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master #11

Manually merged
claudio.atzori merged 275 commits from :master into enrichment_wfs 2020-05-11 15:14:56 +02:00
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20
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromremrel/input_orcidtoresult_parameters.json Normal file
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[
{
"paramName":"mt",
"paramLongName":"master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName":"as",
"paramLongName":"allowedsemrels",
"paramDescription": "the allowed sematinc relations for propagation",
"paramRequired": true
}
]

18
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromremrel/oozie_app/config-default.xml Normal file
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<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>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

55
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/orcidtoresultfromremrel/oozie_app/workflow.xml Normal file
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<workflow-app name="orcid_to_result_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<description>the semantic relationships allowed for propagation</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>
</parameters>
<start to="OrcidToResultFromSemRelPropagation"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="OrcidToResultFromSemRelPropagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>AffiliatioPropagation</name>
<class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory}
--executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

20
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/input_propagationresultcommunityfromsemrel_parameters.json Normal file
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[
{
"paramName":"mt",
"paramLongName":"master",
"paramDescription": "should be local or yarn",
"paramRequired": true
},
{
"paramName":"s",
"paramLongName":"sourcePath",
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName":"as",
"paramLongName":"allowedsemrels",
"paramDescription": "the allowed sematinc relations for propagation",
"paramRequired": true
}
]

18
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/config-default.xml Normal file
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<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>oozie.action.sharelib.for.spark</name>
<value>spark2</value>
</property>
</configuration>

55
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromsemrel/oozie_app/workflow.xml Normal file
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<workflow-app name="result_to_community_from_semrel_propagation" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>allowedsemrels</name>
<description>the semantic relationships allowed for propagation</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>
</parameters>
<start to="ResultToCommunityFromSemRelPropagation"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="ResultToCommunityFromSemRelPropagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<master>yarn-cluster</master>
<mode>cluster</mode>
<name>AffiliatioPropagation</name>
<class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob</class>
<jar>dhp-propagation-${projectVersion}.jar</jar>
<spark-opts>--executor-memory ${sparkExecutorMemory}
--executor-cores ${sparkExecutorCores}
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
--conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--allowedsemrels</arg><arg>${allowedsemrels}</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>