Merge branch 'provision_indexing'

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala

@@ -271,6 +271,26 @@ object DoiBoostMappingUtil {
   }
 
 
+
+  def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String): StructuredProperty = {
+    val sp = new StructuredProperty
+    sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
+    sp.setValue(value)
+    sp
+
+  }
+
+
+
+  def createSP(value: String, classId: String,className:String, schemeId: String, schemeName:String, dataInfo: DataInfo): StructuredProperty = {
+    val sp = new StructuredProperty
+    sp.setQualifier(createQualifier(classId,className, schemeId, schemeName))
+    sp.setValue(value)
+    sp.setDataInfo(dataInfo)
+    sp
+
+  }
+
   def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
     val sp = new StructuredProperty
     sp.setQualifier(createQualifier(classId, schemeId))
@@ -279,6 +299,8 @@ object DoiBoostMappingUtil {
 
   }
 
+
+
   def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
     val sp = new StructuredProperty
     sp.setQualifier(createQualifier(classId, schemeId))

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala

@@ -129,16 +129,16 @@ case object ConversionUtil {
     val fieldOfStudy = item._2
     if (fieldOfStudy != null && fieldOfStudy.subjects != null && fieldOfStudy.subjects.nonEmpty) {
       val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
-        val s1 = createSP(s.DisplayName, "keyword", "dnet:subject_classification_typologies")
+        val s1 = createSP(s.DisplayName, "MAG","Microsoft Academic Graph classification", "dnet:subject_classification_typologies", "dnet:subject_classification_typologies")
         val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
         var resList: List[StructuredProperty] = List(s1)
         if (s.MainType.isDefined) {
           val maintp = s.MainType.get
-          val s2 = createSP(s.MainType.get, "keyword", "dnet:subject_classification_typologies")
+          val s2 = createSP(s.MainType.get, "MAG","Microsoft Academic Graph classification", "dnet:subject_classification_typologies", "dnet:subject_classification_typologies")
           s2.setDataInfo(di)
           resList = resList ::: List(s2)
           if (maintp.contains(".")) {
-            val s3 = createSP(maintp.split("\\.").head, "keyword", "dnet:subject_classification_typologies")
+            val s3 = createSP(maintp.split("\\.").head, "MAG","Microsoft Academic Graph classification", "dnet:subject_classification_typologies", "dnet:subject_classification_typologies")
             s3.setDataInfo(di)
             resList = resList ::: List(s3)
           }

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala

@@ -43,7 +43,7 @@ object SparkPreProcessMAG {
     val distinctPaper: Dataset[MagPapers] = spark.createDataset(result)
     distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct")
 
-    logger.info("Phase 6) Enrich Publication with description")
+    logger.info("Phase 0) Enrich Publication with description")
     val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract]
     pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract")
 

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml

@@ -32,7 +32,7 @@
 
 
 
-    <start to="GenerateActionSet"/>
+    <start to="CreateDOIBoost"/>
 
 
     <kill name="Kill">

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

@@ -18,6 +18,9 @@ class CrossrefMappingTest {
   val mapper = new ObjectMapper()
 
 
+
+
+
   @Test
   def testFunderRelationshipsMapping(): Unit = {
     val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString
@@ -58,6 +61,27 @@ class CrossrefMappingTest {
   }
 
 
+  @Test
+  def testOrcidID() :Unit = {
+    val json = Source.fromInputStream(getClass.getResourceAsStream("orcid_data.json")).mkString
+
+
+    assertNotNull(json)
+    assertFalse(json.isEmpty);
+
+    val resultList: List[Oaf] = Crossref2Oaf.convert(json)
+
+    assertTrue(resultList.nonEmpty)
+
+    val items = resultList.filter(p => p.isInstanceOf[Result])
+
+
+    mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
+    items.foreach(p => println(mapper.writeValueAsString(p)))
+
+
+  }
+
   @Test
   def testEmptyTitle() :Unit = {
     val json = Source.fromInputStream(getClass.getResourceAsStream("empty_title.json")).mkString

dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/orcid_data.json

@@ -0,0 +1,271 @@
+{
+  "DOI":"10.1016/j.carbpol.2020.115930",
+  "issued":{
+    "date-parts":[
+      [
+        2020,
+        4
+      ]
+    ]
+  },
+  "published-print":{
+    "date-parts":[
+      [
+        2020,
+        4
+      ]
+    ]
+  },
+  "prefix":"10.1016",
+  "subject":[
+    "Organic Chemistry",
+    "Materials Chemistry",
+    "Polymers and Plastics"
+  ],
+  "author":[
+    {
+      "affiliation":[
+
+      ],
+      "given":"Lei",
+      "family":"Fang",
+      "sequence":"first"
+    },
+    {
+      "affiliation":[
+
+      ],
+      "given":"Hua",
+      "family":"Lin",
+      "sequence":"additional"
+    },
+    {
+      "affiliation":[
+
+      ],
+      "given":"Zhenfeng",
+      "family":"Wu",
+      "sequence":"additional"
+    },
+    {
+      "affiliation":[
+
+      ],
+      "given":"Zhen",
+      "family":"Wang",
+      "sequence":"additional"
+    },
+    {
+      "affiliation":[
+
+      ],
+      "given":"Xinxin",
+      "family":"Fan",
+      "sequence":"additional"
+    },
+    {
+      "affiliation":[
+
+      ],
+      "given":"Ziting",
+      "family":"Cheng",
+      "sequence":"additional"
+    },
+    {
+      "affiliation":[
+
+      ],
+      "given":"Xiaoya",
+      "family":"Hou",
+      "sequence":"additional"
+    },
+    {
+      "authenticated-orcid":false,
+      "given":"Daquan",
+      "family":"Chen",
+      "sequence":"additional",
+      "affiliation":[
+
+      ],
+      "ORCID":"http://orcid.org/0000-0002-6796-0204"
+    }
+  ],
+  "reference-count":41,
+  "ISSN":[
+    "0144-8617"
+  ],
+  "assertion":[
+    {
+      "name":"publisher",
+      "value":"Elsevier",
+      "label":"This article is maintained by"
+    },
+    {
+      "name":"articletitle",
+      "value":"In vitro/vivo evaluation of novel mitochondrial targeting charge-reversal polysaccharide-based antitumor nanoparticle",
+      "label":"Article Title"
+    },
+    {
+      "name":"journaltitle",
+      "value":"Carbohydrate Polymers",
+      "label":"Journal Title"
+    },
+    {
+      "name":"articlelink",
+      "value":"https://doi.org/10.1016/j.carbpol.2020.115930",
+      "label":"CrossRef DOI link to publisher maintained version"
+    },
+    {
+      "name":"content_type",
+      "value":"article",
+      "label":"Content Type"
+    },
+    {
+      "name":"copyright",
+      "value":"\\u00a9 2020 Elsevier Ltd. All rights reserved.",
+      "label":"Copyright"
+    }
+  ],
+  "member":"78",
+  "source":"Crossref",
+  "score":1.0,
+  "deposited":{
+    "timestamp":1584590965000,
+    "date-time":"2020-03-19T04:09:25Z",
+    "date-parts":[
+      [
+        2020,
+        3,
+        19
+      ]
+    ]
+  },
+  "indexed":{
+    "timestamp":1584592912467,
+    "date-time":"2020-03-19T04:41:52Z",
+    "date-parts":[
+      [
+        2020,
+        3,
+        19
+      ]
+    ]
+  },
+  "type":"journal-article",
+  "URL":"http://dx.doi.org/10.1016/j.carbpol.2020.115930",
+  "is-referenced-by-count":0,
+  "volume":"234",
+  "issn-type":[
+    {
+      "type":"print",
+      "value":"0144-8617"
+    }
+  ],
+  "link":[
+    {
+      "URL":"https://api.elsevier.com/content/article/PII:S0144861720301041?httpAccept=text/xml",
+      "intended-application":"text-mining",
+      "content-version":"vor",
+      "content-type":"text/xml"
+    },
+    {
+      "URL":"https://api.elsevier.com/content/article/PII:S0144861720301041?httpAccept=text/plain",
+      "intended-application":"text-mining",
+      "content-version":"vor",
+      "content-type":"text/plain"
+    }
+  ],
+  "update-policy":"http://dx.doi.org/10.1016/elsevier_cm_policy",
+  "references-count":41,
+  "short-container-title":[
+    "Carbohydrate Polymers"
+  ],
+  "publisher":"Elsevier BV",
+  "content-domain":{
+    "domain":[
+      "elsevier.com",
+      "sciencedirect.com"
+    ],
+    "crossmark-restriction":true
+  },
+  "language":"en",
+  "license":[
+    {
+      "URL":"https://www.elsevier.com/tdm/userlicense/1.0/",
+      "start":{
+        "timestamp":1585699200000,
+        "date-time":"2020-04-01T00:00:00Z",
+        "date-parts":[
+          [
+            2020,
+            4,
+            1
+          ]
+        ]
+      },
+      "content-version":"tdm",
+      "delay-in-days":0
+    }
+  ],
+  "created":{
+    "timestamp":1581759678000,
+    "date-time":"2020-02-15T09:41:18Z",
+    "date-parts":[
+      [
+        2020,
+        2,
+        15
+      ]
+    ]
+  },
+  "title":[
+    "In vitro/vivo evaluation of novel mitochondrial targeting charge-reversal polysaccharide-based antitumor nanoparticle"
+  ],
+  "alternative-id":[
+    "S0144861720301041"
+  ],
+  "container-title":[
+    "Carbohydrate Polymers"
+  ],
+  "funder":[
+    {
+      "doi-asserted-by":"publisher",
+      "DOI":"10.13039/501100007129",
+      "name":"Natural Science Foundation of Shandong Province",
+      "award":[
+        "ZR2019ZD24",
+        "ZR2019YQ30"
+      ]
+    },
+    {
+      "doi-asserted-by":"publisher",
+      "DOI":"10.13039/100010449",
+      "name":"Ministry of Education, Libya",
+      "award":[
+
+      ]
+    },
+    {
+      "doi-asserted-by":"publisher",
+      "DOI":"10.13039/501100012249",
+      "name":"Jiangxi University of Traditional Chinese Medicine",
+      "award":[
+        "TCM-0906"
+      ]
+    },
+    {
+      "name":"Taishan Scholar Program",
+      "award":[
+        "qnts20161035"
+      ]
+    },
+    {
+      "name":"Open fund project of Key Laboratory of Modern Preparation of TCM",
+      "award":[
+
+      ]
+    }
+  ],
+  "page":"115930",
+  "article-number":"115930"
+}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleanGraphSparkJob.java

@@ -147,6 +147,9 @@ public class CleanGraphSparkJob {
 					if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
 						i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
 					}
+					if (Objects.isNull(i.getRefereed())) {
+						i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
+					}
 				}
 			}
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/CreateRelatedEntitiesJob_phase1.java

@@ -25,9 +25,7 @@ import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.oa.provision.model.ProvisionModelSupport;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
-import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
 import eu.dnetlib.dhp.schema.common.EntityType;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import scala.Tuple2;
 
@@ -109,11 +107,12 @@ public class CreateRelatedEntitiesJob_phase1 {
 		Class<E> clazz,
 		String outputPath) {
 
-		Dataset<Tuple2<String, SortableRelation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
+		Dataset<Tuple2<String, Relation>> relsByTarget = readPathRelation(spark, inputRelationsPath)
 			.filter("dataInfo.deletedbyinference == false")
 			.map(
-				(MapFunction<SortableRelation, Tuple2<String, SortableRelation>>) r -> new Tuple2<>(r.getTarget(), r),
+				(MapFunction<Relation, Tuple2<String, Relation>>) r -> new Tuple2<>(r.getTarget(),
-				Encoders.tuple(Encoders.STRING(), Encoders.kryo(SortableRelation.class)))
+					r),
+				Encoders.tuple(Encoders.STRING(), Encoders.kryo(Relation.class)))
 			.cache();
 
