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master #11

Manually merged
claudio.atzori merged 275 commits from :master into enrichment_wfs 2020-05-11 15:14:56 +02:00
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1 changed files with 70 additions and 77 deletions
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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>
<description>writes new version of the graph after the propagation step</description>
</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>
@ -59,17 +51,16 @@
<mode>cluster</mode>
<name>PrepareDatasourceCountryAssociation</name>
<class>eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
@ -80,8 +71,8 @@
<error to="Kill"/>
</action>
<fork name="fork_join_apply_country_propagation">
<!-- <path start="join_propagation_publication"/>-->
<!-- <path start="join_propagation_dataset"/>-->
<path start="join_propagation_publication"/>
<path start="join_propagation_dataset"/>
<path start="join_propagation_otherresearchproduct"/>
<path start="join_propagation_software"/>
</fork>
@ -92,18 +83,19 @@
<mode>cluster</mode>
<name>countryPropagationForPublications</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
@ -111,7 +103,7 @@
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark>
<ok to="end"/>
<ok to="wait"/>
<error to="Kill"/>
</action>
@ -121,26 +113,27 @@
<mode>cluster</mode>
<name>countryPropagationForDataset</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</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>${workingDir}/country_propagation/preparedInfo</arg>
</spark>
<ok to="end"/>
<ok to="wait"/>
<error to="Kill"/>
</action>
@ -150,26 +143,27 @@
<mode>cluster</mode>
<name>countryPropagationForORP</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Otherresearchproduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/otherresearchproduct</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark>
<ok to="end"/>
<ok to="wait"/>
<error to="Kill"/>
</action>
@ -179,15 +173,47 @@
<mode>cluster</mode>
<name>countryPropagationForSoftware</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</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/software</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark>
<ok to="wait"/>
<error to="Kill"/>
</action>
<action name="CountryPropagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>countryPropagationForSoftware</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
@ -198,42 +224,9 @@
<arg>--outputPath</arg><arg>${workingDir}/country_propagation/publication</arg>
<arg>--preparedInfoPath</arg><arg>${workingDir}/country_propagation/preparedInfo</arg>
</spark>
<ok to="end"/>
<error to="Kill"/>
</action>
<action name="CountryPropagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>CountryPropagation</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>
--num-executors=${sparkExecutorNumber}
--executor-memory=${sparkExecutorMemory}
--executor-cores=${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.enabled=true
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<join name="wait" to="End"/>
<end name="End"/>
</workflow-app>