kwargs = {}
# check systemID
if args.systemID is None:
args.systemID = vdjpy.prompt_user('system ID')
kwargs['systemId'] = args.systemID
# check username
if args.username is not '':
if args.username is None:
args.username = vdjpy.prompt_user('username')
kwargs['username'] = args.username
# -l
if args.limit is None:
args.limit = vdjpy.prompt_for_integer('limit', 250)
kwargs['limit'] = args.limit
# -o
if args.offset is None:
args.offset = vdjpy.prompt_for_integer('offset', 0)
kwargs['offset'] = args.offset
# get systems
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
# if -u
if args.username is not '':
roles_list = my_agave.systems.getRoleForUser(**kwargs)
# if no -u
projects_cache = './.vdjprojects'
# make Agave object and kwargs
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
kwargs = {}
# -p
if args.project is None:
args.project = vdjpy.prompt_user('project name')
project_uuid = vdjpy.get_uuid(args.project, my_agave)
if project_uuid is None:
sys.exit()
# -l (for listMetadata)
if args.limit is None:
args.limit = vdjpy.prompt_for_integer('limit', 5000)
kwargs['limit'] = args.limit
# -o (for listMetadata)
if args.offset is None:
args.offset = vdjpy.prompt_for_integer('offset value', 0)
kwargs['offset'] = args.offset
# SET UP FILETYPE
# -f
if args.projectfile is not '' and args.jobfile is '':
filetype = 'projectFile'
# -j
elif args.jobfile is not '' and args.projectfile is '':
filetype = 'projectJobFile'
else:
kwargs = {}
# -s
if args.systemID is None:
args.systemID = vdjpy.prompt_user("system")
kwargs["systemId"] = args.systemID
# -p
if args.path is None:
args.path = vdjpy.prompt_user("path")
kwargs["filePath"] = args.path
# -l
if args.limit is None:
args.limit = vdjpy.prompt_for_integer("limit", 250)
kwargs["limit"] = args.limit
# -o
if args.offset is None:
args.offset = vdjpy.prompt_for_integer("offset", 0)
kwargs["offset"] = args.offset
# list permissions
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
permissions = my_agave.files.listPermissions(**kwargs)
# if -v
if args.verbose:
print json.dumps(permissions, default=vdjpy.json_serial, sort_keys=True, indent=4, separators=(",", ": "))
args.description_file = vdjpy.prompt_user("path to description file")
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)
# else, build body
else:
# -u
if args.url is None:
args.url = vdjpy.prompt_user("url of postit")
kwargs["body"] = '{"url": "' + args.url + '"'
# -x
if args.max_uses is None:
args.max_uses = vdjpy.prompt_for_integer("max number of uses", 25)
kwargs["body"] += ', "maxUses": "' + str(args.max_uses) + '"'
# -a
no_auth = "false"
if args.no_auth:
no_auth = "true"
kwargs["body"] += ', "noauth": ' + no_auth
# -l
if args.lifetime is None:
args.lifetime = vdjpy.prompt_for_integer("lifetime in seconds", 2592000)
kwargs["body"] += ', "lifetime": ' + str(args.lifetime)
# -m
if args.method is None:
)
parser.add_argument(
"-o", "--offset", dest="offset", type=int, default=0, nargs="?", help="number of results to skip from the start"
)
parser.add_argument("-z", "--accesstoken", dest="accesstoken", nargs="?", help="access token")
args = parser.parse_args()
kwargs = {}
# -q
if args.query is None:
args.query = vdjpy.prompt_user("metadata query")
args.query = re.sub(r"^\'|\'$", "", args.query)
args.query = urllib.quote(args.query)
kwargs["q"] = args.query
# -l
if args.limit is None:
args.limit = vdjpy.prompt_for_integer("limit", 5000)
kwargs["limit"] = args.limit
# -o
if args.offset is None:
args.offset = vdjpy.prompt_for_integer("offset value", 0)
kwargs["offset"] = args.offset
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
metadata = my_agave.meta.listMetadata(**kwargs)
print json.dumps(metadata, default=vdjpy.json_serial, sort_keys=True, indent=4, separators=(",", ": "))
