dedup workflow using the common PidComparator

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

@@ -0,0 +1,27 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+
+public class OrganizationPidComparator implements Comparator<PidType> {
+
+	@Override
+	public int compare(PidType pLeft, PidType pRight) {
+		if (pLeft.equals(PidType.GRID))
+			return -1;
+		if (pRight.equals(PidType.GRID))
+			return 1;
+
+		if (pLeft.equals(PidType.mag_id))
+			return -1;
+		if (pRight.equals(PidType.mag_id))
+			return 1;
+
+		if (pLeft.equals(PidType.urn))
+			return -1;
+		if (pRight.equals(PidType.urn))
+			return 1;
+
+		return 0;
+	}
+}

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

@@ -45,70 +45,10 @@ public class PidComparator<T extends OafEntity> implements Comparator<Structured
 	}
 
 	private int compareResultPids(PidType lClass, PidType rClass) {
-		if (lClass.equals(PidType.doi))
+		return new ResultPidComparator().compare(lClass, rClass);
-			return -1;
-		if (rClass.equals(PidType.doi))
-			return 1;
-
-		if (lClass.equals(PidType.pmid))
-			return -1;
-		if (rClass.equals(PidType.pmid))
-			return 1;
-
-		if (lClass.equals(PidType.pmc))
-			return -1;
-		if (rClass.equals(PidType.pmc))
-			return 1;
-
-		if (lClass.equals(PidType.handle))
-			return -1;
-		if (rClass.equals(PidType.handle))
-			return 1;
-
-		if (lClass.equals(PidType.arXiv))
-			return -1;
-		if (rClass.equals(PidType.arXiv))
-			return 1;
-
-		if (lClass.equals(PidType.NCID))
-			return -1;
-		if (rClass.equals(PidType.NCID))
-			return 1;
-
-		if (lClass.equals(PidType.GBIF))
-			return -1;
-		if (rClass.equals(PidType.GBIF))
-			return 1;
-
-		if (lClass.equals(PidType.nct))
-			return -1;
-		if (rClass.equals(PidType.nct))
-			return 1;
-
-		if (lClass.equals(PidType.urn))
-			return -1;
-		if (rClass.equals(PidType.urn))
-			return 1;
-
-		return 0;
 	}
 
 	private int compareOrganizationtPids(PidType lClass, PidType rClass) {
-		if (lClass.equals(PidType.GRID))
+		return new OrganizationPidComparator().compare(lClass, rClass);
-			return -1;
-		if (rClass.equals(PidType.GRID))
-			return 1;
-
-		if (lClass.equals(PidType.mag_id))
-			return -1;
-		if (rClass.equals(PidType.mag_id))
-			return 1;
-
-		if (lClass.equals(PidType.urn))
-			return -1;
-		if (rClass.equals(PidType.urn))
-			return 1;
-
-		return 0;
 	}
 }

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

@@ -9,10 +9,21 @@ public enum PidType {
 	doi, pmid, pmc, handle, arXiv, NCID, GBIF, nct, pdb,
 
 	// Organization
-	GRID, mag_id, urn;
+	GRID, mag_id, urn,
+
+	// Used by dedup
+	undefined, original;
 
 	public static boolean isValid(String type) {
 		return EnumUtils.isValidEnum(PidType.class, type);
 	}
 
+	public static PidType tryValueOf(String s) {
+		try {
+			return PidType.valueOf(s);
+		} catch (Exception e) {
+			return PidType.original;
+		}
+	}
+
 }

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

@@ -0,0 +1,57 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import java.util.Comparator;
+
+public class ResultPidComparator implements Comparator<PidType> {
+
+	@Override
+	public int compare(PidType pLeft, PidType pRight) {
+		if (pLeft.equals(PidType.doi))
+			return -1;
+		if (pRight.equals(PidType.doi))
+			return 1;
+
+		if (pLeft.equals(PidType.pmid))
+			return -1;
+		if (pRight.equals(PidType.pmid))
+			return 1;
+
+		if (pLeft.equals(PidType.pmc))
+			return -1;
+		if (pRight.equals(PidType.pmc))
+			return 1;
+
+		if (pLeft.equals(PidType.handle))
+			return -1;
+		if (pRight.equals(PidType.handle))
+			return 1;
+
+		if (pLeft.equals(PidType.arXiv))
+			return -1;
+		if (pRight.equals(PidType.arXiv))
+			return 1;
+
+		if (pLeft.equals(PidType.NCID))
+			return -1;
+		if (pRight.equals(PidType.NCID))
+			return 1;
+
+		if (pLeft.equals(PidType.GBIF))
+			return -1;
+		if (pRight.equals(PidType.GBIF))
+			return 1;
+
+		if (pLeft.equals(PidType.nct))
+			return -1;
+		if (pRight.equals(PidType.nct))
+			return 1;
+
+		if (pLeft.equals(PidType.urn))
+			return -1;
+		if (pRight.equals(PidType.urn))
+			return 1;
+
+		return 0;
+	}
+}

