Merge pull request 'Fix for missing collectedfrom after dedup' (#442) from fix_mergedcliquesort into beta_to_master_may2024

Reviewed-on: #442

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

@@ -0,0 +1,104 @@
+
+package eu.dnetlib.dhp.schema.oaf.utils;
+
+import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
+
+import java.util.*;
+import java.util.stream.Collectors;
+
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class MergeEntitiesComparator implements Comparator<Oaf> {
+	static final List<String> PID_AUTHORITIES = Arrays
+		.asList(
+			ModelConstants.ARXIV_ID,
+			ModelConstants.PUBMED_CENTRAL_ID,
+			ModelConstants.EUROPE_PUBMED_CENTRAL_ID,
+			ModelConstants.DATACITE_ID,
+			ModelConstants.CROSSREF_ID);
+
+	static final List<String> RESULT_TYPES = Arrays
+		.asList(
+			ModelConstants.ORP_RESULTTYPE_CLASSID,
+			ModelConstants.SOFTWARE_RESULTTYPE_CLASSID,
+			ModelConstants.DATASET_RESULTTYPE_CLASSID,
+			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID);
+
+	public static final Comparator<Oaf> INSTANCE = new MergeEntitiesComparator();
+
+	@Override
+	public int compare(Oaf left, Oaf right) {
+		if (left == null && right == null)
+			return 0;
+		if (left == null)
+			return -1;
+		if (right == null)
+			return 1;
+
+		int res = 0;
+
+		// pid authority
+		int cfp1 = left
+			.getCollectedfrom()
+			.stream()
+			.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+			.max(Integer::compare)
+			.orElse(-1);
+		int cfp2 = right
+			.getCollectedfrom()
+			.stream()
+			.map(kv -> PID_AUTHORITIES.indexOf(kv.getKey()))
+			.max(Integer::compare)
+			.orElse(-1);
+
+		if (cfp1 >= 0 && cfp1 > cfp2) {
+			return 1;
+		} else if (cfp2 >= 0 && cfp2 > cfp1) {
+			return -1;
+		}
+
+		// trust
+		if (left.getDataInfo() != null && right.getDataInfo() != null) {
+			res = left.getDataInfo().getTrust().compareTo(right.getDataInfo().getTrust());
+		}
+
+		// result type
+		if (res == 0) {
+			if (left instanceof Result && right instanceof Result) {
+				Result r1 = (Result) left;
+				Result r2 = (Result) right;
+
+				if (r1.getResulttype() == null || r1.getResulttype().getClassid() == null) {
+					if (r2.getResulttype() != null && r2.getResulttype().getClassid() != null) {
+						return -1;
+					}
+				} else if (r2.getResulttype() == null || r2.getResulttype().getClassid() == null) {
+					return 1;
+				}
+
+				int rt1 = RESULT_TYPES.indexOf(r1.getResulttype().getClassid());
+				int rt2 = RESULT_TYPES.indexOf(r2.getResulttype().getClassid());
+
+				if (rt1 >= 0 && rt1 > rt2) {
+					return 1;
+				} else if (rt2 >= 0 && rt2 > rt1) {
+					return -1;
+				}
+			}
+		}
+
+		// id
+		if (res == 0) {
+			if (left instanceof OafEntity && right instanceof OafEntity) {
+				res = ((OafEntity) left).getId().compareTo(((OafEntity) right).getId());
+			}
+		}
+
+		return res;
+	}
+
+}

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

@@ -40,27 +40,12 @@ public class MergeUtils {
 
 	public static <T extends Oaf> T mergeGroup(String s, Iterator<T> oafEntityIterator,
 		boolean checkDelegateAuthority) {
-		TreeSet<T> sortedEntities = new TreeSet<>((o1, o2) -> {
-			int res = 0;
 
-			if (o1.getDataInfo() != null && o2.getDataInfo() != null) {
+		ArrayList<T> sortedEntities = new ArrayList<>();
-				res = o1.getDataInfo().getTrust().compareTo(o2.getDataInfo().getTrust());
+		oafEntityIterator.forEachRemaining(sortedEntities::add);
-			}
+		sortedEntities.sort(MergeEntitiesComparator.INSTANCE.reversed());
 
-			if (res == 0) {
+		Iterator<T> it = sortedEntities.iterator();
-				if (o1 instanceof Result && o2 instanceof Result) {
-					return ResultTypeComparator.INSTANCE.compare((Result) o1, (Result) o2);
-				}
-			}
-
-			return res;
-		});
-
-		while (oafEntityIterator.hasNext()) {
-			sortedEntities.add(oafEntityIterator.next());
-		}
-
-		Iterator<T> it = sortedEntities.descendingIterator();
 		T merged = it.next();
 
