Hi David and Bastal,
We have been able to reproduce this behavior under certain conditions and are working on a fix. Until this fix is available, you can disable ajax uploads, which should allow the upload tool to work properly. In tools/data_source/upload.xml change
<param name="file_data" type="file" size="30" label="File" ajax-upload="true" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator).">
to
<param name="file_data" type="file" size="30" label="File" ajax-upload="False" help="TIP: Due to browser limitations, uploading files larger than 2GB is guaranteed to fail. To upload large files, use the URL method (below) or FTP (if enabled by the site administrator).">
Please let us know if this workaround doesn't work for you.
Thanks for using Galaxy,
Dan
On Aug 3, 2012, at 4:20 AM, David Roquis wrote:
Hi Batsal,
I have the exact same problem, on 2 different instances of Galaxy, on two different servers. I can replicate this problem on a cloned instance with no modification, and one using multiple galaxay server, nginx proxy and postgresql, both instances being on different machines (one on fedora 13, the other one on fedora 17). From what I have seen, it seems to be browser related. I can sometimes (rarely) upload data with firefox, chrome or safary, but for me it has worked ALL the time using internet explorer 8/9. The thing is that when you start the upload, the browser shows you that it is uploaded, but the upload.py script is never launched, and hence, the upload seems to be running forever. Seems we are not the only ones with this problem, but no real solution until now.
Two options for you at the moment
- try using IE 8/9 to upload the data
- upload your data using data libraries under the admin menu (this works on any browser).
Keep me in touch if you find a solution
David
From: batsal@gmail.com Date: Thu, 2 Aug 2012 15:48:40 -0400 To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Upload issue in local installation
I installed galaxy locally in a linux server. However, I cannot upload the files (no matter how small, I have tried few kb size fasta files). When I try to upload, the link to the file shows up in the History and gets a new number (purple box). When I click on the link I get 'Dataset is uploading' forever.
In the terminal window where I start galaxy, I get the following error report:
92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /root/tool_menu HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:32 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:33 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:40 -0400] "GET /tool_runner?tool_id=upload1 HTTP/1.1" 200 - "http://redhat:8080/root/tool_menu" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /tool_runner/upload_async_create HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /tool_runner/upload_async_message HTTP/1.1" 200 - "http://redhat:8080/" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "GET /history HTTP/1.1" 200 - "http://redhat:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:33:59 -0400] "POST /root/user_get_usage HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:04 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1" 92.17.41.13 - - [02/Aug/2012:15:34:08 -0400] "POST /root/history_item_updates HTTP/1.1" 200 - "http://redhat:8080/history" "Mozilla/5.0 (Windows NT 5.2; rv:13.0) Gecko/20100101 Firefox/13.0.1"
The last line keeps going for ever... writes new line every 4 secs.
I am stuck and don't know where to look. Please help.
Batsal.
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