def main(options):
"""
@param input_csv: e.g. GSE_species_GSM.csv
"""
input_csv = options.input_csv
outdir = gen_outdir(options)
soft_outdir = gen_soft_outdir(outdir)
download_soft(input_csv, soft_outdir)
def test_gen_outdir_with_specified_outdir(self, mock_mkdir):
p = rp_prep.get_parser()
options = p.parse_args(['gen-csv', '-f', 'any_dir/input.csv', '--outdir', 'specified_outdir'])
self.assertEqual('specified_outdir', gen_csv.gen_outdir(options))
mock_mkdir.called_once_with('specified_outdir')
def test_gen_outdir_as_temp_outdir(self):
self.assertEqual(self.temp_outdir,
os.path.abspath(gen_csv.gen_outdir(self.options2)))
def test_gen_outdir_without_specified_outdir(self, mock_mkdir):
p = rp_prep.get_parser()
options = p.parse_args(['gen-csv', '-f', 'any_dir/input.csv'])
self.assertEqual('any_dir', gen_csv.gen_outdir(options))
self.assertFalse(mock_mkdir.called, "mkdir shouldn't have been called with -f is specified")
def test_gen_outdir_as_dirname_of_input_csv(self):
self.assertEqual(os.path.dirname(__file__),
# since __file__ contains absolute path
os.path.abspath(gen_csv.gen_outdir(self.options1)))
