Bump staging to 879ccf

[github-actions]

@anna-parker wants to update the staging deployment from pathoplexus/pathoplexus@b1a6c9b to pathoplexus/pathoplexus@879ccfa.

Commit date: 2026-09-29T15:49:27Z

Changelog

• 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...879ccfa

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)

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.

We discovered users have been using an old template for submissions so we are not mapping submissions with host:

BEGIN;

UPDATE public.sequence_entries
SET submitted_data = jsonb_set(
    submitted_data,
    '{metadata,host}',
    submitted_data->'metadata'->'hostNameScientific'
)
WHERE group_id != 1
      AND is_revocation IS NOT TRUE
      AND (
          submitted_data->'metadata'->'host' IS NULL
          OR submitted_data->'metadata'->'host' = 'null'::jsonb
          OR submitted_data->'metadata'->'host' = '""'::jsonb
      )
      AND submitted_data->'metadata' ? 'hostNameScientific';

UPDATE public.sequence_entries
SET submitted_data = jsonb_set(
    submitted_data,
    '{metadata,host}',
    '"Homo sapiens"'
)
WHERE submitted_data->'metadata'->>'hostNameCommon' = 'Human'
  AND NOT (submitted_data->'metadata' ? 'host')
  AND NOT (submitted_data->'metadata' ? 'hostNameScientific');

COMMIT;