Update Loculus version to 0481a8 and update RSV-A dataset

[pathoplexus-bot]

@anna-parker wants to update the Loculus version from loculus-project/loculus@03a17ea to loculus-project/loculus@0481a82.

🚨 Breaking Changes

• feat!(backend): cleanup compression dictionary migration loculus-project/loculus#5461
• feat!(config): make stop codon perSegment loculus-project/loculus#5480

Changelog

• feat!(backend): cleanup compression dictionary migration loculus-project/loculus#5461
• chore(backend): refactor dependencies to use BOMs loculus-project/loculus#5587
• chore(backend): document gradle upgrade steps loculus-project/loculus#5589
• fix(backend): validate fileId exists in submit edited endpoint, do validation in same place as file existence checks loculus-project/loculus#5502
• chore(config): use standardized silo lineage hierarchy definition paths loculus-project/loculus#5567
• docs(ingest): document grouping_override in README loculus-project/loculus#5565
• Revert "refactor(prepro): simple split up of enrich_with_nextclade into subfunctions" loculus-project/loculus#5580
• refactor(prepro): simple split up of enrich_with_nextclade into subfunctions loculus-project/loculus#5540
• test: remove E2E tests with all remaining coverage moved to integration tests loculus-project/loculus#5536
• chore(preprocessing): fix spelling in embl file error message loculus-project/loculus#5553
• chore(website): log something when the details.json endpoint fails loculus-project/loculus#5548
• chore(deps): bump actions/checkout from 5 to 6 loculus-project/loculus#5527
• chore(deps): bump org.jlleitschuh.gradle.ktlint from 13.1.0 to 14.0.1 in /backend loculus-project/loculus#5530
• fix(ci): Switch website image waiting from wait-on-check-action to polling docker for image existence loculus-project/loculus#5547
• feat(preprocessing): add "merged" metadata fields that contain the value of the only segment loculus-project/loculus#5467
• chore(deps-dev): bump the minorandpatch group in /integration-tests with 3 updates loculus-project/loculus#5535
• fix(ci): build website image on native runners, then merge, to avoid qemu hangs loculus-project/loculus#5514
• chore(ci): in integration-test action, only install browser that's used loculus-project/loculus#5515
• feat(prepro): fix stop codons loculus-project/loculus#5544
• chore(deps): bump the minor group in /website with 4 updates loculus-project/loculus#5529
• feat(prepro): improve error handling if nextclade returns unexpected … loculus-project/loculus#5538
• chore(deps): bump the minorandpatch group across 1 directory with 2 updates loculus-project/loculus#5537
• chore(deps): bump the patch group in /website with 7 updates loculus-project/loculus#5533
• chore(integration-test): deflake new revise test by increasing test timeout, add todo for inefficient setup loculus-project/loculus#5525
• chore(ci): log basic details of downloaded ncbi datasets loculus-project/loculus#5513
• refactor(prepro): split up process_single into cleaner steps loculus-project/loculus#5510
• test: move many E2E tests to integration tests loculus-project/loculus#5476
• refactor(prepro): move Nextclade functionality into its own file loculus-project/loculus#5520
• doc: improve READMEs with links to installation pages and tips loculus-project/loculus#5436
• chore(deployment): refactor dataset mirror workflows with priority tiers to reduce load for non-Pathoplexus organisms loculus-project/loculus#5352
• fix(website): allow mobile menu scrolling loculus-project/loculus#5506
• ci(prepro): check formatting in ci loculus-project/loculus#5505
• refactor(backend): move data use terms validation to more logical place, use condition-based when/expression-style branching loculus-project/loculus#5492
• chore: add marburg to mirror loculus-project/loculus#5498
• docs(website): explain why the runtime config is separate from the WebsiteConfig loculus-project/loculus#5499
• refactor(preprocessing): pull length fields out of loop loculus-project/loculus#5488
• feat!(config): make stop codon perSegment loculus-project/loculus#5480
• chore(deps): bump glob from 10.4.5 to 10.5.0 in /keycloak/keycloakify loculus-project/loculus#5485
• chore(deps): bump glob from 10.4.5 to 10.5.0 in /website loculus-project/loculus#5484
• chore(deps): bump glob from 10.4.5 to 10.5.0 in /docs loculus-project/loculus#5483
• chore(deps): bump astro from 5.15.8 to 5.15.9 in /docs loculus-project/loculus#5482
• refactor(backend): don't create empty concatenation, slight rewording of variables for clarity loculus-project/loculus#5477
• refactor(integration tests): Refactor integration test fixtures pattern loculus-project/loculus#5469
• fix(integration-tests): unflake extra file upload, refactor file-sharing tests generally loculus-project/loculus#5462
• refactor(kubernetes): add indent to Helm template function loculus-project/loculus#5465

Comparison

loculus-project/loculus@03a17ea...0481a82

Preview

https://preview-update-loculus-0481a8.pathoplexus.org

[anna-parker]

In #752 (comment) I tested that the prepro changes were not breaking and did not require a prepro pipeline version bump. Here I now only update the rsv-a dataset (adding a new reference for the M2_1 gene). I check that:

1. RSV-a is usable (revisable, searchable) during pipeline rollout and after
2. backend compression migration is successful:

• fields removed from database
• old sequences are revisable by a curator

3. submission of new rsv-a sequences is successful

[anna-parker]

Staging testing notes:

1. I see that the migration has started but it seems to then be blocked:
   2025-12-01 15:32:28,788 INFO [main] [] [] - org.flywaydb.core.internal.logging.slf4j.Slf4jLog: Migrating schema "public" to version "1.21 - drop migration check column"
   oh no I see the logs
   Message : ERROR: Cannot drop column compression_migration_checked_at: NULL values exist in sequence_entries_preprocessed_data - this means not all rows have been migrated. Where: PL/pgSQL function inline_code_block line 7 at RAISE
   now I see Caused by: org.postgresql.util.PSQLException: ERROR: deadlock detected only...