Re: [galaxy-dev] Problem in uploading file

23 Jul 2013


      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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Himanshu Gupta

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