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cleanup of non necessary dhp-monitor-update workflow

This commit is contained in:
Claudio Atzori 2023-02-22 10:10:22 +01:00
parent a590c371a9
commit 99cd7761aa
5 changed files with 0 additions and 307 deletions
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32
dhp-workflows/dhp-monitor-update/pom.xml
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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
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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>

18
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/monitor.sh
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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 SCRIPT_PATH=$3
echo "Getting file from " $3
hdfs dfs -copyToLocal $3
echo "Updating monitor database"
cat createMonitorDB.sql | sed s/SOURCE/$1/g | sed s/TARGET/$2/g1 | impala-shell -f -
echo "Impala shell finished"

146
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/scripts/createMonitorDB.sql
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DROP TABLE IF EXISTS TARGET.result_new;
create table TARGET.result_new as
select distinct * from (
select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in (
-- 'openorgs____::b8b8ca674452579f3f593d9f5e557483', -- University College Cork
-- 'openorgs____::38d7097854736583dde879d12dacafca' -- Brown University
'openorgs____::57784c9e047e826fefdb1ef816120d92' --Arts et Métiers ParisTech
) )) foo;
COMPUTE STATS TARGET.result_new;
INSERT INTO TARGET.result select * from TARGET.result_new;
COMPUTE STATS TARGET.result;
INSERT INTO TARGET.result_citations select * from TARGET.result_citations orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_citations;
INSERT INTO TARGET.result_references_oc select * from TARGET.result_references_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_references_oc;
INSERT INTO TARGET.result_citations_oc select * from TARGET.result_citations_oc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_citations_oc;
INSERT INTO TARGET.result_classifications select * from TARGET.result_classifications orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_classifications;
INSERT INTO TARGET.result_apc select * from TARGET.result_apc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_apc;
INSERT INTO TARGET.result_concepts select * from TARGET.result_concepts orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_concepts;
INSERT INTO TARGET.result_datasources select * from TARGET.result_datasources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_datasources;
INSERT INTO TARGET.result_fundercount select * from TARGET.result_fundercount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_fundercount;
INSERT INTO TARGET.result_gold select * from TARGET.result_gold orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_gold;
INSERT INTO TARGET.result_greenoa select * from TARGET.result_greenoa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_greenoa;
INSERT INTO TARGET.result_languages select * from TARGET.result_languages orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_languages;
INSERT INTO TARGET.result_licenses select * from TARGET.result_licenses orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_licenses;
INSERT INTO TARGET.result_oids select * from TARGET.result_oids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_oids;
INSERT INTO TARGET.result_organization select * from TARGET.result_organization orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_organization;
INSERT INTO TARGET.result_peerreviewed select * from TARGET.result_peerreviewed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_peerreviewed;
INSERT INTO TARGET.result_pids select * from TARGET.result_pids orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_pids;
INSERT INTO TARGET.result_projectcount select * from TARGET.result_projectcount orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_projectcount;
INSERT INTO TARGET.result_projects select * from TARGET.result_projects orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_projects;
INSERT INTO TARGET.result_refereed select * from TARGET.result_refereed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_refereed;
INSERT INTO TARGET.result_sources select * from TARGET.result_sources orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_sources;
INSERT INTO TARGET.result_topics select * from TARGET.result_topics orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_topics;
INSERT INTO TARGET.result_fos select * from TARGET.result_fos orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.result_fos;
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;
COMPUTE STATS TARGET.result_result;
-- indicators
-- Sprint 1 ----
INSERT INTO TARGET.indi_pub_green_oa select * from TARGET.indi_pub_green_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_green_oa;
INSERT INTO TARGET.indi_pub_grey_lit select * from TARGET.indi_pub_grey_lit orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_grey_lit;
INSERT INTO TARGET.indi_pub_doi_from_crossref select * from TARGET.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_doi_from_crossref;
-- Sprint 2 ----
INSERT INTO TARGET.indi_result_has_cc_licence select * from TARGET.indi_result_has_cc_licence orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_result_has_cc_licence;
INSERT INTO TARGET.indi_result_has_cc_licence_url select * from TARGET.indi_result_has_cc_licence_url orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_result_has_cc_licence_url;
INSERT INTO TARGET.indi_pub_has_abstract select * from TARGET.indi_pub_has_abstract orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_has_abstract;
INSERT INTO TARGET.indi_result_with_orcid select * from TARGET.indi_result_with_orcid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_result_with_orcid;
---- Sprint 3 ----
INSERT INTO TARGET.indi_funded_result_with_fundref select * from TARGET.indi_funded_result_with_fundref orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_funded_result_with_fundref;
---- Sprint 4 ----
INSERT INTO TARGET.indi_pub_diamond select * from TARGET.indi_pub_diamond orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_diamond;
INSERT INTO TARGET.indi_pub_in_transformative select * from TARGET.indi_pub_in_transformative orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_in_transformative;
INSERT INTO TARGET.indi_pub_closed_other_open select * from TARGET.indi_pub_closed_other_open orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_closed_other_open;
---- Sprint 5 ----
INSERT INTO TARGET.indi_result_no_of_copies select * from TARGET.indi_result_no_of_copies orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_result_no_of_copies;
---- Sprint 6 ----
INSERT INTO TARGET.indi_pub_hybrid_oa_with_cc select * from TARGET.indi_pub_hybrid_oa_with_cc orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_hybrid_oa_with_cc;
INSERT INTO TARGET.indi_pub_downloads select * from TARGET.indi_pub_downloads orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
COMPUTE STATS TARGET.indi_pub_downloads;
INSERT INTO TARGET.indi_pub_downloads_datasource select * from TARGET.indi_pub_downloads_datasource orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
COMPUTE STATS TARGET.indi_pub_downloads_datasource;
INSERT INTO TARGET.indi_pub_downloads_year select * from TARGET.indi_pub_downloads_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
COMPUTE STATS TARGET.indi_pub_downloads_year;
INSERT INTO TARGET.indi_pub_downloads_datasource_year select * from TARGET.indi_pub_downloads_datasource_year orig where exists (select 1 from TARGET.result_new r where r.id=orig.result_id);
COMPUTE STATS TARGET.indi_pub_downloads_datasource_year;
---- Sprint 7 ----
INSERT INTO TARGET.indi_pub_gold_oa select * from TARGET.indi_pub_gold_oa orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_gold_oa;
INSERT INTO TARGET.indi_pub_hybrid select * from TARGET.indi_pub_hybrid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_hybrid;
INSERT INTO TARGET.indi_pub_has_preprint select * from TARGET.indi_pub_has_preprint orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_has_preprint;
INSERT INTO TARGET.indi_pub_in_subscribed select * from TARGET.indi_pub_in_subscribed orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_pub_in_subscribed;
INSERT INTO TARGET.indi_result_with_pid select * from TARGET.indi_result_with_pid orig where exists (select 1 from TARGET.result_new r where r.id=orig.id);
COMPUTE STATS TARGET.indi_result_with_pid;
--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;

77
dhp-workflows/dhp-monitor-update/src/main/resources/eu/dnetlib/dhp/oa/graph/monitor/oozie_app/workflow.xml
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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>${monitor_db_name}</argument>
<argument>${wf:appPath()}/scripts/createMonitorDB.sql</argument>
<file>monitor.sh</file>
</shell>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>