wip: include new table to show the locus to gene setting a study and …

…a locus

app/models/Backend.scala

@@ -579,7 +579,7 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
     val topLociEnrich =
       sql"""
             |SELECT *
-            |FROM ot.manhattan
+            |FROM ot.manhattan_with_l2g
             |WHERE study = $studyId
             |#$limitClause
          """.stripMargin.as[V2DByStudy]
@@ -592,7 +592,7 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
           ManhattanAssociation(el.variantId, el.pval,
             el.pval_mantissa, el.pval_exponent,
             el.v2dOdds, el.v2dBeta,
-            el.topGenes, el.topColocGenes,
+            el.topGenes, el.topColocGenes, el.topL2Genes,
             el.credibleSetSize, el.ldSetSize, el.totalSetSize)
         })
       )
@@ -602,6 +602,103 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
     }
   }
 
+  def buildSLGTable(studyId: String, variantId: String, pageIndex: Option[Int], pageSize: Option[Int]):
+  Future[Entities.SLGTable] = {
+    val limitClause = parsePaginationTokens(pageIndex, pageSize)
+    val variant = Variant.fromString(variantId)
+
+    variant match {
+      case Right(v) =>
+        val slgQ =
+          sql"""
+               |SELECT
+               |    gene_id,
+               |    y_proba_logi_distance,
+               |    y_proba_logi_interaction,
+               |    y_proba_logi_interlocus,
+               |    y_proba_logi_molecularQTL,
+               |    y_proba_logi_pathogenicity,
+               |    y_proba_full_model,
+               |    has_coloc,
+               |    d AS distance_to_locus
+               |FROM
+               |(
+               |    SELECT
+               |        study_id,
+               |        chrom,
+               |        CAST(chrom, 'Enum8(\'1\' = 1, \'2\' = 2, \'3\' = 3, \'4\' = 4, \'5\' = 5, \'6\' = 6, \'7\' = 7, \'8\' = 8, \'9\' = 9, \'10\' = 10, \'11\' = 11, \'12\'
+               |= 12, \'13\' = 13, \'14\' = 14, \'15\' = 15, \'16\' = 16, \'17\' = 17, \'18\' = 18, \'19\' = 19, \'20\' = 20, \'21\' = 21, \'22\' = 22, \'X\' = 23, \'Y\' = 24,
+               | \'MT\' = 25)') AS enumChrom,
+               |        pos,
+               |        ref,
+               |        alt,
+               |        gene_id,
+               |        y_proba_logi_distance,
+               |        y_proba_logi_interaction,
+               |        y_proba_logi_interlocus,
+               |        y_proba_logi_molecularQTL,
+               |        y_proba_logi_pathogenicity,
+               |        y_proba_full_model,
+               |        C.has_coloc AS has_coloc
+               |    FROM ot.l2g_by_slg AS L
+               |    ANY LEFT JOIN
+               |    (
+               |        SELECT
+               |            left_study AS study_id,
+               |            right_gene_id AS gene_id,
+               |            left_chrom as enumChrom,
+               |            left_pos as pos,
+               |            left_ref as ref,
+               |            left_alt as alt,
+               |            count() > 0 AS has_coloc
+               |        FROM ot.v2d_coloc
+               |        PREWHERE coloc_h4 > 0.8
+               |        GROUP BY
+               |            left_study,
+               |            left_chrom,
+               |            left_pos,
+               |            left_ref,
+               |            left_alt,
+               |            right_gene_id
+               |    ) AS C USING (study_id, enumChrom, pos, ref, alt, gene_id)
+               |    PREWHERE (study_id = $studyId) AND
+               |      (chrom = ${v.chromosome}) AND
+               |      (pos = ${v.position}) AND
+               |      (ref = ${v.refAllele}) AND
+               |      (alt = ${v.altAllele})
+               |) AS LL
+               |ANY LEFT JOIN
+               |(
+               |    SELECT
+               |        chr_id AS chrom,
+               |        position AS pos,
+               |        ref_allele AS ref,
+               |        alt_allele AS alt,
+               |        gene_id,
+               |        d
+               |    FROM ot.v2g
+               |    PREWHERE (type_id = 'distance') AND
+               |    (source_id = 'canonical_tss') AND
+               |    (chrom = ${v.chromosome}) AND
+               |      (pos = ${v.position}) AND
+               |      (ref = ${v.refAllele}) AND
+               |      (alt = ${v.altAllele})
+               |) AS G ON (LL.enumChrom = G.chrom) AND (LL.pos = G.pos) AND (LL.ref = G.ref) AND (LL.alt = G.alt) AND (LL.gene_id = G.gene_id)
+               |#$limitClause
+         """.stripMargin.as[SLGRow]
+
+        // WHERE (study_id = $studyId) AND (chrom = '20') AND (pos = 35437976) AND (ref = 'A') AND (alt = 'G')
+        db.run(slgQ.asTry).map {
+          case Success(v) => SLGTable(studyId, variant.right.get.id, v)
+          case Failure(ex) =>
+            logger.error(ex.getMessage)
+            SLGTable(studyId, variant.right.get.id, Vector.empty)
+        }
+      case Left(violation) =>
+        Future.failed(InputParameterCheckError(Vector(violation)))
+    }
+  }
+
   def buildIndexVariantAssocTable(variantID: String, pageIndex: Option[Int], pageSize: Option[Int]):
   Future[VariantToDiseaseTable] = {
     val limitPair = parsePaginationTokensForSlick(pageIndex, pageSize)

