forked from D-Net/dnet-hadoop
Added a new generation of the dump for scholexplorer tested with last version of spark, and strongly refactored
This commit is contained in:
parent
0d628cd62b
commit
9cd3bc0f10
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@ -154,5 +154,13 @@
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"unknown":{
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"original":"Unknown",
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"inverse":"Unknown"
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},
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"isamongtopnsimilardocuments": {
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"original": "IsAmongTopNSimilarDocuments",
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"inverse": "HasAmongTopNSimilarDocuments"
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},
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"hasamongtopnsimilardocuments": {
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"original": "HasAmongTopNSimilarDocuments",
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"inverse": "IsAmongTopNSimilarDocuments"
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}
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}
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@ -65,7 +65,11 @@ object ScholixUtils extends Serializable {
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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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val sum = ScholixUtils.resultToSummary(r)
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if (sum != null)
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generateScholixResourceFromSummary(ScholixUtils.resultToSummary(r))
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else
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null
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}
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val statsAggregator: Aggregator[(String, String, Long), RelatedEntities, RelatedEntities] =
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@ -153,6 +157,14 @@ object ScholixUtils extends Serializable {
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}
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def invRel(rel: String): String = {
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val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
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if (semanticRelation != null)
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semanticRelation.inverse
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else
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null
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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 { d =>
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@ -377,10 +389,7 @@ object ScholixUtils extends Serializable {
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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.setTypology(r.getResulttype.getClassid)
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s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
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@ -0,0 +1,5 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the scholix dump", "paramRequired": true}
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]
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@ -0,0 +1,166 @@
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{
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"cites":{
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"original":"Cites",
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"inverse":"IsCitedBy"
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},
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"compiles":{
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"original":"Compiles",
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"inverse":"IsCompiledBy"
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},
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"continues":{
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"original":"Continues",
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"inverse":"IsContinuedBy"
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},
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"derives":{
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"original":"IsSourceOf",
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"inverse":"IsDerivedFrom"
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},
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"describes":{
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"original":"Describes",
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"inverse":"IsDescribedBy"
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},
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"documents":{
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"original":"Documents",
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"inverse":"IsDocumentedBy"
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},
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"hasmetadata":{
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"original":"HasMetadata",
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"inverse":"IsMetadataOf"
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},
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"hasassociationwith":{
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"original":"HasAssociationWith",
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"inverse":"HasAssociationWith"
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},
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"haspart":{
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"original":"HasPart",
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"inverse":"IsPartOf"
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},
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"hasversion":{
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"original":"HasVersion",
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"inverse":"IsVersionOf"
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},
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"iscitedby":{
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"original":"IsCitedBy",
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"inverse":"Cites"
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},
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"iscompiledby":{
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"original":"IsCompiledBy",
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"inverse":"Compiles"
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},
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"iscontinuedby":{
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"original":"IsContinuedBy",
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"inverse":"Continues"
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},
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"isderivedfrom":{
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"original":"IsDerivedFrom",
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"inverse":"IsSourceOf"
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},
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"isdescribedby":{
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"original":"IsDescribedBy",
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"inverse":"Describes"
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},
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"isdocumentedby":{
