def start(context, ccp, config, executable, gene_list, email, priority, dryrun,
customer, family):
"""Start a new analysis."""
ccp_abs = (Path(ccp).abspath() if ccp else
Path(context.obj['analysis_root']).joinpath(customer))
# parse pedigree yaml
pedigree_path = ccp_abs.joinpath("{0}/{0}_pedigree.yaml".format(family))
if not pedigree_path.exists():
log.error("pedigree YAML doesn't exist")
context.abort()
# check if case is already running
case_id = "{}-{}".format(customer, family)
if api.is_running(case_id):
log.error("case already running!")
context.abort()
global_config = config or context.obj['mip_config']
executable = executable or context.obj['mip_exe']
gene_list = gene_list or context.obj.get('mip_genelist')
email = email or environ_email()
process = start_mip(
config=global_config,
family_id=family,
ccp=ccp_abs,
executable=executable,
gene_list=gene_list,
dryrun=dryrun,
email=email,
priority=priority,
)
process.wait()
if process.returncode != 0:
log.error("error starting analysis, check the output")
context.abort()
# add pending entry to database
new_entry = build_pending(case_id, ccp_abs)
if email:
user = api.user(email)
new_entry.user = user
commit_analysis(context.obj['manager'], new_entry)
context.obj['manager'].commit()
def commit_analysis(manager, new_entry, email=None):
"""Store new analysis in the database."""
# look up previous runs for the same case
old_runs = api.case(case_id=new_entry.case_id)
latest_run = old_runs.first()
if latest_run is None or not same_entry(latest_run, new_entry):
if new_entry.status == 'completed':
# set failed runs to not be visible in dashboard
for old_run in old_runs:
old_runs.is_visible = False
manager.commit()
# save the new entry to the database
if latest_run and latest_run.status in ('running', 'pending'):
# replace old temporary entries
log.debug("deleting existing entry: %s", new_entry.case_id)
latest_run.delete()
manager.commit()
if email:
new_entry.user = api.user(email)
manager.add_commit(new_entry)
log.info("added new entry: {entry.case_id} - {entry.status}"
.format(entry=new_entry))
