added inverse relations to datacite mapping

This commit is contained in:
Sandro La Bruzzo 2021-06-04 15:10:20 +02:00
parent 5b724d9972
commit 0cdb7ccdaa
3 changed files with 80 additions and 50 deletions

View File

@ -3,9 +3,8 @@ package eu.dnetlib.dhp.actionmanager.datacite
import com.fasterxml.jackson.databind.ObjectMapper
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
import eu.dnetlib.dhp.schema.action.AtomicAction
import eu.dnetlib.dhp.schema.common.{ModelConstants, ModelSupport}
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils, PidType}
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
import eu.dnetlib.dhp.schema.oaf.{AccessRight, Author, DataInfo, Instance, KeyValue, Oaf, OtherResearchProduct, Publication, Qualifier, Relation, Result, Software, StructuredProperty, Dataset => OafDataset}
import eu.dnetlib.dhp.utils.DHPUtils
import org.apache.commons.lang3.StringUtils
@ -17,8 +16,9 @@ import java.nio.charset.CodingErrorAction
import java.text.SimpleDateFormat
import java.time.LocalDate
import java.time.format.DateTimeFormatter
import java.util.{Date, Locale}
import java.util
import java.util.regex.Pattern
import java.util.{Date, Locale}
import scala.collection.JavaConverters._
import scala.io.{Codec, Source}
@ -46,32 +46,32 @@ object DataciteToOAFTransformation {
val REL_TYPE_VALUE:String = "resultResult"
val subRelTypeMapping: Map[String,String] = Map(
"References" ->"relationship",
"IsSupplementTo" ->"supplement",
"IsPartOf" ->"part",
"HasPart" ->"part",
"IsVersionOf" ->"version",
"HasVersion" ->"version",
"IsIdenticalTo" ->"relationship",
"IsPreviousVersionOf" ->"version",
"IsContinuedBy" ->"relationship",
"Continues" ->"relationship",
"IsNewVersionOf" ->"version",
"IsSupplementedBy" ->"supplement",
"IsDocumentedBy" ->"relationship",
"IsSourceOf" ->"relationship",
"Cites" ->"citation",
"IsCitedBy" ->"citation",
"IsDerivedFrom" ->"relationship",
"IsVariantFormOf" ->"version",
"IsReferencedBy" ->"relationship",
"IsObsoletedBy" ->"version",
"Reviews" ->"review",
"Documents" ->"relationship",
"IsCompiledBy" ->"relationship",
"Compiles" ->"relationship",
"IsReviewedBy" ->"review"
val subRelTypeMapping: Map[String,(String,String)] = Map(
"References" ->("IsReferencedBy","relationship"),
"IsSupplementTo" ->("IsSupplementedBy","supplement"),
"IsPartOf" ->("HasPart","part"),
"HasPart" ->("IsPartOf","part"),
"IsVersionOf" ->("HasVersion","version"),
"HasVersion" ->("IsVersionOf","version"),
"IsIdenticalTo" ->("IsIdenticalTo","relationship"),
"IsPreviousVersionOf" ->("IsNewVersionOf","version"),
"IsContinuedBy" ->("Continues","relationship"),
"Continues" ->("IsContinuedBy","relationship"),
"IsNewVersionOf" ->("IsPreviousVersionOf","version"),
"IsSupplementedBy" ->("IsSupplementTo","supplement"),
"IsDocumentedBy" ->("Documents","relationship"),
"IsSourceOf" ->("IsDerivedFrom","relationship"),
"Cites" ->("IsCitedBy","citation"),
"IsCitedBy" ->("Cites","citation"),
"IsDerivedFrom" ->("IsSourceOf","relationship"),
"IsVariantFormOf" ->("IsDerivedFrom","version"),
"IsReferencedBy" ->("References","relationship"),
"IsObsoletedBy" ->("IsNewVersionOf","version"),
"Reviews" ->("IsReviewedBy","review"),
"Documents" ->("IsDocumentedBy","relationship"),
"IsCompiledBy" ->("Compiles","relationship"),
"Compiles" ->("IsCompiledBy","relationship"),
"IsReviewedBy" ->("Reviews","review")
)
implicit val codec: Codec = Codec("UTF-8")
@ -523,26 +523,7 @@ val REL_TYPE_VALUE:String = "resultResult"
} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
relations = relations ::: rels
.filter(r =>
subRelTypeMapping.contains(r.relationType) && (
r.relatedIdentifierType.equalsIgnoreCase("doi") ||
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
r.relatedIdentifierType.equalsIgnoreCase("arxiv") )
)
.map(r => {
val rel = new Relation
val subRelType = subRelTypeMapping.get(r.relationType)
rel.setRelType(REL_TYPE_VALUE)
rel.setSubRelType(subRelType.get)
rel.setRelClass(r.relationType)
rel.setSource(result.getId)
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.setDataInfo(dataInfo)
rel.setTarget(createDNetTargetIdentifier(r.relatedIdentifier, r.relatedIdentifierType, "50|"))
rel
})
relations = relations ::: generateRelations(rels,result.getId)
}
if (relations != null && relations.nonEmpty) {
List(result) ::: relations
@ -551,6 +532,47 @@ val REL_TYPE_VALUE:String = "resultResult"
List(result)
}
private def generateRelations(rels: List[RelatedIdentifierType], id:String):List[Relation] = {
rels
.filter(r =>
subRelTypeMapping.contains(r.relationType) && (
r.relatedIdentifierType.equalsIgnoreCase("doi") ||
r.relatedIdentifierType.equalsIgnoreCase("pmid") ||
r.relatedIdentifierType.equalsIgnoreCase("arxiv"))
)
.flatMap(r => {
val rel = new Relation
val inverseRel = new Relation
rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
rel.setDataInfo(dataInfo)
inverseRel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
inverseRel.setDataInfo(dataInfo)
val subRelType = subRelTypeMapping(r.relationType)._2
val inverseRelSemantic = subRelTypeMapping(r.relationType)._1
val inversesubRelType = subRelTypeMapping(inverseRelSemantic)._2
rel.setRelType(REL_TYPE_VALUE)
rel.setSubRelType(subRelType)
rel.setRelClass(r.relationType)
inverseRel.setRelType(REL_TYPE_VALUE)
inverseRel.setSubRelType(inversesubRelType)
inverseRel.setRelClass(inverseRelSemantic)
rel.setSource(id)
rel.setTarget(createDNetTargetIdentifier(r.relatedIdentifier, r.relatedIdentifierType, "50|"))
inverseRel.setTarget(id)
inverseRel.setSource(createDNetTargetIdentifier(r.relatedIdentifier, r.relatedIdentifierType, "50|"))
List(rel, inverseRel)
})
}
def generateDataInfo(trust: String): DataInfo = {
val di = new DataInfo
di.setDeletedbyinference(false)

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@ -23,5 +23,12 @@
"paramLongName": "isLookupUrl",
"paramDescription": "the isLookup URL",
"paramRequired": true
},
{
"paramName": "l",
"paramLongName": "exportLinks",
"paramDescription": "should export also links",
"paramRequired": false
}
]

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@ -16,7 +16,7 @@
</parameters>
<start to="ImportDatacite"/>
<start to="TransformJob"/>
<kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
@ -70,6 +70,7 @@
<arg>--sourcePath</arg><arg>${mainPath}/datacite_dump</arg>
<arg>--targetPath</arg><arg>${mainPath}/datacite_oaf</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--exportLinks</arg><arg>true</arg>
<arg>--master</arg><arg>yarn-cluster</arg>
</spark>
<ok to="End"/>