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 extend(context, no_link, date, category, sample, archive_type, case_name,
asset_path):
"""Add an additional asset to a run."""
manager = api.manager(context.obj['database'])
run_obj = run_orabort(context, case_name, date)
if sample:
sample_map = {smpl.name: smpl for smpl in run_obj.samples}
sample_obj = sample_map[sample]
else:
sample_obj = None
new_asset = api.add_asset(run_obj, asset_path, category, archive_type,
sample=sample_obj)
root_path = context.obj['root']
run_root = get_rundir(root_path, run_obj.case.name, run_obj)
filename = new_asset.basename()
if no_link:
new_path = asset_path
else:
new_path = run_root.joinpath(filename)
log.debug("link asset: %s -> %s", new_asset.original_path, new_path)
path(new_asset.original_path).link(new_path)
new_asset.path = new_path
run_obj.assets.append(new_asset)
log.info("add asset: %s", new_asset.path)
manager.commit()
