def validate_column(self, validators, error_handler, **kwargs):
"""
Run the given validators on this column
Parameters
----------
validators : [func or validator like] or func or validator like
A validator or list of validators to apply to the hed strings in the columns.
error_handler : ErrorHandler or None
Used to report errors. Uses a default one if none passed in.
kwargs:
See util.translate_ops or the specific validators for additional options
Returns
-------
col_issues: [{}]
A list of issues found by the given validators.
"""
if error_handler is None:
error_handler = error_reporter.ErrorHandler()
if not isinstance(validators, list):
validators = [validators]
validators = validators.copy()
validators.append(self._validate_pound_sign_count)
error_handler.push_error_context(ErrorContext.SIDECAR_COLUMN_NAME,
self.column_name)
col_validation_issues = self._run_ops(validators,
allow_placeholders=True,
error_handler=error_handler,
**kwargs)
col_validation_issues += self._validate_column_structure(error_handler)
col_validation_issues += self.get_definition_issues()
error_handler.pop_error_context()
return col_validation_issues
def setUpClass(cls):
if cls.schema_file:
hed_xml = os.path.join(os.path.dirname(os.path.abspath(__file__)),
cls.schema_file)
cls.hed_schema = schema.load_schema(hed_xml)
elif not cls.hed_schema:
raise ValueError("No schema set for test case")
cls.error_handler = error_reporter.ErrorHandler()
def setUpClass(cls):
super().setUpClass()
cls.error_handler = error_reporter.ErrorHandler()
cls.syntactic_hed_input_reader = HedValidator(
hed_schema=None, run_semantic_validation=False)
cls.syntactic_tag_validator = cls.syntactic_hed_input_reader._tag_validator
cls.semantic_hed_input_reader = HedValidator(
hed_schema=cls.hed_schema, run_semantic_validation=True)
cls.semantic_tag_validator = cls.semantic_hed_input_reader._tag_validator
def setUpClass(cls):
schema_file = '../data/hed_pairs/HED8.0.0t.xml'
hed_xml = os.path.join(os.path.dirname(os.path.abspath(__file__)), schema_file)
hed_schema1 = schema.load_schema(hed_xml)
hed_schema2 = schema.load_schema(hed_xml, library_prefix="tl:")
cls.hed_schema = HedSchemaGroup([hed_schema1, hed_schema2])
cls.error_handler = error_reporter.ErrorHandler()
super().setUpClass()
def validate_entries(self, validators=None, name=None, extra_def_dicts=None,
error_handler=None, **kwargs):
"""Run the given validators on all columns in this sidecar
Parameters
----------
validators : [func or validator like] or func or validator like
A validator or list of validators to apply to the hed strings in this sidecar.
name: str
If present, will use this as the filename for context, rather than using the actual filename
Useful for temp filenames.
extra_def_dicts: [DefDict] or DefDict or None
If present, also use these in addition to the sidecars def dicts.
error_handler : ErrorHandler or None
Used to report errors. Uses a default one if none passed in.
kwargs:
See util.translate_ops or the specific validators for additional options
Returns
-------
validation_issues: [{}]
The list of validation issues found
"""
if error_handler is None:
error_handler = error_reporter.ErrorHandler()
if not name:
name = self.name
if name:
error_handler.push_error_context(ErrorContext.FILE_NAME, name, False)
validators = self._add_definition_mapper(validators, extra_def_dicts)
all_validation_issues = []
for column_data in self:
all_validation_issues += column_data.validate_column(validators,
error_handler=error_handler,
**kwargs)
if name:
error_handler.pop_error_context()
return all_validation_issues
def check_compliance(hed_schema,
also_check_for_warnings=True,
name=None,
error_handler=None):
"""
Checks for hed3 compliance of a schema object.
Parameters
----------
hed_schema : HedSchema
HedSchema object to check for hed3 compliance
also_check_for_warnings : bool, default True
If True, also checks for formatting issues like invalid characters, capitalization, etc.
name: str
If present, will use this as the filename for context, rather than using the actual filename
Useful for temp filenames.
error_handler : ErrorHandler or None
Used to report errors. Uses a default one if none passed in.
Returns
-------
issue_list : [{}]
A list of all warnings and errors found in the file.
"""
if not isinstance(hed_schema, HedSchema):
raise ValueError(
"To check compliance of a HedGroupSchema, call self.check_compliance on the schema itself."
)
if error_handler is None:
error_handler = error_reporter.ErrorHandler()
issues_list = []
if not name:
name = hed_schema.filename
error_handler.push_error_context(ErrorContext.FILE_NAME, name)
unknown_attributes = hed_schema.get_all_unknown_attributes()
if unknown_attributes:
for attribute_name, source_tags in unknown_attributes.items():
for tag in source_tags:
issues_list += error_handler.format_error_with_context(
SchemaErrors.HED_SCHEMA_ATTRIBUTE_INVALID,
attribute_name,
source_tag=tag)
schema_attribute_validators = {
HedKey.SuggestedTag: tag_exists_check,
HedKey.RelatedTag: tag_exists_check,
HedKey.UnitClass: tag_is_placeholder_check,
HedKey.ValueClass: tag_is_placeholder_check,
}
# Check attributes
for section_key in hed_schema._sections:
error_handler.push_error_context(ErrorContext.SCHEMA_SECTION,
section_key)
# Check attributes
for tag_entry in hed_schema[section_key].values():
error_handler.push_error_context(ErrorContext.SCHEMA_TAG,
tag_entry.name)
for attribute_name in tag_entry.attributes:
validator = schema_attribute_validators.get(attribute_name)
if validator:
error_handler.push_error_context(
ErrorContext.SCHEMA_ATTRIBUTE, attribute_name, False)
new_issues = validator(
hed_schema, tag_entry,
tag_entry.attributes[attribute_name])
error_handler.add_context_to_issues(new_issues)
issues_list += new_issues
error_handler.pop_error_context()
error_handler.pop_error_context()
# Check duplicate names
for name, duplicate_entries in hed_schema[
section_key].duplicate_names.items():
issues_list += error_handler.format_error_with_context(
SchemaErrors.HED_SCHEMA_DUPLICATE_NODE,
name,
duplicate_tag_list=[entry.name for entry in duplicate_entries],
section=section_key)
error_handler.pop_error_context()
if also_check_for_warnings:
hed_terms = hed_schema.get_all_schema_tags(True)
for hed_term in hed_terms:
issues_list += validate_schema_term(hed_term)
for tag_name, desc in hed_schema.get_desc_iter():
issues_list += validate_schema_description(tag_name, desc)
error_handler.pop_error_context()
return issues_list