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, make_root=True)
_LOGGER.debug("refgenie {}".format(__version__))
_LOGGER.debug("Args: {}".format(args))
if not args.command:
parser.print_help()
_LOGGER.error("No command given")
sys.exit(1)
gencfg = refgenconf.select_genome_config(
filename=args.genome_config,
check_exist=not args.command == INIT_CMD,
on_missing=lambda fp: fp,
strict_env=True)
if gencfg is None:
raise MissingGenomeConfigError(args.genome_config)
_LOGGER.debug("Determined genome config: {}".format(gencfg))
# From user input we want to construct a list of asset dicts, where each
# asset has a genome name, asset name, and tag
if "asset_registry_paths" in args and args.asset_registry_paths:
_LOGGER.debug("Found registry_path: {}".format(
args.asset_registry_paths))
asset_list = [
parse_registry_path(x) for x in args.asset_registry_paths
]
for a in asset_list:
# every asset must have a genome, either provided via registry path
# or the args.genome arg.
if not a["genome"]:
if args.genome:
a["genome"] = args.genome
else:
_LOGGER.error(
"Provided asset registry path ({}/{}:{}) is invalid. See help for usage reference."
.format(a["genome"], a["asset"], a["tag"]))
sys.exit(1)
else:
if args.genome and args.genome != a["genome"]:
_LOGGER.warn(
"Two different genomes specified for asset '{}'.".
format(a["asset"]))
else:
if args.command in GENOME_ONLY_REQUIRED and not args.genome:
parser.error("You must provide either a genome or a registry path")
sys.exit(1)
if args.command in ASSET_REQUIRED:
parser.error("You must provide an asset registry path")
sys.exit(1)
if args.command == INIT_CMD:
_LOGGER.debug("Initializing refgenie genome configuration")
rgc = RefGenConf(entries=OrderedDict(
{
CFG_VERSION_KEY: REQ_CFG_VERSION,
CFG_FOLDER_KEY: os.path.dirname(os.path.abspath(gencfg)),
CFG_SERVERS_KEY: args.genome_server or [DEFAULT_SERVER],
CFG_GENOMES_KEY: None
}))
rgc.initialize_config_file(os.path.abspath(gencfg))
elif args.command == BUILD_CMD:
if not all(
[x["genome"] == asset_list[0]["genome"] for x in asset_list]):
_LOGGER.error("Build can only build assets for one genome")
sys.exit(1)
recipe_name = None
if args.recipe:
if len(asset_list) > 1:
_LOGGER.error(
"Recipes cannot be specified for multi-asset builds")
sys.exit(1)
recipe_name = args.recipe
if args.requirements:
for a in asset_list:
recipe = recipe_name or a["asset"]
if recipe not in asset_build_packages.keys():
_raise_missing_recipe_error(recipe)
_LOGGER.info("'{}' recipe requirements: ".format(recipe))
_make_asset_build_reqs(recipe)
sys.exit(0)
refgenie_build(gencfg, asset_list[0]["genome"], asset_list,
recipe_name, args)
elif args.command == GET_ASSET_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
check = args.check_exists if args.check_exists else None
for a in asset_list:
_LOGGER.debug("getting asset: '{}/{}.{}:{}'".format(
a["genome"], a["asset"], a["seek_key"], a["tag"]))
print(
rgc.seek(a["genome"],
a["asset"],
a["tag"],
a["seek_key"],
strict_exists=check))
return
elif args.command == INSERT_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
if len(asset_list) > 1:
raise NotImplementedError("Can only add 1 asset at a time")
else:
refgenie_add(rgc, asset_list[0], args.path, args.force)
elif args.command == PULL_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
force = None if not args.force else True
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
for a in asset_list:
rgc.pull(a["genome"],
a["asset"],
a["tag"],
unpack=not args.no_untar,
force=force)
elif args.command in [LIST_LOCAL_CMD, LIST_REMOTE_CMD]:
rgc = RefGenConf(filepath=gencfg, writable=False)
if args.command == LIST_REMOTE_CMD:
num_servers = 0
# Keep all servers so that child updates maintain server list
server_list = rgc[CFG_SERVERS_KEY]
bad_servers = []
for server_url in rgc[CFG_SERVERS_KEY]:
num_servers += 1
try:
rgc[CFG_SERVERS_KEY] = server_url
pfx, genomes, assets, recipes = _exec_list(
rgc, args.command == LIST_REMOTE_CMD, args.genome)
if assets is None and genomes is None:
continue
_LOGGER.info("{} genomes: {}".format(pfx, genomes))
if args.command != LIST_REMOTE_CMD: # Not implemented yet
_LOGGER.info("{} recipes: {}".format(pfx, recipes))
_LOGGER.info("{} assets:\n{}\n".format(pfx, assets))
except (DownloadJsonError, ConnectionError):
bad_servers.append(server_url)
continue
if num_servers >= len(server_list) and bad_servers:
_LOGGER.error(
"Could not list assets from the following server(s): {}".
