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? -- Thanks, Shantanu.
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. --nate
-- Thanks, Shantanu. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
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. -- Shantanu.
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
-- Shantanu.
On Nov 3, 2011, at 8:36 AM, Nate Coraor wrote: 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 Thanks for explaining it Nate. That's helpful. -- Shantanu.
participants (2)
-
Nate Coraor -
Shantanu Pavgi