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[orcidenrichment] refactoring

This commit is contained in:
Miriam Baglioni 2024-11-06 14:15:34 +01:00
parent 939c84ede6
commit e4f89f9800
2 changed files with 26 additions and 244 deletions
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23
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json
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@ -1,21 +1,32 @@
[ [
{ {
"paramName":"s", "paramName":"s",
"paramLongName":"sourcePath", "paramLongName":"graphPath",
"paramDescription": "the path of the sequencial file to read", "paramDescription": "the path of the sequencial file to read",
"paramRequired": true "paramRequired": true
}, },
{ {
"paramName": "out", "paramName": "out",
"paramLongName": "outputPath", "paramLongName": "targetPath",
"paramDescription": "the path used to store temporary output files", "paramDescription": "the path used to store temporary output files",
"paramRequired": true "paramRequired": true
}, }, {
"paramName": "o",
"paramLongName": "orcidPath",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
}, {
"paramName": "w",
"paramLongName": "workingDir",
"paramDescription": "the path used to store temporary output files",
"paramRequired": true
},
{ {
"paramName": "ssm", "paramName": "m",
"paramLongName": "isSparkSessionManaged", "paramLongName": "matchingSource",
"paramDescription": "true if the spark session is managed, false otherwise", "paramDescription": "the path used to store temporary output files",
"paramRequired": false "paramRequired": false
} }
] ]

247
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml
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@ -92,21 +92,14 @@
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<join name="copy_wait" to="fork_prepare_assoc_step1"/> <join name="copy_wait" to="exec_propagation"/>
<fork name="fork_prepare_assoc_step1"> <action name="exec_propagation">
<path start="join_prepare_publication"/>
<path start="join_prepare_dataset"/>
<path start="join_prepare_otherresearchproduct"/>
<path start="join_prepare_software"/>
</fork>
<action name="join_prepare_publication">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>ORCIDPropagation-PreparePhase1-Publications</name> <name>ORCIDPropagation-PreparePhase1-Publications</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class> <class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkPropagateOrcidAuthor</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar> <jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
@ -119,239 +112,17 @@
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=8000 --conf spark.sql.shuffle.partitions=8000
</spark-opts> </spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--graphPath</arg><arg>${sourcePath}/</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--orcidPath</arg><arg>${sourcePath}/</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg> <arg>--workingDir</arg><arg>${workingDir}/</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg> <arg>--targetPath</arg><arg>${outputPath}/</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg> <arg>--matchingSource</arg><arg>graph</arg>
</spark> </spark>
<ok to="wait"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="join_prepare_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-PreparePhase1-Dataset</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_prepare_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-PreparePhase1-ORP</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="join_prepare_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-PreparePhase1-Software</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<join name="wait" to="prepare_assoc_step2"/>
<action name="prepare_assoc_step2">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-PreparePhase2</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep2</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/orcid/targetOrcidAssoc</arg>
<arg>--outputPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
</spark>
<ok to="fork-join-exec-propagation"/>
<error to="Kill"/>
</action>
<fork name="fork-join-exec-propagation">
<path start="join_propagate_publication"/>
<path start="join_propagate_dataset"/>
<path start="join_propagate_otherresearchproduct"/>
<path start="join_propagate_software"/>
</fork>
<action name="join_propagate_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-Publication</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=15000
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-Dataset</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=8000
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-ORP</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=8000
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
</action>
<action name="join_propagate_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>ORCIDPropagation-Software</name>
<class>eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.executor.memoryOverhead=${sparkExecutorMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=4000
</spark-opts>
<arg>--possibleUpdatesPath</arg><arg>${workingDir}/orcid/mergedOrcidAssoc</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${outputPath}/software</arg>
</spark>
<ok to="wait2"/>
<error to="Kill"/>
</action>
<join name="wait2" to="End"/>
<end name="End"/> <end name="End"/>