forked from D-Net/dnet-hadoop
defined a single oozie workflow for the generation of doiboost
This commit is contained in:
parent
7185158942
commit
b0dc92786f
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@ -39,6 +39,7 @@ object SparkGenerateDOIBoostActionSet {
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val dbaffiliationRelationPath = parser.get("dbaffiliationRelationPath")
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val dbOrganizationPath = parser.get("dbOrganizationPath")
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val workingDirPath = parser.get("targetPath")
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val sequenceFilePath = parser.get("sFilePath")
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spark.read.load(dbDatasetPath).as[OafDataset]
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.map(d =>DoiBoostMappingUtil.fixResult(d))
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@ -65,7 +66,7 @@ object SparkGenerateDOIBoostActionSet {
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val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
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d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
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d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
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@ -5,5 +5,6 @@
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{"paramName": "cr", "paramLongName":"crossRefRelation", "paramDescription": "the UnpayWall Publication Path", "paramRequired": true},
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{"paramName": "da", "paramLongName":"dbaffiliationRelationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
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{"paramName": "do", "paramLongName":"dbOrganizationPath", "paramDescription": "the MAG Publication Path", "paramRequired": true},
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{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true}
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{"paramName": "w", "paramLongName":"targetPath", "paramDescription": "the Working Path", "paramRequired": true},
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{"paramName": "sp", "paramLongName":"sFilePath", "paramDescription": "the Sequence file Path", "paramRequired": true},
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]
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@ -0,0 +1,42 @@
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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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@ -0,0 +1,326 @@
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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>crossrefTimestamp</name>
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<description>Timestamp for the Crossref incremental Harvesting</description>
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</property>
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<!-- MAG Parameters -->
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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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<!-- UnpayWall Parameters -->
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<property>
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<name>inputPathUnpayWall</name>
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<description>the UnpayWall 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 working path</description>
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</property>
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</parameters>
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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="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
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<case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
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<case to="PreprocessMag">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
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<case to="PreprocessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
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<case to="PreprocessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
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<case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
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<case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
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<default to="ImportCrossRef"/>
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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[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="ImportCrossRef">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
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<arg>-t</arg><arg>${inputPathCrossref}/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="GenerateCrossrefDataset"/>
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<error to="Kill"/>
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</action>
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<!-- CROSSREF SECTION -->
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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>GenerateCrossrefDataset</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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${sparkExtraOPT}
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</spark-opts>
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<arg>--workingPath</arg><arg>${inputPathCrossref}</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="${inputPathCrossref}/crossref_ds"/>
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<move source="${inputPathCrossref}/crossref_ds_updated"
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target="${inputPathCrossref}/crossref_ds"/>
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</fs>
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<ok to="ConvertCrossrefToOAF"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertCrossrefToOAF">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>ConvertCrossrefToOAF</name>
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<class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
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<jar>dhp-doiboost-${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>${inputPathCrossref}/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="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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<delete path='${inputPathMAG}/dataset'/>
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</fs>
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<ok to="ConvertMagToDataset"/>
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<error to="Kill"/>
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</action>
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<action name="ConvertMagToDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert Mag to Dataset</name>
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<class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
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<jar>dhp-doiboost-${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>${inputPathMAG}/input</arg>
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<arg>--targetPath</arg><arg>${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="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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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
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<arg>--workingPath</arg><arg>${inputPathMAG}/process</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="PreprocessUW"/>
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<error to="Kill"/>
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</action>
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<!-- UnpayWall SECTION -->
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<action name="PreprocessUW">
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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 UnpayWall to Dataset</name>
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<class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</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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${sparkExtraOPT}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="PreprocessORCID"/>
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<error to="Kill"/>
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</action>
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<!-- ORCID SECTION -->
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<action name="PreprocessORCID">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Convert ORCID to Dataset</name>
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<class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
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<jar>dhp-doiboost-${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>${inputPathOrcid}</arg>
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<arg>--targetPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="CreateDOIBoost"/>
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<error to="Kill"/>
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</action>
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<!-- INTERSECTION SECTION-->
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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>${inputPathMAG}/process/Affiliations</arg>
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<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/process/PaperAuthorAffiliations</arg>
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<arg>--workingDirPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="GenerateActionSet"/>
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<error to="Kill"/>
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</action>
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<action name="GenerateActionSet">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Generate DOIBoost ActionSet</name>
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<class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
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<jar>dhp-doiboost-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorIntersectionMemory}
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--executor-cores=${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>${workingPath}/doiBoostPublicationFiltered</arg>
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<arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
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<arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
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<arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
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<arg>-do</arg><arg>${workingPath}/doiBoostOrganization</arg>
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<arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
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<arg>--sFilePath</arg><arg>${outputPath}</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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