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 <james@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 <himanshucse10@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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