def test_json2isatab_convert_source_split_study_table(self):
with open(os.path.join(self._json_data_dir, 'TEST-ISA-source-split.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(os.path.join(self._tmp_dir, 's_TEST-Template1-Splitting.txt')) as out_fp:
with open(os.path.join(self._tab_data_dir, 'TEST-ISA-source-split', 's_TEST-Template1-Splitting.txt')) \
as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
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_assert_tab_content_equal_assay_table(self):
with open(os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
's_BII-S-1.txt')) as s_tab1:
with open(
os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
's_BII-S-1.txt')) as s_tab2:
self.assertTrue(utils.assert_tab_content_equal(s_tab1, s_tab2))
def test_assert_tab_content_equal_investigation(self):
with open(
os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
'i_investigation.txt')) as i_tab1:
with open(
os.path.join(utils.TAB_DATA_DIR, 'BII-I-1',
'i_investigation.txt')) as i_tab2:
self.assertTrue(utils.assert_tab_content_equal(i_tab1, i_tab2))
def test_json2isatab_convert_bii_s_3_study_table(self):
with open(os.path.join(self._json_data_dir, 'BII-S-3',
'BII-S-3.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(os.path.join(self._tmp_dir, 's_BII-S-3.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-3',
's_BII-S-3.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_study2_table(self):
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 's_BII-S-2.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-I-1',
's_BII-S-2.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_metabolome(self):
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'a_metabolome.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_metabolome.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_s_7_assay_table_Gx(self):
with open(os.path.join(self._json_data_dir, 'BII-S-7',
'BII-S-7.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(os.path.join(self._tmp_dir,
'a_matteo-assay-Gx.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-7',
'a_matteo-assay-Gx.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_proteome(self):
# FIXME: Same duplication problem as above
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'a_proteome.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_proteome.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_s_3_investigation(self):
with open(os.path.join(self._json_data_dir, 'BII-S-3',
'BII-S-3.json')) as json_fp:
json2isatab.convert(json_fp,
self._tmp_dir,
i_file_name='i_gilbert.txt',
validate_first=False)
with open(os.path.join(self._tmp_dir, 'i_gilbert.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir, 'BII-S-3',
'i_gilbert.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_transcriptome(self):
# FIXME: Has inserted Protocol REFs but Array Design REF, Scan Name, Factor Values
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir,
'a_transcriptome.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_transcriptome.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))
def test_json2isatab_convert_bii_i_1_assay_table_microarray(self):
# FIXME: ArrayExpress comments come out twice (on Assay AND Derived Data File output from assay),
# missing Data Transformation Name and Factor Values
with open(os.path.join(self._json_data_dir, 'BII-I-1',
'BII-I-1.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir)
with open(os.path.join(self._tmp_dir, 'a_microarray.txt')) as out_fp:
with open(
os.path.join(self._tab_data_dir,
'BII-I-1_written_by_isatab',
'a_microarray.txt')) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, 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_json2isatab_convert_source_split_assay_table(self):
with open(
os.path.join(self._json_data_dir,
'TEST-ISA-source-split.json')) as json_fp:
json2isatab.convert(json_fp, self._tmp_dir, validate_first=False)
with open(
os.path.join(
self._tmp_dir,
'a_test-template1-splitting_transcription_profiling_DNA_microarray.txt'
)) as out_fp:
with open(
os.path.join(
self._tab_data_dir, 'TEST-ISA-source-split',
'a_test-template1-splitting_transcription_profiling_DNA_microarray.txt'
)) as reference_fp:
self.assertTrue(assert_tab_content_equal(out_fp, reference_fp))