feat(website): use segment displayName and collapse sequences container if an organism is muti-segmented

[anna-parker]

resolves #

Screenshot

Use segment displayName in search UI, details page, download UI:

Collapse sequences dropdown:

PR Checklist

• The implemented feature is covered by appropriate, automated tests.
• Any manual testing that has been done is documented (i.e. what exactly was tested?) -> tested on preview, used in private virus 4 preview

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

[claude]

This PR may be related to: #3557 (Improve how we display segment names: main isn't a thing that we should ever show to users)

[claude]

Claude finished @anna-parker's task in 4m 28s —— View job

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Code Review

• Read changed files
• Review code quality
• Check testing coverage
• Review Kubernetes templates
• Provide final feedback

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Good PR overall — the displayName plumbing is clean and the collapsed-tab UX for highly-segmented organisms is a real improvement. A few things to address:

Bug: 2-segment tabs still use name not displayName

The collapsed dropdown (SegmentDropdown) correctly uses segment.displayName ?? segment.name, but the per-segment tab labels rendered when segments.length === 2 (i.e., useCollapsedTab is false) still hardcode segmentName.name:

SequencesContainer.tsx line 216:

label={`${segmentName.name} (unaligned)`}

SequencesContainer.tsx line 265:

label={`${segmentName.name} (aligned)`}

These should be segmentName.displayName ?? segmentName.name to be consistent. For any 2-segment organism that has display names configured, the tabs would still show the raw segment identifier. Fix this →

lapisNameToDisplayName not updated

sequenceTypeHelpers.ts line 286 maps lapis names to segmentName (not displayName):

map.set(refData.lapisName, referenceGenomesInfo.isMultiSegmented ? segmentName : undefined);

This function is used in getTableData.ts to populate segment labels in the mutations/insertions tables on the sequence details page. For organisms with display names, those tables would still show L, M, S instead of Large, Medium, Small. Worth fixing here too: referenceGenomesInfo.segmentDisplayNames[segmentName] ?? segmentName. Fix this →

Minor: Unnecessary dependency in useMemo

DownloadForm.tsx line 69:

const referenceSelected = useMemo(() => nucleotideSegmentInfos.length !== 0, [nucleotideSegmentInfos, geneInfos]);

geneInfos is not used inside the memo — it can be removed from the dependency array.

Testing

The new THREE_SEG_SINGLE_REF_REFERENCEGENOMES fixture is used in SequencesContainer.spec.tsx and correctly verifies that display names appear in the dropdown. The toReferenceGenomes tests in referenceGenomes.spec.ts cover the existing schema conversion cases well. One gap: there's no THREE_SEG_SINGLE_REF_REFERENCEGENOMES_SCHEMA variant to verify the schema→info conversion path includes segmentDisplayNames for 3-segment organisms (though MULTI_SEG_MULTI_REF covers the multi-segment display name mapping).

Kubernetes templates

The _merged-reference-genomes.tpl and _common-metadata.tpl changes look correct — displayNames is now extracted from the segment data and propagated through loculus.getNucleotideSegmentNames and loculus.generateWebsiteMetadata, making per-segment field headers use the display name ($segmentDisplayName) rather than the raw segment identifier.

[theosanderson]

@codex review

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[theosanderson]

lgtm!