implementation of the dedup_id generation using pids to make the graph more stable

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

@@ -114,7 +114,7 @@ public class DatePicker {
 		}
 	}
 
-	private static boolean inRange(final String date) {
+	public static boolean inRange(final String date) {
 		final int year = Integer.parseInt(substringBefore(date, "-"));
 		return year >= YEAR_LB && year <= YEAR_UB;
 	}

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

@@ -1,11 +1,12 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
-import java.io.Serializable;
+import com.fasterxml.jackson.databind.DeserializationFeature;
-import java.util.Collection;
+import com.fasterxml.jackson.databind.ObjectMapper;
-import java.util.Iterator;
+import com.google.common.collect.Lists;
-import java.util.List;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
-
+import eu.dnetlib.dhp.schema.oaf.*;
+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;
@@ -13,15 +14,12 @@ import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.DeserializationFeature;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.google.common.collect.Lists;
-
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.*;
 import scala.Tuple2;
 
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 public class DedupRecordFactory {
 
 	private static final Logger log = LoggerFactory.getLogger(DedupRecordFactory.class);
@@ -77,15 +75,23 @@ public class DedupRecordFactory {
 		String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
 		throws IllegalAccessException, InstantiationException {
 
+		SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
+
 		T entity = clazz.newInstance();
 
 		final Collection<String> dates = Lists.newArrayList();
 		final List<List<Author>> authors = Lists.newArrayList();
+		final List<Identifier> bestPids = Lists.newArrayList();  //best pids list
 
 		entities
 			.forEachRemaining(
 				t -> {
 					T duplicate = t._2();
+
+					StructuredProperty bestPid = bestPid(duplicate.getPid());
+					if (bestPid != null)
+						bestPids.add(new Identifier(bestPid, extractDate(duplicate, sdf), PidType.classidValueOf(bestPid.getQualifier().getClassid())));
+
 					entity.mergeFrom(duplicate);
 					if (ModelSupport.isSubClass(duplicate, Result.class)) {
 						Result r1 = (Result) duplicate;
@@ -94,6 +100,7 @@ public class DedupRecordFactory {
 						if (r1.getDateofacceptance() != null)
 							dates.add(r1.getDateofacceptance().getValue());
 					}
+
 				});
 
 		// set authors and date
@@ -102,10 +109,73 @@ public class DedupRecordFactory {
 			((Result) entity).setAuthor(AuthorMerger.merge(authors));
 		}
 
+		Identifier bestPid = winnerPid(bestPids);
+		if (bestPid == null)
 			entity.setId(id);
+		else
+			entity.setId(id.split("\\|")[0] + "|" + createPrefix(bestPid.getPid().getQualifier().getClassid()) + "::" + DedupUtility.md5(bestPid.getPid().getValue()));
+
 		entity.setLastupdatetimestamp(ts);
 		entity.setDataInfo(dataInfo);
 
 		return entity;
 	}
+
+	//pick the best pid from the list (consider date and pidtype)
+	public static Identifier winnerPid(List<Identifier> pids) {
+		if (pids == null || pids.size() == 0)
+			return null;
+		Optional<Identifier> bp = pids.stream()
+				.filter(pid -> pid.getType() != PidType.undefined)
+				.max(Identifier::compareTo);
+		return bp.orElse(null);
+	}
+
+	//pick the best pid from the entity
+	public static StructuredProperty bestPid(List<StructuredProperty> pids) {
+
+		if (pids == null || pids.size() == 0)
+			return null;
+		Optional<StructuredProperty> bp = pids.stream()
+				.filter(pid -> PidType.classidValueOf(pid.getQualifier().getClassid()) != PidType.undefined)
+				.max(Comparator.comparing(pid -> PidType.classidValueOf(pid.getQualifier().getClassid())));
+
+		return bp.orElse(null);
+	}
+
+	//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);
+
+	}
+
+	//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 = "2000-01-01";
+		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("\\d{4}-\\d{2}-\\d{2}") && DatePicker.inRange(date.getValue());
+	}
+
 }

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

@@ -0,0 +1,55 @@
+package eu.dnetlib.dhp.oa.dedup;
+
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+
+import java.io.Serializable;
+import java.util.Date;
+
+public class Identifier implements Serializable, Comparable<Identifier>{
+
+    StructuredProperty pid;
+    Date date;
+    PidType type;
+
+    public Identifier(StructuredProperty pid, Date date, PidType type) {
+        this.pid = pid;
+        this.date = date;
+        this.type = type;
+    }
+
+    public StructuredProperty getPid() {
+        return pid;
+    }
+
+    public void setPid(StructuredProperty pidValue) {
+        this.pid = pid;
+    }
+
+    public Date getDate() {
+        return date;
+    }
+
+    public void setDate(Date date) {
+        this.date = date;
+    }
+
+    public PidType getType() {
+        return type;
+    }
+
+    public void setType(PidType type) {
+        this.type = type;
+    }
+
+    @Override
+    public int compareTo(Identifier i) {
+        //priority in comparisons: 1) pidtype, 2) date
+        if (this.getType().compareTo(i.getType()) == 0){ //same type
+            return this.getDate().compareTo(date);
+        }
+        else {
+            return this.getType().compareTo(i.getType());
+        }
+
+    }
+}

