Merge branch 'beta' into dump
This commit is contained in:
commit
be0acccf42
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@ -12,7 +12,7 @@ import org.json4s.jackson.JsonMethods.parse
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import scala.collection.JavaConverters._
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import scala.io.Source
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object ScholixUtils {
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object ScholixUtils extends Serializable {
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val DNET_IDENTIFIER_SCHEMA: String = "DNET Identifier"
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@ -24,7 +24,7 @@ object ScholixUtils {
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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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val input = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/scholexplorer/relation/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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@ -53,8 +53,6 @@ object ScholixUtils {
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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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@ -64,11 +62,15 @@ object ScholixUtils {
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}
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def generateScholixResourceFromResult(r:Result) :ScholixResource = {
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generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
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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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@ -142,6 +144,14 @@ object ScholixUtils {
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}
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def extractCollectedFrom(summary: ScholixResource): List[ScholixEntityId] = {
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if (summary.getCollectedFrom != null && !summary.getCollectedFrom.isEmpty) {
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val l: List[ScholixEntityId] = summary.getCollectedFrom.asScala.map {
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d => new ScholixEntityId(d.getProvider.getName, d.getProvider.getIdentifiers)
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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(summary: ScholixSummary): List[ScholixEntityId] = {
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if (summary.getDatasources != null && !summary.getDatasources.isEmpty) {
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@ -160,7 +170,7 @@ object ScholixUtils {
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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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}.toList
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l
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} else List()
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}
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@ -179,6 +189,19 @@ object ScholixUtils {
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}
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def generateCompleteScholix(scholix: Scholix, target: ScholixResource): 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(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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@ -222,6 +245,38 @@ object ScholixUtils {
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}
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def scholixFromSource(relation: Relation, source: ScholixResource):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 = source.getPublicationDate
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s.setPublicationDate(d)
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if (source.getPublisher != null && !source.getPublisher.isEmpty) {
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s.setPublisher(source.getPublisher)
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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(source)
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s
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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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@ -303,7 +358,7 @@ object ScholixUtils {
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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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val titles: List[String] = r.getTitle.asScala.map(t => t.getValue).toList
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if (titles.nonEmpty)
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s.setTitle(titles.asJava)
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else
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@ -311,12 +366,12 @@ object ScholixUtils {
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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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val authors: List[String] = r.getAuthor.asScala.map(a => a.getFullname).toList
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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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val dt: List[String] = r.getInstance().asScala.filter(i => i.getDateofacceptance != null).map(i => i.getDateofacceptance.getValue).toList
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if (dt.nonEmpty)
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s.setDate(dt.distinct.asJava)
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}
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@ -327,7 +382,7 @@ object ScholixUtils {
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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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val subjects: List[SchemeValue] = r.getSubject.asScala.map(s => new SchemeValue(s.getQualifier.getClassname, s.getValue)).toList
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if (subjects.nonEmpty)
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s.setSubject(subjects.asJava)
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}
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@ -336,7 +391,7 @@ object ScholixUtils {
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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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val cf: List[CollectedFromType] = r.getCollectedfrom.asScala.map(c => new CollectedFromType(c.getValue, c.getKey, "complete")).toList
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if (cf.nonEmpty)
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s.setDatasources(cf.distinct.asJava)
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}
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@ -0,0 +1,19 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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</configuration>
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@ -0,0 +1,62 @@
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<workflow-app name="Retrieve Scholix Update" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the source path of scholix graph</description>
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</property>
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<property>
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<name>datacitePath</name>
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<description>the datacite native path</description>
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</property>
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<property>
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<name>workingSupportPath</name>
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<description>the working Support path</description>
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</property>
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<property>
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<name>isLookupUrl</name>
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<description>The IS lookUp service endopoint</description>
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</property>
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<property>
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<name>updateDS</name>
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<value>false</value>
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<description>The transformation Rule to apply</description>
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</property>
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</parameters>
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<start to="RetrieveDeltaDatacite"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="RetrieveDeltaDatacite">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>New Update from Datacite to Scholix</name>
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<class>eu.dnetlib.dhp.sx.graph.SparkRetrieveDataciteDelta</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=6000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--datacitePath</arg><arg>${datacitePath}</arg>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--workingSupportPath</arg><arg>${workingSupportPath}</arg>
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<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
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<arg>--updateDS</arg><arg>${updateDS}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
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||||
<error to="Kill"/>
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||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
|
||||
</workflow-app>
|
||||
|
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@ -0,0 +1,41 @@
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[
|
||||
{
|
||||
"paramName": "s",
|
||||
"paramLongName": "sourcePath",
|
||||
"paramDescription": "the source mdstore path",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
||||
{
|
||||
"paramName": "d",
|
||||
"paramLongName": "datacitePath",
|
||||
"paramDescription": "the datacite native path",
|
||||
"paramRequired": true
|
||||
},
|
||||
|
||||
{
|
||||
"paramName": "w",
|
||||
"paramLongName": "workingSupportPath",
|
||||
"paramDescription": "the working Support path",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "isLookupUrl",
