def main(argsv):
parser = argparse.ArgumentParser(
description='Add one or more methods to Broad Methods Repository')
parser.add_argument('-n',
'--namespace',
dest='namespace',
action='store',
required=True,
help='Methods namespace')
parser.add_argument('-p',
'--public',
dest='public',
action='store_true',
help='Make methods publicly readable')
parser.add_argument(dest='wdl', help='Path to WDL file.', nargs='+')
args = parser.parse_args(argsv)
namespace = args.namespace
public = args.public
for wdl in args.wdl:
method_name = os.path.basename(wdl)
suffix = method_name.lower().rfind('.wdl')
if suffix != -1:
method_name = method_name[0:suffix]
method_acl = []
try:
existing_method = alto.get_method(namespace, method_name)
method_acl = fapi.get_repository_method_acl(
namespace=existing_method['namespace'],
method=existing_method['name'],
snapshot_id=existing_method['snapshotId']).json()
except ValueError:
pass
if public:
existing_public_user = False
for i in range(len(method_acl)):
if method_acl[i]['user'] == 'public':
existing_public_user = True
method_acl[i] = dict(user="******", role="READER")
break
if not existing_public_user:
method_acl.append(dict(user="******", role="READER"))
result = fapi.update_repository_method(namespace=namespace,
method=method_name,
wdl=wdl,
synopsis='')
if result.status_code == 201:
result = result.json()
if len(method_acl) > 0:
fapi.update_repository_method_acl(
namespace=result['namespace'],
method=result['name'],
snapshot_id=result['snapshotId'],
acl_updates=method_acl)
print(
'import "https://api.firecloud.org/ga4gh/v1/tools/{}:{}/versions/{}/plain-WDL/descriptor"'
.format(result['namespace'], result['name'],
result['snapshotId']))
else:
print('Unable to add {}'.format(method_name))
print(result.json())
def main(argv):
parser = argparse.ArgumentParser(description='Add one or more methods to Broad Methods Repository.')
parser.add_argument('-n', '--namespace', dest='namespace', action='store', required=True, help='Methods namespace')
parser.add_argument('-p', '--public', dest='public', action='store_true', help='Make methods publicly readable')
parser.add_argument(dest='wdl', help='Path to WDL file.', nargs='+')
args = parser.parse_args(argv)
namespace = args.namespace
public = args.public
n_success = 0
for wdl in args.wdl:
method_name = os.path.basename(wdl)
suffix = method_name.lower().rfind('.wdl')
if suffix != -1:
method_name = method_name[0:suffix]
method_acl = []
try:
existing_method = get_firecloud_workflow(namespace, method_name)
method_acl = fapi.get_repository_method_acl(namespace=existing_method['namespace'], method=existing_method['name'], snapshot_id=existing_method['snapshotId']).json()
except ValueError:
pass
if public:
existing_public_user = False
for i in range(len(method_acl)):
if method_acl[i]['user'] == 'public':
existing_public_user = True
method_acl[i] = dict(user='******', role='READER')
break
if not existing_public_user:
method_acl.append(dict(user='******', role='READER'))
result = fapi.update_repository_method(namespace=namespace, method=method_name, wdl=wdl, synopsis='')
if result.status_code == 201:
result = result.json()
if len(method_acl) > 0:
fapi.update_repository_method_acl(namespace=result['namespace'], method=result['name'], snapshot_id=result['snapshotId'], acl_updates=method_acl)
print(f'Workflow {method_name} is imported! See https://api.firecloud.org/ga4gh/v1/tools/{result["namespace"]}:{result["name"]}/versions/{result["snapshotId"]}/plain-WDL/descriptor')
n_success += 1
else:
print(f'Unable to add workflow {method_name} - {result.json()}')
print(f'Successfully added {n_success} workflows.')
def set_acl(self, role, users):
"""Set permissions for this method.
Args:
role (str): Access level
one of {one of "OWNER", "READER", "WRITER", "NO ACCESS"}
users (list(str)): List of users to give role to
"""
acl_updates = [{"user": user, "role": role} for user in users]
r = fapi.update_repository_method_acl(
self.namespace, self.name, self.snapshot_id,
acl_updates, self.api_url
)
fapi._check_response_code(r, 200)
z = fapi.update_repository_method(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, synopsis='run sims and compute component stats',
wdl=os.path.abspath(f'./Dockstore.wdl'))
#print('UPDATE IS', z, z.json())
new_method = z.json()
print('NEW_METHOD IS', new_method)
#z = fapi.list_repository_methods(namespace=SEL_NAMESPACE, name=TERRA_METHOD_NAME).json()
#print('METHODS LIST AFT', z)
snapshot_id = new_method['snapshotId']
z = fapi.get_repository_method_acl(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, snapshot_id=snapshot_id)
print('ACL:', z, z.json())
z = fapi.update_repository_method_acl(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, snapshot_id=snapshot_id,
acl_updates=[{'role': 'OWNER', 'user': '******'},
{'role': 'OWNER', 'user': '******'}])
print('ACL UPDATE:', z, z.json())
z = fapi.get_repository_method_acl(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, snapshot_id=snapshot_id)
print('ACL AFTER UPDATE:', z, z.json())
z = fapi.get_config_template(namespace=SEL_NAMESPACE, method=TERRA_METHOD_NAME, version=snapshot_id)
#print('CONFIG TEMPLATE AFT IS', z, z.json())
config_template = z.json()
#z = fapi.list_workspace_configs(namespace=SEL_NAMESPACE, workspace=SEL_WORKSPACE, allRepos=True).json()
#print('LIST_WORKSPACE_CONFIGS allRepos', z)
TERRA_CONFIG_NAME += f'_cfg_{snapshot_id}'
# z = fapi.get_workspace_config(workspace=SEL_WORKSPACE, namespace=SEL_NAMESPACE,
# config=TERRA_CONFIG_NAME, cnamespace=SEL_NAMESPACE)