Merge branch 'master' into provision_indexing

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java

@@ -1,21 +1,24 @@
-package eu.dnetlib.dhp.oa.dedup;
 
-import com.wcohen.ss.JaroWinkler;
+package eu.dnetlib.dhp.oa.dedup;
-import eu.dnetlib.dhp.schema.oaf.Author;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-import eu.dnetlib.pace.model.Person;
-import org.apache.commons.lang3.StringUtils;
-import scala.Tuple2;
 
 import java.text.Normalizer;
 import java.util.*;
 import java.util.stream.Collectors;
 
+import org.apache.commons.lang3.StringUtils;
+
+import com.wcohen.ss.JaroWinkler;
+
+import eu.dnetlib.dhp.schema.oaf.Author;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.pace.model.Person;
+import scala.Tuple2;
+
 public class AuthorMerger {
 
 	private static final Double THRESHOLD = 0.95;
 
-    public static List<Author> merge(List<List<Author>> authors){
+	public static List<Author> merge(List<List<Author>> authors) {
 
 		authors.sort(new Comparator<List<Author>>() {
 			@Override
@@ -26,7 +29,7 @@ public class AuthorMerger {
 
 		List<Author> author = new ArrayList<>();
 
-        for(List<Author> a : authors){
+		for (List<Author> a : authors) {
 			author = mergeAuthor(author, a);
 		}
 
@@ -93,8 +96,10 @@ public class AuthorMerger {
 				});
 	}
 
-    public static String pidToComparableString(StructuredProperty pid){
+	public static String pidToComparableString(StructuredProperty pid) {
-        return (pid.getQualifier()!=null? pid.getQualifier().getClassid()!=null?pid.getQualifier().getClassid().toLowerCase():"":"") + (pid.getValue()!=null? pid.getValue().toLowerCase():"");
+		return (pid.getQualifier() != null
+			? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
+			: "") + (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
 	}
 
 	public static int countAuthorsPids(List<Author> authors) {

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupRecordFactory.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.io.Serializable;
@@ -73,7 +74,8 @@ public class DedupRecordFactory {
 	}
 
 	public static <T extends OafEntity> T entityMerger(
-		String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz) throws IllegalAccessException, InstantiationException {
+		String id, Iterator<Tuple2<String, T>> entities, long ts, DataInfo dataInfo, Class<T> clazz)
+		throws IllegalAccessException, InstantiationException {
 
 		T entity = clazz.newInstance();
 
@@ -87,14 +89,14 @@ public class DedupRecordFactory {
 					entity.mergeFrom(duplicate);
 					if (ModelSupport.isSubClass(duplicate, Result.class)) {
 						Result r1 = (Result) duplicate;
-						if (r1.getAuthor() != null && r1.getAuthor().size()>0)
+						if (r1.getAuthor() != null && r1.getAuthor().size() > 0)
 							authors.add(r1.getAuthor());
 						if (r1.getDateofacceptance() != null)
 							dates.add(r1.getDateofacceptance().getValue());
 					}
 				});
 
-		//set authors and date
+		// set authors and date
 		if (ModelSupport.isSubClass(entity, Result.class)) {
 			((Result) entity).setDateofacceptance(DatePicker.pick(dates));
 			((Result) entity).setAuthor(AuthorMerger.merge(authors));

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

@@ -1,5 +1,8 @@
+
 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;
@@ -7,15 +10,13 @@ import java.io.Serializable;
 import java.nio.file.Paths;
 import java.util.*;
 
-import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.pace.util.MapDocumentUtil;
 import org.codehaus.jackson.map.ObjectMapper;
 import org.junit.jupiter.api.BeforeEach;
-
 import org.junit.jupiter.api.Test;
-import scala.Tuple2;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+import scala.Tuple2;
 
 public class EntityMergerTest implements Serializable {
 
@@ -45,7 +46,8 @@ public class EntityMergerTest implements Serializable {
 	@Test
 	public void publicationMergerTest() throws InstantiationException, IllegalAccessException {
 
-		Publication pub_merged = DedupRecordFactory.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
+		Publication pub_merged = DedupRecordFactory
+			.entityMerger(dedupId, publications.iterator(), 0, dataInfo, Publication.class);
 
 		assertEquals(dedupId, pub_merged.getId());
 
@@ -59,36 +61,36 @@ public class EntityMergerTest implements Serializable {
 		assertEquals(pub_merged.getDateoftransformation(), pub_top.getDateoftransformation());
 		assertEquals(pub_merged.getOaiprovenance(), pub_top.getOaiprovenance());
 		assertEquals(pub_merged.getDateofcollection(), pub_top.getDateofcollection());
-		assertEquals(pub_merged.getInstance().size(),3);
+		assertEquals(pub_merged.getInstance().size(), 3);
 		assertEquals(pub_merged.getCountry().size(), 2);
 		assertEquals(pub_merged.getSubject().size(), 0);
 		assertEquals(pub_merged.getTitle().size(), 2);
-		assertEquals(pub_merged.getRelevantdate().size(),0);
+		assertEquals(pub_merged.getRelevantdate().size(), 0);
-		assertEquals(pub_merged.getDescription().size(),0);
+		assertEquals(pub_merged.getDescription().size(), 0);
-		assertEquals(pub_merged.getSource().size(),0);
+		assertEquals(pub_merged.getSource().size(), 0);
-		assertEquals(pub_merged.getFulltext().size(),0);
+		assertEquals(pub_merged.getFulltext().size(), 0);
-		assertEquals(pub_merged.getFormat().size(),0);
+		assertEquals(pub_merged.getFormat().size(), 0);
-		assertEquals(pub_merged.getContributor().size(),0);
+		assertEquals(pub_merged.getContributor().size(), 0);
-		assertEquals(pub_merged.getCoverage().size(),0);
+		assertEquals(pub_merged.getCoverage().size(), 0);
-		assertEquals(pub_merged.getContext().size(),0);
+		assertEquals(pub_merged.getContext().size(), 0);
-		assertEquals(pub_merged.getExternalReference().size(),0);
+		assertEquals(pub_merged.getExternalReference().size(), 0);
-		assertEquals(pub_merged.getOriginalId().size(),3);
+		assertEquals(pub_merged.getOriginalId().size(), 3);
-		assertEquals(pub_merged.getCollectedfrom().size(),3);
+		assertEquals(pub_merged.getCollectedfrom().size(), 3);
-		assertEquals(pub_merged.getPid().size(),1);
+		assertEquals(pub_merged.getPid().size(), 1);
-		assertEquals(pub_merged.getExtraInfo().size(),0);
+		assertEquals(pub_merged.getExtraInfo().size(), 0);
 
-		//verify datainfo
+		// verify datainfo
 		assertEquals(pub_merged.getDataInfo(), dataInfo);
 
-		//verify datepicker
+		// verify datepicker
 		assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30");
 
-		//verify authors
+		// verify authors
 		assertEquals(pub_merged.getAuthor().size(), 9);
 		assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4);
 	}
 
-	public DataInfo setDI(){
+	public DataInfo setDI() {
 		DataInfo dataInfo = new DataInfo();
 		dataInfo.setTrust("0.9");
 		dataInfo.setDeletedbyinference(false);
@@ -97,13 +99,13 @@ public class EntityMergerTest implements Serializable {
 		return dataInfo;
 	}
 
-	public Publication getTopPub(List<Tuple2<String, Publication>> publications){
+	public Publication getTopPub(List<Tuple2<String, Publication>> publications) {
 
 		Double maxTrust = 0.0;
 		Publication maxPub = new Publication();
 		for (Tuple2<String, Publication> publication : publications) {
 			Double pubTrust = Double.parseDouble(publication._2().getDataInfo().getTrust());
-			if(pubTrust > maxTrust){
+			if (pubTrust > maxTrust) {
 				maxTrust = pubTrust;
 				maxPub = publication._2();
 			}
@@ -118,11 +120,11 @@ public class EntityMergerTest implements Serializable {
 			reader = new BufferedReader(new FileReader(path));
 			String line = reader.readLine();
 			while (line != null) {
-				res.add(
+				res
+					.add(
 						new Tuple2<>(
 							MapDocumentUtil.getJPathString("$.id", line),
-								new ObjectMapper().readValue(line, clazz))
+							new ObjectMapper().readValue(line, clazz)));
-				);
 				// read next line
 				line = reader.readLine();
 			}
@@ -134,5 +136,4 @@ public class EntityMergerTest implements Serializable {
 		return res;
 	}
 
