def do(context, case_path, run_all, step, use_family, force):
"""Perform action on a completed analysis."""
mip_case = info.analysis(case_path)
context.obj["case"] = mip_case
context.obj["use_family"] = use_family
# check if analysis is complete
if not force and not mip_case.is_complete:
logger.warn("analysis not finished")
context.abort()
if run_all:
context.invoke(all_cmd)
elif step:
context.invoke(STEPS[step])
def case(context, case_paths):
"""Monitor the status of an analysis (finished/running)."""
if len(case_paths) == 0:
logger.warn('no case paths given')
context.abort()
scout_db = scout_tools.ScoutDatabase(context.obj['mongodb'])
case_infos = (analysis_info(info.analysis(case_path), scout_db)
for case_path in case_paths)
headers = ['Customer', 'Case', 'Samples', 'MIP', 'Date', 'Complete',
'In Scout', 'Up-to-date', 'Research']
rows = (serialize_status(case_info) for case_info in case_infos)
output = tabulate(rows, headers=headers, tablefmt='fancy_grid')
click.echo(output)
def traverse(context, step, cust_roots):
"""Upload all cases found by traversing the root directories."""
if len(cust_roots) == 0:
cust_roots = expand_paths(*context.obj.get("customer_roots", []))
for case_path in automate.case_roots(*cust_roots):
try:
mip_case = info.analysis(case_path)
if not mip_case.is_complete:
logger.debug("skipping non-complete case: %s", case_path)
elif "Path" not in mip_case._family["VCFFile"]["Clinical"]:
logger.warn("analysis run in non-standard mode")
elif step:
logger.debug("processing %s: %s", case_path, step)
context.invoke(do, case_path=case_path, step=step)
else:
logger.debug("processing case: %s", case_path)
context.invoke(do, case_path=case_path, run_all=True)
except Exception as error:
logger.exception("unexpected error loading: %s", case_path)