dnet-hadoop/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/bioschema/BioschemaToOAFTransformation.scala

package eu.dnetlib.dhp.bioschema

import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.bioschema.BioschemaModelConstants._
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{Dataset => OafDataset, _}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse

import java.time.LocalDate
import scala.collection.JavaConverters._

object BioschemaToOAFTransformation {

  val mapper = new ObjectMapper()

  val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(
    false,
    null,
    false,
    false,
    ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER,
    "0.9"
  )

  val resolvedURL: Map[String, String] = Map(
    "uniprot" -> "https://www.uniprot.org/uniprot/",
    "pubmed"  -> "https://pubmed.ncbi.nlm.nih.gov/"
  )

  val collectedFromMap: Map[String, KeyValue] = {
    val PEDCollectedFrom: KeyValue = OafMapperUtils.keyValue(
      //TODO create pedDatasourceId and update this value
      "10|ped_________::pedDatasourceId",
      "Protein Ensemble Database"
    )
    PEDCollectedFrom.setDataInfo(DATA_INFO)

    Map(
      "ped" -> PEDCollectedFrom
    )
  }

  def extract_date(input: String): Option[String] = {
    val d = Date_regex
      .map(pattern => {
        val matcher = pattern.matcher(input)
        if (matcher.find())
          matcher.group(0)
        else
          null
      })
      .find(s => s != null)

    if (d.isDefined) {
      val a_date = if (d.get.length == 4) s"01-01-${d.get}" else d.get
      try {
        return Some(LocalDate.parse(a_date, df_en).toString)
      } catch {
        case _: Throwable =>
          try {
            return Some(LocalDate.parse(a_date, df_it).toString)
          } catch {
            case _: Throwable =>
              return None
          }
      }
    }
    d
  }

  def getResult(): Result = {
    val i = new Instance
    i.setInstancetype(
      OafMapperUtils.qualifier(
        "0046",
        "Bioentity",
        ModelConstants.DNET_PUBLICATION_RESOURCE,
        ModelConstants.DNET_PUBLICATION_RESOURCE
      )
    )
    val d = new OafDataset
    d.setInstance(List(i).asJava)
    return d
    null
  }

  def createDNetTargetIdentifier(pid: String, pidType: String, idPrefix: String): String = {
    val f_part = s"$idPrefix|${pidType.toLowerCase}".padTo(15, '_')
    s"$f_part::${IdentifierFactory.md5(pid.toLowerCase)}"
  }

  def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = {
    OafMapperUtils.structuredProperty(dt, q, null)
  }

  def generateRelation(
    sourceId: String,
    targetId: String,
    relClass: String,
    cf: KeyValue,
    di: DataInfo
  ): Relation = {

    val r = new Relation
    r.setSource(sourceId)
    r.setTarget(targetId)
    r.setRelType(ModelConstants.RESULT_PROJECT)
    r.setRelClass(relClass)
    r.setSubRelType(ModelConstants.OUTCOME)
    r.setCollectedfrom(List(cf).asJava)
    r.setDataInfo(di)
    r

  }

  def generateOAF(
    input: String,
    exportLinks: Boolean
  ): List[Oaf] = {

    implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
    lazy val json = parse(input)

    val resourceType = (json \ "types" \ "resourceType").extractOrElse[String](null)
    val resourceTypeGeneral =
      (json \ "types" \ "resourceTypeGeneral").extractOrElse[String](null)
    val schemaOrg = (json \ "types" \ "schemaOrg").extractOrElse[String](null)

    val result = getResult(
    )
    if (result == null)
      return List()

    val pid = (json \ "id").extract[String]

    result.setPid(
      List(
        OafMapperUtils.structuredProperty(
          pid,
          "ped",
          "ped",
          ModelConstants.DNET_PID_TYPES,
          ModelConstants.DNET_PID_TYPES,
          DATA_INFO
        )
      ).asJava
    )
    result.setId(OafMapperUtils.createOpenaireId(50, s"ped_________::$pid", true))
    result.setOriginalId(List(pid).asJava)

    result.setDataInfo(dataInfo)

    val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List())

    result.setTitle(
      titles
        .filter(t => t.title.nonEmpty)
        .map(t => {
          OafMapperUtils
            .structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)
        })
        .asJava
    )

    val dates = (json \\ "dates").extract[List[DateType]]
    val publication_year = (json \\ "publicationYear").extractOrElse[String](null)

    val i_date = dates
      .filter(d => d.date.isDefined && d.dateType.isDefined)
      .find(d => d.dateType.get.equalsIgnoreCase("issued"))
      .map(d => extract_date(d.date.get))
    val a_date: Option[String] = dates
      .filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
      .map(d => extract_date(d.date.get))
      .find(d => d != null && d.isDefined)
      .map(d => d.get)

    if (a_date.isDefined) {
      result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
    }
    if (i_date.isDefined && i_date.get.isDefined) {
      result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
      result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
    } else if (publication_year != null) {
      result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
      result
        .getInstance()
        .get(0)
        .setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
    }

