def get_method(method_namespace: str,
method_name: str,
method_version: int = None) -> "JSON":
"""
If method_version is None, get the latest snapshot
"""
if method_version is None:
list_methods = fapi.list_repository_methods(namespace=method_namespace,
name=method_name)
if list_methods.status_code != 200:
raise ValueError('Unable to list methods ' + ' - ' +
str(list_methods.json()))
methods = list_methods.json()
version = -1
for method in methods:
version = max(version, method['snapshotId'])
if version == -1:
raise ValueError(method_name + ' not found')
method_version = version
method_def = fapi.get_repository_method(method_namespace, method_name,
method_version)
if method_def.status_code != 200:
raise ValueError('Unable to fetch method {0}/{1}/{2} - {3}'.format(
method_namespace, method_name, method_version,
str(method_def.json())))
return method_def.json()
def main(argsv):
parser = argparse.ArgumentParser(
description='Download one or more methods from Broad Methods Repository'
)
parser.add_argument('-m',
'--method',
dest='method',
action='store',
required=True,
help=alto.METHOD_HELP)
args = parser.parse_args(argsv)
method_namespace, method_name, method_version = alto.fs_split(args.method)
list_methods = fapi.list_repository_methods(namespace=method_namespace,
name=method_name,
snapshotId=method_version)
if list_methods.status_code != 200:
raise ValueError('Unable to list methods ' + ' - ' +
str(list_methods.json))
methods = list_methods.json()
for method in methods:
wdl = fapi.get_repository_method(
method_namespace, method_name,
method['snapshotId']).json()['payload']
with open('{}_{}.wdl'.format(method_name, method['snapshotId']),
'w') as w:
w.write(wdl)
def download_remote_wdls(namespace, workspace):
"""Update WDL scripts in wdls/production directory, to the ones currently being used in Firecloud
"""
download_method_configs(namespace, workspace)
method_configs = pd.read_table('method_configs/latest_method_configs.txt')
for idx, method in method_configs.iterrows():
res = firecloud_api.get_repository_method('tsca',
method['method_name'],
method['snapshot'])
print("Updating WDL for %s:%s" %
(method['method_name'], method['snapshot']))
if res.status_code == 200:
text_file = open(
"../wdls/production/%s.wdl" % method['method_name'], "w")
text_file.write(res.json()['payload'])
text_file.close()
return
def get_firecloud_workflow(method_namespace: str,
method_name: str,
method_version: int = None) -> dict:
"""Locate a workflow using the method_namespace, method_name and method_version hierachy and return results in a dictionary.
Parameters
----------
method_namespace: `str`
The namespace that workflow belongs to (case-sensitive).
method_name: `str`
The workflow name (case-sensitive).
version: `int`, optional (default: None)
Snapshot ID. By default, the lastest snapshot recorded in Broad Methods Repository would be used.
Returns
-------
`dict` object.
A dictionary object containing the following entries:
'namespace': workflow namespace as recorded in Broad Methods Repository.
'name': workflow name as recorded in Broad Methods Repository.
'snapshotId': workflow version as recorded in Broad Methods Repository.
'url': URL to the WDL file.
'methodUri': Uniform Resource Identifier that is recognized by Terra platform.
Examples
--------
>>> results = get_firecloud_workflow('cumulus', 'cumulus')
"""
method_record = None
if method_version is not None:
method_def = fapi.get_repository_method(method_namespace, method_name,
method_version)
if method_def.status_code != 200:
raise ValueError(
f"Unable to fetch workflow {method_namespace}/{method_name}/{method_version} - {method_def.json()}!"
)
method_record = method_def.json()
else:
list_methods = fapi.list_repository_methods(namespace=method_namespace,
name=method_name)
if list_methods.status_code != 200:
raise ValueError(
f"Unable to list methods - {list_methods.json()}!")
methods = list_methods.json()
if len(methods) == 0:
raise ValueError(
f"Unable to locate workflow {method_namespace}/{method_name}!")
method_record = methods[0]
for method in methods[1:]:
if method_record["snapshotId"] < method["snapshotId"]:
method_record = method
results = {
"namespace":
method_record["namespace"],
"name":
method_record["name"],
"snapshotId":
method_record["snapshotId"],
"url":
f"https://api.firecloud.org/ga4gh/v1/tools/{method_record['namespace']}:{method_record['name']}/versions/{method_record['snapshotId']}/plain-WDL/descriptor",
"methodUri":
f"agora://{method_record['namespace']}/{method_record['name']}/{method_record['snapshotId']}"
}
return results
def do_fc_inputs(method, out, config):
method_namespace, method_name, method_version = kco.fs_split(method)
if method_namespace is None:
raise ValueError(
'Method should be specified as namespace/name (e.g. regev/drop-seq)'
)
if method_version is None:
version = -1
list_methods = fapi.list_repository_methods(method_name)
if list_methods.status_code != 200:
raise ValueError('Unable to list methods ' + ' - ' +
str(list_methods.json))
methods = list_methods.json()
for method in methods:
if method['namespace'] == method_namespace:
version = max(version, method['snapshotId'])
if version == -1:
raise ValueError(method_name + ' not found')
method_version = version
payload = fapi.get_repository_method(method_namespace, method_name,
method_version).json()['payload']
tmp_wdl_file = tempfile.mkstemp(suffix='.wdl')[1]
with open(tmp_wdl_file, 'w') as w:
w.write(payload)
repo_config = None
if config is not None:
config_namespace, config_name, config_version = kco.fs_split(
config)
if config_version is not None:
repo_config = fapi.get_repository_config(
config_namespace, config_name, config_version).json()
else:
repo_configs = fapi.list_repository_configs().json()
for config in repo_configs:
if config['namespace'] == config_namespace and config[
'name'] == config_name and config['method'][
'name'] == method_name and config['method'][
'namespace'] == method_namespace:
repo_config = config
break
if repo_config is not None:
repo_config = fapi.get_repository_config(
repo_config['namespace'], repo_config['name'],
repo_config['snapshotId']).json()
jar = pkg_resources.resource_filename('kco', 'womtool-33.1.jar')
tmp_json_file = tempfile.mkstemp(suffix='.json')[1]
with open(tmp_json_file, 'w') as tmp_json_out:
subprocess.check_call(
['java', '-jar', jar, 'inputs', tmp_wdl_file],
stdout=tmp_json_out)
with open(tmp_json_file, 'r') as tmp_json_in:
inputs = json.loads(tmp_json_in.read())
if repo_config is not None:
repo_config = json.loads(repo_config['payload'])['inputs']
for key in repo_config:
value = repo_config[key]
if inputs.get(key) is not None and value != '':
inputs[key] = value
if out is None:
out = method_name + '_inputs.json'
if not out.lower().endswith('.json'):
out = out + '.json'
with open(out, 'w') as json_out:
json.dump(inputs, json_out, indent=0)
os.remove(tmp_json_file)
os.remove(tmp_wdl_file)