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 refgenie_add(rgc, asset_dict, path, force=False):
"""
Add an external asset to the config.
File existence is checked and asset files are transferred to the selected
tag subdirectory
:param refgenconf.RefGenConf rgc: genome configuration object
:param dict asset_dict: a single parsed registry path
:param str path: the path provided by the user. Must be relative to the
specific genome directory
:param bool force: whether the replacement of a possibly existing asset
should be forced
"""
# remove the first directory from the provided path if it is the genome name
path = (
os.path.join(*path.split(os.sep)[1:])
if path.split(os.sep)[0] == asset_dict["genome"]
else path
)
tag = asset_dict["tag"] or rgc.get_default_tag(
asset_dict["genome"], asset_dict["asset"]
)
outfolder = os.path.abspath(os.path.join(rgc[CFG_FOLDER_KEY], asset_dict["genome"]))
abs_asset_path = os.path.join(outfolder, path)
if asset_dict["seek_key"] is None:
# if seek_key is not specified we're about to move a directory to
# 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) if asset_dict["seek_key"] is not None else "."
)
sk = {asset_dict["seek_key"] or asset_dict["asset"]: seek_key_value}
rgc.update_seek_keys(*gat_bundle, keys=sk)
rgc.set_default_pointer(asset_dict["genome"], asset_dict["asset"], tag)
# a separate update_tags call since we want to use the get_asset method
# that requires a complete asset entry in rgc
td = {CFG_ASSET_CHECKSUM_KEY: get_dir_digest(_seek(rgc, *gat_bundle))}
rgc.update_tags(*gat_bundle, data=td)
# Write the updated refgenie genome configuration
rgc.write()
rgc.make_readonly()
return True
def bulker_init(config_path, template_config_path, container_engine=None):
"""
Initialize a config file.
:param str config_path: path to bulker configuration file to
create/initialize
:param str template_config_path: path to bulker configuration file to
copy FROM
"""
if not config_path:
_LOGGER.error("You must specify a file path to initialize.")
return
if not template_config_path:
_LOGGER.error("You must specify a template config file path.")
return
if not container_engine:
check_engines = ["docker", "singularity"]
for engine in check_engines:
if is_command_callable(engine):
_LOGGER.info("Guessing container engine is {}.".format(engine))
container_engine = engine
break # it's a priority list, stop at the first found engine
if config_path and not (os.path.exists(config_path)
and not query_yes_no("Exists. Overwrite?")):
# dcc.write(config_path)
# Init should *also* write the templates.
dest_folder = os.path.dirname(config_path)
dest_templates_dir = os.path.join(dest_folder, TEMPLATE_SUBDIR)
# templates_subdir = TEMPLATE_SUBDIR
copy_tree(os.path.dirname(template_config_path), dest_templates_dir)
new_template = os.path.join(dest_folder,
os.path.basename(template_config_path))
bulker_config = yacman.YacAttMap(filepath=template_config_path,
writable=True)
_LOGGER.debug("Engine used: {}".format(container_engine))
bulker_config.bulker.container_engine = container_engine
if bulker_config.bulker.container_engine == "docker":
bulker_config.bulker.executable_template = os.path.join(
TEMPLATE_SUBDIR, DOCKER_EXE_TEMPLATE)
bulker_config.bulker.shell_template = os.path.join(
TEMPLATE_SUBDIR, DOCKER_SHELL_TEMPLATE)
bulker_config.bulker.build_template = os.path.join(
TEMPLATE_SUBDIR, DOCKER_BUILD_TEMPLATE)
elif bulker_config.bulker.container_engine == "singularity":
bulker_config.bulker.executable_template = os.path.join(
TEMPLATE_SUBDIR, SINGULARITY_EXE_TEMPLATE)
bulker_config.bulker.shell_template = os.path.join(
TEMPLATE_SUBDIR, SINGULARITY_SHELL_TEMPLATE)
bulker_config.bulker.build_template = os.path.join(
TEMPLATE_SUBDIR, SINGULARITY_BUILD_TEMPLATE)
bulker_config.bulker.rcfile = os.path.join(TEMPLATE_SUBDIR,
RCFILE_TEMPLATE)
bulker_config.bulker.rcfile_strict = os.path.join(
TEMPLATE_SUBDIR, RCFILE_STRICT_TEMPLATE)
bulker_config.write(config_path)
# copyfile(template_config_path, new_template)
# os.rename(new_template, config_path)
_LOGGER.info("Wrote new configuration file: {}".format(config_path))
else:
_LOGGER.warning(
"Can't initialize, file exists: {} ".format(config_path))
def bulker_load(manifest,
cratevars,
bcfg,
exe_jinja2_template,
shell_jinja2_template,
crate_path=None,
build=False,
force=False):
manifest_name = cratevars['crate']
# We store them in folder: namespace/crate/version
if not crate_path:
crate_path = os.path.join(bcfg.bulker.default_crate_folder,
cratevars['namespace'], manifest_name,
cratevars['tag'])
if not os.path.isabs(crate_path):
crate_path = os.path.join(os.path.dirname(bcfg._file_path), crate_path)
_LOGGER.debug("Crate path: {}".format(crate_path))
_LOGGER.debug("cratevars: {}".format(cratevars))
# Update the config file
if not bcfg.bulker.crates:
bcfg.bulker.crates = {}
if not hasattr(bcfg.bulker.crates, cratevars['namespace']):
bcfg.bulker.crates[cratevars['namespace']] = yacman.YacAttMap({})
if not hasattr(bcfg.bulker.crates[cratevars['namespace']],
cratevars['crate']):
bcfg.bulker.crates[cratevars['namespace']][
cratevars['crate']] = yacman.YacAttMap({})
if hasattr(bcfg.bulker.crates[cratevars['namespace']][cratevars['crate']],
cratevars['tag']):
_LOGGER.debug(bcfg.bulker.crates[cratevars['namespace']][
cratevars['crate']].to_dict())
if not (force or query_yes_no(
"That manifest has already been loaded. Overwrite?")):
return
else:
bcfg.bulker.crates[cratevars['namespace']][cratevars['crate']][str(
cratevars['tag'])] = crate_path
_LOGGER.warning(
"Removing all executables in: {}".format(crate_path))
try:
shutil.rmtree(crate_path)
except:
_LOGGER.error(
"Error removing crate at {}. Did your crate path change? Remove it manually."
.format(crate_path))
else:
bcfg.bulker.crates[cratevars['namespace']][cratevars['crate']][str(
cratevars['tag'])] = crate_path
# Now make the crate
# First add any imports
mkdir(crate_path, exist_ok=True)
if hasattr(manifest.manifest, "imports") and manifest.manifest.imports:
for imp in manifest.manifest.imports:
imp_cratevars = parse_registry_path(imp)
imp_crate_path = os.path.join(bcfg.bulker.default_crate_folder,
imp_cratevars['namespace'],
imp_cratevars['crate'],
imp_cratevars['tag'])
if not os.path.isabs(imp_crate_path):
imp_crate_path = os.path.join(os.path.dirname(bcfg._file_path),
imp_crate_path)
if not os.path.exists(imp_crate_path):
_LOGGER.error("Can't import crate '{}' from '{}'".format(
imp, imp_crate_path))
# Recursively load any non-existant imported crates.
imp_manifest, imp_cratevars = load_remote_registry_path(
bcfg, imp, None)
_LOGGER.debug(imp_manifest)
_LOGGER.debug(imp_cratevars)
bulker_load(imp_manifest,
imp_cratevars,
bcfg,
exe_jinja2_template,
shell_jinja2_template,
crate_path=None,
build=build,
force=force)
_LOGGER.info("Importing crate '{}' from '{}'.".format(
imp, imp_crate_path))
copy_tree(imp_crate_path, crate_path)
# should put this in a function
def host_tool_specific_args(bcfg, pkg, hosttool_arg_key):
_LOGGER.debug("Arg key: '{}'".format(hosttool_arg_key))
# Here we're parsing the *image*, not the crate registry path.
imvars = parse_registry_path_image(pkg['docker_image'])
_LOGGER.debug(imvars)
try:
amap = bcfg.bulker.tool_args[imvars['namespace']][imvars['image']]
if imvars['tag'] != 'default' and hasattr(amap, imvars['tag']):
string = amap[imvars['tag']][hosttool_arg_key]
else:
string = amap.default[hosttool_arg_key]
_LOGGER.debug(string)
return string
except:
_LOGGER.debug("No host/tool args found.")
return ""
cmdlist = []
cmd_count = 0
if hasattr(manifest.manifest, "commands") and manifest.manifest.commands:
for pkg in manifest.manifest.commands:
_LOGGER.debug(pkg)
pkg.update(bcfg.bulker) # Add terms from the bulker config
pkg = copy.deepcopy(
yacman.YacAttMap(pkg)) # (otherwise it's just a dict)
