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

add test showing error during import job preparion with latest Galaxy #51

Merged
merged 7 commits into from
Jan 29, 2024

Commits on Jan 22, 2024

  1. add test showing error during import job preparion

    the following Traceback can be found in the logs (the test itself is not
    executed)
    
    ```
    Traceback (most recent call last):
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/jobs/runners/__init__.py", line 291, in prepare_job
        job_wrapper.prepare()
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/jobs/__init__.py", line 1254, in prepare
        ) = tool_evaluator.build()
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 566, in build
        global_tool_logs(self._build_config_files, config_file, "Building Config Files")
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 96, in global_tool_logs
        raise e
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 92, in global_tool_logs
        return func()
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 633, in _build_config_files
        self.__write_workdir_file(config_filename, config_text, param_dict, is_template=is_template)
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/tools/evaluation.py", line 756, in __write_workdir_file
        value = fill_template(content, context=context, python_template_version=self.tool.python_template_version)
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/util/template.py", line 143, in fill_template
        raise first_exception or e
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/util/template.py", line 87, in fill_template
        return unicodify(t, log_exception=False)
      File "/tmp/tmpiottroee/galaxy-dev/lib/galaxy/util/__init__.py", line 1153, in unicodify
        value = str(value)
      File "/home/berntm/.planemo/gx_venv_3/lib/python3.10/site-packages/Cheetah/Template.py", line 1053, in __unicode__
        return getattr(self, mainMethName)()
      File "cheetah_DynamicallyCompiledCheetahTemplate_1705952649_1165519_57877.py", line 119, in respond
      File "cheetah_DynamicallyCompiledCheetahTemplate_1705952649_1165519_57877.py", line 102, in stringify
      File "cheetah_DynamicallyCompiledCheetahTemplate_1705952649_1165519_57877.py", line 113, in stringify
    AttributeError: 'TreeDict' object has no attribute 'is_collection'
    ```
    bernt-matthias committed Jan 22, 2024
    Configuration menu
    Copy the full SHA
    7ae4b68 View commit details
    Browse the repository at this point in the history

Commits on Jan 23, 2024

  1. working test for 23.0

    bernt-matthias committed Jan 23, 2024
    Configuration menu
    Copy the full SHA
    d5569e2 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    87b8fb1 View commit details
    Browse the repository at this point in the history

Commits on Jan 24, 2024

  1. add test for laneless

    bernt-matthias committed Jan 24, 2024
    Configuration menu
    Copy the full SHA
    8d265c5 View commit details
    Browse the repository at this point in the history

Commits on Jan 26, 2024

  1. Configuration menu
    Copy the full SHA
    ff65965 View commit details
    Browse the repository at this point in the history
  2. better fix

    bernt-matthias committed Jan 26, 2024
    Configuration menu
    Copy the full SHA
    9a15f2b View commit details
    Browse the repository at this point in the history
  3. bump tool version

    bernt-matthias committed Jan 26, 2024
    Configuration menu
    Copy the full SHA
    f3a8ece View commit details
    Browse the repository at this point in the history