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 mip_sex(context, sample, case_id):
"""Parse out analysis determined sex of sample."""
if sample and case_id is None:
sample_obj = api.sample(sample)
if sample_obj is None:
log.warn('sorry, sample not found')
context.abort()
case_id = sample_obj.case_id
qc_metrics = api.assets(case_id, category='qc').first()
qcm_data = yaml.load(qc_metrics.path)
sample_sexes = parse_mipsex(qcm_data)
if sample:
click.echo(sample_sexes[sample])
else:
for sample_id, sex in sample_sexes.items():
click.echo("{}: {}".format(sample_id, sex))
