When you say "p.s. there is nothing in the log file."?

Does you mean the Galaxy log file? If there are jobs running and completing there must be something in the log file right? Do you mean there are just not tracebacks indicating errors in the logs?

My guess is the response is just taking a while perhaps because the server is busy processing the workflow request (but that seems baffling given how small the workflow is). I would consider just catching the exception in your script and then continuing to process items. With the next release of Galaxy (Dec/Jan) the workflow request will return an invocation object that you can pull - but for now you can repeatedly check the history for the status of the workflow as it progresses if you need to monitor it.

Have you made any modifications to the job submission code that might significantly slow it down - added sleeps for debugging purposes anywhere or anything like that?

-John

On Tue, Oct 14, 2014 at 2:14 AM, Neil.Burdett@csiro.au wrote:

Hi, when I use the example_watch_folder.py to check for files in an input directory and process them if they are present. The workflow runs to completion successfully, but the "example_watch_folder.py" task crashes with the following errors, thus it can only process one file at a time, as the example_watch_folder.py has to be constantly restarted.

python example_watch_folder.py d2fcd3feb4c6318c496d55fa8869b67c http://barium-rbh/new/api/ /home/galaxy/cte_input /home/galaxy/cte_output "API Imports" f597429621d6eb2b

in_folder [/home/galaxy/cte_input]

fullpath [/home/galaxy/cte_input/141_S_0851_MRI_T1_Screening.nii.gz]

submit library_id [f2db41e1fa331b3e]

libset [[{u'url': u'/new/api/libraries/f2db41e1fa331b3e/contents/82b264d8c3d11790', u'id': u'82b264d8c3d11790', u'name': u'141_S_0851_MRI_T1_Screening.nii.gz'}]]

waits for several minutes ....

Traceback (most recent call last): File "example_watch_folder.py", line 97, in <module> main(api_key, api_url, in_folder, out_folder, data_library, workflow ) File "example_watch_folder.py", line 77, in main res = submit( api_key, api_url + 'workflows', wf_data, return_formatted=False) File "common.py", line 117, in submit r = post( api_key, url, data ) File "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(176 bytes read)

Due to the crash there is no outputs shown on the screen. Any ideas?

Thanks Neil

p.s. there is nothing in the log file.

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