diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index 3a3c2f94d..2422a25db 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -66,6 +66,21 @@ object BioDBToOAF { ) } + def crossrefLinksToOaf(input:String):Oaf = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json = parse(input) + val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase + val source_pid_type = (json \ "Source" \ "Identifier" \ "IDScheme").extract[String].toLowerCase + + val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase + val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase + + 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) + + } + def scholixResolvedToOAF(input:ScholixResolved):Oaf = { @@ -213,11 +228,11 @@ object BioDBToOAF { - - def crossrefLinkToRelation(input:String):Oaf = { - null + def generate_unresolved_id(pid:String, pidType:String) :String = { + s"unresolved::$pid::$pidType" } + def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String):Relation = { val rel = new Relation diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala index 3f81ec3a8..1bca02a73 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -41,6 +41,8 @@ object SparkTransformBioDatabaseToOAF { spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) case "SCHOLIX" => spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).write.mode(SaveMode.Overwrite).save(targetPath) + case "CROSSREF_LINKS"=> + spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml index d7f6538db..90e2ae34f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml @@ -20,6 +20,10 @@ the Scholix Resolved Dataset Path + + CrossrefLinksPath + the CrossrefLinks Path + targetPath the Target Working dir path @@ -134,9 +138,40 @@ --databaseSCHOLIX --targetPath${targetPath}/scholix_resolved_OAF + + + + + + + + yarn + cluster + Convert Crossref Links to OAF Dataset + eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --dbPath${CrossrefLinksPath} + --databaseCROSSREF_LINKS + --targetPath${targetPath}/crossref_unresolved_relation_OAF + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala index f1c6b9e13..a23c6530f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala @@ -131,6 +131,22 @@ class BioScholixTest extends AbstractVocabularyTest{ } + @Test + def testCrossrefLinksToOAF():Unit = { + + val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/crossref_links")).mkString + records.lines.foreach(s => assertTrue(s.nonEmpty)) + + + val result:List[Oaf] =records.lines.map(s => BioDBToOAF.crossrefLinksToOaf(s)).toList + + assertNotNull(result) + assertTrue(result.nonEmpty) + + println(mapper.writeValueAsString(result.head)) + + } + @Test def testEBILinksToOAF():Unit = { val iterator = GzFileIterator(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi_links.gz"), "UTF-8") diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/crossref_links b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/crossref_links index 5eded8390..53f45f7d2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/crossref_links +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/crossref_links @@ -1,10 +1,16 @@ -{"LinkProvider": {"Name": "Elsevier"}, "Target": {"Identifier": {"ID": "P29964", "IDScheme": "ncbi-p", "IDURL": "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=protein&doptcmdl=genbank&term=P29964[accn]"}, "Type": {"Name": 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