 		Dataset<Tuple2<String, RelatedEntity>> entities = readPathEntity(spark, inputEntityPath, clazz)
@@ -129,7 +128,7 @@ public class CreateRelatedEntitiesJob_phase1 {
 		relsByTarget
 			.joinWith(entities, entities.col("_1").equalTo(relsByTarget.col("_1")), "inner")
 			.map(
-				(MapFunction<Tuple2<Tuple2<String, SortableRelation>, Tuple2<String, RelatedEntity>>, RelatedEntityWrapper>) t -> new RelatedEntityWrapper(
+				(MapFunction<Tuple2<Tuple2<String, Relation>, Tuple2<String, RelatedEntity>>, RelatedEntityWrapper>) t -> new RelatedEntityWrapper(
 					t._1()._2(), t._2()._2()),
 				Encoders.kryo(RelatedEntityWrapper.class))
 			.write()
@@ -232,11 +231,11 @@ public class CreateRelatedEntitiesJob_phase1 {
 	 * @param relationPath
 	 * @return the Dataset<SortableRelation> containing all the relationships
 	 */
-	private static Dataset<SortableRelation> readPathRelation(
+	private static Dataset<Relation> readPathRelation(
 		SparkSession spark, final String relationPath) {
 
 		log.info("Reading relations from: {}", relationPath);
-		return spark.read().load(relationPath).as(Encoders.bean(SortableRelation.class));
+		return spark.read().load(relationPath).as(Encoders.bean(Relation.class));
 	}
 
 	private static void removeOutputDir(SparkSession spark, String path) {

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

@@ -1,39 +1,33 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+import com.fasterxml.jackson.databind.ObjectMapper;
-
+import com.google.common.base.Splitter;
-import java.util.*;
+import com.google.common.collect.Iterables;
-import java.util.function.Function;
+import com.google.common.collect.Sets;
-
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey;
+import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.*;
 import org.apache.spark.rdd.RDD;
-import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
-import com.clearspring.analytics.util.Lists;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.common.base.Splitter;
-import com.google.common.collect.Iterables;
-import com.google.common.collect.Iterators;
-import com.google.common.collect.Sets;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.FunctionalInterfaceSupport;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
-import eu.dnetlib.dhp.oa.provision.utils.RelationPartitioner;
-import scala.Function1;
 import scala.Tuple2;
 
+import java.util.HashSet;
+import java.util.Optional;
+import java.util.Set;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
 /**
  * Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects. The
  * operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization, and
@@ -133,22 +127,35 @@ public class PrepareRelationsJob {
 		SparkSession spark, String inputRelationsPath, String outputPath, Set<String> relationFilter, int maxRelations,
 		int relPartitions) {
 
-		RDD<SortableRelation> cappedRels = readPathRelationRDD(spark, inputRelationsPath)
+		// group by SOURCE and apply limit
-			.repartition(relPartitions)
+		RDD<Relation> bySource = readPathRelationRDD(spark, inputRelationsPath)
-			.filter(rel -> !rel.getDataInfo().getDeletedbyinference())
+			.filter(rel -> rel.getDataInfo().getDeletedbyinference() == false)
-			.filter(rel -> !relationFilter.contains(rel.getRelClass()))
+			.filter(rel -> relationFilter.contains(rel.getRelClass()) == false)
-			// group by SOURCE and apply limit
+			.mapToPair(r -> new Tuple2<>(SortableRelationKey.create(r, r.getSource()), r))
-			.mapToPair(rel -> new Tuple2<>(rel.getSource(), rel))
+			.repartitionAndSortWithinPartitions(new RelationPartitioner(relPartitions))
-			.groupByKey(new RelationPartitioner(relPartitions))
+			.groupBy(Tuple2::_1)
-			.flatMap(group -> Iterables.limit(group._2(), maxRelations).iterator())
+			.map(Tuple2::_2)
-			// group by TARGET and apply limit
+			.map(t -> Iterables.limit(t, maxRelations))
-			.mapToPair(rel -> new Tuple2<>(rel.getTarget(), rel))
+			.flatMap(Iterable::iterator)
-			.groupByKey(new RelationPartitioner(relPartitions))
+			.map(Tuple2::_2)
-			.flatMap(group -> Iterables.limit(group._2(), maxRelations).iterator())
+			.rdd();
+
+		// group by TARGET and apply limit
+		RDD<Relation> byTarget = readPathRelationRDD(spark, inputRelationsPath)
+			.filter(rel -> rel.getDataInfo().getDeletedbyinference() == false)
+			.filter(rel -> relationFilter.contains(rel.getRelClass()) == false)
+			.mapToPair(r -> new Tuple2<>(SortableRelationKey.create(r, r.getTarget()), r))
+			.repartitionAndSortWithinPartitions(new RelationPartitioner(relPartitions))
+			.groupBy(Tuple2::_1)
+			.map(Tuple2::_2)
+			.map(t -> Iterables.limit(t, maxRelations))
+			.flatMap(Iterable::iterator)
+			.map(Tuple2::_2)
 			.rdd();
 
 		spark
-			.createDataset(cappedRels, Encoders.bean(SortableRelation.class))
+			.createDataset(bySource.union(byTarget), Encoders.bean(Relation.class))
+			.repartition(relPartitions)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.parquet(outputPath);
@@ -162,10 +169,10 @@ public class PrepareRelationsJob {
 	 * @param inputPath
 	 * @return the JavaRDD<SortableRelation> containing all the relationships
 	 */
-	private static JavaRDD<SortableRelation> readPathRelationRDD(
+	private static JavaRDD<Relation> readPathRelationRDD(
 		SparkSession spark, final String inputPath) {
 		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-		return sc.textFile(inputPath).map(s -> OBJECT_MAPPER.readValue(s, SortableRelation.class));
+		return sc.textFile(inputPath).map(s -> OBJECT_MAPPER.readValue(s, Relation.class));
 	}
 
 	private static void removeOutputDir(SparkSession spark, String path) {

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

@@ -19,7 +19,7 @@ public class ProvisionModelSupport {
 						RelatedEntityWrapper.class,
 						JoinedEntity.class,
 						RelatedEntity.class,
-						SortableRelation.class));
+						SortableRelationKey.class));
 		return modelClasses.toArray(new Class[] {});
 	}
 }

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

@@ -5,28 +5,30 @@ import java.io.Serializable;
 
 import com.google.common.base.Objects;
 
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
 public class RelatedEntityWrapper implements Serializable {
 
-	private SortableRelation relation;
+	private Relation relation;
 	private RelatedEntity target;
 
 	public RelatedEntityWrapper() {
 	}
 
-	public RelatedEntityWrapper(SortableRelation relation, RelatedEntity target) {
+	public RelatedEntityWrapper(Relation relation, RelatedEntity target) {
 		this(null, relation, target);
 	}
 
-	public RelatedEntityWrapper(TypedRow entity, SortableRelation relation, RelatedEntity target) {
+	public RelatedEntityWrapper(TypedRow entity, Relation relation, RelatedEntity target) {
 		this.relation = relation;
 		this.target = target;
 	}
 
-	public SortableRelation getRelation() {
+	public Relation getRelation() {
 		return relation;
 	}
 
-	public void setRelation(SortableRelation relation) {
+	public void setRelation(Relation relation) {
 		this.relation = relation;
 	}
 

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

@@ -1,38 +0,0 @@
-
-package eu.dnetlib.dhp.oa.provision.model;
-
-import java.io.Serializable;
-import java.util.Map;
-
-import com.google.common.collect.ComparisonChain;
-import com.google.common.collect.Maps;
-
-import eu.dnetlib.dhp.schema.oaf.Relation;
-
-public class SortableRelation extends Relation implements Comparable<Relation>, Serializable {
-
-	private static final Map<String, Integer> weights = Maps.newHashMap();
-
-	static {
-		weights.put("outcome", 0);
-		weights.put("supplement", 1);
-		weights.put("affiliation", 2);
-		weights.put("relationship", 3);
-		weights.put("publicationDataset", 4);
-		weights.put("similarity", 5);
-
-		weights.put("provision", 6);
-		weights.put("participation", 7);
-		weights.put("dedup", 8);
-	}
-
-	@Override
-	public int compareTo(Relation o) {
-		return ComparisonChain
-			.start()
-			.compare(weights.get(getSubRelType()), weights.get(o.getSubRelType()))
-			.compare(getSource(), o.getSource())
-			.compare(getTarget(), o.getTarget())
-			.result();
-	}
-}

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

@@ -0,0 +1,90 @@
+
+package eu.dnetlib.dhp.oa.provision.model;
+
+import java.io.Serializable;
+import java.util.Map;
+import java.util.Optional;
+
+import com.google.common.base.Objects;
+import com.google.common.collect.ComparisonChain;
+import com.google.common.collect.Maps;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class SortableRelationKey implements Comparable<SortableRelationKey>, Serializable {
+
+	private static final Map<String, Integer> weights = Maps.newHashMap();
+
+	static {
+		weights.put("outcome", 0);
+		weights.put("supplement", 1);
+		weights.put("review", 2);
+		weights.put("citation", 3);
+		weights.put("affiliation", 4);
+		weights.put("relationship", 5);
+		weights.put("publicationDataset", 6);
+		weights.put("similarity", 7);
+
+		weights.put("provision", 8);
+		weights.put("participation", 9);
+		weights.put("dedup", 10);
+	}
+
+	private static final long serialVersionUID = 3232323;
+
+	private String groupingKey;
+
+	private String subRelType;
+
+	public static SortableRelationKey create(Relation r, String groupingKey) {
+		SortableRelationKey sr = new SortableRelationKey();
+		sr.setGroupingKey(groupingKey);
+		sr.setSubRelType(r.getSubRelType());
+		return sr;
+	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o)
+			return true;
+		if (o == null || getClass() != o.getClass())
+			return false;
+		SortableRelationKey that = (SortableRelationKey) o;
+		return getGroupingKey().equals(that.getGroupingKey());
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hashCode(getGroupingKey());
+	}
+
+	@Override
+	public int compareTo(SortableRelationKey o) {
+		return ComparisonChain
+			.start()
+			.compare(getGroupingKey(), o.getGroupingKey())
+			.compare(getWeight(this), getWeight(o))
+			.result();
+	}
+
+	private Integer getWeight(SortableRelationKey o) {
+		return Optional.ofNullable(weights.get(o.getSubRelType())).orElse(Integer.MAX_VALUE);
+	}
+
+	public String getSubRelType() {
+		return subRelType;
+	}
+
+	public void setSubRelType(String subRelType) {
+		this.subRelType = subRelType;
+	}
+
+	public String getGroupingKey() {
+		return groupingKey;
+	}
+
+	public void setGroupingKey(String groupingKey) {
+		this.groupingKey = groupingKey;
+	}
+
+}

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

@@ -4,12 +4,16 @@ package eu.dnetlib.dhp.oa.provision.utils;
 import org.apache.spark.Partitioner;
 import org.apache.spark.util.Utils;
 
+import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey;
+
 /**
  * Used in combination with SortableRelationKey, allows to partition the records by source id, therefore allowing to
  * sort relations sharing the same source id by the ordering defined in SortableRelationKey.
  */
 public class RelationPartitioner extends Partitioner {
 
+	private static final long serialVersionUID = 343434456L;
+
 	private final int numPartitions;
 
 	public RelationPartitioner(int numPartitions) {
@@ -23,8 +27,18 @@ public class RelationPartitioner extends Partitioner {
 
 	@Override
 	public int getPartition(Object key) {
-		String partitionKey = (String) key;
+		SortableRelationKey partitionKey = (SortableRelationKey) key;
-		return Utils.nonNegativeMod(partitionKey.hashCode(), numPartitions());
+		return Utils.nonNegativeMod(partitionKey.getGroupingKey().hashCode(), numPartitions());
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (obj instanceof RelationPartitioner) {
+			RelationPartitioner p = (RelationPartitioner) obj;
+			if (p.numPartitions() == numPartitions())
+				return true;
+		}
+		return false;
 	}
 
 }

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

@@ -276,7 +276,7 @@ public class XmlRecordFactory implements Serializable {
 																			pidType,
 																			pidValue
 																				.toLowerCase()
-																				.replaceAll("orcid", "")));
+																				.replaceAll("^.*orcid\\.org\\/", "")));
 														}
 													}
 												});

