feat(graphql-api): v4 variants include LoF curation results

Author: rileyhgrant

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

@@ -1,8 +1,9 @@
-type GnomadVersion = 'ExAC' | 'v2'
+type GnomadVersion = 'ExAC' | 'v2' | 'v4'
 
 const GNOMAD_LOF_CURATION_RESULTS_INDICES = {
   ExAC: 'gnomad_v2_lof_curation_results',
   v2: 'gnomad_v2_lof_curation_results',
+  v4: 'gnomad_v4_lof_curation_results',
 }
 
 // ================================================================================================

graphql-api/src/queries/variant-datasets/gnomad-v4-variant-queries.ts

@@ -7,6 +7,11 @@ import { UserVisibleError } from '../../errors'
 import { fetchLocalAncestryPopulationsByVariant } from '../local-ancestry-queries'
 import { fetchAllSearchResults } from '../helpers/elasticsearch-helpers'
 import { mergeOverlappingRegions } from '../helpers/region-helpers'
+import {
+  fetchLofCurationResultsByVariant,
+  fetchLofCurationResultsByGene,
+  fetchLofCurationResultsByRegion,
+} from '../lof-curation-result-queries'
 
 import { getFlagsForContext } from './shared/flags'
 import { getConsequenceForContext } from './shared/transcriptConsequence'
@@ -113,6 +118,12 @@ const fetchVariantById = async (esClient: any, variantId: any, subset: Subset) =
 
   const { variantFlags, exomeFlags, genomeFlags } = getFlagsForContext({ type: 'region' }, variant)
 
+  const lofCurationResults = await fetchLofCurationResultsByVariant(
+    esClient,
+    'v4',
+    variant.variant_id
+  )
+
   let genome_ancestry_groups = subsetGenomeFreq.ancestry_groups || []
   // Include HGDP and 1KG populations with gnomAD subsets
   if (variant.genome.freq.hgdp.ac_raw > 0) {
@@ -232,6 +243,7 @@ const fetchVariantById = async (esClient: any, variantId: any, subset: Subset) =
       : null,
     flags: variantFlags,
     // TODO: Include RefSeq transcripts once the browser supports them.
+    lof_curations: lofCurationResults,
     transcript_consequences: (variant.transcript_consequences || []).filter((csq: any) =>
       csq.gene_id.startsWith('ENSG')
     ),
@@ -466,6 +478,20 @@ const fetchVariantsByGene = async (esClient: any, gene: any, subset: Subset) =>
       )
       .map(shapeVariantSummary(subset, { type: 'gene', geneId: gene.gene_id }))
 
+    const lofCurationResults = await fetchLofCurationResultsByGene(esClient, 'v4', 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
+      lofCurationResultsByVariant[result.variant_id] = result.lof_curations.find(
+        (c: any) => c.gene_id === gene.gene_id
+      )
+    })
+
+    shapedHits.forEach((variant: any) => {
+      // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+      variant.lof_curation = lofCurationResultsByVariant[variant.variant_id] // eslint-disable-line no-param-reassign
+    })
+
     return shapedHits
   } catch (error) {
     throw new Error(`'Error fetching variants by gene:', ${error}`)
@@ -506,14 +532,41 @@ const fetchVariantsByRegion = async (esClient: any, region: any, subset: Subset)
     },
   })
 
-  return hits
+  const variants = hits
     .map((hit: any) => hit._source.value)
     .filter(
       (variant: any) =>
         (variant.genome.freq.all && variant.genome.freq.all.ac_raw > 0) ||
         variant.exome.freq[subset].ac_raw > 0
     )
     .map(shapeVariantSummary(subset, { type: 'region' }))
+
+  const lofCurationResults = await fetchLofCurationResultsByRegion(esClient, 'v2', region)
+
+  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
+    lofCurationResultsByVariant[result.variant_id] = result.lof_curations.reduce(
+      // @ts-expect-error TS(7006) FIXME: Parameter 'acc' implicitly has an 'any' type.
+      (acc, c) => ({
+        ...acc,
+        [c.gene_id]: c,
+      }),
+      {}
+    )
+  })
+
+  variants.forEach((variant: any) => {
+    if (variant.transcript_consequence) {
+      // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
+      // eslint-disable-next-line no-param-reassign
+      variant.lof_curation = (lofCurationResultsByVariant[variant.variant_id] || {})[
+        variant.transcript_consequence.gene_id
+      ]
+    }
+  })
+
+  return variants
 }
 
 // ================================================================================================