feat(wasap): add GenSpectrum collections analysis mode#1327
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Also converts WasapAnalysisMode, SignatureType, ExcludeSetName to const-object pattern (matching VARIANT_TIME_FRAME), adds SEQUENCE_TYPE for the external SequenceType, exports fetchWasapPageData for direct testing, and adds BackendRouteMocker.mockGetCollection to routeMocker.ts. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
… customColumns Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…eFrame tests Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Waiting for #1332 so we can add some more tests. |
Adds a new 'collection' analysis mode to the WASAP dashboard that browses GenSpectrum's own collection system, enabling RSV-A and RSV-B to have a collections mode (CovSpectrum collections only exist for COVID). - Config: CollectionAnalysisModeConfig discriminated union; no extra URL needed since the backend is our own - Data fetch: getBackendServiceForClientside().getCollection(), handles both 'query' and 'filterObject' variant types via parseQuery validation - Filter UI: GsCollectionAnalysisFilter lists collections by organism via getCollectionSummaries() - COVID gets both modes; RSV-A and RSV-B get only the new mode - CollectionInfo now accepts sourceLabel/collectionUrl to distinguish CovSpectrum vs GenSpectrum collection links in the page view Closes #1324 Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…llection link
- Deduplicate display labels in fetchCollectionModeData: duplicate names
get a counter suffix ("Resistance", "Resistance (2)") so GsQueriesOverTime
doesn't throw on collections like the RSV-A resistance set
- Add clickable link to the GenSpectrum collection info box using
Page.viewCollection(config.internalName, id)
See #1328 for the same fix on the CovSpectrum path.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…pdown Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…isFilter Also auto-selects the first collection on load via useEffect and removes the empty placeholder option from the dropdown. 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>
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Closes #1324, closes #1328
Summary
'collection'analysis mode to WASAP that uses GenSpectrum's own backend collections, separate from the existing'covSpectrumCollection'mode (CovSpectrum API)collectionmode (CovSpectrum collections don't exist for RSV)CollectionInfocomponent updated to acceptsourceLabeland optionalcollectionUrlto show appropriate links per sourceNew files
CollectionAnalysisFilter.tsx— filter dropdown that lists collections for the current organism viagetCollectionSummaries({ organism })Key implementation notes
getBackendServiceForClientside().getCollection({ id })queryvariants (countQuery used directly) andfilterObjectvariants (mutation arrays joined into a query string)parseQuery+validateGenomeOnlybefore display, same as the CovSpectrum pathfilterObjectvariants with only mutation arrays (no lineage catchall fields) are converted; empty results are marked invalidTest plan
npx tsc --noEmit)GsQueriesOverTimewith the collection's variantsTODO
WasapPage.browser.spec.tsxthat mocksgetCollectionviaBackendRouteMockerand asserts the "No valid variants" message renders when all variants are empty/invalid🤖 Generated with Claude Code