Merge pull request #49 from opentargets/mk-refactor-clickhouse-queries

refactor clickhouse queries and minor cleanups

.travis.yml

@@ -4,18 +4,6 @@ scala:
   - 2.12.6
 jdk:
   - oraclejdk8
-branches:
-  only:
-  - master
-  - "/\\d+\\.\\d+\\.\\d+/"
-  - "/mk.*/"
-  - "/af.*/"
-  - "/ck.*/"
-  - "/ms.*/"
-  - "/MS.*/"
-  - "/gp.*/"
-  - "/pl.*/"
-  - "/gk.*/"
 services:
 - docker
 env:

app.yaml

@@ -14,12 +14,3 @@ automatic_scaling:
 
 health_check:
   enable_health_check: True
-
-
-# NOTE: Values below are commonly inserted by our CI system..
-# env_variables:
-
-# endpoints_api_service:
-#  name: ${APPENG_VERSION}.${GOOGLE_PROJECT_ID}.appspot.com
-#  config_id: ${GCENDPOINT_VERSION}
-# TODO make sure this config_id updates for every deployment

app/models/Backend.scala

@@ -324,7 +324,7 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
     *
     * NOTE! WARNING! THERE IS A DIFF AT THE MOMENT BETWEEN THE VARIANTS COMING FROM VCF FILE
     * AND THE ONES COMING FROM UKB AND WE NEED TO FILL THAT GAP WHILE THIS ISSUE IS NOT
-    * ADDRESSED. AT THE MOMENT, THE WAY TO DO IS USING THE VARIANT APPLY CONTRUCTOR FROM A
+    * ADDRESSED. AT THE MOMENT, THE WAY TO DO IS USING THE VARIANT APPLY CONSTRUCTOR FROM A
     * STRING TO GET A WHITE-LABEL VARIANT WITH ANY OTHER REFERENCES FROM RSID OR NEAREST GENES
     * (NONCODING AND PROTCODING)
     */
@@ -337,9 +337,9 @@ class Backend @Inject()(@NamedDatabase("default") protected val dbConfigProvider
 
       db.run(q.result.asTry).map {
         case Success(v) =>
-          val missingVIds = (variantIds diff v.map(_.id))
+          val missingVIds = variantIds diff v.map(_.id)
 
-          v ++ (missingVIds.map(DNA.Variant(_)).withFilter(_.isRight).map(_.right.get))
+          v ++ missingVIds.map(DNA.Variant(_)).withFilter(_.isRight).map(_.right.get)
         case Failure(ex) =>
           logger.error("BDIOAction failed with " + ex.getMessage)
           Seq.empty

app/models/DNA.scala

@@ -48,7 +48,7 @@ object DNA {
           /** match a region (chr:start-end) in a list of highly dense regions true if overlaps false otherwise
             *
             * @param region the region to match against dense regions
-            * @return Some matched or not | None if denseregion map is None too
+            * @return matched or not
             */
           override def matchRegion(region: Region): Boolean = {
             denseRegions.get(region.chrId) match {

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: