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Merge branch 'beta' of code-repo.d4science.org:D-Net/dnet-hadoop into beta

This commit is contained in:
Sandro La Bruzzo 2022-04-26 09:56:34 +02:00
parent 8c22e5c30a 81242538e6
commit 78015a5733
1 changed files with 142 additions and 1 deletions
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143
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml
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@ -13,6 +13,23 @@
<name>isLookupUrl</name>
<description>the address of the lookUp service</description>
</property>
<property>
<name>shouldCleanContext</name>
<description>true if the context have to be cleaned</description>
</property>
<property>
<name>contextId</name>
<value>sobigdata</value>
<description>It is the context id that should be removed from the result if the condition is matched.
Now it is just sobigdata. In a futere implementation I plan to have the contextId as value in a json
where to specify also the constraints that should be verified to remove the context from the result</description>
</property>
<property>
<name>verifyParam</name>
<value>gcube </value>
<description>It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in
the title. If title starts with gcube than the context sobigdata will be removed by the result if present</description>
</property>
<property>
<name>sparkDriverMemory</name>
@ -275,7 +292,131 @@
<error to="Kill"/>
</action>
<join name="wait_clean" to="End"/>
<join name="wait_clean" to="clean_context"/>
<decision name="clean_context">
<switch>
<case to="fork_clean_context">${wf:conf('shouldCleanContext') eq true}</case>
<default to="End"/>
</switch>
</decision>
<fork name="fork_clean_context">
<path start="clean_publication_context"/>
<path start="clean_dataset_context"/>
<path start="clean_otherresearchproduct_context"/>
<path start="clean_software_context"/>
</fork>
<action name="clean_publication_context">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean publications context</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--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.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphOutputPath}/publication</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
<arg>--workingPath</arg><arg>${workingDir}/working/publication</arg>
<arg>--contextId</arg><arg>${contextId}</arg>
<arg>--verifyParam</arg><arg>${verifyParam}</arg>
</spark>
<ok to="wait_clean_context"/>
<error to="Kill"/>
</action>
<action name="clean_dataset_context">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean datasets Context</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphOutputPath}/dataset</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
<arg>--workingPath</arg><arg>${workingDir}/working/dataset</arg>
<arg>--contextId</arg><arg>${contextId}</arg>
<arg>--verifyParam</arg><arg>${verifyParam}</arg>
</spark>
<ok to="wait_clean_context"/>
<error to="Kill"/>
</action>
<action name="clean_otherresearchproduct_context">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean otherresearchproducts context</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--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.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphOutputPath}/otherresearchproduct</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
<arg>--workingPath</arg><arg>${workingDir}/working/otherresearchproduct</arg>
<arg>--contextId</arg><arg>${contextId}</arg>
<arg>--verifyParam</arg><arg>${verifyParam}</arg>
</spark>
<ok to="wait_clean_context"/>
<error to="Kill"/>
</action>
<action name="clean_software_context">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Clean softwares context</name>
<class>eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCores}
--executor-memory=${sparkExecutorMemory}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--inputPath</arg><arg>${graphOutputPath}/software</arg>
<arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
<arg>--workingPath</arg><arg>${workingDir}/working/software</arg>
<arg>--contextId</arg><arg>${contextId}</arg>
<arg>--verifyParam</arg><arg>${verifyParam}</arg>
</spark>
<ok to="wait_clean_context"/>
<error to="Kill"/>
</action>
<join name="wait_clean_context" to="End"/>
<end name="End"/>
</workflow-app>