Merge branch 'deduptesting'

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/RelationAggregator.java

@@ -0,0 +1,57 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import java.util.Objects;
+
+import org.apache.spark.sql.Encoder;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.expressions.Aggregator;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class RelationAggregator extends Aggregator<Relation, Relation, Relation> {
+
+	private static Relation ZERO = new Relation();
+
+	@Override
+	public Relation zero() {
+		return ZERO;
+	}
+
+	@Override
+	public Relation reduce(Relation b, Relation a) {
+		return mergeRel(b, a);
+	}
+
+	@Override
+	public Relation merge(Relation b, Relation a) {
+		return mergeRel(b, a);
+	}
+
+	@Override
+	public Relation finish(Relation r) {
+		return r;
+	}
+
+	private Relation mergeRel(Relation b, Relation a) {
+		if (Objects.equals(b, ZERO)) {
+			return a;
+		}
+		if (Objects.equals(a, ZERO)) {
+			return b;
+		}
+
+		b.mergeFrom(a);
+		return b;
+	}
+
+	@Override
+	public Encoder<Relation> bufferEncoder() {
+		return Encoders.kryo(Relation.class);
+	}
+
+	@Override
+	public Encoder<Relation> outputEncoder() {
+		return Encoders.kryo(Relation.class);
+	}
+}

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateMergeRels.java

@@ -5,11 +5,13 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.PairFunction;
 import org.apache.spark.graphx.Edge;
 import org.apache.spark.rdd.RDD;
@@ -75,7 +77,11 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 		final String workingPath = parser.get("workingPath");
 		final String isLookUpUrl = parser.get("isLookUpUrl");
 		final String actionSetId = parser.get("actionSetId");
-
+		int cut = Optional
+				.ofNullable(parser.get("cutConnectedComponent"))
+				.map(Integer::valueOf)
+				.orElse(0);
+		log.info("connected component cut: '{}'", cut);
 		log.info("graphBasePath: '{}'", graphBasePath);
 		log.info("isLookUpUrl:   '{}'", isLookUpUrl);
 		log.info("actionSetId:   '{}'", actionSetId);
@@ -100,8 +106,10 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 
 			final RDD<Edge<String>> edgeRdd = spark
 				.read()
-				.load(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
+				.textFile(DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity))
-				.as(Encoders.bean(Relation.class))
+				.map(
+					(MapFunction<String, Relation>) r -> OBJECT_MAPPER.readValue(r, Relation.class),
+					Encoders.bean(Relation.class))
 				.javaRDD()
 				.map(it -> new Edge<>(hash(it.getSource()), hash(it.getTarget()), it.getRelClass()))
 				.rdd();
@@ -109,7 +117,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 			final Dataset<Relation> mergeRels = spark
 				.createDataset(
 					GraphProcessor
-						.findCCs(vertexes.rdd(), edgeRdd, maxIterations)
+						.findCCs(vertexes.rdd(), edgeRdd, maxIterations, cut)
 						.toJavaRDD()
 						.filter(k -> k.getDocIds().size() > 1)
 						.flatMap(cc -> ccToMergeRel(cc, dedupConf))
@@ -117,6 +125,7 @@ public class SparkCreateMergeRels extends AbstractSparkAction {
 					Encoders.bean(Relation.class));
 
 			mergeRels.write().mode(SaveMode.Append).parquet(mergeRelPath);
+
 		}
 	}
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.io.IOException;
+import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
@@ -34,6 +35,8 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 
 	private static final Logger log = LoggerFactory.getLogger(SparkCreateSimRels.class);
 
+	public static final int NUM_PARTITIONS = 1000;
+
 	public SparkCreateSimRels(ArgumentApplicationParser parser, SparkSession spark) {
 		super(parser, spark);
 	}
@@ -48,13 +51,6 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 		parser.parseArgument(args);
 
 		SparkConf conf = new SparkConf();
-		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
-		conf
-			.registerKryoClasses(
-				new Class[] {
-					MapDocument.class, FieldListImpl.class, FieldValueImpl.class, Block.class
-				});
-
 		new SparkCreateSimRels(parser, getSparkSession(conf))
 			.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
 	}
@@ -68,7 +64,12 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 		final String isLookUpUrl = parser.get("isLookUpUrl");
 		final String actionSetId = parser.get("actionSetId");
 		final String workingPath = parser.get("workingPath");
+		final int numPartitions = Optional
+				.ofNullable(parser.get("numPartitions"))
+				.map(Integer::valueOf)
+				.orElse(NUM_PARTITIONS);
 
+		log.info("numPartitions: '{}'", numPartitions);
 		log.info("graphBasePath: '{}'", graphBasePath);
 		log.info("isLookUpUrl:   '{}'", isLookUpUrl);
 		log.info("actionSetId:   '{}'", actionSetId);
@@ -88,6 +89,7 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 
 			JavaPairRDD<String, MapDocument> mapDocuments = sc
 				.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
+				.repartition(numPartitions)
 				.mapToPair(
 					(PairFunction<String, String, MapDocument>) s -> {
 						MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s);
@@ -95,19 +97,17 @@ public class SparkCreateSimRels extends AbstractSparkAction {
 					});
 
 			// create blocks for deduplication
-			JavaPairRDD<String, Block> blocks = Deduper.createSortedBlocks(mapDocuments, dedupConf);
+			JavaPairRDD<String, Block> blocks = Deduper
+				.createSortedBlocks(mapDocuments, dedupConf)
+				.repartition(numPartitions);
 
 			// create relations by comparing only elements in the same group
-			JavaRDD<Relation> relations = Deduper
+			Deduper
 				.computeRelations(sc, blocks, dedupConf)
-				.map(t -> createSimRel(t._1(), t._2(), entity));
+				.map(t -> createSimRel(t._1(), t._2(), entity))
-
+				.repartition(numPartitions)
-			// save the simrel in the workingdir
+				.map(r -> OBJECT_MAPPER.writeValueAsString(r))
-			spark
+				.saveAsTextFile(outputPath);
-				.createDataset(relations.rdd(), Encoders.bean(Relation.class))
-				.write()
-				.mode(SaveMode.Append)
-				.save(outputPath);
 		}
 	}
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkPropagateRelation.java

@@ -3,8 +3,11 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static org.apache.spark.sql.functions.col;
 
+import com.google.common.base.Joiner;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.*;
 import org.slf4j.Logger;
@@ -95,7 +98,20 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 			FieldType.TARGET,
 			getDeletedFn());
 
-		save(newRels.union(updated).union(mergeRels), outputRelationPath, SaveMode.Overwrite);
+		save(
+			distinctRelations(newRels
+				.union(updated)
+				.union(mergeRels)
+				.map((MapFunction<Relation, Relation>) r -> r, Encoders.kryo(Relation.class))),
+			outputRelationPath, SaveMode.Overwrite);
+	}
+
+	private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
+		return rels
+			.filter(getRelationFilterFunction())
+			.groupByKey((MapFunction<Relation, String>) r -> String.join(r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()), Encoders.STRING())
+			.agg(new RelationAggregator().toColumn())
+			.map((MapFunction<Tuple2<String, Relation>, Relation>) t -> t._2(), Encoders.bean(Relation.class));
 	}
 
 	private static Dataset<Relation> processDataset(
@@ -112,6 +128,14 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 			.map(mapFn, Encoders.bean(Relation.class));
 	}
 
+	private FilterFunction<Relation> getRelationFilterFunction() {
+		return (FilterFunction<Relation>) r -> StringUtils.isNotBlank(r.getSource()) ||
+			StringUtils.isNotBlank(r.getTarget()) ||
+			StringUtils.isNotBlank(r.getRelClass()) ||
+			StringUtils.isNotBlank(r.getSubRelType()) ||
+			StringUtils.isNotBlank(r.getRelClass());
+	}
+
 	private static MapFunction<String, Relation> patchRelFn() {
 		return value -> {
 			final Relation rel = OBJECT_MAPPER.readValue(value, Relation.class);

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/ConnectedComponent.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.dedup.graph;
 import java.io.IOException;
 import java.io.Serializable;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.commons.lang.StringUtils;
 import org.codehaus.jackson.annotate.JsonIgnore;
@@ -18,12 +19,17 @@ public class ConnectedComponent implements Serializable {
 	private Set<String> docIds;
 	private String ccId;
 
