def post_pedigree(cust_id, case_id):
"""Write pedigree to correct location."""
logger.debug('gather information from LIMS')
samples_res = glue.get('lims', 'samples', params={'cust_id': cust_id,
'case_id': case_id})
analysis_type = utils.get_analysis_type(samples_res.json['analysis_types'])
ped_content = get_pedigree(cust_id, case_id)
docase_res = glue.post('assemble', 'cases', 'prepare', cust_id, case_id,
data={'analysis_type': analysis_type,
'ped_content': ped_content})
return docase_res.json
def post_start_analysis(cust_id, case_id, gene_list=None, mip_config=None,
add_only=False):
"""Start analysis for a case."""
filters = {'cust_id': cust_id, 'case_id': case_id}
samples_res = glue.get('lims', 'samples', params=filters)
analysis_types = samples_res.json['analysis_types']
analysis_type = get_analysis_type(analysis_types)
if add_only:
case_res = glue.get('analyze', 'analyses', cust_id, case_id)
else:
start_payload = {'seq_type': analysis_type, 'gene_list': gene_list,
'mip_config': mip_config}
case_res = glue.post('analyze', 'analyses', 'start', cust_id, case_id,
data=start_payload)
logger.debug('persist the analysis to the database')
analyzed_at = case_res.json['analyzed_at']
add_payload = {'cust_id': cust_id, 'case_id': case_id,
'analysis_type': analysis_type, 'analyzed_at': analyzed_at}
add_res = glue.post('moneypenny', 'analyses', data=add_payload)
return add_res.json
