Use url helper to create refget urls in refget api slice (#1116)

Instead of generating the url to refget in useRefgetSequenceQuery, call urlHelper.refget to get the prepared url. This fixes the inconsistency when urlHelper.refget was expecting the start coordinate in the Ensembl coordinate system (1-based), and automatically translated the coordinate into the 0-based coordinate system used by refget; but `useRefgetSequenceQuery` was not doing this correction. As a result, this also fixed an off-by-one error while fetching gene and transcript sequences in genome browser drawer.
Ensembl · Apr 16, 2024 · 70b4ac1 · 70b4ac1
1 parent 77eb3f7
commit 70b4ac1
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Showing 3 changed files with 7 additions and 21 deletions.
diff --git a/src/content/app/entity-viewer/variant-view/transcript-consequences/useTranscriptDetails.ts b/src/content/app/entity-viewer/variant-view/transcript-consequences/useTranscriptDetails.ts
@@ -178,7 +178,7 @@ const useGenomicRegionData = (params: {
   } = useRefgetSequenceQuery(
     {
       checksum: regionChecksum ?? '',
-      start: genomicSliceStart - 1, // translate to 0-based coordinate system that refget uses
+      start: genomicSliceStart,
       end: genomicSliceEnd
     },
     {
@@ -270,7 +270,7 @@ const useProteinData = (params: {
   } = useRefgetSequenceQuery(
     {
       checksum: proteinChecksum ?? '',
-      start: proteinSliceCoordinates.proteinSliceStart - 1, // FIXME: undo the (- 1) after useRefgetSequenceQuery hook is updated to use urlFor.refget
+      start: proteinSliceCoordinates.proteinSliceStart,
       end: proteinSliceCoordinates.proteinSliceEnd
     },
     {

diff --git a/src/content/app/entity-viewer/variant-view/variant-image/useVariantImageData.ts b/src/content/app/entity-viewer/variant-view/variant-image/useVariantImageData.ts
@@ -107,7 +107,7 @@ const useVariantImageData = (params: {
   } = useRefgetSequenceQuery(
     {
       checksum: regionChecksum ?? '',
-      start: sliceStart - 1, // translate to 0-based coordinate system that refget uses
+      start: sliceStart,
       end: sliceEnd
     },
     {

diff --git a/src/shared/state/api-slices/refgetSlice.ts b/src/shared/state/api-slices/refgetSlice.ts
@@ -14,7 +14,7 @@
  * limitations under the License.
  */
 
-import config from 'config';
+import * as urlFor from 'src/shared/helpers/urlHelper';
 
 import restApiSlice from 'src/shared/state/api-slices/restSlice';
 
@@ -24,7 +24,7 @@ import { Strand } from 'src/shared/types/core-api/strand';
 
 export type SequenceQueryParams = {
   checksum: string;
-  start?: number;
+  start?: number; // In Ensembl (1-based) coordinate system!
   end?: number;
   strand?: Strand;
 };
@@ -33,23 +33,9 @@ const refgetApiSlice = restApiSlice.injectEndpoints({
   endpoints: (builder) => ({
     refgetSequence: builder.query<string, SequenceQueryParams>({
       query: (params) => {
-        const { checksum, start, end } = params;
-        const queryParameters = new URLSearchParams();
-        if (start) {
-          queryParameters.set('start', `${start}`);
-        }
-        if (end) {
-          queryParameters.set('end', `${end}`);
-        }
-
-        const queryString = [...queryParameters].length
-          ? `?${queryParameters.toString()}`
-          : '';
-
-        // FIXME:
-        // Use urlFor.refget helper. !!!Remember that urlFor.refget helper accepts start in Ensembl coordinates
+        const refgetUrl = urlFor.refget(params);
         return {
-          url: `${config.refgetBaseUrl}/sequence/${checksum}${queryString}`,
+          url: refgetUrl,
           responseHandler: 'text'
         };
       },