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new workflow for country propagation: it is composed of the preparation step and in the propagation. The propagation part runs in parallel on the result types

This commit is contained in:
Miriam Baglioni 2020-04-11 16:40:22 +02:00
parent a562080b0b
commit 87f802821e
1 changed files with 70 additions and 77 deletions
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107
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml
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@ -36,14 +36,6 @@
<name>saveGraph</name> <name>saveGraph</name>
<description>writes new version of the graph after the propagation step</description> <description>writes new version of the graph after the propagation step</description>
</property> </property>
<property>
<name>outputPath</name>
<description>the path used to store temporary output files</description>
</property>
<property>
<name>preparedInfoPath</name>
<description>the path where prepared info have been stored</description>
</property>
</parameters> </parameters>
@ -59,17 +51,16 @@
<mode>cluster</mode> <mode>cluster</mode>
<name>PrepareDatasourceCountryAssociation</name> <name>PrepareDatasourceCountryAssociation</name>
<class>eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation</class> <class>eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar> <jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCoresForJoining} --executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemoryForJoining} --executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemoryForJoining} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg> <arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg> <arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
@ -80,8 +71,8 @@
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<fork name="fork_join_apply_country_propagation"> <fork name="fork_join_apply_country_propagation">
<!-- <path start="join_propagation_publication"/>--> <path start="join_propagation_publication"/>
<!-- <path start="join_propagation_dataset"/>--> <path start="join_propagation_dataset"/>
<path start="join_propagation_otherresearchproduct"/> <path start="join_propagation_otherresearchproduct"/>
<path start="join_propagation_software"/> <path start="join_propagation_software"/>
</fork> </fork>
@ -92,18 +83,19 @@
<mode>cluster</mode> <mode>cluster</mode>
<name>countryPropagationForPublications</name> <name>countryPropagationForPublications</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class> <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar> <jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCoresForJoining} --executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemoryForJoining} --executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemoryForJoining} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg> <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg> <arg>--saveGraph</arg><arg>${saveGraph}</arg>
@ -111,7 +103,7 @@
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg> <arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark> </spark>
<ok to="end"/> <ok to="wait"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
@ -121,26 +113,27 @@
<mode>cluster</mode> <mode>cluster</mode>
<name>countryPropagationForDataset</name> <name>countryPropagationForDataset</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class> <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar> <jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCoresForJoining} --executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemoryForJoining} --executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemoryForJoining} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg> <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg> <arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg> <arg>--outputPath</arg><arg>${workingDir}/country_propagation/dataset</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark> </spark>
<ok to="end"/> <ok to="wait"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
@ -150,26 +143,27 @@
<mode>cluster</mode> <mode>cluster</mode>
<name>countryPropagationForORP</name> <name>countryPropagationForORP</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class> <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar> <jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCoresForJoining} --executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemoryForJoining} --executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemoryForJoining} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg> <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg> <arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Otherresearchproduct</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg> <arg>--outputPath</arg><arg>${workingDir}/country_propagation/otherresearchproduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark> </spark>
<ok to="end"/> <ok to="wait"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
@ -179,42 +173,40 @@
<mode>cluster</mode> <mode>cluster</mode>
<name>countryPropagationForSoftware</name> <name>countryPropagationForSoftware</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class> <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar> <jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-cores=${sparkExecutorCoresForJoining} --executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemoryForJoining} --executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemoryForJoining} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg> <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg> <arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg> <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg> <arg>--outputPath</arg><arg>${workingDir}/country_propagation/software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg> <arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark> </spark>
<ok to="end"/> <ok to="wait"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<action name="CountryPropagation"> <action name="CountryPropagation">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker> <master>yarn</master>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>CountryPropagation</name> <name>countryPropagationForSoftware</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob</class> <class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-propagation-${projectVersion}.jar</jar> <jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory} --driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
@ -225,15 +217,16 @@
</spark-opts> </spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg> <arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg> <arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg> <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg> <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg> <arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark> </spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>
<join name="wait" to="End"/>
<end name="End"/> <end name="End"/>
</workflow-app> </workflow-app>