forked from D-Net/dnet-hadoop
added alternateIdentifiers to oaf
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2f5caef77b
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@ -28,6 +28,11 @@ case class RelatedIdentifierType(
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relatedIdentifierType: String
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) {}
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case class IdentifierType(
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identifier: String,
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identifierType: String
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) {}
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case class NameIdentifiersType(
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nameIdentifierScheme: Option[String],
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schemeUri: Option[String],
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@ -29,15 +29,15 @@ object BioschemaToOAFTransformation {
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)
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val resolvedURL: Map[String, String] = Map(
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"uniprot" -> "https://www.uniprot.org/uniprot/",
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"pubmed" -> "https://pubmed.ncbi.nlm.nih.gov/"
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"uniprot" -> "https://www.uniprot.org/uniprot/",
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"pubmed" -> "https://pubmed.ncbi.nlm.nih.gov/"
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)
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val collectedFromMap: Map[String, KeyValue] = {
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val PEDCollectedFrom: KeyValue = OafMapperUtils.keyValue(
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//TODO create pedDatasourceId and update this value
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"10|ped_________::pedDatasourceId",
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"PED"
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"Protein Ensemble Database"
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)
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PEDCollectedFrom.setDataInfo(DATA_INFO)
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@ -254,19 +254,8 @@ object BioschemaToOAFTransformation {
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titles
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.filter(t => t.title.nonEmpty)
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.map(t => {
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if (t.titleType.isEmpty) {
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OafMapperUtils
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.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, null)
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} else {
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OafMapperUtils.structuredProperty(
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t.title.get,
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t.titleType.get,
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t.titleType.get,
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ModelConstants.DNET_DATACITE_TITLE,
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ModelConstants.DNET_DATACITE_TITLE,
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null
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)
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}
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OafMapperUtils
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.structuredProperty(t.title.get, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)
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})
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.asJava
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)
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@ -339,8 +328,20 @@ object BioschemaToOAFTransformation {
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val instance = result.getInstance().get(0)
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val ids: List[IdentifierType] = for {
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JObject(identifiers) <- json \\ "identifiers"
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JField("identifier", JString(identifier)) <- identifiers
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JField("identifierType", JString(identifierType)) <- identifiers
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} yield IdentifierType(identifier, identifierType)
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instance.setUrl(
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ids
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.map(id => {
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id.identifier
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})
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.asJava
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)
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instance.setCollectedfrom(collectedFromMap("ped"))
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instance.setUrl(List(s"https://proteinensemble.org/$pid").asJava)
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instance.setPid(result.getPid)
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result.setId(IdentifierFactory.createIdentifier(result))
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@ -349,12 +350,39 @@ object BioschemaToOAFTransformation {
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if (result.getId == null)
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return List()
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val alternativeIdentifierUrls: List[String] = for {
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JObject(alternateIdentifiers) <- json \\ "alternateIdentifiers"
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JField("alternateIdentifier", JString(alternateIdentifier)) <- alternateIdentifiers
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foundResolvedURLId = resolvedURL
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.map(k => {
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if (alternateIdentifier.contains(s"${k._1}:"))
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k._1
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else
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null
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})
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.find(s => s != null)
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alternativeIdentifierUrl = StringUtils.substringAfter(alternateIdentifier, s"${foundResolvedURLId.get}:")
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} yield alternativeIdentifierUrl
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alternativeIdentifierUrls.map(id => {
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var alternateIdentifier: StructuredProperty = null
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alternateIdentifier = OafMapperUtils.structuredProperty(
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id,
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"uniprot",
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"uniprot",
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ModelConstants.DNET_PID_TYPES,
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ModelConstants.DNET_PID_TYPES,
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dataInfo
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)
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instance.setAlternateIdentifier(List(alternateIdentifier).asJava)
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})
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if (exportLinks) {
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val rels: List[RelatedIdentifierType] = for {
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JObject(relIdentifier) <- json \\ "relatedIdentifiers"
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JField("relationType", JString(relationType)) <- relIdentifier
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JObject(relIdentifier) <- json \\ "relatedIdentifiers"
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JField("relationType", JString(relationType)) <- relIdentifier
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JField("relatedIdentifierType", JString(relatedIdentifierType)) <- relIdentifier
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JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
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JField("relatedIdentifier", JString(relatedIdentifier)) <- relIdentifier
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} yield RelatedIdentifierType(relationType, relatedIdentifier, relatedIdentifierType)
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relations = relations ::: generateRelations(
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@ -364,18 +392,6 @@ object BioschemaToOAFTransformation {
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pid
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)
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val identifiers: List[RelatedIdentifierType] = for {
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JObject(alternateIdentifier) <- json \\ "alternateIdentifiers"
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JField("alternateIdentifier", JString(alternateIdentifierValue)) <- alternateIdentifier
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} yield RelatedIdentifierType("IsIdenticalTo", alternateIdentifierValue, "URL")
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relations = relations ::: generateRelations(
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identifiers,
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result.getId,
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if (i_date.isDefined && i_date.get.isDefined) i_date.get.get else null,
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pid
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)
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}
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if (relations != null && relations.nonEmpty) {
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List(result) ::: relations
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@ -404,12 +420,14 @@ object BioschemaToOAFTransformation {
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rel.setProperties(List(dateProps).asJava)
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val foundResolvedURLId = resolvedURL.map(k => {
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if (r.relatedIdentifier.contains(s"${k._1}:"))
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k._1
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else
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null
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}).find(s => s != null);
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val foundResolvedURLId = resolvedURL
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.map(k => {
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if (r.relatedIdentifier.contains(s"${k._1}:"))
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k._1
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else
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null
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})
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.find(s => s != null);
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if (foundResolvedURLId.nonEmpty) {
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val relatedId = StringUtils.substringAfter(r.relatedIdentifier, s"${foundResolvedURLId.get}:")
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rel.setTarget(s"${resolvedURL(foundResolvedURLId.get)}${relatedId}")
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