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@achave11-ucsc achave11-ucsc commented Dec 8, 2025

Linked issues: #7474, #7548

Note

  • It is likely that the system administrator (@hannes-ucsc) will be required to increase the scope of the token used by the action invoking schedule.py to fully include project scope

Checklist

Author

  • PR is assigned to the author
  • Status of PR is In progress
  • PR is a draft
  • Target branch is develop
  • Name of PR branch matches issues/<GitHub handle of author>/<issue#>-<slug>
  • PR is linked to all issues it (partially) resolves
  • 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
  • For each linked 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 linked issues
  • This PR partially resolves each of the linked issues or does not have the partial label

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
  • 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

Author (API changes)

  • This PR and its linked 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 linked issues or the none of the stable branches (anvilprod and prod) have temporary hotfixes for any of the issues linked 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 Dockerfile, environment, requirements*.txt, common.mk, Makefile or environment.boot
  • 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
  • PR is awaiting requested review from a peer
  • Status of PR is Review requested
  • PR is assigned to only the peer and the author

Peer reviewer (after approval)

Note that after requesting changes, the PR must be assigned to only the author.

  • Actually approved the PR
  • 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
  • Labeled linked issues as demo or no demo
  • Commented on linked issues about demo expectations or all linked 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
  • Status of PR is Approved
  • PR is assigned to only the operator and the author

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)

  • Added sandbox label or PR is labeled no sandbox
  • Pushed PR branch to GitLab dev or PR is labeled no sandbox
  • Pushed PR branch to GitLab anvildev or PR is labeled no sandbox
  • Build passes in sandbox deployment or PR is labeled no sandbox
  • Build passes in anvilbox deployment or PR is labeled no sandbox
  • Reviewed build logs for anomalies in sandbox deployment or PR is labeled no sandbox
  • Reviewed build logs for anomalies in anvilbox deployment or PR is labeled no sandbox
  • Deleted unreferenced indices in sandbox or this PR does not remove catalogs or otherwise causes unreferenced indices in dev
  • Deleted unreferenced indices in anvilbox or this PR does not remove catalogs or otherwise causes unreferenced indices in anvildev
  • Started reindex in sandbox or this PR is not labeled reindex:dev
  • Started reindex in anvilbox or this PR is not labeled reindex:anvildev
  • Checked for failures in sandbox or this PR is not labeled reindex:dev
  • Checked for failures in anvilbox or this PR is not labeled reindex:anvildev

Operator (merge the branch)

  • All status checks passed and the PR is mergeable or PR is labeled no sandbox
  • 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
  • Requested from PR author that the last remaining CL item in Remove priority labels #7474 (comment) be completed
  • PR author confirmed full completion of CL items in Remove priority labels #7474

Operator (main build)

  • Pushed merge commit to GitLab dev
  • Pushed merge commit to GitLab anvildev
  • Build passes on GitLab dev
  • Reviewed build logs for anomalies on GitLab dev
  • Build passes on GitLab anvildev
  • Reviewed build logs for anomalies on GitLab anvildev
  • Ran _select dev.shared && make -C terraform/shared apply or this PR is not labeled deploy:shared
  • Ran _select anvildev.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 dev
  • 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
  • Deindexed all unreferenced catalogs in anvildev or this PR is neither labeled reindex:partial nor reindex:anvildev
  • 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
  • Indexed specific sources in dev or this PR is neither labeled reindex:partial nor reindex:dev
  • 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

url
]
log.info('Running %r …', command)
process = subprocess.run(command, check=True, stdout=subprocess.PIPE)

Check notice

Code scanning / CodeQL

Unused local variable Note

Variable process is not used.
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False positive, the variable is used on the next line

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coveralls commented Dec 8, 2025

Coverage Status

coverage: 85.046%. remained the same
when pulling 4c9fc98 on issues/achave11-ucsc/7474-remove-priority-labels
into 9e9805f on develop.

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codecov bot commented Dec 8, 2025

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.82%. Comparing base (9e9805f) to head (4c9fc98).
⚠️ Report is 7 commits behind head on develop.

