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

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

@@ -139,12 +139,26 @@ abstract class AbstractSparkAction implements Serializable {
 	protected boolean isOpenorgs(Relation rel) {
 		return Optional
 			.ofNullable(rel.getCollectedfrom())
-			.map(
+			.map(c -> isCollectedFromOpenOrgs(c))
-				c -> c
+			.orElse(false);
+	}
+
+	protected boolean isOpenorgsDedupRel(Relation rel) {
+		return isOpenorgs(rel) && isOpenOrgsDedupMergeRelation(rel);
+	}
+
+	private boolean isCollectedFromOpenOrgs(List<KeyValue> c) {
+		return c
 			.stream()
 			.filter(Objects::nonNull)
-					.anyMatch(kv -> ModelConstants.OPENORGS_NAME.equals(kv.getValue())))
+			.anyMatch(kv -> ModelConstants.OPENORGS_NAME.equals(kv.getValue()));
-			.orElse(false);
+	}
+
+	private boolean isOpenOrgsDedupMergeRelation(Relation rel) {
+		return ModelConstants.ORG_ORG_RELTYPE.equals(rel.getRelType()) &&
+			ModelConstants.DEDUP.equals(rel.getSubRelType())
+			&& (ModelConstants.IS_MERGED_IN.equals(rel.getRelClass()) ||
+				ModelConstants.MERGES.equals(rel.getRelClass()));
 	}
 
 	protected static Boolean parseECField(Field<String> field) {

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

@@ -61,7 +61,7 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction {
 			.textFile(relationPath)
 			.map(patchRelFn(), Encoders.bean(Relation.class))
 			.toJavaRDD()
-			.filter(x -> !isOpenorgs(x));
+			.filter(x -> !isOpenorgsDedupRel(x));
 
 		if (log.isDebugEnabled()) {
 			log.debug("Number of non-Openorgs relations collected: {}", simRels.count());

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

@@ -11,6 +11,8 @@ import java.io.IOException;
 import java.io.Serializable;
 import java.net.URISyntaxException;
 import java.nio.file.Paths;
+import java.util.List;
+import java.util.stream.Collectors;
 
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
@@ -29,6 +31,8 @@ import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
@@ -226,9 +230,10 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 
 		new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService);
 
-		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
+		final JavaRDD<String> rels = jsc.textFile(testDedupGraphBasePath + "/relation");
+
+		assertEquals(2382, rels.count());
 
-		assertEquals(2380, relations);
 	}
 
 	@Test
@@ -250,7 +255,7 @@ public class SparkOpenorgsProvisionTest implements Serializable {
 
 		long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count();
 
-		assertEquals(4894, relations);
+		assertEquals(4896, relations);
 
 		// check deletedbyinference
 		final Dataset<Relation> mergeRels = spark

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/openorgs/provision/relation/part-00000

@@ -2518,3 +2518,5 @@
 {"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::5c351d85f02db01ca291acd119f0bd78", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|opendoar____::37248e2f6987b18670dd2b8a51d6ef55", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
 {"subRelType": "dedup", "relClass": "merges", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
 {"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
+{"subRelType": "relationship", "relClass": "IsParentOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}
+{"subRelType": "relationship", "relClass": "IsChildOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []}