Shantanu Pavgi wrote:

On Nov 2, 2011, at 3:39 PM, Nate Coraor wrote:

Shantanu Pavgi wrote:

Hi,

It seems like modification of 'citation_url'  in the universe_wsgi.ini config file has no effect in the UI (Help --> How to Cite Galaxy). Is it something hard-coded in the source?

Hi Shantanu,

Whoops.  This has been fixed in 6205:9a9479f7e53f.

Thanks Nate. I was wondering if 'lib/galaxy/config.py' file needs to be modified as well.

{{{

$ hg diff ./lib/galaxy/config.py

diff -r 9e90faf2cb1c lib/galaxy/config.py

--- a/lib/galaxy/config.py Wed Nov 02 14:15:08 2011 -0700

+++ b/lib/galaxy/config.py Wed Nov 02 16:46:08 2011 -0500

@@ -113,6 +113,7 @@

        self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly,sgd_yeast" ).lower().split(",")

        self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",")

        self.brand = kwargs.get( 'brand', None )

+       self.citation_url = kwargs.get('citation_url', 'http://wiki.g2.bx.psu.edu/Citing%20Galaxy')

        self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' )

        self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' )

        self.blog_url = kwargs.get( 'blog_url', None )

}}}

Also, it seems like the default values are being passed twice here - in the mako templates and initialization method of Configuration class. I was wondering if default values can be passed only once during initialization and then other get methods would only query the necessary configuration option.   I don't know all the code in detail, so I might be wrong here.

The template is using Config's get() method, which allows for a default
if the option is not in the kwargs passed to Config.__init__().  It's a
shorthand we've used for config options that are only used in one place
in the code.

--nate