Disabling viewing of very large files
Hi, We've come across a problem in our local Galaxy install with users trying to view extremely large files. This makes Galaxy slow to a crawl and has actually brought the server down due to out-of-memory errors. In order to avoid this is there a way to disable the view button for files of a certain type or above a certain size? Thanks for any help, Chris
Hello Chris, This is not currently possible, but the following bitbucket ticket was opened by Brad Chapman which relates to this issue. Providing this ability is on our development road map, but has not yet been completed. http://bitbucket.org/galaxy/galaxy-central/issue/104/displaying-large-data-f... You can "follow" the ticket in bitbucket if you want, and you'll be alerted when the feature has been added to Galaxy. Thanks very much, Greg Von Kuster Galaxy Development Team Chris Cole wrote:
Hi,
We've come across a problem in our local Galaxy install with users trying to view extremely large files. This makes Galaxy slow to a crawl and has actually brought the server down due to out-of-memory errors.
In order to avoid this is there a way to disable the view button for files of a certain type or above a certain size? Thanks for any help,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
Greg Von Kuster wrote:
This is not currently possible, but the following bitbucket ticket was opened by Brad Chapman which relates to this issue. Providing this ability is on our development road map, but has not yet been completed.
http://bitbucket.org/galaxy/galaxy-central/issue/104/displaying-large-data-f...
You can "follow" the ticket in bitbucket if you want, and you'll be alerted when the feature has been added to Galaxy.
Also, although you can't disable it, you can work around the memory issue by setting debug = False in universe_wsgi.ini. This will prevent Galaxy from attempting to load the entire response into memory before sending. --nate
Hi Nate, Nate Coraor wrote:
Greg Von Kuster wrote:
This is not currently possible, but the following bitbucket ticket was opened by Brad Chapman which relates to this issue. Providing this ability is on our development road map, but has not yet been completed.
http://bitbucket.org/galaxy/galaxy-central/issue/104/displaying-large-data-f...
You can "follow" the ticket in bitbucket if you want, and you'll be alerted when the feature has been added to Galaxy.
Also, although you can't disable it, you can work around the memory issue by setting debug = False in universe_wsgi.ini. This will prevent Galaxy from attempting to load the entire response into memory before sending.
I don't fully understand. Does this mean it will complain before trying to load it into memory or what? Thanks, Chris
It won't load it into memory at all. Part of the debugging framework requires loading the whole request into memory to check it for potential errors. This should be disabled for production sites. When it is disabled, large files are streamed directly to the client without being loaded into memory. On Sep 2, 2009, at 10:11 AM, Chris Cole wrote:
I don't fully understand. Does this mean it will complain before trying to load it into memory or what?
Ah, right. So the browser will still more than likely die, but the server will be fine. Correct? That suits me. Thanks, Chris James Taylor wrote:
It won't load it into memory at all. Part of the debugging framework requires loading the whole request into memory to check it for potential errors. This should be disabled for production sites. When it is disabled, large files are streamed directly to the client without being loaded into memory.
On Sep 2, 2009, at 10:11 AM, Chris Cole wrote:
I don't fully understand. Does this mean it will complain before trying to load it into memory or what?
Hi Greg, Greg Von Kuster wrote:
Hello Chris,
This is not currently possible, but the following bitbucket ticket was opened by Brad Chapman which relates to this issue. Providing this ability is on our development road map, but has not yet been completed.
http://bitbucket.org/galaxy/galaxy-central/issue/104/displaying-large-data-f...
You can "follow" the ticket in bitbucket if you want, and you'll be alerted when the feature has been added to Galaxy.
Done. Thanks. However, I can't download the patch file associated with that ticket; it returns a 404. Chris
Thanks very much,
Greg Von Kuster Galaxy Development Team
Chris Cole wrote:
Hi,
We've come across a problem in our local Galaxy install with users trying to view extremely large files. This makes Galaxy slow to a crawl and has actually brought the server down due to out-of-memory errors.
In order to avoid this is there a way to disable the view button for files of a certain type or above a certain size? Thanks for any help,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-dev
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
A bug on the bitbucket side - the URL is: http://media-static.bitbucket.org//http://bitbucket.org/m/attch/2009/07/data... but should be: http://bitbucket.org/m/attch/2009/07/dataset.diff Chris Cole wrote:
However, I can't download the patch file associated with that ticket; it returns a 404.
Chris
participants (4)
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Chris Cole -
Greg Von Kuster -
James Taylor -
Nate Coraor