WIP: pid cleaning

pom.xml

@@ -5,7 +5,7 @@
     <groupId>eu.dnetlib.dhp</groupId>
     <artifactId>dhp-schemas</artifactId>
     <packaging>jar</packaging>
-    <version>3.16.1-SNAPSHOT</version>
+    <version>3.17.1-SNAPSHOT</version>
 
     <licenses>
         <license>

src/main/java/eu/dnetlib/dhp/schema/oaf/Instance.java

@@ -21,7 +21,7 @@ public class Instance implements Serializable {
 
 	private KeyValue collectedfrom;
 
-	private List<StructuredProperty> pid;
+	private List<Pid> pid;
 
 	private List<StructuredProperty> alternateIdentifier;
 
@@ -95,11 +95,11 @@ public class Instance implements Serializable {
 		this.collectedfrom = collectedfrom;
 	}
 
-	public List<StructuredProperty> getPid() {
+	public List<Pid> getPid() {
 		return pid;
 	}
 
-	public void setPid(List<StructuredProperty> pid) {
+	public void setPid(List<Pid> pid) {
 		this.pid = pid;
 	}
 

src/main/java/eu/dnetlib/dhp/schema/oaf/OafEntity.java

@@ -11,7 +11,7 @@ public abstract class OafEntity extends Oaf implements Serializable {
 
 	private List<String> originalId;
 
-	private List<StructuredProperty> pid;
+	private List<Pid> pid;
 
 	private String dateofcollection;
 
@@ -60,11 +60,11 @@ public abstract class OafEntity extends Oaf implements Serializable {
 		this.originalId = originalId;
 	}
 
-	public List<StructuredProperty> getPid() {
+	public List<Pid> getPid() {
 		return pid;
 	}
 
-	public void setPid(List<StructuredProperty> pid) {
+	public void setPid(List<Pid> pid) {
 		this.pid = pid;
 	}
 

src/main/java/eu/dnetlib/dhp/schema/oaf/Pid.java

@@ -0,0 +1,6 @@
+package eu.dnetlib.dhp.schema.oaf;
+
+import java.io.Serializable;
+
+public class Pid extends StructuredProperty implements Serializable {
+}

src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java

@@ -570,7 +570,21 @@ public class Result extends OafEntity implements Serializable {
 	private static String extractKeyFromPid(final StructuredProperty pid) {
 		if (pid == null)
 			return null;
-		final  StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
+		final  Pid normalizedPid = CleaningFunctions.normalizePidValue((Pid) pid);
+
+		return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
+	}
+
+	/**
+	 * Normalize pid string.
+	 *
+	 * @param pid the pid
+	 * @return the string
+	 */
+	private static String extractKeyFromAltId(final StructuredProperty pid) {
+		if (pid == null)
+			return null;
+		final  StructuredProperty normalizedPid = CleaningFunctions.normalizeSPValue(pid);
 
 		return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
 	}
@@ -595,8 +609,6 @@ public class Result extends OafEntity implements Serializable {
 	 * @return the result map
 	 */
 	public static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
-
-
 		return ri
 				.stream()
 				.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
@@ -622,7 +634,7 @@ public class Result extends OafEntity implements Serializable {
 	 * @param enrichments the List of enrichment instances having the same pid
 	 * @return the list
 	 */
-	private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids, final Map<String,Instance> enrichments) {
+	private static List<Instance> findEnrichmentsByPID(final List<Pid> pids, final Map<String,Instance> enrichments) {
 		if (pids == null || enrichments == null)
 			return null;
 		return pids
@@ -633,6 +645,25 @@ public class Result extends OafEntity implements Serializable {
 				.collect(Collectors.toList());
 	}
 
+	/**
+	 * This utility method finds the list of enrichment instances
+	 * that match one or more PIDs in the input list
+	 *
+	 * @param pids        the list of PIDs
+	 * @param enrichments the List of enrichment instances having the same pid
+	 * @return the list
+	 */
+	private static List<Instance> findEnrichmentsByAlternateIdentifier(final List<StructuredProperty> pids, final Map<String,Instance> enrichments) {
+		if (pids == null || enrichments == null)
+			return null;
+		return pids
+				.stream()
+				.map(Result::extractKeyFromAltId)
+				.map(enrichments::get)
+				.filter(Objects::nonNull)
+				.collect(Collectors.toList());
+	}
+
 	/**
 	 * This method apply enrichment on a single instance
 	 * The enrichment consists of replacing values on
@@ -712,11 +743,11 @@ public class Result extends OafEntity implements Serializable {
 
 		toEnrichInstances.forEach(i -> {
 			final List<Instance> e = findEnrichmentsByPID(i.getPid(), ri);
-			if (e!= null && e.size()> 0) {
+			if (e!= null && !e.isEmpty()) {
 				e.forEach(enr -> applyEnrichment(i, enr));
 			} else {
-				final List<Instance> a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri);
-				if (a!= null && a.size()> 0) {
+				final List<Instance> a = findEnrichmentsByAlternateIdentifier(i.getAlternateIdentifier(), ri);
+				if (a!= null && !a.isEmpty()) {
 					a.forEach(enr -> applyEnrichment(i, enr));
 				}
 			}

src/main/java/eu/dnetlib/dhp/schema/oaf/utils/CleaningFunctions.java

@@ -8,6 +8,7 @@ import java.util.Set;
 
 import org.apache.commons.lang3.StringUtils;
 
+import eu.dnetlib.dhp.schema.oaf.Pid;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
 public class CleaningFunctions {
@@ -29,7 +30,7 @@ public class CleaningFunctions {
 	 * @param s the PID whose value will be checked.
 	 * @return false if the pid matches the filter criteria, true otherwise.
 	 */
-	public static boolean pidFilter(StructuredProperty s) {
+	public static boolean pidFilter(Pid s) {
 		final String pidValue = s.getValue();
 		if (Objects.isNull(s.getQualifier()) ||
 			StringUtils.isBlank(pidValue) ||
@@ -47,7 +48,7 @@ public class CleaningFunctions {
 	 * @param pid the PID whose value will be normalised.
 	 * @return the PID containing the normalised value.
 	 */
-	public static StructuredProperty normalizePidValue(StructuredProperty pid) {
+	public static Pid normalizePidValue(Pid pid) {
 		pid.setValue(
 				normalizePidValue(
 					pid.getQualifier().getClassid(),
@@ -56,6 +57,20 @@ public class CleaningFunctions {
 		return pid;
 	}
 
+	/**
+	 * Utility method that normalises PID values on a per-type basis.
+	 * @param pid the PID whose value will be normalised.
+	 * @return the PID containing the normalised value.
+	 */
+	public static StructuredProperty normalizeSPValue(StructuredProperty pid) {
+		pid.setValue(
+				normalizePidValue(
+						pid.getQualifier().getClassid(),
+						pid.getValue()));
+
+		return pid;
+	}
+
 	public static String normalizePidValue(String pidType, String pidValue) {
 		String value = Optional
 				.ofNullable(pidValue)

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

@@ -95,7 +95,7 @@ public class IdentifierFactory implements Serializable {
 				.collect(Collectors.toCollection(HashSet::new));
 	}
 
-	public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
+	public static List<StructuredProperty> getPids(List<Pid> pid, KeyValue collectedFrom) {
 		return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
 	}
 
@@ -143,7 +143,7 @@ public class IdentifierFactory implements Serializable {
 
 		checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
 
-		final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
+		final Map<String, Set<Pid>> pids = extractPids(entity);
 
 		return pids
 			.values()
@@ -164,7 +164,7 @@ public class IdentifierFactory implements Serializable {
 			.orElseGet(entity::getId);
 	}
 
-	private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
+	private static <T extends OafEntity> Map<String, Set<Pid>> extractPids(T entity) {
 		if (entity instanceof Result) {
 			return Optional
 				.ofNullable(((Result) entity).getInstance())
@@ -184,7 +184,7 @@ public class IdentifierFactory implements Serializable {
 		}
 	}
 
-	private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
+	private static Map<String, Set<Pid>> mapPids(List<Instance> instance) {
 		return instance
 			.stream()
 			.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
@@ -196,7 +196,7 @@ public class IdentifierFactory implements Serializable {
 						Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
 	}
 
-	private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
+	private static Stream<Pid> pidFromInstance(List<Pid> pid, KeyValue collectedFrom,
 		boolean mapHandles) {
 		return Optional
 			.ofNullable(pid)

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

@@ -4,12 +4,13 @@ package eu.dnetlib.dhp.schema.oaf.utils;
 import java.util.Comparator;
 import java.util.Optional;
 
+import eu.dnetlib.dhp.schema.oaf.Pid;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
-public class PidValueComparator implements Comparator<StructuredProperty> {
+public class PidValueComparator implements Comparator<Pid> {
 
 	@Override
-	public int compare(StructuredProperty left, StructuredProperty right) {
+	public int compare(Pid left, Pid right) {
 
 		if (left == null && right == null)
 			return 0;
@@ -18,15 +19,15 @@ public class PidValueComparator implements Comparator<StructuredProperty> {
 		if (right == null)
 			return -1;
 
-		StructuredProperty l = CleaningFunctions.normalizePidValue(left);
-		StructuredProperty r = CleaningFunctions.normalizePidValue(right);
+		Pid l = CleaningFunctions.normalizePidValue(left);
+		Pid r = CleaningFunctions.normalizePidValue(right);
 
 		return Optional
 			.ofNullable(l.getValue())
 			.map(
 				lv -> Optional
 					.ofNullable(r.getValue())
-					.map(rv -> lv.compareTo(rv))
+					.map(lv::compareTo)
 					.orElse(-1))
 			.orElse(1);
 	}

src/test/java/eu/dnetlib/dhp/schema/oaf/MergeTest.java

@@ -109,10 +109,20 @@ class MergeTest {
 			final Result currentPub = source.get(i);
 			final Result currentEnrichment = enrichment.get(i);
 			final Instance currentInstance = Objects.requireNonNull(currentPub.getInstance()).get(0);
-			if (overrideAlternateIdentifier)
-				currentInstance.setAlternateIdentifier(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
-			else
-				currentInstance.setPid(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
+			final List<Pid> pid = Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid();
+			if (overrideAlternateIdentifier) {
+				currentInstance.setAlternateIdentifier(pid.stream()
+						.map(p -> {
+							StructuredProperty sp = new StructuredProperty();
+							sp.setValue(p.getValue());
+							sp.setQualifier(p.getQualifier());
+							sp.setDataInfo(p.getDataInfo());
+							return sp;
+						})
+						.collect(Collectors.toList()));
+			} else {
+				currentInstance.setPid(pid);
+			}
 		}
 	}