genomedata-erase-data doesn't work

[EricR86]

Original report (archived issue) by Rachel Chan (Bitbucket: rcwchan).

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Specifically, the arg parser (if called from commandline) is searching for attributes that don't exist:

From _erase_data.py:

#!python

38 def parse_options(args):
 39 
 40     description = ("Erase the specified tracks from the Genomedata archive"
 41                    " in such a way that the track data can be replaced"
 42                    " (via genomedata-load-data).")
 43 
 44     parser = ArgumentParser(description=description,
 45                             prog='genomedata-erase-data',
 46                             version=__version__)
 47 
 48     parser.add_argument('gdarchive', help='genomedata archive')
 49 
 50     parser.add_argument("--trackname", required=True, nargs='+',
 51                         help="tracknames to erase")
 52 
 53     parser.add_argument("--verbose", default=False, action="store_true",
 54                         help="Print status updates and diagnostic messages")
 55 
 56     args = parser.parse_args(args)
 57 
 58     return args
 59 
 60 def main(argv=sys.argv[1:]):
 61     args = parse_options(argv)
 62     gdarchive = args.archive
 63 
 64     for trackname in args.tracknames:
 65         erase_data(gdarchive, trackname, verbose=args.verbose)
 66 
 67 if __name__ == "__main__":
 68     sys.exit(main())                                   

In particular, args.archive should be args.gdarchive, args.tracknames doesn't exist, etc. Edit: Possibly a test should be added for it in the genomedata test suite?

[EricR86]

Original comment by Rachel Chan (Bitbucket: rcwchan).

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• Edited issue description

[EricR86]

Original comment by Rachel Chan (Bitbucket: rcwchan).

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• Edited issue description

[EricR86]

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

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It appears to be documented, just there is no test coverage. I think better to fix it.

[EricR86]

Original comment by Rachel Chan (Bitbucket: rcwchan).

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• Edited issue description

[EricR86]

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

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A smoke test alone would have caught this.