feat(website): show resistance mutation annotations on COVID and RSV dashboards

[fhennig]

Summary

Extract resistance mutation collection configs and helpers from the wasap subtree into a shared util file (resistanceMutations.ts). Add byEnv as a pure selector to dbIdSpace.ts. Wire COVID, RSV-A, and RSV-B constants to factory functions that build collection configs; have the generic Astro page components fetch annotations server-side and pass them down through the React layout tree.

Screenshot

PR Checklist

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

[vercel]

The latest updates on your projects. Learn more about Vercel for GitHub.

Project	Deployment	Actions	Updated (UTC)
dashboards	Ready	Preview	Jul 30, 2026 8:54am

[Copilot]

Pull request overview

This PR adds support for displaying resistance mutation annotations on organism dashboards (COVID, RSV-A, RSV-B) by extracting resistance-collection configuration and annotation-building utilities into shared helpers, and by fetching these annotations server-side in the generic Astro pages before passing them down into the React layout tree.

Changes:

• Introduces shared resistance-mutation utilities (resistanceMutations.ts) and an SSR fetch helper (fetchOrganismMutationAnnotations.ts).
• Extends organism constants with a factory hook to build resistance-collection configs by environment, and wires COVID/RSV-A/RSV-B to these factories.
• Updates the generic Astro pages + React layouts to accept and forward mutationAnnotations.

Reviewed changes

Copilot reviewed 22 out of 22 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
website/src/views/rsvB.ts	Removes empty per-organism annotations and wires RSV-B to the shared resistance-collection factory.
website/src/views/rsvA.ts	Removes empty per-organism annotations and wires RSV-A to the shared resistance-collection factory.
website/src/views/OrganismConstants.ts	Adds optional buildResistanceMutationCollections hook to organism constants.
website/src/views/covid.ts	Removes empty per-organism annotations and wires COVID to the shared resistance-collection factory.
website/src/util/resistanceMutations.ts	New shared utilities: collection config types, env-specific collection builders, annotation building, and collection fetch-to-annotations helper.
website/src/util/fetchOrganismMutationAnnotations.ts	New SSR helper to fetch organism mutation annotations safely (tolerates failures).
website/src/types/wastewaterConfig.ts	Reuses shared resistance-collection factory functions and central byEnv selector.
website/src/types/dbIdSpace.ts	Adds exported byEnv selector for env-dependent constants.
website/src/layouts/OrganismPage/SingleVariantOrganismPageLayout.tsx	Adds optional mutationAnnotations prop and forwards to OrganismViewPageLayout.
website/src/layouts/OrganismPage/OrganismViewPageLayout.tsx	Accepts optional mutationAnnotations prop and prioritizes it over constants’ annotations.
website/src/components/views/wasap/wasapPageConfig.ts	Moves ResistanceMutationCollectionConfig type import to shared util.
website/src/components/views/wasap/resistanceData.ts	Reuses shared buildMutationAnnotations to avoid duplication.
website/src/components/views/sequencingEfforts/GenericSequencingEffortsReactPage.tsx	Threads optional mutationAnnotations prop into the layout tree.
website/src/components/views/sequencingEfforts/GenericSequencingEffortsPage.astro	Fetches mutation annotations server-side and passes to the React page.
website/src/components/views/compareVariants/GenericCompareVariantsReactPage.tsx	Threads optional mutationAnnotations prop into the layout tree.
website/src/components/views/compareVariants/GenericCompareVariantsPage.astro	Fetches mutation annotations server-side and passes to the React page.
website/src/components/views/compareToBaseline/GenericCompareToBaselineReactPage.tsx	Threads optional mutationAnnotations prop into the layout tree.
website/src/components/views/compareToBaseline/GenericCompareToBaselinePage.astro	Fetches mutation annotations server-side and passes to the React page.
website/src/components/views/compareSideBySide/GenericCompareSideBySideReactPage.tsx	Threads optional mutationAnnotations prop into the layout tree.
website/src/components/views/compareSideBySide/GenericCompareSideBySidePage.astro	Fetches mutation annotations server-side and passes to the React page.
website/src/components/views/analyzeSingleVariant/GenericAnalyzeSingleVariantPage.astro	Fetches mutation annotations server-side and passes to the React page.
website/src/components/views/analyzeSingleVariant/GenericAnalyseSingleVariantReactPage.tsx	Threads optional mutationAnnotations prop into the layout tree.

[Copilot]

Pull request overview

Copilot reviewed 26 out of 26 changed files in this pull request and generated no new comments.

Comments suppressed due to low confidence (6)

website/src/types/dbIdSpace.ts:18

• byEnv is declared to return T but the switch has no default/exhaustiveness guard, so at runtime it can return undefined if env is ever an unexpected value (and TypeScript may also warn that not all code paths return a value). Add a default branch that throws to make the function total and fail fast.

export function byEnv<T>(env: DbIdSpace, vars: { prod: T; staging: T; local: T }): T {
    switch (env) {
        case dbIdSpaces.prod:
            return vars.prod;
        case dbIdSpaces.staging:
            return vars.staging;
        case dbIdSpaces.local:
            return vars.local;
    }
}

website/src/layouts/OrganismPage/OrganismViewPageLayout.tsx:35

• mutationAnnotations can now be undefined when the server-side fetch fails and view.organismConstants.mutationAnnotations is not set (e.g. COVID/RSV after this change). Passing undefined into <gs-app mutationAnnotations={...}> risks runtime errors if the web component assumes an array. Coalesce to an empty array as a safe default.

            <gs-app
                lapis={lapisUrl}
                mutationAnnotations={mutationAnnotations ?? view.organismConstants.mutationAnnotations}
            >

website/src/util/resistanceMutations.ts:32

• buildMutationAnnotations indexes collections[i] without validating that collections and setConfigs have matching lengths. Since this is an exported helper, a mismatch will currently throw a cryptic Cannot read properties of undefined at collections[i].variants. Add an explicit length check with a clear error.

    return setConfigs.map((setConfig, i) => {
        const filterVariants = collections[i].variants.filter((v) => v.type === 'filterObject');
        return {

website/src/views/covid.ts:32

• In website/src/views/*, internal util imports consistently include the .ts extension (e.g. website/src/views/mpox.ts:36). This new import is missing the extension, which is inconsistent with the established pattern and can be problematic under stricter ESM module resolution. Consider updating it to include .ts.

import { buildCovidResistanceMutationCollections } from '../util/resistanceMutations';

website/src/views/rsvA.ts:37

• In website/src/views/*, internal util imports consistently include the .ts extension (e.g. website/src/views/mpox.ts:36). This new import is missing the extension, which is inconsistent with the established pattern and can be problematic under stricter ESM module resolution. Consider updating it to include .ts.

import { buildRsvAResistanceMutationCollections } from '../util/resistanceMutations';

website/src/views/rsvB.ts:37

• In website/src/views/*, internal util imports consistently include the .ts extension (e.g. website/src/views/mpox.ts:36). This new import is missing the extension, which is inconsistent with the established pattern and can be problematic under stricter ESM module resolution. Consider updating it to include .ts.

import { buildRsvBResistanceMutationCollections } from '../util/resistanceMutations';