relation fetcher for l2g, pagingation max size for variant

opentargets · Oct 25, 2024 · 66e2d64 · 66e2d64
1 parent f7b0ef3
commit 66e2d64
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Showing 6 changed files with 22 additions and 15 deletions.
diff --git a/Makefile b/Makefile
@@ -28,7 +28,7 @@ ch_tunnel: ## Create tunnel connection to Clickhouse eg. make ch_tunnel zone eur
 	@gcloud compute ssh ${instance} --zone="${zone}" --tunnel-through-iap -- -L 8123:localhost:8123
 
 run_with_standalone: ## Runs API with standalone platform
-	@sbt "run 8090" -DELASTICSEARCH_HOST=elasticsearch -DSLICK_CLICKHOUSE_URL=jdbc:clickhouse://clickhouse:8123 -DPLATFORM_API_IGNORE_CACHE=true
+	@sbt "run 8090" -J-Xms2g -J-Xmx7g -DELASTICSEARCH_HOST=elasticsearch -DSLICK_CLICKHOUSE_URL=jdbc:clickhouse://clickhouse:8123 -DPLATFORM_API_IGNORE_CACHE=true
 
 debug_with_standalone: ## Runs API with standalone platform
 	@sbt -jvm-debug 9999 run 8090 -DSLICK_CLICKHOUSE_URL=jdbc:clickhouse://clickhouse:8123 -DPLATFORM_API_IGNORE_CACHE=true

diff --git a/app/models/Backend.scala b/app/models/Backend.scala
@@ -152,13 +152,15 @@ class Backend @Inject() (implicit
 
   def getVariants(ids: Seq[String]): Future[IndexedSeq[VariantIndex]] = {
     val indexName = getIndexOrDefault("variant_index")
-    esRetriever
+    val pag = Pagination(Pagination.indexDefault, Pagination.sizeMax)
+    val r = esRetriever
       .getByIndexedTermsMust(indexName,
                              Map("variantId.keyword" -> ids),
-                             Pagination.mkDefault,
+                             pag,
                              fromJsValue[VariantIndex]
       )
       .map(_._1)
+    r
   }
 
   def getBiosamples(ids: Seq[String]): Future[IndexedSeq[Biosample]] = {

diff --git a/app/models/entities/Configuration.scala b/app/models/entities/Configuration.scala
@@ -5,7 +5,7 @@ import play.api.libs.json.Reads._
 import play.api.libs.functional.syntax._
 
 object Configuration {
-  val batchSize = 100
+  val batchSize = 5000
 
   case class Logging(otHeader: String, ignoredQueries: Seq[String])
 

diff --git a/app/models/entities/CredibleSet.scala b/app/models/entities/CredibleSet.scala
@@ -4,7 +4,7 @@ import models.Backend
 import models.gql.StudyTypeEnum
 import models.gql.Arguments.StudyType
 import models.entities.GwasIndex.{gwasImp, gwasWithoutCredSetsImp}
-import models.gql.Fetchers.{gwasFetcher, l2gFetcher, targetsFetcher, variantFetcher}
+import models.gql.Fetchers.{gwasFetcher, l2gFetcher, l2gByStudyLocusIdRel, targetsFetcher, variantFetcher}
 import models.gql.Objects.{logger, targetImp, variantIndexImp, colocalisationImp, l2gPredictionsImp}
 import play.api.Logging
 import play.api.libs.json.{JsValue, Json, OFormat, OWrites}
@@ -106,7 +106,7 @@ object CredibleSet extends Logging {
         resolve = r => {
           val variantId = r.value.variantId.getOrElse("")
           logger.debug(s"Finding variant index: $variantId")
-          DeferredValue(variantFetcher.deferOpt(variantId))
+          variantFetcher.deferOpt(variantId)
         }
       )
     )
@@ -128,18 +128,18 @@ object CredibleSet extends Logging {
       OptionType(variantIndexImp),
       description = None,
       resolve = js => {
-        val id = (js.value \ "variantId").asOpt[String]
+        val id = (js.value \ "variantId").as[String]
         logger.debug(s"Finding variant for id: $id")
-        DeferredValue(variantFetcher.deferOpt(id))
+        variantFetcher.deferOpt(id)
       }
     ),
     Field(
       "l2Gpredictions",
-      OptionType(l2gPredictionsImp),
+      OptionType(ListType(l2gPredictionsImp)),
       description = None,
       resolve = js => {
         val id = (js.value \ "studyLocusId").as[String]
-        DeferredValue(l2gFetcher.deferOpt(id))
+        l2gFetcher.deferRelSeq(l2gByStudyLocusIdRel, id)
       }
     ),
     Field(
@@ -310,7 +310,7 @@ object CredibleSet extends Logging {
     resolve = js => {
       val studyId = (js.value \ "studyId").asOpt[String]
       logger.debug(s"Finding gwas study: $studyId")
-      DeferredValue(gwasFetcher.deferOpt(studyId))
+      gwasFetcher.deferOpt(studyId)
     }
   )
   val credibleSetImp: ObjectType[Backend, JsValue] = ObjectType(

diff --git a/app/models/entities/GwasIndex.scala b/app/models/entities/GwasIndex.scala
@@ -239,7 +239,7 @@ object GwasIndex extends Logging {
       description = Some("Credible sets"),
       resolve = js => {
         val studyId = (js.value \ "studyId").as[String]
-        DeferredValue(credibleSetFetcher.deferRelSeq(credibleSetByStudyRel, studyId))
+        credibleSetFetcher.deferRelSeq(credibleSetByStudyRel, studyId)
       }
     )
   lazy val gwasImp: ObjectType[Backend, JsValue] = ObjectType(

diff --git a/app/models/gql/Fetchers.scala b/app/models/gql/Fetchers.scala
@@ -171,13 +171,18 @@ object Fetchers extends Logging {
     )
   }
 
-  implicit val l2gFetcherId: HasId[L2GPredictions, String] =
-    HasId[L2GPredictions, String](_.studyLocusId)
+
   val l2gFetcherCache = FetcherCache.simple
-  val l2gFetcher: Fetcher[Backend, L2GPredictions, L2GPredictions, String] = Fetcher(
+  implicit val l2gHasId: HasId[L2GPredictions, String] = HasId[L2GPredictions, String](_.studyLocusId)
+  val l2gByStudyLocusIdRel =
+    Relation[L2GPredictions, String]("byStudyLocus", l2g => Seq(l2g.studyLocusId))
+  val l2gFetcher: Fetcher[Backend, L2GPredictions, L2GPredictions, String] = Fetcher.rel(
     config = FetcherConfig.maxBatchSize(entities.Configuration.batchSize).caching(l2gFetcherCache),
     fetch = (ctx: Backend, ids: Seq[String]) => {
       ctx.getL2GPredictions(ids)
+    },
+    fetchRel = (ctx: Backend, ids: RelationIds[L2GPredictions]) => {
+      ctx.getL2GPredictions(ids(l2gByStudyLocusIdRel))
     }
   )