-Renamed RelationInverse into RelationLabel.

-Removed findRelation from ModelSupport
-code formatted

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java

@@ -9,13 +9,13 @@ import java.util.concurrent.TimeUnit;
 
 import org.apache.http.HttpHeaders;
 import org.apache.http.entity.ContentType;
+import org.jetbrains.annotations.NotNull;
 
 import com.google.gson.Gson;
 
 import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
 import eu.dnetlib.dhp.common.api.zenodo.ZenodoModelList;
 import okhttp3.*;
-import org.jetbrains.annotations.NotNull;
 
 public class ZenodoAPIClient implements Serializable {
 
@@ -155,7 +155,6 @@ public class ZenodoAPIClient implements Serializable {
 		conn.setDoOutput(true);
 		conn.setRequestMethod("PUT");
 
-
 		try (OutputStream os = conn.getOutputStream()) {
 			byte[] input = metadata.getBytes("utf-8");
 			os.write(input, 0, input.length);
@@ -169,7 +168,6 @@ public class ZenodoAPIClient implements Serializable {
 
 		return responseCode;
 
-
 	}
 
 	private boolean checkOKStatus(int responseCode) {
@@ -233,7 +231,6 @@ public class ZenodoAPIClient implements Serializable {
 		conn.setDoOutput(true);
 		conn.setRequestMethod("POST");
 
-
 		try (OutputStream os = conn.getOutputStream()) {
 			byte[] input = json.getBytes("utf-8");
 			os.write(input, 0, input.length);
@@ -296,7 +293,6 @@ public class ZenodoAPIClient implements Serializable {
 		ZenodoModel zenodoModel = new Gson().fromJson(body, ZenodoModel.class);
 		bucket = zenodoModel.getLinks().getBucket();
 
-
 		return responseCode;
 
 	}
@@ -331,8 +327,6 @@ public class ZenodoAPIClient implements Serializable {
 		conn.setDoOutput(true);
 		conn.setRequestMethod("GET");
 
-
-
 		String body = getBody(conn);
 
 		int responseCode = conn.getResponseCode();
@@ -341,12 +335,8 @@ public class ZenodoAPIClient implements Serializable {
 		if (!checkOKStatus(responseCode))
 			throw new IOException("Unexpected code " + responseCode + body);
 
-
-
 		return body;
 
-
-
 	}
 
 	private String getBucket(String inputUurl) throws IOException {
@@ -370,8 +360,6 @@ public class ZenodoAPIClient implements Serializable {
 
 		return zenodoModel.getLinks().getBucket();
 
-
-
 	}
 
 }

dhp-common/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java

@@ -86,7 +86,6 @@ public class ModelConstants {
 	public static final Qualifier PROVENANCE_ACTION_SET_QUALIFIER = qualifier(
 		SYSIMPORT_ACTIONSET, SYSIMPORT_ACTIONSET, DNET_PROVENANCE_ACTIONS);
 
-
 	public static final String UNKNOWN = "UNKNOWN";
 	public static final String NOT_AVAILABLE = "not available";
 

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupport.java

@@ -2,16 +2,12 @@
 package eu.dnetlib.dhp.schema.oaf.common;
 
 import static com.google.common.base.Preconditions.checkArgument;
-import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
 
 import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.text.ParseException;
-import java.util.Date;
+import java.util.*;
-import java.util.Map;
-import java.util.Objects;
-import java.util.Optional;
 import java.util.function.Function;
 
 import org.apache.commons.codec.binary.Hex;
@@ -96,26 +92,6 @@ public class ModelSupport {
 		idPrefixEntity.put("50", "result");
 	}
 
-	private static void set(Map<String, RelationInverse> relationInverseMap, String relType, String subRelType,
-		String relClass, String inverseRelClass) {
-		relationInverseMap
-			.put(
-				rel(relType, subRelType, relClass), new RelationInverse()
-					.setInverseRelClass(inverseRelClass)
-					.setRelClass(relClass)
-					.setRelType(relType)
-					.setSubReltype(subRelType));
-		if (!relClass.equals(inverseRelClass)) {
-			relationInverseMap
-				.put(
-					rel(relType, subRelType, inverseRelClass), new RelationInverse()
-						.setInverseRelClass(relClass)
-						.setRelClass(inverseRelClass)
-						.setRelType(relType)
-						.setSubReltype(subRelType));
-		}
-	}
-
 	/**
 	 * Helper method: combines the relation attributes
 	 * @param relType
@@ -127,6 +103,24 @@ public class ModelSupport {
 		return String.format("%s_%s_%s", relType, subRelType, relClass);
 	}
 
+	/**
+	 * Helper method: deserialize the relation attributes serialized with rel
+	 * @param relType
+	 * @param subRelType
+	 * @param relClass
+	 * @return
+	 */
+	public static RelationLabel unRel(String deserialization) {
+		final String[] s = deserialization.split("_");
+		if (s!= null && s.length==3) {
+			final Relation.RELTYPE currentRelType = Relation.RELTYPE.valueOf(s[0]);
+			final Relation.SUBRELTYPE currentSubRelType = Relation.SUBRELTYPE.valueOf(s[1]);
+			final Relation.RELCLASS currentRelClass = Relation.RELCLASS.valueOf(s[2]);
+			return new RelationLabel(currentRelClass, currentRelType, currentSubRelType);
+		}
+		throw new IllegalArgumentException("Invalid relationship format for "+ deserialization);
+	}
+
 	private static final String schemeTemplate = "dnet:%s_%s_relations";
 
 	public static final String DATE_FORMAT = "yyyy-MM-dd";

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/RelationInverse.java

@@ -1,46 +0,0 @@
-
-package eu.dnetlib.dhp.schema.oaf.common;
-
-public class RelationInverse {
-	private String relClass;
-	private String inverseRelClass;
-	private String relType;
-	private String subReltype;
-
-	public String getRelType() {
-		return relType;
-	}
-
-	public RelationInverse setRelType(String relType) {
-		this.relType = relType;
-		return this;
-	}
-
-	public String getSubReltype() {
-		return subReltype;
-	}
-
-	public RelationInverse setSubReltype(String subReltype) {
-		this.subReltype = subReltype;
-		return this;
-	}
-
-	public String getRelClass() {
-		return relClass;
-	}
-
-	public RelationInverse setRelClass(String relClass) {
-		this.relClass = relClass;
-		return this;
-	}
-
-	public String getInverseRelClass() {
-		return inverseRelClass;
-	}
-
-	public RelationInverse setInverseRelClass(String inverseRelClass) {
-		this.inverseRelClass = inverseRelClass;
-		return this;
-	}
-
-}

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/common/RelationLabel.java

@@ -0,0 +1,33 @@
+
+package eu.dnetlib.dhp.schema.oaf.common;
+
+import eu.dnetlib.dhp.schema.oaf.Relation;
+
+public class RelationLabel {
+	private final Relation.RELCLASS relClass;
+	private final Relation.RELTYPE relType;
+	private final Relation.SUBRELTYPE subReltype;
+
+	public RelationLabel(Relation.RELCLASS relClass, Relation.RELTYPE relType, Relation.SUBRELTYPE subReltype) {
+		this.relClass = relClass;
+		this.relType = relType;
+		this.subReltype = subReltype;
+
+	}
+
+	public RelationLabel inverse() {
+		return  new RelationLabel(relClass.getInverse(), relType, subReltype);
+	}
+
+	public Relation.RELTYPE getRelType() {
+		return relType;
+	}
+
+	public Relation.SUBRELTYPE getSubReltype() {
+		return subReltype;
+	}
+
+	public Relation.RELCLASS getRelClass() {
+		return relClass;
+	}
+}

dhp-common/src/main/java/eu/dnetlib/dhp/schema/sx/OafUtils.scala

@@ -1,59 +0,0 @@
-package eu.dnetlib.dhp.schema.sx
-
-import eu.dnetlib.dhp.schema.common.ModelConstants
-import eu.dnetlib.dhp.schema.oaf._
-
-object OafUtils {
-
-  def generateKeyValue(key: String, value: String): KeyValue = {
-    val kv: KeyValue = new KeyValue()
-    kv.setKey(key)
-    kv.setValue(value)
-    kv
-  }
-
-  def generateDataInfo(trust: Float = 0.9f, invisible: Boolean = false): DataInfo = {
-    val di = new DataInfo
-    di.setInferred(false)
-    di.setTrust(trust)
-    di.setProvenanceaction(createQualifier(ModelConstants.SYSIMPORT_ACTIONSET, ModelConstants.DNET_PROVENANCE_ACTIONS))
-    di
-  }
-
-  def createQualifier(cls: String, sch: String): Qualifier = {
-    createQualifier(cls, cls, sch)
-  }
-
-  def createQualifier(classId: String, className: String, schemeId: String): Qualifier = {
-    val q: Qualifier = new Qualifier
-    q.setClassid(classId)
-    q.setClassname(className)
-    q.setSchemeid(schemeId)
-    q
-  }
-
-  def createAccessRight(classId: String, className: String, schemeId: String): AccessRight = {
-    val accessRight: AccessRight = new AccessRight
-    accessRight.setClassid(classId)
-    accessRight.setClassname(className)
-    accessRight.setSchemeid(schemeId)
-    accessRight
-  }
-
-  def createSP(value: String, classId: String,className:String, schemeId: String): StructuredProperty = {
-    val sp = new StructuredProperty
-    sp.setQualifier(createQualifier(classId,className, schemeId))
-    sp.setValue(value)
-    sp
-
-  }
-
-  def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
-    val sp = new StructuredProperty
-    sp.setQualifier(createQualifier(classId, schemeId))
-    sp.setValue(value)
-    sp
-
-  }
-
-}

dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelInfo.java

@@ -1,25 +0,0 @@
-
-package eu.dnetlib.scholexplorer.relation;
-
-import java.io.Serializable;
-
-public class RelInfo implements Serializable {
-	private String original;
-	private String inverse;
-
-	public String getOriginal() {
-		return original;
-	}
-
-	public void setOriginal(String original) {
-		this.original = original;
-	}
-
-	public String getInverse() {
-		return inverse;
-	}
-
-	public void setInverse(String inverse) {
-		this.inverse = inverse;
-	}
-}

dhp-common/src/main/java/eu/dnetlib/scholexplorer/relation/RelationMapper.java

@@ -1,20 +0,0 @@
-
-package eu.dnetlib.scholexplorer.relation;
-
-import java.io.Serializable;
-import java.util.HashMap;
-
-import org.apache.commons.io.IOUtils;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-public class RelationMapper extends HashMap<String, RelInfo> implements Serializable {
-
-	public static RelationMapper load() throws Exception {
-
-		final String json = IOUtils.toString(RelationMapper.class.getResourceAsStream("relations.json"));
-
-		ObjectMapper mapper = new ObjectMapper();
-		return mapper.readValue(json, RelationMapper.class);
-	}
-}

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/common/ModelSupportTest.java

@@ -36,15 +36,4 @@ public class ModelSupportTest {
 		}
 	}
 
-	@Nested
-	class InverseRelation {
-
-		@Test
-		void findRelations() {
-			assertNotNull(ModelSupport.findRelation("isMetadataFor"));
-			assertNotNull(ModelSupport.findRelation("ismetadatafor"));
-			assertNotNull(ModelSupport.findRelation("ISMETADATAFOR"));
-			assertNotNull(ModelSupport.findRelation("isRelatedTo"));
-		}
-	}
 }

dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java

@@ -1,16 +0,0 @@
-
-package eu.dnetlib.scholexplorer.relation;
-
-import static org.junit.jupiter.api.Assertions.assertFalse;
-
-import org.junit.jupiter.api.Test;
-
-class RelationMapperTest {
-
-	@Test
-	void testLoadRels() throws Exception {
-
-		RelationMapper relationMapper = RelationMapper.load();
-		assertFalse(relationMapper.isEmpty());
-	}
-}

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala

@@ -2,7 +2,7 @@ package eu.dnetlib.dhp.datacite
 
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
-import eu.dnetlib.dhp.schema.oaf.{DataInfo, EntityDataInfo, KeyValue}
+import eu.dnetlib.dhp.schema.oaf.{DataInfo, EntityDataInfo, KeyValue, Relation}
 
 import java.io.InputStream
 import java.time.format.DateTimeFormatter
@@ -66,12 +66,13 @@ class DataciteModelConstants extends Serializable {}
 
 object DataciteModelConstants {
 
-  val REL_TYPE_VALUE: String = "resultResult"
+  val REL_TYPE_VALUE =Relation.RELTYPE.resultResult
   val DATE_RELATION_KEY = "RelationDate"
   val DATACITE_FILTER_PATH = "/eu/dnetlib/dhp/datacite/datacite_filter"
-  val DOI_CLASS = "doi"
   val SUBJ_CLASS = "keywords"
   val DATACITE_NAME = "Datacite"
+  val PMID = "pmid"
+  val ARXIV = "arxiv"
   val dataInfo: EntityDataInfo = dataciteDataInfo(0.9f)
   val relDataInfo = OafMapperUtils.fromEntityDataInfo(dataInfo);
 
@@ -138,4 +139,8 @@ object DataciteModelConstants {
     Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE)
   )
 
+  def validIdentifiersInRelation(relatedIdentifierType:String):Boolean = {
+    relatedIdentifierType.equalsIgnoreCase(ModelConstants.DOI) || relatedIdentifierType.equalsIgnoreCase(PMID) ||
+      relatedIdentifierType.equalsIgnoreCase(ARXIV)
+  }
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala

@@ -100,7 +100,7 @@ object DataciteToOAFTransformation {
   }
 
   /** This utility method indicates whether the embargo date has been reached
-    * @param embargo_end_date
+    * @param embargo_end_date the end date of embargo
     * @return True if the embargo date has been reached, false otherwise
     */
   def embargo_end(embargo_end_date: String): Boolean = {
@@ -345,8 +345,8 @@ object DataciteToOAFTransformation {
 
     // DOI is mapped on a PID inside a Instance object
     val doi_q = OafMapperUtils.qualifier(
-      "doi",
+      ModelConstants.DOI,
-      "doi",
+      ModelConstants.DOI,
       ModelConstants.DNET_PID_TYPES
     )
     val pid = OafMapperUtils.structuredProperty(doi, doi_q)
@@ -615,44 +615,52 @@ object DataciteToOAFTransformation {
       List(result)
   }
 
+
+  //TODO @CLAUDIO we need to define relation in which verse
+
+  /**
+   * This function generate unresolved relation from the original Datacite document
+   * @param rels the related identifier section on the document
+   * @param id the source record Identifier
+   * @param date the date of collection
+   * @return a List of OAF relation
+   */
   private def generateRelations(
     rels: List[RelatedIdentifierType],
     id: String,
     date: String
   ): List[Relation] = {
+
+    // TODO We need to check how to generate realtions
+    // in the previous implementation we create all Bidirection Relations
+    // related to a DOI pid or arxiv,
     val bidirectionalRels: List[Relation] = rels
       .filter(r =>
-        Relation.RELCLASS.exists(r.relationType) && (r.relatedIdentifierType.equalsIgnoreCase("doi") ||
+        Relation.RELCLASS.exists(r.relationType) && validIdentifiersInRelation(r.relatedIdentifierType)
-        r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
-        r.relatedIdentifierType.equalsIgnoreCase("arxiv"))
       )
       .map(r => {
-        val subRelType = subRelTypeMapping(r.relationType).relType
+        val subRelType = Relation.SUBRELTYPE.valueOf(r.relationType)
         val target = DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
-        relation(id, target, subRelType, r.relationType, date)
+        relation(id, target, subRelType, Relation.RELCLASS.valueOf(r.relationType), date)
       })
     val citationRels: List[Relation] = rels
-      .filter(r =>
+      .filter(r =>validIdentifiersInRelation(r.relatedIdentifierType) &&
-        (r.relatedIdentifierType.equalsIgnoreCase("doi") ||
-        r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
-        r.relatedIdentifierType.equalsIgnoreCase("arxiv")) &&
         (r.relationType.toLowerCase.contains("cite") || r.relationType.toLowerCase.contains("reference"))
       )
       .map(r => {
         r.relationType match {
-          case ModelConstants.CITES | ModelConstants.REFERENCES =>
+          case  Relation.RELCLASS.Cites.toString | Relation.RELCLASS.References.toString =>
             val target = DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
-            relation(id, target, ModelConstants.CITATION, ModelConstants.CITES, date)
+            relation(id, target, Relation.SUBRELTYPE.citation, Relation.RELCLASS.Cites, date)
-          case ModelConstants.IS_CITED_BY | ModelConstants.IS_REFERENCED_BY =>
+          case Relation.RELCLASS.IsCitedBy.toString | Relation.RELCLASS.IsReferencedBy.toString =>
             val source = DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
-            relation(source, id, ModelConstants.CITATION, ModelConstants.CITES, date)
+            relation(source, id, Relation.SUBRELTYPE.citation, Relation.RELCLASS.Cites, date)
         }
       })
-
     citationRels ::: bidirectionalRels
   }
 
-  def relation(source: String, target: String, subRelType: String, relClass: String, date: String): Relation = {
+  def relation(source: String, target: String, subRelType: Relation.SUBRELTYPE, relClass: Relation.RELCLASS, date: String): Relation = {
     val rel = new Relation
     rel.setProvenance(Lists.newArrayList(OafMapperUtils.getProvenance(DATACITE_COLLECTED_FROM, relDataInfo)))
 

dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java

@@ -14,7 +14,7 @@ import java.util.function.Consumer;
 import java.util.function.Function;
 
 import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.common.RelationInverse;
+import eu.dnetlib.dhp.schema.oaf.common.RelationLabel;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
@@ -76,30 +76,22 @@ public class ReadBlacklistFromDB implements Closeable {
 	public List<Relation> processBlacklistEntry(ResultSet rs) {
 		try {
 			Relation direct = new Relation();
-			Relation inverse = new Relation();
+
 
 			String source_prefix = ModelSupport.entityIdPrefix.get(rs.getString("source_type"));
 			String target_prefix = ModelSupport.entityIdPrefix.get(rs.getString("target_type"));
 
 			String source_direct = source_prefix + "|" + rs.getString("source");
 			direct.setSource(source_direct);
-			inverse.setTarget(source_direct);
 
 			String target_direct = target_prefix + "|" + rs.getString("target");
 			direct.setTarget(target_direct);
-			inverse.setSource(target_direct);
-
 			String encoding = rs.getString("relationship");
-			RelationInverse ri = ModelSupport.findInverse(encoding);
+			final RelationLabel directLabel = ModelSupport.unRel(encoding);
-			direct.setRelClass(ri.getRelClass());
+			direct.setRelClass(directLabel.getRelClass());
-			inverse.setRelClass(ri.getInverseRelClass());
+			direct.setRelType(directLabel.getRelType());
-			direct.setRelType(ri.getRelType());
+			direct.setSubRelType(directLabel.getSubReltype());
-			inverse.setRelType(ri.getRelType());
+			return Arrays.asList(direct, direct.inverse());
-			direct.setSubRelType(ri.getSubReltype());
-			inverse.setSubRelType(ri.getSubReltype());
-
-			return Arrays.asList(direct, inverse);
-
 		} catch (final SQLException e) {
 			throw new RuntimeException(e);
 		}

dhp-workflows/dhp-blacklist/src/test/java/eu/dnetlib/dhp/blacklist/BlacklistRelationTest.java

@@ -5,7 +5,7 @@ import java.util.Arrays;
 import java.util.List;
 
 import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.common.RelationInverse;
+import eu.dnetlib.dhp.schema.oaf.common.RelationLabel;
 import org.junit.jupiter.api.Assertions;
 import org.junit.jupiter.api.Test;
 
@@ -25,7 +25,7 @@ public class BlacklistRelationTest {
 				"resultProject_outcome_isProducedBy");
 
 		rels.forEach(r -> {
-			RelationInverse inverse = ModelSupport.relationInverseMap.get(r);
+			RelationLabel inverse = ModelSupport.relationInverseMap.get(r);
 			Assertions.assertNotNull(inverse);
 			Assertions.assertNotNull(inverse.getRelType());
 			Assertions.assertNotNull(inverse.getSubReltype());

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala

@@ -203,9 +203,9 @@ object SparkGenerateDoiBoost {
         val r: Relation = new Relation
         r.setSource(pub.getId)
         r.setTarget(affId)
-        r.setRelType(ModelConstants.RESULT_ORGANIZATION)
+        r.setRelType(Relation.RELTYPE.resultOrganization)
-        r.setRelClass(ModelConstants.HAS_AUTHOR_INSTITUTION)
+        r.setRelClass(Relation.RELCLASS.hasAuthorInstitution)
-        r.setSubRelType(ModelConstants.AFFILIATION)
+        r.setSubRelType(Relation.SUBRELTYPE.affiliation)
         r.setProvenance(OafMapperUtils.getProvenance(pub.getCollectedfrom, dataInfo))
 
         List(r)

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

@@ -11,7 +11,7 @@ import java.util.*;
 import java.util.stream.Collectors;
 
 import eu.dnetlib.dhp.schema.oaf.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.common.RelationInverse;
+import eu.dnetlib.dhp.schema.oaf.common.RelationLabel;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.Element;
@@ -401,7 +401,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
 	protected List<Oaf> getRelations(final String reltype, final String entityId, final String otherId,
 		final Entity entity) {
 		final List<Oaf> res = new ArrayList<>();
-		RelationInverse rel = ModelSupport.findRelation(reltype);
+		RelationLabel rel = ModelSupport.findRelation(reltype);
 		if (rel != null) {
 			res
 				.add(