package eu.dnetlib.doiboost.orcid

import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.schema.oaf.Publication
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}

object SparkConvertORCIDToOAF {
  val logger: Logger = LoggerFactory.getLogger(SparkConvertORCIDToOAF.getClass)

  def run(spark:SparkSession,sourcePath:String,workingPath:String, targetPath:String):Unit = {
    import spark.implicits._
    implicit val mapEncoderPubs: Encoder[Publication] = Encoders.kryo[Publication]

    val inputRDD:RDD[OrcidAuthor]  = spark.sparkContext.textFile(s"$sourcePath/authors").map(s => ORCIDToOAF.convertORCIDAuthor(s)).filter(s => s!= null).filter(s => ORCIDToOAF.authorValid(s))

    spark.createDataset(inputRDD).as[OrcidAuthor].write.mode(SaveMode.Overwrite).save(s"$workingPath/author")

    val res = spark.sparkContext.textFile(s"$sourcePath/works").flatMap(s => ORCIDToOAF.extractDOIWorks(s)).filter(s => s!= null)

    spark.createDataset(res).as[OrcidWork].write.mode(SaveMode.Overwrite).save(s"$workingPath/works")

    val authors :Dataset[OrcidAuthor] = spark.read.load(s"$workingPath/author").as[OrcidAuthor]

    val works :Dataset[OrcidWork] = spark.read.load(s"$workingPath/works").as[OrcidWork]

    works.joinWith(authors, authors("oid").equalTo(works("oid")))
      .map(i =>{
        val doi = i._1.doi
        val author = i._2
        (doi, author)
      }).groupBy(col("_1").alias("doi"))
      .agg(collect_list(col("_2")).alias("authors"))
      .write.mode(SaveMode.Overwrite).save(s"$workingPath/orcidworksWithAuthor")

    val dataset: Dataset[ORCIDItem] =spark.read.load(s"$workingPath/orcidworksWithAuthor").as[ORCIDItem]

    logger.info("Converting ORCID to OAF")
    dataset.map(o => ORCIDToOAF.convertTOOAF(o)).write.mode(SaveMode.Overwrite).save(targetPath)
  }

  def main(args: Array[String]): Unit = {
    val conf: SparkConf = new SparkConf()
    val parser = new ArgumentApplicationParser(IOUtils.toString(SparkConvertORCIDToOAF.getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/convert_map_to_oaf_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")
    run(spark, sourcePath, workingPath, targetPath)

  }

}