-	public ConnectedComponent() {
+	public ConnectedComponent(Set<String> docIds, final int cut) {
-	}
-
-	public ConnectedComponent(Set<String> docIds) {
 		this.docIds = docIds;
 		createID();
+		if (cut > 0 && docIds.size() > cut) {
+			this.docIds = docIds
+				.stream()
+				.filter(s -> !ccId.equalsIgnoreCase(s))
+				.limit(cut - 1)
+				.collect(Collectors.toSet());
+			this.docIds.add(ccId);
+		}
 	}
 
 	public String createID() {
@@ -41,6 +47,7 @@ public class ConnectedComponent implements Serializable {
 	public String getMin() {
 
 		final StringBuilder min = new StringBuilder();
+
 		docIds
 			.forEach(
 				i -> {

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/graph/GraphProcessor.scala

@@ -7,7 +7,7 @@ import scala.collection.JavaConversions;
 
 object GraphProcessor {
 
-  def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int): RDD[ConnectedComponent] = {
+  def findCCs(vertexes: RDD[(VertexId, String)], edges: RDD[Edge[String]], maxIterations: Int, cut:Int): RDD[ConnectedComponent] = {
     val graph: Graph[String, String] = Graph(vertexes, edges).partitionBy(PartitionStrategy.RandomVertexCut) //TODO remember to remove partitionby
     val cc = graph.connectedComponents(maxIterations).vertices
 
@@ -22,15 +22,15 @@ object GraphProcessor {
       }
     }
     val connectedComponents = joinResult.groupByKey()
-      .map[ConnectedComponent](cc => asConnectedComponent(cc))
+      .map[ConnectedComponent](cc => asConnectedComponent(cc, cut))
     connectedComponents
   }
 
 
 
-  def asConnectedComponent(group: (VertexId, Iterable[String])): ConnectedComponent = {
+  def asConnectedComponent(group: (VertexId, Iterable[String]), cut:Int): ConnectedComponent = {
     val docs = group._2.toSet[String]
-    val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs));
+    val connectedComponent = new ConnectedComponent(JavaConversions.setAsJavaSet[String](docs), cut);
     connectedComponent
   }
 

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json

@@ -17,6 +17,12 @@
     "paramDescription": "the url for the lookup service",
     "paramRequired": true
   },
+  {
+    "paramName": "cc",
+    "paramLongName": "cutConnectedComponent",
+    "paramDescription": "the number of maximum elements that belongs to a connected components",
+    "paramRequired": false
+  },
   {
     "paramName": "w",
     "paramLongName": "workingPath",

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/createSimRels_parameters.json

@@ -22,5 +22,11 @@
     "paramLongName": "workingPath",
     "paramDescription": "path of the working directory",
     "paramRequired": true
+  },
+  {
+    "paramName": "np",
+    "paramLongName": "numPartitions",
+    "paramDescription": "number of partitions for the similarity relations intermediate phases",
+    "paramRequired": false
   }
 ]

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/scan/oozie_app/workflow.xml

@@ -20,6 +20,10 @@
             <name>dedupGraphPath</name>
             <description>path for the output graph</description>
         </property>
+        <property>
+            <name>cutConnectedComponent</name>
+            <description>max number of elements in a connected component</description>
+        </property>
         <property>
             <name>sparkDriverMemory</name>
             <description>memory for driver process</description>
@@ -106,10 +110,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
+            <arg>--actionSetId</arg><arg>${actionSetId}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--numPartitions</arg><arg>8000</arg>
         </spark>
         <ok to="CreateMergeRel"/>
         <error to="Kill"/>
@@ -132,10 +137,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
+            <arg>--actionSetId</arg><arg>${actionSetId}</arg>
+            <arg>--cutConnectedComponent</arg><arg>${cutConnectedComponent}</arg>
         </spark>
         <ok to="CreateDedupRecord"/>
         <error to="Kill"/>
@@ -158,10 +164,10 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--la</arg><arg>${isLookUpUrl}</arg>
+            <arg>--isLookUpUrl</arg><arg>${isLookUpUrl}</arg>
-            <arg>--asi</arg><arg>${actionSetId}</arg>
+            <arg>--actionSetId</arg><arg>${actionSetId}</arg>
         </spark>
         <ok to="UpdateEntity"/>
         <error to="Kill"/>
@@ -184,9 +190,9 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--i</arg><arg>${graphBasePath}</arg>
+            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--w</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
-            <arg>--o</arg><arg>${dedupGraphPath}</arg>
+            <arg>--dedupGraphPath</arg><arg>${dedupGraphPath}</arg>
         </spark>
         <ok to="copyRelations"/>
         <error to="Kill"/>

dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json

@@ -1,17 +1,17 @@
 [
-{
+  {
-  "paramName": "i",
+    "paramName": "i",
-  "paramLongName": "graphBasePath",
+    "paramLongName": "graphBasePath",
-  "paramDescription": "the base path of raw graph",
+    "paramDescription": "the base path of raw graph",
-  "paramRequired": true
+    "paramRequired": true
-},
+  },
-{
+  {
-  "paramName": "w",
+    "paramName": "w",
-  "paramLongName": "workingPath",
+    "paramLongName": "workingPath",
-  "paramDescription": "the working directory path",
+    "paramDescription": "the working directory path",
-  "paramRequired": true
+    "paramRequired": true
-},
+  },
-{
+  {
     "paramName": "o",
     "paramLongName": "dedupGraphPath",
     "paramDescription": "the path of the dedup graph",

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java

@@ -3,6 +3,8 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static java.nio.file.Files.createTempDirectory;
 
+import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.count;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.lenient;
 
@@ -11,6 +13,9 @@ import java.io.IOException;
 import java.io.Serializable;
 import java.net.URISyntaxException;
 import java.nio.file.Paths;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
@@ -18,6 +23,7 @@ import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.PairFunction;
 import org.apache.spark.sql.Dataset;
@@ -71,11 +77,13 @@ public class SparkDedupTest implements Serializable {
 		FileUtils.deleteDirectory(new File(testOutputBasePath));
 		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
 
+		final SparkConf conf = new SparkConf();
+		conf.set("spark.sql.shuffle.partitions", "200");
 		spark = SparkSession
 			.builder()
 			.appName(SparkDedupTest.class.getSimpleName())
 			.master("local[*]")
-			.config(new SparkConf())
+			.config(conf)
 			.getOrCreate();
 
 		jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
@@ -152,37 +160,42 @@ public class SparkDedupTest implements Serializable {
 		parser
 			.parseArgument(
 				new String[] {
-					"-i",
+					"-i", testGraphBasePath,
-					testGraphBasePath,
+					"-asi", testActionSetId,
-					"-asi",
+					"-la", "lookupurl",
-					testActionSetId,
+					"-w", testOutputBasePath,
-					"-la",
+					"-np", "50"
-					"lookupurl",
-					"-w",
-					testOutputBasePath
 				});
 
 		new SparkCreateSimRels(parser, spark).run(isLookUpService);
 
 		long orgs_simrel = spark
 			.read()
-			.load(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
+			.textFile(testOutputBasePath + "/" + testActionSetId + "/organization_simrel")
 			.count();
+
 		long pubs_simrel = spark
 			.read()
-			.load(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
+			.textFile(testOutputBasePath + "/" + testActionSetId + "/publication_simrel")
 			.count();
-		long sw_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/software_simrel").count();
 
-		long ds_simrel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel").count();
+		long sw_simrel = spark
+			.read()
+			.textFile(testOutputBasePath + "/" + testActionSetId + "/software_simrel")
+			.count();
+
+		long ds_simrel = spark
+			.read()
+			.textFile(testOutputBasePath + "/" + testActionSetId + "/dataset_simrel")
+			.count();
 
 		long orp_simrel = spark
 			.read()
-			.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
+			.textFile(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_simrel")
 			.count();
 
 		assertEquals(3432, orgs_simrel);
-		assertEquals(7054, pubs_simrel);
+		assertEquals(7152, pubs_simrel);
 		assertEquals(344, sw_simrel);
 		assertEquals(458, ds_simrel);
 		assertEquals(6750, orp_simrel);
@@ -190,6 +203,100 @@ public class SparkDedupTest implements Serializable {
 
