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
=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
