def test_isatab2json_convert_source_split_with_error(self):
test_case = 'TEST-ISA-source-split-with-error'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_sample_pool(self):
test_case = 'TEST-ISA-sample-pool'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_charac_param_factor(self):
test_case = 'TEST-ISA-charac-param-factor'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_json2isatab_isatab2json_2way_convert_source_split(self):
test_case = 'TEST-ISA-source-split'
with open(os.path.join(self._json_data_dir,
test_case + '.json')) as test_json:
json2isatab.convert(test_json, self._tmp_dir, validate_first=False)
test_json.seek(0) # reset pointer
expected_json = json.load(test_json)
actual_json = isatab2json.convert(self._tmp_dir,
validate_first=False)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_bii_s_7(self):
test_case = 'BII-S-7'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
validate_first=False)
with open(
os.path.join(self._json_data_dir, test_case,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2json_convert_mtbls1(self):
test_case = 'MTBLS1'
actual_json = isatab2json.convert(os.path.join(self._tab_data_dir,
test_case),
self.identifier_type,
validate_first=False)
with open(
os.path.join(self._json_data_dir, test_case,
test_case + '.json')) as expected_file:
expected_json = json.load(expected_file)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_isatab2cedar_convert_mtbls2(self):
test_case = 'MTBLS2'
isa2cedar = ISATab2CEDAR("http://www.isa-tools.org/")
isa2cedar.createCEDARjson(os.path.join(self._tab_data_dir, test_case),
self._tmp_dir, True)
with open(os.path.join(self._json_data_dir, 'cedar', test_case + '.json')) as expected_file, \
open(os.path.join(self._tmp_dir, test_case + '.json')) as actual_file:
expected_json = json.load(expected_file)
actual_json = json.load(actual_file)
utils.strip_ids(expected_json)
utils.strip_ids(actual_json)
self.assertTrue(utils.assert_json_equal(expected_json,
actual_json))
def test_assert_json_equal(self):
self.assertTrue(utils.assert_json_equal(self.j1, self.j2))
self.assertFalse(utils.assert_json_equal(self.j1, self.j3))