forked from D-Net/dnet-hadoop
cleanup old doiboost workflows
This commit is contained in:
parent
fddbc8364e
commit
a3948c1f6e
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</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>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>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
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</property>
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</configuration>
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@ -1,372 +0,0 @@
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<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorIntersectionMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<!-- Itersection Parameters -->
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<property>
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<name>workingPath</name>
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<description>the working Path</description>
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</property>
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<property>
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<name>hostedByMapPath</name>
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<description>the hostedByMap Path</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the Path of the sequence file action set</description>
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</property>
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<!-- Crossref Parameters -->
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<property>
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<name>inputPathCrossref</name>
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<description>the Crossref input path</description>
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</property>
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<property>
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<name>crossrefTimestamp</name>
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<description>Timestamp for the Crossref incremental Harvesting</description>
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</property>
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<property>
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<name>esServer</name>
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<description>elasticsearch server url for the Crossref Harvesting</description>
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</property>
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<property>
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<name>esIndex</name>
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<description>elasticsearch index name for the Crossref Harvesting</description>
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</property>
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<!-- MAG Parameters -->
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<property>
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<name>MAGDumpPath</name>
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<description>the MAG dump working path</description>
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</property>
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<property>
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<name>inputPathMAG</name>
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<description>the MAG working path</description>
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</property>
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<!-- UnpayWall Parameters -->
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<property>
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<name>inputPathUnpayWall</name>
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<description>the UnpayWall working path</description>
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</property>
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<!-- ORCID Parameters -->
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<property>
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<name>inputPathOrcid</name>
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<description>the ORCID input path</description>
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</property>
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<property>
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<name>workingPathOrcid</name>
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<description>the ORCID working path</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="resume_from"/>
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<decision name="resume_from">
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<switch>
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<case to="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
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<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
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<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
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<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
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<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
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<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
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<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
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<default to="ImportCrossRef"/>
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</switch>
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</decision>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportCrossRef">
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<java>
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<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/index_update</arg>
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<arg>--namenode</arg><arg>${nameNode}</arg>
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<arg>--esServer</arg><arg>${esServer}</arg>
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<arg>--esIndex</arg><arg>${esIndex}</arg>
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<arg>--timestamp</arg><arg>${crossrefTimestamp}</arg>
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</java>
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<ok to="GenerateCrossrefDataset"/>
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<error to="Kill"/>
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</action>
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<!-- CROSSREF SECTION -->
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<action name="GenerateCrossrefDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>GenerateCrossrefDataset</name>
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<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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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}${spark2EventLogDir}
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</spark-opts>
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<arg>--workingPath</arg><arg>${inputPathCrossref}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="RenameDataset"/>
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<error to="Kill"/>
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</action>
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<action name="RenameDataset">
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<fs>
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<delete path="${inputPathCrossref}/crossref_ds"/>
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<move source="${inputPathCrossref}/crossref_ds_updated"
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target="${inputPathCrossref}/crossref_ds"/>
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</fs>
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<ok to="ResetMagWorkingPath"/>
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<error to="Kill"/>
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</action>
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<!-- MAG SECTION -->
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<action name="ResetMagWorkingPath">
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<fs>
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<delete path="${inputPathMAG}/dataset"/>
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<delete path="${inputPathMAG}/process"/>
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</fs>
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<ok to="ConvertMagToDataset"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertMagToDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert Mag to Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${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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</spark-opts>
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<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
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<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="ConvertCrossrefToOAF"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertCrossrefToOAF">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ConvertCrossrefToOAF</name>
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<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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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}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="ProcessMAG"/>
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<error to="Kill"/>
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</action>
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<action name="ProcessMAG">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert Mag to OAF Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkProcessMAG</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorIntersectionMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${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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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
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<arg>--workingPath</arg><arg>${inputPathMAG}/process</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="ProcessUW"/>
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<error to="Kill"/>
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</action>
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<!-- UnpayWall SECTION -->
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<action name="ProcessUW">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert UnpayWall to Dataset</name>
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<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${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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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
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<arg>--targetPath</arg><arg>${workingPath}/uwPublication</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="ProcessORCID"/>
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<error to="Kill"/>
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</action>
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<!-- ORCID SECTION -->
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<action name="ProcessORCID">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert ORCID to Dataset</name>
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<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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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}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
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<arg>--workingPath</arg><arg>${workingPathOrcid}</arg>
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<arg>--targetPath</arg><arg>${workingPath}/orcidPublication</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="CreateDOIBoost"/>
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<error to="Kill"/>
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</action>
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<!-- INTERSECTION SECTION-->
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<action name="CreateDOIBoost">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Create DOIBoost Infospace</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorIntersectionMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.sql.shuffle.partitions=3840
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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}${spark2EventLogDir}
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</spark-opts>
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<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
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<arg>--affiliationPath</arg><arg>${inputPathMAG}/dataset/Affiliations</arg>
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<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/dataset/PaperAuthorAffiliations</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="GenerateActionSet"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateActionSet">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Generate DOIBoost ActionSet</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${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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</spark-opts>
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<arg>--dbPublicationPath</arg><arg>${workingPath}/doiBoostPublicationFiltered</arg>
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<arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
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<arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
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<arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
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<arg>--dbOrganizationPath</arg><arg>${workingPath}/doiBoostOrganization</arg>
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<arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
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<arg>--sFilePath</arg><arg>${outputPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</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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<end name="End"/>
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</workflow-app>
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