def get_errors(self):
# This creates a deeply nested dict.
# Keys are present only if there is actually an error to report.
errors = {}
tsv_errors = get_tsv_errors(self.path, schema_name='sample')
if tsv_errors:
errors['Sample TSV Errors'] = tsv_errors
return errors
def __get_ref_errors(self, ref_type, path, assay_type):
if ref_type == 'data':
return get_data_dir_errors(
assay_type, path, dataset_ignore_globs=self.dataset_ignore_globs)
else:
return get_tsv_errors(
schema_name=ref_type, tsv_path=path,
offline=self.offline, encoding=self.encoding)
def main():
args = parser.parse_args()
try:
schema_name = (args.schema if args.schema != 'metadata' else
get_schema_version(args.path, 'ascii').schema_name)
except PreflightError as e:
errors = {'Preflight': str(e)}
else:
errors = get_tsv_errors(args.path, schema_name=schema_name)
errors = {f'{schema_name} TSV errors': errors} if errors else {}
report = ErrorReport(errors)
print(getattr(report, args.output)())
return exit_codes.INVALID if errors else exit_codes.VALID
def _get_assay_internal_errors(self, assay_type, path):
return get_tsv_errors(
type=assay_type, tsv_path=path,
offline=self.offline, encoding=self.encoding,
optional_fields=self.optional_fields)
def _get_antibodies_errors(self, antibodies_path):
return get_tsv_errors(
type='antibodies', tsv_path=antibodies_path,
offline=self.offline, encoding=self.encoding)
def _get_contributors_errors(self, contributors_path):
return get_tsv_errors(
type='contributors', tsv_path=contributors_path,
offline=self.offline, encoding=self.encoding)