# We have to deepcopy it so that changes we make to pkg aren't reflected in bcfg.
if pkg.container_engine == "singularity" and "singularity_image_folder" in pkg:
pkg["singularity_image"] = os.path.basename(
pkg["docker_image"])
pkg["namespace"] = os.path.dirname(pkg["docker_image"])
if os.path.isabs(pkg["singularity_image_folder"]):
sif = pkg["singularity_image_folder"]
else:
sif = os.path.join(os.path.dirname(bcfg._file_path),
pkg["singularity_image_folder"])
pkg["singularity_fullpath"] = os.path.join(
sif, pkg["namespace"], pkg["singularity_image"])
mkdir(os.path.dirname(pkg["singularity_fullpath"]),
exist_ok=True)
command = pkg["command"]
path = os.path.join(crate_path, command)
_LOGGER.debug("Writing {cmd}".format(cmd=path))
cmdlist.append(command)
# Add any host-specific tool-specific args
hosttool_arg_key = "{engine}_args".format(
engine=bcfg.bulker.container_engine)
hts = host_tool_specific_args(bcfg, pkg, hosttool_arg_key)
_LOGGER.debug("Adding host-tool args: {}".format(hts))
if hasattr(pkg, hosttool_arg_key):
pkg[hosttool_arg_key] += " " + hts
else:
pkg[hosttool_arg_key] = hts
# Remove any excluded volumes from the package
exclude_vols = host_tool_specific_args(bcfg, pkg,
"exclude_volumes")
_LOGGER.debug("Volume list: {}".format(pkg["volumes"]))
_LOGGER.debug("pkg: {}".format(pkg))
if len(exclude_vols) > 0:
for item in exclude_vols:
_LOGGER.debug("Excluding volume: '{}'".format(item))
try:
pkg["volumes"].remove(item)
except:
pass
_LOGGER.debug("Volume list: {}".format(pkg["volumes"]))
else:
_LOGGER.debug("No excluded volumes")
with open(path, "w") as fh:
fh.write(exe_jinja2_template.render(pkg=pkg))
os.chmod(path, 0o755)
# shell commands
path_shell = os.path.join(crate_path, "_" + command)
_LOGGER.debug(
"Writing shell command: '{cmd}'".format(cmd=path_shell))
with open(path_shell, "w") as fh:
fh.write(shell_jinja2_template.render(pkg=pkg))
os.chmod(path_shell, 0o755)
if build:
buildscript = build.render(pkg=pkg)
x = os.system(buildscript)
if x != 0:
_LOGGER.error(
"------ Error building. Build script used: ------")
_LOGGER.error(buildscript)
_LOGGER.error(
"------------------------------------------------")
_LOGGER.info("Container available at: {cmd}".format(
cmd=pkg["singularity_fullpath"]))
# host commands
host_cmdlist = []
if hasattr(manifest.manifest,
"host_commands") and manifest.manifest.host_commands:
_LOGGER.info("Populating host commands")
for cmd in manifest.manifest.host_commands:
_LOGGER.debug(cmd)
if not is_command_callable(cmd):
_LOGGER.warning("Requested host command is not callable and "
"therefore not created: '{}'".format(cmd))
continue
local_exe = find_executable(cmd)
path = os.path.join(crate_path, cmd)
host_cmdlist.append(cmd)
os.symlink(local_exe, path)
# The old way: TODO: REMOVE THIS
if False:
populated_template = LOCAL_EXE_TEMPLATE.format(cmd=local_exe)
with open(path, "w") as fh:
fh.write(populated_template)
os.chmod(path, 0o755)
cmd_count = len(cmdlist)
host_cmd_count = len(host_cmdlist)
if cmd_count < 1 and host_cmd_count < 1:
_LOGGER.error("No commands provided. Crate not created.")
os.rmdir(crate_path)
crate_path_parent = os.path.dirname(crate_path)
if not os.listdir(crate_path_parent):
os.rmdir(crate_path_parent)
sys.exit(1)
rp = "{namespace}/{crate}:{tag}".format(namespace=cratevars['namespace'],
crate=cratevars['crate'],
tag=cratevars['tag'])
_LOGGER.info("Loading manifest: '{rp}'."
" Activate with 'bulker activate {rp}'.".format(rp=rp))
if cmd_count > 0:
_LOGGER.info("Commands available: {}".format(", ".join(cmdlist)))
if host_cmd_count > 0:
_LOGGER.info("Host commands available: {}".format(
", ".join(host_cmdlist)))
bcfg.write()
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
)
def test_query_yesno_input(question, default, response, expected):
""" Yes/No interaction responds to user input. """
with mock.patch(READ_INPUT_PATH, return_value=response):
assert query_yes_no(question, default) is expected
def test_response_sequence(question, default, responses, expected):
""" The interaction re-prompts and then responds as intended. """
with mock.patch(READ_INPUT_PATH, side_effect=responses):
assert expected is query_yes_no(question, default)
def test_query_yesno_empty_with_default(question, default, expected, capsys):
""" Default response is used when user input is empty. """
with mock.patch(READ_INPUT_PATH, return_value=""):
assert expected is query_yes_no(question, default)
def test_illegal_default_yields_value_error(question, default):
""" Illegal default response causes ValueError. """
with pytest.raises(ValueError):
query_yes_no(question, default)