Description
Expected Behavior
When the source of a step input in a workflow is invalid, cwltool should report that error by printing a normal hierarchical validation error.
Actual Behavior
When cwltool encounters this source error, it tries to throw an exception, but in doing so calls the shortname method on the invalid ID, which causes the exception 'CommentedMap' object has no attribute 'decode' that is hard to decipher.
Workflow Code
Unfortunately I have found it difficult to create a minimal example of this error. However, if you clone this repository: https://github.com/TMiguelT/CWL-Bug, you should be able to replicate it. If you run (from the repository root), cwltool --validate --debug workflows/cpipe.broken.cwl, the bug should occur. If instead you run cwltool --validate --debug workflows/cpipe.cwl, which does not have this invalid input source, this bug will not occur. Not that the difference between these two files is on line 222: https://github.com/TMiguelT/CWL-Bug/blob/master/workflows/cpipe.broken.cwl#L222.
Full Traceback
/vlsci/VR0320/milton/CWL-Bug/venv/bin/cwltool 1.0.20170928192020
Resolved 'workflows/cpipe.broken.cwl' to 'file:///vlsci/VR0320/milton/cwl_bug/cpipe-out-rabix/workflows/cpipe.broken.cwl'
I'm sorry, I couldn't load this CWL file. The error was:
Traceback (most recent call last):
File "/vlsci/VR0320/milton/CWL-Bug/venv/lib/python3.5/site-packages/cwltool/main.py", line 837, in main
makeTool, make_tool_kwds)
File "/vlsci/VR0320/milton/CWL-Bug/venv/lib/python3.5/site-packages/cwltool/load_tool.py", line 263, in make_tool
tool = makeTool(processobj, **kwargs)
File "/vlsci/VR0320/milton/CWL-Bug/venv/lib/python3.5/site-packages/cwltool/workflow.py", line 40, in defaultMakeTool
return Workflow(toolpath_object, **kwargs)
File "/vlsci/VR0320/milton/CWL-Bug/venv/lib/python3.5/site-packages/cwltool/workflow.py", line 522, in __init__
self.steps.append(WorkflowStep(step, n, **kwargs))
File "/vlsci/VR0320/milton/CWL-Bug/venv/lib/python3.5/site-packages/cwltool/workflow.py", line 716, in __init__
+ "\n" + SourceLine(self.embedded_tool.tool, "outputs").makeError(
File "/vlsci/VR0320/milton/CWL-Bug/venv/lib/python3.5/site-packages/cwltool/process.py", line 170, in shortname
d = urllib.parse.urlparse(inputid)
File "/usr/local/python/3.5.2-intel/lib/python3.5/urllib/parse.py", line 294, in urlparse
url, scheme, _coerce_result = _coerce_args(url, scheme)
File "/usr/local/python/3.5.2-intel/lib/python3.5/urllib/parse.py", line 114, in _coerce_args
return _decode_args(args) + (_encode_result,)
File "/usr/local/python/3.5.2-intel/lib/python3.5/urllib/parse.py", line 98, in _decode_args
return tuple(x.decode(encoding, errors) if x else '' for x in args)
File "/usr/local/python/3.5.2-intel/lib/python3.5/urllib/parse.py", line 98, in <genexpr>
return tuple(x.decode(encoding, errors) if x else '' for x in args)
AttributeError: 'CommentedMap' object has no attribute 'decode'Your Environment
- cwltool version: 1.0.20170928192020
- Python version: Python 3.5.2
- Red Hat Enterprise Linux Server release 6.9 (Santiago) (also replicated on Ubuntu 16.04)