[Enrichment single step] modification of workflow ans some change in the classes

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java

@@ -8,6 +8,8 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
 
+import eu.dnetlib.dhp.countrypropagation.pojo.CountrySbs;
+import eu.dnetlib.dhp.countrypropagation.pojo.DatasourceCountry;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.FilterFunction;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareResultCountrySet.java

@@ -7,12 +7,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Set;
-import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.countrypropagation.pojo.CountrySbs;
+import eu.dnetlib.dhp.countrypropagation.pojo.DatasourceCountry;
+import eu.dnetlib.dhp.countrypropagation.pojo.ResultCountrySet;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
 import org.apache.spark.sql.*;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java

@@ -9,6 +9,8 @@ import java.util.List;
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.countrypropagation.pojo.CountrySbs;
+import eu.dnetlib.dhp.countrypropagation.pojo.ResultCountrySet;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.MapFunction;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/pojo/CountrySbs.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.countrypropagation;
+package eu.dnetlib.dhp.countrypropagation.pojo;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/pojo/DatasourceCountry.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.countrypropagation;
+package eu.dnetlib.dhp.countrypropagation.pojo;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/pojo/ResultCountrySet.java

@@ -1,5 +1,7 @@
 
-package eu.dnetlib.dhp.countrypropagation;
+package eu.dnetlib.dhp.countrypropagation.pojo;
+
+import eu.dnetlib.dhp.countrypropagation.pojo.CountrySbs;
 
 import java.io.Serializable;
 import java.util.ArrayList;

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/projecttoresult/SparkResultToProjectThroughSemRelJob.java

@@ -51,8 +51,7 @@ public class SparkResultToProjectThroughSemRelJob {
 		final String alreadyLinkedPath = parser.get("alreadyLinkedPath");
 		log.info("alreadyLinkedPath {}: ", alreadyLinkedPath);
 
-		final Boolean saveGraph = Boolean.valueOf(parser.get("saveGraph"));
+
-		log.info("saveGraph: {}", saveGraph);
 
 		SparkConf conf = new SparkConf();
 
@@ -60,11 +59,9 @@ public class SparkResultToProjectThroughSemRelJob {
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				if (isTest(parser)) {
+
-					removeOutputDir(spark, outputPath);
-				}
 				execPropagation(
-					spark, outputPath, alreadyLinkedPath, potentialUpdatePath, saveGraph);
+					spark, outputPath, alreadyLinkedPath, potentialUpdatePath);
 			});
 	}
 
@@ -72,13 +69,12 @@ public class SparkResultToProjectThroughSemRelJob {
 		SparkSession spark,
 		String outputPath,
 		String alreadyLinkedPath,
-		String potentialUpdatePath,
+		String potentialUpdatePath) {
-		Boolean saveGraph) {
 
 		Dataset<ResultProjectSet> toaddrelations = readPath(spark, potentialUpdatePath, ResultProjectSet.class);
 		Dataset<ResultProjectSet> alreadyLinked = readPath(spark, alreadyLinkedPath, ResultProjectSet.class);
 
-		if (saveGraph) {
+
 			toaddrelations
 				.joinWith(
 					alreadyLinked,
@@ -89,7 +85,7 @@ public class SparkResultToProjectThroughSemRelJob {
 				.mode(SaveMode.Append)
 				.option("compression", "gzip")
 				.json(outputPath);
-		}
+
 	}
 
 	private static FlatMapFunction<Tuple2<ResultProjectSet, ResultProjectSet>, Relation> mapRelationRn() {

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromorganization/SparkResultToCommunityFromOrganizationJob.java

@@ -56,11 +56,7 @@ public class SparkResultToCommunityFromOrganizationJob {
 		final String resultClassName = parser.get("resultTableName");
 		log.info("resultTableName: {}", resultClassName);
 
-		final Boolean saveGraph = Optional
+
-			.ofNullable(parser.get("saveGraph"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("saveGraph: {}", saveGraph);
 
