feat(website): rsv resistance mutations in wastewater dashboard#1257
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Pull request overview
Adds support for RSV resistance mutation annotations in the W‑ASAP (wastewater) dashboards by introducing an explicit annotationMode on resistance mutation collections and updating resistance annotation building logic to support both COVID-style (“per variant”) and RSV-style (“per collection”) annotations.
Changes:
- Added required
annotationMode: 'per-variant' | 'per-collection'toResistanceMutationCollectionConfig. - Updated
buildResistanceDatato emit mutation annotations differently depending onannotationMode(per-mutation vs flattened per-collection). - Enabled resistance analysis for RSV-A/RSV-B in
wastewaterConfig.tsand configured their resistance mutation collections + defaults; updated tests accordingly.
Reviewed changes
Copilot reviewed 5 out of 5 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 include required annotationMode for resistance sets. |
| website/src/types/wastewaterConfig.ts | Adds RSV-A/RSV-B resistance mode + collection config; adds staging override mappings. |
| website/src/components/views/wasap/wasapPageConfig.ts | Extends resistance collection config type with required annotationMode. |
| website/src/components/views/wasap/resistanceData.ts | Implements annotationMode branching in resistance data/annotation building. |
| website/src/components/views/wasap/resistanceData.spec.ts | Adds/updates unit tests for both per-variant and per-collection annotation modes. |
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Adds a `per-collection` annotation mode to `ResistanceMutationCollectionConfig` so RSV resistance data (already in protein coordinates) can be surfaced as one annotation per collection rather than one per mutation. Enables resistance analysis mode on the RSV-A and RSV-B wastewater dashboards using collection IDs 5001–5004 from the ViralZone seeder. Existing COVID configs explicitly opt in to the original `per-variant` behaviour so the refactor is backwards-compatible. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
… spec Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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| if (setConfig.annotationMode === annotationMode.perVariant) { | ||
| filterVariants.forEach((variant) => { | ||
| (variant.filterObject.aminoAcidMutations ?? []).forEach((aminoAcidMutation) => { | ||
| mutationAnnotations.push({ | ||
| name: variant.name, | ||
| symbol: setConfig.annotationSymbol, | ||
| description: setConfig.description, | ||
| aminoAcidMutations: [aminoAcidMutation], | ||
| }); | ||
| }); | ||
| }); | ||
| } else { | ||
| mutationAnnotations.push({ | ||
| name: setConfig.name, | ||
| symbol: setConfig.annotationSymbol, | ||
| description: setConfig.description, | ||
| aminoAcidMutations: [aminoAcidMutation], | ||
| })), | ||
| ); | ||
| aminoAcidMutations: allMutations, | ||
| }); | ||
| } |
fengelniederhammer
approved these changes
Jun 11, 2026
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Closes #1242
Summary
Adds RSV resistance mutation annotations. They are different from the covid annotations, in that we really use only one annotation for multiple mutations, whereas with covid we use one annotation per mutation. We do this because we want to name each mutation individually. This difference is now encoded with
annotationMode, see below.annotationMode: 'per-variant' | 'per-collection'(required, no default) toResistanceMutationCollectionConfigbuildResistanceDatato branch on the mode:per-variantkeeps existing COVID behaviour (one annotation per mutation, name = variant name);per-collectionemits one annotation for the whole collection with all mutations flattenedresistanceAnalysisModeEnabledon RSV-A and RSV-B. Prod collection IDs are 4983/4984 (RSV-A) and 4985/4986 (RSV-B); staging overrides these to 5001/5002 (RSV-A) and 5003/5004 (RSV-B) viawastewaterOrganismStagingConfigs.annotationMode: 'per-variant'on all three existing COVID collectionsScreenshot
Test plan
resistanceData.spec.ts— existing per-variant tests still pass; new per-collection describe block covers flattened annotation and query-variant skippingtsc --noEmit)🤖 Generated with Claude Code