|
||||
"paramDescription": "the isLookup URL",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "m",
|
||||
"paramLongName": "master",
|
||||
"paramDescription": "the master name",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "u",
|
||||
"paramLongName": "updateDS",
|
||||
"paramDescription": "Need to regenerate all support Dataset",
|
||||
"paramRequired": false
|
||||
}
|
||||
|
||||
]
|
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|
|
@ -0,0 +1,305 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import eu.dnetlib.dhp.application.AbstractScalaApplication
|
||||
import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.datacite.{DataciteToOAFTransformation, DataciteType}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
|
||||
import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
|
||||
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
||||
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
|
||||
import eu.dnetlib.dhp.utils.{DHPUtils, ISLookupClientFactory}
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
import org.apache.spark.sql.functions.max
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
import java.text.SimpleDateFormat
|
||||
|
||||
class SparkRetrieveDataciteDelta (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) {
|
||||
|
||||
val ISO_DATE_PATTERN = "yyyy-MM-dd'T'HH:mm:ssZ"
|
||||
val simpleFormatter = new SimpleDateFormat(ISO_DATE_PATTERN)
|
||||
|
||||
val SCHOLIX_RESOURCE_PATH_NAME = "scholixResource"
|
||||
val DATACITE_OAF_PATH_NAME = "dataciteOAFUpdate"
|
||||
val PID_MAP_PATH_NAME = "pidMap"
|
||||
val RESOLVED_REL_PATH_NAME ="resolvedRelation"
|
||||
val SCHOLIX_PATH_NAME = "scholix"
|
||||
|
||||
|
||||
def scholixResourcePath(workingPath:String) = s"$workingPath/$SCHOLIX_RESOURCE_PATH_NAME"
|
||||
def dataciteOAFPath(workingPath:String) = s"$workingPath/$DATACITE_OAF_PATH_NAME"
|
||||
def pidMapPath(workingPath:String) = s"$workingPath/$PID_MAP_PATH_NAME"
|
||||
def resolvedRelationPath(workingPath:String) = s"$workingPath/$RESOLVED_REL_PATH_NAME"
|
||||
def scholixPath(workingPath:String) = s"$workingPath/$SCHOLIX_PATH_NAME"
|
||||
|
||||
|
||||
/**
|
||||
* Utility to parse Date in ISO8601 to epochMillis
|
||||
* @param inputDate The String represents an input date in ISO8601
|
||||
* @return The relative epochMillis of parsed date
|
||||
*/
|
||||
def ISO8601toEpochMillis(inputDate:String):Long = {
|
||||
simpleFormatter.parse(inputDate).getTime
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* This method tries to retrieve the last collection date from all datacite
|
||||
* records in HDFS.
|
||||
* This method should be called before indexing scholexplorer to retrieve
|
||||
* the delta of Datacite record to download, since from the generation of
|
||||
* raw graph to the generation of Scholexplorer sometimes it takes 20 days
|
||||
* @param spark
|
||||
* @param entitiesPath
|
||||
* @return the last collection date from the current scholexplorer Graph of the datacite records
|
||||
*/
|
||||
def retrieveLastCollectedFrom(spark:SparkSession, entitiesPath:String):Long = {
|
||||
log.info("Retrieve last entities collected From")
|
||||
|
||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
||||
import spark.implicits._
|
||||
|
||||
val entitiesDS = spark.read.load(s"$entitiesPath/*").as[Oaf].filter(o =>o.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
|
||||
|
||||
val date = entitiesDS.filter(r => r.getDateofcollection!= null).map(_.getDateofcollection).select(max("value")).first.getString(0)
|
||||
|
||||
ISO8601toEpochMillis(date) / 1000
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* The method of update Datacite relationships on Scholexplorer
|
||||
* needs some utilities data structures
|
||||
* One is the scholixResource DS that stores all the nodes in the Scholix Graph
|
||||
* in format ScholixResource
|
||||
* @param summaryPath the path of the summary in Scholix
|
||||
* @param workingPath the working path
|
||||
* @param spark the spark session
|
||||
*/
|
||||
def generateScholixResource(summaryPath:String, workingPath: String, spark:SparkSession) :Unit = {
|
||||
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
|
||||
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||
|
||||
log.info("Convert All summary to ScholixResource")
|
||||
spark.read.load(summaryPath).as[ScholixSummary]
|
||||
.map(ScholixUtils.generateScholixResourceFromSummary)(scholixResourceEncoder)
|
||||
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
||||
.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_native")
|
||||
}
|
||||
|
||||
/**
|
||||
* This method convert the new Datacite Resource into Scholix Resource
|
||||
* Needed to fill the source and the type of Scholix Relationships
|
||||
* @param workingPath the Working Path
|
||||
* @param spark The spark Session
|
||||
*/
|
||||
def addMissingScholixResource(workingPath:String, spark:SparkSession ) :Unit = {
|
||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
||||
import spark.implicits._
|
||||
|
||||
spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
|
||||
.filter(_.isInstanceOf[Result])
|
||||
.map(_.asInstanceOf[Result])
|
||||
.map(ScholixUtils.generateScholixResourceFromResult)
|
||||
.filter(r => r.getIdentifier!= null && r.getIdentifier.size>0)
