Re: [galaxy-dev] uploads stuck in history
Hello, We don't use the nginx module kind regards, Leandro On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: 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 -
Re: [galaxy-dev] uploads stuck in history
The same for us. We never changed anything on our local dev or prod server. The dev server which runs the latest central edition is still suffering from it. Earlier there was no problem at all. Why is it the ngnix issue? Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Leandro Hermida Verzonden: donderdag 8 maart 2012 12:43 Aan: Jorrit Boekel CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] uploads stuck in history Hello, We don't use the nginx module kind regards, Leandro On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: 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
Re: [galaxy-dev] uploads stuck in history
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 -
Re: [galaxy-dev] uploads stuck in history
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;
Re: [galaxy-dev] uploads stuck in history
I had same issue recently. I tried to upload files locally and give same error (from 50Mb or 17Gb as admin). The files never finish uploading. A few days ago I tried to upload around 20 files (up to 200Mb), most of them uploaded normally, but some wouldn't. I will try a different browser them Thanks. 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 Luciano ___ 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/
Re: [galaxy-dev] uploads stuck in history
Hi,
I was trying to upload data again and here is the error message that I
get:
Can't create peek [Errno 2] No such file or directory:
'/home/koala2/galaxy-dist/database/files/000/dataset_24.dat'
Exception happened during processing of request from ('127.0.0.1', 52338)
Traceback (most recent call last):
File
/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 1053, in process_request_in_thread
self.finish_request(request, client_address)
File /usr/lib/python2.7/SocketServer.py, line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File /usr/lib/python2.7/SocketServer.py, line 639, in __init__
self.handle()
File
/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 432, in handle
BaseHTTPRequestHandler.handle(self)
File /usr/lib/python2.7/BaseHTTPServer.py, line 343, in handle
self.handle_one_request()
File
/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 427, in handle_one_request
self.wsgi_execute()
File
/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 287, in wsgi_execute
self.wsgi_start_response)
File /home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/urlmap.py,
line 202, in __call__
return app(environ, start_response)
File
/home/koala2/galaxy-dist/lib/galaxy/web/framework/middleware/xforwardedhost.py,
line 21, in __call__
return self.app( environ, start_response )
File
/home/koala2/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/config.py,
line 164, in __call__
app_iter = self.application(environ, start_response)
File
/home/koala2/galaxy-dist/lib/galaxy/web/framework/middleware/translogger.py,
line 68, in __call__
return self.application(environ, replacement_start_response)
File
/home/koala2/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py,
line 226, in __call__
return self.respond(environ, start_response)
File
/home/koala2/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py,
line 399, in respond
if self.xmlhttp_key in req.params:
File
/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py,
line 900, in params
params = self.str_params
File
/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py,
line 892, in str_params
return NestedMultiDict(self.str_GET, self.str_POST)
File
/home/koala2/galaxy-dist/eggs/WebOb-0.8.5-py2.7.egg/webob/__init__.py,
line 818, in str_POST
keep_blank_values=True)
File /usr/lib/python2.7/cgi.py, line 508, in __init__
self.read_multi(environ, keep_blank_values, strict_parsing)
File /usr/lib/python2.7/cgi.py, line 632, in read_multi
environ, keep_blank_values, strict_parsing)
File /usr/lib/python2.7/cgi.py, line 510, in __init__
self.read_single()
File /usr/lib/python2.7/cgi.py, line 647, in read_single
self.read_lines()
File /home/koala2/galaxy-dist/lib/galaxy/web/framework/base.py, line
268, in read_lines
self.read_lines_to_outerboundary()
File /usr/lib/python2.7/cgi.py, line 697, in read_lines_to_outerboundary
line = self.fp.readline(116)
File
/home/koala2/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py,
line 467, in readline
data = self.file.readline(self.length - self._consumed)
File /usr/lib/python2.7/socket.py, line 412, in readline
bline = buf.readline(size)
OverflowError: signed integer is greater than maximum
On Mon, Mar 5, 2012 at 3:24 PM, Luciano Cosme cosme.sim...@gmail.comwrote:
I had same issue recently. I tried to upload files locally and give same
error (from 50Mb or 17Gb as admin). The files never finish uploading. A few
days ago I tried to upload around 20 files (up to 200Mb), most of them
uploaded normally, but some wouldn't. I will try a different browser them
Thanks.
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
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Re: [galaxy-dev] uploads stuck in history
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
Re: [galaxy-dev] uploads stuck in history
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)
Re: [galaxy-dev] uploads stuck in history
Hi all, We get the behavior mentioned some times too, its not reproducible just like you mentioned. Some times it happens with small files, some times with large files and again as you said it doesn't happen all the time. Now I haven't seen this yet on our Galaxy dev server which is the latest galaxy-dist, only see this on our Galaxy production which is an older version of galaxy-dist from last winter. regards, Leandro On Wed, Feb 22, 2012 at 3:59 PM, Hans-Rudolf Hotz h...@fmi.ch wrote: 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
Re: [galaxy-dev] uploads stuck in history
Hi, I haven't been patient enough to wait really long, but I can give that a try. As Leandro mentioned, I've also seen it in kilobyte to megabyte sized files. My Galaxy is forked from the latest galaxy-dist. cheers, jorrit On 02/22/2012 04:47 PM, Leandro Hermida wrote: Hi all, We get the behavior mentioned some times too, its not reproducible just like you mentioned. Some times it happens with small files, some times with large files and again as you said it doesn't happen all the time. Now I haven't seen this yet on our Galaxy dev server which is the latest galaxy-dist, only see this on our Galaxy production which is an older version of galaxy-dist from last winter. regards, Leandro On Wed, Feb 22, 2012 at 3:59 PM, Hans-Rudolf Hotzh...@fmi.ch wrote: 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 -
