Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[23.1] Make sort_collection tool require terminal datasets #16661

Conversation

mvdbeek
Copy link
Member

@mvdbeek mvdbeek commented Sep 7, 2023

It would be nice if we could limit this just to the dataset that we're reading the element identifiers from, but this will do as a bugfix.

Fixes

Exception: Number of lines must match number of list elements (2), but file has 0 lines
  File "galaxy/tools/__init__.py", line 1937, in handle_single_execution
    rval = self.execute(
  File "galaxy/tools/__init__.py", line 2034, in execute
    return self.tool_action.execute(
  File "galaxy/tools/actions/model_operations.py", line 88, in execute
    self._produce_outputs(
  File "galaxy/tools/actions/model_operations.py", line 119, in _produce_outputs
    tool.produce_outputs(
  File "galaxy/tools/__init__.py", line 3545, in produce_outputs
    raise Exception(message)

because in a workflow the dataset with identifiers might not be ready at the time the tool is run.

Broken in 314f135

How to test the changes?

(Select all options that apply)

  • I've included appropriate automated tests.
  • This is a refactoring of components with existing test coverage.
  • Instructions for manual testing are as follows:
    1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

  • I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

It would be nice if we could limit this just to the dataset that we're
reading the element identifiers from, but this will do as a bugfix.
@github-actions github-actions bot added this to the 23.2 milestone Sep 7, 2023
@dannon dannon merged commit c77636b into galaxyproject:release_23.1 Sep 7, 2023
34 of 36 checks passed
@wm75
Copy link
Contributor

wm75 commented Sep 7, 2023

Thanks a lot @mvdbeek!

@dannon dannon modified the milestones: 23.2, 23.1 Sep 22, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging this pull request may close these issues.

None yet

4 participants