[orcidenrichment] refactoring
This commit is contained in:
parent
939c84ede6
commit
e4f89f9800
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@ -1,21 +1,32 @@
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[
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{
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"paramName":"s",
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"paramLongName":"sourcePath",
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"paramLongName":"graphPath",
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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": "out",
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"paramLongName": "outputPath",
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"paramLongName": "targetPath",
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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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"paramName": "o",
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"paramLongName": "orcidPath",
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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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"paramName": "w",
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"paramLongName": "workingDir",
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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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"paramName": "m",
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"paramLongName": "matchingSource",
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"paramDescription": "the path used to store temporary output files",
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"paramRequired": false
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}
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]
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@ -92,21 +92,14 @@
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<error to="Kill"/>
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</action>
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<join name="copy_wait" to="fork_prepare_assoc_step1"/>
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<join name="copy_wait" to="exec_propagation"/>
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<fork name="fork_prepare_assoc_step1">
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<path start="join_prepare_publication"/>
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<path start="join_prepare_dataset"/>
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<path start="join_prepare_otherresearchproduct"/>
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<path start="join_prepare_software"/>
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</fork>
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<action name="join_prepare_publication">
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<action name="exec_propagation">
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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>ORCIDPropagation-PreparePhase1-Publications</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkPropagateOrcidAuthor</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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@ -119,239 +112,17 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=8000
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--hive_metastore_uris</arg><arg>${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>${workingDir}/orcid/targetOrcidAssoc</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
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<arg>--graphPath</arg><arg>${sourcePath}/</arg>
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<arg>--orcidPath</arg><arg>${sourcePath}/</arg>
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<arg>--workingDir</arg><arg>${workingDir}/</arg>
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<arg>--targetPath</arg><arg>${outputPath}/</arg>
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<arg>--matchingSource</arg><arg>graph</arg>
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</spark>
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<ok to="wait"/>
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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="join_prepare_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>ORCIDPropagation-PreparePhase1-Dataset</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--hive_metastore_uris</arg><arg>${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>${workingDir}/orcid/targetOrcidAssoc</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<action name="join_prepare_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>ORCIDPropagation-PreparePhase1-ORP</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--hive_metastore_uris</arg><arg>${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>${workingDir}/orcid/targetOrcidAssoc</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<action name="join_prepare_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>ORCIDPropagation-PreparePhase1-Software</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--hive_metastore_uris</arg><arg>${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>${workingDir}/orcid/targetOrcidAssoc</arg>
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<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<join name="wait" to="prepare_assoc_step2"/>
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<action name="prepare_assoc_step2">
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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>ORCIDPropagation-PreparePhase2</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep2</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
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<arg>--outputPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
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</spark>
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<ok to="fork-join-exec-propagation"/>
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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>ORCIDPropagation-Publication</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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--conf spark.extraListeners=${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.shuffle.partitions=15000
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</spark-opts>
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<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
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<arg>--sourcePath</arg><arg>${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>${outputPath}/publication</arg>
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</spark>
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<ok to="wait2"/>
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<error to="Kill"/>
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</action>
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<action name="join_propagate_dataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDPropagation-Dataset</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
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<jar>dhp-enrichment-${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=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=8000
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</spark-opts>
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<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--outputPath</arg><arg>${outputPath}/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>ORCIDPropagation-ORP</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
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<jar>dhp-enrichment-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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--conf spark.extraListeners=${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.shuffle.partitions=8000
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</spark-opts>
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<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
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<arg>--sourcePath</arg><arg>${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>${outputPath}/otherresearchproduct</arg>
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</spark>
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<ok to="wait2"/>
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<error to="Kill"/>
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</action>
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<action name="join_propagate_software">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>ORCIDPropagation-Software</name>
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<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
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<jar>dhp-enrichment-${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=${sparkDriverMemory}
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--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
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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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=4000
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</spark-opts>
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<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
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<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--outputPath</arg><arg>${outputPath}/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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