def test_mzml2isa_convert_investigation(self):
study_id = 'MTBLS267'
report = mzml2isa.convert(os.path.join(self._mzml_data_dir,
study_id + '-partial'),
self._tmp_dir,
study_id,
validate_output=True)
self.assertTrue(report['validation_finished'])
self.assertEqual(len(report['errors']), 0)
# Strip out the line with Comment[Created With Tool] to avoid changes in version number generated by mzml2isa
with open(os.path.join(self._tmp_dir, study_id, 'i_Investigation.txt')
) as in_fp, StringIO() as stripped_actual_file:
stripped_actual_file.name = 'i_Investigation.txt'
for row in in_fp:
if row.startswith('Comment[Created With Tool]'):
pass
else:
stripped_actual_file.write(row)
stripped_actual_file.seek(0)
with open(
os.path.join(self._tab_data_dir, study_id + '-partial',
'i_Investigation.txt')) as reference_fp:
self.assertTrue(
assert_tab_content_equal(stripped_actual_file,
reference_fp))
def test_mzml2isa_convert_study_table(self):
study_id = 'MTBLS267'
report = mzml2isa.convert(os.path.join(self._mzml_data_dir,
study_id + '-partial'),
self._tmp_dir,
study_id,
validate_output=True)
self.assertTrue(report['validation_finished'])
self.assertEqual(len(report['errors']), 0)
with open(os.path.join(self._tmp_dir,
's_{}.txt'.format(study_id))) as out_fp:
with open(
os.path.join(self._tab_data_dir, study_id + '-partial',
's_{}.txt'.format(study_id))) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_mzml2isa_convert_assay_table(self):
study_id = 'MTBLS267'
report = mzml2isa.convert(os.path.join(self._mzml_data_dir,
study_id + '-partial'),
self._tmp_dir,
study_id,
validate_output=True)
self.assertTrue(report['validation_finished'])
self.assertEqual(len(report['errors']), 0)
self.assertTrue(
assert_tab_content_equal(
open(
os.path.join(
self._tmp_dir, study_id,
'a_{}_metabolite_profiling_mass_spectrometry.txt'.
format(study_id))),
open(
os.path.join(
self._tab_data_dir, study_id + '-partial',
'a_{}_metabolite_profiling_mass_spectrometry.txt'.
format(study_id)))))