feat: implement the last needed table to serve locus to gene data

opentargets · Jan 16, 2020 · 4ee36e6 · 4ee36e6
1 parent d68176e
commit 4ee36e6
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Showing 3 changed files with 100 additions and 1 deletion.
diff --git a/app/models/Backend.scala b/app/models/Backend.scala
@@ -496,6 +496,56 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
     }
   }
 
+  def getStudiesAndLeadVariantsForGeneByL2G(geneId: String,
+                                            pageIndex: Option[Int],
+                                            pageSize: Option[Int]): Future[Vector[V2DL2GRowByGene]] = {
+    val limitClause = parsePaginationTokens(pageIndex, pageSize)
+
+    val topLociEnrich =
+      sql"""
+           |SELECT study_id,
+           |       chrom,
+           |       pos,
+           |       ref,
+           |       alt,
+           |       y_proba_logi_distance,
+           |       y_proba_logi_interaction,
+           |       y_proba_logi_interlocus,
+           |       y_proba_logi_molecularQTL,
+           |       y_proba_logi_pathogenicity,
+           |       y_proba_full_model,
+           |       odds_ratio,
+           |       oddsr_ci_lower,
+           |       oddsr_ci_upper,
+           |       direction,
+           |       beta,
+           |       beta_ci_lower,
+           |       beta_ci_upper,
+           |       pval,
+           |       pval_exponent,
+           |       pval_mantissa
+           |FROM ot.l2g_by_gsl l
+           |ANY INNER JOIN (
+           |    SELECT *,
+           |           CAST(lead_chrom, 'String') as stringChrom
+           |    FROM ot.v2d_by_stchr
+           |    ) v on (v.study_id = l.study_id and
+           |            v.stringChrom = l.chrom and
+           |            v.lead_pos = l.pos and
+           |            v.lead_ref = l.ref and
+           |            v.lead_alt = l.alt)
+           |PREWHERE gene_id = $geneId
+           |#$limitClause
+         """.stripMargin.as[V2DL2GRowByGene]
+
+    db.run(topLociEnrich.asTry).map {
+      case Success(v) => v
+      case Failure(ex) =>
+        logger.error(ex.getMessage)
+        Vector.empty
+    }
+  }
+
   def getGenesByRegion(chromosome: String, startPos: Long, endPos: Long): Future[Seq[Gene]] = {
     (parseChromosome(chromosome), parseRegion(startPos, endPos)) match {
       case (Right(chr), Right((start, end))) =>

diff --git a/app/models/Entities.scala b/app/models/Entities.scala
@@ -43,6 +43,11 @@ object Entities {
   case class V2DRow(tag: SimpleVariant, lead: SimpleVariant, study: Study, association: V2DAssociation,
                     odds: V2DOdds, beta: V2DBeta)
 
+  case class V2DL2GRowByGene(studyId: String, variantId: String, odds: V2DOdds, beta: V2DBeta, pval: Double,
+                             pvalExponent: Long, pvalMantissa: Double, yProbaDistance: Double,
+                             yProbaInteraction: Double, yProbaInterlocus: Double, yProbaMolecularQTL: Double,
+                             yProbaPathogenicity: Double, yProbaModel: Double)
+
   case class OverlapRow(stid: String, numOverlapLoci: Int)
 
   case class OverlappedLociStudy(studyId: String, topOverlappedStudies: IndexedSeq[OverlapRow])
@@ -375,6 +380,31 @@ object Entities {
       GetResult(r => SLGRow(r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<))
     }
 
+    implicit val getV2DL2GRowByGene: GetResult[V2DL2GRowByGene] = {
+      GetResult(r => {
+        val studyId: String = r.<<
+        val svID: String = SimpleVariant(r.<<, r.<<, r.<<, r.<<).id
+
+        val yProbaLogiDistance: Double = r.<<
+        val yProbaLogiInteraction: Double = r.<<
+        val yProbaLogiInterlocus: Double = r.<<
+        val yProbaLogiMolecularQTL: Double = r.<<
+        val yProbaLogiPathogenicity: Double = r.<<
+        val yProbaFullModel: Double = r.<<
+
+        val odds = V2DOdds(r.<<?, r.<<?, r.<<?)
+        val beta = V2DBeta(r.<<?, r.<<?, r.<<?, r.<<?)
+        val pval: Double = r.<<
+        val pvalExponent: Long = r.<<
+        val pvalMantissa: Double = r.<<
+
+        V2DL2GRowByGene(studyId, svID, odds, beta, pval, pvalExponent, pvalMantissa,
+          yProbaLogiDistance, yProbaLogiInteraction, yProbaLogiInterlocus, yProbaLogiMolecularQTL,
+          yProbaLogiPathogenicity, yProbaFullModel)
+
+      })
+    }
+
     implicit val getV2DByStudy: GetResult[V2DByStudy] = {
       def toGeneScoreTupleWithDuplicates(geneIds: Seq[String], geneScores: Seq[Double]): Seq[(String, Double)] = {
         val ordScored = geneIds zip geneScores

diff --git a/app/models/GQLSchema.scala b/app/models/GQLSchema.scala
@@ -1133,6 +1133,20 @@ object GQLSchema extends GQLGene with GQLVariant with GQLStudy with GQLIndexVari
     ExcludeFields("studyId", "variantId")
   )
 
+  implicit val V2DOddsImp = deriveObjectType[Backend, V2DOdds]()
+  implicit val V2DBetaImp = deriveObjectType[Backend, V2DBeta]()
+  implicit val V2DL2GRowByGeneImp = deriveObjectType[Backend, V2DL2GRowByGene](
+    AddFields(
+      Field("study", study,
+        description = Some("Study"),
+        resolve = ctx => studiesFetcher.defer(ctx.value.studyId)),
+      Field("variant", variant,
+        description = Some("Variant"),
+        resolve = ctx => variantsFetcher.defer(ctx.value.variantId))
+    ),
+    ExcludeFields("studyId", "variantId")
+  )
+
   val query = ObjectType(
     "Query", fields[Backend, Unit](
       Field("search", searchResult,
@@ -1215,9 +1229,14 @@ object GQLSchema extends GQLGene with GQLVariant with GQLStudy with GQLIndexVari
         arguments = studyId :: variantId :: Nil,
         resolve = ctx =>
           ctx.ctx.qtlColocalisation(ctx.arg(studyId), ctx.arg(variantId))),
+      // getStudiesAndLeadVariantsForGeneByL2G
       Field("studiesAndLeadVariantsForGene", ListType(studiesAndLeadVariantsForGene),
         arguments = geneId :: Nil,
-        resolve = ctx => ctx.ctx.getStudiesAndLeadVariantsForGene(ctx.arg(geneId)))
+        resolve = ctx => ctx.ctx.getStudiesAndLeadVariantsForGene(ctx.arg(geneId))),
+      Field("studiesAndLeadVariantsForGeneByL2G", ListType(V2DL2GRowByGeneImp),
+        arguments = geneId :: pageIndex :: pageSize :: Nil,
+        resolve = ctx => ctx.ctx.getStudiesAndLeadVariantsForGeneByL2G(ctx.arg(geneId),
+          ctx.arg(pageIndex), ctx.arg(pageSize)))
     ))
 
   val schema = Schema(query)