cleanup and refinements

Reviewed-on: D-Net/dnet-hadoop#333

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/DispatchEntitiesSparkJob.java

@@ -1,98 +0,0 @@
-
-package eu.dnetlib.dhp.oa.merge;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.util.Objects;
-import java.util.Optional;
-
-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;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-
-public class DispatchEntitiesSparkJob {
-
-	private static final Logger log = LoggerFactory.getLogger(DispatchEntitiesSparkJob.class);
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				Objects
-					.requireNonNull(
-						DispatchEntitiesSparkJob.class
-							.getResourceAsStream(
-								"/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json")));
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String inputPath = parser.get("inputPath");
-		log.info("inputPath: {}", inputPath);
-
-		String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
-		log.info("filterInvisible: {}", filterInvisible);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				dispatchEntities(spark, inputPath, outputPath, filterInvisible);
-			});
-	}
-
-	private static void dispatchEntities(
-		SparkSession spark,
-		String inputPath,
-		String outputPath,
-		boolean filterInvisible) {
-
-		Dataset<String> df = spark.read().textFile(inputPath);
-
-		ModelSupport.oafTypes.entrySet().parallelStream().forEach(entry -> {
-			String entityType = entry.getKey();
-			Class<?> clazz = entry.getValue();
-
-			if (!entityType.equalsIgnoreCase("relation")) {
-				Dataset<Row> entityDF = spark
-					.read()
-					.schema(Encoders.bean(clazz).schema())
-					.json(
-						df
-							.filter((FilterFunction<String>) s -> s.startsWith(clazz.getName()))
-							.map(
-								(MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"),
-								Encoders.STRING()));
-
-				if (filterInvisible) {
-					entityDF = entityDF.filter("dataInfo.invisible != true");
-				}
-
-				entityDF
-					.write()
-					.mode(SaveMode.Overwrite)
-					.option("compression", "gzip")
-					.json(outputPath + "/" + entityType);
-			}
-		});
-	}
-}

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/GroupEntitiesSparkJob.java

@@ -2,36 +2,28 @@
 package eu.dnetlib.dhp.oa.merge;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static eu.dnetlib.dhp.utils.DHPUtils.toSeq;
+import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.when;
 
-import java.io.IOException;
-import java.util.List;
-import java.util.Objects;
+import java.util.Map;
 import java.util.Optional;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ForkJoinPool;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
-import org.apache.spark.sql.expressions.Aggregator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.jayway.jsonpath.Configuration;
-import com.jayway.jsonpath.DocumentContext;
-import com.jayway.jsonpath.JsonPath;
-import com.jayway.jsonpath.Option;
-
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
@@ -39,13 +31,9 @@ import scala.Tuple2;
  * Groups the graph content by entity identifier to ensure ID uniqueness
  */
 public class GroupEntitiesSparkJob {
-
 	private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class);
 
-	private static final String ID_JPATH = "$.id";
-
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
-		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+	private static final Encoder<OafEntity> OAFENTITY_KRYO_ENC =  Encoders.kryo(OafEntity.class);
 
 	public static void main(String[] args) throws Exception {
 
@@ -66,9 +54,15 @@ public class GroupEntitiesSparkJob {
 		String graphInputPath = parser.get("graphInputPath");
 		log.info("graphInputPath: {}", graphInputPath);
 
+		String checkpointPath = parser.get("checkpointPath");
+		log.info("checkpointPath: {}", checkpointPath);
+
 		String outputPath = parser.get("outputPath");
 		log.info("outputPath: {}", outputPath);
 
+		boolean filterInvisible = Boolean.valueOf(parser.get("filterInvisible"));
+		log.info("filterInvisible: {}", filterInvisible);
+
 		SparkConf conf = new SparkConf();
 		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
 		conf.registerKryoClasses(ModelSupport.getOafModelClasses());
@@ -78,126 +72,95 @@ public class GroupEntitiesSparkJob {
 			isSparkSessionManaged,
 			spark -> {
 				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				groupEntities(spark, graphInputPath, outputPath);
+				groupEntities(spark, graphInputPath, checkpointPath, outputPath, filterInvisible);
 			});
 	}
 
 	private static void groupEntities(
 		SparkSession spark,
 		String inputPath,
-		String outputPath) {
+		String checkpointPath,
+		String outputPath,
+		boolean filterInvisible) {
 
-		final TypedColumn<OafEntity, OafEntity> aggregator = new GroupingAggregator().toColumn();
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-		spark
-			.read()
-			.textFile(toSeq(listEntityPaths(inputPath, sc)))
-			.map((MapFunction<String, OafEntity>) GroupEntitiesSparkJob::parseOaf, Encoders.kryo(OafEntity.class))
-			.filter((FilterFunction<OafEntity>) e -> StringUtils.isNotBlank(ModelSupport.idFn().apply(e)))
-			.groupByKey((MapFunction<OafEntity, String>) oaf -> ModelSupport.idFn().apply(oaf), Encoders.STRING())
-			.agg(aggregator)
+		Dataset<OafEntity> allEntities = spark.emptyDataset(OAFENTITY_KRYO_ENC);
+
+		for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
+			String entity = e.getKey().name();
+			Class<? extends OafEntity> entityClass = e.getValue();
+			String entityInputPath = inputPath + "/" + entity;
+
+			if (!HdfsSupport.exists(entityInputPath, spark.sparkContext().hadoopConfiguration())) {
+				continue;
+			}
+
+			allEntities = allEntities
+				.union(
+					((Dataset<OafEntity>) spark
+						.read()
+						.schema(Encoders.bean(entityClass).schema())
+						.json(entityInputPath)
+						.filter("length(id) > 0")
+						.as(Encoders.bean(entityClass)))
+							.map((MapFunction<OafEntity, OafEntity>) r -> r, OAFENTITY_KRYO_ENC));
+		}
+
+		Dataset<?> groupedEntities = allEntities
+			.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
+			.reduceGroups((ReduceFunction<OafEntity>) (b, a) -> OafMapperUtils.mergeEntities(b, a))
 			.map(
-				(MapFunction<Tuple2<String, OafEntity>, String>) t -> t._2().getClass().getName() +
-					"|" + OBJECT_MAPPER.writeValueAsString(t._2()),
-				Encoders.STRING())
+				(MapFunction<Tuple2<String, OafEntity>, Tuple2<String, OafEntity>>) t -> new Tuple2(
+					t._2().getClass().getName(), t._2()),
+				Encoders.tuple(Encoders.STRING(), OAFENTITY_KRYO_ENC));
+
+		// pivot on "_1" (classname of the entity)
+		// created columns  containing only entities of the same class
+		for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
+			String entity = e.getKey().name();
+			Class<? extends OafEntity> entityClass = e.getValue();
+
+			groupedEntities = groupedEntities
+				.withColumn(
+					entity,
+					when(col("_1").equalTo(entityClass.getName()), col("_2")));
+		}
+
+		groupedEntities
+			.drop("_1", "_2")
 			.write()
-			.option("compression", "gzip")
 			.mode(SaveMode.Overwrite)
-			.text(outputPath);
-	}
+			.option("compression", "gzip")
+			.save(checkpointPath);
 
-	public static class GroupingAggregator extends Aggregator<OafEntity, OafEntity, OafEntity> {
+		ForkJoinPool parPool = new ForkJoinPool(ModelSupport.entityTypes.size());
 
-		@Override
-		public OafEntity zero() {
-			return null;
-		}
-
-		@Override
-		public OafEntity reduce(OafEntity b, OafEntity a) {
-			return mergeAndGet(b, a);
-		}
-
-		private OafEntity mergeAndGet(OafEntity b, OafEntity a) {
-			if (Objects.nonNull(a) && Objects.nonNull(b)) {
-				return OafMapperUtils.mergeEntities(b, a);
-			}
-			return Objects.isNull(a) ? b : a;
-		}
-
-		@Override
-		public OafEntity merge(OafEntity b, OafEntity a) {
-			return mergeAndGet(b, a);
-		}
-
-		@Override
-		public OafEntity finish(OafEntity j) {
-			return j;
-		}
-
-		@Override
-		public Encoder<OafEntity> bufferEncoder() {
-			return Encoders.kryo(OafEntity.class);
-		}
-
-		@Override
-		public Encoder<OafEntity> outputEncoder() {
-			return Encoders.kryo(OafEntity.class);
-		}
-
-	}
-
-	private static OafEntity parseOaf(String s) {
-
-		DocumentContext dc = JsonPath
-			.parse(s, Configuration.defaultConfiguration().addOptions(Option.SUPPRESS_EXCEPTIONS));
-		final String id = dc.read(ID_JPATH);
-		if (StringUtils.isNotBlank(id)) {
-
-			String prefix = StringUtils.substringBefore(id, "|");
-			switch (prefix) {
-				case "10":
-					return parse(s, Datasource.class);
-				case "20":
-					return parse(s, Organization.class);
-				case "40":
-					return parse(s, Project.class);
-				case "50":
-					String resultType = dc.read("$.resulttype.classid");
-					switch (resultType) {
-						case "publication":
-							return parse(s, Publication.class);
-						case "dataset":
-							return parse(s, eu.dnetlib.dhp.schema.oaf.Dataset.class);
-						case "software":
-							return parse(s, Software.class);
-						case "other":
-							return parse(s, OtherResearchProduct.class);
-						default:
-							throw new IllegalArgumentException(String.format("invalid resultType: '%s'", resultType));
-					}
-				default:
-					throw new IllegalArgumentException(String.format("invalid id prefix: '%s'", prefix));
-			}
-		} else {
-			throw new IllegalArgumentException(String.format("invalid oaf: '%s'", s));
-		}
-	}
-
-	private static <T extends OafEntity> OafEntity parse(String s, Class<T> clazz) {
-		try {
-			return OBJECT_MAPPER.readValue(s, clazz);
-		} catch (IOException e) {
-			throw new IllegalArgumentException(e);
-		}
-	}
-
-	private static List<String> listEntityPaths(String inputPath, JavaSparkContext sc) {
-		return HdfsSupport
-			.listFiles(inputPath, sc.hadoopConfiguration())
+		ModelSupport.entityTypes
+			.entrySet()
 			.stream()
-			.filter(f -> !f.toLowerCase().contains("relation"))
-			.collect(Collectors.toList());
-	}
+			.map(e -> parPool.submit(() -> {
+				String entity = e.getKey().name();
+				Class<? extends OafEntity> entityClass = e.getValue();
 
+				spark
+					.read()
+					.load(checkpointPath)
+					.select(col(entity).as("value"))
+					.filter("value IS NOT NULL")
+					.as(OAFENTITY_KRYO_ENC)
+					.map((MapFunction<OafEntity, OafEntity>) r -> r, (Encoder<OafEntity>) Encoders.bean(entityClass))
+					.filter(filterInvisible ? "dataInfo.invisible != TRUE" : "TRUE")
+					.write()
+					.mode(SaveMode.Overwrite)
+					.option("compression", "gzip")
+					.json(outputPath + "/" + entity);
+			}))
+			.collect(Collectors.toList())
+			.forEach(t -> {
+				try {
+					t.get();
+				} catch (InterruptedException | ExecutionException e) {
+					throw new RuntimeException(e);
+				}
+			});
+	}
 }

dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/dispatch_entities_parameters.json

@@ -1,26 +0,0 @@
-[
-  {
-    "paramName": "issm",
-    "paramLongName": "isSparkSessionManaged",
-    "paramDescription": "when true will stop SparkSession after job execution",
-    "paramRequired": false
-  },
-  {
-    "paramName": "i",
-    "paramLongName": "inputPath",
-    "paramDescription": "the source path",
-    "paramRequired": true
-  },
-  {
-    "paramName": "o",
-    "paramLongName": "outputPath",
-    "paramDescription": "path of the output graph",
-    "paramRequired": true
-  },
-  {
-    "paramName": "fi",
-    "paramLongName": "filterInvisible",
-    "paramDescription": "if true filters out invisible entities",
-    "paramRequired": true
-  }
-]

dhp-common/src/main/resources/eu/dnetlib/dhp/oa/merge/group_graph_entities_parameters.json

@@ -8,13 +8,25 @@
   {
     "paramName": "gin",
     "paramLongName": "graphInputPath",
-    "paramDescription": "the graph root path",
+    "paramDescription": "the input graph root path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "cp",
+    "paramLongName": "checkpointPath",
+    "paramDescription": "checkpoint directory",
     "paramRequired": true
   },
   {
     "paramName": "out",
     "paramLongName": "outputPath",
-    "paramDescription": "the output merged graph root path",
+    "paramDescription": "the output graph root path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "fi",
+    "paramLongName": "filterInvisible",
+    "paramDescription": "if true filters out invisible entities",
     "paramRequired": true
   }
 ]

dhp-pace-core/src/main/java/eu/dnetlib/pace/model/SparkModel.scala

@@ -81,7 +81,7 @@ case class SparkModel(conf: DedupConfig) {
               MapDocumentUtil.truncateList(
                 MapDocumentUtil.getJPathList(fdef.getPath, documentContext, fdef.getType),
                 fdef.getSize
-              ).toArray
+              ).asScala
 
             case Type.StringConcat =>
               val jpaths = CONCAT_REGEX.split(fdef.getPath)

dhp-pace-core/src/main/java/eu/dnetlib/pace/util/DiffPatchMatch.java

@@ -1,6 +1,23 @@
 
 package eu.dnetlib.pace.util;
 
+/*
+ * Diff Match and Patch
+ * Copyright 2018 The diff-match-patch Authors.
+ * https://github.com/google/diff-match-patch
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *   http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 /*
  * Diff Match and Patch
  * Copyright 2018 The diff-match-patch Authors.

dhp-pace-core/src/main/java/eu/dnetlib/pace/util/MapDocumentUtil.java

@@ -117,6 +117,11 @@ public class MapDocumentUtil {
 			return result;
 		}
 
+		if (type == Type.List && jresult instanceof List) {
+			((List<?>) jresult).forEach(x -> result.add(x.toString()));
+			return result;
+		}
+
 		if (jresult instanceof JSONArray) {
 			((JSONArray) jresult).forEach(it -> {
 				try {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java

@@ -12,6 +12,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
 import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
@@ -30,15 +31,29 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
+import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
 
 public class CreateActionSetSparkJob implements Serializable {
 	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
 	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
-	private static final String ID_PREFIX = "50|doi_________::";
+
+	// DOI-to-DOI citations
+	public static final String COCI = "COCI";
+
+	// PMID-to-PMID citations
+	public static final String POCI = "POCI";
+
+	private static final String DOI_PREFIX = "50|doi_________::";
+
+	private static final String PMID_PREFIX = "50|pmid________::";
+
 	private static final String TRUST = "0.91";
 
 	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
+
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(final String[] args) throws IOException, ParseException {
@@ -62,7 +77,7 @@ public class CreateActionSetSparkJob implements Serializable {
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
 		final String inputPath = parser.get("inputPath");
-		log.info("inputPath {}", inputPath.toString());
+		log.info("inputPath {}", inputPath);
 
 		final String outputPath = parser.get("outputPath");
 		log.info("outputPath {}", outputPath);
@@ -76,41 +91,68 @@ public class CreateActionSetSparkJob implements Serializable {
 		runWithSparkSession(
 			conf,
 			isSparkSessionManaged,
-			spark -> {
-				extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
-			});
+			spark -> extractContent(spark, inputPath, outputPath, shouldDuplicateRels));
 
 	}
 
 	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
 		boolean shouldDuplicateRels) {
-		spark
+
+		getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, COCI)
+			.union(getTextTextJavaPairRDD(spark, inputPath, shouldDuplicateRels, POCI))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
+	}
+
+	private static JavaPairRDD<Text, Text> getTextTextJavaPairRDD(SparkSession spark, String inputPath,
+		boolean shouldDuplicateRels, String prefix) {
+		return spark
 			.read()
-			.textFile(inputPath + "/*")
+			.textFile(inputPath + "/" + prefix + "/" + prefix + "_JSON/*")
 			.map(
 				(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
 				Encoders.bean(COCI.class))
 			.flatMap(
-				(FlatMapFunction<COCI, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
+				(FlatMapFunction<COCI, Relation>) value -> createRelation(
+					value, shouldDuplicateRels, prefix)
+						.iterator(),
 				Encoders.bean(Relation.class))
-			.filter((FilterFunction<Relation>) value -> value != null)
+			.filter((FilterFunction<Relation>) Objects::nonNull)
 			.toJavaRDD()
 			.map(p -> new AtomicAction(p.getClass(), p))
 			.mapToPair(
 				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
-
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
-	private static List<Relation> createRelation(COCI value, boolean duplicate) {
+	private static List<Relation> createRelation(COCI value, boolean duplicate, String p) {
 
 		List<Relation> relationList = new ArrayList<>();
+		String prefix;
+		String citing;
+		String cited;
 
-		String citing = ID_PREFIX
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
-		final String cited = ID_PREFIX
-			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
+		switch (p) {
+			case COCI:
+				prefix = DOI_PREFIX;
+				citing = prefix
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.doi.toString(), value.getCiting()));
+				cited = prefix
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.doi.toString(), value.getCited()));
+				break;
+			case POCI:
+				prefix = PMID_PREFIX;
+				citing = prefix
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.pmid.toString(), value.getCiting()));
+				cited = prefix
+					+ IdentifierFactory
+						.md5(CleaningFunctions.normalizePidValue(PidType.pmid.toString(), value.getCited()));
+				break;
+			default:
+				throw new IllegalStateException("Invalid prefix: " + p);
+		}
 
 		if (!citing.equals(cited)) {
 			relationList
@@ -120,7 +162,7 @@ public class CreateActionSetSparkJob implements Serializable {
 						cited, ModelConstants.CITES));
 
 			if (duplicate && value.getCiting().endsWith(".refs")) {
-				citing = ID_PREFIX + IdentifierFactory
+				citing = prefix + IdentifierFactory
 					.md5(
 						CleaningFunctions
 							.normalizePidValue(
@@ -132,59 +174,30 @@ public class CreateActionSetSparkJob implements Serializable {
 		return relationList;
 	}
 
-	private static Collection<Relation> getRelations(String citing, String cited) {
-
-		return Arrays
-			.asList(
-				getRelation(citing, cited, ModelConstants.CITES),
-				getRelation(cited, citing, ModelConstants.IS_CITED_BY));
-	}
-
 	public static Relation getRelation(
 		String source,
 		String target,
-		String relclass) {
-		Relation r = new Relation();
-		r.setCollectedfrom(getCollectedFrom());
-		r.setSource(source);
-		r.setTarget(target);
-		r.setRelClass(relclass);
-		r.setRelType(ModelConstants.RESULT_RESULT);
-		r.setSubRelType(ModelConstants.CITATION);
-		r
-			.setDataInfo(
-				getDataInfo());
-		return r;
-	}
+		String relClass) {
 
-	public static List<KeyValue> getCollectedFrom() {
-		KeyValue kv = new KeyValue();
-		kv.setKey(ModelConstants.OPENOCITATIONS_ID);
-		kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
-
-		return Arrays.asList(kv);
-	}
-
-	public static DataInfo getDataInfo() {
-		DataInfo di = new DataInfo();
-		di.setInferred(false);
-		di.setDeletedbyinference(false);
-		di.setTrust(TRUST);
-
-		di
-			.setProvenanceaction(
-				getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
-		return di;
-	}
-
-	public static Qualifier getQualifier(String class_id, String class_name,
-		String qualifierSchema) {
-		Qualifier pa = new Qualifier();
-		pa.setClassid(class_id);
-		pa.setClassname(class_name);
-		pa.setSchemeid(qualifierSchema);
-		pa.setSchemename(qualifierSchema);
-		return pa;
+		return OafMapperUtils
+			.getRelation(
+				source,
+				target,
+				ModelConstants.RESULT_RESULT,
+				ModelConstants.CITATION,
+				relClass,
+				Arrays
+					.asList(
+						OafMapperUtils.keyValue(ModelConstants.OPENOCITATIONS_ID, ModelConstants.OPENOCITATIONS_NAME)),
+				OafMapperUtils
+					.dataInfo(
+						false, null, false, false,
+						OafMapperUtils
+							.qualifier(
+								OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME,
+								ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS),
+						TRUST),
+				null);
 	}
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.actionmanager.opencitations;
 
 import java.io.*;
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.Objects;
 import java.util.zip.GZIPOutputStream;
 import java.util.zip.ZipEntry;
@@ -37,7 +38,7 @@ public class GetOpenCitationsRefs implements Serializable {
 		parser.parseArgument(args);
 
 		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
+		log.info("inputFile {}", Arrays.asList(inputFile));
 
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath {}", workingPath);
@@ -45,6 +46,9 @@ public class GetOpenCitationsRefs implements Serializable {
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 		log.info("hdfsNameNode {}", hdfsNameNode);
 
+		final String prefix = parser.get("prefix");
+		log.info("prefix {}", prefix);
+
 		Configuration conf = new Configuration();
 		conf.set("fs.defaultFS", hdfsNameNode);
 
@@ -53,30 +57,31 @@ public class GetOpenCitationsRefs implements Serializable {
 		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
 
 		for (String file : inputFile) {
-			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
+			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem, prefix);
 		}
 
 	}
 
-	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
+	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem, String prefix)
 		throws IOException {
 
 		final Path path = new Path(inputFile);
 
 		FSDataInputStream oc_zip = fileSystem.open(path);
 
-		int count = 1;
+		// int count = 1;
 		try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
 			ZipEntry entry = null;
 			while ((entry = zis.getNextEntry()) != null) {
 
 				if (!entry.isDirectory()) {
 					String fileName = entry.getName();
-					fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
-					count++;
+					// fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
+					fileName = fileName.substring(0, fileName.lastIndexOf("."));
+					// count++;
 					try (
 						FSDataOutputStream out = fileSystem
-							.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
+							.create(new Path(workingPath + "/" + prefix + "/" + fileName + ".gz"));
 						GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
 
 						IOUtils.copy(zis, gzipOs);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/ReadCOCI.java

@@ -7,6 +7,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.IOException;
 import java.io.Serializable;
+import java.util.Arrays;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -42,13 +43,16 @@ public class ReadCOCI implements Serializable {
 		log.info("outputPath: {}", outputPath);
 
 		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
+		log.info("inputFile {}", Arrays.asList(inputFile));
 		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
 		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 
 		final String workingPath = parser.get("workingPath");
 		log.info("workingPath {}", workingPath);
 
+		final String format = parser.get("format");
+		log.info("format {}", format);
+
 		SparkConf sconf = new SparkConf();
 
 		final String delimiter = Optional
@@ -64,16 +68,17 @@ public class ReadCOCI implements Serializable {
 					workingPath,
 					inputFile,
 					outputPath,
-					delimiter);
+					delimiter,
+					format);
 			});
 	}
 
 	private static void doRead(SparkSession spark, String workingPath, String[] inputFiles,
 		String outputPath,
-		String delimiter) throws IOException {
+		String delimiter, String format) {
 
 		for (String inputFile : inputFiles) {
-			String p_string = workingPath + "/" + inputFile + ".gz";
+			String pString = workingPath + "/" + inputFile + ".gz";
 
 			Dataset<Row> cociData = spark
 				.read()
@@ -82,14 +87,20 @@ public class ReadCOCI implements Serializable {
 				.option("inferSchema", "true")
 				.option("header", "true")
 				.option("quotes", "\"")
-				.load(p_string)
+				.load(pString)
 				.repartition(100);
 
 			cociData.map((MapFunction<Row, COCI>) row -> {
 				COCI coci = new COCI();
+				if (format.equals("COCI")) {
+					coci.setCiting(row.getString(1));
+					coci.setCited(row.getString(2));
+				} else {
+					coci.setCiting(String.valueOf(row.getInt(1)));
+					coci.setCited(String.valueOf(row.getInt(2)));
+				}
 				coci.setOci(row.getString(0));
-				coci.setCiting(row.getString(1));
-				coci.setCited(row.getString(2));
+
 				return coci;
 			}, Encoders.bean(COCI.class))
 				.write()

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json

@@ -16,10 +16,11 @@
     "paramLongName": "isSparkSessionManaged",
     "paramDescription": "the hdfs name node",
     "paramRequired": false
-  },  {
-  "paramName": "sdr",
-  "paramLongName": "shouldDuplicateRels",
-  "paramDescription": "the hdfs name node",
-  "paramRequired": false
-}
+  },
+  {
+    "paramName": "sdr",
+    "paramLongName": "shouldDuplicateRels",
+    "paramDescription": "activates/deactivates the construction of bidirectional relations Cites/IsCitedBy",
+    "paramRequired": false
+  }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json

@@ -16,5 +16,11 @@
     "paramLongName": "hdfsNameNode",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
+  },
+  {
+    "paramName": "p",
+    "paramLongName": "prefix",
+    "paramDescription": "COCI or POCI",
+    "paramRequired": true
   }
 ]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json

@@ -30,7 +30,12 @@
     "paramLongName": "inputFile",
     "paramDescription": "the hdfs name node",
     "paramRequired": true
-  }
+  }, {
+  "paramName": "f",
+  "paramLongName": "format",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": true
+}
 ]
 
 

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml

@@ -34,6 +34,7 @@
     <kill name="Kill">
         <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
     </kill>
+
     <action name="download">
         <shell xmlns="uri:oozie:shell-action:0.2">
             <job-tracker>${jobTracker}</job-tracker>
@@ -46,7 +47,7 @@
             </configuration>
             <exec>download.sh</exec>
             <argument>${filelist}</argument>
-            <argument>${workingPath}/Original</argument>
+            <argument>${workingPath}/${prefix}/Original</argument>
             <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
             <file>download.sh</file>
             <capture-output/>
@@ -54,12 +55,14 @@
         <ok to="extract"/>
         <error to="Kill"/>
     </action>
+
     <action name="extract">
         <java>
             <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
             <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
             <arg>--inputFile</arg><arg>${inputFile}</arg>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}/${prefix}</arg>
+            <arg>--prefix</arg><arg>${prefix}</arg>
         </java>
         <ok to="read"/>
         <error to="Kill"/>
@@ -82,10 +85,11 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}/COCI</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/COCI_JSON/</arg>
+            <arg>--workingPath</arg><arg>${workingPath}/${prefix}/${prefix}</arg>
+            <arg>--outputPath</arg><arg>${workingPath}/${prefix}/${prefix}_JSON/</arg>
             <arg>--delimiter</arg><arg>${delimiter}</arg>
             <arg>--inputFile</arg><arg>${inputFileCoci}</arg>
+            <arg>--format</arg><arg>${prefix}</arg>
         </spark>
         <ok to="create_actionset"/>
         <error to="Kill"/>
@@ -108,7 +112,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
             </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/COCI_JSON</arg>
+            <arg>--inputPath</arg><arg>${workingPath}</arg>
             <arg>--outputPath</arg><arg>${outputPath}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json

@@ -1,4 +1,9 @@
 {
+ "ETHZ.UNIGENF": {
+  "openaire_id": "opendoar____::1400",
+  "datacite_name": "Uni Genf",
+  "official_name": "Archive ouverte UNIGE"
+ },
  "GESIS.RKI": {
   "openaire_id": "re3data_____::r3d100010436",
   "datacite_name": "Forschungsdatenzentrum  am Robert Koch Institut",

dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/TrustUtils.java

@@ -2,7 +2,9 @@
 package eu.dnetlib.dhp.broker.oa.util;
 
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.spark.sql.Row;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -27,10 +29,14 @@ public class TrustUtils {
 	static {
 		mapper = new ObjectMapper();
 		try {
-			dedupConfig = mapper
-				.readValue(
-					DedupConfig.class.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
-					DedupConfig.class);
+			dedupConfig = DedupConfig
+				.load(
+					IOUtils
+						.toString(
+							DedupConfig.class
+								.getResourceAsStream("/eu/dnetlib/dhp/broker/oa/dedupConfig/dedupConfig.json"),
+							StandardCharsets.UTF_8));
+
 			deduper = new SparkDeduper(dedupConfig);
 		} catch (final IOException e) {
 			log.error("Error loading dedupConfig, e");
@@ -57,7 +63,7 @@ public class TrustUtils {
 			return TrustUtils.rescale(score, threshold);
 		} catch (final Exception e) {
 			log.error("Error computing score between results", e);
-			return BrokerConstants.MIN_TRUST;
+			throw new RuntimeException(e);
 		}
 	}
 

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

@@ -1,57 +0,0 @@
-
-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 final 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/SparkCleanRelation.scala

@@ -1,78 +0,0 @@
-package eu.dnetlib.dhp.oa.dedup
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.common.HdfsSupport
-import eu.dnetlib.dhp.schema.oaf.Relation
-import eu.dnetlib.dhp.utils.ISLookupClientFactory
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService
-import org.apache.commons.io.IOUtils
-import org.apache.spark.SparkConf
-import org.apache.spark.sql._
-import org.apache.spark.sql.functions.col
-import org.apache.spark.sql.types.{DataTypes, StructField, StructType}
-import org.slf4j.LoggerFactory
-
-object SparkCleanRelation {
-  private val log = LoggerFactory.getLogger(classOf[SparkCleanRelation])
-
-  @throws[Exception]
-  def main(args: Array[String]): Unit = {
-    val parser = new ArgumentApplicationParser(
-      IOUtils.toString(
-        classOf[SparkCleanRelation].getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json")
-      )
-    )
-    parser.parseArgument(args)
-    val conf = new SparkConf
-
-    new SparkCleanRelation(parser, AbstractSparkAction.getSparkSession(conf))
-      .run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")))
-  }
-}
-
-class SparkCleanRelation(parser: ArgumentApplicationParser, spark: SparkSession)
-    extends AbstractSparkAction(parser, spark) {
-  override def run(isLookUpService: ISLookUpService): Unit = {
-    val graphBasePath = parser.get("graphBasePath")
-    val inputPath = parser.get("inputPath")
-    val outputPath = parser.get("outputPath")
-
-    SparkCleanRelation.log.info("graphBasePath: '{}'", graphBasePath)
-    SparkCleanRelation.log.info("inputPath: '{}'", inputPath)
-    SparkCleanRelation.log.info("outputPath: '{}'", outputPath)
-
-    AbstractSparkAction.removeOutputDir(spark, outputPath)
-
-    val entities =
-      Seq("datasource", "project", "organization", "publication", "dataset", "software", "otherresearchproduct")
-
-    val idsSchema = StructType.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>")
-
-    val emptyIds = spark.createDataFrame(spark.sparkContext.emptyRDD[Row].setName("empty"),
-      idsSchema)
-
-    val ids = entities
-      .foldLeft(emptyIds)((ds, entity) => {
-        val entityPath = graphBasePath + '/' + entity
-        if (HdfsSupport.exists(entityPath, spark.sparkContext.hadoopConfiguration)) {
-          ds.union(spark.read.schema(idsSchema).json(entityPath))
-        } else {
-          ds
-        }
-      })
-      .filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
-      .select("id")
-      .distinct()
-
-    val relations = spark.read.schema(Encoders.bean(classOf[Relation]).schema).json(inputPath)
-      .filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
-
-    AbstractSparkAction.save(
-      relations
-        .join(ids, col("source") === ids("id"), "leftsemi")
-        .join(ids, col("target") === ids("id"), "leftsemi"),
-      outputPath,
-      SaveMode.Overwrite
-    )
-  }
-}

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

@@ -3,23 +3,19 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static org.apache.spark.sql.functions.col;
 
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.Objects;
-
-import org.apache.commons.beanutils.BeanUtils;
 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.api.java.function.ReduceFunction;
 import org.apache.spark.sql.*;
+import org.apache.spark.sql.catalyst.encoders.RowEncoder;
+import org.apache.spark.sql.types.StructType;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
@@ -70,73 +66,63 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 		log.info("workingPath: '{}'", workingPath);
 		log.info("graphOutputPath: '{}'", graphOutputPath);
 
-		final String outputRelationPath = DedupUtility.createEntityPath(graphOutputPath, "relation");
-		removeOutputDir(spark, outputRelationPath);
-
 		Dataset<Relation> mergeRels = spark
-			.read()
-			.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
-			.as(REL_BEAN_ENC);
+				.read()
+				.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
+				.as(REL_BEAN_ENC);
 
 		// <mergedObjectID, dedupID>
-		Dataset<Row> mergedIds = mergeRels
-			.where(col("relClass").equalTo(ModelConstants.MERGES))
-			.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
-			.distinct()
-			.cache();
+		Dataset<Row> idsToMerge = mergeRels
+				.where(col("relClass").equalTo(ModelConstants.MERGES))
+				.select(col("source").as("dedupID"), col("target").as("mergedObjectID"))
+				.distinct();
 
 		Dataset<Row> allRels = spark
-			.read()
-			.schema(REL_BEAN_ENC.schema())
-			.json(DedupUtility.createEntityPath(graphBasePath, "relation"));
+				.read()
+				.schema(REL_BEAN_ENC.schema())
+				.json(graphBasePath + "/relation");
 
 		Dataset<Relation> dedupedRels = allRels
-			.joinWith(mergedIds, allRels.col("source").equalTo(mergedIds.col("mergedObjectID")), "left_outer")
-			.joinWith(mergedIds, col("_1.target").equalTo(mergedIds.col("mergedObjectID")), "left_outer")
-			.select("_1._1", "_1._2.dedupID", "_2.dedupID")
-			.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
-			.flatMap(SparkPropagateRelation::addInferredRelations, REL_KRYO_ENC);
+				.joinWith(idsToMerge, allRels.col("source").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
+				.joinWith(idsToMerge, col("_1.target").equalTo(idsToMerge.col("mergedObjectID")), "left_outer")
+				.select("_1._1", "_1._2.dedupID", "_2.dedupID")
+				.as(Encoders.tuple(REL_BEAN_ENC, Encoders.STRING(), Encoders.STRING()))
+				.map((MapFunction<Tuple3<Relation, String, String>, Relation>) t -> {
+					Relation rel = t._1();
+					String newSource = t._2();
+					String newTarget = t._3();
 
-		Dataset<Relation> processedRelations = distinctRelations(
-			dedupedRels.union(mergeRels.map((MapFunction<Relation, Relation>) r -> r, REL_KRYO_ENC)))
-				.filter((FilterFunction<Relation>) r -> !Objects.equals(r.getSource(), r.getTarget()));
+					if (rel.getDataInfo() == null) {
+						rel.setDataInfo(new DataInfo());
+					}
 
-		save(processedRelations, outputRelationPath, SaveMode.Overwrite);
-	}
+					if (newSource != null || newTarget != null) {
+						rel.getDataInfo().setDeletedbyinference(false);
 
-	private static Iterator<Relation> addInferredRelations(Tuple3<Relation, String, String> t) throws Exception {
-		Relation existingRel = t._1();
-		String newSource = t._2();
-		String newTarget = t._3();
+						if (newSource != null)
+							rel.setSource(newSource);
 
-		if (newSource == null && newTarget == null) {
-			return Collections.singleton(t._1()).iterator();
-		}
+						if (newTarget != null)
+							rel.setTarget(newTarget);
+					}
 
-		// update existing relation
-		if (existingRel.getDataInfo() == null) {
-			existingRel.setDataInfo(new DataInfo());
-		}
-		existingRel.getDataInfo().setDeletedbyinference(true);
+					return rel;
+				}, REL_BEAN_ENC);
 
-		// Create new relation inferred by dedupIDs
-		Relation inferredRel = (Relation) BeanUtils.cloneBean(existingRel);
+		// ids of records that are both not deletedbyinference and not invisible
+		Dataset<Row> ids = validIds(spark, graphBasePath);
 
-		inferredRel.setDataInfo((DataInfo) BeanUtils.cloneBean(existingRel.getDataInfo()));
-		inferredRel.getDataInfo().setDeletedbyinference(false);
+		// filter relations that point to valid records, can force them to be visible
+		Dataset<Relation> cleanedRels = dedupedRels
+				.join(ids, col("source").equalTo(ids.col("id")), "leftsemi")
+				.join(ids, col("target").equalTo(ids.col("id")), "leftsemi")
+				.as(REL_BEAN_ENC)
+				.map((MapFunction<Relation, Relation>) r -> {
+					r.getDataInfo().setInvisible(false);
+					return r;
+				}, REL_KRYO_ENC);
 
-		if (newSource != null)
-			inferredRel.setSource(newSource);
-
-		if (newTarget != null)
-			inferredRel.setTarget(newTarget);
-
-		return Arrays.asList(existingRel, inferredRel).iterator();
-	}
-
-	private Dataset<Relation> distinctRelations(Dataset<Relation> rels) {
-		return rels
-			.filter(getRelationFilterFunction())
+		Dataset<Relation> distinctRels = cleanedRels
 			.groupByKey(
 				(MapFunction<Relation, String>) r -> String
 					.join(" ", r.getSource(), r.getTarget(), r.getRelType(), r.getSubRelType(), r.getRelClass()),
@@ -146,13 +132,33 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 				return b;
 			})
 			.map((MapFunction<Tuple2<String, Relation>, Relation>) Tuple2::_2, REL_BEAN_ENC);
+
+		final String outputRelationPath = graphOutputPath + "/relation";
+		removeOutputDir(spark, outputRelationPath);
+		save(
+			distinctRels
+				.union(mergeRels)
+				.filter("source != target AND dataInfo.deletedbyinference != true AND dataInfo.invisible != true"),
+			outputRelationPath,
+			SaveMode.Overwrite);
 	}
 