 		@SuppressWarnings("unchecked")
 		Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
@@ -72,10 +68,9 @@ public class SparkResultToCommunityFromOrganizationJob {
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				removeOutputDir(spark, outputPath);
+
-				if (saveGraph) {
 					execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
-				}
+
 			});
 	}
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/SparkResultToCommunityThroughSemRelJob.java

@@ -70,13 +70,10 @@ public class SparkResultToCommunityThroughSemRelJob {
 			conf,
 			isSparkSessionManaged,
 			spark -> {
-				if (isTest(parser)) {
+
-					removeOutputDir(spark, outputPath);
-				}
-				if (saveGraph) {
 					execPropagation(
 						spark, inputPath, outputPath, preparedInfoPath, resultClazz);
-				}
+
 			});
 	}
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/SparkResultToOrganizationFromSemRel.java

@@ -98,13 +98,13 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
 		String leavesPath,
 		String childParentPath,
 		String resultOrganizationPath,
-		String graphPath,
+		String relationPath,
 		String workingPath,
 		String outputPath,
 		int iterations) {
 		if (iterations == 1) {
 			doPropagateOnce(
-				spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
+				spark, leavesPath, childParentPath, resultOrganizationPath, relationPath,
 				workingPath, outputPath);
 		} else {
 
@@ -123,26 +123,26 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
 				notReachedFirstParent);
 
 			doPropagate(
-				spark, leavesPath, childParentPath, resultOrganizationPath, graphPath,
+				spark, leavesPath, childParentPath, resultOrganizationPath, relationPath,
 				workingPath, outputPath, propagationCounter);
 		}
 
 	}
 
 	private static void doPropagateOnce(SparkSession spark, String leavesPath, String childParentPath,
-		String resultOrganizationPath, String graphPath, String workingPath,
+		String resultOrganizationPath, String relationPath, String workingPath,
 		String outputPath) {
 
 		StepActions
 			.execStep(
-				spark, graphPath, workingPath + NEW_RELATION_PATH,
+				spark, relationPath, workingPath + NEW_RELATION_PATH,
 				leavesPath, childParentPath, resultOrganizationPath);
 
 		addNewRelations(spark, workingPath + NEW_RELATION_PATH, outputPath);
 	}
 
 	private static void doPropagate(SparkSession spark, String leavesPath, String childParentPath,
-		String resultOrganizationPath, String graphPath, String workingPath, String outputPath,
+		String resultOrganizationPath, String relationPath, String workingPath, String outputPath,
 		PropagationCounter propagationCounter) {
 		int iteration = 0;
 		long leavesCount;
@@ -151,7 +151,7 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
 			iteration++;
 			StepActions
 				.execStep(
-					spark, graphPath, workingPath + NEW_RELATION_PATH,
+					spark, relationPath, workingPath + NEW_RELATION_PATH,
 					leavesPath, childParentPath, resultOrganizationPath);
 			StepActions
 				.prepareForNextStep(

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttoorganizationfromsemrel/StepActions.java

@@ -27,10 +27,10 @@ import scala.Tuple2;
 public class StepActions implements Serializable {
 
 	public static void execStep(SparkSession spark,
-		String graphPath, String newRelationPath,
+		String relationPath, String newRelationPath,
 		String leavesPath, String chldParentOrgPath, String resultOrgPath) {
 
-		Dataset<Relation> relationGraph = readPath(spark, graphPath, Relation.class);
+		Dataset<Relation> relationGraph = readPath(spark, relationPath, Relation.class);
 		// select only the relation source target among those proposed by propagation that are not already existent
 		getNewRels(
 			newRelationPath, relationGraph,

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/main/oozie_app/workflow.xml

