def process(db, cust_roots):
"""Process all MIP output."""
family_dirs = list(automate.case_roots(*cust_roots))
analyses = (load_analysis(family_dir, insanity=True) for family_dir in
family_dirs)
total = len(family_dirs)
with click.progressbar(analyses, label='mip | analyses',
length=total) as bar:
for analysis in bar:
process_one(db, analysis)
try:
db.commit()
except (OperationalError, IntegrityError):
logger.exception('error in saving mip analysis')
db.session.rollback()
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)
def test_case_roots():
cases = automate.case_roots('tests/fixtures/analysis/customers/cust000',
'tests/fixtures/analysis/customers/cust001')
assert len(list(cases)) == 3
