Merge branch 'beta' into dedup_whitelist

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java

@@ -12,6 +12,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.AccessRight;
 import eu.dnetlib.dhp.schema.oaf.Country;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.Relation;
 
 public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Object>> implements Serializable {
 
@@ -24,17 +25,31 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
 		CleaningRuleMap mapping = new CleaningRuleMap();
 		mapping.put(Qualifier.class, o -> cleanQualifier(vocabularies, (Qualifier) o));
 		mapping.put(AccessRight.class, o -> cleanQualifier(vocabularies, (AccessRight) o));
-		mapping.put(Country.class, o -> {
+		mapping.put(Country.class, o -> cleanCountry(vocabularies, (Country) o));
-			final Country c = (Country) o;
+		mapping.put(Relation.class, o -> cleanRelation(vocabularies, (Relation) o));
-			if (StringUtils.isBlank(c.getSchemeid())) {
-				c.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
-				c.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
-			}
-			cleanQualifier(vocabularies, c);
-		});
 		return mapping;
 	}
 
+	private static void cleanRelation(VocabularyGroup vocabularies, Relation r) {
+		if (vocabularies.vocabularyExists(ModelConstants.DNET_RELATION_SUBRELTYPE)) {
+			Qualifier newValue = vocabularies.lookup(ModelConstants.DNET_RELATION_SUBRELTYPE, r.getSubRelType());
+			r.setSubRelType(newValue.getClassid());
+		}
+		if (vocabularies.vocabularyExists(ModelConstants.DNET_RELATION_RELCLASS)) {
+			Qualifier newValue = vocabularies.lookup(ModelConstants.DNET_RELATION_RELCLASS, r.getRelClass());
+			r.setRelClass(newValue.getClassid());
+		}
+	}
+
+	private static void cleanCountry(VocabularyGroup vocabularies, Country o) {
+		final Country c = o;
+		if (StringUtils.isBlank(c.getSchemeid())) {
+			c.setSchemeid(ModelConstants.DNET_COUNTRY_TYPE);
+			c.setSchemename(ModelConstants.DNET_COUNTRY_TYPE);
+		}
+		cleanQualifier(vocabularies, c);
+	}
+
 	private static <Q extends Qualifier> void cleanQualifier(VocabularyGroup vocabularies, Q q) {
 		if (vocabularies.vocabularyExists(q.getSchemeid())) {
 			Qualifier newValue = vocabularies.lookup(q.getSchemeid(), q.getClassid());

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java

@@ -5,6 +5,7 @@ import static org.junit.jupiter.api.Assertions.*;
 import static org.mockito.Mockito.lenient;
 
 import java.io.IOException;
+import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 import java.util.stream.Stream;
@@ -16,12 +17,12 @@ import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.GraphCleaningFunctions;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
@@ -29,7 +30,8 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 @ExtendWith(MockitoExtension.class)
 public class GraphCleaningFunctionsTest {
 
-	public static final ObjectMapper MAPPER = new ObjectMapper();
+	public static final ObjectMapper MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
 	@Mock
 	private ISLookUpService isLookUpService;
@@ -49,6 +51,23 @@ public class GraphCleaningFunctionsTest {
 		mapping = CleaningRuleMap.create(vocabularies);
 	}
 
+	@Test
+	void testCleanRelations() throws Exception {
+
+		List<String> lines = IOUtils
+			.readLines(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/relation.json"));
+		for (String json : lines) {
+			Relation r_in = MAPPER.readValue(json, Relation.class);
+			assertNotNull(r_in);
+
+			assertFalse(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r_in.getRelClass()));
+
+			Relation r_out = OafCleaner.apply(r_in, mapping);
+			assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_RELCLASS).contains(r_out.getRelClass()));
+			assertTrue(vocabularies.getTerms(ModelConstants.DNET_RELATION_SUBRELTYPE).contains(r_out.getSubRelType()));
+		}
+	}
+
 	@Test
 	void testCleaning() throws Exception {
 
