Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop

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

@@ -15,7 +15,7 @@
   "official_name": "Aperta TÜBİTAK Open Archive"
  },
  "BL.CAM": {
-  "openaire_id": "re3data_____::r3d100010620",
+  "openaire_id": "opendoar____::109",
   "datacite_name": "Apollo",
   "official_name": "Apollo"
  },
@@ -196,7 +196,7 @@
  },
  "CSIC.DIGITAL": {
   "openaire_id": "re3data_____::r3d100011076",
-  "datacite_name": "DIGITAL.CSIC",
+  "datacite_name": "Digital CSIC",
   "official_name": "DIGITAL.CSIC"
  },
  "BL.DRI": {
@@ -644,6 +644,11 @@
   "datacite_name": "PANGAEA",
   "official_name": "PANGAEA"
  },
+ "TIB.PANGAEA": {
+  "openaire_id": "re3data_____::r3d100010134",
+  "datacite_name": "PANGAEA",
+  "official_name": "PANGAEA"
+ },
  "NASAPDS.NASAPDS": {
   "openaire_id": "re3data_____::r3d100010121",
   "datacite_name": "PDS",
@@ -896,7 +901,7 @@
  },
  "FIGSHARE.UCT": {
   "openaire_id": "re3data_____::r3d100012633",
-  "datacite_name": "ZivaHub",
+  "datacite_name": "University of Cape Town (UCT)",
   "official_name": "ZivaHub"
  },
  "BL.UCLAN": {
@@ -1030,9 +1035,9 @@
   "official_name": "ZBW Journal Data Archive"
  },
  "CERN.ZENODO": {
-  "openaire_id": "re3data_____::r3d100010468",
+  "openaire_id": "opendoar____::2659",
   "datacite_name": "Zenodo",
-  "official_name": "Zenodo"
+  "official_name": "ZENODO"
  },
  "ZBW.ZEW": {
   "openaire_id": "re3data_____::r3d100010399",

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

@@ -60,7 +60,7 @@ object SparkGenerateDoiBoost {
     val openaireOrganizationPath = parser.get("openaireOrganizationPath")
 
     val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable {
-      override def zero: Publication = new Publication
+      override def zero: Publication = null
 
       override def reduce(b: Publication, a: (String, Publication)): Publication = {
 
@@ -177,8 +177,33 @@ object SparkGenerateDoiBoost {
       .map(DoiBoostMappingUtil.fixPublication)
       .map(p => (p.getId, p))
       .groupByKey(_._1)
-      .agg(crossrefAggregator.toColumn)
-      .map(p => p._2)
+      .reduceGroups((left, right) => {
+        //Check left is not  null
+        if (left != null && left._1 != null) {
+          //If right is null then return left
+          if (right == null || right._2 == null)
+            left
+          else {
+            // Here Left and Right are not null
+            // So we have to merge
+            val b1 = left._2
+            val b2 = right._2
+            b1.mergeFrom(b2)
+            b1.mergeOAFDataInfo(b2)
+            val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
+            b1.setAuthor(authors)
+            if (b2.getId != null && b2.getId.nonEmpty)
+              b1.setId(b2.getId)
+            //Return publication Merged
+            (b1.getId, b1)
+          }
+        } else {
+          // Left is Null so we return right
+          right
+        }
+      })
+      .filter(s => s != null && s._2 != null)
+      .map(s => s._2._2)
       .write
       .mode(SaveMode.Overwrite)
       .save(s"$workingDirPath/doiBoostPublicationFiltered")

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

@@ -711,10 +711,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 			final Relation r = new Relation();
 			r.setRelType(ORG_ORG_RELTYPE);
 			r.setSubRelType(ModelConstants.RELATIONSHIP);
-			r
-				.setRelClass(
-					rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF
-						: ModelConstants.IS_CHILD_OF);
+			r.setRelClass(rs.getString("type"));
 			r.setSource(orgId1);
 			r.setTarget(orgId2);
 			r.setCollectedfrom(collectedFrom);

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

@@ -283,7 +283,15 @@
         <error to="Kill"/>
     </action>
 
-    <join name="wait_dispatch" to="copy_relation"/>
+    <join name="wait_dispatch" to="delete_target_relation"/>
+
+    <action name="delete_target_relation">
+        <fs>
+            <delete path="${nameNode}/${graphOutputPath}/relation"/>
+        </fs>
+        <ok to="copy_relation"/>
+        <error to="Kill"/>
+    </action>
 
     <action name="copy_relation">
         <distcp xmlns="uri:oozie:distcp-action:0.2">

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql

@@ -10,4 +10,4 @@ SELECT
 	'OpenOrgs Database'                                            AS collectedfromname,
 	'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction
 FROM relationships
-WHERE reltype = 'Child' OR reltype = 'Parent'
+WHERE reltype = 'IsChildOf' OR reltype = 'IsParentOf'