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

@@ -82,7 +82,7 @@ public class DedupRecordFactory {
 
 		final Collection<String> dates = Lists.newArrayList();
 		final List<List<Author>> authors = Lists.newArrayList();
-		final List<Identifier> bestPids = Lists.newArrayList(); // best pids list
+		final List<Identifier<T>> bestPids = Lists.newArrayList(); // best pids list
 
 		entities
 			.forEachRemaining(
@@ -90,7 +90,7 @@ public class DedupRecordFactory {
 					T duplicate = t._2();
 
 					// prepare the list of pids to use for the id generation
-					bestPids.addAll(IdGenerator.bestPidToIdentifier(duplicate));
+					bestPids.add(Identifier.newInstance(duplicate));
 
 					entity.mergeFrom(duplicate);
 					if (ModelSupport.isSubClass(duplicate, Result.class)) {

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

@@ -1,124 +1,46 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
+import static org.apache.commons.lang3.StringUtils.substringAfter;
+import static org.apache.commons.lang3.StringUtils.substringBefore;
+
 import java.io.Serializable;
-import java.text.ParseException;
+import java.util.List;
-import java.text.SimpleDateFormat;
-import java.util.*;
-
-import org.apache.commons.lang.StringUtils;
-
-import com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.oa.dedup.model.Identifier;
-import eu.dnetlib.dhp.oa.dedup.model.PidType;
-import eu.dnetlib.dhp.schema.common.EntityType;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Field;
 import eu.dnetlib.dhp.schema.oaf.OafEntity;
-import eu.dnetlib.dhp.schema.oaf.Result;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class IdGenerator implements Serializable {
 
-	public static String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2";
-	public static String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254";
-	public static String BASE_DATE = "2000-01-01";
-
 	// pick the best pid from the list (consider date and pidtype)
-	public static String generate(List<Identifier> pids, String defaultID) {
+	public static <T extends OafEntity> String generate(List<Identifier<T>> pids, String defaultID) {
 		if (pids == null || pids.size() == 0)
 			return defaultID;
 
-		Optional<Identifier> bp = pids
+		Identifier<T> bp = pids
 			.stream()
-			.max(Identifier::compareTo);
+			.min(Identifier::compareTo)
+			.get();
 
-		if (bp.get().isUseOriginal() || bp.get().getPid().getValue() == null) {
+		String prefix = substringBefore(bp.getOriginalID(), "|");
-			return bp.get().getOriginalID().split("\\|")[0] + "|dedup_wf_001::"
+		String ns = substringBefore(substringAfter(bp.getOriginalID(), "|"), "::");
-				+ DHPUtils.md5(bp.get().getOriginalID());
+		String suffix = substringAfter(bp.getOriginalID(), "::");
+
+		final String pidType = substringBefore(ns, "_");
+		if (PidType.isValid(pidType)) {
+			return prefix + "|" + dedupify(ns) + "::" + suffix;
 		} else {
-			return bp.get().getOriginalID().split("\\|")[0] + "|"
+			return prefix + "|dedup_wf_001::" + suffix;
-				+ createPrefix(bp.get().getPid().getQualifier().getClassid()) + "::"
-				+ DHPUtils.md5(bp.get().getPid().getValue());
 		}
-
 	}
 
-	public static <T extends OafEntity> ArrayList<Identifier> createBasePid(T entity, SimpleDateFormat sdf) {
+	private static String dedupify(String ns) {
-
+		StringBuilder prefix = new StringBuilder(substringBefore(ns, "_")).append("_dedup");
-		Date date;
-		try {
-			date = sdf.parse(BASE_DATE);
-		} catch (ParseException e) {
-			date = new Date();
-		}
-		return Lists
-			.newArrayList(
-				new Identifier(new StructuredProperty(), date, PidType.original, entity.getCollectedfrom(),
-					EntityType.fromClass(entity.getClass()), entity.getId()));
-	}
-
-	// pick the best pid from the entity. Returns a list (length 1) to save time in the call
-	public static <T extends OafEntity> List<Identifier> bestPidToIdentifier(T entity) {
-
-		SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
-
-		if (entity.getPid() == null || entity.getPid().size() == 0)
-			return createBasePid(entity, sdf);
-
-		Optional<StructuredProperty> bp = entity
-			.getPid()
-			.stream()
-			.filter(pid -> PidType.classidValueOf(pid.getQualifier().getClassid()) != PidType.undefined)
-			.max(Comparator.comparing(pid -> PidType.classidValueOf(pid.getQualifier().getClassid())));
-
-		return bp
-			.map(
-				structuredProperty -> Lists
-					.newArrayList(
-						new Identifier(structuredProperty, extractDate(entity, sdf),
-							PidType.classidValueOf(structuredProperty.getQualifier().getClassid()),
-							entity.getCollectedfrom(), EntityType.fromClass(entity.getClass()), entity.getId())))
-			.orElseGet(() -> createBasePid(entity, sdf));
-
-	}
-
-	// create the prefix (length = 12): dedup_+ pidType
-	public static String createPrefix(String pidType) {
-
-		StringBuilder prefix = new StringBuilder("dedup_" + pidType);
-
 		while (prefix.length() < 12) {
 			prefix.append("_");
 		}
-		return prefix.toString().substring(0, 12);
+		return prefix.substring(0, 12);
-
 	}
 
-	// extracts the date from the record. If the date is not available or is not wellformed, it returns a base date:
-	// 00-01-01
-	public static <T extends OafEntity> Date extractDate(T duplicate, SimpleDateFormat sdf) {
-
-		String date = BASE_DATE;
-		if (ModelSupport.isSubClass(duplicate, Result.class)) {
-			Result result = (Result) duplicate;
-			if (isWellformed(result.getDateofacceptance())) {
-				date = result.getDateofacceptance().getValue();
-			}
-		}
-
-		try {
-			return sdf.parse(date);
-		} catch (ParseException e) {
-			return new Date();
-		}
-
-	}
-
-	public static boolean isWellformed(Field<String> date) {
-		return date != null && StringUtils.isNotBlank(date.getValue())
-			&& date.getValue().matches(DatePicker.DATE_PATTERN) && DatePicker.inRange(date.getValue());
-	}
 }

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

@@ -2,94 +2,85 @@
 package eu.dnetlib.dhp.oa.dedup.model;
 
 import java.io.Serializable;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.List;
+import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import org.apache.commons.lang3.StringUtils;
+
 import com.google.common.collect.Sets;
 
-import eu.dnetlib.dhp.oa.dedup.IdGenerator;
+import eu.dnetlib.dhp.oa.dedup.DatePicker;
 import eu.dnetlib.dhp.schema.common.EntityType;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.PidComparator;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 
-public class Identifier implements Serializable, Comparable<Identifier> {
+public class Identifier<T extends OafEntity> implements Serializable, Comparable<Identifier> {
 
-	StructuredProperty pid;
+	public static String CROSSREF_ID = "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2";
-	Date date;
+	public static String DATACITE_ID = "10|openaire____::9e3be59865b2c1c335d32dae2fe7b254";
-	PidType type;
+	public static String BASE_DATE = "2000-01-01";
-	List<KeyValue> collectedFrom;
-	EntityType entityType;
-	String originalID;
 
-	boolean useOriginal = false; // to know if the top identifier won because of the alphabetical order of the original
+	private static SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
-									// ID
 
-	public Identifier(StructuredProperty pid, Date date, PidType type, List<KeyValue> collectedFrom,
+	private T entity;
-		EntityType entityType, String originalID) {
+
-		this.pid = pid;
+	public static <T extends OafEntity> Identifier newInstance(T entity) {
-		this.date = date;
+		return new Identifier(entity);
-		this.type = type;
-		this.collectedFrom = collectedFrom;
-		this.entityType = entityType;
-		this.originalID = originalID;
 	}
 
-	public StructuredProperty getPid() {
+	public Identifier(T entity) {
-		return pid;
+		this.entity = entity;
 	}
 
-	public void setPid(StructuredProperty pid) {
+	public T getEntity() {
-		this.pid = pid;
+		return entity;
+	}
+
+	public void setEntity(T entity) {
+		this.entity = entity;
 	}
 
 	public Date getDate() {
-		return date;
+		String date = BASE_DATE;
+		if (ModelSupport.isSubClass(getEntity(), Result.class)) {
+			Result result = (Result) getEntity();
+			if (isWellformed(result.getDateofacceptance())) {
+				date = result.getDateofacceptance().getValue();
+			}
+		}
+		try {
+			return sdf.parse(date);
+		} catch (ParseException e) {
+			return new Date();
+		}
 	}
 
-	public void setDate(Date date) {
+	private static boolean isWellformed(Field<String> date) {
-		this.date = date;
+		return date != null && StringUtils.isNotBlank(date.getValue())
-	}
+			&& date.getValue().matches(DatePicker.DATE_PATTERN) && DatePicker.inRange(date.getValue());
-
-	public PidType getType() {
-		return type;
-	}
-
-	public void setType(PidType type) {
-		this.type = type;
 	}
 
 	public List<KeyValue> getCollectedFrom() {
-		return collectedFrom;
+		return entity.getCollectedfrom();
-	}
-
-	public void setCollectedFrom(List<KeyValue> collectedFrom) {
-		this.collectedFrom = collectedFrom;
 	}
 
 	public EntityType getEntityType() {
-		return entityType;
+		return EntityType.fromClass(entity.getClass());
-	}
-
-	public void setEntityType(EntityType entityType) {
-		this.entityType = entityType;
 	}
 
 	public String getOriginalID() {
-		return originalID;
+		return entity.getId();
 	}
 
-	public void setOriginalID(String originalID) {
+	private PidType getPidType() {
-		this.originalID = originalID;
+		return PidType.tryValueOf(StringUtils.substringBefore(StringUtils.substringAfter(entity.getId(), "|"), "_"));
-	}
-
-	public boolean isUseOriginal() {
-		return useOriginal;
-	}
-
-	public void setUseOriginal(boolean useOriginal) {
-		this.useOriginal = useOriginal;
 	}
 
 	@Override
@@ -97,50 +88,50 @@ public class Identifier implements Serializable, Comparable<Identifier> {
 		// priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4)
 		// alphabetical order of the originalID
 
-		Set<String> lKeys = Sets.newHashSet();
+		Set<String> lKeys = Optional
-		if (this.collectedFrom != null)
+			.ofNullable(getCollectedFrom())
-			lKeys = this.collectedFrom.stream().map(KeyValue::getKey).collect(Collectors.toSet());
+			.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
+			.orElse(Sets.newHashSet());
 
-		Set<String> rKeys = Sets.newHashSet();
+		final Optional<List<KeyValue>> cf = Optional.ofNullable(i.getCollectedFrom());
-		if (i.getCollectedFrom() != null)
+		Set<String> rKeys = cf
-			rKeys = i.getCollectedFrom().stream().map(KeyValue::getKey).collect(Collectors.toSet());
+			.map(c -> c.stream().map(KeyValue::getKey).collect(Collectors.toSet()))
+			.orElse(Sets.newHashSet());
 
-		if (this.getType().compareTo(i.getType()) == 0) { // same type
+		if (this.getPidType().compareTo(i.getPidType()) == 0) { // same type
-			if (entityType == EntityType.publication) {
+			if (getEntityType() == EntityType.publication) {
-				if (isFromDatasourceID(lKeys, IdGenerator.CROSSREF_ID)
+				if (isFromDatasourceID(lKeys, CROSSREF_ID)
-					&& !isFromDatasourceID(rKeys, IdGenerator.CROSSREF_ID))
+					&& !isFromDatasourceID(rKeys, CROSSREF_ID))
-					return 1;
-				if (isFromDatasourceID(rKeys, IdGenerator.CROSSREF_ID)
-					&& !isFromDatasourceID(lKeys, IdGenerator.CROSSREF_ID))
 					return -1;
+				if (isFromDatasourceID(rKeys, CROSSREF_ID)
+					&& !isFromDatasourceID(lKeys, CROSSREF_ID))
+					return 1;
 			}
-			if (entityType == EntityType.dataset) {
+			if (getEntityType() == EntityType.dataset) {
-				if (isFromDatasourceID(lKeys, IdGenerator.DATACITE_ID)
+				if (isFromDatasourceID(lKeys, DATACITE_ID)
-					&& !isFromDatasourceID(rKeys, IdGenerator.DATACITE_ID))
+					&& !isFromDatasourceID(rKeys, DATACITE_ID))
-					return 1;
-				if (isFromDatasourceID(rKeys, IdGenerator.DATACITE_ID)
-					&& !isFromDatasourceID(lKeys, IdGenerator.DATACITE_ID))
 					return -1;
+				if (isFromDatasourceID(rKeys, DATACITE_ID)
+					&& !isFromDatasourceID(lKeys, DATACITE_ID))
+					return 1;
 			}
 
 			if (this.getDate().compareTo(i.getDate()) == 0) {// same date
-
-				if (this.originalID.compareTo(i.originalID) < 0)
-					this.useOriginal = true;
-				else
-					i.setUseOriginal(true);
-
 				// the minus because we need to take the alphabetically lower id
-				return -this.originalID.compareTo(i.originalID);
+				return this.getOriginalID().compareTo(i.getOriginalID());
 			} else
 				// the minus is because we need to take the elder date
-				return -this.getDate().compareTo(i.getDate());
+				return this.getDate().compareTo(i.getDate());
 		} else {
-			return this.getType().compareTo(i.getType());
+			return new PidComparator<>(getEntity()).compare(toSP(getPidType()), toSP(i.getPidType()));
 		}
 
