Code refactor:
- removed old workflows in doiboost - splitted workflow of doiboost in preprocess and processpull/124/head
parent
1cdd09cd8e
commit
10068c00ea
@ -1,101 +0,0 @@
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<workflow-app name="import Crossref from index into HDFS" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>workingPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>timestamp</name>
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<description>Timestamp for incremental Harvesting</description>
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</property>
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</parameters>
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<start to="ImportCrossRef"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportCrossRef">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
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<arg>-t</arg><arg>${workingPath}/input/crossref/index_update</arg>
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<arg>-n</arg><arg>${nameNode}</arg>
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<arg>-ts</arg><arg>${timestamp}</arg>
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</java>
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<ok to="GenerateDataset"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ExtractCrossrefToOAF</name>
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<class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--workingPath</arg><arg>/data/doiboost/input/crossref</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="RenameDataset"/>
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<error to="Kill"/>
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</action>
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<action name="RenameDataset">
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<fs>
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<delete path='${workingPath}/input/crossref/crossref_ds'/>
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<move source="${workingPath}/input/crossref/crossref_ds_updated"
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target="${workingPath}/input/crossref/crossref_ds"/>
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</fs>
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<ok to="ConvertCrossrefToOAF"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertCrossrefToOAF">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ConvertCrossrefToOAF</name>
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<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingPath}/input/crossref/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${workingPath}/process/</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="End"/>
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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>
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@ -1,38 +0,0 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
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</property>
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</configuration>
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@ -1,96 +0,0 @@
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<workflow-app name="Create DOIBoostActionSet" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>hostedByMapPath</name>
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<description>the Hosted By Map Path</description>
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</property>
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<property>
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<name>affiliationPath</name>
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<description>the Affliation Path</description>
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</property>
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<property>
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<name>paperAffiliationPath</name>
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<description>the paperAffiliation Path</description>
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</property>
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<property>
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<name>workingDirPath</name>
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<description>the Working Path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="CreateDOIBoost"/>
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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="CreateDOIBoost">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Create DOIBoost Infospace</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
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<arg>--affiliationPath</arg><arg>${affiliationPath}</arg>
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<arg>--paperAffiliationPath</arg><arg>${paperAffiliationPath}</arg>
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<arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="GenerateActionSet"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateActionSet">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Generate DOIBoost ActionSet</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--dbPublicationPath</arg><arg>${workingDirPath}/doiBoostPublicationFiltered</arg>
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<arg>--dbDatasetPath</arg><arg>${workingDirPath}/crossrefDataset</arg>
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<arg>--crossRefRelation</arg><arg>${workingDirPath}/crossrefRelation</arg>
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<arg>--dbaffiliationRelationPath</arg><arg>${workingDirPath}/doiBoostPublicationAffiliation</arg>
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<arg>-do</arg><arg>${workingDirPath}/doiBoostOrganization</arg>
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<arg>--targetPath</arg><arg>${workingDirPath}/actionDataSet</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="End"/>
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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>
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@ -1,42 +0,0 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>oozie.wf.rerun.failnodes</name>
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<value>false</value>
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</property>
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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
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</property>
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</configuration>
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@ -1,92 +0,0 @@
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<workflow-app name="import MAG into HDFS" 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 working dir base path</description>
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</property>
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<property>
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<name>targetPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>workingPath</name>
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<description>the working dir base path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="ResetWorkingPath"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ResetWorkingPath">
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<fs>
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<delete path='${workingPath}'/>
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<mkdir path='${workingPath}'/>
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</fs>
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<ok to="ConvertMagToDataset"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertMagToDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert Mag to Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="PreprocessMag"/>
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<error to="Kill"/>
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</action>
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<action name="PreprocessMag">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert Mag to OAF Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkPreProcessMAG</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingPath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}/process</arg>
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<arg>--targetPath</arg><arg>${targetPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="End"/>
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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>
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@ -1,42 +0,0 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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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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<property>
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<name>hive_metastore_uris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<value>/user/spark/spark2ApplicationHistory</value>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
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</property>
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</configuration>
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@ -1,453 +0,0 @@
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<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorIntersectionMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<!-- Itersection Parameters -->
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<property>
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<name>workingPath</name>
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<description>the working Path</description>
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</property>
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<property>
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<name>hostedByMapPath</name>
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<description>the hostedByMap Path</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the Path of the sequence file action set</description>
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</property>
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<!-- Crossref Parameters -->
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<property>
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<name>inputPathCrossref</name>
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<description>the Crossref input path</description>
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</property>
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<property>
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<name>crossrefDumpPath</name>
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<description>the Crossref dump path</description>
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</property>
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<!-- <property>-->
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<!-- <name>crossrefTimestamp</name>-->
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<!-- <description>Timestamp for the Crossref incremental Harvesting</description>-->
|
||||
<!-- </property>-->
|
||||
<!-- <property>-->
|
||||
<!-- <name>esServer</name>-->
|
||||
<!-- <description>elasticsearch server url for the Crossref Harvesting</description>-->
|
||||
<!-- </property>-->
|
||||
<!-- <property>-->
|
||||
<!-- <name>esIndex</name>-->
|
||||
<!-- <description>elasticsearch index name for the Crossref Harvesting</description>-->
|
||||
<!-- </property>-->
|
||||
|
||||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
<name>MAGDumpPath</name>
|
||||
<description>the MAG dump working path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>inputPathMAG</name>
|
||||
<description>the MAG working path</description>
|
||||
</property>
|
||||
|
||||
|
||||
<!-- UnpayWall Parameters -->
|
||||
<property>
|
||||
<name>inputPathUnpayWall</name>
|
||||
<description>the UnpayWall working path</description>
|
||||
</property>
|
||||
|
||||
<!-- ORCID Parameters -->
|
||||
<property>
|
||||
<name>inputPathOrcid</name>
|
||||
<description>the ORCID input path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>workingPathOrcid</name>
|
||||
<description>the ORCID working path</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
|
||||
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
|
||||
<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
|
||||
<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
|
||||
<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
|
||||
<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
|
||||
<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
|
||||
<case to="GenerateCrossrefDataset">${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'}</case>
|
||||
<default to="ImportCrossRef"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<!-- <action name="ImportCrossRef">-->
|
||||
<!-- <java>-->
|
||||
<!-- <main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>-->
|
||||
<!-- <arg>--targetPath</arg><arg>${inputPathCrossref}/index_update</arg>-->
|
||||
<!-- <arg>--namenode</arg><arg>${nameNode}</arg>-->
|
||||
<!-- <arg>--esServer</arg><arg>${esServer}</arg>-->
|
||||
<!-- <arg>--esIndex</arg><arg>${esIndex}</arg>-->
|
||||
<!-- <arg>--timestamp</arg><arg>${crossrefTimestamp}</arg>-->
|
||||
<!-- </java>-->
|
||||
<!-- <ok to="GenerateCrossrefDataset"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
|
||||
</java>
|
||||
<ok to="UnpackCrossrefEntries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UnpackCrossrefEntries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkUnpackCrossrefEntries</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="GenerateCrossrefDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkGenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=7G
|
||||
--executor-cores=2
|
||||
--driver-memory=7G
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="removeFiles"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<!-- <delete path="${crossrefDumpPath}/files"/>-->
|
||||
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
|
||||
</fs>
|
||||
<ok to="ResetMagWorkingPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<!-- CROSSREF SECTION -->
|
||||
|
||||
<!-- <action name="GenerateCrossrefDataset">-->
|
||||
<!-- <spark xmlns="uri:oozie:spark-action:0.2">-->
|
||||
<!-- <master>yarn-cluster</master>-->
|
||||
<!-- <mode>cluster</mode>-->
|
||||
<!-- <name>GenerateCrossrefDataset</name>-->
|
||||
<!-- <class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>-->
|
||||
<!-- <jar>dhp-doiboost-${projectVersion}.jar</jar>-->
|
||||
<!-- <spark-opts>-->
|
||||
<!-- --executor-memory=${sparkExecutorMemory}-->
|
||||
<!-- --executor-cores=${sparkExecutorCores}-->
|
||||
<!-- --driver-memory=${sparkDriverMemory}-->
|
||||
<!-- --conf spark.sql.shuffle.partitions=3840-->
|
||||
<!-- --conf spark.extraListeners=${spark2ExtraListeners}-->
|
||||
<!-- --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
|
||||
<!-- --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
|
||||
<!-- --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
|
||||
<!-- </spark-opts>-->
|
||||
<!-- <arg>--workingPath</arg><arg>${inputPathCrossref}</arg>-->
|
||||
<!-- <arg>--master</arg><arg>yarn-cluster</arg>-->
|
||||
<!-- </spark>-->
|
||||
<!-- <ok to="RenameDataset"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
<!-- <action name="RenameDataset">-->
|
||||
<!-- <fs>-->
|
||||
<!-- <delete path="${inputPathCrossref}/crossref_ds"/>-->
|
||||
<!-- <move source="${inputPathCrossref}/crossref_ds_updated"-->
|
||||
<!-- target="${inputPathCrossref}/crossref_ds"/>-->
|
||||
<!-- </fs>-->
|
||||
<!-- <ok to="ResetMagWorkingPath"/>-->
|
||||
<!-- <error to="Kill"/>-->
|
||||
<!-- </action>-->
|
||||
|
||||
|
||||
|
||||
<!-- MAG SECTION -->
|
||||
<action name="ResetMagWorkingPath">
|
||||
<fs>
|
||||
<delete path="${inputPathMAG}/dataset"/>
|
||||
<delete path="${inputPathMAG}/process"/>
|
||||
</fs>
|
||||
<ok to="ConvertMagToDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ConvertMagToDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Mag to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ConvertCrossrefToOAF"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<action name="ConvertCrossrefToOAF">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>ConvertCrossrefToOAF</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ProcessMAG"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ProcessMAG">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Mag to OAF Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.mag.SparkProcessMAG</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorIntersectionMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--workingPath</arg><arg>${inputPathMAG}/process</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ProcessUW"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- UnpayWall SECTION -->
|
||||
|
||||
<action name="ProcessUW">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert UnpayWall to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/uwPublication</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="ProcessORCID"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- ORCID SECTION -->
|
||||
<action name="ProcessORCID">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert ORCID to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkPreprocessORCID</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPathOrcid}</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/orcidPublication</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="CreateDOIBoost"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- INTERSECTION SECTION-->
|
||||
<action name="CreateDOIBoost">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Create DOIBoost Infospace</name>
|
||||
<class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorIntersectionMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
|
||||
<arg>--affiliationPath</arg><arg>${inputPathMAG}/dataset/Affiliations</arg>
|
||||
<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/dataset/PaperAuthorAffiliations</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="GenerateActionSet"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<action name="GenerateActionSet">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Generate DOIBoost ActionSet</name>
|
||||
<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--dbPublicationPath</arg><arg>${workingPath}/doiBoostPublicationFiltered</arg>
|
||||
<arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
|
||||
<arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
|
||||
<arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
|
||||
<arg>--dbOrganizationPath</arg><arg>${workingPath}/doiBoostOrganization</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
|
||||
<arg>--sFilePath</arg><arg>${outputPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
@ -0,0 +1,216 @@
|
||||
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
|
||||
<!-- Crossref Parameters -->
|
||||
<property>
|
||||
<name>inputPathCrossref</name>
|
||||
<description>the Crossref input path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>crossrefDumpPath</name>
|
||||
<description>the Crossref dump path</description>
|
||||
</property>
|
||||
|
||||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
<name>MAGDumpPath</name>
|
||||
<description>the MAG dump working path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>inputPathMAG</name>
|
||||
<description>the MAG working path</description>
|
||||
</property>
|
||||
|
||||
|
||||
<!-- ORCID Parameters -->
|
||||
<property>
|
||||
<name>inputPathOrcid</name>
|
||||
<description>the ORCID input path</description>
|
||||
</property>
|
||||
|
||||
<property>
|
||||
<name>workingPathOrcid</name>
|
||||
<description>the ORCID working path</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<global>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>${oozieActionShareLibForSpark2}</value>
|
||||
</property>
|
||||
</configuration>
|
||||
</global>
|
||||
|
||||
<start to="resume_from"/>
|
||||
|
||||
<decision name="resume_from">
|
||||
<switch>
|
||||
<case to="UnpackCrossrefEntries">${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'}</case>
|
||||
<case to="GenerateCrossrefDataset">${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'}</case>
|
||||
<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
|
||||
<case to="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
|
||||
<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
|
||||
<default to="ImportCrossRef"/>
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ImportCrossRef">
|
||||
<java>
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
|
||||
<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
|
||||
</java>
|
||||
<ok to="UnpackCrossrefEntries"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="UnpackCrossrefEntries">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkUnpackCrossrefEntries</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
|
||||
<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="GenerateCrossrefDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="GenerateCrossrefDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>SparkGenerateCrossrefDataset</name>
|
||||
<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=7G
|
||||
--executor-cores=2
|
||||
--driver-memory=7G
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="removeFiles"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="removeFiles">
|
||||
<fs>
|
||||
<!-- <delete path="${crossrefDumpPath}/files"/>-->
|
||||
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
|
||||
</fs>
|
||||
<ok to="ResetMagWorkingPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- MAG SECTION -->
|
||||
<action name="ResetMagWorkingPath">
|
||||
<fs>
|
||||
<delete path="${inputPathMAG}/dataset"/>
|
||||
<delete path="${inputPathMAG}/process"/>
|
||||
</fs>
|
||||
<ok to="ConvertMagToDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ConvertMagToDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Mag to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
|
||||
<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="PreProcessORCID"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<!-- ORCID SECTION -->
|
||||
<action name="PreProcessORCID">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert ORCID to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.orcid.SparkPreprocessORCID</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPathOrcid}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
@ -1,38 +0,0 @@
|
||||
<configuration>
|
||||
<property>
|
||||
<name>jobTracker</name>
|
||||
<value>yarnRM</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>nameNode</name>
|
||||
<value>hdfs://nameservice1</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>hive_metastore_uris</name>
|
||||
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2YarnHistoryServerAddress</name>
|
||||
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2EventLogDir</name>
|
||||
<value>/user/spark/spark2ApplicationHistory</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2ExtraListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>spark2SqlQueryExecutionListeners</name>
|
||||
<value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
|
||||
</property>
|
||||
</configuration>
|
||||
@ -1,55 +0,0 @@
|
||||
<workflow-app name="import UnpayWall into HDFS" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="PreprocessUW"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="PreprocessUW">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert UnpayWall to Dataset</name>
|
||||
<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
|
||||
<jar>dhp-doiboost-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/uw_extracted</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
Loading…
Reference in New Issue