I execute a number of workflows via the API which all work fine. However,
the longest one I use (consists of three linked tasks), returns an error. I
call the workflow in the python script using popen and has the format:
f597429621d6eb2b hist_id=f597429621d6eb2b 4=hda=c8c00aa41dc69085
The task appears on the history panel and all tasks eventually complete in the
workflow, however, the task that calls the workflow using the above popen call
returns the following error:
Traceback (most recent call last):
File "/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py", line 31,
File "/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py", line 28,
submit( sys.argv, sys.argv, data )
File "/home/galaxy/milxcloud-new/scripts/api/common.py", line 117, in submit
r = post( api_key, url, data )
File "/home/galaxy/milxcloud-new/scripts/api/common.py", line 51, in post
return json.loads( urllib2.urlopen( req ).read() )
File "/usr/lib/python2.7/socket.py", line 351, in read
data = self._sock.recv(rbufsize)
File "/usr/lib/python2.7/httplib.py", line 541, in read
File "/usr/lib/python2.7/httplib.py", line 586, in _read_chunked
httplib.IncompleteRead: IncompleteRead(147 bytes read)
This worked on older versions of Galaxy. I need this to work so I can "monitor"
the workflow so know when all tasks are complete.
has anyone seen this error? Or got an idea how to solve it.
hg summary reports:
% hg summary
parent: 13771:7a4d321c0e38 tip
Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae
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