Merge remote-tracking branch 'origin/beta' into crossref_mapping_improvement

.gitignore

@@ -28,3 +28,4 @@ spark-warehouse
 /**/.scalafmt.conf
 /.java-version
 /dhp-shade-package/dependency-reduced-pom.xml
+/**/job.properties

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

@@ -2,8 +2,7 @@
 package eu.dnetlib.dhp.oa.merge;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-import static org.apache.spark.sql.functions.col;
+import static org.apache.spark.sql.functions.*;
-import static org.apache.spark.sql.functions.when;
 
 import java.util.Map;
 import java.util.Optional;
@@ -135,7 +134,9 @@ public class GroupEntitiesSparkJob {
 					.applyCoarVocabularies(entity, vocs),
 				OAFENTITY_KRYO_ENC)
 			.groupByKey((MapFunction<OafEntity, String>) OafEntity::getId, Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, OafEntity, OafEntity>) MergeUtils::mergeById, OAFENTITY_KRYO_ENC)
+			.mapGroups(
+				(MapGroupsFunction<String, OafEntity, OafEntity>) (key, group) -> MergeUtils.mergeById(group, vocs),
+				OAFENTITY_KRYO_ENC)
 			.map(
 				(MapFunction<OafEntity, Tuple2<String, OafEntity>>) t -> new Tuple2<>(
 					t.getClass().getName(), t),

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java

@@ -2,7 +2,6 @@
 package eu.dnetlib.dhp.schema.oaf.utils;
 
 import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
 
 import java.net.MalformedURLException;
@@ -696,6 +695,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						}
 					}
 
+					// set ORCID_PENDING to all orcid values that are not coming from ORCID provenance
 					for (Author a : r.getAuthor()) {
 						if (Objects.isNull(a.getPid())) {
 							a.setPid(Lists.newArrayList());
@@ -752,6 +752,40 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 										.collect(Collectors.toList()));
 						}
 					}
+
+					// Identify clashing ORCIDS:that is same ORCID associated to multiple authors in this result
+					Map<String, Integer> clashing_orcid = new HashMap<>();
+
+					for (Author a : r.getAuthor()) {
+						a
+							.getPid()
+							.stream()
+							.filter(
+								p -> StringUtils
+									.contains(StringUtils.lowerCase(p.getQualifier().getClassid()), ORCID_PENDING))
+							.map(StructuredProperty::getValue)
+							.distinct()
+							.forEach(orcid -> clashing_orcid.compute(orcid, (k, v) -> (v == null) ? 1 : v + 1));
+					}
+
+					Set<String> clashing = clashing_orcid
+						.entrySet()
+						.stream()
+						.filter(ee -> ee.getValue() > 1)
+						.map(Map.Entry::getKey)
+						.collect(Collectors.toSet());
+
+					// filter out clashing orcids
+					for (Author a : r.getAuthor()) {
+						a
+							.setPid(
+								a
+									.getPid()
+									.stream()
+									.filter(p -> !clashing.contains(p.getValue()))
+									.collect(Collectors.toList()));
+					}
+
 				}
 				if (value instanceof Publication) {
 

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java

@@ -23,24 +23,30 @@ import org.apache.commons.lang3.tuple.Pair;
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.base.Joiner;
 
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.common.AccessRightComparator;
+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.*;
 
 public class MergeUtils {
 
-	public static <T extends Oaf> T mergeById(String s, Iterator<T> oafEntityIterator) {
+	public static <T extends Oaf> T mergeById(Iterator<T> oafEntityIterator, VocabularyGroup vocs) {
-		return mergeGroup(s, oafEntityIterator, true);
+		return mergeGroup(oafEntityIterator, true, vocs);
 	}
 
-	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator) {
+	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator) {
-		return mergeGroup(s, oafEntityIterator, false);
+		return mergeGroup(oafEntityIterator, false);
 	}
 
-	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
+	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator, boolean checkDelegateAuthority) {
-		boolean checkDelegateAuthority) {
+		return mergeGroup(oafEntityIterator, checkDelegateAuthority, null);
+	}
+
+	public static <T extends Oaf> T mergeGroup(Iterator<T> oafEntityIterator,
+		boolean checkDelegateAuthority, VocabularyGroup vocs) {
 
 		ArrayList<T> sortedEntities = new ArrayList<>();
 		oafEntityIterator.forEachRemaining(sortedEntities::add);
@@ -49,13 +55,55 @@ public class MergeUtils {
 		Iterator<T> it = sortedEntities.iterator();
 		T merged = it.next();
 
-		while (it.hasNext()) {
+		if (!it.hasNext() && merged instanceof Result && vocs != null) {
-			merged = checkedMerge(merged, it.next(), checkDelegateAuthority);
+			return enforceResultType(vocs, (Result) merged);
+		} else {
+			while (it.hasNext()) {
+				merged = checkedMerge(merged, it.next(), checkDelegateAuthority);
+			}
 		}
-
 		return merged;
 	}
 
+	private static <T extends Oaf> T enforceResultType(VocabularyGroup vocs, Result mergedResult) {
+		if (Optional.ofNullable(mergedResult.getInstance()).map(List::isEmpty).orElse(true)) {
+			return (T) mergedResult;
+		} else {
+			final Instance i = mergedResult.getInstance().get(0);
+
+			if (!vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
+				return (T) mergedResult;
+			} else {
+				final String expectedResultType = Optional
+					.ofNullable(
+						vocs
+							.lookupTermBySynonym(
+								ModelConstants.DNET_RESULT_TYPOLOGIES, i.getInstancetype().getClassid()))
+					.orElse(ModelConstants.ORP_DEFAULT_RESULTTYPE)
+					.getClassid();
+
+				// there is a clash among the result types
+				if (!expectedResultType.equals(mergedResult.getResulttype().getClassid())) {
+
+					Result result = (Result) Optional
+						.ofNullable(ModelSupport.oafTypes.get(expectedResultType))
+						.map(r -> {
+							try {
+								return r.newInstance();
+							} catch (InstantiationException | IllegalAccessException e) {
+								throw new IllegalStateException(e);
+							}
+						})
+						.orElse(new OtherResearchProduct());
+					result.setId(mergedResult.getId());
+					return (T) mergeResultFields(result, mergedResult);
+				} else {
+					return (T) mergedResult;
+				}
+			}
+		}
+	}
+
 	public static <T extends Oaf> T checkedMerge(final T left, final T right, boolean checkDelegateAuthority) {
 		return (T) merge(left, right, checkDelegateAuthority);
 	}
@@ -106,7 +154,7 @@ public class MergeUtils {
 				return mergeSoftware((Software) left, (Software) right);
 			}
 
-			return mergeResultFields((Result) left, (Result) right);
+			return left;
 		} else if (sameClass(left, right, Datasource.class)) {
 			// TODO
 			final int trust = compareTrust(left, right);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java

@@ -104,22 +104,22 @@ public class PrepareAffiliationRelations implements Serializable {
 			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 
 		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelationsNewModel(
-			spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::crossref");
+			spark, crossrefInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":crossref");
 
 		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-			spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::pubmed");
+			spark, pubmedInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":pubmed");
 
 		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelationsNewModel(
-			spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::openapc");
+			spark, openapcInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":openapc");
 
 		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelationsNewModel(
-			spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::datacite");
+			spark, dataciteInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":datacite");
 
 		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelationsNewModel(
-			spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::rawaff");
+			spark, webcrawlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":rawaff");
 
 		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisherNewModel(
-			spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + "::webcrawl");
+			spark, publisherlInputPath, collectedfromOpenAIRE, BIP_INFERENCE_PROVENANCE + ":webcrawl");
 
 		crossrefRelations
 			.union(pubmedRelations)

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/personentity/ExtractPerson.java

@@ -15,6 +15,7 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.StringUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
@@ -193,8 +194,8 @@ public class ExtractPerson implements Serializable {
 	private static Relation getProjectRelation(String project, String orcid, String role) {
 
 		String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
-		String target = PROJECT_ID_PREFIX + project.substring(0, 14)
+		String target = PROJECT_ID_PREFIX + StringUtils.substringBefore(project, "::") + "::"
-			+ IdentifierFactory.md5(project.substring(15));
+			+ IdentifierFactory.md5(StringUtils.substringAfter(project, "::"));
 		List<KeyValue> properties = new ArrayList<>();
 
 		Relation relation = OafMapperUtils
@@ -345,7 +346,16 @@ public class ExtractPerson implements Serializable {
 					OafMapperUtils
 						.structuredProperty(
 							op.getOrcid(), ModelConstants.ORCID, ModelConstants.ORCID_CLASSNAME,
-							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, null));
+							ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,
+								OafMapperUtils.dataInfo(false,
+										null,
+										false,
+										false,
+										OafMapperUtils.qualifier(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
+												ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY,
+												ModelConstants.DNET_PID_TYPES,
+												ModelConstants.DNET_PID_TYPES),
+								"0.91")));
 			person.setDateofcollection(op.getLastModifiedDate());
 			person.setOriginalId(Arrays.asList(op.getOrcid()));
 			person.setDataInfo(ORCIDDATAINFO);

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala

@@ -667,11 +667,12 @@ case object Crossref2Oaf {
     val doi = input.getString(0)
     val rorId = input.getString(1)
 
-    val pubId = s"50|${PidType.doi.toString.padTo(12, "_")}::${DoiCleaningRule.clean(doi)}"
+
+    val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true)
     val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
 
     val r: Relation = new Relation
-    DoiCleaningRule.clean(doi)
+
     r.setSource(pubId)
     r.setTarget(affId)
     r.setRelType(ModelConstants.RESULT_ORGANIZATION)
@@ -955,7 +956,26 @@ case object Crossref2Oaf {
             case "10.13039/501100010790" =>
               generateSimpleRelationFromAward(funder, "erasmusplus_", a => a)
             case _ => logger.debug("no match for " + funder.DOI.get)
-
+            //Add for Danish funders
+            //Independent Research Fund Denmark (IRFD)
+            case "10.13039/501100004836" =>
+              generateSimpleRelationFromAward(funder, "irfd________", a => a)
+              val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Carlsberg Foundation (CF)
+            case "10.13039/501100002808" =>
+              generateSimpleRelationFromAward(funder, "cf__________", a => a)
+              val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Novo Nordisk Foundation (NNF)
+            case "10.13039/501100009708" =>
+              generateSimpleRelationFromAward(funder, "nnf___________", a => a)
+              val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            case _ => logger.debug("no match for " + funder.DOI.get)
           }
 
         } else {

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

@@ -135,7 +135,7 @@ public class DedupRecordFactory {
 						return Collections.emptyIterator();
 					}
 
-					OafEntity mergedEntity = MergeUtils.mergeGroup(dedupId, cliques.iterator());
+					OafEntity mergedEntity = MergeUtils.mergeGroup(cliques.iterator());
 					// dedup records do not have date of transformation attribute
 					mergedEntity.setDateoftransformation(null);
 					mergedEntity

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

@@ -69,6 +69,7 @@ public class SparkPropagateRelation extends AbstractSparkAction {
 
 		Dataset<Relation> mergeRels = spark
 			.read()
+			.schema(REL_BEAN_ENC.schema())
 			.load(DedupUtility.createMergeRelPath(workingPath, "*", "*"))
 			.as(REL_BEAN_ENC);
 

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

@@ -46,8 +46,8 @@ class DatasetMergerTest implements Serializable {
 	}
 
 	@Test
-	void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
+	void datasetMergerTest() {
-		Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
+		Dataset pub_merged = MergeUtils.mergeGroup(datasets.stream().map(Tuple2::_2).iterator());
 
 		// verify id
 		assertEquals(dedupId, pub_merged.getId());

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -566,7 +566,26 @@ case object Crossref2Oaf {
               queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
               queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
             case _ => logger.debug("no match for " + funder.DOI.get)
-
+            //Add for Danish funders
+            //Independent Research Fund Denmark (IRFD)
+            case "10.13039/501100004836" =>
+              generateSimpleRelationFromAward(funder, "irfd________", a => a)
+              val targetId = getProjectId("irfd________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Carlsberg Foundation (CF)
+            case "10.13039/501100002808" =>
+              generateSimpleRelationFromAward(funder, "cf__________", a => a)
+              val targetId = getProjectId("cf__________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            //Novo Nordisk Foundation (NNF)
+            case "10.13039/501100009708" =>
+              generateSimpleRelationFromAward(funder, "nnf___________", a => a)
+              val targetId = getProjectId("nnf_________", "1e5e62235d094afd01cd56e65112fc63")
+              queue += generateRelation(sourceId, targetId, ModelConstants.IS_PRODUCED_BY)
+              queue += generateRelation(targetId, sourceId, ModelConstants.PRODUCES)
+            case _ => logger.debug("no match for " + funder.DOI.get)
           }
 
