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")