result pids (new xpaths + IS vocabularies)

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

@@ -10,10 +10,27 @@ import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.listFields;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.oaiIProvenance;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.qualifier;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DATASET_DEFAULT_RESULTTYPE;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PID_TYPES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.NOT_AVAILABLE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.ORP_DEFAULT_RESULTTYPE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.OUTCOME;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
@@ -47,10 +64,8 @@ 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(
+	protected static final Qualifier ORCID_PID_TYPE = qualifier("ORCID", "Open Researcher and Contributor ID", 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 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<>();
 
@@ -64,8 +79,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		nsContext.put("datacite", DATACITE_SCHEMA_KERNEL_3);
 	}
 
-	protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier(
+	protected static final Qualifier MAIN_TITLE_QUALIFIER = qualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
-		"main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
 
 	protected AbstractMdRecordToOafMapper(final Map<String, String> code2name) {
 		this.code2name = code2name;
@@ -79,20 +93,15 @@ 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(
+			final KeyValue collectedFrom = getProvenanceDatasource(doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
-				doc, "//oaf:collectedFrom/@id", "//oaf:collectedFrom/@name");
 
-			if (collectedFrom == null) {
+			if (collectedFrom == null) { return 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) {
+			if (hostedBy == null) { return null; }
-				return null;
-			}
 
 			final DataInfo info = prepareDataInfo(doc);
 			final long lastUpdateTimestamp = new Date().getTime();
@@ -107,9 +116,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		final String dsId = doc.valueOf(xpathId);
 		final String dsName = doc.valueOf(xpathName);
 
-		if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) {
+		if (StringUtils.isBlank(dsId) | StringUtils.isBlank(dsName)) { return null; }
-			return null;
-		}
 
 		return keyValue(createOpenaireId(10, dsId, true), dsName);
 	}
@@ -125,47 +132,47 @@ public abstract class AbstractMdRecordToOafMapper {
 		final List<Oaf> oafs = new ArrayList<>();
 
 		switch (type.toLowerCase()) {
-			case "publication":
+		case "publication":
-				final Publication p = new Publication();
+			final Publication p = new Publication();
-				populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
+			populateResultFields(p, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
-				p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
+			p.setResulttype(PUBLICATION_DEFAULT_RESULTTYPE);
-				p.setJournal(prepareJournal(doc, info));
+			p.setJournal(prepareJournal(doc, info));
-				oafs.add(p);
+			oafs.add(p);
-				break;
+			break;
-			case "dataset":
+		case "dataset":
-				final Dataset d = new Dataset();
+			final Dataset d = new Dataset();
-				populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
+			populateResultFields(d, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
-				d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
+			d.setResulttype(DATASET_DEFAULT_RESULTTYPE);
-				d.setStoragedate(prepareDatasetStorageDate(doc, info));
+			d.setStoragedate(prepareDatasetStorageDate(doc, info));
-				d.setDevice(prepareDatasetDevice(doc, info));
+			d.setDevice(prepareDatasetDevice(doc, info));
-				d.setSize(prepareDatasetSize(doc, info));
+			d.setSize(prepareDatasetSize(doc, info));
-				d.setVersion(prepareDatasetVersion(doc, info));
+			d.setVersion(prepareDatasetVersion(doc, info));
-				d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
+			d.setLastmetadataupdate(prepareDatasetLastMetadataUpdate(doc, info));
-				d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
+			d.setMetadataversionnumber(prepareDatasetMetadataVersionNumber(doc, info));
-				d.setGeolocation(prepareDatasetGeoLocations(doc, info));
+			d.setGeolocation(prepareDatasetGeoLocations(doc, info));
-				oafs.add(d);
+			oafs.add(d);
-				break;
+			break;
-			case "software":
+		case "software":
-				final Software s = new Software();
+			final Software s = new Software();
-				populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
+			populateResultFields(s, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
-				s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
+			s.setResulttype(SOFTWARE_DEFAULT_RESULTTYPE);
-				s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
+			s.setDocumentationUrl(prepareSoftwareDocumentationUrls(doc, info));
-				s.setLicense(prepareSoftwareLicenses(doc, info));
+			s.setLicense(prepareSoftwareLicenses(doc, info));
-				s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
+			s.setCodeRepositoryUrl(prepareSoftwareCodeRepositoryUrl(doc, info));
-				s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
+			s.setProgrammingLanguage(prepareSoftwareProgrammingLanguage(doc, info));
-				oafs.add(s);
+			oafs.add(s);
-				break;
+			break;
-			case "":
+		case "":
-			case "otherresearchproducts":
+		case "otherresearchproducts":
-			default:
+		default:
-				final OtherResearchProduct o = new OtherResearchProduct();
+			final OtherResearchProduct o = new OtherResearchProduct();
-				populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
+			populateResultFields(o, doc, collectedFrom, hostedBy, info, lastUpdateTimestamp);
-				o.setResulttype(ORP_DEFAULT_RESULTTYPE);
+			o.setResulttype(ORP_DEFAULT_RESULTTYPE);
-				o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
+			o.setContactperson(prepareOtherResearchProductContactPersons(doc, info));
-				o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
+			o.setContactgroup(prepareOtherResearchProductContactGroups(doc, info));
-				o.setTool(prepareOtherResearchProductTools(doc, info));
+			o.setTool(prepareOtherResearchProductTools(doc, info));
-				oafs.add(o);
+			oafs.add(o);
-				break;
+			break;
 		}
 