         } else {

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java

@@ -153,34 +153,40 @@ public abstract class AbstractMdRecordToOafMapper {
 			final DataInfo entityInfo = prepareDataInfo(doc, this.invisible);
 			final long lastUpdateTimestamp = new Date().getTime();
 
-			final List<Instance> instances = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
+			final Instance instance = prepareInstances(doc, entityInfo, collectedFrom, hostedBy);
 
-			final String type = getResultType(doc, instances);
+			if (!Optional
+				.ofNullable(instance.getInstancetype())
+				.map(Qualifier::getClassid)
+				.filter(StringUtils::isNotBlank)
+				.isPresent()) {
+				return Lists.newArrayList();
+			}
 
-			return createOafs(doc, type, instances, collectedFrom, entityInfo, lastUpdateTimestamp);
+			final String type = getResultType(instance);
+
+			return createOafs(doc, type, instance, collectedFrom, entityInfo, lastUpdateTimestamp);
 		} catch (final DocumentException e) {
 			log.error("Error with record:\n" + xml);
 			return Lists.newArrayList();
 		}
 	}
 
-	protected String getResultType(final Document doc, final List<Instance> instances) {
+	protected String getResultType(final Instance instance) {
-		final String type = doc.valueOf("//dr:CobjCategory/@type");
+		if (this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
-
-		if (StringUtils.isBlank(type) && this.vocs.vocabularyExists(ModelConstants.DNET_RESULT_TYPOLOGIES)) {
-			final String instanceType = instances
-				.stream()
-				.map(i -> i.getInstancetype().getClassid())
-				.findFirst()
-				.filter(s -> !UNKNOWN.equalsIgnoreCase(s))
-				.orElse("0000"); // Unknown
 			return Optional
-				.ofNullable(this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
+				.ofNullable(instance.getInstancetype())
 				.map(Qualifier::getClassid)
+				.map(
+					instanceType -> Optional
+						.ofNullable(
+							this.vocs.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, instanceType))
+						.map(Qualifier::getClassid)
+						.orElse("0000"))
 				.orElse("0000");
+		} else {
+			throw new IllegalStateException("Missing vocabulary: " + ModelConstants.DNET_RESULT_TYPOLOGIES);
 		}
-
-		return type;
 	}
 
 	private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) {
@@ -197,12 +203,12 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected List<Oaf> createOafs(
 		final Document doc,
 		final String type,
-		final List<Instance> instances,
+		final Instance instance,
 		final KeyValue collectedFrom,
 		final DataInfo info,
 		final long lastUpdateTimestamp) {
 
-		final OafEntity entity = createEntity(doc, type, instances, collectedFrom, info, lastUpdateTimestamp);
+		final OafEntity entity = createEntity(doc, type, instance, collectedFrom, info, lastUpdateTimestamp);
 
 		final Set<String> originalId = Sets.newHashSet(entity.getOriginalId());
 		originalId.add(entity.getId());
@@ -235,19 +241,19 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	private OafEntity createEntity(final Document doc,
 		final String type,
-		final List<Instance> instances,
+		final Instance instance,
 		final KeyValue collectedFrom,
 		final DataInfo info,
 		final long lastUpdateTimestamp) {
 		switch (type.toLowerCase()) {
 			case "publication":
 				final Publication p = new Publication();
-				populateResultFields(p, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(p, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				p.setJournal(prepareJournal(doc, info));
 				return p;
 			case "dataset":
 				final Dataset d = new Dataset();
-				populateResultFields(d, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(d, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				d.setStoragedate(prepareDatasetStorageDate(doc, info));
 				d.setDevice(prepareDatasetDevice(doc, info));
 				d.setSize(prepareDatasetSize(doc, info));
@@ -258,7 +264,7 @@ public abstract class AbstractMdRecordToOafMapper {
 				return d;
 			case "software":
 				final Software s = new Software();
-				populateResultFields(s, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(s, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
 				s.setLicense(prepareSoftwareLicenses(doc, info));
 				s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
@@ -268,7 +274,7 @@ public abstract class AbstractMdRecordToOafMapper {
 			case "otherresearchproducts":
 			default:
 				final OtherResearchProduct o = new OtherResearchProduct();
-				populateResultFields(o, doc, instances, collectedFrom, info, lastUpdateTimestamp);
+				populateResultFields(o, doc, instance, collectedFrom, info, lastUpdateTimestamp);
 				o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
 				o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
 				o.setTool(prepareOtherResearchProductTools(doc, info));
@@ -415,7 +421,7 @@ public abstract class AbstractMdRecordToOafMapper {
 	private void populateResultFields(
 		final Result r,
 		final Document doc,
-		final List<Instance> instances,
+		final Instance instance,
 		final KeyValue collectedFrom,
 		final DataInfo info,
 		final long lastUpdateTimestamp) {
@@ -449,8 +455,8 @@ public abstract class AbstractMdRecordToOafMapper {
 		r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
 		r.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
 		r.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
-		r.setInstance(instances);
+		r.setInstance(Arrays.asList(instance));
-		r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances));
+		r.setBestaccessright(OafMapperUtils.createBestAccessRights(Arrays.asList(instance)));
 		r.setEoscifguidelines(prepareEOSCIfGuidelines(doc, info));
 	}
 
