IdentifierFactory: in case a record provides more than one pid of the same type, the the lexicographically lower value is chosen as best pick

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

@@ -2,7 +2,12 @@
 package eu.dnetlib.dhp.schema.oaf.utils;
 
 import java.io.Serializable;
+import java.util.List;
+import java.util.Map;
 import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.apache.commons.lang.StringUtils;
 
@@ -42,13 +47,27 @@ public class IdentifierFactory implements Serializable {
 			return entity.getId();
 		}
 
-		return entity
+		Map<String, List<StructuredProperty>> pids = entity
 				.getPid()
 				.stream()
 				.filter(s -> pidFilter(s))
+				.collect(
+						Collectors.groupingBy(p -> p.getQualifier().getClassid(),
+								Collectors.mapping(p -> p, Collectors.toList()))
+				);
+
+		return pids
+				.values()
+				.stream()
+				.flatMap(s -> s.stream())
 				.min(new PidComparator<>(entity))
+				.map(min -> Optional.ofNullable(pids.get(min.getQualifier().getClassid()))
+						.map(p -> p.stream()
+								.sorted(new PidValueComparator())
+								.findFirst()
 								.map(s -> idFromPid(entity, s))
-			.map(IdentifierFactory::verifyIdSyntax)
+								.orElseGet(entity::getId))
+						.orElseGet(entity::getId))
 				.orElseGet(entity::getId);
 	}
 

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

@@ -1,25 +1,31 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
 import java.util.Comparator;
 
-public class OrganizationPidComparator implements Comparator<PidType> {
+public class OrganizationPidComparator implements Comparator<StructuredProperty> {
 
 	@Override
-	public int compare(PidType pLeft, PidType pRight) {
+	public int compare(StructuredProperty left, StructuredProperty right) {
-		if (pLeft.equals(PidType.GRID))
+
+		PidType lClass = PidType.valueOf(left.getQualifier().getClassid());
+		PidType rClass = PidType.valueOf(right.getQualifier().getClassid());
+		
+		if (lClass.equals(PidType.GRID))
 			return -1;
-		if (pRight.equals(PidType.GRID))
+		if (rClass.equals(PidType.GRID))
 			return 1;
 
-		if (pLeft.equals(PidType.mag_id))
+		if (lClass.equals(PidType.mag_id))
 			return -1;
-		if (pRight.equals(PidType.mag_id))
+		if (rClass.equals(PidType.mag_id))
 			return 1;
 
-		if (pLeft.equals(PidType.urn))
+		if (lClass.equals(PidType.urn))
 			return -1;
-		if (pRight.equals(PidType.urn))
+		if (rClass.equals(PidType.urn))
 			return 1;
 
 		return 0;

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

@@ -27,28 +27,22 @@ public class PidComparator<T extends OafEntity> implements Comparator<Structured
 		if (right == null)
 			return -1;
 
-		PidType lClass = PidType.valueOf(left.getQualifier().getClassid());
-		PidType rClass = PidType.valueOf(right.getQualifier().getClassid());
-
-		if (lClass.equals(rClass))
-			return 0;
-
 		if (ModelSupport.isSubClass(entity, Result.class)) {
-			return compareResultPids(lClass, rClass);
+			return compareResultPids(left, right);
 		}
 		if (ModelSupport.isSubClass(entity, Organization.class)) {
-			return compareOrganizationtPids(lClass, rClass);
+			return compareOrganizationtPids(left, right);
 		}
 
 		// Else (but unlikely), lexicographical ordering will do.
-		return lClass.compareTo(rClass);
+		return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
 	}
 
-	private int compareResultPids(PidType lClass, PidType rClass) {
+	private int compareResultPids(StructuredProperty left, StructuredProperty right) {
-		return new ResultPidComparator().compare(lClass, rClass);
+		return new ResultPidComparator().compare(left, right);
 	}
 
-	private int compareOrganizationtPids(PidType lClass, PidType rClass) {
+	private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
-		return new OrganizationPidComparator().compare(lClass, rClass);
+		return new OrganizationPidComparator().compare(left, right);
 	}
 }