|
||||
.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_update")
|
||||
|
||||
val update = spark.read.load(s"${scholixResourcePath(workingPath)}_update").as[ScholixResource]
|
||||
val native = spark.read.load(s"${scholixResourcePath(workingPath)}_native").as[ScholixResource]
|
||||
val graph = update.union(native)
|
||||
.groupByKey(_.getDnetIdentifier)
|
||||
.reduceGroups((a,b) => if (a!= null && a.getDnetIdentifier!= null) a else b)
|
||||
.map(_._2)
|
||||
graph.write.mode(SaveMode.Overwrite).save(s"${scholixResourcePath(workingPath)}_graph")
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* This method get and Transform only datacite records with
|
||||
* timestamp greater than timestamp
|
||||
* @param datacitePath the datacite input Path
|
||||
* @param timestamp the timestamp
|
||||
* @param workingPath the working path where save the generated Dataset
|
||||
* @param spark SparkSession
|
||||
* @param vocabularies Vocabularies needed for transformation
|
||||
*/
|
||||
|
||||
def getDataciteUpdate(datacitePath:String, timestamp:Long, workingPath:String, spark:SparkSession,vocabularies: VocabularyGroup): Long = {
|
||||
import spark.implicits._
|
||||
val ds = spark.read.load(datacitePath).as[DataciteType]
|
||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
val total = ds.filter(_.timestamp>=timestamp).count()
|
||||
if (total >0) {
|
||||
ds.filter(_.timestamp >= timestamp)
|
||||
.flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks = true))
|
||||
.flatMap(i => fixRelations(i)).filter(i => i != null)
|
||||
.write.mode(SaveMode.Overwrite).save(dataciteOAFPath(workingPath))
|
||||
}
|
||||
total
|
||||
}
|
||||
|
||||
/**
|
||||
* After added the new ScholixResource, we need to update the scholix Pid Map
|
||||
* to intersected with the new Datacite Relations
|
||||
|
||||
* @param workingPath The working Path starting from save the new Map
|
||||
* @param spark the spark session
|
||||
*/
|
||||
def generatePidMap(workingPath:String, spark:SparkSession ) :Unit = {
|
||||
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||
import spark.implicits._
|
||||
spark.read.load(s"${scholixResourcePath(workingPath)}_graph").as[ScholixResource]
|
||||
.flatMap(r=>
|
||||
r.getIdentifier.asScala
|
||||
.map(i =>DHPUtils.generateUnresolvedIdentifier(i.getIdentifier, i.getSchema))
|
||||
.map(t =>(t, r.getDnetIdentifier))
|
||||
)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||
.groupByKey(_._1)
|
||||
.reduceGroups((a,b) => if (a!= null && a._2!= null) a else b)
|
||||
.map(_._2)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
||||
.write.mode(SaveMode.Overwrite).save(pidMapPath(workingPath))
|
||||
}
|
||||
|
||||
/**
|
||||
* This method resolve the datacite relation and filter the resolved
|
||||
* relation
|
||||
* @param workingPath the working path
|
||||
* @param spark the spark session
|
||||
*/
|
||||
|
||||
def resolveUpdateRelation(workingPath:String, spark:SparkSession) :Unit = {
|
||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
||||
import spark.implicits._
|
||||
|
||||
val pidMap = spark.read.load(pidMapPath(workingPath)).as[(String,String)]
|
||||
|
||||
val unresolvedRelations:Dataset[(String,Relation)] = spark.read.load(dataciteOAFPath(workingPath)).as[Oaf]
|
||||
.filter(_.isInstanceOf[Relation])
|
||||
.map(_.asInstanceOf[Relation])
|
||||
.map { r =>
|
||||
if (r.getSource.startsWith("unresolved"))
|
||||
(r.getSource, r)
|
||||
else
|
||||
(r.getTarget, r)
|
||||
}(Encoders.tuple(Encoders.STRING, relationEncoder))
|
||||
|
||||
unresolvedRelations
|
||||
.joinWith(pidMap, unresolvedRelations("_1").equalTo(pidMap("_1")))
|
||||
.map(t => {
|
||||
val r =t._1._2
|
||||
val resolvedIdentifier = t._2._2
|
||||
if (r.getSource.startsWith("unresolved"))
|
||||
r.setSource(resolvedIdentifier)
|
||||
else
|
||||
r.setTarget(resolvedIdentifier)
|
||||
r
|
||||
})(relationEncoder)
|
||||
.filter(r => !(r.getSource.startsWith("unresolved") || r.getTarget.startsWith("unresolved") ))
|
||||
.write.mode(SaveMode.Overwrite)
|
||||
.save(resolvedRelationPath(workingPath))
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* This method generate scholix starting from resolved relation
|
||||
*
|
||||
*
|
||||
* @param workingPath
|
||||
* @param spark
|
||||
*/
|
||||
def generateScholixUpdate(workingPath:String, spark:SparkSession) :Unit = {
|
||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
implicit val scholixEncoder:Encoder[Scholix] = Encoders.kryo[Scholix]
|
||||
implicit val scholixResourceEncoder:Encoder[ScholixResource] = Encoders.kryo[ScholixResource]
|
||||
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
||||
implicit val intermediateEncoder :Encoder[(String,Scholix)] = Encoders.tuple(Encoders.STRING, scholixEncoder)
|
||||
|
||||
|
||||
val relations:Dataset[(String, Relation)] = spark.read.load(resolvedRelationPath(workingPath)).as[Relation].map(r =>(r.getSource,r))(Encoders.tuple(Encoders.STRING, relationEncoder))
|
||||
|
||||
val id_summary:Dataset[(String,ScholixResource)] = spark.read.load(s"${scholixResourcePath(workingPath)}_graph").as[ScholixResource].map(r => (r.getDnetIdentifier,r))(Encoders.tuple(Encoders.STRING, scholixResourceEncoder))
|
||||
|
||||
id_summary.cache()
|
||||
|
||||
relations.joinWith(id_summary, relations("_1").equalTo(id_summary("_1")),"inner")
|
||||
.map(t => (t._1._2.getTarget,ScholixUtils.scholixFromSource(t._1._2, t._2._2)))
|
||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix_one_verse")
|
||||
|
||||
val source_scholix:Dataset[(String, Scholix)] =spark.read.load(s"$workingPath/scholix_one_verse").as[(String,Scholix)]
|
||||
|
||||
source_scholix.joinWith(id_summary, source_scholix("_1").equalTo(id_summary("_1")),"inner")
|
||||
.map(t => {
|
||||
val target:ScholixResource =t._2._2
|
||||
val scholix:Scholix = t._1._2
|
||||
ScholixUtils.generateCompleteScholix(scholix,target)
|
||||
})(scholixEncoder).write.mode(SaveMode.Overwrite).save(s"$workingPath/scholix")
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Here all the spark applications runs this method
|
||||
* where the whole logic of the spark node is defined
|
||||
*/
|
||||
override def run(): Unit = {
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"SourcePath is '$sourcePath'")
|
||||
|
||||
val datacitePath = parser.get("datacitePath")
|
||||
log.info(s"DatacitePath is '$datacitePath'")
|
||||
|
||||
val workingPath = parser.get("workingSupportPath")
|
||||
log.info(s"workingPath is '$workingPath'")
|
||||
|
||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||
log.info("isLookupUrl: {}", isLookupUrl)
|
||||
|
||||
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||
require(vocabularies != null)
|
||||
|
||||
|
||||
val updateDS:Boolean = "true".equalsIgnoreCase(parser.get("updateDS"))
|
||||
log.info(s"updateDS is '$updateDS'")
|
||||
|
||||
var lastCollectionDate = 0L
|
||||
if (updateDS) {
|
||||
generateScholixResource(s"$sourcePath/provision/summaries", workingPath, spark)
|
||||
log.info("Retrieve last entities collected From starting from scholix Graph")
|
||||
lastCollectionDate = retrieveLastCollectedFrom(spark, s"$sourcePath/entities")
|
||||
}
|
||||
else {
|
||||
val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration)
|
||||
fs.delete(new Path(s"${scholixResourcePath(workingPath)}_native"), true)
|
||||
fs.rename(new Path(s"${scholixResourcePath(workingPath)}_graph"), new Path(s"${scholixResourcePath(workingPath)}_native"))
|
||||
lastCollectionDate = retrieveLastCollectedFrom(spark, dataciteOAFPath(workingPath))
|
||||
}
|
||||
|
||||
val numRecords = getDataciteUpdate(datacitePath, lastCollectionDate, workingPath, spark, vocabularies)
|
||||
if (numRecords>0) {
|
||||
addMissingScholixResource(workingPath,spark)
|
||||
generatePidMap(workingPath, spark)
|
||||
resolveUpdateRelation(workingPath,spark)
|
||||
generateScholixUpdate(workingPath, spark)
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
object SparkRetrieveDataciteDelta {
|
||||
val log: Logger = LoggerFactory.getLogger(SparkRetrieveDataciteDelta.getClass)
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
new SparkRetrieveDataciteDelta("/eu/dnetlib/dhp/sx/graph/retrieve_datacite_delta_params.json", args, log).initialize().run()
|
||||
}
|
||||
}
|
||||
|
|
@ -33,13 +33,14 @@ public class PrepareInfo implements Serializable {
|
|||
private static final Logger log = LoggerFactory.getLogger(PrepareInfo.class);
|
||||
|
||||
// associate orgs with all their parent
|
||||
private static final String ORGANIZATION_ORGANIZATION_QUERY = "SELECT target key, collect_set(source) as valueSet " +
|
||||
private static final String ORGANIZATION_ORGANIZATION_QUERY = "SELECT target key, collect_set(source) as valueSet "
|
||||
+
|
||||
"FROM relation " +
|
||||
"WHERE lower(relclass) = '" + ModelConstants.IS_PARENT_OF.toLowerCase() +
|
||||
"' and datainfo.deletedbyinference = false " +
|
||||
"GROUP BY target";
|
||||
|
||||
//associates results with all the orgs they are affiliated to
|
||||
// associates results with all the orgs they are affiliated to
|
||||
private static final String RESULT_ORGANIZATION_QUERY = "SELECT source key, collect_set(target) as valueSet " +
|
||||
"FROM relation " +
|
||||
"WHERE lower(relclass) = '" + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase() +
|
||||
|
|
@ -88,7 +89,7 @@ public class PrepareInfo implements Serializable {
|
|||
childParentPath,
|
||||
leavesPath,
|
||||
resultOrganizationPath,
|
||||
relationPath));
|
||||
relationPath));
|
||||
}
|
||||
|
||||
private static void prepareInfo(SparkSession spark, String inputPath, String childParentOrganizationPath,
|
||||
|
|
@ -113,13 +114,13 @@ public class PrepareInfo implements Serializable {
|
|||
.json(resultOrganizationPath);
|
||||
|
||||
relation
|
||||
.filter(
|
||||
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
|
||||
r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression","gzip")
|
||||
.json(relationPath);
|
||||
.filter(
|
||||
(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
|
||||
r.getRelClass().equals(ModelConstants.HAS_AUTHOR_INSTITUTION))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(relationPath);
|
||||
|
||||
Dataset<String> children = spark
|
||||
.sql(
|
||||
|
|
|
|||
|
|
@ -2,7 +2,6 @@
|
|||
package eu.dnetlib.dhp.resulttoorganizationfromsemrel;
|
||||
|
||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
||||
|
||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
|
@ -22,13 +21,11 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.KeyValueSet;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.resulttoorganizationfrominstrepo.SparkResultToOrganizationFromIstRepoJob;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
