Promotion 2026-08-25 anvilprod (#8245, #8255, #8282, DataBiosphere/azul-private#377, DataBiosphere/azul-private#414)

[hannes-ucsc]

Linked issues: #8245, #8255, #8282, DataBiosphere/azul-private#377, DataBiosphere/azul-private#414

Checklist

Author

• PR is assigned to the author
• Status of PR is In progress
• Target branch is anvilprod
• Name of PR branch matches promotions/yyyy-mm-dd-anvilprod
• PR is linked to the promotion issues it resolves
• Status of linked issue is In progress
• PR description links to linked issues
• Title of linked issue matches Promotion yyyy-mm-dd
• PR title starts with title of linked issue followed by anvilprod
• PR title references the linked issues

Author (reindex)

• This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
• This PR is labeled reindex:partial and its description documents the specific reindexing procedure for anvilprod _{or requires a full reindex or is not labeledreindex:anvilprod}

Author (mirror)

• This PR is labeled mirror:anvilprod _{or the changes introduced by it will not require mirroring of anvilprod}
• This PR is labeled mirror:partial and its description documents the specific mirroring procedure for anvilprod _{or requires a full mirroring or is not labeledmirror:anvilprod}

Author (upgrading deployments)

• This PR is labeled upgrade _{or does not require upgrading deployments}
• This PR is labeled deploy:shared _{or does not modify docker_images.json, and does not require deploying the shared component for any other reason}
• This PR is labeled deploy:gitlab _{or does not require deploying the gitlab component}
• This PR is labeled deploy:runner _{or does not require deploying the runner image}

Author (before every review)

• PR branch is up to date (if not, merge anvilprod into PR branch to integrate upstream changes)
• PR is not a draft
• PR is awaiting requested review from system administrator
• Status of PR is Review requested
• PR is assigned to only the system administrator and the author

System administrator (after approval)

• Actually approved the PR
• Decided if PR can be labeled no sandbox
• N reviews label is accurate
• Status of PR is Approved
• PR is assigned to only the operator and the author

Operator

• Pushed PR branch to GitHub

Operator (deploy .shared and .gitlab components)

• Ran _select anvilprod.shared && CI_COMMIT_REF_NAME=anvilprod make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
• Ran _select anvilprod.gitlab && python scripts/create_gitlab_snapshot.py --no-restart (see operator manual for details) _{or this PR is not labeled backup:gitlab}
• Ran _select anvilprod.gitlab && CI_COMMIT_REF_NAME=anvilprod make -C terraform/gitlab apply(an error from _login_docker_gitlab is benign if the instance was stopped for backup) _{or this PR is not labeled deploy:gitlab}
• Checked the items in the next section _{or this PR is labeled deploy:gitlab}
• PR is assigned to only the system administrator and the author _{or this PR is not labeled deploy:gitlab}

System administrator (post-deploy of .gitlab component)

• Background migrations for anvilprod.gitlab are complete _{or this PR is not labeled deploy:gitlab}
• PR is assigned to only the operator and the author

Operator (deploy runner image)

• Ran _select anvilprod.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}

Operator (sandbox build)

• Added sandbox label _{or PR is labeled no sandbox}
• Pushed PR branch to GitLab anvilprod _{or PR is labeled no sandbox}
• Build passes in hammerbox deployment _{or PR is labeled no sandbox}
• Reviewed build logs for anomalies in hammerbox deployment _{or PR is labeled no sandbox}
• Applied upgrade instructions from UPGRADING.rst to hammerbox _{or this PR is not labeled upgrade, or upgrade instructions do not apply to hammerbox}
• In hammerbox, deleted the catalogs specified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• In hammerbox, deindexed the sources sepcified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• In hammerbox, indexed the sources specified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• In hammerbox, indexed the catalogs specified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• Started full reindex in hammerbox _{or this PR is not labeled reindex:anvilprod or it is labeled reindex:partial}
• Checked for failures in hammerbox _{or this PR is not labeled reindex:anvilprod}
• Started mirroring in hammerbox _{or this PR is not labeled mirror:anvilprod}
• Checked for failures in hammerbox _{or this PR is not labeled mirror:anvilprod}

Operator (merge the branch)

• All status checks passed and the PR is mergeable
• The title of the merge commit starts with the title of this PR
• Added PR # reference to merge commit title
• Collected commit title tags in merge commit title _{but excluded any p tags}
• Pushed merge commit to GitHub
• Status of PR is Merged stable

Operator (main build)

• Pushed merge commit to GitLab anvilprod
• Build passes on GitLab anvilprod
• Reviewed build logs for anomalies on GitLab anvilprod
• Applied upgrade instructions from UPGRADING.rst to anvilprod _{or this PR is not labeled upgrade, or upgrade instructions do not apply to anvilprod}
• Ran _select anvilprod.shared && make -C terraform/shared apply _{or this PR is not labeled deploy:shared}
• Deleted PR branch from GitHub
• PR is assigned to only the operator
• Deleted PR branch from GitLab anvilprod
• Status of linked issue is Stable
• Status of promoted¹ PRs is Merged stable
• Status of promoted¹ issues is Stable

¹ Promoted issues and PRs are referenced in the titles of the commits
that the promotion branch introduces to the stable branch. Prior to the
promotion, the status of promoted issues (PRs) is Lower (Merged lower).
Promoted PRs in status Done do not need to be moved.

Operator (reindex)

• In anvilprod, deleted the catalogs specified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• In anvilprod, deindexed the sources sepcified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• In anvilprod, indexed the sources specified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• In anvilprod, indexed the catalogs specified in the notes _{or this PR is missing either the reindex:partial or the reindex:anvilprod label, or both}
• Started full reindex in anvilprod _{or this PR is not labeled reindex:anvilprod or it is labeled reindex:partial}
• Checked for, triaged and possibly requeued messages in both fail queues in anvilprod _{or this PR is not labeled reindex:anvilprod or it is labeled reindex:partial}
• Emptied fail queues in anvilprod _{or this PR is not labeled reindex:anvilprod or it is labeled reindex:partial}
• Restarted the Data Browser pipeline for the ucsc/anvil/anvilprod branch on GitLab in anvilprod _{or this PR is not labeled reindex:anvilprod}
• Restarted deploy_browser job in the GitLab pipeline for this PR in anvilprod _{or this PR is not labeled reindex:anvilprod}

Operator (mirroring)

• Started mirroring in anvilprod _{or this PR is not labelled mirror:anvilprod}
• Checked for, triaged and possibly requeued messages in mirror fail queue in anvilprod _{or this PR is not labelled mirror:anvilprod}
• Emptied mirror fail queue in anvilprod _{or this PR is not labelled mirror:anvilprod}

Operator

• PR is assigned to only the system administrator

System administrator

• Removed unused image tags from pycharm image on DockerHub _{or this promotion does not alter references to that image}
• Removed unused image tags from bigquery_emulator image on DockerHub _{or this promotion does not alter references to that image}
• PR is assigned to no one

Shorthand for review comments

• L line is too long
• W line wrapping is wrong
• Q bad quotes
• F other formatting problem

[codecov]

Codecov Report

❌ Patch coverage is 87.63557% with 114 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.54%. Comparing base (38041a3) to head (5e419ec).
⚠️ Report is 1 commits behind head on anvilprod.

Files with missing lines	Patch %	Lines
test/integration_test.py	0.00%	52 Missing ⚠️
src/azul/indexer/cache_service.py	79.47%	47 Missing ⚠️
src/azul/terra.py	54.54%	5 Missing ⚠️
src/azul/oauth2.py	33.33%	2 Missing ⚠️
src/azul/plugins/metadata/hca/indexer/aggregate.py	96.15%	2 Missing ⚠️
src/azul/lib/urls.py	94.44%	1 Missing ⚠️
src/azul/plugins/repository/tdr_anvil/__init__.py	97.56%	1 Missing ⚠️
src/azul/service/manifest_service.py	50.00%	1 Missing ⚠️
src/azul/service/user_controller.py	80.00%	1 Missing ⚠️
src/azul/service/user_service.py	50.00%	1 Missing ⚠️
... and 1 more

Additional details and impacted files

@@              Coverage Diff              @@
##           anvilprod    #8262      +/-   ##
=============================================
- Coverage      84.54%   84.54%   -0.01%     
=============================================
  Files            166      169       +3     
  Lines          24577    25248     +671     
=============================================
+ Hits           20779    21345     +566     
- Misses          3798     3903     +105     

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[coveralls]

coverage: 84.619% (-0.007%) from 84.626% — promotions/2026-08-25-anvilprod into anvilprod