable {
 				source, target, ModelConstants.PROJECT_PERSON_RELTYPE, ModelConstants.PROJECT_PERSON_SUBRELTYPE,
 				ModelConstants.PROJECT_PERSON_PARTICIPATES,
 				collectedfromOpenAIRE,
-				DATAINFO,
+					FUNDERDATAINFO,
 				null);
 		relation.setValidated(true);
 
@@ -328,7 +344,7 @@ public class ExtractPerson implements Serializable {
 							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null));
 			person.setDateofcollection(op.getLastModifiedDate());
 			person.setOriginalId(Arrays.asList(op.getOrcid()));
-			person.setDataInfo(DATAINFO);
+			person.setDataInfo(ORCIDDATAINFO);
 			return person;
 		}, Encoders.bean(Person.class))
 			.write()
@@ -415,7 +431,7 @@ public class ExtractPerson implements Serializable {
 				source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE,
 				ModelConstants.ORG_PERSON_PARTICIPATES,
 				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				DATAINFO,
+					ORCIDDATAINFO,
 				null);
 		relation.setValidated(true);
 
@@ -438,31 +454,6 @@ public class ExtractPerson implements Serializable {
 
 	}
 
-	private static Collection<? extends Relation> getCoAuthorshipRelations(String orcid1, String orcid2) {
-		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid1);
-		String target = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid2);
-
-		return Arrays
-			.asList(
-				OafMapperUtils
-					.getRelation(
-						source, target, ModelConstants.PERSON_PERSON_RELTYPE,
-						ModelConstants.PERSON_PERSON_SUBRELTYPE,
-						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						DATAINFO,
-						null),
-				OafMapperUtils
-					.getRelation(
-						target, source, ModelConstants.PERSON_PERSON_RELTYPE,
-						ModelConstants.PERSON_PERSON_SUBRELTYPE,
-						ModelConstants.PERSON_PERSON_HASCOAUTHORED,
-						Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-						DATAINFO,
-						null));
-
-	}
-
 	private static @NotNull Iterator<Relation> getAuthorshipRelationIterator(Work w) {
 
 		if (Optional.ofNullable(w.getPids()).isPresent())
@@ -511,7 +502,7 @@ public class ExtractPerson implements Serializable {
 				ModelConstants.RESULT_PERSON_SUBRELTYPE,
 				ModelConstants.RESULT_PERSON_HASAUTHORED,
 				Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
-				DATAINFO,
+					ORCIDDATAINFO,
 				null);
 		relation.setValidated(true);
 		return relation;
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
index ac63d8a68..b9325bcb7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/personentity/job.properties
@@ -1,5 +1,5 @@
 inputPath=/data/orcid_2023/tables/
 outputPath=/user/miriam.baglioni/peopleAS
 postgresUrl=jdbc:postgresql://beta.services.openaire.eu:5432/dnet_openaireplus
-postgresUser=dnet'
+postgresUser=dnet
 postgresPassword=dnetPwd
\ No newline at end of file

From 0e34b0ece13f4d6dfeb5a4f0cb274168327c954a Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Mon, 21 Oct 2024 09:05:13 +0200
Subject: [PATCH 161/239] Fix imports: point them from the main distribution
 packages

---
 .../src/test/java/eu/dnetlib/pace/util/UtilTest.java        | 1 -
 .../dhp/actionmanager/personentity/ExtractPerson.java       | 6 +++---
 .../eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala   | 2 +-
 .../scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala   | 2 +-
 .../main/scala/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala   | 2 +-
 .../src/main/java/eu/dnetlib/dhp/api/Utils.java             | 4 ++--
 .../java/eu/dnetlib/dhp/bulktag/community/Constraint.java   | 2 +-
 .../dhp/oa/graph/hive/GraphHiveTableImporterJob.java        | 6 +++---
 .../main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java  | 2 +-
 9 files changed, 13 insertions(+), 14 deletions(-)

diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java
index be5c1ebb9..93db552c1 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/util/UtilTest.java
@@ -11,7 +11,6 @@ import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 import eu.dnetlib.pace.model.Person;
-import jdk.nashorn.internal.ir.annotations.Ignore;
 
 public class UtilTest {
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index e63a50984..debf7e38e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -11,6 +11,7 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.io.compress.BZip2Codec;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -20,7 +21,6 @@ import org.apache.spark.sql.*;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.spark_project.jetty.util.StringUtil;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -317,13 +317,13 @@ public class ExtractPerson implements Serializable {
 						"0.91"),
 				null);
 
-		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
+		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtils.isNotBlank(row.getStartDate())) {
 			KeyValue kv = new KeyValue();
 			kv.setKey("startDate");
 			kv.setValue(row.getStartDate());
 			properties.add(kv);
 		}
-		if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
+		if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtils.isNotBlank(row.getEndDate())) {
 			KeyValue kv = new KeyValue();
 			kv.setKey("endDate");
 			kv.setValue(row.getEndDate());
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index 7c45234f6..e7d68920b 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -14,7 +14,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.{
   PidType
 }
 import eu.dnetlib.dhp.utils.DHPUtils
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 import org.apache.spark.sql.Row
 import org.json4s
 import org.json4s.DefaultFormats
diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
index d8292a631..a2c36041d 100644
--- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
@@ -7,7 +7,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactor
 import eu.dnetlib.dhp.utils.DHPUtils
 import eu.dnetlib.doiboost.DoiBoostMappingUtil
 import eu.dnetlib.doiboost.DoiBoostMappingUtil._
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 import org.json4s
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST._
diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
index 7c58afc09..6ec75f5c3 100644
--- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
+++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala
@@ -6,7 +6,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
 import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
 import eu.dnetlib.doiboost.DoiBoostMappingUtil
 import eu.dnetlib.doiboost.DoiBoostMappingUtil.{createSP, generateDataInfo}
-import org.apache.commons.lang.StringUtils
+import org.apache.commons.lang3.StringUtils
 import org.json4s
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST._
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
index 27fb37e5b..6079da365 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
@@ -6,11 +6,11 @@ import java.io.Serializable;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import org.apache.commons.lang3.StringUtils;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.amazonaws.util.StringUtils;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Maps;
 
@@ -81,7 +81,7 @@ public class Utils implements Serializable {
 		Community c = new Community();
 		c.setId(cm.getId());
 		c.setZenodoCommunities(cm.getOtherZenodoCommunities());
-		if (!StringUtils.isNullOrEmpty(cm.getZenodoCommunity()))
+		if (StringUtils.isNotBlank(cm.getZenodoCommunity()))
 			c.getZenodoCommunities().add(cm.getZenodoCommunity());
 		c.setSubjects(cm.getSubjects());
 		c.getSubjects().addAll(cm.getFos());
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java
index 82a6a3b85..51525e4d3 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/Constraint.java
@@ -4,7 +4,7 @@ package eu.dnetlib.dhp.bulktag.community;
 import java.io.Serializable;
 import java.lang.reflect.InvocationTargetException;
 
-import org.apache.htrace.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 
 import eu.dnetlib.dhp.bulktag.criteria.Selection;
 import eu.dnetlib.dhp.bulktag.criteria.VerbResolver;
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
index 73243dbc5..d4fec3f52 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hive/GraphHiveTableImporterJob.java
@@ -72,9 +72,9 @@ public class GraphHiveTableImporterJob {
 		final Encoder<T> clazzEncoder = Encoders.bean(clazz);
 
 		Dataset<Row> dataset = spark
-				.read()
-				.schema(clazzEncoder.schema())
-				.json(inputPath);
+			.read()
+			.schema(clazzEncoder.schema())
+			.json(inputPath);
 
 		if (numPartitions > 0) {
 			log.info("repartitioning {} to {} partitions", clazz.getSimpleName(), numPartitions);
diff --git a/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java b/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java
index 5e705716c..0461e2f94 100644
--- a/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java
+++ b/dhp-workflows/dhp-swh/src/main/java/eu/dnetlib/dhp/swh/models/LastVisitData.java
@@ -3,8 +3,8 @@ package eu.dnetlib.dhp.swh.models;
 
 import java.io.Serializable;
 
-import com.cloudera.com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonProperty;
 
 @JsonIgnoreProperties(ignoreUnknown = true)
 public class LastVisitData implements Serializable {

From aa7b8fd014f8b1a3855330806efa40cec1fc11d6 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Mon, 21 Oct 2024 18:05:01 +0200
Subject: [PATCH 162/239] Use workingDir parameter for temporary data of ORCID
 enrichment

---
 .../enrich/orcid/enrich_graph_orcid_parameters.json  |  6 ++++++
 .../orcid/SparkEnrichGraphWithOrcidAuthors.scala     | 12 +++++++-----
 2 files changed, 13 insertions(+), 5 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json
index 765c0e8ff..772e1381f 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/enrich_graph_orcid_parameters.json
@@ -22,5 +22,11 @@
     "paramLongName": "targetPath",
     "paramDescription": "the output path of the graph enriched",
     "paramRequired": true
+  },
+  {
+    "paramName": "wp",
+    "paramLongName": "workingDir",
+    "paramDescription": "the working dir",
+    "paramRequired": true
   }
 ]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala
index 0824c2a71..847a5f090 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala
@@ -47,13 +47,15 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String]
     log.info(s"orcidPath is '$orcidPath'")
     val targetPath = parser.get("targetPath")
     log.info(s"targetPath is '$targetPath'")
+    val workingDir = parser.get("workingDir")
+    log.info(s"targetPath is '$workingDir'")
 
-    createTemporaryData(graphPath, orcidPath, targetPath)
-    analisys(targetPath)
-    generateGraph(graphPath, targetPath)
+    createTemporaryData(graphPath, orcidPath, workingDir)
+    analisys(workingDir)
+    generateGraph(graphPath, workingDir, targetPath)
   }
 
-  private def generateGraph(graphPath: String, targetPath: String): Unit = {
+  private def generateGraph(graphPath: String, workingDir: String, targetPath: String): Unit = {
 
     ModelSupport.entityTypes.asScala
       .filter(e => ModelSupport.isResult(e._1))
@@ -63,7 +65,7 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String]
 
         val matched = spark.read
           .schema(Encoders.bean(classOf[ORCIDAuthorEnricherResult]).schema)
-          .parquet(s"${targetPath}/${resultType}_matched")
+          .parquet(s"${workingDir}/${resultType}_matched")
           .selectExpr("id", "enriched_author")
 
         spark.read

From 6bc741715c08a4b71e3b737b3d8befdbfa743aab Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Wed, 23 Oct 2024 14:01:12 +0200
Subject: [PATCH 163/239] Fix OafMapperUtilsTest.testMergePubs

---
 .../eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
index 9317c0ce4..1ee8e52de 100644
--- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
+++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
@@ -179,7 +179,7 @@ class OafMapperUtilsTest {
 		assertEquals(
 			ModelConstants.DATASET_RESULTTYPE_CLASSID,
 			((Result) MergeUtils
-				.merge(p2, d1))
+				.merge(p2, d1, true))
 					.getResulttype()
 					.getClassid());
 	}

From c921cf7ee033053eaf00ccf876e3bb2edc8bfa3e Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 09:57:20 +0200
Subject: [PATCH 164/239] [personEntity] removed the deletedbyinference results
 (not indexed, but still in the graph). Changed the writing mode: append
 instead of overwrite

---
 .../common/person}/CoAuthorshipIterator.java  |  2 +-
 .../dnetlib/dhp/common/person}/Coauthors.java |  5 +-
 .../personentity/ExtractPerson.java           |  2 +
 dhp-workflows/dhp-enrichment/pom.xml          |  7 +-
 .../input_personpropagation_parameters.json   | 21 ++++++
 .../dhp/wf/subworkflows/person/job.properties |  1 +
 .../person/oozie_app/config-default.xml       | 58 ++++++++++++++++
 .../person/oozie_app/workflow.xml             | 68 +++++++++++++++++++
 8 files changed, 153 insertions(+), 11 deletions(-)
 rename {dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity => dhp-common/src/main/java/eu/dnetlib/dhp/common/person}/CoAuthorshipIterator.java (98%)
 rename {dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity => dhp-common/src/main/java/eu/dnetlib/dhp/common/person}/Coauthors.java (70%)
 create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/input_personpropagation_parameters.json
 create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/job.properties
 create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/config-default.xml
 create mode 100644 dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/workflow.xml

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/person/CoAuthorshipIterator.java
similarity index 98%
rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
rename to dhp-common/src/main/java/eu/dnetlib/dhp/common/person/CoAuthorshipIterator.java
index 131f3f466..853f223d0 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/CoAuthorshipIterator.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/person/CoAuthorshipIterator.java
@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.actionmanager.personentity;
+package eu.dnetlib.dhp.common.person;
 
 import java.util.Arrays;
 import java.util.Iterator;
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/person/Coauthors.java
similarity index 70%
rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
rename to dhp-common/src/main/java/eu/dnetlib/dhp/common/person/Coauthors.java
index 17f46d5c7..ff9324d2e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/Coauthors.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/person/Coauthors.java
@@ -1,12 +1,9 @@
 
-package eu.dnetlib.dhp.actionmanager.personentity;
+package eu.dnetlib.dhp.common.person;
 
 import java.io.Serializable;
-import java.util.ArrayList;
 import java.util.List;
 
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
 public class Coauthors implements Serializable {
 	private List<String> coauthors;
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 7b04d4d52..3ee89e772 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -13,6 +13,8 @@ import java.sql.SQLException;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.common.person.CoAuthorshipIterator;
+import eu.dnetlib.dhp.common.person.Coauthors;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.conf.Configuration;
diff --git a/dhp-workflows/dhp-enrichment/pom.xml b/dhp-workflows/dhp-enrichment/pom.xml
index 9698dee03..41f57e6df 100644
--- a/dhp-workflows/dhp-enrichment/pom.xml
+++ b/dhp-workflows/dhp-enrichment/pom.xml
@@ -48,12 +48,7 @@
             <groupId>io.github.classgraph</groupId>
             <artifactId>classgraph</artifactId>
         </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-aggregation</artifactId>
-            <version>1.2.5-SNAPSHOT</version>
-            <scope>compile</scope>
-        </dependency>
+
 
 
     </dependencies>
diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/input_personpropagation_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/input_personpropagation_parameters.json
new file mode 100644
index 000000000..df65d5320
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/input_personpropagation_parameters.json
@@ -0,0 +1,21 @@
+[
+  {
+    "paramName":"s",
+    "paramLongName":"sourcePath",
+    "paramDescription": "the path of the sequencial file to read",
+    "paramRequired": true
+  },
+  {
+    "paramName": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path used to store temporary output files",
+    "paramRequired": true
+  },
+
+  {
+    "paramName": "ssm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "true if the spark session is managed, false otherwise",
+    "paramRequired": false
+  }
+]
diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/job.properties b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/job.properties
new file mode 100644
index 000000000..61bd3d121
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/job.properties
@@ -0,0 +1 @@
+sourcePath=/tmp/miriam/13_graph_copy
\ No newline at end of file
diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/config-default.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/config-default.xml
new file mode 100644
index 000000000..1cb0b8a5e
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/config-default.xml
@@ -0,0 +1,58 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>sparkDriverMemory</name>
+        <value>15G</value>
+    </property>
+    <property>
+        <name>sparkExecutorMemory</name>
+        <value>5G</value>
+    </property>
+    <property>
+        <name>sparkExecutorCores</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>spark2MaxExecutors</name>
+        <value>50</value>
+    </property>
+</configuration>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/workflow.xml
new file mode 100644
index 000000000..c9b914384
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/person/oozie_app/workflow.xml
@@ -0,0 +1,68 @@
+<workflow-app name="person_propagation" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sourcePath</name>
+            <description>the source path</description>
+        </property>
+
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="reset_outputpath"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="reset_outputpath">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="extract_person_relation_from_graph"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="extract_person_relation_from_graph">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>personPropagation</name>
+            <class>eu.dnetlib.dhp.person.SparkExtractPersonRelations</class>
+            <jar>dhp-enrichment-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.speculation=false
+                --conf spark.hadoop.mapreduce.map.speculative=false
+                --conf spark.hadoop.mapreduce.reduce.speculative=false
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}/</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+    <end name="End"/>
+
+</workflow-app>
\ No newline at end of file

From cf07ed90584b8d792f7868f325404eb35fbd3fbf Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 14:35:14 +0200
Subject: [PATCH 165/239] [person] refactoring

---
 .../person/SparkExtractPersonRelations.java   | 271 ++++++++++++++++++
 1 file changed, 271 insertions(+)
 create mode 100644 dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
new file mode 100644
index 000000000..34bd976ea
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
@@ -0,0 +1,271 @@
+
+package eu.dnetlib.dhp.person;
+
+import static com.ibm.icu.text.PluralRules.Operand.w;
+import static eu.dnetlib.dhp.PropagationConstant.*;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+import java.util.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SaveMode;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.person.CoAuthorshipIterator;
+import eu.dnetlib.dhp.common.person.Coauthors;
+import eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import scala.Tuple2;
+
+public class SparkExtractPersonRelations {
+
+	private static final Logger log = LoggerFactory.getLogger(SparkCountryPropagationJob.class);
+	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
+
+	public static final DataInfo DATAINFO = OafMapperUtils
+		.dataInfo(
+			false,
+			"openaire",
+			true,
+			false,
+			OafMapperUtils
+				.qualifier(
+					ModelConstants.SYSIMPORT_CROSSWALK_REPOSITORY,
+					ModelConstants.SYSIMPORT_CROSSWALK_REPOSITORY,
+					ModelConstants.DNET_PROVENANCE_ACTIONS,
+					ModelConstants.DNET_PROVENANCE_ACTIONS),
+			"0.85");
+
+	public static void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				SparkCountryPropagationJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/wf/subworkflows/person/input_personpropagation_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		String sourcePath = parser.get("sourcePath");
+		log.info("sourcePath: {}", sourcePath);
+
+		final String workingPath = parser.get("outputPath");
+		log.info("workingPath: {}", workingPath);
+
+		SparkConf conf = new SparkConf();
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+
+				extractRelations(
+					spark,
+					sourcePath,
+					workingPath);
+			});
+	}
+
+	private static void extractRelations(SparkSession spark, String sourcePath, String workingPath) {
+
+		Dataset<Tuple2<String, Relation>> relationDataset = spark
+			.read()
+			.schema(Encoders.bean(Relation.class).schema())
+			.json(sourcePath + "relation")
+			.as(Encoders.bean(Relation.class))
+			.map(
+				(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(
+					r.getSource() + r.getRelClass() + r.getTarget(), r),
+				Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class)));
+
+		ModelSupport.entityTypes
+			.keySet()
+			.stream()
+			.filter(ModelSupport::isResult)
+			.forEach(
+				e -> {
+					// 1. search for results having orcid_pending and orcid in the set of pids for the authors
+					Dataset<Result> resultWithOrcids = spark
+						.read()
+						.schema(Encoders.bean(Result.class).schema())
+						.json(sourcePath + e.name())
+						.as(Encoders.bean(Result.class))
+						.filter(
+							(FilterFunction<Result>) r -> !r.getDataInfo().getDeletedbyinference() &&
+								!r.getDataInfo().getInvisible() &&
+								Optional
+									.ofNullable(r.getAuthor())
+									.isPresent())
+						.filter(
+							(FilterFunction<Result>) r -> r
+								.getAuthor()
+								.stream()
+								.anyMatch(
+									a -> Optional
+										.ofNullable(
+											a
+												.getPid())
+										.isPresent() &&
+										a
+											.getPid()
+											.stream()
+											.anyMatch(
+												p -> Arrays
+													.asList("orcid", "orcid_pending")
+													.contains(p.getQualifier().getClassid().toLowerCase()))));
+					// 2. create authorship relations between the result identifier and the person entity with
+					// orcid_pending.
+					Dataset<Tuple2<String, Relation>> newRelations = resultWithOrcids
+						.flatMap(
+							(FlatMapFunction<Result, Relation>) r -> getAuthorshipRelations(r),
+							Encoders.bean(Relation.class))
+						.map(
+							(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(
+								r.getSource() + r.getRelClass() + r.getTarget(), r),
+							Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class)));
+					newRelations
+						.joinWith(relationDataset, newRelations.col("_1").equalTo(relationDataset.col("_1")), "left")
+						.map((MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, Relation>>, Relation>) t2 -> {
+							if (t2._2() == null)
+								return t2._1()._2();
+							return null;
+						}, Encoders.bean(Relation.class))
+						.filter((FilterFunction<Relation>) r -> r != null)
+						.write()
+						.mode(SaveMode.Append)
+						.option("compression", "gzip")
+						.json(workingPath);
+
+					// 2.1 store in a separate location the relation between the person and the pids for the result?
+
+					// 3. create co_authorship relations between the pairs of authors with orcid/orcid_pending pids
+					newRelations = resultWithOrcids
+						.map((MapFunction<Result, Coauthors>) r -> getAuthorsPidList(r), Encoders.bean(Coauthors.class))
+						.flatMap(
+							(FlatMapFunction<Coauthors, Relation>) c -> new CoAuthorshipIterator(c.getCoauthors()),
+							Encoders.bean(Relation.class))
+						.groupByKey(
+							(MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
+						.mapGroups(
+							(MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(),
+							Encoders.bean(Relation.class))
+						.map(
+							(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(
+								r.getSource() + r.getRelClass() + r.getTarget(), r),
+							Encoders.tuple(Encoders.STRING(), Encoders.bean(Relation.class)));
+					newRelations
+						.joinWith(relationDataset, newRelations.col("_1").equalTo(relationDataset.col("_1")), "left")
+						.map((MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, Relation>>, Relation>) t2 -> {
+							if (t2._2() == null)
+								return t2._1()._2();
+							return null;
+						}, Encoders.bean(Relation.class))
+						.filter((FilterFunction<Relation>) r -> r != null)
+						.write()
+						.mode(SaveMode.Append)
+						.option("compression", "gzip")
+						.json(workingPath);
+
+				});
+		spark
+			.read()
+			.schema(Encoders.bean(Relation.class).schema())
+			.json(workingPath)
+			.write()
+			.mode(SaveMode.Append)
+			.option("compression", "gzip")
+			.json(sourcePath + "relation");
+
+	}
+
+	private static Coauthors getAuthorsPidList(Result r) {
+		Coauthors coauth = new Coauthors();
+		coauth
+			.setCoauthors(
+				r
+					.getAuthor()
+					.stream()
+					.filter(
+						a -> a
+							.getPid()
+							.stream()
+							.anyMatch(
+								p -> Arrays.asList("orcid", "orcid_pending").contains(p.getQualifier().getClassid())))
+					.map(a -> {
+						Optional<StructuredProperty> tmp = a
+							.getPid()
+							.stream()
+							.filter(p -> p.getQualifier().getClassid().equalsIgnoreCase("orcid"))
+							.findFirst();
+						if (tmp.isPresent())
+							return tmp.get().getValue();
+						tmp = a
+							.getPid()
+							.stream()
+							.filter(p -> p.getQualifier().getClassid().equalsIgnoreCase("orcid_pending"))
+							.findFirst();
+						if (tmp.isPresent())
+							return tmp.get().getValue();
+
+						return null;
+					})
+					.filter(Objects::nonNull)
+					.collect(Collectors.toList()));
+		return coauth;
+
+	}
+
+	private static Iterator<Relation> getAuthorshipRelations(Result r) {
+		List<Relation> relationList = new ArrayList<>();
+		for (Author a : r.getAuthor())
+
+			relationList.addAll(a.getPid().stream().map(p -> {
+
+				if (p.getQualifier().getClassid().equalsIgnoreCase("orcid_pending"))
+					return getRelation(p.getValue(), r.getId());
+				return null;
+			})
+				.filter(Objects::nonNull)
+				.collect(Collectors.toList()));
+
+		return relationList.iterator();
+	}
+
+	private static Relation getRelation(String orcid, String resultId) {
+
+		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
+
+		Relation relation = OafMapperUtils
+			.getRelation(
+				source, resultId, ModelConstants.RESULT_PERSON_RELTYPE,
+				ModelConstants.RESULT_PERSON_SUBRELTYPE,
+				ModelConstants.RESULT_PERSON_HASAUTHORED,
+				null, // collectedfrom = null
+				DATAINFO,
+				null);
+
+		return relation;
+	}
+
+}

From c773421cc73531dce34ee869f5dce44296ea425c Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 14:44:13 +0200
Subject: [PATCH 166/239] [person] added new substep in propagation worflow
 main

---
 .../dnetlib/dhp/wf/main/oozie_app/import.txt  |  3 ++-
 .../dhp/wf/main/oozie_app/workflow.xml        | 19 ++++++++++++++++++-
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/import.txt
index b20259414..8922b6ac6 100644
--- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/import.txt
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/import.txt
@@ -7,4 +7,5 @@ community_organization classpath eu/dnetlib/dhp/wf/subworkflows/resulttocommunit
 result_project classpath eu/dnetlib/dhp/wf/subworkflows/projecttoresult/oozie_app
 community_project classpath eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromproject/oozie_app
 community_sem_rel classpath eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/oozie_app
-country_propagation classpath eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app
\ No newline at end of file
+country_propagation classpath eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app
+person_propagation classpath eu/dnetlib/dhp/wf/subworkflows/person/oozie_app
\ No newline at end of file
diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml
index 8e91707b6..4351cd595 100644
--- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml
@@ -122,6 +122,7 @@
             <case to="community_project">${wf:conf('resumeFrom') eq 'CommunityProject'}</case>
             <case to="community_sem_rel">${wf:conf('resumeFrom') eq 'CommunitySemanticRelation'}</case>
             <case to="country_propagation">${wf:conf('resumeFrom') eq 'CountryPropagation'}</case>
+            <case to="person_propagation">${wf:conf('resumeFrom') eq 'PersonPropagation'}</case>
             <default to="orcid_propagation"/>
         </switch>
     </decision>
@@ -291,10 +292,24 @@
                 </property>
             </configuration>
         </sub-workflow>
+        <ok to="person_propagation" />
+        <error to="Kill" />
+    </action>
+    <action name="person_propagation">
+        <sub-workflow>
+            <app-path>${wf:appPath()}/person_propagation
+            </app-path>
+            <propagate-configuration/>
+            <configuration>
+                <property>
+                    <name>sourcePath</name>
+                    <value>${outputPath}</value>
+                </property>
+            </configuration>
+        </sub-workflow>
         <ok to="country_propagation" />
         <error to="Kill" />
     </action>
-
     <action name="country_propagation">
         <sub-workflow>
             <app-path>${wf:appPath()}/country_propagation
@@ -319,6 +334,8 @@
         <error to="Kill" />
     </action>
 
+
+
     <end name="End"/>
 
 </workflow-app>

From 01679c935a96c796a45eac96a7e15e5ea44f312d Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 15:27:06 +0200
Subject: [PATCH 167/239] [person] added test class to be implemented

---
 .../dhp/person/PersonPropagationJobTest.java  | 95 +++++++++++++++++++
 .../dhp/person/graph/dataset/part-00000       |  0
 .../graph/otherresearchproduct/part-00000     |  0
 .../dhp/person/graph/publication/part-00000   |  0
 .../dhp/person/graph/relation/part-00000      |  1 +
 .../dhp/person/graph/software/part-00000      |  0
 6 files changed, 96 insertions(+)
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/person/PersonPropagationJobTest.java
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/dataset/part-00000
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/software/part-00000

diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/person/PersonPropagationJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/person/PersonPropagationJobTest.java
new file mode 100644
index 000000000..43f913d3d
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/person/PersonPropagationJobTest.java
@@ -0,0 +1,95 @@
+
+package eu.dnetlib.dhp.person;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.ArrayList;
+import java.util.List;
+
+import eu.dnetlib.dhp.schema.oaf.*;
+import org.apache.commons.io.FileUtils;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob;
+import scala.Tuple2;
+
+public class PersonPropagationJobTest {
+
+	private static final Logger log = LoggerFactory.getLogger(PersonPropagationJobTest.class);
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files.createTempDirectory(PersonPropagationJobTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(PersonPropagationJobTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(PersonPropagationJobTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testPersonPropagation() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/personpropagation/graph")
+			.getPath();
+
+		SparkExtractPersonRelations
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+					"--outputPath", workingDir.toString()
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.textFile(workingDir.toString() + "/relation")
+			.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
+
+		//TODO write assertions and find relevant information for hte resource files
+	}
+
+
+
+}
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/dataset/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/dataset/part-00000
new file mode 100644
index 000000000..e69de29bb
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000
new file mode 100644
index 000000000..e69de29bb
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000
new file mode 100644
index 000000000..e69de29bb
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000
new file mode 100644
index 000000000..a17560e55
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000
@@ -0,0 +1 @@
+{"clazz":"eu.dnetlib.dhp.schema.oaf.Relation","payload":{"collectedfrom":[{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.91","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:orcid","classname":"Imported from ORCID","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":null,"relType":"personPerson","subRelType":"coAuthorship","relClass":"hasCoAuthor","source":"30|orcid_______::028da52095190c6573d6bf9dba4c8ede","target":"30|orcid_______::8791a84ea413592878d6fe191f0ed35f","validated":true,"validationDate":null,"properties":[]}}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/software/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/software/part-00000
new file mode 100644
index 000000000..e69de29bb

From a7699558ed38382618911b1d7bca62f9e738d36d Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 16:15:12 +0200
Subject: [PATCH 168/239] [person] -

---
 .../java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java | 2 ++
 .../eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000 | 1 +
 2 files changed, 3 insertions(+)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
index 34bd976ea..6caeef478 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
@@ -140,6 +140,8 @@ public class SparkExtractPersonRelations {
 						.flatMap(
 							(FlatMapFunction<Result, Relation>) r -> getAuthorshipRelations(r),
 							Encoders.bean(Relation.class))
+//							.groupByKey((MapFunction<Relation, String>) r-> r.getSource()+r.getTarget(), Encoders.STRING() )
+//							.mapGroups((MapGroupsFunction<String, Relation, Relation>) (k,it) -> it.next(), Encoders.bean(Relation.class) )
 						.map(
 							(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(
 								r.getSource() + r.getRelClass() + r.getTarget(), r),
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000
index e69de29bb..47a3fdccb 100644
--- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/otherresearchproduct/part-00000
@@ -0,0 +1 @@
+{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "resourcetype": {"classid": "Taxonomic treatment", "classname": "Taxonomic treatment", "schemename": "dnet:dataCite_resource", "schemeid": "dnet:dataCite_resource"}, "pid": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.5281/zenodo.10249277"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.5281/zenodo.10249277"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.5281/zenodo.10249277"}], "bestaccessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "relevantdate": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "issued", "classname": "issued", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2023-11-28"}], "contributor": [], "id": "50|doi_________::fa6db8629c4a8d13ec21e445b309d1c8", "description": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "11.1 Saltia papposa (Forrsk.) Moq., Prodr. [A. P. de Candolle] 13(2): 325. 1849 \\u2261 Achyranthes papposa Forssk., Fl. Aegypt.-Arab.: 48. 1775. Lectotype (designate here): \\u2014 YEMEN. Zabid, s.d., Forssk\\u00e5l 205 (C10001569!, image of the lectotype available at https://plants.jstor. org/stable/viewer/10.5555/al.ap.specimen.c10001569?page=1); isolectotypes: C10001570! (image of the isolectotype available at https://plants.jstor.org/stable/viewer/10.5555/al.ap.specimen.c10001570?page=1) and BM000950560! (image of the isolectotype available at https://data.nhm.ac.uk/object/c634a45c-983a-42f3-9c4d-1d1b06f5f88b/1691539200000). Typification of the name Achyranthes papposa:\\u2014 Forssk\\u00e5l (1775: 48) published Achyranthes papposa by giving a short diagnosis (\\u201c foliis alternis; crassiusculis; lineari-cuneatis, obtusis \\u201d) and a detailed description; the provenance [\\u201c Zeb\\u00edd \\u201d (currently Zabid), a city of W-Yemen] is reported [see also Forssk\\u00e5l (1775: CVII) who indicated \\u201cMi.\\u201d as provenance of A. papposa, \\u201cMi.\\u201d meaning \\u201cMontium Regionis Inferior\\u201d (Forssk\\u00e5l 1775: CI)]. We traced two specimens at C, where Forsskal\\u2019s herbarium and types are mostly preserved (HUH Index of Botanists 2013c), i.e. viz. C10001569 and C10001570, both collected at Zabid; a further specimen is kept at BM (BM000950560) and it was annotated by Frank Nigel Hepper as an isotype. These three specimens are part of the original material for A. papposa (see also Hepper & Friis 1994). C10001569 bears a branch of a plant with more flowers than in C10001570. Since the morphology of the flowers is important to identify Saltia papposa (Townsend 1993), we here designate C10001569 as the lectotype of A. papposa. C10001570 and BM000950560 are isolectotypes. Chorology:\\u2015 Endemic to the Arabian Peninsula (Saudi Arabia and Yemen; POWO 2023). Occurrence in Saudi Arabia:\\u2015 Doubtfully in Makkah (Miller & Cope 1996). We did not trace any specimen collected in Saudi Arabia, but it is not impossible that Saltia papposa occurs in the country, probably in the south-eastern coastal area (Jazan?) (see also Ghazanfar & Fisher 2013: 178\\u2013179)."}], "eoscifguidelines": [], "author": [{"surname": "Hassan", "name": "Walaa A.", "pid": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "orcid_pending", "classname": "Open Researcher and Contributor ID", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "0000-0001-7605-9058"}], "rank": 1, "affiliation": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef, Egypt & azmeyw @ gmail. com; https: // orcid. org / 0000 - 0001 - 7605 - 9058"}], "fullname": "Hassan, Walaa A."}, {"surname": "Al-Shaye", "name": "Najla A.", "pid": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "orcid_pending", "classname": "Open Researcher and Contributor ID", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "0000-0002-0447-8613"}], "rank": 2, "affiliation": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia & naaalshaye @ pnu. edu. sa; https: // orcid. org / 0000 - 0002 - 0447 - 8613"}], "fullname": "Al-Shaye, Najla A."}, {"surname": "Iamonico", "name": "Duilio", "pid": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "orcid_pending", "classname": "Open Researcher and Contributor ID", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "0000-0001-5491-7568"}], "rank": 3, "affiliation": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "Department of Environmental Biology, Univeristy of Rome Sapienza, 00185 Rome, Italy & duilio. iamonico @ uniroma 1. it; https: // orcid. org / 0000 - 0001 - 5491 - 7568"}], "fullname": "Iamonico, Duilio"}], "contactgroup": [], "collectedfrom": [{"value": "ZENODO", "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69"}], "instance": [{"refereed": {"classid": "0002", "classname": "nonPeerReviewed", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"value": "ZENODO", "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69"}, "license": {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "CC 0"}, "url": ["http://dx.doi.org/10.5281/zenodo.10249277", "http://treatment.plazi.org/id/97224201FFE29001FF4C6AB685F912EB"], "pid": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.5281/zenodo.10249277"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.5281/zenodo.10249277"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.5281/zenodo.10249277"}], "instanceTypeMapping": [{"originalType": "Taxonomic treatment", "vocabularyName": "openaire::coar_resource_types_3_1"}], "alternateIdentifier": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "oai", "classname": "Open Archives Initiative", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "oai:zenodo.org:10249277"}], "dateofacceptance": {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "2023-11-28"}, "collectedfrom": {"value": "ZENODO", "key": "10|opendoar____::358aee4cc897452c00244351e4d91f69"}, "accessright": {"classid": "OPEN", "classname": "Open Access", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0020", "classname": "Other ORP type", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}], "dateofcollection": "2023-12-21T22:24:48+0000", "fulltext": [], "dateoftransformation": "2024-01-18T06:50:15.691Z", "dateofacceptance": {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "2023-11-28"}, "format": [], "tool": [], "subject": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Tracheophyta"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Magnoliopsida"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Amaranthaceae"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Saltia"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Saltia papposa"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Biodiversity"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Plantae"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Caryophyllales"}, {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "keyword", "classname": "keyword", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "Taxonomy"}], "coverage": [], "externalReference": [], "publisher": {"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "value": "Zenodo"}, "lastupdatetimestamp": 1721832280654, "language": {"classid": "und", "classname": "Undetermined", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "resulttype": {"classid": "other", "classname": "other", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "country": [], "extraInfo": [], "originalId": ["oai:zenodo.org:10249277", "50|od______2659::42fc9730cd6f5de3b0e3bfacdc347177"], "contactperson": [], "source": [], "context": [], "title": [{"dataInfo": {"invisible": false, "trust": "0.9", "deletedbyinference": false, "inferred": false, "provenanceaction": {"classid": "sysimport:crosswalk:repository", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Saltia papposa Moq., Prodr."}]}
\ No newline at end of file

From c93bf824875fb3ffdb2220ac62fc52495e17fa01 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 17:34:34 +0200
Subject: [PATCH 169/239] [affroNewModel] extended wf definition

---
 .../actionmanager/bipaffiliations/oozie_app/workflow.xml   | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
index 2e89c07fd..88ff42dc2 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
@@ -21,6 +21,10 @@
             <name>webCrawlInputPath</name>
             <description>the path where to find the inferred affiliation relations from webCrawl</description>
         </property>
+        <property>
+            <name>publisherInputPath</name>
+            <description>the path where to find the inferred affiliation relations from publisher websites</description>
+        </property>
         <property>
             <name>outputPath</name>
             <description>the path where to store the actionset</description>
@@ -99,7 +103,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>Produces the atomic action with the inferred by BIP! affiliation relations (from Crossref and Pubmed)</name>
+            <name>Produces the atomic action with the inferred by OpenAIRE affiliation relations</name>
             <class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
             <jar>dhp-aggregation-${projectVersion}.jar</jar>
             <spark-opts>
@@ -117,6 +121,7 @@
             <arg>--openapcInputPath</arg><arg>${openapcInputPath}</arg>
             <arg>--dataciteInputPath</arg><arg>${dataciteInputPath}</arg>
             <arg>--webCrawlInputPath</arg><arg>${webCrawlInputPath}</arg>
+            <arg>--publisherInputPath</arg><arg>${publisherInputPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

From cab8f1135fd82d2721cb8051d44550ac24b0b3eb Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 17:44:33 +0200
Subject: [PATCH 170/239] [affroNewModel] -

---
 .../bipaffiliations/PrepareAffiliationRelations.java        | 2 +-
 .../dhp/actionmanager/bipaffiliations/job.properties        | 6 ++++--
 .../bipaffiliations/PrepareAffiliationRelationsTest.java    | 2 +-
 3 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 61a018a41..15c1cc376 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -34,7 +34,7 @@ import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
 /**
- * Creates action sets for Crossref affiliation relations inferred by BIP!
+ * Creates action sets for Crossref affiliation relations inferred by OpenAIRE
  */
 public class PrepareAffiliationRelations implements Serializable {
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
index ded4fe409..58124c9d1 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
@@ -32,8 +32,10 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
 oozie.wf.application.path=${oozieTopWfApplicationPath}
 
 crossrefInputPath=/data/bip-affiliations/crossref-data.json
-pubmedInputPath=/data/bip-affiliations/pubmed-data.json
+pubmedInputPath=/data/bip-affiliations/pubmed-data-v4.json
 openapcInputPath=/data/bip-affiliations/openapc-data.json
 dataciteInputPath=/data/bip-affiliations/datacite-data.json
+webCrawlInputPath=/data/bip-affiliations/webCrawl
+publisherInputPath=/data/bip-affiliations/publishers
 
-outputPath=/tmp/crossref-affiliations-output-v5
+outputPath=/tmp/affRoAS
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
index c704bb99b..16d60f7da 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java
@@ -112,7 +112,7 @@ public class PrepareAffiliationRelationsTest {
 			.map(aa -> ((Relation) aa.getPayload()));
 
 		// count the number of relations
-		assertEquals(162, tmp.count());// 18 + 24  + 30 * 4 =
+		assertEquals(162, tmp.count());// 18 + 24 + 30 * 4 =
 
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");

From 32f444984e3a6277c3ffc32f45408e4033b7ba3b Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 24 Oct 2024 17:51:42 +0200
Subject: [PATCH 171/239] [person] -

---
 .../resources/eu/dnetlib/dhp/person/graph/publication/part-00000 | 1 +
 .../resources/eu/dnetlib/dhp/person/graph/relation/part-00000    | 1 -
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000
index e69de29bb..af1b5d55c 100644
--- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/publication/part-00000
@@ -0,0 +1 @@
+{"dataInfo": {"invisible": false, "trust": "0.91", "deletedbyinference": true, "inferred": false, "provenanceaction": {"classid": "sysimport:actionset", "classname": "Harvested", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}}, "resourcetype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "pid": [{"qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.11646/phytotaxa.379.3.5"}], "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "created", "classname": "created", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2018-11-29"}, {"qualifier": {"classid": "published-online", "classname": "published-online", "schemename": "dnet:dataCite_date", "schemeid": "dnet:dataCite_date"}, "value": "2018-11-29"}], "collectedfrom": [{"value": "Crossref", "key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2"}], "id": "50|doi_________::b2eae15cfe9b0d7f416b6dcfc84c09f9", "description": [{"value": "<jats:p>As part of the ongoing studies on the genus Polycarpon Linnaeus (1759: 859, 881) (see e.g., Iamonico 2015a, 2015b, 2015c, Iamonico &amp; Domina 2015), and on the Italian loci classici (see e.g., Peruzzi et al. 2015, Brundu et al. 2015, Domina et al. 2016, Di Gristina et al. 2017, Domina et al. 2017, 2018a, 2018b), we present here a note regarding Hagaea alsinifolia Bivona-Bernardi (1815: 7\\u20138) [currently accepted (see Bartolucci et al. 2018) as Polycarpon tetraphyllum Linnaeus (1759: 881) subsp. alsinifolium (Biv.) Ball (1877: 370)].</jats:p>"}], "lastupdatetimestamp": 1648743612067, "author": [{"surname": "IAMONICO", "fullname": "DUILIO IAMONICO", "pid": [], "name": "DUILIO", "rank": 1}, {"surname": "DOMINA", "fullname": "GIANNIANTONIO DOMINA", "pid": [], "name": "GIANNIANTONIO", "rank": 2}], "instance": [{"refereed": {"classid": "0001", "classname": "peerReviewed", "schemename": "dnet:review_levels", "schemeid": "dnet:review_levels"}, "hostedby": {"dataInfo": {"invisible": false, "deletedbyinference": false}, "value": "Phytotaxa", "key": "10|issn___print::9336d3bbf63c241b54726a55fa38c0ef"}, "url": ["https://doi.org/10.11646/phytotaxa.379.3.5"], "pid": [{"qualifier": {"classid": "doi", "classname": "Digital Object Identifier", "schemename": "dnet:pid_types", "schemeid": "dnet:pid_types"}, "value": "10.11646/phytotaxa.379.3.5"}], "instanceTypeMapping": [{"originalType": "journal-article", "typeLabel": "research article", "vocabularyName": "openaire::coar_resource_types_3_1", "typeCode": "http://purl.org/coar/resource_type/c_2df8fbb1"}, {"originalType": "http://purl.org/coar/resource_type/c_2df8fbb1", "typeLabel": "Article", "vocabularyName": "openaire::user_resource_types", "typeCode": "Article"}], "dateofacceptance": {"value": "2018-11-29"}, "collectedfrom": {"value": "Crossref", "key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemename": "dnet:access_modes", "schemeid": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemename": "dnet:publication_resource", "schemeid": "dnet:publication_resource"}}], "dateofcollection": "2024-07-26T02:32:47.105", "metaResourceType": {"classid": "Research Literature", "classname": "Research Literature", "schemename": "openaire::meta_resource_types", "schemeid": "openaire::meta_resource_types"}, "context": [], "journal": {"issnPrinted": "1179-3155", "vol": "379", "sp": "267", "issnOnline": "1179-3163", "name": "Phytotaxa"}, "subject": [{"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "0106 biological sciences"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "0301 basic medicine"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "03 medical and health sciences"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "03010801 Mycology/Symbiosis"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "030108 mycology & parasitology"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "010603 evolutionary biology"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "01 natural sciences"}, {"dataInfo": {"deletedbyinference": false, "provenanceaction": {"classid": "subject:fos", "classname": "Inferred by OpenAIRE", "schemename": "dnet:provenanceActions", "schemeid": "dnet:provenanceActions"}, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": "0.5"}, "qualifier": {"classid": "FOS", "classname": "Fields of Science and Technology classification", "schemename": "dnet:subject_classification_typologies", "schemeid": "dnet:subject_classification_typologies"}, "value": "01060304 Pollination/Angiosperms"}], "externalReference": [], "publisher": {"value": "Magnolia Press"}, "eoscifguidelines": [], "language": {"classid": "und", "classname": "Undetermined", "schemename": "dnet:languages", "schemeid": "dnet:languages"}, "resulttype": {"classid": "publication", "classname": "publication", "schemename": "dnet:result_typologies", "schemeid": "dnet:result_typologies"}, "country": [], "title": [{"qualifier": {"classid": "main title", "classname": "main title", "schemename": "dnet:dataCite_title", "schemeid": "dnet:dataCite_title"}, "value": "Epitypification of Hagaea alsinifolia (Polyycarpon tetraphyllum subsp. Alsinifolium, Caryophyllaceae)"}], "originalId": ["10.11646/phytotaxa.379.3.5", "50|doiboost____|b2eae15cfe9b0d7f416b6dcfc84c09f9"], "source": [{"value": "Crossref"}], "dateofacceptance": {"value": "2018-11-29"}}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000 b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000
index a17560e55..e69de29bb 100644
--- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/person/graph/relation/part-00000
@@ -1 +0,0 @@
-{"clazz":"eu.dnetlib.dhp.schema.oaf.Relation","payload":{"collectedfrom":[{"key":"10|openaire____::806360c771262b4d6770e7cdf04b5c5a","value":"ORCID","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.91","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:orcid","classname":"Imported from ORCID","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":null,"relType":"personPerson","subRelType":"coAuthorship","relClass":"hasCoAuthor","source":"30|orcid_______::028da52095190c6573d6bf9dba4c8ede","target":"30|orcid_______::8791a84ea413592878d6fe191f0ed35f","validated":true,"validationDate":null,"properties":[]}}
\ No newline at end of file

From e75326d6ec712d534c34efd50a48c5a18a7a358a Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 25 Oct 2024 09:13:54 +0200
Subject: [PATCH 172/239] [FundersMatchFromCrossref] added match from CrossRef
 to DFG unidentified project

---
 .../scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala   | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
index d8292a631..824c7ff52 100644
--- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
@@ -560,7 +560,11 @@ case object Crossref2Oaf {
                 "10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" |
                 "10.13039/501100013589" | "10.13039/501100000271" =>
               generateSimpleRelationFromAward(funder, "ukri________", a => a)
-
+            //DFG
+            case "10.13039/501100001659" =>
+              val targetId = getProjectId("dfgf________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             case _ => logger.debug("no match for " + funder.DOI.get)
 
           }

From 842cc75dae0b11bcc0f4974cf6fe199813f7696d Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 25 Oct 2024 09:42:52 +0200
Subject: [PATCH 173/239] [AffRo] fix name

---
 .../dhp/actionmanager/bipaffiliations/job.properties | 12 ++++++------
 .../bipaffiliations/oozie_app/workflow.xml           |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
index 58124c9d1..c61830cba 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties
@@ -31,11 +31,11 @@ spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListen
 # The following is needed as a property of a workflow
 oozie.wf.application.path=${oozieTopWfApplicationPath}
 
-crossrefInputPath=/data/bip-affiliations/crossref-data.json
-pubmedInputPath=/data/bip-affiliations/pubmed-data-v4.json
-openapcInputPath=/data/bip-affiliations/openapc-data.json
-dataciteInputPath=/data/bip-affiliations/datacite-data.json
-webCrawlInputPath=/data/bip-affiliations/webCrawl
-publisherInputPath=/data/bip-affiliations/publishers
+crossrefInputPath=/data/openaire-affiliations/crossref-data.json
+pubmedInputPath=/data/openaire-affiliations/pubmed-data-v4.json
+openapcInputPath=/data/openaire-affiliations/openapc-data.json
+dataciteInputPath=/data/openaire-affiliations/datacite-data.json
+webCrawlInputPath=/data/openaire-affiliations/webCrawl
+publisherInputPath=/data/openaire-affiliations/publishers
 
 outputPath=/tmp/affRoAS
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
index 88ff42dc2..2e65aaa5e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml
@@ -1,4 +1,4 @@
-<workflow-app name="BipAffiliations" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="OpenAIREAffiliations" xmlns="uri:oozie:workflow:0.5">
     <parameters>
 
         <property>

From 1fce7d5a0f467b478993d408c1103dbd7d895acf Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 25 Oct 2024 10:05:17 +0200
Subject: [PATCH 174/239] [Person] remove the isolated nodes from the person
 set

---
 .../person/SparkExtractPersonRelations.java   | 28 +++++++++++++++++--
 1 file changed, 25 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
index 6caeef478..3892498df 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/person/SparkExtractPersonRelations.java
@@ -16,10 +16,8 @@ import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.sql.*;
 import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -84,9 +82,33 @@ public class SparkExtractPersonRelations {
 					spark,
 					sourcePath,
 					workingPath);
+				removeIsolatedPerson(spark,sourcePath, workingPath);
 			});
 	}
 
+	private static void removeIsolatedPerson(SparkSession spark, String sourcePath, String workingPath) {
+		Dataset<Person> personDataset = spark.read().schema(Encoders.bean(Person.class).schema())
+				.json(sourcePath + "person")
+				.as(Encoders.bean(Person.class));
+
+		Dataset<Relation> relationDataset = spark.read().schema(Encoders.bean(Relation.class).schema())
+				.json(sourcePath + "relation")
+				.as(Encoders.bean(Relation.class));
+
+		personDataset.join(relationDataset, personDataset.col("id").equalTo(relationDataset.col("source")), "left_semi")
+				.write()
+				.option("compression","gzip")
+				.mode(SaveMode.Overwrite)
+				.json(workingPath + "person");
+
+		spark.read().schema(Encoders.bean(Person.class).schema())
+				.json(workingPath + "person")
+				.write()
+				.mode(SaveMode.Overwrite)
+				.option("compression","gzip")
+				.json(sourcePath + "person");
+	}
+
 	private static void extractRelations(SparkSession spark, String sourcePath, String workingPath) {
 
 		Dataset<Tuple2<String, Relation>> relationDataset = spark

From 0fb6af5586ac0532745bd9fde1347b1c972fcf8a Mon Sep 17 00:00:00 2001
From: "miriam.baglioni" <miriam.baglioni@isti.cnr.it>
Date: Mon, 29 Jan 2024 18:12:33 +0100
Subject: [PATCH 175/239] Updated main pom dependency against dhp-schema, from
 8.0.1 to 9.0.0. The new fields included in the updated schema module are
 populated by the Solr JSON payload mapping, which also limits the number of
 authors serialised to 200.

---
 .../dhp/schema/oaf/utils/ModelHardLimits.java |  1 +
 .../model/ProvisionModelSupport.java          | 19 ++++++++++++++++++-
 pom.xml                                       |  2 +-
 3 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
index 36d138ba1..74cd1b42a 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ModelHardLimits.java
@@ -12,6 +12,7 @@ public class ModelHardLimits {
 
 	public static final int MAX_EXTERNAL_ENTITIES = 50;
 	public static final int MAX_AUTHORS = 200;
+	public static final int MAX_RELATED_AUTHORS = 20;
 	public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
 	public static final int MAX_TITLE_LENGTH = 5000;
 	public static final int MAX_TITLES = 10;
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 4a2326453..bc02b595f 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,6 +5,7 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.oaf.utils.ModelHardLimits;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -150,6 +151,12 @@ public class ProvisionModelSupport {
 		rr.setPublisher(re.getPublisher());
 		rr.setResulttype(mapQualifier(re.getResulttype()));
 		rr.setTitle(Optional.ofNullable(re.getTitle()).map(StructuredProperty::getValue).orElse(null));
+		rr.setDescription(StringUtils.left(re.getDescription(), ModelHardLimits.MAX_RELATED_ABSTRACT_LENGTH));
+		rr.setAuthor(Optional.ofNullable(re.getAuthor())
+				.map(aa -> aa.stream()
+						.limit(ModelHardLimits.MAX_RELATED_AUTHORS)
+						.collect(Collectors.toList()))
+				.orElse(null));
 
 		if (relation.getValidated() == null) {
 			relation.setValidated(false);
@@ -378,6 +385,7 @@ public class ProvisionModelSupport {
 		rs.setPubliclyFunded(r.getPubliclyFunded());
 		rs.setTransformativeAgreement(r.getTransformativeAgreement());
 		rs.setExternalReference(mapExternalReference(r.getExternalReference()));
+		rs.setBestinstancetype(mapQualifier(r.getBestInstancetype()));
 		rs.setInstance(mapInstances(r.getInstance()));
 
 		if (r instanceof Publication) {
@@ -667,14 +675,23 @@ public class ProvisionModelSupport {
 	}
 
 	private static List<Author> asAuthor(List<eu.dnetlib.dhp.schema.oaf.Author> authorList) {
+		return asAuthor(authorList, ModelHardLimits.MAX_AUTHORS);
+	}
+
+	private static List<Author> asAuthor(List<eu.dnetlib.dhp.schema.oaf.Author> authorList, int maxAuthors) {
 		return Optional
 			.ofNullable(authorList)
 			.map(
 				authors -> authors
 					.stream()
+					.limit(maxAuthors)
 					.map(
 						a -> Author
-							.newInstance(a.getFullname(), a.getName(), a.getSurname(), a.getRank(), asPid(a.getPid())))
+							.newInstance(
+									StringUtils.left(a.getFullname(), ModelHardLimits.MAX_AUTHOR_FULLNAME_LENGTH),
+									a.getName(),
+									a.getSurname(),
+									a.getRank(), asPid(a.getPid())))
 					.collect(Collectors.toList()))
 			.orElse(null);
 	}
diff --git a/pom.xml b/pom.xml
index e1d99f25b..9480ddfc0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[8.0.1]</dhp-schemas.version>
+        <dhp-schemas.version>[9.0.0]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From 32fa579b809138f9ae5d52d661423b1cebf4fbe4 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 28 Oct 2024 10:03:02 +0100
Subject: [PATCH 176/239] [graph provision] select the longest abstract

---
 .../dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
index 63f3c2ead..add1c80fa 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java
@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.provision;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
+import java.util.Comparator;
 import java.util.List;
 import java.util.Objects;
 import java.util.Optional;
@@ -167,8 +168,9 @@ public class CreateRelatedEntitiesJob_phase1 {
 					result
 						.getDescription()
 						.stream()
-						.findFirst()
+						.filter(d -> Objects.nonNull(d.getValue()))
 						.map(Field::getValue)
+						.max(Comparator.comparingInt(String::length))
 						.ifPresent(
 							d -> re.setDescription(StringUtils.left(d, ModelHardLimits.MAX_RELATED_ABSTRACT_LENGTH)));
 				}

From 6fd50266f11c39d7b71600d8da9fc010da4037e5 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 28 Oct 2024 10:42:46 +0100
Subject: [PATCH 177/239] translate 'otherresearchproduct' into 'other' when
 setting the related record type

---
 .../dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index bc02b595f..69aa940c9 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -109,7 +109,7 @@ public class ProvisionModelSupport {
 		RelatedRecord rr = new RelatedRecord();
 
 		final RelatedEntity re = rew.getTarget();
-		final RecordType relatedRecordType = RecordType.valueOf(re.getType());
+		final RecordType relatedRecordType = RecordType.fromString(re.getType());
 		final Relation relation = rew.getRelation();
 		final String relationProvenance = Optional
 			.ofNullable(relation.getDataInfo())

From 5916346ba17cfcbc8a9ba378e4f6f1972c1b729e Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 28 Oct 2024 12:18:50 +0100
Subject: [PATCH 178/239] [TransformativeAgreement] fix to remove the file
 downloaded from a previous run of the workflow

---
 .../transformativeagreement/oozie_app/workflow.xml     | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml
index 0c5b1c119..a11e3350e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/transformativeagreement/oozie_app/workflow.xml
@@ -24,7 +24,7 @@
 
     <decision name="resume_from">
         <switch>
-            <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
+            <case to="reset_workingDir">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
             <default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
         </switch>
     </decision>
@@ -33,6 +33,14 @@
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="download"/>
+        <error to="Kill"/>
+    </action>
     <action name="download">
         <shell xmlns="uri:oozie:shell-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>

From 56224e034ab1b19bfc21d5dab38ea49d6da62529 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Mon, 28 Oct 2024 12:05:56 +0100
Subject: [PATCH 179/239] Fill the new mergedIds field when generating dedup
 records Filter out dedup records composed of invisible records only Filter
 out mergerels that have not been used when creating the dedup record
 (ungrouping of cliques)

---
 .../dhp/oa/dedup/DedupRecordFactory.java      | 15 ++++++--
 .../dhp/oa/dedup/SparkCreateDedupRecord.java  | 36 +++++++++++++++++--
 pom.xml                                       |  2 +-
 3 files changed, 47 insertions(+), 6 deletions(-)

diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
index 36ed4d7c1..44482cfdb 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
@@ -2,14 +2,13 @@
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.util.*;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.apache.commons.beanutils.BeanUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.FlatMapGroupsFunction;
 import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
 
 import eu.dnetlib.dhp.oa.dedup.model.Identifier;
@@ -107,6 +106,8 @@ public class DedupRecordFactory {
 
 					final HashSet<String> acceptanceDate = new HashSet<>();
 
+					boolean isVisible = false;
+
 					while (it.hasNext()) {
 						Tuple3<String, String, OafEntity> t = it.next();
 						OafEntity entity = t._3();
@@ -114,6 +115,7 @@ public class DedupRecordFactory {
 						if (entity == null) {
 							aliases.add(t._2());
 						} else {
+							isVisible = isVisible || !entity.getDataInfo().getInvisible();
 							cliques.add(entity);
 
 							if (acceptanceDate.size() < MAX_ACCEPTANCE_DATE) {
@@ -129,13 +131,20 @@ public class DedupRecordFactory {
 
 					}
 
-					if (acceptanceDate.size() >= MAX_ACCEPTANCE_DATE || cliques.isEmpty()) {
+					if (!isVisible || acceptanceDate.size() >= MAX_ACCEPTANCE_DATE || cliques.isEmpty()) {
 						return Collections.emptyIterator();
 					}
 
 					OafEntity mergedEntity = MergeUtils.mergeGroup(dedupId, cliques.iterator());
 					// dedup records do not have date of transformation attribute
 					mergedEntity.setDateoftransformation(null);
+					mergedEntity
+						.setMergedIds(
+							Stream
+								.concat(cliques.stream().map(OafEntity::getId), aliases.stream())
+								.distinct()
+								.sorted()
+								.collect(Collectors.toList()));
 
 					return Stream
 						.concat(
diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
index 6989ec54b..6f5f40e43 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
@@ -5,11 +5,11 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTION
 import static eu.dnetlib.dhp.schema.common.ModelConstants.PROVENANCE_DEDUP;
 
 import java.io.IOException;
+import java.util.Arrays;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
+import org.apache.spark.sql.*;
 import org.dom4j.DocumentException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -17,6 +17,7 @@ import org.xml.sax.SAXException;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.common.EntityType;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
@@ -25,6 +26,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import eu.dnetlib.pace.config.DedupConfig;
+import scala.collection.JavaConverters;
 
 public class SparkCreateDedupRecord extends AbstractSparkAction {
 
@@ -85,6 +87,36 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
 				.mode(SaveMode.Overwrite)
 				.option("compression", "gzip")
 				.json(outputPath);
+
+			log.info("Updating mergerels for: '{}'", subEntity);
+			final Dataset<Row> dedupIds = spark
+				.read()
+				.schema("`id` STRING, `mergedIds` ARRAY<STRING>")
+				.json(outputPath)
+				.selectExpr("id as source", "explode(mergedIds) as target");
+			spark
+				.read()
+				.load(mergeRelPath)
+				.where("relClass == 'merges'")
+				.join(dedupIds, JavaConverters.asScalaBuffer(Arrays.asList("source", "target")).toSeq(), "left_semi")
+				.write()
+				.mode(SaveMode.Overwrite)
+				.option("compression", "gzip")
+				.save(workingPath + "/mergerel_filtered");
+
+			final Dataset<Row> validRels = spark.read().load(workingPath + "/mergerel_filtered");
+
+			final Dataset<Row> filteredMergeRels = validRels
+				.union(
+					validRels
+						.withColumnRenamed("source", "source_tmp")
+						.withColumnRenamed("target", "target_tmp")
+						.withColumn("relClass", functions.lit(ModelConstants.IS_MERGED_IN))
+						.withColumnRenamed("target_tmp", "source")
+						.withColumnRenamed("source_tmp", "target"));
+
+			saveParquet(filteredMergeRels, mergeRelPath, SaveMode.Overwrite);
+			removeOutputDir(spark, workingPath + "/mergerel_filtered");
 		}
 	}
 
diff --git a/pom.xml b/pom.xml
index e1d99f25b..9480ddfc0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[8.0.1]</dhp-schemas.version>
+        <dhp-schemas.version>[9.0.0]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From e6ca382debc8c9ee96e008bfa71a6ebd4083a76a Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 28 Oct 2024 13:52:06 +0100
Subject: [PATCH 180/239] using scala 2.11 converters

---
 .../java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java  | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
index 6f5f40e43..29394cb12 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
@@ -98,7 +98,9 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
 				.read()
 				.load(mergeRelPath)
 				.where("relClass == 'merges'")
-				.join(dedupIds, JavaConverters.asScalaBuffer(Arrays.asList("source", "target")).toSeq(), "left_semi")
+				.join(
+					dedupIds, JavaConverters.asScalaBufferConverter(Arrays.asList("source", "target")).asScala(),
+					"left_semi")
 				.write()
 				.mode(SaveMode.Overwrite)
 				.option("compression", "gzip")

From 9b4415cb674c5fedfa8644a035c2bfc66414dfe2 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 28 Oct 2024 13:56:25 +0100
Subject: [PATCH 181/239] using _the right_ scala 2.11 converters

---
 .../java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
index 29394cb12..bd17d05eb 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateDedupRecord.java
@@ -26,6 +26,7 @@ import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import eu.dnetlib.pace.config.DedupConfig;
+import scala.collection.JavaConversions;
 import scala.collection.JavaConverters;
 
 public class SparkCreateDedupRecord extends AbstractSparkAction {
@@ -98,9 +99,7 @@ public class SparkCreateDedupRecord extends AbstractSparkAction {
 				.read()
 				.load(mergeRelPath)
 				.where("relClass == 'merges'")
-				.join(
-					dedupIds, JavaConverters.asScalaBufferConverter(Arrays.asList("source", "target")).asScala(),
-					"left_semi")
+				.join(dedupIds, JavaConversions.asScalaBuffer(Arrays.asList("source", "target")), "left_semi")
 				.write()
 				.mode(SaveMode.Overwrite)
 				.option("compression", "gzip")

From e4504fd98de52f20b201ff3985a18792241751f1 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Mon, 28 Oct 2024 15:32:09 +0100
Subject: [PATCH 182/239] [Person] fixed project identifier creation

---
 .../personentity/ExtractPerson.java              | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 1131f85e9..bf2c19c3d 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -25,6 +25,7 @@ import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.*;
 import org.apache.spark.sql.*;
+import org.apache.spark.sql.Dataset;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -43,10 +44,7 @@ import eu.dnetlib.dhp.common.person.Coauthors;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.DataInfo;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Person;
-import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
@@ -70,7 +68,11 @@ public class ExtractPerson implements Serializable {
 
 	private static final String PMCID_PREFIX = "50|pmcid_______::";
 	private static final String ROR_PREFIX = "20|ror_________::";
-	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
+	private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class)
+		+ IdentifierFactory.ID_PREFIX_SEPARATOR + ModelConstants.ORCID + "_______";
+	private static final String PROJECT_ID_PREFIX = ModelSupport.getIdPrefix(Project.class)
+		+ IdentifierFactory.ID_PREFIX_SEPARATOR;
+
 	public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
 	public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
 	public static final String FUNDER_AUTHORS_CLASSID = "sysimport:crosswalk:funderdatabase";
@@ -173,7 +175,7 @@ public class ExtractPerson implements Serializable {
 			}
 
 		} catch (IOException e) {
-			e.printStackTrace();
+			throw new RuntimeException(e);
 		}
 
 	}
@@ -191,7 +193,7 @@ public class ExtractPerson implements Serializable {
 	private static Relation getProjectRelation(String project, String orcid, String role) {
 
 		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
-		String target = project.substring(0, 14)
+		String target = PROJECT_ID_PREFIX + project.substring(0, 14)
 			+ IdentifierFactory.md5(project.substring(15));
 		List<KeyValue> properties = new ArrayList<>();
 

From 499892b67c4549bd0cebe6bc07873a4e553eda3a Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 29 Oct 2024 09:51:30 +0100
Subject: [PATCH 183/239] [graph raw] rule out empty PIDs

---
 .../graph/raw/AbstractMdRecordToOafMapper.java | 18 +++++++++++++-----
 1 file changed, 13 insertions(+), 5 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
index a85f47d99..2436a272c 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
@@ -657,13 +657,21 @@ public abstract class AbstractMdRecordToOafMapper {
 			final Node n = (Node) o;
 			final String classId = n.valueOf(xpathClassId).trim();
 			if (this.vocs.termExists(schemeId, classId)) {
-				res
-					.add(
-						HashableStructuredProperty
-							.newInstance(n.getText(), this.vocs.getTermAsQualifier(schemeId, classId), info));
+				final String value = n.getText();
+				if (StringUtils.isNotBlank(value)) {
+					res
+						.add(
+							HashableStructuredProperty
+								.newInstance(value, this.vocs.getTermAsQualifier(schemeId, classId), info));
+				}
 			}
 		}
-		return Lists.newArrayList(res);
+		return res
+			.stream()
+			.filter(Objects::nonNull)
+			.filter(p -> StringUtils.isNotBlank(p.getValue()))
+			.filter(p -> StringUtils.isNotBlank(p.getValue().trim()))
+			.collect(Collectors.toList());
 	}
 
 	protected List<StructuredProperty> prepareListStructProps(

From 5ca031c8d6a780b46adc2b1b0b4a7a5307cf9c73 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 29 Oct 2024 13:48:41 +0100
Subject: [PATCH 184/239] [graph raw] rule out empty PIDs

---
 .../java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java | 1 +
 .../main/java/eu/dnetlib/dhp/schema/oaf/utils/PidCleaner.java   | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
index 2c77c3b37..da245d67c 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactory.java
@@ -204,6 +204,7 @@ public class IdentifierFactory implements Serializable {
 			.map(
 				pp -> pp
 					.stream()
+					.filter(p -> StringUtils.isNotBlank(p.getValue()))
 					// filter away PIDs provided by a DS that is not considered an authority for the
 					// given PID Type
 					.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidCleaner.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidCleaner.java
index 114c2b3af..678ed71dd 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidCleaner.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PidCleaner.java
@@ -26,7 +26,7 @@ public class PidCleaner {
 		String value = Optional
 			.ofNullable(pidValue)
 			.map(String::trim)
-			.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
+			.orElseThrow(() -> new IllegalArgumentException("PID (" + pidType + ") value cannot be empty"));
 
 		switch (pidType) {
 

From 69aee609ef32c6e8121e08042b25d779f8a40dcb Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 29 Oct 2024 15:53:04 +0100
Subject: [PATCH 185/239] [bulktag] align type to community api

---
 .../eu/dnetlib/dhp/api/model/CommunityContentprovider.java  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java
index 9fab5a80c..8e0ea598c 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/model/CommunityContentprovider.java
@@ -13,13 +13,13 @@ public class CommunityContentprovider {
 	private String openaireId;
 	private SelectionConstraints selectioncriteria;
 
-	private String enabled;
+	private Boolean enabled;
 
-	public String getEnabled() {
+	public Boolean getEnabled() {
 		return enabled;
 	}
 
-	public void setEnabled(String enabled) {
+	public void setEnabled(Boolean enabled) {
 		this.enabled = enabled;
 	}
 

From 323c76eafca0e992c7b7dd749fd31fdc2eb840e2 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 30 Oct 2024 07:35:30 +0100
Subject: [PATCH 186/239] patch relations job: removed non necessary logging

---
 .../eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
index 615b4a824..dce6cd39d 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/PatchRelationsApplication.java
@@ -80,9 +80,6 @@ public class PatchRelationsApplication {
 		final Dataset<Relation> rels = readPath(spark, relationPath, Relation.class);
 		final Dataset<RelationIdMapping> idMapping = readPath(spark, idMappingPath, RelationIdMapping.class);
 
-		log.info("relations: {}", rels.count());
-		log.info("idMapping: {}", idMapping.count());
-
 		final Dataset<Relation> bySource = rels
 			.joinWith(idMapping, rels.col("source").equalTo(idMapping.col("oldId")), "left")
 			.map((MapFunction<Tuple2<Relation, RelationIdMapping>, Relation>) t -> {

From 26cdc7e439e8035a31a21f4895a4d521aa85d1e0 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 30 Oct 2024 07:35:47 +0100
Subject: [PATCH 187/239] Avoid NPEs in MergeUtils

---
 .../main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index e01813110..79a12d630 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -715,7 +715,9 @@ public class MergeUtils {
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
 			.ofNullable(sp)
-			.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
+			.map(s -> Joiner.on("||")
+					.useForNull("")
+					.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
 			.orElse(null);
 	}
 

From a877c76d70a10afdd888f84a33cbe683c2f78755 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 30 Oct 2024 11:24:25 +0100
Subject: [PATCH 188/239] make MergeUtils.selectOldestDate less prone to errors
 when receiving invalid date formats

---
 .../schema/oaf/utils/GraphCleaningFunctions.java  |  2 +-
 .../dnetlib/dhp/schema/oaf/utils/MergeUtils.java  | 15 +++++----------
 2 files changed, 6 insertions(+), 11 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
index fdfd63a15..b6574da16 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@@ -810,7 +810,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 		return author;
 	}
 
-	private static Optional<String> cleanDateField(Field<String> dateofacceptance) {
+	public static Optional<String> cleanDateField(Field<String> dateofacceptance) {
 		return Optional
 			.ofNullable(dateofacceptance)
 			.map(Field::getValue)
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index 79a12d630..4c411a155 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -654,16 +654,9 @@ public class MergeUtils {
 	}
 
 	private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
-		if (d1 == null || StringUtils.isBlank(d1.getValue())) {
+		if (!GraphCleaningFunctions.cleanDateField(d1).isPresent()) {
 			return d2;
-		} else if (d2 == null || StringUtils.isBlank(d2.getValue())) {
-			return d1;
-		}
-
-		if (StringUtils.contains(d1.getValue(), "null")) {
-			return d2;
-		}
-		if (StringUtils.contains(d2.getValue(), "null")) {
+		} else if (!GraphCleaningFunctions.cleanDateField(d2).isPresent()) {
 			return d1;
 		}
 
@@ -715,7 +708,9 @@ public class MergeUtils {
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
 			.ofNullable(sp)
-			.map(s -> Joiner.on("||")
+			.map(
+				s -> Joiner
+					.on("||")
 					.useForNull("")
 					.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
 			.orElse(null);

From a42c8b7c8541d3225d5d087469af9b7ff5fb9aa7 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 30 Oct 2024 11:25:17 +0100
Subject: [PATCH 189/239] person table directory produced by the workflows
 raw_all and merge graphs

---
 .../dhp/oa/graph/merge/oozie_app/workflow.xml | 28 +++++++++++++++++++
 .../oa/graph/raw_all/oozie_app/workflow.xml   | 27 ++++++++++++++++++
 2 files changed, 55 insertions(+)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml
index a8d0d5068..3444e3afe 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/merge/oozie_app/workflow.xml
@@ -68,6 +68,7 @@
         <path start="merge_datasource"/>
         <path start="merge_organization"/>
         <path start="merge_project"/>
+        <path start="merge_person"/>
         <path start="merge_relation"/>
     </fork>
 
@@ -260,6 +261,33 @@
         <error to="Kill"/>
     </action>
 
+    <action name="merge_person">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Merge person</name>
+            <class>eu.dnetlib.dhp.oa.graph.merge.MergeGraphTableSparkJob</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--betaInputPath</arg><arg>${betaInputGraphPath}/person</arg>
+            <arg>--prodInputPath</arg><arg>${prodInputGraphPath}/person</arg>
+            <arg>--outputPath</arg><arg>${graphOutputPath}/person</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+            <arg>--priority</arg><arg>${priority}</arg>
+        </spark>
+        <ok to="wait_merge"/>
+        <error to="Kill"/>
+    </action>
+
     <action name="merge_relation">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
index ff927fe52..1b3cb1111 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml
@@ -649,6 +649,7 @@
         <path start="merge_claims_datasource"/>
         <path start="merge_claims_organization"/>
         <path start="merge_claims_project"/>
+        <path start="merge_claims_person"/>
         <path start="merge_claims_relation"/>
     </fork>
 
@@ -860,6 +861,32 @@
         <error to="Kill"/>
     </action>
 
+    <action name="merge_claims_person">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>MergeClaims_person</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.MergeClaimsApplication</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores ${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=200
+            </spark-opts>
+            <arg>--rawGraphPath</arg><arg>${workingDir}/graph_raw</arg>
+            <arg>--claimsGraphPath</arg><arg>${workingDir}/graph_claims</arg>
+            <arg>--outputRawGaphPath</arg><arg>${graphOutputPath}</arg>
+            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Person</arg>
+        </spark>
+        <ok to="wait_merge"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="wait_merge" to="decisionPatchRelations"/>
 
     <decision name="decisionPatchRelations">

From a8ed5a3b048b560a6c2b794834e27e4adcdcac97 Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@gmail.com>
Date: Mon, 4 Nov 2024 17:45:28 +0100
Subject: [PATCH 190/239] Organized getters and setters in the PMArticle class
 for better readability and maintainability.

---
 dhp-shade-package/pom.xml                     | 122 +++----
 .../personentity/ExtractPerson.java           |   8 +-
 .../dnetlib/dhp/sx/bio/pubmed/PMArticle.java  | 312 +++++-------------
 .../sx/bio/ebi/baseline_to_oaf_params.json    |   7 +-
 .../sx/bio/ebi/SparkCreatePubmedDump.scala    |  90 +++++
 .../dnetlib/dhp/sx/bio/pubmed/PMParser2.scala | 264 +++++++++++++++
 .../dhp/sx/graph/bio/single_pubmed.xml        | 222 +++++++++++++
 .../dnetlib/dhp/sx/bio/BioScholixTest.scala   |  28 +-
 8 files changed, 754 insertions(+), 299 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml

diff --git a/dhp-shade-package/pom.xml b/dhp-shade-package/pom.xml
index d8e17ed46..c4f9b262e 100644
--- a/dhp-shade-package/pom.xml
+++ b/dhp-shade-package/pom.xml
@@ -26,16 +26,16 @@
 
     <dependencies>
 
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-actionmanager</artifactId>
-            <version>${project.version}</version>
-        </dependency>
 <!--        <dependency>-->
 <!--            <groupId>eu.dnetlib.dhp</groupId>-->
-<!--            <artifactId>dhp-aggregation</artifactId>-->
+<!--            <artifactId>dhp-actionmanager</artifactId>-->
 <!--            <version>${project.version}</version>-->
 <!--        </dependency>-->
+        <dependency>
+            <groupId>eu.dnetlib.dhp</groupId>
+            <artifactId>dhp-aggregation</artifactId>
+            <version>${project.version}</version>
+        </dependency>
 <!--        <dependency>-->
 <!--            <groupId>eu.dnetlib.dhp</groupId>-->
 <!--            <artifactId>dhp-blacklist</artifactId>-->
@@ -56,61 +56,61 @@
 <!--            <artifactId>dhp-enrichment</artifactId>-->
 <!--            <version>${project.version}</version>-->
 <!--        </dependency>-->
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-graph-mapper</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-graph-provision</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-impact-indicators</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-actionsets</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-hist-snaps</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-monitor-irish</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-promote</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-stats-update</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-swh</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-usage-raw-data-update</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>eu.dnetlib.dhp</groupId>
-            <artifactId>dhp-usage-stats-build</artifactId>
-            <version>${project.version}</version>
-        </dependency>
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-graph-mapper</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-graph-provision</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-impact-indicators</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-stats-actionsets</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-stats-hist-snaps</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-stats-monitor-irish</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-stats-promote</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-stats-update</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-swh</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-usage-raw-data-update</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
+<!--        <dependency>-->
+<!--            <groupId>eu.dnetlib.dhp</groupId>-->
+<!--            <artifactId>dhp-usage-stats-build</artifactId>-->
+<!--            <version>${project.version}</version>-->
+<!--        </dependency>-->
     </dependencies>
 
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index bf2c19c3d..db31bb43f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -15,6 +15,7 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
@@ -29,7 +30,6 @@ import org.apache.spark.sql.Dataset;
 import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.spark_project.jetty.util.StringUtil;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
@@ -206,7 +206,7 @@ public class ExtractPerson implements Serializable {
 				null);
 		relation.setValidated(true);
 
-		if (StringUtil.isNotBlank(role)) {
+		if (StringUtils.isNotBlank(role)) {
 			KeyValue kv = new KeyValue();
 			kv.setKey("role");
 			kv.setValue(role);
@@ -439,13 +439,13 @@ public class ExtractPerson implements Serializable {
 				null);
 		relation.setValidated(true);
 
-		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())) {
+		if (Optional.ofNullable(row.getStartDate()).isPresent() && StringUtils.isNotBlank(row.getStartDate())) {
 			KeyValue kv = new KeyValue();
 			kv.setKey("startDate");
 			kv.setValue(row.getStartDate());
 			properties.add(kv);
 		}
-		if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
+		if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtils.isNotBlank(row.getEndDate())) {
 			KeyValue kv = new KeyValue();
 			kv.setKey("endDate");
 			kv.setValue(row.getEndDate());
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java
index 3fb814606..6191f6446 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java
@@ -8,259 +8,115 @@ import java.util.List;
 /**
  * This class represent an instance of Pubmed Article extracted from the native XML
  *
- * @author Sandro La Bruzzo
  */
-
 public class PMArticle implements Serializable {
 
-	/**
-	 * the Pubmed Identifier
-	 */
 	private String pmid;
-
 	private String pmcId;
-
-	/**
-	 * the DOI
-	 */
 	private String doi;
-	/**
-	 * the Pubmed Date extracted from <PubmedPubDate> Specifies a date significant to either the article's history or the citation's processing.
-	 * All <History> dates will have a <Year>, <Month>, and <Day> elements. Some may have an <Hour>, <Minute>, and <Second> element(s).
-	 */
 	private String date;
-	/**
-	 * This is an 'envelop' element that contains various elements describing the journal cited; i.e., ISSN, Volume, Issue, and PubDate and author name(s), however, it does not contain data itself.
-	 */
 	private PMJournal journal;
-	/**
-	 * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. The NLM journal title abbreviation is exported in the <MedlineTA> element.
-	 */
 	private String title;
-	/**
-	 * English-language abstracts are taken directly from the published article.
-	 * If the article does not have a published abstract, the National Library of Medicine does not create one,
-	 * thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
-	 * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
-	 */
 	private String description;
-	/**
-	 * the language in which an article was published is recorded in <Language>.
-	 * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single
-	 * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value.
-	 *  Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined.
-	 */
 	private String language;
-
-	/**
-	 * NLM controlled vocabulary, Medical Subject Headings (MeSH®), is used to characterize the content of the articles represented by MEDLINE citations.	 *
-	 */
-	private final List<PMSubject> subjects = new ArrayList<>();
-	/**
-	 * This element is used to identify the type of article indexed for MEDLINE;
-	 * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
-	 * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
-	 */
-	private final List<PMSubject> publicationTypes = new ArrayList<>();
-	/**
-	 * Personal and collective (corporate) author names published with the article are found in <AuthorList>.
-	 */
+	private List<PMSubject> subjects;
+	private List<PMSubject> publicationTypes = new ArrayList<>();
 	private List<PMAuthor> authors = new ArrayList<>();
+	private List<PMGrant> grants = new ArrayList<>();
 
-	/**
-	 * <GrantID> contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service
-	 * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations.
-	 */
-	private final List<PMGrant> grants = new ArrayList<>();
-
-	/**
-	 * get the DOI
-	 * @return a DOI
-	 */
-	public String getDoi() {
-		return doi;
-	}
-
-	/**
-	 * Set the DOI
-	 * @param doi a DOI
-	 */
-	public void setDoi(String doi) {
-		this.doi = doi;
-	}
-
-	/**
-	 * get the Pubmed Identifier
-	 * @return the PMID
-	 */
 	public String getPmid() {
 		return pmid;
 	}
 
-	/**
-	 * set the Pubmed Identifier
-	 * @param pmid the Pubmed Identifier
-	 */
 	public void setPmid(String pmid) {
 		this.pmid = pmid;
 	}
 
-	/**
-	 * the Pubmed Date extracted from <PubmedPubDate> Specifies a date significant to either the article's history or the citation's processing.
-	 * All <History> dates will have a <Year>, <Month>, and <Day> elements. Some may have an <Hour>, <Minute>, and <Second> element(s).
-	 *
-	 * @return the Pubmed Date
-	 */
-	public String getDate() {
-		return date;
-	}
-
-	/**
-	 * Set the pubmed Date
-	 * @param date
-	 */
-	public void setDate(String date) {
-		this.date = date;
-	}
-
-	/**
-	 * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element.
-	 * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles.
-	 * The NLM journal title abbreviation is exported in the <MedlineTA> element.
-	 *
-	 * @return the pubmed Journal Extracted
-	 */
-	public PMJournal getJournal() {
-		return journal;
-	}
-
-	/**
-	 * Set the mapped pubmed Journal
-	 * @param journal
-	 */
-	public void setJournal(PMJournal journal) {
-		this.journal = journal;
-	}
-
-	/**
-	 * <ArticleTitle> contains the entire title of the journal article. <ArticleTitle> is always in English;
-	 * those titles originally published in a non-English language and translated for <ArticleTitle> are enclosed in square brackets.
-	 * All titles end with a period unless another punctuation mark such as a question mark or bracket is present.
-	 * Explanatory information about the title itself is enclosed in parentheses, e.g.: (author's transl).
-	 * Corporate/collective authors may appear at the end of <ArticleTitle> for citations up to about the year 2000.
-	 *
-	 *  @return the extracted pubmed Title
-	 */
-	public String getTitle() {
-		return title;
-	}
-
-	/**
-	 * set the pubmed title
-	 * @param title
-	 */
-	public void setTitle(String title) {
-		this.title = title;
-	}
-
-	/**
-	 * English-language abstracts are taken directly from the published article.
-	 * If the article does not have a published abstract, the National Library of Medicine does not create one,
-	 * thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
-	 * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
-	 *
-	 * @return the Mapped Pubmed Article Abstracts
-	 */
-	public String getDescription() {
-		return description;
-	}
-
-	/**
-	 * Set the Mapped Pubmed Article Abstracts
-	 * @param description
-	 */
-	public void setDescription(String description) {
-		this.description = description;
-	}
-
-	/**
-	 * Personal and collective (corporate) author names published with the article are found in <AuthorList>.
-	 *
-	 * @return get the Mapped Authors lists
-	 */
-	public List<PMAuthor> getAuthors() {
-		return authors;
-	}
-
-	/**
-	 * Set the Mapped Authors lists
-	 * @param authors
-	 */
-	public void setAuthors(List<PMAuthor> authors) {
-		this.authors = authors;
-	}
-
-	/**
-	 * This element is used to identify the type of article indexed for MEDLINE;
-	 * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
-	 * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
-	 *
-	 * @return the mapped Subjects
-	 */
-	public List<PMSubject> getSubjects() {
-		return subjects;
-	}
-
-	/**
-	 *
-	 * the language in which an article was published is recorded in <Language>.
-	 * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single
-	 * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value.
-	 *  Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined.
-	 *
-	 * @return The mapped Language
-	 */
-	public String getLanguage() {
-		return language;
-	}
-
-	/**
-	 *
-	 *  Set The mapped Language
-	 *
-	 * @param language the mapped Language
-	 */
-	public void setLanguage(String language) {
-		this.language = language;
-	}
-
-	/**
-	 *  This element is used to identify the type of article indexed for MEDLINE;
-	 * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
-	 * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
-	 *
-	 * @return the mapped Publication Type
-	 */
-	public List<PMSubject> getPublicationTypes() {
-		return publicationTypes;
-	}
-
-	/**
-	 * <GrantID> contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service
-	 * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations.
-	 * @return the mapped grants
-	 */
-
-	public List<PMGrant> getGrants() {
-		return grants;
-	}
-
 	public String getPmcId() {
 		return pmcId;
 	}
 
-	public PMArticle setPmcId(String pmcId) {
+	public void setPmcId(String pmcId) {
 		this.pmcId = pmcId;
-		return this;
+	}
+
+	public String getDoi() {
+		return doi;
+	}
+
+	public void setDoi(String doi) {
+		this.doi = doi;
+	}
+
+	public String getDate() {
+		return date;
+	}
+
+	public void setDate(String date) {
+		this.date = date;
+	}
+
+	public PMJournal getJournal() {
+		return journal;
+	}
+
+	public void setJournal(PMJournal journal) {
+		this.journal = journal;
+	}
+
+	public String getTitle() {
+		return title;
+	}
+
+	public void setTitle(String title) {
+		this.title = title;
+	}
+
+	public String getDescription() {
+		return description;
+	}
+
+	public void setDescription(String description) {
+		this.description = description;
+	}
+
+	public String getLanguage() {
+		return language;
+	}
+
+	public void setLanguage(String language) {
+		this.language = language;
+	}
+
+	public List<PMSubject> getSubjects() {
+		return subjects;
+	}
+
+	public void setSubjects(List<PMSubject> subjects) {
+		this.subjects = subjects;
+	}
+
+	public List<PMSubject> getPublicationTypes() {
+		return publicationTypes;
+	}
+
+	public void setPublicationTypes(List<PMSubject> publicationTypes) {
+		this.publicationTypes = publicationTypes;
+	}
+
+	public List<PMAuthor> getAuthors() {
+		return authors;
+	}
+
+	public void setAuthors(List<PMAuthor> authors) {
+		this.authors = authors;
+	}
+
+	public List<PMGrant> getGrants() {
+		return grants;
+	}
+
+	public void setGrants(List<PMGrant> grants) {
+		this.grants = grants;
 	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
index 3ba83764d..8326fab0f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
@@ -1,8 +1,7 @@
 [
   {"paramName":"mt",  "paramLongName":"master",         "paramDescription": "should be local or yarn",                  "paramRequired": true},
   {"paramName":"i",   "paramLongName":"isLookupUrl",    "paramDescription": "isLookupUrl",                              "paramRequired": true},
-  {"paramName":"w",   "paramLongName":"workingPath",    "paramDescription": "the path of the sequencial file to read",  "paramRequired": true},
-  {"paramName":"mo",   "paramLongName":"mdstoreOutputVersion",     "paramDescription": "the oaf path ",                            "paramRequired": true},
-  {"paramName":"s",   "paramLongName":"skipUpdate",     "paramDescription": "skip update ",                             "paramRequired": false},
-  {"paramName":"h",   "paramLongName":"hdfsServerUri",  "paramDescription": "the  working path ",                       "paramRequired": true}
+  {"paramName":"s",   "paramLongName":"sourcePath",    "paramDescription": "the baseline path",  "paramRequired": true},
+  {"paramName":"t",   "paramLongName":"targetPath",     "paramDescription": "the mdstore path to save",                 "paramRequired": true}
+
 ]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
new file mode 100644
index 000000000..c21bfd7c3
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
@@ -0,0 +1,90 @@
+package eu.dnetlib.dhp.sx.bio.ebi
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import eu.dnetlib.dhp.application.{AbstractScalaApplication, ArgumentApplicationParser}
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
+import eu.dnetlib.dhp.schema.oaf.Oaf
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PMParser2, PubMedToOaf}
+import eu.dnetlib.dhp.utils.ISLookupClientFactory
+import org.apache.spark.sql.functions._
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+import java.io.ByteArrayInputStream
+import javax.xml.stream.XMLInputFactory
+
+class SparkCreatePubmedDump(propertyPath: String, args: Array[String], log: Logger)
+    extends AbstractScalaApplication(propertyPath, args, log: Logger) {
+
+  /** Here all the spark applications runs this method
+    * where the whole logic of the spark node is defined
+    */
+  override def run(): Unit = {
+    val isLookupUrl: String = parser.get("isLookupUrl")
+    log.info("isLookupUrl: {}", isLookupUrl)
+    val sourcePath = parser.get("sourcePath")
+    log.info(s"SourcePath is '$sourcePath'")
+    val targetPath = parser.get("targetPath")
+    log.info(s"TargetPath is '$targetPath'")
+
+    val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
+    val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
+
+    createPubmedDump(spark, sourcePath, targetPath, vocabularies)
+
+  }
+
+  def createPubmedDump(
+    spark: SparkSession,
+    sourcePath: String,
+    targetPath: String,
+    vocabularies: VocabularyGroup
+  ): Unit = {
+    require(spark != null)
+
+    implicit val PMEncoder: Encoder[PMArticle] = Encoders.bean(classOf[PMArticle])
+
+    import spark.implicits._
+    val df = spark.read.option("lineSep", "</PubmedArticle>").text(sourcePath)
+    val mapper = new ObjectMapper()
+    df.as[String]
+      .map(s => {
+        val id = s.indexOf("<PubmedArticle>")
+        if (id >= 0) s"${s.substring(id)}</PubmedArticle>" else null
+      })
+      .filter(s => s != null)
+      .map { i =>
+        try {
+          new PMParser2().parse(i)
+        } catch {
+          case _: Exception => {
+            throw new RuntimeException(s"Error parsing article: $i")
+          }
+        }
+      }
+      .dropDuplicates("pmid")
+      .map { a =>
+        val oaf = PubMedToOaf.convert(a, vocabularies)
+        if (oaf != null)
+          mapper.writeValueAsString(oaf)
+        else
+          null
+      }
+      .as[String]
+      .filter(s => s != null)
+      .write
+      .option("compression", "gzip")
+      .mode("overwrite")
+      .text(targetPath)
+  }
+}
+
+object SparkCreatePubmedDump {
+
+  def main(args: Array[String]): Unit = {
+    val log: Logger = LoggerFactory.getLogger(getClass)
+
+    new SparkCreatePubmedDump("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json", args, log).initialize().run()
+
+  }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
new file mode 100644
index 000000000..c9e868185
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
@@ -0,0 +1,264 @@
+package eu.dnetlib.dhp.sx.bio.pubmed
+
+import org.apache.commons.lang3.StringUtils
+
+import javax.xml.stream.XMLEventReader
+import scala.collection.JavaConverters._
+import scala.xml.{MetaData, NodeSeq}
+import scala.xml.pull.{EvElemEnd, EvElemStart, EvText}
+
+class PMParser2 {
+
+  /** Extracts the value of an attribute from a MetaData object.
+    * @param attrs the MetaData object
+    * @param key the key of the attribute
+    * @return the value of the attribute or null if the attribute is not found
+    */
+  private def extractAttributes(attrs: MetaData, key: String): String = {
+
+    val res = attrs.get(key)
+    if (res.isDefined) {
+      val s = res.get
+      if (s != null && s.nonEmpty)
+        s.head.text
+      else
+        null
+    } else null
+  }
+
+  /** Validates and formats a date given the year, month, and day as strings.
+    *
+    * @param year  the year as a string
+    * @param month the month as a string
+    * @param day   the day as a string
+    * @return      the formatted date as "YYYY-MM-DD" or null if the date is invalid
+    */
+  private def validate_Date(year: String, month: String, day: String): String = {
+    try {
+      f"${year.toInt}-${month.toInt}%02d-${day.toInt}%02d"
+
+    } catch {
+      case _: Throwable => null
+    }
+  }
+
+  /** Extracts the grant information from a NodeSeq object.
+    *
+    * @param gNode the NodeSeq object
+    * @return the grant information or an empty list if the grant information is not found
+    */
+  private def extractGrant(gNode: NodeSeq): List[PMGrant] = {
+    gNode
+      .map(node => {
+        val grantId = (node \ "GrantID").text
+        val agency = (node \ "Agency").text
+        val country = (node \ "Country").text
+        new PMGrant(grantId, agency, country)
+      })
+      .toList
+  }
+
+  /** Extracts the journal information from a NodeSeq object.
+    *
+    * @param jNode the NodeSeq object
+    * @return the journal information or null if the journal information is not found
+    */
+  private def extractJournal(jNode: NodeSeq): PMJournal = {
+    val journal = new PMJournal
+    journal.setTitle((jNode \ "Title").text)
+    journal.setIssn((jNode \ "ISSN").text)
+    journal.setVolume((jNode \ "JournalIssue" \ "Volume").text)
+    journal.setIssue((jNode \ "JournalIssue" \ "Issue").text)
+    if (journal.getTitle != null && StringUtils.isNotEmpty(journal.getTitle))
+      journal
+    else
+      null
+  }
+
+  private def extractAuthors(aNode: NodeSeq): List[PMAuthor] = {
+    aNode
+      .map(author => {
+        val a = new PMAuthor
+        a.setLastName((author \ "LastName").text)
+        a.setForeName((author \ "ForeName").text)
+        a
+      })
+      .toList
+  }
+
+  def parse(input: String): PMArticle = {
+    val xml = scala.xml.XML.loadString(input)
+    val article = new PMArticle
+
+    val grantNodes = xml \ "MedlineCitation" \\ "Grant"
+    article.setGrants(extractGrant(grantNodes).asJava)
+
+    val journal = xml \ "MedlineCitation" \ "Article" \ "Journal"
+    article.setJournal(extractJournal(journal))
+
+    val authors = xml \ "MedlineCitation" \ "Article" \ "AuthorList" \ "Author"
+
+    article.setAuthors(
+      authors
+        .map(author => {
+          val a = new PMAuthor
+          a.setLastName((author \ "LastName").text)
+          a.setForeName((author \ "ForeName").text)
+          a
+        })
+        .toList
+        .asJava
+    )
+
+    val pmId = xml \ "MedlineCitation" \ "PMID"
+
+    val articleIds = xml \ "PubmedData" \ "ArticleIdList" \ "ArticleId"
+    articleIds.foreach(articleId => {
+      val idType = (articleId \ "@IdType").text
+      val id = articleId.text
+      if ("doi".equalsIgnoreCase(idType)) article.setDoi(id)
+      if ("pmc".equalsIgnoreCase(idType)) article.setPmcId(id)
+    })
+    article.setPmid(pmId.text)
+
+    val pubMedPubDate = xml \ "MedlineCitation" \ "DateCompleted"
+    val currentDate =
+      validate_Date((pubMedPubDate \ "Year").text, (pubMedPubDate \ "Month").text, (pubMedPubDate \ "Day").text)
+    if (currentDate != null) article.setDate(currentDate)
+
+    val articleTitle = xml \ "MedlineCitation" \ "Article" \ "ArticleTitle"
+    article.setTitle(articleTitle.text)
+
+    val abstractText = xml \ "MedlineCitation" \ "Article" \ "Abstract" \ "AbstractText"
+    if (abstractText != null && abstractText.text != null && abstractText.text.nonEmpty)
+      article.setDescription(abstractText.text.split("\n").map(s => s.trim).mkString(" ").trim)
+
+    val language = xml \ "MedlineCitation" \ "Article" \ "Language"
+    article.setLanguage(language.text)
+
+    val subjects = xml \ "MedlineCitation" \ "MeshHeadingList" \ "MeshHeading"
+    article.setSubjects(
+      subjects
+        .take(20)
+        .map(subject => {
+          val descriptorName = (subject \ "DescriptorName").text
+          val ui = (subject \ "DescriptorName" \ "@UI").text
+          val s = new PMSubject
+          s.setValue(descriptorName)
+          s.setMeshId(ui)
+          s
+        })
+        .toList
+        .asJava
+    )
+    val publicationTypes = xml \ "MedlineCitation" \ "Article" \ "PublicationTypeList" \ "PublicationType"
+    article.setPublicationTypes(
+      publicationTypes
+        .map(pt => {
+          val s = new PMSubject
+          s.setValue(pt.text)
+          s
+        })
+        .toList
+        .asJava
+    )
+
+    article
+  }
+
+  def parse2(xml: XMLEventReader): PMArticle = {
+    var currentArticle: PMArticle = null
+    var currentSubject: PMSubject = null
+    var currentAuthor: PMAuthor = null
+    var currentJournal: PMJournal = null
+    var currentGrant: PMGrant = null
+    var currNode: String = null
+    var currentYear = "0"
+    var currentMonth = "01"
+    var currentDay = "01"
+    var currentArticleType: String = null
+
+    while (xml.hasNext) {
+      val ne = xml.next
+      ne match {
+        case EvElemStart(_, label, attrs, _) =>
+          currNode = label
+
+          label match {
+            case "PubmedArticle" => currentArticle = new PMArticle
+            case "Author"        => currentAuthor = new PMAuthor
+            case "Journal"       => currentJournal = new PMJournal
+            case "Grant"         => currentGrant = new PMGrant
+            case "PublicationType" | "DescriptorName" =>
+              currentSubject = new PMSubject
+              currentSubject.setMeshId(extractAttributes(attrs, "UI"))
+            case "ArticleId" => currentArticleType = extractAttributes(attrs, "IdType")
+            case _           =>
+          }
+        case EvElemEnd(_, label) =>
+          label match {
+            case "PubmedArticle" => return currentArticle
+            case "Author"        => currentArticle.getAuthors.add(currentAuthor)
+            case "Journal"       => currentArticle.setJournal(currentJournal)
+            case "Grant"         => currentArticle.getGrants.add(currentGrant)
+            case "PubMedPubDate" =>
+              if (currentArticle.getDate == null)
+                currentArticle.setDate(validate_Date(currentYear, currentMonth, currentDay))
+            case "PubDate"         => currentJournal.setDate(s"$currentYear-$currentMonth-$currentDay")
+            case "DescriptorName"  => currentArticle.getSubjects.add(currentSubject)
+            case "PublicationType" => currentArticle.getPublicationTypes.add(currentSubject)
+            case _                 =>
+          }
+        case EvText(text) =>
+          if (currNode != null && text.trim.nonEmpty)
+            currNode match {
+              case "ArticleTitle" => {
+                if (currentArticle.getTitle == null)
+                  currentArticle.setTitle(text.trim)
+                else
+                  currentArticle.setTitle(currentArticle.getTitle + text.trim)
+              }
+              case "AbstractText" => {
+                if (currentArticle.getDescription == null)
+                  currentArticle.setDescription(text.trim)
+                else
+                  currentArticle.setDescription(currentArticle.getDescription + text.trim)
+              }
+              case "PMID" => currentArticle.setPmid(text.trim)
+              case "ArticleId" =>
+                if ("doi".equalsIgnoreCase(currentArticleType)) currentArticle.setDoi(text.trim)
+                if ("pmc".equalsIgnoreCase(currentArticleType)) currentArticle.setPmcId(text.trim)
+              case "Language"                           => currentArticle.setLanguage(text.trim)
+              case "ISSN"                               => currentJournal.setIssn(text.trim)
+              case "GrantID"                            => currentGrant.setGrantID(text.trim)
+              case "Agency"                             => currentGrant.setAgency(text.trim)
+              case "Country"                            => if (currentGrant != null) currentGrant.setCountry(text.trim)
+              case "Year"                               => currentYear = text.trim
+              case "Month"                              => currentMonth = text.trim
+              case "Day"                                => currentDay = text.trim
+              case "Volume"                             => currentJournal.setVolume(text.trim)
+              case "Issue"                              => currentJournal.setIssue(text.trim)
+              case "PublicationType" | "DescriptorName" => currentSubject.setValue(text.trim)
+              case "LastName" => {
+                if (currentAuthor != null)
+                  currentAuthor.setLastName(text.trim)
+              }
+              case "ForeName" =>
+                if (currentAuthor != null)
+                  currentAuthor.setForeName(text.trim)
+              case "Title" =>
+                if (currentJournal.getTitle == null)
+                  currentJournal.setTitle(text.trim)
+                else
+                  currentJournal.setTitle(currentJournal.getTitle + text.trim)
+              case _ =>
+
+            }
+        case _ =>
+      }
+
+    }
+    null
+  }
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml
new file mode 100644
index 000000000..4b4d860d7
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml
@@ -0,0 +1,222 @@
+<PubmedArticle>
+    <MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM">
+        <PMID Version="1">37885214</PMID>
+        <DateCompleted>
+            <Year>2024</Year>
+            <Month>02</Month>
+            <Day>14</Day>
+        </DateCompleted>
+        <DateRevised>
+            <Year>2024</Year>
+            <Month>02</Month>
+            <Day>14</Day>
+        </DateRevised>
+        <Article PubModel="Print-Electronic">
+            <Journal>
+                <ISSN IssnType="Electronic">2752-7549</ISSN>
+                <JournalIssue CitedMedium="Internet">
+                    <Volume>40</Volume>
+                    <Issue>5</Issue>
+                    <PubDate>
+                        <MedlineDate>2023 Sep-Oct</MedlineDate>
+                    </PubDate>
+                </JournalIssue>
+                <Title>Journal of pediatric hematology/oncology nursing</Title>
+                <ISOAbbreviation>J Pediatr Hematol Oncol Nurs</ISOAbbreviation>
+            </Journal>
+            <ArticleTitle>Care Needs of Parents of Children With Cancer in a Low-Middle-Income Country.</ArticleTitle>
+            <Pagination>
+                <MedlinePgn>295-304</MedlinePgn>
+            </Pagination>
+            <ELocationID EIdType="doi" ValidYN="Y">10.1177/27527530231193972</ELocationID>
+            <Abstract>
+                <AbstractText><b>Background:</b> Mapping out actual supportive care needs assists nurses in providing holistic individualized care. This study aimed to explore the care needs of parents of children with cancer in the Philippines. <b>Method:</b> Guided by the Supportive Care Needs Framework (SCNF), this study used an embedded mixed-method design with the quantitative revised Cancer Patient Needs Questionnaire and qualitative semistructured interviews to describe parents' care needs and priorities. <b>Results:</b> Filipino parents (<i>N</i> = 156) of children with cancer have various care needs which could be classified along the SCNF categories-practical, informational, spiritual, physical, emotional, and physical needs as ranked from highest to lowest. A number of variables were significantly associated with care needs. Solid tumor diagnosis was associated with greater practical, emotional, and psychosocial care needs; having a child who had undergone surgery was associated with more practical and spiritual care needs; and being within one year of the child's diagnosis was associated with practical, psychosocial, and spiritual care needs. Parent priority needs included (a) addressing financial needs; (b) access to temporary housing to minimize treatment-related costs; (c) support groups among parents of children with cancer as a source of information; (d) financial and social support between members of family and partners of parents of children with cancer; and (e) using prayer to facilitate acceptance. <b>Conclusions:</b> Supportive care needs of parents of children with cancer are important components of care that should be given recognition to enhance holistic individualized care throughout the childhood cancer experience.</AbstractText>
+            </Abstract>
+            <AuthorList CompleteYN="Y">
+                <Author ValidYN="Y">
+                    <LastName>Banayat</LastName>
+                    <ForeName>Aprille Campos</ForeName>
+                    <Initials>AC</Initials>
+                    <Identifier Source="ORCID">0000-0001-9339-9871</Identifier>
+                    <AffiliationInfo>
+                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                    </AffiliationInfo>
+                </Author>
+                <Author ValidYN="Y">
+                    <LastName>Abad</LastName>
+                    <ForeName>Peter James B</ForeName>
+                    <Initials>PJB</Initials>
+                    <AffiliationInfo>
+                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                    </AffiliationInfo>
+                </Author>
+                <Author ValidYN="Y">
+                    <LastName>Bonito</LastName>
+                    <ForeName>Sheila R</ForeName>
+                    <Initials>SR</Initials>
+                    <AffiliationInfo>
+                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                    </AffiliationInfo>
+                </Author>
+                <Author ValidYN="Y">
+                    <LastName>Manahan</LastName>
+                    <ForeName>Lydia T</ForeName>
+                    <Initials>LT</Initials>
+                    <AffiliationInfo>
+                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                    </AffiliationInfo>
+                </Author>
+                <Author ValidYN="Y">
+                    <LastName>Peralta</LastName>
+                    <ForeName>Arnold B</ForeName>
+                    <Initials>AB</Initials>
+                    <AffiliationInfo>
+                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                    </AffiliationInfo>
+                </Author>
+            </AuthorList>
+            <Language>eng</Language>
+            <PublicationTypeList>
+                <PublicationType UI="D016428">Journal Article</PublicationType>
+            </PublicationTypeList>
+            <ArticleDate DateType="Electronic">
+                <Year>2023</Year>
+                <Month>10</Month>
+                <Day>26</Day>
+            </ArticleDate>
+        </Article>
+        <MedlineJournalInfo>
+            <Country>United States</Country>
+            <MedlineTA>J Pediatr Hematol Oncol Nurs</MedlineTA>
+            <NlmUniqueID>9918282681506676</NlmUniqueID>
+            <ISSNLinking>2752-7530</ISSNLinking>
+        </MedlineJournalInfo>
+        <CitationSubset>IM</CitationSubset>
+        <MeshHeadingList>
+            <MeshHeading>
+                <DescriptorName UI="D002648" MajorTopicYN="N">Child</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D010290" MajorTopicYN="Y">Parents</DescriptorName>
+                <QualifierName UI="Q000523" MajorTopicYN="N">psychology</QualifierName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D012944" MajorTopicYN="N">Social Support</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D029181" MajorTopicYN="N">Spirituality</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D012067" MajorTopicYN="N">Religion</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D009369" MajorTopicYN="Y">Neoplasms</DescriptorName>
+                <QualifierName UI="Q000628" MajorTopicYN="N">therapy</QualifierName>
+            </MeshHeading>
+        </MeshHeadingList>
+        <KeywordList Owner="NOTNLM">
+            <Keyword MajorTopicYN="N">cancer</Keyword>
+            <Keyword MajorTopicYN="N">mixed methods</Keyword>
+            <Keyword MajorTopicYN="N">parent</Keyword>
+            <Keyword MajorTopicYN="N">pediatric</Keyword>
+            <Keyword MajorTopicYN="N">research</Keyword>
+            <Keyword MajorTopicYN="N">supportive care</Keyword>
+        </KeywordList>
+        <CoiStatement>Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.</CoiStatement>
+    </MedlineCitation>
+    <PubmedData>
+        <History>
+            <PubMedPubDate PubStatus="medline">
+                <Year>2024</Year>
+                <Month>2</Month>
+                <Day>12</Day>
+                <Hour>18</Hour>
+                <Minute>42</Minute>
+            </PubMedPubDate>
+            <PubMedPubDate PubStatus="pubmed">
+                <Year>2023</Year>
+                <Month>10</Month>
+                <Day>27</Day>
+                <Hour>6</Hour>
+                <Minute>42</Minute>
+            </PubMedPubDate>
+            <PubMedPubDate PubStatus="entrez">
+                <Year>2023</Year>
+                <Month>10</Month>
+                <Day>27</Day>
+                <Hour>3</Hour>
+                <Minute>43</Minute>
+            </PubMedPubDate>
+        </History>
+        <PublicationStatus>ppublish</PublicationStatus>
+        <ArticleIdList>
+            <ArticleId IdType="pubmed">37885214</ArticleId>
+            <ArticleId IdType="doi">10.1177/27527530231193972</ArticleId>
+        </ArticleIdList>
+    </PubmedData>
+</PubmedArticle>
+<DeleteCitation>
+<PMID Version="1">30522158</PMID>
+<PMID Version="1">32769323</PMID>
+<PMID Version="1">34061701</PMID>
+<PMID Version="1">34661197</PMID>
+<PMID Version="1">34837091</PMID>
+<PMID Version="1">35035475</PMID>
+<PMID Version="1">35211699</PMID>
+<PMID Version="1">35557982</PMID>
+<PMID Version="1">35782783</PMID>
+<PMID Version="1">35795240</PMID>
+<PMID Version="1">35832688</PMID>
+<PMID Version="1">35847411</PMID>
+<PMID Version="1">36081602</PMID>
+<PMID Version="1">36081858</PMID>
+<PMID Version="1">36468085</PMID>
+<PMID Version="1">36468934</PMID>
+<PMID Version="1">36580086</PMID>
+<PMID Version="1">36589526</PMID>
+<PMID Version="1">36619609</PMID>
+<PMID Version="1">36649460</PMID>
+<PMID Version="1">36654909</PMID>
+<PMID Version="1">36655054</PMID>
+<PMID Version="1">36700856</PMID>
+<PMID Version="1">36705625</PMID>
+<PMID Version="1">36713939</PMID>
+<PMID Version="1">36714172</PMID>
+<PMID Version="1">36741203</PMID>
+<PMID Version="1">36741905</PMID>
+<PMID Version="1">36743825</PMID>
+<PMID Version="1">36788221</PMID>
+<PMID Version="1">36844926</PMID>
+<PMID Version="1">36846546</PMID>
+<PMID Version="1">36935776</PMID>
+<PMID Version="1">36946757</PMID>
+<PMID Version="1">36972191</PMID>
+<PMID Version="1">37034422</PMID>
+<PMID Version="1">37124311</PMID>
+<PMID Version="1">37152108</PMID>
+<PMID Version="1">37171968</PMID>
+<PMID Version="1">37273889</PMID>
+<PMID Version="1">37333905</PMID>
+<PMID Version="1">37387733</PMID>
+<PMID Version="1">37431449</PMID>
+<PMID Version="1">37576947</PMID>
+<PMID Version="1">37601162</PMID>
+<PMID Version="1">37711214</PMID>
+<PMID Version="1">37901290</PMID>
+<PMID Version="1">37981909</PMID>
+<PMID Version="1">37981945</PMID>
+<PMID Version="1">37982005</PMID>
+<PMID Version="1">38037601</PMID>
+<PMID Version="1">38037602</PMID>
+<PMID Version="1">38150730</PMID>
+<PMID Version="1">38274640</PMID>
+<PMID Version="1">38332671</PMID>
+<PMID Version="1">38334184</PMID>
+<PMID Version="1">38335456</PMID>
+<PMID Version="1">38349506</PMID>
+<PMID Version="1">38349576</PMID>
+<PMID Version="1">38353676</PMID>
+</DeleteCitation>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
index c4af14c40..1374b741d 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
@@ -5,7 +5,10 @@ import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
 import eu.dnetlib.dhp.schema.oaf.utils.PidType
 import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result}
 import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
-import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PMSubject, PubMedToOaf}
+import eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PMParser2, PMSubject, PubMedToOaf}
+import org.apache.commons.io.IOUtils
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.parse
@@ -13,8 +16,9 @@ import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.extension.ExtendWith
 import org.junit.jupiter.api.{BeforeEach, Test}
 import org.mockito.junit.jupiter.MockitoExtension
+import org.slf4j.LoggerFactory
 
-import java.io.{BufferedReader, InputStream, InputStreamReader}
+import java.io.{BufferedReader, ByteArrayInputStream, InputStream, InputStreamReader}
 import java.util.zip.GZIPInputStream
 import javax.xml.stream.XMLInputFactory
 import scala.collection.JavaConverters._
@@ -48,6 +52,17 @@ class BioScholixTest extends AbstractVocabularyTest {
     }
   }
 
+  @Test
+  def testParsingPubmed2(): Unit = {
+    val mapper = new ObjectMapper()
+    val xml = IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml"))
+    val parser = new PMParser2()
+    val article = parser.parse(xml)
+
+    println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(article))
+
+  }
+
   @Test
   def testEBIData() = {
     val inputFactory = XMLInputFactory.newInstance
@@ -124,6 +139,15 @@ class BioScholixTest extends AbstractVocabularyTest {
     }
   }
 
+  @Test
+  def testPubmedSplitting(): Unit = {
+
+    val spark: SparkSession = SparkSession.builder().appName("test").master("local").getOrCreate()
+    new SparkCreatePubmedDump("", Array.empty, LoggerFactory.getLogger(getClass))
+      .createPubmedDump(spark, "/home/sandro/Downloads/pubmed", "/home/sandro/Downloads/pubmed_mapped", vocabularies)
+
+  }
+
   @Test
   def testPubmedOriginalID(): Unit = {
     val article: PMArticle = new PMArticle

From c1cef5d685373ad28dac341b56fc459cd43ff606 Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@gmail.com>
Date: Tue, 5 Nov 2024 10:38:40 +0100
Subject: [PATCH 191/239] removed old library joda time replaced with standard
 java.time introduced in java 8

---
 .../plugin/gtr2/Gtr2PublicationsIterator.java | 26 +++++++++----------
 1 file changed, 13 insertions(+), 13 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
index 5b8f48680..779c43712 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
@@ -1,6 +1,8 @@
 
 package eu.dnetlib.dhp.collection.plugin.gtr2;
 
+import java.nio.charset.StandardCharsets;
+import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -16,9 +18,7 @@ import org.dom4j.Document;
 import org.dom4j.DocumentException;
 import org.dom4j.DocumentHelper;
 import org.dom4j.Element;
-import org.joda.time.DateTime;
-import org.joda.time.format.DateTimeFormat;
-import org.joda.time.format.DateTimeFormatter;
+import java.time.format.DateTimeFormatter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -33,7 +33,7 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 	private static final Logger log = LoggerFactory.getLogger(Gtr2PublicationsIterator.class);
 
 	private final HttpConnector2 connector;
-	private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormat.forPattern("yyyy-MM-dd");
+	private static final DateTimeFormatter simpleDateTimeFormatter = DateTimeFormatter.ofPattern("yyyy-MM-dd");
 
 	private static final int MAX_ATTEMPTS = 10;
 
@@ -41,7 +41,7 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 	private int currPage;
 	private int endPage;
 	private boolean incremental = false;
-	private DateTime fromDate;
+	private LocalDate fromDate;
 
 	private final Map<String, String> cache = new HashMap<>();
 
@@ -188,28 +188,28 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 
 	private Document loadURL(final String cleanUrl, final int attempt) {
 		try {
-			log.debug("  * Downloading Url: " + cleanUrl);
-			final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes("UTF-8");
+            log.debug("  * Downloading Url: {}", cleanUrl);
+			final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes(StandardCharsets.UTF_8);
 			return DocumentHelper.parseText(new String(bytes));
 		} catch (final Throwable e) {
-			log.error("Error dowloading url: " + cleanUrl + ", attempt = " + attempt, e);
+            log.error("Error dowloading url: {}, attempt = {}", cleanUrl, attempt, e);
 			if (attempt >= MAX_ATTEMPTS) {
-				throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
+				throw new RuntimeException("Error downloading url: " + cleanUrl, e);
 			}
 			try {
 				Thread.sleep(60000); // I wait for a minute
 			} catch (final InterruptedException e1) {
-				throw new RuntimeException("Error dowloading url: " + cleanUrl, e);
+				throw new RuntimeException("Error downloading url: " + cleanUrl, e);
 			}
 			return loadURL(cleanUrl, attempt + 1);
 		}
 	}
 
-	private DateTime parseDate(final String s) {
-		return DateTime.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter);
+	private LocalDate parseDate(final String s) {
+		return LocalDate.parse(s.contains("T") ? s.substring(0, s.indexOf("T")) : s, simpleDateTimeFormatter);
 	}
 
-	private boolean isAfter(final String d, final DateTime fromDate) {
+	private boolean isAfter(final String d, final LocalDate fromDate) {
 		return StringUtils.isNotBlank(d) && parseDate(d).isAfter(fromDate);
 	}
 }

From 973aa7dca6508e2c1e82fa7c775b3d40c18fe45b Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 6 Nov 2024 12:29:06 +0100
Subject: [PATCH 192/239] [dedup] force the Relation schema when reading the
 merge rels

---
 .../java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java     | 1 +
 1 file changed, 1 insertion(+)

diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
index c7efce4d7..b0bc314e2 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java
@@ -69,6 +69,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 
 		Dataset<Relation> mergeRels = spark
 			.read()
+			.schema(REL_BEAN_ENC.schema())
 			.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
 			.as(REL_BEAN_ENC);
 

From f7bb53fe7895105f4a7a73b7de14cd6b4121589e Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Thu, 7 Nov 2024 01:04:43 +0100
Subject: [PATCH 193/239] [orcid enrichment] added missing workflow parameter:
 workingDir

---
 .../resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml
index 4031da15a..1ece2c0be 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml
@@ -51,6 +51,7 @@
             <arg>--orcidPath</arg><arg>${orcidPath}</arg>
             <arg>--targetPath</arg><arg>${targetPath}</arg>
             <arg>--graphPath</arg><arg>${graphPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
             <arg>--master</arg><arg>yarn</arg>
         </spark>
         <ok to="reset_outputpath"/>

From 8f5171557e20ed58f69f7abe3af1ad0a85b10ba3 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Thu, 7 Nov 2024 12:22:34 +0100
Subject: [PATCH 194/239] Remove ORCID information when the same ORCID ID is
 used multiple times in the same result for different authors

---
 .../oaf/utils/GraphCleaningFunctions.java     | 36 ++++++++++++++++++-
 1 file changed, 35 insertions(+), 1 deletion(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
index b6574da16..9153a6476 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
@@ -2,7 +2,6 @@
 package eu.dnetlib.dhp.schema.oaf.utils;
 
 import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
 
 import java.net.MalformedURLException;
@@ -696,6 +695,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						}
 					}
 
+					// set ORCID_PENDING to all orcid values that are not coming from ORCID provenance
 					for (Author a : r.getAuthor()) {
 						if (Objects.isNull(a.getPid())) {
 							a.setPid(Lists.newArrayList());
@@ -752,6 +752,40 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 										.collect(Collectors.toList()));
 						}
 					}
+
+					// Identify clashing ORCIDS:that is same ORCID associated to multiple authors in this result
+					Map<String, Integer> clashing_orcid = new HashMap<>();
+
+					for (Author a : r.getAuthor()) {
+						a
+							.getPid()
+							.stream()
+							.filter(
+								p -> StringUtils
+									.contains(StringUtils.lowerCase(p.getQualifier().getClassid()), ORCID_PENDING))
+							.map(StructuredProperty::getValue)
+							.distinct()
+							.forEach(orcid -> clashing_orcid.compute(orcid, (k, v) -> (v == null) ? 1 : v + 1));
+					}
+
+					Set<String> clashing = clashing_orcid
+						.entrySet()
+						.stream()
+						.filter(ee -> ee.getValue() > 1)
+						.map(Map.Entry::getKey)
+						.collect(Collectors.toSet());
+
+					// filter out clashing orcids
+					for (Author a : r.getAuthor()) {
+						a
+							.setPid(
+								a
+									.getPid()
+									.stream()
+									.filter(p -> !clashing.contains(p.getValue()))
+									.collect(Collectors.toList()));
+					}
+
 				}
 				if (value instanceof Publication) {
 

From 6fd9ec856608c3ca9baeedfa3677a64287483d92 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 7 Nov 2024 13:55:31 +0100
Subject: [PATCH 195/239] [danishfunders] added link for danish funders versus
 the unidentified project for IRFD (501100004836) CF (501100002808) and
 NNF(501100009708)

---
 .../doiboost/crossref/Crossref2Oaf.scala       | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
index f284a063e..bf11ed0a8 100644
--- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
@@ -566,7 +566,23 @@ case object Crossref2Oaf {
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             case _ => logger.debug("no match for " + funder.DOI.get)
-
+            //Add for Danish funders
+            //Independent Research Fund Denmark (IRFD)
+            case "10.13039/501100004836" =>
+              val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Carlsberg Foundation (CF)
+            case "10.13039/501100002808" =>
+              val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Novo Nordisk Foundation (NNF)
+            case "10.13039/501100009708" =>
+              val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            case _ => logger.debug("no match for " + funder.DOI.get)
           }
 
         } else {

From 0d0904f4ec2b1d4424d5d8d5d6d782049c0544cd Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@gmail.com>
Date: Mon, 11 Nov 2024 10:27:23 +0100
Subject: [PATCH 196/239] updated workflow baseline to direct transform on OAF

---
 .../sx/bio/ebi/baseline_to_oaf_params.json    |  8 ++---
 .../dhp/sx/bio/pubmed/oozie_app/workflow.xml  | 17 ++++-------
 .../sx/bio/ebi/SparkCreatePubmedDump.scala    | 29 ++++++++++++-------
 3 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
index 8326fab0f..0fcc03266 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json
@@ -1,7 +1,7 @@
 [
-  {"paramName":"mt",  "paramLongName":"master",         "paramDescription": "should be local or yarn",                  "paramRequired": true},
-  {"paramName":"i",   "paramLongName":"isLookupUrl",    "paramDescription": "isLookupUrl",                              "paramRequired": true},
-  {"paramName":"s",   "paramLongName":"sourcePath",    "paramDescription": "the baseline path",  "paramRequired": true},
-  {"paramName":"t",   "paramLongName":"targetPath",     "paramDescription": "the mdstore path to save",                 "paramRequired": true}
+  {"paramName":"mt",  "paramLongName":"master",               "paramDescription": "should be local or yarn",                  "paramRequired": true},
+  {"paramName":"i",   "paramLongName":"isLookupUrl",          "paramDescription": "isLookupUrl",                              "paramRequired": true},
+  {"paramName":"s",   "paramLongName":"sourcePath",           "paramDescription": "the baseline path",                        "paramRequired": true},
+  {"paramName":"mo",  "paramLongName":"mdstoreOutputVersion", "paramDescription": "the mdstore path to save",                 "paramRequired": true}
 
 ]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
index 30eb41469..0f4c5c249 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
@@ -16,11 +16,6 @@
             <name>mdStoreManagerURI</name>
             <description>the path of the cleaned mdstore</description>
         </property>
-        <property>
-            <name>skipUpdate</name>
-            <value>false</value>
-            <description>The request block size</description>
-        </property>
     </parameters>
 
     <start to="StartTransaction"/>
@@ -44,16 +39,16 @@
             <arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
             <capture-output/>
         </java>
-        <ok to="ConvertDataset"/>
+        <ok to="TransformPubMed"/>
         <error to="RollBack"/>
     </action>
 
-    <action name="ConvertDataset">
+    <action name="TransformPubMed">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>Convert Baseline to OAF Dataset</name>
-            <class>eu.dnetlib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
+            <name>Convert Baseline Pubmed to OAF Dataset</name>
+            <class>eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump</class>
             <jar>dhp-aggregation-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}
@@ -65,12 +60,10 @@
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
-            <arg>--workingPath</arg><arg>${baselineWorkingPath}</arg>
+            <arg>--sourcePath</arg><arg>${baselineWorkingPath}</arg>
             <arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
             <arg>--master</arg><arg>yarn</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
-            <arg>--skipUpdate</arg><arg>${skipUpdate}</arg>
         </spark>
         <ok to="CommitVersion"/>
         <error to="RollBack"/>
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
index c21bfd7c3..1bdd2a4bc 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
@@ -1,18 +1,14 @@
 package eu.dnetlib.dhp.sx.bio.ebi
 
 import com.fasterxml.jackson.databind.ObjectMapper
-import eu.dnetlib.dhp.application.{AbstractScalaApplication, ArgumentApplicationParser}
+import eu.dnetlib.dhp.application.AbstractScalaApplication
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
-import eu.dnetlib.dhp.schema.oaf.Oaf
-import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PMParser2, PubMedToOaf}
+import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
+import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser2, PubMedToOaf}
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
-import org.apache.spark.sql.functions._
-import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
+import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
 
-import java.io.ByteArrayInputStream
-import javax.xml.stream.XMLInputFactory
-
 class SparkCreatePubmedDump(propertyPath: String, args: Array[String], log: Logger)
     extends AbstractScalaApplication(propertyPath, args, log: Logger) {
 
@@ -24,16 +20,26 @@ class SparkCreatePubmedDump(propertyPath: String, args: Array[String], log: Logg
     log.info("isLookupUrl: {}", isLookupUrl)
     val sourcePath = parser.get("sourcePath")
     log.info(s"SourcePath is '$sourcePath'")
-    val targetPath = parser.get("targetPath")
-    log.info(s"TargetPath is '$targetPath'")
+    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
+    log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")
+    val mapper = new ObjectMapper()
+    val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
+    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
+    log.info(s"outputBasePath is '$outputBasePath'")
 
     val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
     val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
 
-    createPubmedDump(spark, sourcePath, targetPath, vocabularies)
+    createPubmedDump(spark, sourcePath, outputBasePath, vocabularies)
 
   }
 
+  /** This method creates a dump of the pubmed articles
+    * @param spark the spark session
+    * @param sourcePath the path of the source file
+    * @param targetPath the path of the target file
+    * @param vocabularies the vocabularies
+    */
   def createPubmedDump(
     spark: SparkSession,
     sourcePath: String,
@@ -54,6 +60,7 @@ class SparkCreatePubmedDump(propertyPath: String, args: Array[String], log: Logg
       })
       .filter(s => s != null)
       .map { i =>
+        //remove try catch
         try {
           new PMParser2().parse(i)
         } catch {

From 19ce783e58f4f9176f4dc9a98d9bb250dc615e0d Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Mon, 11 Nov 2024 12:28:02 +0100
Subject: [PATCH 197/239] renamed workflow

---
 .../eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
index 0f4c5c249..2a51b4050 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml
@@ -1,4 +1,4 @@
-<workflow-app name="Download_Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>baselineWorkingPath</name>

From 474f365286b7f83b8d58e4969277b3e67ebdd0cc Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Mon, 11 Nov 2024 12:37:27 +0100
Subject: [PATCH 198/239] removed wrong test

---
 .../test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
index 1374b741d..c942ca132 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
@@ -6,9 +6,9 @@ import eu.dnetlib.dhp.schema.oaf.utils.PidType
 import eu.dnetlib.dhp.schema.oaf.{Oaf, Publication, Relation, Result}
 import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
 import eu.dnetlib.dhp.sx.bio.ebi.SparkCreatePubmedDump
-import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PMParser2, PMSubject, PubMedToOaf}
+import eu.dnetlib.dhp.sx.bio.pubmed._
 import org.apache.commons.io.IOUtils
-import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
+import org.apache.spark.sql.SparkSession
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.parse
@@ -18,13 +18,12 @@ import org.junit.jupiter.api.{BeforeEach, Test}
 import org.mockito.junit.jupiter.MockitoExtension
 import org.slf4j.LoggerFactory
 
-import java.io.{BufferedReader, ByteArrayInputStream, InputStream, InputStreamReader}
+import java.io.{BufferedReader, InputStream, InputStreamReader}
 import java.util.zip.GZIPInputStream
 import javax.xml.stream.XMLInputFactory
 import scala.collection.JavaConverters._
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
-import scala.xml.pull.XMLEventReader
 
 @ExtendWith(Array(classOf[MockitoExtension]))
 class BioScholixTest extends AbstractVocabularyTest {
@@ -139,7 +138,6 @@ class BioScholixTest extends AbstractVocabularyTest {
     }
   }
 
-  @Test
   def testPubmedSplitting(): Unit = {
 
     val spark: SparkSession = SparkSession.builder().appName("test").master("local").getOrCreate()

From b0283fe94c168b87176f283f414ef2c4dfd3cdab Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 11 Nov 2024 14:57:57 +0100
Subject: [PATCH 199/239] [person] fix provenance of pid in person when it is
 orcid (classid entityregistry to avoid the cleaning put orcid_pending)

---
 .../dhp/actionmanager/personentity/ExtractPerson.java | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index bf2c19c3d..6830f2291 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -345,7 +345,16 @@ public class ExtractPerson implements Serializable {
 					OafMapperUtils
 						.structuredProperty(
 							op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME,
-							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null));
+							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,
+								OafMapperUtils.dataInfo(false,
+										null,
+										false,
+										false,
+										OafMapperUtils.qualifier(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
+												ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
+												ModelConstants.DNET_PID_TYPES,
+												ModelConstants.DNET_PID_TYPES),
+								"0.91")));
 			person.setDateofcollection(op.getLastModifiedDate());
 			person.setOriginalId(Arrays.asList(op.getOrcid()));
 			person.setDataInfo(ORCIDDATAINFO);

From f1ea9da5bcda277451416253982c24233e40d87b Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 11 Nov 2024 15:37:56 +0100
Subject: [PATCH 200/239] [person] checked type in inferenceprovenance

---
 .../bipaffiliations/PrepareAffiliationRelations.java | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
index 15c1cc376..75e58e665 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java
@@ -104,22 +104,22 @@ public class PrepareAffiliationRelations implements Serializable {
 			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
 		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
-			spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::crossref");
+			spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":crossref");
 
 		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-			spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::pubmed");
+			spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":pubmed");
 
 		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel(
-			spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::openapc");
+			spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":openapc");
 
 		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelationsNewModel(
-			spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::datacite");
+			spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":datacite");
 
 		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelationsNewModel(
-			spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::rawaff");
+			spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":rawaff");
 
 		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisherNewModel(
-			spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::webcrawl");
+			spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":webcrawl");
 
 		crossrefRelations
 			.union(pubmedRelations)

From 250f101779a16ffbec1c16d3e0dc1050d6533c87 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 11 Nov 2024 16:04:06 +0100
Subject: [PATCH 201/239] [person] fixed issue in creating project identifier
 for the graph for person->project relations

---
 .../dhp/actionmanager/personentity/ExtractPerson.java        | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 6830f2291..6976def4c 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -15,6 +15,7 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.StringUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
@@ -193,8 +194,8 @@ public class ExtractPerson implements Serializable {
 	private static Relation getProjectRelation(String project, String orcid, String role) {
 
 		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
-		String target = PROJECT_ID_PREFIX + project.substring(0, 14)
-			+ IdentifierFactory.md5(project.substring(15));
+		String target = PROJECT_ID_PREFIX + StringUtils.substringBefore(project, "::") + "::"
+			+ IdentifierFactory.md5(StringUtils.substringAfter(project, "::"));
 		List<KeyValue> properties = new ArrayList<>();
 
 		Relation relation = OafMapperUtils

From 6c5df761e21d5aea6c203cb2ca2374b33a9219e5 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 12 Nov 2024 14:18:04 +0100
Subject: [PATCH 202/239] enforce resulttype based on the
 dnet:result_typologies vocabulary and upon merge

---
 .../dhp/oa/merge/GroupEntitiesSparkJob.java   |  7 ++-
 .../dhp/schema/oaf/utils/MergeUtils.java      | 62 ++++++++++++++++---
 .../dhp/oa/dedup/DedupRecordFactory.java      |  2 +-
 .../dhp/oa/dedup/DatasetMergerTest.java       |  4 +-
 .../raw/AbstractMdRecordToOafMapper.java      | 11 ++--
 .../raw/GenerateEntitiesApplication.java      |  2 +-
 .../dhp/sx/graph/SparkCreateInputGraph.scala  |  2 +-
 7 files changed, 66 insertions(+), 24 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java
index 24de1a787..98ec09277 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java
@@ -2,8 +2,7 @@
 package eu.dnetlib.dhp.oa.merge;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.col;
-import static org.apache.spark.sql.functions.when;
+import static org.apache.spark.sql.functions.*;
 
 import java.util.Map;
 import java.util.Optional;
@@ -135,7 +134,9 @@ public class GroupEntitiesSparkJob {
 					.applyCoarVocabularies(entity, vocs),
 				OAFENTITY_KRYO_ENC)
 			.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, OafEntity, OafEntity>) MergeUtils::mergeById, OAFENTITY_KRYO_ENC)
+			.mapGroups(
+				(MapGroupsFunction<String, OafEntity, OafEntity>) (key, group) -> MergeUtils.mergeById(group, vocs),
+				OAFENTITY_KRYO_ENC)
 			.map(
 				(MapFunction<OafEntity, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
 					t.getClass().getName(), t),
diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index 4c411a155..d7e08fca7 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -23,24 +23,30 @@ import org.apache.commons.lang3.tuple.Pair;
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.base.Joiner;
 
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 
 public class MergeUtils {
 
-	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
-		return mergeGroup(s, oafEntityIterator, true);
+	public static <T extends Oaf> T mergeById(Iterator<T> oafEntityIterator, VocabularyGroup vocs) {
+		return mergeGroup(oafEntityIterator, true, vocs);
 	}
 
-	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator) {
-		return mergeGroup(s, oafEntityIterator, false);
+	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator) {
+		return mergeGroup(oafEntityIterator, false);
 	}
 
-	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
-		boolean checkDelegateAuthority) {
+	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator, boolean checkDelegateAuthority) {
+		return mergeGroup(oafEntityIterator, checkDelegateAuthority, null);
+	}
+
+	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator,
+		boolean checkDelegateAuthority, VocabularyGroup vocs) {
 
 		ArrayList<T> sortedEntities = new ArrayList<>();
 		oafEntityIterator.forEachRemaining(sortedEntities::add);
@@ -49,13 +55,49 @@ public class MergeUtils {
 		Iterator<T> it = sortedEntities.iterator();
 		T merged = it.next();
 
-		while (it.hasNext()) {
-			merged = checkedMerge(merged, it.next(), checkDelegateAuthority);
+		if (!it.hasNext() && merged instanceof Result && vocs != null) {
+			return enforceResultType(vocs, (Result) merged);
+		} else {
+			while (it.hasNext()) {
+				merged = checkedMerge(merged, it.next(), checkDelegateAuthority);
+			}
 		}
-
 		return merged;
 	}
 
+	private static <T extends Oaf> T enforceResultType(VocabularyGroup vocs, Result mergedResult) {
+		if (Optional.ofNullable(mergedResult.getInstance()).map(List::isEmpty).orElse(true)) {
+			return (T) mergedResult;
+		} else {
+			final Instance i = mergedResult.getInstance().get(0);
+
+			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
+				return (T) mergedResult;
+			} else {
+				final Qualifier expectedResultType = vocs
+					.getSynonymAsQualifier(
+						ModelConstants.DNET_RESULT_TYPOLOGIES,
+						i.getInstancetype().getClassid());
+
+				// there is a clash among the result types
+				if (!expectedResultType.getClassid().equals(mergedResult.getResulttype().getClassid())) {
+					try {
+						String resulttype = expectedResultType.getClassid();
+						if (EntityType.otherresearchproduct.toString().equals(resulttype)) {
+							resulttype = "other";
+						}
+						Result result = (Result) ModelSupport.oafTypes.get(resulttype).newInstance();
+						return (T) mergeResultFields(result, mergedResult);
+					} catch (InstantiationException | IllegalAccessException e) {
+						throw new IllegalStateException(e);
+					}
+				} else {
+					return (T) mergedResult;
+				}
+			}
+		}
+	}
+
 	public static <T extends Oaf> T checkedMerge(final T left, final T right, boolean checkDelegateAuthority) {
 		return (T) merge(left, right, checkDelegateAuthority);
 	}
@@ -106,7 +148,7 @@ public class MergeUtils {
 				return mergeSoftware((Software) left, (Software) right);
 			}
 
-			return mergeResultFields((Result) left, (Result) right);
+			return left;
 		} else if (sameClass(left, right, Datasource.class)) {
 			// TODO
 			final int trust = compareTrust(left, right);
diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
index 44482cfdb..f6a436543 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java
@@ -135,7 +135,7 @@ public class DedupRecordFactory {
 						return Collections.emptyIterator();
 					}
 
-					OafEntity mergedEntity = MergeUtils.mergeGroup(dedupId, cliques.iterator());
+					OafEntity mergedEntity = MergeUtils.mergeGroup(cliques.iterator());
 					// dedup records do not have date of transformation attribute
 					mergedEntity.setDateoftransformation(null);
 					mergedEntity
diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java
index 726814c43..a79047590 100644
--- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java
+++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/DatasetMergerTest.java
@@ -46,8 +46,8 @@ class DatasetMergerTest implements Serializable {
 	}
 
 	@Test
-	void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
-		Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
+	void datasetMergerTest() {
+		Dataset pub_merged = MergeUtils.mergeGroup(datasets.stream().map(Tuple2::_2).iterator());
 
 		// verify id
 		assertEquals(dedupId, pub_merged.getId());
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
index 2436a272c..ba6887a2e 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
@@ -155,7 +155,7 @@ public abstract class AbstractMdRecordToOafMapper {
 
 			final List<Instance> instances = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
 
-			final String type = getResultType(doc, instances);
+			final String type = getResultType(instances);
 
 			return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp);
 		} catch (final DocumentException e) {
@@ -164,10 +164,9 @@ public abstract class AbstractMdRecordToOafMapper {
 		}
 	}
 
-	protected String getResultType(final Document doc, final List<Instance> instances) {
-		final String type = doc.valueOf("//dr:CobjCategory/@type");
+	protected String getResultType(final List<Instance> instances) {
 
-		if (StringUtils.isBlank(type) && this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
+		if (this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
 			final String instanceType = instances
 				.stream()
 				.map(i -> i.getInstancetype().getClassid())
@@ -178,9 +177,9 @@ public abstract class AbstractMdRecordToOafMapper {
 				.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
 				.map(Qualifier::getClassid)
 				.orElse("0000");
+		} else {
+			throw new IllegalStateException("Missing vocabulary: " + ModelConstants.DNET_RESULT_TYPOLOGIES);
 		}
-
-		return type;
 	}
 
 	private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) {
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
index c3806c211..357fae470 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
@@ -133,7 +133,7 @@ public class GenerateEntitiesApplication extends AbstractMigrationApplication {
 					inputRdd
 						.keyBy(oaf -> ModelSupport.idFn().apply(oaf))
 						.groupByKey()
-						.map(t -> MergeUtils.mergeGroup(t._1, t._2.iterator())),
+						.map(t -> MergeUtils.mergeGroup(t._2.iterator())),
 					// .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
 					// .reduceByKey(MergeUtils::merge)
 					// .map(Tuple2::_2),
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala
index d94a23947..42299cd34 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkCreateInputGraph.scala
@@ -133,7 +133,7 @@ object SparkCreateInputGraph {
     val ds: Dataset[T] = spark.read.load(sourcePath).as[T]
 
     ds.groupByKey(_.getId)
-      .mapGroups { (id, it) => MergeUtils.mergeGroup(id, it.asJava).asInstanceOf[T] }
+      .mapGroups { (id, it) => MergeUtils.mergeGroup(it.asJava).asInstanceOf[T] }
 //      .reduceGroups { (x: T, y: T) => MergeUtils.merge(x, y).asInstanceOf[T] }
 //      .map(_)
       .write

From 07f267bb10911d62e30a2b299db3c50fcd1746a2 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 13 Nov 2024 08:14:26 +0100
Subject: [PATCH 203/239] fix vocabulary lookup in mergeutils

---
 .../dhp/schema/oaf/utils/MergeUtils.java      | 425 +++++++++---------
 1 file changed, 215 insertions(+), 210 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index d7e08fca7..dc76860f8 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -16,6 +16,8 @@ import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -23,10 +25,8 @@ import org.apache.commons.lang3.tuple.Pair;
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.base.Joiner;
 
-import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
-import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -46,7 +46,7 @@ public class MergeUtils {
 	}
 
 	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator,
-		boolean checkDelegateAuthority, VocabularyGroup vocs) {
+											   boolean checkDelegateAuthority, VocabularyGroup vocs) {
 
 		ArrayList<T> sortedEntities = new ArrayList<>();
 		oafEntityIterator.forEachRemaining(sortedEntities::add);
@@ -74,11 +74,16 @@ public class MergeUtils {
 			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
 				return (T) mergedResult;
 			} else {
-				final Qualifier expectedResultType = vocs
-					.getSynonymAsQualifier(
+				final Qualifier expectedResultType = vocs.lookupTermBySynonym(
 						ModelConstants.DNET_RESULT_TYPOLOGIES,
 						i.getInstancetype().getClassid());
 
+				if (Objects.isNull(expectedResultType)) {
+					throw new IllegalArgumentException(
+							"instance type not bound to any result type in dnet:result_typologies: " +
+									i.getInstancetype().getClassid());
+				}
+
 				// there is a clash among the result types
 				if (!expectedResultType.getClassid().equals(mergedResult.getResulttype().getClassid())) {
 					try {
@@ -117,10 +122,10 @@ public class MergeUtils {
 			return mergeRelation((Relation) left, (Relation) right);
 		} else {
 			throw new RuntimeException(
-				String
-					.format(
-						"MERGE_FROM_AND_GET incompatible types: %s, %s",
-						left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+					String
+							.format(
+									"MERGE_FROM_AND_GET incompatible types: %s, %s",
+									left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
 		}
 	}
 
@@ -159,10 +164,10 @@ public class MergeUtils {
 			return mergeProject((Project) left, (Project) right);
 		} else {
 			throw new RuntimeException(
-				String
-					.format(
-						"MERGE_FROM_AND_GET incompatible types: %s, %s",
-						left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+					String
+							.format(
+									"MERGE_FROM_AND_GET incompatible types: %s, %s",
+									left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
 		}
 	}
 
@@ -253,7 +258,7 @@ public class MergeUtils {
 	}
 
 	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
-		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
+											 Function<T, K> keyExtractor, BinaryOperator<T> merger) {
 		if (left == null || left.isEmpty()) {
 			return right != null ? right : new ArrayList<>();
 		} else if (right == null || right.isEmpty()) {
@@ -264,11 +269,11 @@ public class MergeUtils {
 		List<T> l = trust >= 0 ? right : left;
 
 		return new ArrayList<>(Stream
-			.concat(h.stream(), l.stream())
-			.filter(Objects::nonNull)
-			.distinct()
-			.collect(Collectors.toMap(keyExtractor, v -> v, merger, LinkedHashMap::new))
-			.values());
+				.concat(h.stream(), l.stream())
+				.filter(Objects::nonNull)
+				.distinct()
+				.collect(Collectors.toMap(keyExtractor, v -> v, merger, LinkedHashMap::new))
+				.values());
 	}
 
 	private static <T, K> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
@@ -282,10 +287,10 @@ public class MergeUtils {
 		List<T> l = trust >= 0 ? right : left;
 
 		return Stream
-			.concat(h.stream(), l.stream())
-			.filter(Objects::nonNull)
-			.distinct()
-			.collect(Collectors.toList());
+				.concat(h.stream(), l.stream())
+				.filter(Objects::nonNull)
+				.distinct()
+				.collect(Collectors.toList());
 	}
 
 	private static List<String> unionDistinctListOfString(final List<String> l, final List<String> r) {
@@ -296,10 +301,10 @@ public class MergeUtils {
 		}
 
 		return Stream
-			.concat(l.stream(), r.stream())
-			.filter(StringUtils::isNotBlank)
-			.distinct()
-			.collect(Collectors.toList());
+				.concat(l.stream(), r.stream())
+				.filter(StringUtils::isNotBlank)
+				.distinct()
+				.collect(Collectors.toList());
 	}
 
 	// TODO review
@@ -325,7 +330,7 @@ public class MergeUtils {
 	}
 
 	private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right,
-		int trust) {
+													   int trust) {
 		if (left == null) {
 			return right;
 		} else if (right == null) {
@@ -336,10 +341,10 @@ public class MergeUtils {
 		List<StructuredProperty> l = trust >= 0 ? right : left;
 
 		return Stream
-			.concat(h.stream(), l.stream())
-			.filter(Objects::isNull)
-			.distinct()
-			.collect(Collectors.toList());
+				.concat(h.stream(), l.stream())
+				.filter(Objects::isNull)
+				.distinct()
+				.collect(Collectors.toList());
 	}
 
 	/**
@@ -374,8 +379,8 @@ public class MergeUtils {
 		merged.setPid(mergeLists(merged.getPid(), enrich.getPid(), trust, MergeUtils::spKeyExtractor, (p1, p2) -> p1));
 		merged.setDateofcollection(LocalDateTime.now().toString());
 		merged
-			.setDateoftransformation(
-				chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
+				.setDateoftransformation(
+						chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
 		merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
 		// When merging records OAI provenance becomes null
 		merged.setOaiprovenance(null);
@@ -392,7 +397,7 @@ public class MergeUtils {
 		checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal");
 		checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal");
 		checkArgument(
-			Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
+				Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
 		checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal");
 
 		// merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance()));
@@ -403,10 +408,10 @@ public class MergeUtils {
 			merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate()));
 		} catch (ParseException e) {
 			throw new IllegalArgumentException(String
-				.format(
-					"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
-					merge.getTarget(),
-					merge.getValidationDate()));
+					.format(
+							"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
+							merge.getTarget(),
+							merge.getValidationDate()));
 		}
 
 		// TODO keyvalue merge
@@ -420,7 +425,7 @@ public class MergeUtils {
 		T merge = mergeOafEntityFields(original, enrich, trust);
 
 		if (merge.getProcessingchargeamount() == null
-			|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
+				|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
 			merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
 			merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
 		}
@@ -452,8 +457,8 @@ public class MergeUtils {
 		}
 
 		merge
-			.setDateofacceptance(
-				mergeDateOfAcceptance(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
+				.setDateofacceptance(
+						mergeDateOfAcceptance(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
 
 		merge.setPublisher(coalesce(merge.getPublisher(), enrich.getPublisher()));
 		merge.setEmbargoenddate(coalesce(merge.getEmbargoenddate(), enrich.getEmbargoenddate()));
@@ -468,7 +473,7 @@ public class MergeUtils {
 		merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust));
 
 		if (enrich.getBestaccessright() != null
-			&& new AccessRightComparator<>()
+				&& new AccessRightComparator<>()
 				.compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) {
 			merge.setBestaccessright(enrich.getBestaccessright());
 		}
@@ -481,8 +486,8 @@ public class MergeUtils {
 
 		// ok
 		merge
-			.setExternalReference(
-				mergeExternalReference(merge.getExternalReference(), enrich.getExternalReference(), trust));
+				.setExternalReference(
+						mergeExternalReference(merge.getExternalReference(), enrich.getExternalReference(), trust));
 
 		// instance enrichment or union
 		// review instance equals => add pid to comparision
@@ -490,17 +495,17 @@ public class MergeUtils {
 			merge.setInstance(mergeInstances(merge.getInstance(), enrich.getInstance(), trust));
 		} else {
 			final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
-				: enrich.getInstance();
+					: enrich.getInstance();
 			final List<Instance> enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance()
-				: merge.getInstance();
+					: merge.getInstance();
 			if (isAnEnrichment(merge))
 				merge.setDataInfo(enrich.getDataInfo());
 			merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances));
 		}
 
 		merge
-			.setEoscifguidelines(
-				mergeEosciifguidelines(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
+				.setEoscifguidelines(
+						mergeEosciifguidelines(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
 		merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen()));
 		// OK but should be list of values
 		merge.setOpenAccessColor(coalesce(merge.getOpenAccessColor(), enrich.getOpenAccessColor()));
@@ -526,7 +531,7 @@ public class MergeUtils {
 						LocalDate enrich_date = LocalDate.parse(enrich.getValue(), DateTimeFormatter.ISO_DATE);
 
 						if (enrich_date.getYear() > 1300
-							&& (merge_date.getYear() < 1300 || merge_date.isAfter(enrich_date))) {
+								&& (merge_date.getYear() < 1300 || merge_date.isAfter(enrich_date))) {
 							return enrich;
 						}
 					} catch (NullPointerException | DateTimeParseException e) {
@@ -544,56 +549,56 @@ public class MergeUtils {
 
 	private static List<Instance> mergeInstances(List<Instance> v1, List<Instance> v2, int trust) {
 		return mergeLists(
-			v1, v2, trust,
-			MergeUtils::instanceKeyExtractor,
-			MergeUtils::instanceMerger);
+				v1, v2, trust,
+				MergeUtils::instanceKeyExtractor,
+				MergeUtils::instanceMerger);
 	}
 
 	private static List<EoscIfGuidelines> mergeEosciifguidelines(List<EoscIfGuidelines> v1, List<EoscIfGuidelines> v2,
-		int trust) {
+																 int trust) {
 		return mergeLists(
-			v1, v2, trust, er -> Joiner
-				.on("||")
-				.useForNull("")
-				.join(er.getCode(), er.getLabel(), er.getUrl(), er.getSemanticRelation()),
-			(r, l) -> r);
+				v1, v2, trust, er -> Joiner
+						.on("||")
+						.useForNull("")
+						.join(er.getCode(), er.getLabel(), er.getUrl(), er.getSemanticRelation()),
+				(r, l) -> r);
 
 	}
 
 	private static List<ExternalReference> mergeExternalReference(List<ExternalReference> v1,
-		List<ExternalReference> v2, int trust) {
+																  List<ExternalReference> v2, int trust) {
 		return mergeLists(
-			v1, v2, trust, er -> Joiner
-				.on(',')
-				.useForNull("")
-				.join(
-					er.getSitename(), er.getLabel(),
-					er.getUrl(), toString(er.getQualifier()), er.getRefidentifier(),
-					er.getQuery(), toString(er.getDataInfo())),
-			(r, l) -> r);
+				v1, v2, trust, er -> Joiner
+						.on(',')
+						.useForNull("")
+						.join(
+								er.getSitename(), er.getLabel(),
+								er.getUrl(), toString(er.getQualifier()), er.getRefidentifier(),
+								er.getQuery(), toString(er.getDataInfo())),
+				(r, l) -> r);
 	}
 
 	private static String toString(DataInfo di) {
 		return Joiner
-			.on(',')
-			.useForNull("")
-			.join(
-				di.getInvisible(), di.getInferred(), di.getDeletedbyinference(), di.getTrust(),
-				di.getInferenceprovenance(), toString(di.getProvenanceaction()));
+				.on(',')
+				.useForNull("")
+				.join(
+						di.getInvisible(), di.getInferred(), di.getDeletedbyinference(), di.getTrust(),
+						di.getInferenceprovenance(), toString(di.getProvenanceaction()));
 	}
 
 	private static String toString(Qualifier q) {
 		return Joiner
-			.on(',')
-			.useForNull("")
-			.join(q.getClassid(), q.getClassname(), q.getSchemeid(), q.getSchemename());
+				.on(',')
+				.useForNull("")
+				.join(q.getClassid(), q.getClassname(), q.getSchemeid(), q.getSchemename());
 	}
 
 	private static String toString(StructuredProperty sp) {
 		return Joiner
-			.on(',')
-			.useForNull("")
-			.join(toString(sp.getQualifier()), sp.getValue());
+				.on(',')
+				.useForNull("")
+				.join(toString(sp.getQualifier()), sp.getValue());
 	}
 
 	private static <T extends StructuredProperty> List<T> mergeStructuredProperties(List<T> v1, List<T> v2, int trust) {
@@ -632,17 +637,17 @@ public class MergeUtils {
 		// 2. @@
 		// 3. ||
 		return String
-			.join(
-				"::",
-				kvKeyExtractor(i.getHostedby()),
-				kvKeyExtractor(i.getCollectedfrom()),
-				qualifierKeyExtractor(i.getAccessright()),
-				qualifierKeyExtractor(i.getInstancetype()),
-				Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
-				Optional
-					.ofNullable(i.getPid())
-					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
-					.orElse(null));
+				.join(
+						"::",
+						kvKeyExtractor(i.getHostedby()),
+						kvKeyExtractor(i.getCollectedfrom()),
+						qualifierKeyExtractor(i.getAccessright()),
+						qualifierKeyExtractor(i.getInstancetype()),
+						Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
+						Optional
+								.ofNullable(i.getPid())
+								.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
+								.orElse(null));
 	}
 
 	private static Instance instanceMerger(Instance i1, Instance i2) {
@@ -653,30 +658,30 @@ public class MergeUtils {
 		i.setInstancetype(i1.getInstancetype());
 		i.setPid(mergeLists(i1.getPid(), i2.getPid(), 0, MergeUtils::spKeyExtractor, (sp1, sp2) -> sp1));
 		i
-			.setAlternateIdentifier(
-				mergeLists(
-					i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
-					(sp1, sp2) -> sp1));
+				.setAlternateIdentifier(
+						mergeLists(
+								i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
+								(sp1, sp2) -> sp1));
 
 		i
-			.setRefereed(
-				Collections
-					.min(
-						Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
-						new RefereedComparator()));
+				.setRefereed(
+						Collections
+								.min(
+										Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
+										new RefereedComparator()));
 		i
-			.setInstanceTypeMapping(
-				mergeLists(
-					i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
-					MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
+				.setInstanceTypeMapping(
+						mergeLists(
+								i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
+								MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
 		i.setFulltext(selectFulltext(i1.getFulltext(), i2.getFulltext()));
 		i.setDateofacceptance(selectOldestDate(i1.getDateofacceptance(), i2.getDateofacceptance()));
 		i.setLicense(coalesce(i1.getLicense(), i2.getLicense()));
 		i.setProcessingchargeamount(coalesce(i1.getProcessingchargeamount(), i2.getProcessingchargeamount()));
 		i.setProcessingchargecurrency(coalesce(i1.getProcessingchargecurrency(), i2.getProcessingchargecurrency()));
 		i
-			.setMeasures(
-				mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
+				.setMeasures(
+						mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
 
 		i.setUrl(unionDistinctListOfString(i1.getUrl(), i2.getUrl()));
 
@@ -685,14 +690,14 @@ public class MergeUtils {
 
 	private static String measureKeyExtractor(Measure m) {
 		return String
-			.join(
-				"::",
-				m.getId(),
-				m
-					.getUnit()
-					.stream()
-					.map(KeyValue::getKey)
-					.collect(Collectors.joining("::")));
+				.join(
+						"::",
+						m.getId(),
+						m
+								.getUnit()
+								.stream()
+								.map(KeyValue::getKey)
+								.collect(Collectors.joining("::")));
 	}
 
 	private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
@@ -703,16 +708,16 @@ public class MergeUtils {
 		}
 
 		return Stream
-			.of(d1, d2)
-			.min(
-				Comparator
-					.comparing(
-						f -> DateParserUtils
-							.parseDate(f.getValue())
-							.toInstant()
-							.atZone(ZoneId.systemDefault())
-							.toLocalDate()))
-			.orElse(d1);
+				.of(d1, d2)
+				.min(
+						Comparator
+								.comparing(
+										f -> DateParserUtils
+												.parseDate(f.getValue())
+												.toInstant()
+												.atZone(ZoneId.systemDefault())
+												.toLocalDate()))
+				.orElse(d1);
 	}
 
 	private static String selectFulltext(String ft1, String ft2) {
@@ -727,12 +732,12 @@ public class MergeUtils {
 
 	private static String instanceTypeMappingKeyExtractor(InstanceTypeMapping itm) {
 		return String
-			.join(
-				"::",
-				itm.getOriginalType(),
-				itm.getTypeCode(),
-				itm.getTypeLabel(),
-				itm.getVocabularyName());
+				.join(
+						"::",
+						itm.getOriginalType(),
+						itm.getTypeCode(),
+						itm.getTypeLabel(),
+						itm.getVocabularyName());
 	}
 
 	private static String kvKeyExtractor(KeyValue kv) {
@@ -749,13 +754,13 @@ public class MergeUtils {
 
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
-			.ofNullable(sp)
-			.map(
-				s -> Joiner
-					.on("||")
-					.useForNull("")
-					.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
-			.orElse(null);
+				.ofNullable(sp)
+				.map(
+						s -> Joiner
+								.on("||")
+								.useForNull("")
+								.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
+				.orElse(null);
 	}
 
 	private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
@@ -777,8 +782,8 @@ public class MergeUtils {
 		merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
 		merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
 		merge
-			.setProgrammingLanguage(
-				chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
+				.setProgrammingLanguage(
+						chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
 
 		return merge;
 	}
@@ -792,11 +797,11 @@ public class MergeUtils {
 		merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
 		merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
 		merge
-			.setLastmetadataupdate(
-				chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
+				.setLastmetadataupdate(
+						chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
 		merge
-			.setMetadataversionnumber(
-				chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
+				.setMetadataversionnumber(
+						chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
 		merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
 
 		return merge;
@@ -818,26 +823,26 @@ public class MergeUtils {
 		merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
 		merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
 		merged
-			.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
+				.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
 		merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
 		merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
 		merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
 		merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
 		merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
 		merged
-			.setEcresearchorganization(
-				chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
+				.setEcresearchorganization(
+						chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
 		merged
-			.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
+				.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
 		merged
-			.setEcinternationalorganizationeurinterests(
-				chooseReference(
-					merged.getEcinternationalorganizationeurinterests(),
-					enrich.getEcinternationalorganizationeurinterests(), trust));
+				.setEcinternationalorganizationeurinterests(
+						chooseReference(
+								merged.getEcinternationalorganizationeurinterests(),
+								enrich.getEcinternationalorganizationeurinterests(), trust));
 		merged
-			.setEcinternationalorganization(
-				chooseReference(
-					merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
+				.setEcinternationalorganization(
+						chooseReference(
+								merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
 		merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
 		merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
 		merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
@@ -861,8 +866,8 @@ public class MergeUtils {
 		merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
 		merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
 		merged
-			.setOamandatepublications(
-				chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
+				.setOamandatepublications(
+						chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
 		merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
 		merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
 		merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
@@ -888,8 +893,8 @@ public class MergeUtils {
 		}
 
 		merged
-			.setH2020classification(
-				unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
+				.setH2020classification(
+						unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
 
 		return merged;
 	}
@@ -916,7 +921,7 @@ public class MergeUtils {
 	 * @return list of instances possibly enriched
 	 */
 	private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,
-		final List<Instance> enrichmentInstances) {
+												  final List<Instance> enrichmentInstances) {
 		final List<Instance> enrichmentResult = new ArrayList<>();
 
 		if (toEnrichInstances == null) {
@@ -954,42 +959,42 @@ public class MergeUtils {
 	 */
 	private static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
 		return ri
-			.stream()
-			.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
-			.flatMap(i -> {
-				final List<Pair<String, Instance>> result = new ArrayList<>();
-				if (i.getPid() != null)
-					i
-						.getPid()
-						.stream()
-						.filter(MergeUtils::validPid)
-						.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
-				if (i.getAlternateIdentifier() != null)
-					i
-						.getAlternateIdentifier()
-						.stream()
-						.filter(MergeUtils::validPid)
-						.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
-				return result.stream();
-			})
-			.collect(
-				Collectors
-					.toMap(
-						Pair::getLeft,
-						Pair::getRight,
-						(a, b) -> a));
+				.stream()
+				.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
+				.flatMap(i -> {
+					final List<Pair<String, Instance>> result = new ArrayList<>();
+					if (i.getPid() != null)
+						i
+								.getPid()
+								.stream()
+								.filter(MergeUtils::validPid)
+								.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+					if (i.getAlternateIdentifier() != null)
+						i
+								.getAlternateIdentifier()
+								.stream()
+								.filter(MergeUtils::validPid)
+								.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+					return result.stream();
+				})
+				.collect(
+						Collectors
+								.toMap(
+										Pair::getLeft,
+										Pair::getRight,
+										(a, b) -> a));
 	}
 
 	private static boolean isFromDelegatedAuthority(Result r) {
 		return Optional
-			.ofNullable(r.getInstance())
-			.map(
-				instance -> instance
-					.stream()
-					.filter(i -> Objects.nonNull(i.getCollectedfrom()))
-					.map(i -> i.getCollectedfrom().getKey())
-					.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
-			.orElse(false);
+				.ofNullable(r.getInstance())
+				.map(
+						instance -> instance
+								.stream()
+								.filter(i -> Objects.nonNull(i.getCollectedfrom()))
+								.map(i -> i.getCollectedfrom().getKey())
+								.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
+				.orElse(false);
 	}
 
 	/**
@@ -1025,15 +1030,15 @@ public class MergeUtils {
 	 * @return the list
 	 */
 	private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids,
-		final Map<String, Instance> enrichments) {
+													   final Map<String, Instance> enrichments) {
 		if (pids == null || enrichments == null)
 			return null;
 		return pids
-			.stream()
-			.map(MergeUtils::extractKeyFromPid)
-			.map(enrichments::get)
-			.filter(Objects::nonNull)
-			.collect(Collectors.toList());
+				.stream()
+				.map(MergeUtils::extractKeyFromPid)
+				.map(enrichments::get)
+				.filter(Objects::nonNull)
+				.collect(Collectors.toList());
 	}
 
 	/**
@@ -1044,8 +1049,8 @@ public class MergeUtils {
 	 */
 	private static boolean isAnEnrichment(OafEntity e) {
 		return e.getDataInfo() != null &&
-			e.getDataInfo().getProvenanceaction() != null
-			&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
+				e.getDataInfo().getProvenanceaction() != null
+				&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
 	}
 
 	/**
@@ -1068,17 +1073,17 @@ public class MergeUtils {
 		merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
 		merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
 		merge
-			.setDistributionlocation(
-				firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
+				.setDistributionlocation(
+						firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
 		merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
 		// pid and alternateId are used for matching
 		merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
 		merge
-			.setProcessingchargeamount(
-				firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
+				.setProcessingchargeamount(
+						firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
 		merge
-			.setProcessingchargecurrency(
-				firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
+				.setProcessingchargecurrency(
+						firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
 		merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
 		merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
 		merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
@@ -1086,14 +1091,14 @@ public class MergeUtils {
 
 	private static int compareTrust(Oaf a, Oaf b) {
 		String left = Optional
-			.ofNullable(a.getDataInfo())
-			.map(DataInfo::getTrust)
-			.orElse("0.0");
+				.ofNullable(a.getDataInfo())
+				.map(DataInfo::getTrust)
+				.orElse("0.0");
 
 		String right = Optional
-			.ofNullable(b.getDataInfo())
-			.map(DataInfo::getTrust)
-			.orElse("0.0");
+				.ofNullable(b.getDataInfo())
+				.map(DataInfo::getTrust)
+				.orElse("0.0");
 
 		return left.compareTo(right);
 	}

From a1d5ad5c2609c91b60b97600163072d551dcc440 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Wed, 13 Nov 2024 09:51:13 +0100
Subject: [PATCH 204/239] code formatted

---
 .../dhp/schema/oaf/utils/MergeUtils.java      | 423 +++++++++---------
 .../personentity/ExtractPerson.java           |  22 +-
 .../plugin/gtr2/Gtr2PublicationsIterator.java |   6 +-
 3 files changed, 228 insertions(+), 223 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index dc76860f8..cd8506583 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -16,8 +16,6 @@ import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
-import eu.dnetlib.dhp.schema.common.EntityType;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -25,8 +23,10 @@ import org.apache.commons.lang3.tuple.Pair;
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.base.Joiner;
 
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -46,7 +46,7 @@ public class MergeUtils {
 	}
 
 	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator,
-											   boolean checkDelegateAuthority, VocabularyGroup vocs) {
+		boolean checkDelegateAuthority, VocabularyGroup vocs) {
 
 		ArrayList<T> sortedEntities = new ArrayList<>();
 		oafEntityIterator.forEachRemaining(sortedEntities::add);
@@ -74,14 +74,15 @@ public class MergeUtils {
 			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
 				return (T) mergedResult;
 			} else {
-				final Qualifier expectedResultType = vocs.lookupTermBySynonym(
+				final Qualifier expectedResultType = vocs
+					.lookupTermBySynonym(
 						ModelConstants.DNET_RESULT_TYPOLOGIES,
 						i.getInstancetype().getClassid());
 
 				if (Objects.isNull(expectedResultType)) {
 					throw new IllegalArgumentException(
-							"instance type not bound to any result type in dnet:result_typologies: " +
-									i.getInstancetype().getClassid());
+						"instance type not bound to any result type in dnet:result_typologies: " +
+							i.getInstancetype().getClassid());
 				}
 
 				// there is a clash among the result types
@@ -122,10 +123,10 @@ public class MergeUtils {
 			return mergeRelation((Relation) left, (Relation) right);
 		} else {
 			throw new RuntimeException(
-					String
-							.format(
-									"MERGE_FROM_AND_GET incompatible types: %s, %s",
-									left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+				String
+					.format(
+						"MERGE_FROM_AND_GET incompatible types: %s, %s",
+						left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
 		}
 	}
 
