feat(chore): Update to silo 0.3.0, lapis to 0.3.7 and fix e2e tests (#…

…3077) * dummyOrganism: Remove pangoLineage type, remove partitionBy * fix: request FASTA format explicitly for sequences --------- Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>
loculus-project · Oct 26, 2024 · 335f12f · 335f12f
1 parent a1897df
commit 335f12f
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Showing 5 changed files with 27 additions and 18 deletions.
diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1243,9 +1243,9 @@ defaultOrganisms:
           header: "Collection Details"
         - name: pangoLineage
           initiallyVisible: true
-          type: pango_lineage
           autocomplete: true
           required: true
+          type: string
       website:
         tableColumns:
           - country
@@ -1256,7 +1256,6 @@ defaultOrganisms:
         defaultOrderBy: date
       silo:
         dateToSortBy: date
-        partitionBy: pangoLineage
     preprocessing:
       - version: 1
         image: ghcr.io/loculus-project/preprocessing-dummy
@@ -1451,8 +1450,8 @@ insecureCookies: false
 bannerMessage: "This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly."
 additionalHeadHTML: '<script defer data-domain="loculus.org" src="https://plausible.io/js/script.js"></script>'
 images:
-  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.2.23"
-  lapis: "ghcr.io/genspectrum/lapis:0.3.5"
+  lapisSilo: "ghcr.io/genspectrum/lapis-silo:0.3.0"
+  lapis: "ghcr.io/genspectrum/lapis:0.3.7"
 secrets:
   smtp-password:
     type: raw

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
@@ -54,14 +54,15 @@ export class LapisClient extends ZodiosWrapperClient<typeof lapisApi> {
         });
     }
 
-    public getSequenceEntryVersionDetailsTsv(accessionVersion: string): Promise<Result<string, ProblemDetail>> {
-        return this.call('details', {
+    public async getSequenceEntryVersionDetailsTsv(accessionVersion: string): Promise<Result<string, ProblemDetail>> {
+        const result = await this.call('details', {
             [this.schema.primaryKey]: accessionVersion,
             dataFormat: 'TSV',
-            // This type cast isn't pretty, but if the API would be typed correctly, the union type
-            // of the actual details resonse and the potential 'string' would polute the whole API,
-            // so I decided to just do this cast here. We know that the return value is a TSV string.
-        }).then((result) => result.map((data) => data as unknown as string));
+        });
+        // This type cast isn't pretty, but if the API would be typed correctly, the union type
+        // of the actual details resonse and the potential 'string' would pollute the whole API,
+        // so I (@fhennig) decided to just do this cast here. We know that the return value is a TSV string.
+        return result.map((data) => data as unknown as string);
     }
 
     public async getLatestAccessionVersion(accession: string): Promise<Result<AccessionVersion, ProblemDetail>> {
@@ -149,6 +150,7 @@ export class LapisClient extends ZodiosWrapperClient<typeof lapisApi> {
     public getUnalignedSequences(accessionVersion: string) {
         return this.call('unalignedNucleotideSequences', {
             [this.schema.primaryKey]: accessionVersion,
+            dataFormat: 'FASTA',
         });
     }
 
@@ -159,6 +161,7 @@ export class LapisClient extends ZodiosWrapperClient<typeof lapisApi> {
                     'unalignedNucleotideSequencesMultiSegment',
                     {
                         [this.schema.primaryKey]: accessionVersion,
+                        dataFormat: 'FASTA',
                     },
                     { params: { segment } },
                 ),

diff --git a/website/src/services/serviceHooks.ts b/website/src/services/serviceHooks.ts
@@ -6,7 +6,7 @@ import { backendApi } from './backendApi.ts';
 import { lapisApi } from './lapisApi.ts';
 import { seqSetCitationApi } from './seqSetCitationApi.ts';
 import { problemDetail } from '../types/backend.ts';
-import type { LapisBaseRequest } from '../types/lapis.ts';
+import type { SequenceRequest } from '../types/lapis.ts';
 import type { ClientConfig } from '../types/runtimeConfig.ts';
 import { fastaEntries } from '../utils/parseFasta.ts';
 import { isAlignedSequence, isUnalignedSequence, type SequenceType } from '../utils/sequenceTypeHelpers.ts';
@@ -23,7 +23,10 @@ export function lapisClientHooks(lapisUrl: string) {
             useGetSequence(accessionVersion: string, sequenceType: SequenceType, isMultiSegmented: boolean) {
                 const { data, error, isLoading } = getSequenceHook(
                     zodiosHooks,
-                    { accessionVersion },
+                    {
+                        accessionVersion,
+                        dataFormat: 'FASTA',
+                    },
                     sequenceType,
                     isMultiSegmented,
                 );
@@ -63,7 +66,7 @@ export function lapisClientHooks(lapisUrl: string) {
 
 function getSequenceHook(
     hooks: ZodiosHooksInstance<typeof lapisApi>,
-    request: LapisBaseRequest,
+    request: SequenceRequest,
     sequenceType: SequenceType,
     isMultiSegmented: boolean,
 ) {

diff --git a/website/src/types/lapis.ts b/website/src/types/lapis.ts
@@ -24,6 +24,9 @@ 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 type SequenceRequest = z.infer<typeof sequenceRequest>;
+
 export const mutationProportionCount = z.object({
     mutation: z.string(),
     proportion: z.number(),