Ok, I found some tape I can put on it. Here:
http://misc.feedfury.com/content/45712644-anton-bobrov-bad-servers-chunked-encoding-and-incompleteread.html
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=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:
IncompleteRead(118 bytes read)
Therefore, I cannot get the results within the script.
Any idea?
Best,
L-A
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