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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