package eu.dnetlib.dhp.sx.bio.ebi

import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.application.AbstractScalaApplication
import eu.dnetlib.dhp.collection.CollectionUtils
import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion
import eu.dnetlib.dhp.schema.oaf.Oaf
import eu.dnetlib.dhp.sx.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
import org.slf4j.{Logger, LoggerFactory}

class SparkTransformEBILinksToOaf(propertyPath: String, args: Array[String], log: Logger)
    extends AbstractScalaApplication(propertyPath, args, log: Logger) {

  def transformLinks(spark: SparkSession, sourcePath: String, outputBasePath: String, targetPath: String) = {
    implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
    import spark.implicits._
    val ebLinks: Dataset[EBILinkItem] = spark.read
      .load(sourcePath)
      .as[EBILinkItem]
      .filter(l => l.links != null && l.links.startsWith("{"))

    CollectionUtils.saveDataset(
      ebLinks
        .flatMap(j => BioDBToOAF.parse_ebi_links(j.links))
        .filter(p => BioDBToOAF.EBITargetLinksFilter(p))
        .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)),
      targetPath
    )
    reportTotalSize(targetPath, outputBasePath)
  }

  /** Here all the spark applications runs this method
    * where the whole logic of the spark node is defined
    */
  override def run(): Unit = {

    val sourcePath = parser.get("sourcePath")
    log.info(s"sourcePath is '$sourcePath'")

    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
    log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'")

    val mapper = new ObjectMapper()
    val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
    log.info(s"outputBasePath is '$outputBasePath'")

    val targetPath = s"$outputBasePath$MDSTORE_DATA_PATH"
    log.info(s"targetPath is '$targetPath'")
    transformLinks(spark, sourcePath, outputBasePath, targetPath)

  }
}

object SparkTransformEBILinksToOaf {
  val log: Logger = LoggerFactory.getLogger(SparkTransformEBILinksToOaf.getClass)

  def main(args: Array[String]): Unit = {
    new SparkTransformEBILinksToOaf("/eu/dnetlib/dhp/sx/bio/ebi/transform_ebi_to_df_params.json", args, log)
      .initialize()
      .run()
  }
}