Enable mirroring in anvildev and anvilbox (#7154, #7214) #7223

nadove-ucsc · 2025-06-16T21:59:37Z

Connected issues: #7154, #7214

Checklist

Author

PR is a draft
Target branch is develop
Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
On ZenHub, PR is connected to all issues it (partially) resolves
PR description links to connected issues
PR title matches¹ that of a connected issue _{or comment in PR explains why they're different}
PR title references all connected issues
For each connected issue, there is at least one commit whose title references that issue

¹ when the issue title describes a problem, the corresponding PR
title is Fix: followed by the issue title

Author (partiality)

Added p tag to titles of partial commits
This PR is labeled partial _{or completely resolves all connected issues}
This PR partially resolves each of the connected issues _{or does not have the partial label}

Author (chains)

This PR is blocked by previous PR in the chain _{or is not chained to another PR}
The blocking PR is labeled base _{or this PR is not chained to another PR}
This PR is labeled chained _{or is not chained to another PR}

Author (reindex, API changes)

Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
This PR is labeled reindex:dev _{or the changes introduced by it will not require reindexing of dev}
This PR is labeled reindex:anvildev _{or the changes introduced by it will not require reindexing of anvildev}
This PR is labeled reindex:anvilprod _{or the changes introduced by it will not require reindexing of anvilprod}
This PR is labeled reindex:prod _{or the changes introduced by it will not require reindexing of prod}
This PR is labeled reindex:partial and its description documents the specific reindexing procedure for dev, anvildev, anvilprod and prod _{or requires a full reindex or carries none of the labels reindex:dev, reindex:anvildev, reindex:anvilprod and reindex:prod}
This PR and its connected issues are labeled API _{or this PR does not modify a REST API}
Added a (A) tag to commit title for backwards (in)compatible changes _{or this PR does not modify a REST API}
Updated REST API version number in app.py _{or this PR does not modify a REST API}

Author (upgrading deployments)

Ran make docker_images.json and committed the resulting changes _{or this PR does not modify azul_docker_images, or any other variables referenced in the definition of that variable}
Documented upgrading of deployments in UPGRADING.rst _{or this PR does not require upgrading deployments}
Added u tag to commit title _{or this PR does not require 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 (hotfixes)

Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
Reverted the temporary hotfixes for any connected issues _{or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues connected to this PR}

Author (before every review)

Rebased PR branch on develop, squashed fixups from prior reviews
Ran make requirements_update _{or this PR does not modify requirements*.txt, common.mk, Makefile and Dockerfile}
Added R tag to commit title _{or this PR does not modify requirements*.txt}
This PR is labeled reqs _{or does not modify requirements*.txt}
make integration_test passes in personal deployment _{or this PR does not modify functionality that could affect the IT outcome}

Peer reviewer (after approval)

Actually approved the PR
PR is not a draft
Ticket is in Review requested column
PR is awaiting requested review from system administrator
PR is assigned to only the system administrator

System administrator (after approval)

Actually approved the PR
Labeled connected issues as demo or no demo
Commented on connected issues about demo expectations _{or all connected issues are labeled no demo}
Decided if PR can be labeled no sandbox
A comment to this PR details the completed security design review
PR title is appropriate as title of merge commit
N reviews label is accurate
Moved connected issues to Approved column
PR is assigned to only the operator

Operator (before pushing merge the commit)

System administrator

Background migrations for dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
PR is assigned to only the operator

Operator

Checked reindex:… labels and r commit title tag
Checked that demo expectations are clear _{or all linked issues are labeled no demo}
Squashed PR branch and rebased onto develop
Sanity-checked history
Pushed PR branch to GitHub

Operator (deploy `.shared` and `.gitlab` components)

Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select dev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{or this PR is not labeled deploy:gitlab}
Ran _select anvildev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
Ran _select anvildev.gitlab && CI_COMMIT_REF_NAME=develop make -C terraform/gitlab apply _{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 dev.gitlab are complete _{or this PR is not labeled deploy:gitlab}
Background migrations for anvildev.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 dev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
Ran _select anvildev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}

