feat(website): resistance mutation sets as collections by fhennig · Pull Request #1181 · GenSpectrum/dashboards

fhennig · 2026-04-28T15:07:57Z

Summary

Resistance mutation sets are now sourced from backend collections (IDs 1/2/3) rather than hard-coded arrays in TypeScript
Collections are fetched server-side in Wasap.astro (SSR) and passed as a prop to WasapPage, so no client-side fetch or loading state is needed for resistance data
The config is resolved server-side in Wasap.astro, picking prod vs staging collection IDs — staging overrides live in wastewaterOrganismStagingConfigs
resistanceData.ts contains the plain async fetch logic; useResistanceMutationSets hook deleted
Prod collections visible at: https://genspectrum.org/api/collections - I already created them so we don't break prod!

Screenshot

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PR Checklist

~~All necessary documentation has been adapted.~~
~~The implemented feature is covered by an appropriate test.~~

Creates three COVID collections (3CLpro, RdRp, Spike mAb) from the resistance mutation sets defined in resistanceMutations.ts, each with one filterObject variant per individual mutation. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

vercel · 2026-04-28T15:08:02Z

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Project	Deployment	Actions	Updated (UTC)
dashboards	Ready	Preview, Comment	Apr 30, 2026 11:29am

…cript When SESSION_TOKEN is set, the script hits the website proxy at /api/collections (which injects the user ID from the session) and passes the auth cookie. Automatically uses the __Secure- cookie prefix for HTTPS targets. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Instead of hard-coding mutation lists in the codebase, fetch them at runtime from the backend collections API (one collection per set: 3CLpro, RdRp, Spike). The seed script now uses mature protein names (offset-adjusted) as variant names, so the name calculation is no longer needed in client code. Offset and matureName are removed from the frontend entirely. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

useResistanceMutationSets now returns ResistanceData directly (mutationAnnotations + displayMutationsBySet), removing the intermediate ResistanceMutationSet type and resistanceMutations.ts entirely. The selector/filter chain now takes plain string[] for set names. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

The example data seeder on feat/example-data-seeder handles this now. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…errides Add wastewaterOrganismStagingConfigs with staging resistance collection IDs (1/2/3 for 3CLpro/RdRp/Spike). Wasap.astro now selects prod vs staging config and passes it directly to WasapPage, removing the env dependency from React. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…tance collections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

IDs confirmed at https://genspectrum.org/api/collections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

…2, 3) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Moves resistance collection fetching from a React Query hook to the Astro SSR layer, so data is available before the page reaches the browser. WasapPage now receives resistanceData as a prop instead of fetching it client-side. Removes useResistanceMutationSets hook; logic lives in resistanceData.ts as a plain async function. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

fhennig · 2026-04-29T12:26:54Z

Hey Fabian, the resistance stuff is fetched in the astro frontmatter, I think that's better because it's a simple Docker internal call. But I had it before with a React hook, the change is all in this commit: 2b50741 - Both approaches have pros and cons I'd say, we can also revert this commit if the hook approach is better.

Copilot

Pull request overview

Moves W-ASAP resistance mutation sets from hard-coded TypeScript arrays to backend collections, fetching them server-side in Wasap.astro and passing the resolved config + resistance data into the React page to avoid client-side loading.

Changes:

Replace resistanceMutationSets with resistanceMutationCollections (collection IDs + metadata) across config/types/tests.
Add server-side resistance collection fetching/building (resistanceData.ts) and plumb it through Wasap.astro → WasapPage.
Remove the old hard-coded resistance mutations module and update the resistance filter UI to use set names derived from fetched data.

Reviewed changes

Copilot reviewed 12 out of 12 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
website/src/views/pageStateHandlers/WasapPageStateHandler.spec.ts	Updates test config to use `resistanceMutationCollections`.
website/src/types/wastewaterConfig.ts	Switches COVID resistance config to collection-based IDs; adds staging config override export.
website/src/types/wastewaterConfig.spec.ts	Adjusts config validation test to new property name.
website/src/components/views/wasap/wasapPageConfig.ts	Updates `WasapPageConfig` to use `ResistanceMutationCollectionConfig`.
website/src/components/views/wasap/useWasapPageData.ts	Threads `displayMutationsBySet` into the query path for resistance mode.
website/src/components/views/wasap/resistanceMutations.ts	Deletes hard-coded resistance mutation sets + conversion helper.
website/src/components/views/wasap/resistanceData.ts	Adds SSR fetch + transformation from collections to mutation annotations + display mutations.
website/src/components/views/wasap/WasapPage.tsx	Accepts SSR-provided `config` + `resistanceData`, wiring them into gs-app + filters.
website/src/components/views/wasap/Wasap.astro	Resolves prod vs staging config and fetches resistance collections server-side.
website/src/components/pageStateSelectors/wasap/filters/ResistanceMutationsFilter.tsx	Switches selector inputs from full sets to set-name list.
website/src/components/pageStateSelectors/wasap/filters/ResistanceMutationsFilter.browser.spec.tsx	Updates browser test to pass set names instead of mutation sets.
website/src/components/pageStateSelectors/wasap/WasapPageStateSelector.tsx	Wires `resistanceSetNames` through to the resistance filter.

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Copilot

Pull request overview

Copilot reviewed 12 out of 12 changed files in this pull request and generated 3 comments.

                        <WasapPageStateSelector
                            config={config}
                            pageStateHandler={pageStateHandler}
                            initialBaseFilterState={base}
                            initialAnalysisFilterState={analysis}
                            setPageState={setPageState}
+                            resistanceSetNames={Object.keys(displayMutationsBySet)}
                        />


+} catch (error) {
+    getInstanceLogger('WasapPage').error(
+        `Failed to fetch resistance data for WASAP page (organism: ${wastewaterOrganism}): ${error}`,
+    );


+function withResistanceCollectionOverrides(config: WasapPageConfig): WasapPageConfig {
+    if (!config.resistanceAnalysisModeEnabled) return config;
+    // eslint-disable-next-line @typescript-eslint/naming-convention
+    const stagingIds: Record<string, number> = { '3CLpro': 1, 'RdRp': 2, 'Spike': 3 };
+    return {
+        ...config,
+        resistanceMutationCollections: config.resistanceMutationCollections.map((set) => ({
+            ...set,
+            collectionId: stagingIds[set.name] ?? set.collectionId,
+        })),
+    };


fengelniederhammer · 2026-05-12T07:16:35Z

        type: 'mutations',
-        displayMutations:
-            config.resistanceMutationSets.find((set) => set.name === analysis.resistanceSet)?.mutations ?? [],
+        displayMutations: displayMutationsBySet[analysis.resistanceSet ?? ''] ?? [],


Can analysis.resistanceSet ever be undefined?

fengelniederhammer · 2026-05-12T07:21:07Z

Let's maybe add a simple unit test to test the mapping here?

fengelniederhammer · 2026-05-12T07:27:24Z

 type Props = {
    wastewaterOrganism: WastewaterOrganismName;
 };

 const { wastewaterOrganism } = Astro.props;
-const { name } = wastewaterOrganismConfigs[wastewaterOrganism];
+const config = (isStaging() ? wastewaterOrganismStagingConfigs : wastewaterOrganismConfigs)[wastewaterOrganism];
+const backendService = new BackendService(getBackendHost());
+let resistanceData: ResistanceData = { mutationAnnotations: [], displayMutationsBySet: {} };
+
+try {
+    resistanceData = await fetchResistanceData(config, backendService);
+} catch (error) {


AI: If fetchResistanceData fails, the page renders with empty resistance data — the resistance mode dropdown will show zero options, but the user can still select the "resistance" tab and see an empty dropdown. Should we show some kind of user-facing warning in this case, or hide the resistance mode tab entirely when the data is unavailable?

fhennig and others added 2 commits April 28, 2026 15:58

initial implementation

88f9d5a

fhennig changed the title ~~feat(backend): add script to seed resistance mutation collections~~ resistance mutation sets as collections Apr 29, 2026

fhennig self-assigned this Apr 29, 2026

fhennig and others added 2 commits April 29, 2026 09:13

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chore(backend): remove resistance mutation collection seeding script

7ec3e98

The example data seeder on feat/example-data-seeder handles this now. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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chore(website): remove resolved TODOs and set 1h stale time for resis…

6f56af5

…tance collections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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fix(website): set correct prod resistance collection IDs (1, 2, 3)

c59d24f

IDs confirmed at https://genspectrum.org/api/collections Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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chore(website): update test fixture collection IDs to match prod (1, …

831288a

…2, 3) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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chore(website): remove parallel fetching TODO from WasapPage

45caf50

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

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format

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fhennig changed the title ~~resistance mutation sets as collections~~ feat(website): resistance mutation sets as collections Apr 29, 2026

fhennig requested a review from fengelniederhammer April 29, 2026 12:24

fhennig force-pushed the resistance-collections branch from 5ca6a5d to 2b50741 Compare April 29, 2026 12:25

fhennig marked this pull request as ready for review April 29, 2026 12:25

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Comment thread website/src/components/views/wasap/useWasapPageData.ts Outdated

Comment thread website/src/components/views/wasap/useWasapPageData.ts

Comment thread website/src/components/views/wasap/Wasap.astro Outdated

Comment thread website/src/types/wastewaterConfig.ts

fhennig requested a review from chaoran-chen April 30, 2026 11:09

fix typo

a7d8212

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feat(website): resistance mutation sets as collections#1181

feat(website): resistance mutation sets as collections#1181
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