improvement DOIBoost

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

@@ -1,7 +1,7 @@
 package eu.dnetlib.doiboost
 
 import eu.dnetlib.dhp.schema.action.AtomicAction
-import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
+import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
 import eu.dnetlib.dhp.utils.DHPUtils
 import org.apache.commons.lang3.StringUtils
 import org.codehaus.jackson.map.ObjectMapper
@@ -14,11 +14,21 @@ import scala.collection.JavaConverters._
 import scala.io.Source
 
 
-case class HostedByItemType(id: String, officialName: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
+case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
 
-case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:String){}
+case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){}
 
 object DoiBoostMappingUtil {
+  def getUnknownCountry(): Qualifier = {
+    createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries")
+  }
+
+
+
+  def generateMAGAffiliationId(affId: String): String = {
+    s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}"
+  }
+
 
   val logger: Logger = LoggerFactory.getLogger(getClass)
 
@@ -52,6 +62,11 @@ object DoiBoostMappingUtil {
         a.setClazz(classOf[Publication])
         a.setPayload(publication)
         (publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
+      case organization: Organization =>
+        val a: AtomicAction[Organization] = new AtomicAction[Organization]
+        a.setClazz(classOf[Organization])
+        a.setPayload(organization)
+        (organization.getClass.getCanonicalName, mapper.writeValueAsString(a))
       case relation: Relation =>
         val a: AtomicAction[Relation] = new AtomicAction[Relation]
         a.setClazz(classOf[Relation])
@@ -64,27 +79,33 @@ object DoiBoostMappingUtil {
   }
 
 
-  def retrieveHostedByMap(): Map[String, HostedByItemType] = {
+  def toHostedByItem(input:String): (String, HostedByItemType) = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
-    val jsonMap = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/hbMap.json")).mkString
+
-    lazy val json: json4s.JValue = parse(jsonMap)
+    lazy val json: json4s.JValue = parse(input)
-    json.extract[Map[String, HostedByItemType]]
+    val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]]
+    (c.keys.head, c.values.head)
   }
 
-  def retrieveHostedByItem(issn: String, eissn: String, lissn: String, hostedByMap: Map[String, HostedByItemType]): HostedByItemType = {
-    if (issn != null && issn.nonEmpty && hostedByMap.contains(issn))
-      return hostedByMap(issn)
 
-    if (eissn != null && eissn.nonEmpty && hostedByMap.contains(eissn))
+  def toISSNPair(publication: Publication) : (String, Publication) = {
-      return hostedByMap(eissn)
+    val issn = if (publication.getJournal == null) null else publication.getJournal.getIssnPrinted
-
+    val eissn =if (publication.getJournal == null) null else  publication.getJournal.getIssnOnline
-    if (lissn != null && lissn.nonEmpty && hostedByMap.contains(lissn))
+    val lissn =if (publication.getJournal == null) null else  publication.getJournal.getIssnLinking
-      return hostedByMap(lissn)
-
-    null
 
+    if (issn!= null && issn.nonEmpty)
+      (issn, publication)
+    else if(eissn!= null && eissn.nonEmpty)
+      (eissn, publication)
+    else if(lissn!= null && lissn.nonEmpty)
+      (lissn, publication)
+    else
+      (publication.getId, publication)
   }
 
+
+
+
   def generateGridAffiliationId(gridId:String) :String = {
     s"20|grid________::${DHPUtils.md5(gridId.toLowerCase().trim())}"
   }
@@ -96,18 +117,36 @@ object DoiBoostMappingUtil {
       result.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype))
     }
     result.getInstance().asScala.foreach(i => {
-      val hb = new KeyValue
+      i.setHostedby(getUbknownHostedBy())
-      hb.setValue("Unknown Repository")
-      hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c")
-      i.setHostedby(hb)
     })
     result
   }
 
-  def fixPublication(publication: Publication, hostedByMap: Map[String, HostedByItemType]): Publication = {
+  def getUbknownHostedBy():KeyValue = {
-    val issn = if (publication.getJournal == null) null else publication.getJournal.getIssnPrinted
+    val hb = new KeyValue
-    val eissn =if (publication.getJournal == null) null else  publication.getJournal.getIssnOnline
+    hb.setValue("Unknown Repository")
-    val lissn =if (publication.getJournal == null) null else  publication.getJournal.getIssnLinking
+    hb.setKey(s"10|$OPENAIRE_PREFIX::55045bd2a65019fd8e6741a755395c8c")
+    hb
+
+  }
+
+
+  def getOpenAccessQualifier():Qualifier = {
+    createQualifier("OPEN","Open Access","dnet:access_modes", "dnet:access_modes")
+
+  }
+
+  def getRestrictedQualifier():Qualifier = {
+    createQualifier("RESTRICTED","Restricted","dnet:access_modes", "dnet:access_modes")
+
+  }
+
+  def fixPublication(input:((String,Publication), (String,HostedByItemType))): Publication = {
+
+    val publication = input._1._2
+
+    val item = if (input._2 != null) input._2._2 else null
+
 
     val instanceType = publication.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty)
 
