bug fix and minor changes

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

@@ -1,11 +1,8 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
 import java.util.*;
 
-import org.apache.commons.lang.StringUtils;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.MapGroupsFunction;
 import org.apache.spark.sql.Dataset;
@@ -18,7 +15,6 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Lists;
 
-import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import scala.Tuple2;
@@ -90,7 +86,7 @@ public class DedupRecordFactory {
 					T duplicate = t._2();
 
 					// prepare the list of pids to use for the id generation
-					bestPids.addAll(IdGenerator.bestPidtoIdentifier(duplicate));
+					bestPids.addAll(IdGenerator.bestPidToIdentifier(duplicate));
 
 					entity.mergeFrom(duplicate);
 					if (ModelSupport.isSubClass(duplicate, Result.class)) {

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

@@ -70,17 +70,6 @@ public class DedupUtility {
 		return Sets.newHashSet(BlacklistAwareClusteringCombiner.filterAndCombine(doc, conf));
 	}
 
-	public static String md5(final String s) {
-		try {
-			final MessageDigest md = MessageDigest.getInstance("MD5");
-			md.update(s.getBytes(StandardCharsets.UTF_8));
-			return new String(Hex.encodeHex(md.digest()));
-		} catch (final Exception e) {
-			System.err.println("Error creating id");
-			return null;
-		}
-	}
-
 	public static String createDedupRecordPath(
 		final String basePath, final String actionSetId, final String entityType) {
 		return String.format("%s/%s/%s_deduprecord", basePath, actionSetId, entityType);

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

@@ -6,6 +6,7 @@ import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.*;
 
+import eu.dnetlib.dhp.utils.DHPUtils;
 import org.apache.commons.lang.NullArgumentException;
 import org.apache.commons.lang.StringUtils;
 
@@ -34,17 +35,17 @@ public class IdGenerator implements Serializable {
 
 		if (bp.get().isUseOriginal() || bp.get().getPid().getValue() == null) {
 			return bp.get().getOriginalID().split("\\|")[0] + "|dedup_wf_001::"
-				+ DedupUtility.md5(bp.get().getOriginalID());
+				+ DHPUtils.md5(bp.get().getOriginalID());
 		} else {
 			return bp.get().getOriginalID().split("\\|")[0] + "|"
 				+ createPrefix(bp.get().getPid().getQualifier().getClassid()) + "::"
-				+ DedupUtility.md5(bp.get().getPid().getValue());
+				+ DHPUtils.md5(bp.get().getPid().getValue());
 		}
 
 	}
 
 	// 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) {
+	public static <T extends OafEntity> List<Identifier> bestPidToIdentifier(T entity) {
 
 		if (entity.getPid() == null || entity.getPid().size() == 0)
 			return Lists

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

@@ -4,6 +4,8 @@ package eu.dnetlib.dhp.oa.dedup;
 import java.io.Serializable;
 import java.util.Date;
 import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 import eu.dnetlib.dhp.schema.common.EntityType;
 import eu.dnetlib.dhp.schema.oaf.KeyValue;
@@ -35,7 +37,7 @@ public class Identifier implements Serializable, Comparable<Identifier> {
 		return pid;
 	}
 
-	public void setPid(StructuredProperty pidValue) {
+	public void setPid(StructuredProperty pid) {
 		this.pid = pid;
 	}
 
@@ -91,25 +93,29 @@ public class Identifier implements Serializable, Comparable<Identifier> {
 	public int compareTo(Identifier i) {
 		// priority in comparisons: 1) pidtype, 2) collectedfrom (depending on the entity type) , 3) date 4)
 		// alphabetical order of the originalID
+
+		Set<String> lKeys = this.collectedFrom.stream().map(KeyValue::getKey).collect(Collectors.toSet());
+		Set<String> rKeys = i.getCollectedFrom().stream().map(KeyValue::getKey).collect(Collectors.toSet());
+
 		if (this.getType().compareTo(i.getType()) == 0) { // same type
 			if (entityType == EntityType.publication) {
-				if (isFromDatasourceID(this.collectedFrom, IdGenerator.CROSSREF_ID)
+				if (isFromDatasourceID(lKeys, IdGenerator.CROSSREF_ID)
-					&& !isFromDatasourceID(i.collectedFrom, IdGenerator.CROSSREF_ID))
+					&& !isFromDatasourceID(rKeys, IdGenerator.CROSSREF_ID))
 					return 1;
-				if (isFromDatasourceID(i.collectedFrom, IdGenerator.CROSSREF_ID)
+				if (isFromDatasourceID(rKeys, IdGenerator.CROSSREF_ID)
-					&& !isFromDatasourceID(this.collectedFrom, IdGenerator.CROSSREF_ID))
+					&& !isFromDatasourceID(lKeys, IdGenerator.CROSSREF_ID))
 					return -1;
 			}
 			if (entityType == EntityType.dataset) {
-				if (isFromDatasourceID(this.collectedFrom, IdGenerator.DATACITE_ID)
+				if (isFromDatasourceID(lKeys, IdGenerator.DATACITE_ID)
-					&& !isFromDatasourceID(i.collectedFrom, IdGenerator.DATACITE_ID))
+					&& !isFromDatasourceID(rKeys, IdGenerator.DATACITE_ID))
 					return 1;
-				if (isFromDatasourceID(i.collectedFrom, IdGenerator.DATACITE_ID)
+				if (isFromDatasourceID(rKeys, IdGenerator.DATACITE_ID)
-					&& !isFromDatasourceID(this.collectedFrom, IdGenerator.DATACITE_ID))
+					&& !isFromDatasourceID(lKeys, IdGenerator.DATACITE_ID))
 					return -1;
 			}
 
-			if (this.getDate().compareTo(date) == 0) {// same date
+			if (this.getDate().compareTo(i.getDate()) == 0) {// same date
 
 				if (this.originalID.compareTo(i.originalID) > 0)
 					this.useOriginal = true;
@@ -120,19 +126,14 @@ public class Identifier implements Serializable, Comparable<Identifier> {
 				return -this.originalID.compareTo(i.originalID);
 			} else
 				// the minus is because we need to take the elder date
-				return -this.getDate().compareTo(date);
+				return -this.getDate().compareTo(i.getDate());
 		} else {
 			return this.getType().compareTo(i.getType());
 		}
 
 	}
 
-	public boolean isFromDatasourceID(List<KeyValue> collectedFrom, String dsId) {
+	public boolean isFromDatasourceID(Set<String> collectedFrom, String dsId) {
-
+		return collectedFrom.contains(dsId);
-		for (KeyValue cf : collectedFrom) {
-			if (cf.getKey().equals(dsId))
-				return true;
-		}
-		return false;
 	}
 }

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

@@ -4,7 +4,7 @@ package eu.dnetlib.dhp.oa.dedup;
 public enum PidType {
 
 	// from the less to the more important
-	undefined, original, orcid, ror, grid, pdb, arXiv, pmid, doi;
+	undefined, original, orcid, ror, grid, pdb, arXiv, pmid, pmc, doi;
 
 	public static PidType classidValueOf(String s) {
 		try {

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

@@ -6,6 +6,7 @@ import java.io.Serializable;
 import java.util.Set;
 import java.util.stream.Collectors;
 
+import eu.dnetlib.dhp.utils.DHPUtils;
 import org.apache.commons.lang.StringUtils;
 import org.codehaus.jackson.annotate.JsonIgnore;
 
@@ -36,7 +37,7 @@ public class ConnectedComponent implements Serializable {
 		if (docIds.size() > 1) {
 			final String s = getMin();
 			String prefix = s.split("\\|")[0];
-			ccId = prefix + "|dedup_wf_001::" + DedupUtility.md5(s);
+			ccId = prefix + "|dedup_wf_001::" + DHPUtils.md5(s);
 			return ccId;
 		} else {
 			return docIds.iterator().next();