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

@@ -0,0 +1,35 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import eu.dnetlib.dhp.oa.graph.clean.CleaningFunctions;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+import java.util.Comparator;
+import java.util.Optional;
+
+public class PidValueComparator implements Comparator<StructuredProperty> {
+
+	@Override
+	public int compare(StructuredProperty left, StructuredProperty right) {
+
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return 1;
+		if (right == null)
+			return -1;
+
+		StructuredProperty l = CleaningFunctions.normalizePidValue(left);
+		StructuredProperty r = CleaningFunctions.normalizePidValue(right);
+
+		return Optional.ofNullable(l.getValue())
+				.map(lv -> Optional.ofNullable(r.getValue())
+						.map(rv -> lv.compareTo(rv))
+						.orElse(-1))
+				.orElse(1);
+	}
+}

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

@@ -1,55 +1,61 @@
 
 package eu.dnetlib.dhp.schema.oaf.utils;
 
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
 import java.util.Comparator;
 
-public class ResultPidComparator implements Comparator<PidType> {
+public class ResultPidComparator implements Comparator<StructuredProperty> {
 
 	@Override
-	public int compare(PidType pLeft, PidType pRight) {
+	public int compare(StructuredProperty left, StructuredProperty right) {
-		if (pLeft.equals(PidType.doi))
+
+		PidType lClass = PidType.valueOf(left.getQualifier().getClassid());
+		PidType rClass = PidType.valueOf(right.getQualifier().getClassid());
+
+		if (lClass.equals(PidType.doi))
 			return -1;
-		if (pRight.equals(PidType.doi))
+		if (rClass.equals(PidType.doi))
 			return 1;
 
-		if (pLeft.equals(PidType.pmid))
+		if (lClass.equals(PidType.pmid))
 			return -1;
-		if (pRight.equals(PidType.pmid))
+		if (rClass.equals(PidType.pmid))
 			return 1;
 
-		if (pLeft.equals(PidType.pmc))
+		if (lClass.equals(PidType.pmc))
 			return -1;
-		if (pRight.equals(PidType.pmc))
+		if (rClass.equals(PidType.pmc))
 			return 1;
 
-		if (pLeft.equals(PidType.handle))
+		if (lClass.equals(PidType.handle))
 			return -1;
-		if (pRight.equals(PidType.handle))
+		if (rClass.equals(PidType.handle))
 			return 1;
 
-		if (pLeft.equals(PidType.arXiv))
+		if (lClass.equals(PidType.arXiv))
 			return -1;
-		if (pRight.equals(PidType.arXiv))
+		if (rClass.equals(PidType.arXiv))
 			return 1;
 
-		if (pLeft.equals(PidType.NCID))
+		if (lClass.equals(PidType.NCID))
 			return -1;
-		if (pRight.equals(PidType.NCID))
+		if (rClass.equals(PidType.NCID))
 			return 1;
 
-		if (pLeft.equals(PidType.GBIF))
+		if (lClass.equals(PidType.GBIF))
 			return -1;
-		if (pRight.equals(PidType.GBIF))
+		if (rClass.equals(PidType.GBIF))
 			return 1;
 
-		if (pLeft.equals(PidType.nct))
+		if (lClass.equals(PidType.nct))
 			return -1;
-		if (pRight.equals(PidType.nct))
+		if (rClass.equals(PidType.nct))
 			return 1;
 
-		if (pLeft.equals(PidType.urn))
+		if (lClass.equals(PidType.urn))
 			return -1;
-		if (pRight.equals(PidType.urn))
+		if (rClass.equals(PidType.urn))
 			return 1;
 
 		return 0;

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/IdentifierFactoryTest.java

@@ -22,10 +22,11 @@ public class IdentifierFactoryTest {
 	@Test
 	public void testCreateIdentifierForPublication() throws IOException {
 
-		verifyIdentifier("publication_doi.json", "50|doi_________::" + DHPUtils.md5("10.1016/j.cmet.2011.03.013"));
+		verifyIdentifier("publication_doi1.json", "50|doi_________::" + DHPUtils.md5("10.1016/j.cmet.2011.03.013"));
-		verifyIdentifier("publication_pmc.json", "50|pmc_________::" + DHPUtils.md5("21459329"));
+		verifyIdentifier("publication_doi2.json", "50|doi_________::" + DHPUtils.md5("10.1016/j.cmet.2010.03.013"));
+		verifyIdentifier("publication_pmc1.json", "50|pmc_________::" + DHPUtils.md5("21459329"));
 		verifyIdentifier(
-			"publication_urn.json",
+			"publication_urn1.json",
 			"50|urn_________::" + DHPUtils.md5("urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"));
 
 		final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";

dhp-common/src/test/resources/eu/dnetlib/dhp/schema/oaf/utils/publication_doi2.json

@@ -0,0 +1 @@
+{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2010.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}]}