fixed implementation of PatchRelationsApplication, refined the relative unit test

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml

@@ -548,42 +548,7 @@
         <error to="Kill"/>
     </action>
 
-    <join name="wait_graphs" to="patchRelations"/>
+    <join name="wait_graphs" to="fork_merge_claims"/>
-
-    <decision name="decisionPatchRelations">
-        <switch>
-            <case to="patchRelations">
-                ${(shouldPatchRelations eq "true") and
-                (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")}
-            </case>
-            <default to="fork_merge_claims"/>
-        </switch>
-    </decision>
-
-    <action name="patchRelations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>PatchRelations</name>
-            <class>eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory ${sparkExecutorMemory}
-                --executor-cores ${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--graphBasePath</arg><arg>${workingDir}/graph_raw</arg>
-            <arg>--workingDir</arg><arg>${workingDir}/patch_relations</arg>
-            <arg>--idMappingPath</arg><arg>${idMappingPath}</arg>
-        </spark>
-        <ok to="fork_merge_claims"/>
-        <error to="Kill"/>
-    </action>
 
     <fork name="fork_merge_claims">
         <path start="merge_claims_publication"/>
@@ -596,7 +561,6 @@
         <path start="merge_claims_relation"/>
     </fork>
 
-
     <action name="merge_claims_publication">
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
@@ -805,7 +769,42 @@
         <error to="Kill"/>
     </action>
 
-    <join name="wait_merge" to="End"/>
+    <join name="wait_merge" to="decisionPatchRelations"/>
+
+    <decision name="decisionPatchRelations">
+        <switch>
+            <case to="patchRelations">
+                ${(shouldPatchRelations eq "true") and
+                (fs:exists(concat(concat(wf:conf('nameNode'),'/'),wf:conf('idMappingPath'))) eq "true")}
+            </case>
+            <default to="End"/>
+        </switch>
+    </decision>
+
+    <action name="patchRelations">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>PatchRelations</name>
+            <class>eu.dnetlib.dhp.oa.graph.raw.PatchRelationsApplication</class>
+            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory ${sparkExecutorMemory}
+                --executor-cores ${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.shuffle.partitions=7680
+            </spark-opts>
+            <arg>--graphBasePath</arg><arg>${graphOutputPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}/patch_relations</arg>
+            <arg>--idMappingPath</arg><arg>${idMappingPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
 
     <end name="End"/>
 </workflow-app>

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/PrepareRelationsJob.java

@@ -10,6 +10,7 @@ import java.util.Set;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
@@ -81,6 +82,7 @@ public class PrepareRelationsJob {
 
 		Set<String> relationFilter = Optional
 			.ofNullable(parser.get("relationFilter"))
+			.map(String::toLowerCase)
 			.map(s -> Sets.newHashSet(Splitter.on(",").split(s)))
 			.orElse(new HashSet<>());
 		log.info("relationFilter: {}", relationFilter);
@@ -130,7 +132,7 @@ public class PrepareRelationsJob {
 
 		JavaRDD<Relation> rels = readPathRelationRDD(spark, inputRelationsPath)
 			.filter(rel -> rel.getDataInfo().getDeletedbyinference() == false)
-			.filter(rel -> relationFilter.contains(rel.getRelClass()) == false);
+			.filter(rel -> relationFilter.contains(StringUtils.lowerCase(rel.getRelClass())) == false);
 
 		JavaRDD<Relation> pruned = pruneRels(
 			pruneRels(