-
 }

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

@@ -10,7 +10,16 @@ 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_PID_TYPES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PRODUCED_BY;
+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 java.util.ArrayList;
 import java.util.Arrays;
@@ -50,6 +59,10 @@ 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 MAG_PID_TYPE = qualifier(
+		"MAGIdentifier", "Microsoft Academic Graph Identifier", DNET_PID_TYPES, DNET_PID_TYPES);
 
 	protected static final Map<String, String> nsContext = new HashMap<>();
 
@@ -75,8 +88,7 @@ public abstract class AbstractMdRecordToOafMapper {
 			DocumentFactory.getInstance().setXPathNamespaceURIs(nsContext);
 
 			final Document doc = DocumentHelper
-				.parseText(
+				.parseText(xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
-					xml.replaceAll(DATACITE_SCHEMA_KERNEL_4, DATACITE_SCHEMA_KERNEL_3));
 
 			final String type = doc.valueOf("//dr:CobjCategory/@type");
 			final KeyValue collectedFrom = getProvenanceDatasource(
@@ -103,7 +115,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		}
 	}
 
-	private KeyValue getProvenanceDatasource(Document doc, String xpathId, String xpathName) {
+	private KeyValue getProvenanceDatasource(final Document doc, final String xpathId, final String xpathName) {
 		final String dsId = doc.valueOf(xpathId);
 		final String dsName = doc.valueOf(xpathName);
 
@@ -111,9 +123,7 @@ public abstract class AbstractMdRecordToOafMapper {
 			return null;
 		}
 
-		return keyValue(
+		return keyValue(createOpenaireId(10, dsId, true), dsName);
-			createOpenaireId(10, dsId, true),
-			dsName);
 	}
 
 	protected List<Oaf> createOafs(
@@ -211,8 +221,14 @@ public abstract class AbstractMdRecordToOafMapper {
 		return res;
 	}
 
-	protected Relation getRelation(String source, String target, String relType, String subRelType, String relClass,
+	protected Relation getRelation(final String source,
-		KeyValue collectedFrom, DataInfo info, long lastUpdateTimestamp) {
+		final String target,
+		final String relType,
+		final String subRelType,
+		final String relClass,
+		final KeyValue collectedFrom,
+		final DataInfo info,
+		final long lastUpdateTimestamp) {
 		final Relation rel = new Relation();
 		rel.setRelType(relType);
 		rel.setSubRelType(subRelType);
@@ -289,7 +305,10 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected abstract Qualifier prepareResourceType(Document doc, DataInfo info);
 
 	protected abstract List<Instance> prepareInstances(
-		Document doc, DataInfo info, KeyValue collectedfrom, KeyValue hostedby);
+		Document doc,
+		DataInfo info,
+		KeyValue collectedfrom,
+		KeyValue hostedby);
 
 	protected abstract List<Field<String>> prepareSources(Document doc, DataInfo info);
 
@@ -314,13 +333,16 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected abstract List<Author> prepareAuthors(Document doc, DataInfo info);
 
 	protected abstract List<Field<String>> prepareOtherResearchProductTools(
-		Document doc, DataInfo info);
+		Document doc,
+		DataInfo info);
 
 	protected abstract List<Field<String>> prepareOtherResearchProductContactGroups(
-		Document doc, DataInfo info);
+		Document doc,
+		DataInfo info);
 
 	protected abstract List<Field<String>> prepareOtherResearchProductContactPersons(
-		Document doc, DataInfo info);
+		Document doc,
+		DataInfo info);
 
 	protected abstract Qualifier prepareSoftwareProgrammingLanguage(Document doc, DataInfo info);
 
@@ -329,7 +351,8 @@ public abstract class AbstractMdRecordToOafMapper {
 	protected abstract List<StructuredProperty> prepareSoftwareLicenses(Document doc, DataInfo info);
 
 	protected abstract List<Field<String>> prepareSoftwareDocumentationUrls(
-		Document doc, DataInfo info);
+		Document doc,
+		DataInfo info);
 
 	protected abstract List<GeoLocation> prepareDatasetGeoLocations(Document doc, DataInfo info);
 
@@ -358,26 +381,17 @@ public abstract class AbstractMdRecordToOafMapper {
 			final String vol = n.valueOf("@vol");
 			final String edition = n.valueOf("@edition");
 			if (StringUtils.isNotBlank(name)) {
-				return journal(
+				return journal(name, issnPrinted, issnOnline, issnLinking, ep, iss, sp, vol, edition, null, null, info);
-					name,
-					issnPrinted,
-					issnOnline,
-					issnLinking,
-					ep,
-					iss,
-					sp,
-					vol,
-					edition,
-					null,
-					null,
-					info);
 			}
 		}
 		return null;
 	}
 
 	protected Qualifier prepareQualifier(
-		final Node node, final String xpath, final String schemeId, final String schemeName) {
+		final Node node,
+		final String xpath,
+		final String schemeId,
+		final String schemeName) {
 		final String classId = node.valueOf(xpath);
 		final String className = code2name.get(classId);
 		return qualifier(classId, className, schemeId, schemeName);
@@ -401,7 +415,10 @@ public abstract class AbstractMdRecordToOafMapper {
 	}
 
 	protected List<StructuredProperty> prepareListStructProps(
-		final Node node, final String xpath, final Qualifier qualifier, final DataInfo info) {
+		final Node node,
+		final String xpath,
+		final Qualifier qualifier,
+		final DataInfo info) {
 		final List<StructuredProperty> res = new ArrayList<>();
 		for (final Object o : node.selectNodes(xpath)) {
 			final Node n = (Node) o;
@@ -411,19 +428,17 @@ public abstract class AbstractMdRecordToOafMapper {
 	}
 
 	protected List<StructuredProperty> prepareListStructProps(
-		final Node node, final String xpath, final DataInfo info) {
+		final Node node,
+		final String xpath,
+		final DataInfo info) {
 		final List<StructuredProperty> res = new ArrayList<>();
 		for (final Object o : node.selectNodes(xpath)) {
 			final Node n = (Node) o;
 			res
 				.add(
 					structuredProperty(
-						n.getText(),
+						n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
-						n.valueOf("@classid"),
+						n.valueOf("@schemename"), info));
-						n.valueOf("@classname"),
-						n.valueOf("@schemeid"),
-						n.valueOf("@schemename"),
-						info));
 		}
 		return res;
 	}
@@ -449,8 +464,7 @@ public abstract class AbstractMdRecordToOafMapper {
 		final Node n = doc.selectSingleNode("//oaf:datainfo");
 
 		if (n == null) {
-			return dataInfo(
+			return dataInfo(false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
-				false, null, false, false, REPOSITORY_PROVENANCE_ACTIONS, "0.9");
 		}
 
 		final String paClassId = n.valueOf("./oaf:provenanceaction/@classid");
@@ -464,12 +478,8 @@ public abstract class AbstractMdRecordToOafMapper {
 		final String trust = n.valueOf("./oaf:trust");
 
 		return dataInfo(
-			deletedbyinference,
+			deletedbyinference, inferenceprovenance, inferred, false,
-			inferenceprovenance,
+			qualifier(paClassId, paClassName, paSchemeId, paSchemeName), trust);
-			inferred,
-			false,
-			qualifier(paClassId, paClassName, paSchemeId, paSchemeName),
-			trust);
 	}
 
 	protected Field<String> prepareField(final Node node, final String xpath, final DataInfo info) {
@@ -477,7 +487,9 @@ public abstract class AbstractMdRecordToOafMapper {
 	}
 
 	protected List<Field<String>> prepareListFields(
-		final Node node, final String xpath, final DataInfo info) {
+		final Node node,
+		final String xpath,
+		final DataInfo info) {
 		return listFields(info, prepareListString(node, xpath));
 	}
 

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

@@ -1,10 +1,19 @@
 
 package eu.dnetlib.dhp.oa.graph.raw;
 
-import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.*;
+import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
+import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
+import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.structuredProperty;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_ACCESS_MODES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_RELATED_TO;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.PUBLICATION_DATASET;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
@@ -15,8 +24,15 @@ import org.dom4j.Node;
 import com.google.common.collect.Lists;
 
 import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Author;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.DataInfo;
+import eu.dnetlib.dhp.schema.oaf.Field;
+import eu.dnetlib.dhp.schema.oaf.GeoLocation;
+import eu.dnetlib.dhp.schema.oaf.Instance;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
 public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
@@ -39,14 +55,25 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 				author.setSurname(p.getNormalisedSurname());
 			}
 
-			final String pid = e.attributeValue("nameIdentifier");
+			final String pid = e.valueOf("./@nameIdentifier");
-			final String pidType = e.attributeValue("nameIdentifierScheme");
+			final String type = e
+				.valueOf("./@nameIdentifierScheme")
+				.trim()
+				.toUpperCase()
+				.replaceAll(" ", "")
+				.replaceAll("_", "");
 
 			author.setPid(new ArrayList<>());
-			if (StringUtils.isNotBlank(pid) && StringUtils.isNotBlank(pidType)) {
+
-				author
+			if (StringUtils.isNotBlank(pid)) {
-					.getPid()
+				if (type.startsWith("ORCID")) {
-					.add(structuredProperty(pid, qualifier(pidType, pidType, DNET_PID_TYPES, DNET_PID_TYPES), info));
+					final String cleanedId = pid
+						.replaceAll("http://orcid.org/", "")
+						.replaceAll("https://orcid.org/", "");
+					author.getPid().add(structuredProperty(cleanedId, ORCID_PID_TYPE, info));
+				} else if (type.startsWith("MAGID")) {
+					author.getPid().add(structuredProperty(pid, MAG_PID_TYPE, info));
+				}
 			}
 
 			res.add(author);
@@ -104,28 +131,21 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 		final Instance instance = new Instance();
 		instance
 			.setInstancetype(
-				prepareQualifier(
+				prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
-					doc,
-					"//dr:CobjCategory",
-					DNET_PUBLICATION_RESOURCE,
-					DNET_PUBLICATION_RESOURCE));
 		instance.setCollectedfrom(collectedfrom);
 		instance.setHostedby(hostedby);
 		instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
 		instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
 		instance
-			.setAccessright(
+			.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES));
-				prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES));
 		instance.setLicense(field(doc.valueOf("//oaf:license"), info));
 		instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
 		instance
-			.setProcessingchargeamount(
+			.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
-				field(doc.valueOf("//oaf:processingchargeamount"), info));
 		instance
-			.setProcessingchargecurrency(
+			.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
-				field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
 
-		List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
+		final List<Node> nodes = Lists.newArrayList(doc.selectNodes("//dc:identifier"));
 		instance
 			.setUrl(
 				nodes
@@ -158,19 +178,22 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected Field<String> prepareSoftwareCodeRepositoryUrl(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return null; // NOT PRESENT IN OAF
 	}
 
 	@Override
 	protected List<StructuredProperty> prepareSoftwareLicenses(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // NOT PRESENT IN OAF
 	}
 
 	@Override
 	protected List<Field<String>> prepareSoftwareDocumentationUrls(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // NOT PRESENT IN OAF
 	}
 
@@ -182,13 +205,15 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected Field<String> prepareDatasetMetadataVersionNumber(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return null; // NOT PRESENT IN OAF
 	}
 
 	@Override
 	protected Field<String> prepareDatasetLastMetadataUpdate(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return null; // NOT PRESENT IN OAF
 	}
 
@@ -216,19 +241,22 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductTools(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // NOT PRESENT IN OAF
 	}
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductContactGroups(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // NOT PRESENT IN OAF
 	}
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductContactPersons(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // NOT PRESENT IN OAF
 	}
 

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

@@ -4,16 +4,31 @@ package eu.dnetlib.dhp.oa.graph.raw;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.createOpenaireId;
 import static eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils.field;
 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.DNET_ACCESS_MODES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_DATE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_DATA_CITE_RESOURCE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_LANGUAGES;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PUBLICATION_RESOURCE;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.HAS_PARTS;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_PART_OF;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENTED_BY;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.IS_SUPPLEMENT_TO;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.PART;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
+import static eu.dnetlib.dhp.schema.common.ModelConstants.SUPPLEMENT;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.Node;
 
 import eu.dnetlib.dhp.oa.graph.raw.common.PacePerson;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Author;
 import eu.dnetlib.dhp.schema.oaf.DataInfo;
 import eu.dnetlib.dhp.schema.oaf.Field;
@@ -22,7 +37,6 @@ import eu.dnetlib.dhp.schema.oaf.Instance;
 import eu.dnetlib.dhp.schema.oaf.KeyValue;
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 import eu.dnetlib.dhp.schema.oaf.Qualifier;
-import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 
 public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
@@ -48,7 +62,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 			final String fullname = n.valueOf("./datacite:creatorName");
 			author.setFullname(fullname);
 
-			PacePerson pp = new PacePerson(fullname, false);
+			final PacePerson pp = new PacePerson(fullname, false);
 			final String name = n.valueOf("./datacite:givenName");
 			if (StringUtils.isBlank(name) & pp.isAccurate()) {
 				author.setName(pp.getNormalisedFirstName());
@@ -63,6 +77,10 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 				author.setSurname(surname);
 			}
 
+			if (StringUtils.isBlank(author.getFullname())) {
+				author.setFullname(String.format("%s, %s", author.getSurname(), author.getName()));
+			}
+
 			author.setAffiliation(prepareListFields(n, "./datacite:affiliation", info));
 			author.setPid(preparePids(n, info));
 			author.setRank(pos++);
@@ -74,13 +92,21 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	private List<StructuredProperty> preparePids(final Node n, final DataInfo info) {
 		final List<StructuredProperty> res = new ArrayList<>();
 		for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
-			res
+
-				.add(
+			final String id = ((Node) o).getText();
-					structuredProperty(
+			final String type = ((Node) o)
-						((Node) o).getText(),
+				.valueOf("./@nameIdentifierScheme")
-						prepareQualifier(
+				.trim()
-							(Node) o, "./@nameIdentifierScheme", DNET_PID_TYPES, DNET_PID_TYPES),
+				.toUpperCase()
-						info));
+				.replaceAll(" ", "")
+				.replaceAll("_", "");
+
+			if (type.startsWith("ORCID")) {
+				final String cleanedId = id.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", "");
+				res.add(structuredProperty(cleanedId, ORCID_PID_TYPE, info));
+			} else if (type.startsWith("MAGID")) {
+				res.add(structuredProperty(id, MAG_PID_TYPE, info));
+			}
 		}
 		return res;
 	}
@@ -95,21 +121,18 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 		final Instance instance = new Instance();
 		instance
 			.setInstancetype(
-				prepareQualifier(
+				prepareQualifier(doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
-					doc, "//dr:CobjCategory", DNET_PUBLICATION_RESOURCE, DNET_PUBLICATION_RESOURCE));
 		instance.setCollectedfrom(collectedfrom);
 		instance.setHostedby(hostedby);
 		instance.setDateofacceptance(field(doc.valueOf("//oaf:dateAccepted"), info));
 		instance.setDistributionlocation(doc.valueOf("//oaf:distributionlocation"));
 		instance
-			.setAccessright(
+			.setAccessright(prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES));
-				prepareQualifier(doc, "//oaf:accessrights", DNET_ACCESS_MODES, DNET_ACCESS_MODES));
 		instance.setLicense(field(doc.valueOf("//oaf:license"), info));
 		instance.setRefereed(field(doc.valueOf("//oaf:refereed"), info));
 		instance.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
 		instance
-			.setProcessingchargecurrency(
+			.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
-				field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
 
 		final Set<String> url = new HashSet<>();
 		for (final Object o : doc.selectNodes("//datacite:alternateIdentifier[@alternateIdentifierType='URL']")) {
@@ -149,11 +172,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 				res
 					.add(
 						structuredProperty(
-							((Node) o).getText(),
+							((Node) o).getText(), "UNKNOWN", "UNKNOWN", DNET_DATA_CITE_DATE, DNET_DATA_CITE_DATE,
-							"UNKNOWN",
-							"UNKNOWN",
-							DNET_DATA_CITE_DATE,
-							DNET_DATA_CITE_DATE,
 							info));
 			}
 		}
@@ -197,53 +216,52 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductTools(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // Not present in ODF ???
 	}
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductContactGroups(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return prepareListFields(
-			doc,
+			doc, "//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName", info);
-			"//datacite:contributor[@contributorType='ContactGroup']/datacite:contributorName",
-			info);
 	}
 
 	@Override
 	protected List<Field<String>> prepareOtherResearchProductContactPersons(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return prepareListFields(
-			doc,
+			doc, "//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName", info);
-			"//datacite:contributor[@contributorType='ContactPerson']/datacite:contributorName",
-			info);
 	}
 
 	@Override
 	protected Qualifier prepareSoftwareProgrammingLanguage(final Document doc, final DataInfo info) {
-		return prepareQualifier(
+		return prepareQualifier(doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages");
-			doc, "//datacite:format", "dnet:programming_languages", "dnet:programming_languages");
 	}
 
 	@Override
 	protected Field<String> prepareSoftwareCodeRepositoryUrl(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return null; // Not present in ODF ???
 	}
 
 	@Override
 	protected List<StructuredProperty> prepareSoftwareLicenses(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return new ArrayList<>(); // Not present in ODF ???
 	}
 
 	@Override
 	protected List<Field<String>> prepareSoftwareDocumentationUrls(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return prepareListFields(
-			doc,
+			doc, "//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']", info);
-			"//datacite:relatedIdentifier[@relatedIdentifierType='URL' and @relationType='IsDocumentedBy']",
-			info);
 	}
 
 	// DATASETS
@@ -264,13 +282,15 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 
 	@Override
 	protected Field<String> prepareDatasetMetadataVersionNumber(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return null; // Not present in ODF ???
 	}
 
 	@Override
 	protected Field<String> prepareDatasetLastMetadataUpdate(
-		final Document doc, final DataInfo info) {
+		final Document doc,
+		final DataInfo info) {
 		return prepareField(doc, "//datacite:date[@dateType='Updated']", info);
 	}
 
@@ -346,9 +366,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	@Override
 	protected Qualifier prepareResourceType(final Document doc, final DataInfo info) {
 		return prepareQualifier(
-			doc,
+			doc, "//*[local-name() = 'resource']//*[local-name() = 'resourceType']", DNET_DATA_CITE_RESOURCE,
-			"//*[local-name() = 'resource']//*[local-name() = 'resourceType']",
-			DNET_DATA_CITE_RESOURCE,
 			DNET_DATA_CITE_RESOURCE);
 	}
 }

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

@@ -21,7 +21,14 @@ import org.mockito.Mock;
 import org.mockito.junit.jupiter.MockitoExtension;
 
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.Author;
+import eu.dnetlib.dhp.schema.oaf.Dataset;
+import eu.dnetlib.dhp.schema.oaf.Field;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+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.schema.oaf.StructuredProperty;
 
 @ExtendWith(MockitoExtension.class)
 public class MappersTest {
@@ -54,13 +61,13 @@ public class MappersTest {
 		assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue()));
 
 		assertTrue(p.getAuthor().size() > 0);
-		Optional<Author> author = p
+		final Optional<Author> author = p
 			.getAuthor()
 			.stream()
 			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
 			.findFirst();
 		assertTrue(author.isPresent());
-		StructuredProperty pid = author
+		final StructuredProperty pid = author
 			.get()
 			.getPid()
 			.stream()
@@ -68,7 +75,7 @@ public class MappersTest {
 			.get();
 		assertEquals("0000-0001-6651-1178", pid.getValue());
 		assertEquals("ORCID", pid.getQualifier().getClassid());
-		assertEquals("ORCID", pid.getQualifier().getClassname());
+		assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname());
 		assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
 		assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
 		assertEquals("Votsi,Nefta", author.get().getFullname());
@@ -121,13 +128,13 @@ public class MappersTest {
 		assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
 		assertTrue(d.getAuthor().size() > 0);
 
-		Optional<Author> author = d
+		final Optional<Author> author = d
 			.getAuthor()
 			.stream()
 			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
 			.findFirst();
 		assertTrue(author.isPresent());
-		StructuredProperty pid = author
+		final StructuredProperty pid = author
 			.get()
 			.getPid()
 			.stream()
@@ -135,7 +142,7 @@ public class MappersTest {
 			.get();
 		assertEquals("0000-0001-9074-1619", pid.getValue());
 		assertEquals("ORCID", pid.getQualifier().getClassid());
-		assertEquals("ORCID", pid.getQualifier().getClassname());
+		assertEquals("Open Researcher and Contributor ID", pid.getQualifier().getClassname());
 		assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemeid());
 		assertEquals(ModelConstants.DNET_PID_TYPES, pid.getQualifier().getSchemename());
 		assertEquals("Baracchini, Theo", author.get().getFullname());
@@ -143,13 +150,13 @@ public class MappersTest {
 		assertEquals("Theo", author.get().getName());
 
 		assertEquals(1, author.get().getAffiliation().size());
-		Optional<Field<String>> opAff = author
+		final Optional<Field<String>> opAff = author
 			.get()
 			.getAffiliation()
 			.stream()
 			.findFirst();
 		assertTrue(opAff.isPresent());
-		Field<String> affiliation = opAff.get();
+		final Field<String> affiliation = opAff.get();
 		assertEquals("ISTI-CNR", affiliation.getValue());
 
 		assertTrue(d.getSubject().size() > 0);