Hi, Can someone help me understand the automagic (un)zipping in Galaxy? In my universe_wsgi.ini there an option to enable gzip compression like this: # ---- HTTP gzip compression ---- # If planning to run Galaxy as a production service, we recommend running Galaxy # through a proxy and enabling gzip compression there (instructions at # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer ) # but you may also turn on Paste's built-in gzip compressor by uncommenting the following lines # and also the 'filter-with = gzip' line under [app:main]. This will reduce network traffic # and should speed up the interface, especially the visualization module. # [filter:gzip] use = egg:Paste#gzip ... filter-with = gzip 1. I cannot find instructions on how to enable gzip compression in Apache at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer, but I have enabled "Paste's built-in gzip compressor" and that does not generate errors, so I guess it works. 2. This is not the part that is responsible for automatically detecting *.gz files and unzipping them, or is it? Enabling or disabling the code above does not affect automagic unzipping of uploaded *.gz, which works for me with or without the code above. 2. Can I make automagic unzipping also work for *.zip files? Personally I prefer gzip, but many people in our lab are more familiar with things like winzip.... Cheers, Pi
On 5 February 2010 13:24, Pieter Neerincx <pieter.neerincx@gmail.com> wrote:
Hi,
Can someone help me understand the automagic (un)zipping in Galaxy?
In my universe_wsgi.ini there an option to enable gzip compression like this:
# ---- HTTP gzip compression ---- # If planning to run Galaxy as a production service, we recommend running Galaxy # through a proxy and enabling gzip compression there (instructions at # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer )
This means you should use something such as mod deflate: http://httpd.apache.org/docs/2.0/mod/mod_deflate.html
2. Can I make automagic unzipping also work for *.zip files? Personally I prefer gzip, but many people in our lab are more familiar with things like winzip....
This is handled transparently by negotiation between the browser and the server. Your end user does not have to do anything - the browser unzips before rendering. hope this helps, James
James Casbon wrote:
On 5 February 2010 13:24, Pieter Neerincx <pieter.neerincx@gmail.com> wrote:
Hi,
Can someone help me understand the automagic (un)zipping in Galaxy?
In my universe_wsgi.ini there an option to enable gzip compression like this:
# ---- HTTP gzip compression ---- # If planning to run Galaxy as a production service, we recommend running Galaxy # through a proxy and enabling gzip compression there (instructions at # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer )
This means you should use something such as mod deflate: http://httpd.apache.org/docs/2.0/mod/mod_deflate.html
I've also added the missing information to the wiki: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
2. Can I make automagic unzipping also work for *.zip files? Personally I prefer gzip, but many people in our lab are more familiar with things like winzip....
This is handled transparently by negotiation between the browser and the server. Your end user does not have to do anything - the browser unzips before rendering.
It may help to clarify that this only refers to compression of data sent from Apache to the client, so it does not include uploads or any data handling by Galaxy itself. In response to one of the original questions, we chose not to allow uploading zip files since they can contain multiple files and upload is only designed to handle one file at a time. gzip is not a file container, so it is always guaranteed to contain one file (even if that file is a tar archive). However, detecting the contents of a zip is simple, and we could simply reject any zips with > 1 file. So if people would find this to be useful, it's something we could add to our enhancements wishlist. --nate
hope this helps, James _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Hi Nate and James, On Feb 5, 2010, at 4:59 PM, Nate Coraor wrote:
James Casbon wrote:
On 5 February 2010 13:24, Pieter Neerincx <pieter.neerincx@gmail.com> wrote:
Hi,
Can someone help me understand the automagic (un)zipping in Galaxy?
In my universe_wsgi.ini there an option to enable gzip compression like this:
# ---- HTTP gzip compression ---- # If planning to run Galaxy as a production service, we recommend running Galaxy # through a proxy and enabling gzip compression there (instructions at # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer ) This means you should use something such as mod deflate: http://httpd.apache.org/docs/2.0/mod/mod_deflate.html
I've also added the missing information to the wiki:
http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
Thanks!
2. Can I make automagic unzipping also work for *.zip files? Personally I prefer gzip, but many people in our lab are more familiar with things like winzip.... This is handled transparently by negotiation between the browser and the server. Your end user does not have to do anything - the browser unzips before rendering.
It may help to clarify that this only refers to compression of data sent from Apache to the client, so it does not include uploads or any data handling by Galaxy itself.
Thanks for clarifying.
In response to one of the original questions, we chose not to allow uploading zip files since they can contain multiple files and upload is only designed to handle one file at a time. gzip is not a file container, so it is always guaranteed to contain one file (even if that file is a tar archive).
However, detecting the contents of a zip is simple, and we could simply reject any zips with > 1 file. So if people would find this to be useful, it's something we could add to our enhancements wishlist.
Yes that would be useful, please do! Cheers, Pi
--nate
hope this helps, James _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
Pieter Neerincx wrote:
In response to one of the original questions, we chose not to allow uploading zip files since they can contain multiple files and upload is only designed to handle one file at a time. gzip is not a file container, so it is always guaranteed to contain one file (even if that file is a tar archive).
However, detecting the contents of a zip is simple, and we could simply reject any zips with > 1 file. So if people would find this to be useful, it's something we could add to our enhancements wishlist.
Yes that would be useful, please do!
Okay, I've created a bitbucket for that issue (which you may "follow") here: http://bitbucket.org/galaxy/galaxy-central/issue/280/allow-zip-file-uploads
Cheers,
Pi
--nate
hope this helps, James _______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
participants (3)
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James Casbon -
Nate Coraor -
Pieter Neerincx