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Fix scores & Workflow

This commit is contained in:
Ilias Kanellos 2023-07-06 15:06:28 +03:00
parent d5c39a1059 60f25b780d
commit 0c433eccdd
2 changed files with 53 additions and 46 deletions
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2
dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/job.properties
View File

@ -102,4 +102,4 @@ actionSetOutputPath=${workingDir}/bip_actionsets/
# The directory to store project impact indicators # The directory to store project impact indicators
projectImpactIndicatorsOutput=${workingDir}/project_indicators projectImpactIndicatorsOutput=${workingDir}/project_indicators
resume=create-openaire-ranking-graph resume=entry-point-decision

97
dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml
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@ -36,7 +36,7 @@
<default to="create-openaire-ranking-graph" /> <default to="create-openaire-ranking-graph" />
</switch> </switch>
</decision> </decision>
<!-- Script here written by Serafeim: maps openaire ids to their synonyms --> <!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
<action name="create-openaire-ranking-graph"> <action name="create-openaire-ranking-graph">
<!-- This is required as a tag for spark jobs, regardless of programming language --> <!-- This is required as a tag for spark jobs, regardless of programming language -->
@ -47,12 +47,12 @@
<prepare> <prepare>
<delete path="${synonymFolder}"/> <delete path="${synonymFolder}"/>
</prepare> </prepare>
--> -->
<!-- using configs from an example on openaire --> <!-- using configs from an example on openaire -->
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<!-- This is the name of our job --> <!-- This is the name of our job -->
<name>Openaire Ranking Graph Creation</name> <name>Openaire Ranking Graph Creation</name>
<!-- Script name goes here --> <!-- Script name goes here -->
@ -144,8 +144,8 @@
<!-- This is required as a tag for spark jobs, regardless of programming language --> <!-- This is required as a tag for spark jobs, regardless of programming language -->
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<!-- using configs from an example on openaire --> <!-- using configs from an example on openaire -->
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<!-- This is the name of our job --> <!-- This is the name of our job -->
@ -250,8 +250,8 @@
<!-- Reference says: The mode element if present indicates the mode of spark, where to run spark driver program. Ex: client,cluster. | In my case I always have a client --> <!-- Reference says: The mode element if present indicates the mode of spark, where to run spark driver program. Ex: client,cluster. | In my case I always have a client -->
<!-- <mode>client</mode> --> <!-- <mode>client</mode> -->
<!-- using configs from an example on openaire --> <!-- using configs from an example on openaire -->
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<!-- This is the name of our job --> <!-- This is the name of our job -->
@ -295,8 +295,8 @@
<!-- This is required as a tag for spark jobs, regardless of programming language --> <!-- This is required as a tag for spark jobs, regardless of programming language -->
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<!-- using configs from an example on openaire --> <!-- using configs from an example on openaire -->
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<!-- This is the name of our job --> <!-- This is the name of our job -->
@ -340,12 +340,18 @@
</action> </action>
<<<<<<< HEAD
<!-- Removed for ser --> <!-- Removed for ser -->
<!-- <!--
JOIN ITERATIVE METHODS AND THEN END = JOIN ITERATIVE METHODS AND THEN END =
<join name="join-iterative-rankings" to="end" /> <join name="join-iterative-rankings" to="end" />
to="get-file-names"/> to="get-file-names"/>
--> -->
=======
<!-- JOIN ITERATIVE METHODS AND THEN END -->
<join name="join-iterative-rankings" to="get-file-names" />
<!-- to="get-file-names"/> -->
>>>>>>> 60f25b780de1c456762003cbb8b0011c9c82f93d
<!-- This will be a shell action that will output key-value pairs for output files --> <!-- This will be a shell action that will output key-value pairs for output files -->
@ -358,7 +364,7 @@
<!-- name of script to run --> <!-- name of script to run -->
<argument>get_ranking_files.sh</argument> <argument>get_ranking_files.sh</argument>
<!-- We only pass the directory where we expect to find the rankings --> <!-- We only pass the directory where we expect to find the rankings -->
