forked from D-Net/dnet-hadoop
added proeprties for the preparation step and actual propagation. Added the new parametrized workflow
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6f35f5ca42
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15656684b9
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@ -1,21 +1,51 @@
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[
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{
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"paramName":"mt",
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"paramLongName":"master",
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"paramDescription": "should be local or yarn",
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"paramRequired": true
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},
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramDescription": "the path of the sequencial file to read",
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"paramRequired": true
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},
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{
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"paramName":"ocm",
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"paramLongName":"organizationtoresultcommunitymap",
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"paramDescription": "the map in json format assocaition the organization original id with the list of communities",
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"paramName":"h",
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"paramLongName":"hive_metastore_uris",
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"paramDescription": "the hive metastore uris",
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"paramRequired": true
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},
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{
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"paramName":"sg",
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"paramLongName":"saveGraph",
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"paramDescription": "true if the new version of the graph must be saved",
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"paramRequired": false
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},
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{
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"paramName":"test",
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"paramLongName":"isTest",
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"paramDescription": "true if it is executing a test",
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"paramRequired": false
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},
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{
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"paramName": "out",
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"paramLongName": "outputPath",
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"paramDescription": "the path used to store temporary output files",
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"paramRequired": true
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},
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{
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"paramName": "ssm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "true if the spark session is managed, false otherwise",
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"paramRequired": false
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},
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{
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"paramName":"tn",
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"paramLongName":"resultTableName",
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"paramDescription": "the name of the result table we are currently working on",
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"paramRequired": true
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},
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{
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"paramName": "p",
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"paramLongName": "preparedInfoPath",
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"paramDescription": "the path where prepared info have been stored",
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"paramRequired": true
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}
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]
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@ -28,6 +28,12 @@
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"paramLongName":"isTest",
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"paramDescription": "true if it is executing a test",
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"paramRequired": false
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},
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{
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"paramName": "out",
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"paramLongName": "outputPath",
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"paramDescription": "the path used to store temporary output files",
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"paramRequired": true
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}
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]
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@ -15,4 +15,44 @@
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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>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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<property>
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<name>sparkExecutorNumber</name>
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<value>4</value>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<value>15G</value>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<value>6G</value>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<value>1</value>
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</property>
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<property>
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<name>spark2MaxExecutors</name>
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<value>50</value>
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</property>
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</configuration>
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@ -9,47 +9,185 @@
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<description>organization community map</description>
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</property>
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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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<name>writeUpdate</name>
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<description>writes the information found for the update. No double check done if the information is already present</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>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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<name>saveGraph</name>
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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="CommunityToResultFromOrganizationPropagation"/>
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<start to="reset-outputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="CommunityToResultFromOrganizationPropagation">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ProjectToResultPropagation</name>
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<class>eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>--executor-memory ${sparkExecutorMemory}
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--executor-cores ${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
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--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
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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>${sourcePath}</arg>
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<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
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</spark>
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<ok to="End"/>
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<action name="reset-outputpath">
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<fs>
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<delete path='${workingDir}/resulttocommunityorganization_propagation'/>
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</fs>
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<ok to="copy_relation"/>
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<error to="Kill"/>
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</action>
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<action name="copy_relation">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/relation</arg>
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<arg>${nameNode}/${workingDir}/projecttoresult_propagation/relation</arg>
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</distcp>
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<ok to="prepare_result_communitylist"/>
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<error to="Kill"/>
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</action>
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<action name="prepare_result_communitylist">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Prepare-Community-Result-Organization</name>
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<class>eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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=${spark2MaxExecutors}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
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<arg>--organizationtoresultcommunitymap</arg><arg>${organizationtoresultcommunitymap}</arg>
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</spark>
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<ok to="fork-join-exec-propagation"/>
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<!-- <ok to="End"/>-->
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<error to="Kill"/>
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</action>
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<fork name="fork-join-exec-propagation">
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<path start="join_propagate_publication"/>
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<path start="join_propagate_dataset"/>
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<path start="join_propagate_otherresearchproduct"/>
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<path start="join_propagate_software"/>
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</fork>
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<action name="join_propagate_publication">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>community2resultfromorganization-Publication</name>
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<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob2</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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=${spark2MaxExecutors}
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</spark-opts>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
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</spark>
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<ok to="wait2"/>
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<error to="Kill"/>
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</action>
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<action name="join_propagate_dataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>community2resultfromorganization-Dataset</name>
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<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob2</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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=${spark2MaxExecutors}
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</spark-opts>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
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</spark>
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<ok to="wait2"/>
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<error to="Kill"/>
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</action>
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<action name="join_propagate_otherresearchproduct">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>community2resultfromorganization-ORP</name>
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<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob2</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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=${spark2MaxExecutors}
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</spark-opts>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
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</spark>
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<ok to="wait2"/>
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<error to="Kill"/>
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</action>
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<action name="join_propagate_software">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>community2resultfromorganization-Software</name>
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<class>eu.dnetlib.dhp.resulttocommunityfromorganization.SparkResultToCommunityFromOrganizationJob2</class>
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<jar>dhp-propagation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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=${spark2MaxExecutors}
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</spark-opts>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
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<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--outputPath</arg><arg>${workingDir}/software</arg>
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</spark>
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<ok to="wait2"/>
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<error to="Kill"/>
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</action>
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<join name="wait2" to="End"/>
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<end name="End"/>
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</workflow-app>
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