new input parameters and workflow definition to be used in the provision pipeline

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

@@ -11,17 +11,11 @@
     "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
+    "paramRequired": false
   },
   {
     "paramName":"dop",

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

@@ -5,12 +5,8 @@
         <description>the source path</description>
     </property>
     <property>
-        <name>writeUpdate</name>
-        <description>writes the information found for the update. No double check done if the information is already present</description>
-    </property>
-    <property>
-        <name>saveGraph</name>
-        <description>writes new version of the graph after the propagation step</description>
+        <name>outputPath</name>
+        <description>sets the outputPath</description>
     </property>
 </parameters>
 
@@ -22,18 +18,29 @@
 
     <action name="reset-outputpath">
         <fs>
-            <delete path='${workingDir}/resulttoorganization_propagation'/>
+            <delete path='${outputPath}/relation'/>
+            <delete path='${outputPath}/datasource'/>
+            <delete path='${outputPath}/organization'/>
+            <delete path='${outputPath}/project'/>
+            <delete path='${outputPath}/publication'/>
+            <delete path='${outputPath}/dataset'/>
+            <delete path='${outputPath}/software'/>
+            <delete path='${outputPath}/otherresearchproduct'/>
+            <delete path='${workingDir}/preparedInfo'/>
         </fs>
-        <ok to="copy_relations"/>
+        <ok to="copy_entities"/>
         <error to="Kill"/>
     </action>
 
-    <fork name="copy_relations">
+    <fork name="copy_entities">
         <path start="copy_relation"/>
         <path start="copy_publication"/>
         <path start="copy_dataset"/>
         <path start="copy_orp"/>
         <path start="copy_software"/>
+        <path start="copy_organization"/>
+        <path start="copy_projects"/>
+        <path start="copy_datasources"/>
     </fork>
 
     <action name="copy_relation">
@@ -41,18 +48,17 @@
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/relation</arg>
-            <arg>${nameNode}/${workingDir}/resulttoorganization_propagation/relation</arg>
+            <arg>${nameNode}/${outputPath}/relation</arg>
         </distcp>
         <ok to="wait"/>
         <error to="Kill"/>
     </action>
-
     <action name="copy_publication">
         <distcp xmlns="uri:oozie:distcp-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/publication</arg>
-            <arg>${nameNode}/${workingDir}/resulttoorganization_propagation/publication</arg>
+            <arg>${nameNode}/${outputPath}/publication</arg>
         </distcp>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -63,7 +69,7 @@
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/dataset</arg>
-            <arg>${nameNode}/${workingDir}/resulttoorganization_propagation/dataset</arg>
+            <arg>${nameNode}/${outputPath}/dataset</arg>
         </distcp>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -74,7 +80,7 @@
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/otherresearchproduct</arg>
-            <arg>${nameNode}/${workingDir}/resulttoorganization_propagation/otherresearchproduct</arg>
+            <arg>${nameNode}/${outputPath}/otherresearchproduct</arg>
         </distcp>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -84,11 +90,44 @@
             <job-tracker>${jobTracker}</job-tracker>
             <name-node>${nameNode}</name-node>
             <arg>${nameNode}/${sourcePath}/software</arg>
-            <arg>${nameNode}/${workingDir}/resulttoorganization_propagation/software</arg>
+            <arg>${nameNode}/${outputPath}/software</arg>
         </distcp>
         <ok to="wait"/>
         <error to="Kill"/>
     </action>
+    <action name="copy_organization">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/organization</arg>
+            <arg>${nameNode}/${outputPath}/organization</arg>
+        </distcp>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_projects">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/project</arg>
+            <arg>${nameNode}/${outputPath}/project</arg>
+        </distcp>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="copy_datasources">
+        <distcp xmlns="uri:oozie:distcp-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <arg>${nameNode}/${sourcePath}/datasource</arg>
+            <arg>${nameNode}/${outputPath}/datasource</arg>
+        </distcp>
+        <ok to="wait"/>
+        <error to="Kill"/>
+    </action>
+
     <join name="wait" to="prepare_result_organization_association"/>
     <action name="prepare_result_organization_association">
         <spark xmlns="uri:oozie:spark-action:0.2">
@@ -108,8 +147,8 @@
             </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>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
         </spark>
         <ok to="fork_join_apply_resulttoorganization_propagation"/>
         <!--        <ok to="End"/>-->
@@ -142,12 +181,11 @@
             </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>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -173,17 +211,15 @@
             </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>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
     </action>
-
     <action name="join_propagation_otherresearchproduct">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -204,12 +240,11 @@
             </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>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -235,12 +270,30 @@
             </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>${workingDir}/resulttoorganization_propagation/preparedInfo/alreadyLinked</arg>
+            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
+            <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>--saveGraph</arg><arg>${saveGraph}</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
+            <arg>--datasourceOrganizationPath</arg><arg>${workingDir}/preparedInfo/datasourceOrganization</arg>
+            <arg>--alreadyLinkedPath</arg><arg>${workingDir}/preparedInfo/alreadyLinked</arg>
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>