dnet-hadoop/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala

package eu.dnetlib.doiboost.mag

import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
import org.apache.spark.rdd.RDD
import org.apache.spark.sql.functions._
import org.apache.spark.sql._
import org.slf4j.{Logger, LoggerFactory}

import scala.collection.JavaConverters._

object SparkProcessMAG {

  def getDistinctResults (d:Dataset[MagPapers]):Dataset[MagPapers]={
    d.where(col("Doi").isNotNull)
      .groupByKey(mp => DoiBoostMappingUtil.normalizeDoi(mp.Doi))(Encoders.STRING)
      .reduceGroups((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2))
      .map(_._2)(Encoders.product[MagPapers])
      .map(mp => {
        new MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi),
          mp.DocType, mp.PaperTitle, mp.OriginalTitle,
          mp.BookTitle, mp.Year, mp.Date, mp.Publisher: String,
          mp.JournalId, mp.ConferenceSeriesId, mp.ConferenceInstanceId,
          mp.Volume, mp.Issue, mp.FirstPage, mp.LastPage,
          mp.ReferenceCount, mp.CitationCount, mp.EstimatedCitation,
          mp.OriginalVenue, mp.FamilyId, mp.CreatedDate)
      })(Encoders.product[MagPapers])
  }

  def main(args: Array[String]): Unit = {

    val logger: Logger = LoggerFactory.getLogger(getClass)
    val conf: SparkConf = new SparkConf()
    val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/mag/preprocess_mag_params.json")))
    parser.parseArgument(args)
    val spark: SparkSession =
      SparkSession
        .builder()
        .config(conf)
        .appName(getClass.getSimpleName)
        .master(parser.get("master")).getOrCreate()

    val sourcePath = parser.get("sourcePath")
    val workingPath = parser.get("workingPath")
    val targetPath = parser.get("targetPath")

    import spark.implicits._
    implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication]
    implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs)

    logger.info("Phase 1) make uninue DOI in Papers:")
    val d: Dataset[MagPapers] = spark.read.load(s"$sourcePath/Papers").as[MagPapers]

    // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one
    val distinctPaper: Dataset[MagPapers] = getDistinctResults(d)

    distinctPaper.write.mode(SaveMode.Overwrite).save(s"$workingPath/Papers_distinct")

    logger.info("Phase 0) Enrich Publication with description")
    val pa = spark.read.load(s"$sourcePath/PaperAbstractsInvertedIndex").as[MagPaperAbstract]
    pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"$workingPath/PaperAbstract")

    logger.info("Phase 3) Group Author by PaperId")
    val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor]

    val affiliation = spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation]
    val paperAuthorAffiliation = spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation]

    paperAuthorAffiliation.joinWith(authors, paperAuthorAffiliation("AuthorId").equalTo(authors("AuthorId")))
      .map { case (a: MagPaperAuthorAffiliation, b: MagAuthor) => (a.AffiliationId, MagPaperAuthorDenormalized(a.PaperId, b, null, a.AuthorSequenceNumber)) }
      .joinWith(affiliation, affiliation("AffiliationId").equalTo(col("_1")), "left")
      .map(s => {
        val mpa = s._1._2
        val af = s._2
        if (af != null) {
          MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName, mpa.sequenceNumber)
        } else
          mpa
      }).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation", $"sequenceNumber")).as("authors"))
      .write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_1_paper_authors")

    logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors")

    val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal]

    val papers = spark.read.load((s"$workingPath/Papers_distinct")).as[MagPapers]

    val paperWithAuthors = spark.read.load(s"$workingPath/merge_step_1_paper_authors").as[MagPaperWithAuthorList]

    val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left")
    firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left")
      .map { a => ConversionUtil.createOAFFromJournalAuthorPaper(a) }
      .write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_2")


    var magPubs: Dataset[(String, Publication)] =
      spark.read.load(s"$workingPath/merge_step_2").as[Publication]
      .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]


    val conference = spark.read.load(s"$sourcePath/ConferenceInstances")
      .select($"ConferenceInstanceId".as("ci"), $"DisplayName", $"Location", $"StartDate",$"EndDate" )
    val conferenceInstance = conference.joinWith(papers, papers("ConferenceInstanceId").equalTo(conference("ci")))
      .select($"_1.ci", $"_1.DisplayName", $"_1.Location", $"_1.StartDate",$"_1.EndDate", $"_2.PaperId").as[MagConferenceInstance]


    magPubs.joinWith(conferenceInstance, col("_1").equalTo(conferenceInstance("PaperId")), "left")
      .map(item => ConversionUtil.updatePubsWithConferenceInfo(item))
      .write
      .mode(SaveMode.Overwrite)
      .save(s"$workingPath/merge_step_3")


    val paperAbstract = spark.read.load((s"$workingPath/PaperAbstract")).as[MagPaperAbstract]


    magPubs = spark.read.load(s"$workingPath/merge_step_3").as[Publication]
      .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]

    magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left")
      .map(item => ConversionUtil.updatePubsWithDescription(item)
    ).write.mode(SaveMode.Overwrite).save(s"$workingPath/merge_step_4")


    logger.info("Phase 7) Enrich Publication with FieldOfStudy")

    magPubs = spark.read.load(s"$workingPath/merge_step_4").as[Publication]
      .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)]

    val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType")

    val pfos = spark.read.load(s"$sourcePath/PaperFieldsOfStudy")

    val paperField = pfos.joinWith(fos, fos("fos").equalTo(pfos("FieldOfStudyId")))
      .select($"_1.FieldOfStudyId", $"_2.DisplayName", $"_2.MainType", $"_1.PaperId", $"_1.Score")
      .groupBy($"PaperId").agg(collect_list(struct($"FieldOfStudyId", $"DisplayName", $"MainType", $"Score")).as("subjects"))
      .as[MagFieldOfStudy]

    magPubs.joinWith(paperField, col("_1")
      .equalTo(paperField("PaperId")), "left")
      .map(item => ConversionUtil.updatePubsWithSubject(item))
      .write.mode(SaveMode.Overwrite)
      .save(s"$workingPath/mag_publication")

    spark.read.load(s"$workingPath/mag_publication").as[Publication]
      .filter(p => p.getId != null)
      .groupByKey(p => p.getId)
      .reduceGroups((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b))
      .map(_._2)
      .write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication")



  }
}