I just tried setting up galaxy to use xSendFile[1] but that didn't
make any difference.

What's odd is that I'm still getting the same error in the galaxy log.
 By using xsendfile shouldn't I now be avoiding using Galaxy to
process the upload over a socket?

Perhaps xsendfile isn't working?

-Greg


[1] 
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy#Sending_files_using_Apache

On Thu, Nov 29, 2012 at 12:57 PM, greg <margeem...@gmail.com> wrote:
> Hmm, no luck on the large uploads.
>
> I tried using a recent version of Google Chrome.
>
> I added these settings to /etc/httpd/conf/httpd.conf
>
> Timeout 6000
> LimitRequestBody 32147483647
>
> And restarted apache.
>
> But when I try to upload a 3.7GB file I get this error in Galaxy:
>
> "Bad Gateway
>
> The proxy server received an invalid response from an upstream server."
>
>
> Now I do see this error in the Galaxy log, so I'm thinking I'm not
> hitting an Apache issue, and I'm not hitting a browser issue.  Perhaps
> it's a paste issue?
>
>
> Exception happened during processing of request from ('127.0.0.1', 52128)
> Traceback (most recent call last):
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 1053, in process_request_in_thread
>     self.finish_request(request, client_address)
>   File "/usr/local/python27/lib/python2.7/SocketServer.py", line 323,
> in finish_request
>     self.RequestHandlerClass(request, client_address, self)
>   File "/usr/local/python27/lib/python2.7/SocketServer.py", line 639,
> in __init__
>     self.handle()
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 432, in handle
>     BaseHTTPRequestHandler.handle(self)
>   File "/usr/local/python27/lib/python2.7/BaseHTTPServer.py", line
> 337, in handle
>     self.handle_one_request()
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 427, in handle_one_request
>     self.wsgi_execute()
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 287, in wsgi_execute
>     self.wsgi_start_response)
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py",
> line 202, in __call__
>     return app(environ, start_response)
>   File 
> "/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py",
> line 21, in __call__
>     return self.app( environ, start_response )
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py",
> line 164, in __call__
>     app_iter = self.application(environ, start_response)
>   File 
> "/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py",
> line 68, in __call__
>     return self.application(environ, replacement_start_response)
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
> line 226, in __call__
>     return self.respond(environ, start_response)
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py",
> line 399, in respond
>     if self.xmlhttp_key in req.params:
>   File "build/bdist.linux-x86_64/egg/webob/__init__.py", line 900, in params
>     params = self.str_params
>   File "build/bdist.linux-x86_64/egg/webob/__init__.py", line 892, in 
> str_params
>     return NestedMultiDict(self.str_GET, self.str_POST)
>   File "build/bdist.linux-x86_64/egg/webob/__init__.py", line 818, in str_POST
>     keep_blank_values=True)
>   File "/usr/local/python27/lib/python2.7/cgi.py", line 508, in __init__
>     self.read_multi(environ, keep_blank_values, strict_parsing)
>   File "/usr/local/python27/lib/python2.7/cgi.py", line 632, in read_multi
>     environ, keep_blank_values, strict_parsing)
>   File "/usr/local/python27/lib/python2.7/cgi.py", line 510, in __init__
>     self.read_single()
>   File "/usr/local/python27/lib/python2.7/cgi.py", line 647, in read_single
>     self.read_lines()
>   File "/misc/local/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py",
> line 268, in read_lines
>     self.read_lines_to_outerboundary()
>   File "/usr/local/python27/lib/python2.7/cgi.py", line 697, in
> read_lines_to_outerboundary
>     line = self.fp.readline(1<<16)
>   File 
> "/misc/local/galaxy/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py",
> line 467, in readline
>     data = self.file.readline(self.length - self._consumed)
>   File "/usr/local/python27/lib/python2.7/socket.py", line 412, in readline
>     bline = buf.readline(size)
> OverflowError: signed integer is greater than maximum
>
>
>
>
>
>
> On Thu, Nov 29, 2012 at 11:26 AM, greg <margeem...@gmail.com> wrote:
>> This says Google Chrome can support uploads larger than 4 GB.
>> http://www.motobit.com/help/scptutl/pa98.htm
>>
>> Maybe I just need to configure Apache?
>>
>> I'll let you guys know what I find.
>>
>> -Greg
>>
>> On Thu, Nov 29, 2012 at 11:22 AM, greg <margeem...@gmail.com> wrote:
>>> Follow up question.  What's the deal with the 2GB limit it mentions?
>>>
>>> I think it would be pretty convienent to allow larger uploads.  We're
>>> on a fast local network so even 10 or 20 GB uploads pretty fast.
>>>
>>> Can I increase the limit in Apache?  Which browsers are limited?  This
>>> is an internal install so I can tell users to only use certain
>>> browsers for uploads.
>>>
>>> -Greg
>>>
>>> On Thu, Nov 29, 2012 at 11:01 AM, Nate Coraor <n...@bx.psu.edu> wrote:
>>>> On Nov 29, 2012, at 10:54 AM, greg wrote:
>>>>
>>>>> Thanks.  That seemed to have worked.  Can you explain what happened?
>>>>> (I'm curious)
>>>>
>>>> It's due to a bug that we've done quite a bit of work to investigate, but 
>>>> haven't yet found  the cause.  It seems to have cropped up more frequently 
>>>> in the past few weeks, so we'll be working on it in depth in the next few 
>>>> days.
>>>>
>>>> --nate
>>>>
>>>>>
>>>>> -Greg
>>>>>
>>>>> On Thu, Nov 29, 2012 at 8:43 AM, Nate Coraor <n...@bx.psu.edu> wrote:
>>>>>> On Nov 28, 2012, at 1:23 PM, greg wrote:
>>>>>>
>>>>>>> I just finished setting up a local install on our cluster but I'm
>>>>>>> having trouble uploading files.
>>>>>>>
>>>>>>> I was able to (successfully?) upload one 160MB fasta file.  But any
>>>>>>> further uploads I try, they just hang.
>>>>>>
>>>>>> Hi Greg,
>>>>>>
>>>>>> Could you try the following:
>>>>>>
>>>>>> Open tools/data_source/upload.xml
>>>>>>
>>>>>> In the following line, set 'ajax-upload="false"':
>>>>>>
>>>>>> <param name="file_data" type="file" size="30" label="File" 
>>>>>> ajax-upload="false" help="TIP: Due to browser limitations, uploading 
>>>>>> files larger than 2GB is guaranteed to fail.  To upload large files, use 
>>>>>> the URL method (below) or FTP (if enabled by the site administrator).">
>>>>>>
>>>>>> Then restart Galaxy and retry the upload and let us know if it succeeds.
>>>>>>
>>>>>> --nate
>>>>>>
>>>>>>>
>>>>>>> Here's the information from the log file:
>>>>>>>
>>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:15:18,190
>>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>>> galaxy.tools.actions.upload_common INFO 2012-11-28 12:20:36,597 tool
>>>>>>> upload1 created job id 4
>>>>>>> galaxy.jobs.handler INFO 2012-11-28 12:20:38,386 (4) Job dispatched
>>>>>>> galaxy.jobs.runners.drmaa INFO 2012-11-28 12:20:38,930 (4) queued as 
>>>>>>> 3718641
>>>>>>> galaxy.objectstore CRITICAL 2012-11-28 12:21:03,071
>>>>>>> /home/galaxy/job_working_directory/000/4 delete error [Errno 39]
>>>>>>> Directory not empty: '/home/galaxy/job_working_directory/000/4'
>>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:21:55,763
>>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:28:26,466
>>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:35:09,662
>>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>>> paste.httpserver.ThreadPool INFO 2012-11-28 12:46:35,565
>>>>>>> kill_hung_threads status: 10 threads (0 working, 10 idle, 0 starting)
>>>>>>> ave time N/A, max time 0.00sec, killed 0 workers
>>>>>>>
>>>>>>>
>>>>>>> The first upload that worked was around 12:20 (above), and the second
>>>>>>> failed one was at 12:40.  The log file doesn't seem to even mention
>>>>>>> it? Could that error have killed the server somehow?
>>>>>>>
>>>>>>> Let me know if I can provide more info.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Greg
>>>>>>> ___________________________________________________________
>>>>>>> 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/
>>>>>>
>>>>>
>>>>

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