-	private FilterFunction<Relation> getRelationFilterFunction() {
-		return r -> StringUtils.isNotBlank(r.getSource()) ||
-			StringUtils.isNotBlank(r.getTarget()) ||
-			StringUtils.isNotBlank(r.getRelType()) ||
-			StringUtils.isNotBlank(r.getSubRelType()) ||
-			StringUtils.isNotBlank(r.getRelClass());
+	static Dataset<Row> validIds(SparkSession spark, String graphBasePath) {
+		StructType idsSchema = StructType
+			.fromDDL("`id` STRING, `dataInfo` STRUCT<`deletedbyinference`:BOOLEAN,`invisible`:BOOLEAN>");
+
+		Dataset<Row> allIds = spark.emptyDataset(RowEncoder.apply(idsSchema));
+
+		for (EntityType entityType : ModelSupport.entityTypes.keySet()) {
+			String entityPath = graphBasePath + '/' + entityType.name();
+			if (HdfsSupport.exists(entityPath, spark.sparkContext().hadoopConfiguration())) {
+				allIds = allIds.union(spark.read().schema(idsSchema).json(entityPath));
+			}
+		}
+
+		return allIds
+			.filter("dataInfo.deletedbyinference != true AND dataInfo.invisible != true")
+			.select("id")
+			.distinct();
 	}
 }

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

@@ -1,20 +0,0 @@
-[
-  {
-    "paramName": "i",
-    "paramLongName": "graphBasePath",
-    "paramDescription": "the base path of raw graph",
-    "paramRequired": true
-  },
-  {
-    "paramName": "w",
-    "paramLongName": "inputPath",
-    "paramDescription": "the path to the input relation to cleanup",
-    "paramRequired": true
-  },
-  {
-    "paramName": "o",
-    "paramLongName": "outputPath",
-    "paramDescription": "the path of the output relation cleaned",
-    "paramRequired": true
-  }
-]

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

@@ -100,35 +100,9 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--graphOutputPath</arg><arg>${workingPath}/propagaterelation/</arg>
+            <arg>--graphOutputPath</arg><arg>${graphOutputPath}</arg>
             <arg>--workingPath</arg><arg>${workingPath}</arg>
         </spark>
-        <ok to="CleanRelation"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="CleanRelation">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Clean Relations</name>
-            <class>eu.dnetlib.dhp.oa.dedup.SparkCleanRelation</class>
-            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=15000
-            </spark-opts>
-            <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
-            <arg>--inputPath</arg><arg>${workingPath}/propagaterelation/relation</arg>
-            <arg>--outputPath</arg><arg>${graphOutputPath}/relation</arg>
-        </spark>
         <ok to="group_entities"/>
         <error to="Kill"/>
     </action>
@@ -152,31 +126,7 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
-        </spark>
-        <ok to="dispatch_entities"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="dispatch_entities">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Dispatch grouped entitities</name>
-            <class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
-            <jar>dhp-dedup-openaire-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-memory=${sparkExecutorMemory}
-                --conf spark.executor.memoryOverhead=${sparkExecutorMemoryOverhead}
-                --executor-cores=${sparkExecutorCores}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
+            <arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}</arg>
             <arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
         </spark>

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

@@ -3,7 +3,6 @@ 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.*;
 import static org.mockito.Mockito.lenient;
@@ -23,14 +22,13 @@ import java.util.stream.Collectors;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 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.*;
 import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
@@ -46,8 +44,6 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import eu.dnetlib.pace.util.MapDocumentUtil;
-import scala.Tuple2;
 
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@@ -62,6 +58,8 @@ public class SparkDedupTest implements Serializable {
 	private static String testGraphBasePath;
 	private static String testOutputBasePath;
 	private static String testDedupGraphBasePath;
+	private static String testConsistencyGraphBasePath;
+
 	private static final String testActionSetId = "test-orchestrator";
 	private static String whitelistPath;
 	private static List<String> whiteList;
@@ -75,6 +73,7 @@ public class SparkDedupTest implements Serializable {
 			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/entities").toURI())
 			.toFile()
 			.getAbsolutePath();
+
 		testOutputBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
 			.toAbsolutePath()
 			.toString();
@@ -83,6 +82,10 @@ public class SparkDedupTest implements Serializable {
 			.toAbsolutePath()
 			.toString();
 
+		testConsistencyGraphBasePath = createTempDirectory(SparkDedupTest.class.getSimpleName() + "-")
+			.toAbsolutePath()
+			.toString();
+
 		whitelistPath = Paths
 			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/whitelist.simrels.txt").toURI())
 			.toFile()
@@ -674,22 +677,45 @@ public class SparkDedupTest implements Serializable {
 		assertEquals(mergedOrp, deletedOrp);
 	}
 
+	@Test
+	@Order(6)
+	void copyRelationsNoOpenorgsTest() throws Exception {
+
+		ArgumentApplicationParser parser = new ArgumentApplicationParser(
+			IOUtils
+				.toString(
+					SparkCopyRelationsNoOpenorgs.class
+						.getResourceAsStream(
+							"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
+		parser
+			.parseArgument(
+				new String[] {
+					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
+				});
+
+		new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
+
+		final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
+
+		System.out.println(outputRels.count());
+		// assertEquals(2382, outputRels.count());
+	}
+
 	@Test
 	@Order(7)
 	void propagateRelationTest() throws Exception {
 
 		ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/propagateRelation_parameters.json"));
-		String outputRelPath = testDedupGraphBasePath + "/propagaterelation";
 		parser
 			.parseArgument(
 				new String[] {
-					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", outputRelPath
+					"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
 				});
 
 		new SparkPropagateRelation(parser, spark).run(isLookUpService);
 
-		long relations = jsc.textFile(outputRelPath + "/relation").count();
+		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
 //		assertEquals(4860, relations);
 		System.out.println("relations = " + relations);
@@ -699,95 +725,52 @@ public class SparkDedupTest implements Serializable {
 			.read()
 			.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
 			.as(Encoders.bean(Relation.class));
-		final JavaPairRDD<String, String> mergedIds = mergeRels
-			.where("relClass == 'merges'")
-			.select(mergeRels.col("target"))
-			.distinct()
-			.toJavaRDD()
-			.mapToPair(
-				(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
 
-		JavaRDD<String> toCheck = jsc
-			.textFile(outputRelPath + "/relation")
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
-			.join(mergedIds)
-			.map(t -> t._2()._1())
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
-			.join(mergedIds)
-			.map(t -> t._2()._1());
+		Dataset<Row> inputRels = spark
+			.read()
+			.json(testDedupGraphBasePath + "/relation");
 
-		long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
-		long updated = toCheck.count();
+		Dataset<Row> outputRels = spark
+			.read()
+			.json(testConsistencyGraphBasePath + "/relation");
 
-		assertEquals(updated, deletedbyinference);
+		assertEquals(
+			0, outputRels
+				.filter("dataInfo.deletedbyinference == true OR dataInfo.invisible == true")
+				.count());
+
+		assertEquals(
+			5, outputRels
+				.filter("relClass NOT IN ('merges', 'isMergedIn')")
+				.count());
+
+		assertEquals(5 + mergeRels.count(), outputRels.count());
 	}
 
 	@Test
 	@Order(8)
-	void testCleanBaseRelations() throws Exception {
-		ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
-
-		// append dangling relations to be cleaned up
+	void testCleanedPropagatedRelations() throws Exception {
 		Dataset<Row> df_before = spark
 			.read()
 			.schema(Encoders.bean(Relation.class).schema())
-			.json(testGraphBasePath + "/relation");
-		Dataset<Row> df_input = df_before
-			.unionByName(df_before.drop("source").withColumn("source", functions.lit("n/a")))
-			.unionByName(df_before.drop("target").withColumn("target", functions.lit("n/a")));
-		df_input.write().mode(SaveMode.Overwrite).json(testOutputBasePath + "_tmp");
-
-		parser
-			.parseArgument(
-				new String[] {
-					"--graphBasePath", testGraphBasePath,
-					"--inputPath", testGraphBasePath + "/relation",
-					"--outputPath", testDedupGraphBasePath + "/relation"
-				});
-
-		new SparkCleanRelation(parser, spark).run(isLookUpService);
+			.json(testDedupGraphBasePath + "/relation");
 
 		Dataset<Row> df_after = spark
 			.read()
 			.schema(Encoders.bean(Relation.class).schema())
-			.json(testDedupGraphBasePath + "/relation");
-
-		assertNotEquals(df_before.count(), df_input.count());
-		assertNotEquals(df_input.count(), df_after.count());
-		assertEquals(5, df_after.count());
-	}
-
-	@Test
-	@Order(9)
-	void testCleanDedupedRelations() throws Exception {
-		ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			classPathResourceAsString("/eu/dnetlib/dhp/oa/dedup/cleanRelation_parameters.json"));
-
-		String inputRelPath = testDedupGraphBasePath + "/propagaterelation/relation";
-
-		// append dangling relations to be cleaned up
-		Dataset<Row> df_before = spark.read().schema(Encoders.bean(Relation.class).schema()).json(inputRelPath);
-
-		df_before.filter(col("dataInfo.deletedbyinference").notEqual(true)).show(50, false);
-
-		parser
-			.parseArgument(
-				new String[] {
-					"--graphBasePath", testGraphBasePath,
-					"--inputPath", inputRelPath,
-					"--outputPath", testDedupGraphBasePath + "/relation"
-				});
-
-		new SparkCleanRelation(parser, spark).run(isLookUpService);
-
-		Dataset<Row> df_after = spark
-			.read()
-			.schema(Encoders.bean(Relation.class).schema())
-			.json(testDedupGraphBasePath + "/relation");
+			.json(testConsistencyGraphBasePath + "/relation");
 
 		assertNotEquals(df_before.count(), df_after.count());
-		assertEquals(0, df_after.count());
+
+		assertEquals(
+			0, df_after
+				.filter("dataInfo.deletedbyinference == true OR dataInfo.invisible == true")
+				.count());
+
+		assertEquals(
+			5, df_after
+				.filter("relClass NOT IN ('merges', 'isMergedIn')")
+				.count());
 	}
 
