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)
