def prepare_assembly_data(args, aclient, usage):
"""Parses args and uploads files
returns data spec for submission in run/upload commands"""
if not (args.pair or args.single or args.pair_url or args.single_url or args.contigs):
sys.exit(usage)
adata = client.AssemblyData()
curl = args.curl
res_ids = []
files = []
file_sizes = []
file_list = []
file_lists = []
all_lists = [args.pair, args.pair_url, args.single, args.single_url,
args.reference, args.reference_url, args.contigs]
all_types = ['paired', 'paired_url', 'single', 'single_url',
'reference', 'reference_url', 'contigs']
for li in all_lists:
if li is None:
file_lists.append([])
else:
file_lists.append(li)
seen = {}
for f_list in file_lists:
for ls in f_list:
for word in ls:
if '=' not in word:
if word in seen:
sys.exit('Input error: duplicated file: {}'.format(word))
else:
seen[word] = True
for f_list, f_type in zip(file_lists, all_types):
for ls in f_list:
f_infos = []
f_set_args = {}
for word in ls:
if '=' in word:
key, val = word.split('=')
f_set_args[key] = val
elif os.path.isfile(word):
f_info = aclient.upload_data_file_info(word, curl=curl)
f_infos.append(f_info)
elif f_type.endswith('_url'):
file_url = utils.verify_url(word)
f_info = asmtypes.FileInfo(direct_url=file_url)
f_infos.append(f_info)
else:
sys.exit('Invalid input: {}: {}'.format(f_type, word))
f_set = asmtypes.FileSet(f_type, f_infos, **f_set_args)
adata.add_set(f_set)
return adata
def run_command():
parser = get_parser()
args = parser.parse_args()
usage = parser.format_usage()
frmt = logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s")
sh = logging.StreamHandler()
sh.setLevel(logging.DEBUG)
sh.setFormatter(frmt)
clientlog = logging.getLogger("client")
clientlog.setLevel(logging.INFO)
clientlog.addHandler(sh)
if args.verbose:
clientlog.setLevel(logging.DEBUG)
clientlog.debug("Logger Debugging mode")
if args.command == "login":
cmd_login(args)
sys.exit()
if args.command == "logout":
cmd_logout(args)
sys.exit()
a_user, a_token = auth.verify_token(ARAST_AUTH_USER, ARAST_AUTH_TOKEN)
if not a_user or not a_token:
if ARAST_ENVIRON:
sys.exit("Please use the {} controls to authenticate".format(ARAST_ENVIRON))
else:
sys.stderr.write("You can use the login/logout commands to authenticate\n")
a_user, a_token = auth.authenticate()
# main command options
a_url = args.arast_url or ARAST_URL
a_url = utils.verify_url(a_url)
logging.info("ARAST_URL: {}".format(a_url))
aclient = client.Client(a_url, a_user, a_token)
if args.command == "upload":
cmd_upload(args, aclient, usage, clientlog)
elif args.command == "run":
cmd_run(args, aclient, usage, clientlog)
elif args.command == "stat":
cmd_stat(args, aclient)
elif args.command == "get":
cmd_get(args, aclient)
elif args.command == "avail":
cmd_avail(args, aclient)
elif args.command == "kill":
print aclient.kill_jobs(args.job)
def run_command():
parser = get_parser()
args = parser.parse_args()
usage = parser.format_usage()
frmt = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
sh = logging.StreamHandler()
sh.setLevel(logging.DEBUG)
sh.setFormatter(frmt)
clientlog = logging.getLogger('client')
clientlog.setLevel(logging.INFO)
clientlog.addHandler(sh)
if args.verbose:
clientlog.setLevel(logging.DEBUG)
clientlog.debug("Logger Debugging mode")
if args.command == 'login':
cmd_login(args)
sys.exit()
if args.command == 'logout':
cmd_logout(args)
sys.exit()
a_user, a_token = auth.verify_token(ARAST_AUTH_USER,ARAST_AUTH_TOKEN)
if not a_user or not a_token:
if ARAST_ENVIRON:
sys.exit('Please use the {} controls to authenticate'.format(ARAST_ENVIRON))
else:
sys.stderr.write('You can use the login/logout commands to authenticate\n')
a_user, a_token = auth.authenticate()
# main command options
a_url = args.arast_url or ARAST_URL
a_url = utils.verify_url(a_url)
logging.info('ARAST_URL: {}'.format(a_url))
aclient = client.Client(a_url, a_user, a_token)
if args.command == 'upload':
cmd_upload(args, aclient, usage, clientlog)
elif args.command == 'run':
cmd_run(args, aclient, usage, clientlog)
elif args.command == 'stat':
cmd_stat(args, aclient)
elif args.command == 'get':
cmd_get(args, aclient)
elif args.command == 'avail':
cmd_avail(args, aclient)
elif args.command == 'kill':
print aclient.kill_jobs(args.job)