 	@Test
@@ -813,6 +796,7 @@ public class SparkDedupTest implements Serializable {
 	public static void finalCleanUp() throws IOException {
 		FileUtils.deleteDirectory(new File(testOutputBasePath));
 		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
+		FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
 	}
 
 	public boolean isDeletedByInference(String s) {

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

@@ -3,6 +3,7 @@ package eu.dnetlib.dhp.oa.dedup;
 
 import static java.nio.file.Files.createTempDirectory;
 
+import static org.apache.spark.sql.functions.col;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.mockito.Mockito.lenient;
 
@@ -15,10 +16,6 @@ import java.nio.file.Paths;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 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.PairFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.Row;
@@ -33,8 +30,6 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import eu.dnetlib.pace.util.MapDocumentUtil;
-import scala.Tuple2;
 
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
@@ -44,11 +39,11 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 	ISLookUpService isLookUpService;
 
 	private static SparkSession spark;
-	private static JavaSparkContext jsc;
 
 	private static String testGraphBasePath;
 	private static String testOutputBasePath;
 	private static String testDedupGraphBasePath;
+	private static String testConsistencyGraphBasePath;
 	private static final String testActionSetId = "test-orchestrator";
 
 	@BeforeAll
@@ -64,6 +59,9 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 		testDedupGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
 			.toAbsolutePath()
 			.toString();
+		testConsistencyGraphBasePath = createTempDirectory(SparkOpenorgsProvisionTest.class.getSimpleName() + "-")
+			.toAbsolutePath()
+			.toString();
 
 		FileUtils.deleteDirectory(new File(testOutputBasePath));
 		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
@@ -76,8 +74,13 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 			.master("local[*]")
 			.config(conf)
 			.getOrCreate();
+	}
 
-		jsc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+	@AfterAll
+	public static void finalCleanUp() throws IOException {
+		FileUtils.deleteDirectory(new File(testOutputBasePath));
+		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
+		FileUtils.deleteDirectory(new File(testConsistencyGraphBasePath));
 	}
 
 	@BeforeEach
@@ -186,26 +189,21 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 
 		new SparkUpdateEntity(parser, spark).run(isLookUpService);
 
-		long organizations = jsc.textFile(testDedupGraphBasePath + "/organization").count();
+		Dataset<Row> organizations = spark.read().json(testDedupGraphBasePath + "/organization");
 
-		long mergedOrgs = spark
+		Dataset<Row> mergedOrgs = spark
 			.read()
 			.load(testOutputBasePath + "/" + testActionSetId + "/organization_mergerel")
-			.as(Encoders.bean(Relation.class))
 			.where("relClass=='merges'")
-			.javaRDD()
-			.map(Relation::getTarget)
-			.distinct()
-			.count();
+			.select("target")
+			.distinct();
 
-		assertEquals(80, organizations);
+		assertEquals(80, organizations.count());
 
-		long deletedOrgs = jsc
-			.textFile(testDedupGraphBasePath + "/organization")
-			.filter(this::isDeletedByInference)
-			.count();
+		Dataset<Row> deletedOrgs = organizations
+			.filter("dataInfo.deletedbyinference = TRUE");
 
-		assertEquals(mergedOrgs, deletedOrgs);
+		assertEquals(mergedOrgs.count(), deletedOrgs.count());
 	}
 
 	@Test
@@ -226,10 +224,9 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 
 		new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
 
-		final JavaRDD<String> rels = jsc.textFile(testDedupGraphBasePath + "/relation");
-
-		assertEquals(2382, rels.count());
+		final Dataset<Row> outputRels = spark.read().text(testDedupGraphBasePath + "/relation");
 
+		assertEquals(2382, outputRels.count());
 	}
 
 	@Test
@@ -244,51 +241,41 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 		parser
 			.parseArgument(
 				new String[] {
-					"-i", testGraphBasePath, "-w", testOutputBasePath, "-o", testDedupGraphBasePath
+					"-i", testDedupGraphBasePath, "-w", testOutputBasePath, "-o", testConsistencyGraphBasePath
 				});
 
 		new SparkPropagateRelation(parser, spark).run(isLookUpService);
 
-		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
-
-		assertEquals(4896, relations);
-
-		// check deletedbyinference
 		final Dataset<Relation> mergeRels = spark
 			.read()
 			.load(DedupUtility.createMergeRelPath(testOutputBasePath, "*", "*"))
 			.as(Encoders.bean(Relation.class));
-		final JavaPairRDD<String, String> mergedIds = mergeRels
+
+		Dataset<Row> inputRels = spark
+			.read()
+			.json(testDedupGraphBasePath + "/relation");
+
+		Dataset<Row> outputRels = spark
+			.read()
+			.json(testConsistencyGraphBasePath + "/relation");
+
+		final Dataset<Row> mergedIds = mergeRels
 			.where("relClass == 'merges'")
-			.select(mergeRels.col("target"))
-			.distinct()
-			.toJavaRDD()
-			.mapToPair(
-				(PairFunction<Row, String, String>) r -> new Tuple2<String, String>(r.getString(0), "d"));
+			.select(col("target").as("id"))
+			.distinct();
 
-		JavaRDD<String> toCheck = jsc
-			.textFile(testDedupGraphBasePath + "/relation")
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.source", json), json))
-			.join(mergedIds)
-			.map(t -> t._2()._1())
-			.mapToPair(json -> new Tuple2<>(MapDocumentUtil.getJPathString("$.target", json), json))
-			.join(mergedIds)
-			.map(t -> t._2()._1());
+		Dataset<Row> toUpdateRels = inputRels
+			.as("rel")
+			.join(mergedIds.as("s"), col("rel.source").equalTo(col("s.id")), "left_outer")
+			.join(mergedIds.as("t"), col("rel.target").equalTo(col("t.id")), "left_outer")
+			.filter("s.id IS NOT NULL OR t.id IS NOT NULL")
+			.distinct();
 
-		long deletedbyinference = toCheck.filter(this::isDeletedByInference).count();
-		long updated = toCheck.count();
+		Dataset<Row> updatedRels = inputRels
+			.select("source", "target", "relClass")
+			.except(outputRels.select("source", "target", "relClass"));
 
-		assertEquals(updated, deletedbyinference);
+		assertEquals(toUpdateRels.count(), updatedRels.count());
+		assertEquals(140, outputRels.count());
 	}
-
-	@AfterAll
-	public static void finalCleanUp() throws IOException {
-		FileUtils.deleteDirectory(new File(testOutputBasePath));
-		FileUtils.deleteDirectory(new File(testDedupGraphBasePath));
-	}
-
-	public boolean isDeletedByInference(String s) {
-		return s.contains("\"deletedbyinference\":true");
-	}
-
 }

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

@@ -96,30 +96,7 @@
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
-            <arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>
-        </spark>
-        <ok to="dispatch_entities"/>
-        <error to="Kill"/>
-    </action>
-
-    <action name="dispatch_entities">
-        <spark xmlns="uri:oozie:spark-action:0.2">
-            <master>yarn</master>
-            <mode>cluster</mode>
-            <name>Dispatch grouped entities</name>
-            <class>eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob</class>
-            <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
-            <spark-opts>
-                --executor-cores=${sparkExecutorCores}
-                --executor-memory=${sparkExecutorMemory}
-                --driver-memory=${sparkDriverMemory}
-                --conf spark.extraListeners=${spark2ExtraListeners}
-                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
-                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
-                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
-            </spark-opts>
-            <arg>--inputPath</arg><arg>${workingPath}/grouped_entities</arg>
+            <arg>--checkpointPath</arg><arg>${workingPath}/grouped_entities</arg>
             <arg>--outputPath</arg><arg>${graphOutputPath}</arg>
             <arg>--filterInvisible</arg><arg>${filterInvisible}</arg>
         </spark>

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/group/GroupEntitiesSparkJobTest.java

@@ -1,16 +1,15 @@
 
 package eu.dnetlib.dhp.oa.graph.group;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
-
-import java.io.IOException;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.utils.DHPUtils;
 import org.apache.commons.io.FileUtils;
-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;
@@ -19,118 +18,108 @@ import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.junit.jupiter.api.*;
 
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
+import java.io.IOException;
+import java.net.URISyntaxException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.oa.merge.DispatchEntitiesSparkJob;
-import eu.dnetlib.dhp.oa.merge.GroupEntitiesSparkJob;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.utils.DHPUtils;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
 public class GroupEntitiesSparkJobTest {
 
-	private static SparkSession spark;
+    private static SparkSession spark;
 
-	private static ObjectMapper mapper = new ObjectMapper()
-		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
+    private static ObjectMapper mapper = new ObjectMapper()
+            .configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
-	private static Path workingDir;
-	private Path dataInputPath;
+    private static Path workingDir;
+    private Path dataInputPath;
 
-	private Path groupEntityPath;
-	private Path dispatchEntityPath;
+    private Path checkpointPath;
 
-	@BeforeAll
-	public static void beforeAll() throws IOException {
-		workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
+    private Path outputPath;
 
-		SparkConf conf = new SparkConf();
-		conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
-		conf.setMaster("local");
-		conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
-		conf.registerKryoClasses(ModelSupport.getOafModelClasses());
-		spark = SparkSession.builder().config(conf).getOrCreate();
-	}
+    @BeforeAll
+    public static void beforeAll() throws IOException {
+        workingDir = Files.createTempDirectory(GroupEntitiesSparkJob.class.getSimpleName());
 
-	@BeforeEach
-	public void beforeEach() throws IOException, URISyntaxException {
-		dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
-		groupEntityPath = workingDir.resolve("grouped_entity");
-		dispatchEntityPath = workingDir.resolve("dispatched_entity");
-	}
+        SparkConf conf = new SparkConf();
+        conf.setAppName(GroupEntitiesSparkJob.class.getSimpleName());
+        conf.setMaster("local");
+        conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
+        conf.registerKryoClasses(ModelSupport.getOafModelClasses());
+        spark = SparkSession.builder().config(conf).getOrCreate();
+    }
 