@@ -115,15 +154,15 @@ object DoiBoostMappingUtil {
       publication.getInstance().asScala.foreach(i => i.setInstancetype(instanceType.get.getInstancetype))
     }
 
-    val item = retrieveHostedByItem(issn, eissn, lissn, hostedByMap)
+
     publication.getInstance().asScala.foreach(i => {
       val hb = new KeyValue
       if (item != null) {
-        hb.setValue(item.officialName)
+        hb.setValue(item.officialname)
         hb.setKey(generateDSId(item.id))
         if (item.openAccess)
-          i.setAccessright(createQualifier("OPEN", "dnet:access_modes"))
+          i.setAccessright(getOpenAccessQualifier())
-        publication.setBestaccessright(createQualifier("OPEN", "dnet:access_modes"))
+        publication.setBestaccessright(getOpenAccessQualifier())
       }
       else {
         hb.setValue("Unknown Repository")
@@ -135,10 +174,10 @@ object DoiBoostMappingUtil {
     val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid)
     if (ar.nonEmpty) {
       if(ar.contains("OPEN")){
-        publication.setBestaccessright(createQualifier("OPEN", "dnet:access_modes"))
+        publication.setBestaccessright(getOpenAccessQualifier())
       }
       else {
-        publication.setBestaccessright(createQualifier(ar.head, "dnet:access_modes"))
+        publication.setBestaccessright(getRestrictedQualifier())
       }
     }
     publication
@@ -298,6 +337,8 @@ object DoiBoostMappingUtil {
   }
 
 
+
+
   def createMAGCollectedFrom(): KeyValue = {
 
     val cf = new KeyValue

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala

@@ -2,10 +2,13 @@ package eu.dnetlib.doiboost
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.schema.action.AtomicAction
-import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
+import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
 import org.apache.commons.io.IOUtils
+import org.apache.hadoop.io.Text
+import org.apache.hadoop.io.compress.GzipCodec
+import org.apache.hadoop.mapred.SequenceFileOutputFormat
 import org.apache.spark.SparkConf
-import org.apache.spark.sql.{ Encoder, Encoders, SaveMode, SparkSession}
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.slf4j.{Logger, LoggerFactory}
 
 object SparkGenerateDOIBoostActionSet {
@@ -23,8 +26,10 @@ object SparkGenerateDOIBoostActionSet {
         .master(parser.get("master")).getOrCreate()
 
     implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
+    implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
     implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
     implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
+    implicit val mapEncoderAS: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
 
     implicit val mapEncoderAtomiAction: Encoder[AtomicAction[OafDataset]] = Encoders.kryo[AtomicAction[OafDataset]]
 
@@ -32,17 +37,23 @@ object SparkGenerateDOIBoostActionSet {
     val dbDatasetPath               = parser.get("dbDatasetPath")
     val crossRefRelation            = parser.get("crossRefRelation")
     val dbaffiliationRelationPath   = parser.get("dbaffiliationRelationPath")
+    val dbOrganizationPath          = parser.get("dbOrganizationPath")
     val workingDirPath              = parser.get("targetPath")
 
     spark.read.load(dbDatasetPath).as[OafDataset]
       .map(d =>DoiBoostMappingUtil.fixResult(d))
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
-      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
+      .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
 
     spark.read.load(dbPublicationPath).as[Publication]
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
       .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
 
+    spark.read.load(dbOrganizationPath).as[Organization]
+      .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
+      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
+
+
     spark.read.load(crossRefRelation).as[Relation]
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
       .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
@@ -52,15 +63,9 @@ object SparkGenerateDOIBoostActionSet {
       .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
 
 
-//    implicit val mapEncoderPub: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
+    val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
-//
-//    val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
-//
-//
-//
-//    d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset_a8c2f90b-a3ae-4d6e-8187-47a437156e18_1590223414", classOf[Text], classOf[Text], classOf[TextOutputFormat[Text,Text]], classOf[GzipCodec])
-
 
