def schema_convert(hed_schema, display_name):
"""Return a string representation of hed_schema in the desired format
Parameters
----------
hed_schema: HedSchema object
A HedSchema object containing the schema to be processed.
display_name: str
The display name associated with this schema object.
Returns
-------
result: dict
A dictionary in the standard results format containing the results of the operation
"""
schema_version = hed_schema.header_attributes.get('version', 'Unknown')
schema_format = get_file_extension(display_name)
if schema_format == file_constants.SCHEMA_XML_EXTENSION:
data = hed_schema.get_as_mediawiki_string()
extension = '.mediawiki'
else:
data = hed_schema.get_as_xml_string()
extension = '.xml'
file_name = generate_filename(display_name, extension=extension)
return {
'command': base_constants.COMMAND_CONVERT,
'data': data,
'output_display_name': file_name,
'schema_version': schema_version,
'msg_category': 'success',
'msg': 'Schema was successfully converted'
}
def _run_tag_compare(local_xml_path):
"""Runs tag compare for the given XML file.
returns: A dictionary with converter.constants filled in.
"""
input_extension = get_file_extension(local_xml_path)
if input_extension != file_extension_constants.HED_XML_EXTENSION:
raise ValueError(f"Invalid extension type: {input_extension}")
return duplicate_tags.check_for_duplicate_tags(local_xml_path)
def _run_conversion(hed_file_path):
"""Runs the appropriate xml<>mediawiki converter depending on input filetype.
returns: A dictionary with converter.constants filled in.
"""
input_extension = get_file_extension(hed_file_path)
if input_extension == file_extension_constants.HED_XML_EXTENSION:
conversion_function = xml2wiki.convert_hed_xml_2_wiki
elif input_extension == file_extension_constants.HED_WIKI_EXTENSION:
conversion_function = wiki2xml.convert_hed_wiki_2_xml
else:
raise ValueError(f"Invalid extension type: {input_extension}")
return conversion_function(None, hed_file_path)
def get_input_from_form(request):
"""Gets input argument dictionary from the spreadsheet form request.
Parameters
----------
request: Request object
A Request object containing user data from the spreadsheet form.
Returns
-------
dictionary
A dictionary containing input arguments for calling the underlying spreadsheet functions
"""
arguments = {
base_constants.SCHEMA:
get_hed_schema_from_pull_down(request),
base_constants.SPREADSHEET:
None,
base_constants.SPREADSHEET_TYPE:
file_constants.TSV_EXTENSION,
base_constants.WORKSHEET_NAME:
request.form.get(base_constants.WORKSHEET_SELECTED, None),
base_constants.COMMAND:
request.form.get(base_constants.COMMAND_OPTION, ''),
base_constants.HAS_COLUMN_NAMES:
form_has_option(request, base_constants.HAS_COLUMN_NAMES, 'on'),
base_constants.CHECK_FOR_WARNINGS:
form_has_option(request, base_constants.CHECK_FOR_WARNINGS, 'on'),
}
tag_columns, prefix_dict = get_prefix_dict(request.form)
filename = request.files[base_constants.SPREADSHEET_FILE].filename
file_ext = get_file_extension(filename)
if file_ext in file_constants.EXCEL_FILE_EXTENSIONS:
arguments[
base_constants.SPREADSHEET_TYPE] = file_constants.EXCEL_EXTENSION
spreadsheet = models.HedInput(
file=request.files[base_constants.SPREADSHEET_FILE],
file_type=arguments[base_constants.SPREADSHEET_TYPE],
worksheet_name=arguments.get(base_constants.WORKSHEET_NAME, None),
tag_columns=tag_columns,
has_column_names=arguments.get(base_constants.HAS_COLUMN_NAMES, None),
column_prefix_dictionary=prefix_dict,
name=filename)
arguments[base_constants.SPREADSHEET] = spreadsheet
return arguments
def save_hed_to_upload_folder(hed_file_object):
"""Save an spreadsheet other to the upload folder.
Parameters
----------
hed_file_object: File object
A other object that points to a HED XML other that was first saved in a temporary location.
Returns
-------
string
The path to the HED XML other that was saved to the upload folder.
"""
hed_file_extension = get_file_extension(hed_file_object.filename)
hed_file_path = _save_file_to_upload_folder(hed_file_object, hed_file_extension)
return hed_file_path
def report_eeg_events_validation_status(request):
"""Reports validation status of hed strings associated with EEG events
received from EEGLAB plugin HEDTools
Parameters
----------
request: Request object
A Request object containing user data submitted by HEDTools.
Keys include "hed_strings", "check_for_warnings", and "hed_xml_file"
Returns
-------
string
A serialized JSON string containing information related to the hed strings validation result.
If the validation fails then a 500 error message is returned.
"""
validation_status = {}
# Parse uploaded data
form_data = request.form
check_for_warnings = form_data["check_for_warnings"] == '1' if "check_for_warnings" in form_data else False
# if hed_xml_file was submitted, it's accessed by request.files, otherwise empty
if "hed_xml_file" in request.files and get_file_extension(request.files["hed_xml_file"].filename) == "xml":
hed_xml_file = _save_hed_to_upload_folder_if_present(request.files["hed_xml_file"])
else:
hed_xml_file = ''
try:
# parse hed_strings from json
hed_strings = json.loads(form_data["hed_strings"])
# hed_strings is a list of HED strings associated with events in EEG.event (order preserved)
hed_input_reader = HedValidator(hed_strings, check_for_warnings=check_for_warnings, hed_xml_file=hed_xml_file)
# issues is a list of lists. Element list is empty if no error,
# else is a list of dictionaries, each dictionary contains an error-message key-value pair
issues = hed_input_reader.get_validation_issues()
# Prepare response
validation_status["issues"] = issues
except:
validation_status[error_constants.ERROR_KEY] = traceback.format_exc()
finally:
delete_file_if_it_exist(hed_xml_file)
return validation_status
def _get_column_delimiter_based_on_file_extension(file_name_or_path):
"""Gets the spreadsheet column delimiter based on the other extension.
Parameters
----------
file_name_or_path: string
A other name or path.
Returns
-------
string
The spreadsheet column delimiter based on the other extension.
"""
column_delimiter = ''
file_extension = get_file_extension(file_name_or_path)
if file_extension in spreadsheet_constants.SPREADSHEET_FILE_EXTENSION_TO_DELIMITER_DICTIONARY:
column_delimiter = spreadsheet_constants.SPREADSHEET_FILE_EXTENSION_TO_DELIMITER_DICTIONARY.get(file_extension)
return column_delimiter
def test_get_file_extension(self):
expected_extension = '.xml'
file_extension = file_util.get_file_extension(self.hed_xml_file)
self.assertTrue(file_extension)
self.assertEqual(expected_extension, file_extension)