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