+    d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
 
 
 

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

@@ -1,7 +1,7 @@
 package eu.dnetlib.doiboost
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
+import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset, Organization}
 import eu.dnetlib.doiboost.mag.ConversionUtil
 import org.apache.commons.io.IOUtils
 import org.apache.spark.SparkConf
@@ -26,22 +26,13 @@ object SparkGenerateDoiBoost {
         .master(parser.get("master")).getOrCreate()
 
     import spark.implicits._
-    val crossrefPublicationPath = parser.get("crossrefPublicationPath")
+
-    val crossrefDatasetPath = parser.get("crossrefDatasetPath")
+    val hostedByMapPath = parser.get("hostedByMapPath")
-    val uwPublicationPath = parser.get("uwPublicationPath")
-    val magPublicationPath = parser.get("magPublicationPath")
-    val orcidPublicationPath = parser.get("orcidPublicationPath")
     val workingDirPath = parser.get("workingDirPath")
 
 
-//    logger.info("Phase 1) repartition and move all the dataset in a same working folder")
-//    spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefPublication")
-//    spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s => s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset")
-//    spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication")
-//    spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication")
-//    spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication")
-
     implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
+    implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization]
     implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
     implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
     implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
@@ -75,23 +66,26 @@ object SparkGenerateDoiBoost {
     sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication")
 
 
-    val doiBoostPublication: Dataset[Publication] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication]
+    val doiBoostPublication: Dataset[(String,Publication)] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication].filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(DoiBoostMappingUtil.toISSNPair)(tupleForJoinEncoder)
 
-    val map = DoiBoostMappingUtil.retrieveHostedByMap()
+    val hostedByDataset : Dataset[(String, HostedByItemType)] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(DoiBoostMappingUtil.toHostedByItem))
 
-    doiBoostPublication.filter(p=>DoiBoostMappingUtil.filterPublication(p)).map(p => DoiBoostMappingUtil.fixPublication(p, map)).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered")
 
+    doiBoostPublication.joinWith(hostedByDataset, doiBoostPublication("_1").equalTo(hostedByDataset("_1")), "left")
+      .map(DoiBoostMappingUtil.fixPublication)
+      .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered")
 
     val affiliationPath = parser.get("affiliationPath")
     val paperAffiliationPath = parser.get("paperAffiliationPath")
 
-    val affiliation = spark.read.load(affiliationPath).where(col("GridId").isNotNull).select(col("AffiliationId"), col("GridId"))
+    val affiliation = spark.read.load(affiliationPath).select(col("AffiliationId"), col("GridId"), col("OfficialPage"), col("DisplayName"))
 
     val paperAffiliation = spark.read.load(paperAffiliationPath).select(col("AffiliationId").alias("affId"), col("PaperId"))
 
 
     val a:Dataset[DoiBoostAffiliation] = paperAffiliation
-      .joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId"))).select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId")).as[DoiBoostAffiliation]
+      .joinWith(affiliation, paperAffiliation("affId").equalTo(affiliation("AffiliationId")))
+      .select(col("_1.PaperId"), col("_2.AffiliationId"), col("_2.GridId"), col("_2.OfficialPage"), col("_2.DisplayName")).as[DoiBoostAffiliation]
 
 
 
@@ -102,24 +96,45 @@ object SparkGenerateDoiBoost {
     magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
       val pub:Publication = item._1._2
       val affiliation = item._2
+      val affId:String = if (affiliation.GridId.isDefined) DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId.get) else  DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
       val r:Relation = new Relation
       r.setSource(pub.getId)
-      r.setTarget(DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId))
+      r.setTarget(affId)
       r.setRelType("resultOrganization")
       r.setRelClass("hasAuthorInstitution")
       r.setSubRelType("affiliation")
       r.setDataInfo(pub.getDataInfo)
-      r.setCollectedfrom(pub.getCollectedfrom)
+      r.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
       val r1:Relation = new Relation
       r1.setTarget(pub.getId)
-      r1.setSource(DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId))
+      r1.setSource(affId)
       r1.setRelType("resultOrganization")
       r1.setRelClass("isAuthorInstitutionOf")
       r1.setSubRelType("affiliation")
       r1.setDataInfo(pub.getDataInfo)
-      r1.setCollectedfrom(pub.getCollectedfrom)
+      r1.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
       List(r, r1)
     })(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
+
+
+    magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
+      val affiliation = item._2
+      if (affiliation.GridId.isEmpty) {
+        val o = new Organization
+        o.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
+        o.setDataInfo(DoiBoostMappingUtil.generateDataInfo())
+        o.setId(DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString))
+        o.setOriginalId(List(affiliation.AffiliationId.toString).asJava)
+        if (affiliation.DisplayName.nonEmpty)
+          o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get))
+        if (affiliation.OfficialPage.isDefined)
+          o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get))
+        o.setCountry(DoiBoostMappingUtil.getUnknownCountry())
+        o
+      }
+      else
+        null
+    }).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization")
     }
 
 }

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

@@ -106,8 +106,10 @@ case object Crossref2Oaf {
 
     // Publisher ( Name of work's publisher mapped into  Result/Publisher)
     val publisher = (json \ "publisher").extractOrElse[String](null)
+    if (publisher!= null && publisher.nonEmpty)
       result.setPublisher(asField(publisher))
 
+
     // TITLE
     val mainTitles = for {JString(title) <- json \ "title" if title.nonEmpty} yield createSP(title, "main title", "dnet:dataCite_title")
     val originalTitles = for {JString(title) <- json \ "original-title" if title.nonEmpty} yield createSP(title, "alternative title", "dnet:dataCite_title")
@@ -120,7 +122,7 @@ case object Crossref2Oaf {
     result.setDescription(descriptionList.asJava)
 
     // Source
-    val sourceList = for {JString(source) <- json \ "source" if source.nonEmpty} yield asField(source)
+    val sourceList = for {JString(source) <- json \ "source" if source!= null && source.nonEmpty} yield asField(source)
     result.setSource(sourceList.asJava)
 
     //RELEVANT DATE Mapping
@@ -168,7 +170,7 @@ case object Crossref2Oaf {
       instance.setRefereed(asField("peerReviewed"))
 
 
-    instance.setAccessright(createQualifier("RESTRICTED", "dnet:access_modes"))
+    instance.setAccessright(getRestrictedQualifier())
     result.setInstance(List(instance).asJava)
     instance.setInstancetype(createQualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), "dnet:publication_resource", "dnet:publication_resource"))
     result.setResourcetype(createQualifier(cobjCategory.substring(0, 4),"dnet:dataCite_resource"))

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

@@ -115,7 +115,7 @@ case object ConversionUtil {
       j.setName(ci.DisplayName.get)
       if (ci.StartDate.isDefined && ci.EndDate.isDefined)
       {
-        j.setConferencedate(s"${ci.StartDate.get.toString} - ${ci.EndDate.get.toString}")
+        j.setConferencedate(s"${ci.StartDate.get.toString.substring(0,10)} - ${ci.EndDate.get.toString.substring(0,10)}")
       }
 
       publication.setJournal(j)
@@ -214,7 +214,7 @@ case object ConversionUtil {
 
 
     if (paper.Date != null && paper.Date.isDefined) {
-      pub.setDateofacceptance(asField(paper.Date.get.toString))
+      pub.setDateofacceptance(asField(paper.Date.get.toString.substring(0,10)))
     }
     pub.setPublisher(asField(paper.Publisher))
 
@@ -280,7 +280,7 @@ case object ConversionUtil {
 
 
     if (paper.Date != null) {
-      pub.setDateofacceptance(asField(paper.Date.toString))
+      pub.setDateofacceptance(asField(paper.Date.toString.substring(0,10)))
     }
 
     pub.setAuthor(authorsOAF.asJava)

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/SparkMapUnpayWallToOAF.scala

@@ -27,7 +27,7 @@ object SparkMapUnpayWallToOAF {
         .appName(getClass.getSimpleName)
         .master(parser.get("master")).getOrCreate()
 
-    implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication])
+    implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]
 
 
     val sourcePath = parser.get("sourcePath")
@@ -35,7 +35,8 @@ object SparkMapUnpayWallToOAF {
     val inputRDD:RDD[String] = spark.sparkContext.textFile(s"$sourcePath")
 
     logger.info("Converting UnpayWall to OAF")
-    val d:Dataset[Publication] = spark.createDataset(inputRDD.repartition(1000).map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
+
+    val d:Dataset[Publication] = spark.createDataset(inputRDD.map(UnpayWallToOAF.convertToOAF).filter(p=>p!=null)).as[Publication]
     d.write.mode(SaveMode.Overwrite).save(targetPath)
   }
 

