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 restart(context, max_gaussian, restart, email, case, extras, disable,
start_from, config_path):
"""Restart MIP with modifications to the config file."""
if not case and not config_path:
log.error("you must provide either case of config path")
context.abort()
if case:
most_recent = api.case(case).first()
config_path = most_recent.config_path
if max_gaussian:
new_values = restart_api.update_maxgaussian(config_path)
else:
extras = dict(extras)
new_values = restart_api.update_config(config_path,
start_step=start_from,
disable_branches=disable,
**extras)
log.info("update config: {}".format(config_path))
restart_api.write_config(config_path, new_values)
if restart:
email = email or environ_email() or new_values.get('email')
kwargs = dict(executable=context.obj['mip_exe'], email=email)
process = start_mip(config=config_path, **kwargs)
process.wait()
if process.returncode != 0:
log.error("error starting analysis, check the output")
context.abort()
if case:
new_entry = build_pending(most_recent.case_id,
most_recent.root_dir)
commit_analysis(context.obj['manager'], new_entry)