format(bad_servers))
# Restore original server list, even when we couldn't find assets on a server
rgc[CFG_SERVERS_KEY] = server_list
else: # Only check local assets once
_LOGGER.info("Server subscriptions: {}".format(", ".join(
rgc[CFG_SERVERS_KEY])))
pfx, genomes, assets, recipes = _exec_list(
rgc, args.command == LIST_REMOTE_CMD, args.genome)
_LOGGER.info("{} genomes: {}".format(pfx, genomes))
if args.command != LIST_REMOTE_CMD: # Not implemented yet
_LOGGER.info("{} recipes: {}".format(pfx, recipes))
_LOGGER.info("{} assets:\n{}".format(pfx, assets))
elif args.command == GETSEQ_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
rgc.getseq(rgc, args.genome, args.locus)
elif args.command == REMOVE_CMD:
force = args.force
rgc = RefGenConf(filepath=gencfg)
for a in asset_list:
a["tag"] = a["tag"] or rgc.get_default_tag(
a["genome"], a["asset"], use_existing=False)
_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)
sys.exit(0)
rgc.tag(a["genome"], a["asset"], a["tag"], args.tag)
elif args.command == ID_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
if len(asset_list) == 1:
g, a = asset_list[0]["genome"], asset_list[0]["asset"]
t = asset_list[0]["tag"] or rgc.get_default_tag(g, a)
print(rgc.id(g, a, t))
return
for asset in asset_list:
g, a = asset["genome"], asset["asset"]
t = asset["tag"] or rgc.get_default_tag(g, a)
print("{}/{}:{},".format(g, a, t) + rgc.id(g, a, t))
return
elif args.command == SUBSCRIBE_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
rgc.subscribe(urls=args.genome_server, reset=args.reset)
return
elif args.command == UNSUBSCRIBE_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False)
rgc.unsubscribe(urls=args.genome_server)
return
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, make_root=True)
_LOGGER.debug(f"versions: refgenie {__version__} | refgenconf {rgc_version}")
_LOGGER.debug(f"Args: {args}")
if not args.command:
parser.print_help()
_LOGGER.error("No command given")
sys.exit(1)
if args.command == ALIAS_CMD and not args.subcommand:
parser.print_help()
_LOGGER.error("No alias subcommand command given")
sys.exit(1)
gencfg = select_genome_config(
filename=args.genome_config,
check_exist=not args.command == INIT_CMD,
on_missing=lambda fp: fp,
strict_env=True,
)
if gencfg is None:
raise MissingGenomeConfigError(args.genome_config)
_LOGGER.debug("Determined genome config: {}".format(gencfg))
skip_read_lock = _skip_lock(args.skip_read_lock, gencfg)
# From user input we want to construct a list of asset dicts, where each
# asset has a genome name, asset name, and tag
if "asset_registry_paths" in args and args.asset_registry_paths:
_LOGGER.debug("Found registry_path: {}".format(args.asset_registry_paths))
asset_list = [parse_registry_path(x) for x in args.asset_registry_paths]
for a in asset_list:
# every asset must have a genome, either provided via registry path
# or the args.genome arg.
if not a["genome"]:
if args.genome:
a["genome"] = args.genome
else:
_LOGGER.error(
"Provided asset registry path ({}/{}:{}) is invalid. See help for usage reference.".format(
a["genome"], a["asset"], a["tag"]
)
)
sys.exit(1)
else:
if args.genome and args.genome != a["genome"]:
_LOGGER.warn(
"Two different genomes specified for asset '{}'.".format(
a["asset"]
)
)
else:
if args.command in GENOME_ONLY_REQUIRED and not args.genome:
parser.error("You must provide either a genome or a registry path")
sys.exit(1)
if args.command in ASSET_REQUIRED:
parser.error("You must provide an asset registry path")
sys.exit(1)
if args.command == INIT_CMD:
_LOGGER.debug("Initializing refgenie genome configuration")
entries = OrderedDict(
{
CFG_VERSION_KEY: REQ_CFG_VERSION,
CFG_FOLDER_KEY: os.path.dirname(os.path.abspath(gencfg)),
CFG_SERVERS_KEY: args.genome_server or [DEFAULT_SERVER],
CFG_GENOMES_KEY: None,
}
)
if args.settings_json:
if os.path.isfile(args.settings_json):
with open(args.settings_json, "r") as json_file:
data = json.load(json_file)
entries.update(data)
else:
raise FileNotFoundError(
"JSON file with config init settings does not exist: {}".format(
args.settings_json
)
)
if args.genome_folder:
entries.update({CFG_FOLDER_KEY: args.genome_folder})
if args.remote_url_base:
entries.update({CFG_REMOTE_URL_BASE_KEY: args.remote_url_base})
if args.genome_archive_folder:
entries.update({CFG_ARCHIVE_KEY: args.genome_archive_folder})
if args.genome_archive_config:
entries.update({CFG_ARCHIVE_CONFIG_KEY: args.genome_archive_config})
_LOGGER.debug("initializing with entries: {}".format(entries))
rgc = RefGenConf(entries=entries, skip_read_lock=skip_read_lock)
rgc.initialize_config_file(os.path.abspath(gencfg))
elif args.command == BUILD_CMD:
if not all([x["genome"] == asset_list[0]["genome"] for x in asset_list]):
_LOGGER.error("Build can only build assets for one genome")
sys.exit(1)
recipe_name = None
if args.recipe:
if len(asset_list) > 1:
_LOGGER.error("Recipes cannot be specified for multi-asset builds")
sys.exit(1)
recipe_name = args.recipe
if args.requirements:
for a in asset_list:
recipe = recipe_name or a["asset"]
if recipe not in asset_build_packages.keys():
_raise_missing_recipe_error(recipe)
_LOGGER.info("'{}' recipe requirements: ".format(recipe))
_make_asset_build_reqs(recipe)
sys.exit(0)
refgenie_build(gencfg, asset_list[0]["genome"], asset_list, recipe_name, args)
elif args.command == GET_ASSET_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
check = args.check_exists if args.check_exists else None
for a in asset_list:
_LOGGER.debug(
"getting asset: '{}/{}.{}:{}'".format(
a["genome"], a["asset"], a["seek_key"], a["tag"]
)
)
print(
rgc.seek(
a["genome"],
a["asset"],
a["tag"],
a["seek_key"],
strict_exists=check,
)
)
return
elif args.command == INSERT_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
if len(asset_list) > 1:
raise NotImplementedError("Can only add 1 asset at a time")
else:
sk = args.seek_keys
if sk:
sk = json.loads(args.seek_keys)
rgc.add(
path=args.path,
genome=asset_list[0]["genome"],
asset=asset_list[0]["asset"],
tag=asset_list[0]["tag"],
seek_keys=sk,
force=args.force,
)
elif args.command == PULL_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
# existing assets overwriting
if args.no_overwrite:
force = False
elif args.force_overwrite:
force = True
else:
force = None
# large archive pulling
if args.no_large:
force_large = False
elif args.pull_large:
force_large = True
else:
force_large = None
# batch mode takes precedence over other choices
if args.batch:
force_large = True
force = False
outdir = rgc.data_dir
if not os.path.exists(outdir):
raise MissingFolderError(outdir)
if not perm_check_x(outdir):
return
if not _single_folder_writeable(outdir):
_LOGGER.error("Insufficient permissions to write to: {}".format(outdir))
return
for a in asset_list:
rgc.pull(
a["genome"],
a["asset"],
a["tag"],
force=force,
force_large=force_large,
size_cutoff=args.size_cutoff,
)
elif args.command in [LIST_LOCAL_CMD, LIST_REMOTE_CMD]:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
console = Console()
if args.command == LIST_REMOTE_CMD:
num_servers = 0
bad_servers = []
for server_url in rgc[CFG_SERVERS_KEY]:
num_servers += 1
try:
table = rgc.get_asset_table(
genomes=args.genome, server_url=server_url
)
except (DownloadJsonError, ConnectionError, MissingSchema):
bad_servers.append(server_url)
continue
else:
console.print(table)
if num_servers >= len(rgc[CFG_SERVERS_KEY]) and bad_servers:
_LOGGER.error(
"Could not list assets from the following servers: {}".format(
bad_servers
)
)
else:
if args.recipes:
print(", ".join(sorted(list(asset_build_packages.keys()))))
else:
console.print(rgc.get_asset_table(genomes=args.genome))
elif args.command == GETSEQ_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
print(rgc.getseq(args.genome, args.locus))
elif args.command == REMOVE_CMD:
force = args.force
rgc = RefGenConf(filepath=gencfg, skip_read_lock=skip_read_lock)
for a in asset_list:
a["tag"] = a["tag"] or rgc.get_default_tag(
a["genome"], a["asset"], use_existing=False
)
_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.")
gat = {"genome": a["genome"], "asset": a["asset"], "tag": a["tag"]}
try:
if not rgc.is_asset_complete(**gat):
with rgc as r:
r.cfg_remove_assets(**gat)
_LOGGER.info(
"Removed an incomplete asset "
"'{genome}/{asset}:{tag}'".format(*gat)
)
return
except (KeyError, MissingAssetError, MissingGenomeError):
_LOGGER.info(
"Asset '{genome}/{asset}:{tag}' does not exist".format(**gat)
)
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, skip_read_lock=skip_read_lock)
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)
sys.exit(0)
rgc.tag(a["genome"], a["asset"], a["tag"], args.tag, force=args.force)
elif args.command == ID_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
if len(asset_list) == 1:
g, a = asset_list[0]["genome"], asset_list[0]["asset"]
t = asset_list[0]["tag"] or rgc.get_default_tag(g, a)
print(rgc.id(g, a, t))
return
for asset in asset_list:
g, a = asset["genome"], asset["asset"]
t = asset["tag"] or rgc.get_default_tag(g, a)
print("{}/{}:{},".format(g, a, t) + rgc.id(g, a, t))
return
elif args.command == SUBSCRIBE_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
rgc.subscribe(urls=args.genome_server, reset=args.reset)
return
elif args.command == UNSUBSCRIBE_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
rgc.unsubscribe(urls=args.genome_server)
return
elif args.command == ALIAS_CMD:
rgc = RefGenConf(filepath=gencfg, skip_read_lock=skip_read_lock)
if args.subcommand == ALIAS_GET_CMD:
if args.aliases is not None:
for a in args.aliases:
print(rgc.get_genome_alias_digest(alias=a))
return
console = Console()
console.print(rgc.genome_aliases_table)
if args.subcommand == ALIAS_SET_CMD:
rgc.set_genome_alias(
digest=args.digest,
genome=args.aliases,
reset_digest=args.reset,
create_genome=args.force,
)
return
elif args.subcommand == ALIAS_REMOVE_CMD:
rgc.remove_genome_aliases(digest=args.digest, aliases=args.aliases)
return
elif args.command == COMPARE_CMD:
rgc = RefGenConf(filepath=gencfg, writable=False, skip_read_lock=skip_read_lock)
res = rgc.compare(
args.genome1[0], args.genome2[0], explain=not args.no_explanation
)
if args.no_explanation:
print(res)
elif args.command == UPGRADE_CMD:
upgrade_config(
target_version=args.target_version, filepath=gencfg, force=args.force
)