My optimism was short lived. I think I've hit a galaxy bug in Unicode processing. Having managed to get the deseq tool not to crash galaxy in the sqlalchemy layer, I now get a crash when clicking on the info->stderr for the tool output dataset, probably because it contains Unicode. Here's the traceback from paster.log:
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 47124)
Traceback (most recent call last):
File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/SocketServer.py", line 617, in __init__
self.handle()
File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 442, in handle
BaseHTTPRequestHandler.handle(self)
File "/usr/lib64/python2.6/BaseHTTPServer.py", line 329, in handle
self.handle_one_request()
File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 437, in handle_one_request
self.wsgi_execute()
File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute
self.wsgi_write_chunk(chunk)
File "/home/galaxy-dev/galaxy/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py", line 150, in wsgi_write_chunk
self.wfile.write(chunk)
File "/usr/lib64/python2.6/socket.py", line 316, in write
data = str(data) # XXX Should really reject non-string non-buffers
UnicodeEncodeError: 'ascii' codec can't encode character u'\u2018' in position 169: ordinal not in range(128)
----------------------------------------
I don't know where to look to find the actual stderr output. Any pointers?
Is this actually a galaxy bug now?
cheers,
Simon
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