feat(collection-seeder): add influenza resistance mutation collections#1316
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Adds four new Source classes (h1n1pdm, h3n2, h5n1, victoria) that fetch antiviral resistance mutation data from the BU-ISCIII flu_resistance repo and produce one Collection per antiviral per organism. NA inhibitors (Oseltamivir, Zanamivir, Peramivir, Laninamivir) are sourced from NA-inhibitors.json with NI/RI/HRI classification. Baloxavir is sourced from PA-inhibitors.json with fold-change values. NI-only and unknown (?, ?e) entries are excluded. Open questions about strain mapping, fold-change thresholds, LAPIS gene name conventions, and additional data files are documented in QUESTIONS.md. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Baloxavir variants now named by mutation (e.g. 'PA:I38T') with fold-change surfaced in the new variant description field - Add description field to Variant TypedDict (NotRequired[str]) - Remove QUESTIONS.md (all questions resolved) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Some entries in NA-inhibitors.json have leading spaces (e.g. " S227N"), which produced invalid strings like "NA: S227N" in aminoAcidMutations. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ction descriptions Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Pull request overview
Adds a new collection-seeding source that pulls influenza antiviral resistance mutations from the BU-ISCIII flu_resistance repository and generates seeded collections for the influenza dashboards (H1N1pdm, H3N2, H5N1, and B/Victoria), resolving #1272.
Changes:
- Introduces
influenza_resistance_mutationsseeding sources that fetch NA- and PA-inhibitor mutation datasets and build collections/variants per subtype. - Registers the new influenza sources in the seeder source registry so they run in the default seed flow.
- Extends the shared
Varianttyped model to allow an optionaldescription, and adds a dedicated test suite for the influenza sources and parsing.
Reviewed changes
Copilot reviewed 4 out of 4 changed files in this pull request and generated 3 comments.
| File | Description |
|---|---|
| collection-seeding/sources/influenza_resistance_mutations.py | New influenza resistance mutation sources and JSON fetching/parsing to produce collections. |
| collection-seeding/sources/registry.py | Registers the new influenza sources in ALL_SOURCES. |
| collection-seeding/models.py | Makes Variant.description optional via NotRequired. |
| collection-seeding/tests/test_influenza_resistance_mutations.py | Adds unit tests for parsing and for collection/variant generation across influenza subtypes. |
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resolves #1272
Summary
Adds resistance mutations for all influenza viruses.
Screenshot
Screen.Recording.2026-07-14.at.15.10.05.mov
PR Checklist