Bump staging to 8b8f81

[github-actions]

@maverbiest wants to update the staging deployment from pathoplexus/pathoplexus@a12f630 to pathoplexus/pathoplexus@8b8f81a.

Commit date: 2026-09-08T08:56:43Z

Changelog

• Add zika viral usher linkout pathoplexus#1134
• Update Loculus version to 94efc2 pathoplexus#1136

Comparison

pathoplexus/pathoplexus@a12f630...8b8f81a

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)

Three cchf that were ingested on staging and prod (or ingested right as I was doing DB clone?) and released with slightly different timestamps (https://pathoplexus.org/cchf/search?visibility_releasedAtTimestamp=true&releasedAtTimestampFrom=1788856341&releasedAtTimestampTo=1788856343&isRevocation=&versionStatus=&visibility_versionStatus=true&visibility_isRevocation=true):

  accessionVersion: PP_007L167.1
    submittedAtTimestamp: "1788856332" => "1788856712"
    releasedAtTimestamp: "1788856342" => "1788856743"

  accessionVersion: PP_007L175.1
    submittedAtTimestamp: "1788856332" => "1788856712"
    releasedAtTimestamp: "1788856342" => "1788856743"

  accessionVersion: PP_007L183.1
    submittedAtTimestamp: "1788856332" => "1788856712"
    releasedAtTimestamp: "1788856342" => "1788856743"

As well as the CCHF that I submitted to staging here #836

  accessionVersion: PP_007L258.1
  accession: PP_007L258
  version: 1
  submissionId: test_NIHPAK-19
  isRevocation: false
  submitter: mverbiest_curator
  groupName: Epidemiology and Virus Evolution, Swiss TPH, Switzerland
  ...

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

Regression tests are clean, apart from testing sequences I submitted and the newly ingested CCHF listed above

• 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 (CCHF: PP_007L52B.1, WNV: PP_007L539.1, PP_007L547.1, PP_007L555.1, ...)
  • Revise a test sequence (Revising PP_007L52B.1)
    • Confirm revision goes through (revised version is PP_007L52B.2)
  • Revoke a test sequence (revoking PP_007L539.1)
    • Confirm revocation goes through (revocation is PP_007L539.2)

Rollout-specific checklist:

• Confirm Zika UShER linkout works on staging

• @anna-parker checked that metadata docs look as expected (host no longer in uncategorized)

[anna-parker]

I just checked that the metadata docs look good and show the extra input field host correctly for e.g. dengue (also the excel download is correct)

[anna-parker]

I will also delete the liveness times of all ncbi nuccore accessions as our pipeline was incorrectly marking all Genbank nuccore accessions live (even when not live, see loculus-project/loculus#7220), I know this started happening sometime since loculus-project/loculus#7151 (at this point tests passed) so I only need to do this for liveness times set in the last 2 weeks:

SELECT *
FROM ena_deposition_schema.assembly_table
WHERE ncbi_nucleotide_first_publicly_visible >= NOW() - INTERVAL '2 weeks';

returns 55 entries.

UPDATE ena_deposition_schema.assembly_table
SET ncbi_nucleotide_first_publicly_visible = NULL
WHERE ncbi_nucleotide_first_publicly_visible >= NOW() - INTERVAL '2 weeks';

awesome, I forced a rerun and now only 53 entries and not live assemblies e.g. https://www.ncbi.nlm.nih.gov/nuccore?term=OZ545432.1 is not included