def main():
""" main workflow """
parser = build_argparser()
args, remaining_args = parser.parse_known_args()
cfg = refgenconf.select_genome_config(
filename=args.config, check_exist=True, strict_env=True
)
if not cfg:
raise MissingGenomeConfigError(args.config)
rgc = refgenconf.RefGenConf(filepath=cfg, writable=False)
pths = [args.path, mkabs(args.path, rgc.genome_folder)]
if not untar_or_copy(
pths[0], os.path.join(rgc.genome_folder, args.genome)
) and not untar_or_copy(pths[1], os.path.join(rgc.genome_folder, args.genome)):
raise OSError(
"Path '{}' does not exist. Tried: {}".format(args.path, " and ".join(pths))
)
path_components = [rgc.genome_folder] + [args.genome] + ["*"] * 3 + ["Sequence"]
assets_paths = glob(os.path.join(*path_components))
assert len(assets_paths) > 0, OSError(
"Your iGenomes directory is corrupted, more than one directory matched by {}."
"\nMatched dirs: {}".format(
os.path.join(*path_components), ", ".join(assets_paths)
)
)
assets_path = assets_paths[0]
asset_names = [d for d in os.listdir(assets_path) if os.path.isdir(assets_path)]
processed = []
for a in asset_names:
asset_dict = {"genome": args.genome, "asset": a, "tag": None, "seek_key": None}
asset_path = os.path.relpath(os.path.join(assets_path, a), rgc.genome_folder)
if refgenie_add(rgc, asset_dict, asset_path):
processed.append("{}/{}".format(asset_dict["genome"], asset_dict["asset"]))
print("Added assets: \n- {}".format("\n- ".join(processed)))
def main():
global rgc, _LOGGER
parser = build_parser()
args = parser.parse_args()
if not args.command:
parser.print_help()
print("No subcommand given")
sys.exit(1)
logger_args = (dict(name=PKG_NAME, fmt=LOG_FORMAT, level=5)
if args.debug else dict(name=PKG_NAME, fmt=LOG_FORMAT))
_LOGGER = logmuse.setup_logger(**logger_args)
selected_cfg = select_genome_config(args.config)
assert (
selected_cfg is not None
), "You must provide a config file or set the {} environment variable".format(
"or ".join(CFG_ENV_VARS))
# this RefGenConf object will be used in the server, so it's read-only
rgc = RefGenConf(filepath=selected_cfg, writable=False)
if args.command == "archive":
arp = ([parse_registry_path(x) for x in args.asset_registry_paths]
if args.asset_registry_paths is not None else None)
archive(rgc, arp, args.force, args.remove, selected_cfg,
args.genomes_desc)
elif args.command == "serve":
# the router imports need to be after the RefGenConf object is declared
with rgc as r:
purge_nonservable(r)
from .routers import private, version1, version2, version3
app.include_router(version3.router)
app.include_router(version1.router, prefix="/v1")
app.include_router(version2.router, prefix="/v2")
app.include_router(version3.router, prefix="/v3")
app.include_router(private.router, prefix=f"/{PRIVATE_API}")
uvicorn.run(app, host="0.0.0.0", port=args.port)
def test_select_via_env_var_implicit(env_var, tmpdir):
"""Config file selection can leverage default environmanent variables."""
conf_file = tmpdir.join("test-refgenconf-conf.yaml").strpath
assert not os.path.exists(conf_file)
with open(conf_file, "w"):
pass
assert os.path.isfile(conf_file)
with TmpEnv(overwrite=True, **{env_var: conf_file}):
assert conf_file == select_genome_config(None)
def test_select_null():
"""Test prioritized selection of genome configuration file."""
with TmpEnv(overwrite=True, **{ev: "" for ev in CFG_ENV_VARS}):
_check_no_env_vars()
assert select_genome_config(None) is None
def main():
""" Primary workflow """
parser = logmuse.add_logging_options(arguments.build_argparser())
args, remaining_args = parser.parse_known_args()
global _LOGGER
_LOGGER = logmuse.logger_via_cli(args)
_LOGGER.info("Welcome to bedshift version {}".format(__version__))
_LOGGER.info("Shifting file: '{}'".format(args.bedfile))
if not args.bedfile:
parser.print_help()
_LOGGER.error("No BED file given")
sys.exit(1)
if args.chrom_lengths:
pass
elif args.genome:
try:
import refgenconf
rgc = refgenconf.RefGenConf(refgenconf.select_genome_config())
args.chrom_lengths = rgc.seek(args.genome, "fasta", None,
"chrom_sizes")
except ModuleNotFoundError:
_LOGGER.error(
"You must have package refgenconf installed to use a refgenie genome"
)
sys.exit(1)
msg = arguments.param_msg
if args.repeat < 1:
_LOGGER.error("repeats specified is less than 1")
sys.exit(1)
if args.outputfile:
outfile_base = args.outputfile
else:
outfile_base = "bedshifted_{}".format(os.path.basename(args.bedfile))
_LOGGER.info(
msg.format(
bedfile=args.bedfile,
chromsizes=args.chrom_lengths,
droprate=args.droprate,
dropfile=args.dropfile,
addrate=args.addrate,
addmean=args.addmean,
addstdev=args.addstdev,
addfile=args.addfile,
valid_regions=args.valid_regions,
shiftrate=args.shiftrate,
shiftmean=args.shiftmean,
shiftstdev=args.shiftstdev,
shiftfile=args.shiftfile,
cutrate=args.cutrate,
mergerate=args.mergerate,
outputfile=outfile_base,
repeat=args.repeat,
yaml_config=args.yaml_config,
))
bedshifter = Bedshift(args.bedfile, args.chrom_lengths)
_LOGGER.info(f"Generating {args.repeat} repetitions...")
pct_reports = [int(x * args.repeat / 100) for x in [5, 25, 50, 75, 100]]
for i in range(args.repeat):
n = bedshifter.all_perturbations(
args.addrate,
args.addmean,
args.addstdev,
args.addfile,
args.valid_regions,
args.shiftrate,
args.shiftmean,
args.shiftstdev,
args.shiftfile,
args.cutrate,
args.mergerate,
args.droprate,
args.dropfile,
args.yaml_config,
)
if args.repeat == 1:
bedshifter.to_bed(outfile_base)
_LOGGER.info(
"REGION COUNT | original: {}\tnew: {}\tchanged: {}\t\noutput file: {}"
.format(
bedshifter.original_num_regions,
bedshifter.bed.shape[0],
str(n),
outfile_base,
))
else:
basename, ext = os.path.splitext(os.path.basename(outfile_base))
dirname = os.path.dirname(outfile_base)
digits = int(math.log10(args.repeat)) + 1
rep = str(i + 1).zfill(digits)
modified_outfile_path = os.path.join(dirname,
f"{basename}_rep{rep}{ext}")
bedshifter.to_bed(modified_outfile_path)
pct_finished = int((100 * (i + 1)) / args.repeat)
if i + 1 in pct_reports:
_LOGGER.info(
f"Rep {i+1}. Finished: {pct_finished}%. Output file: {modified_outfile_path}"
)
bedshifter.reset_bed()
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
)