||||
|
||||
public class SparkResultToOrganizationFromSemRel implements Serializable {
|
||||
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromSemRel.class);
|
||||
private static final int MAX_ITERATION = 5;
|
||||
|
|
@ -201,6 +198,4 @@ public class SparkResultToOrganizationFromSemRel implements Serializable {
|
|||
.json(outputPath);
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -75,8 +75,8 @@ public class StepActions implements Serializable {
|
|||
ret.setValueSet(orgs);
|
||||
return ret;
|
||||
}, Encoders.bean(KeyValueSet.class))
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(outputPath);
|
||||
}
|
||||
|
|
@ -179,7 +179,6 @@ public class StepActions implements Serializable {
|
|||
"GROUP BY resId")
|
||||
.as(Encoders.bean(KeyValueSet.class));
|
||||
|
||||
|
||||
// create new relations from result to organization for each result linked to a leaf
|
||||
return resultParent
|
||||
.flatMap(
|
||||
|
|
@ -200,7 +199,6 @@ public class StepActions implements Serializable {
|
|||
.iterator(),
|
||||
Encoders.bean(Relation.class));
|
||||
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -84,7 +84,7 @@ public class PrepareInfoJobTest {
|
|||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
|
||||
});
|
||||
|
||||
|
|
@ -229,7 +229,7 @@ public class PrepareInfoJobTest {
|
|||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
|
||||
});
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
|
@ -335,34 +335,35 @@ public class PrepareInfoJobTest {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void relationTest()throws Exception {
|
||||
public void relationTest() throws Exception {
|
||||
|
||||
PrepareInfo
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-graphPath", getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
|
||||
.getPath(),
|
||||
"-hive_metastore_uris", "",
|
||||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-graphPath", getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/resulttoorganizationfromsemrel/resultorganizationtest")
|
||||
.getPath(),
|
||||
"-hive_metastore_uris", "",
|
||||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
|
||||
});
|
||||
});
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Relation> tmp = sc
|
||||
.textFile(workingDir.toString() + "/relation")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
|
||||
.textFile(workingDir.toString() + "/relation")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Relation.class));
|
||||
|
||||
Dataset<Relation> verificationDs = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
Assertions.assertEquals(7, verificationDs.count());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void resultOrganizationTest1() throws Exception {
|
||||
|
||||
|
|
@ -378,7 +379,7 @@ public class PrepareInfoJobTest {
|
|||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
|
||||
});
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
|
@ -512,7 +513,7 @@ public class PrepareInfoJobTest {
|
|||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
|
||||
});
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
|
@ -539,7 +540,7 @@ public class PrepareInfoJobTest {
|
|||
"-leavesPath", workingDir.toString() + "/currentIteration/",
|
||||
"-resultOrgPath", workingDir.toString() + "/resultOrganization/",
|
||||
"-childParentPath", workingDir.toString() + "/childParentOrg/",
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
"-relationPath", workingDir.toString() + "/relation"
|
||||
|
||||
});
|
||||
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
|
||||
{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"su", "paramLongName":"scholixUpdatePath", "paramDescription": "the scholix updated Path", "paramRequired": false},
|
||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true},
|
||||
{"paramName":"o", "paramLongName":"objectType", "paramDescription": "should be scholix or Summary", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -79,7 +79,7 @@
|
|||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=20000
|
||||
--conf spark.sql.shuffle.partitions=30000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
|
|
@ -90,68 +90,6 @@
|
|||
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="DropJSONPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="DropJSONPath">
|
||||
<fs>
|
||||
<delete path='${targetPath}/index'/>
|
||||
<mkdir path='${targetPath}/index/'/>
|
||||
</fs>
|
||||
<ok to="SerializeScholix"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="SerializeScholix">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Serialize scholix to JSON</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=6000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
|
||||
<arg>--objectType</arg><arg>scholix</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="SerializeSummary"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="SerializeSummary">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Serialize summary to JSON</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=6000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
|
||||
<arg>--objectType</arg><arg>summary</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
|||
|
|
@ -1,158 +0,0 @@
|
|||
{
|
||||
