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.