input parameters and workflow definition for propagation of result to organization from institutional repositories

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_prepareresultorg_parameters.json

@@ -11,18 +11,6 @@
     "paramDescription": "the hive metastore uris",
     "paramRequired": true
   },
-  {
-    "paramName":"wu",
-    "paramLongName":"writeUpdate",
-    "paramDescription": "true if the update must be writte. No double check if information is already present",
-    "paramRequired": true
-  },
-  {
-    "paramName":"sg",
-    "paramLongName":"saveGraph",
-    "paramDescription": "true if the new version of the graph must be saved",
-    "paramRequired": true
-  },
   {
     "paramName":"dop",
     "paramLongName":"datasourceOrganizationPath",

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json

@@ -1,10 +1,4 @@
 [
-  {
-    "paramName":"mt",
-    "paramLongName":"master",
-    "paramDescription": "should be local or yarn",
-    "paramRequired": true
-  },
   {
     "paramName":"s",
     "paramLongName":"sourcePath",
@@ -16,5 +10,53 @@
     "paramLongName":"hive_metastore_uris",
     "paramDescription": "the hive metastore uris",
     "paramRequired": true
+  },
+  {
+    "paramName":"wu",
+    "paramLongName":"writeUpdate",
+    "paramDescription": "true if the update must be writte. No double check if information is already present",
+    "paramRequired": true
+  },
+  {
+    "paramName":"sg",
+    "paramLongName":"saveGraph",
+    "paramDescription": "true if the new version of the graph must be saved",
+    "paramRequired": true
+  },
+  {
+    "paramName":"dop",
+    "paramLongName":"datasourceOrganizationPath",
+    "paramDescription": "path where to store/find association from datasource and organization",
+    "paramRequired": true
+  },
+  {
+    "paramName":"alp",
+    "paramLongName":"alreadyLinkedPath",
+    "paramDescription": "path where to store/find already linked results and organizations",
+    "paramRequired": true
+  },
+  {
+    "paramName": "ssm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the path where prepared info have been stored",
+    "paramRequired": false
+  },
+  {
+    "paramName": "test",
+    "paramLongName": "isTest",
+    "paramDescription": "true if it is a test running",
+    "paramRequired": false
+  },
+  {
+    "paramName":"tn",
+    "paramLongName":"resultTableName",
+    "paramDescription": "the name of the result table we are currently working on",
+    "paramRequired": true
+  },
+  {
+    "paramName": "out",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path used to store temporary output files",
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/config-default.xml

@@ -19,4 +19,40 @@
         <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>

dhp-workflows/dhp-propagation/src/main/resources/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/oozie_app/workflow.xml

@@ -5,47 +5,227 @@
         <description>the source path</description>
     </property>
     <property>
-        <name>sparkDriverMemory</name>
+        <name>writeUpdate</name>
-        <description>memory for driver process</description>
+        <description>writes the information found for the update. No double check done if the information is already present</description>
     </property>
     <property>
-        <name>sparkExecutorMemory</name>
+        <name>saveGraph</name>
-        <description>memory for individual executor</description>
+        <description>writes new version of the graph after the propagation step</description>
-    </property>
-    <property>
-        <name>sparkExecutorCores</name>
-        <description>number of cores used by single executor</description>
     </property>
 </parameters>
 
-<start to="AffiliationPropagation"/>
+<start to="reset-outputpath"/>
-
+<!--<start to="prepare_result_organization_association"/>-->
 <kill name="Kill">
     <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
 </kill>
 