 	}
 
+	private StructuredProperty toSP(PidType pidType) {
+		return OafMapperUtils.structuredProperty("", pidType.toString(), pidType.toString(), "", "", new DataInfo());
+	}
+
 	public boolean isFromDatasourceID(Set<String> collectedFrom, String dsId) {
 		return collectedFrom.contains(dsId);
 	}

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

@@ -1,17 +0,0 @@
-
-package eu.dnetlib.dhp.oa.dedup.model;
-
-public enum PidType {
-
-	// from the less to the more important
-	undefined, original, orcid, ror, grid, pdb, arXiv, pmid, pmc, doi;
-
-	public static PidType classidValueOf(String s) {
-		try {
-			return PidType.valueOf(s);
-		} catch (Exception e) {
-			return PidType.undefined;
-		}
-	}
-
-}

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

@@ -9,6 +9,7 @@ import java.io.IOException;
 import java.io.Serializable;
 import java.nio.file.Paths;
 import java.util.*;
+import java.util.stream.Collectors;
 
 import org.codehaus.jackson.map.ObjectMapper;
 import org.junit.jupiter.api.BeforeEach;
@@ -21,16 +22,16 @@ import scala.Tuple2;
 
 public class EntityMergerTest implements Serializable {
 
-	List<Tuple2<String, Publication>> publications;
+	private List<Tuple2<String, Publication>> publications;
-	List<Tuple2<String, Publication>> publications2;
+	private List<Tuple2<String, Publication>> publications2;
-	List<Tuple2<String, Publication>> publications3;
+	private List<Tuple2<String, Publication>> publications3;
-	List<Tuple2<String, Publication>> publications4;
+	private List<Tuple2<String, Publication>> publications4;
-	List<Tuple2<String, Publication>> publications5;
+	private List<Tuple2<String, Publication>> publications5;
 
-	String testEntityBasePath;
+	private String testEntityBasePath;
-	DataInfo dataInfo;
+	private DataInfo dataInfo;
-	String dedupId = "00|dedup_id::1";
+	private String dedupId = "00|dedup_id::1";
-	Publication pub_top;
+	private Publication pub_top;
 
 	@BeforeEach
 	public void setUp() throws Exception {
@@ -61,9 +62,9 @@ public class EntityMergerTest implements Serializable {
 		Software merged = DedupRecordFactory
 			.entityMerger(dedupId, softwares.iterator(), 0, dataInfo, Software.class);
 
-		assertEquals(merged.getBestaccessright().getClassid(), "OPEN SOURCE");
+		assertEquals("OPEN SOURCE", merged.getBestaccessright().getClassid());
 
-		assertEquals(merged.getId(), "50|dedup_doi___::0968af610a356656706657e4f234b340");
+		assertEquals("50|doi_dedup___::0968af610a356656706657e4f234b340", merged.getId());
 
 	}
 
@@ -74,45 +75,45 @@ public class EntityMergerTest implements Serializable {
 			.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
 
 		// verify id
-		assertEquals(pub_merged.getId(), "50|dedup_doi___::0968af610a356656706657e4f234b340");
+		assertEquals("50|doi_dedup___::0968af610a356656706657e4f234b340", pub_merged.getId());
 
-		assertEquals(pub_merged.getJournal(), pub_top.getJournal());
+		assertEquals(pub_top.getJournal(), pub_merged.getJournal());
-		assertEquals(pub_merged.getBestaccessright().getClassid(), "OPEN");
+		assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
-		assertEquals(pub_merged.getResulttype(), pub_top.getResulttype());
+		assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
-		assertEquals(pub_merged.getLanguage(), pub_merged.getLanguage());
+		assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());
-		assertEquals(pub_merged.getPublisher(), pub_top.getPublisher());
+		assertEquals(pub_top.getPublisher(), pub_merged.getPublisher());
-		assertEquals(pub_merged.getEmbargoenddate(), pub_top.getEmbargoenddate());
+		assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate());
-		assertEquals(pub_merged.getResourcetype().getClassid(), "0004");
+		assertEquals(pub_top.getResourcetype().getClassid(), "");
-		assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation());
+		assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation());
-		assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance());
+		assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance());
-		assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection());
+		assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
-		assertEquals(pub_merged.getInstance().size(), 3);
+		assertEquals(3, pub_merged.getInstance().size());
-		assertEquals(pub_merged.getCountry().size(), 2);
+		assertEquals(2, pub_merged.getCountry().size());
-		assertEquals(pub_merged.getSubject().size(), 0);
+		assertEquals(0, pub_merged.getSubject().size());
-		assertEquals(pub_merged.getTitle().size(), 2);
+		assertEquals(2, pub_merged.getTitle().size());
-		assertEquals(pub_merged.getRelevantdate().size(), 0);
+		assertEquals(0, pub_merged.getRelevantdate().size());
-		assertEquals(pub_merged.getDescription().size(), 0);
+		assertEquals(0, pub_merged.getDescription().size());
-		assertEquals(pub_merged.getSource().size(), 0);
+		assertEquals(0, pub_merged.getSource().size());
-		assertEquals(pub_merged.getFulltext().size(), 0);
+		assertEquals(0, pub_merged.getFulltext().size());
-		assertEquals(pub_merged.getFormat().size(), 0);
+		assertEquals(0, pub_merged.getFormat().size());
-		assertEquals(pub_merged.getContributor().size(), 0);
+		assertEquals(0, pub_merged.getContributor().size());
-		assertEquals(pub_merged.getCoverage().size(), 0);
+		assertEquals(0, pub_merged.getCoverage().size());
-		assertEquals(pub_merged.getContext().size(), 0);
+		assertEquals(0, pub_merged.getContext().size());
-		assertEquals(pub_merged.getExternalReference().size(), 0);
+		assertEquals(0, pub_merged.getExternalReference().size());
-		assertEquals(pub_merged.getOriginalId().size(), 3);
+		assertEquals(3, pub_merged.getOriginalId().size());
-		assertEquals(pub_merged.getCollectedfrom().size(), 3);
+		assertEquals(3, pub_merged.getCollectedfrom().size());
-		assertEquals(pub_merged.getPid().size(), 1);
+		assertEquals(1, pub_merged.getPid().size());
-		assertEquals(pub_merged.getExtraInfo().size(), 0);
+		assertEquals(0, pub_merged.getExtraInfo().size());
 
 		// verify datainfo
-		assertEquals(pub_merged.getDataInfo(), dataInfo);
+		assertEquals(dataInfo, pub_merged.getDataInfo());
 
 		// verify datepicker
-		assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30");
+		assertEquals("2018-09-30", pub_merged.getDateofacceptance().getValue());
 
 		// verify authors
-		assertEquals(pub_merged.getAuthor().size(), 9);
+		assertEquals(9, pub_merged.getAuthor().size());
-		assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4);
+		assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor()));
 
 		// verify title
 		int count = 0;
@@ -120,7 +121,7 @@ public class EntityMergerTest implements Serializable {
 			if (title.getQualifier().getClassid().equals("main title"))
 				count++;
 		}
-		assertEquals(count, 1);
+		assertEquals(1, count);
 	}
 
 	@Test
@@ -130,9 +131,9 @@ public class EntityMergerTest implements Serializable {
 			.entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class);
 
 		// verify id
-		assertEquals("50|dedup_doi___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId());
+		assertEquals("50|doi_dedup___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId());
 
-		assertEquals(pub_merged.getAuthor().size(), 27);
+		assertEquals(27, pub_merged.getAuthor().size());
 	}
 
 	@Test
@@ -142,7 +143,7 @@ public class EntityMergerTest implements Serializable {
 			.entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class);
 
 		// verify id
-		assertEquals("50|dedup_doi___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId());
+		assertEquals("50|doi_dedup___::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId());
 	}
 
 	@Test
@@ -152,17 +153,24 @@ public class EntityMergerTest implements Serializable {
 			.entityMerger(dedupId, publications4.iterator(), 0, dataInfo, Publication.class);
 
 		// verify id
-		assertEquals("50|dedup_wf_001::2d2bbbbcfb285e3fb3590237b79e2fa8", pub_merged.getId());
+		assertEquals("50|dedup_wf_001::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId());
 	}
 
 	@Test
 	public void publicationMergerTest5() throws InstantiationException, IllegalStateException, IllegalAccessException {
 
+		System.out
+			.println(
+				publications5
+					.stream()
+					.map(p -> p._2().getId())
+					.collect(Collectors.toList()));
+
 		Publication pub_merged = DedupRecordFactory
 			.entityMerger(dedupId, publications5.iterator(), 0, dataInfo, Publication.class);
 
