feat!(config, website): split mutation search by segment and remove segment prefix

[anna-parker]

resolves #5842, #5945, #5943

Summary

A. Allows mutation search for multi-seg, multi-ref organisms without having to select all references.

1. SearchUI is now split between sample and sequence related fields, in turn sequence-related fields are split between segments. Each segment has its own mutation search field and reference seletor in the case it has multiple references.
2. Url parameters are now adapted to have mutation_<segmentName> in the case where an organism has multiple segments.
3. The segment prefix is removed from mucleotide mutations as the segment is now known from the mutation box, this is also extended to the sequenceDetails page to allow easier copying of mutations.
4. Insertions and deletions are now also split by segment on the sequenceDetails page.
5. The mutation info box now included a list of valid names

B. It is now possible to configure segment and reference displayNames which are shown in the searchUI and reference selection dropdowns and on the sequenceDetails page (in the mutation section)

Screenshot

Screen.Recording.2026-02-13.at.09.49.52.mov

Config Changes

Metadata relating to the sequence should now be marked with the argument isSequenceFilter: true (the default is false):

- name: length
  perSegment: true

becomes

- name: length
  isSequenceFilter: true
  perSegment: true

If a sequence-related field should be created/shown only for one segment add the field relatesToSegment: S. Additionally, the config will now populate preprocessing args related to the reference and segment for you from these fields, this means you should change:

- name: lineage
  preprocessing:
    args: 
      segment: S
    inputs: {input: nextclade.clade}

to:

- name: lineage
  isSequenceFilter: true
  relatesToSegment: S
  preprocessing:
    inputs: {input: nextclade.clade}

This is also true for fields with onlyForReference, for example:

- name: clade_cv_a16
  onlyForReference: CV-A16
  preprocessing:
    args:
      reference: CV-A16
    inputs: {input: nextclade.clade}

can be changed to:

- name: clade_cv_a16
  onlyForReference: CV-A16
  preprocessing:
    inputs: {input: nextclade.clade}

If you would like to use a displayName instead of the segment or reference name you can add this to the referenceGenomes section, for example:

referenceGenomes:
- name: M
        displayName: M segment
        references:
          - name: MH396653
            displayName: "M (MH396653.1)"
            sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/M/MH396653/reference.fasta]]"
            insdcAccessionFull: MH396653.1
            genes:
              - name: GPC
                sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/cchf/M/MH396653/GPC.fasta]]"

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?) -> see preview

🚀 Preview: https://search-ui-demo.loculus.org

[claude]

This PR may be related to: #5566 (feature: add option to hide metadata fields from web interface)

[anna-parker]

Comments from @rneher and @theosanderson in https://loculus.slack.com/archives/C094HTT8XEJ/p1770225352248569 (I made issues only for the more complicated sections:

• rename sections to sequence/sample filters
• make subsections more prominent
• "Sample Metadata" should probably be above sequence filters.
• Search UI multi-seg, multi-ref: Remove segment name from mutations in search and on details page #5943
• Search UI multi-path multi-ref: Add custom displayName for segments and references #5944
• Search UI multi-seg multi-ref: Make sequence and sample filter sections collapsable but avoid over-nesting for single segmented organisms #5945
• Rethink displayName of segmented metadata fields on details page

Other issues:

• Make aligned sequence download segment-dependent (now need to select references for all to download any sequence)
• Fix integration tests

[theosanderson]

@codex review

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 9fa4c93d8d

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

[theosanderson]

@codex review

[theosanderson]

LGTM!

[chatgpt-codex-connector]

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: b2db5e3b8a

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

• Open a pull request for review
• Mark a draft as ready
• Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".