def test_complex_file_validation_invalid(self):
schema_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'../data/validator_tests/bids_schema.mediawiki')
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../data/validator_tests/bids_events.tsv')
hed_schema = schema.load_schema(schema_path)
json_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../data/validator_tests/bids_events_bad_defs.json")
validator = HedValidator(hed_schema=hed_schema)
sidecar = Sidecar(json_path)
issues = sidecar.validate_entries(validators=validator,
check_for_warnings=True)
self.assertEqual(len(issues), 4)
input_file = EventsInput(events_path, sidecars=sidecar)
validation_issues = input_file.validate_file_sidecars(
validator, check_for_warnings=True)
self.assertEqual(len(validation_issues), 4)
validation_issues = input_file.validate_file(validator,
check_for_warnings=True)
self.assertEqual(len(validation_issues), 42)
def test_loading_and_reset_mapper(self):
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../data/validator_tests/bids_events.tsv')
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../data/validator_tests/bids_events.json")
sidecar = Sidecar(json_path)
self.assertEqual(len(sidecar.validate_entries()), 0)
input_file_1 = EventsInput(events_path, sidecars=sidecar)
input_file_2 = EventsInput(events_path, sidecars=sidecar)
input_file_2.reset_column_mapper()
for (row_number, column_dict), (row_number2, column_dict2) in zip(
input_file_1.iter_dataframe(), input_file_2.iter_dataframe()):
self.assertEqual(
row_number, row_number2,
f"EventsInput should have row {row_number} equal to {row_number2} after reset"
)
self.assertTrue(
len(column_dict) == 5,
f"The column dictionary for row {row_number} should have the right length"
)
self.assertTrue(
len(column_dict2) == 11,
f"The reset column dictionary for row {row_number2} should have the right length"
)
def test_name(self):
invalid_json = "invalidxmlfile.json"
name = "PrettyDisplayName.json"
try:
json_dict = Sidecar(invalid_json)
self.assertTrue(False)
except HedFileError as e:
self.assertTrue(name in e.format_error_message(
return_string_only=True, name=name))
def test_invalid_filenames(self):
# Handle missing or invalid files.
invalid_json = "invalidxmlfile.json"
self.assertRaises(HedFileError, Sidecar, invalid_json)
json_dict = None
try:
json_dict = Sidecar(None)
except HedFileError:
pass
self.assertTrue(len(json_dict._column_data) == 0)
json_dict = None
try:
json_dict = Sidecar("")
except HedFileError:
pass
self.assertTrue(len(json_dict._column_data) == 0)
def test_file_as_string(self):
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../data/validator_tests/bids_events.tsv')
json_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"../data/validator_tests/bids_events.json")
sidecar = Sidecar(json_path)
self.assertEqual(len(sidecar.validate_entries(expand_defs=True)), 0)
input_file = EventsInput(events_path, sidecars=sidecar)
with open(events_path) as file:
events_file_as_string = io.StringIO(file.read())
input_file_from_string = EventsInput(file=events_file_as_string,
sidecars=sidecar)
for (row_number, column_dict), (row_number2, column_dict) in zip(
input_file, input_file_from_string):
self.assertEqual(row_number, row_number2)
self.assertEqual(column_dict, column_dict)
def setUpClass(cls):
cls.base_data_dir = os.path.join(
os.path.dirname(os.path.abspath(__file__)), '../data/')
hed_xml_file = os.path.join(cls.base_data_dir,
"hed_pairs/HED8.0.0t.xml")
cls.hed_schema = schema.load_schema(hed_xml_file)
cls.json_filename = os.path.join(
cls.base_data_dir, "sidecar_tests/both_types_events.json")
cls.json_def_filename = os.path.join(
cls.base_data_dir,
"sidecar_tests/both_types_events_with_defs.json")
cls.json_without_definitions_filename = \
os.path.join(cls.base_data_dir, "sidecar_tests/both_types_events_without_definitions.json")
cls.json_errors_filename = os.path.join(
cls.base_data_dir, "sidecar_tests/json_errors.json")
cls.default_sidecar = Sidecar(cls.json_filename)
cls.json_def_sidecar = Sidecar(cls.json_def_filename)
cls.errors_sidecar = Sidecar(cls.json_errors_filename)
cls.json_without_definitions_sidecar = Sidecar(
cls.json_without_definitions_filename)
def test_complex_file_validation_invalid_definitions_removed(self):
# This verifies definitions are being removed from sidecar strings before being added, or it will produce
# extra errors.
schema_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'../data/validator_tests/bids_schema.mediawiki')
events_path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../data/validator_tests/bids_events.tsv')
hed_schema = schema.load_schema(schema_path)
json_path = os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../data/validator_tests/bids_events_bad_defs2.json")
sidecar = Sidecar(json_path)
input_file = EventsInput(events_path, sidecars=sidecar)
validator = HedValidator(hed_schema=hed_schema)
validation_issues1 = input_file.validate_file_sidecars(validator)
self.assertEqual(len(validation_issues1), 4)
validation_issues = input_file.validate_file(validator)
self.assertEqual(len(validation_issues), 42)
def test_add_json_string(self):
with open(self.json_filename) as file:
file_as_string = io.StringIO(file.read())
json_file = Sidecar(file_as_string)
self.assertTrue(json_file)