feat!(backend): refactor multi-segment submission (2/n) #5398

anna-parker · 2025-11-10T07:46:19Z

partially resolves #5392, #5185 (comment)

Builds on #5382

BREAKING CHANGES

When users submit to multi-segmented organisms and want to group multiple segments under one metadata entry they are now required to add an additional fastaId column with a space (or comma) -separated list of the fastaIds (fasta header IDs) of the respective sequences. If no fastaId column is supplied the submissionId will be used instead and the backend will assume that (as in the single-segmented case) there is a one-to-one mapping of metadata submissionId to fastaId.

This new submission structure was voted for in microbioinfo: https://microbial-bioinfo.slack.com/archives/CB0HYT53M/p1760961465729399 and discussed in https://app.nuclino.com/Loculus/Development/2025-10-20-Weekly-6d5fe89f-8ded-4286-b892-d215e0a498f6 (and in other meetings)

Nextclade sort will be used to assign segments/subtypes for all aligned sequences:

minimizer_index: <url_to_minimizer_index_used_by_nextclade_sort>

For organisms without a nextclade dataset we still allow the fasta headers to be used to determine the segment/subtype - entries must have the format _ (as in current set up).

As preprocessing now assigns segments it will return a map from the segment (or subtype) to the fastaHeader in the processedData: sequenceNameToFastaHeaderMap. This allows us to surface this assignment on the edit page.

Testing

You can use pathoplexus/dev_example_data#2 for testing.

Prepro config changes

Instead of having a dictionary for the nextclade datasets and servers we make nucleotideSequences a list of sequences:

nextclade_dataset_name: 
    L: nextstrain/cchfv/linked/L
    M: nextstrain/cchfv/linked/M
    S: nextstrain/cchfv/linked/S
nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output
genes: [RdRp, GPC, NP]

nucleotideSequences:
  - name: L
    nextclade_dataset_name: nextstrain/cchfv/linked/L
    nextclade_dataset_tag: <optional - was previously incorrectly placed on an organism level> 
    nextclade_dataset_server: <optional overwrites nextclade_dataset_server for this seq>
    accepted_sort_matches: <optional, used for classify_with_nextclade_sort and require_nextclade_sort_match, if not given nextclade_dataset_name is used> 
    gene_prefix: <optional, prefix to add to genes produced by nextclade run, e.g. nextclade labels genes as `AV1` but we expect `EV1_AV1`, here `EV1` would be the prefix >
  - name: M
    nextclade_dataset_name: nextstrain/cchfv/linked/M
  - name: S
    nextclade_dataset_name: nextstrain/cchfv/linked/S
nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output

Note the templates now also generate the genes list from the merged config.

PR Checklist

Update values.schema.json
keep tests for alignment NONE case
Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator
Any manual testing that has been done is documented: submission of EVs from test folder were submitted with the same fastaHeader as the submissionId -> this succeeded, additionally the submission of CCHF with a fastaID column in the metadata was tested (also in folder above), additionally revision of a segment was tested
Have preprocessing send back a segment: fastaHeader mapping

Future Work

add integration testing for full EV submission user journey
improve CCHF minimizer (some segments are again not assigned)
discuss if the originalData dictionary should be migrated (persistent DB has segmentName as key, now we have fastaHeader as key)
update PPX docs with new multi-segment submission format

🚀 Preview: https://multi-segment-submission.loculus.org

website/src/components/Submission/FormOrUploadWrapper.tsx

anna-parker · 2025-11-10T10:29:40Z

@codex review

website/src/components/Submission/FormOrUploadWrapper.tsx

website/src/components/Edit/SequencesForm.tsx

fengelniederhammer · 2025-11-12T09:00:32Z

Nitpick: IMO the commit message shouldn't be "refactor" but instead describe that
it's a significant change to the sequence structure. Maybe something like "don't require the segment name in sequence submissions"?

fengelniederhammer · 2025-11-12T09:27:53Z

When users submit to multi-segmented organisms and want to group multiple segments under one metadata entry they are required to add an additional fastaId column with a space (or comma) -separated list of the fastaIds (fasta header IDs) of the respective sequences. If no fastaId column is supplied the submissionId will be used instead and the backend will assume that (as in the single-segmented case) there is a one-to-one mapping of metadata submissionId to fastaId.