Operator (sandbox build)

System administrator

Mirrored anvilbox
PR is assigned to only the operator

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 only included p if the PR is also labeled partial}
Pushed merge commit to GitHub
Status of PR is Merged lower
Status of blocked issues is Triage _{or no issues are blocked on the linked issues}

Operator (main build)

Operator (reindex)

System administrator

Mirrored anvildev
PR is assigned to only the operator

Operator (mirroring)

~~Started mirroring in dev _{or this PR does not require mirroring dev}~~
~~Started mirroring in anvildev _{or this PR does not require mirroring anvildev}~~
Checked for, triaged and possibly requeued messages in mirror fail queue in dev _{or this PR does not require mirroring dev}
Checked for, triaged and possibly requeued messages in mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}
Emptied mirror fail queue in dev _{or this PR does not require mirroring dev}
Emptied mirror fail queue in anvildev _{or this PR does not require mirroring anvildev}

Operator

Propagated the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels to the next promotion PRs _{or this PR carries none of these labels}
Propagated any specific instructions related to the deploy:shared, deploy:gitlab, deploy:runner, API, reindex:partial, reindex:anvilprod and reindex:prod labels, from the description of this PR to that of the next promotion PRs _{or this PR carries none of these labels}
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 · 2025-06-17T07:52:13Z

Codecov Report

❌ Patch coverage is 75.00000% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.86%. Comparing base (9b68251) to head (8c1d149).
⚠️ Report is 8 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/azul/plugins/repository/tdr_anvil/__init__.py	77.27%	5 Missing ⚠️
src/azul/indexer/mirror_file_service.py	0.00%	2 Missing ⚠️
test/integration_test.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7223      +/-   ##
===========================================
- Coverage    84.88%   84.86%   -0.02%     
===========================================
  Files          157      157              
  Lines        22796    22816      +20     
===========================================
+ Hits         19350    19363      +13     
- Misses        3446     3453       +7

☔ View full report in Codecov by Sentry.
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coveralls · 2025-06-17T09:29:02Z

coverage: 85.087% (-0.02%) from 85.104%
when pulling 8c1d149 on issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding
into 9b68251 on develop.

dsotirho-ucsc

Approved.

hannes-ucsc

This will get conflicts once the backport I just approved land on develop.

It's not evident from the title of that commit that removes the snapshot what the defect is. Either add a ticket reference or describe the defect in the body of the commit message. Probably the former is warranted so that we can point our collaborators at it.

The base branch was changed.

hannes-ucsc

While the link in the message body of the middle commit is helpful, the body should be self-contained and include a description of the alleged defect.

hannes-ucsc · 2025-12-11T08:04:23Z

hannes-ucsc · 2025-12-11T08:08:04Z

Security design review

This change copies data files from mock managed-access snapshots in TDR's GCP bucket to an Azul-managed S3 bucket. The snapshots are actually public, we just pretend they are managed-access. Since there simply is no actual managed-access (meta)data in the platform-anvil-dev zone, neither a software defect nor an outage introduce the risk of leaking managed access data.

and document use case for default value

Previously disabled due to the issues with MD5 encoding

…7634)

nadove-ucsc added reindex:anvildev [process] PR requires reindexing anvildev reindex:anvilprod [process] PR requires reindexing anvilprod labels Jun 16, 2025

github-actions bot added the orange label Jun 16, 2025

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch 3 times, most recently from 85448b8 to 1cb13db Compare June 17, 2025 07:28

