Fix: GH Action schedule failed to create promotion ticket (#8041) by achave11-ucsc · Pull Request #8110 · DataBiosphere/azul

achave11-ucsc · 2026-06-11T17:35:01Z

Linked issues: #8041

Checklist

Author

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 (mirror)

This PR is labeled mirror:dev _{or the changes introduced by it will not require mirroring of dev}
This PR is labeled mirror:anvildev _{or the changes introduced by it will not require mirroring of anvildev}
This PR is labeled mirror:anvilprod _{or the changes introduced by it will not require mirroring of anvilprod}
This PR is labeled mirror:prod _{or the changes introduced by it will not require mirroring of prod}
This PR is labeled mirror:partial and its description documents the specific mirroring procedure for dev, anvildev, anvilprod and prod _{or requires a full mirroring or carries none of the labels mirror:dev, mirror:anvildev, mirror:anvilprod and mirror: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)

Operator

Checked reindex:… labels and r commit title tag
Checked mirror:… labels
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)

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)

Operator (mirroring)

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

Operator

Propagated the upgrade and API labels to the next promotion PRs _{or this PR carries neither of these labels}
Propagated the deploy:shared, deploy:gitlab, deploy:runner, reindex:partial, reindex:anvilprod, reindex:prod, mirror:partial, mirror:anvilprod and mirror: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, reindex:partial, reindex:anvilprod, reindex:prod, mirror:partial, mirror:anvilprod and mirror: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 · 2026-06-11T17:47:22Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.35%. Comparing base (dda3db9) to head (eab7c7a).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #8110   +/-   ##
========================================
  Coverage    84.35%   84.35%           
========================================
  Files          166      166           
  Lines        24460    24460           
========================================
  Hits         20633    20633           
  Misses        3827     3827

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coveralls · 2026-06-11T17:47:40Z

coverage: 84.435%. remained the same — issues/achave11-ucsc/8041-add-GL-schdule into develop

dsotirho-ucsc

Merge conflicts.

hannes-ucsc · 2026-07-03T08:35:18Z

+- Optionally, [GitHub CLI], which is used by the scheduled GitLab job,
+  `github_schedule`, to create the GitHub issues from templates. You may install
+  the version set at `azul_ghcli_version` in [environment.py](environment.py),
+  or any compatible recent version.


Suggested change

- Optionally, [GitHub CLI], which is used by the scheduled GitLab job,

`github_schedule`, to create the GitHub issues from templates. You may install

the version set at `azul_ghcli_version` in [environment.py](environment.py),

or any compatible recent version.

- Optionally, the [GitHub CLI]. You should install

the version set at `azul_ghcli_version` in [environment.py](environment.py),

or a more recent, compatible version.

hannes-ucsc · 2026-07-03T08:40:26Z

+
+Next, confirm with the SA that the ``azul_github_access_token`` used in both
+instances' ``environment.local.py`` is set, and that its permissions are
+equivalent to the ``AZUL_GITHUB_TOKEN`` in the GitHub Action secrets.


Suggested change

equivalent to the ``AZUL_GITHUB_TOKEN`` in the GitHub Action secrets.

equivalent to that of the token deposited in the ``AZUL_GITHUB_TOKEN`` GitHub Action secret.

hannes-ucsc · 2026-07-03T08:40:50Z

+2) Set the interval pattern to ``0 * * * *`` on ``dev`` and ``30 * * * *`` on
+``anvildev``.
+
+3) Set the cron timezone to ``Pacific Time (US & Canada)``


Suggested change

3) Set the cron timezone to ``Pacific Time (US & Canada)``

3) Set the Cron timezone to ``Pacific Time (US & Canada)``

hannes-ucsc · 2026-07-03T08:49:34Z

+instances' ``environment.local.py`` is set, and that its permissions are
+equivalent to the ``AZUL_GITHUB_TOKEN`` in the GitHub Action secrets.
+
+Lastly, remove ``AZUL_GITHUB_TOKEN`` from the GitHub Action secrets.


I'm not sure that operators have the necessary permissions to do this.

hannes-ucsc · 2026-07-07T07:34:47Z

(Posted by Claude Code)

Superseded — see updated security design review.

Security Design Review

PR Summary: This PR migrates the scheduled GitHub issue creation from a GitHub Action to a GitLab CI job. It installs the GitHub CLI (gh) in the Docker image, adds a github_schedule GitLab CI job that runs .github/workflows/schedule.py using azul_github_access_token, and moves the old GitHub Actions workflow to attic/. The PR also includes routine dependency updates (certifi, click, greenlet, etc.).