@@ -176,10 +176,6 @@
                     <name>pathMap</name>
                     <value>${pathMap}</value>
                 </property>
-                <property>
-                    <name>outputPath</name>
-                    <value>${workingDir}/results</value>
-                </property>
             </configuration>
         </sub-workflow>
         <ok to="affiliation_inst_repo" />
@@ -220,10 +216,6 @@
                     <name>sourcePath</name>
                     <value>${outputPath}</value>
                 </property>
-<!--                <property>-->
-<!--                    <name>outputPath</name>-->
-<!--                    <value>${outputPath}</value>-->
-<!--                </property>-->
             </configuration>
         </sub-workflow>
         <ok to="community_organization" />
@@ -240,10 +232,6 @@
                     <name>sourcePath</name>
                     <value>${outputPath}</value>
                 </property>
-                <property>
-                    <name>outputPath</name>
-                    <value>${outputPath}</value>
-                </property>
                 <property>
                     <name>organizationtoresultcommunitymap</name>
                     <value>${organizationtoresultcommunitymap}</value>
@@ -264,10 +252,6 @@
                     <name>sourcePath</name>
                     <value>${outputPath}</value>
                 </property>
-                <property>
-                    <name>outputPath</name>
-                    <value>${outputPath}</value>
-                </property>
                 <property>
                     <name>allowedsemrels</name>
                     <value>${allowedsemrelsresultproject}</value>
@@ -280,7 +264,7 @@
 
     <action name="community_sem_rel">
         <sub-workflow>
-            <app-path>${wf:appPath()}/result_project
+            <app-path>${wf:appPath()}/community_sem_rel
             </app-path>
             <propagate-configuration/>
             <configuration>
@@ -288,10 +272,7 @@
                     <name>sourcePath</name>
                     <value>${outputPath}</value>
                 </property>
-                <property>
+              
-                    <name>outputPath</name>
-                    <value>${workingDir}/communitysemrel</value>
-                </property>
                 <property>
                     <name>allowedsemrels</name>
                     <value>${allowedsemrelscommunitysemrel}</value>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/bulktag/oozie_app/workflow.xml

@@ -186,7 +186,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${outputPath}</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/eoscTag</arg>
+            <arg>--workingPath</arg><arg>${workingDir}/bulktag</arg>
         </spark>
         <ok to="eosc_get_datasource_master"/>
         <error to="Kill"/>
@@ -230,7 +230,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${outputPath}/publication</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/publication</arg>
+            <arg>--workingPath</arg><arg>${workingDir}/bulktag/publication</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
             <arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
         </spark>
@@ -256,7 +256,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${outputPath}/dataset</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/dataset</arg>
+            <arg>--workingPath</arg><arg>${workingDir}/bulktag/dataset</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
             <arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
         </spark>
@@ -281,7 +281,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${outputPath}/software</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/software</arg>
+            <arg>--workingPath</arg><arg>${workingDir}/bulktag/software</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
             <arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
         </spark>
@@ -306,14 +306,24 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
             </spark-opts>
             <arg>--sourcePath</arg><arg>${outputPath}/otherresearchproduct</arg>
-            <arg>--workingPath</arg><arg>${workingDir}/eoscContextTag/otherresearchproduct</arg>
+            <arg>--workingPath</arg><arg>${workingDir}/bulktag/otherresearchproduct</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
             <arg>--datasourceMapPath</arg><arg>${workingDir}/datasourcemaster</arg>
         </spark>
         <ok to="wait_eosc_context_tag"/>
         <error to="Kill"/>
     </action>
-    <join name="wait_eosc_context_tag" to="End"/>
+    <join name="wait_eosc_context_tag" to="reset_workingDir"/>
+
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/countrypropagation/oozie_app/workflow.xml

@@ -30,20 +30,13 @@
         </configuration>
     </global>
 
-    <start to="reset_outputpath"/>
+    <start to="prepare_datasource_country_association"/>
 
     <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="prepare_datasource_country_association"/>
-        <error to="Kill"/>
-    </action>
 