 	@Test
 	@Order(2)
+	public void cutMergeRelsTest() throws Exception {
+
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SparkCreateMergeRels.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/createCC_parameters.json")));
+		parser
+			.parseArgument(
+				new String[] {
+					"-i",
+					testGraphBasePath,
+					"-asi",
+					testActionSetId,
+					"-la",
+					"lookupurl",
+					"-w",
+					testOutputBasePath,
+					"-cc",
+					"3"
+				});
+
+		new SparkCreateMergeRels(parser, spark).run(isLookUpService);
+
+		long orgs_mergerel = spark
+			.read()
+			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
+			.as(Encoders.bean(Relation.class))
+			.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
+			.groupBy("source")
+			.agg(count("target").alias("cnt"))
+			.select("source", "cnt")
+			.where("cnt > 3")
+			.count();
+
+		long pubs_mergerel = spark
+			.read()
+			.load(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel")
+			.as(Encoders.bean(Relation.class))
+			.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
+			.groupBy("source")
+			.agg(count("target").alias("cnt"))
+			.select("source", "cnt")
+			.where("cnt > 3")
+			.count();
+		long sw_mergerel = spark
+			.read()
+			.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
+			.as(Encoders.bean(Relation.class))
+			.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
+			.groupBy("source")
+			.agg(count("target").alias("cnt"))
+			.select("source", "cnt")
+			.where("cnt > 3")
+			.count();
+
+		long ds_mergerel = spark
+			.read()
+			.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
+			.as(Encoders.bean(Relation.class))
+			.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
+			.groupBy("source")
+			.agg(count("target").alias("cnt"))
+			.select("source", "cnt")
+			.where("cnt > 3")
+			.count();
+
+		long orp_mergerel = spark
+			.read()
+			.load(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel")
+			.as(Encoders.bean(Relation.class))
+			.filter((FilterFunction<Relation>) r -> r.getRelClass().equalsIgnoreCase("merges"))
+			.groupBy("source")
+			.agg(count("target").alias("cnt"))
+			.select("source", "cnt")
+			.where("cnt > 3")
+			.count();
+
+		assertEquals(0, orgs_mergerel);
+		assertEquals(0, pubs_mergerel);
+		assertEquals(0, sw_mergerel);
+		assertEquals(0, ds_mergerel);
+		assertEquals(0, orp_mergerel);
+
+		FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel"));
+		FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/publication_mergerel"));
+		FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/software_mergerel"));
+		FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel"));
+		FileUtils.deleteDirectory(new File(testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_mergerel"));
+	}
+
+	@Test
+	@Order(3)
 	public void createMergeRelsTest() throws Exception {
 
 		ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -225,8 +332,10 @@ public class SparkDedupTest implements Serializable {
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/software_mergerel")
 			.count();
-
+		long ds_mergerel = spark
-		long ds_mergerel = spark.read().load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel").count();
+			.read()
+			.load(testOutputBasePath + "/" + testActionSetId + "/dataset_mergerel")
+			.count();
 
 		long orp_mergerel = spark
 			.read()
@@ -234,14 +343,14 @@ public class SparkDedupTest implements Serializable {
 			.count();
 
 		assertEquals(1276, orgs_mergerel);
-		assertEquals(1440, pubs_mergerel);
+		assertEquals(1442, pubs_mergerel);
 		assertEquals(288, sw_mergerel);
 		assertEquals(472, ds_mergerel);
 		assertEquals(718, orp_mergerel);
 	}
 
 	@Test
-	@Order(3)
+	@Order(4)
 	public void createDedupRecordTest() throws Exception {
 
 		ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -288,7 +397,7 @@ public class SparkDedupTest implements Serializable {
 	}
 
 	@Test
-	@Order(4)
+	@Order(5)
 	public void updateEntityTest() throws Exception {
 
 		ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -404,7 +513,7 @@ public class SparkDedupTest implements Serializable {
 	}
 
 	@Test
-	@Order(5)
+	@Order(6)
 	public void propagateRelationTest() throws Exception {
 
 		ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -423,7 +532,7 @@ public class SparkDedupTest implements Serializable {
 
 		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
-		assertEquals(4971, relations);
+		assertEquals(4866, relations);
 
