def test_validator(self):
events = BidsEventFiles(Test.root_path)
hed_schema = \
load_schema('https://raw.githubusercontent.com/hed-standard/hed-specification/master/hedxml/HED8.0.0.xml')
validator = HedValidator(hed_schema)
validation_issues = events.validate(validators=[validator],
check_for_warnings=False)
self.assertFalse(validation_issues,
"BidsEventFiles should have no validation errors")
validation_issues = events.validate(validators=[validator],
check_for_warnings=True)
self.assertTrue(validation_issues,
"BidsEventFiles should have validation warnings")
self.assertEqual(
len(validation_issues), 6,
"BidsEventFiles should have 2 validation warnings for missing columns"
)
""" Examples of creating a HedValidator and validating various Hed Strings with it.
Classes Demonstrated:
HedValidator - Validates a given input string or file
"""
from hed.errors.error_reporter import get_printable_issue_string
from hed.models.hed_string import HedString
from hed.schema.hed_schema_io import load_schema
from hed.validator.hed_validator import HedValidator
if __name__ == '__main__':
hed_xml_url = 'https://raw.githubusercontent.com/hed-standard/hed-specification/master/hedxml/HED8.0.0.xml'
hed_schema = load_schema(hed_xml_url)
hed_validator = HedValidator(hed_schema)
hed_validator_no_semantic = HedValidator(run_semantic_validation=False)
hed_string_1 = \
"Sensory-event,Visual-presentation,Experimental-stimulus,Green,Non-target," + \
"(Letter/D, (Center-of, Computer-screen))"
string_obj_1 = HedString(hed_string_1)
validation_issues = string_obj_1.validate(hed_validator)
print(
get_printable_issue_string(
validation_issues,
title=
'[Example 1] hed_string_1 should have no issues with HEDv8.0.0'))
string_1_long, issues = string_obj_1.convert_to_short(hed_schema)
print(
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])
validation_issues = input_file.validate_file(hed_validator_local)
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}")
hed_string_obj = HedString(input_string)
return hed_string_obj.convert_to_short(hed_schema)
def short_to_long_string(input_string, hed_schema):
hed_string_obj = HedString(input_string)
return hed_string_obj.convert_to_long(hed_schema)
if __name__ == '__main__':
# Convert a spreadsheet to
data_path = '../../data/spreadsheet_data'
base_name = 'ExcelOneSheet'
single_sheet = os.path.join(data_path, base_name + '.xlsx')
loaded_schema = load_schema(local_hed)
prefixed_needed_tag_columns = {2: 'Property/Informational-property/Label/',
3: 'Property/Informational-property/Description/'}
loaded_file = HedInput(single_sheet, tag_columns=[4],
column_prefix_dictionary=prefixed_needed_tag_columns,
worksheet_name='LKT 8HED3')
filename = os.path.join(data_path, base_name + '_short_form.xlsx')
long_to_short_file(loaded_file, filename, loaded_schema)
filename = os.path.join(data_path, base_name + '_long_form.xlsx')
loaded_file = HedInput(single_sheet, tag_columns=[4],
column_prefix_dictionary=prefixed_needed_tag_columns,
worksheet_name='LKT 8HED3')
short_to_long_file(loaded_file, filename, loaded_schema)
inputs = 'Attribute/Sensory/Visual/Color/CSS-color/White-color/White'
import os
from hed.errors.error_reporter import get_printable_issue_string
from hed.models.sidecar import Sidecar
from hed.models.events_input import EventsInput
from hed.validator.hed_validator import HedValidator
from hed.schema.hed_schema_io import load_schema
from hed.schema.hed_schema_group import HedSchemaGroup
if __name__ == '__main__':
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)
""" Example of converting a hed schema from .mediawiki format to .xml format. """
from hed.util.file_util import write_strings_to_file
from hed.schema.hed_schema_io import load_schema
if __name__ == '__main__':
# Convert mediawiki to XML and write to a temporary file
hed_wiki_url = 'https://raw.githubusercontent.com/hed-standard/hed-specification/master' + \
'/hedwiki/HED8.0.0.mediawiki'
print("Converting HED8.0.0.mediawiki to XML:")
hed_schema = load_schema(hed_wiki_url)
xml_file_string = hed_schema.get_as_xml_string()
if xml_file_string:
xml_location = write_strings_to_file(xml_file_string)
print(f"XML temporary file: {xml_location}")