def validate_metadata_file(convention_path, metadata_path):
with open(convention_path) as f:
convention = json.load(f)
metadata = CellMetadata(metadata_path, '', '')
print(f'Validating {metadata_path}')
collect_jsonschema_errors(metadata, convention)
validate_collected_ontology_data(metadata, convention)
serialize_issues(metadata)
report_issues(metadata)
exit_if_errors(metadata)
def validate_metadata_file(metadata_path):
placeholder = 'SCP555' # TODO: Refactor CellMetadata to not require this
metadata = CellMetadata(metadata_path, '', '', study_accession=placeholder)
print(f'Validating {metadata_path}')
convention_path = download_from_bucket(IngestPipeline.JSON_CONVENTION)
with open(convention_path) as file:
convention = json.load(file)
validate_input_metadata(metadata, convention)
serialize_issues(metadata)
report_issues(metadata)
exit_if_errors(metadata)
def validate_metadata_file(parsed_args, connection):
metadata_path = parsed_args.metadata_file
study_name = parsed_args.study_name
dry_run = parsed_args.dry_run
verbose = parsed_args.verbose
study_accession_res = connection.get_study_attribute(study_name=study_name,
attribute='accession',
dry_run=dry_run)
# Needed dummy values for CellMetadata
study_file = ObjectId('addedfeed000000000000000')
study_file_id = ObjectId('addedfeed000000000000001')
if succeeded(study_accession_res):
if verbose:
print(
f'Study accession {study_accession_res} retrieved for {study_name}'
)
study_accession = study_accession_res.get('study_attribute')
metadata = CellMetadata(
metadata_path,
study_file,
study_file_id,
study_accession=str(study_accession),
)
convention_res = connection.do_get(
command=get_api_base(parsed_args) +
'metadata_schemas/alexandria_convention/latest/json',
dry_run=dry_run,
)
if succeeded(convention_res):
if verbose:
print(f'Retreieved file for latest metdata convention')
convention = convention_res["response"].json()
validate_input_metadata(metadata, convention)
serialize_issues(metadata)
report_issues(metadata)
exit_if_errors(metadata)