@@ -164,10 +165,10 @@ public class MergeUtils {
 			return mergeProject((Project) left, (Project) right);
 		} else {
 			throw new RuntimeException(
-					String
-							.format(
-									"MERGE_FROM_AND_GET incompatible types: %s, %s",
-									left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+				String
+					.format(
+						"MERGE_FROM_AND_GET incompatible types: %s, %s",
+						left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
 		}
 	}
 
@@ -258,7 +259,7 @@ public class MergeUtils {
 	}
 
 	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
-											 Function<T, K> keyExtractor, BinaryOperator<T> merger) {
+		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
 		if (left == null || left.isEmpty()) {
 			return right != null ? right : new ArrayList<>();
 		} else if (right == null || right.isEmpty()) {
@@ -269,11 +270,11 @@ public class MergeUtils {
 		List<T> l = trust >= 0 ? right : left;
 
 		return new ArrayList<>(Stream
-				.concat(h.stream(), l.stream())
-				.filter(Objects::nonNull)
-				.distinct()
-				.collect(Collectors.toMap(keyExtractor, v -> v, merger, LinkedHashMap::new))
-				.values());
+			.concat(h.stream(), l.stream())
+			.filter(Objects::nonNull)
+			.distinct()
+			.collect(Collectors.toMap(keyExtractor, v -> v, merger, LinkedHashMap::new))
+			.values());
 	}
 
 	private static <T, K> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
@@ -287,10 +288,10 @@ public class MergeUtils {
 		List<T> l = trust >= 0 ? right : left;
 
 		return Stream
-				.concat(h.stream(), l.stream())
-				.filter(Objects::nonNull)
-				.distinct()
-				.collect(Collectors.toList());
+			.concat(h.stream(), l.stream())
+			.filter(Objects::nonNull)
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	private static List<String> unionDistinctListOfString(final List<String> l, final List<String> r) {
@@ -301,10 +302,10 @@ public class MergeUtils {
 		}
 
 		return Stream
-				.concat(l.stream(), r.stream())
-				.filter(StringUtils::isNotBlank)
-				.distinct()
-				.collect(Collectors.toList());
+			.concat(l.stream(), r.stream())
+			.filter(StringUtils::isNotBlank)
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	// TODO review
@@ -330,7 +331,7 @@ public class MergeUtils {
 	}
 
 	private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right,
-													   int trust) {
+		int trust) {
 		if (left == null) {
 			return right;
 		} else if (right == null) {
@@ -341,10 +342,10 @@ public class MergeUtils {
 		List<StructuredProperty> l = trust >= 0 ? right : left;
 
 		return Stream
-				.concat(h.stream(), l.stream())
-				.filter(Objects::isNull)
-				.distinct()
-				.collect(Collectors.toList());
+			.concat(h.stream(), l.stream())
+			.filter(Objects::isNull)
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	/**
@@ -379,8 +380,8 @@ public class MergeUtils {
 		merged.setPid(mergeLists(merged.getPid(), enrich.getPid(), trust, MergeUtils::spKeyExtractor, (p1, p2) -> p1));
 		merged.setDateofcollection(LocalDateTime.now().toString());
 		merged
-				.setDateoftransformation(
-						chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
+			.setDateoftransformation(
+				chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
 		merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
 		// When merging records OAI provenance becomes null
 		merged.setOaiprovenance(null);
@@ -397,7 +398,7 @@ public class MergeUtils {
 		checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal");
 		checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal");
 		checkArgument(
-				Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
+			Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
 		checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal");
 
 		// merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance()));
@@ -408,10 +409,10 @@ public class MergeUtils {
 			merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate()));
 		} catch (ParseException e) {
 			throw new IllegalArgumentException(String
-					.format(
-							"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
-							merge.getTarget(),
-							merge.getValidationDate()));
+				.format(
+					"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
+					merge.getTarget(),
+					merge.getValidationDate()));
 		}
 
 		// TODO keyvalue merge
@@ -425,7 +426,7 @@ public class MergeUtils {
 		T merge = mergeOafEntityFields(original, enrich, trust);
 
 		if (merge.getProcessingchargeamount() == null
-				|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
+			|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
 			merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
 			merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
 		}
@@ -457,8 +458,8 @@ public class MergeUtils {
 		}
 
 		merge
-				.setDateofacceptance(
-						mergeDateOfAcceptance(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
+			.setDateofacceptance(
+				mergeDateOfAcceptance(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
 
 		merge.setPublisher(coalesce(merge.getPublisher(), enrich.getPublisher()));
 		merge.setEmbargoenddate(coalesce(merge.getEmbargoenddate(), enrich.getEmbargoenddate()));
@@ -473,7 +474,7 @@ public class MergeUtils {
 		merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust));
 
 		if (enrich.getBestaccessright() != null
-				&& new AccessRightComparator<>()
+			&& new AccessRightComparator<>()
 				.compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) {
 			merge.setBestaccessright(enrich.getBestaccessright());
 		}
@@ -486,8 +487,8 @@ public class MergeUtils {
 
 		// ok
 		merge
-				.setExternalReference(
-						mergeExternalReference(merge.getExternalReference(), enrich.getExternalReference(), trust));
+			.setExternalReference(
+				mergeExternalReference(merge.getExternalReference(), enrich.getExternalReference(), trust));
 
 		// instance enrichment or union
 		// review instance equals => add pid to comparision
@@ -495,17 +496,17 @@ public class MergeUtils {
 			merge.setInstance(mergeInstances(merge.getInstance(), enrich.getInstance(), trust));
 		} else {
 			final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
-					: enrich.getInstance();
+				: enrich.getInstance();
 			final List<Instance> enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance()
-					: merge.getInstance();
+				: merge.getInstance();
 			if (isAnEnrichment(merge))
 				merge.setDataInfo(enrich.getDataInfo());
 			merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances));
 		}
 
 		merge
-				.setEoscifguidelines(
-						mergeEosciifguidelines(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
+			.setEoscifguidelines(
+				mergeEosciifguidelines(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
 		merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen()));
 		// OK but should be list of values
 		merge.setOpenAccessColor(coalesce(merge.getOpenAccessColor(), enrich.getOpenAccessColor()));
@@ -531,7 +532,7 @@ public class MergeUtils {
 						LocalDate enrich_date = LocalDate.parse(enrich.getValue(), DateTimeFormatter.ISO_DATE);
 
 						if (enrich_date.getYear() > 1300
-								&& (merge_date.getYear() < 1300 || merge_date.isAfter(enrich_date))) {
+							&& (merge_date.getYear() < 1300 || merge_date.isAfter(enrich_date))) {
 							return enrich;
 						}
 					} catch (NullPointerException | DateTimeParseException e) {
@@ -549,56 +550,56 @@ public class MergeUtils {
 
 	private static List<Instance> mergeInstances(List<Instance> v1, List<Instance> v2, int trust) {
 		return mergeLists(
-				v1, v2, trust,
-				MergeUtils::instanceKeyExtractor,
-				MergeUtils::instanceMerger);
+			v1, v2, trust,
+			MergeUtils::instanceKeyExtractor,
+			MergeUtils::instanceMerger);
 	}
 
 	private static List<EoscIfGuidelines> mergeEosciifguidelines(List<EoscIfGuidelines> v1, List<EoscIfGuidelines> v2,
-																 int trust) {
+		int trust) {
 		return mergeLists(
-				v1, v2, trust, er -> Joiner
-						.on("||")
-						.useForNull("")
-						.join(er.getCode(), er.getLabel(), er.getUrl(), er.getSemanticRelation()),
-				(r, l) -> r);
+			v1, v2, trust, er -> Joiner
+				.on("||")
+				.useForNull("")
+				.join(er.getCode(), er.getLabel(), er.getUrl(), er.getSemanticRelation()),
+			(r, l) -> r);
 
 	}
 
 	private static List<ExternalReference> mergeExternalReference(List<ExternalReference> v1,
-																  List<ExternalReference> v2, int trust) {
+		List<ExternalReference> v2, int trust) {
 		return mergeLists(
-				v1, v2, trust, er -> Joiner
-						.on(',')
-						.useForNull("")
-						.join(
-								er.getSitename(), er.getLabel(),
-								er.getUrl(), toString(er.getQualifier()), er.getRefidentifier(),
-								er.getQuery(), toString(er.getDataInfo())),
-				(r, l) -> r);
+			v1, v2, trust, er -> Joiner
+				.on(',')
+				.useForNull("")
+				.join(
+					er.getSitename(), er.getLabel(),
+					er.getUrl(), toString(er.getQualifier()), er.getRefidentifier(),
+					er.getQuery(), toString(er.getDataInfo())),
+			(r, l) -> r);
 	}
 
 	private static String toString(DataInfo di) {
 		return Joiner
-				.on(',')
-				.useForNull("")
-				.join(
-						di.getInvisible(), di.getInferred(), di.getDeletedbyinference(), di.getTrust(),
-						di.getInferenceprovenance(), toString(di.getProvenanceaction()));
+			.on(',')
+			.useForNull("")
+			.join(
+				di.getInvisible(), di.getInferred(), di.getDeletedbyinference(), di.getTrust(),
+				di.getInferenceprovenance(), toString(di.getProvenanceaction()));
 	}
 
 	private static String toString(Qualifier q) {
 		return Joiner
-				.on(',')
-				.useForNull("")
-				.join(q.getClassid(), q.getClassname(), q.getSchemeid(), q.getSchemename());
+			.on(',')
+			.useForNull("")
+			.join(q.getClassid(), q.getClassname(), q.getSchemeid(), q.getSchemename());
 	}
 
 	private static String toString(StructuredProperty sp) {
 		return Joiner
-				.on(',')
-				.useForNull("")
-				.join(toString(sp.getQualifier()), sp.getValue());
+			.on(',')
+			.useForNull("")
+			.join(toString(sp.getQualifier()), sp.getValue());
 	}
 
 	private static <T extends StructuredProperty> List<T> mergeStructuredProperties(List<T> v1, List<T> v2, int trust) {
@@ -637,17 +638,17 @@ public class MergeUtils {
 		// 2. @@
 		// 3. ||
 		return String
-				.join(
-						"::",
-						kvKeyExtractor(i.getHostedby()),
-						kvKeyExtractor(i.getCollectedfrom()),
-						qualifierKeyExtractor(i.getAccessright()),
-						qualifierKeyExtractor(i.getInstancetype()),
-						Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
-						Optional
-								.ofNullable(i.getPid())
-								.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
-								.orElse(null));
+			.join(
+				"::",
+				kvKeyExtractor(i.getHostedby()),
+				kvKeyExtractor(i.getCollectedfrom()),
+				qualifierKeyExtractor(i.getAccessright()),
+				qualifierKeyExtractor(i.getInstancetype()),
+				Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
+				Optional
+					.ofNullable(i.getPid())
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
+					.orElse(null));
 	}
 
 	private static Instance instanceMerger(Instance i1, Instance i2) {
@@ -658,30 +659,30 @@ public class MergeUtils {
 		i.setInstancetype(i1.getInstancetype());
 		i.setPid(mergeLists(i1.getPid(), i2.getPid(), 0, MergeUtils::spKeyExtractor, (sp1, sp2) -> sp1));
 		i
-				.setAlternateIdentifier(
-						mergeLists(
-								i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
-								(sp1, sp2) -> sp1));
+			.setAlternateIdentifier(
+				mergeLists(
+					i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
+					(sp1, sp2) -> sp1));
 
 		i
-				.setRefereed(
-						Collections
-								.min(
-										Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
-										new RefereedComparator()));
+			.setRefereed(
+				Collections
+					.min(
+						Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
+						new RefereedComparator()));
 		i
-				.setInstanceTypeMapping(
-						mergeLists(
-								i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
-								MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
+			.setInstanceTypeMapping(
+				mergeLists(
+					i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
+					MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
 		i.setFulltext(selectFulltext(i1.getFulltext(), i2.getFulltext()));
 		i.setDateofacceptance(selectOldestDate(i1.getDateofacceptance(), i2.getDateofacceptance()));
 		i.setLicense(coalesce(i1.getLicense(), i2.getLicense()));
 		i.setProcessingchargeamount(coalesce(i1.getProcessingchargeamount(), i2.getProcessingchargeamount()));
 		i.setProcessingchargecurrency(coalesce(i1.getProcessingchargecurrency(), i2.getProcessingchargecurrency()));
 		i
-				.setMeasures(
-						mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
+			.setMeasures(
+				mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
 
 		i.setUrl(unionDistinctListOfString(i1.getUrl(), i2.getUrl()));
 
@@ -690,14 +691,14 @@ public class MergeUtils {
 
 	private static String measureKeyExtractor(Measure m) {
 		return String
-				.join(
-						"::",
-						m.getId(),
-						m
-								.getUnit()
-								.stream()
-								.map(KeyValue::getKey)
-								.collect(Collectors.joining("::")));
+			.join(
+				"::",
+				m.getId(),
+				m
+					.getUnit()
+					.stream()
+					.map(KeyValue::getKey)
+					.collect(Collectors.joining("::")));
 	}
 
 	private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
@@ -708,16 +709,16 @@ public class MergeUtils {
 		}
 
 		return Stream
-				.of(d1, d2)
-				.min(
-						Comparator
-								.comparing(
-										f -> DateParserUtils
-												.parseDate(f.getValue())
-												.toInstant()
-												.atZone(ZoneId.systemDefault())
-												.toLocalDate()))
-				.orElse(d1);
+			.of(d1, d2)
+			.min(
+				Comparator
+					.comparing(
+						f -> DateParserUtils
+							.parseDate(f.getValue())
+							.toInstant()
+							.atZone(ZoneId.systemDefault())
+							.toLocalDate()))
+			.orElse(d1);
 	}
 
 	private static String selectFulltext(String ft1, String ft2) {
@@ -732,12 +733,12 @@ public class MergeUtils {
 
 	private static String instanceTypeMappingKeyExtractor(InstanceTypeMapping itm) {
 		return String
-				.join(
-						"::",
-						itm.getOriginalType(),
-						itm.getTypeCode(),
-						itm.getTypeLabel(),
-						itm.getVocabularyName());
+			.join(
+				"::",
+				itm.getOriginalType(),
+				itm.getTypeCode(),
+				itm.getTypeLabel(),
+				itm.getVocabularyName());
 	}
 
 	private static String kvKeyExtractor(KeyValue kv) {
@@ -754,13 +755,13 @@ public class MergeUtils {
 
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
-				.ofNullable(sp)
-				.map(
-						s -> Joiner
-								.on("||")
-								.useForNull("")
-								.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
-				.orElse(null);
+			.ofNullable(sp)
+			.map(
+				s -> Joiner
+					.on("||")
+					.useForNull("")
+					.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
+			.orElse(null);
 	}
 
 	private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
@@ -782,8 +783,8 @@ public class MergeUtils {
 		merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
 		merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
 		merge
-				.setProgrammingLanguage(
-						chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
+			.setProgrammingLanguage(
+				chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
 
 		return merge;
 	}
@@ -797,11 +798,11 @@ public class MergeUtils {
 		merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
 		merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
 		merge
-				.setLastmetadataupdate(
-						chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
+			.setLastmetadataupdate(
+				chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
 		merge
-				.setMetadataversionnumber(
-						chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
+			.setMetadataversionnumber(
+				chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
 		merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
 
 		return merge;
@@ -823,26 +824,26 @@ public class MergeUtils {
 		merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
 		merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
 		merged
-				.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
+			.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
 		merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
 		merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
 		merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
 		merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
 		merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
 		merged
-				.setEcresearchorganization(
-						chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
+			.setEcresearchorganization(
+				chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
 		merged
-				.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
+			.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
 		merged
-				.setEcinternationalorganizationeurinterests(
-						chooseReference(
-								merged.getEcinternationalorganizationeurinterests(),
-								enrich.getEcinternationalorganizationeurinterests(), trust));
+			.setEcinternationalorganizationeurinterests(
+				chooseReference(
+					merged.getEcinternationalorganizationeurinterests(),
+					enrich.getEcinternationalorganizationeurinterests(), trust));
 		merged
-				.setEcinternationalorganization(
-						chooseReference(
-								merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
+			.setEcinternationalorganization(
+				chooseReference(
+					merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
 		merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
 		merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
 		merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
@@ -866,8 +867,8 @@ public class MergeUtils {
 		merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
 		merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
 		merged
-				.setOamandatepublications(
-						chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
+			.setOamandatepublications(
+				chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
 		merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
 		merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
 		merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
@@ -893,8 +894,8 @@ public class MergeUtils {
 		}
 
 		merged
-				.setH2020classification(
-						unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
+			.setH2020classification(
+				unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
 
 		return merged;
 	}
@@ -921,7 +922,7 @@ public class MergeUtils {
 	 * @return list of instances possibly enriched
 	 */
 	private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,
-												  final List<Instance> enrichmentInstances) {
+		final List<Instance> enrichmentInstances) {
 		final List<Instance> enrichmentResult = new ArrayList<>();
 
 		if (toEnrichInstances == null) {
@@ -959,42 +960,42 @@ public class MergeUtils {
 	 */
 	private static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
 		return ri
-				.stream()
-				.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
-				.flatMap(i -> {
-					final List<Pair<String, Instance>> result = new ArrayList<>();
-					if (i.getPid() != null)
-						i
-								.getPid()
-								.stream()
-								.filter(MergeUtils::validPid)
-								.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
-					if (i.getAlternateIdentifier() != null)
-						i
-								.getAlternateIdentifier()
-								.stream()
-								.filter(MergeUtils::validPid)
-								.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
-					return result.stream();
-				})
-				.collect(
-						Collectors
-								.toMap(
-										Pair::getLeft,
-										Pair::getRight,
-										(a, b) -> a));
+			.stream()
+			.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
+			.flatMap(i -> {
+				final List<Pair<String, Instance>> result = new ArrayList<>();
+				if (i.getPid() != null)
+					i
+						.getPid()
+						.stream()
+						.filter(MergeUtils::validPid)
+						.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+				if (i.getAlternateIdentifier() != null)
+					i
+						.getAlternateIdentifier()
+						.stream()
+						.filter(MergeUtils::validPid)
+						.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+				return result.stream();
+			})
+			.collect(
+				Collectors
+					.toMap(
+						Pair::getLeft,
+						Pair::getRight,
+						(a, b) -> a));
 	}
 
 	private static boolean isFromDelegatedAuthority(Result r) {
 		return Optional
-				.ofNullable(r.getInstance())
-				.map(
-						instance -> instance
-								.stream()
-								.filter(i -> Objects.nonNull(i.getCollectedfrom()))
-								.map(i -> i.getCollectedfrom().getKey())
-								.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
-				.orElse(false);
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.filter(i -> Objects.nonNull(i.getCollectedfrom()))
+					.map(i -> i.getCollectedfrom().getKey())
+					.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
+			.orElse(false);
 	}
 
 	/**
@@ -1030,15 +1031,15 @@ public class MergeUtils {
 	 * @return the list
 	 */
 	private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids,
-													   final Map<String, Instance> enrichments) {
+		final Map<String, Instance> enrichments) {
 		if (pids == null || enrichments == null)
 			return null;
 		return pids
-				.stream()
-				.map(MergeUtils::extractKeyFromPid)
-				.map(enrichments::get)
-				.filter(Objects::nonNull)
-				.collect(Collectors.toList());
+			.stream()
+			.map(MergeUtils::extractKeyFromPid)
+			.map(enrichments::get)
+			.filter(Objects::nonNull)
+			.collect(Collectors.toList());
 	}
 
 	/**
@@ -1049,8 +1050,8 @@ public class MergeUtils {
 	 */
 	private static boolean isAnEnrichment(OafEntity e) {
 		return e.getDataInfo() != null &&
-				e.getDataInfo().getProvenanceaction() != null
-				&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
+			e.getDataInfo().getProvenanceaction() != null
+			&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
 	}
 
 	/**
@@ -1073,17 +1074,17 @@ public class MergeUtils {
 		merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
 		merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
 		merge
-				.setDistributionlocation(
-						firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
+			.setDistributionlocation(
+				firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
 		merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
 		// pid and alternateId are used for matching
 		merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
 		merge
-				.setProcessingchargeamount(
-						firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
+			.setProcessingchargeamount(
+				firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
 		merge
-				.setProcessingchargecurrency(
-						firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
+			.setProcessingchargecurrency(
+				firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
 		merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
 		merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
 		merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
@@ -1091,14 +1092,14 @@ public class MergeUtils {
 
 	private static int compareTrust(Oaf a, Oaf b) {
 		String left = Optional
-				.ofNullable(a.getDataInfo())
-				.map(DataInfo::getTrust)
-				.orElse("0.0");
+			.ofNullable(a.getDataInfo())
+			.map(DataInfo::getTrust)
+			.orElse("0.0");
 
 		String right = Optional
-				.ofNullable(b.getDataInfo())
-				.map(DataInfo::getTrust)
-				.orElse("0.0");
+			.ofNullable(b.getDataInfo())
+			.map(DataInfo::getTrust)
+			.orElse("0.0");
 
 		return left.compareTo(right);
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
index 06924f05a..05f083740 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java
@@ -346,15 +346,19 @@ public class ExtractPerson implements Serializable {
 						.structuredProperty(
 							op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME,
 							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,
-								OafMapperUtils.dataInfo(false,
-										null,
-										false,
-										false,
-										OafMapperUtils.qualifier(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
-												ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
-												ModelConstants.DNET_PID_TYPES,
-												ModelConstants.DNET_PID_TYPES),
-								"0.91")));
+							OafMapperUtils
+								.dataInfo(
+									false,
+									null,
+									false,
+									false,
+									OafMapperUtils
+										.qualifier(
+											ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
+											ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
+											ModelConstants.DNET_PID_TYPES,
+											ModelConstants.DNET_PID_TYPES),
+									"0.91")));
 			person.setDateofcollection(op.getLastModifiedDate());
 			person.setOriginalId(Arrays.asList(op.getOrcid()));
 			person.setDataInfo(ORCIDDATAINFO);
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
index 779c43712..1b1ff8db4 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/gtr2/Gtr2PublicationsIterator.java
@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.collection.plugin.gtr2;
 
 import java.nio.charset.StandardCharsets;
 import java.time.LocalDate;
+import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -18,7 +19,6 @@ import org.dom4j.Document;
 import org.dom4j.DocumentException;
 import org.dom4j.DocumentHelper;
 import org.dom4j.Element;
-import java.time.format.DateTimeFormatter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -188,11 +188,11 @@ public class Gtr2PublicationsIterator implements Iterator<String> {
 
 	private Document loadURL(final String cleanUrl, final int attempt) {
 		try {
-            log.debug("  * Downloading Url: {}", cleanUrl);
+			log.debug("  * Downloading Url: {}", cleanUrl);
 			final byte[] bytes = this.connector.getInputSource(cleanUrl).getBytes(StandardCharsets.UTF_8);
 			return DocumentHelper.parseText(new String(bytes));
 		} catch (final Throwable e) {
-            log.error("Error dowloading url: {}, attempt = {}", cleanUrl, attempt, e);
+			log.error("Error dowloading url: {}, attempt = {}", cleanUrl, attempt, e);
 			if (attempt >= MAX_ATTEMPTS) {
 				throw new RuntimeException("Error downloading url: " + cleanUrl, e);
 			}

From 03c262ccb981bed4d6351705026e699963c9e4fc Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Wed, 13 Nov 2024 10:56:17 +0100
Subject: [PATCH 205/239] Crossref: generate canonical openaire id for results
 in affiliation relationship

---
 .gitignore                                                   | 1 +
 .../eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala    | 5 +++--
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.gitignore b/.gitignore
index 6fafc7055..ef9144ae3 100644
--- a/.gitignore
+++ b/.gitignore
@@ -28,3 +28,4 @@ spark-warehouse
 /**/.scalafmt.conf
 /.java-version
 /dhp-shade-package/dependency-reduced-pom.xml
+/**/job.properties
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index e7d68920b..d3a68c92e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -673,11 +673,12 @@ case object Crossref2Oaf {
     val doi = input.getString(0)
     val rorId = input.getString(1)
 
-    val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.clean(doi)}"
+
+    val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true)
     val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
 
     val r: Relation = new Relation
-    DoiCleaningRule.clean(doi)
+
     r.setSource(pubId)
     r.setTarget(affId)
     r.setRelType(ModelConstants.RESULT_ORGANIZATION)

From fb1f0f8850b867f758fffdf9751ec9e4d2543db5 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 7 Nov 2024 14:05:02 +0100
Subject: [PATCH 206/239] [danishfunders] added the possibility to link also
 versus a specif award if present in the metadata

---
 .../collection/crossref/Crossref2Oaf.scala    | 21 ++++++++++++++++++-
 .../doiboost/crossref/Crossref2Oaf.scala      |  3 +++
 2 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index e7d68920b..59a12bc03 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -978,7 +978,26 @@ case object Crossref2Oaf {
             case "10.13039/501100010790" =>
               generateSimpleRelationFromAward(funder, "erasmusplus_", a => a)
             case _ => logger.debug("no match for " + funder.DOI.get)
-
+            //Add for Danish funders
+            //Independent Research Fund Denmark (IRFD)
+            case "10.13039/501100004836" =>
+              generateSimpleRelationFromAward(funder, "irfd________", a => a)
+              val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Carlsberg Foundation (CF)
+            case "10.13039/501100002808" =>
+              generateSimpleRelationFromAward(funder, "cf__________", a => a)
+              val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Novo Nordisk Foundation (NNF)
+            case "10.13039/501100009708" =>
+              generateSimpleRelationFromAward(funder, "nnf___________", a => a)
+              val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            case _ => logger.debug("no match for " + funder.DOI.get)
           }
 
         } else {
diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
index bf11ed0a8..031a04058 100644
--- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
@@ -569,16 +569,19 @@ case object Crossref2Oaf {
             //Add for Danish funders
             //Independent Research Fund Denmark (IRFD)
             case "10.13039/501100004836" =>
+              generateSimpleRelationFromAward(funder, "irfd________", a => a)
               val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             //Carlsberg Foundation (CF)
             case "10.13039/501100002808" =>
+              generateSimpleRelationFromAward(funder, "cf__________", a => a)
               val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             //Novo Nordisk Foundation (NNF)
             case "10.13039/501100009708" =>
+              generateSimpleRelationFromAward(funder, "nnf___________", a => a)
               val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63")
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)

From ac0a94d62d7c34fc3953d47a9a2263ac5cfadb82 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Wed, 13 Nov 2024 16:26:59 +0100
Subject: [PATCH 207/239] updated pubmed parser to add also ORCID id and
 affiliation string to authors

---
 .../dhp/sx/bio/pubmed/PMAffiliation.java      |  39 +++
 .../dnetlib/dhp/sx/bio/pubmed/PMAuthor.java   |  39 +++
 .../dhp/sx/bio/pubmed/PMIdentifier.java       |  53 +++++
 .../dnetlib/dhp/sx/bio/pubmed/PMParser2.scala |  30 ++-
 .../dhp/sx/bio/pubmed/PubMedToOaf.scala       |   6 +
 .../dhp/sx/graph/bio/single_pubmed.xml        | 223 +++++++-----------
 .../dnetlib/dhp/sx/bio/BioScholixTest.scala   |  64 ++++-
 7 files changed, 300 insertions(+), 154 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
new file mode 100644
index 000000000..54aba8715
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
@@ -0,0 +1,39 @@
+package eu.dnetlib.dhp.sx.bio.pubmed;
+
+/**
+ * The type Pubmed Affiliation.
+ *
+ * @author Sandro La Bruzzo
+ */
+public class PMAffiliation {
+
+    private  String name;
+
+    private PMIdentifier identifier;
+
+    public PMAffiliation() {
+
+    }
+    public PMAffiliation(String name, PMIdentifier identifier) {
+        this.name = name;
+        this.identifier = identifier;
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public PMAffiliation setName(String name) {
+        this.name = name;
+        return this;
+    }
+
+    public PMIdentifier getIdentifier() {
+        return identifier;
+    }
+
+    public PMAffiliation setIdentifier(PMIdentifier identifier) {
+        this.identifier = identifier;
+        return this;
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
index 68ef6459e..b0df25663 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
@@ -12,6 +12,8 @@ public class PMAuthor implements Serializable {
 
 	private String lastName;
 	private String foreName;
+	private PMIdentifier identifier;
+	private PMAffiliation affiliation;
 
 	/**
 	 * Gets last name.
@@ -59,4 +61,41 @@ public class PMAuthor implements Serializable {
 			.format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : "");
 	}
 
+	/**
+	 * Gets identifier.
+	 *
+	 * @return the identifier
+	 */
+	public PMIdentifier getIdentifier() {
+		return identifier;
+	}
+
+	/**
+	 * Sets identifier.
+	 *
+	 * @param identifier the identifier
+	 */
+	public void setIdentifier(PMIdentifier identifier) {
+		this.identifier = identifier;
+	}
+
+	/**
+	 * Gets affiliation.
+	 *
+	 * @return the affiliation
+	 */
+	public PMAffiliation getAffiliation() {
+		return affiliation;
+	}
+
+	/**
+	 * Sets affiliation.
+	 *
+	 * @param affiliation the affiliation
+	 */
+	public void setAffiliation(PMAffiliation affiliation) {
+		this.affiliation = affiliation;
+	}
+
+
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
new file mode 100644
index 000000000..0c8c55e40
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
@@ -0,0 +1,53 @@
+package eu.dnetlib.dhp.sx.bio.pubmed;
+
+public class PMIdentifier {
+
+    private String pid;
+    private String type;
+
+
+    public PMIdentifier(String pid, String type) {
+        this.pid = cleanPid(pid);
+        this.type = type;
+    }
+
+    public PMIdentifier() {
+
+    }
+
+    private String cleanPid(String pid) {
+
+        if (pid == null) {
+            return null;
+        }
+
+        // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
+        if (pid.matches("[0-9]{15}[0-9X]")) {
+            return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
+        }
+
+        // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
+        if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
+            return pid.replaceAll("http://orcid.org/", "");
+        }
+        return pid;
+    }
+
+    public String getPid() {
+        return pid;
+    }
+
+    public PMIdentifier setPid(String pid) {
+        this.pid = cleanPid(pid);
+        return this;
+    }
+
+    public String getType() {
+        return type;
+    }
+
+    public PMIdentifier setType(String type) {
+        this.type = type;
+        return this;
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
index c9e868185..2eb4bea65 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
@@ -81,6 +81,26 @@ class PMParser2 {
         val a = new PMAuthor
         a.setLastName((author \ "LastName").text)
         a.setForeName((author \ "ForeName").text)
+        val id = (author \ "Identifier").text
+        val idType =(author \ "Identifier" \ "@Source").text
+
+        if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
+          a.setIdentifier(new PMIdentifier(id, idType))
+        }
+
+
+        val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text
+        val affiliationId  = (author \ "AffiliationInfo" \ "Identifier").text
+        val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text
+
+        if(affiliation != null && affiliation.nonEmpty) {
+          val aff = new PMAffiliation()
+          aff.setName(affiliation)
+          if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) {
+            aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType))
+          }
+          a.setAffiliation(aff)
+        }
         a
       })
       .toList
@@ -99,15 +119,7 @@ class PMParser2 {
     val authors = xml \ "MedlineCitation" \ "Article" \ "AuthorList" \ "Author"
 
     article.setAuthors(
-      authors
-        .map(author => {
-          val a = new PMAuthor
-          a.setLastName((author \ "LastName").text)
-          a.setForeName((author \ "ForeName").text)
-          a
-        })
-        .toList
-        .asJava
+      extractAuthors(authors).asJava
     )
 
     val pmId = xml \ "MedlineCitation" \ "PMID"
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
index d59d73bd0..5e14c731a 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
@@ -294,6 +294,12 @@ object PubMedToOaf {
       author.setName(a.getForeName)
       author.setSurname(a.getLastName)
       author.setFullname(a.getFullName)
+      if(a.getIdentifier != null) {
+        author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid,
+          OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava)
+      }
+      if (a.getAffiliation!= null)
+        author.setRawAffiliationString(List(a.getAffiliation.getName).asJava)
       author.setRank(index + 1)
       author
     }(collection.breakOut)
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml
index 4b4d860d7..c2e503f57 100644
--- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/single_pubmed.xml
@@ -1,77 +1,56 @@
 <PubmedArticle>
-    <MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM">
-        <PMID Version="1">37885214</PMID>
+    <MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM">
+        <PMID Version="1">37318999</PMID>
         <DateCompleted>
             <Year>2024</Year>
             <Month>02</Month>
-            <Day>14</Day>
+            <Day>09</Day>
         </DateCompleted>
         <DateRevised>
             <Year>2024</Year>
             <Month>02</Month>
-            <Day>14</Day>
+            <Day>09</Day>
         </DateRevised>
         <Article PubModel="Print-Electronic">
             <Journal>
-                <ISSN IssnType="Electronic">2752-7549</ISSN>
+                <ISSN IssnType="Electronic">1522-1229</ISSN>
                 <JournalIssue CitedMedium="Internet">
-                    <Volume>40</Volume>
-                    <Issue>5</Issue>
+                    <Volume>47</Volume>
+                    <Issue>3</Issue>
                     <PubDate>
-                        <MedlineDate>2023 Sep-Oct</MedlineDate>
+                        <Year>2023</Year>
+                        <Month>Sep</Month>
+                        <Day>01</Day>
                     </PubDate>
                 </JournalIssue>
-                <Title>Journal of pediatric hematology/oncology nursing</Title>
-                <ISOAbbreviation>J Pediatr Hematol Oncol Nurs</ISOAbbreviation>
+                <Title>Advances in physiology education</Title>
+                <ISOAbbreviation>Adv Physiol Educ</ISOAbbreviation>
             </Journal>
-            <ArticleTitle>Care Needs of Parents of Children With Cancer in a Low-Middle-Income Country.</ArticleTitle>
+            <ArticleTitle>Providing the choice of in-person or videoconference attendance in a clinical physiology course may harm learning outcomes for the entire cohort.</ArticleTitle>
             <Pagination>
-                <MedlinePgn>295-304</MedlinePgn>
+                <MedlinePgn>548-556</MedlinePgn>
             </Pagination>
-            <ELocationID EIdType="doi" ValidYN="Y">10.1177/27527530231193972</ELocationID>
+            <ELocationID EIdType="doi" ValidYN="Y">10.1152/advan.00160.2022</ELocationID>
             <Abstract>
-                <AbstractText><b>Background:</b> Mapping out actual supportive care needs assists nurses in providing holistic individualized care. This study aimed to explore the care needs of parents of children with cancer in the Philippines. <b>Method:</b> Guided by the Supportive Care Needs Framework (SCNF), this study used an embedded mixed-method design with the quantitative revised Cancer Patient Needs Questionnaire and qualitative semistructured interviews to describe parents' care needs and priorities. <b>Results:</b> Filipino parents (<i>N</i> = 156) of children with cancer have various care needs which could be classified along the SCNF categories-practical, informational, spiritual, physical, emotional, and physical needs as ranked from highest to lowest. A number of variables were significantly associated with care needs. Solid tumor diagnosis was associated with greater practical, emotional, and psychosocial care needs; having a child who had undergone surgery was associated with more practical and spiritual care needs; and being within one year of the child's diagnosis was associated with practical, psychosocial, and spiritual care needs. Parent priority needs included (a) addressing financial needs; (b) access to temporary housing to minimize treatment-related costs; (c) support groups among parents of children with cancer as a source of information; (d) financial and social support between members of family and partners of parents of children with cancer; and (e) using prayer to facilitate acceptance. <b>Conclusions:</b> Supportive care needs of parents of children with cancer are important components of care that should be given recognition to enhance holistic individualized care throughout the childhood cancer experience.</AbstractText>
+                <AbstractText>Clinical Physiology 1 and 2 are flipped classes in which students watch prerecorded videos before class. During the 3-h class, students take practice assessments, work in groups on critical thinking exercises, work through case studies, and engage in drawing exercises. Due to the COVID pandemic, these courses were transitioned from in-person classes to online classes. Despite the university's return-to-class policy, some students were reluctant to return to in-person classes; therefore during the 2021-2022 academic year, Clinical Physiology 1 and 2 were offered as flipped, hybrid courses. In a hybrid format, students either attended the synchronous class in person or online. Here we evaluate the learning outcomes and the perceptions of the learning experience for students who attended Clinical Physiology 1 and 2 either online (2020-2021) or in a hybrid format (2021-2022). In addition to exam scores, in-class surveys and end of course evaluations were compiled to describe the student experience in the flipped hybrid setting. Retrospective linear mixed-model regression analysis of exam scores revealed that a hybrid modality (2021-2022) was associated with lower exam scores when controlling for sex, graduate/undergraduate status, delivery method, and the order in which the courses were taken (<i>F</i> test: <i>F</i> = 8.65, df1 = 2, df2 = 179.28, <i>P</i> = 0.0003). In addition, being a Black Indigenous Person of Color (BIPOC) student is associated with a lower exam score, controlling for the same previous factors (<i>F</i> test: <i>F</i> = 4.23, df1 = 1, df2 = 130.28, <i>P</i> = 0.04), albeit with lower confidence; the BIPOC representation in this sample is small (BIPOC: <i>n</i> = 144; total: <i>n</i> = 504). There is no significant interaction between the hybrid modality and race, meaning that BIPOC and White students are both negatively affected in a hybrid flipped course. Instructors should consider carefully about offering hybrid courses and build in extra student support.<b>NEW &amp; NOTEWORTHY</b> The transition from online to in-person teaching has been as challenging as the original transition to remote teaching with the onset of the pandemic. Since not all students were ready to return to the classroom, students could choose to take this course in person or online. This arrangement provided flexibility and opportunities for innovative class activities for students but introduced tradeoffs in lower test scores from the hybrid modality than fully online or fully in-person modalities.</AbstractText>
             </Abstract>
             <AuthorList CompleteYN="Y">
                 <Author ValidYN="Y">
-                    <LastName>Banayat</LastName>
-                    <ForeName>Aprille Campos</ForeName>
-                    <Initials>AC</Initials>
-                    <Identifier Source="ORCID">0000-0001-9339-9871</Identifier>
+                    <LastName>Anderson</LastName>
+                    <ForeName>Lisa Carney</ForeName>
+                    <Initials>LC</Initials>
+                    <Identifier Source="ORCID">0000-0003-2261-1921</Identifier>
                     <AffiliationInfo>
-                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                        <Affiliation>Department of Integrative Biology and Physiology, University of Minnesota, Minneapolis, Minnesota, United States.</Affiliation>
+                        <Identifier Source="ROR">https://ror.org/017zqws13</Identifier>
                     </AffiliationInfo>
                 </Author>
                 <Author ValidYN="Y">
-                    <LastName>Abad</LastName>
-                    <ForeName>Peter James B</ForeName>
-                    <Initials>PJB</Initials>
+                    <LastName>Jacobson</LastName>
+                    <ForeName>Tate</ForeName>
+                    <Initials>T</Initials>
                     <AffiliationInfo>
-                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
-                    </AffiliationInfo>
-                </Author>
-                <Author ValidYN="Y">
-                    <LastName>Bonito</LastName>
-                    <ForeName>Sheila R</ForeName>
-                    <Initials>SR</Initials>
-                    <AffiliationInfo>
-                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
-                    </AffiliationInfo>
-                </Author>
-                <Author ValidYN="Y">
-                    <LastName>Manahan</LastName>
-                    <ForeName>Lydia T</ForeName>
-                    <Initials>LT</Initials>
-                    <AffiliationInfo>
-                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
-                    </AffiliationInfo>
-                </Author>
-                <Author ValidYN="Y">
-                    <LastName>Peralta</LastName>
-                    <ForeName>Arnold B</ForeName>
-                    <Initials>AB</Initials>
-                    <AffiliationInfo>
-                        <Affiliation>College of Nursing, University of the Philippines Manila, Manila, Philippines.</Affiliation>
+                        <Affiliation>Department of Statistics, University of Minnesota, Minneapolis, Minnesota, United States.</Affiliation>
                     </AffiliationInfo>
                 </Author>
             </AuthorList>
@@ -81,142 +60,98 @@
             </PublicationTypeList>
             <ArticleDate DateType="Electronic">
                 <Year>2023</Year>
-                <Month>10</Month>
-                <Day>26</Day>
+                <Month>06</Month>
+                <Day>15</Day>
             </ArticleDate>
         </Article>
         <MedlineJournalInfo>
             <Country>United States</Country>
-            <MedlineTA>J Pediatr Hematol Oncol Nurs</MedlineTA>
-            <NlmUniqueID>9918282681506676</NlmUniqueID>
-            <ISSNLinking>2752-7530</ISSNLinking>
+            <MedlineTA>Adv Physiol Educ</MedlineTA>
+            <NlmUniqueID>100913944</NlmUniqueID>
+            <ISSNLinking>1043-4046</ISSNLinking>
         </MedlineJournalInfo>
         <CitationSubset>IM</CitationSubset>
         <MeshHeadingList>
             <MeshHeading>
-                <DescriptorName UI="D002648" MajorTopicYN="N">Child</DescriptorName>
+                <DescriptorName UI="D010827" MajorTopicYN="Y">Physiology</DescriptorName>
+                <QualifierName UI="Q000193" MajorTopicYN="N">education</QualifierName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D012189" MajorTopicYN="N">Retrospective Studies</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D007858" MajorTopicYN="N">Learning</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D058873" MajorTopicYN="N">Pandemics</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D000086382" MajorTopicYN="N">COVID-19</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D012044" MajorTopicYN="N">Regression Analysis</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D013334" MajorTopicYN="N">Students</DescriptorName>
             </MeshHeading>
             <MeshHeading>
                 <DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
             </MeshHeading>
             <MeshHeading>
-                <DescriptorName UI="D010290" MajorTopicYN="Y">Parents</DescriptorName>
-                <QualifierName UI="Q000523" MajorTopicYN="N">psychology</QualifierName>
+                <DescriptorName UI="D008297" MajorTopicYN="N">Male</DescriptorName>
             </MeshHeading>
             <MeshHeading>
-                <DescriptorName UI="D012944" MajorTopicYN="N">Social Support</DescriptorName>
+                <DescriptorName UI="D005260" MajorTopicYN="N">Female</DescriptorName>
             </MeshHeading>
             <MeshHeading>
-                <DescriptorName UI="D029181" MajorTopicYN="N">Spirituality</DescriptorName>
+                <DescriptorName UI="D044465" MajorTopicYN="N">White People</DescriptorName>
             </MeshHeading>
             <MeshHeading>
-                <DescriptorName UI="D012067" MajorTopicYN="N">Religion</DescriptorName>
+                <DescriptorName UI="D044383" MajorTopicYN="N">Black People</DescriptorName>
             </MeshHeading>
             <MeshHeading>
-                <DescriptorName UI="D009369" MajorTopicYN="Y">Neoplasms</DescriptorName>
-                <QualifierName UI="Q000628" MajorTopicYN="N">therapy</QualifierName>
+                <DescriptorName UI="D020375" MajorTopicYN="N">Education, Distance</DescriptorName>
+            </MeshHeading>
+            <MeshHeading>
+                <DescriptorName UI="D003479" MajorTopicYN="N">Curriculum</DescriptorName>
             </MeshHeading>
         </MeshHeadingList>
         <KeywordList Owner="NOTNLM">
-            <Keyword MajorTopicYN="N">cancer</Keyword>
-            <Keyword MajorTopicYN="N">mixed methods</Keyword>
-            <Keyword MajorTopicYN="N">parent</Keyword>
-            <Keyword MajorTopicYN="N">pediatric</Keyword>
-            <Keyword MajorTopicYN="N">research</Keyword>
-            <Keyword MajorTopicYN="N">supportive care</Keyword>
+            <Keyword MajorTopicYN="N">flipped teaching</Keyword>
+            <Keyword MajorTopicYN="N">hybrid teaching</Keyword>
+            <Keyword MajorTopicYN="N">inequity</Keyword>
+            <Keyword MajorTopicYN="N">learning outcomes</Keyword>
+            <Keyword MajorTopicYN="N">responsive teaching</Keyword>
         </KeywordList>
-        <CoiStatement>Declaration of Conflicting InterestsThe author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.</CoiStatement>
     </MedlineCitation>
     <PubmedData>
         <History>
             <PubMedPubDate PubStatus="medline">
-                <Year>2024</Year>
-                <Month>2</Month>
-                <Day>12</Day>
-                <Hour>18</Hour>
-                <Minute>42</Minute>
+                <Year>2023</Year>
+                <Month>7</Month>
+                <Day>21</Day>
+                <Hour>6</Hour>
+                <Minute>44</Minute>
             </PubMedPubDate>
             <PubMedPubDate PubStatus="pubmed">
                 <Year>2023</Year>
-                <Month>10</Month>
-                <Day>27</Day>
-                <Hour>6</Hour>
-                <Minute>42</Minute>
+                <Month>6</Month>
+                <Day>15</Day>
+                <Hour>19</Hour>
+                <Minute>14</Minute>
             </PubMedPubDate>
             <PubMedPubDate PubStatus="entrez">
                 <Year>2023</Year>
-                <Month>10</Month>
-                <Day>27</Day>
-                <Hour>3</Hour>
-                <Minute>43</Minute>
+                <Month>6</Month>
+                <Day>15</Day>
+                <Hour>12</Hour>
+                <Minute>53</Minute>
             </PubMedPubDate>
         </History>
         <PublicationStatus>ppublish</PublicationStatus>
         <ArticleIdList>
-            <ArticleId IdType="pubmed">37885214</ArticleId>
-            <ArticleId IdType="doi">10.1177/27527530231193972</ArticleId>
+            <ArticleId IdType="pubmed">37318999</ArticleId>
+            <ArticleId IdType="doi">10.1152/advan.00160.2022</ArticleId>
         </ArticleIdList>
     </PubmedData>
 </PubmedArticle>
-<DeleteCitation>
-<PMID Version="1">30522158</PMID>
-<PMID Version="1">32769323</PMID>
-<PMID Version="1">34061701</PMID>
-<PMID Version="1">34661197</PMID>
-<PMID Version="1">34837091</PMID>
-<PMID Version="1">35035475</PMID>
-<PMID Version="1">35211699</PMID>
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-<PMID Version="1">35782783</PMID>
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-<PMID Version="1">36972191</PMID>
-<PMID Version="1">37034422</PMID>
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-<PMID Version="1">37152108</PMID>
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-<PMID Version="1">37273889</PMID>
-<PMID Version="1">37333905</PMID>
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-<PMID Version="1">37981909</PMID>
-<PMID Version="1">37981945</PMID>
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-<PMID Version="1">38274640</PMID>
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-<PMID Version="1">38335456</PMID>
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-<PMID Version="1">38349576</PMID>
-<PMID Version="1">38353676</PMID>
-</DeleteCitation>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
index c942ca132..4a926df01 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
@@ -19,9 +19,11 @@ import org.mockito.junit.jupiter.MockitoExtension
 import org.slf4j.LoggerFactory
 
 import java.io.{BufferedReader, InputStream, InputStreamReader}
+import java.util.regex.Pattern
 import java.util.zip.GZIPInputStream
 import javax.xml.stream.XMLInputFactory
 import scala.collection.JavaConverters._
+import scala.collection.mutable
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
 
@@ -51,6 +53,64 @@ class BioScholixTest extends AbstractVocabularyTest {
     }
   }
 
+  @Test
+  def testPid(): Unit = {
+    val pids = List(
+      "0000000163025705",
+      "000000018494732X",
+      "0000000308873343",
+      "0000000335964515",
+      "0000000333457333",
+      "0000000335964515",
+      "0000000302921949",
+
+      "http://orcid.org/0000-0001-8567-3543",
+      "http://orcid.org/0000-0001-7868-8528",
+      "0000-0001-9189-1440",
+      "0000-0003-3727-9247",
+      "0000-0001-7246-1058",
+      "000000033962389X",
+      "0000000330371470",
+      "0000000171236123",
+      "0000000272569752",
+      "0000000293231371",
+      "http://orcid.org/0000-0003-3345-7333",
+      "0000000340145688",
+      "http://orcid.org/0000-0003-4894-1689"
+    )
+
+    pids.foreach(pid => {
+      val pidCleaned = new PMIdentifier(pid, "ORCID").getPid
+      // assert pid is in the format of ORCID
+      println(pidCleaned)
+      assertTrue(pidCleaned.matches("[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{3}[0-9X]"))
+    })
+  }
+
+  def extractAffiliation(s: String): List[String] = {
+    val regex: String = "<Affiliation>(.*)<\\/Affiliation>"
+    val pattern = Pattern.compile(regex, Pattern.MULTILINE)
+    val matcher = pattern.matcher(s)
+    val l: mutable.ListBuffer[String] = mutable.ListBuffer()
+    while (matcher.find()) {
+      l += matcher.group(1)
+    }
+    l.toList
+  }
+
+  case class AuthorPID(pidType: String, pid: String) {}
+
+  def extractAuthorIdentifier(s: String): List[AuthorPID] = {
+    val regex: String = "<Identifier Source=\"(.*)\">(.*)<\\/Identifier>"
+    val pattern = Pattern.compile(regex, Pattern.MULTILINE)
+    val matcher = pattern.matcher(s)
+    val l: mutable.ListBuffer[AuthorPID] = mutable.ListBuffer()
+    while (matcher.find()) {
+      l += AuthorPID(pidType = matcher.group(1), pid = matcher.group(2))
+    }
+    l.toList
+  }
+
   @Test
   def testParsingPubmed2(): Unit = {
     val mapper = new ObjectMapper()
@@ -58,7 +118,9 @@ class BioScholixTest extends AbstractVocabularyTest {
     val parser = new PMParser2()
     val article = parser.parse(xml)
 
-    println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(article))
+//    println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(article))
+
+    println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(PubMedToOaf.convert(article, vocabularies)))
 
   }
 

From 4a3b173ca2d917c52de1671c352d1296ac211736 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 13 Nov 2024 16:27:00 +0100
Subject: [PATCH 208/239] defaults to 0000 - Unknown in case the instance type
 lookup in the dnet:result_typologies doesn't find a corresponding result type
 binding

---
 .../dhp/schema/oaf/utils/MergeUtils.java      | 12 +---
 .../raw/AbstractMdRecordToOafMapper.java      | 55 ++++++++++---------
 .../dhp/oa/graph/raw/OafToOafMapper.java      |  4 +-
 .../dhp/oa/graph/raw/OdfToOafMapper.java      |  4 +-
 4 files changed, 36 insertions(+), 39 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index dc76860f8..c9b235fd6 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -74,15 +74,9 @@ public class MergeUtils {
 			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
 				return (T) mergedResult;
 			} else {
-				final Qualifier expectedResultType = vocs.lookupTermBySynonym(
-						ModelConstants.DNET_RESULT_TYPOLOGIES,
-						i.getInstancetype().getClassid());
-
-				if (Objects.isNull(expectedResultType)) {
-					throw new IllegalArgumentException(
-							"instance type not bound to any result type in dnet:result_typologies: " +
-									i.getInstancetype().getClassid());
-				}
+				final Qualifier expectedResultType = Optional
+						.ofNullable(vocs.lookupTermBySynonym(ModelConstants.DNET_RESULT_TYPOLOGIES, i.getInstancetype().getClassid()))
+						.orElse(OafMapperUtils.unknown(ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES));
 
 				// there is a clash among the result types
 				if (!expectedResultType.getClassid().equals(mergedResult.getResulttype().getClassid())) {
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
index ba6887a2e..be84778f5 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
@@ -153,30 +153,33 @@ public abstract class AbstractMdRecordToOafMapper {
 			final DataInfo entityInfo = prepareDataInfo(doc, this.invisible);
 			final long lastUpdateTimestamp = new Date().getTime();
 
-			final List<Instance> instances = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
+			final Instance instance = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
 
-			final String type = getResultType(instances);
+			if (!Optional.ofNullable(instance.getInstancetype())
+					.map(Qualifier::getClassid)
+					.filter(StringUtils::isNotBlank)
+					.isPresent()) {
+				return Lists.newArrayList();
+			}
 
-			return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp);
+			final String type = getResultType(instance);
+
+			return createOafs(doc, type, instance, collectedFrom, entityInfo, lastUpdateTimestamp);
 		} catch (final DocumentException e) {
 			log.error("Error with record:\n" + xml);
 			return Lists.newArrayList();
 		}
 	}
 
-	protected String getResultType(final List<Instance> instances) {
-
+	protected String getResultType(final Instance instance) {
 		if (this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
-			final String instanceType = instances
-				.stream()
-				.map(i -> i.getInstancetype().getClassid())
-				.findFirst()
-				.filter(s -> !UNKNOWN.equalsIgnoreCase(s))
-				.orElse("0000"); // Unknown
-			return Optional
-				.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
-				.map(Qualifier::getClassid)
-				.orElse("0000");
+			return Optional.ofNullable(instance.getInstancetype())
+					.map(Qualifier::getClassid)
+					.map(instanceType -> Optional
+								.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
+								.map(Qualifier::getClassid)
+								.orElse("0000"))
+					.orElse("0000");
 		} else {
 			throw new IllegalStateException("Missing vocabulary: " + ModelConstants.DNET_RESULT_TYPOLOGIES);
 		}
@@ -196,12 +199,12 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected List<Oaf> createOafs(
 		final Document doc,
 		final String type,
-		final List<Instance> instances,
+		final Instance instance,
 		final KeyValue collectedFrom,
 		final DataInfo info,
 		final long lastUpdateTimestamp) {
 
-		final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
+		final OafEntity entity = createEntity(doc, type, instance, collectedFrom, info, lastUpdateTimestamp);
 
 		final Set<String> originalId = Sets.newHashSet(entity.getOriginalId());
 		originalId.add(entity.getId());
@@ -234,19 +237,19 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	private OafEntity createEntity(final Document doc,
 		final String type,
-		final List<Instance> instances,
+		final Instance instance,
 		final KeyValue collectedFrom,
 		final DataInfo info,
 		final long lastUpdateTimestamp) {
 		switch (type.toLowerCase()) {
 			case "publication":
 				final Publication p = new Publication();
-				populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(p, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				p.setJournal(prepareJournal(doc, info));
 				return p;
 			case "dataset":
 				final Dataset d = new Dataset();
-				populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(d, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				d.setStoragedate(prepareDatasetStorageDate(doc, info));
 				d.setDevice(prepareDatasetDevice(doc, info));
 				d.setSize(prepareDatasetSize(doc, info));
@@ -257,7 +260,7 @@ public abstract class AbstractMdRecordToOafMapper {
 				return d;
 			case "software":
 				final Software s = new Software();
-				populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(s, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
 				s.setLicense(prepareSoftwareLicenses(doc, info));
 				s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
@@ -267,7 +270,7 @@ public abstract class AbstractMdRecordToOafMapper {
 			case "otherresearchproducts":
 			default:
 				final OtherResearchProduct o = new OtherResearchProduct();
-				populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(o, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
 				o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
 				o.setTool(prepareOtherResearchProductTools(doc, info));
@@ -414,7 +417,7 @@ public abstract class AbstractMdRecordToOafMapper {
 	private void populateResultFields(
 		final Result r,
 		final Document doc,
-		final List<Instance> instances,
+		final Instance instance,
 		final KeyValue collectedFrom,
 		final DataInfo info,
 		final long lastUpdateTimestamp) {
@@ -448,8 +451,8 @@ public abstract class AbstractMdRecordToOafMapper {
 		r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
 		r.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
 		r.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
-		r.setInstance(instances);
-		r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances));
+		r.setInstance(Arrays.asList(instance));
+		r.setBestaccessright(OafMapperUtils.createBestAccessRights(Arrays.asList(instance)));
 		r.setEoscifguidelines(prepareEOSCIfGuidelines(doc, info));
 	}
 
@@ -508,7 +511,7 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
 
-	protected abstract List<Instance> prepareInstances(
+	protected abstract Instance prepareInstances(
 		Document doc,
 		DataInfo info,
 		KeyValue collectedfrom,
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
index 98da48f9e..33351e91f 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
@@ -135,7 +135,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 	}
 
 	@Override
-	protected List<Instance> prepareInstances(
+	protected Instance prepareInstances(
 		final Document doc,
 		final DataInfo info,
 		final KeyValue collectedfrom,
@@ -197,7 +197,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 			instance.getUrl().addAll(validUrl);
 		}
 
-		return Lists.newArrayList(instance);
+		return instance;
 	}
 
 	/**
diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
index ad61304a0..a811aad46 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
@@ -126,7 +126,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	}
 
 	@Override
-	protected List<Instance> prepareInstances(
+	protected Instance prepareInstances(
 		final Document doc,
 		final DataInfo info,
 		final KeyValue collectedfrom,
@@ -210,7 +210,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 			instance.setUrl(new ArrayList<>());
 			instance.getUrl().addAll(validUrl);
 		}
-		return Arrays.asList(instance);
+		return instance;
 	}
 
 	protected String trimAndDecodeUrl(String url) {

From b95672b4204667f1b011a7b6ed281b7fcbb3525c Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 15 Nov 2024 09:16:18 +0100
Subject: [PATCH 209/239] mergeUtils set the result identifier when enforcing
 the result type

---
 .../dhp/schema/oaf/utils/MergeUtils.java      | 451 +++++++++---------
 1 file changed, 229 insertions(+), 222 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index c9b235fd6..c092f6035 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -16,8 +16,6 @@ import java.util.function.Function;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
-import eu.dnetlib.dhp.schema.common.EntityType;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -25,8 +23,10 @@ import org.apache.commons.lang3.tuple.Pair;
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.base.Joiner;
 
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
@@ -46,7 +46,7 @@ public class MergeUtils {
 	}
 
 	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator,
-											   boolean checkDelegateAuthority, VocabularyGroup vocs) {
+		boolean checkDelegateAuthority, VocabularyGroup vocs) {
 
 		ArrayList<T> sortedEntities = new ArrayList<>();
 		oafEntityIterator.forEachRemaining(sortedEntities::add);
@@ -74,22 +74,29 @@ public class MergeUtils {
 			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
 				return (T) mergedResult;
 			} else {
-				final Qualifier expectedResultType = Optional
-						.ofNullable(vocs.lookupTermBySynonym(ModelConstants.DNET_RESULT_TYPOLOGIES, i.getInstancetype().getClassid()))
-						.orElse(OafMapperUtils.unknown(ModelConstants.DNET_RESULT_TYPOLOGIES, ModelConstants.DNET_RESULT_TYPOLOGIES));
+				final String expectedResultType = Optional
+					.ofNullable(
+						vocs
+							.lookupTermBySynonym(
+								ModelConstants.DNET_RESULT_TYPOLOGIES, i.getInstancetype().getClassid()))
+					.orElse(ModelConstants.ORP_DEFAULT_RESULTTYPE)
+					.getClassid();
 
 				// there is a clash among the result types
-				if (!expectedResultType.getClassid().equals(mergedResult.getResulttype().getClassid())) {
-					try {
-						String resulttype = expectedResultType.getClassid();
-						if (EntityType.otherresearchproduct.toString().equals(resulttype)) {
-							resulttype = "other";
-						}
-						Result result = (Result) ModelSupport.oafTypes.get(resulttype).newInstance();
-						return (T) mergeResultFields(result, mergedResult);
-					} catch (InstantiationException | IllegalAccessException e) {
-						throw new IllegalStateException(e);
-					}
+				if (!expectedResultType.equals(mergedResult.getResulttype().getClassid())) {
+
+					Result result = (Result) Optional
+						.ofNullable(ModelSupport.oafTypes.get(expectedResultType))
+						.map(r -> {
+							try {
+								return r.newInstance();
+							} catch (InstantiationException | IllegalAccessException e) {
+								throw new IllegalStateException(e);
+							}
+						})
+						.orElse(new OtherResearchProduct());
+					result.setId(mergedResult.getId());
+					return (T) mergeResultFields(result, mergedResult);
 				} else {
 					return (T) mergedResult;
 				}
@@ -116,10 +123,10 @@ public class MergeUtils {
 			return mergeRelation((Relation) left, (Relation) right);
 		} else {
 			throw new RuntimeException(
-					String
-							.format(
-									"MERGE_FROM_AND_GET incompatible types: %s, %s",
-									left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+				String
+					.format(
+						"MERGE_FROM_AND_GET incompatible types: %s, %s",
+						left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
 		}
 	}
 
@@ -158,10 +165,10 @@ public class MergeUtils {
 			return mergeProject((Project) left, (Project) right);
 		} else {
 			throw new RuntimeException(
-					String
-							.format(
-									"MERGE_FROM_AND_GET incompatible types: %s, %s",
-									left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
+				String
+					.format(
+						"MERGE_FROM_AND_GET incompatible types: %s, %s",
+						left.getClass().getCanonicalName(), right.getClass().getCanonicalName()));
 		}
 	}
 
@@ -252,7 +259,7 @@ public class MergeUtils {
 	}
 
 	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
-											 Function<T, K> keyExtractor, BinaryOperator<T> merger) {
+		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
 		if (left == null || left.isEmpty()) {
 			return right != null ? right : new ArrayList<>();
 		} else if (right == null || right.isEmpty()) {
@@ -263,11 +270,11 @@ public class MergeUtils {
 		List<T> l = trust >= 0 ? right : left;
 
 		return new ArrayList<>(Stream
-				.concat(h.stream(), l.stream())
-				.filter(Objects::nonNull)
-				.distinct()
-				.collect(Collectors.toMap(keyExtractor, v -> v, merger, LinkedHashMap::new))
-				.values());
+			.concat(h.stream(), l.stream())
+			.filter(Objects::nonNull)
+			.distinct()
+			.collect(Collectors.toMap(keyExtractor, v -> v, merger, LinkedHashMap::new))
+			.values());
 	}
 
 	private static <T, K> List<T> unionDistinctLists(final List<T> left, final List<T> right, int trust) {
@@ -281,10 +288,10 @@ public class MergeUtils {
 		List<T> l = trust >= 0 ? right : left;
 
 		return Stream
-				.concat(h.stream(), l.stream())
-				.filter(Objects::nonNull)
-				.distinct()
-				.collect(Collectors.toList());
+			.concat(h.stream(), l.stream())
+			.filter(Objects::nonNull)
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	private static List<String> unionDistinctListOfString(final List<String> l, final List<String> r) {
@@ -295,10 +302,10 @@ public class MergeUtils {
 		}
 
 		return Stream
-				.concat(l.stream(), r.stream())
-				.filter(StringUtils::isNotBlank)
-				.distinct()
-				.collect(Collectors.toList());
+			.concat(l.stream(), r.stream())
+			.filter(StringUtils::isNotBlank)
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	// TODO review
@@ -324,7 +331,7 @@ public class MergeUtils {
 	}
 
 	private static List<StructuredProperty> unionTitle(List<StructuredProperty> left, List<StructuredProperty> right,
-													   int trust) {
+		int trust) {
 		if (left == null) {
 			return right;
 		} else if (right == null) {
@@ -335,10 +342,10 @@ public class MergeUtils {
 		List<StructuredProperty> l = trust >= 0 ? right : left;
 
 		return Stream
-				.concat(h.stream(), l.stream())
-				.filter(Objects::isNull)
-				.distinct()
-				.collect(Collectors.toList());
+			.concat(h.stream(), l.stream())
+			.filter(Objects::isNull)
+			.distinct()
+			.collect(Collectors.toList());
 	}
 
 	/**
@@ -373,8 +380,8 @@ public class MergeUtils {
 		merged.setPid(mergeLists(merged.getPid(), enrich.getPid(), trust, MergeUtils::spKeyExtractor, (p1, p2) -> p1));
 		merged.setDateofcollection(LocalDateTime.now().toString());
 		merged
-				.setDateoftransformation(
-						chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
+			.setDateoftransformation(
+				chooseString(merged.getDateoftransformation(), enrich.getDateoftransformation(), trust));
 		merged.setExtraInfo(unionDistinctLists(merged.getExtraInfo(), enrich.getExtraInfo(), trust));
 		// When merging records OAI provenance becomes null
 		merged.setOaiprovenance(null);
@@ -391,7 +398,7 @@ public class MergeUtils {
 		checkArgument(Objects.equals(merge.getTarget(), enrich.getTarget()), "target ids must be equal");
 		checkArgument(Objects.equals(merge.getRelType(), enrich.getRelType()), "relType(s) must be equal");
 		checkArgument(
-				Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
+			Objects.equals(merge.getSubRelType(), enrich.getSubRelType()), "subRelType(s) must be equal");
 		checkArgument(Objects.equals(merge.getRelClass(), enrich.getRelClass()), "relClass(es) must be equal");
 
 		// merge.setProvenance(mergeLists(merge.getProvenance(), enrich.getProvenance()));
@@ -402,10 +409,10 @@ public class MergeUtils {
 			merge.setValidationDate(ModelSupport.oldest(merge.getValidationDate(), enrich.getValidationDate()));
 		} catch (ParseException e) {
 			throw new IllegalArgumentException(String
-					.format(
-							"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
-							merge.getTarget(),
-							merge.getValidationDate()));
+				.format(
+					"invalid validation date format in relation [s:%s, t:%s]: %s", merge.getSource(),
+					merge.getTarget(),
+					merge.getValidationDate()));
 		}
 
 		// TODO keyvalue merge
@@ -419,7 +426,7 @@ public class MergeUtils {
 		T merge = mergeOafEntityFields(original, enrich, trust);
 
 		if (merge.getProcessingchargeamount() == null
-				|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
+			|| StringUtils.isBlank(merge.getProcessingchargeamount().getValue())) {
 			merge.setProcessingchargeamount(enrich.getProcessingchargeamount());
 			merge.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
 		}
@@ -451,8 +458,8 @@ public class MergeUtils {
 		}
 
 		merge
-				.setDateofacceptance(
-						mergeDateOfAcceptance(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
+			.setDateofacceptance(
+				mergeDateOfAcceptance(merge.getDateofacceptance(), enrich.getDateofacceptance(), trust));
 
 		merge.setPublisher(coalesce(merge.getPublisher(), enrich.getPublisher()));
 		merge.setEmbargoenddate(coalesce(merge.getEmbargoenddate(), enrich.getEmbargoenddate()));
@@ -467,7 +474,7 @@ public class MergeUtils {
 		merge.setCoverage(unionDistinctLists(merge.getCoverage(), enrich.getCoverage(), trust));
 
 		if (enrich.getBestaccessright() != null
-				&& new AccessRightComparator<>()
+			&& new AccessRightComparator<>()
 				.compare(enrich.getBestaccessright(), merge.getBestaccessright()) < 0) {
 			merge.setBestaccessright(enrich.getBestaccessright());
 		}
@@ -480,8 +487,8 @@ public class MergeUtils {
 
 		// ok
 		merge
-				.setExternalReference(
-						mergeExternalReference(merge.getExternalReference(), enrich.getExternalReference(), trust));
+			.setExternalReference(
+				mergeExternalReference(merge.getExternalReference(), enrich.getExternalReference(), trust));
 
 		// instance enrichment or union
 		// review instance equals => add pid to comparision
@@ -489,17 +496,17 @@ public class MergeUtils {
 			merge.setInstance(mergeInstances(merge.getInstance(), enrich.getInstance(), trust));
 		} else {
 			final List<Instance> enrichmentInstances = isAnEnrichment(merge) ? merge.getInstance()
-					: enrich.getInstance();
+				: enrich.getInstance();
 			final List<Instance> enrichedInstances = isAnEnrichment(merge) ? enrich.getInstance()
-					: merge.getInstance();
+				: merge.getInstance();
 			if (isAnEnrichment(merge))
 				merge.setDataInfo(enrich.getDataInfo());
 			merge.setInstance(enrichInstances(enrichedInstances, enrichmentInstances));
 		}
 
 		merge
-				.setEoscifguidelines(
-						mergeEosciifguidelines(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
+			.setEoscifguidelines(
+				mergeEosciifguidelines(merge.getEoscifguidelines(), enrich.getEoscifguidelines(), trust));
 		merge.setIsGreen(booleanOR(merge.getIsGreen(), enrich.getIsGreen()));
 		// OK but should be list of values
 		merge.setOpenAccessColor(coalesce(merge.getOpenAccessColor(), enrich.getOpenAccessColor()));
@@ -525,7 +532,7 @@ public class MergeUtils {
 						LocalDate enrich_date = LocalDate.parse(enrich.getValue(), DateTimeFormatter.ISO_DATE);
 
 						if (enrich_date.getYear() > 1300
-								&& (merge_date.getYear() < 1300 || merge_date.isAfter(enrich_date))) {
+							&& (merge_date.getYear() < 1300 || merge_date.isAfter(enrich_date))) {
 							return enrich;
 						}
 					} catch (NullPointerException | DateTimeParseException e) {
@@ -543,56 +550,56 @@ public class MergeUtils {
 
 	private static List<Instance> mergeInstances(List<Instance> v1, List<Instance> v2, int trust) {
 		return mergeLists(
-				v1, v2, trust,
-				MergeUtils::instanceKeyExtractor,
-				MergeUtils::instanceMerger);
+			v1, v2, trust,
+			MergeUtils::instanceKeyExtractor,
+			MergeUtils::instanceMerger);
 	}
 
 	private static List<EoscIfGuidelines> mergeEosciifguidelines(List<EoscIfGuidelines> v1, List<EoscIfGuidelines> v2,
-																 int trust) {
+		int trust) {
 		return mergeLists(
-				v1, v2, trust, er -> Joiner
-						.on("||")
-						.useForNull("")
-						.join(er.getCode(), er.getLabel(), er.getUrl(), er.getSemanticRelation()),
-				(r, l) -> r);
+			v1, v2, trust, er -> Joiner
+				.on("||")
+				.useForNull("")
+				.join(er.getCode(), er.getLabel(), er.getUrl(), er.getSemanticRelation()),
+			(r, l) -> r);
 
 	}
 
 	private static List<ExternalReference> mergeExternalReference(List<ExternalReference> v1,
-																  List<ExternalReference> v2, int trust) {
+		List<ExternalReference> v2, int trust) {
 		return mergeLists(
-				v1, v2, trust, er -> Joiner
-						.on(',')
-						.useForNull("")
-						.join(
-								er.getSitename(), er.getLabel(),
-								er.getUrl(), toString(er.getQualifier()), er.getRefidentifier(),
-								er.getQuery(), toString(er.getDataInfo())),
-				(r, l) -> r);
+			v1, v2, trust, er -> Joiner
+				.on(',')
+				.useForNull("")
+				.join(
+					er.getSitename(), er.getLabel(),
+					er.getUrl(), toString(er.getQualifier()), er.getRefidentifier(),
+					er.getQuery(), toString(er.getDataInfo())),
+			(r, l) -> r);
 	}
 
 	private static String toString(DataInfo di) {
 		return Joiner
-				.on(',')
-				.useForNull("")
-				.join(
-						di.getInvisible(), di.getInferred(), di.getDeletedbyinference(), di.getTrust(),
-						di.getInferenceprovenance(), toString(di.getProvenanceaction()));
+			.on(',')
+			.useForNull("")
+			.join(
+				di.getInvisible(), di.getInferred(), di.getDeletedbyinference(), di.getTrust(),
+				di.getInferenceprovenance(), toString(di.getProvenanceaction()));
 	}
 
 	private static String toString(Qualifier q) {
 		return Joiner
-				.on(',')
-				.useForNull("")
-				.join(q.getClassid(), q.getClassname(), q.getSchemeid(), q.getSchemename());
+			.on(',')
+			.useForNull("")
+			.join(q.getClassid(), q.getClassname(), q.getSchemeid(), q.getSchemename());
 	}
 
 	private static String toString(StructuredProperty sp) {
 		return Joiner
-				.on(',')
-				.useForNull("")
-				.join(toString(sp.getQualifier()), sp.getValue());
+			.on(',')
+			.useForNull("")
+			.join(toString(sp.getQualifier()), sp.getValue());
 	}
 
 	private static <T extends StructuredProperty> List<T> mergeStructuredProperties(List<T> v1, List<T> v2, int trust) {
@@ -631,17 +638,17 @@ public class MergeUtils {
 		// 2. @@
 		// 3. ||
 		return String
-				.join(
-						"::",
-						kvKeyExtractor(i.getHostedby()),
-						kvKeyExtractor(i.getCollectedfrom()),
-						qualifierKeyExtractor(i.getAccessright()),
-						qualifierKeyExtractor(i.getInstancetype()),
-						Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
-						Optional
-								.ofNullable(i.getPid())
-								.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
-								.orElse(null));
+			.join(
+				"::",
+				kvKeyExtractor(i.getHostedby()),
+				kvKeyExtractor(i.getCollectedfrom()),
+				qualifierKeyExtractor(i.getAccessright()),
+				qualifierKeyExtractor(i.getInstancetype()),
+				Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
+				Optional
+					.ofNullable(i.getPid())
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
+					.orElse(null));
 	}
 
 	private static Instance instanceMerger(Instance i1, Instance i2) {
@@ -652,30 +659,30 @@ public class MergeUtils {
 		i.setInstancetype(i1.getInstancetype());
 		i.setPid(mergeLists(i1.getPid(), i2.getPid(), 0, MergeUtils::spKeyExtractor, (sp1, sp2) -> sp1));
 		i
-				.setAlternateIdentifier(
-						mergeLists(
-								i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
-								(sp1, sp2) -> sp1));
+			.setAlternateIdentifier(
+				mergeLists(
+					i1.getAlternateIdentifier(), i2.getAlternateIdentifier(), 0, MergeUtils::spKeyExtractor,
+					(sp1, sp2) -> sp1));
 
 		i
-				.setRefereed(
-						Collections
-								.min(
-										Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
-										new RefereedComparator()));
+			.setRefereed(
+				Collections
+					.min(
+						Stream.of(i1.getRefereed(), i2.getRefereed()).collect(Collectors.toList()),
+						new RefereedComparator()));
 		i
-				.setInstanceTypeMapping(
-						mergeLists(
-								i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
-								MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
+			.setInstanceTypeMapping(
+				mergeLists(
+					i1.getInstanceTypeMapping(), i2.getInstanceTypeMapping(), 0,
+					MergeUtils::instanceTypeMappingKeyExtractor, (itm1, itm2) -> itm1));
 		i.setFulltext(selectFulltext(i1.getFulltext(), i2.getFulltext()));
 		i.setDateofacceptance(selectOldestDate(i1.getDateofacceptance(), i2.getDateofacceptance()));
 		i.setLicense(coalesce(i1.getLicense(), i2.getLicense()));
 		i.setProcessingchargeamount(coalesce(i1.getProcessingchargeamount(), i2.getProcessingchargeamount()));
 		i.setProcessingchargecurrency(coalesce(i1.getProcessingchargecurrency(), i2.getProcessingchargecurrency()));
 		i
-				.setMeasures(
-						mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
+			.setMeasures(
+				mergeLists(i1.getMeasures(), i2.getMeasures(), 0, MergeUtils::measureKeyExtractor, (m1, m2) -> m1));
 
 		i.setUrl(unionDistinctListOfString(i1.getUrl(), i2.getUrl()));
 
@@ -684,14 +691,14 @@ public class MergeUtils {
 
 	private static String measureKeyExtractor(Measure m) {
 		return String
-				.join(
-						"::",
-						m.getId(),
-						m
-								.getUnit()
-								.stream()
-								.map(KeyValue::getKey)
-								.collect(Collectors.joining("::")));
+			.join(
+				"::",
+				m.getId(),
+				m
+					.getUnit()
+					.stream()
+					.map(KeyValue::getKey)
+					.collect(Collectors.joining("::")));
 	}
 
 	private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
@@ -702,16 +709,16 @@ public class MergeUtils {
 		}
 
 		return Stream
-				.of(d1, d2)
-				.min(
-						Comparator
-								.comparing(
-										f -> DateParserUtils
-												.parseDate(f.getValue())
-												.toInstant()
-												.atZone(ZoneId.systemDefault())
-												.toLocalDate()))
-				.orElse(d1);
+			.of(d1, d2)
+			.min(
+				Comparator
+					.comparing(
+						f -> DateParserUtils
+							.parseDate(f.getValue())
+							.toInstant()
+							.atZone(ZoneId.systemDefault())
+							.toLocalDate()))
+			.orElse(d1);
 	}
 
 	private static String selectFulltext(String ft1, String ft2) {
@@ -726,12 +733,12 @@ public class MergeUtils {
 
 	private static String instanceTypeMappingKeyExtractor(InstanceTypeMapping itm) {
 		return String
-				.join(
-						"::",
-						itm.getOriginalType(),
-						itm.getTypeCode(),
-						itm.getTypeLabel(),
-						itm.getVocabularyName());
+			.join(
+				"::",
+				itm.getOriginalType(),
+				itm.getTypeCode(),
+				itm.getTypeLabel(),
+				itm.getVocabularyName());
 	}
 
 	private static String kvKeyExtractor(KeyValue kv) {
@@ -748,13 +755,13 @@ public class MergeUtils {
 
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
-				.ofNullable(sp)
-				.map(
-						s -> Joiner
-								.on("||")
-								.useForNull("")
-								.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
-				.orElse(null);
+			.ofNullable(sp)
+			.map(
+				s -> Joiner
+					.on("||")
+					.useForNull("")
+					.join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
+			.orElse(null);
 	}
 
 	private static <T extends OtherResearchProduct> T mergeORP(T original, T enrich) {
@@ -776,8 +783,8 @@ public class MergeUtils {
 		merge.setLicense(unionDistinctLists(merge.getLicense(), enrich.getLicense(), trust));
 		merge.setCodeRepositoryUrl(chooseReference(merge.getCodeRepositoryUrl(), enrich.getCodeRepositoryUrl(), trust));
 		merge
-				.setProgrammingLanguage(
-						chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
+			.setProgrammingLanguage(
+				chooseReference(merge.getProgrammingLanguage(), enrich.getProgrammingLanguage(), trust));
 
 		return merge;
 	}
@@ -791,11 +798,11 @@ public class MergeUtils {
 		merge.setSize(chooseReference(merge.getSize(), enrich.getSize(), trust));
 		merge.setVersion(chooseReference(merge.getVersion(), enrich.getVersion(), trust));
 		merge
-				.setLastmetadataupdate(
-						chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
+			.setLastmetadataupdate(
+				chooseReference(merge.getLastmetadataupdate(), enrich.getLastmetadataupdate(), trust));
 		merge
-				.setMetadataversionnumber(
-						chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
+			.setMetadataversionnumber(
+				chooseReference(merge.getMetadataversionnumber(), enrich.getMetadataversionnumber(), trust));
 		merge.setGeolocation(unionDistinctLists(merge.getGeolocation(), enrich.getGeolocation(), trust));
 
 		return merge;
@@ -817,26 +824,26 @@ public class MergeUtils {
 		merged.setLegalshortname(chooseReference(merged.getLegalshortname(), enrich.getLegalshortname(), trust));
 		merged.setLegalname(chooseReference(merged.getLegalname(), enrich.getLegalname(), trust));
 		merged
-				.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
+			.setAlternativeNames(unionDistinctLists(enrich.getAlternativeNames(), merged.getAlternativeNames(), trust));
 		merged.setWebsiteurl(chooseReference(merged.getWebsiteurl(), enrich.getWebsiteurl(), trust));
 		merged.setLogourl(chooseReference(merged.getLogourl(), enrich.getLogourl(), trust));
 		merged.setEclegalbody(chooseReference(merged.getEclegalbody(), enrich.getEclegalbody(), trust));
 		merged.setEclegalperson(chooseReference(merged.getEclegalperson(), enrich.getEclegalperson(), trust));
 		merged.setEcnonprofit(chooseReference(merged.getEcnonprofit(), enrich.getEcnonprofit(), trust));
 		merged
-				.setEcresearchorganization(
-						chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
+			.setEcresearchorganization(
+				chooseReference(merged.getEcresearchorganization(), enrich.getEcresearchorganization(), trust));
 		merged
-				.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
+			.setEchighereducation(chooseReference(merged.getEchighereducation(), enrich.getEchighereducation(), trust));
 		merged
-				.setEcinternationalorganizationeurinterests(
-						chooseReference(
-								merged.getEcinternationalorganizationeurinterests(),
-								enrich.getEcinternationalorganizationeurinterests(), trust));
+			.setEcinternationalorganizationeurinterests(
+				chooseReference(
+					merged.getEcinternationalorganizationeurinterests(),
+					enrich.getEcinternationalorganizationeurinterests(), trust));
 		merged
-				.setEcinternationalorganization(
-						chooseReference(
-								merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
+			.setEcinternationalorganization(
+				chooseReference(
+					merged.getEcinternationalorganization(), enrich.getEcinternationalorganization(), trust));
 		merged.setEcenterprise(chooseReference(merged.getEcenterprise(), enrich.getEcenterprise(), trust));
 		merged.setEcsmevalidated(chooseReference(merged.getEcsmevalidated(), enrich.getEcsmevalidated(), trust));
 		merged.setEcnutscode(chooseReference(merged.getEcnutscode(), enrich.getEcnutscode(), trust));
@@ -860,8 +867,8 @@ public class MergeUtils {
 		merged.setDuration(chooseReference(merged.getDuration(), enrich.getDuration(), trust));
 		merged.setEcsc39(chooseReference(merged.getEcsc39(), enrich.getEcsc39(), trust));
 		merged
-				.setOamandatepublications(
-						chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
+			.setOamandatepublications(
+				chooseReference(merged.getOamandatepublications(), enrich.getOamandatepublications(), trust));
 		merged.setEcarticle29_3(chooseReference(merged.getEcarticle29_3(), enrich.getEcarticle29_3(), trust));
 		merged.setSubjects(unionDistinctLists(merged.getSubjects(), enrich.getSubjects(), trust));
 		merged.setFundingtree(unionDistinctLists(merged.getFundingtree(), enrich.getFundingtree(), trust));
@@ -887,8 +894,8 @@ public class MergeUtils {
 		}
 
 		merged
-				.setH2020classification(
-						unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
+			.setH2020classification(
+				unionDistinctLists(merged.getH2020classification(), enrich.getH2020classification(), trust));
 
 		return merged;
 	}
@@ -915,7 +922,7 @@ public class MergeUtils {
 	 * @return list of instances possibly enriched
 	 */
 	private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,
-												  final List<Instance> enrichmentInstances) {
+		final List<Instance> enrichmentInstances) {
 		final List<Instance> enrichmentResult = new ArrayList<>();
 
 		if (toEnrichInstances == null) {
@@ -953,42 +960,42 @@ public class MergeUtils {
 	 */
 	private static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
 		return ri
-				.stream()
-				.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
-				.flatMap(i -> {
-					final List<Pair<String, Instance>> result = new ArrayList<>();
-					if (i.getPid() != null)
-						i
-								.getPid()
-								.stream()
-								.filter(MergeUtils::validPid)
-								.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
-					if (i.getAlternateIdentifier() != null)
-						i
-								.getAlternateIdentifier()
-								.stream()
-								.filter(MergeUtils::validPid)
-								.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
-					return result.stream();
-				})
-				.collect(
-						Collectors
-								.toMap(
-										Pair::getLeft,
-										Pair::getRight,
-										(a, b) -> a));
+			.stream()
+			.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
+			.flatMap(i -> {
+				final List<Pair<String, Instance>> result = new ArrayList<>();
+				if (i.getPid() != null)
+					i
+						.getPid()
+						.stream()
+						.filter(MergeUtils::validPid)
+						.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+				if (i.getAlternateIdentifier() != null)
+					i
+						.getAlternateIdentifier()
+						.stream()
+						.filter(MergeUtils::validPid)
+						.forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
+				return result.stream();
+			})
+			.collect(
+				Collectors
+					.toMap(
+						Pair::getLeft,
+						Pair::getRight,
+						(a, b) -> a));
 	}
 
 	private static boolean isFromDelegatedAuthority(Result r) {
 		return Optional
-				.ofNullable(r.getInstance())
-				.map(
-						instance -> instance
-								.stream()
-								.filter(i -> Objects.nonNull(i.getCollectedfrom()))
-								.map(i -> i.getCollectedfrom().getKey())
-								.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
-				.orElse(false);
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.filter(i -> Objects.nonNull(i.getCollectedfrom()))
+					.map(i -> i.getCollectedfrom().getKey())
+					.anyMatch(cfId -> IdentifierFactory.delegatedAuthorityDatasourceIds().contains(cfId)))
+			.orElse(false);
 	}
 
 	/**
@@ -1024,15 +1031,15 @@ public class MergeUtils {
 	 * @return the list
 	 */
 	private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids,
-													   final Map<String, Instance> enrichments) {
+		final Map<String, Instance> enrichments) {
 		if (pids == null || enrichments == null)
 			return null;
 		return pids
-				.stream()
-				.map(MergeUtils::extractKeyFromPid)
-				.map(enrichments::get)
-				.filter(Objects::nonNull)
-				.collect(Collectors.toList());
+			.stream()
+			.map(MergeUtils::extractKeyFromPid)
+			.map(enrichments::get)
+			.filter(Objects::nonNull)
+			.collect(Collectors.toList());
 	}
 
 	/**
@@ -1043,8 +1050,8 @@ public class MergeUtils {
 	 */
 	private static boolean isAnEnrichment(OafEntity e) {
 		return e.getDataInfo() != null &&
-				e.getDataInfo().getProvenanceaction() != null
-				&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
+			e.getDataInfo().getProvenanceaction() != null
+			&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
 	}
 
 	/**
@@ -1067,17 +1074,17 @@ public class MergeUtils {
 		merge.setHostedby(firstNonNull(merge.getHostedby(), enrichment.getHostedby()));
 		merge.setUrl(unionDistinctLists(merge.getUrl(), enrichment.getUrl(), 0));
 		merge
-				.setDistributionlocation(
-						firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
+			.setDistributionlocation(
+				firstNonNull(merge.getDistributionlocation(), enrichment.getDistributionlocation()));
 		merge.setCollectedfrom(firstNonNull(merge.getCollectedfrom(), enrichment.getCollectedfrom()));
 		// pid and alternateId are used for matching
 		merge.setDateofacceptance(firstNonNull(merge.getDateofacceptance(), enrichment.getDateofacceptance()));
 		merge
-				.setProcessingchargeamount(
-						firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
+			.setProcessingchargeamount(
+				firstNonNull(merge.getProcessingchargeamount(), enrichment.getProcessingchargeamount()));
 		merge
-				.setProcessingchargecurrency(
-						firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
+			.setProcessingchargecurrency(
+				firstNonNull(merge.getProcessingchargecurrency(), enrichment.getProcessingchargecurrency()));
 		merge.setRefereed(firstNonNull(merge.getRefereed(), enrichment.getRefereed()));
 		merge.setMeasures(unionDistinctLists(merge.getMeasures(), enrichment.getMeasures(), 0));
 		merge.setFulltext(firstNonNull(merge.getFulltext(), enrichment.getFulltext()));
@@ -1085,14 +1092,14 @@ public class MergeUtils {
 
 	private static int compareTrust(Oaf a, Oaf b) {
 		String left = Optional
-				.ofNullable(a.getDataInfo())
-				.map(DataInfo::getTrust)
-				.orElse("0.0");
+			.ofNullable(a.getDataInfo())
+			.map(DataInfo::getTrust)
+			.orElse("0.0");
 
 		String right = Optional
-				.ofNullable(b.getDataInfo())
-				.map(DataInfo::getTrust)
-				.orElse("0.0");
+			.ofNullable(b.getDataInfo())
+			.map(DataInfo::getTrust)
+			.orElse("0.0");
 
 		return left.compareTo(right);
 	}

From 5f512f510e92a717f1e536b9be9db15399d42805 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 15 Nov 2024 09:16:51 +0100
Subject: [PATCH 210/239] code formatting

---
 .../raw/AbstractMdRecordToOafMapper.java      | 26 +++++++++++--------
 1 file changed, 15 insertions(+), 11 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
index be84778f5..881d3202c 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
@@ -155,10 +155,11 @@ public abstract class AbstractMdRecordToOafMapper {
 
 			final Instance instance = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
 
-			if (!Optional.ofNullable(instance.getInstancetype())
-					.map(Qualifier::getClassid)
-					.filter(StringUtils::isNotBlank)
-					.isPresent()) {
+			if (!Optional
+				.ofNullable(instance.getInstancetype())
+				.map(Qualifier::getClassid)
+				.filter(StringUtils::isNotBlank)
+				.isPresent()) {
 				return Lists.newArrayList();
 			}
 
@@ -173,13 +174,16 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	protected String getResultType(final Instance instance) {
 		if (this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
-			return Optional.ofNullable(instance.getInstancetype())
-					.map(Qualifier::getClassid)
-					.map(instanceType -> Optional
-								.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
-								.map(Qualifier::getClassid)
-								.orElse("0000"))
-					.orElse("0000");
+			return Optional
+				.ofNullable(instance.getInstancetype())
+				.map(Qualifier::getClassid)
+				.map(
+					instanceType -> Optional
+						.ofNullable(
+							this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
+						.map(Qualifier::getClassid)
+						.orElse("0000"))
+				.orElse("0000");
 		} else {
 			throw new IllegalStateException("Missing vocabulary: " + ModelConstants.DNET_RESULT_TYPOLOGIES);
 		}

From cf7d9a32ab847d50bcafe03bc66795d2719e7d03 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 15 Nov 2024 09:17:28 +0100
Subject: [PATCH 211/239] disable autoBroadcastJoin in the cleaning workflow

---
 .../eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
index 2512fc5bc..01aaadae5 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
@@ -162,6 +162,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
@@ -197,6 +198,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
@@ -232,6 +234,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=5000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
@@ -267,6 +270,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
@@ -302,6 +306,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
@@ -337,6 +342,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
@@ -372,6 +378,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
@@ -407,6 +414,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/person</arg>
@@ -442,6 +450,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=20000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>

From 9e439f5ecaea8c92ca7db4e62158289766fee84e Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 15 Nov 2024 12:19:26 +0100
Subject: [PATCH 212/239] map the abstracts considering both the datacite and
 the dc nsPrefix

---
 .../dhp/oa/graph/raw/OdfToOafMapper.java      |  2 +-
 .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 23 +++++
 .../dhp/oa/graph/raw/odf_guidelines4.xml      | 95 +++++++++++++++++++
 3 files changed, 119 insertions(+), 1 deletion(-)
 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
index a811aad46..efe05eb68 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
@@ -319,7 +319,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected List<Field<String>> prepareDescriptions(final Document doc, final DataInfo info) {
-		return prepareListFields(doc, "//*[local-name()='description' and ./@descriptionType='Abstract']", info);
+		return prepareListFields(doc, "//datacite:description[./@descriptionType='Abstract'] | //dc:description", info);
 	}
 
 	@Override
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
index 2cf3ea0c0..ea9503d17 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@@ -906,6 +906,29 @@ class MappersTest {
 		assertEquals("IT", p.getCountry().get(0).getClassid());
 		assertEquals("FR", p.getCountry().get(1).getClassid());
 		assertEquals("DE", p.getCountry().get(2).getClassid());
+
+		assertNotNull(p.getDescription());
+		assertEquals(1, p.getDescription().size());
+		assertNotNull(p.getDescription().get(0));
+		assertTrue(StringUtils.isNotBlank(p.getDescription().get(0).getValue()));
+	}
+
+	@Test
+	void testODFRecord_guidelines4() throws IOException {
+		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml")));
+		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
+
+		final Publication p = (Publication) list.get(0);
+		assertValidId(p.getId());
+		assertValidId(p.getCollectedfrom().get(0).getKey());
+		assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
+
+		assertNotNull(p.getDescription());
+		assertEquals(2, p.getDescription().size());
+		assertNotNull(p.getDescription().get(0));
+		assertTrue(StringUtils.isNotBlank(p.getDescription().get(0).getValue()));
+		assertNotNull(p.getDescription().get(1));
+		assertTrue(StringUtils.isNotBlank(p.getDescription().get(1).getValue()));
 	}
 
 	@Test
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml
new file mode 100644
index 000000000..4f390afb7
--- /dev/null
+++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_guidelines4.xml
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<record xmlns:datacite="http://datacite.org/schema/kernel-3"
+        xmlns:dr="http://www.driver-repository.eu/namespace/dr"
+        xmlns:oaf="http://namespace.openaire.eu/oaf"
+        xmlns:oai="http://www.openarchives.org/OAI/2.0/">
+    <header xmlns="http://www.openarchives.org/OAI/2.0/" xmlns:dri="http://www.driver-repository.eu/namespace/dri">
+        <dri:objIdentifier>od______1261::66de86a37fa980b9b8f4cefdf1c5a0c5</dri:objIdentifier>
+        <dri:recordIdentifier>oai:air.unimi.it:2434/636308</dri:recordIdentifier>
+        <dri:dateOfCollection>2020-09-04T14:36:48.411Z</dri:dateOfCollection>
+        <oaf:datasourceprefix>od______1261</oaf:datasourceprefix>
+        <identifier>oai:air.unimi.it:2434/636308</identifier>
+        <datestamp>2022-10-14T14:17:28Z</datestamp>
+        <setSpec>com_2434_73555</setSpec>
+        <setSpec>col_2434_73557</setSpec>
+        <setSpec>openaire</setSpec>
+        <dr:dateOfTransformation>2024-11-07T06:17:52.454Z</dr:dateOfTransformation>
+    </header>
+    <metadata>
+        <oaire:resource xmlns:oaire="http://namespace.openaire.eu/schema/oaire/"
+                        xmlns:exslt="http://exslt.org/common"
+                        xmlns:xs="http://www.w3.org/2001/XMLSchema"
+                        xmlns:rdf="http://www.w3.org/TR/rdf-concepts/"
+                        xmlns:doc="http://www.lyncode.com/xoai"
+                        xmlns:dc="http://purl.org/dc/elements/1.1/"
+                        xmlns:datacite="http://datacite.org/schema/kernel-4"
+                        xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                        xmlns:vc="http://www.w3.org/2007/XMLSchema-versioning"
+                        xmlns="http://www.openarchives.org/OAI/2.0/"
+                        xsi:schemaLocation="http://namespace.openaire.eu/schema/oaire/ https://www.openaire.eu/schema/repo-lit/4.0/openaire.xsd">
+            <datacite:titles>
+                <datacite:title xml:lang="en">I processi incorpati di costruzione della conoscenza nelle pratiche di cura</datacite:title>
+            </datacite:titles>
+            <datacite:creators>
+                <datacite:creator>
+                    <datacite:creatorName>S. Visioli</datacite:creatorName>
+                    <nameIdentifier nameIdentifierScheme="IRIS">rp17381</nameIdentifier>
+                    <affiliation affiliationIdentifierScheme="ROR"
+                                 affiliationIdentifier="https://ror.org/00wjc7c48">University of Milan</affiliation>
+                    <nameIdentifier nameIdentifierScheme="UGOV">53567</nameIdentifier>
+                </datacite:creator>
+                <datacite:creator>
+                    <datacite:creatorName>L. Zannini</datacite:creatorName>
+                    <datacite:nameIdentifier schemeURI="https://orcid.org" nameIdentifierScheme="ORCID">0000-0001-7287-6616</datacite:nameIdentifier>
+                    <nameIdentifier nameIdentifierScheme="IRIS">rp31993</nameIdentifier>
+                    <affiliation affiliationIdentifierScheme="ROR"
+                                 affiliationIdentifier="https://ror.org/00wjc7c48">University of Milan</affiliation>
+                    <nameIdentifier nameIdentifierScheme="UGOV">5556</nameIdentifier>
+                </datacite:creator>
+            </datacite:creators>
+            <oaire:citationStartPage>487</oaire:citationStartPage>
+            <oaire:citationIssue>2</oaire:citationIssue>
+            <oaire:citationEndPage>506</oaire:citationEndPage>
+            <oaire:citationVolume>8</oaire:citationVolume>
+            <oaire:citationTitle>METIS</oaire:citationTitle>
+            <datacite:alternateIdentifiers>
+                <datacite:alternateIdentifier alternateIdentifierType="DOI">10.30557/MT00041</datacite:alternateIdentifier>
+                <datacite:alternateIdentifier alternateIdentifierType="URN">http://hdl.handle.net/2434/636308</datacite:alternateIdentifier>
+            </datacite:alternateIdentifiers>
+            <datacite:dates>
+                <datacite:date dateType="Accepted">2018</datacite:date>
+                <datacite:date dateType="Issued">2018</datacite:date>
+                <datacite:date dateType="Available">2019-05-23</datacite:date>
+            </datacite:dates>
+            <dc:language>ita</dc:language>
+            <oaire:resourceType resourceTypeGeneral="literature"
+                                uri="http://purl.org/coar/resource_type/c_6501">journal article</oaire:resourceType>
+            <dc:description>In ambito educativo, il corpo è stato tradizionalmente marginalizzato o rifiutato come fonte di conoscenza. Negli ultimi decenni, la letteratura pedagogica ha manifestato crescente interesse per il ruolo che ha il corpo dell’insegnante, nel pianificare e realizzare l’insegnamento, sfidando le ideologie e le epistemologie dominanti, secondo le quali la nostra mente è la fonte primaria di apprendimento. Al contrario, una pedagogia della conoscenza incorpata (embodiment) considera il corpo centrale nel nostro conoscere (le pratiche d’insegnamento) e nel nostro essere (insegnanti). Analogamente, la letteratura delle professioni del caring si è rivelata molto attenta ai temi della conoscenza incorpata, ossia di quel sapere che è presente in un corpo, spesso in modo tacito. Le infermiere hanno da tempo esplorato il ruolo del loro corpo nei processi di costruzione della conoscenza, come anche il ruolo del corpo dello studente, e addirittura del paziente, nel conoscere la malattia. In questo paper riportiamo alcune riflessioni ed esperienze sulla conoscenza incorpata nelle pratiche assistenziali, mettendo in luce come questa, benché spesso tacita, abbia un ruolo centrale nell’aver cura delle persone malate.</dc:description>
+            <dc:description>In educational contexts, the body has been traditionally marginalized or rejected as a source of knowledge. In the last decades, some pedagogical contributions have shown interest for the role that the teacher’s body has in planning and implementing teaching, challenging dominant ideologies and epistemologies that tell us our minds are the primary sources of learning. Conversely, a pedagogy of embodiment makes the body central in our knowing (educational practices) and being (a teacher). Similarly, literature from the caring professions has revealed very receptive to-ward issues related to embodied knowledge, that is to say the knowledge that the body owns, which is frequently tacit. Since many years, nurses have explored the role of body in the processes of knowledge building, as well as the role of the student’s body, and even the patient’s body, in knowing the illness. In this paper we report some reflections and experiences concerning embodied knowledge in the nursing practice, highlighting that embodied knowledge, even if tacit, has a pivotal role when caring for sick people.</dc:description>
+            <dc:format>application/pdf</dc:format>
+            <datacite:identifier xmlns:datacite="http://datacite.org/schema/kernel-3"
+                                 identifierType="Handle">2434/636308</datacite:identifier>
+            <datacite:rights rightsURI="http://purl.org/coar/access_right/c_abf2">open access</datacite:rights>
+            <datacite:subjects>
+                <datacite:subject>body; educational practices; embodied knowledge; nursing; teaching</datacite:subject>
+            </datacite:subjects>
+            <datacite:sizes/>
+            <datacite:sizes>
+                <datacite:size>413926 bytes</datacite:size>
+            </datacite:sizes>
+            <datacite:sizes/>
+            <oaire:file accessRightsURI="http://purl.org/coar/access_right/c_14cb"
+                        mimeType="application/pdf"
+                        objectType="fulltext">https://air.unimi.it/bitstream/2434/636308/2/Finale%20pubblicato.pdf</oaire:file>
+        </oaire:resource>
+        <oaf:fulltext>https://air.unimi.it/bitstream/2434/636308/2/Finale%20pubblicato.pdf</oaf:fulltext>
+        <dr:CobjCategory type="publication">0001</dr:CobjCategory>
+        <oaf:dateAccepted>2018-01-01</oaf:dateAccepted>
+        <oaf:accessrights>OPEN</oaf:accessrights>
+        <oaf:language>ita</oaf:language>
+        <oaf:hostedBy name="Archivio Istituzionale della Ricerca dell'Università degli Studi di Milano"
+                      id="opendoar____::1261"/>
+        <oaf:collectedFrom name="Archivio Istituzionale della Ricerca dell'Università degli Studi di Milano"
+                           id="opendoar____::1261"/>
+    </metadata>
+</record>
\ No newline at end of file

From a1297082e2df74e672512334238143542ad323ce Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Tue, 19 Nov 2024 14:57:18 +0100
Subject: [PATCH 213/239] Crossref Enhancements:

-Accurate Review Type Assignment: Resolved an issue identified in ticket https://support.openaire.eu/issues/9525#note-13. When a relationship of "is-review-of" is detected, the publication type is now correctly set to "Review."
-Enhanced Author Affiliation Data: Implemented Miriam's suggestion by including a new field, "RawAffiliationString," in each author entry. This additional data provides a more granular level of detail regarding author affiliations, potentially improving discoverability and research analysis.
---
 .../collection/crossref/Crossref2Oaf.scala    |  67 ++---
 .../collection/crossref/affiliationTest.json  | 232 ++++++++++++++++++
 .../crossref/CrossrefMappingTest.scala        |  12 +-
 3 files changed, 265 insertions(+), 46 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json

diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index e7d68920b..e15312e43 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -37,7 +37,7 @@ case class mappingAuthor(
   family: Option[String],
   sequence: Option[String],
   ORCID: Option[String],
-  affiliation: Option[mappingAffiliation]
+  affiliation: Option[List[mappingAffiliation]]
 ) {}
 
 case class funderInfo(id: String, uri: String, name: String, synonym: List[String]) {}
@@ -457,15 +457,14 @@ case object Crossref2Oaf {
     }
 
     //Mapping Author
-    val authorList: List[mappingAuthor] =
-      (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined)
+    val authorList: List[mappingAuthor] = (json \ "author").extract[List[mappingAuthor]].filter(a => a.family.isDefined)
 
     val sorted_list = authorList.sortWith((a: mappingAuthor, b: mappingAuthor) =>
       a.sequence.isDefined && a.sequence.get.equalsIgnoreCase("first")
     )
 
     result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) =>
-      generateAuhtor(a.given.orNull, a.family.get, a.ORCID.orNull, index)
+      generateAuthor(a.given.orNull, a.family.get, a.ORCID.orNull, index, a.affiliation)
     }.asJava)
 
     // Mapping instance
@@ -504,18 +503,6 @@ case object Crossref2Oaf {
       )
     }
 
-    val is_review = json \ "relation" \ "is-review-of" \ "id"
-
-    if (is_review != JNothing) {
-      instance.setInstancetype(
-        OafMapperUtils.qualifier(
-          "0015",
-          "peerReviewed",
-          ModelConstants.DNET_REVIEW_LEVELS,
-          ModelConstants.DNET_REVIEW_LEVELS
-        )
-      )
-    }
 
     if (doi.startsWith("10.3410") || doi.startsWith("10.12703"))
       instance.setHostedby(
@@ -569,17 +556,24 @@ case object Crossref2Oaf {
       result
   }
 
+
+
   def generateIdentifier(oaf: Result, doi: String): String = {
     val id = DHPUtils.md5(doi.toLowerCase)
     s"50|doiboost____|$id"
   }
 
-  def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = {
+  private def generateAuthor(given: String, family: String, orcid: String, index: Int, affiliation: Option[List[mappingAffiliation]]): Author = {
     val a = new Author
     a.setName(given)
     a.setSurname(family)
     a.setFullname(s"$given $family")
     a.setRank(index + 1)
+
+    // Adding Raw affiliation if it's defined
+    if (affiliation.isDefined) {
+      a.setRawAffiliationString(affiliation.get.map(a => a.name).asJava)
+    }
     if (StringUtils.isNotBlank(orcid))
       a.setPid(
         List(
@@ -705,11 +699,21 @@ case object Crossref2Oaf {
     val objectType = (json \ "type").extractOrElse[String](null)
     if (objectType == null)
       return resultList
-    val typology = getTypeQualifier(objectType, vocabularies)
+
+
+    // If the item has a relations is-review-of, then we force it to a peer-review
+    val is_review = json \ "relation" \ "is-review-of" \ "id"
+    var force_to_review = false
+    if (is_review != JNothing) {
+      force_to_review = true
+    }
+
+    val typology = getTypeQualifier(if (force_to_review) "peer-review" else objectType, vocabularies)
 
     if (typology == null)
       return List()
 
+
     val result = generateItemFromType(typology._2)
     if (result == null)
       return List()
@@ -757,33 +761,6 @@ case object Crossref2Oaf {
       else
         resultList
     }
-
-    //    if (uw != null) {
-//      result.getCollectedfrom.add(createUnpayWallCollectedFrom())
-//      val i: Instance = new Instance()
-//      i.setCollectedfrom(createUnpayWallCollectedFrom())
-//      if (uw.best_oa_location != null) {
-//
-//        i.setUrl(List(uw.best_oa_location.url).asJava)
-//        if (uw.best_oa_location.license.isDefined) {
-//          i.setLicense(field[String](uw.best_oa_location.license.get, null))
-//        }
-//
-//        val colour = get_unpaywall_color(uw.oa_status)
-//        if (colour.isDefined) {
-//          val a = new AccessRight
-//          a.setClassid(ModelConstants.ACCESS_RIGHT_OPEN)
-//          a.setClassname(ModelConstants.ACCESS_RIGHT_OPEN)
-//          a.setSchemeid(ModelConstants.DNET_ACCESS_MODES)
-//          a.setSchemename(ModelConstants.DNET_ACCESS_MODES)
-//          a.setOpenAccessRoute(colour.get)
-//          i.setAccessright(a)
-//        }
-//        i.setPid(result.getPid)
-//        result.getInstance().add(i)
-//      }
-//    }
-
   }
 
   private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json
new file mode 100644
index 000000000..201138e45
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/crossref/affiliationTest.json
@@ -0,0 +1,232 @@
+{
+  "indexed": {
+    "date-parts": [
+      [
+        2022,
+        4,
+        3
+      ]
+    ],
+    "date-time": "2022-04-03T01:45:59Z",
+    "timestamp": 1648950359167
+  },
+  "reference-count": 0,
+  "publisher": "American Society of Clinical Oncology (ASCO)",
+  "issue": "18_suppl",
+  "content-domain": {
+    "domain": [],
+    "crossmark-restriction": false
+  },
+  "short-container-title": [
+    "JCO"
+  ],
+  "published-print": {
+    "date-parts": [
+      [
+        2007,
+        6,
+        20
+      ]
+    ]
+  },
+  "abstract": "<jats:p> 3507 </jats:p><jats:p> Purpose: To detect IGF-1R on circulating tumor cells (CTCs) as a biomarker in the clinical development of a monoclonal human antibody, CP-751,871, targeting IGF-1R. Experimental Design: An automated sample preparation and analysis system for enumerating CTCs (Celltracks) was adapted for detecting IGF-1R positive CTCs with a diagnostic antibody targeting a different IGF-1R epitope to CP-751,871. This assay was utilized in three phase I trials of CP-751,871 as a single agent or with chemotherapy and was validated using cell lines and blood samples from healthy volunteers and patients with metastatic carcinoma. Results: There was no interference between the analytical and therapeutic antibodies. CP-751,871 was well tolerated as a single agent, and in combination with docetaxel or carboplatin and paclitaxel, at doses ranging from 0.05 mg/kg to 20 mg/kg. Eighty patients were enrolled on phase 1 studies of CP-751,871, with 47 (59%) patients having CTCs detected during the study. Prior to treatment 26 patients (33%) had CTCs, with 23 having detectable IGF-1R positive CTCs. CP-751,871 alone, and CP-751,871 with cytotoxic chemotherapy, decreased CTCs and IGF-1R positive CTCs; these increased towards the end of the 21-day cycle in some patients, falling again with retreatment. CTCs were commonest in advanced hormone refractory prostate cancer (11/20). Detectable IGF-1R expression on CTCs before treatment with CP-751,871 and docetaxel was associated with a higher frequency of PSA decline by more than 50% (6/10 vs 2/8 patients). A relationship was observed between sustained falls in CTCs counts and PSA declines by more than 50%. Conclusions: IGF-1R expression is detectable by immunofluorescence on CTCs. These data support the further evaluation of CTCs in pharmacodynamic studies and patient selection, particularly in advanced prostate cancer. </jats:p><jats:p> No significant financial relationships to disclose. </jats:p>",
+  "DOI": "10.1200/jco.2007.25.18_suppl.3507",
+  "type": "journal-article",
+  "created": {
+    "date-parts": [
+      [
+        2020,
+        3,
+        6
+      ]
+    ],
+    "date-time": "2020-03-06T20:50:42Z",
+    "timestamp": 1583527842000
+  },
+  "page": "3507-3507",
+  "source": "Crossref",
+  "is-referenced-by-count": 0,
+  "title": [
+    "Circulating tumor cells expressing the insulin growth factor-1 receptor (IGF-1R): Method of detection, incidence and potential applications"
+  ],
+  "prefix": "10.1200",
+  "volume": "25",
+  "author": [
+    {
+      "given": "J. S.",
+      "family": "de Bono",
+      "sequence": "first",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "A.",
+      "family": "Adjei",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "G.",
+      "family": "Attard",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "M.",
+      "family": "Pollak",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "P.",
+      "family": "Fong",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "P.",
+      "family": "Haluska",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "L.",
+      "family": "Roberts",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "D.",
+      "family": "Chainese",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "L.",
+      "family": "Terstappen",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    },
+    {
+      "given": "A.",
+      "family": "Gualberto",
+      "sequence": "additional",
+      "affiliation": [
+        {
+          "name": "Royal Marsden Hospital, Surrey, United Kingdom; Mayo Clinic, Rochester, MN; McGill University & Lady Davis Research Institute, Montreal, PQ, Canada; Pfizer Global Research & Development, New London, CT; Immunicon Corporation, Huntingdon Valley, PA"
+        }
+      ]
+    }
+  ],
+  "member": "233",
+  "container-title": [
+    "Journal of Clinical Oncology"
+  ],
+  "original-title": [],
+  "language": "en",
+  "deposited": {
+    "date-parts": [
+      [
+        2020,
+        3,
+        6
+      ]
+    ],
+    "date-time": "2020-03-06T20:51:03Z",
+    "timestamp": 1583527863000
+  },
+  "score": 1,
+  "resource": {
+    "primary": {
+      "URL": "http://ascopubs.org/doi/10.1200/jco.2007.25.18_suppl.3507"
+    }
+  },
+  "subtitle": [],
+  "short-title": [],
+  "issued": {
+    "date-parts": [
+      [
+        2007,
+        6,
+        20
+      ]
+    ]
+  },
+  "references-count": 0,
+  "journal-issue": {
+    "issue": "18_suppl",
+    "published-print": {
+      "date-parts": [
+        [
+          2007,
+          6,
+          20
+        ]
+      ]
+    }
+  },
+  "alternative-id": [
+    "10.1200/jco.2007.25.18_suppl.3507"
+  ],
+  "URL": "http://dx.doi.org/10.1200/jco.2007.25.18_suppl.3507",
+  "relation": {},
+  "ISSN": [
+    "0732-183X",
+    "1527-7755"
+  ],
+  "issn-type": [
+    {
+      "value": "0732-183X",
+      "type": "print"
+    },
+    {
+      "value": "1527-7755",
+      "type": "electronic"
+    }
+  ],
+  "subject": [],
+  "published": {
+    "date-parts": [
+      [
+        2007,
+        6,
+        20
+      ]
+    ]
+  }
+}
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
index c3ea884eb..f6f71ca66 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
@@ -25,8 +25,18 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
     val input =
       IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
 
-    println(Crossref2Oaf.convert(input, vocabularies, TransformationType.All))
+    Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => {
+      println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(record))
+    })
 
   }
 
+
+  @Test
+  def mappingAffiliation(): Unit = {
+    val input =
+      IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8")
+    val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult)
+    println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head))
+  }
 }

From 5d344323983e5aa6cff4cd02557bf40d0dc6c5dd Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 19 Nov 2024 15:12:04 +0100
Subject: [PATCH 214/239] align MergeUtils with beta branch

---
 .../dhp/schema/oaf/utils/MergeUtils.java      | 42 +++++++++----------
 1 file changed, 21 insertions(+), 21 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
index cd8506583..c092f6035 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
@@ -74,29 +74,29 @@ public class MergeUtils {
 			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
 				return (T) mergedResult;
 			} else {
-				final Qualifier expectedResultType = vocs
-					.lookupTermBySynonym(
-						ModelConstants.DNET_RESULT_TYPOLOGIES,
-						i.getInstancetype().getClassid());
-
-				if (Objects.isNull(expectedResultType)) {
-					throw new IllegalArgumentException(
-						"instance type not bound to any result type in dnet:result_typologies: " +
-							i.getInstancetype().getClassid());
-				}
+				final String expectedResultType = Optional
+					.ofNullable(
+						vocs
+							.lookupTermBySynonym(
+								ModelConstants.DNET_RESULT_TYPOLOGIES, i.getInstancetype().getClassid()))
+					.orElse(ModelConstants.ORP_DEFAULT_RESULTTYPE)
+					.getClassid();
 
 				// there is a clash among the result types
-				if (!expectedResultType.getClassid().equals(mergedResult.getResulttype().getClassid())) {
-					try {
-						String resulttype = expectedResultType.getClassid();
-						if (EntityType.otherresearchproduct.toString().equals(resulttype)) {
-							resulttype = "other";
-						}
-						Result result = (Result) ModelSupport.oafTypes.get(resulttype).newInstance();
-						return (T) mergeResultFields(result, mergedResult);
-					} catch (InstantiationException | IllegalAccessException e) {
-						throw new IllegalStateException(e);
-					}
+				if (!expectedResultType.equals(mergedResult.getResulttype().getClassid())) {
+
+					Result result = (Result) Optional
+						.ofNullable(ModelSupport.oafTypes.get(expectedResultType))
+						.map(r -> {
+							try {
+								return r.newInstance();
+							} catch (InstantiationException | IllegalAccessException e) {
+								throw new IllegalStateException(e);
+							}
+						})
+						.orElse(new OtherResearchProduct());
+					result.setId(mergedResult.getId());
+					return (T) mergeResultFields(result, mergedResult);
 				} else {
 					return (T) mergedResult;
 				}

From 4e55ddc547451c18b9e14cce8244015e6825b3cf Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Tue, 19 Nov 2024 16:50:42 +0100
Subject: [PATCH 215/239] [PubMed aggregation] storing contents into
 mdStoreVersion/store

---
 .../dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala   | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
index 1bdd2a4bc..adac9ffb6 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreatePubmedDump.scala
@@ -2,9 +2,13 @@ package eu.dnetlib.dhp.sx.bio.ebi
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.application.AbstractScalaApplication
+import eu.dnetlib.dhp.common.Constants
+import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH}
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
 import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
 import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser2, PubMedToOaf}
+import eu.dnetlib.dhp.transformation.TransformSparkJobNode
+import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
 import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
@@ -82,7 +86,10 @@ class SparkCreatePubmedDump(propertyPath: String, args: Array[String], log: Logg
       .write
       .option("compression", "gzip")
       .mode("overwrite")
-      .text(targetPath)
+      .text(targetPath + MDSTORE_DATA_PATH)
+
+    val mdStoreSize = spark.read.text(targetPath + MDSTORE_DATA_PATH).count
+    writeHdfsFile(spark.sparkContext.hadoopConfiguration, "" + mdStoreSize, targetPath + MDSTORE_SIZE_PATH)
   }
 }
 

From 496007188a720b18ce8301b6050c6e0b924522d1 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Wed, 20 Nov 2024 09:50:09 +0100
Subject: [PATCH 216/239] Added assertion on CrossrefMappingTest

---
 .../crossref/CrossrefMappingTest.scala          | 17 +++++++++++++++--
 1 file changed, 15 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
index f6f71ca66..12ca14ba1 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
@@ -3,12 +3,15 @@ package eu.dnetlib.dhp.collection.crossref
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
 import eu.dnetlib.dhp.collection.crossref.Crossref2Oaf.TransformationType
+import eu.dnetlib.dhp.schema.oaf.Publication
 import org.apache.commons.io.IOUtils
-import org.junit.jupiter.api.{BeforeEach, Test}
+import org.junit.jupiter.api.{Assertions, BeforeEach, Test}
 import org.junit.jupiter.api.extension.ExtendWith
 import org.mockito.junit.jupiter.MockitoExtension
 import org.slf4j.{Logger, LoggerFactory}
 
+import scala.collection.JavaConverters.asScalaBufferConverter
+
 @ExtendWith(Array(classOf[MockitoExtension]))
 class CrossrefMappingTest extends AbstractVocabularyTest {
 
@@ -26,7 +29,7 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
       IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
 
     Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => {
-      println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(record))
+      Assertions.assertNotNull(record)
     })
 
   }
@@ -37,6 +40,16 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
     val input =
       IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8")
     val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult)
+    data.foreach(record => {
+      Assertions.assertNotNull(record)
+      Assertions.assertTrue(record.isInstanceOf[Publication])
+      val publication = record.asInstanceOf[Publication]
+      publication.getAuthor.asScala.foreach(author => {
+        Assertions.assertNotNull(author.getRawAffiliationString)
+        Assertions.assertTrue(author.getRawAffiliationString.size()>0)
+
+        })
+      })
     println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head))
   }
 }

From 15227f82b8acecaf7b51cddba83d68bde5f10169 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Wed, 20 Nov 2024 15:52:40 +0100
Subject: [PATCH 217/239] added related author's given name and family name in
 the solr json payload serialisation

---
 .../model/ProvisionModelSupport.java          | 23 +++++++++++++++++--
 pom.xml                                       |  2 +-
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 738d75189..0da0f6955 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,6 +5,7 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -39,7 +40,6 @@ import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
 import eu.dnetlib.dhp.schema.solr.Person;
-import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import eu.dnetlib.dhp.schema.solr.Pid;
 import eu.dnetlib.dhp.schema.solr.Project;
 import eu.dnetlib.dhp.schema.solr.Result;
@@ -174,6 +174,8 @@ public class ProvisionModelSupport {
 			&& StringUtils.isNotBlank(relation.getValidationDate())) {
 			rr.setValidationDate(relation.getValidationDate());
 		}
+		rr.setGivenName(re.getGivenName());
+		rr.setFamilyName(re.getFamilyName());
 
 		return rr;
 	}
@@ -208,11 +210,28 @@ public class ProvisionModelSupport {
 		ps.setAlternativeNames(p.getAlternativeNames());
 		ps.setBiography(p.getBiography());
 		ps.setConsent(p.getConsent());
-		// ps.setSubject(...));
+		ps.setSubject(mapPersonTopics(p.getSubject()));
 
 		return ps;
 	}
 
+	private static List<PersonTopic> mapPersonTopics(List<eu.dnetlib.dhp.schema.oaf.PersonTopic> subjects) {
+		return Optional.ofNullable(subjects)
+				.map(ss -> ss.stream()
+						.map(ProvisionModelSupport::mapPersonTopic)
+						.collect(Collectors.toList()))
+				.orElse(null);
+	}
+
+	private static PersonTopic mapPersonTopic(eu.dnetlib.dhp.schema.oaf.PersonTopic pt) {
+		PersonTopic topic = new PersonTopic();
+		topic.setValue(pt.getValue());
+		topic.setSchema(pt.getSchema());
+		topic.setFromYear(pt.getFromYear());
+		topic.setToYear(pt.getToYear());
+		return topic;
+	}
+
 	private static Funding mapFunding(List<String> fundingtree, VocabularyGroup vocs) {
 		SAXReader reader = new SAXReader();
 		return Optional
diff --git a/pom.xml b/pom.xml
index 9480ddfc0..033d88b0b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -937,7 +937,7 @@
         <commons.logging.version>1.1.3</commons.logging.version>
         <commons-validator.version>1.7</commons-validator.version>
         <dateparser.version>1.0.7</dateparser.version>
-        <dhp-schemas.version>[9.0.0]</dhp-schemas.version>
+        <dhp-schemas.version>[10.0.0]</dhp-schemas.version>
         <dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
         <dhp.commons.lang.version>3.5</dhp.commons.lang.version>
         <dhp.guava.version>11.0.2</dhp.guava.version>

From e5b04e61ff8f7f7b1d80f607e0fcb4da7c7c9f37 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Thu, 21 Nov 2024 10:20:12 +0100
Subject: [PATCH 218/239] [CommunityPatents] extends the community propagation
 considering also the results of type patents linked with a isrelatedto
 semantcis

---
 .../main/java/eu/dnetlib/dhp/api/Utils.java   |  2 +-
 .../PrepareResultCommunitySetStep1.java       | 51 ++++++++++++++++---
 .../PrepareResultCommunitySetStep2.java       | 18 ++-----
 3 files changed, 49 insertions(+), 22 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
index 6079da365..1e39d99c3 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/api/Utils.java
@@ -171,7 +171,7 @@ public class Utils implements Serializable {
 	public static List<String> getCommunityIdList(String baseURL) throws IOException {
 		return getValidCommunities(baseURL)
 			.stream()
-			.map(community -> community.getId())
+			.map(CommunityModel::getId)
 			.collect(Collectors.toList());
 	}
 
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
index aede9ef05..ff496bb87 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
@@ -3,11 +3,14 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
+import static java.lang.String.join;
 
 import java.io.IOException;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.*;
@@ -45,7 +48,7 @@ public class PrepareResultCommunitySetStep1 {
 
 	/**
 	 * a dataset for example could be linked to more than one publication. For each publication linked to that dataset
-	 * the previous query will produce a row: targetId set of community context the target could possibly inherit with
+	 * the previous query will produce a row: targetId, set of community context the target could possibly inherit. With
 	 * the following query there will be a single row for each result linked to more than one result of the result type
 	 * currently being used
 	 */
@@ -56,6 +59,16 @@ public class PrepareResultCommunitySetStep1 {
 		+ "where length(co) > 0 "
 		+ "group by resultId";
 
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context  "
+			+ "from (select id, collect_set(co.id) community_context "
+			+ "       from  result "
+			+ "       lateral view explode (context) c as co "
+			+ "       where datainfo.deletedbyinference = false %s "
+			+ "       and array_contains(instance.instancetype.classname, 'Patent') group by id) p "
+			+ " JOIN "
+			+ " (select source, target from relation "
+			+ "  where datainfo.deletedbyinference = false %s ) r ON p.id = r.source";
+
 	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
 			.toString(
@@ -82,15 +95,20 @@ public class PrepareResultCommunitySetStep1 {
 		SparkConf conf = new SparkConf();
 		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
-		final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
+		final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
+				.map(value -> "'" + value.toLowerCase() + "'")
+				.toArray(String[]::new));
+
 		log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
 
 		final String baseURL = parser.get("baseURL");
 		log.info("baseURL: {}", baseURL);
 
-		final List<String> communityIdList = getCommunityList(baseURL);
-		log.info("communityIdList: {}", new Gson().toJson(communityIdList));
+		final String communityIdList = join(",", getCommunityList(baseURL).stream()
+				.map(value -> "'" + value.toLowerCase() + "'")
+				.toArray(String[]::new));
 
+		log.info("communityIdList: {}", new Gson().toJson(communityIdList));
 		final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
 		log.info("resultType: {}", resultType);
 
@@ -118,10 +136,10 @@ public class PrepareResultCommunitySetStep1 {
 		SparkSession spark,
 		String inputPath,
 		String outputPath,
-		List<String> allowedsemrel,
+		String allowedsemrel,
 		Class<R> resultClazz,
 		String resultType,
-		List<String> communityIdList) {
+		String communityIdList) {
 
 		final String inputResultPath = inputPath + "/" + resultType;
 		log.info("Reading Graph table from: {}", inputResultPath);
@@ -141,8 +159,15 @@ public class PrepareResultCommunitySetStep1 {
 		String resultContextQuery = String
 			.format(
 				RESULT_CONTEXT_QUERY_TEMPLATE,
-				getConstraintList(" lower(co.id) = '", communityIdList),
-				getConstraintList(" lower(relClass) = '", allowedsemrel));
+				" lower(co.id) IN " + communityIdList,
+				" AND lower(relClass) IN " +  allowedsemrel);
+
+		String resultContextQueryIsRelatedTo = String
+				.format(
+						RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO,
+						" AND lower(co.id) IN " + communityIdList,
+						"AND  lower(relClass) = '"+
+								ModelConstants.IS_RELATED_TO.toLowerCase() + "'");
 
 		Dataset<Row> result_context = spark.sql(resultContextQuery);
 		result_context.createOrReplaceTempView("result_context");
@@ -154,6 +179,16 @@ public class PrepareResultCommunitySetStep1 {
 			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
 			.json(outputResultPath);
+
+		result_context = spark.sql(resultContextQueryIsRelatedTo);
+		result_context.createOrReplaceTempView("result_context");
+		spark
+				.sql(RESULT_COMMUNITY_LIST_QUERY)
+				.as(Encoders.bean(ResultCommunityList.class))
+				.write()
+				.option("compression", "gzip")
+				.mode(SaveMode.Append)
+				.json(outputResultPath);
 	}
 
 	public static List<String> getCommunityList(final String baseURL) throws IOException {
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
index a53d3dfe3..9bebc36e5 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
+import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Set;
 
@@ -76,22 +77,13 @@ public class PrepareResultCommunitySetStep2 {
 					if (b == null) {
 						return a;
 					}
-					Set<String> community_set = new HashSet<>();
-					a.getCommunityList().stream().forEach(aa -> community_set.add(aa));
-					b
-						.getCommunityList()
-						.stream()
-						.forEach(
-							aa -> {
-								if (!community_set.contains(aa)) {
-									a.getCommunityList().add(aa);
-									community_set.add(aa);
-								}
-							});
+                    Set<String> community_set = new HashSet<>(a.getCommunityList());
+					community_set.addAll(b.getCommunityList());
+					a.setCommunityList(new ArrayList<>(community_set));
 					return a;
 				})
 			.map(Tuple2::_2)
-			.map(r -> OBJECT_MAPPER.writeValueAsString(r))
+			.map(OBJECT_MAPPER::writeValueAsString)
 			.saveAsTextFile(outputPath, GzipCodec.class);
 	}
 

From 821700299a31e5201f616fd4235dcd599018d19b Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 22 Nov 2024 17:21:58 +0100
Subject: [PATCH 219/239] [patents] added test and resources

---
 .../PrepareResultCommunitySetStep1.java       | 93 +++++++++++--------
 .../ResultToCommunityJobTest.java             | 55 +++++++++++
 .../graph/publication/part-00000.json         | 13 +++
 .../graph/relation/part-00000.json            | 24 +++++
 4 files changed, 147 insertions(+), 38 deletions(-)
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json
 create mode 100644 dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/relation/part-00000.json

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
index ff496bb87..8f23a4cfd 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
@@ -37,7 +37,8 @@ public class PrepareResultCommunitySetStep1 {
 	 * relation
 	 */
 	// TODO
-	private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context  "
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE =
+			"select target resultId, community_context  "
 		+ "from (select id, collect_set(co.id) community_context "
 		+ "       from  result "
 		+ "       lateral view explode (context) c as co "
@@ -59,15 +60,26 @@ public class PrepareResultCommunitySetStep1 {
 		+ "where length(co) > 0 "
 		+ "group by resultId";
 
-	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target resultId, community_context  "
-			+ "from (select id, collect_set(co.id) community_context "
-			+ "       from  result "
-			+ "       lateral view explode (context) c as co "
-			+ "       where datainfo.deletedbyinference = false %s "
-			+ "       and array_contains(instance.instancetype.classname, 'Patent') group by id) p "
-			+ " JOIN "
-			+ " (select source, target from relation "
-			+ "  where datainfo.deletedbyinference = false %s ) r ON p.id = r.source";
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO =
+			"select target as resultId, community_context " +
+			"from resultWithContext rwc " +
+			"join relatedToRelations r " +
+			"join patents p  " +
+			"on rwc.id = r.source and r.target = p.id";
+
+	private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context        \n" +
+			"    from  result        " +
+			"    lateral view explode (context) c as co     " +
+			"    where datainfo.deletedbyinference = false  AND lower(co.id) IN %s" +
+			"    group by id";
+
+	private static final String RESULT_PATENT = "select id " +
+			"    from result " +
+			"    where array_contains(instance.instancetype.classname, 'Patent')";
+
+	private static final String IS_RELATED_TO_RELATIONS = "select source, target " +
+			"    from relation " +
+			"    where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false";
 
 	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
@@ -95,20 +107,18 @@ public class PrepareResultCommunitySetStep1 {
 		SparkConf conf = new SparkConf();
 		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
-		final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
-				.map(value -> "'" + value.toLowerCase() + "'")
-				.toArray(String[]::new));
-
-		log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
+		final String allowedsemrel ="(" + join(",",
+				Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'")
+						.toArray(String[]::new)) + ")";
+		log.info("allowedSemRel: {}", allowedsemrel);
 
 		final String baseURL = parser.get("baseURL");
 		log.info("baseURL: {}", baseURL);
 
-		final String communityIdList = join(",", getCommunityList(baseURL).stream()
+		final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream()
 				.map(value -> "'" + value.toLowerCase() + "'")
-				.toArray(String[]::new));
+				.toArray(String[]::new)) + ")";
 
-		log.info("communityIdList: {}", new Gson().toJson(communityIdList));
 		final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
 		log.info("resultType: {}", resultType);
 
@@ -156,32 +166,38 @@ public class PrepareResultCommunitySetStep1 {
 		final String outputResultPath = outputPath + "/" + resultType;
 		log.info("writing output results to: {}", outputResultPath);
 
+
 		String resultContextQuery = String
 			.format(
 				RESULT_CONTEXT_QUERY_TEMPLATE,
-				" lower(co.id) IN " + communityIdList,
-				" AND lower(relClass) IN " +  allowedsemrel);
-
-		String resultContextQueryIsRelatedTo = String
-				.format(
-						RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO,
-						" AND lower(co.id) IN " + communityIdList,
-						"AND  lower(relClass) = '"+
-								ModelConstants.IS_RELATED_TO.toLowerCase() + "'");
-
+					"AND  lower(co.id) IN " + communityIdList,
+					"AND lower(relClass) IN " + allowedsemrel);
 		Dataset<Row> result_context = spark.sql(resultContextQuery);
+		//result_context.createOrReplaceTempView("result_context");
+
+//		spark
+//			.sql(RESULT_COMMUNITY_LIST_QUERY)
+//			.as(Encoders.bean(ResultCommunityList.class))
+//			.write()
+//			.option("compression", "gzip")
+//			.mode(SaveMode.Overwrite)
+//			.json(outputResultPath);
+
+		Dataset<Row> rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList));
+		Dataset<Row> patents = spark.sql(RESULT_PATENT);
+		Dataset<Row> relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS);
+
+		rwc.createOrReplaceTempView("resultWithContext");
+
+		patents.createOrReplaceTempView("patents");
+
+		relatedToRelations.createOrReplaceTempView("relatedTorelations");
+
+
+		result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO));
+
 		result_context.createOrReplaceTempView("result_context");
 
-		spark
-			.sql(RESULT_COMMUNITY_LIST_QUERY)
-			.as(Encoders.bean(ResultCommunityList.class))
-			.write()
-			.option("compression", "gzip")
-			.mode(SaveMode.Overwrite)
-			.json(outputResultPath);
-
-		result_context = spark.sql(resultContextQueryIsRelatedTo);
-		result_context.createOrReplaceTempView("result_context");
 		spark
 				.sql(RESULT_COMMUNITY_LIST_QUERY)
 				.as(Encoders.bean(ResultCommunityList.class))
@@ -189,6 +205,7 @@ public class PrepareResultCommunitySetStep1 {
 				.option("compression", "gzip")
 				.mode(SaveMode.Append)
 				.json(outputResultPath);
+
 	}
 
 	public static List<String> getCommunityList(final String baseURL) throws IOException {
diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
index 0d5b12c80..4361b6f39 100644
--- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
+++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
@@ -6,8 +6,11 @@ import static org.apache.spark.sql.functions.desc;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.ArrayList;
 import java.util.List;
+import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -25,6 +28,7 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.oaf.Dataset;
+import scala.collection.Seq;
 
 public class ResultToCommunityJobTest {
 
@@ -271,4 +275,55 @@ public class ResultToCommunityJobTest {
 					.get(0)
 					.getString(0));
 	}
+
+	@Test
+	public void prepareStep1Test() throws Exception {
+		/*
+
+
+		final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
+				.map(value -> "'" + value.toLowerCase() + "'")
+				.toArray(String[]::new));
+
+		log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
+
+		final String baseURL = parser.get("baseURL");
+		log.info("baseURL: {}", baseURL);
+		 */
+		PrepareResultCommunitySetStep1
+				.main(
+						new String[] {
+								"-isSparkSessionManaged", Boolean.FALSE.toString(),
+								"-sourcePath", getClass()
+								.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph")
+								.getPath(),
+								"-hive_metastore_uris", "",
+								"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
+								"-outputPath", workingDir.toString() + "/preparedInfo",
+								"-allowedsemrels","issupplementto;issupplementedby",
+								"-baseURL","https://dev-openaire.d4science.org/openaire/community/"
+						});
+
+
+		org.apache.spark.sql.Dataset<ResultCommunityList> resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema())
+				.json(workingDir.toString() + "/preparedInfo/publication")
+				.as(Encoders.bean(ResultCommunityList.class));
+
+		Assertions.assertEquals(2, resultCommunityList.count());
+		Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count());
+		Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count());
+
+		ArrayList<String> communities = resultCommunityList
+				.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'")
+				.first().getCommunityList();
+		Assertions.assertEquals(2, communities.size());
+		Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid)));
+		Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid)));
+
+		communities = resultCommunityList
+				.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'")
+				.first().getCommunityList();
+		Assertions.assertEquals(1, communities.size());
+		Assertions.assertEquals("dh-ch", communities.get(0));
+	}
 }
diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json
new file mode 100644
index 000000000..7957bcfd5
--- /dev/null
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json
@@ -0,0 +1,13 @@
+{"author":[{"fullname":"Tanouayi, Gnon","name":"Gnon","pid":[],"rank":1,"surname":"Tanouayi"},{"fullname":"GNANDI, Kissao","name":"Kissao","pid":[],"rank":2,"surname":"Gnandi"},{"fullname":"Ouro-Sama, Kamilou","name":"Kamilou","pid":[],"rank":3,"surname":"Ouro-Sama"},{"fullname":"Ahoudi, Housséni","name":"Housséni","pid":[],"rank":4,"surname":"Ahoudi"},{"fullname":"Solitoke, Hodabalo Dhéoulaba","name":"Hodabalo Dhéoulaba","pid":[],"rank":5,"surname":"Solitoke"},{"fullname":"Badassan, Tchaa Esso-Essinam","name":"Tchaa Esso-Essinam","pid":[],"rank":6,"surname":"Badassan"},{"fullname":"Nyametso, A. Yawovi","name":"A. Yawovi","pid":[],"rank":7,"surname":"Nyametso"},{"fullname":"Agbéko, Aduayi-Akué Adoté","name":"Aduayi-Akué Adoté","pid":[],"rank":8,"surname":"Agbéko"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|eurocrisdris::fe4903425d9040f680d8610d9079ea14","value":"Episciences"}],"context":[],"contributor":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Importer of dst articles previously hosted by inist Eid system account"}],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2017-05-01"},"dateofcollection":"2022-03-01T00:17:08.896Z","dateoftransformation":"2022-03-01T02:57:50.566Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"This study is a contribution to the development of adsorption techniques for the removal of fluoride in natural waters. The work is carried out on a laboratory scale using local geo-materials sorbents, on the one hand the residues from the treatment of natural phosphorite of Hahotoé-Kpogamé and on the other hand the attapulgite clay mineral from the costal basin of Togo. The work carried out concerns the adsorption of fluoride on those sorbents. The following parameters are batch tested on synthetic fluoride solutions: time, solution pH, geo-material dose and fluoride concentration. The fluoride is analyzed by absorption spectrometry. The adsorption yields on the phosphorite treatment residues for aqueous fluoride solutions at an initial concentration of 10 mg/L and an adsorbent concentration of 10 g/L are 49 % at pH 6.5 and 66 % at pH 4.0. In the same experimental conditions, the yields on clay minerals are 28.2 % and 36.3 %. These yields are logically improved by increasing the adsorbent dosage (from 2 to 30 g/L). Additional tests are carried out on natural water at an initial fluoride concentration of 3.76 mg/L."},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Cette étude est une contribution au développement de techniques d’adsorption pour l’élimination du fluor dans les eaux naturelles. Les travaux ont été réalisés à l’échelle du laboratoire en utilisant comme sorbants des géo-matériaux locaux, d’une part les résidus du traitement des phosphates naturels de Hahotoé-Kpogamé et d’autre part l’argilite feuilletée du bassin sédimentaire côtier du Togo. Les travaux réalisés concernent l’adsorption du fluor sur les sorbants considérés. Les paramètres suivants ont été testés en batch sur des solutions synthétiques de fluor : le temps, le pH de la solution, la dose du géo-matériau et la concentration du fluor. Le fluor a été dosé par spectromètrie d’absorption. Les rendements d’adsorption sur les résidus de traitement des phosphates pour des solutions aqueuses de fluor à concentration initiale de 10 mg/L et une concentration en adsorbant de 10 g/L ont été de 49 % à pH 6,5 et 66 % à pH de 4,0. Dans les mêmes conditions expérimentales, les rendements sur les argilites ont été de 28,2 % et 36,3 %. Ces rendements ont logiquement été améliorés en augmentant le dosage en adsorbant (de 2 à 30 g/L). Des essais complémentaires ont été réalisés sur une eau naturelle à une concentration initiale en fluor de 3,76 mg/L."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.4267/dechets-sciences-techniques.3534"}],"collectedfrom":{"key":"10|openaire____::6824b298c96ba906a3e6a70593affbf5","value":"Episciences"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2017-05-01"},"distributionlocation":"","hostedby":{"key":"10|openaire____::6824b298c96ba906a3e6a70593affbf5","value":"Episciences"},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"pid":[],"refereed":{"classid":"0000","classname":"UNKNOWN","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://eid.episciences.org/7781"]}],"language":{"classid":"fra/fre","classname":"French","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1646506202085,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Foai.episciences.org%2F","datestamp":"2017-05-01","harvestDate":"2022-03-01T00:17:08.896Z","identifier":"oai:episciences.org:eid:7781","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"originalId":["oai:episciences.org:eid:7781","50|06cdd3ff4700::49ec404cee4e1452808aabeaffbd3072"],"pid":[],"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"ISSN: 2778-844X"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Environnement, Ingénierie & Développement"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Episciences.org"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"eid:7781 - 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+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","subRelType":"affiliation","target":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::0f488ad00253126c14a21abe6b2d406c","subRelType":"affiliation","target":"20|openorgs____::548cbb0c5a93722f3a9aa62aa17a1ba1","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"isAuthorInstitutionOf","relType":"resultOrganization","source":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","subRelType":"affiliation","target":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","validated":false}
+{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"propagation","inferred":true,"invisible":false,"provenanceaction":{"classid":"result:organization:instrepo","classname":"Propagation of affiliation to result collected from datasources of type institutional repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.85"},"properties":[],"relClass":"hasAuthorInstitution","relType":"resultOrganization","source":"50|dedup_wf_001::12206bf78aabd7d52132477182d19147","subRelType":"affiliation","target":"20|pending_org_::c522a7c935f9fd9578122e60eeec282c","validated":false}
\ No newline at end of file

From 189a7c255a52127f79db59d7cde171f216d76152 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Mon, 25 Nov 2024 16:52:13 +0100
Subject: [PATCH 220/239] [patents] added test and resources

---
 .../PrepareResultCommunitySetStep1.java               | 11 -----------
 .../ResultToCommunityJobTest.java                     |  2 ++
 2 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
index 8f23a4cfd..5af2bf481 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
@@ -173,24 +173,13 @@ public class PrepareResultCommunitySetStep1 {
 					"AND  lower(co.id) IN " + communityIdList,
 					"AND lower(relClass) IN " + allowedsemrel);
 		Dataset<Row> result_context = spark.sql(resultContextQuery);
-		//result_context.createOrReplaceTempView("result_context");
-
-//		spark
-//			.sql(RESULT_COMMUNITY_LIST_QUERY)
-//			.as(Encoders.bean(ResultCommunityList.class))
-//			.write()
-//			.option("compression", "gzip")
-//			.mode(SaveMode.Overwrite)
-//			.json(outputResultPath);
 
 		Dataset<Row> rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList));
 		Dataset<Row> patents = spark.sql(RESULT_PATENT);
 		Dataset<Row> relatedToRelations = spark.sql(IS_RELATED_TO_RELATIONS);
 
 		rwc.createOrReplaceTempView("resultWithContext");
-
 		patents.createOrReplaceTempView("patents");
-
 		relatedToRelations.createOrReplaceTempView("relatedTorelations");
 
 
diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
index 4361b6f39..c1fcff4d9 100644
--- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
+++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
@@ -326,4 +326,6 @@ public class ResultToCommunityJobTest {
 		Assertions.assertEquals(1, communities.size());
 		Assertions.assertEquals("dh-ch", communities.get(0));
 	}
+
+
 }

From 2e54715d715426cd66cca94f1b63fe29abbcc8ce Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 22 Nov 2024 10:05:56 +0100
Subject: [PATCH 221/239] Applying PR#512 - Sequential ActionSet promotion

---
 .../wf/main/oozie_app/workflow.xml            | 47 ++++---------------
 1 file changed, 9 insertions(+), 38 deletions(-)

diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
index 7ccfb342e..cdb4de908 100644
--- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/main/oozie_app/workflow.xml
@@ -135,22 +135,10 @@
             <arg>--outputPath</arg><arg>${workingDir}/action_payload_by_type</arg>
             <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
         </spark>
-        <ok to="ForkPromote"/>
+        <ok to="PromoteActionPayloadForDatasetTable"/>
         <error to="Kill"/>
     </action>
 
-    <fork name="ForkPromote">
-        <path start="PromoteActionPayloadForDatasetTable"/>
-        <path start="PromoteActionPayloadForDatasourceTable"/>
-        <path start="PromoteActionPayloadForOrganizationTable"/>
-        <path start="PromoteActionPayloadForOtherResearchProductTable"/>
-        <path start="PromoteActionPayloadForProjectTable"/>
-        <path start="PromoteActionPayloadForPublicationTable"/>
-        <path start="PromoteActionPayloadForRelationTable"/>
-        <path start="PromoteActionPayloadForSoftwareTable"/>
-        <path start="PromoteActionPayloadForPersonTable"/>
-    </fork>
-
     <action name="PromoteActionPayloadForDatasetTable">
         <sub-workflow>
             <app-path>${wf:appPath()}/promote_action_payload_for_dataset_table</app-path>
@@ -162,7 +150,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForDatasourceTable"/>
         <error to="Kill"/>
     </action>
 
@@ -177,7 +165,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForOrganizationTable"/>
         <error to="Kill"/>
     </action>
 
@@ -192,7 +180,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForOtherResearchProductTable"/>
         <error to="Kill"/>
     </action>
 
@@ -207,7 +195,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForProjectTable"/>
         <error to="Kill"/>
     </action>
 
@@ -222,7 +210,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForPublicationTable"/>
         <error to="Kill"/>
     </action>
 
@@ -237,7 +225,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForRelationTable"/>
         <error to="Kill"/>
     </action>
 
@@ -252,7 +240,7 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="PromoteActionPayloadForSoftwareTable"/>
         <error to="Kill"/>
     </action>
 
@@ -267,26 +255,9 @@
                 </property>
             </configuration>
         </sub-workflow>
-        <ok to="JoinPromote"/>
+        <ok to="End"/>
         <error to="Kill"/>
     </action>
 
-    <action name="PromoteActionPayloadForPersonTable">
-        <sub-workflow>
-            <app-path>${wf:appPath()}/promote_action_payload_for_person_table</app-path>
-            <propagate-configuration/>
-            <configuration>
-                <property>
-                    <name>inputActionPayloadRootPath</name>
-                    <value>${workingDir}/action_payload_by_type</value>
-                </property>
-            </configuration>
-        </sub-workflow>
-        <ok to="JoinPromote"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="JoinPromote" to="End"/>
-
     <end name="End"/>
 </workflow-app>
\ No newline at end of file

From ca2d480df372b174d92f141f38cdf14b19130979 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Tue, 26 Nov 2024 13:36:27 +0100
Subject: [PATCH 222/239] [BulkTagging] added fix to consider when the set of
 constraints for the datasource is empty. Added check for remove constraints
 and advanced constraints to verify if the constraints list is empty and in
 that case do nothing

---
 .../dhp/bulktag/community/ResultTagger.java       | 15 +++++++++------
 .../bulktag/community/SelectionConstraints.java   |  2 ++
 2 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
index 2ea229e3e..64cbd70ba 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
@@ -130,6 +130,7 @@ public class ResultTagger implements Serializable {
 					// log.info("Remove constraints for " + communityId);
 					if (conf.getRemoveConstraintsMap().keySet().contains(communityId) &&
 						conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
+							!conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() &&
 						conf
 							.getRemoveConstraintsMap()
 							.get(communityId)
@@ -161,29 +162,30 @@ public class ResultTagger implements Serializable {
 
 		// Tagging for datasource
 		final Set<String> datasources = new HashSet<>();
-		final Set<String> collfrom = new HashSet<>();
+		final Set<String> cfhb = new HashSet<>();
 		final Set<String> hostdby = new HashSet<>();
 
 		if (Objects.nonNull(result.getInstance())) {
 			for (Instance i : result.getInstance()) {
 				if (Objects.nonNull(i.getCollectedfrom()) && Objects.nonNull(i.getCollectedfrom().getKey())) {
-					collfrom.add(i.getCollectedfrom().getKey());
+					cfhb.add(i.getCollectedfrom().getKey());
 				}
 				if (Objects.nonNull(i.getHostedby()) && Objects.nonNull(i.getHostedby().getKey())) {
+					cfhb.add(i.getHostedby().getKey());
 					hostdby.add(i.getHostedby().getKey());
 				}
 
 			}
 
-			collfrom
+			cfhb
 				.forEach(
 					dsId -> datasources
 						.addAll(
 							conf.getCommunityForDatasource(dsId, param)));
 			hostdby.forEach(dsId -> {
-				datasources
-					.addAll(
-						conf.getCommunityForDatasource(dsId, param));
+//				datasources
+//					.addAll(
+//						conf.getCommunityForDatasource(dsId, param));
 				if (conf.isEoscDatasource(dsId)) {
 					datasources.add("eosc");
 				}
@@ -226,6 +228,7 @@ public class ResultTagger implements Serializable {
 			.forEach(communityId -> {
 				if (!removeCommunities.contains(communityId) &&
 					conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null &&
+						!conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() &&
 					conf
 						.getSelectionConstraintsMap()
 						.get(communityId)
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java
index 57cc658fc..8a23a7017 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/SelectionConstraints.java
@@ -33,6 +33,8 @@ public class SelectionConstraints implements Serializable {
 
 	// Constraints in or
 	public boolean verifyCriteria(final Map<String, List<String>> param) {
+		if (criteria.isEmpty())
+			return true;
 		for (Constraints selc : criteria) {
 			if (selc.verifyCriteria(param)) {
 				return true;

From 0517e452e34cf30d471552f5930983a9435a91c5 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Mon, 2 Dec 2024 14:00:59 +0100
Subject: [PATCH 223/239] Fixed error on empty affiliation

---
 .../main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java  | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
index 54aba8715..a8dacd132 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
@@ -23,9 +23,8 @@ public class PMAffiliation {
         return name;
     }
 
-    public PMAffiliation setName(String name) {
+    public void setName(String name) {
         this.name = name;
-        return this;
     }
 
     public PMIdentifier getIdentifier() {

From cc6bbbb80474553a4d3e71bc0fa80c4b84035194 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Tue, 3 Dec 2024 14:31:11 +0100
Subject: [PATCH 224/239] make setter void

---
 .../main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java  | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
index a8dacd132..e3dcc95dd 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
@@ -31,8 +31,7 @@ public class PMAffiliation {
         return identifier;
     }
 
-    public PMAffiliation setIdentifier(PMIdentifier identifier) {
+    public void setIdentifier(PMIdentifier identifier) {
         this.identifier = identifier;
-        return this;
     }
 }

From 65902a87e3ae7b161cd8e682f4a3535df996e3cd Mon Sep 17 00:00:00 2001
From: "michele.artini" <michele.artini@isti.cnr.it>
Date: Wed, 4 Dec 2024 13:18:17 +0100
Subject: [PATCH 225/239] support of the new apis

---
 .../plugin/researchfi/ResearchFiIterator.java | 54 +++++++++----------
 1 file changed, 27 insertions(+), 27 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
index 269a89f71..cad499962 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/researchfi/ResearchFiIterator.java
@@ -6,7 +6,7 @@ import java.util.Queue;
 import java.util.concurrent.PriorityBlockingQueue;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.apache.http.Header;
@@ -27,25 +27,25 @@ public class ResearchFiIterator implements Iterator<String> {
 
 	private final String baseUrl;
 	private final String authToken;
-	private int currPage;
-	private int nPages;
+	private String nextUrl;
+	private int nCalls = 0;
 
 	private final Queue<String> queue = new PriorityBlockingQueue<>();
 
 	public ResearchFiIterator(final String baseUrl, final String authToken) {
 		this.baseUrl = baseUrl;
 		this.authToken = authToken;
-		this.currPage = 0;
-		this.nPages = 0;
+		this.nextUrl = null;
 	}
 
 	private void verifyStarted() {
-		if (this.currPage == 0) {
-			try {
-				nextCall();
-			} catch (final CollectorException e) {
-				throw new IllegalStateException(e);
+
+		try {
+			if (this.nCalls == 0) {
+				this.nextUrl = invokeUrl(this.baseUrl);
 			}
+		} catch (final CollectorException e) {
+			throw new IllegalStateException(e);
 		}
 	}
 
@@ -62,9 +62,9 @@ public class ResearchFiIterator implements Iterator<String> {
 		synchronized (this.queue) {
 			verifyStarted();
 			final String res = this.queue.poll();
-			while (this.queue.isEmpty() && (this.currPage < this.nPages)) {
+			while (this.queue.isEmpty() && StringUtils.isNotBlank(this.nextUrl)) {
 				try {
-					nextCall();
+					this.nextUrl = invokeUrl(this.nextUrl);
 				} catch (final CollectorException e) {
 					throw new IllegalStateException(e);
 				}
@@ -73,18 +73,11 @@ public class ResearchFiIterator implements Iterator<String> {
 		}
 	}
 
-	private void nextCall() throws CollectorException {
+	private String invokeUrl(final String url) throws CollectorException {
 
-		this.currPage += 1;
+		this.nCalls += 1;
+		String next = null;
 
-		final String url;
-		if (!this.baseUrl.contains("?")) {
-			url = String.format("%s?PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
-		} else if (!this.baseUrl.contains("PageSize=")) {
-			url = String.format("%s&PageNumber=%d&PageSize=%d", this.baseUrl, this.currPage, PAGE_SIZE);
-		} else {
-			url = String.format("%s&PageNumber=%d", this.baseUrl, this.currPage);
-		}
 		log.info("Calling url: " + url);
 
 		try (final CloseableHttpClient client = HttpClients.createDefault()) {
@@ -94,11 +87,15 @@ public class ResearchFiIterator implements Iterator<String> {
 			try (final CloseableHttpResponse response = client.execute(req)) {
 				for (final Header header : response.getAllHeaders()) {
 					log.debug("HEADER: " + header.getName() + " = " + header.getValue());
-					if ("x-page-count".equals(header.getName())) {
-						final int totalPages = NumberUtils.toInt(header.getValue());
-						if (this.nPages != totalPages) {
-							this.nPages = NumberUtils.toInt(header.getValue());
-							log.info("Total pages: " + totalPages);
+					if ("link".equals(header.getName())) {
+						final String s = StringUtils.substringBetween(header.getValue(), "<", ">");
+						final String token = StringUtils
+							.substringBefore(StringUtils.substringAfter(s, "NextPageToken="), "&");
+
+						if (this.baseUrl.contains("?")) {
+							next = this.baseUrl + "&NextPageToken=" + token;
+						} else {
+							next = this.baseUrl + "?NextPageToken=" + token;
 						}
 					}
 				}
@@ -108,6 +105,9 @@ public class ResearchFiIterator implements Iterator<String> {
 
 				jsonArray.forEach(obj -> this.queue.add(JsonUtils.convertToXML(obj.toString())));
 			}
+
+			return next;
+
 		} catch (final Throwable e) {
 			log.warn("Error calling url: " + url, e);
 			throw new CollectorException("Error calling url: " + url, e);

From 32e2a8b34053dc8162bf20bb91c977d544d05b94 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Wed, 4 Dec 2024 13:36:21 +0100
Subject: [PATCH 226/239] implemented zenodo dump collector plugin

---
 .../CollectZenodoDumpCollectorPlugin.java     |  96 ++++++++++++++++++
 .../plugin/zenodo/ZenodoTarIterator.java      |  59 +++++++++++
 .../zenodo/ZenodoPluginCollectionTest.java    |  35 +++++++
 .../dhp/collection/zenodo/zenodo.tar.gz       | Bin 0 -> 7412 bytes
 4 files changed, 190 insertions(+)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java
new file mode 100644
index 000000000..3ea29a9b0
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/CollectZenodoDumpCollectorPlugin.java
@@ -0,0 +1,96 @@
+
+package eu.dnetlib.dhp.collection.plugin.zenodo;
+
+import static eu.dnetlib.dhp.utils.DHPUtils.getHadoopConfiguration;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.fs.FSDataOutputStream;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.compress.CompressionCodec;
+import org.apache.hadoop.io.compress.CompressionCodecFactory;
+import org.apache.http.client.config.RequestConfig;
+import org.apache.http.client.methods.CloseableHttpResponse;
+import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class CollectZenodoDumpCollectorPlugin implements CollectorPlugin {
+
+	final private Logger log = LoggerFactory.getLogger(getClass());
+
+	private void downloadItem(final String name, final String itemURL, final String basePath,
+		final FileSystem fileSystem) {
+		try {
+			final Path hdfsWritePath = new Path(String.format("%s/%s", basePath, name));
+			final FSDataOutputStream fsDataOutputStream = fileSystem.create(hdfsWritePath, true);
+			final HttpGet request = new HttpGet(itemURL);
+			final int timeout = 60; // seconds
+			final RequestConfig config = RequestConfig
+				.custom()
+				.setConnectTimeout(timeout * 1000)
+				.setConnectionRequestTimeout(timeout * 1000)
+				.setSocketTimeout(timeout * 1000)
+				.build();
+			log.info("Downloading url {} into {}", itemURL, hdfsWritePath.getName());
+			try (CloseableHttpClient client = HttpClientBuilder.create().setDefaultRequestConfig(config).build();
+				CloseableHttpResponse response = client.execute(request)) {
+				int responseCode = response.getStatusLine().getStatusCode();
+				log.info("Response code is {}", responseCode);
+				if (responseCode >= 200 && responseCode < 400) {
+					IOUtils.copy(response.getEntity().getContent(), fsDataOutputStream);
+				}
+			} catch (Throwable eu) {
+				throw new RuntimeException(eu);
+			}
+		} catch (Throwable e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	@Override
+	public Stream<String> collect(ApiDescriptor api, AggregatorReport report) throws CollectorException {
+		try {
+			final String zenodoURL = api.getBaseUrl();
+			final String hdfsURI = api.getParams().get("hdfsURI");
+			final FileSystem fileSystem = FileSystem.get(getHadoopConfiguration(hdfsURI));
+			downloadItem("zenodoDump.tar.gz", zenodoURL, "/tmp", fileSystem);
+			CompressionCodecFactory factory = new CompressionCodecFactory(fileSystem.getConf());
+
+			Path sourcePath = new Path("/tmp/zenodoDump.tar.gz");
+			CompressionCodec codec = factory.getCodec(sourcePath);
+			InputStream gzipInputStream = null;
+			try {
+				gzipInputStream = codec.createInputStream(fileSystem.open(sourcePath));
+				return iterateTar(gzipInputStream);
+
+			} catch (IOException e) {
+				throw new CollectorException(e);
+			} finally {
+				log.info("Closing gzip stream");
+				org.apache.hadoop.io.IOUtils.closeStream(gzipInputStream);
+			}
+		} catch (Exception e) {
+			throw new CollectorException(e);
+		}
+	}
+
+	private Stream<String> iterateTar(InputStream gzipInputStream) throws Exception {
+
+		Iterable<String> iterable = () -> new ZenodoTarIterator(gzipInputStream);
+		return StreamSupport.stream(iterable.spliterator(), false);
+
+	}
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java
new file mode 100644
index 000000000..8e627683e
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoTarIterator.java
@@ -0,0 +1,59 @@
+
+package eu.dnetlib.dhp.collection.plugin.zenodo;
+
+import java.io.Closeable;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.Iterator;
+
+import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
+import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
+import org.apache.commons.io.IOUtils;
+
+public class ZenodoTarIterator implements Iterator<String>, Closeable {
+
+	private final InputStream gzipInputStream;
+	private final StringBuilder currentItem = new StringBuilder();
+	private TarArchiveInputStream tais;
+	private boolean hasNext;
+
+	public ZenodoTarIterator(InputStream gzipInputStream) {
+		this.gzipInputStream = gzipInputStream;
+		tais = new TarArchiveInputStream(gzipInputStream);
+		hasNext = getNextItem();
+	}
+
+	private boolean getNextItem() {
+		try {
+			TarArchiveEntry entry;
+			while ((entry = tais.getNextTarEntry()) != null) {
+				if (entry.isFile()) {
+					currentItem.setLength(0);
+					currentItem.append(IOUtils.toString(new InputStreamReader(tais)));
+					return true;
+				}
+			}
+			return false;
+		} catch (Throwable e) {
+			throw new RuntimeException(e);
+		}
+	}
+
+	@Override
+	public boolean hasNext() {
+		return hasNext;
+	}
+
+	@Override
+	public String next() {
+		final String data = currentItem.toString();
+		hasNext = getNextItem();
+		return data;
+	}
+
+	@Override
+	public void close() throws IOException {
+		gzipInputStream.close();
+	}
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java
new file mode 100644
index 000000000..9b5cf1850
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/zenodo/ZenodoPluginCollectionTest.java
@@ -0,0 +1,35 @@
+
+package eu.dnetlib.dhp.collection.plugin.zenodo;
+
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+
+import java.util.zip.GZIPInputStream;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.collection.ApiDescriptor;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+
+public class ZenodoPluginCollectionTest {
+
+	@Test
+	public void testZenodoIterator() throws Exception {
+
+		final GZIPInputStream gis = new GZIPInputStream(
+			getClass().getResourceAsStream("/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz"));
+		try (ZenodoTarIterator it = new ZenodoTarIterator(gis)) {
+			Assertions.assertTrue(it.hasNext());
+			int i = 0;
+			while (it.hasNext()) {
+				Assertions.assertNotNull(it.next());
+				i++;
+			}
+			Assertions.assertEquals(10, i);
+
+		}
+	}
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/zenodo/zenodo.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..6c06bf4e5a5d568aa6c534cc4636796d9938f97e
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zo29?SET9s%5(JN1a(Od#al2UHn_4XJE$tSvT`cg8Efy$0#2y%%TrAM2x7*e9TY*)l
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zI0R}3;KddQ?$tJ=_&fH~#RUSoHP&z&=hS@wz8nh?QXr1S5Ikwbu*&ZLw|6zmZQDTj
zRdBRtL<-<Pa<gdBl_!opmeS7jlA$TaW+I6iQnZtt@(z81w5Ogsz4TbWNuQ*<AZ1$-
z>DZQJI59BektIP(a0%=m7T=PsqyFn{o$O}e#RSh99O-0`Ou@|!^Xz#YH!z(a=D0zX
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zc&g)cGK(?$1zr3WI^_5%SnFdUR6&<*`Q=B+cshzd!24bCJ_^StpfIZ6p&z`}Eh%Dc
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z^P+LvV26z3{0uz#*+rVYCvaCW$!EpzqbO)ROitlRjtF}HDan&l+$fo5X@n3#lT%UI
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z<~?ARuFeddu9~O6(&Op%eP3ssySl>=-&EpI_Irl|<cg;oo?&uV?o5FpS@J+UtEn=H
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zO@;}GU9q%1$C8C>T~3~Gc$P+$n1PioYcyg#<+yu5B?2eIq}lQPZoiL<iRuP-ZDvWr
z{5EaJGTPZ#KerR6OM@Q2R!7tDv}6mTw!zkq;D5*AcwU>i7}GSF-L@>=W^Kw0YRcjd
zPMSgQpk$3nspD)Q&F3L2n!4}_Xai}CvFtX8Tx#2nE?ym(%HY61tSn5hV5qZ!av1kf
zOx;1RJ2<X1lWlNnN~>;wHq}nQ(g2(>(~xOtR_0x~l(-?w5vZ)*qnG|%O@lQfb<UI`
zMwq?KqMkHuK;1SN-5U28NMH?|HLCG9(iAp`7|;mZHBG&Il~s*Gh?xFSDPau9HC$Vo
zQ^37;mQO=;*gPF(ue2HvLLCkB={&!{H28}1_IoHZ(6|kckhS&u#Vyjf(b*z(n{X}C
zybaYN&D%1fih;5Hf~;}(LNAY!04aeLaRwc7vh^y)^h(6y%C`w~$rgvJg3P#CexNo1
m<<{y04Jj)sD^WGoR8vhg)l^eWHPuvmZtZ{1`;Gtr@BjcT^mtAH

literal 0
HcmV?d00001


From 4034da757915f7400edc93e20f35c9a8cfb03e0b Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Wed, 4 Dec 2024 13:37:14 +0100
Subject: [PATCH 227/239] code formatted

---
 .../dhp/sx/bio/pubmed/PMAffiliation.java      | 42 ++++++-----
 .../dnetlib/dhp/sx/bio/pubmed/PMAuthor.java   |  1 -
 .../dhp/sx/bio/pubmed/PMIdentifier.java       | 74 +++++++++----------
 .../collection/crossref/Crossref2Oaf.scala    |  1 -
 .../dnetlib/dhp/sx/bio/pubmed/PMParser2.scala | 13 ++--
 .../dhp/sx/bio/pubmed/PubMedToOaf.scala       | 20 ++++-
 .../dnetlib/dhp/sx/bio/BioScholixTest.scala   |  1 -
 7 files changed, 82 insertions(+), 70 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
index e3dcc95dd..427eb2725 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
 /**
@@ -7,31 +8,32 @@ package eu.dnetlib.dhp.sx.bio.pubmed;
  */
 public class PMAffiliation {
 
-    private  String name;
+	private String name;
 
-    private PMIdentifier identifier;
+	private PMIdentifier identifier;
 
-    public PMAffiliation() {
+	public PMAffiliation() {
 
-    }
-    public PMAffiliation(String name, PMIdentifier identifier) {
-        this.name = name;
-        this.identifier = identifier;
-    }
+	}
 
-    public String getName() {
-        return name;
-    }
+	public PMAffiliation(String name, PMIdentifier identifier) {
+		this.name = name;
+		this.identifier = identifier;
+	}
 
-    public void setName(String name) {
-        this.name = name;
-    }
+	public String getName() {
+		return name;
+	}
 
-    public PMIdentifier getIdentifier() {
-        return identifier;
-    }
+	public void setName(String name) {
+		this.name = name;
+	}
 
-    public void setIdentifier(PMIdentifier identifier) {
-        this.identifier = identifier;
-    }
+	public PMIdentifier getIdentifier() {
+		return identifier;
+	}
+
+	public void setIdentifier(PMIdentifier identifier) {
+		this.identifier = identifier;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
index b0df25663..e023f2e62 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
@@ -97,5 +97,4 @@ public class PMAuthor implements Serializable {
 		this.affiliation = affiliation;
 	}
 
-
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
index 0c8c55e40..6cd17a90c 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
@@ -1,53 +1,53 @@
+
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
 public class PMIdentifier {
 
-    private String pid;
-    private String type;
+	private String pid;
+	private String type;
 
+	public PMIdentifier(String pid, String type) {
+		this.pid = cleanPid(pid);
+		this.type = type;
+	}
 
-    public PMIdentifier(String pid, String type) {
-        this.pid = cleanPid(pid);
-        this.type = type;
-    }
+	public PMIdentifier() {
 
-    public PMIdentifier() {
+	}
 
-    }
+	private String cleanPid(String pid) {
 
-    private String cleanPid(String pid) {
+		if (pid == null) {
+			return null;
+		}
 
-        if (pid == null) {
-            return null;
-        }
+		// clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
+		if (pid.matches("[0-9]{15}[0-9X]")) {
+			return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
+		}
 
-        // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
-        if (pid.matches("[0-9]{15}[0-9X]")) {
-            return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
-        }
+		// clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
+		if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
+			return pid.replaceAll("http://orcid.org/", "");
+		}
+		return pid;
+	}
 
-        // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
-        if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
-            return pid.replaceAll("http://orcid.org/", "");
-        }
-        return pid;
-    }
+	public String getPid() {
+		return pid;
+	}
 
-    public String getPid() {
-        return pid;
-    }
+	public PMIdentifier setPid(String pid) {
+		this.pid = cleanPid(pid);
+		return this;
+	}
 
-    public PMIdentifier setPid(String pid) {
-        this.pid = cleanPid(pid);
-        return this;
-    }
+	public String getType() {
+		return type;
+	}
 
-    public String getType() {
-        return type;
-    }
-
-    public PMIdentifier setType(String type) {
-        this.type = type;
-        return this;
-    }
+	public PMIdentifier setType(String type) {
+		this.type = type;
+		return this;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index e4a238c8f..de68ebb58 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -673,7 +673,6 @@ case object Crossref2Oaf {
     val doi = input.getString(0)
     val rorId = input.getString(1)
 
-
     val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true)
     val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
index 2eb4bea65..bc9a2cf02 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
@@ -82,21 +82,22 @@ class PMParser2 {
         a.setLastName((author \ "LastName").text)
         a.setForeName((author \ "ForeName").text)
         val id = (author \ "Identifier").text
-        val idType =(author \ "Identifier" \ "@Source").text
+        val idType = (author \ "Identifier" \ "@Source").text
 
-        if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
+        if (id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
           a.setIdentifier(new PMIdentifier(id, idType))
         }
 
-
         val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text
-        val affiliationId  = (author \ "AffiliationInfo" \ "Identifier").text
+        val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text
         val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text
 
-        if(affiliation != null && affiliation.nonEmpty) {
+        if (affiliation != null && affiliation.nonEmpty) {
           val aff = new PMAffiliation()
           aff.setName(affiliation)
-          if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) {
+          if (
+            affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty
+          ) {
             aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType))
           }
           a.setAffiliation(aff)
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
index 5e14c731a..281ca0e07 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
@@ -294,11 +294,23 @@ object PubMedToOaf {
       author.setName(a.getForeName)
       author.setSurname(a.getLastName)
       author.setFullname(a.getFullName)
-      if(a.getIdentifier != null) {
-        author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid,
-          OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava)
+      if (a.getIdentifier != null) {
+        author.setPid(
+          List(
+            OafMapperUtils.structuredProperty(
+              a.getIdentifier.getPid,
+              OafMapperUtils.qualifier(
+                a.getIdentifier.getType,
+                a.getIdentifier.getType,
+                ModelConstants.DNET_PID_TYPES,
+                ModelConstants.DNET_PID_TYPES
+              ),
+              dataInfo
+            )
+          ).asJava
+        )
       }
-      if (a.getAffiliation!= null)
+      if (a.getAffiliation != null)
         author.setRawAffiliationString(List(a.getAffiliation.getName).asJava)
       author.setRank(index + 1)
       author
diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
index 4a926df01..cb7826dbf 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
@@ -63,7 +63,6 @@ class BioScholixTest extends AbstractVocabularyTest {
       "0000000333457333",
       "0000000335964515",
       "0000000302921949",
-
       "http://orcid.org/0000-0001-8567-3543",
       "http://orcid.org/0000-0001-7868-8528",
       "0000-0001-9189-1440",

From 730a7751b68b0dc2c5a8fa1f97ee4e82bdb2b3f2 Mon Sep 17 00:00:00 2001
From: "sandro.labruzzo" <sandro.labruzzo@gmail.com>
Date: Wed, 4 Dec 2024 15:03:59 +0100
Subject: [PATCH 228/239] added zenodoDump to enum of CollectorPlugin

---
 .../main/java/eu/dnetlib/dhp/collection/CollectorWorker.java   | 3 +++
 .../java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java | 2 +-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
index f63bfcb48..4c6d0653e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
@@ -7,6 +7,7 @@ import java.io.IOException;
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicInteger;
 
+import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.IntWritable;
@@ -129,6 +130,8 @@ public class CollectorWorker extends ReportingJob {
 				return new Gtr2PublicationsCollectorPlugin(this.clientParams);
 			case osfPreprints:
 				return new OsfPreprintsCollectorPlugin(this.clientParams);
+			case zenodoDump:
+				return new CollectZenodoDumpCollectorPlugin();
 			case other:
 				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
 					.ofNullable(this.api.getParams().get("other_plugin_type"))
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
index 72e691579..93e65b6a7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java
@@ -11,7 +11,7 @@ public interface CollectorPlugin {
 
 	enum NAME {
 
-		oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints;
+		oai, other, rest_json2xml, file, fileGzip, baseDump, gtr2Publications, osfPreprints, zenodoDump;
 
 		public enum OTHER_NAME {
 			mdstore_mongodb_dump, mdstore_mongodb

From bde59a7c8f49cd964317a9e240dacb3be1eeec01 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Thu, 5 Dec 2024 11:09:30 +0100
Subject: [PATCH 229/239] implementation of the utilities for the inclusion of
 raids in the graph

---
 .../java/eu/dnetlib/dhp/common/Constants.java |   4 +
 .../dnetlib/dhp/actionmanager/Constants.java  |   8 +
 .../raid/GenerateRAiDActionSetJob.java        | 190 ++++++++++++++++++
 .../raid/model/GenerateRAiDActionSetJob.java  |   2 +
 .../actionmanager/raid/model/RAiDEntity.java  | 102 ++++++++++
 .../ror/GenerateRorActionSetJob.java          |   8 +-
 .../raid/action_set_parameters.json           |  14 ++
 .../raid/oozie_app/action_set_parameters.json |   0
 .../raid/oozie_app/config-default.xml         |  58 ++++++
 .../actionmanager/raid/oozie_app/workflow.xml |  55 +++++
 .../raid/GenerateRAiDActionSetJobTest.java    | 112 +++++++++++
 .../dhp/actionmanager/raid/raid_example.json  |   6 +
 12 files changed, 552 insertions(+), 7 deletions(-)
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml
 create mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java
 create mode 100644 dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
index 0477d6399..b00199ea5 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
@@ -10,6 +10,10 @@ public class Constants {
 	public static final Map<String, String> accessRightsCoarMap = Maps.newHashMap();
 	public static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
 
+	public static final String RAID_NS_PREFIX = "raid________";
+	public static final String RAID_DATASOURCE_NAME = "Research Activity Identifier Service (RAiD)";
+	public static final String RAID_OPENAIRE_ID = "";
+
 	public static final String ROR_NS_PREFIX = "ror_________";
 
 	public static final String ROR_OPENAIRE_ID = "10|openaire____::993a7ae7a863813cf95028b50708e222";
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
index 73b4b77cb..722415c2e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
@@ -3,6 +3,8 @@ package eu.dnetlib.dhp.actionmanager;
 
 import java.util.Optional;
 
+import eu.dnetlib.dhp.schema.oaf.Instance;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
@@ -110,6 +112,12 @@ public class Constants {
 
 	}
 
+	public static Instance getInstance(Qualifier qualifier) {
+		Instance instance = new Instance();
+		instance.setInstancetype(qualifier);
+		return instance;
+	}
+
 	public static void removeOutputDir(SparkSession spark, String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
new file mode 100644
index 000000000..8e5e1bdcb
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
@@ -0,0 +1,190 @@
+package eu.dnetlib.dhp.actionmanager.raid;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.Constants;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.utils.DHPUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import scala.Tuple2;
+
+import java.util.*;
+import java.util.stream.Collectors;
+
+import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID;
+import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
+import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
+
+public class GenerateRAiDActionSetJob {
+
+    private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class);
+
+    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+    private static final List<KeyValue> RAID_COLLECTED_FROM = listKeyValues(
+            OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+
+    private static final Qualifier RAID_QUALIFIER = qualifier("raid:openaireinference", "raid:openaireinference", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
+
+    private static final DataInfo RAID_DATA_INFO = dataInfo(
+            false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_QUALIFIER, "0.92");
+
+    public static void main(final String[] args) throws Exception {
+
+        final String jsonConfiguration = IOUtils
+                .toString(
+                        eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class
+                                .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json"));
+
+        final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+        parser.parseArgument(args);
+
+        final Boolean isSparkSessionManaged = Optional
+                .ofNullable(parser.get("isSparkSessionManaged"))
+                .map(Boolean::valueOf)
+                .orElse(Boolean.TRUE);
+
+        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+        final String inputPath = parser.get("inputPath");
+        log.info("inputPath: {}", inputPath);
+
+        final String outputPath = parser.get("outputPath");
+        log.info("outputPath {}: ", outputPath);
+
+        final SparkConf conf = new SparkConf();
+
+        runWithSparkSession(conf, isSparkSessionManaged, spark -> {
+            removeOutputDir(spark, outputPath);
+            processRAiDEntities(spark, inputPath, outputPath);
+        });
+    }
+
+    private static void removeOutputDir(final SparkSession spark, final String path) {
+        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+    }
+
+    static void processRAiDEntities(final SparkSession spark,
+                                            final String inputPath,
+                                            final String outputPath) {
+        readInputPath(spark, inputPath)
+                .map(GenerateRAiDActionSetJob::prepareRAiD)
+                .flatMap(List::iterator)
+                .mapToPair(
+                        aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+                                new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+                .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
+
+    }
+
+    protected static List<AtomicAction<? extends Oaf>> prepareRAiD(final RAiDEntity r) {
+
+        final Date now = new Date();
+        final OtherResearchProduct orp = new OtherResearchProduct();
+        final List<AtomicAction<? extends Oaf>> res = new ArrayList<>();
+        String raidId = calculateOpenaireId(r.getRaid());
+
+        orp.setId(raidId);
+        orp.setCollectedfrom(RAID_COLLECTED_FROM);
+        orp.setDataInfo(RAID_DATA_INFO);
+        orp.setResourcetype(RAID_QUALIFIER);
+        orp.setTitle(
+                Collections.singletonList(
+                        structuredProperty(
+                                r.getTitle(),
+                                qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE),
+                                RAID_DATA_INFO))
+        );
+        orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary()));
+        orp.setAuthor(createAuthors(r.getAuthors()));
+        orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER)));
+        orp.setSubject(
+                r.getSubjects()
+                    .stream()
+                    .map(s -> subject(s, qualifier(DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES, DNET_SUBJECT_TYPOLOGIES), RAID_DATA_INFO))
+                    .collect(Collectors.toList())
+        );
+        orp.setRelevantdate(
+                Arrays.asList(
+                        structuredProperty(r.getEndDate(), qualifier("endDate","endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO),
+                        structuredProperty(r.getStartDate(), qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO)
+                )
+        );
+        orp.setLastupdatetimestamp(now.getTime());
+        orp.setDateofcollection(r.getStartDate());
+
+        res.add(new AtomicAction<>(OtherResearchProduct.class, orp));
+
+        for(String resultId: r.getIds()) {
+            Relation rel1 = OafMapperUtils.getRelation(
+                    raidId,
+                    resultId,
+                    ModelConstants.RESULT_RESULT,
+                    ModelConstants.OUTCOME,
+                    PART,
+                    RAID_COLLECTED_FROM,
+                    RAID_DATA_INFO,
+                    now.getTime(),
+                    null,
+                    null
+            );
+            Relation rel2 = OafMapperUtils.getRelation(
+                    resultId,
+                    raidId,
+                    ModelConstants.RESULT_RESULT,
+                    ModelConstants.OUTCOME,
+                    IS_PART_OF,
+                    RAID_COLLECTED_FROM,
+                    RAID_DATA_INFO,
+                    now.getTime(),
+                    null,
+                    null
+            );
+            res.add(new AtomicAction<>(Relation.class, rel1));
+            res.add(new AtomicAction<>(Relation.class, rel2));
+        }
+
+        return res;
+    }
+
+    public static String calculateOpenaireId(final String raid) {
+        return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid));
+    }
+
+    public static List<Author> createAuthors(final List<String> author) {
+        return author.stream().map(s-> {
+            Author a = new Author();
+            a.setFullname(s);
+            return a;
+        }).collect(Collectors.toList());
+    }
+
+    private static JavaRDD<RAiDEntity> readInputPath(
+            final SparkSession spark,
+            final String path) {
+
+        return spark
+                .read()
+                .json(path)
+                .as(Encoders.bean(RAiDEntity.class))
+                .toJavaRDD();
+
+    }
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java
new file mode 100644
index 000000000..b0aec71d3
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java
@@ -0,0 +1,2 @@
+package eu.dnetlib.dhp.actionmanager.raid.model;public class GenerateRAiDActionSetJob {
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java
new file mode 100644
index 000000000..bd7e28926
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java
@@ -0,0 +1,102 @@
+package eu.dnetlib.dhp.actionmanager.raid.model;
+
+import java.io.Serializable;
+import java.util.List;
+
+public class RAiDEntity implements Serializable {
+
+    String raid;
+    List<String> authors;
+    String startDate;
+    String endDate;
+    List<String> subjects;
+    List<String> titles;
+    List<String> ids;
+    String title;
+    String summary;
+
+    public RAiDEntity(){}
+    public RAiDEntity(String raid, List<String> authors, String startDate, String endDate, List<String> subjects, List<String> titles, List<String> ids, String title, String summary) {
+        this.raid = raid;
+        this.authors = authors;
+        this.startDate = startDate;
+        this.endDate = endDate;
+        this.subjects = subjects;
+        this.titles = titles;
+        this.ids = ids;
+        this.title = title;
+        this.summary = summary;
+    }
+
+    public String getRaid() {
+        return raid;
+    }
+
+    public void setRaid(String raid) {
+        this.raid = raid;
+    }
+
+    public List<String> getAuthors() {
+        return authors;
+    }
+
+    public void setAuthors(List<String> authors) {
+        this.authors = authors;
+    }
+
+    public String getStartDate() {
+        return startDate;
+    }
+
+    public void setStartDate(String startDate) {
+        this.startDate = startDate;
+    }
+
+    public String getEndDate() {
+        return endDate;
+    }
+
+    public void setEndDate(String endDate) {
+        this.endDate = endDate;
+    }
+
+    public List<String> getSubjects() {
+        return subjects;
+    }
+
+    public void setSubjects(List<String> subjects) {
+        this.subjects = subjects;
+    }
+
+    public List<String> getTitles() {
+        return titles;
+    }
+
+    public void setTitles(List<String> titles) {
+        this.titles = titles;
+    }
+
+    public List<String> getIds() {
+        return ids;
+    }
+
+    public void setIds(List<String> ids) {
+        this.ids = ids;
+    }
+
+    public String getTitle() {
+        return title;
+    }
+
+    public void setTitle(String title) {
+        this.title = title;
+    }
+
+    public String getSummary() {
+        return summary;
+    }
+
+    public void setSummary(String summary) {
+        this.summary = summary;
+    }
+}
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
index 5f3493d56..ce1973a7f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
@@ -21,6 +21,7 @@ import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.schema.oaf.*;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.conf.Configuration;
@@ -44,13 +45,6 @@ import eu.dnetlib.dhp.common.Constants;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.DataInfo;
-import eu.dnetlib.dhp.schema.oaf.Field;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.Organization;
-import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json
new file mode 100644
index 000000000..2049630d2
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json
@@ -0,0 +1,14 @@
+[
+  {
+    "paramName": "i",
+    "paramLongName": "inputPath",
+    "paramDescription": "the path of the input json",
+    "paramRequired": true
+  },
+  {
+    "paramName": "o",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path of the new ActionSet",
+    "paramRequired": true
+  }
+]
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json
new file mode 100644
index 000000000..e69de29bb
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml
new file mode 100644
index 000000000..a1755f329
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/config-default.xml
@@ -0,0 +1,58 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>sparkDriverMemory</name>
+        <value>15G</value>
+    </property>
+    <property>
+        <name>sparkExecutorMemory</name>
+        <value>6G</value>
+    </property>
+    <property>
+        <name>sparkExecutorCores</name>
+        <value>1</value>
+    </property>
+</configuration>
\ No newline at end of file
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml
new file mode 100644
index 000000000..9b5aa5905
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml
@@ -0,0 +1,55 @@
+<workflow-app name="Update_RAiD_action_set" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>raidJsonInputPath</name>
+            <description>the path of the json</description>
+        </property>
+        <property>
+            <name>raidActionSetPath</name>
+            <description>path where to store the action set</description>
+        </property>
+    </parameters>
+
+    <start to="deleteoutputpath"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="deleteoutputpath">
+        <fs>
+            <delete path='${raidActionSetPath}'/>
+            <mkdir path='${raidActionSetPath}'/>
+            <delete path='${workingDir}'/>
+            <mkdir path='${workingDir}'/>
+        </fs>
+        <ok to="processRAiDFile"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="processRAiDFile">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>ProcessRAiDFile</name>
+            <class>eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${sparkExecutorCores}
+                --executor-memory=${sparkExecutorMemory}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=3840
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${raidJsonInputPath}</arg>
+            <arg>--outputPath</arg><arg>${raidActionSetPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java
new file mode 100644
index 000000000..1f33f45b2
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java
@@ -0,0 +1,112 @@
+package eu.dnetlib.dhp.actionmanager.raid;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest;
+import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.rdd.RDD;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Disabled;
+import org.junit.jupiter.api.Test;
+import scala.Tuple2;
+
+import java.io.File;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.List;
+
+import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER;
+import static java.nio.file.Files.createTempDirectory;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+public class GenerateRAiDActionSetJobTest {
+    private static String input_path;
+    private static String output_path;
+    static SparkSession spark;
+
+    @BeforeEach
+    void setUp() throws Exception {
+
+        input_path = Paths
+                .get(GenerateRAiDActionSetJobTest.class.getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json").toURI())
+                .toFile()
+                .getAbsolutePath();
+
+        output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-")
+                .toAbsolutePath()
+                .toString();
+
+        SparkConf conf = new SparkConf();
+        conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName());
+
+        conf.setMaster("local[*]");
+        conf.set("spark.driver.host", "localhost");
+        conf.set("hive.metastore.local", "true");
+        conf.set("spark.ui.enabled", "false");
+        conf.set("spark.sql.warehouse.dir", output_path);
+        conf.set("hive.metastore.warehouse.dir", output_path);
+
+        spark = SparkSession
+                .builder()
+                .appName(GenerateRAiDActionSetJobTest.class.getSimpleName())
+                .config(conf)
+                .getOrCreate();
+    }
+
+    @AfterAll
+    static void cleanUp() throws Exception {
+        FileUtils.deleteDirectory(new File(output_path));
+    }
+
+    @Test
+    @Disabled
+    void testProcessRAiDEntities() {
+        GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set");
+
+        JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+        JavaRDD<? extends Oaf> result = sc
+                .sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class)
+                .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+                .map(AtomicAction::getPayload);
+
+        assertEquals(80, result.count());
+    }
+
+    @Test
+    void testPrepareRAiD() {
+
+        List<AtomicAction<? extends Oaf>> atomicActions = GenerateRAiDActionSetJob.prepareRAiD(new RAiDEntity(
+                "-92190526",
+                Arrays.asList("Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"),
+                "2021-09-10",
+                "2024-02-16",
+                Arrays.asList("cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"),
+                Arrays.asList("Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment 'More is Less' from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"),
+                Arrays.asList("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"),
+                "Exploring Multi-Scale Map Generalization and Design",
+                "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval."
+        ));
+
+        OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload();
+        Relation rel = (Relation) atomicActions.get(1).getPayload();
+
+        assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue());
+        assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource());
+        assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget());
+
+    }
+
+}
diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json
new file mode 100644
index 000000000..7694b605c
--- /dev/null
+++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/raid/raid_example.json
@@ -0,0 +1,6 @@
+{"raid": "-9222092103004099540", "authors": ["Department of Archaeology & Museums", "Department of Archaeology and Museums", "Department Of Archaeology & Museums"], "subjects": ["Begamganj", "Raisen", "Bhopal", "Budhni", "Malwa site survey", "सीहोर", "Gauharganj", "बुधनी", "Budni", "Berasia"], "titles": ["Malwa site survey : Raisen District, Begamganj Tahsīl, photographic documentation", "Malwa site survey : Bhopal District, photographic documentation (version 1, TIFF files)", "Malwa site survey : Raisen District, Gauharganj Tahsīl, village finds", "Malwa site survey : Sehore सीहोर District, Budni Tahsīl, photographic documentation (part 1)", "Malwa site survey: Bhopal District, Berasia Tahsīl, photographic documentation (with villages named)", "Malwa site survey : Sehore सीहोर District, Budni Tahsīl, photographic documentation (part 2)", "Malwa site survey : Bhopal District, photographic documentation (version 2, JPEG files)"], "ids": ["50|doi_dedup___::7523d165970830dd857e6cbea4302adf", "50|doi_dedup___::02309ae8a9fae291df321e317f5c5330", "50|doi_dedup___::95347ba2c4264414fab39712ee7fe481", "50|doi_dedup___::970aa708fe667596754fd02a708780f5", "50|doi_dedup___::b7cd9128cc53b1257a4f000347f339b0", "50|doi_dedup___::c7d65da0ecedef4d2c702b9db197d90c", "50|doi_dedup___::addbb67cf5046e340f342ba091bcebfa"], "title": "Documentation of Malwa Region", "summary": "This project involves the documentation of the Malwa region through photographic surveys. The surveys were conducted by the Department of Archaeology and Museums, Madhya Pradesh, and cover various districts and tahsils. The documentation includes photographic records of sites, villages, and other relevant features. The project aims to provide a comprehensive understanding of the region's cultural and historical significance.", "startDate": "2019-03-06", "endDate": "2019-03-08"}
+{"raid": "-9221424331076109424", "authors": ["Hutchings, Judy", "Ward, Catherine", "Baban, Adriana", "D��nil��, Ingrid", "Frantz, Inga", "Gardner, Frances", "Lachman, Jamie", "Lachman, Jamie M.", "Foran, Heather", "Heinrichs, Nina", "Murphy, Hugh", "B��ban, Adriana", "Raleva, Marija", "Fang, Xiangming", "Jansen, Elena", "Taut, Diana", "Foran, Heather M.", "T��ut, Diana", "Ward, Catherine L.", "Williams, Margiad", "Lesco, Galina", "Brühl, Antonia"], "subjects": ["3. Good health", "5. Gender equality", "Criminology not elsewhere classified", "1. No poverty", "2. Zero hunger"], "titles": ["sj-docx-1-vaw-10.1177_10778012231188090 - Supplemental material for Co-Occurrence of Intimate Partner Violence Against Mothers and Maltreatment of Their Children With Behavioral Problems in Eastern Europe", "Hunger in vulnerable families in Southeastern Europe: Associations with health and violence", "Prevention of child mental health problems through parenting interventions in Southeastern Europe (RISE): study protocol for a multi-site randomised controlled trial"], "ids": ["50|doi_dedup___::a70015063e5400dae2e097ee10b4a589", "50|doi_dedup___::6e1d12026fcde9087724622ccdeed430", "50|doi_dedup___::5b7bd5d46c5d95e2ef5b36663504a67e"], "title": "Exploring the Impact of Hunger and Violence on Child Health in Southeastern Europe", "summary": "This study aims to investigate the relationship between hunger, violence, and child health in vulnerable families in Southeastern Europe. The research will explore the experiences of families in FYR Macedonia, Republic of Moldova, and Romania, and examine the associations between hunger, maltreatment, and other health indicators. The study will also test the efficacy of a parenting intervention targeting child behavioral problems in alleviating these issues. The findings of this research will contribute to the development of effective interventions to address the complex needs of vulnerable families in the region.", "startDate": "2019-06-04", "endDate": "2023-01-01"}
+{"raid": "-9219052635741785098", "authors": ["Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"], "subjects": ["cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"], "titles": ["Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment \"More is Less\" from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"], "ids": ["50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"], "title": "Exploring Multi-Scale Map Generalization and Design", "summary": "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval.", "startDate": "2021-09-10", "endDate": "2024-02-16"}
+{"raid": "-9216828847055450272", "authors": ["Grey, Alan", "Gorelov, Sergey", "Pall, Szilard", "Merz, Pascal", "Justin A., Lemkul", "Szilárd Páll", "Pasquadibisceglie, Andrea", "Kutzner, Carsten", "Schulz, Roland", "Nabet, Julien", "Abraham, Mark", "Jalalypour, Farzaneh", "Lundborg, Magnus", "Gray, Alan", "Villa, Alessandra", "Berk Hess", "Santuz, Hubert", "Irrgang, M. Eric", "Wingbermuehle, Sebastian", "Lemkul, Justin A.", "Jordan, Joe", "Pellegrino, Michele", "Doijade, Mahesh", "Shvetsov, Alexey", "Hess, Berk", "Behera, Sudarshan", "Andrey Alekseenko", "Shugaeva, Tatiana", "Fleischmann, Stefan", "Bergh, Cathrine", "Morozov, Dmitry", "Adam Hospital", "Briand, Eliane", "Lindahl, Erik", "Brown, Ania", "Marta Lloret Llinares", "Miletic, Vedran", "Alekseenko, Andrey", "Gouaillardet, Gilles", "Fiorin, Giacomo", "Basov, Vladimir"], "subjects": ["webinar"], "titles": ["Introduction to HPC: molecular dynamics simulations with GROMACS: log files", "BioExcel webinar #73: Competency frameworks to support training design and professional development", "Introduction to HPC: molecular dynamics simulations with GROMACS: output files - Devana", "GROMACS 2024.0 Manual", "BioExcel Webinar #71: GROMACS-PMX for accurate estimation of free energy differences", "Introduction to HPC: molecular dynamics simulations with GROMACS: input files", "BioExcel Webinar #68: What's new in GROMACS 2023", "BioExcel Webinar #69: BioBB-Wfs and BioBB-API, integrated web-based platform and programmatic interface for biomolecular simulations workflows using the BioExcel Building Blocks library", "GROMACS 2024-beta Source code"], "ids": ["50|doi_dedup___::8318fbc815ee1943c3269be7567f220b", "50|doi_dedup___::9530e03fb2aac63e82b18a40dc09e32c", "50|doi_dedup___::30174ab31075e76a428ca5b4f4d236b8", "50|doi_________::70b7c6dce09ae6f1361d22913fdf95eb", "50|doi_dedup___::337dd48600618f3c06257edd750d6201", "50|doi_dedup___::d622992ba9077617f37ebd268b3e806d", "50|doi_dedup___::0b0bcc6825d6c052c37882fd5cfc1e8c", "50|doi_dedup___::4b1541a7cee32527c65ace5d1ed57335", "50|doi_dedup___::1379861df59bd755e4fb39b9f95ffbd3"], "title": "Exploring High-Performance Computing and Biomolecular Simulations", "summary": "This project involves exploring high-performance computing (HPC) and biomolecular simulations using GROMACS. The objectives include understanding molecular dynamics simulations, log files, input files, and output files. Additionally, the project aims to explore competency frameworks for professional development, specifically in the field of computational biomolecular research. The tools and techniques used will include GROMACS, BioExcel Building Blocks, and competency frameworks. The expected outcomes include a deeper understanding of HPC and biomolecular simulations, as well as the development of skills in using GROMACS and BioExcel Building Blocks. The project will also contribute to the development of competency frameworks for professional development in the field of computational biomolecular research.", "startDate": "2023-04-25", "endDate": "2024-01-30"}
+{"raid": "-9210544816395499758", "authors": ["Bateson, Melissa", "Andrews, Clare", "Verhulst, Simon", "Nettle, Daniel", "Zuidersma, Erica"], "subjects": ["2. Zero hunger"], "titles": ["Exposure to food insecurity increases energy storage and reduces somatic maintenance in European starlings", "Data and code archive for Andrews et al. 'Exposure to food insecurity increases energy storage and reduces somatic maintenance in European starlings'"], "ids": ["50|doi_dedup___::176117239be06189523c253e0ca9c5ec", "50|doi_dedup___::343e0b0ddf0d54763a89a62af1f7a379"], "title": "Investigating the Effects of Food Insecurity on Energy Storage and Somatic Maintenance in European Starlings", "summary": "This study examines the impact of food insecurity on energy storage and somatic maintenance in European starlings. The research involved exposing juvenile starlings to either uninterrupted food availability or a regime of unpredictable food unavailability. The results show that birds exposed to food insecurity stored more energy, but at the expense of somatic maintenance and repair. The study provides insights into the adaptive responses of birds to food scarcity and the trade-offs involved in energy storage and maintenance.", "startDate": "2021-06-28", "endDate": "2021-06-28"}
+{"raid": "-9208499171224730388", "authors": ["Maniati, Eleni", "Bakker, Bjorn", "McClelland, Sarah E.", "Shaikh, Nadeem", "De Angelis, Simone", "Johnson, Sarah C.", "Wang, Jun", "Foijer, Floris", "Spierings, Diana C. J.", "Boemo, Michael A.", "Wardenaar, René", "Mazzagatti, Alice"], "subjects": [], "titles": ["Additional file 2 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses", "Additional file 5 of Replication stress generates distinctive landscapes of DNA copy number alterations and chromosome scale losses"], "ids": ["50|doi_dedup___::a1bfeb173971f74a274fab8bdd78a4bc", "50|doi_dedup___::3d6e151aaeb2f7c40a320207fdd80ade"], "title": "Analysis of DNA Copy Number Alterations and Chromosome Scale Losses", "summary": "This study analyzed the effects of replication stress on DNA copy number alterations and chromosome scale losses. The results show distinctive landscapes of these alterations and losses, which were further investigated in additional files. The study provides valuable insights into the mechanisms of replication stress and its impact on genomic stability.", "startDate": "2022-01-01", "endDate": "2022-01-01"}
\ No newline at end of file

From 6af3fd16b6362c4a9357f44ba779b7822f5b7033 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Thu, 5 Dec 2024 14:39:42 +0100
Subject: [PATCH 230/239] attributes fixes

---
 .../java/eu/dnetlib/pace/tree/DateRange.java  |  90 ++---
 .../eu/dnetlib/pace/tree/JsonListMatch.java   |   2 +-
 .../pace/comparators/ComparatorTest.java      |  30 +-
 .../dnetlib/dhp/actionmanager/Constants.java  |   4 +-
 .../raid/GenerateRAiDActionSetJob.java        | 309 ++++++++++--------
 .../raid/model/GenerateRAiDActionSetJob.java  |   5 +-
 .../actionmanager/raid/model/RAiDEntity.java  | 154 ++++-----
 .../ror/GenerateRorActionSetJob.java          |   2 +-
 .../dhp/sx/bio/pubmed/PMAffiliation.java      |  44 +--
 .../dnetlib/dhp/sx/bio/pubmed/PMAuthor.java   |   1 -
 .../dhp/sx/bio/pubmed/PMIdentifier.java       |  74 ++---
 .../raid/oozie_app/action_set_parameters.json |   0
 .../actionmanager/raid/oozie_app/workflow.xml |   2 -
 .../collection/crossref/Crossref2Oaf.scala    |   1 -
 .../dnetlib/dhp/sx/bio/pubmed/PMParser2.scala |  13 +-
 .../dhp/sx/bio/pubmed/PubMedToOaf.scala       |  20 +-
 .../raid/GenerateRAiDActionSetJobTest.java    | 203 +++++++-----
 .../dnetlib/dhp/sx/bio/BioScholixTest.scala   |   1 -
 .../dhp/bulktag/community/ResultTagger.java   |   4 +-
 .../dnetlib/dhp/oa/graph/raw/MappersTest.java |   3 +-
 .../model/ProvisionModelSupport.java          |  15 +-
 21 files changed, 546 insertions(+), 431 deletions(-)
 delete mode 100644 dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
index c913109a4..194677e6e 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
@@ -1,10 +1,5 @@
-package eu.dnetlib.pace.tree;
 
-import com.wcohen.ss.AbstractStringDistance;
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-import org.joda.time.DateTime;
+package eu.dnetlib.pace.tree;
 
 import java.time.DateTimeException;
 import java.time.LocalDate;
@@ -13,55 +8,62 @@ import java.time.format.DateTimeFormatter;
 import java.util.Locale;
 import java.util.Map;
 
+import org.joda.time.DateTime;
+
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
 @ComparatorClass("dateRange")
 public class DateRange extends AbstractStringComparator {
 
-    int YEAR_RANGE;
+	int YEAR_RANGE;
 
-    public DateRange(Map<String, String> params) {
-        super(params, new com.wcohen.ss.JaroWinkler());
-        YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3"));
-    }
+	public DateRange(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3"));
+	}
 
-    public DateRange(final double weight) {
-        super(weight, new com.wcohen.ss.JaroWinkler());
-    }
+	public DateRange(final double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
 
-    protected DateRange(final double weight, final AbstractStringDistance ssalgo) {
-        super(weight, ssalgo);
-    }
+	protected DateRange(final double weight, final AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
 
-    public static boolean isNumeric(String str) {
-        return str.matches("\\d+");  //match a number with optional '-' and decimal.
-    }
+	public static boolean isNumeric(String str) {
+		return str.matches("\\d+"); // match a number with optional '-' and decimal.
+	}
 
-    @Override
-    public double distance(final String a, final String b, final Config conf) {
-        if (a.isEmpty() || b.isEmpty()) {
-            return -1.0; // return -1 if a field is missing
-        }
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+		if (a.isEmpty() || b.isEmpty()) {
+			return -1.0; // return -1 if a field is missing
+		}
 
-        try {
-            DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH);
-            LocalDate d1 = LocalDate.parse(a, formatter);
-            LocalDate d2 = LocalDate.parse(b, formatter);
-            Period period = Period.between(d1, d2);
+		try {
+			DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH);
+			LocalDate d1 = LocalDate.parse(a, formatter);
+			LocalDate d2 = LocalDate.parse(b, formatter);
+			Period period = Period.between(d1, d2);
 
-            return period.getYears() <= YEAR_RANGE? 1.0 : 0.0;
-        }
-        catch (DateTimeException e) {
-            return -1.0;
-        }
+			return period.getYears() <= YEAR_RANGE ? 1.0 : 0.0;
+		} catch (DateTimeException e) {
+			return -1.0;
+		}
 
-    }
+	}
 
-    @Override
-    public double getWeight() {
-        return super.weight;
-    }
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
 
-    @Override
-    protected double normalize(final double d) {
-        return d;
-    }
+	@Override
+	protected double normalize(final double d) {
+		return d;
+	}
 }
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
index e95d9206e..d9558df90 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
@@ -62,7 +62,7 @@ public class JsonListMatch extends AbstractListComparator {
 
 				Set<String> types = Sets.intersection(typesA, typesB);
 
-				if (types.isEmpty())  // if no common type, it is impossible to compare
+				if (types.isEmpty()) // if no common type, it is impossible to compare
 					return -1;
 
 				ca = ca.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet());
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index 83539de4a..0abde84bc 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -72,14 +72,34 @@ public class ComparatorTest extends AbstractPaceTest {
 		CodeMatch codeMatch = new CodeMatch(params);
 
 		// names have different codes
-		assertEquals(0.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ir02", conf));
+		assertEquals(
+			0.0,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998 ev02a",
+					"physical oceanography at ctd station june 1998 ir02", conf));
 
 		// names have same code
-		assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ev02a", conf));
+		assertEquals(
+			1.0,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998 ev02a",
+					"physical oceanography at ctd station june 1998 ev02a", conf));
 
 		// code is not in both names
-		assertEquals(-1, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998 ev02a", conf));
-		assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998", conf));
+		assertEquals(
+			-1,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998",
+					"physical oceanography at ctd station june 1998 ev02a", conf));
+		assertEquals(
+			1.0,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998",
+					conf));
 	}
 
 	@Test
@@ -275,7 +295,7 @@ public class ComparatorTest extends AbstractPaceTest {
 			Arrays
 				.asList(
 					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}",
-						"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"),
+					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"),
 			"authors");
 		List<String> b = createFieldList(
 			Arrays
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
index 722415c2e..394cc22a3 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
@@ -3,8 +3,6 @@ package eu.dnetlib.dhp.actionmanager;
 
 import java.util.Optional;
 
-import eu.dnetlib.dhp.schema.oaf.Instance;
-import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
@@ -15,6 +13,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Instance;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.Subject;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
index 8e5e1bdcb..3b2405956 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
@@ -1,15 +1,15 @@
+
 package eu.dnetlib.dhp.actionmanager.raid;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.Constants;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.utils.DHPUtils;
+import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID;
+import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME;
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
+import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
+
+import java.util.*;
+import java.util.stream.Collectors;
+
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -19,172 +19,191 @@ import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.Constants;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
-import java.util.*;
-import java.util.stream.Collectors;
-
-import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID;
-import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
-import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
-
 public class GenerateRAiDActionSetJob {
 
-    private static final Logger log = LoggerFactory.getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class);
+	private static final Logger log = LoggerFactory
+		.getLogger(eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class);
 
-    private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-    private static final List<KeyValue> RAID_COLLECTED_FROM = listKeyValues(
-            OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+	private static final List<KeyValue> RAID_COLLECTED_FROM = listKeyValues(
+		OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
-    private static final Qualifier RAID_QUALIFIER = qualifier("raid:openaireinference", "raid:openaireinference", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
+	private static final Qualifier RAID_QUALIFIER = qualifier("0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE);
 
-    private static final DataInfo RAID_DATA_INFO = dataInfo(
-            false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_QUALIFIER, "0.92");
+	private static final Qualifier RAID_INFERENCE_QUALIFIER = qualifier(
+		"raid:openaireinference", "Inferred by OpenAIRE", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);
 
-    public static void main(final String[] args) throws Exception {
+	private static final DataInfo RAID_DATA_INFO = dataInfo(
+		false, OPENAIRE_DATASOURCE_NAME, true, false, RAID_INFERENCE_QUALIFIER, "0.92");
 
-        final String jsonConfiguration = IOUtils
-                .toString(
-                        eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class
-                                .getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json"));
+	public static void main(final String[] args) throws Exception {
 
-        final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+		final String jsonConfiguration = IOUtils
+			.toString(
+				eu.dnetlib.dhp.actionmanager.raid.GenerateRAiDActionSetJob.class
+					.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/raid/action_set_parameters.json"));
 
-        parser.parseArgument(args);
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
 
-        final Boolean isSparkSessionManaged = Optional
-                .ofNullable(parser.get("isSparkSessionManaged"))
-                .map(Boolean::valueOf)
-                .orElse(Boolean.TRUE);
+		parser.parseArgument(args);
 
-        log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+		final Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
 
-        final String inputPath = parser.get("inputPath");
-        log.info("inputPath: {}", inputPath);
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
-        final String outputPath = parser.get("outputPath");
-        log.info("outputPath {}: ", outputPath);
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath: {}", inputPath);
 
-        final SparkConf conf = new SparkConf();
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}: ", outputPath);
 
-        runWithSparkSession(conf, isSparkSessionManaged, spark -> {
-            removeOutputDir(spark, outputPath);
-            processRAiDEntities(spark, inputPath, outputPath);
-        });
-    }
+		final SparkConf conf = new SparkConf();
 
-    private static void removeOutputDir(final SparkSession spark, final String path) {
-        HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
-    }
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
+			removeOutputDir(spark, outputPath);
+			processRAiDEntities(spark, inputPath, outputPath);
+		});
+	}
 
-    static void processRAiDEntities(final SparkSession spark,
-                                            final String inputPath,
-                                            final String outputPath) {
-        readInputPath(spark, inputPath)
-                .map(GenerateRAiDActionSetJob::prepareRAiD)
-                .flatMap(List::iterator)
-                .mapToPair(
-                        aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-                                new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-                .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
+	private static void removeOutputDir(final SparkSession spark, final String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
 
-    }
+	static void processRAiDEntities(final SparkSession spark,
+		final String inputPath,
+		final String outputPath) {
+		readInputPath(spark, inputPath)
+			.map(GenerateRAiDActionSetJob::prepareRAiD)
+			.flatMap(List::iterator)
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
 
-    protected static List<AtomicAction<? extends Oaf>> prepareRAiD(final RAiDEntity r) {
+	}
 
-        final Date now = new Date();
-        final OtherResearchProduct orp = new OtherResearchProduct();
-        final List<AtomicAction<? extends Oaf>> res = new ArrayList<>();
-        String raidId = calculateOpenaireId(r.getRaid());
+	protected static List<AtomicAction<? extends Oaf>> prepareRAiD(final RAiDEntity r) {
 
-        orp.setId(raidId);
-        orp.setCollectedfrom(RAID_COLLECTED_FROM);
-        orp.setDataInfo(RAID_DATA_INFO);
-        orp.setResourcetype(RAID_QUALIFIER);
-        orp.setTitle(
-                Collections.singletonList(
-                        structuredProperty(
-                                r.getTitle(),
-                                qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE),
-                                RAID_DATA_INFO))
-        );
-        orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary()));
-        orp.setAuthor(createAuthors(r.getAuthors()));
-        orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER)));
-        orp.setSubject(
-                r.getSubjects()
-                    .stream()
-                    .map(s -> subject(s, qualifier(DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES, DNET_SUBJECT_TYPOLOGIES), RAID_DATA_INFO))
-                    .collect(Collectors.toList())
-        );
-        orp.setRelevantdate(
-                Arrays.asList(
-                        structuredProperty(r.getEndDate(), qualifier("endDate","endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO),
-                        structuredProperty(r.getStartDate(), qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE), RAID_DATA_INFO)
-                )
-        );
-        orp.setLastupdatetimestamp(now.getTime());
-        orp.setDateofcollection(r.getStartDate());
+		final Date now = new Date();
+		final OtherResearchProduct orp = new OtherResearchProduct();
+		final List<AtomicAction<? extends Oaf>> res = new ArrayList<>();
+		String raidId = calculateOpenaireId(r.getRaid());
 
-        res.add(new AtomicAction<>(OtherResearchProduct.class, orp));
+		orp.setId(raidId);
+		orp.setCollectedfrom(RAID_COLLECTED_FROM);
+		orp.setDataInfo(RAID_DATA_INFO);
+		orp
+			.setTitle(
+				Collections
+					.singletonList(
+						structuredProperty(
+							r.getTitle(),
+							qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE),
+							RAID_DATA_INFO)));
+		orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary()));
+//		orp.setAuthor(createAuthors(r.getAuthors()));
+		orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER)));
+		orp
+			.setSubject(
+				r
+					.getSubjects()
+					.stream()
+					.map(
+						s -> subject(
+							s,
+							qualifier(
+								DNET_SUBJECT_KEYWORD, DNET_SUBJECT_KEYWORD, DNET_SUBJECT_TYPOLOGIES,
+								DNET_SUBJECT_TYPOLOGIES),
+							RAID_DATA_INFO))
+					.collect(Collectors.toList()));
+		orp
+			.setRelevantdate(
+				Arrays
+					.asList(
+						structuredProperty(
+							r.getEndDate(), qualifier("endDate", "endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE),
+							RAID_DATA_INFO),
+						structuredProperty(
+							r.getStartDate(),
+							qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE),
+							RAID_DATA_INFO)));
+		orp.setLastupdatetimestamp(now.getTime());
+		orp.setDateofacceptance(field(r.getStartDate(), RAID_DATA_INFO));
 
-        for(String resultId: r.getIds()) {
-            Relation rel1 = OafMapperUtils.getRelation(
-                    raidId,
-                    resultId,
-                    ModelConstants.RESULT_RESULT,
-                    ModelConstants.OUTCOME,
-                    PART,
-                    RAID_COLLECTED_FROM,
-                    RAID_DATA_INFO,
-                    now.getTime(),
-                    null,
-                    null
-            );
-            Relation rel2 = OafMapperUtils.getRelation(
-                    resultId,
-                    raidId,
-                    ModelConstants.RESULT_RESULT,
-                    ModelConstants.OUTCOME,
-                    IS_PART_OF,
-                    RAID_COLLECTED_FROM,
-                    RAID_DATA_INFO,
-                    now.getTime(),
-                    null,
-                    null
-            );
-            res.add(new AtomicAction<>(Relation.class, rel1));
-            res.add(new AtomicAction<>(Relation.class, rel2));
-        }
+		res.add(new AtomicAction<>(OtherResearchProduct.class, orp));
 
-        return res;
-    }
+		for (String resultId : r.getIds()) {
+			Relation rel1 = OafMapperUtils
+				.getRelation(
+					raidId,
+					resultId,
+					ModelConstants.RESULT_RESULT,
+					PART,
+					HAS_PART,
+					RAID_COLLECTED_FROM,
+					RAID_DATA_INFO,
+					now.getTime(),
+					null,
+					null);
+			Relation rel2 = OafMapperUtils
+				.getRelation(
+					resultId,
+					raidId,
+					ModelConstants.RESULT_RESULT,
+					PART,
+					IS_PART_OF,
+					RAID_COLLECTED_FROM,
+					RAID_DATA_INFO,
+					now.getTime(),
+					null,
+					null);
+			res.add(new AtomicAction<>(Relation.class, rel1));
+			res.add(new AtomicAction<>(Relation.class, rel2));
+		}
 
-    public static String calculateOpenaireId(final String raid) {
-        return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid));
-    }
+		return res;
+	}
 
-    public static List<Author> createAuthors(final List<String> author) {
-        return author.stream().map(s-> {
-            Author a = new Author();
-            a.setFullname(s);
-            return a;
-        }).collect(Collectors.toList());
-    }
+	public static String calculateOpenaireId(final String raid) {
+		return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid));
+	}
 
-    private static JavaRDD<RAiDEntity> readInputPath(
-            final SparkSession spark,
-            final String path) {
+	public static List<Author> createAuthors(final List<String> author) {
+		return author.stream().map(s -> {
+			Author a = new Author();
+			a.setFullname(s);
+			return a;
+		}).collect(Collectors.toList());
+	}
 
-        return spark
-                .read()
-                .json(path)
-                .as(Encoders.bean(RAiDEntity.class))
-                .toJavaRDD();
+	private static JavaRDD<RAiDEntity> readInputPath(
+		final SparkSession spark,
+		final String path) {
 
-    }
+		return spark
+			.read()
+			.json(path)
+			.as(Encoders.bean(RAiDEntity.class))
+			.toJavaRDD();
+
+	}
 
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java
index b0aec71d3..856b52e18 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/GenerateRAiDActionSetJob.java
@@ -1,2 +1,5 @@
-package eu.dnetlib.dhp.actionmanager.raid.model;public class GenerateRAiDActionSetJob {
+
+package eu.dnetlib.dhp.actionmanager.raid.model;
+
+public class GenerateRAiDActionSetJob {
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java
index bd7e28926..1203b28a7 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/model/RAiDEntity.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.actionmanager.raid.model;
 
 import java.io.Serializable;
@@ -5,98 +6,101 @@ import java.util.List;
 
 public class RAiDEntity implements Serializable {
 
-    String raid;
-    List<String> authors;
-    String startDate;
-    String endDate;
-    List<String> subjects;
-    List<String> titles;
-    List<String> ids;
-    String title;
-    String summary;
+	String raid;
+	List<String> authors;
+	String startDate;
+	String endDate;
+	List<String> subjects;
+	List<String> titles;
+	List<String> ids;
+	String title;
+	String summary;
 
-    public RAiDEntity(){}
-    public RAiDEntity(String raid, List<String> authors, String startDate, String endDate, List<String> subjects, List<String> titles, List<String> ids, String title, String summary) {
-        this.raid = raid;
-        this.authors = authors;
-        this.startDate = startDate;
-        this.endDate = endDate;
-        this.subjects = subjects;
-        this.titles = titles;
-        this.ids = ids;
-        this.title = title;
-        this.summary = summary;
-    }
+	public RAiDEntity() {
+	}
 
-    public String getRaid() {
-        return raid;
-    }
+	public RAiDEntity(String raid, List<String> authors, String startDate, String endDate, List<String> subjects,
+		List<String> titles, List<String> ids, String title, String summary) {
+		this.raid = raid;
+		this.authors = authors;
+		this.startDate = startDate;
+		this.endDate = endDate;
+		this.subjects = subjects;
+		this.titles = titles;
+		this.ids = ids;
+		this.title = title;
+		this.summary = summary;
+	}
 
-    public void setRaid(String raid) {
-        this.raid = raid;
-    }
+	public String getRaid() {
+		return raid;
+	}
 
-    public List<String> getAuthors() {
-        return authors;
-    }
+	public void setRaid(String raid) {
+		this.raid = raid;
+	}
 
-    public void setAuthors(List<String> authors) {
-        this.authors = authors;
-    }
+	public List<String> getAuthors() {
+		return authors;
+	}
 
-    public String getStartDate() {
-        return startDate;
-    }
+	public void setAuthors(List<String> authors) {
+		this.authors = authors;
+	}
 
-    public void setStartDate(String startDate) {
-        this.startDate = startDate;
-    }
+	public String getStartDate() {
+		return startDate;
+	}
 
-    public String getEndDate() {
-        return endDate;
-    }
+	public void setStartDate(String startDate) {
+		this.startDate = startDate;
+	}
 
-    public void setEndDate(String endDate) {
-        this.endDate = endDate;
-    }
+	public String getEndDate() {
+		return endDate;
+	}
 
-    public List<String> getSubjects() {
-        return subjects;
-    }
+	public void setEndDate(String endDate) {
+		this.endDate = endDate;
+	}
 
-    public void setSubjects(List<String> subjects) {
-        this.subjects = subjects;
-    }
+	public List<String> getSubjects() {
+		return subjects;
+	}
 
-    public List<String> getTitles() {
-        return titles;
-    }
+	public void setSubjects(List<String> subjects) {
+		this.subjects = subjects;
+	}
 
-    public void setTitles(List<String> titles) {
-        this.titles = titles;
-    }
+	public List<String> getTitles() {
+		return titles;
+	}
 
-    public List<String> getIds() {
-        return ids;
-    }
+	public void setTitles(List<String> titles) {
+		this.titles = titles;
+	}
 
-    public void setIds(List<String> ids) {
-        this.ids = ids;
-    }
+	public List<String> getIds() {
+		return ids;
+	}
 
-    public String getTitle() {
-        return title;
-    }
+	public void setIds(List<String> ids) {
+		this.ids = ids;
+	}
 
-    public void setTitle(String title) {
-        this.title = title;
-    }
+	public String getTitle() {
+		return title;
+	}
 
-    public String getSummary() {
-        return summary;
-    }
+	public void setTitle(String title) {
+		this.title = title;
+	}
 
-    public void setSummary(String summary) {
-        this.summary = summary;
-    }
+	public String getSummary() {
+		return summary;
+	}
+
+	public void setSummary(String summary) {
+		this.summary = summary;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
index ce1973a7f..6e8f48bda 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java
@@ -21,7 +21,6 @@ import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.oaf.*;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.conf.Configuration;
@@ -45,6 +44,7 @@ import eu.dnetlib.dhp.common.Constants;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
index a8dacd132..5ac1920ea 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAffiliation.java
@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
 /**
@@ -7,32 +8,33 @@ package eu.dnetlib.dhp.sx.bio.pubmed;
  */
 public class PMAffiliation {
 
-    private  String name;
+	private String name;
 
-    private PMIdentifier identifier;
+	private PMIdentifier identifier;
 
-    public PMAffiliation() {
+	public PMAffiliation() {
 
-    }
-    public PMAffiliation(String name, PMIdentifier identifier) {
-        this.name = name;
-        this.identifier = identifier;
-    }
+	}
 
-    public String getName() {
-        return name;
-    }
+	public PMAffiliation(String name, PMIdentifier identifier) {
+		this.name = name;
+		this.identifier = identifier;
+	}
 
-    public void setName(String name) {
-        this.name = name;
-    }
+	public String getName() {
+		return name;
+	}
 
-    public PMIdentifier getIdentifier() {
-        return identifier;
-    }
+	public void setName(String name) {
+		this.name = name;
+	}
 
-    public PMAffiliation setIdentifier(PMIdentifier identifier) {
-        this.identifier = identifier;
-        return this;
-    }
+	public PMIdentifier getIdentifier() {
+		return identifier;
+	}
+
+	public PMAffiliation setIdentifier(PMIdentifier identifier) {
+		this.identifier = identifier;
+		return this;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
index b0df25663..e023f2e62 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java
@@ -97,5 +97,4 @@ public class PMAuthor implements Serializable {
 		this.affiliation = affiliation;
 	}
 
-
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
index 0c8c55e40..6cd17a90c 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMIdentifier.java
@@ -1,53 +1,53 @@
+
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
 public class PMIdentifier {
 
-    private String pid;
-    private String type;
+	private String pid;
+	private String type;
 
+	public PMIdentifier(String pid, String type) {
+		this.pid = cleanPid(pid);
+		this.type = type;
+	}
 
-    public PMIdentifier(String pid, String type) {
-        this.pid = cleanPid(pid);
-        this.type = type;
-    }
+	public PMIdentifier() {
 
-    public PMIdentifier() {
+	}
 
-    }
+	private String cleanPid(String pid) {
 
-    private String cleanPid(String pid) {
+		if (pid == null) {
+			return null;
+		}
 
-        if (pid == null) {
-            return null;
-        }
+		// clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
+		if (pid.matches("[0-9]{15}[0-9X]")) {
+			return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
+		}
 
-        // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
-        if (pid.matches("[0-9]{15}[0-9X]")) {
-            return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
-        }
+		// clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
+		if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
+			return pid.replaceAll("http://orcid.org/", "");
+		}
+		return pid;
+	}
 
-        // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
-        if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
-            return pid.replaceAll("http://orcid.org/", "");
-        }
-        return pid;
-    }
+	public String getPid() {
+		return pid;
+	}
 
