Merge branch 'beta' into hive

dhp-workflows/dhp-monitor-update/pom.xml

@@ -0,0 +1,32 @@
+<?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/xsd/maven-4.0.0.xsd">
+    <parent>
+        <artifactId>dhp-workflows</artifactId>
+        <groupId>eu.dnetlib.dhp</groupId>
+        <version>1.2.4-SNAPSHOT</version>
+    </parent>
+    <modelVersion>4.0.0</modelVersion>
+    <artifactId>dhp-monitor-update</artifactId>
+    <dependencies>
+        <dependency>
+            <groupId>org.apache.spark</groupId>
+            <artifactId>spark-core_2.11</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.spark</groupId>
+            <artifactId>spark-sql_2.11</artifactId>
+        </dependency>
+    </dependencies>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>pl.project13.maven</groupId>
+				<artifactId>git-commit-id-plugin</artifactId>
+                <version>2.1.11</version>
+				<configuration>
+					<failOnNoGitDirectory>false</failOnNoGitDirectory>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
+</project>

dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql

@@ -1,5 +1,6 @@
 DROP TABLE IF EXISTS TARGET.result_new;
 
+<<<<<<< HEAD
 create table TARGET.result_new stored as parquet as
     select distinct * from (
         select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
@@ -76,18 +77,103 @@ ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS;
 
 INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
 ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS;
+=======
+create table TARGET.result_new as
+    select distinct * from (
+        select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
+--              'openorgs____::b8b8ca674452579f3f593d9f5e557483',  -- University College Cork
+--             'openorgs____::38d7097854736583dde879d12dacafca'	-- Brown University
+                'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech
+        ) )) foo;
+
+COMPUTE STATS TARGET.result_new;
+
+INSERT INTO TARGET.result select * from TARGET.result_new;
+COMPUTE STATS TARGET.result;
+
+INSERT INTO TARGET.result_citations select * from TARGET.result_citations orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_citations;
+
+INSERT INTO TARGET.result_references_oc select * from TARGET.result_references_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_references_oc;
+
+INSERT INTO TARGET.result_citations_oc select * from TARGET.result_citations_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_citations_oc;
+
+INSERT INTO TARGET.result_classifications select * from TARGET.result_classifications orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_classifications;
+
+INSERT INTO TARGET.result_apc select * from TARGET.result_apc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_apc;
+
+INSERT INTO TARGET.result_concepts select * from TARGET.result_concepts orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_concepts;
+
+INSERT INTO TARGET.result_datasources select * from TARGET.result_datasources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_datasources;
+
+INSERT INTO TARGET.result_fundercount select * from TARGET.result_fundercount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_fundercount;
+
+INSERT INTO TARGET.result_gold select * from TARGET.result_gold orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_gold;
+
+INSERT INTO TARGET.result_greenoa select * from TARGET.result_greenoa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_greenoa;
+
+INSERT INTO TARGET.result_languages select * from TARGET.result_languages orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_languages;
+
+INSERT INTO TARGET.result_licenses select * from TARGET.result_licenses orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_licenses;
+
+INSERT INTO TARGET.result_oids select * from TARGET.result_oids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_oids;
+
+INSERT INTO TARGET.result_organization select * from TARGET.result_organization orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_organization;
+
+INSERT INTO TARGET.result_peerreviewed select * from TARGET.result_peerreviewed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_peerreviewed;
+
+INSERT INTO TARGET.result_pids select * from TARGET.result_pids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_pids;
+
+INSERT INTO TARGET.result_projectcount select * from TARGET.result_projectcount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_projectcount;
+
+INSERT INTO TARGET.result_projects select * from TARGET.result_projects orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_projects;
+
+INSERT INTO TARGET.result_refereed select * from TARGET.result_refereed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_refereed;
+
+INSERT INTO TARGET.result_sources select * from TARGET.result_sources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_sources;
+
+INSERT INTO TARGET.result_topics select * from TARGET.result_topics orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_topics;
+
+INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.result_fos;
+>>>>>>> beta
 
 create view TARGET.foo1 as select * from TARGET.result_result rr where rr.source in (select id from TARGET.result_new);
 create view TARGET.foo2 as select * from TARGET.result_result rr where rr.target in (select id from TARGET.result_new);
 INSERT INTO TARGET.result_result select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou;
 drop view TARGET.foo1;
 drop view TARGET.foo2;
+<<<<<<< HEAD
 ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS;
 
+=======
+COMPUTE STATS TARGET.result_result;
+>>>>>>> beta
 
 -- indicators
 -- Sprint 1 ----
 INSERT INTO TARGET.indi_pub_green_oa select * from TARGET.indi_pub_green_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+<<<<<<< HEAD
 ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS;
 INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
 ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS;
@@ -138,6 +224,58 @@ INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subsc
 ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS;
 INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
 ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS;
+=======
+COMPUTE STATS TARGET.indi_pub_green_oa;
+INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_grey_lit;
+INSERT INTO TARGET.indi_pub_doi_from_crossref select * from TARGET.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_doi_from_crossref;
+-- Sprint 2 ----
+INSERT INTO TARGET.indi_result_has_cc_licence select * from TARGET.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_result_has_cc_licence;
+INSERT INTO TARGET.indi_result_has_cc_licence_url select * from TARGET.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_result_has_cc_licence_url;
+INSERT INTO TARGET.indi_pub_has_abstract select * from TARGET.indi_pub_has_abstract orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_has_abstract;
+INSERT INTO TARGET.indi_result_with_orcid select * from TARGET.indi_result_with_orcid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_result_with_orcid;
+---- Sprint 3 ----
+INSERT INTO TARGET.indi_funded_result_with_fundref select * from TARGET.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_funded_result_with_fundref;
+---- Sprint 4 ----
+INSERT INTO TARGET.indi_pub_diamond select * from TARGET.indi_pub_diamond orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_diamond;
+INSERT INTO TARGET.indi_pub_in_transformative select * from TARGET.indi_pub_in_transformative orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_in_transformative;
+INSERT INTO TARGET.indi_pub_closed_other_open select * from TARGET.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_closed_other_open;
+---- Sprint 5 ----
+INSERT INTO TARGET.indi_result_no_of_copies select * from TARGET.indi_result_no_of_copies orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_result_no_of_copies;
+---- Sprint 6 ----
+INSERT INTO TARGET.indi_pub_hybrid_oa_with_cc select * from TARGET.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_hybrid_oa_with_cc;
+INSERT INTO TARGET.indi_pub_downloads select * from TARGET.indi_pub_downloads orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
+COMPUTE STATS TARGET.indi_pub_downloads;
+INSERT INTO TARGET.indi_pub_downloads_datasource select * from TARGET.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
+COMPUTE STATS TARGET.indi_pub_downloads_datasource;
+INSERT INTO TARGET.indi_pub_downloads_year select * from TARGET.indi_pub_downloads_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
+COMPUTE STATS TARGET.indi_pub_downloads_year;
+INSERT INTO TARGET.indi_pub_downloads_datasource_year select * from TARGET.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
+COMPUTE STATS TARGET.indi_pub_downloads_datasource_year;
+---- Sprint 7 ----
+INSERT INTO TARGET.indi_pub_gold_oa select * from TARGET.indi_pub_gold_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_gold_oa;
+INSERT INTO TARGET.indi_pub_hybrid select * from TARGET.indi_pub_hybrid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_hybrid;
+
+INSERT INTO TARGET.indi_pub_has_preprint select * from TARGET.indi_pub_has_preprint orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_has_preprint;
+INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_pub_in_subscribed;
+INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
+COMPUTE STATS TARGET.indi_result_with_pid;
+>>>>>>> beta
 --create table TARGET.indi_datasets_gold_oa stored as parquet as select * from SOURCE.indi_datasets_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
 --compute stats TARGET.indi_datasets_gold_oa;
 --create table TARGET.indi_software_gold_oa stored as parquet as select * from SOURCE.indi_software_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql

@@ -29,12 +29,12 @@ select rcount.pid, sum(case when rcount.type='publication' then rcount.count els
 from rcount
 group by rcount.pid;
 
-create view ${stats_db_name}.rndexpenditure as select * from ${external_stats_db_name}.rndexpediture;
+create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture;
-create view ${stats_db_name}.rndgdpexpenditure as select * from ${external_stats_db_name}.rndgdpexpenditure;
+create view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure;
-create view ${stats_db_name}.doctoratestudents as select * from ${external_stats_db_name}.doctoratestudents;
+create view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents;
-create view ${stats_db_name}.totalresearchers as select * from ${external_stats_db_name}.totalresearchers;
+create view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers;
-create view ${stats_db_name}.totalresearchersft as select * from ${external_stats_db_name}.totalresearchersft;
+create view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft;
-create view ${stats_db_name}.hrrst as select * from ${external_stats_db_name}.hrrst;
+create view ${stats_db_name}.hrrst as select * from stats_ext.hrrst;
 
 create table ${stats_db_name}.result_instance stored as parquet as
 select distinct r.*

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml

@@ -102,7 +102,6 @@
             <case to="Step16_5">${wf:conf('resumeFrom') eq 'Step16_5'}</case>
             <case to="Step19-finalize">${wf:conf('resumeFrom') eq 'Step19-finalize'}</case>
             <case to="step20-createMonitorDB">${wf:conf('resumeFrom') eq 'step20-createMonitorDB'}</case>
-            <case to="step20-createMonitorDB-post">${wf:conf('resumeFrom') eq 'step20-createMonitorDB-post'}</case>
             <case to="step21-createObservatoryDB-pre">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-pre'}</case>
             <case to="step21-createObservatoryDB">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'}</case>
             <case to="step21-createObservatoryDB-post">${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-post'}</case>