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

@@ -97,18 +97,7 @@
         </configuration>
     </global>
 
-    <start to="resume_from"/>
+    <start to="prepare_relations"/>
-
-    <decision name="resume_from">
-        <switch>
-            <case to="prepare_relations">${wf:conf('resumeFrom') eq 'prepare_relations'}</case>
-            <case to="fork_join_related_entities">${wf:conf('resumeFrom') eq 'fork_join_related_entities'}</case>
-            <case to="fork_join_all_entities">${wf:conf('resumeFrom') eq 'fork_join_all_entities'}</case>
-            <case to="convert_to_xml">${wf:conf('resumeFrom') eq 'convert_to_xml'}</case>
-            <case to="to_solr_index">${wf:conf('resumeFrom') eq 'to_solr_index'}</case>
-            <default to="prepare_relations"/>
-        </switch>
-    </decision>
 
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@@ -135,475 +124,12 @@
             <arg>--outputPath</arg><arg>${workingDir}/relation</arg>
             <arg>--relPartitions</arg><arg>5000</arg>
         </spark>
-        <ok to="fork_join_related_entities"/>
-        <error to="Kill"/>
-    </action>
-
-    <fork name="fork_join_related_entities">
-        <path start="join_relation_publication"/>
-        <path start="join_relation_dataset"/>
-        <path start="join_relation_otherresearchproduct"/>
-        <path start="join_relation_software"/>
-        <path start="join_relation_datasource"/>
-        <path start="join_relation_organization"/>
-        <path start="join_relation_project"/>
-    </fork>
-
-    <action name="join_relation_publication">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = publication.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/publication</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_relation_dataset">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = dataset.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/dataset</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_relation_otherresearchproduct">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = otherresearchproduct.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/otherresearchproduct</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_relation_software">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = software.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/software</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_relation_datasource">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = datasource.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/datasource</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/datasource</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_relation_organization">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = organization.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/organization</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/organization</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_relation_project">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[relation.target = project.id]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase1</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputRelationsPath</arg><arg>${workingDir}/relation</arg>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/project</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_partial/project</arg>
-        </spark>
-        <ok to="wait_joins"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_joins" to="fork_join_all_entities"/>
-
-    <fork name="fork_join_all_entities">
-        <path start="join_publication_relations"/>
-        <path start="join_dataset_relations"/>
-        <path start="join_otherresearchproduct_relations"/>
-        <path start="join_software_relations"/>
-        <path start="join_datasource_relations"/>
-        <path start="join_organization_relations"/>
-        <path start="join_project_relations"/>
-    </fork>
-
-    <action name="join_publication_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[publication.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=15360
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/publication</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/publication</arg>
-            <arg>--numPartitions</arg><arg>30000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_dataset_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[dataset.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/dataset</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/dataset</arg>
-            <arg>--numPartitions</arg><arg>20000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_otherresearchproduct_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[otherresearchproduct.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/otherresearchproduct</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/otherresearchproduct</arg>
-            <arg>--numPartitions</arg><arg>10000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_software_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[software.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/software</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/software</arg>
-            <arg>--numPartitions</arg><arg>10000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_datasource_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[datasource.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/datasource</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Datasource</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/datasource</arg>
-            <arg>--numPartitions</arg><arg>1000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_organization_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[organization.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/organization</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Organization</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/organization</arg>
-            <arg>--numPartitions</arg><arg>20000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="join_project_relations">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Join[project.id = relatedEntity.source]</name>
-            <class>eu.dnetlib.dhp.oa.provision.CreateRelatedEntitiesJob_phase2</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputEntityPath</arg><arg>${inputGraphRootPath}/project</arg>
-            <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Project</arg>
-            <arg>--inputRelatedEntitiesPath</arg><arg>${workingDir}/join_partial</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/join_entities/project</arg>
-            <arg>--numPartitions</arg><arg>10000</arg>
-        </spark>
-        <ok to="wait_join_phase2"/>
-        <error to="Kill"/>
-    </action>
-
-    <join name="wait_join_phase2" to="convert_to_xml"/>
-
-    <action name="convert_to_xml">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>convert_to_xml</name>
-            <class>eu.dnetlib.dhp.oa.provision.XmlConverterJob</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCoresForJoining}
-                --executor-memory=${sparkExecutorMemoryForJoining}
-                --driver-memory=${sparkDriverMemoryForJoining}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=3840
-                --conf spark.network.timeout=${sparkNetworkTimeout}
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${workingDir}/join_entities</arg>
-            <arg>--outputPath</arg><arg>${workingDir}/xml</arg>
-            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--otherDsTypeId</arg><arg>${otherDsTypeId}</arg>
-        </spark>
-        <ok to="to_solr_index"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="to_solr_index">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>to_solr_index</name>
-            <class>eu.dnetlib.dhp.oa.provision.XmlIndexingJob</class>
-            <jar>dhp-graph-provision-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemoryForIndexing}
-                --driver-memory=${sparkDriverMemoryForIndexing}
-                --conf spark.dynamicAllocation.enabled=true
-                --conf spark.dynamicAllocation.maxExecutors=${sparkExecutorCoresForIndexing}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.speculation=false
-                --conf spark.hadoop.mapreduce.map.speculative=false
-                --conf spark.hadoop.mapreduce.reduce.speculative=false
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${workingDir}/xml</arg>
-            <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
-            <arg>--format</arg><arg>${format}</arg>
-            <arg>--batchSize</arg><arg>${batchSize}</arg>
-        </spark>
         <ok to="End"/>
         <error to="Kill"/>
     </action>
 