Could you please explain why we need the fastaIds now? Is the submissionId even necessary then?

I think initially we agreed to still stick to the pattern >{submissionid}_{someSegmentId} for the fasta headers. Why don't we keep it?

theosanderson · 2025-11-12T09:33:14Z

Is the submissionId even necessary then?

I think the submissionId is generally part of our model as (in part) a user's id for a sequence. E.g. we surface it on the review cards.

backend/src/main/kotlin/org/loculus/backend/utils/MetadataEntry.kt

backend/src/main/resources/db/migration/V1.21__refactor_aux_tables.sql

backend/src/main/kotlin/org/loculus/backend/utils/MetadataEntry.kt

backend/src/main/resources/db/migration/V1.21__refactor_aux_tables.sql

corneliusroemer · 2025-11-20T10:11:20Z

backend/src/main/kotlin/org/loculus/backend/model/SubmitModel.kt

+            val metadataFastaIds = uploadDatabaseService.getFastaIdsForMetadata(uploadId)
+            val metadataFastaIdsSet = metadataFastaIds.flatten().toSet()
+            if (metadataFastaIdsSet.size < metadataFastaIds.flatten().size) {
+                throw UnprocessableEntityException("Metadata file contains duplicate fastaIds.")
+            }


Put into validate function similar to below for submission ids

backend/src/main/kotlin/org/loculus/backend/model/SubmitModel.kt

...nd/src/main/kotlin/org/loculus/backend/service/submission/dbtables/SequenceUploadAuxTable.kt

backend/src/main/kotlin/org/loculus/backend/service/submission/UploadDatabaseService.kt

resolves #4847 ### Screenshot Improves #4821, comes after #5398 You can use pathoplexus/dev_example_data#2 for testing. Nextclade sort will be used to assign segments/subtypes for all aligned sequences: ``` minimizer_index: <url_to_minimizer_index_used_by_nextclade_sort> ``` For organisms without a nextclade dataset we still allow the fasta headers to be used to determine the segment/subtype - entries must have the format <submissionId>_<segmentName> (as in current set up). As preprocessing now assigns segments it will return a map from the segment (or subtype) to the fastaHeader in the processedData: `sequenceNameToFastaHeaderMap`. This allows us to surface this assignment on the edit page. ## Prepro config changes Instead of having a dictionary for the nextclade datasets and servers we make `nucleotideSequences` a list of sequences: ``` nextclade_dataset_name: L: nextstrain/cchfv/linked/L M: nextstrain/cchfv/linked/M S: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output genes: [RdRp, GPC, NP] ``` ``` nucleotideSequences: - name: L nextclade_dataset_name: nextstrain/cchfv/linked/L nextclade_dataset_tag: <optional - was previously incorrectly placed on an organism level> nextclade_dataset_server: <optional overwrites nextclade_dataset_server for this seq> accepted_sort_matches: <optional, used for classify_with_nextclade_sort and require_nextclade_sort_match, if not given nextclade_dataset_name is used> gene_prefix: <optional, prefix to add to genes produced by nextclade run, e.g. nextclade labels genes as `AV1` but we expect `EV1_AV1`, here `EV1` would be the prefix > - name: M nextclade_dataset_name: nextstrain/cchfv/linked/M - name: S nextclade_dataset_name: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output ``` Note the templates now also generate the genes list from the merged config. ### PR Checklist - [ ] Update values.schema.json - [x] keep tests for alignment NONE case - [x] Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator - [x] Any manual testing that has been done is documented: submission of EVs from test folder were submitted with the same fastaHeader as the submissionId -> this succeeded, additionally the submission of CCHF with a fastaID column in the metadata was tested (also in folder above), additionally revision of a segment was tested - [x] Have preprocessing send back a segment: fastaHeader mapping ## Future Work - [ ] add integration testing for full EV submission user journey - [ ] improve CCHF minimizer (some segments are again not assigned) - [ ] discuss if the originalData dictionary should be migrated (persistent DB has segmentName as key, now we have fastaHeader as key) - [ ] update PPX docs with new multi-segment submission format 🚀 Preview: https://sort-multi-path.loculus.org

