85 lines
2.6 KiB
Scala
85 lines
2.6 KiB
Scala
package eu.dnetlib.dhp.sx.bio
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
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import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation}
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import org.json4s.DefaultFormats
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import org.json4s.jackson.JsonMethods.parse
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import scala.collection.JavaConverters._
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object PDBToOAF {
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val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
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val collectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::d1c373ab1570cfb9a7dbb53c186b37a2", "Protein Data Bank")
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def convert(input:String):List[Oaf]= {
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implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
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lazy val json = parse(input)
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val pdb = (json \ "pdb").extract[String].toLowerCase
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if (pdb.isEmpty)
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return List()
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val d = new Dataset
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d.setPid(
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List(
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OafMapperUtils.structuredProperty(pdb, "pdb", "pdb", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES,dataInfo)
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).asJava
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)
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d.setCollectedfrom(List(collectedFrom).asJava)
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d.setDataInfo(dataInfo)
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d.setId(OafMapperUtils.createOpenaireId(50,s"pdb_________::$pdb", true))
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d.setOriginalId(List(pdb).asJava)
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val title = (json \ "title").extractOrElse[String](null)
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if (title== null)
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return List()
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d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava)
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val authors:List[String] = (json \ "authors").extractOrElse[List[String]](null)
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if (authors!= null)
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{
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val convertedAuthors = authors.zipWithIndex.map{a =>
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val res = new Author
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res.setFullname(a._1)
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res.setRank(a._2+1)
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res
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}
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d.setAuthor(convertedAuthors.asJava)
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}
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val i = new Instance
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i.setPid(d.getPid)
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i.setUrl(List(s"https://www.rcsb.org/structure/$pdb").asJava)
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i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
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i.setCollectedfrom(collectedFrom)
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d.setInstance(List(i).asJava)
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val pmid = (json \ "pmid").extractOrElse[String](null)
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if (pmid != null) {
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val rel = new Relation
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rel.setCollectedfrom(List(collectedFrom).asJava)
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rel.setDataInfo(dataInfo)
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rel.setRelType("resultResult")
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rel.setSubRelType("supplement")
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rel.setRelClass("IsSupplementTo")
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rel.setSource(d.getId)
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rel.setTarget(s"unresolved::$pmid::pmid")
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return List(d,rel)
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}
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List(d)
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}
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}
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