Hi, 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:
/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py d2fcd3feb4c6318c496d55fa8869b67c http://barium-rbh/new/api/workflows 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, in <module> main() File "/home/galaxy/milxcloud-new/scripts/api/workflow_execute.py", line 28, in main submit( sys.argv[1], sys.argv[2], 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 return self._read_chunked(amt) File "/usr/lib/python2.7/httplib.py", line 586, in _read_chunked raise IncompleteRead(''.join(value)) 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 branch: stable commit: (clean) update: (current)
Thanks Neil