Fixed DoiBoost generation to point to correct organization in affiliation relation
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b924276e18
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@ -13,10 +13,30 @@ import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.collection.JavaConverters._
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.{JField, JObject, JString,JArray}
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import org.json4s.jackson.JsonMethods.parse
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object SparkGenerateDoiBoost {
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def extractIdGRID(input:String):List[(String,String)] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: org.json4s.JValue = parse(input)
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val id:String = (json \ "id").extract[String]
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val grids:List[String] = for {
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JObject(pid) <- json \ "pid"
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JField("qualifier", JObject(qualifier)) <- pid
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JField("classid", JString(classid)) <-qualifier
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JField("value", JString(vl)) <- pid
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if classid == "GRID"
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} yield vl
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grids.map(g => (id, s"unresolved::grid::${g.toLowerCase}"))(collection.breakOut)
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}
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def main(args: Array[String]): Unit = {
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@ -36,6 +56,7 @@ object SparkGenerateDoiBoost {
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val hostedByMapPath = parser.get("hostedByMapPath")
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val workingDirPath = parser.get("workingPath")
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val openaireOrganizationPath = parser.get("openaireOrganizationPath")
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val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable {
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override def zero: Publication = new Publication
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@ -156,7 +177,7 @@ object SparkGenerateDoiBoost {
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magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).flatMap(item => {
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val pub:Publication = item._1._2
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val affiliation = item._2
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val affId:String = if (affiliation.GridId.isDefined) DoiBoostMappingUtil.generateGridAffiliationId(affiliation.GridId.get) else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
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val affId:String = if (affiliation.GridId.isDefined) s"unresolved::grid::${affiliation.GridId.get.toLowerCase}" else DoiBoostMappingUtil.generateMAGAffiliationId(affiliation.AffiliationId.toString)
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val r:Relation = new Relation
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r.setSource(pub.getId)
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r.setTarget(affId)
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@ -174,9 +195,35 @@ object SparkGenerateDoiBoost {
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r1.setDataInfo(pub.getDataInfo)
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r1.setCollectedfrom(List(DoiBoostMappingUtil.createMAGCollectedFrom()).asJava)
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List(r, r1)
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})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
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})(mapEncoderRel).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved")
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val unresolvedRels:Dataset[(String, Relation)] = spark.read.load(s"$workingDirPath/doiBoostPublicationAffiliation_unresolved").as[Relation].map(r => {
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if (r.getSource.startsWith("unresolved"))
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(r.getSource, r)
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else if (r.getTarget.startsWith("unresolved"))
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(r.getTarget,r)
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else
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("resolved", r)
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})
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val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2)
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unresolvedRels.joinWith(openaireOrganization,unresolvedRels("_1").equalTo(openaireOrganization("_2")))
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.map { x =>
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val currentRels = x._1._2
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val currentOrgs = x._2
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if (currentOrgs!= null)
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if(currentRels.getSource.startsWith("unresolved"))
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currentRels.setSource(currentOrgs._1)
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else
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currentRels.setTarget(currentOrgs._1)
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currentRels
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}.write.save(s"$workingDirPath/doiBoostPublicationAffiliation")
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magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
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val affiliation = item._2
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if (affiliation.GridId.isEmpty) {
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@ -1,7 +1,8 @@
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[
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{"paramName": "m", "paramLongName":"master", "paramDescription": "the master name", "paramRequired": true},
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{"paramName": "hb", "paramLongName":"hostedByMapPath", "paramDescription": "the hosted By Map Path", "paramRequired": true},
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{"paramName": "oo", "paramLongName":"openaireOrganizationPath", "paramDescription": "the openaire Organization Path", "paramRequired": true},
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{"paramName": "ap", "paramLongName":"affiliationPath", "paramDescription": "the Affliation Path", "paramRequired": true},
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{"paramName": "pa", "paramLongName":"paperAffiliationPath", "paramDescription": "the paperAffiliation Path", "paramRequired": true},
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{"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true}
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{"paramName": "w", "paramLongName":"workingPath", "paramDescription": "the Working Path", "paramRequired": true}
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]
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@ -27,6 +27,12 @@
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<name>hostedByMapPath</name>
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<description>the hostedByMap Path</description>
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</property>
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<property>
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<name>openaireOrganizationPath</name>
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<description>the OpenAire Organizations Path</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the Path of the sequence file action set</description>
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@ -214,6 +220,7 @@
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
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<arg>--openaireOrganizationPath</arg><arg>${openaireOrganizationPath}</arg>
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<arg>--affiliationPath</arg><arg>${inputPathMAG}/dataset/Affiliations</arg>
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<arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/dataset/PaperAuthorAffiliations</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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