 		// check deletedbyinference
 		final Dataset<Relation> mergeRels = spark
@@ -454,7 +563,7 @@ public class SparkDedupTest implements Serializable {
 	}
 
 	@Test
-	@Order(6)
+	@Order(7)
 	public void testRelations() throws Exception {
 		testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_1.json", 12, 10);
 		testUniqueness("/eu/dnetlib/dhp/dedup/test/relation_2.json", 10, 2);

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/ds.curr.conf.json

@@ -6,10 +6,10 @@
     "subEntityType" : "resulttype",
     "subEntityValue" : "dataset",
     "orderField" : "title",
-    "queueMaxSize" : "800",
+    "queueMaxSize" : "100",
     "groupMaxSize" : "100",
     "maxChildren" : "100",
-    "slidingWindowSize" : "80",
+    "slidingWindowSize" : "100",
     "rootBuilder" : ["result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
     "includeChildren" : "true",
     "idPath" : "$.id",
@@ -17,7 +17,8 @@
   },
   "pace" : {
     "clustering" : [
-      { "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
+      { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
       { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
     ],
     "decisionTree" : {

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/orp.curr.conf.json

@@ -6,10 +6,10 @@
     "subEntityType" : "resulttype",
     "subEntityValue" : "otherresearchproduct",
     "orderField" : "title",
-    "queueMaxSize" : "800",
+    "queueMaxSize" : "100",
     "groupMaxSize" : "100",
     "maxChildren" : "100",
-    "slidingWindowSize" : "80",
+    "slidingWindowSize" : "100",
     "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
     "includeChildren" : "true",
     "idPath" : "$.id",
@@ -17,7 +17,8 @@
   },
   "pace" : {
     "clustering" : [
-      { "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
+      { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
       { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
     ],
     "decisionTree" : {

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/pub.curr.conf.json

@@ -6,10 +6,10 @@
     "subEntityType": "resulttype",
     "subEntityValue": "publication",
     "orderField": "title",
-    "queueMaxSize": "800",
+    "queueMaxSize": "100",
     "groupMaxSize": "100",
     "maxChildren": "100",
-    "slidingWindowSize": "80",
+    "slidingWindowSize": "100",
     "rootBuilder": [
       "result",
       "resultProject_outcome_isProducedBy",
@@ -29,7 +29,8 @@
   },
   "pace": {
     "clustering" : [
-      { "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
+      { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
+      { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
       { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
     ],
     "decisionTree": {

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/conf/sw.curr.conf.json

@@ -6,10 +6,10 @@
       "subEntityType" : "resulttype",
       "subEntityValue" : "software",
       "orderField" : "title",
-      "queueMaxSize" : "800",
+      "queueMaxSize" : "100",
       "groupMaxSize" : "100",
       "maxChildren" : "100",
-      "slidingWindowSize" : "80",
+      "slidingWindowSize" : "100",
       "rootBuilder" : [ "result", "resultProject_outcome_isProducedBy", "resultResult_publicationDataset_isRelatedTo", "resultResult_similarity_isAmongTopNSimilarDocuments", "resultResult_similarity_hasAmongTopNSimilarDocuments", "resultOrganization_affiliation_hasAuthorInstitution", "resultResult_part_hasPart", "resultResult_part_isPartOf", "resultResult_supplement_isSupplementTo", "resultResult_supplement_isSupplementedBy", "resultResult_version_isVersionOf" ],
       "includeChildren" : "true",
       "idPath" : "$.id",
@@ -17,8 +17,9 @@
     },
     "pace" : {
       "clustering" : [
-        { "name" : "wordssuffixprefix", "fields" : [ "title" ], "params" : { "max" : "2", "len" : "3" } },
+        { "name" : "ngrampairs", "fields" : [ "title" ], "params" : { "max" : "1", "ngramLen" : "3"} },
-        { "name" : "lowercase", "fields" : [ "doi", "url" ], "params" : { } }
+        { "name" : "suffixprefix", "fields" : [ "title" ], "params" : { "max" : "1", "len" : "3" } },
+        { "name" : "lowercase", "fields" : [ "doi" ], "params" : { } }
       ],
       "decisionTree": {
         "start": {