 		while (it.hasNext()) {
@@ -143,7 +128,7 @@ public class MergeUtils {
 	 * https://graph.openaire.eu/docs/data-model/pids-and-identifiers#delegated-authorities and in that case it prefers
 	 * such version.
 	 * <p>
-	 * Otherwise, it considers a resulttype priority order implemented in {@link ResultTypeComparator}
+	 * Otherwise, it considers a resulttype priority order implemented in {@link MergeEntitiesComparator}
 	 * and proceeds with the canonical property merging.
 	 *
 	 * @param left
@@ -161,8 +146,9 @@ public class MergeUtils {
 		if (!leftFromDelegatedAuthority && rightFromDelegatedAuthority) {
 			return right;
 		}
+
 		// TODO: raise trust to have preferred fields from one or the other??
-		if (new ResultTypeComparator().compare(left, right) < 0) {
+		if (MergeEntitiesComparator.INSTANCE.compare(left, right) > 0) {
 			return mergeResultFields(left, right);
 		} else {
 			return mergeResultFields(right, left);
@@ -225,9 +211,9 @@ public class MergeUtils {
 
 	private static <T, K> List<T> mergeLists(final List<T> left, final List<T> right, int trust,
 		Function<T, K> keyExtractor, BinaryOperator<T> merger) {
-		if (left == null) {
+		if (left == null || left.isEmpty()) {
-			return right;
+			return right != null ? right : new ArrayList<>();
-		} else if (right == null) {
+		} else if (right == null || right.isEmpty()) {
 			return left;
 		}
 
@@ -405,7 +391,7 @@ public class MergeUtils {
 		}
 
 		// should be an instance attribute, get the first non-null value
-		merge.setLanguage(coalesce(merge.getLanguage(), enrich.getLanguage()));
+		merge.setLanguage(coalesceQualifier(merge.getLanguage(), enrich.getLanguage()));
 
 		// distinct countries, do not manage datainfo
 		merge.setCountry(mergeQualifiers(merge.getCountry(), enrich.getCountry(), trust));
@@ -575,6 +561,13 @@ public class MergeUtils {
 		return m != null ? m : e;
 	}
 
+	private static Qualifier coalesceQualifier(Qualifier m, Qualifier e) {
+		if (m == null || m.getClassid() == null || StringUtils.isBlank(m.getClassid())) {
+			return e;
+		}
+		return m;
+	}
+
 	private static List<Author> mergeAuthors(List<Author> author, List<Author> author1, int trust) {
 		List<List<Author>> authors = new ArrayList<>();
 		if (author != null) {
@@ -587,6 +580,10 @@ public class MergeUtils {
 	}
 
 	private static String instanceKeyExtractor(Instance i) {
+		// three levels of concatenating:
+		// 1. ::
+		// 2. @@
+		// 3. ||
 		return String
 			.join(
 				"::",
@@ -594,10 +591,10 @@ public class MergeUtils {
 				kvKeyExtractor(i.getCollectedfrom()),
 				qualifierKeyExtractor(i.getAccessright()),
 				qualifierKeyExtractor(i.getInstancetype()),
-				Optional.ofNullable(i.getUrl()).map(u -> String.join("::", u)).orElse(null),
+				Optional.ofNullable(i.getUrl()).map(u -> String.join("@@", u)).orElse(null),
 				Optional
 					.ofNullable(i.getPid())
-					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("::")))
+					.map(pp -> pp.stream().map(MergeUtils::spKeyExtractor).collect(Collectors.joining("@@")))
 					.orElse(null));
 	}
 
@@ -706,7 +703,7 @@ public class MergeUtils {
 	private static String spKeyExtractor(StructuredProperty sp) {
 		return Optional
 			.ofNullable(sp)
-			.map(s -> Joiner.on("::").join(s, qualifierKeyExtractor(s.getQualifier())))
+			.map(s -> Joiner.on("||").join(qualifierKeyExtractor(s.getQualifier()), s.getValue()))
 			.orElse(null);
 	}
 

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

@@ -1,87 +0,0 @@
-
-package eu.dnetlib.dhp.schema.oaf.utils;
-
-import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
-
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Result;
-
-public class ResultTypeComparator implements Comparator<Result> {
-
-	public static final ResultTypeComparator INSTANCE = new ResultTypeComparator();
-
-	@Override
-	public int compare(Result left, Result right) {
-
-		if (left == null && right == null)
-			return 0;
-		if (left == null)
-			return 1;
-		if (right == null)
-			return -1;
-
-		HashSet<String> lCf = getCollectedFromIds(left);
-		HashSet<String> rCf = getCollectedFromIds(right);
-
-		if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
-			return -1;
-		}
-		if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
-			return 1;
-		}
-
-		if (left.getResulttype() == null || left.getResulttype().getClassid() == null) {
-			if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
-				return 0;
-			}
-			return 1;
-		} else if (right.getResulttype() == null || right.getResulttype().getClassid() == null) {
-			return -1;
-		}
-
-		String lClass = left.getResulttype().getClassid();
-		String rClass = right.getResulttype().getClassid();
-
-		if (!lClass.equals(rClass)) {
-			if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
-				return 1;
-
-			if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
-				return 1;
-
-			if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
-				return 1;
-
-			if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
-				return -1;
-			if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
-				return 1;
-		}
-
-		// Else (but unlikely), lexicographical ordering will do.
-		return lClass.compareTo(rClass);
-	}
-
-	protected HashSet<String> getCollectedFromIds(Result left) {
-		return Optional
-			.ofNullable(left.getCollectedfrom())
-			.map(
-				cf -> cf
-					.stream()
-					.map(KeyValue::getKey)
-					.collect(Collectors.toCollection(HashSet::new)))
-			.orElse(new HashSet<>());
-	}
-}

