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implemented mapping from Crossref Event Data to Oaf

This commit is contained in:
Sandro La Bruzzo 2021-06-29 10:21:23 +02:00
parent 511ec14c63
commit f36f92287d
6 changed files with 87 additions and 13 deletions
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21
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
View File

@ -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

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala
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@ -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)
}
}

35
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/bio/oozie_app/workflow.xml
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@ -20,6 +20,10 @@
<description>the Scholix Resolved Dataset Path</description>
</property>
<property>
<name>CrossrefLinksPath</name>
<description>the CrossrefLinks Path</description>
</property>
<property>
<name>targetPath</name>
<description>the Target Working dir path</description>
@ -134,9 +138,40 @@
<arg>--database</arg><arg>SCHOLIX</arg>
<arg>--targetPath</arg><arg>${targetPath}/scholix_resolved_OAF</arg>
</spark>
<ok to="ConvertCrossrefLinks"/>
<error to="Kill"/>
</action>
<action name="ConvertCrossrefLinks">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>Convert Crossref Links to OAF Dataset</name>
<class>eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--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}
</spark-opts>
<arg>--master</arg><arg>yarn</arg>
<arg>--dbPath</arg><arg>${CrossrefLinksPath}</arg>
<arg>--database</arg><arg>CROSSREF_LINKS</arg>
<arg>--targetPath</arg><arg>${targetPath}/crossref_unresolved_relation_OAF</arg>
</spark>
<ok to="End"/>
<error to="Kill"/>
</action>
<end name="End"/>
</workflow-app>

16
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/bio/pubmed/BioScholixTest.scala
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@ -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")

26
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/bio/crossref_links
View File

@ -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": "dataset"}}, "Source": {"Publisher": {"Identifier": {"ID": "0141-8130", "IDScheme": "ISNI", "IDURL": "http://www.isni.org/isni/0141-8130"}, "Name": "International Journal of Biological Macromolecules"}, "Identifier": {"ID": "10.1016/j.ijbiomac.2017.09.060", "IDScheme": "DOI", "IDURL": "https://doi.org/10.1016/j.ijbiomac.2017.09.060"}, "Type": {"SubType": "journal article", "Name": "literature"}, "PublicationDate": "2018", "Title": "Molecular structure of cyclomaltodextrinase derived from amylolytic lactic acid bacterium "}, "LinkedPublicationDate": "2018", "LicenseURL": "https://creativecommons.org/licenses/by/4.0/", "RelationshipType": {"Name": "IsReferencedBy"}}
{"LinkProvider": {"Name": "Elsevier"}, "Target": {"Identifier": {"ID": "P56942", "IDScheme": "ncbi-p", "IDURL": "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=protein&doptcmdl=genbank&term=P56942[accn]"}, "Type": {"Name": "dataset"}}, "Source": {"Publisher": {"Identifier": {"ID": "0091-3022", "IDScheme": "ISNI", "IDURL": "http://www.isni.org/isni/0091-3022"}, "Name": "Frontiers in Neuroendocrinology"}, "Identifier": {"ID": "10.1016/j.yfrne.2010.09.001", "IDScheme": "DOI", "IDURL": "https://doi.org/10.1016/j.yfrne.2010.09.001"}, "Type": {"SubType": "journal article", "Name": "literature"}, "PublicationDate": "2011", "Title": "New aspects of melanocortin signaling: A role for PRCP in \u03b1-MSH degradation"}, "LinkedPublicationDate": "2018", "LicenseURL": "https://creativecommons.org/licenses/by/4.0/", "RelationshipType": {"Name": "IsReferencedBy"}}
{"LinkProvider": {"Name": "Elsevier"}, "Target": {"Identifier": {"ID": "Q9R0R4", "IDScheme": "ncbi-p", "IDURL": "https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=protein&doptcmdl=genbank&term=Q9R0R4[accn]"}, "Type": {"Name": "dataset"}}, "Source": {"Publisher": {"Identifier": {"ID": "0091-3022", "IDScheme": "ISNI", "IDURL": "http://www.isni.org/isni/0091-3022"}, "Name": "Frontiers in Neuroendocrinology"}, "Identifier": {"ID": "10.1016/j.yfrne.2010.09.001", "IDScheme": "DOI", "IDURL": "https://doi.org/10.1016/j.yfrne.2010.09.001"}, "Type": {"SubType": "journal article", "Name": "literature"}, "PublicationDate": "2011", "Title": "New aspects of melanocortin signaling: A role for PRCP in \u03b1-MSH degradation"}, "LinkedPublicationDate": "2018", "LicenseURL": "https://creativecommons.org/licenses/by/4.0/", "RelationshipType": {"Name": "IsReferencedBy"}}
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