 		if (!oafs.isEmpty()) {
@@ -194,15 +201,9 @@ public abstract class AbstractMdRecordToOafMapper {
 				final String projectId = createOpenaireId(40, originalId, true);
 
 				res
-					.add(
+					.add(getRelation(docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info, lastUpdateTimestamp));
-						getRelation(
-							docId, projectId, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY, collectedFrom, info,
-							lastUpdateTimestamp));
 				res
-					.add(
+					.add(getRelation(projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info, lastUpdateTimestamp));
-						getRelation(
-							projectId, docId, RESULT_PROJECT, OUTCOME, PRODUCES, collectedFrom, info,
-							lastUpdateTimestamp));
 			}
 		}
 
@@ -247,10 +248,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		r.setId(createOpenaireId(50, doc.valueOf("//dri:objIdentifier"), false));
 		r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
 		r.setCollectedfrom(Arrays.asList(collectedFrom));
-		r
+		r.setPid(prepareResultPids(doc, info));
-			.setPid(
-				prepareListStructProps(
-					doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", info));
 		r.setDateofcollection(doc.valueOf("//dr:dateOfCollection"));
 		r.setDateoftransformation(doc.valueOf("//dr:dateOfTransformation"));
 		r.setExtraInfo(new ArrayList<>()); // NOT PRESENT IN MDSTORES
@@ -278,6 +276,8 @@ public abstract class AbstractMdRecordToOafMapper {
 		r.setBestaccessright(getBestAccessRights(instances));
 	}
 
+	protected abstract List<StructuredProperty> prepareResultPids(Document doc, DataInfo info);
+
 	private List<Context> prepareContexts(final Document doc, final DataInfo info) {
 		final List<Context> list = new ArrayList<>();
 		for (final Object o : doc.selectNodes("//oaf:concept")) {
@@ -358,7 +358,7 @@ public abstract class AbstractMdRecordToOafMapper {
 
 	protected abstract Field<String> prepareDatasetStorageDate(Document doc, DataInfo info);
 
-	protected static Qualifier getBestAccessRights(List<Instance> instanceList) {
+	protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
 		if (instanceList != null) {
 			final Optional<Qualifier> min = instanceList
 				.stream()
@@ -398,9 +398,7 @@ 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)) {
+			if (StringUtils.isNotBlank(name)) { return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info); }
-				return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
-			}
 		}
 		return null;
 	}
@@ -453,10 +451,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		for (final Object o : node.selectNodes(xpath)) {
 			final Node n = (Node) o;
 			res
-				.add(
+				.add(structuredProperty(n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"), n.valueOf("@schemename"), info));
-					structuredProperty(
-						n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
-						n.valueOf("@schemename"), info));
 		}
 		return res;
 	}
@@ -464,9 +459,7 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected OAIProvenance prepareOAIprovenance(final Document doc) {
 		final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");
 
-		if (n == null) {
+		if (n == null) { return null; }
-			return null;
-		}
 
 		final String identifier = n.valueOf("./*[local-name()='identifier']");
 		final String baseURL = n.valueOf("./*[local-name()='baseURL']");
@@ -481,9 +474,7 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected DataInfo prepareDataInfo(final Document doc) {
 		final Node n = doc.selectSingleNode("//oaf:datainfo");
 
-		if (n == null) {
+		if (n == null) { return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9"); }
-			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");
@@ -495,9 +486,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		final Boolean inferred = Boolean.parseBoolean(n.valueOf("./oaf:inferred"));
 		final String trust = n.valueOf("./oaf:trust");
 
-		return dataInfo(
+		return dataInfo(deletedbyinference, inferenceprovenance, inferred, false, qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
-			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

@@ -5,7 +5,12 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.IOException;
 import java.sql.SQLException;
-import java.util.*;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
@@ -27,7 +32,19 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.DbClient;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.Datasource;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.OafEntity;
+import eu.dnetlib.dhp.schema.oaf.Organization;
+import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
+import eu.dnetlib.dhp.schema.oaf.Project;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.Software;
+import eu.dnetlib.dhp.utils.ISLookupClientFactory;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import scala.Tuple2;
 
 public class GenerateEntitiesApplication {
@@ -39,14 +56,12 @@ public class GenerateEntitiesApplication {
 	public static void main(final String[] args) throws Exception {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
-				.toString(
+				.toString(GenerateEntitiesApplication.class
-					MigrateMongoMdstoresApplication.class
+					.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
-						.getResourceAsStream(
-							"/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json")));
 
 		parser.parseArgument(args);
 
-		Boolean isSparkSessionManaged = Optional
+		final Boolean isSparkSessionManaged = Optional
 			.ofNullable(parser.get("isSparkSessionManaged"))
 			.map(Boolean::valueOf)
 			.orElse(Boolean.TRUE);
@@ -58,17 +73,17 @@ public class GenerateEntitiesApplication {
 		final String dbUrl = parser.get("postgresUrl");
 		final String dbUser = parser.get("postgresUser");
 		final String dbPassword = parser.get("postgresPassword");
+		final String isLookupUrl = parser.get("isLookupUrl");
 
-		final Map<String, String> code2name = loadClassNames(dbUrl, dbUser, dbPassword);
+		final Map<String, String> code2name = loadVocsFromDB(dbUrl, dbUser, dbPassword);
 
-		SparkConf conf = new SparkConf();
+		code2name.putAll(loadVocsFromIS(isLookupUrl));
-		runWithSparkSession(
+
-			conf,
+		final SparkConf conf = new SparkConf();
-			isSparkSessionManaged,
+		runWithSparkSession(conf, isSparkSessionManaged, spark -> {
-			spark -> {
+			removeOutputDir(spark, targetPath);
-				removeOutputDir(spark, targetPath);
+			generateEntities(spark, code2name, sourcePaths, targetPath);
-				generateEntities(spark, code2name, sourcePaths, targetPath);
+		});
-			});
 	}
 
 	private static void generateEntities(
@@ -77,7 +92,7 @@ public class GenerateEntitiesApplication {
 		final String sourcePaths,
 		final String targetPath) {
 
-		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 		final List<String> existingSourcePaths = Arrays
 			.stream(sourcePaths.split(","))
 			.filter(p -> exists(sc, p))
@@ -90,27 +105,25 @@ public class GenerateEntitiesApplication {
 
 		for (final String sp : existingSourcePaths) {
 			inputRdd = inputRdd
-				.union(
+				.union(sc
-					sc
+					.sequenceFile(sp, Text.class, Text.class)
-						.sequenceFile(sp, Text.class, Text.class)
+					.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
-						.map(k -> new Tuple2<>(k._1().toString(), k._2().toString()))
+					.map(k -> convertToListOaf(k._1(), k._2(), code2name))
-						.map(k -> convertToListOaf(k._1(), k._2(), code2name))
+					.filter(Objects::nonNull)
-						.filter(Objects::nonNull)
+					.flatMap(list -> list.iterator()));
-						.flatMap(list -> list.iterator()));
 		}
 
 		inputRdd
 			.mapToPair(oaf -> new Tuple2<>(ModelSupport.idFn().apply(oaf), oaf))
 			.reduceByKey((o1, o2) -> merge(o1, o2))
 			.map(Tuple2::_2)
-			.map(
+			.map(oaf -> oaf.getClass().getSimpleName().toLowerCase()
-				oaf -> oaf.getClass().getSimpleName().toLowerCase()
+				+ "|"
-					+ "|"
+				+ OBJECT_MAPPER.writeValueAsString(oaf))
-					+ OBJECT_MAPPER.writeValueAsString(oaf))
 			.saveAsTextFile(targetPath, GzipCodec.class);
 	}
 
-	private static Oaf merge(Oaf o1, Oaf o2) {
+	private static Oaf merge(final Oaf o1, final Oaf o2) {
 		if (ModelSupport.isSubClass(o1, OafEntity.class)) {
 			((OafEntity) o1).mergeFrom((OafEntity) o2);
 		} else if (ModelSupport.isSubClass(o1, Relation.class)) {
@@ -122,37 +135,41 @@ public class GenerateEntitiesApplication {
 	}
 
 	private static List<Oaf> convertToListOaf(
-		final String id, final String s, final Map<String, String> code2name) {
+		final String id,
+		final String s,
+		final Map<String, String> code2name) {
 		final String type = StringUtils.substringAfter(id, ":");
 
 		switch (type.toLowerCase()) {
-			case "native_oaf":
+		case "native_oaf":
-				return new OafToOafMapper(code2name).processMdRecord(s);
+			return new OafToOafMapper(code2name).processMdRecord(s);
-			case "native_odf":
+		case "native_odf":
-				return new OdfToOafMapper(code2name).processMdRecord(s);
+			return new OdfToOafMapper(code2name).processMdRecord(s);
-			case "datasource":
+		case "datasource":
-				return Arrays.asList(convertFromJson(s, Datasource.class));
+			return Arrays.asList(convertFromJson(s, Datasource.class));
-			case "organization":
+		case "organization":
-				return Arrays.asList(convertFromJson(s, Organization.class));
+			return Arrays.asList(convertFromJson(s, Organization.class));
-			case "project":
+		case "project":
-				return Arrays.asList(convertFromJson(s, Project.class));
+			return Arrays.asList(convertFromJson(s, Project.class));
-			case "relation":
+		case "relation":
-				return Arrays.asList(convertFromJson(s, Relation.class));
+			return Arrays.asList(convertFromJson(s, Relation.class));
-			case "publication":
+		case "publication":
-				return Arrays.asList(convertFromJson(s, Publication.class));
+			return Arrays.asList(convertFromJson(s, Publication.class));
-			case "dataset":
+		case "dataset":
-				return Arrays.asList(convertFromJson(s, Dataset.class));
+			return Arrays.asList(convertFromJson(s, Dataset.class));
-			case "software":
+		case "software":
-				return Arrays.asList(convertFromJson(s, Software.class));
+			return Arrays.asList(convertFromJson(s, Software.class));
-			case "otherresearchproduct":
+		case "otherresearchproduct":
-				return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
+			return Arrays.asList(convertFromJson(s, OtherResearchProduct.class));
-			default:
+		default:
-				throw new RuntimeException("type not managed: " + type.toLowerCase());
+			throw new RuntimeException("type not managed: " + type.toLowerCase());
 		}
 	}
 
-	private static Map<String, String> loadClassNames(
+	private static Map<String, String> loadVocsFromDB(
-		final String dbUrl, final String dbUser, final String dbPassword) throws IOException {
+		final String dbUrl,
+		final String dbUser,
+		final String dbPassword) throws IOException {
 
 		log.info("Loading vocabulary terms from db...");
 
@@ -160,15 +177,13 @@ public class GenerateEntitiesApplication {
 
 		try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
 			dbClient
-				.processResults(
+				.processResults("select code, name from class", rs -> {
-					"select code, name from class",
+					try {
-					rs -> {
+						map.put(rs.getString("code"), rs.getString("name"));
-						try {
+					} catch (final SQLException e) {
-							map.put(rs.getString("code"), rs.getString("name"));
+						e.printStackTrace();
-						} catch (final SQLException e) {
+					}
-							e.printStackTrace();
+				});
-						}
-					});
 		}
 
 		log.info("Found " + map.size() + " terms.");
@@ -176,6 +191,24 @@ public class GenerateEntitiesApplication {
 		return map;
 	}
 
+	private static Map<String, String> loadVocsFromIS(final String isLookupUrl) throws IOException, ISLookUpException {
+		final ISLookUpService isLookUpService = ISLookupClientFactory.getLookUpService(isLookupUrl);
+
+		final String xquery =
+			IOUtils.toString(GenerateEntitiesApplication.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/xquery/load_vocabularies.xquery"));
+
+		final Map<String, String> map = new HashMap<>();
+
+		for (final String s : isLookUpService.quickSearchProfile(xquery)) {
+			final String[] arr = s.split("@=@");
+			if (arr.length == 4) {
+				map.put(arr[2].trim(), arr[3].trim());
+			}
+		}
+
+		return map;
+	}
+
 	private static Oaf convertFromJson(final String s, final Class<? extends Oaf> clazz) {
 		try {
 			return OBJECT_MAPPER.readValue(s, clazz);
@@ -196,7 +229,7 @@ public class GenerateEntitiesApplication {
 		}
 	}
 
-	private static void removeOutputDir(SparkSession spark, String path) {
+	private static void removeOutputDir(final SparkSession spark, final String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}
 }

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

@@ -130,8 +130,7 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 		final Instance instance = new Instance();
 		instance
-			.setInstancetype(
+			.setInstancetype(prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
-				prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
 		instance.setCollectedfrom(collectedfrom);
 		instance.setHostedby(hostedby);
 		instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
@@ -147,14 +146,13 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 		final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
 		instance
-			.setUrl(
+			.setUrl(nodes
-				nodes
+				.stream()
-					.stream()
+				.filter(n -> StringUtils.isNotBlank(n.getText()))
-					.filter(n -> StringUtils.isNotBlank(n.getText()))
+				.map(n -> n.getText().trim())
-					.map(n -> n.getText().trim())
+				.filter(u -> u.startsWith("http"))
-					.filter(u -> u.startsWith("http"))
+				.distinct()
-					.distinct()
+				.collect(Collectors.toCollection(ArrayList::new)));
-					.collect(Collectors.toCollection(ArrayList::new)));
 
 		return Lists.newArrayList(instance);
 	}
@@ -279,15 +277,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 				final String otherId = createOpenaireId(50, originalId, false);
 
 				res
-					.add(
+					.add(getRelation(docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
-						getRelation(
-							docId, otherId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
-							lastUpdateTimestamp));
 				res
-					.add(
+					.add(getRelation(otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info, lastUpdateTimestamp));
-						getRelation(
-							otherId, docId, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO, collectedFrom, info,
-							lastUpdateTimestamp));
 			}
 		}
 		return res;
@@ -297,4 +289,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 	protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
 		return null; // NOT PRESENT IN OAF
 	}
+
+	@Override
+	protected List<StructuredProperty> prepareResultPids(final Document doc, final DataInfo 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

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

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/generate_entities_parameters.json

@@ -34,6 +34,11 @@
 		"paramLongName": "postgresPassword",
 		"paramDescription": "postgres password",
 		"paramRequired": false
+	},
+	{
+		"paramName": "islookup",
+		"paramLongName": "isLookupUrl",
+		"paramDescription": "the url of the ISLookupService",
+		"paramRequired": true
 	}
-
 ]