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=273c7b4e3aaffd3884ef715aaf780d9a
  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
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