forked from D-Net/dnet-hadoop
workflow for the dump as sub workflows
This commit is contained in:
parent
d70f8c96fd
commit
c028feef4f
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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>hiveMetastoreUris</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>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hiveDbName</name>
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<value>openaire</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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</configuration>
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## This is a classpath-based import file (this header is required)
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dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app
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dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app
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dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app
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<workflow-app name="dump_graph" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>singleDeposition</name>
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<description>Indicates if it is a single community deposition</description>
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</property>
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<property>
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<name>communityId</name>
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<description>the id of the community to be dumped if a dump for a single community should be done</description>
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</property>
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<property>
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<name>dumpType</name>
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<description>the type of the dump one of {complete, community, funder}</description>
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</property>
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<property>
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<name>onlyUpload</name>
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<description>true if the dump is already done and should only be upload in zenodo</description>
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</property>
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<property>
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<name>upload</name>
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<description>true if the dump should be upload in zenodo</description>
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</property>
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<property>
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<name>sourcePath</name>
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<description>the source path</description>
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</property>
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<property>
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<name>isLookUpUrl</name>
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<description>the isLookup service endpoint</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the output path</description>
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</property>
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<property>
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<name>resultAggregation</name>
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<description>true if all the result type have to be dumped under result. false otherwise</description>
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</property>
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<property>
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<name>accessToken</name>
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<description>the access token used for the deposition in Zenodo</description>
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</property>
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<property>
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<name>connectionUrl</name>
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<description>the connection url for Zenodo</description>
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</property>
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<property>
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<name>metadata</name>
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<description> the metadata associated to the deposition</description>
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</property>
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<property>
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<name>depositionType</name>
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<description>the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided)</description>
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</property>
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<property>
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<name>conceptRecordId</name>
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<description>for new version, the id of the record for the old deposition</description>
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</property>
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<property>
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<name>depositionId</name>
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<description>the depositionId of a deposition open that has to be added content</description>
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</property>
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<property>
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<name>organizationCommunityMap</name>
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<description>the organization community map</description>
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</property>
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<property>
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<name>hiveDbName</name>
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<description>the target hive database name</description>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<description>hive server jdbc url</description>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<description>hive server metastore URIs</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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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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<description>spark 2.* extra listeners classname</description>
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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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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</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>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</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>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="only_upload"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<decision name="only_upload">
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<switch>
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<case to="send_zenodo">${wf:conf('onlyUpload') eq true}</case>
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<default to="reset_outputpath"/>
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</switch>
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</decision>
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<action name="reset_outputpath">
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<fs>
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<delete path="${outputPath}"/>
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<mkdir path="${outputPath}"/>
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</fs>
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<ok to="save_community_map"/>
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<error to="Kill"/>
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</action>
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<action name="save_community_map">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap</main-class>
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<arg>--outputPath</arg><arg>${workingDir}/communityMap</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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<arg>--singleDeposition</arg><arg>${singleDeposition}</arg>
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<arg>--communityId</arg><arg>${communityId}</arg>
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</java>
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<ok to="choose_dump"/>
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<error to="Kill"/>
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</action>
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<decision name="choose_dump">
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<switch>
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<case to="dump_funder">${wf:conf('dumpType') eq "funder"}</case>
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<case to="dump_community">${wf:conf('dumpType') eq "community"}</case>
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<default to="dump_complete"/>
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</switch>
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</decision>
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<!-- Sub-workflow which runs the dump for the complete graph -->
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<action name="dump_complete">
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<sub-workflow>
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<app-path>${wf:appPath()}/dump_complete
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</app-path>
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<propagate-configuration/>
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<configuration>
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<property>
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<name>communityMapPath</name>
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<value>${workingDir}/communityMap</value>
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</property>
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<property>
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<name>outputPath</name>
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<value>${workingDir}/tar</value>
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</property>
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<property>
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<name>sourcePath</name>
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<value>${sourcePath}</value>
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</property>
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<property>
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<name>organizationCommunityMap</name>
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<value>${organizationCommunityMap}</value>
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</property>
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<property>
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<name>isLookUpUrl</name>
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<value>${isLookUpUrl}</value>
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</property>
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<property>
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<name>resultAggregation</name>
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<value>${resultAggregation}</value>
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</property>
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</configuration>
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</sub-workflow>
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<ok to="make_archive" />
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<error to="Kill" />
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</action>
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<!-- Sub-workflow which runs the dump for the complete graph -->
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<action name="dump_community">
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<sub-workflow>
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<app-path>${wf:appPath()}/dump_community
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</app-path>
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<propagate-configuration/>
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<configuration>
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<property>
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<name>sourcePath</name>
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<value>${sourcePath}</value>
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</property>
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<property>
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<name>communityMapPath</name>
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<value>${workingDir}/communityMap</value>
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</property>
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<property>
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<name>outputPath</name>
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<value>${workingDir}/tar</value>
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</property>
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</configuration>
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</sub-workflow>
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<ok to="make_archive" />
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<error to="Kill" />
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</action>
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<action name="dump_funder">
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<sub-workflow>
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<app-path>${wf:appPath()}/dump_funder
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</app-path>
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<propagate-configuration/>
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<configuration>
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<property>
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<name>communityMapPath</name>
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<value>${workingDir}/communityMap</value>
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</property>
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<property>
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<name>outputPath</name>
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<value>${workingDir}/tar</value>
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</property>
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<property>
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<name>sourcePath</name>
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<value>${sourcePath}</value>
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</property>
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<property>
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<name>dumpType</name>
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<value>${dumpType}</value>
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</property>
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</configuration>
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</sub-workflow>
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<ok to="make_archive" />
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<error to="Kill" />
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</action>
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<action name="make_archive">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.MakeTar</main-class>
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<arg>--hdfsPath</arg><arg>${outputPath}</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--sourcePath</arg><arg>${workingDir}/tar</arg>
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</java>
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<ok to="should_upload"/>
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<error to="Kill"/>
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</action>
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<decision name="should_upload">
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<switch>
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<case to="send_zenodo">${wf:conf('upload') eq true}</case>
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<default to="End"/>
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</switch>
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</decision>
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<action name="send_zenodo">
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<java>
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<main-class>eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS</main-class>
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<arg>--hdfsPath</arg><arg>${outputPath}</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--accessToken</arg><arg>${accessToken}</arg>
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<arg>--connectionUrl</arg><arg>${connectionUrl}</arg>
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<arg>--metadata</arg><arg>${metadata}</arg>
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<arg>--conceptRecordId</arg><arg>${conceptRecordId}</arg>
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<arg>--depositionType</arg><arg>${depositionType}</arg>
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<arg>--depositionId</arg><arg>${depositionId}</arg>
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</java>
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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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@ -0,0 +1,30 @@
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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>hiveMetastoreUris</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>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hiveDbName</name>
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<value>openaire</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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</configuration>
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@ -0,0 +1,347 @@
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<workflow-app name="sub_dump_community_funder_results" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source 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 output path</description>
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</property>
|
||||||
|
<property>
|
||||||
|
<name>communityMapPath</name>
|
||||||
|
<description>the path to the community map</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>selectedResults</name>
|
||||||
|
<description>the path the the possible subset ot results to be dumped</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveDbName</name>
|
||||||
|
<description>the target hive database name</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveJdbcUrl</name>
|
||||||
|
<description>hive server jdbc url</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveMetastoreUris</name>
|
||||||
|
<description>hive server metastore URIs</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkDriverMemory</name>
|
||||||
|
<description>memory for driver process</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorMemory</name>
|
||||||
|
<description>memory for individual executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorCores</name>
|
||||||
|
<description>number of cores used by single executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozieActionShareLibForSpark2</name>
|
||||||
|
<description>oozie action sharelib for spark 2.*</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2ExtraListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||||
|
<description>spark 2.* extra listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2SqlQueryExecutionListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||||
|
<description>spark 2.* sql query execution listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<description>spark 2.* yarn history server address</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<description>spark 2.* event log dir location</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<global>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>mapreduce.job.queuename</name>
|
||||||
|
<value>${queueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||||
|
<value>${oozieLauncherQueueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>${oozieActionShareLibForSpark2}</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
</configuration>
|
||||||
|
</global>
|
||||||
|
|
||||||
|
<start to="fork_dump"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<fork name="fork_dump">
|
||||||
|
<path start="dump_publication"/>
|
||||||
|
<path start="dump_dataset"/>
|
||||||
|
<path start="dump_orp"/>
|
||||||
|
<path start="dump_software"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="dump_publication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table publication for community/funder related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${selectedResults}/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/publication</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
<arg>--dumpType</arg><arg>${dumpType}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_dataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table dataset for community/funder related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${selectedResults}/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/dataset</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_orp">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table ORP for community related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${selectedResults}/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_software">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table software for community related products</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${selectedResults}/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/dump/software</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_dump" to="prepareResultProject"/>
|
||||||
|
|
||||||
|
<action name="prepareResultProject">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Prepare association result subset of project info</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="fork_extendWithProject"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<fork name="fork_extendWithProject">
|
||||||
|
<path start="extend_publication"/>
|
||||||
|
<path start="extend_dataset"/>
|
||||||
|
<path start="extend_orp"/>
|
||||||
|
<path start="extend_software"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="extend_publication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped publications with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/ext/publication</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="extend_dataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped dataset with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/ext/dataset</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="extend_orp">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped ORP with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/otherresearchproduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/ext/orp</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="extend_software">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extend dumped software with information about project</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/dump/software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/ext/software</arg>
|
||||||
|
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extend"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
<join name="join_extend" to="End"/>
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
|
||||||
|
</workflow-app>
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -0,0 +1,30 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveMetastoreUris</name>
|
||||||
|
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveJdbcUrl</name>
|
||||||
|
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveDbName</name>
|
||||||
|
<value>openaire</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,2 @@
|
||||||
|
## This is a classpath-based import file (this header is required)
|
||||||
|
dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app
|
||||||
|
|
@ -0,0 +1,145 @@
|
||||||
|
<workflow-app name="sub_dump_community_products" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<description>the source path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>outputPath</name>
|
||||||
|
<description>the output path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveDbName</name>
|
||||||
|
<description>the target hive database name</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveJdbcUrl</name>
|
||||||
|
<description>hive server jdbc url</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveMetastoreUris</name>
|
||||||
|
<description>hive server metastore URIs</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkDriverMemory</name>
|
||||||
|
<description>memory for driver process</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorMemory</name>
|
||||||
|
<description>memory for individual executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorCores</name>
