def test_get_experiment_as_isatab_mtab(self, value, mock_ax_get): src = os.path.abspath( os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'magetab', value)) dest = tempfile.mkdtemp() target = shutil.copytree(src, os.path.abspath(os.path.join(dest, value))) mock_ax_get.return_value = target AX.get_isatab(value, self._tmp_dir) with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp: isatab.validate(i_fp)
def test_get_experiment_as_isatab_mtab_3954(self): # Tests assay splitting AX.get_isatab('E-MTAB-3954', self._tmp_dir) self.assertTrue( os.path.isfile(os.path.join(self._tmp_dir, 'i_investigation.txt'))) self.assertTrue( os.path.isfile( os.path.join(self._tmp_dir, 's_E-MTAB-3954_study.txt'))) self.assertTrue( os.path.isfile( os.path.join(self._tmp_dir, 'a_E-MTAB-3954_assay-ChIP-Seq.txt'))) self.assertTrue( os.path.isfile( os.path.join(self._tmp_dir, 'a_E-MTAB-3954_assay-Chromatin-Seq.txt')))
def test_get_experiment_as_isatab(self, mock_ax_get): src = os.path.abspath( os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'magetab', 'E-AFMX-1')) dest = tempfile.mkdtemp() target = shutil.copytree( src, os.path.abspath(os.path.join(dest, 'E-AFMX-1'))) mock_ax_get.return_value = target tmp_dir = AX.get_isatab('E-AFMX-1') # gets E-AFMX-1 MAGE-TAB files self.assertEqual(len(os.listdir(tmp_dir)), 3) self.assertSetEqual(set(os.listdir(tmp_dir)), { 'i_investigation.txt', 'a_E-AFMX-1_assay.txt', 's_E-AFMX-1_study.txt' }) shutil.rmtree(tmp_dir)
def test_get_experiment_as_isatab_mtab_3954( self, mock_ax_get): # Tests assay splitting value = 'E-MTAB-3954' src = os.path.abspath( os.path.join(os.path.dirname(os.path.realpath(__file__)), 'data', 'magetab', value)) dest = tempfile.mkdtemp() target = shutil.copytree(src, os.path.abspath(os.path.join(dest, value))) mock_ax_get.return_value = target AX.get_isatab(value, self._tmp_dir) self.assertTrue( os.path.isfile(os.path.join(self._tmp_dir, 'i_investigation.txt'))) self.assertTrue( os.path.isfile( os.path.join(self._tmp_dir, 's_E-MTAB-3954_study.txt'))) self.assertTrue( os.path.isfile( os.path.join(self._tmp_dir, 'a_E-MTAB-3954_assay-ChIP-Seq.txt'))) self.assertTrue( os.path.isfile( os.path.join(self._tmp_dir, 'a_E-MTAB-3954_assay-Chromatin-Seq.txt')))
def test_get_experiment_as_isatab(self): tmp_dir = AX.get_isatab('E-AFMX-1') # gets E-AFMX-1 MAGE-TAB files self.assertEqual(len(os.listdir(tmp_dir)), 3) self.assertSetEqual(set(os.listdir(tmp_dir)), {'i_investigation.txt', 'a_E-AFMX-1_assay.txt', 's_E-AFMX-1_study.txt'}) shutil.rmtree(tmp_dir)
def test_get_experiment_as_isatab_mtab_20(self): AX.get_isatab('E-MTAB-20', self._tmp_dir) # gets E-MTAB-20 MAGE-TAB files with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp: isatab.validate(i_fp)
def test_get_experiment_as_isatab_mtab_1936(self): # splits three assays AX.get_isatab('E-MTAB-1963', self._tmp_dir) # gets E-MTAB-4649 MAGE-TAB files with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp: isatab.validate(i_fp)
def test_get_experiment_as_isatab_mtab_584(self): AX.get_isatab('E-MTAB-584', self._tmp_dir) with open(os.path.join(self._tmp_dir, 'i_investigation.txt')) as i_fp: isatab.validate(i_fp)