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master #59

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claudio.atzori wants to merge 3221 commits from master into stable_ids
pull from: master
merge into: D-Net:stable_ids
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32
dhp-workflows/dhp-monitor-update/pom.xml Normal file
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<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<parent>
<artifactId>dhp-workflows</artifactId>
<groupId>eu.dnetlib.dhp</groupId>
<version>1.2.4-SNAPSHOT</version>
</parent>
<modelVersion>4.0.0</modelVersion>
<artifactId>dhp-monitor-update</artifactId>
<dependencies>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-core_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.spark</groupId>
<artifactId>spark-sql_2.11</artifactId>
</dependency>
</dependencies>
<build>
<plugins>
<plugin>
<groupId>pl.project13.maven</groupId>
<artifactId>git-commit-id-plugin</artifactId>
<version>2.1.11</version>
<configuration>
<failOnNoGitDirectory>false</failOnNoGitDirectory>
</configuration>
</plugin>
</plugins>
</build>
</project>

34
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/config-default.xml Normal file
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<configuration>
<property>
<name>jobTracker</name>
<value>${jobTracker}</value>
</property>
<property>
<name>nameNode</name>
<value>${nameNode}</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>hive_jdbc_url</name>
<value>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</value>
</property>
<property>
<name>oozie.wf.workflow.notification.url</name>
<value>{serviceUrl}/v1/oozieNotification/jobUpdate?jobId=$jobId%26status=$status</value>
</property>
<property>
<name>stats_tool_api_url</name>
<value>${stats_tool_api_url}</value>
</property>
</configuration>

21
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor-post.sh Normal file
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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!"

24
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh Normal file
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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"

241
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql Normal file
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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;

4
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/updateCache.sh Normal file
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#!/usr/bin/env bash
curl --request GET $1/cache/updateCache
sleep 6h

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dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml Normal file
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<workflow-app name="Monitor DB" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>stats_db_name</name>
<description>the target stats database name</description>
</property>
<property>
<name>stats_db_shadow_name</name>
<description>the name of the shadow schema</description>
</property>
<property>
<name>monitor_db_name</name>
<description>the target monitor db name</description>
</property>
<property>
<name>monitor_db_shadow_name</name>
<description>the name of the shadow monitor db</description>
</property>
<property>
<name>stats_tool_api_url</name>
<description>The url of the API of the stats tool. Is used to trigger the cache update.</description>
</property>
<property>
<name>hive_metastore_uris</name>
<description>hive server metastore URIs</description>
</property>
<property>
<name>hive_jdbc_url</name>
<description>hive server jdbc url</description>
</property>
<property>
<name>hive_timeout</name>
<description>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.</description>
</property>
<property>
<name>context_api_url</name>
<description>the base url of the context api (https://services.openaire.eu/openaire)</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>hive.metastore.uris</name>
<value>${hive_metastore_uris}</value>
</property>
<property>
<name>hive.txn.timeout</name>
<value>${hive_timeout}</value>
</property>
</configuration>
</global>
<start to="Step1-createMonitorDB"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="Step1-createMonitorDB">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>monitor.sh</exec>
<argument>${stats_db_name}</argument>
<argument>${monitor_db_name}</argument>
<argument>${monitor_db_shadow_name}</argument>
<argument>${wf:appPath()}/scripts/createMonitorDB.sql</argument>
<file>monitor.sh</file>
</shell>
<ok to="Step2-createMonitorDB-post"/>
<error to="Kill"/>
</action>
<action name="Step2-createMonitorDB-post">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>monitor-post.sh</exec>
<argument>${stats_db_name}</argument>
<argument>${monitor_db_name}</argument>
<argument>${monitor_db_shadow_name}</argument>
<file>monitor-post.sh</file>
</shell>
<ok to="Step3-updateCache"/>
<error to="Kill"/>
</action>
<action name="Step3-updateCache">
<shell xmlns="uri:oozie:shell-action:0.1">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<exec>updateCache.sh</exec>
<argument>${stats_tool_api_url}</argument>
<file>updateCache.sh</file>
</shell>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>