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)))