@@ -509,7 +515,7 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
 
-	protected abstract List<Instance> prepareInstances(
+	protected abstract Instance prepareInstances(
 		Document doc,
 		DataInfo info,
 		KeyValue collectedfrom,

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java

@@ -133,7 +133,7 @@ public class GenerateEntitiesApplication extends AbstractMigrationApplication {
 					inputRdd
 						.keyBy(oaf -> ModelSupport.idFn().apply(oaf))
 						.groupByKey()
-						.map(t -> MergeUtils.mergeGroup(t._1, t._2.iterator())),
+						.map(t -> MergeUtils.mergeGroup(t._2.iterator())),
 					// .mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
 					// .reduceByKey(MergeUtils::merge)
 					// .map(Tuple2::_2),

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java

@@ -135,7 +135,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 	}
 
 	@Override
-	protected List<Instance> prepareInstances(
+	protected Instance prepareInstances(
 		final Document doc,
 		final DataInfo info,
 		final KeyValue collectedfrom,
@@ -197,7 +197,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 			instance.getUrl().addAll(validUrl);
 		}
 
-		return Lists.newArrayList(instance);
+		return instance;
 	}
 
 	/**

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java

@@ -126,7 +126,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	}
 
 	@Override
-	protected List<Instance> prepareInstances(
+	protected Instance prepareInstances(
 		final Document doc,
 		final DataInfo info,
 		final KeyValue collectedfrom,
@@ -210,7 +210,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 			instance.setUrl(new ArrayList<>());
 			instance.getUrl().addAll(validUrl);
 		}
-		return Arrays.asList(instance);
+		return instance;
 	}
 
 	protected String trimAndDecodeUrl(String url) {

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/enrich/orcid/oozie_app/workflow.xml

@@ -51,6 +51,7 @@
             <arg>--orcidPath</arg><arg>${orcidPath}</arg>
             <arg>--targetPath</arg><arg>${targetPath}</arg>
             <arg>--graphPath</arg><arg>${graphPath}</arg>
+            <arg>--workingDir</arg><arg>${workingDir}</arg>
             <arg>--master</arg><arg>yarn</arg>
         </spark>
         <ok to="reset_outputpath"/>

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

@@ -162,6 +162,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/publication</arg>
@@ -197,6 +198,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=8000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/dataset</arg>
@@ -232,6 +234,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=5000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/otherresearchproduct</arg>
@@ -267,6 +270,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/software</arg>
@@ -302,6 +306,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/datasource</arg>
@@ -337,6 +342,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=1000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/organization</arg>
@@ -372,6 +378,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/project</arg>
@@ -407,6 +414,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=2000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/person</arg>
@@ -442,6 +450,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.autoBroadcastJoinThreshold=-1
                 --conf spark.sql.shuffle.partitions=20000
             </spark-opts>
             <arg>--inputPath</arg><arg>${graphInputPath}/relation</arg>

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

@@ -133,7 +133,7 @@ object SparkCreateInputGraph {
     val ds: Dataset[T] = spark.read.load(sourcePath).as[T]
 
     ds.groupByKey(_.getId)
-      .mapGroups { (id, it) => MergeUtils.mergeGroup(id, it.asJava).asInstanceOf[T] }
+      .mapGroups { (id, it) => MergeUtils.mergeGroup(it.asJava).asInstanceOf[T] }
 //      .reduceGroups { (x: T, y: T) => MergeUtils.merge(x, y).asInstanceOf[T] }
 //      .map(_)
       .write