467 lines
21 KiB
XML
467 lines
21 KiB
XML
<workflow-app name="dump_graph" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source 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 output path</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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</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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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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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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<description>spark 2.* extra listeners classname</description>
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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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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</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>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="dump_result"/>
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<decision name="filter_set">
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<switch>
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<case to="filter">${wf:conf('filter') eq "true"}</case>
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<default to="copy_graph"/>
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</switch>
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</decision>
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<fork name="copy_graph">
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<path start="copy_relation"/>
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<path start="copy_organization"/>
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<path start="copy_projects"/>
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<path start="copy_datasources"/>
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<path start="copy_publication"/>
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<path start="copy_dataset"/>
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<path start="copy_software"/>
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<path start="copy_otherresearchproduct"/>
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</fork>
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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}/graph/relation</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_organization">
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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}/organization</arg>
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<arg>${nameNode}/${workingDir}/graph/organization</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_projects">
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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}/project</arg>
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<arg>${nameNode}/${workingDir}/graph/project</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_datasources">
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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}/datasource</arg>
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<arg>${nameNode}/${workingDir}/graph/datasource</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_publication">
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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}/publication</arg>
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<arg>${nameNode}/${workingDir}/graph/publication</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_dataset">
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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}/dataset</arg>
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<arg>${nameNode}/${workingDir}/graph/dataset</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_software">
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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}/software</arg>
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<arg>${nameNode}/${workingDir}/graph/software</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_otherresearchproduct">
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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}/otherresearchproduct</arg>
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<arg>${nameNode}/${workingDir}/graph/otherresearchproduct</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<join name="copy_wait" to="emit_from_result"/>
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<action name="filter">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Selecting subset of results</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.filterentities.FilterEntities</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=4
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--executor-memory=4G
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=5G
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--conf spark.extraListeners=${spark2ExtraListeners}
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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}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--workingDir</arg><arg>${workingDir}/graph/</arg>
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<arg>--filterPath</arg><arg>${filterPath}</arg>
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</spark>
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<ok to="select_relevant_graph_subset"/>
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<error to="Kill"/>
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</action>
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<action name="select_relevant_graph_subset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Selecting relevant linked relations and entities</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.filterentities.SelectConnectedEntities</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=4
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--executor-memory=4G
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=5G
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--conf spark.extraListeners=${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.sql.warehouse.dir=${sparkSqlWarehouseDir}
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<!-- <arg>--workingDir</arg><arg>${workingDir}/graph/</arg>-->
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<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/graph/</arg>
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<arg>--filterPath</arg><arg>${filterPath}</arg>
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</spark>
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<!-- <ok to="emit_from_result"/>-->
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<ok to="copy_graph_publication"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_publication">
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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>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/publication</arg>
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<arg>${nameNode}/${workingDir}/graph/publication</arg>
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</distcp>
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<ok to="copy_graph_dataset"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_dataset">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/dataset</arg>
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<arg>${nameNode}/${workingDir}/graph/dataset</arg>
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</distcp>
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<ok to="copy_graph_otherresearchproduct"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_otherresearchproduct">
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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>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/otherresearchproduct</arg>
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<arg>${nameNode}/${workingDir}/graph/otherresearchproduct</arg>
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</distcp>
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<ok to="copy_graph_software"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_software">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/software</arg>
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<arg>${nameNode}/${workingDir}/graph/software</arg>
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</distcp>
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<ok to="copy_graph_datasource"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_datasource">
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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>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/datasource</arg>
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<arg>${nameNode}/${workingDir}/graph/datasource</arg>
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</distcp>
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<ok to="copy_graph_project"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_project">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/project</arg>
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<arg>${nameNode}/${workingDir}/graph/project</arg>
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</distcp>
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<ok to="copy_graph_organization"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_organization">
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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>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/organization</arg>
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<arg>${nameNode}/${workingDir}/graph/organization</arg>
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</distcp>
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<ok to="copy_graph_relation"/>
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<error to="Kill"/>
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</action>
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<action name="copy_graph_relation">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/user/miriam.baglioni/oa/graph/dump/temp/graph/relation</arg>
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<arg>${nameNode}/${workingDir}/graph/relation</arg>
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</distcp>
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<ok to="emit_from_result"/>
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<error to="Kill"/>
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</action>
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<action name="emit_from_result">
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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>Emit from Result</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.skgif.EmitFromEntities</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.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}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/graph/</arg>-->
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<!-- <arg>--workingDir</arg><arg>${workingDir}/</arg>-->
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/</arg>
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<arg>--sourcePath</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/graph/</arg>
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</spark>
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<ok to="dump_result"/>
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<error to="Kill"/>
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</action>
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<action name="dump_result">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table results </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.skgif.DumpResult</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=4
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--executor-memory=8G
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=5G
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--conf spark.extraListeners=${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.sql.warehouse.dir=${sparkSqlWarehouseDir}
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--conf spark.sql.shuffle.partitions=15000
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</spark-opts>
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/graph/</arg>-->
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<arg>--sourcePath</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/graph/</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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<!-- <arg>--workingDir</arg><arg>${workingDir}/</arg>-->
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<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/</arg>
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</spark>
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<ok to="dump_datasource"/>
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<error to="Kill"/>
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</action>
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<action name="dump_datasource">
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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>Dump table datasource </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.skgif.DumpDatasource</class>
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<jar>dump-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.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}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/graph/</arg>-->
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<arg>--sourcePath</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/graph/</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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<!-- <arg>--workingDir</arg><arg>${workingDir}/</arg>-->
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<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/</arg>
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</spark>
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<ok to="dump_venue"/>
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<error to="Kill"/>
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</action>
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<action name="dump_venue">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table venues </name>
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<class>eu.dnetlib.dhp.oa.graph.dump.skgif.DumpVenue</class>
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<jar>dump-${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=${sparkDriverMemory}
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--conf spark.extraListeners=${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.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<!-- <arg>--sourcePath</arg><arg>${workingDir}/graph/</arg>-->
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<arg>--sourcePath</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/graph/</arg>
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<arg>--outputPath</arg><arg>${outputPath}</arg>
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<!-- <arg>--workingDir</arg><arg>${workingDir}/</arg>-->
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<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/</arg>
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</spark>
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<ok to="dump_organization"/>
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<error to="Kill"/>
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</action>
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<action name="dump_organization">
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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>
|
|
<name>Dump table organization </name>
|
|
<class>eu.dnetlib.dhp.oa.graph.dump.skgif.DumpOrganization</class>
|
|
<jar>dump-${projectVersion}.jar</jar>
|
|
<spark-opts>
|
|
--executor-memory=${sparkExecutorMemory}
|
|
--executor-cores=${sparkExecutorCores}
|
|
--driver-memory=${sparkDriverMemory}
|
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
|
</spark-opts>
|
|
<!-- <arg>--sourcePath</arg><arg>${workingDir}/graph/</arg>-->
|
|
<arg>--sourcePath</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/graph/</arg>
|
|
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
|
<!-- <arg>--workingDir</arg><arg>${workingDir}/</arg>-->
|
|
<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/</arg>
|
|
</spark>
|
|
<ok to="dump_grant"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
<action name="dump_grant">
|
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
|
<master>yarn</master>
|
|
<mode>cluster</mode>
|
|
<name>Dump table project </name>
|
|
<class>eu.dnetlib.dhp.oa.graph.dump.skgif.DumpGrant</class>
|
|
<jar>dump-${projectVersion}.jar</jar>
|
|
<spark-opts>
|
|
--executor-memory=${sparkExecutorMemory}
|
|
--executor-cores=${sparkExecutorCores}
|
|
--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.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
|
|
|
</spark-opts>
|
|
<!-- <arg>--sourcePath</arg><arg>${workingDir}/graph/</arg>-->
|
|
<arg>--sourcePath</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/graph/</arg>
|
|
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
|
<!-- <arg>--workingDir</arg><arg>${workingDir}/</arg>-->
|
|
<arg>--workingDir</arg><arg>/user/miriam.baglioni/oa/graph/dump/temp/working_dir/</arg>
|
|
</spark>
|
|
<ok to="End"/>
|
|
<error to="Kill"/>
|
|
</action>
|
|
|
|
<end name="End"/>
|
|
</workflow-app> |