fix: request FASTA format explicitly for sequences

Related to: - GenSpectrum/LAPIS#999 - GenSpectrum/LAPIS#971
loculus-project · Oct 25, 2024 · 4beeca2 · 4beeca2
1 parent 4d08864
commit 4beeca2
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Showing 3 changed files with 10 additions and 5 deletions.
diff --git a/website/src/services/lapisApi.ts b/website/src/services/lapisApi.ts
@@ -8,6 +8,7 @@ import {
     lapisBaseRequest,
     mutationsRequest,
     mutationsResponse,
+    sequenceRequest,
 } from '../types/lapis.ts';
 
 function withSample<Path extends `/${string}`>(path: Path) {
@@ -107,7 +108,7 @@ const alignedNucleotideSequencesEndpoint = makeEndpoint({
         {
             name: 'request',
             type: 'Body',
-            schema: lapisBaseRequest,
+            schema: sequenceRequest,
         },
     ],
     response: z.string(),
@@ -122,7 +123,7 @@ const alignedNucleotideSequencesMultiSegmentEndpoint = makeEndpoint({
         {
             name: 'request',
             type: 'Body',
-            schema: lapisBaseRequest,
+            schema: sequenceRequest,
         },
     ],
     response: z.string(),
@@ -137,7 +138,7 @@ const unalignedNucleotideSequencesMultiSegmentEndpoint = makeEndpoint({
         {
             name: 'request',
             type: 'Body',
-            schema: lapisBaseRequest,
+            schema: sequenceRequest,
         },
     ],
     response: z.string(),
@@ -152,7 +153,7 @@ const unalignedNucleotideSequencesEndpoint = makeEndpoint({
         {
             name: 'request',
             type: 'Body',
-            schema: lapisBaseRequest,
+            schema: sequenceRequest,
         },
     ],
     response: z.string(),
@@ -167,7 +168,7 @@ const alignedAminoAcidSequencesEndpoint = makeEndpoint({
         {
             name: 'request',
             type: 'Body',
-            schema: lapisBaseRequest,
+            schema: sequenceRequest,
         },
     ],
     response: z.string(),

diff --git a/website/src/services/lapisClient.ts b/website/src/services/lapisClient.ts
@@ -149,6 +149,7 @@ export class LapisClient extends ZodiosWrapperClient<typeof lapisApi> {
     public getUnalignedSequences(accessionVersion: string) {
         return this.call('unalignedNucleotideSequences', {
             [this.schema.primaryKey]: accessionVersion,
+            dataFormat: 'FASTA',
         });
     }
 
@@ -159,6 +160,7 @@ export class LapisClient extends ZodiosWrapperClient<typeof lapisApi> {
                     'unalignedNucleotideSequencesMultiSegment',
                     {
                         [this.schema.primaryKey]: accessionVersion,
+                        dataFormat: 'FASTA',
                     },
                     { params: { segment } },
                 ),

diff --git a/website/src/types/lapis.ts b/website/src/types/lapis.ts
@@ -24,6 +24,8 @@ export type LapisBaseRequest = z.infer<typeof lapisBaseRequest>;
 
 export const mutationsRequest = lapisBaseRequest.extend({ minProportion: z.number().optional() });
 
+export const sequenceRequest = lapisBaseRequest.extend({ dataFormat: z.enum(['FASTA', 'NDJSON', 'JSON']) });
+
 export const mutationProportionCount = z.object({
     mutation: z.string(),
     proportion: z.number(),