def test_create_isatab_archive(self):
with open(os.path.join(
test_utils.TAB_DATA_DIR, 'BII-S-3', 'i_gilbert.txt')) as fp:
result = utils.create_isatab_archive(inv_fp=fp)
self.assertIsInstance(result, list)
self.assertListEqual(sorted(result),
sorted(['i_gilbert.txt',
's_BII-S-3.txt',
'a_gilbert-assay-Gx.txt',
'a_gilbert-assay-Tx.txt',
'EXHS9OF02.sff', 'EXHS9OF01.sff',
'EWOEPZA01.sff', 'EWOEPZA02.sff',
'EX398L101.sff', 'EX398L102.sff',
'EVHINN105.sff', 'EVNG8PH04.sff',
'EVUSNDQ01.sff', 'EVHINN102.sff',
'EVHINN113.sff', 'EVUSNDQ02.sff',
'EVHINN101.sff', 'EVNG8PH01.sff',
'EVHINN106.sff', 'EVHINN108.sff',
'EVHINN116.sff', 'EVHINN104.sff',
'EVHINN110.sff', 'EVHINN107.sff',
'EVUSNDQ03.sff', 'EVHINN103.sff',
'EVHINN112.sff', 'EVUSNDQ04.sff',
'EVHINN115.sff', 'EVNG8PH02.sff',
'EVHINN114.sff', 'EVHINN111.sff',
'EVNG8PH03.sff', 'EVHINN109.sff']))
def test_create_isatab_archive_filter_on_transcription_profiling(self):
with open(
os.path.join(test_utils.TAB_DATA_DIR, 'BII-S-3',
'i_gilbert.txt')) as fp:
result = utils.create_isatab_archive(
inv_fp=fp, filter_by_measurement='transcription profiling')
self.assertIsInstance(result, list)
self.assertListEqual(
sorted(result),
sorted([
'i_gilbert.txt', 's_BII-S-3.txt', 'a_gilbert-assay-Tx.txt',
'EVHINN105.sff', 'EVNG8PH04.sff', 'EVUSNDQ01.sff',
'EVHINN102.sff', 'EVHINN113.sff', 'EVUSNDQ02.sff',
'EVHINN101.sff', 'EVNG8PH01.sff', 'EVHINN106.sff',
'EVHINN108.sff', 'EVHINN116.sff', 'EVHINN104.sff',
'EVHINN110.sff', 'EVHINN107.sff', 'EVUSNDQ03.sff',
'EVHINN103.sff', 'EVHINN112.sff', 'EVUSNDQ04.sff',
'EVHINN115.sff', 'EVNG8PH02.sff', 'EVHINN114.sff',
'EVHINN111.sff', 'EVNG8PH03.sff', 'EVHINN109.sff'
]))
def test_create_isatab_archive_missing_files(self):
with open(os.path.join(
test_utils.TAB_DATA_DIR, 'BII-I-1',
'i_investigation.txt')) as fp:
result = utils.create_isatab_archive(inv_fp=fp)
self.assertIsNone(result) # returns None if can't create archive