     <action name="prepare_datasource_country_association">
         <spark xmlns="uri:oozie:spark-action:0.2">
@@ -222,7 +215,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
             <arg>--workingPath</arg><arg>${workingDir}/country/publication</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/publication</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/country/result/publication</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -251,7 +244,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
             <arg>--workingPath</arg><arg>${workingDir}/country/dataset</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/country/result/dataset</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -280,7 +273,7 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
             <arg>--workingPath</arg><arg>${workingDir}/country/otherresearchproduct</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/country/result/otherresearchproduct</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
@@ -309,14 +302,21 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
             <arg>--workingPath</arg><arg>${workingDir}/country/software</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/software</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/country/result/software</arg>
         </spark>
         <ok to="wait"/>
         <error to="Kill"/>
     </action>
 
-    <join name="wait" to="End"/>
+    <join name="wait" to="reset_workingDir"/>
-
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/oozie_app/workflow.xml

@@ -390,7 +390,16 @@
         <error to="Kill"/>
     </action>
     
-    <join name="wait2" to="End"/>
+    <join name="wait2" to="reset_workingDir"/>
+
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
     
     <end name="End"/>
     

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/projecttoresult/oozie_app/workflow.xml

@@ -8,10 +8,7 @@
             <name>allowedsemrels</name>
             <description>the allowed semantics </description>
         </property>
-       <property>
+
-           <name>outputPath</name>
-           <description>the output path</description>
-       </property>
     </parameters>
 
     <global>
@@ -76,16 +73,22 @@
                 --conf spark.dynamicAllocation.enabled=true
                 --conf spark.dynamicAllocation.maxExecutors=${spark2MaxExecutors}
             </spark-opts>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/relation</arg>
+            <arg>--outputPath</arg><arg>${sourcePath}/relation</arg>
             <arg>--potentialUpdatePath</arg><arg>${workingDir}/resultproject/preparedInfo/potentialUpdates</arg>
             <arg>--alreadyLinkedPath</arg><arg>${workingDir}/resultproject/preparedInfo/alreadyLinked</arg>
         </spark>
+        <ok to="reset_workingDir"/>
+        <error to="Kill"/>
+    </action>
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
-
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromorganization/oozie_app/workflow.xml

@@ -8,10 +8,7 @@
             <name>organizationtoresultcommunitymap</name>
             <description>organization community map</description>
         </property>
-        <property>
+
-            <name>outputPath</name>
-            <description>the output path</description>
-        </property>
     </parameters>
 
     <global>
@@ -25,21 +22,12 @@
         </configuration>
     </global>
 
-    <start to="reset_outputpath"/>
+    <start to="prepare_result_communitylist"/>
 
     <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="prepare_result_communitylist"/>
-        <error to="Kill"/>
-    </action>
-
     <action name="prepare_result_communitylist">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -97,7 +85,7 @@
             <arg>--outputPath</arg><arg>${workingDir}/communityorganization/publication</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -126,7 +114,7 @@
             <arg>--outputPath</arg><arg>${workingDir}/communityorganization/dataset</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -155,7 +143,7 @@
             <arg>--outputPath</arg><arg>${workingDir}/communityorganization/otherresearchproduct</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -184,14 +172,22 @@
             <arg>--outputPath</arg><arg>${workingDir}/communityorganization/software</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
     </action>
 
-    <join name="wait2" to="End"/>
+    <join name="wait2" to="reset_workingDir"/>
 
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/resulttocommunityfromsemrel/oozie_app/workflow.xml

@@ -18,21 +18,12 @@
         </property>
     </parameters>
 
-    <start to="reset_outputpath"/>
+    <start to="fork_prepare_assoc_step1"/>
 
     <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="fork_prepare_assoc_step1"/>
-        <error to="Kill"/>
-    </action>
-
 
 
     <fork name="fork_prepare_assoc_step1">
@@ -214,8 +205,8 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/publication</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/publication</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/communitysemrel/publication</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -243,8 +234,8 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/dataset</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/dataset</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/communitysemrel/dataset</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -272,8 +263,8 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/otherresearchproduct</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/otherresearchproduct</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/communitysemrel/otherresearchproduct</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
@@ -301,15 +292,22 @@
             <arg>--sourcePath</arg><arg>${sourcePath}/software</arg>
             <arg>--hive_metastore_uris</arg><arg>${hive_metastore_uris}</arg>
             <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--outputPath</arg><arg>${outputPath}/software</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/communitysemrel/software</arg>
-            <arg>--saveGraph</arg><arg>${saveGraph}</arg>
+
         </spark>
         <ok to="wait2"/>
         <error to="Kill"/>
     </action>
 
-    <join name="wait2" to="End"/>
+    <join name="wait2" to="reset_workingDir"/>
-
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/wf/subworkflows/resulttoorganizationfromsemrel/oozie_app/workflow.xml

@@ -4,10 +4,7 @@
             <name>sourcePath</name>
             <description>the source path</description>
         </property>
-<!--        <property>-->
+
-<!--            <name>outputPath</name>-->
-<!--            <description>sets the outputPath</description>-->
-<!--        </property>-->
     </parameters>
 
     <global>
@@ -27,23 +24,6 @@
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
-<!--    <decision name="resume_from">-->
-<!--        <switch>-->
-<!--            <case to="prepare_info">${wf:conf('resumeFrom') eq 'PrepareInfo'}</case>-->
-<!--            <default to="reset_outputpath"/> &lt;!&ndash; first action to be done when downloadDump is to be performed &ndash;&gt;-->
-<!--        </switch>-->
-<!--    </decision>-->
-
-<!--    <action name="reset_outputpath">-->
-<!--        <fs>-->
-<!--            <delete path="${outputPath}"/>-->
-<!--            <mkdir path="${outputPath}"/>-->
-<!--        </fs>-->
-<!--        <ok to="prepare_info"/>-->
-<!--        <error to="Kill"/>-->
-<!--    </action>-->
-
-
     <action name="prepare_info">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -99,12 +79,19 @@
             <arg>--workingDir</arg><arg>${workingDir}/affiliationSemanticRelation/working</arg>
             <arg>--iterations</arg><arg>${iterations}</arg>
         </spark>
+        <ok to="reset_workingDir"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="reset_workingDir">
+        <fs>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
 
-
-
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/DatasourceCountryPreparationTest.java

@@ -5,6 +5,7 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 
+import eu.dnetlib.dhp.countrypropagation.pojo.DatasourceCountry;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/countrypropagation/ResultCountryPreparationTest.java

@@ -1,12 +1,11 @@
 
 package eu.dnetlib.dhp.countrypropagation;
 
-import static eu.dnetlib.dhp.PropagationConstant.isSparkSessionManaged;
-
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 
+import eu.dnetlib.dhp.countrypropagation.pojo.ResultCountrySet;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/projecttoresult/ProjectPropagationJobTest.java

@@ -33,21 +33,21 @@ public class ProjectPropagationJobTest {
 	private static SparkSession spark;
 
 	private static Path workingDir;
+	private static final SparkConf conf = new SparkConf();
 
 	@BeforeAll
 	public static void beforeAll() throws IOException {
-		workingDir = Files.createTempDirectory(ProjectPropagationJobTest.class.getSimpleName());
+
 		log.info("using work dir {}", workingDir);
 
-		SparkConf conf = new SparkConf();
+
 		conf.setAppName(ProjectPropagationJobTest.class.getSimpleName());
 
 		conf.setMaster("local[*]");
 		conf.set("spark.driver.host", "localhost");
 		conf.set("hive.metastore.local", "true");
 		conf.set("spark.ui.enabled", "false");
-		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+
-		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
 
 		spark = SparkSession
 				.builder()
@@ -58,7 +58,7 @@ public class ProjectPropagationJobTest {
 
 	@AfterAll
 	public static void afterAll() throws IOException {
-		FileUtils.deleteDirectory(workingDir.toFile());
+
 		spark.stop();
 	}
 
@@ -71,6 +71,7 @@ public class ProjectPropagationJobTest {
 	@Test
 	void NoUpdateTest() throws Exception {
 
