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@ -2,27 +2,23 @@ package eu.dnetlib.dhp.oa.graph.hostebymap
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.oa.graph.hostebymap.model.{DOAJModel, UnibiGoldModel}
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import eu.dnetlib.dhp.oa.merge.AuthorMerger
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.{Datasource, Organization, Publication, Relation}
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import eu.dnetlib.dhp.schema.oaf.{Datasource}
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.json4s.DefaultFormats
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import org.slf4j.{Logger, LoggerFactory}
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import org.json4s.jackson.Serialization.write
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import scala.collection.mutable.ListBuffer
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import com.fasterxml.jackson.databind.ObjectMapper
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object SparkPrepareHostedByMapData {
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case class HostedByInfo(id: Option[String], officialname: String, journal_id: String, provenance : String, id_type: String) {}
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implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])
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implicit val mapEncoderDats: Encoder[Datasource] = Encoders.bean(classOf[Datasource])
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implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel]
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implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel]
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implicit val mapEncoderHBI: Encoder[HostedByInfo] = Encoders.product[HostedByInfo]
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def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)) : HostedByItemType = {
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@ -32,59 +28,144 @@ object SparkPrepareHostedByMapData {
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val isOpenAccess: Boolean = doaj == null && gold == null
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openaire.journal_id match {
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case Constants.ISSN => return HostedByItemType(openaire.id.get, openaire.officialname, openaire.journal_id, "", "", isOpenAccess)
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case Constants.EISSN => return HostedByItemType(openaire.id.get, openaire.officialname, "", openaire.journal_id, "", isOpenAccess)
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case Constants.ISSNL => return HostedByItemType(openaire.id.get, openaire.officialname, "", "", openaire.journal_id, isOpenAccess)
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case Constants.ISSN => HostedByItemType(openaire.id, openaire.officialname, openaire.journal_id, "", "", isOpenAccess)
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case Constants.EISSN => HostedByItemType(openaire.id, openaire.officialname, "", openaire.journal_id, "", isOpenAccess)
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case Constants.ISSNL => HostedByItemType(openaire.id, openaire.officialname, "", "", openaire.journal_id, isOpenAccess)
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// catch the default with a variable so you can print it
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case whoa => return null
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case whoa => null
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}
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}
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def toHostedByMap(input: HostedByItemType): ListBuffer[String] = {
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implicit val formats = DefaultFormats
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val serializedJSON:String = write(input)
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// def toHostedByMap(input: HostedByItemType): ListBuffer[String] = {
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// implicit val formats = DefaultFormats
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// val serializedJSON:String = write(input)
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//
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// var hostedBy = new ListBuffer[String]()
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// if(!input.issn.equals("")){
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// hostedBy += "{\"" + input.issn + "\":" + serializedJSON + "}"
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// }
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// if(!input.eissn.equals("")){
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// hostedBy += "{\"" + input.eissn + "\":" + serializedJSON + "}"
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// }
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// if(!input.lissn.equals("")){
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// hostedBy += "{\"" + input.lissn + "\":" + serializedJSON + "}"
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// }
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//
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// hostedBy
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//
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// }
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def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = {
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if(issn != null){
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if(eissn != null){
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if(issnl != null){
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HostedByItemType(id, officialname, issn, eissn, issnl , oa)
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}else{
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HostedByItemType(id, officialname, issn, eissn, "" , oa)
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}
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}else{
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if(issnl != null){
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HostedByItemType(id, officialname, issn, "", issnl , oa)
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}else{
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HostedByItemType(id, officialname, issn, "", "" , oa)
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}
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}
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}else{
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if(eissn != null){
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if(issnl != null){
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HostedByItemType(id, officialname, "", eissn, issnl , oa)
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}else{
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HostedByItemType(id, officialname, "", eissn, "" , oa)
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}
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}else{
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if(issnl != null){
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HostedByItemType(id, officialname, "", "", issnl , oa)
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}else{
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HostedByItemType("", "", "", "", "" , oa)
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}
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}
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}
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}
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def oaToHostedbyItemType(dats: Datasource): HostedByItemType = {
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if (dats.getJournal != null) {
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return getHostedByItemType(dats.getId, dats.getOfficialname.getValue, dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, false)
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}
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HostedByItemType("","","","","",false)
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}
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def oaHostedByDataset(spark:SparkSession, datasourcePath : String) : Dataset[HostedByItemType] = {
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import spark.implicits._
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val mapper = new ObjectMapper()
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implicit var encoderD = Encoders.kryo[Datasource]
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val dd : Dataset[Datasource] = spark.read.textFile(datasourcePath)
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.map(r => mapper.readValue(r, classOf[Datasource]))
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dd.map{ddt => oaToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
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}
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def goldToHostedbyItemType(gold: UnibiGoldModel): HostedByItemType = {
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return getHostedByItemType(Constants.UNIBI, gold.getTitle, gold.getIssn, "", gold.getIssn_l, true)
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}
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def goldHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = {
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import spark.implicits._
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implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel]
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var hostedBy = new ListBuffer[String]()
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val mapper = new ObjectMapper()
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val dd : Dataset[UnibiGoldModel] = spark.read.textFile(datasourcePath)
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.map(r => mapper.readValue(r, classOf[UnibiGoldModel]))
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dd.map{ddt => goldToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
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}
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def doajToHostedbyItemType(doaj: DOAJModel): HostedByItemType = {
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return getHostedByItemType(Constants.DOAJ, doaj.getJournalTitle, doaj.getIssn, doaj.getEissn, "", true)
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}
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def doajHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = {
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import spark.implicits._
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implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel]
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val mapper = new ObjectMapper()
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val dd : Dataset[DOAJModel] = spark.read.textFile(datasourcePath)
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.map(r => mapper.readValue(r, classOf[DOAJModel]))
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dd.map{ddt => doajToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals("")))
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}
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def toList(input: HostedByItemType): List[(String, HostedByItemType)] = {
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var lst : List[(String, HostedByItemType)] = List()
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if(!input.issn.equals("")){
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hostedBy += "{\"" + input.issn + "\":" + serializedJSON + "}"
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lst = (input.issn, input) :: lst
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}
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if(!input.eissn.equals("")){
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hostedBy += "{\"" + input.eissn + "\":" + serializedJSON + "}"
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lst = (input.eissn, input) :: lst
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}
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if(!input.lissn.equals("")){
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hostedBy += "{\"" + input.lissn + "\":" + serializedJSON + "}"
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lst = (input.lissn, input) :: lst
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}
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hostedBy
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lst
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}
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def readOADataset(input:String, spark: SparkSession): Dataset[HostedByInfo] = {
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spark.read.textFile(input).as[Datasource].flatMap(ds => {
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val lst = new ListBuffer[HostedByInfo]()
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if (ds.getJournal == null) {
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return null
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}
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val issn: String = ds.getJournal.getIssnPrinted
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val issnl: String = ds.getJournal.getIssnOnline
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val eissn: String = ds.getJournal.getIssnOnline
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val id: String = ds.getId
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val officialname: String = ds.getOfficialname.getValue
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if (issn != null) {
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lst += HostedByInfo(Some(id), officialname, issn, Constants.OPENAIRE, Constants.ISSN)
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}
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if (issnl != null) {
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lst += HostedByInfo(Some(id), officialname, issnl, Constants.OPENAIRE, Constants.ISSNL)
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}
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if (eissn != null) {
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lst += HostedByInfo(Some(id), officialname, eissn, Constants.OPENAIRE, Constants.EISSN)
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}
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lst
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}).filter(i => i != null)
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}
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def main(args: Array[String]): Unit = {
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val logger: Logger = LoggerFactory.getLogger(getClass)
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@ -105,53 +186,34 @@ object SparkPrepareHostedByMapData {
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implicit val formats = DefaultFormats
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logger.info("Getting the Datasources")
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val doajDataset: Dataset[DOAJModel] = spark.read.load(workingDirPath + "/doaj").as[DOAJModel]
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val unibiDataset: Dataset[UnibiGoldModel] = spark.read.load(datasourcePath).as[UnibiGoldModel]
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// val doajDataset: Dataset[DOAJModel] = spark.read.textFile(workingDirPath + "/doaj").as[DOAJModel]
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val oa: Dataset[HostedByInfo] = readOADataset(datasourcePath, spark)
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val dats : Dataset[HostedByItemType] =
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oaHostedByDataset(spark, datasourcePath)
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.union(goldHostedByDataset(spark, workingDirPath + "/unibi_gold"))
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.union(doajHostedByDataset(spark, workingDirPath + "/doaj"))
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dats.flatMap(hbi => toList(hbi))
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.groupByKey(_._1)
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val doaj: Dataset[HostedByInfo] = doajDataset.flatMap(doaj => {
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val lst = new ListBuffer[HostedByInfo]()
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val issn: String = doaj.getIssn
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val eissn: String = doaj.getEissn
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val officialname: String = doaj.getJournalTitle
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if (issn != null) {
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lst += HostedByInfo(null, officialname, issn, Constants.DOAJ, Constants.ISSN)
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}
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if (eissn != null) {
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lst += HostedByInfo(null, officialname, eissn, Constants.DOAJ, Constants.EISSN)
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}
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lst
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})
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val gold: Dataset[HostedByInfo] = unibiDataset.flatMap(gold => {
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val lst = new ListBuffer[HostedByInfo]()
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val issn: String = gold.getIssn
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val issnl: String = gold.getIssn_l
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val officialname: String = gold.getTitle
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if (issn != null) {
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lst += HostedByInfo(null, officialname, issn, Constants.UNIBI, Constants.ISSN)
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}
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if (issnl != null) {
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lst += HostedByInfo(null, officialname, issnl, Constants.UNIBI, Constants.ISSNL)
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}
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lst
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})
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Aggregators.createHostedByItemTypes(oa.joinWith(doaj, oa.col("journal_id").equalTo(doaj.col("journal_id")), "left")
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.joinWith(gold, $"_1.col('journal_id')".equalTo(gold.col("journal_id")), "left").map(toHostedByItemType)
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.filter(i => i != null))
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.flatMap(toHostedByMap)
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// .map(i => (i.id,i))
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// .groupByKey(_._1)
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// .agg(hostedByAggregator.toColumn)
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// .map(p => p._2)
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.write.mode(SaveMode.Overwrite).save(s"$workingDirPath/HostedByMap")
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//
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//
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//
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//
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// Aggregators.createHostedByItemTypes(oa.joinWith(doaj, oa.col("journal_id").equalTo(doaj.col("journal_id")), "left")
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// .joinWith(gold, $"_1.col('journal_id')".equalTo(gold.col("journal_id")), "left").map(toHostedByItemType)
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// .filter(i => i != null))
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// .flatMap(toHostedByMap)
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// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/HostedByMap")
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//
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//
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}
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