Bump staging to c43453

[github-actions]

@corneliusroemer wants to update the staging deployment from pathoplexus/pathoplexus@b1a6c9b to pathoplexus/pathoplexus@c43453a.

Commit date: 2026-10-01T11:33:24Z

Changelog

• Update Loculus version to cbf764 pathoplexus#1177
• Update Loculus version to cdcfec pathoplexus#1176
• chore(taxonomy): use NCBI taxonomy build 2026-09-01 pathoplexus#1175
• feat(website): update the date of CHIKV release pathoplexus#1174
• Update Loculus version to 252763 pathoplexus#1173
• feat: add embl annotation files, reprocess everything pathoplexus#1164
• Add chikungunya pathoplexus#1141
• Update Loculus version to c95869 pathoplexus#1172
• docs: reword focal set requirements in restricted-use summary pathoplexus#1170
• chore(config): remove collection device/method, sample received date and sequencing date from desired fields and metadata template pathoplexus#1168
• Update Loculus version to 9af277 pathoplexus#1167

Comparison

pathoplexus/pathoplexus@b1a6c9b...c43453a

Pre-merge checklists

Before merging this PR and bumping the staging version, clone the production database to staging and confirm this was successful:

• DB clone: ssh bastion "cd pathoplexus/scripts/db-clone/ && ./clone-prod-to-staging.sh"
• Restart staging backend: kubectl rollout restart deployment/loculus-backend -n staging
• Run regressions tests to confirm staging is now identical to production (you will need to wait for SILO pods to import any new data)

7 dengue sequences seem to have been ingested on both prod and staging after clone so submission timestamps differ, otherwise no changes

• run host migration: https://github.com/pathoplexus/db-surgery/pull/1

Post-merge checklists

After merging this PR, work through these checks (or provide justification for anything that was skipped) to confirm functionality and data integrity of Pathoplexus under the new version.

Standard checklist:

• Run regression tests, highlight any observed differences and discuss why they are expected. If the new version includes new preprocessing pipeline versions: wait for reprocessing to finish and for all new SILO pods to come up first
• Confirm submit/revise/revoke flow works (also pay close attention to the UI, document anything out of the ordinary):
  • Submit test data to the staging preview
    • Confirm submission goes through (paste AccessionVersion(s) here)
  • Revise a test sequence (paste AccessionVersion here)
    • Confirm revision goes through
  • Revoke a test sequence (paste AccessionVersion here)
    • Confirm revocation goes through

Rollout-specific checklist:

Document any checks that were performed to test newly added features, database surgeries, etc. here.

[corneliusroemer]

I already ran this surgery now before this rolls to staging - discussed with Anya: https://github.com/pathoplexus/db-surgery/pull/1

[anna-parker]

Regression test results

1. annotations column added everywhere
2. Some modifications in hostNameCommon
   103 for andv e.g.

  accessionVersion: PP_006VQVN.1
    hostNameCommon: "mice and others" => "Magellanic pygmy rice rat"

  accessionVersion: PP_006VQXJ.1
    hostNameCommon: "hairy-tailed bolo mouse" => "Argentine bolo mouse; Temchuk's bolo mouse; hairy-tailed bolo mouse"

3 new hostNameCommon added fields for dengue, 127 for ebola-zaire (same name), 2 for measles (same name), 16 for mpox (same name):

  accessionVersion: PP_00538L8.1
    hostNameCommon: "crab eating macaque; crab-eating macaque; cynomolgus macaque; cynomolgus monkey; cynomolgus monkeys; long-tailed macaque" => "crab-eating macaque; cynomolgus macaque; cynomolgus monkey; cynomolgus monkeys; long-tailed macaque"

1 new hostNameCommon for west-nile virus:

  accessionVersion: PP_00027S4.2
    hostNameCommon: "Russian wild horse; tarpan" => "Russian wild horse; Yukon horse; Yukon wild horse; tarpan"

3. mpox 84 noInput fields that were incorrectly passed through removed

accessionVersion: PP_002XKUV.2
    ncbiVirusName: "Monkeypox virus" => ""
    ncbiVirusTaxId: "10244" => ""

5. Previously erroring author names now passed through, resulting in 39 new zika with Nebenf##hr, M., 7 yf with Guertin Patrick M, [. U. S. ].