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fixing issue on propagation organization. added --config to workflow definition. added oozie_app to communtiy project

This commit is contained in:
Miriam Baglioni 2023-10-20 10:14:20 +02:00
parent f1b898c6b4
commit a4214ced1e
6 changed files with 207 additions and 12 deletions
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4
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/PrepareResultCommunitySet.java
View File

@ -109,12 +109,12 @@ public class PrepareResultCommunitySet {
});
});
if(cl.size() == 0)
if (cl.size() == 0)
return null;
rpl.setCommunityList(cl);
return rpl;
}, Encoders.bean(ResultProjectList.class))
.filter(Objects::nonNull)
.filter(Objects::nonNull)
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")

2
dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromproject/SparkResultToCommunityFromProject.java
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@ -62,10 +62,8 @@ public class SparkResultToCommunityFromProject implements Serializable {
final String possibleupdatespath = parser.get("preparedInfoPath");
log.info("preparedInfoPath: {}", possibleupdatespath);
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,

4
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromorganization/oozie_app/workflow.xml
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@ -92,7 +92,7 @@
<spark-opts>
--executor-cores=6
--executor-memory=5G
--spark.executor.memoryOverhead=3g
--conf spark.executor.memoryOverhead=3g
--conf spark.sql.shuffle.partitions=3284
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
@ -121,7 +121,7 @@
<spark-opts>
--executor-cores=6
--executor-memory=5G
--spark.executor.memoryOverhead=3g
--conf spark.executor.memoryOverhead=3g
--conf spark.sql.shuffle.partitions=3284
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}

7
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/input_preparecommunitytoresult_parameters.json
View File

@ -5,12 +5,7 @@
"paramDescription": "the path of the sequencial file to read",
"paramRequired": true
},
{
"paramName":"h",
"paramLongName":"hive_metastore_uris",
"paramDescription": "the hive metastore uris",
"paramRequired": true
},
{
"paramName": "ssm",
"paramLongName": "isSparkSessionManaged",

58
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/config-default.xml Normal file
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@ -0,0 +1,58 @@
<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>
<property>
<name>hive_metastore_uris</name>
<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
</property>
<property>
<name>spark2YarnHistoryServerAddress</name>
<value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
</property>
<property>
<name>spark2EventLogDir</name>
<value>/user/spark/spark2ApplicationHistory</value>
</property>
<property>
<name>spark2ExtraListeners</name>
<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
</property>
<property>
<name>spark2SqlQueryExecutionListeners</name>
<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
</property>
<property>
<name>sparkExecutorNumber</name>
<value>4</value>
</property>
<property>
<name>sparkDriverMemory</name>
<value>15G</value>
</property>
<property>
<name>sparkExecutorMemory</name>
<value>6G</value>
</property>
<property>
<name>sparkExecutorCores</name>
<value>1</value>
</property>
<property>
<name>spark2MaxExecutors</name>
<value>50</value>
</property>
</configuration>

144
dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/resulttocommunityfromproject/oozie_app/workflow.xml Normal file
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@ -0,0 +1,144 @@
<workflow-app name="community_to_result_propagation_project" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
<description>the source path</description>
</property>
<property>
<name>outputPath</name>
<description>the output path</description>
</property>
</parameters>
<global>
<job-tracker>${jobTracker}</job-tracker>
<name-node>${nameNode}</name-node>
<configuration>
<property>
<name>oozie.action.sharelib.for.spark</name>
<value>${oozieActionShareLibForSpark2}</value>
</property>
</configuration>
</global>
<start to="reset_outputpath"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill>
<action name="reset_outputpath">
<fs>
<delete path="${outputPath}"/>
<mkdir path="${outputPath}"/>
</fs>
<ok to="copy_entities"/>
<error to="Kill"/>
</action>
<fork name="copy_entities">
<path start="copy_relation"/>
<path start="copy_organization"/>
<path start="copy_projects"/>
<path start="copy_datasources"/>
</fork>
<action name="copy_relation">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/relation</arg>
<arg>${nameNode}/${outputPath}/relation</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_organization">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/organization</arg>
<arg>${nameNode}/${outputPath}/organization</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_projects">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/project</arg>
<arg>${nameNode}/${outputPath}/project</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<action name="copy_datasources">
<distcp xmlns="uri:oozie:distcp-action:0.2">
<arg>${nameNode}/${sourcePath}/datasource</arg>
<arg>${nameNode}/${outputPath}/datasource</arg>
</distcp>
<ok to="copy_wait"/>
<error to="Kill"/>
</action>
<join name="copy_wait" to="prepare_result_communitylist"/>
<action name="prepare_result_communitylist">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Prepare-Community-Result-Organization</name>
<class>eu.dnetlib.dhp.resulttocommunityfromproject.PrepareResultCommunitySet</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=6
--executor-memory=5G
--conf spark.executor.memoryOverhead=3g
--conf spark.sql.shuffle.partitions=3284
--driver-memory=${sparkDriverMemory}
--conf spark.extraListeners=${spark2ExtraListeners}
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
--conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--sourcePath</arg><arg>${sourcePath}/relation</arg>
<arg>--outputPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--production</arg><arg>${production}</arg>
</spark>
<ok to="exec-propagation"/>
<error to="Kill"/>
</action>
<action name="exec-propagation">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>community2resultfromproject</name>
<class>eu.dnetlib.dhp.resulttocommunityfromproject.SparkResultToCommunityFromProject</class>
<jar>dhp-enrichment-${projectVersion}.jar</jar>
<spark-opts>
--executor-cores=6
--executor-memory=5G
--conf spark.executor.memoryOverhead=3g
--conf spark.sql.shuffle.partitions=3284
--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.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
</spark-opts>
<arg>--preparedInfoPath</arg><arg>${workingDir}/preparedInfo/resultCommunityList</arg>
<arg>--sourcePath</arg><arg>${sourcePath}/</arg>
<arg>--outputPath</arg><arg>${outputPath}/</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>