Merge pull request #73 from opentargets/update-search-for-slimmed-es

update search for slimmed es

app/components/elasticsearch/ElasticsearchComponent.scala

@@ -14,16 +14,22 @@ import com.sksamuel.elastic4s.http.JavaClient
 import com.sksamuel.elastic4s.requests.searches._
 import com.sksamuel.elastic4s.requests.searches.queries.funcscorer.FieldValueFactorFunctionModifier
 import configuration.ElasticsearchConfiguration
+
 import javax.inject.{Inject, Singleton}
-import models.entities.DNA.{Gene, Variant}
-import models.entities.Entities.{SearchResultSet, Study}
+import models.entities.DNA.Variant
+import models.entities.Entities.SearchResultSet
 import models.entities.Violations.{InputParameterCheckError, SearchStringViolation}
-import models.implicits.{ElasticSearchEntity, EsHitReader}
-import play.api.{Configuration, Logger, Logging}
+import models.implicits.{
+  ElasticSearchEntity,
+  EsHitReader,
+  GeneSearchResult,
+  StudySearchResult,
+  VariantSearchResult
+}
+import play.api.{Configuration, Logger}
 
 import scala.concurrent.ExecutionContext.Implicits.global
 import scala.concurrent.Future
-import scala.util.{Failure, Success}
 
 object GeneticsApiQueries {
 
@@ -142,11 +148,11 @@ class ElasticsearchComponent @Inject() (configuration: Configuration) extends El
           // build output
           SearchResultSet(
             gene.totalHits,
-            gene.hits.asInstanceOf[Seq[Gene]],
+            gene.hits.asInstanceOf[Seq[GeneSearchResult]],
             variant.totalHits,
-            variant.hits.asInstanceOf[Seq[Variant]],
+            variant.hits.asInstanceOf[Seq[VariantSearchResult]],
             study.totalHits,
-            study.hits.asInstanceOf[Seq[Study]]
+            study.hits.asInstanceOf[Seq[StudySearchResult]]
           )
         }
     }

app/models/entities/DNA.scala

@@ -129,8 +129,7 @@ object DNA {
                      gnomadAnnotation: GnomadAnnotation,
                      chromosomeB37: Option[String],
                      positionB37: Option[Long]
-  ) extends ElasticSearchEntity
-      with SkelVariant {
+  ) extends SkelVariant {
 
     lazy val idB37: Option[String] = (chromosomeB37, positionB37) match {
       case (Some(c), Some(p)) =>
@@ -258,7 +257,7 @@ object DNA {
                   end: Option[Long],
                   fwd: Option[Boolean],
                   exons: Seq[Long]
-  ) extends ElasticSearchEntity
+  )
 
   object Gene
       extends ((String,

app/models/entities/Entities.scala

@@ -6,8 +6,8 @@ import models.Functions.{
   defaultIntervalTypes,
   defaultQtlTypes
 }
-import models.entities.DNA.{Gene, SimpleVariant, Variant}
-import models.implicits.ElasticSearchEntity
+import models.entities.DNA.{SimpleVariant, Variant}
+import models.implicits.{GeneSearchResult, StudySearchResult, VariantSearchResult}
 
 import scala.collection.SeqView
 
@@ -220,7 +220,7 @@ object Entities {
       nCases: Option[Long],
       traitCategory: Option[String],
       numAssocLoci: Option[Long]
-  ) extends ElasticSearchEntity
+  )
 
   case class GeneTagVariant(geneId: String, tagVariantId: String, overallScore: Double)
 
@@ -302,16 +302,15 @@ object Entities {
       }
   }
 
-  case class VariantSearchResult(variant: Variant)
-
   case class SearchResultSet(
       totalGenes: Long = 0,
-      genes: Seq[Gene] = Seq(),
+      genes: Seq[GeneSearchResult] = Seq(),
       totalVariants: Long = 0,
-      variants: Seq[Variant] = Seq(),
+      variants: Seq[VariantSearchResult] = Seq(),
       totalStudies: Long = 0,
-      studies: Seq[Study] = Seq()
+      studies: Seq[StudySearchResult] = Seq()
   ) {
+    // fixme: this appears to be unused: remove?
     def combine(that: SearchResultSet): SearchResultSet =
       SearchResultSet(
         totalGenes + that.totalGenes,

app/models/gql/GQLSchema.scala

@@ -276,14 +276,6 @@ object GQLSchema
     )
   )
 
