Hello everyone,
I'm working on a script that uploads files and launchs workflows on them, but I keep getting errors that appear more or less randomly when the display() and submit() functions are called. In a nutshell, there is a 1/3 chance the calls fail this way.
Nevertheless, the actions are properly triggered in Galaxy, surprisingly.
Here is an example:
When I launch a workflow, I get the following traceback even though the workflow is properly executed:
http://localhost/galaxy-dev/api/workflows?key=273c7b4e3aaffd3884ef715aaf780d... File "automated_preprocessing.py", line 61, in expandFile result = submit( api_key, api_url + 'workflows', wf_data, return_formatted=False) File "common.py", line 100, in submit r = post( api_key, url, data ) File "common.py", line 44, in post return simplejson.loads( urllib2.urlopen( req ).read() ) File "/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/socket.py", line 329, in read data = self._sock.recv(rbufsize) File "/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/httplib.py", line 518, in read return self._read_chunked(amt) File "/g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/httplib.py", line 561, in _read_chunked raise IncompleteRead(''.join(value)) Failed to expand file A: Type: <class 'httplib.IncompleteRead'> IncompleteRead(118 bytes read)
Therefore, I cannot get the results within the script.
Any idea?
Best, L-A