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gtrack / gtrackcore

gtrackcore: A Python package supporting parsing, conversion and operations of genomic track files.
GNU General Public License v3.0
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GTools command line parameter validation needs to improve #1

Open sveinugu opened 5 years ago

sveinugu commented 5 years ago

Lacking some essential parameters should provide helpful information instead of exceptions:

19:30 $ python gtrackcore/track_operations/gtools/GTools.py import
Traceback (most recent call last):
  File "gtrackcore/track_operations/gtools/GTools.py", line 201, in <module>
    GTools()
  File "gtrackcore/track_operations/gtools/GTools.py", line 30, in __init__
    self.runOperation()
  File "gtrackcore/track_operations/gtools/GTools.py", line 53, in runOperation
    btrack = BTrack(self._args.btrackPath)
  File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/api/BTrack.py", line 15, in __init__
    self._path = os.path.abspath(path)
  File "/Users/sveinugu/miniconda2/lib/python2.7/posixpath.py", line 360, in abspath
    if not isabs(path):
  File "/Users/sveinugu/miniconda2/lib/python2.7/posixpath.py", line 54, in isabs
    return s.startswith('/')
AttributeError: 'NoneType' object has no attribute 'startswith

Also, it would be prettier if such validation exceptions were only print statements, and not full exceptions with stacktrace:

python gtrackcore/track_operations/gtools/GTools.py create -b test.btrack
Traceback (most recent call last):
  File "gtrackcore/track_operations/gtools/GTools.py", line 201, in <module>
    GTools()
  File "gtrackcore/track_operations/gtools/GTools.py", line 30, in __init__
    self.runOperation()
  File "gtrackcore/track_operations/gtools/GTools.py", line 47, in runOperation
    BTrack(self._args.btrackPath, self._args.genomePath)
  File "/Users/sveinugu/PycharmProjects/gtrackcore/gtrackcore/api/BTrack.py", line 23, in __init__
    raise ValueError('Genome has to be provided')
ValueError: Genome has to be provided