forked from antonis.lempesis/dnet-hadoop
updated mapping scholexplorer to OAF
This commit is contained in:
parent
9bf67f5de1
commit
1681de672d
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@ -4,9 +4,12 @@ import java.time.LocalDateTime
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import java.time.format.DateTimeFormatter
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import eu.dnetlib.dhp.common.PacePerson
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import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Field, Instance, KeyValue, Publication, Qualifier, Relation, StructuredProperty}
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, StructuredProperty}
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import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation}
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import eu.dnetlib.dhp.utils.DHPUtils
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import org.apache.commons.lang3.StringUtils
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import org.codehaus.jackson.map.ObjectMapper
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import scala.collection.JavaConverters._
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@ -77,6 +80,76 @@ object DLIToOAF {
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)
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val rel_inverse: Map[String, String] = Map(
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"isRelatedTo" -> "isRelatedTo",
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"IsSupplementedBy" -> "isSupplementTo",
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"cites" -> "IsCitedBy",
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"IsCitedBy" -> "cites",
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"reviews" -> "IsReviewedBy"
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)
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val PidTypeMap: Map[String, String] = Map(
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"pbmid" -> "pmid",
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"pmcid" -> "pmc",
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"pmid" -> "pmid",
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"pubmedid" -> "pmid",
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"DOI" -> "doi",
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"doi" -> "doi"
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)
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def toActionSet(item: Oaf): (String, String) = {
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val mapper = new ObjectMapper()
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item match {
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case dataset: Dataset =>
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val a: AtomicAction[Dataset] = new AtomicAction[Dataset]
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a.setClazz(classOf[Dataset])
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a.setPayload(dataset)
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(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case publication: Publication =>
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val a: AtomicAction[Publication] = new AtomicAction[Publication]
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a.setClazz(classOf[Publication])
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a.setPayload(publication)
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(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case relation: Relation =>
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val a: AtomicAction[Relation] = new AtomicAction[Relation]
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a.setClazz(classOf[Relation])
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a.setPayload(relation)
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(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case _ =>
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null
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}
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}
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def convertClinicalTrial(dataset: DLIDataset): (String, String) = {
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val currentId = generateId(dataset.getId)
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val pids = dataset.getPid.asScala.filter(p => "clinicaltrials.gov".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => s"50|r3111dacbab5::${DHPUtils.md5(p.getValue.toLowerCase())}")
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if (pids.isEmpty)
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null
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else
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(currentId, pids.head)
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}
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def insertExternalRefs(publication: Publication, externalReferences: List[DLIExternalReference]): Publication = {
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val eRefs = externalReferences.map(e => {
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val result = new ExternalReference()
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result.setSitename(e.sitename)
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result.setLabel(e.label)
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result.setUrl(e.url)
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result.setRefidentifier(e.pid)
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result.setDataInfo(generateDataInfo())
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result.setQualifier(createQualifier(e.classId, "dnet:externalReference_typologies"))
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result
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})
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publication.setExternalReference(eRefs.asJava)
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publication
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}
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def filterPid(p: StructuredProperty): Boolean = {
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if (expectecdPidType.contains(p.getQualifier.getClassname) && p.getQualifier.getClassname.equalsIgnoreCase("url"))