"cites":{
|
||||
"original":"Cites",
|
||||
"inverse":"IsCitedBy"
|
||||
},
|
||||
"compiles":{
|
||||
"original":"Compiles",
|
||||
"inverse":"IsCompiledBy"
|
||||
},
|
||||
"continues":{
|
||||
"original":"Continues",
|
||||
"inverse":"IsContinuedBy"
|
||||
},
|
||||
"derives":{
|
||||
"original":"IsSourceOf",
|
||||
"inverse":"IsDerivedFrom"
|
||||
},
|
||||
"describes":{
|
||||
"original":"Describes",
|
||||
"inverse":"IsDescribedBy"
|
||||
},
|
||||
"documents":{
|
||||
"original":"Documents",
|
||||
"inverse":"IsDocumentedBy"
|
||||
},
|
||||
"hasmetadata":{
|
||||
"original":"HasMetadata",
|
||||
"inverse":"IsMetadataOf"
|
||||
},
|
||||
"hasassociationwith":{
|
||||
"original":"HasAssociationWith",
|
||||
"inverse":"HasAssociationWith"
|
||||
},
|
||||
"haspart":{
|
||||
"original":"HasPart",
|
||||
"inverse":"IsPartOf"
|
||||
},
|
||||
"hasversion":{
|
||||
"original":"HasVersion",
|
||||
"inverse":"IsVersionOf"
|
||||
},
|
||||
"iscitedby":{
|
||||
"original":"IsCitedBy",
|
||||
"inverse":"Cites"
|
||||
},
|
||||
"iscompiledby":{
|
||||
"original":"IsCompiledBy",
|
||||
"inverse":"Compiles"
|
||||
},
|
||||
"iscontinuedby":{
|
||||
"original":"IsContinuedBy",
|
||||
"inverse":"Continues"
|
||||
},
|
||||
"isderivedfrom":{
|
||||
"original":"IsDerivedFrom",
|
||||
"inverse":"IsSourceOf"
|
||||
},
|
||||
"isdescribedby":{
|
||||
"original":"IsDescribedBy",
|
||||
"inverse":"Describes"
|
||||
},
|
||||
"isdocumentedby":{
|
||||
"original":"IsDocumentedBy",
|
||||
"inverse":"Documents"
|
||||
},
|
||||
"isidenticalto":{
|
||||
"original":"IsIdenticalTo",
|
||||
"inverse":"IsIdenticalTo"
|
||||
},
|
||||
"ismetadatafor":{
|
||||
"original":"IsMetadataFor",
|
||||
"inverse":"IsMetadataOf"
|
||||
},
|
||||
"ismetadataof":{
|
||||
"original":"IsMetadataOf",
|
||||
"inverse":"IsMetadataFor"
|
||||
},
|
||||
"isnewversionof":{
|
||||
"original":"IsNewVersionOf",
|
||||
"inverse":"IsPreviousVersionOf"
|
||||
},
|
||||
"isobsoletedby":{
|
||||
"original":"IsObsoletedBy",
|
||||
"inverse":"Obsoletes"
|
||||
},
|
||||
"isoriginalformof":{
|
||||
"original":"IsOriginalFormOf",
|
||||
"inverse":"IsVariantFormOf"
|
||||
},
|
||||
"ispartof":{
|
||||
"original":"IsPartOf",
|
||||
"inverse":"HasPart"
|
||||
},
|
||||
"ispreviousversionof":{
|
||||
"original":"IsPreviousVersionOf",
|
||||
"inverse":"IsNewVersionOf"
|
||||
},
|
||||
"isreferencedby":{
|
||||
"original":"IsReferencedBy",
|
||||
"inverse":"References"
|
||||
},
|
||||
"isrelatedto":{
|
||||
"original":"IsRelatedTo",
|
||||
"inverse":"IsRelatedTo"
|
||||
},
|
||||
"isrequiredby":{
|
||||
"original":"IsRequiredBy",
|
||||
"inverse":"Requires"
|
||||
},
|
||||
"isreviewedby":{
|
||||
"original":"IsReviewedBy",
|
||||
"inverse":"Reviews"
|
||||
},
|
||||
"issourceof":{
|
||||
"original":"IsSourceOf",
|
||||
"inverse":"IsDerivedFrom"
|
||||
},
|
||||
"issupplementedby":{
|
||||
"original":"IsSupplementedBy",
|
||||
"inverse":"IsSupplementTo"
|
||||
},
|
||||
"issupplementto":{
|
||||
"original":"IsSupplementTo",
|
||||
"inverse":"IsSupplementedBy"
|
||||
},
|
||||
"isvariantformof":{
|
||||
"original":"IsVariantFormOf",
|
||||
"inverse":"IsOriginalFormOf"
|
||||
},
|
||||
"isversionof":{
|
||||
"original":"IsVersionOf",
|
||||
"inverse":"HasVersion"
|
||||
},
|
||||
"obsoletes":{
|
||||
"original":"Obsoletes",
|
||||
"inverse":"IsObsoletedBy"
|
||||
},
|
||||
"references":{
|
||||
"original":"References",
|
||||
"inverse":"IsReferencedBy"
|
||||
},
|
||||
"requires":{
|
||||
"original":"Requires",
|
||||
"inverse":"IsRequiredBy"
|
||||
},
|
||||
"related":{
|
||||
"original":"IsRelatedTo",
|
||||
"inverse":"IsRelatedTo"
|
||||
},
|
||||
"reviews":{
|
||||
"original":"Reviews",
|
||||
"inverse":"IsReviewedBy"
|
||||
},
|
||||
"unknown":{
|
||||
"original":"Unknown",
|
||||
"inverse":"Unknown"
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
<configuration>
|
||||
<property>
|
||||
<name>oozie.use.system.libpath</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
<property>
|
||||
<name>oozie.action.sharelib.for.spark</name>
|
||||
<value>spark2</value>
|
||||
</property>
|
||||
</configuration>
|
||||
|
|
@ -0,0 +1,83 @@
|
|||
<workflow-app name="Create Scholix final Graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>scholixUpdatePath</name>
|
||||
<description>the working dir base path of the scholix updated</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the final graph path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="DropJSONPath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="DropJSONPath">
|
||||
<fs>
|
||||
<delete path='${targetPath}/index'/>
|
||||
<mkdir path='${targetPath}/index/'/>
|
||||
</fs>
|
||||
<ok to="SerializeScholix"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="SerializeScholix">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Serialize scholix to JSON</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=6000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/scholix/scholix</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/index/scholix_json</arg>
|
||||
<arg>--scholixUpdatePath</arg><arg>${scholixUpdatePath}</arg>
|
||||
<arg>--objectType</arg><arg>scholix</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="SerializeSummary"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="SerializeSummary">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Serialize summary to JSON</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertObjectToJson</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=6000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/provision/summaries_filtered</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/index/summaries_json</arg>
|
||||
<arg>--objectType</arg><arg>summary</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -30,6 +30,9 @@ object SparkConvertObjectToJson {
|
|||
log.info(s"targetPath -> $targetPath")
|
||||
val objectType = parser.get("objectType")
|
||||
log.info(s"objectType -> $objectType")
|
||||
val scholixUpdatePath = parser.get("scholixUpdatePath")
|
||||
log.info(s"scholixUpdatePath -> $scholixUpdatePath")
|
||||
|
||||
|
||||
|
||||
implicit val scholixEncoder: Encoder[Scholix] = Encoders.kryo[Scholix]
|
||||
|
|
@ -42,7 +45,8 @@ object SparkConvertObjectToJson {
|
|||
case "scholix" =>
|
||||
log.info("Serialize Scholix")
|
||||
val d: Dataset[Scholix] = spark.read.load(sourcePath).as[Scholix]
|
||||
d.map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.repartition(6000).saveAsTextFile(targetPath, classOf[GzipCodec])
|
||||
val u :Dataset[Scholix]= spark.read.load(s"$scholixUpdatePath/scholix").as[Scholix]
|
||||
d.union(u).repartition(8000).map(s => mapper.writeValueAsString(s))(Encoders.STRING).rdd.saveAsTextFile(targetPath, classOf[GzipCodec])
|
||||
case "summary" =>
|
||||
log.info("Serialize Summary")
|
||||
val d: Dataset[ScholixSummary] = spark.read.load(sourcePath).as[ScholixSummary]
|
||||
|
|
|
|||
|
|
@ -2,12 +2,11 @@ package eu.dnetlib.dhp.sx.graph
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Software,Dataset => OafDataset}
|
||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkConvertRDDtoDataset {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
|
@ -32,39 +31,40 @@ object SparkConvertRDDtoDataset {
|
|||
val entityPath = s"$t/entities"
|
||||
val relPath = s"$t/relation"
|
||||
val mapper = new ObjectMapper()
|
||||
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
|
||||
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
|
||||
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
|
||||
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
|
||||
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
|
||||
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
|
||||
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
|
||||
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
|
||||
|
||||
|
||||
log.info("Converting dataset")
|
||||
val rddDataset = spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
|
||||
val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset])).filter(r=> r.getDataInfo!= null && r.getDataInfo.getDeletedbyinference == false)
|
||||
spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset")
|
||||
|
||||
|
||||
log.info("Converting publication")
|
||||
val rddPublication = spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication]))
|
||||
val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication])).filter(r=> r.getDataInfo!= null && r.getDataInfo.getDeletedbyinference == false)
|
||||
spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication")
|
||||
|
||||
log.info("Converting software")
|
||||
val rddSoftware = spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software]))
|
||||
val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software])).filter(r=> r.getDataInfo!= null && r.getDataInfo.getDeletedbyinference == false)
|
||||
spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software")
|
||||
|
||||
log.info("Converting otherresearchproduct")
|
||||
val rddOtherResearchProduct = spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct]))
|
||||
val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct])).filter(r=> r.getDataInfo!= null && r.getDataInfo.getDeletedbyinference == false)
|
||||
spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct")
|
||||
|
||||
|
||||
log.info("Converting Relation")
|
||||
|
||||
|
||||
val relationSemanticFilter = List("cites", "iscitedby", "merges", "ismergedin")
|
||||
val relationSemanticFilter = List("cites", "iscitedby","merges", "ismergedin", "HasAmongTopNSimilarDocuments","IsAmongTopNSimilarDocuments" )
|
||||
|
||||
val rddRelation = spark.sparkContext.textFile(s"$sourcePath/relation")
|
||||
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation")
|
||||
.map(s => mapper.readValue(s, classOf[Relation]))
|
||||
.filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
|
||||
.filter(r=> r.getDataInfo!= null && r.getDataInfo.getDeletedbyinference == false)
|
||||
.filter(r=> r.getSource.startsWith("50") && r.getTarget.startsWith("50"))
|
||||
.filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass)))
|
||||
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,26 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
import java.text.SimpleDateFormat
|
||||
|
||||
|
||||
|
||||
class RetrieveDataciteDeltaTest {
|
||||
|
||||
@Test
|
||||
def testParsingDate(): Unit = {
|
||||
|
||||
|
||||
val inputDate = "2021-12-02T11:17:36+0000"
|
||||
|
||||
val t = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ").parse(inputDate).getTime
|
||||
|
||||
|
||||
println(t)
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue