feat(website): use a custom displayName for segments and references and remove segmentName prefix for nucleotide mutation/insertion/deletion search

[anna-parker]

resolves #5944, #5943

Screenshot

PR Checklist

• All necessary documentation has been adapted.
• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?)

🚀 Preview: https://displayname.loculus.org

[anna-parker]

this is kinda ugly and caused a bug... probably would be good to revisit if there is a tidier way to do this

[claude]

Claude finished @anna-parker's task in 2m 49s —— View job

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Code Review Complete

I've performed a comprehensive review of PR #5953. This PR successfully introduces custom display names for segments and references while removing segment name prefixes from nucleotide mutation/insertion/deletion searches.

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Summary

Strengths:

• ✅ Well-tested with comprehensive coverage across multiple scenarios (single-segmented, multi-segmented, multi-reference)
• ✅ Clear separation between internal LAPIS names and user-facing display names
• ✅ Consistent handling of the displayName pattern throughout the codebase
• ✅ Good backward compatibility - displayName is optional with sensible fallbacks

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Detailed Findings

1. Error Handling in Mutation Parsing

Location: website/src/utils/mutation.ts (lines 133, 166, 208, 243)

Issue: Multiple empty catch blocks silently swallow all errors during mutation parsing. This makes debugging difficult when parsing failures occur.

Current code:

try {
    // parsing logic
} catch (_) {
    return INVALID;
}

Recommendation: Log errors in development mode:

} catch (error) {
    if (process.env.NODE_ENV === 'development') {
        console.warn('Failed to parse mutation query:', text, error);
    }
    return INVALID;
}

Relates to: The author's comment "this is kinda ugly and caused a bug..." - error logging would help catch similar issues in the future.

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2. Empty String Edge Case

Location: website/src/components/SequenceDetailsPage/MutationBadge.tsx:82

Issue: The segment value can be an empty string for single-segmented organisms (set in getTableData.ts:244), rendering an empty <h2> header.

Recommendation:

{segment && <h2 className='py-1 my-1 font-semibold border-b'>{segment}</h2>}

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3. Technical Debt - Type Safety

Location: website/src/components/SearchPage/DownloadDialog/SequenceFilters.tsx:6

Issue: ESLint disable comments for any types with reference to TODO #3451. Using any defeats TypeScript's type safety, which is particularly important for display name transformations.

Recommendation: Prioritize issue #3451 to add proper typing to this file.

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4. Missing Documentation for Display Name Convention

Location: website/src/utils/sequenceTypeHelpers.ts:189

Issue: The lapisNameToDisplayName() function returns undefined for single-segmented organisms but the segment name for multi-segmented organisms. This convention is important but not documented.

Recommendation: Add JSDoc:

/**
 * @param referenceGenomesInfo - The reference genome lightweight schema
 * @returns Map from LAPIS names to display names (segment or gene names).
 * For single-segmented genomes, the segment displayName is `undefined` since 
 * there's no ambiguity. Genes always have their name as the displayName.
 */

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5. Documentation Checklist Incomplete

The PR checklist shows:

• All necessary documentation has been adapted
• Manual testing documentation

Recommendation: Update user-facing documentation for the mutation search feature, particularly since this PR removes segment name prefixes from the search syntax.

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Testing Assessment

✅ Excellent test coverage:

• Comprehensive tests in mutation.spec.ts covering all organism types
• Tests in getTableData.spec.ts verify proper display name mapping
• Tests in ReferenceSelector.spec.tsx verify UI behavior
• Edge cases are well covered

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Security & Performance

✅ No security vulnerabilities identified
✅ No performance concerns
✅ Changes maintain existing patterns without introducing inefficiencies

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Author's Concerns Addressed

1. "not sure I can actually use this..." (config.ts)

• ✅ The optional displayName field is properly implemented
• ✅ The fallback pattern to sentenceCase(name) is consistently applied throughout the codebase
• ✅ This is a solid implementation

2. "this is kinda ugly and caused a bug..." (mutation.ts)

• ⚠️ The mutation parsing logic is complex but necessarily so
• ⚠️ Empty catch blocks could hide bugs (see recommendation #1 above)
• Consider refactoring if this becomes a maintenance burden

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Overall Assessment

This is a well-executed PR that achieves its goals with:

• Solid implementation
• Good test coverage
• Backward compatibility
• Consistent patterns

Main recommendations:

1. Add error logging to mutation parsing
2. Handle empty segment names in UI
3. Complete documentation checklist items
4. Address the type safety technical debt when possible