manually merged PR#139
This commit is contained in:
commit
2c0a05f11a
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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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@ -1,128 +0,0 @@
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<workflow-app name="CROSSREF DUMP - DOWNLOAD" 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>crossrefdumpfilename</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>crossrefdumptoken</name>
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<description>the token for the API dump 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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="removeFiles"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="removeFiles">
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<fs>
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<delete path="${crossrefDumpPath}/${crossrefdumpfilename}"/>
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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="DownloadDump"/>
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<error to="Kill"/>
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</action>
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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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<argument>${crossrefdumptoken}</argument>
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<env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
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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>${nameNode}</arg>
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<arg>--crossrefFileNameTarGz</arg><arg>${crossrefdumpfilename}</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>${crossrefDumpPath}/crossref_unpack/</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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<workflow-app name="Generate DOIBoost ActionSet for BETA - PREPROCESS" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="Generate DOIBoost ActionSet - PREPROCESS" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<parameters>
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<property>
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<property>
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<name>sparkDriverMemory</name>
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<name>sparkDriverMemory</name>
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@ -63,12 +63,10 @@
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<decision name="resume_from">
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<decision name="resume_from">
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<switch>
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<switch>
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<case to="UnpackCrossrefEntries">${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="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="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
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<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
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<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
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<default to="ImportCrossRef"/>
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<default to="GenerateCrossrefDataset"/> <!-- first action to be done when downloadDump is to be performed -->
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</switch>
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</switch>
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</decision>
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</decision>
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</kill>
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</kill>
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<action name="ImportCrossRef">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
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<arg>--hdfsServerUri</arg><arg>${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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<action name="GenerateCrossrefDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<master>yarn-cluster</master>
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@ -139,19 +97,12 @@
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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</spark>
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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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<ok to="ResetMagWorkingPath"/>
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<error to="Kill"/>
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<error to="Kill"/>
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</action>
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</action>
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<!-- MAG SECTION -->
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<!-- MAG SECTION -->
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<action name="ResetMagWorkingPath">
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<action name="ResetMagWorkingPath">
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<fs>
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<fs>
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<workflow-app name="Generate DOIBoost ActionSet for BETA - PROCESS" xmlns="uri:oozie:workflow:0.5">
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<workflow-app name="Generate DOIBoost ActionSet - PROCESS" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<parameters>
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<property>
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<property>
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<name>sparkDriverMemory</name>
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<name>sparkDriverMemory</name>
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@ -75,6 +75,7 @@
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<decision name="resume_from">
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<decision name="resume_from">
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<switch>
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<switch>
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<case to="End">${wf:conf('resumeFrom') eq 'Skip'}</case>
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<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
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<case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
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<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
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<case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
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<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'ProcessORCID'}</case>
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<case to="ProcessORCID">${wf:conf('resumeFrom') eq 'ProcessORCID'}</case>
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