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master #11

Manually merged
claudio.atzori merged 275 commits from :master into enrichment_wfs 2020-05-11 15:14:56 +02:00
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1 changed files with 100 additions and 8 deletions
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dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/projecttoresult/oozie_app/workflow.xml
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@ -20,14 +20,96 @@
<name>sparkExecutorCores</name>
<description>number of cores used by single executor</description>
</property>
<property>
<name>writeUpdate</name>
<description>writes the information found for the update. No double check done if the information is already present</description>
</property>
<property>
<name>saveGraph</name>
<description>writes new version of the graph after the propagation step</description>
</property>
</parameters>
<start to="ProjectPropagation"/>
<start to="reset-outputpath"/>
<!--<start to="prepare_project_results_association"/>-->
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset-outputpath">
<fs>
<delete path='${workingDir}/projecttoresult_propagation/relation'/>
</fs>
<ok to="copy_relation"/>
<error to="Kill"/>
</action>
<action name="copy_relation">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<arg>${nameNode}/${sourcePath}/relation</arg>
<arg>${nameNode}/${workingDir}/projecttoresult_propagation/relation</arg>
</distcp>
<ok to="prepare_project_results_association"/>
<error to="Kill"/>
</action>
<action name="prepare_project_results_association">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>PrepareProjectResultsAssociation</name>
<class>eu.dnetlib.dhp.projecttoresult.PrepareProjectResultsAssociation</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/projecttoresult_propagation/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/projecttoresult_propagation/preparedInfo/alreadyLinked</arg>
</spark>
<ok to="apply_propagation"/>
<error to="Kill"/>
</action>
<action name="apply_propagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ProjectToResultPropagation</name>
<class>eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob3</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--outputPath</arg><arg>${workingDir}/projecttoresult_propagation/relation</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/projecttoresult_propagation/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/projecttoresult_propagation/preparedInfo/alreadyLinked</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<action name="ProjectPropagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
@ -35,17 +117,27 @@
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>ProjectToResultPropagation</name>
<class>eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob</class>
<class>eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob2</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory}
--executor-cores ${sparkExecutorCores}
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--potentialUpdatePath</arg><arg>${workingDir}/projecttoresult_propagation/preparedInfo/potentialUpdates</arg>
<arg>--alreadyLinkedPath</arg><arg>${workingDir}/projecttoresult_propagation/preparedInfo/alreadyLinked</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>