def abs_file_paths(xs, base_dir=None, ignore_keys=None):
"""Normalize any file paths found in a subdirectory of configuration input.
"""
ignore_keys = set([]) if ignore_keys is None else set(ignore_keys)
if base_dir is None:
base_dir = os.getcwd()
orig_dir = os.getcwd()
os.chdir(base_dir)
input_dir = os.path.join(base_dir, "inputs")
if isinstance(xs, dict):
out = {}
for k, v in xs.iteritems():
if k not in ignore_keys and v and isinstance(v, basestring):
if v.lower() == "none":
out[k] = None
elif os.path.exists(v) or v.startswith(
utils.SUPPORTED_REMOTES):
out[k] = os.path.normpath(
os.path.join(base_dir, utils.dl_remotes(v, input_dir)))
else:
out[k] = v
else:
out[k] = v
elif isinstance(xs, basestring):
if os.path.exists(xs) or xs.startswith(utils.SUPPORTED_REMOTES):
out = os.path.normpath(
os.path.join(base_dir, utils.dl_remotes(xs, input_dir)))
else:
out = xs
else:
out = xs
os.chdir(orig_dir)
return out
def abs_file_paths(xs, base_dir=None, ignore_keys=None):
"""Normalize any file paths found in a subdirectory of configuration input.
"""
ignore_keys = set([]) if ignore_keys is None else set(ignore_keys)
if base_dir is None:
base_dir = os.getcwd()
orig_dir = os.getcwd()
os.chdir(base_dir)
input_dir = os.path.join(base_dir, "inputs")
if isinstance(xs, dict):
out = {}
for k, v in xs.iteritems():
if k not in ignore_keys and v and isinstance(v, basestring):
if v.lower() == "none":
out[k] = None
elif os.path.exists(v) or v.startswith(utils.SUPPORTED_REMOTES):
out[k] = os.path.normpath(os.path.join(base_dir, utils.dl_remotes(v, input_dir)))
else:
out[k] = v
else:
out[k] = v
elif isinstance(xs, basestring):
if os.path.exists(xs) or xs.startswith(utils.SUPPORTED_REMOTES):
out = os.path.normpath(os.path.join(base_dir, utils.dl_remotes(xs, input_dir)))
else:
out = xs
else:
out = xs
os.chdir(orig_dir)
return out
def _add_remote_resources(resources):
"""Retrieve remote resources like GATK/MuTect jars present in S3.
"""
out = copy.deepcopy(resources)
for prog, info in resources.iteritems():
for key, val in info.iteritems():
if key == "jar" and val.startswith(utils.SUPPORTED_REMOTES):
store_dir = utils.safe_makedir(os.path.join(os.getcwd(), "inputs", "jars", prog))
fname = utils.dl_remotes(val, store_dir, store_dir)
version_file = os.path.join(store_dir, "version.txt")
if not utils.file_exists(version_file):
version = install.get_gatk_jar_version(prog, fname)
with open(version_file, "w") as out_handle:
out_handle.write(version)
else:
with open(version_file) as in_handle:
version = in_handle.read().strip()
del out[prog][key]
out[prog]["dir"] = store_dir
out[prog]["version"] = version
return out
def _add_remote_resources(resources):
"""Retrieve remote resources like GATK/MuTect jars present in S3.
"""
out = copy.deepcopy(resources)
for prog, info in resources.iteritems():
for key, val in info.iteritems():
if key == "jar" and val.startswith(utils.SUPPORTED_REMOTES):
store_dir = utils.safe_makedir(
os.path.join(os.getcwd(), "inputs", "jars", prog))
fname = utils.dl_remotes(val, store_dir, store_dir)
version_file = os.path.join(store_dir, "version.txt")
if not utils.file_exists(version_file):
version = install.get_gatk_jar_version(prog, fname)
with open(version_file, "w") as out_handle:
out_handle.write(version)
else:
with open(version_file) as in_handle:
version = in_handle.read().strip()
del out[prog][key]
out[prog]["dir"] = store_dir
out[prog]["version"] = version
return out