-    public String getPid() {
-        return pid;
-    }
+	public PMIdentifier setPid(String pid) {
+		this.pid = cleanPid(pid);
+		return this;
+	}
 
-    public PMIdentifier setPid(String pid) {
-        this.pid = cleanPid(pid);
-        return this;
-    }
+	public String getType() {
+		return type;
+	}
 
-    public String getType() {
-        return type;
-    }
-
-    public PMIdentifier setType(String type) {
-        this.type = type;
-        return this;
-    }
+	public PMIdentifier setType(String type) {
+		this.type = type;
+		return this;
+	}
 }
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/action_set_parameters.json
deleted file mode 100644
index e69de29bb..000000000
diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml
index 9b5aa5905..d3392596f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml
+++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/raid/oozie_app/workflow.xml
@@ -20,8 +20,6 @@
         <fs>
             <delete path='${raidActionSetPath}'/>
             <mkdir path='${raidActionSetPath}'/>
-            <delete path='${workingDir}'/>
-            <mkdir path='${workingDir}'/>
         </fs>
         <ok to="processRAiDFile"/>
         <error to="Kill"/>
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index e4a238c8f..de68ebb58 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -673,7 +673,6 @@ case object Crossref2Oaf {
     val doi = input.getString(0)
     val rorId = input.getString(1)
 
-
     val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true)
     val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
index 2eb4bea65..bc9a2cf02 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala
@@ -82,21 +82,22 @@ class PMParser2 {
         a.setLastName((author \ "LastName").text)
         a.setForeName((author \ "ForeName").text)
         val id = (author \ "Identifier").text
-        val idType =(author \ "Identifier" \ "@Source").text
+        val idType = (author \ "Identifier" \ "@Source").text
 
-        if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
+        if (id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
           a.setIdentifier(new PMIdentifier(id, idType))
         }
 
-
         val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text
-        val affiliationId  = (author \ "AffiliationInfo" \ "Identifier").text
+        val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text
         val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text
 
-        if(affiliation != null && affiliation.nonEmpty) {
+        if (affiliation != null && affiliation.nonEmpty) {
           val aff = new PMAffiliation()
           aff.setName(affiliation)
-          if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) {
+          if (
+            affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty
+          ) {
             aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType))
           }
           a.setAffiliation(aff)
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
index 5e14c731a..281ca0e07 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
@@ -294,11 +294,23 @@ object PubMedToOaf {
       author.setName(a.getForeName)
       author.setSurname(a.getLastName)
       author.setFullname(a.getFullName)
-      if(a.getIdentifier != null) {
-        author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid,
-          OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava)
+      if (a.getIdentifier != null) {
+        author.setPid(
+          List(
+            OafMapperUtils.structuredProperty(
+              a.getIdentifier.getPid,
+              OafMapperUtils.qualifier(
+                a.getIdentifier.getType,
+                a.getIdentifier.getType,
+                ModelConstants.DNET_PID_TYPES,
+                ModelConstants.DNET_PID_TYPES
+              ),
+              dataInfo
+            )
+          ).asJava
+        )
       }
-      if (a.getAffiliation!= null)
+      if (a.getAffiliation != null)
         author.setRawAffiliationString(List(a.getAffiliation.getName).asJava)
       author.setRank(index + 1)
       author
diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java
index 1f33f45b2..9417822af 100644
--- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java
+++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJobTest.java
@@ -1,11 +1,16 @@
+
 package eu.dnetlib.dhp.actionmanager.raid;
 
-import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest;
-import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.oaf.Oaf;
-import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
-import eu.dnetlib.dhp.schema.oaf.Relation;
+import static java.nio.file.Files.createTempDirectory;
+
+import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.File;
+import java.nio.file.Paths;
+import java.util.Arrays;
+import java.util.List;
+
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat;
@@ -20,93 +25,141 @@ import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.actionmanager.opencitations.CreateOpenCitationsASTest;
+import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 import scala.Tuple2;
 
-import java.io.File;
-import java.nio.file.Paths;
-import java.util.Arrays;
-import java.util.List;
-
-import static eu.dnetlib.dhp.actionmanager.Constants.OBJECT_MAPPER;
-import static java.nio.file.Files.createTempDirectory;
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
 public class GenerateRAiDActionSetJobTest {
-    private static String input_path;
-    private static String output_path;
-    static SparkSession spark;
+	private static String input_path;
+	private static String output_path;
+	static SparkSession spark;
 
-    @BeforeEach
-    void setUp() throws Exception {
+	@BeforeEach
+	void setUp() throws Exception {
 
-        input_path = Paths
-                .get(GenerateRAiDActionSetJobTest.class.getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json").toURI())
-                .toFile()
-                .getAbsolutePath();
+		input_path = Paths
+			.get(
+				GenerateRAiDActionSetJobTest.class
+					.getResource("/eu/dnetlib/dhp/actionmanager/raid/raid_example.json")
+					.toURI())
+			.toFile()
+			.getAbsolutePath();
 
-        output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-")
-                .toAbsolutePath()
-                .toString();
+		output_path = createTempDirectory(GenerateRAiDActionSetJobTest.class.getSimpleName() + "-")
+			.toAbsolutePath()
+			.toString();
 
-        SparkConf conf = new SparkConf();
-        conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName());
+		SparkConf conf = new SparkConf();
+		conf.setAppName(GenerateRAiDActionSetJobTest.class.getSimpleName());
 
-        conf.setMaster("local[*]");
-        conf.set("spark.driver.host", "localhost");
-        conf.set("hive.metastore.local", "true");
-        conf.set("spark.ui.enabled", "false");
-        conf.set("spark.sql.warehouse.dir", output_path);
-        conf.set("hive.metastore.warehouse.dir", output_path);
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", output_path);
+		conf.set("hive.metastore.warehouse.dir", output_path);
 
-        spark = SparkSession
-                .builder()
-                .appName(GenerateRAiDActionSetJobTest.class.getSimpleName())
-                .config(conf)
-                .getOrCreate();
-    }
+		spark = SparkSession
+			.builder()
+			.appName(GenerateRAiDActionSetJobTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
 
-    @AfterAll
-    static void cleanUp() throws Exception {
-        FileUtils.deleteDirectory(new File(output_path));
-    }
+	@AfterAll
+	static void cleanUp() throws Exception {
+		FileUtils.deleteDirectory(new File(output_path));
+	}
 
-    @Test
-    @Disabled
-    void testProcessRAiDEntities() {
-        GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set");
+	@Test
+	@Disabled
+	void testProcessRAiDEntities() {
+		GenerateRAiDActionSetJob.processRAiDEntities(spark, input_path, output_path + "/test_raid_action_set");
 
-        JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
-        JavaRDD<? extends Oaf> result = sc
-                .sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class)
-                .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
-                .map(AtomicAction::getPayload);
+		JavaRDD<? extends Oaf> result = sc
+			.sequenceFile(output_path + "/test_raid_action_set", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(AtomicAction::getPayload);
 
-        assertEquals(80, result.count());
-    }
+		assertEquals(80, result.count());
+	}
 
-    @Test
-    void testPrepareRAiD() {
+	@Test
+	void testPrepareRAiD() {
 
-        List<AtomicAction<? extends Oaf>> atomicActions = GenerateRAiDActionSetJob.prepareRAiD(new RAiDEntity(
-                "-92190526",
-                Arrays.asList("Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura", "Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume", "Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont", "Maïeul GRUGET", "Cécile Duchêne"),
-                "2021-09-10",
-                "2024-02-16",
-                Arrays.asList("cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps", "pan-scalar map", "Python library", "QGIS", "map design", "landmarks", "Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]", "[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography", "eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency", "General Medicine", "Geography, Planning and Development", "multi-scales", "pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences", "progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design", "cartography, map generalisation, zoom, multi-scale map", "Interactive maps", "Map generalisation", "Earth and Planetary Sciences (miscellaneous)", "Cartographic generalization", "rivers", "Benchmark", "General Environmental Science", "open source", "drawing", "Constraint", "Multi-scale maps"),
-                Arrays.asList("Where do people look at during multi-scale map tasks?", "FogDetector survey raw data", "Collection of cartographic disorientation stories", "Anchorwhat dataset", "BasqueRoads: A Benchmark for Road Network Selection", "Progressive river network selection for pan-scalar maps", "BasqueRoads, a dataset to benchmark road selection algorithms", "Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps", "Empirical approach to advance the generalisation of multi-scale maps", "L'Alpe d'Huez: a dataset to benchmark topographic map generalisation", "eye-tracking data from a survey on zooming in a pan-scalar map", "Material of the experiment 'More is Less' from the MapMuxing project", "Cartagen4py, an open source Python library for map generalisation", "L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"),
-                Arrays.asList("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", "50|doi_dedup___::754e3c283639bc6e104c925ff3e34007", "50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0", "50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a", "50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153", "50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a", "50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13", "50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4", "50|doi_dedup___::a9bc4453273b2d02648a5cb453195042", "50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7", "50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5", "50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283", "50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea", "50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"),
-                "Exploring Multi-Scale Map Generalization and Design",
-                "This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval."
-        ));
+		List<AtomicAction<? extends Oaf>> atomicActions = GenerateRAiDActionSetJob
+			.prepareRAiD(
+				new RAiDEntity(
+					"-92190526",
+					Arrays
+						.asList(
+							"Berli, Justin", "Le Mao, Bérénice", "Guillaume Touya", "Wenclik, Laura",
+							"Courtial, Azelle", "Muehlenhaus, Ian", "Justin Berli", "Touya, Guillaume",
+							"Gruget, Maïeul", "Azelle Courtial", "Ian Muhlenhaus", "Maïeul Gruget", "Marion Dumont",
+							"Maïeul GRUGET", "Cécile Duchêne"),
+					"2021-09-10",
+					"2024-02-16",
+					Arrays
+						.asList(
+							"cartography, zoom, pan, desert fog", "Road network", "zooming", "Pan-scalar maps",
+							"pan-scalar map", "Python library", "QGIS", "map design", "landmarks",
+							"Cartes transscalaires", "anchor", "disorientation", "[INFO]Computer Science [cs]",
+							"[SHS.GEO]Humanities and Social Sciences/Geography", "cognitive cartography",
+							"eye-tracking", "Computers in Earth Sciences", "Topographic map", "National Mapping Agency",
+							"General Medicine", "Geography, Planning and Development", "multi-scales",
+							"pan-scalar maps", "Selection", "cartography", "General Earth and Planetary Sciences",
+							"progressiveness", "map generalisation", "Eye-tracker", "zoom", "algorithms", "Map Design",
+							"cartography, map generalisation, zoom, multi-scale map", "Interactive maps",
+							"Map generalisation", "Earth and Planetary Sciences (miscellaneous)",
+							"Cartographic generalization", "rivers", "Benchmark", "General Environmental Science",
+							"open source", "drawing", "Constraint", "Multi-scale maps"),
+					Arrays
+						.asList(
+							"Where do people look at during multi-scale map tasks?", "FogDetector survey raw data",
+							"Collection of cartographic disorientation stories", "Anchorwhat dataset",
+							"BasqueRoads: A Benchmark for Road Network Selection",
+							"Progressive river network selection for pan-scalar maps",
+							"BasqueRoads, a dataset to benchmark road selection algorithms",
+							"Missing the city for buildings? A critical review of pan-scalar map generalization and design in contemporary zoomable maps",
+							"Empirical approach to advance the generalisation of multi-scale maps",
+							"L'Alpe d'Huez: a dataset to benchmark topographic map generalisation",
+							"eye-tracking data from a survey on zooming in a pan-scalar map",
+							"Material of the experiment 'More is Less' from the MapMuxing project",
+							"Cartagen4py, an open source Python library for map generalisation",
+							"L’Alpe d’Huez: A Benchmark for Topographic Map Generalisation"),
+					Arrays
+						.asList(
+							"50|doi_dedup___::6915135e0aa39f913394513f809ae58a",
+							"50|doi_dedup___::754e3c283639bc6e104c925ff3e34007",
+							"50|doi_dedup___::13517477f3c1261d57a3364363ce6ce0",
+							"50|doi_dedup___::675b16c73accc4e7242bbb4ed9b3724a",
+							"50|doi_dedup___::94ce09906b2d7d37eb2206cea8a50153",
+							"50|dedup_wf_002::cc575d5ca5651ff8c3029a3a76e7e70a",
+							"50|doi_dedup___::c5e52baddda17c755d1bae012a97dc13",
+							"50|doi_dedup___::4f5f38c9e08fe995f7278963183f8ad4",
+							"50|doi_dedup___::a9bc4453273b2d02648a5cb453195042",
+							"50|doi_dedup___::5e893dc0cb7624a33f41c9b428bd59f7",
+							"50|doi_dedup___::c1ecdef48fd9be811a291deed950e1c5",
+							"50|doi_dedup___::9e93c8f2d97c35de8a6a57a5b53ef283",
+							"50|dedup_wf_002::d08be0ed27b13d8a880e891e08d093ea",
+							"50|doi_dedup___::f8d8b3b9eddeca2fc0e3bc9e63996555"),
+					"Exploring Multi-Scale Map Generalization and Design",
+					"This project aims to advance the generalization of multi-scale maps by investigating the impact of different design elements on user experience. The research involves collecting and analyzing data from various sources, including surveys, eye-tracking studies, and user experiments. The goal is to identify best practices for map generalization and design, with a focus on reducing disorientation and improving information retrieval during exploration. The project has led to the development of several datasets, including BasqueRoads, AnchorWhat, and L'Alpe d'Huez, which can be used to benchmark road selection algorithms and topographic map generalization techniques. The research has also resulted in the creation of a Python library, Cartagen4py, for map generalization. The findings of this project have the potential to improve the design and usability of multi-scale maps, making them more effective tools for navigation and information retrieval."));
 
-        OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload();
-        Relation rel = (Relation) atomicActions.get(1).getPayload();
+		OtherResearchProduct orp = (OtherResearchProduct) atomicActions.get(0).getPayload();
+		Relation rel = (Relation) atomicActions.get(1).getPayload();
 
-        assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue());
-        assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource());
-        assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget());
+		assertEquals("Exploring Multi-Scale Map Generalization and Design", orp.getTitle().get(0).getValue());
+		assertEquals("50|raid________::759a564ce5cc7360cab030c517c7366b", rel.getSource());
+		assertEquals("50|doi_dedup___::6915135e0aa39f913394513f809ae58a", rel.getTarget());
 
-    }
+	}
 
 }
diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
index 4a926df01..cb7826dbf 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala
@@ -63,7 +63,6 @@ class BioScholixTest extends AbstractVocabularyTest {
       "0000000333457333",
       "0000000335964515",
       "0000000302921949",
-
       "http://orcid.org/0000-0001-8567-3543",
       "http://orcid.org/0000-0001-7868-8528",
       "0000-0001-9189-1440",
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
index 64cbd70ba..0d6c81627 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
@@ -130,7 +130,7 @@ public class ResultTagger implements Serializable {
 					// log.info("Remove constraints for " + communityId);
 					if (conf.getRemoveConstraintsMap().keySet().contains(communityId) &&
 						conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
-							!conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() &&
+						!conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() &&
 						conf
 							.getRemoveConstraintsMap()
 							.get(communityId)
@@ -228,7 +228,7 @@ public class ResultTagger implements Serializable {
 			.forEach(communityId -> {
 				if (!removeCommunities.contains(communityId) &&
 					conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null &&
-						!conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() &&
+					!conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() &&
 					conf
 						.getSelectionConstraintsMap()
 						.get(communityId)
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
index ea9503d17..e1710db54 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@@ -915,7 +915,8 @@ class MappersTest {
 
 	@Test
 	void testODFRecord_guidelines4() throws IOException {
-		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml")));
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
 		final Publication p = (Publication) list.get(0);
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 0da0f6955..2c977a390 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -40,6 +39,7 @@ import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
 import eu.dnetlib.dhp.schema.solr.Person;
+import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import eu.dnetlib.dhp.schema.solr.Pid;
 import eu.dnetlib.dhp.schema.solr.Project;
 import eu.dnetlib.dhp.schema.solr.Result;
@@ -216,11 +216,14 @@ public class ProvisionModelSupport {
 	}
 
 	private static List<PersonTopic> mapPersonTopics(List<eu.dnetlib.dhp.schema.oaf.PersonTopic> subjects) {
-		return Optional.ofNullable(subjects)
-				.map(ss -> ss.stream()
-						.map(ProvisionModelSupport::mapPersonTopic)
-						.collect(Collectors.toList()))
-				.orElse(null);
+		return Optional
+			.ofNullable(subjects)
+			.map(
+				ss -> ss
+					.stream()
+					.map(ProvisionModelSupport::mapPersonTopic)
+					.collect(Collectors.toList()))
+			.orElse(null);
 	}
 
 	private static PersonTopic mapPersonTopic(eu.dnetlib.dhp.schema.oaf.PersonTopic pt) {

From fed13e083e8d9370d7d16885c17c13a8aa1a8d46 Mon Sep 17 00:00:00 2001
From: Giambattista Bloisi <giambattista.bloisi@openaire.eu>
Date: Thu, 5 Dec 2024 15:21:32 +0100
Subject: [PATCH 231/239] Fix: do not import joda formatting

---
 .../java/eu/dnetlib/pace/tree/DateRange.java  | 88 +++++++++----------
 .../eu/dnetlib/pace/tree/JsonListMatch.java   |  2 +-
 .../pace/comparators/ComparatorTest.java      | 30 +++++--
 .../dhp/bulktag/community/ResultTagger.java   |  4 +-
 .../dnetlib/dhp/oa/graph/raw/MappersTest.java |  3 +-
 .../model/ProvisionModelSupport.java          | 15 ++--
 6 files changed, 83 insertions(+), 59 deletions(-)

diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
index c913109a4..6349c944b 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/DateRange.java
@@ -1,10 +1,5 @@
-package eu.dnetlib.pace.tree;
 
-import com.wcohen.ss.AbstractStringDistance;
-import eu.dnetlib.pace.config.Config;
-import eu.dnetlib.pace.tree.support.AbstractStringComparator;
-import eu.dnetlib.pace.tree.support.ComparatorClass;
-import org.joda.time.DateTime;
+package eu.dnetlib.pace.tree;
 
 import java.time.DateTimeException;
 import java.time.LocalDate;
@@ -13,55 +8,60 @@ import java.time.format.DateTimeFormatter;
 import java.util.Locale;
 import java.util.Map;
 
+import com.wcohen.ss.AbstractStringDistance;
+
+import eu.dnetlib.pace.config.Config;
+import eu.dnetlib.pace.tree.support.AbstractStringComparator;
+import eu.dnetlib.pace.tree.support.ComparatorClass;
+
 @ComparatorClass("dateRange")
 public class DateRange extends AbstractStringComparator {
 
-    int YEAR_RANGE;
+	int YEAR_RANGE;
 
-    public DateRange(Map<String, String> params) {
-        super(params, new com.wcohen.ss.JaroWinkler());
-        YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3"));
-    }
+	public DateRange(Map<String, String> params) {
+		super(params, new com.wcohen.ss.JaroWinkler());
+		YEAR_RANGE = Integer.parseInt(params.getOrDefault("year_range", "3"));
+	}
 
-    public DateRange(final double weight) {
-        super(weight, new com.wcohen.ss.JaroWinkler());
-    }
+	public DateRange(final double weight) {
+		super(weight, new com.wcohen.ss.JaroWinkler());
+	}
 
-    protected DateRange(final double weight, final AbstractStringDistance ssalgo) {
-        super(weight, ssalgo);
-    }
+	protected DateRange(final double weight, final AbstractStringDistance ssalgo) {
+		super(weight, ssalgo);
+	}
 
-    public static boolean isNumeric(String str) {
-        return str.matches("\\d+");  //match a number with optional '-' and decimal.
-    }
+	public static boolean isNumeric(String str) {
+		return str.matches("\\d+"); // match a number with optional '-' and decimal.
+	}
 
-    @Override
-    public double distance(final String a, final String b, final Config conf) {
-        if (a.isEmpty() || b.isEmpty()) {
-            return -1.0; // return -1 if a field is missing
-        }
+	@Override
+	public double distance(final String a, final String b, final Config conf) {
+		if (a.isEmpty() || b.isEmpty()) {
+			return -1.0; // return -1 if a field is missing
+		}
 
-        try {
-            DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH);
-            LocalDate d1 = LocalDate.parse(a, formatter);
-            LocalDate d2 = LocalDate.parse(b, formatter);
-            Period period = Period.between(d1, d2);
+		try {
+			DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd", Locale.ENGLISH);
+			LocalDate d1 = LocalDate.parse(a, formatter);
+			LocalDate d2 = LocalDate.parse(b, formatter);
+			Period period = Period.between(d1, d2);
 
-            return period.getYears() <= YEAR_RANGE? 1.0 : 0.0;
-        }
-        catch (DateTimeException e) {
-            return -1.0;
-        }
+			return period.getYears() <= YEAR_RANGE ? 1.0 : 0.0;
+		} catch (DateTimeException e) {
+			return -1.0;
+		}
 
-    }
+	}
 
-    @Override
-    public double getWeight() {
-        return super.weight;
-    }
+	@Override
+	public double getWeight() {
+		return super.weight;
+	}
 
-    @Override
-    protected double normalize(final double d) {
-        return d;
-    }
+	@Override
+	protected double normalize(final double d) {
+		return d;
+	}
 }
diff --git a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
index e95d9206e..d9558df90 100644
--- a/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
+++ b/dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/JsonListMatch.java
@@ -62,7 +62,7 @@ public class JsonListMatch extends AbstractListComparator {
 
 				Set<String> types = Sets.intersection(typesA, typesB);
 
-				if (types.isEmpty())  // if no common type, it is impossible to compare
+				if (types.isEmpty()) // if no common type, it is impossible to compare
 					return -1;
 
 				ca = ca.stream().filter(s -> types.contains(s.split("::")[0])).collect(Collectors.toSet());
diff --git a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
index 83539de4a..0abde84bc 100644
--- a/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
+++ b/dhp-pace-core/src/test/java/eu/dnetlib/pace/comparators/ComparatorTest.java
@@ -72,14 +72,34 @@ public class ComparatorTest extends AbstractPaceTest {
 		CodeMatch codeMatch = new CodeMatch(params);
 
 		// names have different codes
-		assertEquals(0.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ir02", conf));
+		assertEquals(
+			0.0,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998 ev02a",
+					"physical oceanography at ctd station june 1998 ir02", conf));
 
 		// names have same code
-		assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998 ev02a", "physical oceanography at ctd station june 1998 ev02a", conf));
+		assertEquals(
+			1.0,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998 ev02a",
+					"physical oceanography at ctd station june 1998 ev02a", conf));
 
 		// code is not in both names
-		assertEquals(-1, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998 ev02a", conf));
-		assertEquals(1.0, codeMatch.distance("physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998", conf));
+		assertEquals(
+			-1,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998",
+					"physical oceanography at ctd station june 1998 ev02a", conf));
+		assertEquals(
+			1.0,
+			codeMatch
+				.distance(
+					"physical oceanography at ctd station june 1998", "physical oceanography at ctd station june 1998",
+					conf));
 	}
 
 	@Test
@@ -275,7 +295,7 @@ public class ComparatorTest extends AbstractPaceTest {
 			Arrays
 				.asList(
 					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"grid\",\"classname\":\"GRID Identifier\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"grid_1\"}",
-						"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"),
+					"{\"datainfo\":{\"deletedbyinference\":false,\"inferenceprovenance\":null,\"inferred\":false,\"invisible\":false,\"provenanceaction\":{\"classid\":\"sysimport:actionset\",\"classname\":\"Harvested\",\"schemeid\":\"dnet:provenanceActions\",\"schemename\":\"dnet:provenanceActions\"},\"trust\":\"0.9\"},\"qualifier\":{\"classid\":\"ror\",\"classname\":\"Research Organization Registry\",\"schemeid\":\"dnet:pid_types\",\"schemename\":\"dnet:pid_types\"},\"value\":\"ror_1\"}"),
 			"authors");
 		List<String> b = createFieldList(
 			Arrays
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
index 64cbd70ba..0d6c81627 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java
@@ -130,7 +130,7 @@ public class ResultTagger implements Serializable {
 					// log.info("Remove constraints for " + communityId);
 					if (conf.getRemoveConstraintsMap().keySet().contains(communityId) &&
 						conf.getRemoveConstraintsMap().get(communityId).getCriteria() != null &&
-							!conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() &&
+						!conf.getRemoveConstraintsMap().get(communityId).getCriteria().isEmpty() &&
 						conf
 							.getRemoveConstraintsMap()
 							.get(communityId)
@@ -228,7 +228,7 @@ public class ResultTagger implements Serializable {
 			.forEach(communityId -> {
 				if (!removeCommunities.contains(communityId) &&
 					conf.getSelectionConstraintsMap().get(communityId).getCriteria() != null &&
-						!conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() &&
+					!conf.getSelectionConstraintsMap().get(communityId).getCriteria().isEmpty() &&
 					conf
 						.getSelectionConstraintsMap()
 						.get(communityId)
diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
index ea9503d17..e1710db54 100644
--- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
+++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
@@ -915,7 +915,8 @@ class MappersTest {
 
 	@Test
 	void testODFRecord_guidelines4() throws IOException {
-		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml")));
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_guidelines4.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
 		final Publication p = (Publication) list.get(0);
diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
index 0da0f6955..2c977a390 100644
--- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
+++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java
@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -40,6 +39,7 @@ import eu.dnetlib.dhp.schema.solr.OpenAccessColor;
 import eu.dnetlib.dhp.schema.solr.OpenAccessRoute;
 import eu.dnetlib.dhp.schema.solr.Organization;
 import eu.dnetlib.dhp.schema.solr.Person;
+import eu.dnetlib.dhp.schema.solr.PersonTopic;
 import eu.dnetlib.dhp.schema.solr.Pid;
 import eu.dnetlib.dhp.schema.solr.Project;
 import eu.dnetlib.dhp.schema.solr.Result;
@@ -216,11 +216,14 @@ public class ProvisionModelSupport {
 	}
 
 	private static List<PersonTopic> mapPersonTopics(List<eu.dnetlib.dhp.schema.oaf.PersonTopic> subjects) {
-		return Optional.ofNullable(subjects)
-				.map(ss -> ss.stream()
-						.map(ProvisionModelSupport::mapPersonTopic)
-						.collect(Collectors.toList()))
-				.orElse(null);
+		return Optional
+			.ofNullable(subjects)
+			.map(
+				ss -> ss
+					.stream()
+					.map(ProvisionModelSupport::mapPersonTopic)
+					.collect(Collectors.toList()))
+			.orElse(null);
 	}
 
 	private static PersonTopic mapPersonTopic(eu.dnetlib.dhp.schema.oaf.PersonTopic pt) {

From fd1038b44d10e17146d0aac51841818460872eca Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@isti.cnr.it>
Date: Fri, 6 Dec 2024 09:12:06 +0100
Subject: [PATCH 232/239] removed a sneaky break that was committed by mistake.

---
 .../java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java     | 1 -
 1 file changed, 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java
index 11f4c55d8..8172456bb 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java
@@ -154,7 +154,6 @@ public class ORCIDExtractor extends Thread {
 						extractedItem++;
 						if (extractedItem % 100000 == 0) {
 							log.info("Thread {}: Extracted {} items", id, extractedItem);
-							break;
 						}
 					}
 				}

From 1c144a4dcb951319ed88a7cac4825837c5385316 Mon Sep 17 00:00:00 2001
From: miconis <michele.debonis@isti.cnr.it>
Date: Fri, 6 Dec 2024 09:18:10 +0100
Subject: [PATCH 233/239] minor change

---
 .../dhp/actionmanager/raid/GenerateRAiDActionSetJob.java       | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
index 3b2405956..c82934cdb 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
@@ -43,7 +43,8 @@ public class GenerateRAiDActionSetJob {
 	private static final List<KeyValue> RAID_COLLECTED_FROM = listKeyValues(
 		OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
-	private static final Qualifier RAID_QUALIFIER = qualifier("0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE);
+	private static final Qualifier RAID_QUALIFIER = qualifier(
+		"0049", "Research Activity Identifier", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE);
 
 	private static final Qualifier RAID_INFERENCE_QUALIFIER = qualifier(
 		"raid:openaireinference", "Inferred by OpenAIRE", DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS);

From dade7d5bb86d4030fc2b69f3a26940e055e216eb Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 6 Dec 2024 10:02:07 +0100
Subject: [PATCH 234/239] minor changes

---
 .../java/eu/dnetlib/dhp/common/Constants.java |  5 ++--
 .../raid/GenerateRAiDActionSetJob.java        | 27 +++++++------------
 2 files changed, 13 insertions(+), 19 deletions(-)

diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
index b00199ea5..6a4bb34d3 100644
--- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
+++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java
@@ -11,8 +11,9 @@ public class Constants {
 	public static final Map<String, String> coarCodeLabelMap = Maps.newHashMap();
 
 	public static final String RAID_NS_PREFIX = "raid________";
-	public static final String RAID_DATASOURCE_NAME = "Research Activity Identifier Service (RAiD)";
-	public static final String RAID_OPENAIRE_ID = "";
+
+	public static final String END_DATE = "endDate";
+	public static final String START_DATE = "startDate";
 
 	public static final String ROR_NS_PREFIX = "ror_________";
 
diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
index c82934cdb..e67e7171f 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/raid/GenerateRAiDActionSetJob.java
@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager.raid;
 
 import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_ID;
 import static eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson.OPENAIRE_DATASOURCE_NAME;
+import static eu.dnetlib.dhp.common.Constants.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
@@ -24,7 +25,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.actionmanager.raid.model.RAiDEntity;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.Constants;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
@@ -120,8 +120,10 @@ public class GenerateRAiDActionSetJob {
 							qualifier("main title", "main title", DNET_DATACITE_TITLE, DNET_DATACITE_TITLE),
 							RAID_DATA_INFO)));
 		orp.setDescription(listFields(RAID_DATA_INFO, r.getSummary()));
-//		orp.setAuthor(createAuthors(r.getAuthors()));
-		orp.setInstance(Collections.singletonList(eu.dnetlib.dhp.actionmanager.Constants.getInstance(RAID_QUALIFIER)));
+
+		Instance instance = new Instance();
+		instance.setInstancetype(RAID_QUALIFIER);
+		orp.setInstance(Collections.singletonList(instance));
 		orp
 			.setSubject(
 				r
@@ -140,11 +142,11 @@ public class GenerateRAiDActionSetJob {
 				Arrays
 					.asList(
 						structuredProperty(
-							r.getEndDate(), qualifier("endDate", "endDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE),
+							r.getEndDate(), qualifier(END_DATE, END_DATE, DNET_DATACITE_DATE, DNET_DATACITE_DATE),
 							RAID_DATA_INFO),
 						structuredProperty(
 							r.getStartDate(),
-							qualifier("startDate", "startDate", DNET_DATACITE_DATE, DNET_DATACITE_DATE),
+							qualifier(START_DATE, START_DATE, DNET_DATACITE_DATE, DNET_DATACITE_DATE),
 							RAID_DATA_INFO)));
 		orp.setLastupdatetimestamp(now.getTime());
 		orp.setDateofacceptance(field(r.getStartDate(), RAID_DATA_INFO));
@@ -159,11 +161,7 @@ public class GenerateRAiDActionSetJob {
 					ModelConstants.RESULT_RESULT,
 					PART,
 					HAS_PART,
-					RAID_COLLECTED_FROM,
-					RAID_DATA_INFO,
-					now.getTime(),
-					null,
-					null);
+					orp);
 			Relation rel2 = OafMapperUtils
 				.getRelation(
 					resultId,
@@ -171,11 +169,7 @@ public class GenerateRAiDActionSetJob {
 					ModelConstants.RESULT_RESULT,
 					PART,
 					IS_PART_OF,
-					RAID_COLLECTED_FROM,
-					RAID_DATA_INFO,
-					now.getTime(),
-					null,
-					null);
+					orp);
 			res.add(new AtomicAction<>(Relation.class, rel1));
 			res.add(new AtomicAction<>(Relation.class, rel2));
 		}
@@ -184,7 +178,7 @@ public class GenerateRAiDActionSetJob {
 	}
 
 	public static String calculateOpenaireId(final String raid) {
-		return String.format("50|%s::%s", Constants.RAID_NS_PREFIX, DHPUtils.md5(raid));
+		return String.format("50|%s::%s", RAID_NS_PREFIX, DHPUtils.md5(raid));
 	}
 
 	public static List<Author> createAuthors(final List<String> author) {
@@ -204,7 +198,6 @@ public class GenerateRAiDActionSetJob {
 			.json(path)
 			.as(Encoders.bean(RAiDEntity.class))
 			.toJavaRDD();
-
 	}
 
 }

From 8a5ba8df45d6fb1b570853307fb99f465d0667f5 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 6 Dec 2024 10:03:11 +0100
Subject: [PATCH 235/239] minor changes

---
 .../main/java/eu/dnetlib/dhp/actionmanager/Constants.java   | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
index 394cc22a3..d7ad7fcb9 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
@@ -112,12 +112,6 @@ public class Constants {
 
 	}
 
-	public static Instance getInstance(Qualifier qualifier) {
-		Instance instance = new Instance();
-		instance.setInstancetype(qualifier);
-		return instance;
-	}
-
 	public static void removeOutputDir(SparkSession spark, String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}

From ee84db7a6a5ff1e271f5d6a0cfdfcc07e1a59ac9 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 6 Dec 2024 12:20:13 +0100
Subject: [PATCH 236/239] [communityfromsemrelpropagation] added filtering to
 remove the deletedbyinference and invisible results

---
 .../PrepareResultCommunitySetStep1.java                      | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
index 5af2bf481..764390442 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
@@ -70,7 +70,7 @@ public class PrepareResultCommunitySetStep1 {
 	private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context        \n" +
 			"    from  result        " +
 			"    lateral view explode (context) c as co     " +
-			"    where datainfo.deletedbyinference = false  AND lower(co.id) IN %s" +
+			"    where  lower(co.id) IN %s" +
 			"    group by id";
 
 	private static final String RESULT_PATENT = "select id " +
@@ -160,7 +160,8 @@ public class PrepareResultCommunitySetStep1 {
 		Dataset<Relation> relation = readPath(spark, inputRelationPath, Relation.class);
 		relation.createOrReplaceTempView("relation");
 
-		Dataset<R> result = readPath(spark, inputResultPath, resultClazz);
+		Dataset<R> result = readPath(spark, inputResultPath, resultClazz)
+				.where("datainfo.deletedbyinference != true AND datainfo.invisible != true");
 		result.createOrReplaceTempView("result");
 
 		final String outputResultPath = outputPath + "/" + resultType;

From 666155bafaa04db7153c98d91b911d88e9cb2f01 Mon Sep 17 00:00:00 2001
From: Miriam Baglioni <miriam.baglioni@isti.cnr.it>
Date: Fri, 6 Dec 2024 12:26:41 +0100
Subject: [PATCH 237/239] [communityfromsemrelpropagation] changed resource to
 have deletedbyinference = false.

---
 .../graph/publication/part-00000.json                           | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json
index 7957bcfd5..ae9083c65 100644
--- a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json
+++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph/publication/part-00000.json
@@ -7,7 +7,7 @@
 {"author":[{"fullname":"Turkia, Heidi","name":"Heidi","pid":[],"rank":1,"surname":"Turkia"},{"fullname":"Sirén, Heli","name":"Heli","pid":[],"rank":2,"surname":"Sirén"},{"fullname":"Penttilä, Merja","name":"Merja","pid":[],"rank":3,"surname":"Penttilä"},{"fullname":"Pitkänen, Juha Pekka","name":"Juha Pekka","pid":[],"rank":4,"surname":"Pitkänen"}],"bestaccessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"}],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":true,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2013-02-22"},"dateofcollection":"2022-02-28T12:29:51.291Z","dateoftransformation":"2022-02-28T16:19:35.201Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"<p>Hydrolysates of lignocellulosic biomass, used as substrates for the sustainable production of fuels and chemicals often contain high amounts of phenolic compounds inhibiting the production microbiota. Quantification of these inhibitor compounds may help to understand possible difficulties in bioprocessing and further the development of more efficient, robust and tolerable processes. A separation method based on capillary electrophoresis with UV detection was developed for the simultaneous quantification of 10 phenolic compounds that may have inhibitor properties. Intraday relative standard deviations were less than 0.7% for migration times and between 2.6% and 6.4% for peak areas. Interday relative standard deviations were less than 3.0% for migration times and between 5.0% and 7.2% for peak areas. The method was applied to demonstrate that Saccharomyces cerevisiae was able to decrease the concentrations of vanillin, coniferyl aldehyde, syringaldehyde, acetoguaiacone and cinnamic acid during the cultivation, whereas the concentrations of phenols increased.</p>"}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::6c232359e3b3165574cb88f0554d9264","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.1016/j.chroma.2013.01.004"}],"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2013-02-22"},"distributionlocation":"","hostedby":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information 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splitter"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Method for the rotational alignment of polarization-maintaining optical fibers and waveguides"}]}
 {"author":[{"fullname":"Aalto, Timo","name":"Timo","pid":[],"rank":1,"surname":"Aalto"},{"fullname":"Harjanne, Mikko","name":"Mikko","pid":[],"rank":2,"surname":"Harjanne"},{"fullname":"Kapulainen, Markku","name":"Markku","pid":[],"rank":3,"surname":"Kapulainen"}],"bestaccessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"}],"context":[{"dataInfo": null,"id": "beopen"}],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2003-01-01"},"dateofcollection":"2022-02-28T12:32:37.581Z","dateoftransformation":"2022-02-28T19:39:18.717Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"A novel method has been developed for measuring the rotational angle of a fiber's or a waveguide's polarization axis with respect to a reference angle. The reference angle is the polarization axis of the measuring device. The method also gives the true polarization extinction ratio of the measured fiber or waveguide. The method is suitable for the characterization and rotational alignment of polarization-maintaining waveguides and fibers. In particular, the method can be used to rotationally align the fiber-waveguide interconnections during waveguide characterization. The measuring device is either a linear polarizer or a polarization splitter that is accurately rotated with respect to the device under test. According to the experiments with a polarization-maintaining fiber, the method is very easy and inexpensive to implement, and the angular accuracy can be better than 0.2 deg."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|openorgs____::64badd35233ba2cd4946368ef2f4cf57","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"doi","classname":"Digital Object Identifier","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"value":"10.1117/1.1600730"}],"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2003-01-01"},"distributionlocation":"","hostedby":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"pid":[],"refereed":{"classid":"0000","classname":"UNKNOWN","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://cris.vtt.fi/en/publications/8cd538fb-6484-4655-81dd-47348d358fd4"]}],"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1646505829230,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Fcris.vtt.fi%2Fws%2Foai","datestamp":"2022-01-31T21:47:37Z","harvestDate":"2022-02-28T12:32:37.581Z","identifier":"oai:cris.vtt.fi:publications/8cd538fb-6484-4655-81dd-47348d358fd4","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"originalId":["50|355e65625b88::df0143af011fd82af8ac2d07b03ee8cd","oai:cris.vtt.fi:publications/8cd538fb-6484-4655-81dd-47348d358fd4"],"pid":[],"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Aalto , T , Harjanne , M & Kapulainen , M 2003 , ' Method for the rotational alignment of polarization-maintaining optical fibers and waveguides ' , Optical Engineering , vol. 42 , no. 10 , pp. 2861-2867 . https://doi.org/10.1117/1.1600730"}],"subject":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"optical waveguide"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"polarization-maintaining fiber"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"characterization"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"fiber-waveguide coupling"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"polarization"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"polarization axis"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"polarizer"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"value":"polarization splitter"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Method for the rotational alignment of polarization-maintaining optical fibers and waveguides"}]}
 {"author":[{"fullname":"Penttilä, Raimo","name":"Raimo","pid":[],"rank":1,"surname":"Penttilä"},{"fullname":"Vanttaja, Ilkka","name":"Ilkka","pid":[],"rank":2,"surname":"Vanttaja"},{"fullname":"Haapamäki, Petteri","name":"Petteri","pid":[],"rank":3,"surname":"Haapamäki"},{"fullname":"Kujanpää, Veli","name":"Veli","pid":[],"rank":4,"surname":"Kujanpää"}],"bestaccessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|opendoar____::f0dd4a99fba6075a9494772b58f95280","value":"VTT Research Information System"}],"context": [{"dataInfo":null, "id":"dh-ch"}],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"1994-01-01"},"dateofcollection":"2022-02-28T12:35:26.769Z","dateoftransformation":"2022-02-28T19:54:10.494Z","description":[],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6","instance":[{"accessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"1994-01-01"},"distributionlocation":"","hostedby":{"key":"10|eurocrisdris::9ae43d14471c4b33661fedda6f06b539","value":"VTT Research Information System"},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"pid":[],"refereed":{"classid":"0000","classname":"UNKNOWN","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://cris.vtt.fi/en/publications/ddbd28ea-5fbf-43e1-896f-e69856870c26"]}],"language":{"classid":"fin","classname":"Finnish","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1646505838552,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Fcris.vtt.fi%2Fws%2Foai","datestamp":"2019-08-08T07:09:42Z","harvestDate":"2022-02-28T12:35:26.769Z","identifier":"oai:cris.vtt.fi:publications/ddbd28ea-5fbf-43e1-896f-e69856870c26","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"originalId":["oai:cris.vtt.fi:publications/ddbd28ea-5fbf-43e1-896f-e69856870c26","50|355e65625b88::e7d48a470b13bda61f7ebe3513e20cb6"],"pid":[],"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"UNKNOWN","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Penttilä , R , Vanttaja , I , Haapamäki , P & Kujanpää , V 1994 , ' Liimauksen ja puristusliittämisen yhdistämisellä lisää lujuutta, jäykkyyttä ja tiiveyttä ' , Ohutlevyuutiset , no. 2 , pp. 17-19 ."}],"subject":[],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Liimauksen ja puristusliittämisen yhdistämisellä lisää lujuutta, jäykkyyttä ja tiiveyttä"}]}
\ No newline at end of file

From e4b814b3f1bdb3ab52a439aff82aa56359a80cb7 Mon Sep 17 00:00:00 2001
From: Claudio Atzori <claudio.atzori@isti.cnr.it>
Date: Fri, 6 Dec 2024 13:58:39 +0100
Subject: [PATCH 238/239] code formatting

---
 .../dhp/collection/CollectorWorker.java       |  2 +-
 .../collection/crossref/Crossref2Oaf.scala    | 13 ++--
 .../crossref/CrossrefMappingTest.scala        | 18 +++--
 .../PrepareResultCommunitySetStep1.java       | 76 ++++++++++---------
 .../PrepareResultCommunitySetStep2.java       |  2 +-
 .../ResultToCommunityJobTest.java             | 70 ++++++++---------
 6 files changed, 97 insertions(+), 84 deletions(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
index 4c6d0653e..67966d523 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java
@@ -7,7 +7,6 @@ import java.io.IOException;
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.IntWritable;
@@ -29,6 +28,7 @@ import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.osf.OsfPreprintsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
+import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;
diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
index c72b366a0..ea2177497 100644
--- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
+++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala
@@ -503,7 +503,6 @@ case object Crossref2Oaf {
       )
     }
 
-
     if (doi.startsWith("10.3410") || doi.startsWith("10.12703"))
       instance.setHostedby(
         OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true), "H1Connect")
@@ -556,14 +555,18 @@ case object Crossref2Oaf {
       result
   }
 
-
-
   def generateIdentifier(oaf: Result, doi: String): String = {
     val id = DHPUtils.md5(doi.toLowerCase)
     s"50|doiboost____|$id"
   }
 
-  private def generateAuthor(given: String, family: String, orcid: String, index: Int, affiliation: Option[List[mappingAffiliation]]): Author = {
+  private def generateAuthor(
+    given: String,
+    family: String,
+    orcid: String,
+    index: Int,
+    affiliation: Option[List[mappingAffiliation]]
+  ): Author = {
     val a = new Author
     a.setName(given)
     a.setSurname(family)
@@ -700,7 +703,6 @@ case object Crossref2Oaf {
     if (objectType == null)
       return resultList
 
-
     // If the item has a relations is-review-of, then we force it to a peer-review
     val is_review = json \ "relation" \ "is-review-of" \ "id"
     var force_to_review = false
@@ -713,7 +715,6 @@ case object Crossref2Oaf {
     if (typology == null)
       return List()
 
-
     val result = generateItemFromType(typology._2)
     if (result == null)
       return List()
diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
index 12ca14ba1..ebe247d8a 100644
--- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
+++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala
@@ -28,17 +28,21 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
     val input =
       IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
 
-    Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => {
-      Assertions.assertNotNull(record)
-    })
+    Crossref2Oaf
+      .convert(input, vocabularies, TransformationType.All)
+      .foreach(record => {
+        Assertions.assertNotNull(record)
+      })
 
   }
 
-
   @Test
   def mappingAffiliation(): Unit = {
     val input =
-      IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8")
+      IOUtils.toString(
+        getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"),
+        "utf-8"
+      )
     val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult)
     data.foreach(record => {
       Assertions.assertNotNull(record)
@@ -46,10 +50,10 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
       val publication = record.asInstanceOf[Publication]
       publication.getAuthor.asScala.foreach(author => {
         Assertions.assertNotNull(author.getRawAffiliationString)
-        Assertions.assertTrue(author.getRawAffiliationString.size()>0)
+        Assertions.assertTrue(author.getRawAffiliationString.size() > 0)
 
-        })
       })
+    })
     println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head))
   }
 }
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
index 764390442..ecb7cc827 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java
@@ -1,16 +1,16 @@
 
 package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 
+import static java.lang.String.join;
+
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
-import static java.lang.String.join;
 
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
-import eu.dnetlib.dhp.schema.common.ModelConstants;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.*;
@@ -22,6 +22,7 @@ import com.google.gson.Gson;
 import eu.dnetlib.dhp.api.Utils;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
@@ -37,8 +38,7 @@ public class PrepareResultCommunitySetStep1 {
 	 * relation
 	 */
 	// TODO
-	private static final String RESULT_CONTEXT_QUERY_TEMPLATE =
-			"select target resultId, community_context  "
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context  "
 		+ "from (select id, collect_set(co.id) community_context "
 		+ "       from  result "
 		+ "       lateral view explode (context) c as co "
@@ -60,26 +60,26 @@ public class PrepareResultCommunitySetStep1 {
 		+ "where length(co) > 0 "
 		+ "group by resultId";
 
-	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO =
-			"select target as resultId, community_context " +
-			"from resultWithContext rwc " +
-			"join relatedToRelations r " +
-			"join patents p  " +
-			"on rwc.id = r.source and r.target = p.id";
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target as resultId, community_context "
+		+
+		"from resultWithContext rwc " +
+		"join relatedToRelations r " +
+		"join patents p  " +
+		"on rwc.id = r.source and r.target = p.id";
 
 	private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context        \n" +
-			"    from  result        " +
-			"    lateral view explode (context) c as co     " +
-			"    where  lower(co.id) IN %s" +
-			"    group by id";
+		"    from  result        " +
+		"    lateral view explode (context) c as co     " +
+		"    where  lower(co.id) IN %s" +
+		"    group by id";
 
 	private static final String RESULT_PATENT = "select id " +
-			"    from result " +
-			"    where array_contains(instance.instancetype.classname, 'Patent')";
+		"    from result " +
+		"    where array_contains(instance.instancetype.classname, 'Patent')";
 
 	private static final String IS_RELATED_TO_RELATIONS = "select source, target " +
-			"    from relation " +
-			"    where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false";
+		"    from relation " +
+		"    where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false";
 
 	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
@@ -107,17 +107,25 @@ public class PrepareResultCommunitySetStep1 {
 		SparkConf conf = new SparkConf();
 		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
-		final String allowedsemrel ="(" + join(",",
-				Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'")
-						.toArray(String[]::new)) + ")";
+		final String allowedsemrel = "(" + join(
+			",",
+			Arrays
+				.asList(parser.get("allowedsemrels").split(";"))
+				.stream()
+				.map(value -> "'" + value.toLowerCase() + "'")
+				.toArray(String[]::new))
+			+ ")";
 		log.info("allowedSemRel: {}", allowedsemrel);
 
 		final String baseURL = parser.get("baseURL");
 		log.info("baseURL: {}", baseURL);
 
-		final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream()
+		final String communityIdList = "(" + join(
+			",", getCommunityList(baseURL)
+				.stream()
 				.map(value -> "'" + value.toLowerCase() + "'")
-				.toArray(String[]::new)) + ")";
+				.toArray(String[]::new))
+			+ ")";
 
 		final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
 		log.info("resultType: {}", resultType);
@@ -161,18 +169,17 @@ public class PrepareResultCommunitySetStep1 {
 		relation.createOrReplaceTempView("relation");
 
 		Dataset<R> result = readPath(spark, inputResultPath, resultClazz)
-				.where("datainfo.deletedbyinference != true AND datainfo.invisible != true");
+			.where("datainfo.deletedbyinference != true AND datainfo.invisible != true");
 		result.createOrReplaceTempView("result");
 
 		final String outputResultPath = outputPath + "/" + resultType;
 		log.info("writing output results to: {}", outputResultPath);
 
-
 		String resultContextQuery = String
 			.format(
 				RESULT_CONTEXT_QUERY_TEMPLATE,
-					"AND  lower(co.id) IN " + communityIdList,
-					"AND lower(relClass) IN " + allowedsemrel);
+				"AND  lower(co.id) IN " + communityIdList,
+				"AND lower(relClass) IN " + allowedsemrel);
 		Dataset<Row> result_context = spark.sql(resultContextQuery);
 
 		Dataset<Row> rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList));
@@ -183,18 +190,17 @@ public class PrepareResultCommunitySetStep1 {
 		patents.createOrReplaceTempView("patents");
 		relatedToRelations.createOrReplaceTempView("relatedTorelations");
 
-
-		result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO));
+		result_context = result_context.unionAll(spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO));
 
 		result_context.createOrReplaceTempView("result_context");
 
 		spark
-				.sql(RESULT_COMMUNITY_LIST_QUERY)
-				.as(Encoders.bean(ResultCommunityList.class))
-				.write()
-				.option("compression", "gzip")
-				.mode(SaveMode.Append)
-				.json(outputResultPath);
+			.sql(RESULT_COMMUNITY_LIST_QUERY)
+			.as(Encoders.bean(ResultCommunityList.class))
+			.write()
+			.option("compression", "gzip")
+			.mode(SaveMode.Append)
+			.json(outputResultPath);
 
 	}
 
diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
index 9bebc36e5..9801b1bf6 100644
--- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
+++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java
@@ -77,7 +77,7 @@ public class PrepareResultCommunitySetStep2 {
 					if (b == null) {
 						return a;
 					}
-                    Set<String> community_set = new HashSet<>(a.getCommunityList());
+					Set<String> community_set = new HashSet<>(a.getCommunityList());
 					community_set.addAll(b.getCommunityList());
 					a.setCommunityList(new ArrayList<>(community_set));
 					return a;
diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
index c1fcff4d9..2b52c91de 100644
--- a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
+++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java
@@ -10,7 +10,6 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -27,6 +26,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
 import eu.dnetlib.dhp.schema.oaf.Dataset;
 import scala.collection.Seq;
 
@@ -279,53 +279,55 @@ public class ResultToCommunityJobTest {
 	@Test
 	public void prepareStep1Test() throws Exception {
 		/*
-
-
-		final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
-				.map(value -> "'" + value.toLowerCase() + "'")
-				.toArray(String[]::new));
-
-		log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
-
-		final String baseURL = parser.get("baseURL");
-		log.info("baseURL: {}", baseURL);
+		 * final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) .map(value ->
+		 * "'" + value.toLowerCase() + "'") .toArray(String[]::new)); log.info("allowedSemRel: {}", new
+		 * Gson().toJson(allowedsemrel)); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}",
+		 * baseURL);
 		 */
 		PrepareResultCommunitySetStep1
-				.main(
-						new String[] {
-								"-isSparkSessionManaged", Boolean.FALSE.toString(),
-								"-sourcePath", getClass()
-								.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph")
-								.getPath(),
-								"-hive_metastore_uris", "",
-								"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
-								"-outputPath", workingDir.toString() + "/preparedInfo",
-								"-allowedsemrels","issupplementto;issupplementedby",
-								"-baseURL","https://dev-openaire.d4science.org/openaire/community/"
-						});
+			.main(
+				new String[] {
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath", getClass()
+						.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph")
+						.getPath(),
+					"-hive_metastore_uris", "",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
+					"-outputPath", workingDir.toString() + "/preparedInfo",
+					"-allowedsemrels", "issupplementto;issupplementedby",
+					"-baseURL", "https://dev-openaire.d4science.org/openaire/community/"
+				});
 
-
-		org.apache.spark.sql.Dataset<ResultCommunityList> resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema())
-				.json(workingDir.toString() + "/preparedInfo/publication")
-				.as(Encoders.bean(ResultCommunityList.class));
+		org.apache.spark.sql.Dataset<ResultCommunityList> resultCommunityList = spark
+			.read()
+			.schema(Encoders.bean(ResultCommunityList.class).schema())
+			.json(workingDir.toString() + "/preparedInfo/publication")
+			.as(Encoders.bean(ResultCommunityList.class));
 
 		Assertions.assertEquals(2, resultCommunityList.count());
-		Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count());
-		Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count());
+		Assertions
+			.assertEquals(
+				1,
+				resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count());
+		Assertions
+			.assertEquals(
+				1,
+				resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count());
 
 		ArrayList<String> communities = resultCommunityList
-				.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'")
-				.first().getCommunityList();
+			.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'")
+			.first()
+			.getCommunityList();
 		Assertions.assertEquals(2, communities.size());
 		Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid)));
 		Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid)));
 
 		communities = resultCommunityList
-				.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'")
-				.first().getCommunityList();
+			.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'")
+			.first()
+			.getCommunityList();
 		Assertions.assertEquals(1, communities.size());
 		Assertions.assertEquals("dh-ch", communities.get(0));
 	}
 
-
 }

From 0d050061146fc8fb7dfb1f619601719b3892da82 Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@isti.cnr.it>
Date: Fri, 6 Dec 2024 14:23:47 +0100
Subject: [PATCH 239/239] code formatted

---
 .../java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java
index 8172456bb..1adad104e 100644
--- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java
+++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/ORCIDExtractor.java
@@ -160,7 +160,7 @@ public class ORCIDExtractor extends Thread {
 			}
 		} finally {
 			for (SequenceFile.Writer k : fileMap.values()) {
-				log.info("Thread {}: Completed processed {} items", id, extractedItem);
+					log.info("Thread {}: Completed processed {} items", id, extractedItem);
 				k.hflush();
 				k.close();
 			}