-  val variantSearchResult: ObjectType[Backend, VariantSearchResult] = ObjectType(
-    "VariantSearchResult",
-    "Variant search result object",
-    fields[Backend, VariantSearchResult](
-      Field("variant", variant, Some("A variant"), resolve = _.value.variant)
-    )
-  )
-
   val searchResult: ObjectType[Backend, SearchResultSet] = ObjectType(
     "SearchResult",
     "Search data by a query string",
@@ -303,13 +295,28 @@ object GQLSchema
             Some("Total number of studies found"),
             resolve = _.value.totalStudies
       ),
-      Field("genes", ListType(gene), Some("Gene search result list"), resolve = _.value.genes),
-      Field("variants",
-            ListType(variant),
-            Some("Variant search result list"),
-            resolve = _.value.variants
+      Field(
+        "genes",
+        ListType(gene),
+        Some("Gene search result list"),
+        resolve = searchResultSet => {
+          val geneIds = searchResultSet.value.genes.map(_.id)
+          genesFetcher.deferSeq(geneIds)
+        }
       ),
-      Field("studies", ListType(study), Some("Study search result list"), resolve = _.value.studies)
+      Field(
+        "variants",
+        ListType(variant),
+        Some("Variant search result list"),
+        resolve =
+          searchResultSet => variantsFetcher.deferSeq(searchResultSet.value.variants.map(_.id))
+      ),
+      Field("studies",
+            ListType(study),
+            Some("Study search result list"),
+            resolve =
+              searchResultSet => studiesFetcher.deferSeq(searchResultSet.value.studies.map(_.id))
+      )
     )
   )
 

app/models/implicits/Elastic4sHitReaders.scala

@@ -1,18 +1,25 @@
 package models.implicits
 
 import com.sksamuel.elastic4s.{Hit, HitReader}
-import models.entities.DNA.{Gene, Variant}
-import models.entities.Entities.Study
-import play.api.{Logger, Logging}
-import play.api.libs.json.{JsError, JsResult, JsSuccess, Json, Reads}
+import play.api.Logging
+import play.api.libs.json.{JsError, JsPath, JsSuccess, Json, Reads}
 
-import scala.util
 import scala.util.{Failure, Success, Try}
 
-trait ElasticSearchEntity
+sealed trait ElasticSearchEntity
+case class GeneSearchResult(id: String) extends ElasticSearchEntity
+case class VariantSearchResult(id: String) extends ElasticSearchEntity
+case class StudySearchResult(id: String) extends ElasticSearchEntity
 
 object EsHitReader extends HitReader[ElasticSearchEntity] with Logging {
 
+  implicit val gsrReader: Reads[GeneSearchResult] =
+    (JsPath \ "gene_id").read[String].map(GeneSearchResult)
+  implicit val vsrReader: Reads[VariantSearchResult] =
+    (JsPath \ "variant_id").read[String].map(VariantSearchResult)
+  implicit val ssrReader: Reads[StudySearchResult] =
+    (JsPath \ "study_id").read[String].map(StudySearchResult)
+
   def convertHit[T](hit: Hit)(implicit r: Reads[T]): Try[T] =
     Json.parse(hit.sourceAsString).validate[T] match {
       case JsSuccess(value, _) => Success(value)
@@ -21,13 +28,11 @@ object EsHitReader extends HitReader[ElasticSearchEntity] with Logging {
         Failure(new RuntimeException(errors.mkString(" ")))
     }
 
-  override def read(hit: Hit): Try[ElasticSearchEntity] = {
-    import models.implicits.EsImplicits._
-
+  override def read(hit: Hit): Try[ElasticSearchEntity] =
     hit.index match {
-      case "genes"                            => convertHit[Gene](hit)
-      case "studies"                          => convertHit[Study](hit)
-      case s: String if s.contains("variant") => convertHit[Variant](hit)
+      case "genes"                            => convertHit[GeneSearchResult](hit)
+      case "studies"                          => convertHit[StudySearchResult](hit)
+      case s: String if s.contains("variant") => convertHit[VariantSearchResult](hit)
       case _ =>
         Failure(
           new RuntimeException(
@@ -36,6 +41,4 @@ object EsHitReader extends HitReader[ElasticSearchEntity] with Logging {
         )
     }
 
-  }
-
 }

test/components/BackendSpec.scala

@@ -219,10 +219,10 @@ class BackendSpec
 
   "Search expression yields results" taggedAs IntegrationTestTag in {
     // given
-    val searchExpr = "BRCA1"
+    val searchExpr = "ENSG00000012048"
 
     whenReady(backend.search(searchExpr, None))(r =>
-      all(List(r.genes must have length (1), r.genes.head.symbol.get must be(searchExpr)))
+      all(List(r.genes must have length (1), r.genes.head.id must be(searchExpr)))
     )
   }