result pids (new xpaths + IS vocabularies)

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java

@@ -314,7 +314,8 @@ public class Result extends OafEntity implements Serializable {
 	}
 
 	private StructuredProperty getMainTitle(List<StructuredProperty> titles) {
-		//need to check if the list of titles contains more than 1 main title? (in that case, we should chose which main title select in the list)
+		// need to check if the list of titles contains more than 1 main title? (in that case, we should chose which
+		// main title select in the list)
 		for (StructuredProperty title : titles) {
 			if (title.getQualifier() != null && title.getQualifier().getClassid() != null)
 				if (title.getQualifier().getClassid().equals("main title"))

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

@@ -64,8 +64,10 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	protected static final String DATACITE_SCHEMA_KERNEL_4 = "http://datacite.org/schema/kernel-4";
 	protected static final String DATACITE_SCHEMA_KERNEL_3 = "http://datacite.org/schema/kernel-3";
-	protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
+	protected static final Qualifier ORCID_PID_TYPE = qualifier(
-	protected static final Qualifier MAG_PID_TYPE = qualifier("MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
+		"ORCID", "Open Researcher and Contributor ID", DNET_PID_TYPES, DNET_PID_TYPES);
+	protected static final Qualifier MAG_PID_TYPE = qualifier(
+		"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
 
 	protected static final Map<String, String> nsContext = new HashMap<>();
 
@@ -79,7 +81,8 @@ public abstract class AbstractMdRecordToOafMapper {
 		nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
 	}
 
-	protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
+	protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
+		"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
 
 	protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
 		this.code2name = code2name;
@@ -93,15 +96,20 @@ public abstract class AbstractMdRecordToOafMapper {
 				.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
 
 			final String type = doc.valueOf("//dr:CobjCategory/@type");
-			final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
+			final KeyValue collectedFrom = getProvenanceDatasource(
+				doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
 
-			if (collectedFrom == null) { return null; }
+			if (collectedFrom == null) {
+				return null;
+			}
 
 			final KeyValue hostedBy = StringUtils.isBlank(doc.valueOf("//oaf:hostedBy/@id"))
 				? collectedFrom
 				: getProvenanceDatasource(doc, "//oaf:hostedBy/@id", "//oaf:hostedBy/@name");
 
-			if (hostedBy == null) { return null; }
+			if (hostedBy == null) {
+				return null;
+			}
 
 			final DataInfo info = prepareDataInfo(doc);
 			final long lastUpdateTimestamp = new Date().getTime();
@@ -116,7 +124,9 @@ public abstract class AbstractMdRecordToOafMapper {
 		final String dsId = doc.valueOf(xpathId);
 		final String dsName = doc.valueOf(xpathName);
 
-		if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; }
+		if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) {
+			return null;
+		}
 
 		return keyValue(createOpenaireId(10, dsId, true), dsName);
 	}
@@ -201,9 +211,15 @@ public abstract class AbstractMdRecordToOafMapper {
 				final String projectId = createOpenaireId(40, originalId, true);
 
 				res
-					.add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp));
+					.add(
+						getRelation(
+							docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
+							lastUpdateTimestamp));
 				res
-					.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp));
+					.add(
+						getRelation(
+							projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
+							lastUpdateTimestamp));
 			}
 		}
 
@@ -398,7 +414,9 @@ public abstract class AbstractMdRecordToOafMapper {
 			final String sp = n.valueOf("@sp");
 			final String vol = n.valueOf("@vol");
 			final String edition = n.valueOf("@edition");
-			if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
+			if (StringUtils.isNotBlank(name)) {
+				return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
+			}
 		}
 		return null;
 	}
@@ -451,7 +469,10 @@ public abstract class AbstractMdRecordToOafMapper {
 		for (final Object o : node.selectNodes(xpath)) {
 			final Node n = (Node) o;
 			res
-				.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
+				.add(
+					structuredProperty(
+						n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
+						n.valueOf("@schemename"), info));
 		}
 		return res;
 	}
@@ -459,7 +480,9 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected OAIProvenance prepareOAIprovenance(final Document doc) {
 		final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
 
-		if (n == null) { return null; }
+		if (n == null) {
+			return null;
+		}
 
 		final String identifier = n.valueOf("./*[local-name()='identifier']");
 		final String baseURL = n.valueOf("./*[local-name()='baseURL']");
@@ -474,7 +497,9 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected DataInfo prepareDataInfo(final Document doc) {
 		final Node n = doc.selectSingleNode("//oaf:datainfo");
 
-		if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
+		if (n == null) {
+			return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
+		}
 
 		final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
 		final String paClassName = n.valueOf("./oaf:provenanceaction/@classname");
@@ -486,7 +511,9 @@ public abstract class AbstractMdRecordToOafMapper {
 		final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
 		final String trust = n.valueOf("./oaf:trust");
 
-		return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
+		return dataInfo(
+			deletedbyinference, inferenceprovenance, inferred, false,
+			qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
 	}
 
 	protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {

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

@@ -56,7 +56,8 @@ public class GenerateEntitiesApplication {
 	public static void main(final String[] args) throws Exception {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
-				.toString(GenerateEntitiesApplication.class
+				.toString(
+					GenerateEntitiesApplication.class
 						.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
 
 		parser.parseArgument(args);
@@ -105,7 +106,8 @@ public class GenerateEntitiesApplication {
 
 		for (final String sp : existingSourcePaths) {
 			inputRdd = inputRdd
-				.union(sc
+				.union(
+					sc
 						.sequenceFile(sp, Text.class, Text.class)
 						.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
 						.map(k -> convertToListOaf(k._1(), k._2(), code2name))
@@ -117,7 +119,8 @@ public class GenerateEntitiesApplication {
 			.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
 			.reduceByKey((o1, o2) -> merge(o1, o2))
 			.map(Tuple2::_2)
-			.map(oaf -> oaf.getClass().getSimpleName().toLowerCase()
+			.map(
+				oaf -> oaf.getClass().getSimpleName().toLowerCase()
 					+ "|"
 					+ OBJECT_MAPPER.writeValueAsString(oaf))
 			.saveAsTextFile(targetPath, GzipCodec.class);
@@ -194,8 +197,10 @@ public class GenerateEntitiesApplication {
 	private static Map<String, String> loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
 		final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
 
-		final String xquery =
+		final String xquery = IOUtils
-			IOUtils.toString(GenerateEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
+			.toString(
+				GenerateEntitiesApplication.class
+					.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
 
 		final Map<String, String> map = new HashMap<>();
 

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

@@ -130,7 +130,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 		final Instance instance = new Instance();
 		instance
-			.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
+			.setInstancetype(
+				prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
 		instance.setCollectedfrom(collectedfrom);
 		instance.setHostedby(hostedby);
 		instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@@ -146,7 +147,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 		final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
 		instance
-			.setUrl(nodes
+			.setUrl(
+				nodes
 					.stream()
 					.filter(n -> StringUtils.isNotBlank(n.getText()))
 					.map(n -> n.getText().trim())
@@ -277,9 +279,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 				final String otherId = createOpenaireId(50, originalId, false);
 
 				res
-					.add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
+					.add(
+						getRelation(
+							docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
+							lastUpdateTimestamp));
 				res
-					.add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
+					.add(
+						getRelation(
+							otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
+							lastUpdateTimestamp));
 			}
 		}
 		return res;
@@ -292,6 +300,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
-		return prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info);
+		return prepareListStructProps(
+			doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info);
 	}
 }

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

@@ -120,7 +120,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 		final Instance instance = new Instance();
 		instance
-			.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
+			.setInstancetype(
+				prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
 		instance.setCollectedfrom(collectedfrom);
 		instance.setHostedby(hostedby);
 		instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@@ -169,7 +170,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 				&& !dateType.equalsIgnoreCase("Updated")
 				&& !dateType.equalsIgnoreCase("Available")) {
 				res
-					.add(structuredProperty(((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE, info));
+					.add(
+						structuredProperty(
+							((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
+							info));
 			}
 		}
 		return res;
@@ -221,14 +225,16 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	protected List<Field<String>> prepareOtherResearchProductContactGroups(
 		final Document doc,
 		final DataInfo info) {
-		return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
+		return prepareListFields(
+			doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
 	}
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductContactPersons(
 		final Document doc,
 		final DataInfo info) {
-		return prepareListFields(doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
+		return prepareListFields(
+			doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
 	}
 
 	@Override
@@ -254,7 +260,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	protected List<Field<String>> prepareSoftwareDocumentationUrls(
 		final Document doc,
 		final DataInfo info) {
-		return prepareListFields(doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
+		return prepareListFields(
+			doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
 	}
 
 	// DATASETS
@@ -328,16 +335,29 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 				if (type.equalsIgnoreCase("IsSupplementTo")) {
 					res
-						.add(getRelation(docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info, lastUpdateTimestamp));
+						.add(
+							getRelation(
+								docId, otherId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENT_TO, collectedFrom, info,
+								lastUpdateTimestamp));
 					res
-						.add(getRelation(otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info, lastUpdateTimestamp));
+						.add(
+							getRelation(
+								otherId, docId, RESULT_RESULT, SUPPLEMENT, IS_SUPPLEMENTED_BY, collectedFrom, info,
+								lastUpdateTimestamp));
 				} else if (type.equals("IsPartOf")) {
 
 					res
-						.add(getRelation(docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info, lastUpdateTimestamp));
+						.add(
+							getRelation(
+								docId, otherId, RESULT_RESULT, PART, IS_PART_OF, collectedFrom, info,
+								lastUpdateTimestamp));
 					res
-						.add(getRelation(otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info, lastUpdateTimestamp));
+						.add(
-				} else {}
+							getRelation(
+								otherId, docId, RESULT_RESULT, PART, HAS_PARTS, collectedFrom, info,
+								lastUpdateTimestamp));
+				} else {
+				}
 			}
 		}
 		return res;
@@ -345,15 +365,28 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
-		return prepareQualifier(doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE, DNET_DATA_CITE_RESOURCE);
+		return prepareQualifier(
+			doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
+			DNET_DATA_CITE_RESOURCE);
 	}
 
 	@Override
 	protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo info) {
 		final List<StructuredProperty> res = new ArrayList<>();
-		res.addAll(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
+		res
-		res.addAll(prepareListStructProps(doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
+			.addAll(
-		res.addAll(prepareListStructProps(doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']", "@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info));
+				prepareListStructProps(
+					doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
+		res
+			.addAll(
+				prepareListStructProps(
+					doc, "//datacite:identifier[@identifierType != 'URL']", "@identifierType", "dnet:pid_types",
+					"dnet:pid_types", info));
+		res
+			.addAll(
+				prepareListStructProps(
+					doc, "//datacite:alternateIdentifier[@alternateIdentifierType != 'URL']",
+					"@alternateIdentifierType", "dnet:pid_types", "dnet:pid_types", info));
 		return res;
 	}