parser.add_argument('-a', '--appID', dest = 'appID', default = '', nargs = '?', help = 'application ID')
parser.add_argument('-f', '--description_file', dest = 'description_file', nargs = '?', help = 'file containing JSON app description')
parser.add_argument('-v', '--verbose', dest = 'verbose', action = 'store_true', help = 'verbose output')
parser.add_argument('-z', '--accesstoken', dest = 'accesstoken', nargs = '?', help = 'access token')
args = parser.parse_args()
# make agave object and kwargs
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
kwargs = {}
# -f
if args.description_file is None:
args.description_file = vdjpy.prompt_user('path to file containing app description')
# open -f and use as body
body_contents = vdjpy.read_json(args.description_file)
if body_contents is None:
sys.exit('Not a valid file path or does not contain a valid app description.')
kwargs['body'] = json.dumps(body_contents)
# if -a, update app
if args.appID is not '':
if args.appID is None:
args.appID = vdjpy.prompt_user('app ID')
kwargs['appId'] = args.appID
resp = my_agave.apps.update(**kwargs)
# else, add app
else:
resp = my_agave.apps.add(**kwargs)
parser = argparse.ArgumentParser(description = 'Add or update a metadata object. If the uuid of existing metadata is given, the metadata will be updated; otherwise, a new piece of metadata will be created.')
parser.add_argument('-u', '--uuid', dest = 'uuid', default = '', nargs = '?', help = 'uuid of metadata object')
parser.add_argument('-f', '--metadata_file', dest = 'metadata_file', nargs = '?', help = 'file containing JSON metadata description')
parser.add_argument('-z', '--accesstoken', dest = 'accesstoken', nargs = '?', help = 'access token')
args = parser.parse_args()
# make agave object and kwargs
kwargs = {}
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
# -f
if args.metadata_file is None:
args.metadata_file = vdjpy.prompt_user('path to metadata file')
# open -f and use as body
body_contents = vdjpy.read_json(args.metadata_file)
if body_contents is None:
sys.exit('Not a valid file path or does not contain valid JSON.')
kwargs['body'] = json.dumps(body_contents)
# if -u given, use update
if args.uuid is not '':
if args.uuid is None:
args.uuid = vdjpy.prompt_user('uuid of item')
kwargs['uuid'] = args.uuid
resp = my_agave.meta.updateMetadata(**kwargs)
# else, use add
else:
resp = my_agave.meta.addMetadata(**kwargs)
args = parser.parse_args()
# make agave object and kwargs
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
kwargs = {}
# -a
if args.appID is None:
args.appID = vdjpy.prompt_user('ID of app to be cloned')
kwargs['appId'] = args.appID
# -f used if given
if args.description_file is not '':
if args.description_file is None:
args.description_file = vdjpy.prompt_user('file name')
body_contents = vdjpy.read_json(args.description_file)
if body_contents is None:
sys.exit()
kwargs['body'] = json.dumps(body_contents)
# -n, -s, -e, -x, and -d used if no -f
else:
# if -n, -e, or -x not given, load app data (exit if app does not exist)
if args.clone_name or args.execution_system or args.version is '':
apps = my_agave.apps.list()
app_info = None
for app in apps:
if app['id'] == args.appID:
app_info = app
if app_info is None:
sys.exit('Could not find app to be cloned')
user_cache = '~/.vdjapi'
template_cache = './cache-template.json'
if __name__ == '__main__':
# arguments
parser = argparse.ArgumentParser(description = 'Authenticate a user by retrieving a new access and refresh token. If the refresh flag is used, the new tokens are retrieved using the refresh token in the user\'s cache (~/.vdjapi), or one supplied by the user. If the save flag is used, the new tokens are cached.')
parser.add_argument('-u', '--username', dest = 'username', nargs = '?', help = 'user to authenticate')
parser.add_argument('-p', '--password', dest = 'password', nargs = '?', help = 'password of the user')
parser.add_argument('-r', '--refresh', dest = 'refresh', default = '', nargs = '?', help = 'use cached refresh token or one supplied by the user')
parser.add_argument('-s', '--save', dest = 'save', action = 'store_true', help = 'cache tokens once retrieved')
args = parser.parse_args()
# load cache
cache_dict = vdjpy.read_json(user_cache)
if cache_dict is None:
if args.save:
cache_dict = vdjpy.read_json(template_cache)
else:
cache_dict = {}
# -u
if args.username is None:
args.username = cache_dict.get('username')
if args.username is None or args.username == unicode(''):
print 'Username in cache does not exist or is empty'
args.username = vdjpy.prompt_user('username')
# -r
if args.refresh is None: