Add mirror URI column to compact manifest (#7151) #7576

nadove-ucsc · 2025-11-18T01:46:15Z

Linked issues: #7151

Checklist

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

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Added p tag to titles of partial commits
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Added r tag to commit title _{or the changes introduced by this PR will not require reindexing of any deployment}
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This PR and its linked issues are labeled API _{or this PR does not modify a REST API}
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Added F tag to main commit title _{or this PR does not include permanent fix for a temporary hotfix}
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Checked reindex:… labels and r commit title tag
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Squashed PR branch and rebased onto develop
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Ran _select dev.shared && CI_COMMIT_REF_NAME=develop make -C terraform/shared apply_keep_unused _{or this PR is not labeled deploy:shared}
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Checked the items in the next section _{or this PR is labeled deploy:gitlab}
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Ran _select dev.gitlab && make -C terraform/gitlab/runner _{or this PR is not labeled deploy:runner}
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Operator (sandbox build)

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Operator (main build)

Operator (reindex)

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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}

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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

src/azul/plugins/metadata/anvil/__init__.py

+        # FIXME: AnVIL uses uncommon encoding for MD5 digests
+        #        https://github.com/DataBiosphere/azul/issues/7154
+        if False:
+            result[('contents', 'files')]['file_mirror_uri'] = 'files.azul_mirror_uri'


coveralls · 2025-11-19T02:20:17Z

coverage: 85.431% (+0.02%) from 85.409%
when pulling 7b68b86 on issues/nadove-ucsc/7151-add-mirror-uri-column-compact-manifest
into 27e0702 on develop.

codecov · 2025-11-19T03:13:29Z

Codecov Report

❌ Patch coverage is 96.00000% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 85.21%. Comparing base (27e0702) to head (7b68b86).

Files with missing lines	Patch %	Lines
src/azul/service/manifest_service.py	94.44%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #7576      +/-   ##
===========================================
+ Coverage    85.19%   85.21%   +0.02%     
===========================================
  Files          156      156              
  Lines        22571    22592      +21     
===========================================
+ Hits         19229    19252      +23     
+ Misses        3342     3340       -2

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

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dsotirho-ucsc

Approved.

nadove-ucsc self-assigned this Nov 18, 2025

nadove-ucsc linked an issue Nov 18, 2025 that may be closed by this pull request

Add mirror URI column to compact manifest #7151

Open

nadove-ucsc force-pushed the issues/nadove-ucsc/7151-add-mirror-uri-column-compact-manifest branch from 1883281 to e28a965 Compare November 19, 2025 02:04

github-advanced-security bot found potential problems Nov 19, 2025

View reviewed changes

nadove-ucsc added 3 commits November 18, 2025 18:43

Only inject file_url if it is defined in the manifest config

fe27511

Add mirror URI column to compact manifest (#7151)

80eb656

Disable mirror URI column for AnVIL and add FIXME (#7154)

7b68b86

nadove-ucsc force-pushed the issues/nadove-ucsc/7151-add-mirror-uri-column-compact-manifest branch from 13786a3 to fe27511 Compare November 19, 2025 02:58

nadove-ucsc requested a review from dsotirho-ucsc November 19, 2025 04:54

nadove-ucsc assigned dsotirho-ucsc Nov 19, 2025

dsotirho-ucsc approved these changes Nov 19, 2025

View reviewed changes

dsotirho-ucsc marked this pull request as ready for review November 19, 2025 19:00

dsotirho-ucsc requested a review from hannes-ucsc as a code owner November 19, 2025 19:00

dsotirho-ucsc assigned hannes-ucsc and unassigned dsotirho-ucsc Nov 19, 2025

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Add mirror URI column to compact manifest (#7151) #7576

Add mirror URI column to compact manifest (#7151) #7576

nadove-ucsc commented Nov 18, 2025 •

edited by dsotirho-ucsc

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Checklist

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Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

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System administrator (post-deploy of .gitlab component)

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nadove-ucsc commented Nov 18, 2025 •

edited by dsotirho-ucsc

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