Findings

1. No integrity verification for GitHub CLI binary download (Moderate)

The Dockerfile (Dockerfile:64-67) downloads the gh binary from GitHub releases and pipes it directly to tar with no checksum or signature verification:

RUN set -o pipefail \
    && curl --fail --silent --location \
       https://github.com/cli/cli/releases/download/v${azul_ghcli_version}/gh_${azul_ghcli_version}_linux_${TARGETARCH}.tar.gz \
    | tar -xzf - -C /usr/local/bin --strip-components=2 --wildcards "*/bin/gh" --occurrence=1

This contrasts with other tool installations in the same Dockerfile:

AWS CLI: GPG signature verified (gpg --verify)
Docker credential helper: SHA256 checksum verified
Docker packages: signed apt repository

The gh CLI project publishes gh_X.Y.Z_checksums.txt with a detached GPG signature in each release, so verification is feasible. Without it, a compromised release artifact or build-time network attack could inject a malicious binary into the image. Recommend adding checksum verification.

2. Token scope and credential migration (Low)

The azul_github_access_token description in environment.py is expanded from "post status checks" to also "create issues in the Azul repositories." Some issue templates target DataBiosphere/azul-private, requiring a classic PAT with repo scope, which is broad (full access to private repositories the token owner can access). This scope requirement is inherited from the old GitHub Action, not new to this PR.

The credential migration path is sound: UPGRADING.rst properly instructs confirming the GitLab token has equivalent permissions and then removing the old AZUL_GITHUB_TOKEN from GitHub Actions secrets, avoiding lingering unused credentials.

Verified items (no concerns)

No command injection risk. subprocess.run in schedule.py is called with list arguments throughout (no shell=True). Front matter values are passed to gh via -f flags, not shell-interpolated.
No unsafe deserialization. The YAML-like front matter parser (schedule.py:63-82) is a simple line-by-line key-value parser, not yaml.load().
Token not leaked in logs. The gh CLI reads credentials from the GITHUB_TOKEN environment variable, not from command-line arguments. The gh_json logging (Running ['gh', ...]) will not expose the token.
Post-creation verification (schedule.py:196-208). After creating an issue, the script verifies that labels, assignees, and type were correctly applied by inspecting the API response, catching silent permission failures.
Idempotency. Before creating an issue, the script searches for existing issues with the same title (schedule.py:161-168), preventing duplicates if the job runs more than once in the eligible window.
Certifi update (2026.5.20 → 2026.6.17) is a routine CA certificate bundle update — positive security maintenance.

Conclusion

The migration from GitHub Actions to GitLab CI is architecturally sound and the Python script is well-defended against injection and permission issues. The main recommendation is to add checksum or signature verification for the GitHub CLI download in the Dockerfile to match the integrity verification standard established for other tools in the same image.

hannes-ucsc · 2026-07-07T08:19:26Z

(Posted by Claude Code)

Security Design Review

PR Summary: This PR migrates the scheduled GitHub issue creation from a GitHub Action to a GitLab CI job. It installs the GitHub CLI (gh) in the Docker image with SHA-256 checksum verification, adds a github_schedule GitLab CI job that runs .github/workflows/schedule.py using azul_github_access_token, and moves the old GitHub Actions workflow to attic/. The PR also includes routine dependency updates (certifi, click, greenlet, etc.).

Findings

1. Token scope and credential migration (Low)

The azul_github_access_token description in environment.py is expanded from "post status checks" to also "create issues in the Azul repositories." Some issue templates target DataBiosphere/azul-private, requiring a classic PAT with repo scope, which is broad (full access to private repositories the token owner can access). This scope requirement is inherited from the old GitHub Action, not new to this PR.

The credential migration path is sound: UPGRADING.rst properly instructs confirming the GitLab token has equivalent permissions and then removing the old AZUL_GITHUB_TOKEN from GitHub Actions secrets, avoiding lingering unused credentials.

Verified items (no concerns)

GitHub CLI integrity verification. The gh binary is downloaded from GitHub releases over HTTPS, then verified against a SHA-256 checksum committed in bin/checksums/gh_checksums.txt. The checksum file is pinned at review time and can be updated via make gh_checksums. This matches the integrity verification pattern used for other tools in the Dockerfile (ECR credential helper uses SHA-256, AWS CLI uses GPG). Note that the upstream checksums file itself is unsigned, so the trust anchor is the committed checksums file reviewed in this PR, not a cryptographic signature chain.
No command injection risk. subprocess.run in schedule.py is called with list arguments throughout (no shell=True). Front matter values are passed to gh via -f flags, not shell-interpolated.
No unsafe deserialization. The YAML-like front matter parser (schedule.py:63-82) is a simple line-by-line key-value parser, not yaml.load().
Token not leaked in logs. The gh CLI reads credentials from the GITHUB_TOKEN environment variable, not from command-line arguments. The gh_json logging (Running ['gh', ...]) will not expose the token.
Post-creation verification (schedule.py:196-208). After creating an issue, the script verifies that labels, assignees, and type were correctly applied by inspecting the API response, catching silent permission failures.
Idempotency. Before creating an issue, the script searches for existing issues with the same title (schedule.py:161-168), preventing duplicates if the job runs more than once in the eligible window.
Certifi update (2026.5.20 → 2026.6.17) is a routine CA certificate bundle update — positive security maintenance.

