[doiboost] merged workflow from branch beta

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java

@@ -554,7 +554,7 @@ public class PublicationToOaf implements Serializable {
 	private KeyValue createCollectedFrom() {
 		KeyValue cf = new KeyValue();
 		cf.setValue(ModelConstants.ORCID.toUpperCase());
-		cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a");
+		cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "cd0f74b5955dc87fd0605745c4b49ee8");
 		return cf;
 	}
 

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

@@ -391,6 +391,28 @@ object DoiBoostMappingUtil {
     di
   }
 
+  def createSubject(value: String, classId: String, schemeId: String): Subject = {
+    val s = new Subject
+    s.setQualifier(OafMapperUtils.qualifier(classId, classId, schemeId, schemeId))
+    s.setValue(value)
+    s
+
+  }
+
+  def createSubject(
+    value: String,
+    classId: String,
+    className: String,
+    schemeId: String,
+    schemeName: String
+  ): Subject = {
+    val s = new Subject
+    s.setQualifier(OafMapperUtils.qualifier(classId, className, schemeId, schemeName))
+    s.setValue(value)
+    s
+
+  }
+
   def createSP(
     value: String,
     classId: String,

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -201,7 +201,7 @@ case object Crossref2Oaf {
 
     if (subjectList.nonEmpty) {
       result.setSubject(
-        subjectList.map(s => createSP(s, "keywords", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava
+        subjectList.map(s => createSubject(s, "keyword", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava
       )
     }
 
@@ -370,10 +370,40 @@ case object Crossref2Oaf {
       case dataset: Dataset         => convertDataset(dataset)
     }
 
+    val doisReference: List[String] = for {
+      JObject(reference_json)          <- json \ "reference"
+      JField("DOI", JString(doi_json)) <- reference_json
+    } yield doi_json
+
+    if (doisReference != null && doisReference.nonEmpty) {
+      val citation_relations: List[Relation] = generateCitationRelations(doisReference, result)
+      resultList = resultList ::: citation_relations
+    }
     resultList = resultList ::: List(result)
     resultList
   }
 
+  private def createCiteRelation(source: Result, targetPid: String, targetPidType: String): List[Relation] = {
+
+    val targetId = IdentifierFactory.idFromPid("50", targetPidType, targetPid, true)
+
+    val from = new Relation
+    from.setSource(source.getId)
+    from.setTarget(targetId)
+    from.setRelType(ModelConstants.RESULT_RESULT)
+    from.setRelClass(ModelConstants.CITES)
+    from.setSubRelType(ModelConstants.CITATION)
+    from.setCollectedfrom(source.getCollectedfrom)
+    from.setDataInfo(source.getDataInfo)
+    from.setLastupdatetimestamp(source.getLastupdatetimestamp)
+
+    List(from)
+  }
+
+  def generateCitationRelations(dois: List[String], result: Result): List[Relation] = {
+    dois.flatMap(d => createCiteRelation(result, d, "doi"))
+  }
+
   def mappingFunderToRelations(
     funders: List[mappingFunder],
     sourceId: String,

dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala

@@ -2,7 +2,7 @@ package eu.dnetlib.doiboost.mag
 
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
-import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
+import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject}
 import eu.dnetlib.doiboost.DoiBoostMappingUtil
 import eu.dnetlib.doiboost.DoiBoostMappingUtil._
 import org.json4s
@@ -210,8 +210,8 @@ case object ConversionUtil {
       val className = "Microsoft Academic Graph classification"
       val classid = "MAG"
 
-      val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
+      val p: List[Subject] = fieldOfStudy.subjects.flatMap(s => {
-        val s1 = createSP(
+        val s1 = createSubject(
           s.DisplayName,
           classid,
           className,
@@ -219,10 +219,10 @@ case object ConversionUtil {
           ModelConstants.DNET_SUBJECT_TYPOLOGIES
         )
         val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
-        var resList: List[StructuredProperty] = List(s1)
+        var resList: List[Subject] = List(s1)
         if (s.MainType.isDefined) {
           val maintp = s.MainType.get
-          val s2 = createSP(
+          val s2 = createSubject(
             s.MainType.get,
             classid,
             className,
@@ -232,7 +232,7 @@ case object ConversionUtil {
           s2.setDataInfo(di)
           resList = resList ::: List(s2)
           if (maintp.contains(".")) {
-            val s3 = createSP(
+            val s3 = createSubject(
               maintp.split("\\.").head,
               classid,
               className,

dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala

@@ -1,9 +1,14 @@
 package eu.dnetlib.dhp.doiboost.crossref
 
+import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf._
 import eu.dnetlib.dhp.utils.DHPUtils
 import eu.dnetlib.doiboost.crossref.Crossref2Oaf
 import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig}
+import org.json4s
+import org.json4s.JsonAST.{JField, JObject, JString}
+import org.json4s.{DefaultFormats, JValue}
+import org.json4s.jackson.JsonMethods
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.Test
 import org.slf4j.{Logger, LoggerFactory}
@@ -109,6 +114,47 @@ class CrossrefMappingTest {
 
   }
 
+  private def parseJson(input: String): JValue = {
+    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
+    lazy val json: json4s.JValue = JsonMethods.parse(input)
+
+    json
+  }
+
+  @Test
+  def testCitationRelations(): Unit = {
+    val json = Source
+      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/publication_license_embargo.json"))
+      .mkString
+
+    assertNotNull(json)
+    assertFalse(json.isEmpty)
+
+    val result: List[Oaf] = Crossref2Oaf.convert(json)
+
+    assertTrue(result.nonEmpty)
+
+    val j = parseJson(json)
+
+    val doisReference: List[String] = for {
+      JObject(reference_json)          <- j \ "reference"
+      JField("DOI", JString(doi_json)) <- reference_json
+    } yield doi_json
+
+    val relationList: List[Relation] = result
+      .filter(s => s.isInstanceOf[Relation])
+      .map(r => r.asInstanceOf[Relation])
+      .filter(r => r.getSubRelType.equalsIgnoreCase(ModelConstants.CITATION))
+
+    assertNotNull(relationList)
+    assertFalse(relationList.isEmpty)
+
+    assertEquals(doisReference.size, relationList.size)
+
+    mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
+    relationList.foreach(p => println(mapper.writeValueAsString(p)))
+  }
+
   @Test
   def testEmptyTitle(): Unit = {
     val json = Source