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

@@ -0,0 +1,103 @@
+
+package eu.dnetlib.dhp.oa.dedup;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.codehaus.jackson.map.ObjectMapper;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.utils.MergeUtils;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+import scala.Tuple2;
+
+class DatasetMergerTest implements Serializable {
+
+	private List<Tuple2<String, Dataset>> datasets;
+
+	private String testEntityBasePath;
+	private DataInfo dataInfo;
+	private final String dedupId = "50|doi_________::3d18564ef27ebe9ef3bd8b4dec67e148";
+	private Dataset dataset_top;
+
+	@BeforeEach
+	public void setUp() throws Exception {
+		testEntityBasePath = Paths
+			.get(SparkDedupTest.class.getResource("/eu/dnetlib/dhp/dedup/json").toURI())
+			.toFile()
+			.getAbsolutePath();
+
+		datasets = readSample(testEntityBasePath + "/dataset_merge.json", Dataset.class);
+
+		dataset_top = getTopPub(datasets);
+
+		dataInfo = setDI();
+	}
+
+	@Test
+	void datasetMergerTest() throws InstantiationException, IllegalAccessException, InvocationTargetException {
+		Dataset pub_merged = MergeUtils.mergeGroup(dedupId, datasets.stream().map(Tuple2::_2).iterator());
+
+		// verify id
+		assertEquals(dedupId, pub_merged.getId());
+		assertEquals(2, pub_merged.getInstance().size());
+	}
+
+	public DataInfo setDI() {
+		DataInfo dataInfo = new DataInfo();
+		dataInfo.setTrust("0.9");
+		dataInfo.setDeletedbyinference(false);
+		dataInfo.setInferenceprovenance("testing");
+		dataInfo.setInferred(true);
+		return dataInfo;
+	}
+
+	public Dataset getTopPub(List<Tuple2<String, Dataset>> publications) {
+
+		Double maxTrust = 0.0;
+		Dataset maxPub = new Dataset();
+		for (Tuple2<String, Dataset> publication : publications) {
+			Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
+			if (pubTrust > maxTrust) {
+				maxTrust = pubTrust;
+				maxPub = publication._2();
+			}
+		}
+		return maxPub;
+	}
+
+	public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
+		List<Tuple2<String, T>> res = new ArrayList<>();
+		BufferedReader reader;
+		try {
+			reader = new BufferedReader(new FileReader(path));
+			String line = reader.readLine();
+			while (line != null) {
+				res
+					.add(
+						new Tuple2<>(
+							MapDocumentUtil.getJPathString("$.id", line),
+							new ObjectMapper().readValue(line, clazz)));
+				// read next line
+				line = reader.readLine();
+			}
+			reader.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		return res;
+	}
+
+}

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

@@ -93,14 +93,14 @@ class EntityMergerTest implements Serializable {
 		assertEquals(pub_top.getJournal().getConferencedate(), pub_merged.getJournal().getConferencedate());
 		assertEquals(pub_top.getJournal().getConferenceplace(), pub_merged.getJournal().getConferenceplace());
 		assertEquals("OPEN", pub_merged.getBestaccessright().getClassid());
-		assertEquals(pub_top.getResulttype(), pub_merged.getResulttype());
+		assertEquals(pub_top.getResulttype().getClassid(), pub_merged.getResulttype().getClassid());
-		assertEquals(pub_top.getLanguage(), pub_merged.getLanguage());
+		assertEquals(pub_top.getLanguage().getClassid(), pub_merged.getLanguage().getClassid());
-		assertEquals(pub_top.getPublisher(), pub_merged.getPublisher());
+		assertEquals("Elsevier BV", pub_merged.getPublisher().getValue());
-		assertEquals(pub_top.getEmbargoenddate(), pub_merged.getEmbargoenddate());
+		assertEquals(pub_top.getEmbargoenddate().getValue(), pub_merged.getEmbargoenddate().getValue());
 		assertEquals(pub_top.getResourcetype().getClassid(), "");
 		assertEquals(pub_top.getDateoftransformation(), pub_merged.getDateoftransformation());
 		assertEquals(pub_top.getOaiprovenance(), pub_merged.getOaiprovenance());
-		assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
+		// assertEquals(pub_top.getDateofcollection(), pub_merged.getDateofcollection());
 		assertEquals(3, pub_merged.getInstance().size());
 		assertEquals(2, pub_merged.getCountry().size());
 		assertEquals(0, pub_merged.getSubject().size());