feat!(config, website): flip config and website to segment-reference structure #5799

anna-parker · 2026-01-05T16:38:03Z

This adds an example of a multi-reference multi-segment CCHF organism (only the segments S and M have multiple references)

Architecture

As LAPIS does not have a specific way to define references of a segment each reference of a segment is stored as a unique segment in LAPIS - we use a namespaced naming convention to ensure there are no key clashes:

LAPIS Nucleotide sequence naming

    match (multi_reference, multi_segment):
        case (False, _):
            return segmentName
        case (True, True):
            return f"{segmentName}-{referenceName}"
        case (True, False):
            return referenceName

LAPIS Gene sequence naming

    match (multi_reference, multi_segment):
        case (False, _):
            return GeneName
        case (True, _):
            return f"{GeneName}-{referenceName}"

Config Changes

referenceGenomes:
      singleReference:
        nucleotideSequences:
          - name: "main"
            sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/reference.fasta]]"
            insdcAccessionFull: NC_002549.1
        genes:
          - name: NP
            sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/NP.fasta]]"
          ....

becomes:

referenceGenomes:
      - name: main
        references:
          - name: singleReference
            sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/reference.fasta]]"
            insdcAccessionFull: NC_002549.1
            genes:
              - name: NP
                sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/NP.fasta]]"
              - name: VP35
                sequence: "[[URL:https://corneliusroemer.github.io/seqs/artefacts/ebola-sudan/VP35.fasta]]"

PR Checklist

Add the lapisName vs displayName logic to the config structure at the start so that this doesnt have to be recalculated again and again in the code
Get the existing website tests to work
Add integration tests for the multi-segment, multi-reference case
Later steps: ensure ENA deposition works

🚀 Preview: https://restructure-anya.loculus.org

…ing (#5800) partially resolves #5663 and #5664 ## Overview I decided to split out the prepro changes required for #5799 into 1 PR. This change allows multiple `references` per `segment`, prepro will assign sequences to the correct reference within a segment and return the aligned (and unaligned) sequences with the key (of type: `SequenceName`) expected by the backend. Prepro attempts to aligns each sequence to one reference per segment, if a sequence can be aligned to multiple references it chooses the reference with the highest `nextclade alignment` or `nextclade sort` score. If multiple sequences within a submission align to the same segment (also if they align to different references of the same segment) the submission will error. ## Changes 1. The yaml config is changed to reflect segment-reference hierarchy (see breaking changes below), this config is used to create a list of processed `NextcladeSequenceDataset` objects for each reference. 2. Improved typing, introduction of the `SequenceName` type (name of processed sequence as expected by the backend) to distinguish between `SegmentName` objects. For example if the segment `L` has references `A` and `B`, then the `SegmentName` is `L` but the `SequenceName` will be `L_A`. 3. Removal of the `useFirstSegment` config option -`perSegment` metadata fields will always be assigned to results of the reference they best align to. 4. The `ASSIGNED_SEGMENT` field is removed and replaced with `ASSIGNED_REFERENCE` -this is now a `perSegment` field. Note that over 650 lines of this is just to add multi-reference CCHF as a test organism for prepro. ### Breaking changes The prepro config must be changed from ``` configFile: nextclade_sequence_and_datasets: - name: CV-A16 # This does not work yet with multi-segment organisms: #5663 nextclade_dataset_name: enpen/enterovirus/cv-a16 accepted_sort_matches: ["community/hodcroftlab/enterovirus/cva16", "community/hodcroftlab/enterovirus/enterovirus/linked/CV-A16"] gene_prefix: "CV-A16-" genes: ["VP4", "VP2", "VP3", "VP1", "2A", "2B", "2C", "3A", "3B", "3C", "3D"] - name: CV-A10 nextclade_dataset_name: enpen/enterovirus/cv-a10 accepted_sort_matches: ["community/hodcroftlab/enterovirus/enterovirus/linked/CV-A10"] gene_prefix: "CV-A10-" genes: ["VP4", "VP2", "VP3", "VP1", "2A", "2B", "2C", "3A", "3B", "3C", "3D"] ``` to (note we can add more segments with a variable number of references): ``` configFile: segments: - name: main references: -reference: CV-A16 nextclade_dataset_name: enpen/enterovirus/cv-a16 accepted_sort_matches: ["community/hodcroftlab/enterovirus/cva16", "community/hodcroftlab/enterovirus/enterovirus/linked/CV-A16"] genes: ["VP4", "VP2", "VP3", "VP1", "2A", "2B", "2C", "3A", "3B", "3C", "3D"] - reference: CV-A10 nextclade_dataset_name: enpen/enterovirus/cv-a10 accepted_sort_matches: ["community/hodcroftlab/enterovirus/enterovirus/linked/CV-A10"] genes: ["VP4", "VP2", "VP3", "VP1", "2A", "2B", "2C", "3A", "3B", "3C", "3D"] - name: seg2 genes: ... references: -... ``` ## TODO: - [x] check dummy pipeline -> confirmed this works without issues - [x] rename segment to sequence when corresponding to name of `segment/reference` - [x] change `ASSIGNED_SEGMENT` to `ASSIGNED_REFERENCE` and make this per segment - [x] get rid of `useFirstSegment` - [x] fix error for multiple segments of same type exist for multi reference case - [x] All necessary documentation has been adapted. - [x] The implemented feature is covered by appropriate, automated tests. - [x] Any manual testing that has been done is documented (i.e. what exactly was tested?) -> confirmed that all current organisms are unaffected by this change including EVs, integration also all pass 🚀 Preview: https://prepro-multipath.loculus.org