resolves #4708, #4734 partially resolves #5392, #5185 (comment) Builds on #5382 ### BREAKING CHANGES When users submit to multi-segmented organisms and want to group multiple segments under one metadata entry they are now required to add an additional `fastaId` column with a space (or comma) -separated list of the `fastaIds` (fasta header IDs) of the respective sequences. If no `fastaId` column is supplied the `submissionId` will be used instead and the backend will assume that (as in the single-segmented case) there is a one-to-one mapping of metadata `submissionId` to `fastaId`. This new submission structure was voted for in microbioinfo: https://microbial-bioinfo.slack.com/archives/CB0HYT53M/p1760961465729399 and discussed in https://app.nuclino.com/Loculus/Development/2025-10-20-Weekly-6d5fe89f-8ded-4286-b892-d215e0a498f6 (and in other meetings) Nextclade sort will be used to assign segments/subtypes for all aligned sequences: ``` minimizer_index: <url_to_minimizer_index_used_by_nextclade_sort> ``` For organisms without a nextclade dataset we still allow the fasta headers to be used to determine the segment/subtype - entries must have the format <submissionId>_<segmentName> (as in current set up). As preprocessing now assigns segments it will return a map from the segment (or subtype) to the fastaHeader in the processedData: `sequenceNameToFastaHeaderMap`. This allows us to surface this assignment on the edit page. ### Testing You can use pathoplexus/dev_example_data#2 for testing. ### Prepro config changes Instead of having a dictionary for the nextclade datasets and servers we make `nucleotideSequences` a list of sequences: ``` nextclade_dataset_name: L: nextstrain/cchfv/linked/L M: nextstrain/cchfv/linked/M S: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output genes: [RdRp, GPC, NP] ``` ``` nucleotideSequences: - name: L nextclade_dataset_name: nextstrain/cchfv/linked/L nextclade_dataset_tag: <optional - was previously incorrectly placed on an organism level> nextclade_dataset_server: <optional overwrites nextclade_dataset_server for this seq> accepted_sort_matches: <optional, used for classify_with_nextclade_sort and require_nextclade_sort_match, if not given nextclade_dataset_name is used> gene_prefix: <optional, prefix to add to genes produced by nextclade run, e.g. nextclade labels genes as `AV1` but we expect `EV1_AV1`, here `EV1` would be the prefix > - name: M nextclade_dataset_name: nextstrain/cchfv/linked/M - name: S nextclade_dataset_name: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output ``` Note the templates now also generate the genes list from the merged config. ### PR Checklist - [ ] Update values.schema.json - [x] keep tests for alignment NONE case - [x] Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator - [x] Any manual testing that has been done is documented: submission of EVs from test folder were submitted with the same fastaHeader as the submissionId -> this succeeded, additionally the submission of CCHF with a fastaID column in the metadata was tested (also in folder above), additionally revision of a segment was tested - [x] Have preprocessing send back a segment: fastaHeader mapping ## Future Work - [ ] add integration testing for full EV submission user journey - [ ] improve CCHF minimizer (some segments are again not assigned) - [ ] discuss if the originalData dictionary should be migrated (persistent DB has segmentName as key, now we have fastaHeader as key) - [ ] update PPX docs with new multi-segment submission format 🚀 Preview: https://multi-segment-submission.loculus.org --------- Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>