-	@AfterAll
-	public static void afterAll() throws IOException {
-		spark.stop();
-		FileUtils.deleteDirectory(workingDir.toFile());
-	}
+    @BeforeEach
+    public void beforeEach() throws IOException, URISyntaxException {
+        dataInputPath = Paths.get(ClassLoader.getSystemResource("eu/dnetlib/dhp/oa/graph/group").toURI());
+        checkpointPath = workingDir.resolve("grouped_entity");
+        outputPath = workingDir.resolve("dispatched_entity");
+    }
 
-	@Test
-	@Order(1)
-	void testGroupEntities() throws Exception {
-		GroupEntitiesSparkJob.main(new String[] {
-			"-isSparkSessionManaged",
-			Boolean.FALSE.toString(),
-			"-graphInputPath",
-			dataInputPath.toString(),
-			"-outputPath",
-			groupEntityPath.toString()
-		});
+    @AfterAll
+    public static void afterAll() throws IOException {
+        spark.stop();
+        FileUtils.deleteDirectory(workingDir.toFile());
+    }
 
-		Dataset<Result> output = spark
-			.read()
-			.textFile(groupEntityPath.toString())
-			.map((MapFunction<String, String>) s -> StringUtils.substringAfter(s, "|"), Encoders.STRING())
-			.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
+    @Test
+    @Order(1)
+    void testGroupEntities() throws Exception {
+        GroupEntitiesSparkJob.main(new String[]{
+                "-isSparkSessionManaged",
+                Boolean.FALSE.toString(),
+                "-graphInputPath",
+                dataInputPath.toString(),
+                "-checkpointPath",
+                checkpointPath.toString(),
+                "-outputPath",
+                outputPath.toString(),
+                "-filterInvisible",
+                Boolean.FALSE.toString()
+        });
 
-		assertEquals(
-			1,
-			output
-				.filter(
-					(FilterFunction<Result>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
-						.equals(r.getId()) &&
-						r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
-				.count());
-	}
+        Dataset<OafEntity> checkpointTable = spark
+                .read()
+                .load(checkpointPath.toString())
+                .selectExpr("COALESCE(*)")
+                .as(Encoders.kryo(OafEntity.class));
 
-	@Test
-	@Order(2)
-	void testDispatchEntities() throws Exception {
-		DispatchEntitiesSparkJob.main(new String[] {
-			"-isSparkSessionManaged",
-			Boolean.FALSE.toString(),
-			"-inputPath",
-			groupEntityPath.toString(),
-			"-outputPath",
-			dispatchEntityPath.resolve(".").toString(),
-			"-filterInvisible",
-			Boolean.TRUE.toString()
-		});
 
-		Dataset<Result> output = spark
-			.read()
-			.textFile(
-				DHPUtils
-					.toSeq(
-						HdfsSupport
-							.listFiles(dispatchEntityPath.toString(), spark.sparkContext().hadoopConfiguration())))
-			.map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
+        assertEquals(
+                1,
+                checkpointTable
+                        .filter(
+                                (FilterFunction<OafEntity>) r -> "50|doi_________::09821844208a5cd6300b2bfb13bca1b9"
+                                        .equals(r.getId()) &&
+                                        r.getCollectedfrom().stream().anyMatch(kv -> kv.getValue().equalsIgnoreCase("zenodo")))
+                        .count());
 
-		assertEquals(3, output.count());
-		assertEquals(
-			2,
-			output
-				.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
-				.filter((FilterFunction<String>) s -> s.equals("publication"))
-				.count());
-		assertEquals(
-			1,
-			output
-				.map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
-				.filter((FilterFunction<String>) s -> s.equals("dataset"))
-				.count());
-	}
-}
+
+        Dataset<Result> output = spark
+                .read()
+                .textFile(
+                        DHPUtils
+                                .toSeq(
+                                        HdfsSupport
+                                                .listFiles(outputPath.toString(), spark.sparkContext().hadoopConfiguration())))
+                .map((MapFunction<String, Result>) s -> mapper.readValue(s, Result.class), Encoders.bean(Result.class));
+
+        assertEquals(3, output.count());
+        assertEquals(
+                2,
+                output
+                        .map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
+                        .filter((FilterFunction<String>) s -> s.equals("publication"))
+                        .count());
+        assertEquals(
+                1,
+                output
+                        .map((MapFunction<Result, String>) r -> r.getResulttype().getClassid(), Encoders.STRING())
+                        .filter((FilterFunction<String>) s -> s.equals("dataset"))
+                        .count());
+    }
+}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/DownloadCsvTest.java

@@ -49,7 +49,7 @@ public class DownloadCsvTest {
 	@Test
 	void getUnibiFileTest() throws CollectorException, IOException, ClassNotFoundException {
 
-		String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv";
+		String fileURL = "https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_5.csv";
 
 		final String outputFile = workingDir + "/unibi_gold.json";
 		new DownloadCSV()

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java

@@ -1067,6 +1067,28 @@ class MappersTest {
 		System.out.println("***************");
 	}
 
+	@Test
+	public void testD4ScienceTraining() throws IOException {
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-1-training.xml")));
+		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
+		final OtherResearchProduct trainingMaterial = (OtherResearchProduct) list.get(0);
+		System.out.println("***************");
+		System.out.println(new ObjectMapper().writeValueAsString(trainingMaterial));
+		System.out.println("***************");
+	}
+
+	@Test
+	public void testD4ScienceDataset() throws IOException {
+		final String xml = IOUtils
+			.toString(Objects.requireNonNull(getClass().getResourceAsStream("d4science-2-dataset.xml")));
+		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
+		final Dataset trainingMaterial = (Dataset) list.get(0);
+		System.out.println("***************");
+		System.out.println(new ObjectMapper().writeValueAsString(trainingMaterial));
+		System.out.println("***************");
+	}
+
 	@Test
 	void testNotWellFormed() throws IOException {
 		final String xml = IOUtils

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/d4science-1-training.xml

@@ -0,0 +1,93 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<oai:record xmlns:dr="http://www.driver-repository.eu/namespace/dr"
+            xmlns:dri="http://www.driver-repository.eu/namespace/dri"
+            xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:oai="http://www.openarchives.org/OAI/2.0/">
+    <oai:header>
+        <dri:objIdentifier>alessia_____::104c2d4ba8878c16fa824dce5b1bea57</dri:objIdentifier>
+        <dri:recordIdentifier>12d8f77e-d66f-46f5-8d88-af7db23bc4c9</dri:recordIdentifier>
+        <dri:dateOfCollection>2023-09-08T10:12:35.864+02:00</dri:dateOfCollection>
+        <oaf:datasourceprefix>alessia_____</oaf:datasourceprefix>
+        <dr:dateOfTransformation>2023-09-08T11:31:45.692+02:00</dr:dateOfTransformation>
+    </oai:header>
+    <oai:metadata>
+        <datacite:resource
+                xmlns:datacite="http://datacite.org/schema/kernel-4"
+                xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
+            <datacite:identifier identifierType="URL">http://data.d4science.org/ctlg/ResourceCatalogue/visual_analytics_for_data_scientists</datacite:identifier>
+            <datacite:alternateIdentifiers/>
+            <datacite:creators>
+                <datacite:creator>
+                    <datacite:creatorName>BRAGHIERI MARCO</datacite:creatorName>
+                </datacite:creator>
+            </datacite:creators>
+            <datacite:titles>
+                <datacite:title>Visual Analytics for Data Scientists</datacite:title>
+            </datacite:titles>
+            <datacite:publisher>SoBigData++</datacite:publisher>
+            <datacite:publicationYear/>
+            <datacite:dates>
+                <datacite:date dateType="Issued"/>
+            </datacite:dates>
+            <datacite:resourceType resourceTypeGeneral="TrainingMaterial">TrainingMaterial</datacite:resourceType>
+            <datacite:descriptions>
+                <datacite:description descriptionType="Abstract">Participants to this module shall
+                    -    Learn the principles and rules underlying the design of visual data
+                    representations and human-computer interactions
+                    -    Understand, adapt and apply representative visual analytics methods and systems for diverse types
+                    of data and problems
+                    -    Analyse and evaluate the structure and properties
+                    of data to select or devise appropriate methods for data exploration
+                    -    Combine visualization, interactive techniques, and computational
+                    processing to develop practical data analysis for problem solving
+
+                    (This teaching material on Visual Analytics for Data Scientists is part of a MSc module at City University London).
+
+                    The author did not intend to violate any copyright on figures or content. In case you are the legal owner of any copyrighted content, please contact info@sobigdata.eu and we will immediately remove it</datacite:description>
+            </datacite:descriptions>
+            <datacite:subjects>
+                <datacite:subject>Visual analytics</datacite:subject>
+            </datacite:subjects>
+            <datacite:formats>
+                <datacite:format>Slides</datacite:format>
+                <datacite:format>Other</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>PDF</datacite:format>
+                <datacite:format>ZIP</datacite:format>
+            </datacite:formats>
+        </datacite:resource>
+        <oaf:accessrights>OPEN</oaf:accessrights>
+        <dr:CobjCategory type="other">0010</dr:CobjCategory>
+        <oaf:dateAccepted/>
+        <oaf:hostedBy id="alessia_____::alessia" name="Alessia"/>
+        <oaf:collectedFrom id="alessia_____::alessia" name="Alessia"/>
+        <oaf:license>other-open</oaf:license>
+        <oaf:projectid>corda__h2020::871042</oaf:projectid>
+    </oai:metadata>
+    <about xmlns:dc="http://purl.org/dc/elements/1.1/"
+           xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+        <provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
+            <originDescription altered="true" harvestDate="2023-09-08T10:12:35.864+02:00">
+                <baseURL>https%3A%2F%2Fapi.d4science.org%2Fcatalogue%2Fitems</baseURL>
+                <identifier/>
+                <datestamp/>
+                <metadataNamespace/>
+            </originDescription>
+        </provenance>
+        <oaf:datainfo>
+            <oaf:inferred>false</oaf:inferred>
+            <oaf:deletedbyinference>false</oaf:deletedbyinference>
+            <oaf:trust>0.9</oaf:trust>
+            <oaf:inferenceprovenance/>
+            <oaf:provenanceaction classid="sysimport:crosswalk"
+                                  classname="Harvested" schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
+        </oaf:datainfo>
+    </about>
+</oai:record>

