fixed bug on missing relation in ANDS

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/QueryTest.scala

@@ -1,6 +1,6 @@
 package eu.dnetlib.dhp.doiboost
 
-import eu.dnetlib.dhp.schema.oaf.Publication
+import eu.dnetlib.dhp.schema.oaf.{Publication, Relation}
 import org.apache.spark.SparkContext
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
 import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
@@ -21,6 +21,13 @@ class QueryTest {
 
 
 
+  }
+
+
+  def has_ands(r:Relation) :Boolean = {
+
+    r.getCollectedfrom!= null && r.getCollectedfrom.asScala.count(k => k.getValue.contains("Australian")) > 0
+
   }
 
   def hasInstanceWithUrl(p:Publication):Boolean = {

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/IdReplace.scala

@@ -0,0 +1,3 @@
+package eu.dnetlib.dhp.sx.graph
+
+case class IdReplace(newId:String, oldId:String) {}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkSplitOafTODLIEntities.scala

@@ -1,12 +1,15 @@
 package eu.dnetlib.dhp.sx.graph
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation}
+import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
 import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown}
 import eu.dnetlib.dhp.sx.ebi.EBIAggregator
 import org.apache.commons.io.IOUtils
+import org.apache.commons.lang3.StringUtils
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.LoggerFactory
+import org.apache.spark.sql.functions.col
+
 
 object SparkSplitOafTODLIEntities {
 
@@ -83,14 +86,42 @@ object SparkSplitOafTODLIEntities {
   }
 
 
+  def extract_ids(o:Oaf) :(String, String) = {
+
+    o match {
+      case p: DLIPublication =>
+        val prefix = StringUtils.substringBefore(p.getId, "|")
+        val original = StringUtils.substringAfter(p.getOriginalObjIdentifier, "::")
+        (p.getId, s"$prefix|$original")
+      case p: DLIDataset =>
+        val prefix = StringUtils.substringBefore(p.getId, "|")
+        val original = StringUtils.substringAfter(p.getOriginalObjIdentifier, "::")
+        (p.getId, s"$prefix|$original")
+      case _ =>null
+    }
+  }
+
   def extract_relations(spark:SparkSession, workingPath:String) :Unit = {
 
     implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
     implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
+    import spark.implicits._
 
     val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
     val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation].repartition(2000)
 
+
+    OAFDataset
+      .filter(o => o.isInstanceOf[Result])
+      .map(extract_ids)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
+      .filter(r => r != null)
+      .where("_1 != _2")
+      .select(col("_1").alias("newId"), col("_2").alias("oldId"))
+      .distinct()
+      .map(f => IdReplace(f.getString(0), f.getString(1)))
+      .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/id_replace")
+
+
     OAFDataset
       .filter(s => s != null && s.isInstanceOf[Relation])
       .map(s =>s.asInstanceOf[Relation])
@@ -100,7 +131,41 @@ object SparkSplitOafTODLIEntities {
       .agg(EBIAggregator.getRelationAggregator().toColumn)
       .map(p => p._2)
       .repartition(4000)
-      .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation")
+      .write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation_unfixed")
+
+
+    val relations = spark.read.load(s"$workingPath/graph/relation_unfixed").as[Relation]
+    val ids = spark.read.load(s"$workingPath/graph/id_replace").as[IdReplace]
+
+    relations
+      .map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
+      .joinWith(ids, col("_1").equalTo(ids("oldId")), "left")
+      .map(i =>{
+        val r = i._1._2
+        if (i._2 != null)
+          {
+            val id = i._2.newId
+            r.setSource(id)
+          }
+        r
+      }).write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/rel_f_source")
+
+    val rel_source:Dataset[Relation] = spark.read.load(s"$workingPath/graph/rel_f_source").as[Relation]
+
+    rel_source
+      .map(r => (r.getTarget, r))(Encoders.tuple(Encoders.STRING, relEncoder))
+      .joinWith(ids, col("_1").equalTo(ids("oldId")), "left")
+      .map(i =>{
+        val r:Relation = i._1._2
+        if (i._2 != null)
+        {
+          val id = i._2.newId
+          r.setTarget(id)
+        }
+        r
+      }).write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation")
+
+
 
   }
 

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/ScholexplorerParserTest.java

@@ -12,6 +12,7 @@ import com.fasterxml.jackson.databind.SerializationFeature;
 
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.sx.graph.parser.DatasetScholexplorerParser;
+import eu.dnetlib.dhp.sx.graph.parser.PublicationScholexplorerParser;
 import eu.dnetlib.scholexplorer.relation.RelationMapper;
 
 public class ScholexplorerParserTest {
@@ -37,4 +38,26 @@ public class ScholexplorerParserTest {
 					}
 				});
 	}
+
+	@Test
+	public void testPublicationParser() throws Exception {
+		String xml = IOUtils.toString(this.getClass().getResourceAsStream("pmf.xml"));
+
+		PublicationScholexplorerParser p = new PublicationScholexplorerParser();
+		List<Oaf> oaves = p.parseObject(xml, RelationMapper.load());
+
+		ObjectMapper m = new ObjectMapper();
+		m.enable(SerializationFeature.INDENT_OUTPUT);
+
+		oaves
+			.forEach(
+				oaf -> {
+					try {
+						System.out.println(m.writeValueAsString(oaf));
+						System.out.println("----------------------------");
+					} catch (JsonProcessingException e) {
+
+					}
+				});
+	}
 }

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/dmf.xml

@@ -1,51 +1,38 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <oai:record xmlns:oai="http://www.openarchives.org/OAI/2.0/"
-			xmlns:oaf="http://namespace.openaire.eu/oaf"
+			xmlns="http://namespace.openaire.eu/">
-			xmlns:dri="http://www.driver-repository.eu/namespace/dri"
+	<oai:header xmlns="">
-			xmlns:dc="http://purl.org/dc/elements/1.1/">
+		<dri:objIdentifier xmlns:dri="http://www.driver-repository.eu/namespace/dri">r3d100010464::0002882a9d38c4f4612e7666ad768ccd</dri:objIdentifier>
-	<oai:header>
+		<dri:recordIdentifier xmlns:dri="http://www.driver-repository.eu/namespace/dri">https://research.jcu.edu.au/researchdata/published/detail/9079e05370d830eb8d416c77c0b761ce::url</dri:recordIdentifier>
-		<dri:repositoryId>aaadf8b3-01a8-4cc2-9964-63cfb19df3b4_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU=</dri:repositoryId>
+		<dri:dateOfCollection xmlns:dri="http://www.driver-repository.eu/namespace/dri">2020-11-02T16:14:07.831Z</dri:dateOfCollection>
-		<dri:recordIdentifier>oai:pangaea.de:doi:10.1594/PANGAEA.432865</dri:recordIdentifier>
+		<dri:repositoryId xmlns:dri="http://www.driver-repository.eu/namespace/dri">ands_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU=</dri:repositoryId>
-		<dri:datasourceprefix>r3d100010134</dri:datasourceprefix>
+		<dri:datasourceprefix xmlns:dri="http://www.driver-repository.eu/namespace/dri">r3d100010464</dri:datasourceprefix>
-		<dri:objIdentifier>r3d100010134::00002f60593fd1f758fb838fafb46795</dri:objIdentifier>
-		<dri:dateOfCollection>2020-02-18T03:05:02.534Z</dri:dateOfCollection>
-		<oaf:datasourceprefix/>
-		<identifier>oai:pangaea.de:doi:10.1594/PANGAEA.432865</identifier>
-		<setSpec>citable topicOceans</setSpec>
 	</oai:header>
-	<oai:metadata>
+	<metadata xmlns="">
-		<resource xmlns="http://datacite.org/schema/kernel-3">
+		<resource xmlns="http://datacite.org/schema/kernel-3"
-			<identifier identifierType="doi">10.1594/pangaea.432865</identifier>
+				  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-			<titles xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+				  xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
-				<title>Daily sea level from coastal tide gauge station Woods_Hole in 1978 (Research quality database)</title>
+			<identifier xmlns="" identifierType="url">https://research.jcu.edu.au/researchdata/published/detail/9079e05370d830eb8d416c77c0b761ce</identifier>
+			<titles xmlns="">
+				<title>Vertebrate monitoring in the Australian Wet Tropics rainforest at CU6A1 (145.30367623, -16.57767628, 600.0m above MSL) collected by Reptile Surveys</title>
 			</titles>
-			<publisher xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">PANGAEA - Data Publisher for Earth &amp; Environmental Science</publisher>
+			<publisher xmlns="">James Cook University</publisher>
-			<publicationYear xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">2006</publicationYear>
+			<dates xmlns="">
-			<dates xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+				<date dateType="Collected">2013-05-07</date>
-				<date dateType="Collected">1978-01-01T12:00:00/1978-12-31T12:00:00</date>
 			</dates>
-			<creators xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+			<creators xmlns=""/>
-				<creator>
+			<resourceType xmlns="" resourceTypeGeneral="Dataset">Dataset</resourceType>
-					<creatorName>WOCE Sea Level, WSL</creatorName>
+			<relatedIdentifiers xmlns="">
-				</creator>
+				<relatedIdentifier entityType="publication" inverseRelationType="related"
-			</creators>
+								   relatedIdentifierType="dnet"
-			<subjects xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+								   relationType="IsRelatedTo">r3d100010464::57793c5aa995172db237d9da17353f8b</relatedIdentifier>
-				<subject subjectScheme="Parameter">DATE/TIME</subject>
-				<subject subjectScheme="Parameter">Sea level</subject>
-				<subject subjectScheme="Method">Tide gauge station</subject>
-				<subject subjectScheme="Campaign">SeaLevel</subject>
-				<subject subjectScheme="Project">World Ocean Circulation Experiment (WOCE)</subject>
-			</subjects>
-			<resourceType resourceTypeGeneral="Dataset"/>
-			<relatedIdentifiers>
-				<relatedIdentifier relatedIdentifierType="URL" relationType="isDocumentedBy"
-								   inverseRelationType="documents">http://store.pangaea.de/Projects/WOCE/SeaLevel_rqds/Woods_Hole.txt</relatedIdentifier>
 			</relatedIdentifiers>
 		</resource>
-	</oai:metadata>
+	</metadata>
-	<oaf:about>
+	<oaf:about xmlns:oaf="http://namespace.dnet.eu/oaf" xmlns="">
 		<oaf:datainfo>
-			<oaf:collectedFrom completionStatus="complete" id="dli_________::r3d100010134" name="Pangaea"/>
+			<oaf:collectedFrom completionStatus="complete" id="dli_________::r3d100010464"
+							   name="Australian National Data Service"/>
 			<oaf:completionStatus>complete</oaf:completionStatus>
 			<oaf:provisionMode>collected</oaf:provisionMode>
 		</oaf:datainfo>

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/pmf.xml

@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<oai:record xmlns:oai="http://www.openarchives.org/OAI/2.0/"
+            xmlns="http://namespace.openaire.eu/">
+    <oai:header xmlns="">
+        <dri:objIdentifier xmlns:dri="http://www.driver-repository.eu/namespace/dri">r3d100010464::57793c5aa995172db237d9da17353f8b</dri:objIdentifier>
+        <dri:recordIdentifier xmlns:dri="http://www.driver-repository.eu/namespace/dri">10.1111/j.1365-2486.2005.00995.x::doi</dri:recordIdentifier>
+        <dri:dateOfCollection xmlns:dri="http://www.driver-repository.eu/namespace/dri">2020-11-02T16:14:07.831Z</dri:dateOfCollection>
+        <dri:repositoryId xmlns:dri="http://www.driver-repository.eu/namespace/dri">ands_UmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZXMvUmVwb3NpdG9yeVNlcnZpY2VSZXNvdXJjZVR5cGU=</dri:repositoryId>
+        <dri:datasourceprefix xmlns:dri="http://www.driver-repository.eu/namespace/dri">r3d100010464</dri:datasourceprefix>
+    </oai:header>
+    <metadata xmlns="">
+        <oaf:pid xmlns:oaf="http://namespace.dnet.eu/oaf" type="doi">10.1111/j.1365-2486.2005.00995.x</oaf:pid>
+        <dc:identifier xmlns:dc="http://purl.org/dc/elements/1.1/">10.1111/j.1365-2486.2005.00995.x</dc:identifier>
+        <dc:title xmlns:dc="http://purl.org/dc/elements/1.1/">Potential decoupling of trends in distribution area and population size of species with climate change.</dc:title>
+        <dc:type xmlns:dc="http://purl.org/dc/elements/1.1/">publication</dc:type>
+    </metadata>
+    <oaf:about xmlns:oaf="http://namespace.dnet.eu/oaf" xmlns="">
+        <oaf:datainfo>
+            <oaf:collectedFrom completionStatus="complete" id="dli_________::r3d100010464"
+                               name="Australian National Data Service"/>
+            <oaf:completionStatus>complete</oaf:completionStatus>
+            <oaf:provisionMode>collected</oaf:provisionMode>
+        </oaf:datainfo>
+    </oaf:about>
+</oai:record>

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/scholix/Scholix.java

@@ -97,20 +97,25 @@ public class Scholix implements Serializable {
 	}
 
 	private List<ScholixEntityId> mergeScholixEntityId(final List<ScholixEntityId> a, final List<ScholixEntityId> b) {
-		final List<ScholixEntityId> m = new ArrayList<>(a);
+		final List<ScholixEntityId> m = a != null ? new ArrayList<>(a) : new ArrayList<>();
 		if (b != null)
 			b.forEach(s -> {
-				int tt = (int) m.stream().filter(t -> t.getName().equalsIgnoreCase(s.getName())).count();
+				if (s != null) {
+					int tt = (int) m
+						.stream()
+						.filter(t -> t != null && t.getName() != null && t.getName().equalsIgnoreCase(s.getName()))
+						.count();
 					if (tt == 0) {
 						m.add(s);
 					}
+				}
 			});
 		return m;
 	}
 
 	private List<ScholixIdentifier> mergeScholixIdnetifier(final List<ScholixIdentifier> a,
 		final List<ScholixIdentifier> b) {
-		final List<ScholixIdentifier> m = new ArrayList<>(a);
+		final List<ScholixIdentifier> m = a != null ? new ArrayList<>(a) : new ArrayList<>();
 		if (b != null)
 			b.forEach(s -> {
 				int tt = (int) m.stream().filter(t -> t.getIdentifier().equalsIgnoreCase(s.getIdentifier())).count();
@@ -123,7 +128,7 @@ public class Scholix implements Serializable {
 
 	private List<ScholixCollectedFrom> mergeScholixCollectedFrom(final List<ScholixCollectedFrom> a,
 		final List<ScholixCollectedFrom> b) {
-		final List<ScholixCollectedFrom> m = new ArrayList<>(a);
+		final List<ScholixCollectedFrom> m = a != null ? new ArrayList<>(a) : new ArrayList<>();
 		if (b != null)
 			b.forEach(s -> {
 				int tt = (int) m
@@ -139,14 +144,15 @@ public class Scholix implements Serializable {
 
 	private ScholixRelationship mergeRelationships(final ScholixRelationship a, final ScholixRelationship b) {
 		ScholixRelationship result = new ScholixRelationship();
-		result.setName(StringUtils.isEmpty(a.getName()) ? b.getName() : a.getName());
+		result.setName(a == null || StringUtils.isEmpty(a.getName()) ? b.getName() : a.getName());
-		result.setInverse(StringUtils.isEmpty(a.getInverse()) ? b.getInverse() : a.getInverse());
+		result.setInverse(a == null || StringUtils.isEmpty(a.getInverse()) ? b.getInverse() : a.getInverse());
-		result.setSchema(StringUtils.isEmpty(a.getSchema()) ? b.getSchema() : a.getSchema());
+		result.setSchema(a == null || StringUtils.isEmpty(a.getSchema()) ? b.getSchema() : a.getSchema());
 		return result;
 	}
 
 	private ScholixResource mergeResource(final ScholixResource a, final ScholixResource b) {
-
+		if (a == null)
+			return b;
 		final ScholixResource result = new ScholixResource();
 		result.setCollectedFrom(mergeScholixCollectedFrom(a.getCollectedFrom(), b.getCollectedFrom()));
 		result.setCreator(mergeScholixEntityId(a.getCreator(), b.getCreator()));

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/config-default.xml

@@ -7,4 +7,8 @@
         <name>oozie.action.sharelib.for.spark</name>
         <value>spark2</value>
     </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
 </configuration>

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/index/oozie_app/workflow.xml

@@ -1,9 +1,17 @@
-<workflow-app name="Index graph to ElasticSearch" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="Materialize and Index graph to ElasticSearch" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>workingDirPath</name>
             <description>the source path</description>
         </property>
+        <property>
+            <name>index</name>
+            <description>the index name</description>
+        </property>
+        <property>
+            <name>esCluster</name>
+            <description>the Index cluster</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -12,39 +20,43 @@
             <name>sparkExecutorMemory</name>
             <description>memory for individual executor</description>
         </property>
-        <property>
-            <name>index</name>
-            <description>index name</description>
-        </property>
-
-        <property>
-            <name>indexHost</name>
-            <description>index host name</description>
-        </property>
     </parameters>
 
-    <start to="indexSummary"/>
+    <start to="DropAndCreateIndex"/>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
 
+
+    <action name="DropAndCreateIndex">
+        <java>
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <main-class>eu.dnetlib.dhp.provision.DropAndCreateESIndex</main-class>
+            <arg>-i</arg><arg>${index}</arg>
+            <arg>-c</arg><arg>${esCluster}</arg>
+        </java>
+        <ok to="indexSummary"/>
+        <error to="Kill"/>
+    </action>
+
+
     <action name="indexSummary">
         <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>index Summary</name>
+            <name>index summary</name>
             <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
             <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
-            <spark-opts>--executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="32" </spark-opts>
+            <spark-opts>--executor-memory ${sparkExecutorMemory}  --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
             <arg>-mt</arg> <arg>yarn-cluster</arg>
-            <arg>--sourcePath</arg><arg>${workingDirPath}/summary</arg>
+            <arg>--sourcePath</arg><arg>${workingDirPath}/summary_json</arg>
             <arg>--index</arg><arg>${index}_object</arg>
-            <arg>--esHost</arg><arg>${indexHost}</arg>
             <arg>--idPath</arg><arg>id</arg>
-            <arg>--type</arg><arg>summary</arg>
+            <arg>--cluster</arg><arg>${esCluster}</arg>
         </spark>
         <ok to="indexScholix"/>
         <error to="Kill"/>
@@ -63,9 +75,8 @@
             <arg>-mt</arg> <arg>yarn-cluster</arg>
             <arg>--sourcePath</arg><arg>${workingDirPath}/scholix_json</arg>
             <arg>--index</arg><arg>${index}_scholix</arg>
-            <arg>--esHost</arg><arg>${indexHost}</arg>
             <arg>--idPath</arg><arg>identifier</arg>
-            <arg>--type</arg><arg>scholix</arg>
+            <arg>--cluster</arg><arg>${esCluster}</arg>
         </spark>
         <ok to="End"/>
         <error to="Kill"/>

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/resources/eu/dnetlib/dhp/sx/provision/oozie_app/workflow.xml

@@ -112,59 +112,5 @@
         <error to="Kill"/>
     </action>
 
-
-    <action name="DropAndCreateIndex">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-            <main-class>eu.dnetlib.dhp.provision.DropAndCreateESIndex</main-class>
-            <arg>-i</arg><arg>${index}</arg>
-            <arg>-c</arg><arg>${esCluster}</arg>
-        </java>
-        <ok to="indexSummary"/>
-        <error to="Kill"/>
-    </action>
-
-
-    <action name="indexSummary">
-        <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>index summary</name>
-            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
-            <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
-            <spark-opts>--executor-memory ${sparkExecutorMemory}  --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
-            <arg>-mt</arg> <arg>yarn-cluster</arg>
-            <arg>--sourcePath</arg><arg>${workingDirPath}/summary_json</arg>
-            <arg>--index</arg><arg>${index}_object</arg>
-            <arg>--idPath</arg><arg>id</arg>
-            <arg>--cluster</arg><arg>${esCluster}</arg>
-        </spark>
-        <ok to="indexScholix"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="indexScholix">
-        <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>index scholix</name>
-            <class>eu.dnetlib.dhp.provision.SparkIndexCollectionOnES</class>
-            <jar>dhp-graph-provision-scholexplorer-${projectVersion}.jar</jar>
-            <spark-opts>--executor-memory ${sparkExecutorMemory}  --driver-memory=${sparkDriverMemory} ${sparkExtraOPT} --conf spark.dynamicAllocation.maxExecutors="8" </spark-opts>
-            <arg>-mt</arg> <arg>yarn-cluster</arg>
-            <arg>--sourcePath</arg><arg>${workingDirPath}/scholix_json</arg>
-            <arg>--index</arg><arg>${index}_scholix</arg>
-            <arg>--idPath</arg><arg>identifier</arg>
-            <arg>--cluster</arg><arg>${esCluster}</arg>
-        </spark>
-        <ok to="End"/>
-        <error to="Kill"/>
-    </action>
-
     <end name="End"/>
 </workflow-app>