anna-parker · 2026-01-13T13:00:22Z

website/src/components/SearchPage/DownloadDialog/FieldSelector/FieldSelectorModal.tsx

    );
 };

 function getDisplayState(


I really dislike that undefined means that the sequence is visible

anna-parker · 2026-01-13T13:00:53Z

website/src/components/SearchPage/DownloadDialog/DownloadForm.tsx

    );
 };

 export function getSequenceNames(


this should come straight from the config to avoid duplication

anna-parker · 2026-01-13T21:03:12Z

website/src/utils/sequenceTypeHelpers.ts

+ * @param referenceName - The selected reference for this segment (e.g., "CV-A16"), or null
+ * @returns SegmentInfo with appropriate LAPIS naming
+ */
+export function getSegmentInfoWithReference(segmentName: string, referenceName: string | null): SegmentInfo {


again this should just come from the config at the start and then we won't have to call these functions later on

anna-parker changed the base branch from restructure to main January 5, 2026 17:00

This was referenced Jan 5, 2026

demo: flip config to segment-then-reference #5701

Draft

feat!(prepro): multi-pathogen refactor, apply segment-reference ordering #5800

Merged

anna-parker force-pushed the restructure-anya branch from 9c96ac0 to 8a08264 Compare January 9, 2026 19:09

anna-parker changed the base branch from main to prepro_multipath January 9, 2026 19:09

anna-parker force-pushed the prepro_multipath branch from 1e4ff42 to 67cd7e8 Compare January 9, 2026 19:10

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anna-parker changed the title ~~Restructure anya~~ feat!(config, website): flip config and website to segment-reference structure Jan 12, 2026

Base automatically changed from prepro_multipath to main January 12, 2026 14:26

theosanderson and others added 16 commits January 12, 2026 16:15

restructure

ff94dc6

update

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fixup

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update

4d1fb0f

fixup

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up

3faee25

fixup

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fixup

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upd

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up

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u

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format

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remove duplication

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delete unused file

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fix order of reference and segments

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fixup

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anna-parker added 2 commits January 13, 2026 11:52

ugly fix

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fixes

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anna-parker commented Jan 13, 2026

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anna-parker added 8 commits January 13, 2026 14:43

set state correctly

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fix selector

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extend for multi-segment

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add multi-seg, multi-ref example

f22b9ba

also add multiple references for the M segment

a4e5c7e

wupps

8e9c1ae

make reference selectable

654cc02

get rid of warning

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anna-parker added 4 commits January 13, 2026 21:20

improve

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format

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fix reference selector again

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improve more

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anna-parker force-pushed the restructure-anya branch from 62435bc to 613c62d Compare January 13, 2026 20:27

fix some bugs

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anna-parker commented Jan 13, 2026

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anna-parker added 4 commits January 14, 2026 11:19

fix mutation search

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fix download

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fix download button

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fix integration tests

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anna-parker force-pushed the restructure-anya branch from cddd4f5 to 6bffb36 Compare January 14, 2026 12:52

anna-parker added 3 commits January 14, 2026 16:02

fix: dont duplicate reference selection on search page

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Architecture

LAPIS Nucleotide sequence naming

LAPIS Gene sequence naming

Config Changes

PR Checklist

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