Merge pull request #71 from opentargets/rm-credset-add-geneid

Add geneid to credset
opentargets · Aug 16, 2022 · 9959bc4 · 9959bc4
2 parents 7ff4ff2 + 9401cec
commit 9959bc4
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Showing 5 changed files with 16 additions and 12 deletions.
diff --git a/app/components/Backend.scala b/app/components/Backend.scala
@@ -206,7 +206,7 @@ class Backend @Inject() (
 
   def qtlCredibleSet(studyId: String,
                      variantId: String,
-                     phenotypeId: String,
+                     geneId: String,
                      bioFeatureId: String
   ): Future[Seq[(SimpleVariant, CredSetRowStats)]] = {
     val variant = Variant.fromString(variantId)
@@ -221,7 +221,7 @@ class Backend @Inject() (
               (r.leadAltAllele === v.altAllele) &&
               (r.studyId === studyId) &&
               (r.dataType =!= GWASLiteral) &&
-              (r.phenotypeId === phenotypeId) &&
+              (r.geneId === geneId) &&
               (r.bioFeature === bioFeatureId)
           )
           .map(_.tagVariantWithStats)
@@ -261,7 +261,7 @@ class Backend @Inject() (
   def qtlRegionalFromSumstats(
       studyId: String,
       bioFeature: String,
-      phenotypeId: String,
+      geneId: String,
       chromosome: String,
       startPos: Long,
       endPos: Long
@@ -274,7 +274,7 @@ class Backend @Inject() (
             (r.pos >= startPos) &&
             (r.pos <= endPos) &&
             (r.bioFeature === bioFeature) &&
-            (r.phenotypeId === phenotypeId) &&
+            (r.geneId === geneId) &&
             (r.studyId === studyId)
         )
         .map(_.variantAndPVal)

diff --git a/app/models/database/FRM.scala b/app/models/database/FRM.scala
@@ -1042,6 +1042,8 @@ object FRM {
 
     def phenotypeId = column[Option[String]]("phenotype_id")
 
+    def geneId = column[Option[String]]("gene_id")
+
     def dataType = column[String]("data_type")
 
     def tagChromosome = column[String]("tag_chrom")
@@ -1094,7 +1096,8 @@ object FRM {
         ) = (tagVariant, stats)
 
     def * =
-      (studyId, leadVariant, tagVariant, stats, bioFeature, phenotypeId, dataType).mapTo[CredSetRow]
+      (studyId, leadVariant, tagVariant, stats, bioFeature, phenotypeId, geneId, dataType)
+        .mapTo[CredSetRow]
   }
 
   class SumStatsGWAS(tag: Tag) extends Table[SumStatsGWASRow](tag, "v2d_sa_gwas") {

diff --git a/app/models/entities/Entities.scala b/app/models/entities/Entities.scala
@@ -636,6 +636,7 @@ object Entities {
       stats: CredSetRowStats,
       bioFeature: Option[String],
       pehotypeId: Option[String],
+      geneId: Option[String],
       dataType: String
   )
 

diff --git a/app/models/gql/GQLSchema.scala b/app/models/gql/GQLSchema.scala
@@ -54,7 +54,7 @@ object GQLSchema
 
   val credSetTagElement: ObjectType[Backend, (SimpleVariant, CredSetRowStats)] = ObjectType(
     "CredSetTagElement",
-    "Thsi element represents the tag variant with its associated statistics",
+    "This element represents the tag variant with its associated statistics",
     fields[Backend, (SimpleVariant, CredSetRowStats)](
       Field("tagVariant",
             variant,
@@ -613,11 +613,11 @@ object GQLSchema
         "qtlRegional",
         ListType(regionalAssociation),
         arguments =
-          studyId :: bioFeature :: phenotypeId :: chromosome :: dnaPosStart :: dnaPosEnd :: Nil,
+          studyId :: bioFeature :: geneId :: chromosome :: dnaPosStart :: dnaPosEnd :: Nil,
         resolve = ctx =>
           ctx.ctx.qtlRegionalFromSumstats(ctx.arg(studyId),
                                           ctx.arg(bioFeature),
-                                          ctx.arg(phenotypeId),
+                                          ctx.arg(geneId),
                                           ctx.arg(chromosome),
                                           ctx.arg(dnaPosStart),
                                           ctx.arg(dnaPosEnd)
@@ -639,11 +639,11 @@ object GQLSchema
       Field(
         "qtlCredibleSet",
         ListType(credSetTagElement),
-        arguments = studyId :: variantId :: phenotypeId :: bioFeature :: Nil,
+        arguments = studyId :: variantId :: geneId :: bioFeature :: Nil,
         resolve = ctx =>
           ctx.ctx.qtlCredibleSet(ctx.arg(studyId),
                                  ctx.arg(variantId),
-                                 ctx.arg(phenotypeId),
+                                 ctx.arg(geneId),
                                  ctx.arg(bioFeature)
           )
       ),

diff --git a/example_queries.txt b/example_queries.txt
@@ -35,7 +35,7 @@ query exmaple {
       se
     }
   }
-  qtlCredibleSet(studyId: "TWINSUK", variantId: "1_1280044_T_C", phenotypeId: "ENSG00000127054", bioFeature: "LCL") {
+  qtlCredibleSet(studyId: "TWINSUK", variantId: "1_1280044_T_C", geneId: "ENSG00000127054", bioFeature: "LCL") {
     tagVariant {
       id
       rsId
@@ -112,7 +112,7 @@ query exmaple {
       nearestGeneDistance
     }
   }
-  qtlRegional(studyId: "TWINSUK", bioFeature: "FAT", phenotypeId: "ENSG00000224969", chromosome: "1", start: 1000000, end: 1500000) {
+  qtlRegional(studyId: "TWINSUK", bioFeature: "FAT", geneId: "ENSG00000224969", chromosome: "1", start: 1000000, end: 1500000) {
     variant {
       id
       rsId