Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.
_LOGGER.debug("Determined tag for removal: {}".format(a["tag"]))
if a["seek_key"] is not None:
raise NotImplementedError("You can't remove a specific seek_key.")
bundle = [a["genome"], a["asset"], a["tag"]]
try:
if not rgc.is_asset_complete(*bundle):
with rgc as r:
r.cfg_remove_assets(*bundle)
_LOGGER.info("Removed an incomplete asset '{}/{}:{}'".
format(*bundle))
return
except (KeyError, MissingAssetError, MissingGenomeError):
_LOGGER.info("Asset '{}/{}:{}' does not exist".format(*bundle))
return
if len(asset_list) > 1:
if not query_yes_no("Are you sure you want to remove {} assets?".
format(len(asset_list))):
_LOGGER.info("Action aborted by the user")
return
force = True
for a in asset_list:
rgc.remove(genome=a["genome"], asset=a["asset"], tag=a["tag"],
force=force)
elif args.command == TAG_CMD:
rgc = RefGenConf(filepath=gencfg)
if len(asset_list) > 1:
raise NotImplementedError("Can only tag 1 asset at a time")
if args.default:
# set the default tag and exit
with rgc as r:
r.set_default_pointer(a["genome"], a["asset"], a["tag"], True)
# the tag subdir
tag_path = os.path.join(abs_asset_path, tag)
from shutil import copytree as cp
else:
# if seek_key is specified we're about to move just a single file to
# he tag subdir
tag_path = os.path.join(os.path.dirname(abs_asset_path), tag)
if not os.path.exists(tag_path):
os.makedirs(tag_path)
from shutil import copy2 as cp
if os.path.exists(abs_asset_path):
if not os.path.exists(tag_path):
cp(abs_asset_path, tag_path)
else:
if not force and not \
query_yes_no("Path '{}' exists. Do you want to overwrite?".
format(tag_path)):
return False
else:
_remove(tag_path)
cp(abs_asset_path, tag_path)
else:
raise OSError("Absolute path '{}' does not exist. "
"The provided path must be relative to: {}".
format(abs_asset_path, rgc[CFG_FOLDER_KEY]))
rgc.make_writable()
gat_bundle = [asset_dict["genome"], asset_dict["asset"], tag]
td = {CFG_ASSET_PATH_KEY:
path if os.path.isdir(abs_asset_path) else os.path.dirname(path)}
rgc.update_tags(*gat_bundle, data=td)
# seek_key points to the entire dir if not specified
seek_key_value = os.path.basename(abs_asset_path) \