Hi Nate,
I wasn't before, but I switched to nginx now. Non-uploading is still
happening in firefox (10.0.2 on ubuntu 11.10).
I can't be 100% sure that my nginx install was correct, but it's
definitely serving galaxy and not complaining. Is there any way to
verify uploads are processed through nginx?
jorrit
On 03/05/2012 08:37 PM, Nate Coraor wrote:
By any chance, do you all happen to be using the nginx upload module? I am
guessing not.
--nate
On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote:
I confirm the same strange behaviour since some of the last updates on the
central version. We are at the latest now.
It is also with medium (10Mb+ tarballs) AND large files! Furthermore its seems
to be in FireFox only.... They upload fine using IE8 or 9. Didn't test other
browsers though.
Annoying it is indeed.
Alex
-----Oorspronkelijk bericht-----
Van: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Jorrit Boekel
Verzonden: woensdag 22 februari 2012 10:15
Aan: galaxy-dev@lists.bx.psu.edu
Onderwerp: [galaxy-dev] uploads stuck in history
Dear list,
I have stumbled on some strange behaviour when uploading files to galaxy via
the upload.py tool. At times, the upload seems to be stalled in history and is
never actually performed, followed by a seemingly infinite history update (see
log below). My system is Ubuntu 11.10 and runs Python 2.7.2. I find the
behaviour in both my own modified galaxy install (based on galaxy-dist), and in
a fresh clone from galaxy-central.
I have tried to upload different files, and all seem to sometimes trigger the
behaviour, but not all the time. A restart of galaxy sometimes sorts things out.
Common for the debug messages is that it seems there is never a job id generated as
in "galaxy.tools.actions.upload_common INFO 2012-02-22 10:06:36,186 tool
upload1 created job id 2".
Has anyone seen similar things or can it be a problem with my system?
cheers,
jorrit
--------------Debug messa:
galaxy.web.framework DEBUG 2012-02-22 09:47:43,730 Error: this request returned
None from get_history(): http://localhost:8080/
127.0.0.1 - - [22/Feb/2012:09:47:43 +0200] "GET / HTTP/1.1" 200 - "-"
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /root/tool_menu HTTP/1.1" 200 -
"http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101
Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "GET /history HTTP/1.1" 200 -
"http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:44 +0200] "POST /root/user_get_usage HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2)
Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:47:50 +0200] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /tool_runner/upload_async_create HTTP/1.1"
200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /tool_runner/upload_async_message HTTP/1.1"
200 - "http://localhost:8080/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "GET /history HTTP/1.1" 200 -
"http://localhost:8080/tool_runner/upload_async_message"; "Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:11 +0200] "POST /root/user_get_usage HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2)
Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:13 +0200] "GET
/tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://localhost:8080/root/tool_menu";
"Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:15 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:19 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:23 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:27 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:31 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:35 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:39 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:43 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
127.0.0.1 - - [22/Feb/2012:09:48:47 +0200] "POST /root/history_item_updates HTTP/1.1" 200 -
"http://localhost:8080/history"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64;
rv:10.0.2) Gecko/20100101 Firefox/10.0.2"
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___________________________________________________________
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/
___________________________________________________________
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/
