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@nadove-ucsc nadove-ucsc commented Nov 5, 2025

Linked issues: #7503

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  • Target branch is develop
  • Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
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  • Status of linked issues is In progress
  • PR description links to linked issues
  • PR title matches1 that of a linked issue or comment in PR explains why they're different
  • PR title references all linked issues
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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
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Author (reindex)

  • 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
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  • 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
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Author (before every review)

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Operator

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Operator (deploy .shared and .gitlab components)

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Operator (deploy runner image)

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Operator (sandbox build)

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Operator (main build)

  • Pushed merge commit to GitLab dev
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  • Build passes on GitLab dev
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  • Reviewed build logs for anomalies on GitLab anvildev
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  • Ran _select anvildev.shared && make -C terraform/shared apply or this PR is not labeled deploy:shared
  • Deleted PR branch from GitHub
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  • Deleted PR branch from GitLab anvildev
  • Status of linked issues is Lower, or Triage, if PR is partial

Operator (reindex)

  • Deindexed all unreferenced catalogs in dev or this PR is neither labeled reindex:partial nor reindex:dev
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  • Deindexed specific sources in dev or this PR is neither labeled reindex:partial nor reindex:dev
  • Deindexed specific sources in anvildev or this PR is neither labeled reindex:partial nor reindex:anvildev
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  • Indexed specific sources in anvildev or this PR is neither labeled reindex:partial nor reindex:anvildev
  • Started reindex in dev or this PR does not require reindexing dev
  • Started reindex in anvildev or this PR does not require reindexing anvildev
  • Checked for, triaged and possibly requeued messages in both fail queues in dev or this PR does not require reindexing dev
  • Checked for, triaged and possibly requeued messages in both fail queues in anvildev or this PR does not require reindexing anvildev
  • Emptied fail queues in dev or this PR does not require reindexing dev
  • Emptied fail queues in anvildev or this PR does not require reindexing anvildev
  • Restarted the Data Browser pipeline for the ucsc/hca/dev branch on GitLab in dev or this PR does not require reindexing dev
  • Restarted the Data Browser pipeline for the ucsc/lungmap/dev branch on GitLab in dev or this PR does not require reindexing dev
  • Restarted deploy_browser job in the GitLab pipeline for this PR in dev or this PR does not require reindexing dev
  • Restarted the Data Browser pipeline for the ucsc/anvil/anvildev branch on GitLab in anvildev or this PR does not require reindexing anvildev
  • Restarted deploy_browser job in the GitLab pipeline for this PR in anvildev or this PR does not require reindexing anvildev

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

@nadove-ucsc nadove-ucsc self-assigned this Nov 5, 2025
@nadove-ucsc nadove-ucsc linked an issue Nov 5, 2025 that may be closed by this pull request
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/7503-effective-value-azul-current-catalog-sources-not-obvious branch from 734fa0f to 9f13681 Compare November 5, 2025 01:11
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codecov bot commented Nov 5, 2025

Codecov Report

❌ Patch coverage is 12.50000% with 7 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.36%. Comparing base (bd301a9) to head (4177f3b).

Files with missing lines Patch % Lines
src/azul/__init__.py 12.50% 7 Missing ⚠️
Additional details and impacted files
@@             Coverage Diff             @@
##           develop    #7550      +/-   ##
===========================================
- Coverage    85.37%   85.36%   -0.02%     
===========================================
  Files          156      156              
  Lines        22496    22499       +3     
===========================================
  Hits         19206    19206              
- Misses        3290     3293       +3     

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coveralls commented Nov 5, 2025

Coverage Status

coverage: 85.578% (-0.01%) from 85.59%
when pulling 4177f3b on issues/nadove-ucsc/7503-effective-value-azul-current-catalog-sources-not-obvious
into bd301a9 on develop.

@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/7503-effective-value-azul-current-catalog-sources-not-obvious branch from 9f13681 to e2d4a74 Compare November 5, 2025 01:36
config.catalogs[config.current_catalog].name
],
choices=config.catalogs,
help='The names of the catalogs to reindex.')
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Suggested change
help='The names of the catalogs to reindex.')
help='Limit reindexing to a subset of the configured catalogs. This option can alternatively be set via an environment variable.')

@dsotirho-ucsc dsotirho-ucsc removed their assignment Nov 7, 2025
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/7503-effective-value-azul-current-catalog-sources-not-obvious branch 2 times, most recently from 5058166 to e9f12d7 Compare November 7, 2025 02:42
dsotirho-ucsc
dsotirho-ucsc previously approved these changes Nov 7, 2025
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Approved

@dsotirho-ucsc dsotirho-ucsc marked this pull request as ready for review November 7, 2025 17:20
if args.catalogs is None:
catalog_origin = 'environment variable'
if config.current_catalog is None:
catalog_origin += ' (unset)'
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@hannes-ucsc hannes-ucsc Nov 7, 2025

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Using catalog(s) specified via environment variable (unset): …

sounds confusing. How can something that's not set specify something? Maybe use a separate, third source to indicate this case?

@hannes-ucsc hannes-ucsc added the 0 reviews [process] Lead didn't request any changes label Nov 7, 2025
@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/7503-effective-value-azul-current-catalog-sources-not-obvious branch 2 times, most recently from dbc52ee to 50e4567 Compare November 7, 2025 21:42
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Fixup commits had to be squashed during conflict resolution.

@nadove-ucsc nadove-ucsc force-pushed the issues/nadove-ucsc/7503-effective-value-azul-current-catalog-sources-not-obvious branch from 50e4567 to 4177f3b Compare November 7, 2025 22:47
Comment on lines +83 to +84
'All sources must be public. If no values are passed, this argument will be set from the '
'environment variable ``azul_current_sources``. If that variable is unset, all sources in '
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I saw your two edits to this comment but I'm still confused. Where is the logging that shows the effective value and its provenance?

@hannes-ucsc hannes-ucsc removed their assignment Nov 8, 2025
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Effective value of azul_current_{catalog,source} is not obvious

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