+		workingDir = Files.createTempDirectory(ProjectPropagationJobTest.class.getSimpleName());
 		final String potentialUpdateDate = getClass()
 			.getResource(
 				"/eu/dnetlib/dhp/projecttoresult/preparedInfo/noupdates/potentialUpdates")
@@ -82,10 +83,10 @@ public class ProjectPropagationJobTest {
 		SparkResultToProjectThroughSemRelJob
 			.main(
 				new String[] {
-					"-isTest", Boolean.TRUE.toString(),
+
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
 					"-hive_metastore_uris", "",
-					"-saveGraph", "true",
+					
 					"-outputPath", workingDir.toString() + "/relation",
 					"-potentialUpdatePath", potentialUpdateDate,
 					"-alreadyLinkedPath", alreadyLinkedPath,
@@ -98,6 +99,10 @@ public class ProjectPropagationJobTest {
 			.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
 
 		Assertions.assertEquals(0, tmp.count());
+
+		FileUtils.deleteDirectory(workingDir.toFile());
+
+
 	}
 
 	/**
@@ -107,6 +112,12 @@ public class ProjectPropagationJobTest {
 	 */
 	@Test
 	void UpdateTenTest() throws Exception {
+		workingDir = Files.createTempDirectory(ProjectPropagationJobTest.class.getSimpleName());
+		spark = SparkSession
+				.builder()
+				.appName(ProjectPropagationJobTest.class.getSimpleName())
+				.config(conf)
+				.getOrCreate();
 		final String potentialUpdatePath = getClass()
 			.getResource(
 				"/eu/dnetlib/dhp/projecttoresult/preparedInfo/tenupdates/potentialUpdates")
@@ -118,10 +129,10 @@ public class ProjectPropagationJobTest {
 		SparkResultToProjectThroughSemRelJob
 			.main(
 				new String[] {
-					"-isTest", Boolean.TRUE.toString(),
+
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
 					"-hive_metastore_uris", "",
-					"-saveGraph", "true",
+
 					"-outputPath", workingDir.toString() + "/relation",
 					"-potentialUpdatePath", potentialUpdatePath,
 					"-alreadyLinkedPath", alreadyLinkedPath,
@@ -169,6 +180,9 @@ public class ProjectPropagationJobTest {
 					.sql(
 						"Select * from temporary where datainfo.inferenceprovenance = 'propagation'")
 					.count());
+
+		FileUtils.deleteDirectory(workingDir.toFile());
+
 	}
 
 	/**
@@ -179,6 +193,12 @@ public class ProjectPropagationJobTest {
 	 */
 	@Test
 	void UpdateMixTest() throws Exception {
+		workingDir = Files.createTempDirectory(ProjectPropagationJobTest.class.getSimpleName());
+		spark = SparkSession
+				.builder()
+				.appName(ProjectPropagationJobTest.class.getSimpleName())
+				.config(conf)
+				.getOrCreate();
 		final String potentialUpdatepath = getClass()
 			.getResource(
 				"/eu/dnetlib/dhp/projecttoresult/preparedInfo/updatesmixed/potentialUpdates")
@@ -190,10 +210,10 @@ public class ProjectPropagationJobTest {
 		SparkResultToProjectThroughSemRelJob
 			.main(
 				new String[] {
-					"-isTest", Boolean.TRUE.toString(),
+
 					"-isSparkSessionManaged", Boolean.FALSE.toString(),
 					"-hive_metastore_uris", "",
-					"-saveGraph", "true",
+
 					"-outputPath", workingDir.toString() + "/relation",
 					"-potentialUpdatePath", potentialUpdatepath,
 					"-alreadyLinkedPath", alreadyLinkedPath,
@@ -244,5 +264,7 @@ public class ProjectPropagationJobTest {
 					.sql(
 						"Select * from temporary where datainfo.inferenceprovenance = 'propagation'")
 					.count());
+
+		FileUtils.deleteDirectory(workingDir.toFile());
 	}
 }