Simon, using your test tools I was able to reproduce your errors. Pull
request 233 is my attempt to fix them with a lighter touch than just
immediately converting outputs to ascii. Do these patches work on your
end?

Bjoern, do these patches fix your problem as well?

If I don't hear anything from anyone, I will merge these changes in a few days.

Thanks guys,
-John

On Tue, Sep 24, 2013 at 8:29 PM, Guest, Simon
<simon.gu...@agresearch.co.nz> wrote:
> At Thu, 19 Sep 2013 11:44:35 +0200,
> Bjoern Gruening wrote:
>> Hi Simon,
>>
>> it's just a guess but can you try the attached patch if you have a
>> reproducible case. It is not tested, but at least it should point you in
>> the right direction. If its working, I will create a pull request.
>
> Hi Bjoern,
>
> Thanks for your reply and your patch.  (Sorry for the delay in responding, I 
> have been busy with other stuff.)
>
> While your patch didn't solve my problem, it certainly pointed me in the 
> right direction.
>
> I made a new patch based on your idea, which I attach.  The idea is, stdout 
> and stderr of each tool run is converted from possible UTF-8 to ASCII, using 
> a new function asciify which I added to Galaxy util.
>
> I made a repository on the Galaxy test toolshed called unicode_tester, to 
> test this.  This has 2 tools which generates some Unicode output, either on 
> stdout or stderr accordingly.  Log output shows that unicode characters are 
> being removed.
>
> What else should I do to contribute this patch into Galaxy core?
>
> cheers,
> Simon
>
>>
>> > 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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