feat(website): resistance mutation sets as collections #1181
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,34 @@ | ||
| --- | ||
| import { WasapPage } from './WasapPage'; | ||
| import { fetchResistanceData, type ResistanceData } from './resistanceData'; | ||
| import { BackendService } from '../../../backendApi/backendService.ts'; | ||
| import { isStaging, getBackendHost } from '../../../config.ts'; | ||
| import BaseLayout from '../../../layouts/base/BaseLayout.astro'; | ||
| import { getInstanceLogger } from '../../../logger.ts'; | ||
| import { | ||
| wastewaterOrganismConfigs, | ||
| wastewaterOrganismStagingConfigs, | ||
| type WastewaterOrganismName, | ||
| } from '../../../types/wastewaterConfig'; | ||
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| type Props = { | ||
| wastewaterOrganism: WastewaterOrganismName; | ||
| }; | ||
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| const { wastewaterOrganism } = Astro.props; | ||
| const config = (isStaging() ? wastewaterOrganismStagingConfigs : wastewaterOrganismConfigs)[wastewaterOrganism]; | ||
| const backendService = new BackendService(getBackendHost()); | ||
| let resistanceData: ResistanceData = { mutationAnnotations: [], displayMutationsBySet: {} }; | ||
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| try { | ||
| resistanceData = await fetchResistanceData(config, backendService); | ||
| } catch (error) { | ||
| getInstanceLogger('WasapPage').error( | ||
| `Failed to fetch resistance data for WASAP page (organism: ${wastewaterOrganism}): ${error}`, | ||
| ); | ||
|
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| } | ||
| --- | ||
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| <BaseLayout title={`Swiss wastewater - ${config.name}`}> | ||
| <WasapPage config={config} resistanceData={resistanceData} client:only='react' /> | ||
| </BaseLayout> | ||
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|
Contributor
There was a problem hiding this comment. Let's maybe add a simple unit test to test the mapping here? |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| import type { MutationAnnotations } from '@genspectrum/dashboard-components/util'; | ||
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| import type { ResistanceMutationCollectionConfig, WasapPageConfig } from './wasapPageConfig'; | ||
| import type { BackendService } from '../../../backendApi/backendService'; | ||
| import type { Collection } from '../../../types/Collection'; | ||
|
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| export type ResistanceData = { | ||
| /** Flat list of mutation annotations for the genome viewer. */ | ||
| mutationAnnotations: MutationAnnotations; | ||
| /** Map from set name (e.g. "3CLpro") to the genomic amino acid mutations to display. */ | ||
| displayMutationsBySet: Record<string, string[]>; | ||
| }; | ||
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| export async function fetchResistanceData( | ||
| config: WasapPageConfig, | ||
| backendService: BackendService, | ||
| ): Promise<ResistanceData> { | ||
| if (!config.resistanceAnalysisModeEnabled) { | ||
| return { mutationAnnotations: [], displayMutationsBySet: {} }; | ||
| } | ||
| const collections = await Promise.all( | ||
| config.resistanceMutationCollections.map((setConfig) => | ||
| backendService.getCollection({ id: String(setConfig.collectionId) }), | ||
| ), | ||
| ); | ||
| return buildResistanceData(config.resistanceMutationCollections, collections); | ||
| } | ||
|
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| function buildResistanceData( | ||
| setConfigs: ResistanceMutationCollectionConfig[], | ||
| collections: Collection[], | ||
| ): ResistanceData { | ||
| const mutationAnnotations: MutationAnnotations = []; | ||
| const displayMutationsBySet: Record<string, string[]> = {}; | ||
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| setConfigs.forEach((setConfig, i) => { | ||
| const entries = collections[i].variants.flatMap((variant) => { | ||
| if (variant.type !== 'filterObject') return []; | ||
| return (variant.filterObject.aminoAcidMutations ?? []).map((aminoAcidMutation) => ({ | ||
| displayName: variant.name, | ||
| aminoAcidMutation, | ||
| })); | ||
| }); | ||
|
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| displayMutationsBySet[setConfig.name] = entries.map((e) => e.aminoAcidMutation); | ||
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| mutationAnnotations.push( | ||
| ...entries.map(({ displayName, aminoAcidMutation }) => ({ | ||
| name: displayName, | ||
| symbol: setConfig.annotationSymbol, | ||
| description: setConfig.description, | ||
| aminoAcidMutations: [aminoAcidMutation], | ||
| })), | ||
| ); | ||
| }); | ||
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| return { mutationAnnotations, displayMutationsBySet }; | ||
| } |
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AI: If
fetchResistanceDatafails, 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?