fix: show only a set of genes filtered by a list of biotypes

app/models/Backend.scala

@@ -67,6 +67,8 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
     config.get[Int]("ot.elasticsearch.port"))
   val esQ = HttpClient(esUri)
 
+  val geneExclusionList = config.get[Seq[String]]("ot.genes.exclude")
+
   def buildPheWASTable(variantID: String, pageIndex: Option[Int], pageSize: Option[Int]):
   Future[Entities.PheWASTable] = {
     val limitClause = parsePaginationTokens(pageIndex, pageSize)
@@ -485,8 +487,9 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
         } else {
           val geneIdsInLoci = genes.filter(r =>
             (r.chromosome === chr) &&
-              (r.start >= start && r.start <= end) ||
-              (r.end >= start && r.end <= end))
+              ((r.start >= start && r.start <= end) ||
+              (r.end >= start && r.end <= end)) &&
+              !(r.bioType inSet geneExclusionList))
             .map(_.id)
 
           val assocsQ = d2v2gScored.filter(r => (r.leadChromosome === chr) && (

conf/application.conf

@@ -27,6 +27,57 @@ ot.elasticsearch {
   port = 9200
 }
 
+//"3prime_overlapping_ncrna"
+//"antisense"
+//"IG_C_gene"
+//"IG_C_pseudogene"
+//"IG_D_gene"
+//"IG_J_gene"
+//"IG_J_pseudogene"
+//"IG_V_gene"
+//"IG_V_pseudogene"
+//"lincRNA"
+//"miRNA"
+//"misc_RNA"
+//"Mt_rRNA"
+//"Mt_tRNA"
+//"polymorphic_pseudogene"
+//"processed_transcript"
+//"protein_coding"
+//"pseudogene"
+//"rRNA"
+//"sense_intronic"
+//"sense_overlapping"
+//"snoRNA"
+//"snRNA"
+//"TR_C_gene"
+//"TR_D_gene"
+//"TR_J_gene"
+//"TR_J_pseudogene"
+//"TR_V_gene"
+//"TR_V_pseudogene"
+ot.genes {
+  exclude = [
+    "IG_C_pseudogene",
+    "IG_J_pseudogene",
+    "IG_pseudogene",
+    "IG_V_pseudogene",
+    "polymorphic_pseudogene",
+    "processed_pseudogene",
+    "pseudogene",
+    "rRNA",
+    "rRNA_pseudogene",
+    "snoRNA",
+    "snRNA",
+    "transcribed_processed_pseudogene",
+    "transcribed_unitary_pseudogene",
+    "transcribed_unprocessed_pseudogene",
+    "TR_J_pseudogene",
+    "TR_V_pseudogene",
+    "unitary_pseudogene",
+    "unprocessed_pseudogene"]
+}
+
 play.filters.disabled += play.filters.csrf.CSRFFilter
 play.filters.enabled += play.filters.cors.CORSFilter
 

deploy_gcloud.bash

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-gcloud --project=open-targets-genetics beta app deploy \
+gcloud --project=open-targets-genetics app deploy \
     --no-promote \
     -v $(git describe --abbrev=0 \
     --tags | sed "s:\.:-:g")