def setUp(self):
"""setUp and tearDown are run for teach test"""
self.input_csv = os.path.join(os.path.dirname(__file__), '___valid_input.csv')
with open(self.input_csv, 'wb') as opf1:
opf1.write(
"""
GSE59813,GSM1446812;
GSE61491,GSM1506106; GSM1506107;
""")
parser = rp_prep.get_parser()
self.temp_outdir = tempfile.mkdtemp() # mkdtemp returns abspath
self.options1 = parser.parse_args(['gen-csv', '-f', self.input_csv])
self.options2 = parser.parse_args(['gen-csv', '-f', self.input_csv,
'--outdir', self.temp_outdir])
self.gse = 'GSE38003'
self.gsm = 'GSM931711'
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_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")