Ok, I found some tape I can put on it. Here: http://misc.feedfury.com/content/45712644-anton-bobrov-bad-servers-chunked-e...
In scripts/api/common.py I put this piece of code at the beginning of the file, after the imports:
import httplib def patch_http_response_read(func): def inner(*args): try: return func(*args) except httplib.IncompleteRead, e: return e.partial return inner httplib.HTTPResponse.read = patch_http_response_read(httplib.HTTPResponse.read)
And it works fine now.
Le 29/07/2011 17:06, Louise-Amélie Schmitt a écrit :
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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: