def lims(context, limit, sample, start_date):
"""Load all samples from LIMS into the database."""
if start_date:
start_date = datetime.strptime(start_date, "%Y-%m-%d").date()
start_date = start_date or context.obj.get('LIMS_START_DATE')
lims_api = LimsAPI()
lims_api.connect(**context.obj['LIMS_SETTINGS'])
process_lims(context.obj['db'], lims_api, limit=limit, lims_ids=sample,
start_date=start_date)
def parse_payload(db, payload, config, force=False):
"""Analyze a family of samples.
1. generates and writes a new pedigree file from LIMS data
2. generates a start script for the analysis pipeline
Args:
db (Brain): Moneypenny database API
payload (dict): specific data for the analysis mutation type
config (dict): general config for Moneypenny
force (Optional[bool]): not implemented, default: False
"""
analysis_root = config['MIP_ANALYSIS_ROOT']
mip_config = config['MIP_CONFIG_PATH']
cust_id = payload['customer_id']
family_id = payload['family_id']
analysis_type = payload['analysis_type']
gene_list = payload['gene_list']
ccp = os.path.join(analysis_root, cust_id, family_id)
# generate pedigree from LIMS
if not payload.get('skip_pedigree'):
lims_api = LimsAPI()
lims_api.connect(**config['LIMS_SETTINGS'])
ped_content = pedigree(lims_api, cust_id, family_id)
file_name = "{}_pedigree.txt".format(family_id)
ped_path = os.path.join(ccp, analysis_type, family_id, file_name)
with open(ped_path, 'w') as handle:
handle.write(ped_content)
script = start(
analysis_type,
family_id,
mip_config,
ccp,
executable=config['MIP_EXE_PATH'],
customer=cust_id,
gene_list=gene_list,
conda_env=config.get('MIP_CONDA_ENV'),
email=payload.get('email'),
)
script_name = "{}-{}.bash".format(cust_id, family_id)
outfile = os.path.join(config['START_SCRIPTS_DIR'], script_name)
with open(outfile, 'w') as handle:
# overwrite if necessary
handle.write(script)
