def validate_entity(self, entity: Entity):
# identify which attribute cases the error
attribute = 'fake_attribute'
error_msg = 'Example error message'
entity.add_error(attribute, error_msg)
# or if multiple errors occur for the same attribute
error_msgs = ['error 1', 'error 2']
entity.add_errors(attribute, error_msgs)
raise NotImplementedError('Example validate entity used')
def add_errors(self, schema, ena_type: str, entity_type: str, entity: Entity):
for error in schema.error_log:
match = self.regex.match(error.message)
error_message = match.group('error') if match else error.message
error_attribute = error.path.rpartition('/')[2].lower()
if error_attribute not in entity.attributes:
error_attribute = f'{entity_type}_ena_{ena_type}_accession'.lower()
error_message = f'{error.path} {error_message}'
entity.add_error(error_attribute, error_message)
def validate_file(self, entity: Entity, file_attribute: str,
check_attribute: str):
file_name = entity.attributes[file_attribute]
if file_name not in self.file_checksum_map:
entity.add_error(
file_attribute,
f'File has not been uploaded to drag-and-drop: {file_name}')
return
upload_checksum = self.file_checksum_map[file_name]
if check_attribute in entity.attributes:
stated_checksum = entity.attributes[check_attribute]
if stated_checksum != upload_checksum:
entity.add_error(
check_attribute,
f'The checksum found on drag-and-drop {upload_checksum} does not match: {stated_checksum}'
)
return
else:
entity.attributes[check_attribute] = upload_checksum
def convert_experiment(converter: EnaExperimentConverter, data: Submission, experiment: Entity) -> Element:
samples = data.get_linked_entities(experiment, 'sample')
studies = data.get_linked_entities(experiment, 'study')
if len(samples) < 1 or len(studies) < 1:
if len(samples) < 1:
experiment.add_error('run_experiment_ena_experiment_accession', 'No Linked Sample')
if len(studies) < 1:
experiment.add_error('run_experiment_ena_experiment_accession', 'No Linked Study')
else:
len_samples = len(samples)
len_studies = len(studies)
sample = samples.pop()
study = studies.pop()
# ENA Only supports linking one study & sample to an experiment
if len_samples > 1:
experiment.add_error('run_experiment_ena_experiment_accession', f'More than one Sample Linked, using first: {sample.identifier.index}')
if len_studies > 1:
experiment.add_error('run_experiment_ena_experiment_accession', f'More than one Study Linked, using first: {study.identifier.index}')
return converter.convert_experiment(experiment, sample, study)