resolves #4708, #4734 partially resolves #5392, #5185 (comment) Builds on #5382 When users submit to multi-segmented organisms and want to group multiple segments under one metadata entry they are now required to add an additional `fastaId` column with a space (or comma) -separated list of the `fastaIds` (fasta header IDs) of the respective sequences. If no `fastaId` column is supplied the `submissionId` will be used instead and the backend will assume that (as in the single-segmented case) there is a one-to-one mapping of metadata `submissionId` to `fastaId`. This new submission structure was voted for in microbioinfo: https://microbial-bioinfo.slack.com/archives/CB0HYT53M/p1760961465729399 and discussed in https://app.nuclino.com/Loculus/Development/2025-10-20-Weekly-6d5fe89f-8ded-4286-b892-d215e0a498f6 (and in other meetings) Nextclade sort will be used to assign segments/subtypes for all aligned sequences: ``` minimizer_index: <url_to_minimizer_index_used_by_nextclade_sort> ``` For organisms without a nextclade dataset we still allow the fasta headers to be used to determine the segment/subtype - entries must have the format <submissionId>_<segmentName> (as in current set up). As preprocessing now assigns segments it will return a map from the segment (or subtype) to the fastaHeader in the processedData: `sequenceNameToFastaHeaderMap`. This allows us to surface this assignment on the edit page. You can use pathoplexus/dev_example_data#2 for testing. Instead of having a dictionary for the nextclade datasets and servers we make `nucleotideSequences` a list of sequences: ``` nextclade_dataset_name: L: nextstrain/cchfv/linked/L M: nextstrain/cchfv/linked/M S: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output genes: [RdRp, GPC, NP] ``` ``` nucleotideSequences: - name: L nextclade_dataset_name: nextstrain/cchfv/linked/L nextclade_dataset_tag: <optional - was previously incorrectly placed on an organism level> nextclade_dataset_server: <optional overwrites nextclade_dataset_server for this seq> accepted_sort_matches: <optional, used for classify_with_nextclade_sort and require_nextclade_sort_match, if not given nextclade_dataset_name is used> gene_prefix: <optional, prefix to add to genes produced by nextclade run, e.g. nextclade labels genes as `AV1` but we expect `EV1_AV1`, here `EV1` would be the prefix > - name: M nextclade_dataset_name: nextstrain/cchfv/linked/M - name: S nextclade_dataset_name: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output ``` Note the templates now also generate the genes list from the merged config. - [ ] Update values.schema.json - [x] keep tests for alignment NONE case - [x] Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator - [x] Any manual testing that has been done is documented: submission of EVs from test folder were submitted with the same fastaHeader as the submissionId -> this succeeded, additionally the submission of CCHF with a fastaID column in the metadata was tested (also in folder above), additionally revision of a segment was tested - [x] Have preprocessing send back a segment: fastaHeader mapping - [ ] add integration testing for full EV submission user journey - [ ] improve CCHF minimizer (some segments are again not assigned) - [ ] discuss if the originalData dictionary should be migrated (persistent DB has segmentName as key, now we have fastaHeader as key) - [ ] update PPX docs with new multi-segment submission format 🚀 Preview: https://multi-segment-submission.loculus.org --------- Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com>

… refactor multi segment submission in backend and edit page and have prepro assign segments (#5382) resolves #4999 #4708, #4734, #5511 partially resolves #5392, #5185 (comment) includes work done in #5398 and #5402 This PR additionally fixes submission, subtype assignment and search for EVs and other multi-path organisms. ### BREAKING CHANGES When users submit to multi-segmented organisms and want to group multiple segments under one metadata entry they are now required to add an additional `fastaIds` column with a space -separated list of the `fastaId`s (fasta header IDs) of the respective sequences. If no `fastaIds` column is supplied the `submissionId` will be used instead and the backend will assume that (as in the single-segmented case) there is a one-to-one mapping of metadata `submissionId` to `fastaId`. This new submission structure was voted for in microbioinfo: https://microbial-bioinfo.slack.com/archives/CB0HYT53M/p1760961465729399 and discussed in https://app.nuclino.com/Loculus/Development/2025-10-20-Weekly-6d5fe89f-8ded-4286-b892-d215e0a498f6 (and in other meetings) Nextclade sort (uses a minimizer index for fast local alignment) or nextclade align (full sequence alignment to reference) will be used to assign segments/subtypes for all multi-segmented and multi-pathogen sequences (this is also done in ingest for grouping segments): ``` segment_classification_method: "minimizer" or "align" minimizer_url: <url_to_minimizer_index_used_by_nextclade_sort> ``` For organisms without a nextclade dataset we still allow the fasta headers to be used to determine the segment/subtype - entries must have the format `<submissionId>_<segmentName>` (as in current set up). As preprocessing now assigns segments it will return a map from the segment (or subtype) to the fastaId in the processedData, the map is called: `sequenceNameToFastaId`. This allows us to surface the segment assignment on the edit page. ### Nextclade Preprocessing pipeline config changes Instead of having a dictionary for the nextclade datasets and servers we make `nucleotideSequences` a dictionary where each item includes all information required to run nextclade. I.e. we change from: ``` nextclade_dataset_name: L: nextstrain/cchfv/linked/L M: nextstrain/cchfv/linked/M S: nextstrain/cchfv/linked/S nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output genes: [RdRp, GPC, NP] ``` to: ``` nextclade_sequence_and_datasets: - name: L nextclade_dataset_name: nextstrain/cchfv/linked/L nextclade_dataset_tag: <optional - was previously incorrectly placed on an organism level> nextclade_dataset_server: <optional overwrites nextclade_dataset_server for this seq> accepted_sort_matches: <optional, used for classify_with_nextclade_sort and require_nextclade_sort_match, if not given nextclade_dataset_name and name are used> gene_prefix: <optional, prefix to add to genes produced by nextclade run, e.g. nextclade labels genes as `AV1` but we expect `EV1_AV1`, here `EV1` would be the prefix > genes: [RdRp] - name: M nextclade_dataset_name: nextstrain/cchfv/linked/M genes: [GPC] - name: S nextclade_dataset_name: nextstrain/cchfv/linked/S genes: [NP] nextclade_dataset_server: https://raw.githubusercontent.com/nextstrain/nextclade_data/cornelius-cchfv/data_output segment_classification_method: <optional, default for multi segmented viruses is align - if you assign segments in ingest for grouping use the same option here as you use there e.g. "minimizer" or "align"> minimizer_url: <optional, url_to_minimizer_index_used_by_nextclade_sort> ``` ### Ingest Pipeline Config changes `minimizer_index` is changed to `minimizer_url` for consistency (can be used in ingest and preprocessing and should both be the same) ### Optional additional Config changes Limit the number of sequences the backend will accept per submission by using - should be added for multi-segmented organisms: ` submissionDataTypes: &defaultSubmissionDataTypes consensusSequences: true maxSequencesPerEntry: 1 ` ### Testing You can use pathoplexus/example_data#16 and pathoplexus/dev_example_data#2 for testing. ### PR Checklist - [x] Update values.schema.json and other READMEs - [x] add fastaId to commonMetadata (ensure it is downloaded in templates): #5561 - [x] Fix how genes are returned (will cause a config update): #5563 - [x] Improve prepro code (less duplication and more tests): #5554 - [x] ingest EVs as single segmented to ensure search works: #5511 - [x] keep tests for alignment NONE case - [x] Create a minimizer for tests using: https://github.com/loculus-project/nextclade-sort-minimizer-creator - [x] Any manual testing that has been done is documented: submission of EVs from test folder were submitted with the same fastaHeader as the submissionId -> this succeeded, additionally the submission of CCHF with a fastaID column in the metadata was tested (also in folder above), additionally revision of a segment was tested - [x] Have preprocessing send back a segment: fastaHeader mapping - ~add integration testing for full EV submission user journey~ -> will be done in a later PR - [x] improve CCHF minimizer (some segments are again not assigned) - [x] discuss if the originalData dictionary should be migrated (persistent DB has segmentName as key, now we have fastaHeader as key) -> decided against - [x] update PPX docs with new multi-segment submission format -> test PR here: pathoplexus/pathoplexus#759 - [x] update example data for demo 🚀 Preview: https://edit-page-anya.loculus.org --------- Co-authored-by: Cornelius Roemer <cornelius.roemer@gmail.com> Co-authored-by: Fabian Engelniederhammer <92720311+fengelniederhammer@users.noreply.github.com> Co-authored-by: Theo Sanderson <theo@sndrsn.co.uk>

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feat!(backend): refactor multi-segment submission #5261

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Refactor multi-segment submission #5392

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Single sequence revise form does not surface backend error nicely when sequence discarded/missing #4850

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feat!(website, prepro, backend, config, integration):multi pathogen - refactor multi segment submission in backend and edit page and have prepro assign segments #5382

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feat(prepro): assign segment/subtype using nextclade sort (3/n) #5402

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submission_id is text in postgres but varchar 255 in kotlin #5497

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fix(website): only put fasta Id into fastaIds in edit page #5636

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