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"original":"IsDocumentedBy",
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"inverse":"Documents"
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},
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"isidenticalto":{
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"original":"IsIdenticalTo",
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"inverse":"IsIdenticalTo"
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},
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"ismetadatafor":{
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"original":"IsMetadataFor",
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"inverse":"IsMetadataOf"
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},
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"ismetadataof":{
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"original":"IsMetadataOf",
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"inverse":"IsMetadataFor"
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},
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"isnewversionof":{
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"original":"IsNewVersionOf",
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"inverse":"IsPreviousVersionOf"
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},
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"isobsoletedby":{
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"original":"IsObsoletedBy",
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"inverse":"Obsoletes"
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},
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"isoriginalformof":{
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"original":"IsOriginalFormOf",
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"inverse":"IsVariantFormOf"
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},
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"ispartof":{
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"original":"IsPartOf",
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"inverse":"HasPart"
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},
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"ispreviousversionof":{
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"original":"IsPreviousVersionOf",
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"inverse":"IsNewVersionOf"
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},
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"isreferencedby":{
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"original":"IsReferencedBy",
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"inverse":"References"
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},
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"isrelatedto":{
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"original":"IsRelatedTo",
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"inverse":"IsRelatedTo"
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},
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"isrequiredby":{
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"original":"IsRequiredBy",
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"inverse":"Requires"
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},
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"isreviewedby":{
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"original":"IsReviewedBy",
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"inverse":"Reviews"
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},
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"issourceof":{
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"original":"IsSourceOf",
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"inverse":"IsDerivedFrom"
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},
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"issupplementedby":{
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"original":"IsSupplementedBy",
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"inverse":"IsSupplementTo"
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},
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"issupplementto":{
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"original":"IsSupplementTo",
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"inverse":"IsSupplementedBy"
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},
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"isvariantformof":{
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"original":"IsVariantFormOf",
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"inverse":"IsOriginalFormOf"
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},
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"isversionof":{
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"original":"IsVersionOf",
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"inverse":"HasVersion"
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},
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"obsoletes":{
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"original":"Obsoletes",
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"inverse":"IsObsoletedBy"
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},
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"references":{
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"original":"References",
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"inverse":"IsReferencedBy"
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},
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"requires":{
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"original":"Requires",
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"inverse":"IsRequiredBy"
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},
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"related":{
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"original":"IsRelatedTo",
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"inverse":"IsRelatedTo"
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},
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"reviews":{
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"original":"Reviews",
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"inverse":"IsReviewedBy"
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},
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"unknown":{
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"original":"Unknown",
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"inverse":"Unknown"
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},
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"isamongtopnsimilardocuments": {
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"original": "IsAmongTopNSimilarDocuments",
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"inverse": "HasAmongTopNSimilarDocuments"
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},
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"hasamongtopnsimilardocuments": {
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"original": "HasAmongTopNSimilarDocuments",
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"inverse": "IsAmongTopNSimilarDocuments"
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}
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}
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@ -0,0 +1,256 @@
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package eu.dnetlib.dhp.sx.graph
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import eu.dnetlib.dhp.schema.oaf.{KeyValue, Result, StructuredProperty}
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import eu.dnetlib.dhp.schema.sx.scholix.{
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Scholix,
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ScholixCollectedFrom,
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ScholixEntityId,
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ScholixIdentifier,
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ScholixRelationship,
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ScholixResource
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}
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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.collection.JavaConverters._
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import scala.io.Source
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case class RelationInfo(
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source: String,
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target: String,
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relclass: String,
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id: String,
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collectedfrom: Seq[RelKeyValue]
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) {}
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case class RelKeyValue(key: String, value: String) {}
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object ScholexplorerUtils {
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val OPENAIRE_IDENTIFIER_SCHEMA: String = "OpenAIRE Identifier"
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case class RelationVocabulary(original: String, inverse: String) {}
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val relations: Map[String, RelationVocabulary] = {
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val input = Source
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.fromInputStream(
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getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/relation/relations.json")
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)
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.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 invRel(rel: String): String = {
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val semanticRelation = relations.getOrElse(rel.toLowerCase, null)
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if (semanticRelation != null)
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semanticRelation.inverse
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else
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null
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}
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def generateDatasourceOpenAIREURLS(id: String): String = {
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if (id != null && id.length > 12)
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s"https://explore.openaire.eu/search/dataprovider?datasourceId=${id.substring(3)}"
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else
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null
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}
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def findURLForPID(
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pidValue: List[StructuredProperty],
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urls: List[String]
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): List[(StructuredProperty, String)] = {
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pidValue.map { 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()
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.asScala
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.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))
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.distinct
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.toList
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}
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def generateScholixResourceFromResult(result: Result): ScholixResource = {
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if (result.getInstance() == null || result.getInstance().size() == 0)
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return null
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if (result.getPid == null || result.getPid.isEmpty)
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return null
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val r = new ScholixResource
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r.setDnetIdentifier(result.getId)
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val persistentIdentifiers: List[ScholixIdentifier] = extractTypedIdentifierFromInstance(result)
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if (persistentIdentifiers.isEmpty)
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return null
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r.setIdentifier(persistentIdentifiers.asJava)
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r.setObjectType(result.getResulttype.getClassid)
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r.setObjectSubType(
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result
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.getInstance()
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.asScala
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.filter(i => i != null && i.getInstancetype != null)
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.map(i => i.getInstancetype.getClassname)
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.distinct
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.head
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)
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if (result.getTitle != null && result.getTitle.asScala.nonEmpty) {
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val titles: List[String] = result.getTitle.asScala.map(t => t.getValue).toList
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if (titles.nonEmpty)
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r.setTitle(titles.head)
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else
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return null
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}
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if (result.getAuthor != null && !result.getAuthor.isEmpty) {
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val authors: List[ScholixEntityId] =
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result.getAuthor.asScala
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.map(a => {
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val entity = new ScholixEntityId()
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entity.setName(a.getFullname)
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if (a.getPid != null && a.getPid.size() > 0)
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entity.setIdentifiers(
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a.getPid.asScala
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.map(sp => {
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val id = new ScholixIdentifier()
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id.setIdentifier(sp.getValue)
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id.setSchema(sp.getQualifier.getClassid)
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id
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})
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.take(3)
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.toList
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.asJava
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)
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entity
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})
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.toList
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if (authors.nonEmpty)
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r.setCreator(authors.asJava)
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}
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val dt: List[String] = result
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.getInstance()
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.asScala
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.filter(i => i.getDateofacceptance != null)
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.map(i => i.getDateofacceptance.getValue)
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.toList
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if (dt.nonEmpty)
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r.setPublicationDate(dt.distinct.head)
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r.setPublisher(
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result
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.getInstance()
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.asScala
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.map(i => i.getHostedby)
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.filter(h => !"unknown".equalsIgnoreCase(h.getValue))
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.map(h => {
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val eid = new ScholixEntityId()
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eid.setName(h.getValue)
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val id = new ScholixIdentifier()
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id.setIdentifier(h.getKey)
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id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
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id.setUrl(generateDatasourceOpenAIREURLS(h.getKey))
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eid.setIdentifiers(List(id).asJava)
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eid
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})
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.distinct
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.asJava
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)
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r.setCollectedFrom(
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result.getCollectedfrom.asScala
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.map(cf => {
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val scf = new ScholixCollectedFrom()
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scf.setProvisionMode("collected")
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scf.setCompletionStatus("complete")
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val eid = new ScholixEntityId()
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eid.setName(cf.getValue)
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val id = new ScholixIdentifier()
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id.setIdentifier(cf.getKey)
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id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
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id.setUrl(generateDatasourceOpenAIREURLS(cf.getKey))
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eid.setIdentifiers(List(id).asJava)
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scf.setProvider(eid)
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scf
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})
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.asJava
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)
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r
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}
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def generateScholix(relation: RelationInfo, source: ScholixResource): Scholix = {
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val s: Scholix = new Scholix
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s.setSource(source)
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if (relation.collectedfrom != null && relation.collectedfrom.nonEmpty)
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s.setLinkprovider(
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relation.collectedfrom
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.map(cf => {
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val eid = new ScholixEntityId()
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eid.setName(cf.value)
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val id = new ScholixIdentifier()
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id.setIdentifier(cf.key)
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id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
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id.setUrl(generateDatasourceOpenAIREURLS(cf.key))
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eid.setIdentifiers(List(id).asJava)
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eid
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})
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.toList
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.asJava
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)
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else {
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val eid = new ScholixEntityId()
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eid.setName("OpenAIRE")
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val id = new ScholixIdentifier()
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id.setIdentifier("10|infrastruct_::f66f1bd369679b5b077dcdf006089556")
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id.setSchema(OPENAIRE_IDENTIFIER_SCHEMA)
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id.setUrl(generateDatasourceOpenAIREURLS(id.getIdentifier))
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eid.setIdentifiers(List(id).asJava)
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s.setLinkprovider(List(eid).asJava)
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}
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s.setIdentifier(relation.id)
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val semanticRelation = relations.getOrElse(relation.relclass.toLowerCase, null)
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if (semanticRelation == null)
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return null
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s.setRelationship(
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new ScholixRelationship(semanticRelation.original, "datacite", semanticRelation.inverse)
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)
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s.setPublicationDate(source.getPublicationDate)
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s.setPublisher(source.getPublisher)
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val mockTarget = new ScholixResource
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mockTarget.setDnetIdentifier(relation.target)
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s.setTarget(mockTarget)
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s
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}
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def updateTarget(s: Scholix, t: ScholixResource): Scholix = {
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s.setTarget(t)
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val spublishers: Seq[ScholixEntityId] =
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if (s.getPublisher != null && !s.getPublisher.isEmpty) s.getPublisher.asScala else List()
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val tpublishers: Seq[ScholixEntityId] =
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if (t.getPublisher != null && !t.getPublisher.isEmpty) t.getPublisher.asScala else List()
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val mergedPublishers = spublishers.union(tpublishers).distinct.take(10).toList
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s.setPublisher(mergedPublishers.asJava)
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s
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}
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}
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|
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@ -0,0 +1,130 @@
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package eu.dnetlib.dhp.sx.graph
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import eu.dnetlib.dhp.application.AbstractScalaApplication
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import eu.dnetlib.dhp.schema.oaf.{
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KeyValue,
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OtherResearchProduct,
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Publication,
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Relation,
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Result,
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Software,
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Dataset => OafDataset
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}
|
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import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixResource}
|
||||
import org.apache.spark.sql.functions.{col, concat, expr, md5}
|
||||
import org.apache.spark.sql.types.StructType
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
class SparkCreateScholexplorerDump(propertyPath: String, args: Array[String], log: Logger)
|
||||
extends AbstractScalaApplication(propertyPath, args, log: Logger) {
|
||||
|
||||
/** 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("sourcePath: {}", sourcePath)
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info("targetPath: {}", targetPath)
|
||||
generateBidirectionalRelations(sourcePath, targetPath, spark)
|
||||
generateScholixResource(sourcePath, targetPath, spark)
|
||||
generateScholix(targetPath, spark)
|
||||
}
|
||||
|
||||
def generateScholixResource(inputPath: String, outputPath: String, spark: SparkSession): Unit = {
|
||||
val entityMap: Map[String, StructType] = Map(
|
||||
"publication" -> Encoders.bean(classOf[Publication]).schema,
|
||||
"dataset" -> Encoders.bean(classOf[OafDataset]).schema,
|
||||
"software" -> Encoders.bean(classOf[Software]).schema,
|
||||
"otherresearchproduct" -> Encoders.bean(classOf[OtherResearchProduct]).schema
|
||||
)
|
||||
|
||||
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
|
||||
implicit val resultEncoder: Encoder[Result] = Encoders.bean(classOf[Result])
|
||||
|
||||
val resDs = spark.emptyDataset[ScholixResource]
|
||||
val scholixResourceDS = entityMap.foldLeft[Dataset[ScholixResource]](resDs)((res, item) => {
|
||||
println(s"adding ${item._1}")
|
||||
res.union(
|
||||
spark.read
|
||||
.schema(item._2)
|
||||
.json(s"$inputPath/${item._1}")
|
||||
.as[Result]
|
||||
.map(r => ScholexplorerUtils.generateScholixResourceFromResult(r))
|
||||
.filter(s => s != null)
|
||||
)
|
||||
})
|
||||
scholixResourceDS.write.mode(SaveMode.Overwrite).save(s"$outputPath/resource")
|
||||
}
|
||||
|
||||
def generateBidirectionalRelations(inputPath: String, otuputPath: String, spark: SparkSession): Unit = {
|
||||
val relSchema = Encoders.bean(classOf[Relation]).schema
|
||||
|
||||
val relDF = spark.read
|
||||
.schema(relSchema)
|
||||
.json(s"$inputPath/relation")
|
||||
.where(
|
||||
"datainfo.deletedbyinference is false and source like '50%' and target like '50%' " +
|
||||
"and relClass <> 'merges' and relClass <> 'isMergedIn'"
|
||||
)
|
||||
.select("source", "target", "collectedfrom", "relClass")
|
||||
|
||||
def invRel: String => String = { s =>
|
||||
ScholexplorerUtils.invRel(s)
|
||||
}
|
||||
|
||||
import org.apache.spark.sql.functions.udf
|
||||
val inverseRelationUDF = udf(invRel)
|
||||
val inverseRelation = relDF.select(
|
||||
col("target").alias("source"),
|
||||
col("source").alias("target"),
|
||||
col("collectedfrom"),
|
||||
inverseRelationUDF(col("relClass")).alias("relClass")
|
||||
)
|
||||
|
||||
val bidRel = inverseRelation
|
||||
.union(relDF)
|
||||
.withColumn("id", md5(concat(col("source"), col("relClass"), col("target"))))
|
||||
.withColumn("cf", expr("transform(collectedfrom, x -> struct(x.key, x.value))"))
|
||||
.drop("collectedfrom")
|
||||
.withColumnRenamed("cf", "collectedfrom")
|
||||
.distinct()
|
||||
|
||||
bidRel.write.mode(SaveMode.Overwrite).save(s"$otuputPath/relation")
|
||||
|
||||
}
|
||||
|
||||
def generateScholix(outputPath: String, spark: SparkSession): Unit = {
|
||||
implicit val scholixResourceEncoder: Encoder[ScholixResource] = Encoders.bean(classOf[ScholixResource])
|
||||
implicit val scholixEncoder: Encoder[Scholix] = Encoders.bean(classOf[Scholix])
|
||||
|
||||
import spark.implicits._
|
||||
val relations = spark.read.load(s"$outputPath/relation").as[RelationInfo]
|
||||
val resource = spark.read.load(s"$outputPath/resource").as[ScholixResource]
|
||||
|
||||
val scholix_one_verse = relations
|
||||
.joinWith(resource, relations("source") === resource("dnetIdentifier"), "inner")
|
||||
.map(res => ScholexplorerUtils.generateScholix(res._1, res._2))
|
||||
|
||||
scholix_one_verse
|
||||
.joinWith(resource, scholix_one_verse("target.dnetIdentifier") === resource("dnetIdentifier"), "inner")
|
||||
.map(k => ScholexplorerUtils.updateTarget(k._1, k._2))
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.json(s"$outputPath/scholix")
|
||||
}
|
||||
}
|
||||
|
||||
object SparkCreateScholexplorerDump {
|
||||
val logger: Logger = LoggerFactory.getLogger(SparkCreateScholexplorerDump.getClass)
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
new SparkCreateScholexplorerDump(
|
||||
log = logger,
|
||||
args = args,
|
||||
propertyPath = "/eu/dnetlib/dhp/sx/create_scholix_dump_params.json"
|
||||
).initialize().run()
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
package eu.dnetlib.dhp.sx.graph.scholix
|
||||
|
||||
import eu.dnetlib.dhp.sx.graph.SparkCreateScholexplorerDump
|
||||
import org.apache.spark.sql.SparkSession
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
class ScholixGenerationTest {
|
||||
|
||||
@Test
|
||||
def generateScholix(): Unit = {
|
||||
val spark: SparkSession = SparkSession.builder().master("local[*]").getOrCreate()
|
||||
val app = new SparkCreateScholexplorerDump(null, null, null)
|
||||
// app.generateScholixResource("/home/sandro/Downloads/scholix_sample/", "/home/sandro/Downloads/scholix/", spark)
|
||||
// app.generateBidirectionalRelations("/home/sandro/Downloads/scholix_sample/", "/home/sandro/Downloads/scholix/", spark)
|
||||
app.generateScholix("/home/sandro/Downloads/scholix/", spark)
|
||||
}
|
||||
}
|
||||
2
pom.xml
2
pom.xml
|
|
@ -960,7 +960,7 @@
|
|||
<commons.logging.version>1.1.3</commons.logging.version>
|
||||
<commons-validator.version>1.7</commons-validator.version>
|
||||
<dateparser.version>1.0.7</dateparser.version>
|
||||
<dhp-schemas.version>[6.1.1]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[6.1.2-SNAPSHOT]</dhp-schemas.version>
|
||||
<dhp.cdh.version>cdh5.9.2</dhp.cdh.version>
|
||||
<dhp.commons.lang.version>3.5</dhp.commons.lang.version>
|
||||
<dhp.guava.version>11.0.2</dhp.guava.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue