From 2a52a42169ecdede8024fc9fcbadb1008e49f912 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Tue, 6 Dec 2022 10:10:21 +0200 Subject: [PATCH 01/14] Added 4 institutions: -University of Modena and Reggio Emilia -Bilkent University -Saints Cyril and Methodius University of Skopje -University of Milan --- .../stats/oozie_app/scripts/step20-createMonitorDB.sql | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) 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 2bdcbfa3d2..98dca7129b 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 @@ -50,7 +50,11 @@ create table TARGET.result stored as parquet as 'openorgs____::1698a2eb1885ef8adb5a4a969e745ad3', -- École des Ponts ParisTech 'openorgs____::e15adb13c4dadd49de4d35c39b5da93a', -- Nanyang Technological University 'openorgs____::4b34103bde246228fcd837f5f1bf4212', -- Autonomous University of Barcelona - 'openorgs____::72ec75fcfc4e0df1a76dc4c49007fceb' -- McMaster University + '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 ) )) foo; compute stats TARGET.result; From 6449ff42073979226d1c02c08ee608173657bbef Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 22 Dec 2022 10:18:21 +0200 Subject: [PATCH 02/14] 1. Added a decision node to enables the workflow to make a selection on the execution path to follow 2. Added new organization 3. Added 5 new tables from Eurostast --- .../oa/graph/stats/oozie_app/scripts/step15_5.sql | 5 +++++ .../oozie_app/scripts/step20-createMonitorDB.sql | 8 +++++++- .../dhp/oa/graph/stats/oozie_app/workflow.xml | 13 ++++++++++++- 3 files changed, 24 insertions(+), 2 deletions(-) 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 86ead4a2c6..584de0a56c 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 @@ -30,6 +30,11 @@ from rcount group by rcount.pid; create view ${stats_db_name}.rndexpenditure as select * from stats_ext.rndexpediture; +create view ${stats_db_name}.rndgdpexpenditure as select * from stats_ext.rndgdpexpenditure; +create view ${stats_db_name}.doctoratestudents as select * from stats_ext.doctoratestudents; +create view ${stats_db_name}.totalresearchers as select * from stats_ext.totalresearchers; +create view ${stats_db_name}.totalresearchersft as select * from stats_ext.totalresearchersft; +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.* 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 98dca7129b..3e69ff58dc 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 @@ -10,6 +10,11 @@ create view if not exists TARGET.creation_date as select * from SOURCE.creation_ 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 ( @@ -54,7 +59,8 @@ create table TARGET.result stored as parquet as '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____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan + 'openorgs____::b8b8ca674452579f3f593d9f5e557483' -- University College Cork ) )) foo; compute stats TARGET.result; 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 08d33f4e8f..17dcd1fdd7 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 @@ -70,7 +70,18 @@ - + + + + + ${wf:conf('resumeFrom') eq 'Step1'} + ${wf:conf('resumeFrom') eq 'step20-createMonitorDB'} + ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-pre'} + ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'} + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] From 592013d5ddf1bac85dee76bb84931b4a31ad36b0 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Fri, 23 Dec 2022 09:43:16 +0200 Subject: [PATCH 03/14] Added more steps in decision node --- .../dhp/oa/graph/stats/oozie_app/workflow.xml | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) 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 17dcd1fdd7..c68ae46cac 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 @@ -75,9 +75,31 @@ ${wf:conf('resumeFrom') eq 'Step1'} + ${wf:conf('resumeFrom') eq 'Step2'} + ${wf:conf('resumeFrom') eq 'Step3'} + ${wf:conf('resumeFrom') eq 'Step4'} + ${wf:conf('resumeFrom') eq 'Step5'} + ${wf:conf('resumeFrom') eq 'Step6'} + ${wf:conf('resumeFrom') eq 'Step7'} + ${wf:conf('resumeFrom') eq 'Step8'} + ${wf:conf('resumeFrom') eq 'Step9'} + ${wf:conf('resumeFrom') eq 'Step10'} + ${wf:conf('resumeFrom') eq 'Step11'} + ${wf:conf('resumeFrom') eq 'Step12'} + ${wf:conf('resumeFrom') eq 'Step13'} + ${wf:conf('resumeFrom') eq 'Step14'} + ${wf:conf('resumeFrom') eq 'Step15'} + ${wf:conf('resumeFrom') eq 'Step15_5'} + ${wf:conf('resumeFrom') eq 'Contexts'} + ${wf:conf('resumeFrom') eq 'Step16-createIndicatorsTables'} + ${wf:conf('resumeFrom') eq 'Step16_1-definitions'} + ${wf:conf('resumeFrom') eq 'Step16_5'} + ${wf:conf('resumeFrom') eq 'Step19-finalize'} ${wf:conf('resumeFrom') eq 'step20-createMonitorDB'} ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-pre'} ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB'} + ${wf:conf('resumeFrom') eq 'step21-createObservatoryDB-post'} + ${wf:conf('resumeFrom') eq 'Step22'} From becb242c1797b3ba40e5e92b4dd263248d59b14d Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 4 Jan 2023 16:50:29 +0200 Subject: [PATCH 04/14] Monitor DB only Workflow --- dhp-workflows/dhp-monitor-update/pom.xml | 32 +++ .../monitor/oozie_app/config-default.xml | 34 +++ .../graph/monitor/oozie_app/monitor-post.sh | 21 ++ .../dhp/oa/graph/monitor/oozie_app/monitor.sh | 24 ++ .../oozie_app/scripts/createMonitorDB.sql | 241 ++++++++++++++++++ .../oa/graph/monitor/oozie_app/updateCache.sh | 4 + .../oa/graph/monitor/oozie_app/workflow.xml | 105 ++++++++ 7 files changed, 461 insertions(+) create mode 100644 dhp-workflows/dhp-monitor-update/pom.xml create mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh create mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh create mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql create mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh create mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml diff --git a/dhp-workflows/dhp-monitor-update/pom.xml b/dhp-workflows/dhp-monitor-update/pom.xml new file mode 100644 index 0000000000..ca0bb9837d --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/pom.xml @@ -0,0 +1,32 @@ + + + + dhp-workflows + eu.dnetlib.dhp + 1.2.4-SNAPSHOT + + 4.0.0 + dhp-monitor-update + + + org.apache.spark + spark-core_2.11 + + + org.apache.spark + spark-sql_2.11 + + + + + + pl.project13.maven + git-commit-id-plugin + 2.1.11 + + false + + + + + diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml new file mode 100644 index 0000000000..63fc84d75e --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml @@ -0,0 +1,34 @@ + + + jobTracker + ${jobTracker} + + + nameNode + ${nameNode} + + + oozie.use.system.libpath + true + + + oozie.action.sharelib.for.spark + spark2 + + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hive_jdbc_url + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000/;UseNativeQuery=1;?spark.executor.memory=19166291558;spark.yarn.executor.memoryOverhead=3225;spark.driver.memory=11596411699;spark.yarn.driver.memoryOverhead=1228 + + + oozie.wf.workflow.notification.url + {serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status + + + stats_tool_api_url + ${stats_tool_api_url} + + \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh new file mode 100644 index 0000000000..b8c71681a5 --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh @@ -0,0 +1,21 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +export SOURCE=$1 +export TARGET=$2 +export SHADOW=$3 + +impala-shell -q "invalidate metadata;" +impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -f - +echo "Impala shell finished" + +echo "Updating shadow monitor database" +impala-shell -q "create database if not exists ${SHADOW}" +impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - +impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f - +echo "Shadow db ready!" \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh new file mode 100644 index 0000000000..f39bf4893d --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh @@ -0,0 +1,24 @@ +export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs +export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) +if ! [ -L $link_folder ] +then + rm -Rf "$link_folder" + ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} +fi + +export SOURCE=$1 +export TARGET=$2 +export SHADOW=$3 +export SCRIPT_PATH=$4 + +export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228" +export HADOOP_USER_NAME="oozie" + +echo "Getting file from " $SCRIPT_PATH +hdfs dfs -copyToLocal $SCRIPT_PATH + +echo "Creating monitor database" +#cat step20-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 > foo +cat createMonitorDB.sql | sed "s/TARGET/${TARGET}/g" | sed "s/SOURCE/${SOURCE}/g" > foo +hive $HIVE_OPTS -f foo +echo "Hive shell finished" \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql new file mode 100644 index 0000000000..e9e460cb03 --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql @@ -0,0 +1,241 @@ +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 + ) )) foo; + +ANALYZE TABLE TARGET.result COMPUTE STATISTICS; + +create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS; + +create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS; + +create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS; + +create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS; + +create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS; + +create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS; + +create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS; + +create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS; + +create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS; + +create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS; + +create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS; + +create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS; + +create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized; +ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS; + +create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS; + +create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS; + +create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS; + +create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS; + +create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS; + +create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS; + +create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS; + +create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS; + +create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS; + +create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.result_fos COMPUTE STATISTICS; + +create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); +create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); +create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; +drop view TARGET.foo1; +drop view TARGET.foo2; +ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS; + +-- datasources +create view if not exists TARGET.datasource as select * from SOURCE.datasource; +create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids; +create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations; +create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources; + +create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources; +ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS; + +-- organizations +create view if not exists TARGET.organization as select * from SOURCE.organization; +create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources; +create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids; +create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects; +create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources; + +-- projects +create view if not exists TARGET.project as select * from SOURCE.project; +create view if not exists TARGET.project_oids as select * from SOURCE.project_oids; +create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; +create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; +create view if not exists TARGET.project_classification as select * from SOURCE.project_classification; + +create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; +ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS; + +-- indicators +-- Sprint 1 ---- +create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS; +create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS; +create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS; +-- Sprint 2 ---- +create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS; +create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS; +create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS; +create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS; +---- Sprint 3 ---- +create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS; +create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab; +create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab; +create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; +create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; +create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; +create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab; +---- Sprint 4 ---- +create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS; +create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS; +create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS; +---- Sprint 5 ---- +create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS; +---- Sprint 6 ---- +create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS; +create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); +ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS; +create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); +ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS; +create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); +ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS; +create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); +ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS; +---- Sprint 7 ---- +create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS; +create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS; +create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness; +create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; +create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; +create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub; +create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year; +create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year; +create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; +create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; +create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year; +create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS; +create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS; +create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id); +ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS; +--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); +--compute stats TARGET.indi_software_gold_oa; + diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh new file mode 100644 index 0000000000..03aa535e10 --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh @@ -0,0 +1,4 @@ +#!/usr/bin/env bash + +curl --request GET $1/cache/updateCache +sleep 6h \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml new file mode 100644 index 0000000000..2bcff70aca --- /dev/null +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml @@ -0,0 +1,105 @@ + + + + stats_db_name + the target stats database name + + + stats_db_shadow_name + the name of the shadow schema + + + monitor_db_name + the target monitor db name + + + monitor_db_shadow_name + the name of the shadow monitor db + + + stats_tool_api_url + The url of the API of the stats tool. Is used to trigger the cache update. + + + hive_metastore_uris + hive server metastore URIs + + + hive_jdbc_url + hive server jdbc url + + + hive_timeout + the time period, in seconds, after which Hive fails a transaction if a Hive client has not sent a hearbeat. The default value is 300 seconds. + + + context_api_url + the base url of the context api (https://services.openaire.eu/openaire) + + + + + ${jobTracker} + ${nameNode} + + + hive.metastore.uris + ${hive_metastore_uris} + + + hive.txn.timeout + ${hive_timeout} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${jobTracker} + ${nameNode} + monitor.sh + ${stats_db_name} + ${monitor_db_name} + ${monitor_db_shadow_name} + ${wf:appPath()}/scripts/createMonitorDB.sql + monitor.sh + + + + + + + + + ${jobTracker} + ${nameNode} + monitor-post.sh + ${stats_db_name} + ${monitor_db_name} + ${monitor_db_shadow_name} + monitor-post.sh + + + + + + + + ${jobTracker} + ${nameNode} + updateCache.sh + ${stats_tool_api_url} + updateCache.sh + + + + + + + \ No newline at end of file From 686580a22068b6437ff4e8dafccbf919d06e2a77 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 12 Jan 2023 11:18:03 +0200 Subject: [PATCH 05/14] - New Monitor DB workflow - New Organization added --- .../graph/monitor/oozie_app/monitor-post.sh | 21 -- .../dhp/oa/graph/monitor/oozie_app/monitor.sh | 16 +- .../oozie_app/scripts/createMonitorDB.sql | 293 ++++++------------ .../oa/graph/monitor/oozie_app/updateCache.sh | 4 - .../oa/graph/monitor/oozie_app/workflow.xml | 28 -- .../scripts/step20-createMonitorDB.sql | 3 +- 6 files changed, 107 insertions(+), 258 deletions(-) delete mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh delete mode 100644 dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh deleted file mode 100644 index b8c71681a5..0000000000 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh +++ /dev/null @@ -1,21 +0,0 @@ -export PYTHON_EGG_CACHE=/home/$(whoami)/.python-eggs -export link_folder=/tmp/impala-shell-python-egg-cache-$(whoami) -if ! [ -L $link_folder ] -then - rm -Rf "$link_folder" - ln -sfn ${PYTHON_EGG_CACHE}${link_folder} ${link_folder} -fi - -export SOURCE=$1 -export TARGET=$2 -export SHADOW=$3 - -impala-shell -q "invalidate metadata;" -impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -f - -echo "Impala shell finished" - -echo "Updating shadow monitor database" -impala-shell -q "create database if not exists ${SHADOW}" -impala-shell -d ${SHADOW} -q "show tables" --delimited | sed "s/^/drop view if exists ${SHADOW}./" | sed "s/$/;/" | impala-shell -f - -impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/\(.*\)/create view ${SHADOW}.\1 as select * from ${TARGET}.\1;/" | impala-shell -f - -echo "Shadow db ready!" \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh index f39bf4893d..36cfcd3256 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh @@ -8,17 +8,11 @@ fi export SOURCE=$1 export TARGET=$2 -export SHADOW=$3 -export SCRIPT_PATH=$4 +export SCRIPT_PATH=$3 -export HIVE_OPTS="-hiveconf mapred.job.queue.name=analytics -hiveconf hive.spark.client.connect.timeout=120000ms -hiveconf hive.spark.client.server.connect.timeout=300000ms -hiveconf spark.executor.memory=19166291558 -hiveconf spark.yarn.executor.memoryOverhead=3225 -hiveconf spark.driver.memory=11596411699 -hiveconf spark.yarn.driver.memoryOverhead=1228" -export HADOOP_USER_NAME="oozie" - -echo "Getting file from " $SCRIPT_PATH -hdfs dfs -copyToLocal $SCRIPT_PATH +echo "Getting file from " $3 +hdfs dfs -copyToLocal $3 echo "Creating monitor database" -#cat step20-createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 > foo -cat createMonitorDB.sql | sed "s/TARGET/${TARGET}/g" | sed "s/SOURCE/${SOURCE}/g" > foo -hive $HIVE_OPTS -f foo -echo "Hive shell finished" \ No newline at end of file +cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f - +echo "Impala shell finished" diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql index e9e460cb03..2c46082fa1 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql @@ -1,241 +1,148 @@ -drop database if exists TARGET cascade; -create database if not exists TARGET; +DROP TABLE IF EXISTS TARGET.result_new; -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 +create table TARGET.result_new 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____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork + 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University ) )) foo; -ANALYZE TABLE TARGET.result COMPUTE STATISTICS; +COMPUTE STATS TARGET.result_new; -create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_citations COMPUTE STATISTICS; +INSERT INTO TARGET.result select * from TARGET.result_new; -create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_references_oc COMPUTE STATISTICS; +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; -create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_citations_oc COMPUTE STATISTICS; +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; -create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_classifications COMPUTE STATISTICS; +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; -create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_apc COMPUTE STATISTICS; +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; -create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_concepts COMPUTE STATISTICS; +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; -create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_datasources COMPUTE STATISTICS; +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; -create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_fundercount COMPUTE STATISTICS; +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; -create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_gold COMPUTE STATISTICS; +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; -create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_greenoa COMPUTE STATISTICS; +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; -create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_languages COMPUTE STATISTICS; +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; -create table TARGET.result_licenses stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_licenses COMPUTE STATISTICS; +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; -create table TARGET.licenses_normalized STORED AS PARQUET as select * from SOURCE.licenses_normalized; -ANALYZE TABLE TARGET.licenses_normalized COMPUTE STATISTICS; +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; -create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_oids COMPUTE STATISTICS; +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; -create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_organization COMPUTE STATISTICS; +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; -create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_peerreviewed COMPUTE STATISTICS; +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; -create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_pids COMPUTE STATISTICS; +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; -create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_projectcount COMPUTE STATISTICS; +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; -create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_projects COMPUTE STATISTICS; +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; -create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_refereed COMPUTE STATISTICS; +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; -create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_sources COMPUTE STATISTICS; +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; -create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_topics COMPUTE STATISTICS; +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; -create table TARGET.result_fos stored as parquet as select * from SOURCE.result_fos orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.result_fos 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); +COMPUTE STATS TARGET.result_fos; -create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); -create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); -create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; +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; -ANALYZE TABLE TARGET.result_result COMPUTE STATISTICS; - --- datasources -create view if not exists TARGET.datasource as select * from SOURCE.datasource; -create view if not exists TARGET.datasource_oids as select * from SOURCE.datasource_oids; -create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations; -create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources; - -create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources; -ANALYZE TABLE TARGET.datasource_results COMPUTE STATISTICS; - --- organizations -create view if not exists TARGET.organization as select * from SOURCE.organization; -create view if not exists TARGET.organization_datasources as select * from SOURCE.organization_datasources; -create view if not exists TARGET.organization_pids as select * from SOURCE.organization_pids; -create view if not exists TARGET.organization_projects as select * from SOURCE.organization_projects; -create view if not exists TARGET.organization_sources as select * from SOURCE.organization_sources; - --- projects -create view if not exists TARGET.project as select * from SOURCE.project; -create view if not exists TARGET.project_oids as select * from SOURCE.project_oids; -create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; -create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; -create view if not exists TARGET.project_classification as select * from SOURCE.project_classification; - -create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; -ANALYZE TABLE TARGET.project_results COMPUTE STATISTICS; +COMPUTE STATS TARGET.result_result; -- indicators -- Sprint 1 ---- -create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_green_oa COMPUTE STATISTICS; -create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_grey_lit COMPUTE STATISTICS; -create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_doi_from_crossref COMPUTE STATISTICS; +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); +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 ---- -create table TARGET.indi_result_has_cc_licence stored as parquet as select * from SOURCE.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_result_has_cc_licence COMPUTE STATISTICS; -create table TARGET.indi_result_has_cc_licence_url stored as parquet as select * from SOURCE.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_result_has_cc_licence_url COMPUTE STATISTICS; -create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_has_abstract COMPUTE STATISTICS; -create table TARGET.indi_result_with_orcid stored as parquet as select * from SOURCE.indi_result_with_orcid orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_result_with_orcid COMPUTE STATISTICS; +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 ---- -create table TARGET.indi_funded_result_with_fundref stored as parquet as select * from SOURCE.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_funded_result_with_fundref COMPUTE STATISTICS; -create view TARGET.indi_result_org_collab as select * from SOURCE.indi_result_org_collab; -create view TARGET.indi_result_org_country_collab as select * from SOURCE.indi_result_org_country_collab; -create view TARGET.indi_project_collab_org as select * from SOURCE.indi_project_collab_org; -create view TARGET.indi_project_collab_org_country as select * from SOURCE.indi_project_collab_org_country; -create view TARGET.indi_funder_country_collab as select * from SOURCE.indi_funder_country_collab; -create view TARGET.indi_result_country_collab as select * from SOURCE.indi_result_country_collab; +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 ---- -create table TARGET.indi_pub_diamond stored as parquet as select * from SOURCE.indi_pub_diamond orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_diamond COMPUTE STATISTICS; -create table TARGET.indi_pub_in_transformative stored as parquet as select * from SOURCE.indi_pub_in_transformative orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_in_transformative COMPUTE STATISTICS; -create table TARGET.indi_pub_closed_other_open stored as parquet as select * from SOURCE.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_closed_other_open COMPUTE STATISTICS; +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 ---- -create table TARGET.indi_result_no_of_copies stored as parquet as select * from SOURCE.indi_result_no_of_copies orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_result_no_of_copies COMPUTE STATISTICS; +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 ---- -create table TARGET.indi_pub_hybrid_oa_with_cc stored as parquet as select * from SOURCE.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_hybrid_oa_with_cc COMPUTE STATISTICS; -create table TARGET.indi_pub_downloads stored as parquet as select * from SOURCE.indi_pub_downloads orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); -ANALYZE TABLE TARGET.indi_pub_downloads COMPUTE STATISTICS; -create table TARGET.indi_pub_downloads_datasource stored as parquet as select * from SOURCE.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); -ANALYZE TABLE TARGET.indi_pub_downloads_datasource COMPUTE STATISTICS; -create table TARGET.indi_pub_downloads_year stored as parquet as select * from SOURCE.indi_pub_downloads_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); -ANALYZE TABLE TARGET.indi_pub_downloads_year COMPUTE STATISTICS; -create table TARGET.indi_pub_downloads_datasource_year stored as parquet as select * from SOURCE.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result r where r.id=orig.result_id); -ANALYZE TABLE TARGET.indi_pub_downloads_datasource_year COMPUTE STATISTICS; +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 ---- -create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_gold_oa COMPUTE STATISTICS; -create table TARGET.indi_pub_hybrid stored as parquet as select * from SOURCE.indi_pub_hybrid orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_hybrid COMPUTE STATISTICS; -create view TARGET.indi_org_fairness as select * from SOURCE.indi_org_fairness; -create view TARGET.indi_org_fairness_pub_pr as select * from SOURCE.indi_org_fairness_pub_pr; -create view TARGET.indi_org_fairness_pub_year as select * from SOURCE.indi_org_fairness_pub_year; -create view TARGET.indi_org_fairness_pub as select * from SOURCE.indi_org_fairness_pub; -create view TARGET.indi_org_fairness_year as select * from SOURCE.indi_org_fairness_year; -create view TARGET.indi_org_findable_year as select * from SOURCE.indi_org_findable_year; -create view TARGET.indi_org_findable as select * from SOURCE.indi_org_findable; -create view TARGET.indi_org_openess as select * from SOURCE.indi_org_openess; -create view TARGET.indi_org_openess_year as select * from SOURCE.indi_org_openess_year; -create table TARGET.indi_pub_has_preprint stored as parquet as select * from SOURCE.indi_pub_has_preprint orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_has_preprint COMPUTE STATISTICS; -create table TARGET.indi_pub_in_subscribed stored as parquet as select * from SOURCE.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_pub_in_subscribed COMPUTE STATISTICS; -create table TARGET.indi_result_with_pid stored as parquet as select * from SOURCE.indi_result_with_pid orig where exists (select 1 from TARGET.result r where r.id=orig.id); -ANALYZE TABLE TARGET.indi_result_with_pid COMPUTE STATISTICS; +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; --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); --compute stats TARGET.indi_software_gold_oa; - +DROP TABLE TARGET.result_new; diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh deleted file mode 100644 index 03aa535e10..0000000000 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/usr/bin/env bash - -curl --request GET $1/cache/updateCache -sleep 6h \ No newline at end of file diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml index 2bcff70aca..dda645d8f4 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml @@ -66,37 +66,9 @@ monitor.sh ${stats_db_name} ${monitor_db_name} - ${monitor_db_shadow_name} ${wf:appPath()}/scripts/createMonitorDB.sql monitor.sh - - - - - - - - ${jobTracker} - ${nameNode} - monitor-post.sh - ${stats_db_name} - ${monitor_db_name} - ${monitor_db_shadow_name} - monitor-post.sh - - - - - - - - ${jobTracker} - ${nameNode} - updateCache.sh - ${stats_tool_api_url} - updateCache.sh - 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 3e69ff58dc..885f7e4f7d 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 @@ -60,7 +60,8 @@ create table TARGET.result stored as parquet as 'openorgs____::235d7f9ad18ecd7e6dc62ea4990cb9db', -- Bilkent University 'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan - 'openorgs____::b8b8ca674452579f3f593d9f5e557483' -- University College Cork + 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork + 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University ) )) foo; compute stats TARGET.result; From 51f7ab5864ca80023b1cc7d350e4dda38dd1cd99 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 12 Jan 2023 17:15:06 +0200 Subject: [PATCH 06/14] Bug fixes --- .../oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql index 2c46082fa1..7e1333f920 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql @@ -2,11 +2,7 @@ DROP TABLE IF EXISTS TARGET.result_new; create table TARGET.result_new 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 ( + select * from result r where exists (select 1 from result_organization ro where ro.id=r.id and ro.organization in ( -- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University ) )) foo; From dd70c32ad7ab3fccc38dd6c42c04b6ca2c6d15b1 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 12 Jan 2023 17:18:05 +0200 Subject: [PATCH 07/14] Bug fixes --- .../dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql index 7e1333f920..2eb95294a8 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql @@ -2,7 +2,7 @@ DROP TABLE IF EXISTS TARGET.result_new; create table TARGET.result_new stored as parquet as select distinct * from ( - select * from result r where exists (select 1 from result_organization ro where ro.id=r.id and ro.organization in ( + 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 ) )) foo; From db7d625ba9b436060e8be56452215945d80efca6 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Wed, 25 Jan 2023 12:22:21 +0200 Subject: [PATCH 08/14] =?UTF-8?q?Addedd=20Arts=20et=20M=C3=A9tiers=20Paris?= =?UTF-8?q?Tech=20organization?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh | 2 +- .../oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql | 6 ++++-- .../stats/oozie_app/scripts/step20-createMonitorDB.sql | 3 ++- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh index 36cfcd3256..10c1ed4cad 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh @@ -13,6 +13,6 @@ export SCRIPT_PATH=$3 echo "Getting file from " $3 hdfs dfs -copyToLocal $3 -echo "Creating monitor database" +echo "Updating monitor database" cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f - echo "Impala shell finished" diff --git a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql index 2eb95294a8..265610e900 100644 --- a/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql +++ b/dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql @@ -1,15 +1,17 @@ DROP TABLE IF EXISTS TARGET.result_new; -create table TARGET.result_new stored as parquet as +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____::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; 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 885f7e4f7d..c6b7d8ae21 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 @@ -61,7 +61,8 @@ create table TARGET.result stored as parquet as 'openorgs____::31f2fa9e05b49d4cf40a19c3fed8eb06', -- Saints Cyril and Methodius University of Skopje 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork - 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University + 'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University + 'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech ) )) foo; compute stats TARGET.result; From 973d78a4d64718dbeb16ca4857f99419bdfade18 Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Thu, 2 Feb 2023 08:03:54 +0200 Subject: [PATCH 09/14] Update step15_5.sql Added unpaywalls open access colors --- .../dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step15_5.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 584de0a56c..753d61ca0a 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 @@ -39,7 +39,7 @@ 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.* from ( - select substr(r.id, 4) as id, inst.accessright.classname as accessright, substr(inst.collectedfrom.key, 4) as collectedfrom, + 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 explode(inst.pid) pids as p) r join ${stats_db_name}.result res on res.id=r.id; From 98c34263ed54655ca028753552a496392198795d Mon Sep 17 00:00:00 2001 From: dimitrispie Date: Tue, 7 Feb 2023 08:14:48 +0200 Subject: [PATCH 10/14] Update step20-createMonitorDB.sql Add University of Cape Town organization --- .../graph/stats/oozie_app/scripts/step20-createMonitorDB.sql | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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 c6b7d8ae21..237f68fae1 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 @@ -62,8 +62,9 @@ create table TARGET.result stored as parquet as 'openorgs____::db7686f30f22cbe73a4fde872ce812a6', -- University of Milan 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork 'openorgs____::38d7097854736583dde879d12dacafca', -- Brown University - 'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech - ) )) foo; + 'openorgs____::57784c9e047e826fefdb1ef816120d92', --Arts et Métiers ParisTech + 'openorgs____::2530baca8a15936ba2e3297f2bce2e7e' -- University of Cape Town + ))) foo; compute stats TARGET.result; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); From 554df257abfdf5a979bb733f8e25c3231c5ddf01 Mon Sep 17 00:00:00 2001 From: "michele.artini" Date: Mon, 13 Feb 2023 16:05:58 +0100 Subject: [PATCH 11/14] null values in date range conditions --- .../dhp/broker/oa/util/SubscriptionUtils.java | 18 +++++++++++++++--- .../broker/oa/util/SubscriptionUtilsTest.java | 12 ++++++++++++ 2 files changed, 27 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java index cf35621934..4792a7719e 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtils.java @@ -37,12 +37,24 @@ public class SubscriptionUtils { } public static boolean verifyDateRange(final long date, final String min, final String max) { + + long from = 0; + long to = Long.MAX_VALUE; + try { - return date >= DateUtils.parseDate(min, "yyyy-MM-dd").getTime() - && date < DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY; + from = min != null ? DateUtils.parseDate(min, "yyyy-MM-dd").getTime() : 0; } catch (final ParseException e) { - return false; + from = 0; } + + try { + to = max != null ? DateUtils.parseDate(max, "yyyy-MM-dd").getTime() + ONE_DAY : Long.MAX_VALUE; + } catch (final ParseException e) { + to = Long.MAX_VALUE; + } + + return date >= from && date < to; + } public static boolean verifyExact(final String s1, final String s2) { diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java index d93390e4af..63b49d3620 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java @@ -41,6 +41,18 @@ public class SubscriptionUtilsTest { assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "2011-01-01")); assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "2021-01-01")); + + assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", "NULL")); + assertTrue(SubscriptionUtils.verifyDateRange(date, "2010-01-01", null)); + assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "2011-01-01")); + assertTrue(SubscriptionUtils.verifyDateRange(date, null, "2011-01-01")); + assertTrue(SubscriptionUtils.verifyDateRange(date, "NULL", "NULL")); + assertTrue(SubscriptionUtils.verifyDateRange(date, null, null)); + + assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", null)); + assertFalse(SubscriptionUtils.verifyDateRange(date, "2020-01-01", "NULL")); + assertFalse(SubscriptionUtils.verifyDateRange(date, null, "2005-01-01")); + assertFalse(SubscriptionUtils.verifyDateRange(date, "NULL", "2005-01-01")); } @Test From 9a03f71db1ab600743ed34f05d5fe4d4f750ca26 Mon Sep 17 00:00:00 2001 From: Claudio Atzori Date: Mon, 13 Feb 2023 16:25:47 +0100 Subject: [PATCH 12/14] code formatting --- .../oaf/utils/GraphCleaningFunctions.java | 4 +- .../ebi/SparkCreateBaselineDataFrame.scala | 3 +- .../dnetlib/dhp/sx/bio/BioScholixTest.scala | 32 +++++++++------ .../crossref/CrossrefMappingTest.scala | 4 +- .../orcid/MappingORCIDToOAFTest.scala | 8 ++-- .../doiboost/uw/UnpayWallMappingTest.scala | 4 +- .../dhp/oa/graph/clean/CleanCountryTest.java | 41 +++++++++---------- .../resolution/ResolveEntitiesTest.scala | 8 ++-- .../sx/graph/scholix/ScholixGraphTest.scala | 5 ++- 9 files changed, 61 insertions(+), 48 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 b24daaa5d4..fc515b5b13 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 @@ -13,6 +13,8 @@ import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.lang3.StringUtils; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; import com.github.sisyphsu.dateparser.DateParserUtils; import com.google.common.collect.Lists; @@ -23,8 +25,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import me.xuender.unidecode.Unidecode; -import org.apache.spark.api.java.function.MapFunction; -import org.apache.spark.sql.Encoders; public class GraphCleaningFunctions extends CleaningFunctions { diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala index 87116f00a8..8ac8b00bfa 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala @@ -27,7 +27,8 @@ object SparkCreateBaselineDataFrame { def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = { val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") - val result = data.linesWithSeparators.map(l =>l.stripLineEnd) + val result = data.linesWithSeparators + .map(l => l.stripLineEnd) .filter(l => l.startsWith("") 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 24caaa5533..d1611300d2 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 +63,9 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")) .mkString - val r: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList + val r: List[Oaf] = records.linesWithSeparators + .map(l => l.stripLineEnd) + .toList .map(s => mapper.readValue(s, classOf[PMArticle])) .map(a => PubMedToOaf.convert(a, vocabularies)) assertEquals(10, r.size) @@ -173,9 +175,10 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pdb_dump")) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) - val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o)) + val result: List[Oaf] = + records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.pdbTOOaf(o)) assertTrue(result.nonEmpty) result.foreach(r => assertNotNull(r)) @@ -194,9 +197,10 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump")) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) - val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o)) + val result: List[Oaf] = + records.linesWithSeparators.map(l => l.stripLineEnd).toList.flatMap(o => BioDBToOAF.uniprotToOAF(o)) assertTrue(result.nonEmpty) result.foreach(r => assertNotNull(r)) @@ -239,9 +243,10 @@ class BioScholixTest extends AbstractVocabularyTest { val records: String = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/crossref_links")) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) - val result: List[Oaf] = records.linesWithSeparators.map(l =>l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList + val result: List[Oaf] = + records.linesWithSeparators.map(l => l.stripLineEnd).map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList assertNotNull(result) assertTrue(result.nonEmpty) @@ -276,14 +281,17 @@ class BioScholixTest extends AbstractVocabularyTest { getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved") ) .mkString - records.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) + records.linesWithSeparators.map(l => l.stripLineEnd).foreach(s => assertTrue(s.nonEmpty)) implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - val l: List[ScholixResolved] = records.linesWithSeparators.map(l =>l.stripLineEnd).map { input => - lazy val json = parse(input) - json.extract[ScholixResolved] - }.toList + val l: List[ScholixResolved] = records.linesWithSeparators + .map(l => l.stripLineEnd) + .map { input => + lazy val json = parse(input) + json.extract[ScholixResolved] + } + .toList val result: List[Oaf] = l.map(s => BioDBToOAF.scholixResolvedToOAF(s)) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index aba8cee123..12a61454dd 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -31,13 +31,13 @@ class CrossrefMappingTest { .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/funder_doi")) .mkString - for (line <- funder_doi.linesWithSeparators.map(l =>l.stripLineEnd)) { + for (line <- funder_doi.linesWithSeparators.map(l => l.stripLineEnd)) { val json = template.replace("%s", line) val resultList: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(resultList.nonEmpty) checkRelation(resultList) } - for (line <- funder_name.linesWithSeparators.map(l =>l.stripLineEnd)) { + for (line <- funder_name.linesWithSeparators.map(l => l.stripLineEnd)) { val json = template.replace("%s", line) val resultList: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(resultList.nonEmpty) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala index d7a6a94a53..8033f02fb3 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -25,9 +25,11 @@ class MappingORCIDToOAFTest { .mkString assertNotNull(json) assertFalse(json.isEmpty) - json.linesWithSeparators.map(l =>l.stripLineEnd).foreach(s => { - assertNotNull(ORCIDToOAF.extractValueFromInputString(s)) - }) + json.linesWithSeparators + .map(l => l.stripLineEnd) + .foreach(s => { + assertNotNull(ORCIDToOAF.extractValueFromInputString(s)) + }) } @Test diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala index 7fe0e9935a..30001acb55 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/uw/UnpayWallMappingTest.scala @@ -22,7 +22,7 @@ class UnpayWallMappingTest { .mkString var i: Int = 0 - for (line <- Ilist.linesWithSeparators.map(l =>l.stripLineEnd)) { + for (line <- Ilist.linesWithSeparators.map(l => l.stripLineEnd)) { val p = UnpayWallToOAF.convertToOAF(line) if (p != null) { @@ -43,7 +43,7 @@ class UnpayWallMappingTest { i = i + 1 } - val l = Ilist.linesWithSeparators.map(l =>l.stripLineEnd).next() + val l = Ilist.linesWithSeparators.map(l => l.stripLineEnd).next() val item = UnpayWallToOAF.convertToOAF(l) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java index de9e4fc903..3bc69cfd1f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanCountryTest.java @@ -5,7 +5,6 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; -import eu.dnetlib.dhp.schema.oaf.Dataset; 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.oa.graph.clean.country.CleanCountrySparkJob; +import eu.dnetlib.dhp.schema.oaf.Dataset; import eu.dnetlib.dhp.schema.oaf.Publication; public class CleanCountryTest { @@ -151,41 +151,40 @@ public class CleanCountryTest { @Test public void testDatasetClean() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") - .getPath(); + .getResource("/eu/dnetlib/dhp/oa/graph/clean/dataset_clean_country.json") + .getPath(); spark - .read() - .textFile(sourcePath) - .map( - (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), - Encoders.bean(Dataset.class)) - .write() - .json(workingDir.toString() + "/dataset"); + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .json(workingDir.toString() + "/dataset"); CleanCountrySparkJob.main(new String[] { - "--isSparkSessionManaged", Boolean.FALSE.toString(), - "--inputPath", workingDir.toString() + "/dataset", - "-graphTableClassName", Dataset.class.getCanonicalName(), - "-workingDir", workingDir.toString() + "/working", - "-country", "NL", - "-verifyParam", "10.17632", - "-collectedfrom", "NARCIS", - "-hostedBy", getClass() + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/dataset", + "-graphTableClassName", Dataset.class.getCanonicalName(), + "-workingDir", workingDir.toString() + "/working", + "-country", "NL", + "-verifyParam", "10.17632", + "-collectedfrom", "NARCIS", + "-hostedBy", getClass() .getResource("/eu/dnetlib/dhp/oa/graph/clean/hostedBy") .getPath() }); final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/dataset") - .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + .textFile(workingDir.toString() + "/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); Assertions.assertEquals(1, tmp.count()); Assertions.assertEquals(0, tmp.first().getCountry().size()); - } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala index d415b7fc95..022168de57 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala @@ -53,7 +53,8 @@ class ResolveEntitiesTest extends Serializable { def generateUpdates(spark: SparkSession): Unit = { val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString - val pids: List[String] = template.linesWithSeparators.map(l =>l.stripLineEnd) + val pids: List[String] = template.linesWithSeparators + .map(l => l.stripLineEnd) .map { id => val r = new Result r.setId(id.toLowerCase.trim) @@ -127,7 +128,7 @@ class ResolveEntitiesTest extends Serializable { entities.foreach { e => val template = Source.fromInputStream(this.getClass.getResourceAsStream(s"$e")).mkString spark - .createDataset(spark.sparkContext.parallelize(template.linesWithSeparators.map(l =>l.stripLineEnd).toList)) + .createDataset(spark.sparkContext.parallelize(template.linesWithSeparators.map(l => l.stripLineEnd).toList)) .as[String] .write .option("compression", "gzip") @@ -264,7 +265,8 @@ class ResolveEntitiesTest extends Serializable { Source .fromInputStream(this.getClass.getResourceAsStream(s"publication")) .mkString - .linesWithSeparators.map(l =>l.stripLineEnd) + .linesWithSeparators + .map(l => l.stripLineEnd) .next(), classOf[Publication] ) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala index 0ea9082900..b838ae0659 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala @@ -47,7 +47,7 @@ class ScholixGraphTest extends AbstractVocabularyTest { val inputRelations = Source .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/oaf_to_summary")) .mkString - val items = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd).toList + val items = inputRelations.linesWithSeparators.map(l => l.stripLineEnd).toList assertNotNull(items) items.foreach(i => assertTrue(i.nonEmpty)) val result = @@ -69,7 +69,8 @@ class ScholixGraphTest extends AbstractVocabularyTest { getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/merge_result_scholix") ) .mkString - val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators.map(l =>l.stripLineEnd) + val result: List[(Relation, ScholixSummary)] = inputRelations.linesWithSeparators + .map(l => l.stripLineEnd) .sliding(2) .map(s => (s.head, s(1))) .map(p => (mapper.readValue(p._1, classOf[Relation]), mapper.readValue(p._2, classOf[ScholixSummary]))) From a8ac79fa25636a5a7995c148f5536d342feafbc6 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 15 Feb 2023 10:29:13 +0100 Subject: [PATCH 13/14] Added citation relation on crossref Mapping --- .../doiboost/crossref/Crossref2Oaf.scala | 49 + .../crossref/publication_license_embargo.json | 3006 ++++++++--------- .../crossref/CrossrefMappingTest.scala | 43 + 3 files changed, 1564 insertions(+), 1534 deletions(-) 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 7fb10863f6..a271f4c338 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 @@ -309,6 +309,8 @@ case object Crossref2Oaf { result } + + def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = { val a = new Author a.setName(given) @@ -370,10 +372,57 @@ case object Crossref2Oaf { case dataset: Dataset => convertDataset(dataset) } + + val doisReference:List[String] = for { + JObject(reference_json) <- json \ "reference" + JField("DOI", JString(doi_json)) <- reference_json + } yield doi_json + + + + if (doisReference!= null && doisReference.nonEmpty) { + val citation_relations:List[Relation] = generateCitationRelations(doisReference, result) + resultList = resultList ::: citation_relations + } resultList = resultList ::: List(result) resultList } + + + private def createCiteRelation(source:Result, targetPid:String, targetPidType:String) :List[Relation] = { + + + val targetId = IdentifierFactory.idFromPid("50",targetPidType, targetPid, true) + + val from = new Relation + from.setSource(source.getId) + from.setTarget(targetId) + from.setRelType(ModelConstants.RESULT_RESULT) + from.setRelClass(ModelConstants.CITES) + from.setSubRelType(ModelConstants.CITATION) + from.setCollectedfrom(source.getCollectedfrom) + from.setDataInfo(source.getDataInfo) + from.setLastupdatetimestamp(source.getLastupdatetimestamp) + + + val to = new Relation + to.setTarget(source.getId) + to.setSource(targetId) + to.setRelType(ModelConstants.RESULT_RESULT) + to.setRelClass(ModelConstants.IS_CITED_BY) + to.setSubRelType(ModelConstants.CITATION) + to.setCollectedfrom(source.getCollectedfrom) + to.setDataInfo(source.getDataInfo) + to.setLastupdatetimestamp(source.getLastupdatetimestamp) + + List(from,to) + } + + def generateCitationRelations(dois:List[String], result:Result):List[Relation] = { + dois.flatMap(d => createCiteRelation(result, d, "doi")) + } + def mappingFunderToRelations( funders: List[mappingFunder], sourceId: String, diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json index 788946fead..b66147b2d6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/publication_license_embargo.json @@ -1,1537 +1,1475 @@ { -"indexed": { -"date-parts": [ -[ -2021, -7, -2 -] -], -"date-time": "2021-07-02T07:30:10Z", -"timestamp": 1625211010708 -}, -"reference-count": 83, -"publisher": "Springer Science and Business Media LLC", -"issue": "5", -"license": [ -{ -"URL": "https://www.springer.com/tdm", -"start": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T00:00:00Z", -"timestamp": 1613952000000 -}, -"delay-in-days": 0, -"content-version": "tdm" -}, -{ -"URL": "https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model", -"start": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T00:00:00Z", -"timestamp": 1613952000000 -}, -"delay-in-days": 0, -"content-version": "vor" -} -], -"content-domain": { -"domain": [ -"link.springer.com" -], -"crossmark-restriction": false -}, -"short-container-title": [ -"Nat Astron" -], -"published-print": { -"date-parts": [ -[ -2021, -5 -] -] -}, -"DOI": "10.1038/s41550-020-01295-8", -"type": "journal-article", -"created": { -"date-parts": [ -[ -2021, -2, -22 -] -], -"date-time": "2021-02-22T17:03:42Z", -"timestamp": 1614013422000 -}, -"page": "510-518", -"update-policy": "http://dx.doi.org/10.1007/springer_crossmark_policy", -"source": "Crossref", -"is-referenced-by-count": 6, -"title": [ -"A tidal disruption event coincident with a high-energy neutrino" -], -"prefix": "10.1038", -"volume": "5", -"author": [ -{ -"ORCID": "http://orcid.org/0000-0003-2434-0387", -"authenticated-orcid": false, -"given": "Robert", -"family": "Stein", -"sequence": "first", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3859-8074", -"authenticated-orcid": false, -"given": "Sjoert van", -"family": "Velzen", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8594-8666", -"authenticated-orcid": false, -"given": "Marek", -"family": "Kowalski", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Anna", -"family": "Franckowiak", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3703-5154", -"authenticated-orcid": false, -"given": "Suvi", -"family": "Gezari", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3124-2814", -"authenticated-orcid": false, -"given": "James C. A.", -"family": "Miller-Jones", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Sara", -"family": "Frederick", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-0466-3779", -"authenticated-orcid": false, -"given": "Itai", -"family": "Sfaradi", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Michael F.", -"family": "Bietenholz", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-5936-1156", -"authenticated-orcid": false, -"given": "Assaf", -"family": "Horesh", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Rob", -"family": "Fender", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2403-4582", -"authenticated-orcid": false, -"given": "Simone", -"family": "Garrappa", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-2184-6430", -"authenticated-orcid": false, -"given": "Tomás", -"family": "Ahumada", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Igor", -"family": "Andreoni", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Justin", -"family": "Belicki", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8018-5348", -"authenticated-orcid": false, -"given": "Eric C.", -"family": "Bellm", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Markus", -"family": "Böttcher", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Valery", -"family": "Brinnel", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Rick", -"family": "Burruss", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-1673-970X", -"authenticated-orcid": false, -"given": "S. Bradley", -"family": "Cenko", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-8262-2924", -"authenticated-orcid": false, -"given": "Michael W.", -"family": "Coughlin", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2292-0441", -"authenticated-orcid": false, -"given": "Virginia", -"family": "Cunningham", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Andrew", -"family": "Drake", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Glennys R.", -"family": "Farrar", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Michael", -"family": "Feeney", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Ryan J.", -"family": "Foley", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3653-5598", -"authenticated-orcid": false, -"given": "Avishay", -"family": "Gal-Yam", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "V. Zach", -"family": "Golkhou", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-4163-4996", -"authenticated-orcid": false, -"given": "Ariel", -"family": "Goobar", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-3168-0139", -"authenticated-orcid": false, -"given": "Matthew J.", -"family": "Graham", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Erica", -"family": "Hammerstein", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-3367-3415", -"authenticated-orcid": false, -"given": "George", -"family": "Helou", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-9878-7889", -"authenticated-orcid": false, -"given": "Tiara", -"family": "Hung", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Mansi M.", -"family": "Kasliwal", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-5740-7747", -"authenticated-orcid": false, -"given": "Charles D.", -"family": "Kilpatrick", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-5105-344X", -"authenticated-orcid": false, -"given": "Albert K. H.", -"family": "Kong", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-6540-1484", -"authenticated-orcid": false, -"given": "Thomas", -"family": "Kupfer", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2451-5482", -"authenticated-orcid": false, -"given": "Russ R.", -"family": "Laher", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-2242-0244", -"authenticated-orcid": false, -"given": "Ashish A.", -"family": "Mahabal", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-8532-9395", -"authenticated-orcid": false, -"given": "Frank J.", -"family": "Masci", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-0280-7484", -"authenticated-orcid": false, -"given": "Jannis", -"family": "Necker", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-8342-6274", -"authenticated-orcid": false, -"given": "Jakob", -"family": "Nordin", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Daniel A.", -"family": "Perley", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-8121-2560", -"authenticated-orcid": false, -"given": "Mickael", -"family": "Rigault", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-7788-628X", -"authenticated-orcid": false, -"given": "Simeon", -"family": "Reusch", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Hector", -"family": "Rodriguez", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0002-7559-315X", -"authenticated-orcid": false, -"given": "César", -"family": "Rojas-Bravo", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-7648-4142", -"authenticated-orcid": false, -"given": "Ben", -"family": "Rusholme", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-4401-0430", -"authenticated-orcid": false, -"given": "David L.", -"family": "Shupe", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-9898-5597", -"authenticated-orcid": false, -"given": "Leo P.", -"family": "Singer", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0003-1546-6615", -"authenticated-orcid": false, -"given": "Jesper", -"family": "Sollerman", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Maayane T.", -"family": "Soumagnac", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Daniel", -"family": "Stern", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Kirsty", -"family": "Taggart", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Jakob", -"family": "van Santen", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Charlotte", -"family": "Ward", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"given": "Patrick", -"family": "Woudt", -"sequence": "additional", -"affiliation": [ - -] -}, -{ -"ORCID": "http://orcid.org/0000-0001-6747-8509", -"authenticated-orcid": false, -"given": "Yuhan", -"family": "Yao", -"sequence": "additional", -"affiliation": [ - -] -} -], -"member": "297", -"published-online": { -"date-parts": [ -[ -2021, -2, -22 -] -] -}, -"reference": [ -{ -"key": "1295_CR1", -"doi-asserted-by": "crossref", -"first-page": "P03012", -"DOI": "10.1088/1748-0221/12/03/P03012", -"volume": "12", -"author": "MG Aartsen", -"year": "2017", -"unstructured": "Aartsen, M. G. et al. The IceCube Neutrino Observatory: instrumentation and online systems. J. Instrum. 12, P03012 (2017).", -"journal-title": "J. Instrum." -}, -{ -"key": "1295_CR2", -"unstructured": "Stein, R. IceCube-191001A—IceCube observation of a high-energy neutrino candidate event. GCN Circ. 25913 (2019)." -}, -{ -"key": "1295_CR3", -"doi-asserted-by": "crossref", -"first-page": "018002", -"DOI": "10.1088/1538-3873/aaecbe", -"volume": "131", -"author": "EC Bellm", -"year": "2019", -"unstructured": "Bellm, E. C. et al. The Zwicky Transient Facility: system overview, performance, and first results. Publ. Astron. Soc. Pac. 131, 018002 (2019).", -"journal-title": "Publ. Astron. Soc. Pac." -}, -{ -"key": "1295_CR4", -"doi-asserted-by": "crossref", -"first-page": "533", -"DOI": "10.1016/j.astropartphys.2007.03.005", -"volume": "27", -"author": "M Kowalski", -"year": "2007", -"unstructured": "Kowalski, M. & Mohr, A. Detecting neutrino transients with optical follow-up observations. Astropart. Phys. 27, 533–538 (2007).", -"journal-title": "Astropart. Phys." -}, -{ -"key": "1295_CR5", -"doi-asserted-by": "crossref", -"first-page": "329", -"DOI": "10.1088/0004-637X/693/1/329", -"volume": "693", -"author": "GR Farrar", -"year": "2009", -"unstructured": "Farrar, G. R. & Gruzinov, A. Giant AGN flares and cosmic ray bursts. Astrophys. J. 693, 329–332 (2009).", -"journal-title": "Astrophys. J." -}, -{ -"key": "1295_CR6", -"doi-asserted-by": "crossref", -"first-page": "1354", -"DOI": "10.1093/mnras/stx863", -"volume": "469", -"author": "L Dai", -"year": "2017", -"unstructured": "Dai, L. & Fang, K. Can tidal disruption events produce the IceCube neutrinos? Mon. Not. R. Astron. Soc. 469, 1354–1359 (2017).", -"journal-title": "Mon. Not. R. Astron. Soc." -}, -{ -"key": "1295_CR7", -"doi-asserted-by": "crossref", -"first-page": "114", -"DOI": "10.3847/1538-4357/ab44ca", -"volume": "886", -"author": "K Hayasaki", -"year": "2019", -"unstructured": "Hayasaki, K. & Yamazaki, R. 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Astrophys. 594, A116 (2016).", + "DOI": "10.1051/0004-6361/201629178", + "doi-asserted-by": "crossref" + }, + { + "key": "1295_CR65", + "unstructured": "Arnaud, K. A. in Astronomical Data Analysis Software and Systems V (eds Jacoby, G. H. & Barnes, J.) 17 (Astronomical Society of the Pacific, 1996)." + }, + { + "key": "1295_CR66", + "doi-asserted-by": "crossref", + "first-page": "1545", + "DOI": "10.1111/j.1365-2966.2008.13953.x", + "volume": "391", + "author": "JTL Zwart", + "year": "2008", + "unstructured": "Zwart, J. T. L. et al. The Arcminute Microkelvin Imager. Mon. Not. R. Astron. Soc. 391, 1545–1558 (2008).", + "journal-title": "Mon. Not. R. Astron. Soc." + }, + { + "key": "1295_CR67", + "doi-asserted-by": "crossref", + "first-page": "5677", + "DOI": "10.1093/mnras/sty074", + "volume": "475", + "author": "J Hickish", + "year": "2018", + "unstructured": "Hickish, J. et al. A digital correlator upgrade for the Arcminute MicroKelvin Imager. Mon. Not. R. Astron. 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The Large Area Telescope on the Fermi Gamma-ray Space Telescope mission. Astrophys. J. 697, 1071–1102 (2009).", + "journal-title": "Astrophys. J." + }, + { + "key": "1295_CR71", + "unstructured": "Wood, M. et al. Fermipy: an open-source Python package for analysis of Fermi-LAT Data. In Proc. 35th International Cosmic Ray Conference (ICRC2017) 824 (PoS, 2017).", + "DOI": "10.22323/1.301.0824", + "doi-asserted-by": "crossref" + }, + { + "key": "1295_CR72", + "unstructured": "Garrappa, S. & Buson, S. Fermi-LAT gamma-ray observations of IceCube-191001A. GCN Circ. 25932 (2019)." + }, + { + "key": "1295_CR73", + "unstructured": "The Fermi-LAT collaboration. Fermi Large Area Telescope Fourth Source Catalog. Astrophys. J. Suppl. Ser. 247, 33 (2020)." + }, + { + "key": "1295_CR74", + "doi-asserted-by": "crossref", + "first-page": "14", + "DOI": "10.1088/0004-637X/767/1/14", + "volume": "767", + "author": "T Pursimo", + "year": "2013", + "unstructured": "Pursimo, T. et al. The Micro-Arcsecond Scintillation-Induced Variability (MASIV) survey. III. Optical identifications and new redshifts. Astrophys. J. 767, 14 (2013).", + "journal-title": "Astrophys. J." + }, + { + "key": "1295_CR75", + "unstructured": "Garrappa, S., Buson, S. & Fermi-LAT Collaboration. Fermi-LAT gamma-ray observations of IceCube-191001A. GCN Circ. 25932 (2019)." + }, + { + "key": "1295_CR76", + "doi-asserted-by": "crossref", + "first-page": "133", + "DOI": "10.1088/0004-637X/802/2/133", + "volume": "802", + "author": "C Diltz", + "year": "2015", + "unstructured": "Diltz, C., Böttcher, M. & Fossati, G. Time dependent hadronic modeling of flat spectrum radio quasars. Astrophys. J. 802, 133 (2015).", + "journal-title": "Astrophys. J." + }, + { + "key": "1295_CR77", + "doi-asserted-by": "crossref", + "first-page": "88", + "DOI": "10.1038/s41550-018-0610-1", + "volume": "3", + "author": "S Gao", + "year": "2019", + "unstructured": "Gao, S., Fedynitch, A., Winter, W. & Pohl, M. Modelling the coincident observation of a high-energy neutrino and a bright blazar flare. Nat. Astron. 3, 88–92 (2019).", + "journal-title": "Nat. Astron." + }, + { + "key": "1295_CR78", + "unstructured": "Ayala, H. IceCube-191001A: HAWC follow-up. GCN Circ. 25936 (2019)." + }, + { + "key": "1295_CR79", + "doi-asserted-by": "crossref", + "first-page": "62", + "DOI": "10.1126/science.aad1182", + "volume": "351", + "author": "S van Velzen", + "year": "2016", + "unstructured": "van Velzen, S. et al. A radio jet from the optical and x-ray bright stellar tidal disruption flare ASASSN-14li. Science 351, 62–65 (2016).", + "journal-title": "Science" + }, + { + "key": "1295_CR80", + "doi-asserted-by": "crossref", + "first-page": "306", + "DOI": "10.1086/670067", + "volume": "125", + "author": "D Foreman-Mackey", + "year": "2013", + "unstructured": "Foreman-Mackey, D., Hogg, D. W., Lang, D. & Goodman, J. emcee: the MCMC Hammer. Publ. Astron. Soc. Pac. 125, 306 (2013).", + "journal-title": "Publ. Astron. Soc. Pac." + }, + { + "key": "1295_CR81", + "doi-asserted-by": "crossref", + "first-page": "6", + "DOI": "10.3847/1538-4365/aab761", + "volume": "236", + "author": "J Guillochon", + "year": "2018", + "unstructured": "Guillochon, J. et al. MOSFiT: Modular Open Source Fitter for Transients. Astrophys. J. Suppl. Ser. 236, 6 (2018).", + "journal-title": "Astrophys. J. Suppl. Ser." + }, + { + "key": "1295_CR82", + "doi-asserted-by": "crossref", + "first-page": "e008", + "DOI": "10.1017/pasa.2013.44", + "volume": "31", + "author": "J Granot", + "year": "2014", + "unstructured": "Granot, J. & van der Horst, A. J. Gamma-ray burst jets and their radio observations. Publ. Astron. Soc. Aust. 31, e008 (2014).", + "journal-title": "Publ. Astron. Soc. Aust." + }, + { + "key": "1295_CR83", + "doi-asserted-by": "crossref", + "first-page": "102", + "DOI": "10.1088/0004-637X/815/2/102", + "volume": "815", + "author": "W Fong", + "year": "2015", + "unstructured": "Fong, W., Berger, E., Margutti, R. & Zauderer, B. A. A decade of short-duration gamma-ray burst broadband afterglows: energetics, circumburst densities, and jet opening angles. Astrophys. J. 815, 102 (2015).", + "journal-title": "Astrophys. J." + } + ], + "container-title": [ + "Nature Astronomy" + ], + "original-title": [ + ], + "language": "en", + "link": [ + { + "URL": "http://www.nature.com/articles/s41550-020-01295-8.pdf", + "content-type": "application/pdf", + "content-version": "vor", + "intended-application": "text-mining" + }, + { + "URL": "http://www.nature.com/articles/s41550-020-01295-8", + "content-type": "text/html", + "content-version": "vor", + "intended-application": "text-mining" + }, + { + "URL": "http://www.nature.com/articles/s41550-020-01295-8.pdf", + "content-type": "application/pdf", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2021, + 5, + 17 + ] + ], + "date-time": "2021-05-17T15:08:12Z", + "timestamp": 1621264092000 + }, + "score": 1.0, + "subtitle": [ + ], + "short-title": [ + ], + "issued": { + "date-parts": [ + [ + 3021, + 2, + 22 + ] + ] + }, + "references-count": 83, + "journal-issue": { + "published-print": { + "date-parts": [ + [ + 2021, + 5 + ] + ] + }, + "issue": "5" + }, + "alternative-id": [ + "1295" + ], + "URL": "http://dx.doi.org/10.1038/s41550-020-01295-8", + "relation": { + "cites": [ + ] + }, + "ISSN": [ + "2397-3366" + ], + "issn-type": [ + { + "value": "2397-3366", + "type": "electronic" + } + ], + "assertion": [ + { + "value": "21 July 2020", + "order": 1, + "name": "received", + "label": "Received", + "group": { + "name": "ArticleHistory", + "label": "Article History" + } + }, + { + "value": "16 December 2020", + "order": 2, + "name": "accepted", + "label": "Accepted", + "group": { + "name": "ArticleHistory", + "label": "Article History" + } + }, + { + "value": "22 February 2021", + "order": 3, + "name": "first_online", + "label": "First Online", + "group": { + "name": "ArticleHistory", + "label": "Article History" + } + }, + { + "value": "The authors declare no competing interests.", + "order": 1, + "name": "Ethics", + "group": { + "name": "EthicsHeading", + "label": "Competing interests" + } + } + ] } } \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index aba8cee123..bd6dd7cec6 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -1,9 +1,14 @@ package eu.dnetlib.dhp.doiboost.crossref +import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf._ import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.doiboost.crossref.Crossref2Oaf import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} +import org.json4s +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.{DefaultFormats, JValue} +import org.json4s.jackson.JsonMethods import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Test import org.slf4j.{Logger, LoggerFactory} @@ -109,6 +114,44 @@ class CrossrefMappingTest { } + + private def parseJson(input:String):JValue = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = JsonMethods.parse(input) + + json + } + + @Test + def testCitationRelations():Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty) + + val result:List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(result.nonEmpty) + + + val j = parseJson(json) + + val doisReference: List[String] = for { + JObject(reference_json) <- j \ "reference" + JField("DOI", JString(doi_json)) <- reference_json + } yield doi_json + + + + val relationList:List[Relation] = result.filter(s => s.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation]).filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION)) + + assertNotNull(relationList) + assertFalse(relationList.isEmpty) + + assertEquals(doisReference.size*2, relationList.size) + } + @Test def testEmptyTitle(): Unit = { val json = Source From d617c3e812db928e21791ca583013abebf903c5b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 20 Feb 2023 14:45:27 +0100 Subject: [PATCH 14/14] [DOIBoost] extended mapping for funder #8407 --- .../doiboost/crossref/Crossref2Oaf.scala | 54 +++++++++++++------ .../crossref/CrossrefMappingTest.scala | 27 +++++----- 2 files changed, 52 insertions(+), 29 deletions(-) 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 a271f4c338..75aa4a0246 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 @@ -309,8 +309,6 @@ case object Crossref2Oaf { result } - - def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = { val a = new Author a.setName(given) @@ -372,28 +370,22 @@ case object Crossref2Oaf { case dataset: Dataset => convertDataset(dataset) } - - val doisReference:List[String] = for { - JObject(reference_json) <- json \ "reference" + val doisReference: List[String] = for { + JObject(reference_json) <- json \ "reference" JField("DOI", JString(doi_json)) <- reference_json } yield doi_json - - - if (doisReference!= null && doisReference.nonEmpty) { - val citation_relations:List[Relation] = generateCitationRelations(doisReference, result) + if (doisReference != null && doisReference.nonEmpty) { + val citation_relations: List[Relation] = generateCitationRelations(doisReference, result) resultList = resultList ::: citation_relations } resultList = resultList ::: List(result) resultList } + private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = { - - private def createCiteRelation(source:Result, targetPid:String, targetPidType:String) :List[Relation] = { - - - val targetId = IdentifierFactory.idFromPid("50",targetPidType, targetPid, true) + val targetId = IdentifierFactory.idFromPid("50", targetPidType, targetPid, true) val from = new Relation from.setSource(source.getId) @@ -405,7 +397,6 @@ case object Crossref2Oaf { from.setDataInfo(source.getDataInfo) from.setLastupdatetimestamp(source.getLastupdatetimestamp) - val to = new Relation to.setTarget(source.getId) to.setSource(targetId) @@ -416,10 +407,10 @@ case object Crossref2Oaf { to.setDataInfo(source.getDataInfo) to.setLastupdatetimestamp(source.getLastupdatetimestamp) - List(from,to) + List(from, to) } - def generateCitationRelations(dois:List[String], result:Result):List[Relation] = { + def generateCitationRelations(dois: List[String], result: Result): List[Relation] = { dois.flatMap(d => createCiteRelation(result, d, "doi")) } @@ -495,6 +486,7 @@ case object Crossref2Oaf { case "10.13039/501100000781" => generateSimpleRelationFromAward(funder, "corda_______", extractECAward) generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward) + generateSimpleRelationFromAward(funder, "corda_____he", extractECAward) case "10.13039/100000001" => generateSimpleRelationFromAward(funder, "nsf_________", a => a) case "10.13039/501100001665" => generateSimpleRelationFromAward(funder, "anr_________", a => a) case "10.13039/501100002341" => generateSimpleRelationFromAward(funder, "aka_________", a => a) @@ -536,6 +528,34 @@ case object Crossref2Oaf { val targetId = getProjectId("wt__________", "1e5e62235d094afd01cd56e65112fc63") queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //ASAP + case "10.13039/100018231" => generateSimpleRelationFromAward(funder, "asap________", a => a) + //CHIST-ERA + case "10.13039/501100001942" => + val targetId = getProjectId("chistera____", "1e5e62235d094afd01cd56e65112fc63") + queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY) + queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES) + //HE + case "10.13039/100018693" | "10.13039/100018694" | "10.13039/100019188" | "10.13039/100019180" | + "10.13039/100018695" | "10.13039/100019185" | "10.13039/100019186" | "10.13039/100019187" => + generateSimpleRelationFromAward(funder, "corda_____he", extractECAward) + //FCT + case "10.13039/501100001871" => + generateSimpleRelationFromAward(funder, "fct_________", extractECAward) + //NHMRC + case "10.13039/501100000925" => + generateSimpleRelationFromAward(funder, "mhmrc_______", extractECAward) + //NIH + case "10.13039/100000002" => + generateSimpleRelationFromAward(funder, "nih_________", extractECAward) + //NWO + case "10.13039/501100003246" => + generateSimpleRelationFromAward(funder, "nwo_________", extractECAward) + //UKRI + case "10.13039/100014013" | "10.13039/501100000267" | "10.13039/501100000268" | "10.13039/501100000269" | + "10.13039/501100000266" | "10.13039/501100006041" | "10.13039/501100000265" | "10.13039/501100000270" | + "10.13039/501100013589" | "10.13039/501100000271" => + generateSimpleRelationFromAward(funder, "nwo_________", extractECAward) case _ => logger.debug("no match for " + funder.DOI.get) diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 572a48372c..e0ef0e65c0 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -114,8 +114,7 @@ class CrossrefMappingTest { } - - private def parseJson(input:String):JValue = { + private def parseJson(input: String): JValue = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: json4s.JValue = JsonMethods.parse(input) @@ -123,33 +122,37 @@ class CrossrefMappingTest { } @Test - def testCitationRelations():Unit = { - val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")).mkString - + def testCitationRelations(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json")) + .mkString assertNotNull(json) assertFalse(json.isEmpty) - val result:List[Oaf] = Crossref2Oaf.convert(json) + val result: List[Oaf] = Crossref2Oaf.convert(json) assertTrue(result.nonEmpty) - val j = parseJson(json) val doisReference: List[String] = for { - JObject(reference_json) <- j \ "reference" + JObject(reference_json) <- j \ "reference" JField("DOI", JString(doi_json)) <- reference_json } yield doi_json - - - val relationList:List[Relation] = result.filter(s => s.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation]).filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION)) + val relationList: List[Relation] = result + .filter(s => s.isInstanceOf[Relation]) + .map(r => r.asInstanceOf[Relation]) + .filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION)) assertNotNull(relationList) assertFalse(relationList.isEmpty) - assertEquals(doisReference.size*2, relationList.size) + assertEquals(doisReference.size * 2, relationList.size) + + mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT) + relationList.foreach(p => println(mapper.writeValueAsString(p))) } @Test