 		// verify id
-		assertEquals("50|dedup_wf_001::584b89679c3ccd1015b647ec63cc2699", pub_merged.getId());
+		assertEquals("50|dedup_wf_001::0ca46ff10b2b4c756191719d85302b14", pub_merged.getId());
 	}
 
 	public DataInfo setDI() {

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

@@ -7,97 +7,57 @@ import java.io.BufferedReader;
 import java.io.FileReader;
 import java.io.IOException;
 import java.nio.file.Paths;
-import java.text.SimpleDateFormat;
 import java.util.ArrayList;
-import java.util.Date;
 import java.util.List;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
-import org.codehaus.jackson.map.ObjectMapper;
+import org.junit.jupiter.api.BeforeAll;
-import org.junit.jupiter.api.*;
+import org.junit.jupiter.api.MethodOrderer;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestMethodOrder;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.oa.dedup.model.Identifier;
-import eu.dnetlib.dhp.oa.dedup.model.PidType;
+import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.common.EntityType;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.pace.util.MapDocumentUtil;
 import scala.Tuple2;
 
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
 public class IdGeneratorTest {
 
-	private static List<Identifier> bestIds;
+	private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
-	private static List<Tuple2<String, Publication>> pubs;
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
-	private static List<Identifier> bestIds2;
+	private static List<Identifier<Publication>> bestIds;
-	private static List<Identifier> bestIds3;
+	private static List<Identifier<Publication>> bestIds2;
+	private static List<Identifier<Publication>> bestIds3;
 
 	private static String testEntityBasePath;
 
-	private static SimpleDateFormat sdf;
-	private static Date baseDate;
-
 	@BeforeAll
 	public static void setUp() throws Exception {
-
-		sdf = new SimpleDateFormat("yyyy-MM-dd");
-		baseDate = sdf.parse("2000-01-01");
-
-		bestIds = new ArrayList<>();
-		bestIds2 = Lists
-			.newArrayList(
-				new Identifier(pid("pid1", "original", "original"), baseDate, PidType.original,
-					keyValue("key", "value"), EntityType.publication, "50|originalID1"),
-				new Identifier(pid("pid2", "original", "original"), baseDate, PidType.original,
-					keyValue("key", "value"), EntityType.publication, "50|originalID2"),
-				new Identifier(pid("pid3", "original", "original"), baseDate, PidType.original,
-					keyValue("key", "value"), EntityType.publication, "50|originalID3"));
-		bestIds3 = Lists
-			.newArrayList(
-				new Identifier(pid("pid1", "original", "original"), baseDate, PidType.original,
-					keyValue("key", "value"), EntityType.publication, "50|originalID1"),
-				new Identifier(pid("pid2", "doi", "doi"), baseDate, PidType.doi, keyValue("key", "value"),
-					EntityType.publication, "50|originalID2"),
-				new Identifier(pid("pid3", "original", "original"), baseDate, PidType.original,
-					keyValue("key", "value"), EntityType.publication, "50|originalID3"));
-
 		testEntityBasePath = Paths
 			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
 			.toFile()
 			.getAbsolutePath();
 
-		pubs = readSample(testEntityBasePath + "/publication_idgeneration.json", Publication.class);
+		bestIds = createBestIds(testEntityBasePath + "/publication_idgeneration.json", Publication.class);
-
+		bestIds2 = createBestIds(testEntityBasePath + "/publication_idgeneration2.json", Publication.class);
+		bestIds3 = createBestIds(testEntityBasePath + "/publication_idgeneration3.json", Publication.class);
 	}
 
 	@Test
-	@Order(1)
-	public void bestPidToIdentifierTest() {
-
-		List<String> typesForAssertions = Lists
-			.newArrayList(PidType.pmc.toString(), PidType.doi.toString(), PidType.doi.toString());
-
-		for (Tuple2<String, Publication> pub : pubs) {
-			List<Identifier> ids = IdGenerator.bestPidToIdentifier(pub._2());
-			assertEquals(typesForAssertions.get(pubs.indexOf(pub)), ids.get(0).getPid().getQualifier().getClassid());
-			bestIds.addAll(ids);
-		}
-	}
-
-	@Test
-	@Order(2)
 	public void generateIdTest1() {
 		String id1 = IdGenerator.generate(bestIds, "50|defaultID");
 
 		System.out
-			.println("id list 1 = " + bestIds.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList()));
+			.println("id list 1 = " + bestIds.stream().map(i -> i.getOriginalID()).collect(Collectors.toList()));
 
-		assertEquals("50|dedup_wf_001::9c5cfbf993d38476e0f959a301239719", id1);
+		assertEquals("50|doi_dedup___::0968af610a356656706657e4f234b340", id1);
 	}
 
 	@Test
@@ -106,14 +66,22 @@ public class IdGeneratorTest {
 		String id2 = IdGenerator.generate(bestIds3, "50|defaultID");
 
 		System.out
-			.println("id list 2 = " + bestIds2.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList()));
+			.println("id list 2 = " + bestIds2.stream().map(i -> i.getOriginalID()).collect(Collectors.toList()));
 		System.out.println("winner 2 = " + id1);
 		System.out
-			.println("id list 3 = " + bestIds3.stream().map(i -> i.getPid().getValue()).collect(Collectors.toList()));
+			.println("id list 3 = " + bestIds3.stream().map(i -> i.getOriginalID()).collect(Collectors.toList()));
 		System.out.println("winner 3 = " + id2);
 
-		assertEquals("50|dedup_wf_001::2c56cc1914bffdb30fdff354e0099612", id1);
+		assertEquals("50|doi_dedup___::1a77a3bba737f8b669dcf330ad3b37e2", id1);
-		assertEquals("50|dedup_doi___::128ead3ed8d9ecf262704b6fcf592b8d", id2);
+		assertEquals("50|dedup_wf_001::0829b5191605bdbea36d6502b8c1ce1g", id2);
+	}
+
+	protected static <T extends OafEntity> List<Identifier<T>> createBestIds(String path, Class<T> clazz) {
+		final Stream<Identifier<T>> ids = readSample(path, clazz)
+			.stream()
+			.map(Tuple2::_2)
+			.map(Identifier::newInstance);
+		return ids.collect(Collectors.toList());
 	}
 
 	public static <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
@@ -127,7 +95,7 @@ public class IdGeneratorTest {
 					.add(
 						new Tuple2<>(
 							MapDocumentUtil.getJPathString("$.id", line),
-							new ObjectMapper().readValue(line, clazz)));
+							OBJECT_MAPPER.readValue(line, clazz)));
 				// read next line
 				line = reader.readLine();
 			}
@@ -140,23 +108,10 @@ public class IdGeneratorTest {
 	}
 
 	public static StructuredProperty pid(String pid, String classid, String classname) {
-
+		return OafMapperUtils.structuredProperty(pid, classid, classname, "", "", new DataInfo());
-		StructuredProperty sp = new StructuredProperty();
-		sp.setValue(pid);
-		Qualifier q = new Qualifier();
-		q.setSchemeid(classid);
-		q.setSchemename(classname);
-		q.setClassname(classname);
-		q.setClassid(classid);
-		sp.setQualifier(q);
-		return sp;
 	}
 
 	public static List<KeyValue> keyValue(String key, String value) {
-
+		return Lists.newArrayList(OafMapperUtils.keyValue(key, value));
-		KeyValue kv = new KeyValue();
-		kv.setKey(key);
-		kv.setValue(value);
-		return Lists.newArrayList(kv);
 	}
 }

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration2.json

@@ -0,0 +1,3 @@
+{ "id" : "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "pid" : [ { "value" : "pid1", "qualifier" : { "classid" : "original" } } ], "dateofacceptance" :  { "value" :  "2000-01-01"}, "collectedfrom" : [ { "key" : "key", "value" :  "value" } ] }
+{ "id" : "50|doi_________::1a77a3bba737f8b669dcf330ad3b37e2", "pid" : [ { "value" : "pid2", "qualifier" : { "classid" : "doi" } } ], "dateofacceptance" :  { "value" :  "2000-01-01"}, "collectedfrom" : [ { "key" : "key", "value" :  "value" } ] }
+{ "id" : "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "pid" : [ { "value" : "pid3", "qualifier" : { "classid" : "original" } } ], "dateofacceptance" :  { "value" :  "2000-01-01"}, "collectedfrom" : [ { "key" : "key", "value" :  "value" } ] }

dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/json/publication_idgeneration3.json

@@ -0,0 +1,3 @@
+{ "id" : "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "pid" : [ { "value" : "pid1", "qualifier" : { "classid" : "original" } } ], "dateofacceptance" :  { "value" :  "2000-01-01"}, "collectedfrom" : [ { "key" : "key", "value" :  "value" } ] }
+{ "id" : "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1h", "pid" : [ { "value" : "pid2", "qualifier" : { "classid" : "original" } } ], "dateofacceptance" :  { "value" :  "2000-01-01"}, "collectedfrom" : [ { "key" : "key", "value" :  "value" } ] }
+{ "id" : "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1i", "pid" : [ { "value" : "pid3", "qualifier" : { "classid" : "original" } } ], "dateofacceptance" :  { "value" :  "2000-01-01"}, "collectedfrom" : [ { "key" : "key", "value" :  "value" } ] }