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from 1cb13db to 9dc69e5 Compare June 26, 2025 06:39

nadove-ucsc assigned dsotirho-ucsc Jun 26, 2025

nadove-ucsc requested a review from dsotirho-ucsc June 26, 2025 07:05

dsotirho-ucsc previously approved these changes Jun 26, 2025

View reviewed changes

dsotirho-ucsc marked this pull request as ready for review June 26, 2025 18:14

dsotirho-ucsc requested a review from hannes-ucsc as a code owner June 26, 2025 18:14

dsotirho-ucsc assigned hannes-ucsc and unassigned dsotirho-ucsc Jun 26, 2025

hannes-ucsc requested changes Jul 1, 2025

View reviewed changes

hannes-ucsc added the 1 review [process] Lead requested changes once label Jul 1, 2025

hannes-ucsc removed their assignment Jul 1, 2025

nadove-ucsc added the chained [process] PR needs to based of develop before merging label Jul 3, 2025

nadove-ucsc changed the base branch from develop to backports/36999c52 July 3, 2025 00:30

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from 9dc69e5 to a0ad747 Compare July 3, 2025 00:30

achave11-ucsc changed the base branch from backports/36999c52 to develop July 9, 2025 03:46

achave11-ucsc removed the chained [process] PR needs to based of develop before merging label Jul 9, 2025

nadove-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from a0ad747 to 8056e9e Compare July 9, 2025 06:56

nadove-ucsc requested a review from hannes-ucsc July 9, 2025 07:27

nadove-ucsc assigned hannes-ucsc Jul 9, 2025

hannes-ucsc requested changes Jul 14, 2025

View reviewed changes

hannes-ucsc removed their assignment Jul 14, 2025

nadove-ucsc requested a review from hannes-ucsc December 10, 2025 21:43

nadove-ucsc assigned hannes-ucsc Dec 10, 2025

hannes-ucsc approved these changes Dec 11, 2025

View reviewed changes

hannes-ucsc assigned dsotirho-ucsc and unassigned hannes-ucsc Dec 11, 2025

nadove-ucsc added 6 commits December 11, 2025 09:30

Refactor BigQuery column lookup in AnVIL plugin

7ad7065

and document use case for default value

Verify download size in mirror file service

ca60488

[r] Fix: AnVIL uses uncommon encoding for MD5 digests (#7154)

cb35d64

Enable mirror URI column in compact AnVIL manifests (#7151)

43080c8

Previously disabled due to the issues with MD5 encoding

[u] Enable mirroring in anvildev and anvilbox (#7214)

fbfc1cc

[u] Work around unmirrorable files in 1000G snapshot and add FIXME (#…

8c1d149

…7634)

dsotirho-ucsc force-pushed the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch from 4695a1a to 8c1d149 Compare December 11, 2025 17:31

dsotirho-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Dec 11, 2025

dsotirho-ucsc assigned hannes-ucsc and unassigned dsotirho-ucsc and nadove-ucsc Dec 11, 2025

hannes-ucsc assigned dsotirho-ucsc and unassigned hannes-ucsc Dec 11, 2025

dsotirho-ucsc merged commit af7d095 into develop Dec 11, 2025
10 checks passed

dsotirho-ucsc mentioned this pull request Dec 11, 2025

Enable mirroring in hammerbox #7534

Open

dsotirho-ucsc deleted the issues/nadove-ucsc/7154-anvil-uses-nonstandard-md5-enconding branch December 11, 2025 21:29

dsotirho-ucsc assigned hannes-ucsc, dsotirho-ucsc and achave11-ucsc and unassigned dsotirho-ucsc and hannes-ucsc Dec 11, 2025

achave11-ucsc removed their assignment Dec 16, 2025

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Enable mirroring in anvildev and anvilbox (#7154, #7214) #7223

Enable mirroring in anvildev and anvilbox (#7154, #7214) #7223

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Checklist

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Author (chains)

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Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator (before pushing merge the commit)

System administrator

Operator

Operator (deploy .shared and .gitlab components)

System administrator (post-deploy of .gitlab component)

Operator (deploy runner image)

Operator (sandbox build)

System administrator

Operator (merge the branch)

Operator (main build)

Operator (reindex)

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nadove-ucsc commented Jun 16, 2025 •

edited by achave11-ucsc

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