From 080a280bea23f70b70e7e96b0c149b3651035db7 Mon Sep 17 00:00:00 2001
From: Sandro La Bruzzo <sandro.labruzzo@isti.cnr.it>
Date: Mon, 21 Jun 2021 16:23:59 +0200
Subject: [PATCH] added pdb to Oaf Transformation

---
 .../java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala | 58 +++++++++++++++++--
 .../dhp/sx/bio/pubmed/BioScholixTest.scala    | 10 +++-
 2 files changed, 60 insertions(+), 8 deletions(-)

diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala
index e255a2270..a37c6529f 100644
--- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala
+++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/bio/PDBToOAF.scala
@@ -2,17 +2,21 @@ package eu.dnetlib.dhp.sx.bio
 
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
-import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Oaf}
+import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation}
 import org.json4s.DefaultFormats
 import org.json4s.jackson.JsonMethods.parse
+
 import scala.collection.JavaConverters._
 object PDBToOAF {
 
   val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
+
+  val collectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::d1c373ab1570cfb9a7dbb53c186b37a2", "Protein Data Bank")
+
   def convert(input:String):List[Oaf]= {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
     lazy val json = parse(input)
-    val pdb = (json \ "pdb").extract[String]
+    val pdb = (json \ "pdb").extract[String].toLowerCase
 
     if (pdb.isEmpty)
       return List()
@@ -25,12 +29,56 @@ object PDBToOAF {
       ).asJava
     )
 
+    d.setCollectedfrom(List(collectedFrom).asJava)
+    d.setDataInfo(dataInfo)
+    d.setId(OafMapperUtils.createOpenaireId(50,s"pdb_________::$pdb", true))
+    d.setOriginalId(List(pdb).asJava)
+
+    val title = (json \ "title").extractOrElse[String](null)
+
+    if (title== null)
+      return List()
+    d.setTitle(List(OafMapperUtils.structuredProperty(title, ModelConstants.MAIN_TITLE_QUALIFIER, dataInfo)).asJava)
 
 
+    val authors:List[String] = (json \ "authors").extractOrElse[List[String]](null)
 
+    if (authors!= null)
+      {
+        val convertedAuthors = authors.zipWithIndex.map{a =>
+
+          val res = new Author
+          res.setFullname(a._1)
+          res.setRank(a._2+1)
+          res
+        }
+
+        d.setAuthor(convertedAuthors.asJava)
+      }
+
+    val i = new Instance
+
+    i.setPid(d.getPid)
+    i.setUrl(List(s"https://www.rcsb.org/structure/$pdb").asJava)
+    i.setInstancetype(OafMapperUtils.qualifier("0046", "Bioentity", ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
+
+    i.setCollectedfrom(collectedFrom)
+    d.setInstance(List(i).asJava)
+    val pmid = (json \ "pmid").extractOrElse[String](null)
+
+    if (pmid != null) {
+      val rel = new Relation
+      rel.setCollectedfrom(List(collectedFrom).asJava)
+      rel.setDataInfo(dataInfo)
+
+      rel.setRelType("resultResult")
+      rel.setSubRelType("supplement")
+      rel.setRelClass("IsSupplementTo")
+
+      rel.setSource(d.getId)
+      rel.setTarget(s"unresolved::$pmid::pmid")
+      return List(d,rel)
+    }
     List(d)
-
   }
-
-
 }
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 e6699ccb9..f7a5bcd17 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
@@ -1,7 +1,7 @@
 package eu.dnetlib.dhp.sx.bio.pubmed
 
 import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
+import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
 import eu.dnetlib.dhp.sx.bio.PDBToOAF
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.extension.ExtendWith
@@ -55,16 +55,20 @@ class BioScholixTest extends AbstractVocabularyTest{
     assertNotNull(vocabularies)
     assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
 
-//    val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
-//    mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false)
+    val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT)
+    mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false)
     val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/pdb_dump")).mkString
     records.lines.foreach(s => assertTrue(s.nonEmpty))
 
     val result:List[Oaf]=  records.lines.toList.flatMap(o => PDBToOAF.convert(o))
 
+
+
     assertTrue(result.nonEmpty)
     result.foreach(r => assertNotNull(r))
 
+    println(result.count(o => o.isInstanceOf[Relation]))
+    println(mapper.writeValueAsString(result.head))
 
   }