forked from D-Net/dnet-hadoop
removed all the part related to the crossref dump download since it is done in a separate workflow
This commit is contained in:
parent
a5f82f442b
commit
da20fceaf7
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@ -1,21 +0,0 @@
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[
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{
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"paramName": "s",
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"paramLongName": "sourcePath",
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"paramDescription": "the source mdstore path",
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"paramRequired": true
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},
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{
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"paramName": "t",
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"paramLongName": "targetPath",
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"paramDescription": "the target mdstore path",
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"paramRequired": true
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},
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{
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"paramName": "m",
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"paramLongName": "master",
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"paramDescription": "the master name",
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"paramRequired": true
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}
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]
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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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<workflow-app name="read Crossref dump from HDFS" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>crossrefDumpPath</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>inputPathCrossref</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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<value>2</value>
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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="GenerateCrossrefDataset"/>
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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>${nameNode}</name-node>
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<main-class>eu.dnetlib.doiboost.crossref.ExtractCrossrefRecords</main-class>
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<arg>--hdfsServerUri</arg><arg>${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>${workingDir}/files/</arg>
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</java>
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<ok to="UnpackCrossrefEntries"/>
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<error to="Kill"/>
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</action>
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<action name="UnpackCrossrefEntries">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>SparkGenerateCrossrefDataset</name>
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<class>eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries</class>
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<jar>dhp-doiboost-${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>${crossrefDumpPath}/files</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds</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-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${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}${spark2EventLogDir}
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</spark-opts>
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<arg>--master</arg><arg>yarn-cluster</arg>
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<arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
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<arg>--targetPath</arg><arg>${inputPathCrossref}/crossref_ds_updates</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<!-- <action name="removeFiles">-->
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<!-- <fs>-->
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<!-- <delete path="${workingDir}/files"/>-->
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<!-- </fs>-->
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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="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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<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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@ -1,2 +0,0 @@
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#!/bin/bash
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curl -LSs -H "Crossref-Plus-API-Token: Bearer eyJ0eXAiOiJKV1QiLCJhbGciOiJIUzI1NiJ9.eyJpc3MiOiJodHRwOi8vY3Jvc3NyZWYub3JnLyIsImF1ZCI6Im1kcGx1cyIsImp0aSI6Ijk3YTZkNGVkLTg5MjktNGQ2Yi05NWY1LTY2YmMyNDgzNTRjNCJ9.5DPM4gRibUBYBtrUSpRz3RGHYVB-8f61jQBW_q-r-hs" $1 | hdfs dfs -put - $2/$3
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#!/bin/bash
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curl -LSs $1 | hdfs dfs -put - $2/$3
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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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</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[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="DownloadDump">
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<shell xmlns="uri:oozie:shell-action:0.2">
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<job-tracker>${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>${crossrefdumpfilename}</argument>
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<env-var>HADOOP_USER_NAME=${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>${crossrefDumpPath}/crossref_unpack/</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<action name="removeFiles">
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<fs>
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<delete path="${crossrefDumpPath}/files"/>
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<delete path="${crossrefDumpPath}/crossref_unpack/"/>
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</fs>
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<ok to="DownloadDump"/>
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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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@ -1,2 +0,0 @@
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#!/bin/bash
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curl -LSs $1 | hdfs dfs -put - $2/$3
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@ -63,14 +63,10 @@
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<decision name="resume_from">
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<decision name="resume_from">
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<switch>
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<switch>
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<case to="End">${wf:conf('resumeFrom') eq 'Skip'}</case>
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|
||||||
<case to="ImportCrossRef">${wf:conf('resumeFrom') eq 'ImportCrossRef'}</case>
|
|
||||||
<case to="UnpackCrossrefEntries">${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="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
|
||||||
<case to="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
|
<case to="ConvertMagToDataset">${wf:conf('resumeFrom') eq 'ConvertMagToDataset'}</case>
|
||||||
<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
|
<case to="PreProcessORCID">${wf:conf('resumeFrom') eq 'PreProcessORCID'}</case>
|
||||||
<default to="removeFiles"/> <!-- first action to be done when downloadDump is to be performed -->
|
<default to="GenerateCrossrefDataset"/> <!-- first action to be done when downloadDump is to be performed -->
|
||||||
</switch>
|
</switch>
|
||||||
</decision>
|
</decision>
|
||||||
|
|
||||||
|
|
@ -79,67 +75,6 @@
|
||||||
</kill>
|
</kill>
|
||||||
|
|
||||||
|
|
||||||
<action name="DownloadDump">
|
|
||||||
<shell xmlns="uri:oozie:shell-action:0.2">
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<configuration>
|
|
||||||
<property>
|
|
||||||
<name>mapred.job.queue.name</name>
|
|
||||||
<value>${queueName}</value>
|
|
||||||
</property>
|
|
||||||
</configuration>
|
|
||||||
<exec>download.sh</exec>
|
|
||||||
<argument>${url}</argument>
|
|
||||||
<argument>${crossrefDumpPath}</argument>
|
|
||||||
<argument>${crossrefdumpfilename}</argument>
|
|
||||||
<file>download.sh</file>
|
|
||||||
<capture-output/>
|
|
||||||
</shell>
|
|
||||||
<ok to="ImportCrossRef"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ImportCrossRef">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${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>${crossrefdumpfilename}</arg>
|
|
||||||
<arg>--workingPath</arg><arg>${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">
|
<action name="GenerateCrossrefDataset">
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
<master>yarn-cluster</master>
|
<master>yarn-cluster</master>
|
||||||
|
|
@ -166,14 +101,7 @@
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
<action name="removeFiles">
|
|
||||||
<fs>
|
|
||||||
<delete path="${crossrefDumpPath}/files"/>
|
|
||||||
<delete path="${crossrefDumpPath}/crossref_unpack/"/>
|
|
||||||
</fs>
|
|
||||||
<ok to="DownloadDump"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<!-- MAG SECTION -->
|
<!-- MAG SECTION -->
|
||||||
<action name="ResetMagWorkingPath">
|
<action name="ResetMagWorkingPath">
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue