Fix AttributeError when job input dataset association has no dataset#28
Draft
Copilot wants to merge 2 commits into
Draft
Fix AttributeError when job input dataset association has no dataset#28Copilot wants to merge 2 commits into
Copilot wants to merge 2 commits into
Conversation
Owner
|
@copilot so where's the plan ? why did you open an empty PR ? |
Optional/not-provided data inputs are recorded as None in JobToInputDatasetAssociation. Add a filter to skip None datasets when checking for purged input datasets. Agent-Logs-Url: https://github.com/mvdbeek/galaxy/sessions/a79f3cf8-2b82-407f-aadb-144eb1ede32e Co-authored-by: mvdbeek <6804901+mvdbeek@users.noreply.github.com>
Copilot
AI
changed the title
[WIP] Fix AttributeError on dataset access in job files API
Fix AttributeError when job input dataset association has no dataset
Apr 7, 2026
Author
The fix is in commit d30ccfd. It adds an |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Optional/not-provided data inputs are recorded as
NoneinJobToInputDatasetAssociation. The purged-input check in the job files API dereferencesjtid.dataset.dataset.purgedwithout guarding against this, causing:Add
if jtid.datasetfilter to the generator expression to skip null associations.How to test the changes?
FileNotFoundErrorpath in the job files API (e.g. by purging an unrelated input dataset while the job is running).License
Warning
Firewall rules blocked me from connecting to one or more addresses (expand for details)
I tried to connect to the following addresses, but was blocked by firewall rules:
wheels.galaxyproject.org/home/REDACTED/work/galaxy/galaxy/.venv/bin/python python -m pip install -r requirements.txt -r ./lib/galaxy/dependencies/dev-requirements.txt --extra-index-url REDACTED(dns block)/home/REDACTED/work/galaxy/galaxy/.venv/bin/python /home/REDACTED/work/galaxy/galaxy/.venv/bin/python /home/REDACTED/work/galaxy/galaxy/.venv/lib/python3.12/site-packages/pip/__pip-REDACTED__.py install --ignore-installed --no-user --prefix /tmp/pip-build-env-h4t9ifzm/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i REDACTED --extra-index-url REDACTED -- setuptools>=64 setuptools-scm>=8(dns block)/home/REDACTED/work/galaxy/galaxy/.venv/bin/python /home/REDACTED/work/galaxy/galaxy/.venv/bin/python /home/REDACTED/work/galaxy/galaxy/.venv/lib/python3.12/site-packages/pip/__pip-REDACTED__.py install --ignore-installed --no-user --prefix /tmp/pip-build-env-tolnbq59/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i REDACTED --extra-index-url REDACTED -- setuptools>=40.8.0(dns block)If you need me to access, download, or install something from one of these locations, you can either: