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added relation dates in bio mapping

This commit is contained in:
Sandro La Bruzzo 2021-06-29 10:33:09 +02:00
parent f36f92287d
commit 075055eaca
2 changed files with 18 additions and 15 deletions
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24
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
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@ -77,7 +77,9 @@ object BioDBToOAF {
val relation_semantic= (json \ "RelationshipType" \ "Name").extract[String] val relation_semantic= (json \ "RelationshipType" \ "Name").extract[String]
createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type),collectedFromMap("elsevier"),"relationship", relation_semantic) val date = (json \ "LinkedPublicationDate").extract[String]
createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type),collectedFromMap("elsevier"),"relationship", relation_semantic, date)
} }
@ -186,10 +188,10 @@ object BioDBToOAF {
OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null) OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
).asJava) ).asJava)
} }
var i_date:Option[UniprotDate] = None
if (dates.nonEmpty) { if (dates.nonEmpty) {
val i_date = dates.find(d => d.date_info.contains("entry version")) i_date = dates.find(d => d.date_info.contains("entry version"))
if (i_date.isDefined) { if (i_date.isDefined) {
i.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) i.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
@ -214,12 +216,12 @@ object BioDBToOAF {
if (references_pmid != null && references_pmid.nonEmpty) { if (references_pmid != null && references_pmid.nonEmpty) {
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo") val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null)
rel.getCollectedfrom rel.getCollectedfrom
List(d, rel) List(d, rel)
} }
else if (references_doi != null && references_doi.nonEmpty) { else if (references_doi != null && references_doi.nonEmpty) {
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo") val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null)
List(d, rel) List(d, rel)
} }
else else
@ -233,7 +235,7 @@ object BioDBToOAF {
} }
def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String):Relation = { def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String, date:String):Relation = {
val rel = new Relation val rel = new Relation
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava) rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
@ -246,6 +248,8 @@ object BioDBToOAF {
rel.setSource(sourceId) rel.setSource(sourceId)
rel.setTarget(s"unresolved::$pid::$pidType") rel.setTarget(s"unresolved::$pid::$pidType")
rel.setValidationDate(date)
rel.getTarget.startsWith("unresolved") rel.getTarget.startsWith("unresolved")
rel.setCollectedfrom(List(collectedFrom).asJava) rel.setCollectedfrom(List(collectedFrom).asJava)
rel rel
@ -253,8 +257,8 @@ object BioDBToOAF {
} }
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue): Relation = { def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = {
createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo") createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date)
} }
@ -311,7 +315,7 @@ object BioDBToOAF {
val pmid = (json \ "pmid").extractOrElse[String](null) val pmid = (json \ "pmid").extractOrElse[String](null)
if (pmid != null) if (pmid != null)
List(d, createSupplementaryRelation(pmid, "pmid", d.getId, collectedFromMap("pdb"))) List(d, createSupplementaryRelation(pmid, "pmid", d.getId, collectedFromMap("pdb"), null))
else else
List(d) List(d)
} }
@ -383,6 +387,6 @@ object BioDBToOAF {
i.setDateofacceptance(OafMapperUtils.field(input.date, DATA_INFO)) i.setDateofacceptance(OafMapperUtils.field(input.date, DATA_INFO))
d.setDateofacceptance(OafMapperUtils.field(input.date, DATA_INFO)) d.setDateofacceptance(OafMapperUtils.field(input.date, DATA_INFO))
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo")) List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", input.date))
} }
} }

9
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala
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@ -4,20 +4,19 @@ import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, Ser
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
import eu.dnetlib.dhp.sx.bio.BioDBToOAF import eu.dnetlib.dhp.sx.bio.BioDBToOAF
import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved
import eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
import org.junit.jupiter.api.Assertions._ import org.junit.jupiter.api.Assertions._
import org.junit.jupiter.api.extension.ExtendWith import org.junit.jupiter.api.extension.ExtendWith
import org.junit.jupiter.api.{BeforeEach, Test} import org.junit.jupiter.api.{BeforeEach, Test}
import org.mockito.junit.jupiter.MockitoExtension import org.mockito.junit.jupiter.MockitoExtension
import java.io.{BufferedReader, FileInputStream, InputStream, InputStreamReader} import java.io.{BufferedReader, InputStream, InputStreamReader}
import java.util.zip.GZIPInputStream import java.util.zip.GZIPInputStream
import scala.collection.JavaConverters._ import scala.collection.JavaConverters._
import scala.io.Source import scala.io.Source
import scala.xml.pull.XMLEventReader import scala.xml.pull.XMLEventReader
import org.json4s.DefaultFormats
import org.json4s.JsonAST.{JField, JObject, JString}
import org.json4s.jackson.JsonMethods.parse
@ExtendWith(Array(classOf[MockitoExtension])) @ExtendWith(Array(classOf[MockitoExtension]))
class BioScholixTest extends AbstractVocabularyTest{ class BioScholixTest extends AbstractVocabularyTest{