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala

@@ -46,7 +46,7 @@ object UnpayWallToOAF {
     val i :Instance= new Instance()
 
     i.setCollectedfrom(createUnpayWallCollectedFrom())
-    i.setAccessright(createQualifier("OPEN", "dnet:access_modes"))
+    i.setAccessright(getOpenAccessQualifier())
     i.setUrl(List(oaLocation.url.get).asJava)
 
     if (oaLocation.license.isDefined)

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json

@@ -4,5 +4,6 @@
   {"paramName": "dd",   "paramLongName":"dbDatasetPath",                    "paramDescription": "the Crossref Dataset Path",       "paramRequired": true},
   {"paramName": "cr",   "paramLongName":"crossRefRelation",                 "paramDescription": "the UnpayWall Publication Path",  "paramRequired": true},
   {"paramName": "da",   "paramLongName":"dbaffiliationRelationPath",        "paramDescription": "the MAG Publication Path",        "paramRequired": true},
+  {"paramName": "do",   "paramLongName":"dbOrganizationPath",               "paramDescription": "the MAG Publication Path",        "paramRequired": true},
   {"paramName": "w",    "paramLongName":"targetPath",                       "paramDescription": "the Working Path",                "paramRequired": true}
 ]

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json

@@ -1,10 +1,6 @@
 [
   {"paramName": "m",    "paramLongName":"master",                    "paramDescription": "the master name",                 "paramRequired": true},
-  {"paramName": "cp",   "paramLongName":"crossrefPublicationPath",   "paramDescription": "the Crossref Publication Path",   "paramRequired": true},
+  {"paramName": "hb",   "paramLongName":"hostedByMapPath",            "paramDescription": "the hosted By Map Path",         "paramRequired": true},
-  {"paramName": "cd",   "paramLongName":"crossrefDatasetPath",       "paramDescription": "the Crossref Dataset Path",       "paramRequired": true},
-  {"paramName": "up",   "paramLongName":"uwPublicationPath",         "paramDescription": "the UnpayWall Publication Path",  "paramRequired": true},
-  {"paramName": "mp",   "paramLongName":"magPublicationPath",        "paramDescription": "the MAG Publication Path",        "paramRequired": true},
-  {"paramName": "op",   "paramLongName":"orcidPublicationPath",      "paramDescription": "the ORCID Publication Path",      "paramRequired": true},
   {"paramName": "ap",   "paramLongName":"affiliationPath",            "paramDescription": "the Affliation Path",            "paramRequired": true},
   {"paramName": "pa",   "paramLongName":"paperAffiliationPath",      "paramDescription": "the paperAffiliation Path",       "paramRequired": true},
   {"paramName": "w",    "paramLongName":"workingDirPath",            "paramDescription": "the Working Path",                "paramRequired": true}

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/intersection/oozie_app/workflow.xml

@@ -1,37 +1,17 @@
 <workflow-app name="Create DOIBoostActionSet" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
-            <name>crossrefPublicationPath</name>
+            <name>hostedByMapPath</name>
-            <description>the Crossref Publication Path</description>
+            <description>the Hosted By Map Path</description>
         </property>
-        <property>
-            <name>crossrefDatasetPath</name>
-            <description>the Crossref Dataset Path</description>
-        </property>
-        <property>
-            <name>uwPublicationPath</name>
-            <description>the UnpayWall Publication Path</description>
-        </property>
-        <property>
-            <name>magPublicationPath</name>
-            <description>the MAG Publication Path</description>
-        </property>
-        <property>
-            <name>orcidPublicationPath</name>
-            <description>the ORCID Publication Path</description>
-        </property>
-
         <property>
             <name>affiliationPath</name>
             <description>the Affliation Path</description>
         </property>
-
         <property>
             <name>paperAffiliationPath</name>
             <description>the paperAffiliation Path</description>
         </property>
-
-
         <property>
             <name>workingDirPath</name>
             <description>the Working Path</description>
@@ -52,7 +32,7 @@
 
 
 
-    <start to="CreateDOIBoost"/>
+    <start to="GenerateActionSet"/>
 
 
     <kill name="Kill">
@@ -82,17 +62,13 @@
                 --conf spark.sql.shuffle.partitions=3840
                 ${sparkExtraOPT}
             </spark-opts>
-            <arg>--crossrefPublicationPath</arg><arg>${crossrefPublicationPath}</arg>
+            <arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
-            <arg>--crossrefDatasetPath</arg><arg>${crossrefDatasetPath}</arg>
-            <arg>--uwPublicationPath</arg><arg>${uwPublicationPath}</arg>
-            <arg>--magPublicationPath</arg><arg>${magPublicationPath}</arg>
-            <arg>--orcidPublicationPath</arg><arg>${orcidPublicationPath}</arg>
             <arg>--affiliationPath</arg><arg>${affiliationPath}</arg>
             <arg>--paperAffiliationPath</arg><arg>${paperAffiliationPath}</arg>
             <arg>--workingDirPath</arg><arg>${workingDirPath}</arg>
             <arg>--master</arg><arg>yarn-cluster</arg>
         </spark>
-        <ok to="End"/>
+        <ok to="GenerateActionSet"/>
         <error to="Kill"/>
     </action>
 
@@ -115,6 +91,7 @@
             <arg>--dbDatasetPath</arg><arg>${workingDirPath}/crossrefDataset</arg>
             <arg>--crossRefRelation</arg><arg>/data/doiboost/input/crossref/relations</arg>
             <arg>--dbaffiliationRelationPath</arg><arg>${workingDirPath}/doiBoostPublicationAffiliation</arg>
+            <arg>-do</arg><arg>${workingDirPath}/doiBoostOrganization</arg>
             <arg>--targetPath</arg><arg>${workingDirPath}/actionDataSet</arg>
             <arg>--master</arg><arg>yarn-cluster</arg>
         </spark>

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala

@@ -1,7 +1,7 @@
 package eu.dnetlib.dhp.doiboost
 
 import eu.dnetlib.dhp.schema.oaf.{Publication, Dataset => OafDataset}
-import eu.dnetlib.doiboost.DoiBoostMappingUtil
+import eu.dnetlib.doiboost.{DoiBoostMappingUtil, HostedByItemType}
 import eu.dnetlib.doiboost.SparkGenerateDoiBoost.getClass
 import eu.dnetlib.doiboost.mag.ConversionUtil
 import eu.dnetlib.doiboost.orcid.ORCIDElement
@@ -15,45 +15,44 @@ import scala.io.Source
 
 class DoiBoostHostedByMapTest {
 
-  @Test
-  def testLoadMap(): Unit = {
-    println(DoiBoostMappingUtil.retrieveHostedByMap().keys.size)
 
 
-  }
+//  @Test
-
+//  def testMerge():Unit = {
-
+//    val conf: SparkConf = new SparkConf()
-  @Test
+//    val spark: SparkSession =
-  def testMerge():Unit = {
+//      SparkSession
-    val conf: SparkConf = new SparkConf()
+//        .builder()
-    val spark: SparkSession =
+//        .config(conf)
-      SparkSession
+//        .appName(getClass.getSimpleName)
-        .builder()
+//        .master("local[*]").getOrCreate()
-        .config(conf)
+//
-        .appName(getClass.getSimpleName)
+//
-        .master("local[*]").getOrCreate()
+//
-
+//    implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
-
+//    implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
-
+//    implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
-    implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
+//
-    implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
+//
-    implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPub)
+//    import spark.implicits._
-
+//    val dataset:RDD[String]= spark.sparkContext.textFile("/home/sandro/Downloads/hbMap.gz")
-
+//
-    import spark.implicits._
+//
-    val dataset:Dataset[ORCIDElement] = spark.read.json("/home/sandro/orcid").as[ORCIDElement]
+//    val hbMap:Dataset[(String, HostedByItemType)] =spark.createDataset(dataset.map(DoiBoostMappingUtil.toHostedByItem))
-
+//
-
+//
-    dataset.show(false)
+//    hbMap.show()
-
+//
-
+//
-
+//
-
+//
-
+//
-
+//
-
+//
-
+//
-  }
+//
+//
+//  }
 
 
   @Test

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala

@@ -1,5 +1,7 @@
 package eu.dnetlib.doiboost.mag
 
+import java.sql.Timestamp
+
 import eu.dnetlib.dhp.schema.oaf.Publication
 import org.apache.htrace.fasterxml.jackson.databind.SerializationFeature
 import org.apache.spark.SparkConf
@@ -39,6 +41,17 @@ class MAGMappingTest {
 
 
 
+  @Test
+  def testDate() :Unit = {
+
+    val p:Timestamp = Timestamp.valueOf("2011-10-02 00:00:00")
+
+    println(p.toString.substring(0,10))
+
+  }
+
+
+
   @Test
   def buildInvertedIndexTest(): Unit = {
     val json_input = Source.fromInputStream(getClass.getResourceAsStream("invertedIndex.json")).mkString