Zip Vs. Gzip

Question: Zip Vs. Gzip

8.8 years ago by

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

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modified 8.8 years ago by James Casbon • 370 • written 8.8 years ago by Pieter Neerincx • 360

8.8 years ago by

James Casbon • 370

James Casbon • 370 wrote:

This means you should use something such as mod deflate: http://httpd.apache.org/docs/2.0/mod/mod_deflate.html 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

ADD COMMENT • link written 8.8 years ago by James Casbon • 370

I've also added the missing information to the wiki: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy 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

ADD REPLY • link written 8.8 years ago by Nate Coraor ♦ 3.2k

Hi Nate and James, Thanks! Thanks for clarifying. Yes that would be useful, please do! Cheers, Pi

ADD REPLY • link written 8.8 years ago by Pieter Neerincx • 360

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

ADD REPLY • link written 8.8 years ago by Nate Coraor ♦ 3.2k

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