|
||||||
|
<description>number of cores used by single executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozieActionShareLibForSpark2</name>
|
||||||
|
<description>oozie action sharelib for spark 2.*</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2ExtraListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||||
|
<description>spark 2.* extra listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2SqlQueryExecutionListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||||
|
<description>spark 2.* sql query execution listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<description>spark 2.* yarn history server address</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<description>spark 2.* event log dir location</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<global>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>mapreduce.job.queuename</name>
|
||||||
|
<value>${queueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||||
|
<value>${oozieLauncherQueueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>${oozieActionShareLibForSpark2}</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
</configuration>
|
||||||
|
</global>
|
||||||
|
|
||||||
|
<start to="common_action_community_funder"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<action name="common_action_community_funder">
|
||||||
|
<sub-workflow>
|
||||||
|
<app-path>${wf:appPath()}/dump_common
|
||||||
|
</app-path>
|
||||||
|
<propagate-configuration/>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<value>${sourcePath}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>selectedResults</name>
|
||||||
|
<value>${sourcePath}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>communityMapPath</name>
|
||||||
|
<value>${workingDir}/communityMap</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>outputPath</name>
|
||||||
|
<value>${workingDir}</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
</sub-workflow>
|
||||||
|
<ok to="splitForCommunities" />
|
||||||
|
<error to="Kill" />
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<action name="splitForCommunities">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Split dumped result for community</name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/ext</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -0,0 +1,30 @@
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>jobTracker</name>
|
||||||
|
<value>yarnRM</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>nameNode</name>
|
||||||
|
<value>hdfs://nameservice1</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.use.system.libpath</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveMetastoreUris</name>
|
||||||
|
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveJdbcUrl</name>
|
||||||
|
<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveDbName</name>
|
||||||
|
<value>openaire</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||||
|
<value>true</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
|
@ -0,0 +1,537 @@
|
||||||
|
<workflow-app name="sub-dump_complete" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<description>the source path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>outputPath</name>
|
||||||
|
<description>the output path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>resultAggregation</name>
|
||||||
|
<description>true if all the result type have to be dumped under result. false otherwise</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>organizationCommunityMap</name>
|
||||||
|
<description>the organization community map</description>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>hiveDbName</name>
|
||||||
|
<description>the target hive database name</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveJdbcUrl</name>
|
||||||
|
<description>hive server jdbc url</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveMetastoreUris</name>
|
||||||
|
<description>hive server metastore URIs</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkDriverMemory</name>
|
||||||
|
<description>memory for driver process</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorMemory</name>
|
||||||
|
<description>memory for individual executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorCores</name>
|
||||||
|
<description>number of cores used by single executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozieActionShareLibForSpark2</name>
|
||||||
|
<description>oozie action sharelib for spark 2.*</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2ExtraListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||||
|
<description>spark 2.* extra listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2SqlQueryExecutionListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||||
|
<description>spark 2.* sql query execution listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<description>spark 2.* yarn history server address</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<description>spark 2.* event log dir location</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<global>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>mapreduce.job.queuename</name>
|
||||||
|
<value>${queueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||||
|
<value>${oozieLauncherQueueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>${oozieActionShareLibForSpark2}</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
</configuration>
|
||||||
|
</global>
|
||||||
|
|
||||||
|
<start to="fork_dump" />
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<fork name="fork_dump">
|
||||||
|
<path start="dump_publication"/>
|
||||||
|
<path start="dump_dataset"/>
|
||||||
|
<path start="dump_orp"/>
|
||||||
|
<path start="dump_software"/>
|
||||||
|
<path start="dump_organization"/>
|
||||||
|
<path start="dump_project"/>
|
||||||
|
<path start="dump_datasource"/>
|
||||||
|
<path start="select_relation"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="dump_publication">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table publication </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/publication</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_dataset">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table dataset </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/dataset</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_orp">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table ORP </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_software">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table software </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/software</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_organization">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table organization </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/organization</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/organization</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_project">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table project </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/project</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/project</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_datasource">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table datasource </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/datasource</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}/datasource</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${workingDir}/communityMap</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_relation">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Select valid table relation </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/validrelation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="dump_relation"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_relation">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table relation </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/validrelation</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/relation/relation</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_dump"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_dump" to="fork_context"/>
|
||||||
|
|
||||||
|
<fork name="fork_context">
|
||||||
|
<path start="create_entities_fromcontext"/>
|
||||||
|
<path start="create_relation_fromcontext"/>
|
||||||
|
<path start="create_relation_fromorgs"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="create_entities_fromcontext">
|
||||||
|
<java>
|
||||||
|
<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities</main-class>
|
||||||
|
<arg>--hdfsPath</arg><arg>${outputPath}/communities_infrastructures/communities_infrastructure.json.gz</arg>
|
||||||
|
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_context"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="create_relation_fromcontext">
|
||||||
|
<java>
|
||||||
|
<main-class>eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation</main-class>
|
||||||
|
<arg>--hdfsPath</arg><arg>${workingDir}/relation/context</arg>
|
||||||
|
<arg>--nameNode</arg><arg>${nameNode}</arg>
|
||||||
|
<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
|
||||||
|
</java>
|
||||||
|
<ok to="join_context"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="create_relation_fromorgs">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table relation </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/relation/contextOrg</arg>
|
||||||
|
<arg>--organizationCommunityMap</arg><arg>${organizationCommunityMap}</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_context"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_context" to="fork_extract_relations"/>
|
||||||
|
|
||||||
|
<fork name="fork_extract_relations">
|
||||||
|
<path start="rels_from_pubs"/>
|
||||||
|
<path start="rels_from_dats"/>
|
||||||
|
<path start="rels_from_orp"/>
|
||||||
|
<path start="rels_from_sw"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="rels_from_pubs">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Extract Relations from publication </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/relation/publication</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extract_relations"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="rels_from_dats">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table dataset </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/relation/dataset</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extract_relations"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="rels_from_orp">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table ORP </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/relation/orp</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extract_relations"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="rels_from_sw">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump table software </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/relation/software</arg>
|
||||||
|
<arg>--communityMapPath</arg><arg>${communityMapPath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_extract_relations"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_extract_relations" to="collect_and_save"/>
|
||||||
|
|
||||||
|
<action name="collect_and_save">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Collect Results and Relations and put them in the right path </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||||
|
<arg>--resultAggregation</arg><arg>${resultAggregation}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Sub-workflow dump complete failed with error message ${wf:errorMessage()}
|
||||||
|
</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
<end name="End" />
|
||||||
|
</workflow-app>
|
||||||
|
|
@ -0,0 +1,2 @@
|
||||||
|
## This is a classpath-based import file (this header is required)
|
||||||
|
dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app
|
||||||
|
|
@ -0,0 +1,256 @@
|
||||||
|
<workflow-app name="sub_dump_funder_results" xmlns="uri:oozie:workflow:0.5">
|
||||||
|
<parameters>
|
||||||
|
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<description>the source path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>outputPath</name>
|
||||||
|
<description>the output path</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveDbName</name>
|
||||||
|
<description>the target hive database name</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveJdbcUrl</name>
|
||||||
|
<description>hive server jdbc url</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>hiveMetastoreUris</name>
|
||||||
|
<description>hive server metastore URIs</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkDriverMemory</name>
|
||||||
|
<description>memory for driver process</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorMemory</name>
|
||||||
|
<description>memory for individual executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>sparkExecutorCores</name>
|
||||||
|
<description>number of cores used by single executor</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozieActionShareLibForSpark2</name>
|
||||||
|
<description>oozie action sharelib for spark 2.*</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2ExtraListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
|
||||||
|
<description>spark 2.* extra listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2SqlQueryExecutionListeners</name>
|
||||||
|
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
|
||||||
|
<description>spark 2.* sql query execution listeners classname</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2YarnHistoryServerAddress</name>
|
||||||
|
<description>spark 2.* yarn history server address</description>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>spark2EventLogDir</name>
|
||||||
|
<description>spark 2.* event log dir location</description>
|
||||||
|
</property>
|
||||||
|
</parameters>
|
||||||
|
|
||||||
|
<global>
|
||||||
|
<job-tracker>${jobTracker}</job-tracker>
|
||||||
|
<name-node>${nameNode}</name-node>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>mapreduce.job.queuename</name>
|
||||||
|
<value>${queueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.launcher.mapred.job.queue.name</name>
|
||||||
|
<value>${oozieLauncherQueueName}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>oozie.action.sharelib.for.spark</name>
|
||||||
|
<value>${oozieActionShareLibForSpark2}</value>
|
||||||
|
</property>
|
||||||
|
|
||||||
|
</configuration>
|
||||||
|
</global>
|
||||||
|
|
||||||
|
<start to="fork_result_linked_to_projects"/>
|
||||||
|
|
||||||
|
<kill name="Kill">
|
||||||
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
|
</kill>
|
||||||
|
|
||||||
|
|
||||||
|
<fork name="fork_result_linked_to_projects">
|
||||||
|
<path start="select_publication_linked_to_projects"/>
|
||||||
|
<path start="select_dataset_linked_to_projects"/>
|
||||||
|
<path start="select_orp_linked_to_project"/>
|
||||||
|
<path start="select_software_linked_to_projects"/>
|
||||||
|
</fork>
|
||||||
|
|
||||||
|
<action name="select_publication_linked_to_projects">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/publication</arg>
|
||||||
|
<arg>--graphPath</arg><arg>${sourcePath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_dataset_linked_to_projects">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/dataset</arg>
|
||||||
|
<arg>--graphPath</arg><arg>${sourcePath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_orp_linked_to_project">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/otherresearchproduct</arg>
|
||||||
|
<arg>--graphPath</arg><arg>${sourcePath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="select_software_linked_to_projects">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
|
||||||
|
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${workingDir}/result/software</arg>
|
||||||
|
<arg>--graphPath</arg><arg>${sourcePath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="join_link"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<join name="join_link" to="common_action_community_funder"/>
|
||||||
|
|
||||||
|
<action name="common_action_community_funder">
|
||||||
|
<sub-workflow>
|
||||||
|
<app-path>${wf:appPath()}/dump_common
|
||||||
|
</app-path>
|
||||||
|
<propagate-configuration/>
|
||||||
|
<configuration>
|
||||||
|
<property>
|
||||||
|
<name>sourcePath</name>
|
||||||
|
<value>${sourcePath}</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>selectedResults</name>
|
||||||
|
<value>${workingDir}/result</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>communityMapPath</name>
|
||||||
|
<value>${workingDir}/communityMap</value>
|
||||||
|
</property>
|
||||||
|
<property>
|
||||||
|
<name>outputPath</name>
|
||||||
|
<value>${workingDir}</value>
|
||||||
|
</property>
|
||||||
|
</configuration>
|
||||||
|
</sub-workflow>
|
||||||
|
<ok to="dump_funder_results" />
|
||||||
|
<error to="Kill" />
|
||||||
|
</action>
|
||||||
|
|
||||||
|
<action name="dump_funder_results">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Dump funder results </name>
|
||||||
|
<class>eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--sourcePath</arg><arg>${workingDir}/ext</arg>
|
||||||
|
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||||
|
<arg>--graphPath</arg><arg>${sourcePath}</arg>
|
||||||
|
</spark>
|
||||||
|
<ok to="End"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<end name="End"/>
|
||||||
|
|
||||||
|
</workflow-app>
|
||||||
Loading…
Reference in New Issue