app/models/Entities.scala

@@ -70,17 +70,29 @@ object Entities {
                                   v2dOdds: V2DOdds, v2dBeta: V2DBeta,
                                   bestGenes: Seq[(String, Double)],
                                   bestColocGenes: Seq[(String, Double)],
+                                  bestL2Genes: Seq[(String, Double)],
                                   crediblbeSetSize: Option[Long],
                                   ldSetSize: Option[Long], totalSetSize: Long)
 
   case class V2DStructure(typeId: String,
                            sourceId: String,
                           bioFeatureSet: Seq[String])
 
+  case class SLGRow(geneId: String,
+                    yProbaDistance: Double,
+                    yProbaInteraction: Double,
+                    yProbaInterlocus: Double,
+                    yProbaMolecularQTL: Double,
+                    yProbaPathogenicity: Double,
+                    yProbaModel: Double,
+                    hasColoc: Boolean,
+                    distanceToLocus: Long)
+  case class SLGTable(studyId: String, variantId: String, rows: Seq[SLGRow])
   case class V2DByStudy(studyId: String, variantId: String, pval: Double,
                         pval_mantissa: Double, pval_exponent: Long, v2dOdds: V2DOdds, v2dBeta: V2DBeta,
                         credibleSetSize: Option[Long], ldSetSize: Option[Long], totalSetSize: Long,
-                        topGenes: Seq[(String, Double)], topColocGenes: Seq[(String, Double)])
+                        topGenes: Seq[(String, Double)], topColocGenes: Seq[(String, Double)],
+                        topL2Genes: Seq[(String, Double)])
 
   case class StudyInfo(study: Option[Study])
 
@@ -359,8 +371,12 @@ object Entities {
   }
 
   object DBImplicits {
+    implicit val getSLGRow: GetResult[SLGRow] = {
+      GetResult(r => SLGRow(r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<, r.<<))
+    }
+
     implicit val getV2DByStudy: GetResult[V2DByStudy] = {
-      def toGeneScoreTuple(geneIds: Seq[String], geneScores: Seq[Double]): Seq[(String, Double)] = {
+      def toGeneScoreTupleWithDuplicates(geneIds: Seq[String], geneScores: Seq[Double]): Seq[(String, Double)] = {
         val ordScored = geneIds zip geneScores
 
         if (ordScored.isEmpty)
@@ -369,7 +385,7 @@ object Entities {
           ordScored.takeWhile(_._2 == ordScored.head._2)
       }
 
-      def toGeneScoreTupleColoc(geneIds: Seq[String], geneScores: Seq[Double]): Seq[(String, Double)] = {
+      def toGeneScoreTuple(geneIds: Seq[String], geneScores: Seq[Double]): Seq[(String, Double)] = {
         val ordScored = geneIds zip geneScores
 
         if (ordScored.isEmpty)
@@ -393,11 +409,14 @@ object Entities {
         val aggTop10RawScores = DSeqRep(r.<<)
         val aggTop10ColocIds = StrSeqRep(r.<<)
         val aggTop10ColocScores = DSeqRep(r.<<)
+        val aggTop10L2GIds = StrSeqRep(r.<<)
+        val aggTop10L2GScores = DSeqRep(r.<<)
 
         V2DByStudy(studyId, svID, pval, pvalMantissa, pvalExponent, odds, beta,
           credSetSize, ldSetSize, totalSize,
-          toGeneScoreTuple(aggTop10RawIds, aggTop10RawScores),
-          toGeneScoreTupleColoc(aggTop10ColocIds, aggTop10ColocScores))
+          toGeneScoreTupleWithDuplicates(aggTop10RawIds, aggTop10RawScores),
+          toGeneScoreTuple(aggTop10ColocIds, aggTop10ColocScores),
+          toGeneScoreTuple(aggTop10L2GIds, aggTop10L2GScores))
       })
     }
   }

app/models/GQLSchema.scala

@@ -2,6 +2,10 @@ package models
 
 import sangria.execution.deferred._
 import sangria.schema._
+import sangria.macros._
+import sangria.macros.derive._
+import sangria.ast
+import sangria.execution._
 import Entities._
 import Functions._
 import models.DNA.{Gene, SimpleVariant, Variant}
@@ -461,6 +465,9 @@ trait GQLManhattanAssociation {
       Field("bestColocGenes", ListType(scoredGene),
         Some("A list of best genes associated"),
         resolve = _.value.bestColocGenes),
+      Field("bestLocus2Genes", ListType(scoredGene),
+        Some("A list of best L2G scored genes associated"),
+        resolve = _.value.bestL2Genes),
       Field("credibleSetSize", OptionType(LongType),
         Some("The cardinal of the set defined as tag variants for an index variant coming from crediblesets"),
         resolve = _.value.crediblbeSetSize),
@@ -1105,6 +1112,27 @@ object GQLSchema extends GQLGene with GQLVariant with GQLStudy with GQLIndexVari
         resolve = _.value.hs.log2h4h3)
     ))
 
+  implicit val slgRowImp = deriveObjectType[Backend, SLGRow](
+    AddFields(
+      Field("gene", gene,
+        description = Some("Gene"),
+        resolve = ctx => genesFetcher.defer(ctx.value.geneId))
+    ),
+    ExcludeFields("geneId")
+  )
+
+  implicit val slgTableImp = deriveObjectType[Backend, SLGTable](
+    AddFields(
+      Field("study", OptionType(study),
+        description = Some("Study"),
+        resolve = ctx => studiesFetcher.deferOpt(ctx.value.studyId)),
+      Field("variant", OptionType(variant),
+        description = Some("Variant"),
+        resolve = ctx => variantsFetcher.deferOpt(ctx.value.variantId))
+    ),
+    ExcludeFields("studyId", "variantId")
+  )
+
   val query = ObjectType(
     "Query", fields[Backend, Unit](
       Field("search", searchResult,
@@ -1126,6 +1154,9 @@ object GQLSchema extends GQLGene with GQLVariant with GQLStudy with GQLIndexVari
       Field("studiesForGene", ListType(studyForGene),
         arguments = geneId :: Nil,
         resolve = ctx => ctx.ctx.getStudiesForGene(ctx.arg(geneId))),
+      Field("studyLocus2GeneTable", slgTableImp,
+        arguments = studyId :: variantId :: pageIndex :: pageSize :: Nil,
+        resolve = ctx => ctx.ctx.buildSLGTable(ctx.arg(studyId), ctx.arg(variantId), ctx.arg(pageIndex), ctx.arg(pageSize))),
       Field("manhattan", manhattan,
         arguments = studyId :: pageIndex :: pageSize :: Nil,
         resolve = ctx => ctx.ctx.buildManhattanTable(ctx.arg(studyId), ctx.arg(pageIndex), ctx.arg(pageSize))),
@@ -1184,7 +1215,6 @@ 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))),
-
       Field("studiesAndLeadVariantsForGene", ListType(studiesAndLeadVariantsForGene),
         arguments = geneId :: Nil,
         resolve = ctx => ctx.ctx.getStudiesAndLeadVariantsForGene(ctx.arg(geneId)))

build.sbt

@@ -7,7 +7,7 @@ version := "latest"
 
 lazy val root = (project in file(".")).enablePlugins(PlayScala)
 
-scalaVersion := "2.12.8"
+scalaVersion := "2.12.10"
 maintainer := "[email protected]"
 
 javacOptions ++= Seq( "-encoding", "UTF-8" )
@@ -18,7 +18,34 @@ scalacOptions in ThisBuild ++= Seq(
 "-Xfatal-warnings"
 )
 
+/*
+// include resources into the unversal zipped package
+mappings in Universal ++= directory(baseDirectory.value / "resources")
+
+resolvers += Resolver.sonatypeRepo("releases")
+
+libraryDependencies += guice
+libraryDependencies += "com.github.pathikrit" %% "better-files" % "3.8.0"
+libraryDependencies += "com.typesafe.slick" %% "slick" % "3.3.2"
+libraryDependencies += "org.scalatestplus.play" %% "scalatestplus-play" % "4.0.3" % Test
+val playVersion = "2.7.3"
+libraryDependencies += "com.typesafe.play" %% "play" % playVersion
+libraryDependencies += "com.typesafe.play" %% "filters-helpers" % playVersion
+libraryDependencies += "com.typesafe.play" %% "play-logback" % playVersion
+libraryDependencies += "com.typesafe.play" %% "play-json" % playVersion
+libraryDependencies += "com.typesafe.play" %% "play-slick" % "4.0.2"
+libraryDependencies += "ru.yandex.clickhouse" % "clickhouse-jdbc" % "0.2"
+libraryDependencies += "org.sangria-graphql" %% "sangria" % "2.0.0-M1"
+libraryDependencies += "org.sangria-graphql" %% "sangria-play-json" % "2.0.0"
+
+val s4sVersion = "7.3.1"
+libraryDependencies ++= Seq(
+  "com.sksamuel.elastic4s" %% "elastic4s-core" % s4sVersion,
+  "com.sksamuel.elastic4s" %% "elastic4s-client-esjava" % s4sVersion,
+  "com.sksamuel.elastic4s" %% "elastic4s-json-play" % s4sVersion
+)
 
+ */
 // include resources into the unversal zipped package
 mappings in Universal ++= directory(baseDirectory.value / "resources")
 
@@ -34,7 +61,7 @@ libraryDependencies += "com.typesafe.play" %% "play" % "2.6.23"
 libraryDependencies += "com.typesafe.play" %% "play-logback" % "2.6.23"
 libraryDependencies += "com.typesafe.play" %% "play-json" % "2.6.13"
 libraryDependencies += "com.typesafe.play" %% "play-slick" % "3.0.3"
-libraryDependencies += "ru.yandex.clickhouse" % "clickhouse-jdbc" % "0.1.54"
+libraryDependencies += "ru.yandex.clickhouse" % "clickhouse-jdbc" % "0.2.3"
 libraryDependencies += "org.sangria-graphql" %% "sangria" % "1.4.2"
 libraryDependencies += "org.sangria-graphql" %% "sangria-play-json" % "1.0.5"
 libraryDependencies += "com.nrinaudo" %% "kantan.csv" % "0.4.0"

production.conf

@@ -2,7 +2,7 @@ include "application.conf"
 # https://www.playframework.com/documentation/latest/Configuration
 http.port = 8080
 http.port = ${?PLAY_PORT}
-play.http.secret.key = "changeme"
+play.http.secret.key = "@t/PB4rK]zIFsMcFLMMSimE`1bG0Gf^:B`u^=3zh7cBjDoX>[PcNG/y4sSwn]hUZ"
 play.http.secret.key = ${?PLAY_SECRET}
 
 # Root logger:

project/build.properties

@@ -1 +1 @@
-sbt.version=1.2.8
+sbt.version=1.3.6

project/plugins.sbt

@@ -1,2 +1,2 @@
 addSbtPlugin("com.typesafe.play" % "sbt-plugin" % "2.6.23")
-addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.5.1")
+addSbtPlugin("org.scoverage" % "sbt-scoverage" % "1.6.0")