<argument>/${workingDir}</argument> <argument>${workingDir}</argument>
<!-- the name of the file run --> <!-- the name of the file run -->
<file>${wfAppPath}/get_ranking_files.sh#get_ranking_files.sh</file> <file>${wfAppPath}/get_ranking_files.sh#get_ranking_files.sh</file>
@ -490,8 +496,8 @@
<delete path="${synonymFolder}"/> <delete path="${synonymFolder}"/>
</prepare> </prepare>
<!-- using configs from an example on openaire --> <!-- using configs from an example on openaire -->
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<!-- This is the name of our job --> <!-- This is the name of our job -->
@ -512,7 +518,7 @@
</spark-opts> </spark-opts>
<!-- Script arguments here --> <!-- Script arguments here -->
<arg>${openaireDataInput}</arg> <arg>${openaireDataInput}/</arg>
<!-- number of partitions to be used on joins --> <!-- number of partitions to be used on joins -->
<arg>${synonymFolder}</arg> <arg>${synonymFolder}</arg>
<!-- This needs to point to the file on the hdfs i think --> <!-- This needs to point to the file on the hdfs i think -->
@ -532,8 +538,8 @@
<!-- This is required as a tag for spark jobs, regardless of programming language --> <!-- This is required as a tag for spark jobs, regardless of programming language -->
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<!-- using configs from an example on openaire --> <!-- using configs from an example on openaire -->
<master>yarn-cluster</master> <master>yarn-cluster</master>
<mode>cluster</mode> <mode>cluster</mode>
<!-- This is the name of our job --> <!-- This is the name of our job -->
@ -570,47 +576,48 @@
<!-- Do this after finishing okay --> <!-- Do this after finishing okay -->
<ok to="deleteOutputPathForActionSet" /> <ok to="deleteOutputPathForActionSet" />
<!-- This is the initial code <ok to="deleteOutputPathForActionSet" /> -->
<!-- Go there if we have an error --> <!-- Go there if we have an error -->
<error to="map-scores-fail" /> <error to="map-scores-fail" />
</action> </action>
<action name="deleteOutputPathForActionSet"> <action name="deleteOutputPathForActionSet">
<fs> <fs>
<delete path="${actionSetOutputPath}/results/"/> <delete path="${actionSetOutputPath}/results/"/>
<delete path="${actionSetOutputPath}/projects/"/> <delete path="${actionSetOutputPath}/projects/"/>
<mkdir path="${actionSetOutputPath}/results/"/> <mkdir path="${actionSetOutputPath}/results/"/>
<mkdir path="${actionSetOutputPath}/projects/"/> <mkdir path="${actionSetOutputPath}/projects/"/>
</fs> </fs>
<ok to="createActionSetForResults"/> <ok to="createActionSetForResults"/>
<error to="actionset-delete-fail"/> <error to="actionset-delete-fail"/>
</action> </action>
<action name="createActionSetForResults"> <action name="createActionSetForResults">
<spark xmlns="uri:oozie:spark-action:0.2"> <spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master> <master>yarn</master>
<mode>cluster</mode> <mode>cluster</mode>
<name>Produces the atomic action with the bip finder scores for publications</name> <name>Produces the atomic action with the bip finder scores for publications</name>
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class> <class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
<jar>dhp-aggregation-${projectVersion}.jar</jar> <jar>dhp-aggregation-${projectVersion}.jar</jar>
<spark-opts> <spark-opts>
--executor-memory=${sparkNormalExecutorMemory} --executor-memory=${sparkNormalExecutorMemory}
--executor-cores=${sparkExecutorCores} --executor-cores=${sparkExecutorCores}
--driver-memory=${sparkNormalDriverMemory} --driver-memory=${sparkNormalDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners} --conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
</spark-opts> </spark-opts>
<arg>--inputPath</arg><arg>${bipScorePath}</arg> <arg>--inputPath</arg><arg>${bipScorePath}</arg>
<arg>--outputPath</arg><arg>${actionSetOutputPath}/results/</arg> <arg>--outputPath</arg><arg>${actionSetOutputPath}/results/</arg>
<arg>--targetEntity</arg><arg>result</arg> <arg>--targetEntity</arg><arg>result</arg>
</spark> </spark>
<ok to="project-impact-indicators"/> <ok to="project-impact-indicators"/>
<error to="actionset-creation-fail"/> <error to="actionset-creation-fail"/>
</action> </action>
<action name="project-impact-indicators"> <action name="project-impact-indicators">
<!-- This is required as a tag for spark jobs, regardless of programming language --> <!-- This is required as a tag for spark jobs, regardless of programming language -->