added hive parameter and a step of reset of the working dir in the workflow
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parent
6afbd542ca
commit
a9120164aa
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@ -19,6 +19,10 @@
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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@ -17,13 +17,21 @@
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<description>writes new version of the graph after the propagation step</description>
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</property>
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</parameters>
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<start to="reset-outputpath"/>
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<start to="fork_prepare_assoc_step1"/>
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<!-- <start to="fork_prepare_assoc_step1"/>-->
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="reset-outputpath">
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<fs>
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<delete path='${workingDir}/projecttoresult_propagation/relation'/>
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</fs>
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<ok to="fork_prepare_assoc_step1"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_prepare_assoc_step1">
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<path start="join_prepare_publication"/>
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<path start="join_prepare_dataset"/>
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@ -35,7 +43,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-PreparePhase1-Publications</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -63,7 +71,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-PreparePhase1-Dataset</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -91,7 +99,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-PreparePhase1-ORP</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -119,7 +127,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-PreparePhase1-Software</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -139,50 +147,17 @@
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<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/targetOrcidAssoc</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
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</spark>
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<ok to="End"/>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<action name="OrcidToResultFromSemRelPropagation">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>OrcidToResultFromSemRelPropagation</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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--num-executors=${sparkExecutorNumber}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.dynamicAllocation.enabled=true
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--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
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</spark-opts>
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<arg>-mt</arg> <arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
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<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
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<arg>--saveGraph</arg><arg>${saveGraph}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<join name="wait" to="prepare_assoc_step2"/>
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<action name="prepare_assoc_step2">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-PreparePhase2</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep2</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -215,7 +190,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-Publication</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -241,7 +216,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-Dataset</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -267,7 +242,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-ORP</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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@ -293,7 +268,7 @@
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDpropagationFromSemRel</name>
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<name>ORCIDPropagation-Software</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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