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/d4science-2-dataset.xml

@@ -0,0 +1,72 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<oai:record xmlns:dr="http://www.driver-repository.eu/namespace/dr"
+            xmlns:dri="http://www.driver-repository.eu/namespace/dri"
+            xmlns:oaf="http://namespace.openaire.eu/oaf" xmlns:oai="http://www.openarchives.org/OAI/2.0/">
+    <oai:header>
+        <dri:objIdentifier>alessia_____::028879484548f4e1c630e1c503e35231</dri:objIdentifier>
+        <dri:recordIdentifier>4fed018e-c2ff-4afa-b7b5-1ca1beebf850</dri:recordIdentifier>
+        <dri:dateOfCollection>2023-09-08T12:14:27.615+02:00</dri:dateOfCollection>
+        <oaf:datasourceprefix>alessia_____</oaf:datasourceprefix>
+        <dr:dateOfTransformation>2023-09-08T12:14:51.7+02:00</dr:dateOfTransformation>
+    </oai:header>
+    <oai:metadata>
+        <datacite:resource
+                xmlns:datacite="http://datacite.org/schema/kernel-4"
+                xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
+            <datacite:identifier identifierType="URL">http://data.d4science.org/ctlg/ResourceCatalogue/city-to-city_migration</datacite:identifier>
+            <datacite:alternateIdentifiers>
+                <datacite:alternateIdentifier type="URL"/>
+            </datacite:alternateIdentifiers>
+            <datacite:creators>
+                <datacite:creator>
+                    <datacite:creatorName>Pappalardo, Luca</datacite:creatorName>
+                    <datacite:affiliation/>
+                    <datacite:nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org">0000-0002-1547-6007</datacite:nameIdentifier>
+                </datacite:creator>
+            </datacite:creators>
+            <datacite:titles>
+                <datacite:title>City-to-city migration</datacite:title>
+            </datacite:titles>
+            <datacite:publisher>SoBigData++</datacite:publisher>
+            <datacite:publicationYear/>
+            <datacite:dates>
+                <datacite:date dateType="Issued">2018-02-15</datacite:date>
+            </datacite:dates>
+            <datacite:resourceType resourceTypeGeneral="Dataset">Dataset</datacite:resourceType>
+            <datacite:descriptions>
+                <datacite:description descriptionType="Abstract">Census data recording the migration of people between metropolitan areas in
+                    the US</datacite:description>
+            </datacite:descriptions>
+            <datacite:subjects>
+                <datacite:subject>Human Mobility data</datacite:subject>
+            </datacite:subjects>
+            <datacite:formats/>
+        </datacite:resource>
+        <oaf:accessrights>OPEN</oaf:accessrights>
+        <dr:CobjCategory type="dataset">0021</dr:CobjCategory>
+        <oaf:dateAccepted>2018-02-15</oaf:dateAccepted>
+        <oaf:hostedBy id="alessia_____::alessia" name="Alessia"/>
+        <oaf:collectedFrom id="alessia_____::alessia" name="Alessia"/>
+        <oaf:license>AFL-3.0</oaf:license>
+        <oaf:projectid>corda__h2020::871042</oaf:projectid>
+    </oai:metadata>
+    <about xmlns:dc="http://purl.org/dc/elements/1.1/"
+           xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+        <provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
+            <originDescription altered="true" harvestDate="2023-09-08T12:14:27.615+02:00">
+                <baseURL>https%3A%2F%2Fapi.d4science.org%2Fcatalogue%2Fitems</baseURL>
+                <identifier/>
+                <datestamp/>
+                <metadataNamespace/>
+            </originDescription>
+        </provenance>
+        <oaf:datainfo>
+            <oaf:inferred>false</oaf:inferred>
+            <oaf:deletedbyinference>false</oaf:deletedbyinference>
+            <oaf:trust>0.9</oaf:trust>
+            <oaf:inferenceprovenance/>
+            <oaf:provenanceaction classid="sysimport:crosswalk"
+                                  classname="Harvested" schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
+        </oaf:datainfo>
+    </about>
+</oai:record>

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

@@ -24,10 +24,7 @@ import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
 import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
 import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
 import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
-import eu.dnetlib.dhp.schema.oaf.Datasource;
-import eu.dnetlib.dhp.schema.oaf.Project;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.*;
 
 public class XmlRecordFactoryTest {
 
@@ -196,4 +193,51 @@ public class XmlRecordFactoryTest {
 		assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemeid").getValue());
 		assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemename").getValue());
 	}
+
+	@Test
+	public void testD4ScienceTraining() throws DocumentException, IOException {
+		final ContextMapper contextMapper = new ContextMapper();
+
+		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
+			XmlConverterJob.schemaLocation);
+
+		final OtherResearchProduct p = OBJECT_MAPPER
+			.readValue(
+				IOUtils.toString(getClass().getResourceAsStream("d4science-1-training.json")),
+				OtherResearchProduct.class);
+
+		final String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
+
+		assertNotNull(xml);
+
+		final Document doc = new SAXReader().read(new StringReader(xml));
+
+		assertNotNull(doc);
+		System.out.println(doc.asXML());
+
+	}
+
+	@Test
+	public void testD4ScienceDataset() throws DocumentException, IOException {
+		final ContextMapper contextMapper = new ContextMapper();
+
+		final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
+			XmlConverterJob.schemaLocation);
+
+		final OtherResearchProduct p = OBJECT_MAPPER
+			.readValue(
+				IOUtils.toString(getClass().getResourceAsStream("d4science-2-dataset.json")),
+				OtherResearchProduct.class);
+
+		final String xml = xmlRecordFactory.build(new JoinedEntity<>(p));
+
+		assertNotNull(xml);
+
+		final Document doc = new SAXReader().read(new StringReader(xml));
+
+		assertNotNull(doc);
+		System.out.println(doc.asXML());
+
+	}
+
 }

dhp-workflows/dhp-impact-indicators/src/main/resources/eu/dnetlib/dhp/oa/graph/impact_indicators/oozie_app/workflow.xml

@@ -39,7 +39,8 @@
 		<switch>
 			<!-- The default will be set as the normal start, a.k.a. get-doi-synonyms -->
 			<!-- If any different condition is set, go to the corresponding start -->
-			<case to="non-iterative-rankings">${wf:conf('resume') eq "rankings-start"}</case>
+			<case to="spark-cc">${wf:conf('resume') eq "cc"}</case>
+			<case to="spark-ram">${wf:conf('resume') eq "ram"}</case>
 			<case to="spark-impulse">${wf:conf('resume') eq "impulse"}</case>
 			<case to="spark-pagerank">${wf:conf('resume') eq "pagerank"}</case>
 			<case to="spark-attrank">${wf:conf('resume') eq "attrank"}</case>
@@ -89,18 +90,11 @@
 			<file>${nameNode}${wfAppPath}/create_openaire_ranking_graph.py#create_openaire_ranking_graph.py</file>
 		</spark>
 
-		<ok to="non-iterative-rankings" />
+		<ok to="spark-cc"/>
 		<error to="openaire-graph-error" />
 
 	</action>
 
-	<!-- Citation Count and RAM are calculated in parallel-->
-	<fork name="non-iterative-rankings">
-		<path start="spark-cc"/>
-		<!-- <path start="spark-impulse"/> -->
-		<path start="spark-ram"/>
-	</fork>
-
 	<!-- Run Citation Count calculation -->
 	<action name="spark-cc">
 		<spark xmlns="uri:oozie:spark-action:0.2">
@@ -129,7 +123,7 @@
 			<file>${wfAppPath}/bip-ranker/CC.py#CC.py</file>
 		</spark>
 
-		<ok to="join-non-iterative-rankings" />
+		<ok to="spark-ram" />
 		<error to="cc-fail" />
 
 	</action>
@@ -165,14 +159,11 @@
 			<file>${wfAppPath}/bip-ranker/TAR.py#TAR.py</file>
 		</spark>
 
-		<ok to="join-non-iterative-rankings" />
+		<ok to="spark-impulse" />
 		<error to="ram-fail" />
 
 	</action>
 
-	<!-- Join non-iterative methods -->
-	<join name="join-non-iterative-rankings" to="spark-impulse"/>
-
 	<action name="spark-impulse">
 		<spark xmlns="uri:oozie:spark-action:0.2">
 

pom.xml

@@ -112,6 +112,16 @@
 			<url>https://maven.d4science.org/nexus/content/repositories/dnet-deps</url>
 			<layout>default</layout>
 		</repository>
+		<repository>
+			<id>maven-restlet</id>
+			<name>Restlet repository</name>
+			<url>https://maven.restlet.talend.com</url>
+		</repository>
+		<repository>
+			<id>conjars</id>
+			<name>conjars</name>
+			<url>https://conjars.wensel.net/repo/</url>
+		</repository>
 	</repositories>
 
 	<dependencies>