Conclusion

No security concerns. The migration from GitHub Actions to GitLab CI is architecturally sound, the Python script is well-defended against injection and permission issues, and the GitHub CLI download is integrity-verified via committed SHA-256 checksums.

hannes-ucsc · 2026-07-07T12:29:38Z

achave11-ucsc · 2026-07-08T06:59:15Z

The tempdev deployment has been successfully hibernated:

_hibernate
…
Successfully hibernated tempdev

hannes-ucsc · 2026-07-08T08:36:02Z

+You may need to ask a system administrator to perform these changes on your
+behalf.
+
+Add a new ``github_schedule`` pipeline schedule on the ``dev`` and ``anvildev``


It would have been helpful to describe where in the UI this is.

hannes-ucsc · 2026-07-08T08:36:30Z

+
+1) Set the description to "Create Azul scheduled issues on GitHub".
+
+2) Set the interval pattern to ``0 * * * *`` on ``dev`` and ``30 * * * *`` on


2) and 3) should have been swapped since that's the order in which they occur in the UI

hannes-ucsc · 2026-07-08T08:37:18Z

+
+4) Set the variable ``azul_gitlab_schedule`` to ``github_schedule``
+
+Next, confirm with the SA that the ``azul_github_access_token`` used in both


This should occur first in the instructions, as it needs to be done before the schedule is created.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

achave11-ucsc requested a review from hannes-ucsc as a code owner June 11, 2026 17:35

achave11-ucsc self-assigned this Jun 11, 2026

achave11-ucsc linked an issue Jun 11, 2026 that may be closed by this pull request

GH Action schedule failed to create promotion ticket #8041

Open

achave11-ucsc marked this pull request as draft June 11, 2026 17:35

achave11-ucsc force-pushed the issues/achave11-ucsc/8041-add-GL-schdule branch 8 times, most recently from 268e612 to 05a0ec8 Compare June 16, 2026 17:34

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achave11-ucsc and others added 6 commits July 8, 2026 17:27

Fix typo

feacf18

Add GitHub CLI as an Azul dependency

ada9b30

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

[R] Install the GitHub CLI in the runtime & development images

6b3b731

[u] Fix: GH Action schedule failed to create promotion ticket (#8041)

cad95fd

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Verify GitHub CLI checksum during Docker image build (#8041)

ba8c19f

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

[R] Ran make requirements_update

eab7c7a

dsotirho-ucsc approved these changes Jul 9, 2026

View reviewed changes

	equivalent to the ``AZUL_GITHUB_TOKEN`` in the GitHub Action secrets.
	equivalent to that of the token deposited in the ``AZUL_GITHUB_TOKEN`` GitHub Action secret.

	3) Set the cron timezone to ``Pacific Time (US & Canada)``
	3) Set the Cron timezone to ``Pacific Time (US & Canada)``


		1) Set the description to "Create Azul scheduled issues on GitHub".

		2) Set the interval pattern to ``0 * * * `` on ``dev`` and ``30 * * *`` on


		4) Set the variable ``azul_gitlab_schedule`` to ``github_schedule``

		Next, confirm with the SA that the ``azul_github_access_token`` used in both

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Checklist

Author

Author (partiality)

Author (reindex)

Author (mirror)

Author (API changes)

Author (upgrading deployments)

Author (hotfixes)

Author (before every review)

Peer reviewer (after approval)

System administrator (after approval)

Operator

Operator (deploy .shared and .gitlab components)

System administrator (post-deploy of .gitlab component)

Operator (deploy runner image)

Operator (sandbox build)

Operator (merge the branch)

Operator (main build)

Operator (reindex)

Operator (mirroring)

Operator

Shorthand for review comments

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Security Design Review

Findings

Verified items (no concerns)

Conclusion

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hannes-ucsc commented Jul 7, 2026

Security Design Review

Findings

Verified items (no concerns)

Conclusion

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Security design review

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achave11-ucsc commented Jun 11, 2026 •

edited by nadove-ucsc

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