rename variant entity and id

app/models/Backend.scala

@@ -135,10 +135,10 @@ class Backend @Inject() (implicit
     esRetriever.getByIds(targetIndexName, ids, fromJsValue[GeneOntologyTerm])
   }
 
-  def getVariants(ids: Seq[String]): Future[IndexedSeq[VariantIndex]] = {
-    val indexName = getIndexOrDefault("variant_index")
+  def getVariants(ids: Seq[String]): Future[IndexedSeq[Variant]] = {
+    val indexName = getIndexOrDefault("variant")
 
-    esRetriever.getByIds(indexName, ids, fromJsValue[VariantIndex])
+    esRetriever.getByIds(indexName, ids, fromJsValue[Variant])
   }
 
   def getCredibleSets(

app/models/GQLSchema.scala

@@ -140,7 +140,7 @@ object GQLSchema {
       ),
       Field(
         "variant",
-        OptionType(variantIndexImp),
+        OptionType(variantImp),
         description = Some("Return a Variant"),
         arguments = variantId :: Nil,
         resolve = ctx => variantFetcher.deferOpt(ctx.arg(variantId))

app/models/entities/CredibleSet.scala

@@ -3,7 +3,7 @@ package models.entities
 import models.Backend
 import models.entities.GwasIndex.{gwasImp, gwasWithoutCredSetsImp}
 import models.gql.Fetchers.{gwasFetcher, targetsFetcher, variantFetcher}
-import models.gql.Objects.{logger, targetImp, variantIndexImp}
+import models.gql.Objects.{logger, targetImp, variantImp}
 import play.api.Logging
 import play.api.libs.json.{JsValue, Json, OFormat, OWrites}
 import sangria.schema.{
@@ -105,7 +105,7 @@ object CredibleSet extends Logging {
       "variantId",
       Field(
         "variant",
-        OptionType(variantIndexImp),
+        OptionType(variantImp),
         description = None,
         resolve = r => {
           val variantId = (r.value.variantId)
@@ -128,7 +128,7 @@ object CredibleSet extends Logging {
     ),
     Field(
       "variant",
-      OptionType(variantIndexImp),
+      OptionType(variantImp),
       description = None,
       resolve = js => {
         val id = (js.value \ "variantId").asOpt[String]

app/models/entities/VariantIndex.scala → app/models/entities/Variant.scala

@@ -31,25 +31,25 @@ case class DbXref(id: Option[String], source: Option[String])
 
 case class AlleleFrequency(populationName: Option[String], alleleFrequency: Option[Double])
 
-case class VariantIndex(variantId: String,
-                        chromosome: String,
-                        position: Int,
-                        referenceAllele: String,
-                        alternateAllele: String,
-                        inSilicoPredictors: Option[Seq[InSilicoPredictor]],
-                        mostSevereConsequenceId: String,
-                        transcriptConsequences: Option[Seq[TranscriptConsequence]],
-                        rsIds: Option[Seq[String]],
-                        dbXrefs: Option[Seq[DbXref]],
-                        alleleFrequencies: Option[Seq[AlleleFrequency]],
-                        hgvsId: String
+case class Variant(id: String,
+                   chromosome: String,
+                   position: Int,
+                   referenceAllele: String,
+                   alternateAllele: String,
+                   inSilicoPredictors: Option[Seq[InSilicoPredictor]],
+                   mostSevereConsequenceId: String,
+                   transcriptConsequences: Option[Seq[TranscriptConsequence]],
+                   rsIds: Option[Seq[String]],
+                   dbXrefs: Option[Seq[DbXref]],
+                   alleleFrequencies: Option[Seq[AlleleFrequency]],
+                   hgvsId: String
 )
 
-object VariantIndex extends Logging {
+object Variant extends Logging {
   implicit val inSilicoPredictorF: OFormat[InSilicoPredictor] = Json.format[InSilicoPredictor]
   implicit val transcriptConsequenceF: OFormat[TranscriptConsequence] =
     Json.format[TranscriptConsequence]
   implicit val dbXrefF: OFormat[DbXref] = Json.format[DbXref]
   implicit val alleleFrequencyF: OFormat[AlleleFrequency] = Json.format[AlleleFrequency]
-  implicit val variantIndexF: OFormat[VariantIndex] = Json.format[VariantIndex]
+  implicit val variantIndexF: OFormat[Variant] = Json.format[Variant]
 }

app/models/gql/Arguments.scala

@@ -69,7 +69,7 @@ object Arguments {
     Argument("chemblIds", ListInputType(StringType), description = "List of Chembl IDs")
   val goIds: Argument[Seq[String with tag.Tagged[FromInput.CoercedScalaResult]]] =
     Argument("goIds", ListInputType(StringType), description = "List of GO IDs, eg. GO:0005515")
-  val variantId: Argument[String] = Argument("variantId", StringType, description = "Variant ID")
+  val variantId: Argument[String] = Argument("id", StringType, description = "Variant ID")
   val variantIds: Argument[Option[Seq[String]]] =
     Argument("variantIds", OptionInputType(ListInputType(StringType)), description = "Variant IDs")
   val studyId: Argument[String] = Argument("studyId", StringType, description = "Study ID")

app/models/gql/Fetchers.scala

@@ -13,7 +13,7 @@ import models.entities.{
   OtarProjects,
   Reactome,
   Target,
-  VariantIndex
+  Variant
 }
 import models.{Backend, entities}
 import play.api.Logging
@@ -118,10 +118,10 @@ object Fetchers extends Logging {
     }
   )
 
-  implicit val variantFetcherId: HasId[VariantIndex, String] =
-    HasId[VariantIndex, String](_.variantId)
+  implicit val variantFetcherId: HasId[Variant, String] =
+    HasId[Variant, String](_.id)
   val variantFetcherCache = FetcherCache.simple
-  val variantFetcher: Fetcher[Backend, VariantIndex, VariantIndex, String] = Fetcher(
+  val variantFetcher: Fetcher[Backend, Variant, Variant, String] = Fetcher(
     config =
       FetcherConfig.maxBatchSize(entities.Configuration.batchSize).caching(variantFetcherCache),
     fetch = (ctx: Backend, ids: Seq[String]) => {

app/models/gql/Objects.scala

@@ -1176,7 +1176,7 @@ object Objects extends Logging {
     )
 
   lazy val mUnionType: UnionType[Backend] =
-    UnionType("EntityUnionType", types = List(targetImp, drugImp, diseaseImp, variantIndexImp))
+    UnionType("EntityUnionType", types = List(targetImp, drugImp, diseaseImp, variantImp))
 
   implicit val searchResultAggsCategoryImp: ObjectType[Backend, SearchResultAggCategory] =
     deriveObjectType[Backend, models.entities.SearchResultAggCategory]()
@@ -1338,8 +1338,8 @@ object Objects extends Logging {
   implicit val alleleFrequencyImp: ObjectType[Backend, AlleleFrequency] =
     deriveObjectType[Backend, AlleleFrequency]()
   implicit val dbXrefImp: ObjectType[Backend, DbXref] = deriveObjectType[Backend, DbXref]()
-  implicit val variantIndexImp: ObjectType[Backend, VariantIndex] =
-    deriveObjectType[Backend, VariantIndex](
+  implicit val variantImp: ObjectType[Backend, Variant] =
+    deriveObjectType[Backend, Variant](
       ReplaceField(
         "mostSevereConsequenceId",
         Field(
@@ -1360,7 +1360,7 @@ object Objects extends Logging {
           ListType(pharmacogenomicsImp),
           description = Some("Pharmoacogenomics"),
           arguments = pageArg :: Nil,
-          resolve = ctx => ctx.ctx.getPharmacogenomicsByVariant(ctx.value.variantId)
+          resolve = ctx => ctx.ctx.getPharmacogenomicsByVariant(ctx.value.id)
         ),
         Field(
           "evidences",
@@ -1370,7 +1370,7 @@ object Objects extends Logging {
           resolve = ctx => {
             ctx.ctx.getEvidencesByVariantId(
               ctx arg datasourceIdsArg,
-              ctx.value.variantId,
+              ctx.value.id,
               Some(("score", "desc")),
               ctx arg pageSize,
               ctx arg cursor
@@ -1384,7 +1384,7 @@ object Objects extends Logging {
           arguments = pageArg :: studyTypes :: Nil,
           resolve = r => {
             val studyTypesSeq = r.arg(studyTypes).getOrElse(Seq.empty)
-            val variantIdSeq = Seq(r.value.variantId)
+            val variantIdSeq = Seq(r.value.id)
             val credSetQueryArgs =
               CredibleSetQueryArgs(variantIds = variantIdSeq, studyTypes = studyTypesSeq)
             r.ctx.getCredibleSets(credSetQueryArgs, r.arg(pageArg))