Merge pull request #41 from opentargets/mk-fix-studies

fix studies

Dockerfile

@@ -10,6 +10,6 @@ RUN unzip ot-genetics-api-latest.zip
 RUN echo "${CH_URL} ${PLAY_SECRET}"
 
 RUN chmod +x ot-genetics-api-latest/bin/ot-genetics-api
-ENTRYPOINT ot-genetics-api-latest/bin/ot-genetics-api -Dconfig.file=/srv/app/production.conf
+ENTRYPOINT ot-genetics-api-latest/bin/ot-genetics-api -J-Xms2g -J-Xmx4g -J-server -Dconfig.file=/srv/app/production.conf
 #    -Dplay.http.secret.key=${PLAY_SECRET}
 #    -Dslick.dbs.default.db.url=${CH_URL}

README.md

@@ -10,7 +10,28 @@ http.port = 8080
 
 # sbt command playGenerateSecret
 play.http.secret.key = "changeme"
-slick.dbs.default.db.url = "jdbc:clickhouse://clickhouseinternalnodename:8123/ot"
+slick.dbs {
+  default {
+    profile = "clickhouse.ClickHouseProfile$"
+    db {
+      driver = "ru.yandex.clickhouse.ClickHouseDriver"
+      url = "jdbc:clickhouse://clickhouseinternalnodename1:8123/ot"
+    }
+  }
+  sumstats {
+    profile = "clickhouse.ClickHouseProfile$"
+    db {
+      driver = "ru.yandex.clickhouse.ClickHouseDriver"
+      url = "jdbc:clickhouse://clickhouseinternalnodename2:8123/sumstats"
+    }
+  }
+}
+
+ot.elasticsearch {
+  host = "clickhouseinternalnodename3.c.open-targets-genetics.internal"
+  port = 9200
+}
+# slick.dbs.default.db.url = "jdbc:clickhouse://clickhouseinternalnodename:8123/ot"
 ```
 
 # Copyright

app/models/GQLSchema.scala

@@ -401,9 +401,9 @@ object GQLSchema {
   val overlappedVariantsStudies = ObjectType("OverlappedVariantsStudies",
     "This element represent a overlap between two stduies",
     fields[Backend, OverlappedVariantsStudy](
-      Field("study", study,
+      Field("study", OptionType(study),
         Some("A study object"),
-        resolve = rsl => studiesFetcher.defer(rsl.value.studyId)),
+        resolve = rsl => studiesFetcher.deferOpt(rsl.value.studyId)),
       Field("overlaps", ListType(overlap),
         Some("Orig variant id which is been used for computing the " +
           "overlap with the referenced study"),
@@ -413,9 +413,9 @@ object GQLSchema {
   val topOverlappedStudies = ObjectType("TopOverlappedStudies",
     "This element represent a overlap between two stduies",
     fields[Backend, OverlappedLociStudy](
-      Field("study", study,
+      Field("study", OptionType(study),
         Some("A study object"),
-        resolve = rsl => studiesFetcher.defer(rsl.value.studyId)),
+        resolve = rsl => studiesFetcher.deferOpt(rsl.value.studyId)),
       Field("topStudiesByLociOverlap", ListType(overlappedStudy),
         Some("Top N studies ordered by loci overlap"),
         resolve = _.value.topOverlappedStudies)
@@ -430,9 +430,9 @@ object GQLSchema {
 
   val overlappedInfoForStudy = ObjectType("OverlappedInfoForStudy", "",
     fields[Backend, (String, Seq[String])](
-      Field("study", study,
+      Field("study", OptionType(study),
         Some("A study object"),
-        resolve = rsl => studiesFetcher.defer(rsl.value._1)),
+        resolve = rsl => studiesFetcher.deferOpt(rsl.value._1)),
       Field("overlappedVariantsForStudies", ListType(overlappedVariantsStudies),
         Some(""),
         resolve = rsl => rsl.ctx.getOverlapVariantsForStudies(rsl.value._1, rsl.value._2)),
@@ -447,7 +447,7 @@ object GQLSchema {
       Field("associations", ListType(manhattanAssociation),
         Some("A list of associations"),
         resolve = _.value.associations),
-      Field("topOverlappedStudies", topOverlappedStudies,
+      Field("topOverlappedStudies", OptionType(topOverlappedStudies),
         Some("A list of overlapped studies"),
         arguments = pageIndex :: pageSize :: Nil,
         resolve = ctx => ctx.ctx.getTopOverlappedStudies(ctx.value.studyId, ctx.arg(pageIndex), ctx.arg(pageSize)))