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Added workflow

This commit is contained in:
Sandro La Bruzzo 2024-01-10 19:42:22 +01:00
parent 1a42a5c10d
commit 8f61063201
3 changed files with 93 additions and 1 deletions
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2
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/orcid/OrcidGetUpdatesFile.java
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@ -41,7 +41,7 @@ public class OrcidGetUpdatesFile {
final String targetPath = parser.get("targetPath");
log.info("got variable targetPath: {}", targetPath);
//http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar
final String apiURL = parser.get("apiURL");
log.info("got variable apiURL: {}", apiURL);

23
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/config-default.xml Normal file
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@ -0,0 +1,23 @@
<configuration>
<property>
<name>jobTracker</name>
<value>yarnRM</value>
</property>
<property>
<name>nameNode</name>
<value>hdfs://nameservice1</value>
</property>
<property>
<name>oozie.use.system.libpath</name>
<value>true</value>
</property>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>

69
dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/collection/orcid/update/oozie_app/workflow.xml Normal file
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@ -0,0 +1,69 @@
<workflow-app name="download_Update_ORCID" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>targetPath</name>
<description>the path to store the original ORCID dump</description>
</property>
<property>
<name>apiURL</name>
<description>The URL of the update CSV list </description>
<value>http://74804fb637bd8e2fba5b-e0a029c2f87486cddec3b416996a6057.r3.cf1.rackcdn.com/last_modified.csv.tar</value>
</property>
<property>
<name>accessToken</name>
<description>The access tocken</description>
</property>
</parameters>
<start to="startUpdate"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="startUpdate">
<java>
<configuration>
<property>
<name>oozie.launcher.mapreduce.user.classpath.first</name>
<value>true</value>
</property>
</configuration>
<main-class>eu.dnetlib.dhp.collection.orcid.OrcidGetUpdatesFile</main-class>
<arg>--namenode</arg><arg>${nameNode}</arg>
<arg>--targetPath</arg><arg>${targetPath}</arg>
<arg>--apiURL</arg><arg>${apiURL}</arg>
<arg>--accessToken</arg><arg>${accessToken}</arg>
</java>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="generateTables">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Generate ORCID Tables</name>
<class>eu.dnetlib.dhp.collection.orcid.SparkGenerateORCIDTable</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts>
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=2g
--conf spark.sql.shuffle.partitions=3000
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${targetPath}/extracted</arg>
<arg>--targetPath</arg><arg>${targetPath}/tables</arg>
<arg>--master</arg><arg>yarn</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>