def link_records(data):
"""Fetch existing information."""
case_obj = api.case(data['case'])
if case_obj is None:
raise ValueError("case not found: {}".format(data['case']))
for sample_id in data['samples']:
sample_obj = api.sample(sample_id)
if sample_obj is None:
raise ValueError("sample not found: {}".format(sample_id))
data['run'].samples.append(sample_obj)
for new_asset, sample_id in data['assets']:
link_asset(data['run'], new_asset, sample=sample_id)
return {'case': case_obj, 'run': data['run']}
def parse(config_data, reference_data, force=False):
"""Parse MIP analysis output."""
# 1. parse segments of input data
segments = prepare_inputs(config_data)
# 2. post-process the output a bit
prepare_run(segments, force=force)
# 3. build the records
mip_version = segments['family'].get('MIPVersion', 'v2.x')
new_objs = build_analysis(segments, version=mip_version)
# 4. parse references
new_refs = parse_references(reference_data, segments=segments)
# 5. build assets from references + link to new records
new_assets = build_assets(new_refs)
for new_asset, sample in new_assets:
link_asset(new_objs['run'], new_asset, sample=sample)
return new_objs
