resolving conflicts

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java

@@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager.ror;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.ORG_ORG_RELTYPE;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues;
@@ -39,7 +38,6 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.actionmanager.ror.model.ExternalIdType;
-import eu.dnetlib.dhp.actionmanager.ror.model.Relationship;
 import eu.dnetlib.dhp.actionmanager.ror.model.RorOrganization;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
@@ -51,7 +49,6 @@ import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.Organization;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
@@ -168,38 +165,10 @@ public class GenerateRorActionSetJob {
 		final List<AtomicAction<? extends Oaf>> res = new ArrayList<>();
 		res.add(new AtomicAction<>(Organization.class, o));
 
-		for (final Relationship rorRel : r.getRelationships()) {
-			if (rorRel.getType().equalsIgnoreCase("parent")) {
-				final String orgId1 = calculateOpenaireId(r.getId());
-				final String orgId2 = calculateOpenaireId(rorRel.getId());
-				res
-					.add(
-						new AtomicAction<>(Relation.class,
-							calculateHierarchyRel(orgId1, orgId2, ModelConstants.IS_PARENT_OF)));
-				res
-					.add(
-						new AtomicAction<>(Relation.class,
-							calculateHierarchyRel(orgId2, orgId1, ModelConstants.IS_CHILD_OF)));
-			}
-		}
-
 		return res;
 
 	}
 
-	private static Relation calculateHierarchyRel(final String source, final String target, final String relClass) {
-		final Relation rel = new Relation();
-		rel.setSource(source);
-		rel.setTarget(target);
-		rel.setRelType(ORG_ORG_RELTYPE);
-		rel.setSubRelType(ModelConstants.RELATIONSHIP);
-		rel.setRelClass(relClass);
-		rel.setCollectedfrom(ROR_COLLECTED_FROM);
-		rel.setDataInfo(ROR_DATA_INFO);
-		rel.setLastupdatetimestamp(System.currentTimeMillis());
-		return rel;
-	}
-
 	private static String calculateOpenaireId(final String rorId) {
 		return String.format("20|%s::%s", ROR_NS_PREFIX, DHPUtils.md5(rorId));
 	}

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala

@@ -59,6 +59,54 @@ object SparkGenerateDoiBoost {
     val workingDirPath = parser.get("workingPath")
     val openaireOrganizationPath = parser.get("openaireOrganizationPath")
 
+    val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable {
+      override def zero: Publication = null
+
+      override def reduce(b: Publication, a: (String, Publication)): Publication = {
+
+        if (b == null) {
+          if (a != null && a._2 != null) {
+            a._2.setId(a._1)
+            return a._2
+          }
+        } else {
+          if (a != null && a._2 != null) {
+            b.mergeOAFDataInfo(a._2)
+            b.mergeFrom(a._2)
+            b.setId(a._1)
+            val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
+            b.setAuthor(authors)
+            return b
+          }
+        }
+        new Publication
+      }
+
+      override def merge(b1: Publication, b2: Publication): Publication = {
+        if (b1 == null) {
+          if (b2 != null)
+            return b2
+        } else {
+          if (b2 != null) {
+            b1.mergeOAFDataInfo(b2)
+            b1.mergeFrom(b2)
+            val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
+            b1.setAuthor(authors)
+            if (b2.getId != null && b2.getId.nonEmpty)
+              b1.setId(b2.getId)
+            return b1
+          }
+        }
+        new Publication
+      }
+
+      override def finish(reduction: Publication): Publication = reduction
+
+      override def bufferEncoder: Encoder[Publication] = Encoders.kryo[Publication]
+
+      override def outputEncoder: Encoder[Publication] = Encoders.kryo[Publication]
+    }
+
     implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
     implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
     implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
@@ -284,4 +332,4 @@ object SparkGenerateDoiBoost {
       .save(s"$workingDirPath/doiBoostOrganization")
   }
 
-}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java

@@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.util.ArrayList;
+import java.util.Objects;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -102,6 +103,7 @@ public class SparkBulkTagJob {
 		ResultTagger resultTagger = new ResultTagger();
 		readPath(spark, inputPath, resultClazz)
 			.map(patchResult(), Encoders.bean(resultClazz))
+				.filter(Objects::nonNull)
 			.map(
 				(MapFunction<R, R>) value -> resultTagger
 					.enrichContextCriteria(