430 lines
19 KiB
XML
430 lines
19 KiB
XML
<workflow-app name="dump_community_products" 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>isLookUpUrl</name>
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<description>the isLookup service endpoint</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>accessToken</name>
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<description>the access token used for the deposition in Zenodo</description>
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</property>
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<property>
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<name>connectionUrl</name>
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<description>the connection url for Zenodo</description>
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</property>
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<property>
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<name>metadata</name>
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<description> the metadata associated to the deposition</description>
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</property>
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<property>
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<name>newDeposition</name>
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<description>true if it is a brand new depositon. false for new version of an old deposition</description>
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</property>
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<property>
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<name>conceptRecordId</name>
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<description>for new version, the id of the record for the old deposition</description>
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</property>
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<property>
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<name>hiveDbName</name>
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<description>the target hive database name</description>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<description>hive server jdbc url</description>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<description>hive server metastore URIs</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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="reset_outputpath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="reset_outputpath">
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<fs>
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<delete path="${outputPath}"/>
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<mkdir path="${outputPath}"/>
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</fs>
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<ok to="save_community_map"/>
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<error to="Kill"/>
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</action>
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<action name="save_community_map">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap</main-class>
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<arg>--outputPath</arg><arg>${workingDir}/communityMap</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</java>
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<ok to="fork_dump"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_dump">
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<path start="dump_publication"/>
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<path start="dump_dataset"/>
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<path start="dump_orp"/>
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<path start="dump_software"/>
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</fork>
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<action name="dump_publication">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table publication for community related products</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
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<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--outputPath</arg><arg>${workingDir}/publication</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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</spark>
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<ok to="join_dump"/>
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<error to="Kill"/>
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</action>
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<action name="dump_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>Dump table dataset for community related products</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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>${sourcePath}/dataset</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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</spark>
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<ok to="join_dump"/>
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<error to="Kill"/>
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</action>
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<action name="dump_orp">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Dump table ORP for community related products</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
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<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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</spark>
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<ok to="join_dump"/>
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<error to="Kill"/>
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</action>
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<action name="dump_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>Dump table software for community related products</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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>${sourcePath}/software</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--outputPath</arg><arg>${workingDir}/software</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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</spark>
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<ok to="join_dump"/>
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<error to="Kill"/>
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</action>
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<join name="join_dump" to="prepareResultProject"/>
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<action name="prepareResultProject">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Prepare association result subset of project info</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
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<jar>dhp-graph-mapper-${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=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
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</spark>
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<ok to="fork_extendWithProject"/>
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<error to="Kill"/>
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</action>
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<fork name="fork_extendWithProject">
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<path start="extend_publication"/>
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<path start="extend_dataset"/>
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<path start="extend_orp"/>
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<path start="extend_software"/>
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</fork>
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<action name="extend_publication">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Extend dumped publications with information about project</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
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<jar>dhp-graph-mapper-${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}/publication</arg>
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<arg>--outputPath</arg><arg>${workingDir}/ext/publication</arg>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
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</spark>
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<ok to="join_extend"/>
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<error to="Kill"/>
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</action>
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<action name="extend_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>Extend dumped dataset with information about project</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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>${workingDir}/dataset</arg>
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<arg>--outputPath</arg><arg>${workingDir}/ext/dataset</arg>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
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</spark>
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<ok to="join_extend"/>
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<error to="Kill"/>
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</action>
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<action name="extend_orp">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Extend dumped ORP with information about project</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
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<jar>dhp-graph-mapper-${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}/otherresearchproduct</arg>
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<arg>--outputPath</arg><arg>${workingDir}/ext/orp</arg>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
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</spark>
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<ok to="join_extend"/>
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<error to="Kill"/>
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</action>
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<action name="extend_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>Extend dumped software with information about project</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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>${workingDir}/software</arg>
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<arg>--outputPath</arg><arg>${workingDir}/ext/software</arg>
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<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
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</spark>
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<ok to="join_extend"/>
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<error to="Kill"/>
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</action>
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<join name="join_extend" to="splitForCommunities"/>
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<action name="splitForCommunities">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Split dumped result for community</name>
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<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity</class>
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<jar>dhp-graph-mapper-${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}/ext</arg>
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<arg>--outputPath</arg><arg>${workingDir}/split</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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</spark>
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<ok to="make_archive"/>
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<error to="Kill"/>
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</action>
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<action name="make_archive">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.MakeTar</main-class>
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<arg>--hdfsPath</arg><arg>${outputPath}</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--sourcePath</arg><arg>${workingDir}/split</arg>
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</java>
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<ok to="send_zenodo"/>
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<error to="Kill"/>
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</action>
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<action name="send_zenodo">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
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<arg>--hdfsPath</arg><arg>${outputPath}</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--accessToken</arg><arg>${accessToken}</arg>
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<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
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<arg>--metadata</arg><arg>${metadata}</arg>
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<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
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<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
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<arg>--depositionType</arg><arg>${depositionType}</arg>
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</java>
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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> |