-<action name="AffiliationPropagation">
+    <action name="reset-outputpath">
-    <spark xmlns="uri:oozie:spark-action:0.2">
+        <fs>
-        <job-tracker>${jobTracker}</job-tracker>
+            <delete path='${workingDir}/resulttoorganization_propagation/relation'/>
-        <name-node>${nameNode}</name-node>
+        </fs>
-        <master>yarn-cluster</master>
+        <ok to="copy_relation"/>
-        <mode>cluster</mode>
+        <error to="Kill"/>
-        <name>AffiliationPropagation</name>
+    </action>
-        <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob</class>
+    <action name="copy_relation">
-        <jar>dhp-propagation-${projectVersion}.jar</jar>
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
-        <spark-opts>--executor-memory ${sparkExecutorMemory}
+            <job-tracker>${jobTracker}</job-tracker>
-            --executor-cores ${sparkExecutorCores}
+            <name-node>${nameNode}</name-node>
-            --driver-memory=${sparkDriverMemory}
+            <arg>${nameNode}/${sourcePath}/relation</arg>
-            --conf spark.extraListeners="com.cloudera.spark.lineage.NavigatorAppListener"
+            <arg>${nameNode}/${workingDir}/resulttoorganization_propagation/relation</arg>
-            --conf spark.sql.queryExecutionListeners="com.cloudera.spark.lineage.NavigatorQueryListener"
+        </distcp>
-        </spark-opts>
+        <ok to="prepare_result_organization_association"/>
-        <arg>-mt</arg> <arg>yarn-cluster</arg>
+        <error to="Kill"/>
-        <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+    </action>
-        <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+
-    </spark>
+    <action name="prepare_result_organization_association">
-    <ok to="End"/>
+        <spark xmlns="uri:oozie:spark-action:0.2">
-    <error to="Kill"/>
+            <master>yarn</master>
-</action>
+            <mode>cluster</mode>
+            <name>PrepareResultOrganizationAssociation</name>
+            <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.PrepareResultInstRepoAssociation</class>
+            <jar>dhp-propagation-${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}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+        </spark>
+        <ok to="fork_join_apply_resulttoorganization_propagation"/>
+<!--        <ok to="End"/>-->
+        <error to="Kill"/>
+    </action>
+    <fork name="fork_join_apply_resulttoorganization_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>resultToOrganizationFromInstRepoPropagationForPublications</name>
+            <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob2</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${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}${spark2EventLogDir}
+                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
+            <arg>--hive_metastore_uris</arg><arg>${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>
+            <arg>--outputPath</arg><arg>${workingDir}/resulttoorganization_propagation/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+        </spark>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_propagation_dataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>resultToOrganizationFromInstRepoPropagationForDataset</name>
+            <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob2</class>
+            <jar>dhp-propagation-${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.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
+            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/resulttoorganization_propagation/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+        </spark>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_propagation_otherresearchproduct">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>resultToOrganizationFromInstRepoPropagationForORP</name>
+            <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob2</class>
+            <jar>dhp-propagation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-cores=${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}${spark2EventLogDir}
+                --conf spark.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
+            <arg>--hive_metastore_uris</arg><arg>${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>
+            <arg>--outputPath</arg><arg>${workingDir}/resulttoorganization_propagation/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+        </spark>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="join_propagation_software">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>resultToOrganizationFromInstRepoPropagationForSoftware</name>
+            <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob2</class>
+            <jar>dhp-propagation-${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.dynamicAllocation.enabled=true
+                --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
+            <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
+            <arg>--writeUpdate</arg><arg>${writeUpdate}</arg>
+            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/resulttoorganization_propagation/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+        </spark>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="wait" to="End"/>
+    <end name="End"/>
+
+<!--    <action name="AffiliationPropagation">-->
+<!--    <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>AffiliationPropagation</name>-->
+<!--        <class>eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob</class>-->
+<!--        <jar>dhp-propagation-${projectVersion}.jar</jar>-->
+<!--        <spark-opts>-->
+<!--            &#45;&#45;num-executors=${sparkExecutorNumber}-->
+<!--            &#45;&#45;executor-memory=${sparkExecutorMemory}-->
+<!--            &#45;&#45;executor-cores=${sparkExecutorCores}-->
+<!--            &#45;&#45;driver-memory=${sparkDriverMemory}-->
+<!--            &#45;&#45;conf spark.extraListeners=${spark2ExtraListeners}-->
+<!--            &#45;&#45;conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}-->
+<!--            &#45;&#45;conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}-->
+<!--            &#45;&#45;conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}-->
+<!--            &#45;&#45;conf spark.dynamicAllocation.enabled=true-->
+<!--            &#45;&#45;conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}-->
+<!--        </spark-opts>-->
+<!--        <arg>-mt</arg> <arg>yarn-cluster</arg>-->
+<!--        <arg>&#45;&#45;sourcePath</arg><arg>${sourcePath}</arg>-->
+<!--        <arg>&#45;&#45;hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>-->
+<!--        <arg>&#45;&#45;writeUpdate</arg><arg>${writeUpdate}</arg>-->
+<!--        <arg>&#45;&#45;saveGraph</arg><arg>${saveGraph}</arg>-->
+<!--    </spark>-->
+<!--    <ok to="End"/>-->
+<!--    <error to="Kill"/>-->
+<!--</action>-->
 
-<end name="End"/>
 </workflow-app>