+
+
     <end name="End"/>
 
 </workflow-app>

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SortableRelationKeyTest.java

@@ -0,0 +1,42 @@
+
+package eu.dnetlib.dhp.oa.provision;
+
+import java.io.IOException;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.junit.jupiter.api.Test;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.oa.provision.model.SortableRelationKey;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class SortableRelationKeyTest {
+
+	@Test
+	public void doTesSorting() throws IOException {
+		final ObjectMapper mapper = new ObjectMapper();
+		final String json = IOUtils.toString(this.getClass().getResourceAsStream("relations.json"));
+		final List<Relation> relations = mapper.readValue(json, new TypeReference<List<Relation>>() {
+		});
+
+		relations
+			.stream()
+			.map(r -> SortableRelationKey.create(r, r.getSource()))
+			.sorted()
+			.forEach(
+
+				it -> {
+					try {
+						System.out.println(mapper.writeValueAsString(it));
+					} catch (JsonProcessingException e) {
+						e.printStackTrace();
+					}
+				});
+
+	}
+
+}

dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/relations.json

@@ -0,0 +1,90 @@
+[
+  {
+    "collectedfrom": [],
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:entityregistry",
+        "classname": "Harvested",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "lastupdatetimestamp": 1592688952862,
+    "properties": [],
+    "relClass": "hasAuthorInstitution",
+    "relType": "resultOrganization",
+    "source": "1",
+    "subRelType": "affiliation",
+    "target": "2"
+  },
+  {
+    "collectedfrom": [],
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:entityregistry",
+        "classname": "Harvested",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "lastupdatetimestamp": 1592688952862,
+    "properties": [],
+    "relClass": "isAuthorInstitutionOf",
+    "relType": "resultOrganization",
+    "source": "2",
+    "subRelType": "affiliation",
+    "target": "1"
+  },
+  {
+    "collectedfrom": [],
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:entityregistry",
+        "classname": "Harvested",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "lastupdatetimestamp": 1592688952862,
+    "properties": [],
+    "relClass": "isProducedBy",
+    "relType": "resultProject",
+    "source": "1",
+    "subRelType": "outcome",
+    "target": "2"
+  },
+  {
+    "collectedfrom": [],
+    "dataInfo": {
+      "deletedbyinference": false,
+      "inferred": false,
+      "invisible": false,
+      "provenanceaction": {
+        "classid": "sysimport:crosswalk:entityregistry",
+        "classname": "Harvested",
+        "schemeid": "dnet:provenanceActions",
+        "schemename": "dnet:provenanceActions"
+      },
+      "trust": "0.9"
+    },
+    "lastupdatetimestamp": 1592688952862,
+    "properties": [],
+    "relClass": "produces",
+    "relType": "resultProject",
+    "source": "2",
+    "subRelType": "outcome",
+    "target": "1"
+  }
+]