def test_select_config_works_env_vars(self, cfg_file, varname="TEST"):
os.environ[varname] = cfg_file
assert isinstance(yacman.select_config(config_env_vars=varname), str)
assert yacman.select_config(
config_env_vars=varname) == yacman.select_config(
config_filepath=cfg_file)
del os.environ[varname]
def select_bulker_config(filepath):
bulkercfg = yacman.select_config(
filepath,
"BULKERCFG",
default_config_filepath=DEFAULT_CONFIG_FILEPATH,
check_exist=True)
_LOGGER.debug("Selected bulker config: {}".format(bulkercfg))
return bulkercfg
def select_genome_config(filename=None, conf_env_vars=CFG_ENV_VARS, **kwargs):
"""
Get path to genome configuration file.
:param str filename: name/path of genome configuration file
:param Iterable[str] conf_env_vars: names of environment variables to
consider; basically, a prioritized search list
:return str: path to genome configuration file
"""
return select_config(filename, conf_env_vars, **kwargs)
def get_bedbase_cfg(cfg=None):
"""
Determine path to the bedbase configuration file
The path can be either explicitly provided
or read from a $BEDBASE environment variable
:param str cfg: path to the config file.
Optional, the $BEDBASE config env var will be used if not provided
:return str: configuration file path
"""
selected_cfg = select_config(config_filepath=cfg,
config_env_vars=CFG_ENV_VARS)
if not selected_cfg:
raise BedBaseConnectionError(
f"You must provide a config file or set the "
f"{'or '.join(CFG_ENV_VARS)} environment variable")
return selected_cfg
def select_divvy_config(filepath):
"""
Selects the divvy config file path to load.
This uses a priority ordering to first choose a config file path if
it's given, but if not, then look in a priority list of environment
variables and choose the first available file path to return. If none of
these options succeed, the default config path will be returned.
:param str | NoneType filepath: direct file path specification
:return str: path to the config file to read
"""
divcfg = yacman.select_config(
config_filepath=filepath,
config_env_vars=COMPUTE_SETTINGS_VARNAME,
default_config_filepath=DEFAULT_CONFIG_FILEPATH,
check_exist=True,
)
_LOGGER.debug("Selected divvy config: {}".format(divcfg))
return divcfg
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))
def test_select_config_errors_if_no_cfg_found_and_strict_checks_requested(
self, varname="TEST"):
os.environ[varname] = "bogus/path.yaml"
with pytest.raises(Exception):
yacman.select_config(config_env_vars=varname, strict_env=True)
del os.environ[varname]
def test_select_config_returns_none_if_no_cfg_found(self, varname="TEST"):
os.environ[varname] = "bogus/path.yaml"
assert yacman.select_config(config_env_vars=varname) is None
del os.environ[varname]
def test_select_config_returns_default_cfg(self, path="path.yaml"):
assert yacman.select_config(default_config_filepath=path) == path
def test_select_config_works_with_filepath(self, cfg_file):
assert isinstance(yacman.select_config(config_filepath=cfg_file), str)