Merge pull request 'relation-from-odf' (#251) from relation-from-odf into beta

Reviewed-on: D-Net/dnet-hadoop#251

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java

@@ -30,6 +30,7 @@ import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 
 public abstract class AbstractMdRecordToOafMapper {
 
@@ -68,6 +69,17 @@ public abstract class AbstractMdRecordToOafMapper {
 		nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
 	}
 
+	// lowercase pidTypes as keys, normal casing for the values
+	protected static final Map<String, String> pidTypeWithAuthority = new HashMap<>();
+
+	static {
+		IdentifierFactory.PID_AUTHORITY
+			.keySet()
+			.stream()
+			.forEach(entry -> pidTypeWithAuthority.put(entry.toString().toLowerCase(), entry.toString()));
+
+	}
+
 	protected AbstractMdRecordToOafMapper(final VocabularyGroup vocs, final boolean invisible,
 		final boolean shouldHashId, final boolean forceOriginalId) {
 		this.vocs = vocs;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java

@@ -22,9 +22,12 @@ import com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.common.PacePerson;
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
+import eu.dnetlib.dhp.schema.common.ModelSupport;
+import eu.dnetlib.dhp.schema.common.RelationInverse;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+import eu.dnetlib.dhp.schema.oaf.utils.PidType;
 
 public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
@@ -393,36 +396,49 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 		final List<Oaf> res = new ArrayList<>();
 
 		for (final Object o : doc
-			.selectNodes("//*[local-name()='relatedIdentifier' and ./@relatedIdentifierType='OPENAIRE']")) {
+			.selectNodes("//*[local-name()='relatedIdentifier']")) {
 
-			final String originalId = ((Node) o).getText();
+			final String originalId = ((Node) o).getText().trim();
 
 			if (StringUtils.isNotBlank(originalId)) {
-				final String otherId = createOpenaireId(50, originalId, false);
+				final String idType = ((Node) o).valueOf("@relatedIdentifierType");
-				final String type = ((Node) o).valueOf("@relationType");
+				final String relType = ((Node) o).valueOf("@relationType");
+				String otherId = guessRelatedIdentifier(idType, originalId);
+				if (StringUtils.isNotBlank(otherId)) {
+					res.addAll(getRelations(relType, docId, otherId, entity));
+				}
 
-				if (type.equalsIgnoreCase(IS_SUPPLEMENT_TO)) {
-					res
-						.add(
-							getRelation(
-								docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, entity));
-					res
-						.add(
-							getRelation(
-								otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, entity));
-				} else if (type.equalsIgnoreCase(IS_PART_OF)) {
-					res
-						.add(
-							getRelation(
-								docId, otherId, RESULT_RESULT, PART, IS_PART_OF, entity));
-					res
-						.add(
-							getRelation(
-								otherId, docId, RESULT_RESULT, PART, HAS_PART, entity));
-				} else {
-					// TODO catch more semantics
 			}
 		}
+		return res;
+	}
+
+	protected String guessRelatedIdentifier(final String idType, final String value) {
+		if (StringUtils.isBlank(idType) || StringUtils.isBlank(value))
+			return null;
+		if (idType.equalsIgnoreCase("OPENAIRE"))
+			return createOpenaireId(50, value, false);
+		if (pidTypeWithAuthority.containsKey(idType.toLowerCase())) {
+			return IdentifierFactory.idFromPid("50", pidTypeWithAuthority.get(idType.toLowerCase()), value, true);
+		}
+		return null;
+
+	}
+
+	protected List<Oaf> getRelations(final String reltype, final String entityId, final String otherId,
+		final OafEntity entity) {
+		final List<Oaf> res = new ArrayList<>();
+		RelationInverse rel = ModelSupport.findRelation(reltype);
+		if (rel != null) {
+			res
+				.add(
+					getRelation(
+						entityId, otherId, rel.getRelType(), rel.getSubReltype(), rel.getRelClass(), entity));
+			res
+				.add(
+					getRelation(
+						otherId, entityId, rel.getRelType(), rel.getSubReltype(), rel.getInverseRelClass(), entity));
+
 		}
 		return res;
 	}

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java

@@ -579,8 +579,10 @@ class MappersTest {
 
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 
-		assertEquals(1, list.size());
+		assertEquals(3, list.size());
 		assertTrue(list.get(0) instanceof Software);
+		assertTrue(list.get(1) instanceof Relation);
+		assertTrue(list.get(2) instanceof Relation);
 
 		final Software s = (Software) list.get(0);
 
@@ -590,6 +592,22 @@ class MappersTest {
 		assertTrue(s.getAuthor().size() > 0);
 		assertTrue(s.getSubject().size() > 0);
 		assertTrue(s.getInstance().size() > 0);
+
+		final Relation r1 = (Relation) list.get(1);
+		final Relation r2 = (Relation) list.get(2);
+
+		assertEquals(s.getId(), r1.getSource());
+		assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r1.getTarget());
+		assertEquals(ModelConstants.RESULT_RESULT, r1.getRelType());
+		assertEquals(ModelConstants.RELATIONSHIP, r1.getSubRelType());
+		assertEquals(ModelConstants.IS_REFERENCED_BY, r1.getRelClass());
+
+		assertEquals(s.getId(), r2.getTarget());
+		assertEquals("50|doi_________::b453e7b4b2130ace57ff0c3db470a982", r2.getSource());
+		assertEquals(ModelConstants.RESULT_RESULT, r2.getRelType());
+		assertEquals(ModelConstants.RELATIONSHIP, r2.getSubRelType());
+		assertEquals(ModelConstants.REFERENCES, r2.getRelClass());
+
 	}
 
 	@Test
@@ -912,13 +930,13 @@ class MappersTest {
 	}
 
 	@Test
-	void testROHub() throws IOException, DocumentException {
+	void testROHub() throws IOException {
 		final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 		System.out.println("***************");
 		System.out.println(new ObjectMapper().writeValueAsString(list));
 		System.out.println("***************");
-//		final Dataset p = (Dataset) list.get(0);
+//		final OtherResearchProduct p = (OtherResearchProduct) list.get(0);
 //		assertValidId(p.getId());
 //		assertValidId(p.getCollectedfrom().get(0).getKey());
 //		System.out.println(p.getTitle().get(0).getValue());
@@ -926,13 +944,36 @@ class MappersTest {
 	}
 
 	@Test
-	void testROHub2() throws IOException, DocumentException {
+	void testROHub2() throws IOException {
 		final String xml = IOUtils
 			.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml")));
 		final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
 		System.out.println("***************");
 		System.out.println(new ObjectMapper().writeValueAsString(list));
 		System.out.println("***************");
+		assertEquals(7, list.size());
+		final OtherResearchProduct p = (OtherResearchProduct) list.get(0);
+		assertValidId(p.getId());
+		assertValidId(p.getCollectedfrom().get(0).getKey());
+		assertEquals("50|w3id________::afc7592914ae190a50570db90f55f9c2", p.getId());
+		assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
+		assertEquals("w3id", (p.getPid().get(0).getQualifier().getClassid()));
+		assertEquals("https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca", (p.getPid().get(0).getValue()));
+
+		assertEquals(1, list.stream().filter(o -> o instanceof OtherResearchProduct).count());
+		assertEquals(6, list.stream().filter(o -> o instanceof Relation).count());
+
+		for (Oaf oaf : list) {
+			if (oaf instanceof Relation) {
+				String source = ((Relation) oaf).getSource();
+				String target = ((Relation) oaf).getTarget();
+				assertNotEquals(source, target);
+				assertTrue(source.equals(p.getId()) || target.equals(p.getId()));
+				assertNotNull(((Relation) oaf).getSubRelType());
+				assertNotNull(((Relation) oaf).getRelClass());
+				assertNotNull(((Relation) oaf).getRelType());
+			}
+		}
 	}
 
 	@Test

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_dataset.xml

@@ -69,7 +69,6 @@
       </dates>
       <resourceType resourceTypeGeneral="Dataset"/>
       <relatedIdentifiers>
-        <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.3234525</relatedIdentifier>
         <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/epfl</relatedIdentifier>
       </relatedIdentifiers>
       <version>1.0.0</version>

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_software.xml

@@ -20,7 +20,7 @@
       <datacite:publisher>bio.tools</datacite:publisher>
       <datacite:relatedIdentifiers>
         <datacite:relatedIdentifier relatedIdentifierType="URL" relationType="IsDocumentedBy">http://maplab.imppc.org/chainy/</datacite:relatedIdentifier>
-        <datacite:relatedIdentifier relatedIdentifierType="DOI" relationType="isReferencedBy">10.1093/bioinformatics/btw839</datacite:relatedIdentifier>
+        <datacite:relatedIdentifier relatedIdentifierType="DOI" relationType="isreferencedBy">10.1093/bioinformatics/btw839</datacite:relatedIdentifier>
       </datacite:relatedIdentifiers>
       <datacite:alternateIdentifiers>
         <datacite:alternateIdentifier alternateIdentifierType="LandingPage">https://bio.tools/</datacite:alternateIdentifier>

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub-modified.xml

@@ -30,6 +30,9 @@
                 <datacite:relatedIdentifier relatedIdentifierType="w3id" relationType="HasPart">
                     https://w3id.org/ro-id/0ab171a7-45c5-4194-82d4-850955504bca/resources/6d3427a8-352e-49f4-9796-f618c44dc16d
                 </datacite:relatedIdentifier>
+                <datacite:relatedIdentifier relatedIdentifierType="OPENAIRE" relationType="isSupplementedBy">
+                    fsh_____4119::afc7592914ae190a50570db90f55f9c3
+                </datacite:relatedIdentifier>
             </datacite:relatedIdentifiers>
             <datacite:resourceType xs:anyURI="http://purl.org/coar/resource_type/c_1843">RO-crate</datacite:resourceType>
             <datacite:rightsList>

pom.xml

@@ -807,7 +807,7 @@
 		<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>[3.14.0]</dhp-schemas.version>
+		<dhp-schemas.version>[3.15.0]</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>