Hi

I guess we see similar things: a new history item is created, it turns purple, stays like this apparently forever while no job id is created (ie I don't see the job in any of the report tools).


To be honest we ignore them, because:

a) it only (as far as I can tell) happens with big data files (we try to avoid this anyway by using 'Data libraries') while there is heavy load on the storage system

b) ...eventually, unless the user has deleted the history item, it does turn green and the job is listed as 'ok'.


Do you experience this problem with all files, even small ones?


Regards, Hans


On 02/22/2012 10:14 AM, Jorrit Boekel wrote:
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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