Use RNU4ATAC transcript patches in API

Author: phildarnowsky-broad

graphql-api/src/queries/gene-queries.ts

@@ -1,7 +1,10 @@
 import elasticsearch from '@elastic/elasticsearch'
 import { withCache } from '../cache'
 
-import { fetchAllSearchResultsFromMultipleIndices } from './helpers/elasticsearch-helpers'
+import {
+  fetchAllSearchResultsFromMultipleIndices,
+  getFromMultipleIndices,
+} from './helpers/elasticsearch-helpers'
 
 import { ReferenceGenome } from '@gnomad/dataset-metadata/metadata'
 import { LimitedElasticClient, GetResponse, SearchResponse, SearchHit } from '../elasticsearch'
@@ -38,17 +41,7 @@ const _fetchGeneById = async (
           throw err
         }) as Promise<GetResponse | null>
   )
-  return Promise.all(requests).then(
-    (responses) => {
-      const responsesWithValue = responses.filter((response) => response !== null)
-      return responsesWithValue.length > 0
-        ? responsesWithValue[responsesWithValue.length - 1]!.body._source.value
-        : null
-    },
-    (err) => {
-      throw err
-    }
-  )
+  return getFromMultipleIndices(requests)
 }
 
 export const fetchGeneById = withCache(

graphql-api/src/queries/helpers/elasticsearch-helpers.ts

@@ -1,5 +1,5 @@
 import elasticsearch from '@elastic/elasticsearch'
-import { LimitedElasticClient, SearchResponse, SearchHit } from '../../elasticsearch'
+import { LimitedElasticClient, SearchResponse, SearchHit, GetResponse } from '../../elasticsearch'
 
 /**
  * Search and then scroll to retrieve all pages of search results.
@@ -69,3 +69,16 @@ export const fetchIndexMetadata = async (esClient: any, index: any) => {
   // eslint-disable-next-line no-underscore-dangle
   return Object.values(response.body)[0].mappings._meta
 }
+
+export const getFromMultipleIndices = (requests: Promise<GetResponse | null>[]) =>
+  Promise.all(requests).then(
+    (responses) => {
+      const responsesWithValue = responses.filter((response) => response !== null)
+      return responsesWithValue.length > 0
+        ? responsesWithValue[responsesWithValue.length - 1]!.body._source.value
+        : null
+    },
+    (err) => {
+      throw err
+    }
+  )

graphql-api/src/queries/transcript-queries.ts

@@ -1,24 +1,39 @@
-const TRANSCRIPT_INDICES = {
-  GRCh37: 'transcripts_grch37',
-  GRCh38: 'transcripts_grch38',
+import { ReferenceGenome } from '@gnomad/dataset-metadata/metadata'
+import { GetResponse, LimitedElasticClient } from '../elasticsearch'
+import { getFromMultipleIndices } from './helpers/elasticsearch-helpers'
+
+type TranscriptIndex =
+  | 'transcripts_grch37'
+  | 'transcripts_grch38'
+  | 'transcripts_grch38_patched-2025-10-17--18-18'
+
+const TRANSCRIPT_INDICES: Record<ReferenceGenome, TranscriptIndex[]> = {
+  GRCh37: ['transcripts_grch37'],
+  GRCh38: ['transcripts_grch38', 'transcripts_grch38_patched-2025-10-17--18-18'],
 }
 
-export const fetchTranscriptById = async (es: any, transcriptId: any, referenceGenome: any) => {
-  try {
-    const response = await es.get({
-      // @ts-expect-error TS(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
-      index: TRANSCRIPT_INDICES[referenceGenome],
-      type: '_doc',
-      id: transcriptId,
-    })
+export const fetchTranscriptById = async (
+  esClient: LimitedElasticClient,
+  transcriptId: string,
+  referenceGenome: ReferenceGenome
+) => {
+  const indices = TRANSCRIPT_INDICES[referenceGenome]
+  const requests = indices.map(
+    (index) =>
+      esClient
+        .get({
+          index,
+          type: '_doc',
+          id: transcriptId,
+        })
+        .catch((err) => {
+          // meta will not be present if the request times out in the queue before reaching ES
+          if (err.meta && err.meta.body.found === false) {
+            return null
+          }
+          throw err
+        }) as Promise<GetResponse | null>
+  )
 
-    return response.body._source.value
-  } catch (err) {
-    // meta will not be present if the request times out in the queue before reaching ES
-    // @ts-expect-error TS(2571) FIXME: Object is of type 'unknown'.
-    if (err.meta && err.meta.body.found === false) {
-      return null
-    }
-    throw err
-  }
+  return getFromMultipleIndices(requests)
 }