    result.setRelevantdate(
      dates
        .filter(d => d.date.isDefined && d.dateType.isDefined)
        .map(d => (extract_date(d.date.get), d.dateType.get))
        .filter(d => d._1.isDefined)
        .map(d =>
          (
            d._1.get,
            OafMapperUtils.qualifier(
              d._2.toLowerCase(),
              d._2.toLowerCase(),
              ModelConstants.DNET_DATACITE_DATE,
              ModelConstants.DNET_DATACITE_DATE
            )
          )
        )
        .filter(d => d._2 != null)
        .map(d => generateOAFDate(d._1, d._2))
        .asJava
    )

    result.setCollectedfrom(List(collectedFromMap("ped")).asJava)

    val descriptions = (json \\ "descriptions").extract[List[DescriptionType]]

    result.setDescription(
      descriptions
        .filter(d => d.description.isDefined)
        .map(d => OafMapperUtils.field(d.description.get, null))
        .filter(s => s != null)
        .asJava
    )

    val publisher = (json \\ "publisher").extractOrElse[String](null)
    if (publisher != null)
      result.setPublisher(OafMapperUtils.field(publisher, null))

    val instance = result.getInstance().get(0)

    val ids: List[IdentifierType] = for {
      JObject(identifiers)                              <- json \\ "identifiers"
      JField("identifier", JString(identifier))         <- identifiers
      JField("identifierType", JString(identifierType)) <- identifiers
    } yield IdentifierType(identifier, identifierType)

    instance.setUrl(
      ids
        .map(id => {
          id.identifier
        })
        .asJava
    )
    instance.setCollectedfrom(collectedFromMap("ped"))
    instance.setPid(result.getPid)

    result.setId(IdentifierFactory.createIdentifier(result))
    var relations: List[Relation] = List()

    if (result.getId == null)
      return List()

    val alternativeIdentifierUrls: List[String] = for {
      JObject(alternateIdentifiers)                               <- json \\ "alternateIdentifiers"
      JField("alternateIdentifier", JString(alternateIdentifier)) <- alternateIdentifiers
      foundResolvedURLId = resolvedURL
        .map(k => {
          if (alternateIdentifier.contains(s"${k._1}:"))
            k._1
          else
            null
        })
        .find(s => s != null)
      alternativeIdentifierUrl = StringUtils.substringAfter(alternateIdentifier, s"${foundResolvedURLId.get}:")
    } yield alternativeIdentifierUrl

    alternativeIdentifierUrls.map(id => {
      var alternateIdentifier: StructuredProperty = null
      alternateIdentifier = OafMapperUtils.structuredProperty(
        id,
        "uniprot",
        "uniprot",
        ModelConstants.DNET_PID_TYPES,
        ModelConstants.DNET_PID_TYPES,
        dataInfo
      )
      instance.setAlternateIdentifier(List(alternateIdentifier).asJava)
    })

    if (exportLinks) {
      val rels: List[RelatedIdentifierType] = for {
        JObject(relIdentifier)                                          <- json \\ "relatedIdentifiers"
        JField("relationType", JString(relationType))                   <- relIdentifier
        JField("relatedIdentifierType", JString(relatedIdentifierType)) <- relIdentifier
        JField("relatedIdentifier", JString(relatedIdentifier))         <- relIdentifier
      } yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)

      relations = relations ::: generateRelations(
        rels,
        result.getId,
        if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null,
        pid
      )

    }
    if (relations != null && relations.nonEmpty) {
      List(result) ::: relations
    } else
      List(result)
  }

  private def generateRelations(
    rels: List[RelatedIdentifierType],
    id: String,
    date: String,
    pid: String
  ): List[Relation] = {
    rels
      .map(r => {
        val rel = new Relation
        rel.setCollectedfrom(List(collectedFromMap("ped")).asJava)
        rel.setDataInfo(dataInfo)

        val subRelType = subRelTypeMapping(r.relationType).relType
        rel.setRelType(REL_TYPE_VALUE)
        rel.setSubRelType(subRelType)
        rel.setRelClass(r.relationType)

        val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)

        rel.setProperties(List(dateProps).asJava)

        val foundResolvedURLId = resolvedURL
          .map(k => {
            if (r.relatedIdentifier.contains(s"${k._1}:"))
              k._1
            else
              null
          })
          .find(s => s != null);
        if (foundResolvedURLId.nonEmpty) {
          val relatedId = StringUtils.substringAfter(r.relatedIdentifier, s"${foundResolvedURLId.get}:")
          rel.setTarget(s"${resolvedURL(foundResolvedURLId.get)}${relatedId}")
        } else
          rel.setTarget(
            DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier, r.relatedIdentifierType)
          )
        rel.setSource(id)
        rel.setCollectedfrom(List(collectedFromMap("ped")).asJava)
        rel.getCollectedfrom.asScala.map(c => c.getValue).toList
        rel
      })
  }

  def generateDSId(input: String): String = {
    val b = StringUtils.substringBefore(input, "::")
    val a = StringUtils.substringAfter(input, "::")
    s"10|$b::${DHPUtils.md5(a)}"
  }

}