Additional details and impacted files
@@           Coverage Diff            @@
##           develop    #7622   +/-   ##
========================================
  Coverage    84.82%   84.82%           
========================================
  Files          157      157           
  Lines        23060    23060           
========================================
  Hits         19561    19561           
  Misses        3499     3499           

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

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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.
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@achave11-ucsc achave11-ucsc self-assigned this Dec 8, 2025
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch from ed9db65 to 8f71a70 Compare December 9, 2025 19:22
@achave11-ucsc achave11-ucsc changed the title Fix: Remove priority labels (#7474) Fix: Remove priority labels (#7474, #7548) Dec 9, 2025
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch 2 times, most recently from 9fbbec1 to 0938b89 Compare December 10, 2025 03:13
@achave11-ucsc achave11-ucsc changed the title Fix: Remove priority labels (#7474, #7548) Enhancements to schedule.py (#7474, #7548) Dec 10, 2025
@achave11-ucsc
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Title differs from the issue because the PR addresses two issues.

@achave11-ucsc achave11-ucsc changed the title Enhancements to schedule.py (#7474, #7548) Add Azul GitHub project and priority support to schedule.py (#7474, #7548) Dec 10, 2025
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch 2 times, most recently from 31cdffc to 6ac3db6 Compare December 10, 2025 18:26
@achave11-ucsc achave11-ucsc removed the request for review from nadove-ucsc December 10, 2025 22:22
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch from 4d95c72 to 0cf4188 Compare December 10, 2025 22:26
log.info('Successfully created and verfied issue #%s', issue_number)
self.verify_issue(assignees, issue, labels, repository, type, url)

def verify_issue(self, assignees, issue, labels, repository, type, url):
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Type annotations would be nice here

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What's the point of this change? The PR doesn't add any other call sites.

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@achave11-ucsc achave11-ucsc Dec 11, 2025

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What's the point of this change?

To encapsulate the verification logic, but is not as extensive as I originally thought so I've dropped this change.

The PR doesn't add any other call sites.

Respectfully, is that a requirement?

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No, it isn't a requirement. It's the most obvious reason for extracting a method, but there are other valid reasons, including encapsulation. If you had decided to keep the change, I would have accepted your rationale.

assert set(labels) <= actual_labels, (labels, actual_labels)
actual_type = issue['type']['name']
assert type == actual_type, (type, actual_type)
log.info('Successfully created and verfied issue #%s', issue_number)
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Typo in "verfied". Fix in a separate commit.

Comment on lines 236 to 238
assert issue_project['title'] == issue['title'], issue_project['title']
assert issue_project['url'] == url, issue_project['url']
assert issue_project['id'] == project['id'], issue_project['id']
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Suggested change
assert issue_project['title'] == issue['title'], issue_project['title']
assert issue_project['url'] == url, issue_project['url']
assert issue_project['id'] == project['id'], issue_project['id']
assert issue_project['title'] == issue['title'], (issue_project['title'], issue['title'])
assert issue_project['url'] == url, (issue_project['url'], url)
assert issue_project['id'] == project['id'], (issue_project['id'], project['id'])

@nadove-ucsc nadove-ucsc removed their assignment Dec 11, 2025
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch from 7443e1e to a0961b9 Compare December 11, 2025 18:39
process = subprocess.run(command, check=True, stdout=subprocess.PIPE)
item = json.loads(process.stdout)
assert item['id'], item
priority = self.properties.get('_project_item_priority')
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I think using .get is a bad idea here, because if priority is None then line 241 will raise a KeyError.

Suggested change
priority = self.properties.get('_project_item_priority')
priority = self.properties['_project_item_priority']

project = json.loads(process.stdout)
assert project['title'] == title, (project['title'], title)
assert project['url'] == url, (project['url'], url)
assert project['id'] == item['id'], (project['id'], item['id'])
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There are three separate lookups of item['id'], so maybe extract a local for it?

log.info('Successfully created and verfied issue #%s', issue_number)
self.verify_issue(assignees, issue, labels, repository, type, url)

def verify_issue(self, assignees, issue, labels, repository, type, url):
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No, it isn't a requirement. It's the most obvious reason for extracting a method, but there are other valid reasons, including encapsulation. If you had decided to keep the change, I would have accepted your rationale.

@nadove-ucsc nadove-ucsc removed their assignment Dec 11, 2025
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch from a0961b9 to d1a5c69 Compare December 12, 2025 05:24
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch 2 times, most recently from 9668cc0 to 8e36011 Compare January 23, 2026 00:51
import urllib.parse
import zoneinfo

from azul import (
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I'm not sure we're can do this. It might break when the action actually runs.

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It is likely that the system administrator will require increasing the scope of the token used by the action invoking schedule.py to fully include project scope

Do you mean that I may be required to do this?

@hannes-ucsc hannes-ucsc removed their assignment Jan 26, 2026
@achave11-ucsc achave11-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch from 8e36011 to 89624cb Compare January 26, 2026 22:53
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achave11-ucsc commented Jan 27, 2026

Do you mean that I may be required to do this?

Correct, I intended for it to be generic and in the spirit of the CL. I modified the note slightly to @ mention you, didn't mean anything else by the generality.

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Do you mean that I may be required to do this?

Correct, I intended for it to be generic and in the spirit of the CL. I modified the note slightly to @ mention you, didn't mean anything else by the generality.

I updated the note to use passive voice.

@hannes-ucsc hannes-ucsc removed their assignment Jan 27, 2026
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I updated the token permissions:

CleanShot 2026-01-26 at 18 03 14@2x

@hannes-ucsc hannes-ucsc added the no sandbox [process] PR will not be tested in the sandbox label Jan 27, 2026
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Security design review

  • Security design review completed; this PR does not
    • … affect authentication; for example:
      • OAuth 2.0 with the application (API or Swagger UI)
      • Authentication of developers with Google Cloud APIs
      • Authentication of developers with AWS APIs
      • Authentication with a GitLab instance in the system
      • Password and 2FA authentication with GitHub
      • API access token authentication with GitHub
      • Authentication with Terra
    • … affect the permissions of internal users like access to
      • Cloud resources on AWS and GCP
      • GitLab repositories, projects and groups, administration
      • an EC2 instance via SSH
      • GitHub issues, pull requests, commits, commit statuses, wikis, repositories, organizations
    • … affect the permissions of external users like access to
      • TDR snapshots
    • … affect permissions of service or bot accounts
      • Cloud resources on AWS and GCP
    • … affect audit logging in the system, like
      • adding, removing or changing a log message that represents an auditable event
      • changing the routing of log messages through the system
    • … affect monitoring of the system
    • … introduce a new software dependency like
      • Python packages on PYPI
      • Command-line utilities
      • Docker images
      • Terraform providers
    • … add an interface that exposes sensitive or confidential data at the security boundary
    • … affect the encryption of data at rest
    • … require persistence of sensitive or confidential data that might require encryption at rest
    • … require unencrypted transmission of data within the security boundary
    • … affect the network security layer; for example by
      • modifying, adding or removing firewall rules
      • modifying, adding or removing security groups
      • changing or adding a port a service, proxy or load balancer listens on
  • Documentation on any unchecked boxes is provided in comments below

@dsotirho-ucsc dsotirho-ucsc force-pushed the issues/achave11-ucsc/7474-remove-priority-labels branch from 89624cb to 4c9fc98 Compare January 29, 2026 21:21
@hannes-ucsc hannes-ucsc merged commit e8f8149 into develop Jan 30, 2026
8 checks passed
@dsotirho-ucsc dsotirho-ucsc mentioned this pull request Jan 30, 2026
4 tasks
@dsotirho-ucsc dsotirho-ucsc deleted the issues/achave11-ucsc/7474-remove-priority-labels branch January 30, 2026 05:34
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3 reviews [process] Lead requested changes thrice no sandbox [process] PR will not be tested in the sandbox

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Scheduled azul-private issues are not automatically added to Azul project Remove priority labels

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