parser.add_argument('-j', '--jobfile_name', dest = 'jobfile_name', default = '', nargs = '?', help = 'name of jobfile')
parser.add_argument('-l', '--limit', dest = 'limit', default = 250, type = int, nargs = '?', help = 'maximum number of results to return')
parser.add_argument('-o', '--offset', dest = 'offset', default = 0, type = int, nargs = '?', help = 'number of results to skip from the start')
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 = {}
kwargs['systemId'] = 'data.vdjserver.org'
# -p
if args.project is None:
args.project = vdjpy.prompt_user('project')
project_uuid = vdjpy.get_uuid(args.project, my_agave)
if project_uuid is None:
sys.exit()
# -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
# SET UP FILETYPE AND GET FILE NAME IN ARGS.FILE_NAME
# -f (default)
parser = argparse.ArgumentParser(description = 'Move a projectfile or jobfile from one location on data.vdjserver.org to a projectfile destination. This command updates metadata, and the moved file will be visible in its new location on vdjserver.org.')
parser.add_argument('-p', '--current_project', dest = 'current_project', nargs = '?', help = 'name of the file\'s current project')
parser.add_argument('-d', '--destination_project', dest = 'destination_project', nargs = '?', help = 'name of the file\'s destination project')
parser.add_argument('-f', '--file_name', dest = 'file_name', default = '', nargs = '?', help = 'name of projecfile')
parser.add_argument('-j', '--jobfile_name', dest = 'jobfile_name', default = '', nargs = '?', help = 'name of jobfile')
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
my_agave = vdjpy.make_vdj_agave(args.accesstoken)
# -p
if args.current_project is None:
args.current_project = vdjpy.prompt_user('current project')
current_uuid = vdjpy.get_uuid(args.current_project, my_agave)
if current_uuid is None:
sys.exit()
# -d
if args.destination_project is None:
args.destination_project = vdjpy.prompt_user('destination project')
destination_uuid = vdjpy.get_uuid(args.destination_project, my_agave)
if destination_uuid is None:
sys.exit()
# SET UP FILETYPE AND GET FILE NAME IN ARGS.FILE_NAME
# -f (default file type)
if args.file_name is not '' or args.jobfile_name is '':
if args.file_name is None:
args.file_name = vdjpy.prompt_user('file name')
