forked from D-Net/dnet-hadoop
354 lines
12 KiB
Scala
354 lines
12 KiB
Scala
package eu.dnetlib.dhp.sx.graph.scholix
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import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
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import eu.dnetlib.dhp.schema.sx.scholix._
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import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.spark.sql.expressions.Aggregator
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import org.apache.spark.sql.{Encoder, Encoders}
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import org.json4s
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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import scala.io.Source
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import scala.collection.JavaConverters._
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object ScholixUtils {
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val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
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val DATE_RELATION_KEY: String = "RelationDate"
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case class RelationVocabulary(original: String, inverse: String) {}
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case class RelatedEntities(id: String, relatedDataset: Long, relatedPublication: Long) {}
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val relations: Map[String, RelationVocabulary] = {
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val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/relations.json")).mkString
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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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json.extract[Map[String, RelationVocabulary]]
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}
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def extractRelationDate(relation: Relation): String = {
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if (relation.getProperties == null || !relation.getProperties.isEmpty)
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null
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else {
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val date = relation.getProperties.asScala.find(p => DATE_RELATION_KEY.equalsIgnoreCase(p.getKey)).map(p => p.getValue)
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if (date.isDefined)
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date.get
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else
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null
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}
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}
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def extractRelationDate(summary: ScholixSummary): String = {
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if (summary.getDate == null || summary.getDate.isEmpty)
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null
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else {
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summary.getDate.get(0)
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}
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}
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def inverseRelationShip(rel: ScholixRelationship): ScholixRelationship = {
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new ScholixRelationship(rel.getInverse, rel.getSchema, rel.getName)
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}
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val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] = new Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] with Serializable {
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override def zero: RelatedEntities = null
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override def reduce(b: RelatedEntities, a: (String, String, Long)): RelatedEntities = {
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val id = a._1
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val relatedDataset = if ("dataset".equalsIgnoreCase(a._2)) a._3 else 0
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val relatedPublication = if ("publication".equalsIgnoreCase(a._2)) a._3 else 0
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if (b == null)
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RelatedEntities(a._1, relatedDataset, relatedPublication)
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else
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RelatedEntities(a._1, b.relatedDataset + relatedDataset, b.relatedPublication + relatedPublication)
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}
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override def merge(b1: RelatedEntities, b2: RelatedEntities): RelatedEntities = {
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if (b1 != null && b2 != null)
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RelatedEntities(b1.id, b1.relatedDataset + b2.relatedDataset, b1.relatedPublication + b2.relatedPublication)
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else if (b1 != null)
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b1
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else
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b2
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}
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override def finish(reduction: RelatedEntities): RelatedEntities = reduction
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override def bufferEncoder: Encoder[RelatedEntities] = Encoders.bean(classOf[RelatedEntities])
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override def outputEncoder: Encoder[RelatedEntities] = Encoders.bean(classOf[RelatedEntities])
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}
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val scholixAggregator: Aggregator[(String, Scholix), Scholix, Scholix] = new Aggregator[(String, Scholix), Scholix, Scholix] with Serializable {
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override def zero: Scholix = null
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def scholix_complete(s: Scholix): Boolean = {
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if (s == null || s.getIdentifier == null) {
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false
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} else if (s.getSource == null || s.getTarget == null) {
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false
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}
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else if (s.getLinkprovider == null || s.getLinkprovider.isEmpty)
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false
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else
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true
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}
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override def reduce(b: Scholix, a: (String, Scholix)): Scholix = {
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if (scholix_complete(b)) b else a._2
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}
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override def merge(b1: Scholix, b2: Scholix): Scholix = {
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if (scholix_complete(b1)) b1 else b2
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}
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override def finish(reduction: Scholix): Scholix = reduction
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override def bufferEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
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override def outputEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
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}
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def createInverseScholixRelation(scholix: Scholix): Scholix = {
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val s = new Scholix
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s.setPublicationDate(scholix.getPublicationDate)
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s.setPublisher(scholix.getPublisher)
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s.setLinkprovider(scholix.getLinkprovider)
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s.setRelationship(inverseRelationShip(scholix.getRelationship))
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s.setSource(scholix.getTarget)
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s.setTarget(scholix.getSource)
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s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"))
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s
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}
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def extractCollectedFrom(summary: ScholixSummary): List[ScholixEntityId] = {
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if (summary.getDatasources != null && !summary.getDatasources.isEmpty) {
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val l: List[ScholixEntityId] = summary.getDatasources.asScala.map {
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d => new ScholixEntityId(d.getDatasourceName, List(new ScholixIdentifier(d.getDatasourceId, "DNET Identifier", null)).asJava)
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}(collection.breakOut)
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l
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} else List()
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}
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def extractCollectedFrom(relation: Relation): List[ScholixEntityId] = {
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if (relation.getCollectedfrom != null && !relation.getCollectedfrom.isEmpty) {
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val l: List[ScholixEntityId] = relation.getCollectedfrom.asScala.map {
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c =>
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new ScholixEntityId(c.getValue, List(new ScholixIdentifier(c.getKey, DNET_IDENTIFIER_SCHEMA, null)).asJava)
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}(collection breakOut)
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l
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} else List()
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}
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def generateCompleteScholix(scholix: Scholix, target: ScholixSummary): Scholix = {
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val s = new Scholix
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s.setPublicationDate(scholix.getPublicationDate)
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s.setPublisher(scholix.getPublisher)
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s.setLinkprovider(scholix.getLinkprovider)
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s.setRelationship(scholix.getRelationship)
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s.setSource(scholix.getSource)
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s.setTarget(generateScholixResourceFromSummary(target))
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s.setIdentifier(DHPUtils.md5(s"${s.getSource.getIdentifier}::${s.getRelationship.getName}::${s.getTarget.getIdentifier}"))
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s
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}
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def generateScholixResourceFromSummary(summaryObject: ScholixSummary): ScholixResource = {
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val r = new ScholixResource
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r.setIdentifier(summaryObject.getLocalIdentifier)
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r.setDnetIdentifier(summaryObject.getId)
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r.setObjectType(summaryObject.getTypology.toString)
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r.setObjectSubType(summaryObject.getSubType)
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if (summaryObject.getTitle != null && !summaryObject.getTitle.isEmpty)
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r.setTitle(summaryObject.getTitle.get(0))
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if (summaryObject.getAuthor != null && !summaryObject.getAuthor.isEmpty) {
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val l: List[ScholixEntityId] = summaryObject.getAuthor.asScala.map(a => new ScholixEntityId(a, null)).toList
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if (l.nonEmpty)
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r.setCreator(l.asJava)
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}
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if (summaryObject.getDate != null && !summaryObject.getDate.isEmpty)
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r.setPublicationDate(summaryObject.getDate.get(0))
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if (summaryObject.getPublisher != null && !summaryObject.getPublisher.isEmpty) {
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val plist: List[ScholixEntityId] = summaryObject.getPublisher.asScala.map(p => new ScholixEntityId(p, null)).toList
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if (plist.nonEmpty)
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r.setPublisher(plist.asJava)
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}
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if (summaryObject.getDatasources != null && !summaryObject.getDatasources.isEmpty) {
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val l: List[ScholixCollectedFrom] = summaryObject.getDatasources.asScala.map(c => new ScholixCollectedFrom(
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new ScholixEntityId(c.getDatasourceName, List(new ScholixIdentifier(c.getDatasourceId, DNET_IDENTIFIER_SCHEMA, null)).asJava)
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, "collected", "complete"
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)).toList
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if (l.nonEmpty)
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r.setCollectedFrom(l.asJava)
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}
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r
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}
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def scholixFromSource(relation: Relation, source: ScholixSummary): Scholix = {
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if (relation == null || source == null)
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return null
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val s = new Scholix
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var l: List[ScholixEntityId] = extractCollectedFrom(relation)
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if (l.isEmpty)
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l = extractCollectedFrom(source)
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if (l.isEmpty)
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return null
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s.setLinkprovider(l.asJava)
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var d = extractRelationDate(relation)
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if (d == null)
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d = extractRelationDate(source)
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s.setPublicationDate(d)
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if (source.getPublisher != null && !source.getPublisher.isEmpty) {
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val l: List[ScholixEntityId] = source.getPublisher.asScala
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.map {
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p =>
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new ScholixEntityId(p, null)
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}(collection.breakOut)
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if (l.nonEmpty)
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s.setPublisher(l.asJava)
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}
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val semanticRelation = relations.getOrElse(relation.getRelClass.toLowerCase, null)
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if (semanticRelation == null)
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return null
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s.setRelationship(new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse))
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s.setSource(generateScholixResourceFromSummary(source))
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s
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}
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def findURLForPID(pidValue: List[StructuredProperty], urls: List[String]): List[(StructuredProperty, String)] = {
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pidValue.map {
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p =>
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val pv = p.getValue
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val r = urls.find(u => u.toLowerCase.contains(pv.toLowerCase))
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(p, r.orNull)
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}
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}
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def extractTypedIdentifierFromInstance(r: Result): List[ScholixIdentifier] = {
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if (r.getInstance() == null || r.getInstance().isEmpty)
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return List()
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r.getInstance().asScala.filter(i => i.getUrl != null && !i.getUrl.isEmpty)
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.filter(i => i.getPid != null && i.getUrl != null)
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.flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList))
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.map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList
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}
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def resultToSummary(r: Result): ScholixSummary = {
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val s = new ScholixSummary
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s.setId(r.getId)
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if (r.getPid == null || r.getPid.isEmpty)
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return null
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val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
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if (persistentIdentifiers.isEmpty)
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return null
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s.setLocalIdentifier(persistentIdentifiers.asJava)
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if (r.isInstanceOf[Publication])
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s.setTypology(Typology.publication)
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else
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s.setTypology(Typology.dataset)
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s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
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if (r.getTitle != null && r.getTitle.asScala.nonEmpty) {
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val titles: List[String] = r.getTitle.asScala.map(t => t.getValue)(collection breakOut)
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if (titles.nonEmpty)
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s.setTitle(titles.asJava)
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else
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return null
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}
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if (r.getAuthor != null && !r.getAuthor.isEmpty) {
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val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname)(collection breakOut)
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if (authors nonEmpty)
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s.setAuthor(authors.asJava)
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}
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if (r.getInstance() != null) {
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val dt: List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue)(collection.breakOut)
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if (dt.nonEmpty)
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s.setDate(dt.distinct.asJava)
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}
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if (r.getDescription != null && !r.getDescription.isEmpty) {
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val d = r.getDescription.asScala.find(f => f != null && f.getValue != null)
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if (d.isDefined)
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s.setDescription(d.get.getValue)
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}
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if (r.getSubject != null && !r.getSubject.isEmpty) {
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val subjects: List[SchemeValue] = r.getSubject.asScala.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue))(collection breakOut)
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if (subjects.nonEmpty)
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s.setSubject(subjects.asJava)
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}
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if (r.getPublisher != null)
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s.setPublisher(List(r.getPublisher.getValue).asJava)
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if (r.getCollectedfrom != null && !r.getCollectedfrom.isEmpty) {
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val cf: List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete"))(collection breakOut)
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if (cf.nonEmpty)
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s.setDatasources(cf.distinct.asJava)
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}
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s.setRelatedDatasets(0)
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s.setRelatedPublications(0)
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s.setRelatedUnknown(0)
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s
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}
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}
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