implemented filtering step

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

@@ -82,10 +82,11 @@ public class AuthorMerger {
 						.map(ba -> new Tuple2<>(sim(ba, a._2()), ba))
 						.max(Comparator.comparing(Tuple2::_1));
 
-					if(simAuthor.isPresent()) {
+					if (simAuthor.isPresent()) {
 						double th = THRESHOLD;
-						//increase the threshold if the surname is too short
+						// increase the threshold if the surname is too short
-						if (simAuthor.get()._2().getSurname() != null && simAuthor.get()._2().getSurname().length()<=3)
+						if (simAuthor.get()._2().getSurname() != null
+							&& simAuthor.get()._2().getSurname().length() <= 3)
 							th = 0.99;
 
 						if (simAuthor.get()._1() > th) {
@@ -100,8 +101,9 @@ public class AuthorMerger {
 	}
 
 	public static String pidToComparableString(StructuredProperty pid) {
-		return (pid.getQualifier() != null ?
+		return (pid.getQualifier() != null
-						pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" : "")
+			? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
+			: "")
 			+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
 	}
 
@@ -123,14 +125,13 @@ public class AuthorMerger {
 		final Person pa = parse(a);
 		final Person pb = parse(b);
 
-		//if both are accurate (e.g. they have name and surname)
+		// if both are accurate (e.g. they have name and surname)
 		if (pa.isAccurate() & pb.isAccurate()) {
-			return
+			return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5
-					new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString()))*0.5
+				+ new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5;
-							+ new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString()))*0.5;
 		} else {
-			return
+			return new JaroWinkler()
-					new JaroWinkler().score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
+				.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
 		}
 	}
 

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

@@ -1,13 +1,22 @@
 package eu.dnetlib.doiboost
 
-import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, KeyValue, Qualifier, Result, StructuredProperty}
+import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Publication, Qualifier, Result, StructuredProperty}
 import eu.dnetlib.dhp.utils.DHPUtils
+import org.json4s
+import org.json4s.DefaultFormats
+import org.json4s.jackson.JsonMethods.parse
+
+import scala.collection.JavaConverters._
+import scala.io.Source
+
+
+case class HostedByItemType(id: String, officialName: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
 
 object DoiBoostMappingUtil {
 
   //STATIC STRING
   val MAG = "microsoft"
-  val MAG_NAME= "Microsoft Academic Graph"
+  val MAG_NAME = "Microsoft Academic Graph"
   val ORCID = "ORCID"
   val CROSSREF = "Crossref"
   val UNPAYWALL = "UnpayWall"
@@ -19,112 +28,234 @@ object DoiBoostMappingUtil {
   val DNET_LANGUAGES = "dnet:languages"
   val PID_TYPES = "dnet:pid_types"
 
+  val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;")
 
 
-  def generateDataInfo(): DataInfo = {
+  def retrieveHostedByMap(): Map[String, HostedByItemType] = {
-    generateDataInfo("0.9")
+    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)
+    json.extract[Map[String, HostedByItemType]]
   }
 
-  def generateDataInfo(trust:String): DataInfo = {
+  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))
+      return hostedByMap(eissn)
+
+    if (lissn != null && lissn.nonEmpty && hostedByMap.contains(lissn))
+      return hostedByMap(lissn)
+
+    null
+
+  }
+
+
+
+
+  def fixPublication(publication: Publication, hostedByMap: Map[String, HostedByItemType]): Publication = {
+    if (publication.getJournal == null)
+      return publication
+
+    val issn = publication.getJournal.getIssnPrinted
+    val eissn = publication.getJournal.getIssnOnline
+    val lissn = publication.getJournal.getIssnLinking
+
+    val item = retrieveHostedByItem(issn, eissn, lissn, hostedByMap)
+    if (item!= null) {
+      val l = publication.getInstance().asScala.map(i =>{
+        val hb = new KeyValue
+        hb.setValue (item.officialName)
+        hb.setKey (s"10|${item.id}" )
+        i.setHostedby(hb)
+        if(item.openAccess)
+          i.setAccessright(createQualifier("Open", "dnet:access_modes"))
+        i
+      }).asJava
+
+      publication.setInstance(l)
+    }
+    publication
+}
+
+
+def generateDataInfo (): DataInfo = {
+  generateDataInfo ("0.9")
+}
+
+
+  def filterPublication (publication: Publication): Boolean = {
+
+  //Case empty publication
+  if (publication == null)
+  return false
+
+  //Case publication with no title
+  if (publication.getTitle == null || publication.getTitle.size == 0)
+  return false
+
+
+  val s = publication.getTitle.asScala.count (p => p.getValue != null
+  && p.getValue.nonEmpty && ! p.getValue.equalsIgnoreCase ("[NO TITLE AVAILABLE]") )
+
+  if (s == 0)
+  return false
+
+  // fixes #4360 (test publisher)
+  val publisher = if (publication.getPublisher != null) publication.getPublisher.getValue else null
+
+  if (publisher != null && (publisher.equalsIgnoreCase ("Test accounts") || publisher.equalsIgnoreCase ("CrossRef Test Account") ) ) {
+  return false;
+}
+
+  //Publication with no Author
+  if (publication.getAuthor == null || publication.getAuthor.size () == 0)
+  return false
+
+
+  //filter invalid author
+  val authors = publication.getAuthor.asScala.map (s => {
+  if (s.getFullname.nonEmpty) {
+  s.getFullname
+}
+  else
+  s"${
+  s.getName
+} ${
+  s.getSurname
+}"
+})
+
+  val c = authors.count (isValidAuthorName)
+  if (c == 0)
+  return false
+
+  // fixes #4368
+  if (authors.count (s => s.equalsIgnoreCase ("Addie Jackson") ) > 0 && "Elsevier BV".equalsIgnoreCase (publication.getPublisher.getValue) )
+  return false
+
+  true
+}
+
+
+  def isValidAuthorName (fullName: String): Boolean = {
+  if (fullName == null || fullName.isEmpty)
+  return false
+  if (invalidName.contains (fullName.toLowerCase.trim) )
+  return false
+  true
+}
+
+
+  def generateDataInfo (trust: String): DataInfo = {
   val di = new DataInfo
-    di.setDeletedbyinference(false)
+  di.setDeletedbyinference (false)
-    di.setInferred(false)
+  di.setInferred (false)
-    di.setInvisible(false)
+  di.setInvisible (false)
-    di.setTrust(trust)
+  di.setTrust (trust)
-    di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions"))
+  di.setProvenanceaction (createQualifier ("sysimport:actionset", "dnet:provenanceActions") )
   di
-  }
+}
 
 
-  def createSP(value: String, classId: String, schemeId: String): StructuredProperty = {
+  def createSP (value: String, classId: String, schemeId: String): StructuredProperty = {
   val sp = new StructuredProperty
-    sp.setQualifier(createQualifier(classId, schemeId))
+  sp.setQualifier (createQualifier (classId, schemeId) )
-    sp.setValue(value)
+  sp.setValue (value)
   sp
 
-  }
+}
 
-  def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
+  def createSP (value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = {
   val sp = new StructuredProperty
-    sp.setQualifier(createQualifier(classId, schemeId))
+  sp.setQualifier (createQualifier (classId, schemeId) )
-    sp.setValue(value)
+  sp.setValue (value)
-    sp.setDataInfo(dataInfo)
+  sp.setDataInfo (dataInfo)
   sp
 
-  }
+}
 
-  def createCrossrefCollectedFrom(): KeyValue = {
+  def createCrossrefCollectedFrom (): KeyValue = {
 
   val cf = new KeyValue
-    cf.setValue(CROSSREF)
+  cf.setValue (CROSSREF)
-    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(CROSSREF.toLowerCase))
+  cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (CROSSREF.toLowerCase) )
   cf
 
-  }
+}
 
 
-  def createUnpayWallCollectedFrom(): KeyValue = {
+  def createUnpayWallCollectedFrom (): KeyValue = {
 
   val cf = new KeyValue
-    cf.setValue(UNPAYWALL)
+  cf.setValue (UNPAYWALL)
-    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(UNPAYWALL.toLowerCase))
+  cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (UNPAYWALL.toLowerCase) )
   cf
 
-  }
+}
 
-  def createORIDCollectedFrom(): KeyValue = {
+  def createORIDCollectedFrom (): KeyValue = {
 
   val cf = new KeyValue
-    cf.setValue(ORCID)
+  cf.setValue (ORCID)
-    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase))
+  cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (ORCID.toLowerCase) )
   cf
 
-  }
+}
 
 
-
+  def generateIdentifier (oaf: Result, doi: String): String = {
-  def generateIdentifier(oaf: Result, doi: String): String = {
+  val id = DHPUtils.md5 (doi.toLowerCase)
-    val id = DHPUtils.md5(doi.toLowerCase)
+  if (oaf.isInstanceOf[Dataset] )
-    if (oaf.isInstanceOf[Dataset])
+  return s"60|${
-      return s"60|${doiBoostNSPREFIX}${SEPARATOR}${id}"
+  doiBoostNSPREFIX
-    s"50|${doiBoostNSPREFIX}${SEPARATOR}${id}"
+}${
-  }
+  SEPARATOR
+}${
+  id
+}"
+  s"50|${
+  doiBoostNSPREFIX
+}${
+  SEPARATOR
+}${
+  id
+}"
+}
 
 
-
+  def createMAGCollectedFrom (): KeyValue = {
-
-
-  def createMAGCollectedFrom(): KeyValue = {
 
   val cf = new KeyValue
-    cf.setValue(MAG)
+  cf.setValue (MAG)
-    cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(MAG))
+  cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (MAG) )
   cf
 
-  }
+}
 
-  def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = {
+  def createQualifier (clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = {
   val q = new Qualifier
-    q.setClassid(clsName)
+  q.setClassid (clsName)
-    q.setClassname(clsValue)
+  q.setClassname (clsValue)
-    q.setSchemeid(schName)
+  q.setSchemeid (schName)
-    q.setSchemename(schValue)
+  q.setSchemename (schValue)
   q
-  }
+}
 
-  def createQualifier(cls: String, sch: String): Qualifier = {
+  def createQualifier (cls: String, sch: String): Qualifier = {
-    createQualifier(cls, cls, sch, sch)
+  createQualifier (cls, cls, sch, sch)
-  }
+}
 
 
-  def asField[T](value: T): Field[T] = {
+  def asField[T] (value: T): Field[T] = {
   val tmp = new Field[T]
-    tmp.setValue(value)
+  tmp.setValue (value)
   tmp
 
 
-  }
+}
-
 
 
 }

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

@@ -32,11 +32,11 @@ object SparkGenerateDoiBoost {
 
 
     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"$workingDirPath/crossrefPublication")
+//    spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefPublication")
-    spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s => s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset")
+//    spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s => s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset")
-    spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication")
+//    spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication")
-    spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication")
+//    spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication")
-    spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication")
+//    spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication")
 
     implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
     implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset]
@@ -67,14 +67,13 @@ object SparkGenerateDoiBoost {
     logger.info("Phase 3) Join Result with MAG")
     val sj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p))
 
-    sj.where(sj("_1").like())
-
     val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p))
     sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication")
 
 
+    val doiBoostPublication: Dataset[Publication] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication]
 
-
+    doiBoostPublication.filter(p=>DoiBoostMappingUtil.filterPublication(p)).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered")
 
 
 

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

@@ -0,0 +1,16 @@
+package eu.dnetlib.dhp.doiboost
+
+
+import eu.dnetlib.doiboost.DoiBoostMappingUtil
+import org.junit.jupiter.api.Test
+
+class DoiBoostHostedByMapTest {
+
+  @Test
+  def testLoadMap(): Unit = {
+    println(DoiBoostMappingUtil.retrieveHostedByMap().keys.size)
+
+
+  }
+
+}