@@ -87,7 +106,7 @@ public class GraphCleaningFunctionsTest {
 			p_out
 				.getPid()
 				.stream()
-				.map(p -> p.getQualifier())
+				.map(StructuredProperty::getQualifier)
 				.allMatch(q -> pidTerms.contains(q.getClassid())));
 
 		List<Instance> poi = p_out.getInstance();
@@ -101,8 +120,8 @@ public class GraphCleaningFunctionsTest {
 		assertEquals(2, poii.getPid().size());
 
 		assertTrue(
-			poii.getPid().stream().filter(s -> s.getValue().equals("10.1007/s109090161569x")).findFirst().isPresent());
+			poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
-		assertTrue(poii.getPid().stream().filter(s -> s.getValue().equals("10.1008/abcd")).findFirst().isPresent());
+		assertTrue(poii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd")));
 
 		assertNotNull(poii.getAlternateIdentifier());
 		assertEquals(2, poii.getAlternateIdentifier().size());
@@ -111,16 +130,12 @@ public class GraphCleaningFunctionsTest {
 			poii
 				.getAlternateIdentifier()
 				.stream()
-				.filter(s -> s.getValue().equals("10.1007/s109090161569x"))
+				.anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
-				.findFirst()
-				.isPresent());
 		assertTrue(
 			poii
 				.getAlternateIdentifier()
 				.stream()
-				.filter(s -> s.getValue().equals("10.1009/qwerty"))
+				.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
-				.findFirst()
-				.isPresent());
 
 		Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out);
 
@@ -142,8 +157,8 @@ public class GraphCleaningFunctionsTest {
 		assertEquals(2, pcii.getPid().size());
 
 		assertTrue(
-			pcii.getPid().stream().filter(s -> s.getValue().equals("10.1007/s109090161569x")).findFirst().isPresent());
+			pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1007/s109090161569x")));
-		assertTrue(pcii.getPid().stream().filter(s -> s.getValue().equals("10.1008/abcd")).findFirst().isPresent());
+		assertTrue(pcii.getPid().stream().anyMatch(s -> s.getValue().equals("10.1008/abcd")));
 
 		assertNotNull(pcii.getAlternateIdentifier());
 		assertEquals(1, pcii.getAlternateIdentifier().size());
@@ -151,9 +166,7 @@ public class GraphCleaningFunctionsTest {
 			pcii
 				.getAlternateIdentifier()
 				.stream()
-				.filter(s -> s.getValue().equals("10.1009/qwerty"))
+				.anyMatch(s -> s.getValue().equals("10.1009/qwerty")));
-				.findFirst()
-				.isPresent());
 
 		getAuthorPids(p_cleaned).forEach(pid -> {
 			System.out
@@ -172,17 +185,17 @@ public class GraphCleaningFunctionsTest {
 		return pub
 			.getAuthor()
 			.stream()
-			.map(a -> a.getPid())
+			.map(Author::getPid)
-			.flatMap(p -> p.stream())
+			.flatMap(Collection::stream)
-			.map(s -> s.getQualifier());
+			.map(StructuredProperty::getQualifier);
 	}
 
 	private Stream<StructuredProperty> getAuthorPids(Result pub) {
 		return pub
 			.getAuthor()
 			.stream()
-			.map(a -> a.getPid())
+			.map(Author::getPid)
-			.flatMap(p -> p.stream());
+			.flatMap(Collection::stream);
 	}
 
 	private List<String> vocs() throws IOException {

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/relation.json

@@ -0,0 +1,10 @@
+{"relType":"resultResult","subRelType":"citation","relClass":"cites","source":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556","target":"50|openaire____::007a4870b31056f89b768cf508e1538e"}
+{"relType":"resultResult","subRelType":"citation","relClass":"isCitedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"supplement","relClass":"isSupplementedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"part","relClass":"isPartOf","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"part","relClass":"hasPart","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"review","relClass":"isReviewedBy","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"review","relClass":"reviews","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"relationship","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}
+{"relType":"resultResult","subRelType":"publicationDataset","relClass":"isRelatedTo","source":"50|openaire____::007a4870b31056f89b768cf508e1538e","target":"50|4ScienceCRIS::f66f1bd369679b5b077dcdf006089556"}

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt

@@ -1231,4 +1231,14 @@ dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-学術雑誌論文（査
 dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-紀要論文（査読有り）
 dnet:review_levels @=@ 0001 @=@ 印刷物/電子媒体-雑誌記事（査読有り）
 dnet:review_levels @=@ 0001 @=@ 原著論文（査読有り）
-dnet:review_levels @=@ 0001 @=@ 査読論文
+dnet:review_levels @=@ 0001 @=@ 査読論文
+dnet:relation_relClass @=@ Cites @=@ cites
+dnet:relation_relClass @=@ IsCitedBy @=@ isCitedBy
+dnet:relation_relClass @=@ HasPart @=@ hasPart
+dnet:relation_relClass @=@ IsPartOf @=@ isPartOf
+dnet:relation_relClass @=@ IsReviewedBy @=@ isReviewedBy
+dnet:relation_relClass @=@ Reviews @=@ reviews
+dnet:relation_relClass @=@ IsSupplementTo @=@ isSupplementTo
+dnet:relation_relClass @=@ IsSupplementedBy @=@ isSupplementedBy
+dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo
+dnet:relation_subRelType @=@ relationship @=@ publicationDataset

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt

@@ -1079,4 +1079,41 @@ dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/DATASET/IS_SUPPLEMENTED
 dnet:topic_types @=@ dnet:topic_types @=@ ENRICH/MISSING/AUTHOR/ORCID @=@ An Open Researcher and Contributor ID (ORCID) that can be associated to an author of your publications
 dnet:review_levels @=@ dnet:review_levels @=@ 0000 @=@ Unknown
 dnet:review_levels @=@ dnet:review_levels @=@ 0002 @=@ nonPeerReviewed
-dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed
+dnet:review_levels @=@ dnet:review_levels @=@ 0001 @=@ peerReviewed
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ Cites @=@ Cites
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsCitedBy @=@ IsCitedBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ HasPart @=@ HasPart
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsPartOf @=@ IsPartOf
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsReviewedBy @=@ IsReviewedBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ Reviews @=@ Reviews
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsSupplementTo @=@ IsSupplementTo
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsSupplementedBy @=@ IsSupplementedBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsRelatedTo @=@ IsRelatedTo
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ Compiles @=@ Compiles
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ Continues @=@ Continues
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ Documents @=@ Documents
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ HasAmongTopNSimilarDocuments @=@ HasAmongTopNSimilarDocuments
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ HasVersion @=@ HasVersion
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsAmongTopNSimilarDocuments @=@ IsAmongTopNSimilarDocuments
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsCompiledBy @=@ IsCompiledBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsContinuedBy @=@ IsContinuedBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsDerivedFrom @=@ IsDerivedFrom
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsDocumentedBy @=@ IsDocumentedBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsNewVersionOf @=@ IsNewVersionOf
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsObsoletedBy @=@ IsObsoletedBy
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsOriginalFormOf @=@ IsOriginalFormOf
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsPreviousVersionOf @=@ IsPreviousVersionOf
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsSourceOf @=@ IsSourceOf
+dnet:relation_relClass @=@ dnet:relation_relClass @=@ IsVariantFormOf @=@ IsVariantFormOf
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ affiliation @=@ affiliation
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ citation @=@ citation
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ dedup @=@ dedup
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ outcome @=@ outcome
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ part @=@ part
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ participation @=@ participation
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ provision @=@ provision
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ relationship @=@ relationship
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ review @=@ review
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ similarity @=@ similarity
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ supplement @=@ supplement
+dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version

pom.xml

@@ -753,7 +753,7 @@
 		<mockito-core.version>3.3.3</mockito-core.version>
 		<mongodb.driver.version>3.4.2</mongodb.driver.version>
 		<vtd.version>[2.12,3.0)</vtd.version>
-		<dhp-schemas.version>[2.7.17]</dhp-schemas.version>
+		<dhp-schemas.version>[2.7.18]</dhp-schemas.version>
 		<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
 		<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
 		<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>