refactor(graphql-api): parametrize lof curation dataset in query

Author: rileyhgrant

graphql-api/src/queries/lof-curation-result-queries.ts

@@ -1,12 +1,21 @@
-const GNOMAD_V2_LOF_CURATION_RESULTS_INDEX = 'gnomad_v2_lof_curation_results'
+type GnomadVersion = 'ExAC' | 'v2'
+
+const GNOMAD_LOF_CURATION_RESULTS_INDICES = {
+  ExAC: 'gnomad_v2_lof_curation_results',
+  v2: 'gnomad_v2_lof_curation_results',
+}
 
 // ================================================================================================
 // Variant query
 // ================================================================================================
 
-export const fetchLofCurationResultsByVariant = async (esClient: any, variantId: any) => {
+export const fetchLofCurationResultsByVariant = async (
+  esClient: any,
+  gnomadVersion: GnomadVersion,
+  variantId: any
+) => {
   const response = await esClient.search({
-    index: GNOMAD_V2_LOF_CURATION_RESULTS_INDEX,
+    index: GNOMAD_LOF_CURATION_RESULTS_INDICES[gnomadVersion],
     type: '_doc',
     body: {
       query: {
@@ -29,9 +38,13 @@ export const fetchLofCurationResultsByVariant = async (esClient: any, variantId:
 // Gene query
 // ================================================================================================
 
-export const fetchLofCurationResultsByGene = async (esClient: any, gene: any) => {
+export const fetchLofCurationResultsByGene = async (
+  esClient: any,
+  gnomadVersion: GnomadVersion,
+  gene: any
+) => {
   const response = await esClient.search({
-    index: GNOMAD_V2_LOF_CURATION_RESULTS_INDEX,
+    index: GNOMAD_LOF_CURATION_RESULTS_INDICES[gnomadVersion],
     type: '_doc',
     size: 1000,
     body: {
@@ -54,9 +67,13 @@ export const fetchLofCurationResultsByGene = async (esClient: any, gene: any) =>
 // Region query
 // ================================================================================================
 
-export const fetchLofCurationResultsByRegion = async (esClient: any, region: any) => {
+export const fetchLofCurationResultsByRegion = async (
+  esClient: any,
+  gnomadVersion: GnomadVersion,
+  region: any
+) => {
   const response = await esClient.search({
-    index: GNOMAD_V2_LOF_CURATION_RESULTS_INDEX,
+    index: GNOMAD_LOF_CURATION_RESULTS_INDICES[gnomadVersion],
     type: '_doc',
     size: 1000,
     body: {

graphql-api/src/queries/variant-datasets/exac-variant-queries.ts

@@ -78,7 +78,11 @@ export const fetchVariantById = async (esClient: any, variantIdOrRsid: any) => {
 
   const { variantFlags, exomeFlags } = getFlagsForContext({ type: 'region' }, variant)
 
-  const lofCurationResults = await fetchLofCurationResultsByVariant(esClient, variant.variant_id)
+  const lofCurationResults = await fetchLofCurationResultsByVariant(
+    esClient,
+    'ExAC',
+    variant.variant_id
+  )
 
   return {
     ...variant,
@@ -184,7 +188,7 @@ export const fetchVariantsByGene = async (esClient: any, gene: any) => {
     .map((hit: any) => hit._source.value)
     .map(shapeVariantSummary({ type: 'gene', geneId: gene.gene_id }))
 
-  const lofCurationResults = await fetchLofCurationResultsByGene(esClient, gene)
+  const lofCurationResults = await fetchLofCurationResultsByGene(esClient, 'ExAC', gene)
   const lofCurationResultsByVariant = {}
   lofCurationResults.forEach((result: any) => {
     // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
@@ -246,7 +250,7 @@ export const fetchVariantsByRegion = async (esClient: any, region: any) => {
     .map((hit: any) => hit._source.value)
     .map(shapeVariantSummary({ type: 'region' }))
 
-  const lofCurationResults = await fetchLofCurationResultsByRegion(esClient, region)
+  const lofCurationResults = await fetchLofCurationResultsByRegion(esClient, 'ExAC', region)
 
   const lofCurationResultsByVariant = {}
   lofCurationResults.forEach((result: any) => {

graphql-api/src/queries/variant-datasets/gnomad-v2-variant-queries.ts

@@ -119,7 +119,11 @@ const fetchVariantById = async (esClient: any, variantIdOrRsid: any, subset: any
 
   const { variantFlags, exomeFlags, genomeFlags } = getFlagsForContext({ type: 'region' }, variant)
 
-  const lofCurationResults = await fetchLofCurationResultsByVariant(esClient, variant.variant_id)
+  const lofCurationResults = await fetchLofCurationResultsByVariant(
+    esClient,
+    'v2',
+    variant.variant_id
+  )
 
   return {
     ...variant,
@@ -272,7 +276,7 @@ const fetchVariantsByGene = async (esClient: any, gene: any, subset: any) => {
     )
     .map(shapeVariantSummary(exomeSubset, genomeSubset, { type: 'gene', geneId: gene.gene_id }))
 
-  const lofCurationResults = await fetchLofCurationResultsByGene(esClient, gene)
+  const lofCurationResults = await fetchLofCurationResultsByGene(esClient, 'v2', gene)
   const lofCurationResultsByVariant = {}
   lofCurationResults.forEach((result: any) => {
     // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
@@ -344,7 +348,7 @@ const fetchVariantsByRegion = async (esClient: any, region: any, subset: any) =>
     )
     .map(shapeVariantSummary(exomeSubset, genomeSubset, { type: 'region' }))
 
-  const lofCurationResults = await fetchLofCurationResultsByRegion(esClient, region)
+  const lofCurationResults = await fetchLofCurationResultsByRegion(esClient, 'v2', region)
 
   const lofCurationResultsByVariant = {}
   lofCurationResults.forEach((result: any) => {