239 lines
9.6 KiB
XML
239 lines
9.6 KiB
XML
<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>sparkExecutorCores</name>
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<description>number of cores used by single executor</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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<!-- MAG Parameters -->
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<property>
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<name>MAGDumpPath</name>
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<description>the MAG dump working path</description>
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</property>
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<property>
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<name>inputPathMAG</name>
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<description>the MAG working path</description>
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</property>
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<!-- ORCID Parameters -->
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<property>
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<name>inputPathOrcid</name>
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<description>the ORCID input path</description>
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</property>
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<property>
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<name>workingPathOrcid</name>
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<description>the ORCID working path</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="resume_from"/>
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<decision name="resume_from">
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<switch>
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<case to="End">${wf:conf('resumeFrom') eq 'Skip'}</case>
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<case to="ImportCrossRef">${wf:conf('resumeFrom') eq 'ImportCrossRef'}</case>
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<case to="UnpackCrossrefEntries">${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'}</case>
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<case to="GenerateCrossrefDataset">${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'}</case>
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<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
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<case to="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
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<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
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<default to="DownloadDump"/>
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</switch>
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</decision>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="DownloadDump">
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<shell xmlns="uri:oozie:shell-action:0.2">
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapred.job.queue.name</name>
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<value>${queueName}</value>
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</property>
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</configuration>
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<exec>download.sh</exec>
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<argument>${url}</argument>
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<argument>${crossrefDumpPath}</argument>
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<argument>${crossrefdumpfilename}</argument>
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<file>download.sh</file>
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<capture-output/>
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</shell>
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<ok to="ImportCrossRef"/>
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<error to="Kill"/>
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</action>
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<action name="ImportCrossRef">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
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<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
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<arg>--crossrefFileNameTarGz</arg><arg>${crossrefDumpPath}/crossref.tar.gz</arg>
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<arg>--workingPath</arg><arg>${crossrefDumpPath}</arg>
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<arg>--outputPath</arg><arg>${crossrefDumpPath}/files/</arg>
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</java>
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<ok to="UnpackCrossrefEntries"/>
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<error to="Kill"/>
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</action>
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<action name="UnpackCrossrefEntries">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>SparkUnpackCrossrefEntries</name>
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<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${crossrefDumpPath}/files</arg>
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<arg>--targetPath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
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</spark>
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<ok to="GenerateCrossrefDataset"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateCrossrefDataset">
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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>SparkGenerateCrossrefDataset</name>
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<class>eu.dnetlib.doiboost.crossref.GenerateCrossrefDataset</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=7G
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--executor-cores=2
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--driver-memory=7G
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${crossrefDumpPath}/crossref_unpack/</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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</spark>
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<ok to="removeFiles"/>
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<error to="Kill"/>
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</action>
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<action name="removeFiles">
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<fs>
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<!-- <delete path="${crossrefDumpPath}/files"/>-->
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<delete path="${crossrefDumpPath}/crossref_unpack/"/>
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</fs>
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<ok to="ResetMagWorkingPath"/>
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<error to="Kill"/>
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</action>
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<!-- MAG SECTION -->
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<action name="ResetMagWorkingPath">
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<fs>
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<delete path="${inputPathMAG}/dataset"/>
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<delete path="${inputPathMAG}/process"/>
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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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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${MAGDumpPath}</arg>
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<arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="PreProcessORCID"/>
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<error to="Kill"/>
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</action>
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<!-- ORCID SECTION -->
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<action name="PreProcessORCID">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert ORCID to Dataset</name>
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<class>eu.dnetlib.doiboost.orcid.SparkPreprocessORCID</class>
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<jar>dhp-doiboost-${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=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
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<arg>--workingPath</arg><arg>${workingPathOrcid}</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> |