Hello,
It seems you are right. It has nothing to do with the SQLAlchemy. I checked
the Galaxy log and didn't find any other error log. After upgrading the
database to MySQL when I uploaded the first input file, job dispatched to
local runner and everything was fine. But when I tried to upload another
file Galaxy didn't even dispatched the Job. I am pasting below the snapshot
of the Galaxy log for your reference.

galaxy.jobs DEBUG 2013-07-23 09:36:15,579 job 1 ended
galaxy.datatypes.metadata DEBUG 2013-07-23 09:36:15,579 Cleaning up
external metadata files
10.180.4.152 - - [23/Jul/2013:09:36:15 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:36:15 +0600] "GET /api/users/current
HTTP/1.1" 200 - "http://10.180.8.54:6080/"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:36:15 +0600] "GET
/api/histories/f2db41e1fa331b3e/contents?ids=ebfb8f50c6abde6d HTTP/1.1" 200
- "http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:36:33 +0600] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://10.180.8.54:6080/";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:36:38 +0600] "POST
/tool_runner/upload_async_create HTTP/1.1" 200 - "http://10.180.8.54:6080/";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:36:38 +0600] "GET
/tool_runner/upload_async_message HTTP/1.1" 200 - "http://10.180.8.54:6080/";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:01 +0600] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://10.180.8.54:6080/";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:08 +0600] "POST
/tool_runner/upload_async_create HTTP/1.1" 200 - "http://10.180.8.54:6080/";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:08 +0600] "GET
/tool_runner/upload_async_message HTTP/1.1" 200 - "http://10.180.8.54:6080/";
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:53 +0600] "GET /history HTTP/1.1" 200 -
"http://10.180.8.54:6080/"; "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4
(KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:53 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:53 +0600] "GET
/history/get_display_application_links HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET / HTTP/1.1" 200 - "-"
"Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4 (KHTML, like Gecko)
Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET /root/welcome HTTP/1.1"
302 - "http://10.180.8.54:6080/"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET /history HTTP/1.1" 200 -
"http://10.180.8.54:6080/"; "Mozilla/5.0 (X11; Linux i686) AppleWebKit/537.4
(KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET
/history/get_display_application_links HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:37:57 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:02 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:06 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:10 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:14 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:18 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:22 +0600] "GET
/api/histories/f2db41e1fa331b3e HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"
10.180.4.152 - - [23/Jul/2013:09:38:24 +0600] "POST
/datasets/33b43b4e7093c91f/delete_async HTTP/1.1" 200 - "
http://10.180.8.54:6080/history"; "Mozilla/5.0 (X11; Linux i686)
AppleWebKit/537.4 (KHTML, like Gecko) Chrome/22.0.1229.94 Safari/537.4"


Thanks


On Mon, Jul 22, 2013 at 1:05 PM, James Taylor <ja...@jamestaylor.org> wrote:

> The SQLAlchemy warning shouldn't have anything to do with uploads.
> Does Galaxy still start correctly and do you see any other errors on
> the log? What is logged when you try to do the upload?
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Fri, Jul 19, 2013 at 9:19 AM, Himanshu Gupta <himanshucs...@gmail.com>
> wrote:
> > Hello everyone,
> >
> > I had configured galaxy with MySQL database and for some time it was
> working
> > fine. But suddenly it started showing following warning whenever I start
> > galaxy.
> >
> ".../galaxy-dist/eggs/SQLAlchemy-0.7.9-py2.6-linux-x86_64-ucs2.egg/sqlalchemy/sql/expression.py:1927:
> > SAWarning: The IN-predicate on "request_type.id" was invoked with an
> empty
> > sequence. This results in a contradiction, which nonetheless can be
> > expensive to evaluate.  Consider alternative strategies for improved
> > performance."
> >
> > And now I am not able to upload any file. Please help me to resolve it.
> >
> > Thanks
> >
> > ___________________________________________________________
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