507 lines
19 KiB
Scala
507 lines
19 KiB
Scala
package eu.dnetlib.dhp.datacite
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.datacite.DataciteModelConstants._
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
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import eu.dnetlib.dhp.schema.oaf.{AccessRight, Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.commons.lang3.StringUtils
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.{JField, JObject, JString}
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import org.json4s.jackson.JsonMethods.parse
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import java.text.SimpleDateFormat
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import java.time.LocalDate
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import java.time.chrono.ThaiBuddhistDate
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import java.time.format.DateTimeFormatter
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import java.util.{Date, Locale}
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import scala.collection.JavaConverters._
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object DataciteToOAFTransformation {
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val mapper = new ObjectMapper()
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/**
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* This method should skip record if json contains invalid text
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* defined in gile datacite_filter
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* @param json
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* @return True if the record should be skipped
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*/
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def skip_record(json: String): Boolean = {
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datacite_filter.exists(f => json.contains(f))
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}
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@deprecated("this method will be removed", "dhp")
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def toActionSet(item: Oaf): (String, String) = {
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val mapper = new ObjectMapper()
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item match {
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case dataset: OafDataset =>
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val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
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a.setClazz(classOf[OafDataset])
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a.setPayload(dataset)
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(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case publication: Publication =>
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val a: AtomicAction[Publication] = new AtomicAction[Publication]
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a.setClazz(classOf[Publication])
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a.setPayload(publication)
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(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case software: Software =>
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val a: AtomicAction[Software] = new AtomicAction[Software]
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a.setClazz(classOf[Software])
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a.setPayload(software)
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(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case orp: OtherResearchProduct =>
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val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
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a.setClazz(classOf[OtherResearchProduct])
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a.setPayload(orp)
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(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case relation: Relation =>
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val a: AtomicAction[Relation] = new AtomicAction[Relation]
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a.setClazz(classOf[Relation])
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a.setPayload(relation)
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(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case _ =>
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null
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}
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}
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def embargo_end(embargo_end_date: String): Boolean = {
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val dt = LocalDate.parse(embargo_end_date, DateTimeFormatter.ofPattern("[yyyy-MM-dd]"))
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val td = LocalDate.now()
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td.isAfter(dt)
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}
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def extract_date(input: String): Option[String] = {
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val d = Date_regex.map(pattern => {
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val matcher = pattern.matcher(input)
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if (matcher.find())
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matcher.group(0)
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else
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null
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}
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).find(s => s != null)
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if (d.isDefined) {
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val a_date = if (d.get.length == 4) s"01-01-${d.get}" else d.get
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try {
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return Some(LocalDate.parse(a_date, df_en).toString)
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} catch {
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case _: Throwable => try {
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return Some(LocalDate.parse(a_date, df_it).toString)
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} catch {
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case _: Throwable =>
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return None
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}
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}
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}
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d
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}
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def fix_thai_date(input:String, format:String) :String = {
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try {
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val a_date = LocalDate.parse(input,DateTimeFormatter.ofPattern(format))
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val d = ThaiBuddhistDate.of(a_date.getYear, a_date.getMonth.getValue, a_date.getDayOfMonth)
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LocalDate.from(d).toString
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} catch {
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case _: Throwable => ""
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}
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}
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def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): (Qualifier, Qualifier) = {
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if (resourceType != null && resourceType.nonEmpty) {
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val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType)
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if (typeQualifier != null)
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return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid))
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}
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if (schemaOrg != null && schemaOrg.nonEmpty) {
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val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, schemaOrg)
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if (typeQualifier != null)
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return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid))
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}
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if (resourceTypeGeneral != null && resourceTypeGeneral.nonEmpty) {
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val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceTypeGeneral)
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if (typeQualifier != null)
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return (typeQualifier, vocabularies.getSynonymAsQualifier(ModelConstants.DNET_RESULT_TYPOLOGIES, typeQualifier.getClassid))
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}
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null
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}
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def getResult(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): Result = {
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val typeQualifiers: (Qualifier, Qualifier) = getTypeQualifier(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
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if (typeQualifiers == null)
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return null
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val i = new Instance
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i.setInstancetype(typeQualifiers._1)
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typeQualifiers._2.getClassname match {
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case "dataset" =>
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val r = new OafDataset
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r.setInstance(List(i).asJava)
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return r
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case "publication" =>
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val r = new Publication
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r.setInstance(List(i).asJava)
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return r
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case "software" =>
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val r = new Software
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r.setInstance(List(i).asJava)
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return r
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case "other" =>
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val r = new OtherResearchProduct
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r.setInstance(List(i).asJava)
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return r
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}
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null
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}
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def available_date(input: String): Boolean = {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json: org.json4s.JValue = parse(input)
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val l: List[String] = for {
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JObject(dates) <- json \\ "dates"
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JField("dateType", JString(dateTypes)) <- dates
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} yield dateTypes
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l.exists(p => p.equalsIgnoreCase("available"))
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}
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/**
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* As describe in ticket #6377
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* when the result come from figshare we need to remove subject
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* and set Access rights OPEN.
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*
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* @param r
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*/
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def fix_figshare(r: Result): Unit = {
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if (r.getInstance() != null) {
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val hosted_by_figshare = r.getInstance().asScala.exists(i => i.getHostedby != null && "figshare".equalsIgnoreCase(i.getHostedby.getValue))
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if (hosted_by_figshare) {
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r.getInstance().asScala.foreach(i => i.setAccessright(ModelConstants.OPEN_ACCESS_RIGHT()))
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val l: List[StructuredProperty] = List()
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r.setSubject(l.asJava)
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}
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}
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}
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def createDNetTargetIdentifier(pid: String, pidType: String, idPrefix: String): String = {
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val f_part = s"$idPrefix|${pidType.toLowerCase}".padTo(15, '_')
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s"$f_part::${IdentifierFactory.md5(pid.toLowerCase)}"
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}
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def generateOAFDate(dt: String, q: Qualifier): StructuredProperty = {
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OafMapperUtils.structuredProperty(dt, q, null)
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}
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def generateRelation(sourceId: String, targetId: String, relClass: String, cf: KeyValue, di: DataInfo): 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.setCollectedfrom(List(cf).asJava)
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r.setDataInfo(di)
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r
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}
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def get_projectRelation(awardUri: String, sourceId: String): List[Relation] = {
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val match_pattern = funder_regex.find(s => s._1.matcher(awardUri).find())
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if (match_pattern.isDefined) {
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val m = match_pattern.get._1
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val p = match_pattern.get._2
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val grantId = m.matcher(awardUri).replaceAll("$2")
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val targetId = s"$p${DHPUtils.md5(grantId)}"
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List( generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo) )
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}
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else
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List()
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}
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def generateOAF(input: String, ts: Long, dateOfCollection: Long, vocabularies: VocabularyGroup, exportLinks: Boolean): List[Oaf] = {
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if (skip_record(input))
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return List()
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json = parse(input)
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val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null)
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val resourceTypeGeneral = (json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null)
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val schemaOrg = (json \ "attributes" \ "types" \ "schemaOrg").extractOrElse[String](null)
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val doi = (json \ "attributes" \ "doi").extract[String]
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if (doi.isEmpty)
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return List()
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//Mapping type based on vocabularies dnet:publication_resource and dnet:result_typologies
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val result = getResult(resourceType, resourceTypeGeneral, schemaOrg, vocabularies)
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if (result == null)
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return List()
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val doi_q = OafMapperUtils.qualifier("doi", "doi", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES)
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val pid = OafMapperUtils.structuredProperty(doi, doi_q, dataInfo)
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result.setPid(List(pid).asJava)
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result.setId(OafMapperUtils.createOpenaireId(50, s"datacite____::$doi", true))
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result.setOriginalId(List(doi).asJava)
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val d = new Date(dateOfCollection * 1000)
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val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
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result.setDateofcollection(ISO8601FORMAT.format(d))
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result.setDateoftransformation(ISO8601FORMAT.format(d))
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result.setDataInfo(dataInfo)
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val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
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val authors = creators.zipWithIndex.map { case (c, idx) =>
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val a = new Author
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a.setFullname(c.name.orNull)
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a.setName(c.givenName.orNull)
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a.setSurname(c.familyName.orNull)
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if (c.nameIdentifiers != null && c.nameIdentifiers.isDefined && c.nameIdentifiers.get != null) {
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a.setPid(c.nameIdentifiers.get.map(ni => {
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val q = if (ni.nameIdentifierScheme.isDefined) vocabularies.getTermAsQualifier(ModelConstants.DNET_PID_TYPES, ni.nameIdentifierScheme.get.toLowerCase()) else null
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if (ni.nameIdentifier != null && ni.nameIdentifier.isDefined) {
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OafMapperUtils.structuredProperty(ni.nameIdentifier.get, q, dataInfo)
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}
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else
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null
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}
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)
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.asJava)
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}
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if (c.affiliation.isDefined)
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a.setAffiliation(c.affiliation.get.filter(af => af.nonEmpty).map(af => OafMapperUtils.field(af, dataInfo)).asJava)
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a.setRank(idx + 1)
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a
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}
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val titles: List[TitleType] = (json \\ "titles").extractOrElse[List[TitleType]](List())
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result.setTitle(titles.filter(t => t.title.nonEmpty).map(t => {
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if (t.titleType.isEmpty) {
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OafMapperUtils.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
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} else {
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OafMapperUtils.structuredProperty(t.title.get, t.titleType.get, t.titleType.get, ModelConstants.DNET_DATACITE_TITLE, ModelConstants.DNET_DATACITE_TITLE, null)
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}
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}).asJava)
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if (authors == null || authors.isEmpty || !authors.exists(a => a != null))
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return List()
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result.setAuthor(authors.asJava)
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val dates = (json \\ "dates").extract[List[DateType]]
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val publication_year = (json \\ "publicationYear").extractOrElse[String](null)
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val i_date = dates
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.filter(d => d.date.isDefined && d.dateType.isDefined)
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.find(d => d.dateType.get.equalsIgnoreCase("issued"))
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.map(d => extract_date(d.date.get))
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val a_date: Option[String] = dates
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.filter(d => d.date.isDefined && d.dateType.isDefined && d.dateType.get.equalsIgnoreCase("available"))
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.map(d => extract_date(d.date.get))
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.find(d => d != null && d.isDefined)
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.map(d => d.get)
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if (a_date.isDefined) {
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if(doi.startsWith("10.14457"))
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result.setEmbargoenddate(OafMapperUtils.field(fix_thai_date(a_date.get,"[yyyy-MM-dd]"), null))
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else
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result.setEmbargoenddate(OafMapperUtils.field(a_date.get, null))
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}
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if (i_date.isDefined && i_date.get.isDefined) {
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if(doi.startsWith("10.14457")) {
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result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
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result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(i_date.get.get,"[yyyy-MM-dd]"), null))
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}
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else {
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result.setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
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result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(i_date.get.get, null))
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}
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}
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else if (publication_year != null) {
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if(doi.startsWith("10.14457")) {
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result.setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
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result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(fix_thai_date(s"01-01-$publication_year","[dd-MM-yyyy]"), null))
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} else {
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result.setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
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result.getInstance().get(0).setDateofacceptance(OafMapperUtils.field(s"01-01-$publication_year", null))
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}
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}
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result.setRelevantdate(dates.filter(d => d.date.isDefined && d.dateType.isDefined)
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.map(d => (extract_date(d.date.get), d.dateType.get))
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.filter(d => d._1.isDefined)
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.map(d => (d._1.get, vocabularies.getTermAsQualifier(ModelConstants.DNET_DATACITE_DATE, d._2.toLowerCase())))
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.filter(d => d._2 != null)
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.map(d => generateOAFDate(d._1, d._2)).asJava)
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val subjects = (json \\ "subjects").extract[List[SubjectType]]
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result.setSubject(subjects.filter(s => s.subject.nonEmpty)
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.map(s =>
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OafMapperUtils.structuredProperty(s.subject.get, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
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).asJava)
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result.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
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val descriptions = (json \\ "descriptions").extract[List[DescriptionType]]
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result.setDescription(
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descriptions
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.filter(d => d.description.isDefined).
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map(d =>
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OafMapperUtils.field(d.description.get, null)
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).filter(s => s != null).asJava)
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val publisher = (json \\ "publisher").extractOrElse[String](null)
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if (publisher != null)
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result.setPublisher(OafMapperUtils.field(publisher, null))
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val language: String = (json \\ "language").extractOrElse[String](null)
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if (language != null)
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result.setLanguage(vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, language))
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val instance = result.getInstance().get(0)
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val client = (json \ "relationships" \ "client" \\ "id").extractOpt[String]
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val accessRights: List[String] = for {
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JObject(rightsList) <- json \\ "rightsList"
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JField("rightsUri", JString(rightsUri)) <- rightsList
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} yield rightsUri
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val aRights: Option[AccessRight] = accessRights.map(r => {
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vocabularies.getSynonymAsQualifier(ModelConstants.DNET_ACCESS_MODES, r)
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}).find(q => q != null).map(q => {
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val a = new AccessRight
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a.setClassid(q.getClassid)
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a.setClassname(q.getClassname)
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a.setSchemeid(q.getSchemeid)
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a.setSchemename(q.getSchemename)
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a
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})
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val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
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if (client.isDefined) {
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instance.setHostedby(OafMapperUtils.keyValue(generateDSId(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID), ModelConstants.UNKNOWN_REPOSITORY.getValue))
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instance.setCollectedfrom(DATACITE_COLLECTED_FROM)
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instance.setUrl(List(s"https://dx.doi.org/$doi").asJava)
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instance.setAccessright(access_rights_qualifier)
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instance.setPid(result.getPid)
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val license = accessRights
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.find(r => r.startsWith("http") && r.matches(".*(/licenses|/publicdomain|unlicense\\.org/|/legal-and-data-protection-notices|/download/license|/open-government-licence).*"))
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if (license.isDefined)
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instance.setLicense(OafMapperUtils.field(license.get, null))
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}
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val awardUris: List[String] = for {
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JObject(fundingReferences) <- json \\ "fundingReferences"
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JField("awardUri", JString(awardUri)) <- fundingReferences
|
|
} yield awardUri
|
|
|
|
result.setId(IdentifierFactory.createIdentifier(result))
|
|
var relations: List[Relation] = awardUris.flatMap(a => get_projectRelation(a, result.getId)).filter(r => r != null)
|
|
|
|
fix_figshare(result)
|
|
|
|
if (result.getId == null)
|
|
return List()
|
|
|
|
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)
|
|
}
|
|
if (relations != null && relations.nonEmpty) {
|
|
List(result) ::: relations
|
|
}
|
|
else
|
|
List(result)
|
|
}
|
|
|
|
private def generateRelations(rels: List[RelatedIdentifierType], id:String, date:String):List[Relation] = {
|
|
rels
|
|
.filter(r =>
|
|
subRelTypeMapping.contains(r.relationType) && (
|
|
r.relatedIdentifierType.equalsIgnoreCase("doi") ||
|
|
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
|
|
r.relatedIdentifierType.equalsIgnoreCase("arxiv"))
|
|
)
|
|
.map(r => {
|
|
val rel = new Relation
|
|
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).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)
|
|
|
|
rel.setSource(id)
|
|
rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType))
|
|
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).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)}"
|
|
}
|
|
|
|
|
|
} |