galaxyproject / galaxyproject/planemo

Cannot locate xUnit report ... for tests (planemo 0.74.11)

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Dominant language
Python
Stars
110
Forks
102
Avg merge
4d 21h
Merged PRs (30d)
13

Description

### Your operating system name and version, versions of other relevant software such as Galaxy or Docker.
Windows Services for Linux 2
```
$ uname -a
Linux DESKTOP-00J5NN6 5.10.16.3-microsoft-standard-WSL2 #1 SMP Fri Apr 2 22:23:49 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
$ planemo --version
planemo, version 0.74.11
```

### Links to relevant tools.
N/A tool tests don't even commence

### Any details about your local setup that might be helpful in troubleshooting.
Running in WSL2 (a Linux VM running on Windows). The error message does not point to this being the issue:
```
File "/home/art/.planemo/gx_venv_3/lib/python3.10/site-packages/nose/suite.py", line 106, in _set_tests
if isinstance(tests, collections.Callable) and not is_suite:
AttributeError: module 'collections' has no attribute 'Callable'
Testing complete. HTML report is in "/home/art/src/tools-galaxyp/tools/maxquant/tool_test_output.html".
Cannot locate xUnit report [/tmp/tmpy8e0nkxi/xunit.xml] for tests - required to build planemo report and summarize tests.
Traceback (most recent call last):
File "/home/art/bin/planemo", line 8, in
sys.exit(planemo())
File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1130, in __call__
return self.main(*args, **kwargs)
File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1055, in main
rv = self.invoke(ctx)
File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1657, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 1404, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/art/venv/lib/python3.9/site-packages/click/decorators.py", line 84, in new_func
return ctx.invoke(f, obj, *args, **kwargs)
File "/home/art/venv/lib/python3.9/site-packages/click/core.py", line 760, in invoke
return __callback(*args, **kwargs)
File "/home/art/venv/lib/python3.9/site-packages/planemo/cli.py", line 96, in handle_blended_options
return f(*args, **kwds)
File "/home/art/venv/lib/python3.9/site-packages/planemo/commands/cmd_test.py", line 78, in cli
return_value = test_runnables(ctx, runnables, original_paths=uris, **kwds)
File "/home/art/venv/lib/python3.9/site-packages/planemo/engine/test.py", line 33, in test_runnables
return_value = run_in_config(ctx, config, **kwds)
File "/home/art/venv/lib/python3.9/site-packages/planemo/galaxy/test/actions.py", line 109, in run_in_config
_check_test_outputs(xunit_report_file_tracker, structured_report_file_tracker)
File "/home/art/venv/lib/python3.9/site-packages/planemo/galaxy/test/actions.py", line 290, in _check_test_outputs
raise Exception(message)
Exception: Cannot locate xUnit report [/tmp/tmpy8e0nkxi/xunit.xml] for tests - required to build planemo report and summarize tests.
```

### Detailed steps to reproduce the bug.
```
cd ~/src/tools-galaxyp/tools/maxquant
planemo test --biocontainers .
```
The exact same error occurs regardless of which tool is under test or regardless of whether --biocontainers is set.

Contributor guide

Open the contributing guide

Research direction

Reproduce with `planemo test --biocontainers .` from the reported tool directory, then inspect `planemo/galaxy/test/actions.py`, especially `_check_test_outputs`, alongside the displayed `nose` traceback. Trace why `xunit.xml` is absent when tool tests do not commence; done means the command handles this failure coherently and still produces the expected test report behavior.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
cli, testing-qa
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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