Merge pull request 'Oozie workflow for cleancontext' (#216) from cleancontext into beta
Reviewed-on: #216 Looks good. We need to extend the cleaning workflow parameters to enable the extra step only when it is needed.
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commit
81242538e6
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@ -13,6 +13,23 @@
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<name>isLookupUrl</name>
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<description>the address of the lookUp service</description>
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</property>
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<property>
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<name>shouldCleanContext</name>
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<description>true if the context have to be cleaned</description>
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</property>
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<property>
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<name>contextId</name>
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<value>sobigdata</value>
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<description>It is the context id that should be removed from the result if the condition is matched.
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Now it is just sobigdata. In a futere implementation I plan to have the contextId as value in a json
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where to specify also the constraints that should be verified to remove the context from the result</description>
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</property>
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<property>
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<name>verifyParam</name>
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<value>gcube </value>
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<description>It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in
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the title. If title starts with gcube than the context sobigdata will be removed by the result if present</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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@ -275,7 +292,131 @@
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<error to="Kill"/>
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</action>
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<join name="wait_clean" to="End"/>
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<join name="wait_clean" to="clean_context"/>
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<decision name="clean_context">
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<switch>
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<case to="fork_clean_context">${wf:conf('shouldCleanContext') eq true}</case>
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<default to="End"/>
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</switch>
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</decision>
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<fork name="fork_clean_context">
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<path start="clean_publication_context"/>
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<path start="clean_dataset_context"/>
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<path start="clean_otherresearchproduct_context"/>
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<path start="clean_software_context"/>
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</fork>
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<action name="clean_publication_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean publications context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/publication</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<action name="clean_dataset_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean datasets Context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/dataset</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<action name="clean_otherresearchproduct_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean otherresearchproducts context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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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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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/otherresearchproduct</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<action name="clean_software_context">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Clean softwares context</name>
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<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-cores=${sparkExecutorCores}
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--executor-memory=${sparkExecutorMemory}
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--driver-memory=${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}${spark2EventLogDir}
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--conf spark.sql.shuffle.partitions=7680
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</spark-opts>
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<arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
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<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
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<arg>--workingPath</arg><arg>${workingDir}/working/software</arg>
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<arg>--contextId</arg><arg>${contextId}</arg>
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<arg>--verifyParam</arg><arg>${verifyParam}</arg>
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</spark>
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<ok to="wait_clean_context"/>
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<error to="Kill"/>
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</action>
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<join name="wait_clean_context" to="End"/>
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<end name="End"/>
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</workflow-app>
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