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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
Conversation 1 Commits 275 Files Changed 156 +147 -13
2 changed files with 147 additions and 13 deletions
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18
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json
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@ -11,18 +11,6 @@
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName":"wl",
"paramLongName":"whitelist",
"paramDescription": "datasource id that will be considered even if not in the allowed typology list. Split by ;",
"paramRequired": true
},
{
"paramName":"at",
"paramLongName":"allowedtypes",
"paramDescription": "the types of the allowed datasources. Split by ;",
"paramRequired": true
},
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
@ -40,5 +28,11 @@
"paramLongName":"saveGraph",
"paramDescription": "true if the new version of the graph must be saved",
"paramRequired": true
},
{
"paramName":"tn",
"paramLongName":"resultTableName",
"paramDescription": "the name of the result table we are currently working on",
"paramRequired": true
}
]

142
dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/countrypropagation/oozie_app/workflow.xml
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@ -38,12 +38,152 @@
</property>
</parameters>
<start to="CountryPropagation"/>
<start to="prepare_datasource_country_association"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="prepare_datasource_country_association">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>PrepareDatasourceCountryAssociation</name>
<class>eu.dnetlib.dhp.countrypropagation.PrepareDatasourceCountryAssociation</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--whitelist</arg><arg>${whitelist}</arg>
<arg>--allowedtypes</arg><arg>${allowedtypes}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
</spark>
<ok to="fork_join_apply_country_propagation"/>
<error to="Kill"/>
</action>
<fork name="fork_join_apply_country_propagation">
<path start="join_propagation_publication"/>
<path start="join_propagation_dataset"/>
<path start="join_propagation_otherresearchproduct"/>
<path start="join_propagation_software"/>
</fork>
<action name="join_propagation_publication">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>countryPropagationForPublications</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
</spark>
<ok to="end"/>
<error to="Kill"/>
</action>
<action name="join_propagation_dataset">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>countryPropagationForDataset</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
</spark>
<ok to="end"/>
<error to="Kill"/>
</action>
<action name="join_propagation_otherresearchproduct">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>countryPropagationForORP</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Otherresearchproduct</arg>
</spark>
<ok to="end"/>
<error to="Kill"/>
</action>
<action name="join_propagation_software">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>countryPropagationForSoftware</name>
<class>eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2</class>
<jar>dhp-graph-propagation-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=${sparkExecutorCoresForJoining}
--executor-memory=${sparkExecutorMemoryForJoining}
--driver-memory=${sparkDriverMemoryForJoining}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
</spark-opts>
<arg>-mt</arg> <arg>yarn-cluster</arg>
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
<arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
<arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
<arg>--saveGraph</arg><arg>${saveGraph}</arg>
<arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
</spark>
<ok to="end"/>
<error to="Kill"/>
</action>
<action name="CountryPropagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<job-tracker>${jobTracker}</job-tracker>