code formatting

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

@@ -1,16 +1,19 @@
-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;
@@ -94,7 +97,9 @@ public class AuthorMerger {
 	}
 
 	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();
 

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());
 
@@ -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

@@ -59,8 +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 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<>();
 
@@ -74,7 +76,8 @@ 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;
@@ -88,15 +91,20 @@ 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();
@@ -111,7 +119,9 @@ 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);
 	}
@@ -196,9 +206,15 @@ 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));
 			}
 		}
 
@@ -244,7 +260,9 @@ public abstract class AbstractMdRecordToOafMapper {
 		r.setOriginalId(Arrays.asList(doc.valueOf("//dri:objIdentifier")));
 		r.setCollectedfrom(Arrays.asList(collectedFrom));
 		r
-			.setPid(prepareListStructProps(doc, "//oaf:identifier", "@identifierType", "dnet:pid_types", "dnet:pid_types", 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
@@ -362,7 +380,9 @@ 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;
 	}
@@ -415,7 +435,10 @@ 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;
 	}
@@ -423,7 +446,9 @@ 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']");
@@ -438,7 +463,9 @@ 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");
@@ -450,7 +477,9 @@ 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/OafToOafMapper.java

@@ -56,7 +56,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 			}
 
 			final String pid = e.valueOf("./@nameIdentifier");
-			final String type = e.valueOf("./@nameIdentifierScheme")
+			final String type = e
+				.valueOf("./@nameIdentifierScheme")
 				.trim()
 				.toUpperCase()
 				.replaceAll(" ", "")
@@ -66,7 +67,9 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
 
 			if (StringUtils.isNotBlank(pid)) {
 				if (type.startsWith("ORCID")) {
-					final String cleanedId = pid.replaceAll("http://orcid.org/", "").replaceAll("https://orcid.org/", "");
+					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));
@@ -127,7 +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));
@@ -143,7 +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())
@@ -274,9 +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;

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

@@ -94,7 +94,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 		for (final Object o : n.selectNodes("./datacite:nameIdentifier")) {
 
 			final String id = ((Node) o).getText();
-			final String type = ((Node) o).valueOf("./@nameIdentifierScheme")
+			final String type = ((Node) o)
+				.valueOf("./@nameIdentifierScheme")
 				.trim()
 				.toUpperCase()
 				.replaceAll(" ", "")
@@ -119,7 +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));
@@ -168,7 +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;
@@ -220,14 +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
@@ -253,7 +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
@@ -327,16 +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;
@@ -344,6 +365,8 @@ 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);
 	}
 }