Re: [galaxy-dev] galaxy citation_url setting
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.
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Re: [galaxy-dev] galaxy citation_url setting
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.pyWed Nov 02 14:15:08 2011 -0700
> +++ b/lib/galaxy/config.pyWed 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.
>
>
>
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Re: [galaxy-dev] galaxy citation_url setting
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.
___
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:
http://lists.bx.psu.edu/
Re: [galaxy-dev] galaxy citation_url setting
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: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
[galaxy-dev] galaxy citation_url setting
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. ___ 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: http://lists.bx.psu.edu/
