def scout(context, madeline_exe, date, replace, case_name):
"""Prepare a config and files for Scout."""
madeline_exe = madeline_exe or context.obj['madeline_exe']
manager = api.manager(context.obj['database'])
root_path = context.obj['root']
run_obj = run_orabort(context, case_name, date)
if not run_obj.pipeline_version.startswith('v4'):
log.error("unsupported pipeline version: %s", run_obj.pipeline_version)
context.abort()
existing_conf = (api.assets(category='scout-config', run_id=run_obj.id)
.first())
if existing_conf:
if replace:
log.info("deleting existing scout config: %s", existing_conf.path)
api.delete_asset(existing_conf)
existing_mad = (api.assets(category='madeline', run_id=run_obj.id)
.first())
if existing_mad:
log.info("deleting existing madeline: %s", existing_mad.path)
api.delete_asset(existing_mad)
manager.commit()
else:
log.error("scout config already generated")
context.abort()
prepare_scout(run_obj, root_path, madeline_exe)
manager.commit()
def prepare_scout(run_obj, root_path, madeline_exe):
"""Prepare files for Scout upload."""
run_root = Path(get_rundir(root_path, run_obj.case.name, run=run_obj))
config_data = build_config(run_obj)
pedigree = api.assets(category='pedigree', run_id=run_obj.id).one()
# extract external sample ids
ped_yaml = api.assets(category='pedigree-yaml', run_id=run_obj.id).one()
with Path(ped_yaml.path).open() as in_handle:
ped_data = yaml.load(in_handle)
sample_map = {sample['sample_id']: sample['sample_name']
for sample in ped_data['samples']}
madeline_path = build_madeline(pedigree.path, run_root, madeline_exe,
sample_map)
if madeline_path:
mad_asset = api.add_asset(run_obj, madeline_path, 'madeline')
mad_asset.path = str(madeline_path)
log.info("add madeline asset: %s", mad_asset.path)
run_obj.assets.append(mad_asset)
config_data['madeline'] = mad_asset.path
# save the new scout config
config_path = Path(run_root).joinpath('scout.conf.yaml')
with open(config_path, 'w') as out_handle:
yaml.safe_dump(config_data, out_handle, indent=4,
default_flow_style=False)
scout_asset = api.add_asset(run_obj, config_path, 'scout-config')
scout_asset.path = config_path
log.info("add scout config asset: %s", scout_asset.path)
run_obj.assets.append(scout_asset)
def replace_paths(old_root, new_root):
"""Replace root paths for assets."""
all_assets = api.assets()
with click.progressbar(all_assets,
label='updating asset paths',
length=all_assets.count()) as bar:
for asset in bar:
new_path = asset.path.replace(old_root, new_root)
log.debug("replacing path: %s -> %s", asset.path, new_path)
assert Path(new_path).exists(), "can't find asset: {}".format(new_path)
asset.path = new_path
def mip_sex(context, sample, case_id):
"""Parse out analysis determined sex of sample."""
if sample and case_id is None:
sample_obj = api.sample(sample)
if sample_obj is None:
log.warn('sorry, sample not found')
context.abort()
case_id = sample_obj.case_id
qc_metrics = api.assets(case_id, category='qc').first()
qcm_data = yaml.load(qc_metrics.path)
sample_sexes = parse_mipsex(qcm_data)
if sample:
click.echo(sample_sexes[sample])
else:
for sample_id, sex in sample_sexes.items():
click.echo("{}: {}".format(sample_id, sex))