# Set up the file names for the tests
local_hed_file = '../../data/schema_data/HED7.2.0.xml' # path HED v7.1.1 stored locally
example_data_path = '../../data/spreadsheet_data' # path to example data
valid_tsv_file = os.path.join(example_data_path,
'ValidTwoColumnHED7_1_1.tsv')
valid_tsv_file_no_header = os.path.join(
example_data_path, 'ValidTwoColumnHED7_1_1NoHeader.tsv')
valid_tsv_file_separate_cols = os.path.join(example_data_path,
'LKTEventCodesHED2.tsv')
unsupported_csv_format = os.path.join(example_data_path,
'UnsupportedFormatCSV.csv')
multiple_sheet_xlsx_file = os.path.join(example_data_path,
'ExcelMultipleSheets.xlsx')
hed_schema_cached = load_schema_version(xml_version_number='7.1.1')
hed_validator_old = HedValidator(hed_schema=hed_schema_cached)
hed_schema_local = load_schema(local_hed_file)
hed_validator_local = HedValidator(hed_schema=hed_schema_local)
hed_validator_local_warnings = HedValidator(hed_schema=hed_schema_local)
# Example 1a: Valid TSV file with default version of HED
print(valid_tsv_file)
input_file = HedInput(valid_tsv_file, tag_columns=[2])
validation_issues = input_file.validate_file(hed_validator_old,
check_for_warnings=True)
the_title = '[Example 1a] ValidTwoColumnHED7_1_1 is probably okay with default version of HED'
print(get_printable_issue_string(validation_issues, title=the_title))
# Example 1b: Valid TSV file with specified local version of HED
print(valid_tsv_file)
input_file = HedInput(valid_tsv_file, tag_columns=[2])
if issues:
return issues
for event_obj in self.events_dict.values():
contents = event_obj.contents
if not contents:
contents = EventsInput(file=event_obj.file_path, sidecars=event_obj.sidecars)
if keep_events:
event_obj.my_contents = contents
issues += contents.validate_file(validators=validators, check_for_warnings=check_for_warnings)
return issues
if __name__ == '__main__':
path = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'../../../tests/data/bids/eeg_ds003654s_hed')
bids = BidsEventFiles(path)
for file_obj in bids.sidecar_dict.values():
print(file_obj)
for file_obj in bids.events_dict.values():
print(file_obj)
print("Now validating.....")
hed_schema = \
load_schema('https://raw.githubusercontent.com/hed-standard/hed-specification/master/hedxml/HED8.0.0.xml')
validator = HedValidator(hed_schema=hed_schema)
validation_issues = bids.validate(validators=[validator], check_for_warnings=False)
issue_str = get_printable_issue_string(validation_issues, skip_filename=False)
print(f"Issues: {issue_str}")
example_data_path = 'data' # path to example data
valid_tsv_file = os.path.join(example_data_path,
'ValidTwoColumnHED7_1_1.tsv')
valid_tsv_file_no_header = os.path.join(
example_data_path, 'ValidTwoColumnHED7_1_1NoHeader.tsv')
valid_tsv_file_separate_cols = os.path.join(example_data_path,
'ValidSeparateColumnTSV.txt')
unsupported_csv_format = os.path.join(example_data_path,
'UnsupportedFormatCSV.csv')
multiple_sheet_xlsx_file = os.path.join(example_data_path,
'ExcelMultipleSheets.xlsx')
# Example 1a: Valid TSV file with default version of HED
print(valid_tsv_file)
input_file = HedFileInput(valid_tsv_file, tag_columns=[2])
hed_input_reader = HedValidator(input_file)
issues = hed_input_reader.get_validation_issues()
print(
hed_input_reader.get_printable_issue_string(
'[Example 1a] ValidTwoColumnHED7_1_1 is probably okay with default version of HED'
))
# Example 1b: Valid TSV file with specified local version of HED
print(valid_tsv_file)
input_file = HedFileInput(valid_tsv_file, tag_columns=[2])
hed_input_reader = HedValidator(input_file, hed_xml_file=local_hed_file)
print(
hed_input_reader.get_printable_issue_string(
'[Example 1b] ValidTwoColumnHED7_1_1 should have no issues with local version 7.1.1'
))
"""
Examples of HED validation of a tag string
"""
from hed.validator.hed_validator import HedValidator
if __name__ == '__main__':
local_hed_file = 'data/HED7.1.1.xml' # path HED v7.1.1 stored locally
# Example 1a: Valid HED string for HED <= v7.1.1
hed_string_1 = 'Event/Label/ButtonPuskDeny, Event/Description/Button push to deny access to the ID holder,' \
'Event/Category/Participant response, ' \
'(Participant ~ Action/Button press/Keyboard ~ Participant/Effect/Body part/Arm/Hand/Finger)'
hed_input_reader = HedValidator(hed_string_1, hed_xml_file=local_hed_file)
print(
hed_input_reader.get_printable_issue_string(
'[Example 1a] hed_string_1 should have no issues with HEDv7.1.1'))
# Example 1b: Try with the latest version of HED.xml
hed_input_reader = HedValidator(hed_string_1)
print(
hed_input_reader.get_printable_issue_string(
'[Example 1b] hed_string_1 probably has no issues with the latest HED version'
))
# Example 2a: Invalid HED string (junk in last tag)
hed_string_2 = 'Event/Category/Participant response,' \
'(Participant ~ Action/Button press/Keyboard ~ Participant/Effect/Body part/Arm/Hand/Finger),' \
'dskfjkf/dskjdfkj/sdkjdsfkjdf/sdlfdjdsjklj'
hed_input_reader = HedValidator(hed_string_2)
print(
hed_xml_url = 'https://raw.githubusercontent.com/hed-standard/hed-specification/master/hedxml/HED8.0.0.xml'
hed_library_url1 = \
'https://raw.githubusercontent.com/hed-standard/hed-schema-library/main/hedxml/HED_score_0.0.1.xml'
hed_library_url2 = \
'https://raw.githubusercontent.com/hed-standard/hed-schema-library/main/hedxml/HED_test_1.0.2.xml'
hed_schema = load_schema(hed_xml_url)
hed_schema_lib1 = load_schema(hed_library_url1)
hed_schema_lib1.set_library_prefix("sc")
hed_schema_lib2 = load_schema(hed_library_url2)
hed_schema_lib2.set_library_prefix("test")
events_file = os.path.join(
'../../../datasets/eeg_ds003654s_hed_library/sub-003/eeg/sub-003_task-FacePerception_run-2_events.tsv'
)
json_file = os.path.join(
'../../../datasets/eeg_ds003654s_hed_library/task-FacePerception_events.json'
)
schema_group = HedSchemaGroup(
[hed_schema, hed_schema_lib1, hed_schema_lib2])
validator = HedValidator(hed_schema=schema_group)
sidecar = Sidecar(json_file)
input_file = EventsInput(events_file, sidecars=sidecar)
issues = input_file.validate_file_sidecars(validator,
check_for_warnings=False)
issues += input_file.validate_file(validator, check_for_warnings=False)
print(
get_printable_issue_string(
issues, "Validating a Bids event file with its JSON sidecar"))