def test_pull_asset_works_with_nonwritable_and_writable_rgc(
cfg_file, gname, aname, tname, state):
rgc = RefGenConf(filepath=cfg_file, writable=state)
remove_asset_and_file(rgc, gname, aname, tname)
with mock.patch("refgenconf.refgenconf.query_yes_no", return_value=True):
print("\nPulling; genome: {}, asset: {}, tag: {}\n".format(
gname, aname, tname))
rgc.pull_asset(gname, aname, tname)
def test_pull_asset_updates_genome_config(cfg_file, gname, aname, tname):
"""
Test that the object that was identical prior to the asset pull differs afterwards
and the pulled asset metadata has been written to the config file
"""
ori_rgc = RefGenConf(filepath=cfg_file, writable=False)
rgc = RefGenConf(filepath=cfg_file, writable=False)
remove_asset_and_file(rgc, gname, aname, tname)
remove_asset_and_file(ori_rgc, gname, aname, tname)
# ori_rgc.remove_assets(gname, aname, tname)
assert ori_rgc.to_dict() == rgc.to_dict()
with mock.patch("refgenconf.refgenconf.query_yes_no", return_value=True):
print("\nPulling; genome: {}, asset: {}, tag: {}\n".format(
gname, aname, tname))
rgc.pull_asset(gname, aname, tname)
assert not ori_rgc.to_dict() == rgc.to_dict()
post_rgc = RefGenConf(filepath=cfg_file, writable=False)
assert isinstance(post_rgc.get_asset(gname, aname, tname), str)
def main():
""" Primary workflow """
parser = logmuse.add_logging_options(build_argparser())
args, remaining_args = parser.parse_known_args()
global _LOGGER
_LOGGER = logmuse.logger_via_cli(args)
logmuse.logger_via_cli(args, name=refgenconf.__name__)
_LOGGER.debug("Args: {}".format(args))
if not args.command:
parser.print_help()
_LOGGER.error("No command given")
sys.exit(1)
gencfg = yacman.select_config(args.genome_config,
CFG_ENV_VARS,
check_exist=not args.command == INIT_CMD,
on_missing=lambda fp: fp)
if gencfg is None:
raise MissingGenomeConfigError(args.genome_config)
_LOGGER.debug("Determined genome config: {}".format(gencfg))
if args.command == INIT_CMD:
_LOGGER.info("Initializing refgenie genome configuration")
_writeable(os.path.dirname(gencfg), strict_exists=True)
refgenie_init(gencfg, args.genome_server)
sys.exit(0)
rgc = RefGenConf(gencfg)
if args.command == BUILD_CMD:
refgenie_build(rgc, args)
elif args.command == GET_ASSET_CMD:
_LOGGER.debug("getting asset: '{}/{}'".format(args.genome, args.asset))
print(" ".join(
[rgc.get_asset(args.genome, asset) for asset in args.asset]))
return
elif args.command == INSERT_CMD:
if len(args.asset) > 1:
raise NotImplementedError("Can only add 1 asset at a time")
else:
# recast from list to str
args.asset = args.asset[0]
refgenie_add(rgc, args)
elif args.command == PULL_CMD:
outdir = rgc[CFG_FOLDER_KEY]
if not os.path.exists(outdir):
raise MissingFolderError(outdir)
target = _key_to_name(CFG_FOLDER_KEY)
if not perm_check_x(outdir, target):
return
if not _single_folder_writeable(outdir):
_LOGGER.error("Insufficient permissions to write to {}: "
"{}".format(target, outdir))
return
rgc.pull_asset(args.genome,
args.asset,
gencfg,
unpack=not args.no_untar)
elif args.command in [LIST_LOCAL_CMD, LIST_REMOTE_CMD]:
pfx, genomes, assets = _exec_list(rgc, args.command == LIST_REMOTE_CMD)
_LOGGER.info("{} genomes: {}".format(pfx, genomes))
_LOGGER.info("{} assets:\n{}".format(pfx, assets))