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parser.add_argument('-f', '--file', '--path', dest='filepath', default=None)
parser.add_argument('--size-mb', type=int, dest='size_mb')
parser.add_argument('--size-gb', type=int, dest='size_gb')
args = parser.parse_args()
if args.size_mb:
args.file_to_upload_size = args.size_mb * utils.MB
elif args.size_gb:
args.file_to_upload_size = args.size_gb * utils.GB
else:
args.file_to_upload_size = 11*utils.KB
synapseclient.USER_AGENT['User-Agent'] = "test-large-file-upload " + synapseclient.USER_AGENT['User-Agent']
syn = synapseclient.Synapse(debug=args.debug, skip_checks=args.skip_checks)
if args.staging:
print("switching to STAGING endpoints")
syn.setEndpoints(**synapseclient.client.STAGING_ENDPOINTS)
syn.login(args.user, args.password, silent=True)
test_large_file_upload(file_to_upload_size=args.file_to_upload_size, filepath=args.filepath)
def setup_module(module):
print("Python version:", sys.version)
syn = synapseclient.Synapse(debug=False, skip_checks=True)
syn.logger = logging.getLogger(SILENT_LOGGER_NAME)
module.syn = syn
def main(argv):
syn = synapseclient.Synapse()
user = os.environ.get('SYNAPSE_USER', None)
password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=user, password=password)
messages.syn = syn
project_id = conf.CHALLENGE_SYN_ID
for queue_info in conf.evaluation_queues:
#eval_id = argv[0]
if queue_info['id'] > 9603664:
print("sending report reminders for queue {}..."
.format(queue_info['id']))
send_reminders(syn, queue_info['id'])
def setup(module):
module.syn = synapseclient.Synapse()
module.syn.login()
def main(argv):
syn = synapseclient.Synapse()
user = os.environ.get('SYNAPSE_USER', None)
password = os.environ.get('SYNAPSE_PASSWORD', None)
syn.login(email=user, password=password)
project_id = conf.CHALLENGE_SYN_ID
#for queue_info in conf.evaluation_queues:
eval_id = argv[0]
print("updating team annotations for queue {}...".format(eval_id))
update_submissions(syn, eval_id)
def setup(self):
read_session_cache_patcher = patch.object(cached_sessions, "_read_session_cache")
set_most_recent_user_patcher = patch.object(cached_sessions, "set_most_recent_user")
set_api_key_patcher = patch.object(cached_sessions, "set_api_key")
os_patcher = patch.object(cached_sessions, 'os')
equals_path_patcher = patch.object(cached_sessions, 'equal_paths')
self.patchers = [read_session_cache_patcher, set_most_recent_user_patcher, set_api_key_patcher, os_patcher,
equals_path_patcher]
self.mock_syn = create_autospec(Synapse())
self.mock_read_session_cache = read_session_cache_patcher.start()
self.mock_set_most_recent_user = set_most_recent_user_patcher.start()
self.mock_set_api_key = set_api_key_patcher.start()
self.mock_os = os_patcher.start()
self.mock_equals_path = equals_path_patcher.start()
self.file_path = "/asdf/asdf/asdf/.session"
self.mock_os.path.join.return_value = self.file_path
if opt == '--dPSI':
log_fold_cutoff = float(arg)
if opt == '--u':
if string.lower(arg) == 'yes' or string.lower(arg) == 'true':
uniqueDonors=True
use_adjusted_p = False
else:
uniqueDonors = False
if string.lower(arg) == 'both':
runAgain = True
if len(used)>0:
###Upload existing results folder to Synapse
import synapseclient
import os,sys,string,shutil,getopt
syn = synapseclient.Synapse()
syn.login()
synapseDirectoryUpload(target_dir, parent_syn, executed_urls, used)
sys.exit()
elif compareEnrichmentProfiles:
#print expression_files
compareGOEliteEnrichmentProfiles(expression_files[0],expression_files[1])
elif runGOElite:
runGOEliteAnalysis(species,expression_files[0])
elif (len(expression_files)==1 and '.txt' in expression_files[0]) or (len(expression_files)==1 and 'syn' in expression_files[0]):
### Perform a covariate based analysis on the lone input expression file
metadata_file = metadata_files[0]
if 'syn' in metadata_file:
try: metadata_file = downloadSynapseFile(metadata_file,output_dir)
except Exception:
print 'Is the destination file %s already open?' % metadata_file;sys.exit()
expression_file = expression_files[0]
def main():
args = build_parser().parse_args()
synapseclient.USER_AGENT['User-Agent'] = "synapsecommandlineclient " + synapseclient.USER_AGENT['User-Agent']
syn = synapseclient.Synapse(debug=args.debug, skip_checks=args.skip_checks)
if not ('func' in args and args.func == login):
# if we're not executing the "login" operation, automatically authenticate before running operation
login_with_prompt(syn, args.synapseUser, args.synapsePassword, silent=True)
perform_main(args, syn)
def downloadSynapseFile(synid,output_dir):
import synapseclient
import os,sys,string,shutil
syn = synapseclient.Synapse()
syn.login()
matrix = syn.get(synid, downloadLocation=output_dir, ifcollision="keep.local")
return matrix.path