read from blacklist and write the result as relations on hdfs
This commit is contained in:
parent
869f576273
commit
6a47e6191d
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@ -10,6 +10,24 @@
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<modelVersion>4.0.0</modelVersion>
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<artifactId>dhp-blacklist</artifactId>
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<dependencies>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-graph-mapper</artifactId>
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<version>1.1.7-SNAPSHOT</version>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>com.fasterxml.jackson.core</groupId>
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<artifactId>jackson-databind</artifactId>
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<scope>compile</scope>
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</dependency>
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<dependency>
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<groupId>org.apache.hadoop</groupId>
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<artifactId>hadoop-common</artifactId>
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<scope>compile</scope>
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</dependency>
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</dependencies>
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</project>
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@ -5,6 +5,12 @@
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"paramDescription": "the path where storing the sequential file",
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"paramRequired": true
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},
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{
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"paramName": "nn",
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"paramLongName": "hdfsNameNode",
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"paramDescription": "the name node on hdfs",
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"paramRequired": true
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},
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{
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"paramName": "pgurl",
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"paramLongName": "postgresUrl",
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@ -22,11 +28,5 @@
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"paramLongName": "postgresPassword",
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"paramDescription": "postgres password",
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"paramRequired": false
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},
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{
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"paramName": "a",
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"paramLongName": "action",
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"paramDescription": "process claims",
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"paramRequired": false
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}
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]
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@ -1,34 +1,4 @@
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<workflow-app name="bulk_tagging" 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>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>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>pathMap</name>
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<description>the json path associated to each selection field</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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</parameters>
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<workflow-app name="blacklsting" xmlns="uri:oozie:workflow:0.5">
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<start to="reset-outputpath"/>
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@ -38,190 +8,26 @@
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<action name="reset-outputpath">
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<fs>
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<delete path='${outputPath}/relation'/>
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<delete path='${outputPath}/publication'/>
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<delete path='${outputPath}/dataset'/>
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<delete path='${outputPath}/otherresearchproduct'/>
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<delete path='${outputPath}/software'/>
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<delete path='${outputPath}/organization'/>
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<delete path='${outputPath}/project'/>
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<delete path='${outputPath}/datasource'/>
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<delete path='${hdfsPath}'/>
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</fs>
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<ok to="copy_entities"/>
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<ok to="read_blacklist"/>
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<error to="Kill"/>
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</action>
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<fork name="copy_entities">
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<path start="copy_relation"/>
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<path start="copy_organization"/>
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<path start="copy_projects"/>
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<path start="copy_datasources"/>
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</fork>
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<action name="copy_relation">
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<distcp xmlns="uri:oozie:distcp-action:0.2">
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<action name="read_blacklist">
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<java>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<arg>${nameNode}/${sourcePath}/relation</arg>
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<arg>${nameNode}/${outputPath}/relation</arg>
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</distcp>
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<ok to="copy_wait"/>
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<main-class>eu.dnetlib.dhp.blacklist.ReadBlacklistFromDB</main-class>
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<arg>--hdfsPath</arg><arg>${workingDir}/blacklist</arg>
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<arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
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<arg>--postgresUrl</arg><arg>${postgresUrl}</arg>
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<arg>--postgresUser</arg><arg>${postgresUser}</arg>
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<arg>--postgresPassword</arg><arg>${postgresPassword}</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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<action name="copy_organization">
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<distcp xmlns="uri:oozie:distcp-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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<arg>${nameNode}/${sourcePath}/organization</arg>
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<arg>${nameNode}/${outputPath}/organization</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_projects">
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<distcp xmlns="uri:oozie:distcp-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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<arg>${nameNode}/${sourcePath}/project</arg>
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<arg>${nameNode}/${outputPath}/project</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<action name="copy_datasources">
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<distcp xmlns="uri:oozie:distcp-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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<arg>${nameNode}/${sourcePath}/datasource</arg>
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<arg>${nameNode}/${outputPath}/datasource</arg>
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</distcp>
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<ok to="copy_wait"/>
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<error to="Kill"/>
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</action>
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<join name="copy_wait" to="fork_exec_bulktag"/>
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<fork name="fork_exec_bulktag">
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<path start="join_bulktag_publication"/>
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<path start="join_bulktag_dataset"/>
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<path start="join_bulktag_otherresearchproduct"/>
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<path start="join_bulktag_software"/>
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</fork>
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<action name="join_bulktag_publication">
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<spark xmlns="uri:oozie:spark-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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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>bulkTagging-publication</name>
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<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
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<jar>dhp-bulktag-${projectVersion}.jar</jar>
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<spark-opts>
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--num-executors=${sparkExecutorNumber}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--outputPath</arg><arg>${outputPath}/publication</arg>
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<arg>--pathMap</arg><arg>${pathMap}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<action name="join_bulktag_dataset">
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<spark xmlns="uri:oozie:spark-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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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>bulkTagging-dataset</name>
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<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
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<jar>dhp-bulktag-${projectVersion}.jar</jar>
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<spark-opts>
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--num-executors=${sparkExecutorNumber}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
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<arg>--pathMap</arg><arg>${pathMap}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<action name="join_bulktag_otherresearchproduct">
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<spark xmlns="uri:oozie:spark-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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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>bulkTagging-orp</name>
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<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
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<jar>dhp-bulktag-${projectVersion}.jar</jar>
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<spark-opts>
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--num-executors=${sparkExecutorNumber}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
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<arg>--pathMap</arg><arg>${pathMap}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<action name="join_bulktag_software">
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<spark xmlns="uri:oozie:spark-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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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>bulkTagging-software</name>
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<class>eu.dnetlib.dhp.bulktag.SparkBulkTagJob2</class>
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<jar>dhp-bulktag-${projectVersion}.jar</jar>
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<spark-opts>
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--num-executors=${sparkExecutorNumber}
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
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<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--outputPath</arg><arg>${outputPath}/software</arg>
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<arg>--pathMap</arg><arg>${pathMap}</arg>
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<arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
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</spark>
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<ok to="wait"/>
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<error to="Kill"/>
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</action>
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<join name="wait" to="End"/>
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<end name="End"/>
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</workflow-app>
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