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

@@ -0,0 +1,54 @@
+package eu.dnetlib.dhp.oa.dedup;
+
+public enum PidType {
+
+    //from the less to the more important
+    undefined,
+    orcid,
+    ror,
+    grid,
+    pdb,
+    arXiv,
+    pmid,
+    doi;
+
+    public static PidType classidValueOf(String s){
+        try {
+            return PidType.valueOf(s);
+        }
+        catch (Exception e) {
+            return PidType.undefined;
+        }
+    }
+
+}
+
+//dnet:pid_types
+//"actrn"
+//"nct"
+//"euctr"
+//"epo_id"
+//"gsk"
+//"GeoPass"
+//"GBIF"
+//"isrctn"
+//"ISNI"
+//"jprn"
+//"mag_id"
+//"oai"
+//"orcid"
+//"PANGAEA"
+//"epo_nr_epodoc"
+//"UNKNOWN"
+//"VIAF"
+//"arXiv"
+//"doi"
+//"grid"
+//"info:eu-repo/dai"
+//"orcidworkid"
+//"pmc"
+//"pmid"
+//"urn"
+//"who"
+//"drks"
+//"pdb"

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

@@ -22,10 +22,11 @@ public class EntityMergerTest implements Serializable {
 
 	List<Tuple2<String, Publication>> publications;
 	List<Tuple2<String, Publication>> publications2;
+	List<Tuple2<String, Publication>> publications3;
 
 	String testEntityBasePath;
 	DataInfo dataInfo;
-	String dedupId = "dedup_id";
+	String dedupId = "00|dedup_id::1";
 	Publication pub_top;
 
 	@BeforeEach
@@ -38,6 +39,8 @@ public class EntityMergerTest implements Serializable {
 
 		publications = readSample(testEntityBasePath + "/publication_merge.json", Publication.class);
 		publications2 = readSample(testEntityBasePath + "/publication_merge2.json", Publication.class);
+		publications3 = readSample(testEntityBasePath + "/publication_merge3.json", Publication.class);
+
 
 		pub_top = getTopPub(publications);
 
@@ -54,6 +57,9 @@ public class EntityMergerTest implements Serializable {
 			.entityMerger(dedupId, softwares.iterator(), 0, dataInfo, Software.class);
 
 		assertEquals(merged.getBestaccessright().getClassid(), "OPEN SOURCE");
+
+		assertEquals(merged.getId(), "00|dedup_doi___::0968af610a356656706657e4f234b340");
+
 	}
 
 	@Test
@@ -62,7 +68,8 @@ public class EntityMergerTest implements Serializable {
 		Publication pub_merged = DedupRecordFactory
 			.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
 
-		assertEquals(dedupId, pub_merged.getId());
+		// verify id
+		assertEquals(pub_merged.getId(), "00|dedup_doi___::0968af610a356656706657e4f234b340");
 
 		assertEquals(pub_merged.getJournal(), pub_top.getJournal());
 		assertEquals(pub_merged.getBestaccessright(), pub_top.getBestaccessright());
@@ -117,11 +124,25 @@ public class EntityMergerTest implements Serializable {
 		Publication pub_merged = DedupRecordFactory
 			.entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class);
 
+		// verify id
+		assertEquals(pub_merged.getId(), "00|dedup_doi___::0ca46ff10b2b4c756191719d85302b14");
+
 		assertEquals(pub_merged.getAuthor().size(), 27);
-		// insert assertions here
 
 	}
 
+	@Test
+	public void publicationMergerTest3() throws InstantiationException, IllegalAccessException {
+
+		Publication pub_merged = DedupRecordFactory
+				.entityMerger(dedupId, publications3.iterator(), 0, dataInfo, Publication.class);
+
+		// verify id
+		assertEquals(pub_merged.getId(), "00|dedup_doi___::0ca46ff10b2b4c756191719d85302b14");
+
+	}
+
+
 	public DataInfo setDI() {
 		DataInfo dataInfo = new DataInfo();
 		dataInfo.setTrust("0.9");

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

@@ -1,22 +1,12 @@
 
 package eu.dnetlib.dhp.oa.dedup;
 
-import static java.nio.file.Files.createTempDirectory;
+import com.fasterxml.jackson.databind.ObjectMapper;
-
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import static org.apache.spark.sql.functions.col;
+import eu.dnetlib.dhp.schema.oaf.Relation;
-import static org.apache.spark.sql.functions.count;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import static org.mockito.Mockito.lenient;
+import eu.dnetlib.pace.util.MapDocumentUtil;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.Serializable;
-import java.net.URISyntaxException;
-import java.nio.file.Paths;
-import java.util.HashSet;
-import java.util.Set;
-import java.util.stream.Collectors;
-
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
@@ -35,16 +25,19 @@ import org.junit.jupiter.api.extension.ExtendWith;
 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;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
-import eu.dnetlib.pace.util.MapDocumentUtil;
 import scala.Tuple2;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.Serializable;
+import java.net.URISyntaxException;
+import java.nio.file.Paths;
+
+import static java.nio.file.Files.createTempDirectory;
+import static org.apache.spark.sql.functions.count;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.mockito.Mockito.lenient;
+
 @ExtendWith(MockitoExtension.class)
 @TestMethodOrder(MethodOrderer.OrderAnnotation.class)
 public class SparkDedupTest implements Serializable {