580 lines
24 KiB
Scala
580 lines
24 KiB
Scala
package eu.dnetlib.dhp.crossref
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.common.ModelConstants.OPEN_ACCESS_RIGHT
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import eu.dnetlib.dhp.schema.oaf._
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
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import eu.dnetlib.dhp.schema.oaf.utils._
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import org.apache.commons.lang.StringUtils
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST._
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import org.json4s.jackson.JsonMethods.parse
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import org.slf4j.{Logger, LoggerFactory}
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import java.time.LocalDate
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import java.time.format.DateTimeFormatter
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import scala.collection.JavaConverters._
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import scala.collection.mutable.ListBuffer
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import scala.util.matching.Regex
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case class CrossrefDT(doi: String, json: String, timestamp: Long) {}
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case class CrossrefAuthor(givenName:String, familyName:String,ORCID:String, sequence:String, rank:Int ){}
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case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
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object CrossrefUtility {
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val CROSSREF_COLLECTED_FROM = keyValue(ModelConstants.CROSSREF_ID, ModelConstants.CROSSREF_NAME)
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val logger: Logger = LoggerFactory.getLogger(getClass)
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def convert(input: String, vocabularies: VocabularyGroup): List[Oaf] = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: json4s.JValue = parse(input)
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var resultList: List[Oaf] = List()
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val objectType = (json \ "type").extractOrElse[String](null)
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if (objectType == null)
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return resultList
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val resultWithType = generateItemFromType(objectType, vocabularies)
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if (resultWithType == null)
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return List()
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val result = resultWithType._1
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val cOBJCategory = resultWithType._2
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val className = resultWithType._3
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mappingResult(result, json, cOBJCategory, className)
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if (result == null || result.getId == null)
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return List()
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val funderList: List[mappingFunder] =
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(json \ "funder").extractOrElse[List[mappingFunder]](List())
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if (funderList.nonEmpty) {
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resultList = resultList ::: mappingFunderToRelations(funderList, result )
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}
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resultList = resultList ::: List(result)
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resultList
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}
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private def createRelation(sourceId: String, targetId: String, relClass: String): Relation = {
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val r = new Relation
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r.setSource(sourceId)
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r.setTarget(targetId)
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r.setRelType(ModelConstants.RESULT_PROJECT)
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r.setRelClass(relClass)
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r.setSubRelType(ModelConstants.OUTCOME)
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r.setProvenance(List(OafMapperUtils.getProvenance(CROSSREF_COLLECTED_FROM, null)).asJava)
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r
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}
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private def generateSimpleRelationFromAward(
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funder: mappingFunder,
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nsPrefix: String,
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extractField: String => String,
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source:Result
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): List[Relation] = {
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if (funder.award.isDefined && funder.award.get.nonEmpty)
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funder.award.get
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.map(extractField)
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.filter(a => a != null && a.nonEmpty)
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.map(award => {
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val targetId = IdentifierFactory.createOpenaireId("project",s"$nsPrefix::$award", true)
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createRelation(targetId, source.getId, ModelConstants.PRODUCES)
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})
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else List()
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}
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private def extractECAward(award: String): String = {
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val awardECRegex: Regex = "[0-9]{4,9}".r
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if (awardECRegex.findAllIn(award).hasNext)
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return awardECRegex.findAllIn(award).max
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null
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}
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private def snsfRule(award: String): String = {
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val tmp1 = StringUtils.substringAfter(award, "_")
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val tmp2 = StringUtils.substringBefore(tmp1, "/")
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tmp2
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}
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private def mappingFunderToRelations(funders: List[mappingFunder], result: Result): List[Relation] = {
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var relList:List[Relation] = List()
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if (funders != null)
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funders.foreach(funder => {
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if (funder.DOI.isDefined && funder.DOI.get.nonEmpty) {
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funder.DOI.get match {
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case "10.13039/100010663" | "10.13039/100010661" | "10.13039/501100007601" | "10.13039/501100000780" |
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"10.13039/100010665" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward, result)
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case "10.13039/100011199" | "10.13039/100004431" | "10.13039/501100004963" | "10.13039/501100000780" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda_______", extractECAward, result)
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case "10.13039/501100000781" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda_______", extractECAward, result)
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward, result)
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case "10.13039/100000001" => relList =relList ::: generateSimpleRelationFromAward(funder, "nsf_________", a => a, result)
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case "10.13039/501100001665" => relList =relList ::: generateSimpleRelationFromAward(funder, "anr_________", a => a, result)
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case "10.13039/501100002341" => relList =relList ::: generateSimpleRelationFromAward(funder, "aka_________", a => a, result)
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case "10.13039/501100001602" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "sfi_________", a => a.replace("SFI", ""), result)
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case "10.13039/501100000923" => relList =relList ::: generateSimpleRelationFromAward(funder, "arc_________", a => a, result)
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case "10.13039/501100000038" =>
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val targetId = IdentifierFactory.createOpenaireId("project", "nserc_______::1e5e62235d094afd01cd56e65112fc63", false)
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relList =relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES))
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case "10.13039/501100000155" =>
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val targetId = IdentifierFactory.createOpenaireId("project", "sshrc_______::1e5e62235d094afd01cd56e65112fc63", false)
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relList =relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES))
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case "10.13039/501100000024" =>
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val targetId = IdentifierFactory.createOpenaireId("project", "cihr________::1e5e62235d094afd01cd56e65112fc63", false)
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relList =relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES))
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case "10.13039/501100002848" => relList =relList ::: generateSimpleRelationFromAward(funder, "conicytf____", a => a, result)
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case "10.13039/501100003448" => relList =relList ::: generateSimpleRelationFromAward(funder, "gsrt________", extractECAward, result)
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case "10.13039/501100010198" => relList =relList ::: generateSimpleRelationFromAward(funder, "sgov________", a => a, result)
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case "10.13039/501100004564" => relList =relList ::: generateSimpleRelationFromAward(funder, "mestd_______", extractECAward, result)
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case "10.13039/501100003407" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "miur________", a => a, result)
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val targetId = IdentifierFactory.createOpenaireId("project", "miur________::1e5e62235d094afd01cd56e65112fc63", false)
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relList =relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES))
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case "10.13039/501100006588" | "10.13039/501100004488" =>
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relList =relList ::: generateSimpleRelationFromAward(
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funder,
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"irb_hr______",
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a => a.replaceAll("Project No.", "").replaceAll("HRZZ-", ""), result
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)
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case "10.13039/501100006769" => relList =relList ::: generateSimpleRelationFromAward(funder, "rsf_________", a => a, result)
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case "10.13039/501100001711" => relList =relList ::: generateSimpleRelationFromAward(funder, "snsf________", snsfRule, result)
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case "10.13039/501100004410" => relList =relList ::: generateSimpleRelationFromAward(funder, "tubitakf____", a => a, result)
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case "10.13039/100004440" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "wt__________", a => a, result)
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val targetId = IdentifierFactory.createOpenaireId("project", "wt__________::1e5e62235d094afd01cd56e65112fc63", false)
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relList =relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES))
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case _ => logger.debug("no match for " + funder.DOI.get)
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}
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} else {
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funder.name match {
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case "European Union’s Horizon 2020 research and innovation program" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward, result)
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case "European Union's" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda__h2020", extractECAward, result)
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relList =relList ::: generateSimpleRelationFromAward(funder, "corda_______", extractECAward, result)
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case "The French National Research Agency (ANR)" | "The French National Research Agency" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "anr_________", a => a, result)
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case "CONICYT, Programa de Formación de Capital Humano Avanzado" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "conicytf____", extractECAward, result)
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case "Wellcome Trust Masters Fellowship" =>
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relList =relList ::: generateSimpleRelationFromAward(funder, "wt__________", a => a, result)
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val targetId = IdentifierFactory.createOpenaireId("project", "wt__________::1e5e62235d094afd01cd56e65112fc63", false)
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relList =relList ::: List(createRelation(targetId, result.getId, ModelConstants.PRODUCES))
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case _ => logger.debug("no match for " + funder.name)
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}
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}
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})
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relList
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}
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private def mappingResult(result: Result, json: JValue, cobjCategory: String, className:String): Result = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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//MAPPING Crossref DOI into PID
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val doi: String = CleaningFunctions.normalizePidValue(ModelConstants.DOI, (json \ "DOI").extract[String])
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result.setPid(
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List(
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structuredProperty(doi, PidType.doi.toString, PidType.doi.toString, ModelConstants.DNET_PID_TYPES)
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).asJava
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)
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//MAPPING Crossref DOI into OriginalId
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//and Other Original Identifier of dataset like clinical-trial-number
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val clinicalTrialNumbers: List[String] = for (JString(ctr) <- json \ "clinical-trial-number") yield ctr
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val alternativeIds: List[String] = for (JString(ids) <- json \ "alternative-id") yield ids
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val tmp = clinicalTrialNumbers ::: alternativeIds ::: List(doi)
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result.setOriginalId(tmp.filter(id => id != null).asJava)
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// Add DataInfo
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result.setDataInfo(dataInfo(false, false, 0.9f, null, false, ModelConstants.REPOSITORY_PROVENANCE_ACTIONS))
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result.setLastupdatetimestamp((json \ "indexed" \ "timestamp").extract[Long])
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result.setDateofcollection((json \ "indexed" \ "date-time").extract[String])
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result.setCollectedfrom(List(CROSSREF_COLLECTED_FROM).asJava)
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// Publisher ( Name of work's publisher mapped into Result/Publisher)
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val publisher = (json \ "publisher").extractOrElse[String](null)
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if (publisher != null && publisher.nonEmpty)
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result.setPublisher(new Publisher(publisher))
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// TITLE
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val mainTitles =
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for { JString(title) <- json \ "title" if title.nonEmpty } yield structuredProperty(
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title,
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ModelConstants.MAIN_TITLE_QUALIFIER
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)
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val originalTitles = for {
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JString(title) <- json \ "original-title" if title.nonEmpty
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} yield structuredProperty(title, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER)
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val shortTitles = for {
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JString(title) <- json \ "short-title" if title.nonEmpty
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} yield structuredProperty(title, ModelConstants.ALTERNATIVE_TITLE_QUALIFIER)
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val subtitles =
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for { JString(title) <- json \ "subtitle" if title.nonEmpty } yield structuredProperty(
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title, ModelConstants.SUBTITLE_QUALIFIER)
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result.setTitle((mainTitles ::: originalTitles ::: shortTitles ::: subtitles).asJava)
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// DESCRIPTION
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val descriptionList =
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for { JString(description) <- json \ "abstract" } yield description
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result.setDescription(descriptionList.asJava)
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// Source
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val sourceList = for {
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JString(source) <- json \ "source" if source != null && source.nonEmpty
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} yield source
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result.setSource(sourceList.asJava)
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//RELEVANT DATE Mapping
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val createdDate = generateDate(
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(json \ "created" \ "date-time").extract[String],
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(json \ "created" \ "date-parts").extract[List[List[Int]]],
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"created",
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ModelConstants.DNET_DATACITE_DATE
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)
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val postedDate = generateDate(
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(json \ "posted" \ "date-time").extractOrElse[String](null),
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(json \ "posted" \ "date-parts").extract[List[List[Int]]],
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"available",
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ModelConstants.DNET_DATACITE_DATE
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)
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val acceptedDate = generateDate(
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(json \ "accepted" \ "date-time").extractOrElse[String](null),
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(json \ "accepted" \ "date-parts").extract[List[List[Int]]],
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"accepted",
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ModelConstants.DNET_DATACITE_DATE
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)
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val publishedPrintDate = generateDate(
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(json \ "published-print" \ "date-time").extractOrElse[String](null),
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(json \ "published-print" \ "date-parts").extract[List[List[Int]]],
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"published-print",
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ModelConstants.DNET_DATACITE_DATE
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)
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val publishedOnlineDate = generateDate(
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(json \ "published-online" \ "date-time").extractOrElse[String](null),
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(json \ "published-online" \ "date-parts").extract[List[List[Int]]],
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"published-online",
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ModelConstants.DNET_DATACITE_DATE
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)
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val issuedDate = extractDate(
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(json \ "issued" \ "date-time").extractOrElse[String](null),
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(json \ "issued" \ "date-parts").extract[List[List[Int]]]
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)
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if (StringUtils.isNotBlank(issuedDate)) {
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result.setDateofacceptance(issuedDate)
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} else {
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result.setDateofacceptance(createdDate.getValue)
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}
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result.setRelevantdate(
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List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate)
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.filter(p => p != null)
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.asJava
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)
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//Mapping Subject
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val subjectList: List[String] = (json \ "subject").extractOrElse[List[String]](List())
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if (subjectList.nonEmpty) {
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result.setSubject(
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subjectList.map(s =>
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OafMapperUtils.subject(s, OafMapperUtils.qualifier(ModelConstants.DNET_SUBJECT_KEYWORD,ModelConstants.DNET_SUBJECT_KEYWORD,ModelConstants.DNET_SUBJECT_TYPOLOGIES), null)
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).asJava)
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}
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//Mapping Author
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val authorList:List[CrossrefAuthor] =
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for {
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JObject(author) <- json \ "author"
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JField("ORCID", JString(orcid)) <- author
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JField("given", JString(givenName)) <- author
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JField("family", JString(familyName)) <- author
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JField("sequence", JString(sequence)) <- author
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} yield CrossrefAuthor(givenName = givenName, familyName = familyName, ORCID = orcid, sequence = sequence, rank = 0)
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result.setAuthor(authorList.sortWith((a,b) =>{
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if (a.sequence.equalsIgnoreCase("first"))
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true
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else if (b.sequence.equalsIgnoreCase("first"))
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false
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else a.familyName< b.familyName
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}).zipWithIndex.map(k=> k._1.copy(rank = k._2)).map(k => generateAuthor(k)).asJava)
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// Mapping instance
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val instance = new Instance()
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val license = for {
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JObject(license) <- json \ "license"
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JField("URL", JString(lic)) <- license
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JField("content-version", JString(content_version)) <- license
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} yield (new License(lic), content_version)
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val l = license.filter(d => StringUtils.isNotBlank(d._1.getUrl))
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if (l.nonEmpty) {
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if (l exists (d => d._2.equals("vor"))) {
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for (d <- l) {
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if (d._2.equals("vor")) {
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instance.setLicense(d._1)
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}
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}
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} else {
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instance.setLicense(l.head._1)
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}
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}
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// Ticket #6281 added pid to Instance
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instance.setPid(result.getPid)
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val has_review = json \ "relation" \ "has-review" \ "id"
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if (has_review != JNothing) {
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instance.setRefereed(
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OafMapperUtils.qualifier(
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"0001",
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"peerReviewed",
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ModelConstants.DNET_REVIEW_LEVELS
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)
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)
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}
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if (instance.getLicense!= null)
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instance.setAccessright(
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decideAccessRight(instance.getLicense.getUrl, result.getDateofacceptance)
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)
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instance.setInstancetype(
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OafMapperUtils.qualifier(
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cobjCategory,
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className,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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)
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result.setResourcetype(
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OafMapperUtils.qualifier(
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cobjCategory,
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className,
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ModelConstants.DNET_PUBLICATION_RESOURCE
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)
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)
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instance.setCollectedfrom(CROSSREF_COLLECTED_FROM)
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if (StringUtils.isNotBlank(issuedDate)) {
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instance.setDateofacceptance(issuedDate)
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} else {
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instance.setDateofacceptance(createdDate.getValue)
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}
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val s: List[String] = List("https://doi.org/" + doi)
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if (s.nonEmpty) {
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instance.setUrl(s.asJava)
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}
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val containerTitles = for { JString(ct) <- json \ "container-title" } yield ct
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//Mapping book
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if (className.toLowerCase.contains("book")) {
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val ISBN = for {JString(isbn) <- json \ "ISBN"} yield isbn
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if (ISBN.nonEmpty && containerTitles.nonEmpty) {
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val source = s"${containerTitles.head} ISBN: ${ISBN.head}"
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if (result.getSource != null) {
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val l: List[String] = result.getSource.asScala.toList ::: List(source)
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result.setSource(l.asJava)
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} else
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result.setSource(List(source).asJava)
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}
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} else {
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// Mapping Journal
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val issnInfos = for {
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JObject(issn_type) <- json \ "issn-type"
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JField("type", JString(tp)) <- issn_type
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JField("value", JString(vl)) <- issn_type
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} yield Tuple2(tp, vl)
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val volume = (json \ "volume").extractOrElse[String](null)
|
||
if (containerTitles.nonEmpty) {
|
||
val journal = new Journal
|
||
journal.setName(containerTitles.head)
|
||
if (issnInfos.nonEmpty) {
|
||
|
||
issnInfos.foreach(tp => {
|
||
tp._1 match {
|
||
case "electronic" => journal.setIssnOnline(tp._2)
|
||
case "print" => journal.setIssnPrinted(tp._2)
|
||
}
|
||
})
|
||
}
|
||
journal.setVol(volume)
|
||
val page = (json \ "page").extractOrElse[String](null)
|
||
if (page != null) {
|
||
val pp = page.split("-")
|
||
if (pp.nonEmpty)
|
||
journal.setSp(pp.head)
|
||
if (pp.size > 1)
|
||
journal.setEp(pp(1))
|
||
}
|
||
result.setJournal(journal)
|
||
}
|
||
}
|
||
|
||
|
||
result.setInstance(List(instance).asJava)
|
||
result.setId("ID")
|
||
result.setId(IdentifierFactory.createIdentifier(result, true))
|
||
if (result.getId == null || "ID".equalsIgnoreCase(result.getId))
|
||
null
|
||
else
|
||
result
|
||
}
|
||
|
||
def decideAccessRight(license: String, date: String): AccessRight = {
|
||
if (license == null || license.isEmpty) {
|
||
//Default value Unknown
|
||
return ModelConstants.UNKNOWN_ACCESS_RIGHT();
|
||
}
|
||
//CC licenses
|
||
if (
|
||
license.startsWith("cc") ||
|
||
license.startsWith("http://creativecommons.org/licenses") ||
|
||
license.startsWith("https://creativecommons.org/licenses") ||
|
||
|
||
//ACS Publications Author choice licenses (considered OPEN also by Unpaywall)
|
||
license.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html") ||
|
||
license.equals("http://pubs.acs.org/page/policy/authorchoice_termsofuse.html") ||
|
||
license.equals("http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html") ||
|
||
|
||
//APA (considered OPEN also by Unpaywall)
|
||
license.equals("http://www.apa.org/pubs/journals/resources/open-access.aspx")
|
||
) {
|
||
|
||
val oaq: AccessRight = ModelConstants.OPEN_ACCESS_RIGHT()
|
||
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
|
||
return oaq
|
||
}
|
||
|
||
//OUP (BUT ONLY AFTER 12 MONTHS FROM THE PUBLICATION DATE, OTHERWISE THEY ARE EMBARGOED)
|
||
if (
|
||
license.equals(
|
||
"https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model"
|
||
)
|
||
) {
|
||
val now = java.time.LocalDate.now
|
||
|
||
try {
|
||
val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd"))
|
||
if (((now.toEpochDay - pub_date.toEpochDay) / 365.0) > 1) {
|
||
val oaq: AccessRight = ModelConstants.OPEN_ACCESS_RIGHT()
|
||
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
|
||
return oaq
|
||
} else {
|
||
return ModelConstants.EMBARGOED_ACCESS_RIGHT()
|
||
}
|
||
} catch {
|
||
case _: Exception => {
|
||
try {
|
||
val pub_date =
|
||
LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))
|
||
if (((now.toEpochDay - pub_date.toEpochDay) / 365.0) > 1) {
|
||
val oaq: AccessRight = OPEN_ACCESS_RIGHT()
|
||
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
|
||
return oaq
|
||
} else {
|
||
return ModelConstants.EMBARGOED_ACCESS_RIGHT()
|
||
}
|
||
} catch {
|
||
case _: Exception => return ModelConstants.CLOSED_ACCESS_RIGHT()
|
||
}
|
||
}
|
||
|
||
}
|
||
|
||
}
|
||
|
||
ModelConstants.CLOSED_ACCESS_RIGHT()
|
||
}
|
||
|
||
|
||
private def extractDate(dt: String, datePart: List[List[Int]]): String = {
|
||
if (StringUtils.isNotBlank(dt))
|
||
return GraphCleaningFunctions.cleanDate(dt)
|
||
if (datePart != null && datePart.size == 1) {
|
||
val res = datePart.head
|
||
if (res.size == 3) {
|
||
val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d"
|
||
if (dp.length == 10) {
|
||
return GraphCleaningFunctions.cleanDate(dp)
|
||
}
|
||
} else if (res.size == 2) {
|
||
val dp = f"${res.head}-${res(1)}%02d-01"
|
||
return GraphCleaningFunctions.cleanDate(dp)
|
||
} else if (res.size == 1) {
|
||
return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01")
|
||
}
|
||
}
|
||
null
|
||
}
|
||
|
||
private def generateDate(
|
||
dt: String,
|
||
datePart: List[List[Int]],
|
||
classId: String,
|
||
schemeId: String
|
||
): StructuredProperty = {
|
||
val dp = extractDate(dt, datePart)
|
||
if (StringUtils.isNotBlank(dp))
|
||
structuredProperty(dp, classId, classId, schemeId)
|
||
else
|
||
null
|
||
}
|
||
|
||
private def generateItemFromType(objectType: String, vocabularies: VocabularyGroup): (Result, String, String) = {
|
||
val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, objectType)
|
||
if (term != null) {
|
||
val resourceType =
|
||
vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, term.getClassid).getClassname
|
||
|
||
resourceType match {
|
||
case "publication" => (new Publication, resourceType, term.getClassname)
|
||
case "dataset" => (new Dataset, resourceType, term.getClassname)
|
||
case "software" => (new Software, resourceType, term.getClassname)
|
||
case "otherresearchproduct" => (new OtherResearchProduct, resourceType, term.getClassname)
|
||
}
|
||
} else
|
||
null
|
||
}
|
||
|
||
private def generateAuthor(ca: CrossrefAuthor): Author = {
|
||
val a = new Author
|
||
a.setName(ca.givenName)
|
||
a.setSurname(ca.familyName)
|
||
a.setFullname(s"${ca.familyName}, ${ca.givenName}")
|
||
a.setRank(ca.rank + 1)
|
||
if (StringUtils.isNotBlank(ca.ORCID))
|
||
a.setPid(
|
||
List(
|
||
OafMapperUtils.authorPid(ca.ORCID, OafMapperUtils.qualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_PENDING, ModelConstants.DNET_PID_TYPES), null)
|
||
).asJava
|
||
)
|
||
a
|
||
}
|
||
|
||
}
|