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if (filteredURL.exists(u => p.getValue.contains(u)))
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@ -97,7 +170,6 @@ object DLIToOAF {
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}
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def convertDLIDatasetToExternalReference(dataset: DLIDataset): DLIExternalReference = {
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val currentId = generateId(dataset.getId)
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val pids = dataset.getPid.asScala.filter(filterPid)
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if (pids == null || pids.isEmpty)
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@ -109,7 +181,7 @@ object DLIToOAF {
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pid.getQualifier.getClassname match {
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case "uniprot" => DLIExternalReference(generateId(dataset.getId), s"https://www.uniprot.org/uniprot/${pid.getValue}", "UniProt", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
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case "ena" =>
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if(pid.getValue!= null && pid.getValue.nonEmpty && pid.getValue.length>7)
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if (pid.getValue != null && pid.getValue.nonEmpty && pid.getValue.length > 7)
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DLIExternalReference(generateId(dataset.getId), s"https://www.ebi.ac.uk/ena/data/view/${pid.getValue.substring(0, 8)}", "European Nucleotide Archive", extractTitle(dataset.getTitle), pid.getValue, "accessionNumber")
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else
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null
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@ -126,43 +198,50 @@ object DLIToOAF {
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}
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def convertDLIPublicationToOAF(p: DLIPublication): Publication = {
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def convertDLIPublicationToOAF(inputPublication: DLIPublication): Publication = {
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val result = new Publication
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result.setId(generateId(p.getId))
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val cleanedPids = inputPublication.getPid.asScala.filter(p => PidTypeMap.contains(p.getQualifier.getClassid))
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.map(p => {
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p.setQualifier(createQualifier(PidTypeMap(p.getQualifier.getClassid), p.getQualifier.getSchemeid))
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p
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})
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if (cleanedPids.isEmpty)
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return null
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result.setId(generateId(inputPublication.getId))
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result.setDataInfo(generateDataInfo(invisibile = true))
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if (p.getCollectedfrom == null || p.getCollectedfrom.size() == 0 || (p.getCollectedfrom.size() == 1 && p.getCollectedfrom.get(0) == null))
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if (inputPublication.getCollectedfrom == null || inputPublication.getCollectedfrom.size() == 0 || (inputPublication.getCollectedfrom.size() == 1 && inputPublication.getCollectedfrom.get(0) == null))
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return null
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result.setCollectedfrom(p.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).asJava)
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result.setPid(p.getPid)
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result.setDateofcollection(p.getDateofcollection)
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result.setOriginalId(p.getPid.asScala.map(p => p.getValue).asJava)
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result.setCollectedfrom(inputPublication.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava)
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if(result.getCollectedfrom.isEmpty)
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return null
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result.setPid(cleanedPids.asJava)
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result.setDateofcollection(inputPublication.getDateofcollection)
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result.setOriginalId(inputPublication.getPid.asScala.map(p => p.getValue).asJava)
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result.setDateoftransformation(LocalDateTime.now().format(DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'")))
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if (p.getAuthor == null || p.getAuthor.isEmpty)
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if (inputPublication.getAuthor == null || inputPublication.getAuthor.isEmpty)
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return null
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result.setAuthor(p.getAuthor.asScala.map(convertAuthor).asJava)
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result.setResulttype(createQualifier(p.getResulttype.getClassid, p.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies"))
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result.setAuthor(inputPublication.getAuthor.asScala.map(convertAuthor).asJava)
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result.setResulttype(createQualifier(inputPublication.getResulttype.getClassid, inputPublication.getResulttype.getClassname, "dnet:result_typologies", "dnet:result_typologies"))
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if (p.getSubject != null)
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result.setSubject(p.getSubject.asScala.map(convertSubject).asJava)
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if (inputPublication.getSubject != null)
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result.setSubject(inputPublication.getSubject.asScala.map(convertSubject).asJava)
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if (p.getTitle == null || p.getTitle.isEmpty)
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if (inputPublication.getTitle == null || inputPublication.getTitle.isEmpty)
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return null
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result.setTitle(List(patchTitle(p.getTitle.get(0))).asJava)
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result.setTitle(List(patchTitle(inputPublication.getTitle.get(0))).asJava)
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if (p.getRelevantdate == null || p.getRelevantdate.size() == 0)
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if (inputPublication.getRelevantdate == null || inputPublication.getRelevantdate.size() == 0)
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return null
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result.setRelevantdate(p.getRelevantdate.asScala.map(patchRelevantDate).asJava)
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result.setRelevantdate(inputPublication.getRelevantdate.asScala.map(patchRelevantDate).asJava)
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result.setDescription(p.getDescription)
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result.setDescription(inputPublication.getDescription)
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result.setDateofacceptance(asField(p.getRelevantdate.get(0).getValue))
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result.setPublisher(p.getPublisher)
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result.setSource(p.getSource)
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result.setDateofacceptance(asField(inputPublication.getRelevantdate.get(0).getValue))
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result.setPublisher(inputPublication.getPublisher)
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result.setSource(inputPublication.getSource)
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result.setBestaccessright(createQualifier("UNKNOWN", "not available", "dnet:access_modes", "dnet:access_modes"))
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val dois = result.getPid.asScala.filter(p => "doi".equalsIgnoreCase(p.getQualifier.getClassname)).map(p => p.getValue)
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@ -170,7 +249,7 @@ object DLIToOAF {
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return null
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val i: Instance = createInstance(s"https://dx.doi.org/${dois.head}", firstInstanceOrNull(p.getInstance()), result.getDateofacceptance)
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val i: Instance = createInstance(s"https://dx.doi.org/${dois.head}", firstInstanceOrNull(inputPublication.getInstance()), result.getDateofacceptance)
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if (i != null)
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result.setInstance(List(i).asJava)
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@ -211,7 +290,9 @@ object DLIToOAF {
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val result: Dataset = new Dataset
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result.setId(generateId(d.getId))
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result.setDataInfo(generateDataInfo())
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result.setCollectedfrom(d.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).asJava)
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result.setCollectedfrom(d.getCollectedfrom.asScala.map(c => collectedFromMap.getOrElse(c.getKey, null)).filter(p => p != null).asJava)
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if(result.getCollectedfrom.isEmpty)
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return null
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result.setPid(d.getPid)
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@ -280,7 +361,7 @@ object DLIToOAF {
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if (dataset)
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i.setInstancetype(createQualifier("0021", "Dataset", "dnet:publication_resource", "dnet:publication_resource"))
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else
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i.setInstancetype(createQualifier("0000", "UNKNOWN", "dnet:publication_resource", "dnet:publication_resource"))
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i.setInstancetype(createQualifier("0000", "Unknown", "dnet:publication_resource", "dnet:publication_resource"))
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if (originalInstance != null && originalInstance.getHostedby != null)
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i.setHostedby(originalInstance.getHostedby)
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@ -4,10 +4,16 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
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import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIRelation}
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.io.Text
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.hadoop.mapred.SequenceFileOutputFormat
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import org.apache.spark.rdd.RDD
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.apache.spark.sql.functions._
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import org.apache.spark.sql.expressions.Window
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import org.apache.spark.{SparkConf, SparkContext}
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import org.codehaus.jackson.map.ObjectMapper
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import scala.collection.mutable.ArrayBuffer
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@ -36,57 +42,66 @@ object SparkExportContentForOpenAire {
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implicit val dliRelEncoder: Encoder[DLIRelation] = Encoders.bean(classOf[DLIRelation])
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import spark.implicits._
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//
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// val relRDD:RDD[Relation] = sc.textFile(s"$workingPath/relation_j")
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// .map(s => new ObjectMapper().readValue(s, classOf[DLIRelation]))
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// .filter(p => p.getDataInfo.getDeletedbyinference == false)
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// .map(DLIToOAF.convertDLIRelation).filter(p=>p!= null)
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// spark.createDataset(relRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS")
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//
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// val datRDD:RDD[OafDataset] = sc.textFile(s"$workingPath/dataset")
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// .map(s => new ObjectMapper().readValue(s, classOf[DLIDataset]))
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// .filter(p => p.getDataInfo.getDeletedbyinference == false)
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// .map(DLIToOAF.convertDLIDatasetTOOAF).filter(p=>p!= null)
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// spark.createDataset(datRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetDS")
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//
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//
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// val pubRDD:RDD[Publication] = sc.textFile(s"$workingPath/publication")
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// .map(s => new ObjectMapper().readValue(s, classOf[DLIPublication]))
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// .filter(p => p.getDataInfo.getDeletedbyinference == false)
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// .map(DLIToOAF.convertDLIPublicationToOAF).filter(p=>p!= null)
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// spark.createDataset(pubRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationDS")
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//
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//
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//
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// val pubs:Dataset[Publication] = spark.read.load(s"$workingPath/publicationDS").as[Publication]
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// val dats :Dataset[OafDataset] = spark.read.load(s"$workingPath/datasetDS").as[OafDataset]
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var relDS :Dataset[Relation] = spark.read.load(s"$workingPath/relationDS").as[Relation]
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//
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//
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// pubs.joinWith(relDS, pubs("id").equalTo(relDS("source"))).map(k => k._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS_f1")
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//
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// relDS= spark.read.load(s"$workingPath/relationDS_f1").as[Relation]
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//
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// relDS.joinWith(dats, relDS("target").equalTo(dats("id"))).map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS_filtered")
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//
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//
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// val r_source = relDS.select(relDS("source")).distinct()
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// val r_target = relDS.select(relDS("source")).distinct()
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//
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//
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// pubs.joinWith(r_source, pubs("id").equalTo(r_source("source")), "inner").map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationDS_filtered")
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//
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// dats.joinWith(r_target, dats("id").equalTo(r_target("target")), "inner").map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetDS_filtered")
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//
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// spark.createDataset(sc.textFile(s"$workingPath/dataset")
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// .map(s => new ObjectMapper().readValue(s, classOf[DLIDataset]))
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// .map(DLIToOAF.convertDLIDatasetToExternalReference)
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// .filter(p => p != null)).as[DLIExternalReference].write.mode(SaveMode.Overwrite).save(s"$workingPath/externalReference")
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//
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val relRDD:RDD[Relation] = sc.textFile(s"$workingPath/relation_j")
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.map(s => new ObjectMapper().readValue(s, classOf[DLIRelation]))
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.filter(p => p.getDataInfo.getDeletedbyinference == false)
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.map(DLIToOAF.convertDLIRelation).filter(p=>p!= null)
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spark.createDataset(relRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS")
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val datRDD:RDD[OafDataset] = sc.textFile(s"$workingPath/dataset")
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.map(s => new ObjectMapper().readValue(s, classOf[DLIDataset]))
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.filter(p => p.getDataInfo.getDeletedbyinference == false)
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.map(DLIToOAF.convertDLIDatasetTOOAF).filter(p=>p!= null)
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spark.createDataset(datRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetDS")
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val pubRDD:RDD[Publication] = sc.textFile(s"$workingPath/publication")
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.map(s => new ObjectMapper().readValue(s, classOf[DLIPublication]))
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.filter(p => p.getDataInfo.getDeletedbyinference == false)
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.map(DLIToOAF.convertDLIPublicationToOAF).filter(p=>p!= null)
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spark.createDataset(pubRDD).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationDS")
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val pubs:Dataset[Publication] = spark.read.load(s"$workingPath/publicationDS").as[Publication]
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val dats :Dataset[OafDataset] = spark.read.load(s"$workingPath/datasetDS").as[OafDataset]
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val relDS1 :Dataset[Relation] = spark.read.load(s"$workingPath/relationDS").as[Relation]
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val pub_id = pubs.select("id").distinct()
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val dat_id = dats.select("id").distinct()
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pub_id.joinWith(relDS1, pub_id("id").equalTo(relDS1("source"))).map(k => k._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS_f1")
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val relDS2= spark.read.load(s"$workingPath/relationDS_f1").as[Relation]
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relDS2.joinWith(dat_id, relDS2("target").equalTo(dats("id"))).map(k => k._1).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationDS_filtered")
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val r_source = relDS2.select(relDS2("source")).distinct()
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val r_target = relDS2.select(relDS2("target")).distinct()
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val w2 = Window.partitionBy("id").orderBy("lastupdatetimestamp")
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pubs.joinWith(r_source, pubs("id").equalTo(r_source("source")), "inner").map(k => k._1)
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.withColumn("row",row_number.over(w2)).where($"row" === 1).drop("row")
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.write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationDS_filtered")
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dats.joinWith(r_target, dats("id").equalTo(r_target("target")), "inner").map(k => k._1)
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.withColumn("row",row_number.over(w2)).where($"row" === 1).drop("row")
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.write.mode(SaveMode.Overwrite).save(s"$workingPath/datasetAS")
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spark.createDataset(sc.textFile(s"$workingPath/dataset")
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.map(s => new ObjectMapper().readValue(s, classOf[DLIDataset]))
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.map(DLIToOAF.convertDLIDatasetToExternalReference)
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.filter(p => p != null)).as[DLIExternalReference].write.mode(SaveMode.Overwrite).save(s"$workingPath/externalReference")
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val pf = spark.read.load(s"$workingPath/publicationDS_filtered").select("id")
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relDS = spark.read.load(s"$workingPath/relationDS").as[Relation]
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val relationTo = pf.joinWith(relDS, pf("id").equalTo(relDS("source")),"inner").map(t =>t._2)
|
||||
val relDS3 = spark.read.load(s"$workingPath/relationDS").as[Relation]
|
||||
val relationTo = pf.joinWith(relDS3, pf("id").equalTo(relDS3("source")),"inner").map(t =>t._2)
|
||||
|
||||
val extRef = spark.read.load(s"$workingPath/externalReference").as[DLIExternalReference]
|
||||
|
||||
|
|
@ -100,19 +115,70 @@ object SparkExportContentForOpenAire {
|
|||
(f._1, dli_ext)
|
||||
})).write.mode(SaveMode.Overwrite).save(s"$workingPath/externalReference_grouped")
|
||||
|
||||
val pubf :Dataset[Publication] = spark.read.load(s"$workingPath/publicationDS_filtered").as[Publication]
|
||||
|
||||
val groupedERf:Dataset[(String, List[DLIExternalReference])]= spark.read.load(s"$workingPath/externalReference_grouped").as[(String, List[DLIExternalReference])]
|
||||
|
||||
groupedERf.joinWith(pubf,pubf("id").equalTo(groupedERf("_1"))).map(t =>
|
||||
{
|
||||
val publication = t._2
|
||||
if (t._1 != null) {
|
||||
val eRefs = t._1._2
|
||||
DLIToOAF.insertExternalRefs(publication, eRefs)
|
||||
|
||||
} else
|
||||
publication
|
||||
}
|
||||
).write.mode(SaveMode.Overwrite).save(s"$workingPath/publicationAS")
|
||||
|
||||
|
||||
spark.createDataset(sc.textFile(s"$workingPath/dataset")
|
||||
.map(s => new ObjectMapper().readValue(s, classOf[DLIDataset]))
|
||||
.map(DLIToOAF.convertClinicalTrial)
|
||||
.filter(p => p != null))
|
||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/clinicalTrials")
|
||||
|
||||
val ct:Dataset[(String,String)] = spark.read.load(s"$workingPath/clinicalTrials").as[(String,String)]
|
||||
|
||||
val relDS= spark.read.load(s"$workingPath/relationDS_f1").as[Relation]
|
||||
|
||||
relDS.joinWith(ct, relDS("target").equalTo(ct("_1")), "inner")
|
||||
.map(k =>{
|
||||
val currentRel = k._1
|
||||
currentRel.setTarget(k._2._2)
|
||||
currentRel
|
||||
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/clinicalTrialsRels")
|
||||
|
||||
|
||||
val clRels:Dataset[Relation] = spark.read.load(s"$workingPath/clinicalTrialsRels").as[Relation]
|
||||
val rels:Dataset[Relation] = spark.read.load(s"$workingPath/relationDS_filtered").as[Relation]
|
||||
|
||||
rels.union(clRels).flatMap(r => {
|
||||
val inverseRel = new Relation
|
||||
inverseRel.setSource(r.getTarget)
|
||||
inverseRel.setTarget(r.getSource)
|
||||
inverseRel.setDataInfo(r.getDataInfo)
|
||||
inverseRel.setCollectedfrom(r.getCollectedfrom)
|
||||
inverseRel.setRelType(r.getRelType)
|
||||
inverseRel.setSubRelType(r.getSubRelType)
|
||||
inverseRel.setRelClass(DLIToOAF.rel_inverse(r.getRelClass))
|
||||
List(r, inverseRel)
|
||||
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/relationAS")
|
||||
|
||||
|
||||
val fRels:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationAS").as[Relation].map(DLIToOAF.toActionSet)
|
||||
val fpubs:Dataset[(String,String)] = spark.read.load(s"$workingPath/publicationAS").as[Publication].map(DLIToOAF.toActionSet)
|
||||
val fdats:Dataset[(String,String)] = spark.read.load(s"$workingPath/datasetAS").as[OafDataset].map(DLIToOAF.toActionSet)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue