From 3c4baf8b05d6dbfabb507d23028f49ce96909878 Mon Sep 17 00:00:00 2001
From: Miguel C <mkarmona@gmail.com>
Date: Mon, 11 Mar 2019 13:31:57 +0000
Subject: [PATCH] fix: search object mapping to case classes are updated with
 the new fields populated

---
 app/models/Entities.scala  | 35 +++++++++++++++++++++++++----------
 app/models/GQLSchema.scala |  3 +++
 2 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/app/models/Entities.scala b/app/models/Entities.scala
index 3301076..70854d6 100644
--- a/app/models/Entities.scala
+++ b/app/models/Entities.scala
@@ -231,10 +231,6 @@ object Entities {
         else {
           val mv = hit.sourceAsMap
 
-          //  case class Gene(id: String, symbol: Option[String], bioType: Option[String] = None, chromosome: Option[String] = None,
-          //                  tss: Option[Long] = None, start: Option[Long] = None, end: Option[Long] = None,
-          //                  fwd: Option[Boolean] = None, exons: Seq[Long] = Seq.empty)
-
           Right(Gene(mv("gene_id").toString,
             mv.get("gene_name").map(_.toString),
             mv.get("biotype").map(_.toString),
@@ -247,7 +243,7 @@ object Entities {
               case 1 => true
               case _ => false
             }),
-            mv.get("exons").map(_.asInstanceOf[Seq[Long]]).getOrElse(Seq.empty)
+            LSeqRep(mv.get("exons").map(_.toString).getOrElse(""))
           ))
         }
       }
@@ -258,11 +254,30 @@ object Entities {
         if (hit.isSourceEmpty) Left(new NoSuchFieldError("source object is empty"))
         else {
           val mv = hit.sourceAsMap
-
-          val variant = Variant(mv("chr_id").toString, mv("position").asInstanceOf[Int],
-            mv("ref_allele").toString, mv("alt_allele").toString, Option(mv("rs_id").toString))
-
-          Right(variant)
+          Right(Variant(mv("chr_id").toString,
+            mv("position").toString.toLong,
+            mv("ref_allele").toString,
+            mv("alt_allele").toString,
+            mv.get("rs_id").map(_.toString),
+            Annotation(mv.get("gene_id").map(_.toString),
+              mv.get("gene_id_distance").map(_.toString.toLong),
+              mv.get("gene_id_prot_coding").map(_.toString),
+              mv.get("gene_id_prot_coding_distance").map(_.toString.toLong),
+              mv.get("most_severe_consequence").map(_.toString)),
+            CaddAnnotation(mv.get("raw").map(_.toString.toDouble),
+              mv.get("phred").map(_.toString.toDouble)),
+            GnomadAnnotation(mv.get("gnomad_afr").map(_.toString.toDouble),
+              mv.get("gnomad_seu").map(_.toString.toDouble),
+              mv.get("gnomad_amr").map(_.toString.toDouble),
+              mv.get("gnomad_asj").map(_.toString.toDouble),
+              mv.get("gnomad_eas").map(_.toString.toDouble),
+              mv.get("gnomad_fin").map(_.toString.toDouble),
+              mv.get("gnomad_nfe").map(_.toString.toDouble),
+              mv.get("gnomad_nfe_est").map(_.toString.toDouble),
+              mv.get("gnomad_nfe_seu").map(_.toString.toDouble),
+              mv.get("gnomad_nfe_onf").map(_.toString.toDouble),
+              mv.get("gnomad_nfe_nwe").map(_.toString.toDouble),
+              mv.get("gnomad_oth").map(_.toString.toDouble))))
         }
       }
     }
diff --git a/app/models/GQLSchema.scala b/app/models/GQLSchema.scala
index 67413ee..0d01069 100644
--- a/app/models/GQLSchema.scala
+++ b/app/models/GQLSchema.scala
@@ -845,6 +845,9 @@ object GQLSchema extends GQLGene with GQLVariant with GQLStudy with GQLIndexVari
         arguments = queryString :: pageIndex :: pageSize :: Nil,
         resolve = ctx =>
           ctx.ctx.getSearchResultSet(ctx.arg(queryString), ctx.arg(pageIndex), ctx.arg(pageSize))),
+      Field("geneInfo", OptionType(gene),
+        arguments = geneId :: Nil,
+        resolve = ctx => genesFetcher.deferOpt(ctx.arg(geneId))),
       Field("studyInfo", OptionType(study),
         arguments = studyId :: Nil,
         resolve = ctx => studiesFetcher.deferOpt(ctx.arg(studyId))),