forked from D-Net/dnet-hadoop
109 lines
4.4 KiB
XML
109 lines
4.4 KiB
XML
<workflow-app name="Transform_BioEntity_Workflow" 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 PDB Database Working Path</description>
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</property>
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<property>
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<name>database</name>
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<description>the PDB Database Working Path</description>
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</property>
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<property>
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<name>mdStoreOutputId</name>
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<description>the identifier of the cleaned MDStore</description>
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</property>
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<property>
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<name>mdStoreManagerURI</name>
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<description>the path of the cleaned mdstore</description>
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</property>
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</parameters>
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<start to="StartTransaction"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="StartTransaction">
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<java>
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<configuration>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
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<arg>--action</arg><arg>NEW_VERSION</arg>
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<arg>--mdStoreID</arg><arg>${mdStoreOutputId}</arg>
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<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
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<capture-output/>
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</java>
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<ok to="ConvertDB"/>
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<error to="RollBack"/>
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</action>
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<action name="ConvertDB">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Convert Bio DB to OAF Dataset</name>
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<class>eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF</class>
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<jar>dhp-aggregation-${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.shuffle.partitions=2000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--dbPath</arg><arg>${sourcePath}</arg>
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<arg>--database</arg><arg>${database}</arg>
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<arg>--mdstoreOutputVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
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</spark>
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<ok to="CommitVersion"/>
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<error to="RollBack"/>
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</action>
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<action name="CommitVersion">
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<java>
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<configuration>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
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<arg>--action</arg><arg>COMMIT</arg>
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<arg>--namenode</arg><arg>${nameNode}</arg>
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<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
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<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</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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<action name="RollBack">
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<java>
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<configuration>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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<main-class>eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode</main-class>
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<arg>--action</arg><arg>ROLLBACK</arg>
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<arg>--mdStoreVersion</arg><arg>${wf:actionData('StartTransaction')['mdStoreVersion']}</arg>
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<arg>--mdStoreManagerURI</arg><arg>${mdStoreManagerURI}</arg>
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</java>
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<ok to="Kill"/>
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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> |