Re: [Gmod-ajax] Trouble behind cherrypy

[Mariette <jma...@to...>]

Hi everyone,
I have a last question conserning jbrowse, I saw in the doc it is
pssobile to provide to the jbrowse instance the seqRef.js and
the trakInfo.js

*params*
    a dictionary with the following keys:

        * |containerID| - ID of the HTML element that contains the browser
        * |refSeqs| - list of reference sequence information items
          (usually from refSeqs.js)
        * |trackData| - list of track data items (usually from trackInfo.js)
        * |dataRoot| - (optional) URL prefix for the data directory
        * |browserRoot| - (optional) URL prefix for the browser code
        * |tracks| - (optional) comma-delimited string containing
          initial list of tracks to view
        * |location| - (optional) string describing the initial location
        * |defaultTracks| - (optional) comma-delimited string containing
          initial list of tracks to view if there are no cookies and no
          "tracks" parameter
        * |defaultLocation| - (optional) string describing the initial
          location if there are no cookies and no "location" parameter

However I'd like to give it whenever I want so jbrowse take in
consideration different tracks/seqs files without reloading the
page. How could that be done ??

I basicly want to do that because in our application users are allowed
to delete/add/modify 'annotations' so I'd like to update the view
when such actions are performed without reloading the web page (so
.js files cannot be reloaded).

Thanks for your answer,
Jerome







Mariette a écrit :
> Hi Mitch,
>
> so I'm getting further thanks for your help.
> To explain you how we configure our site : we have multiple users, each 
> with his own directory.
> This directory is not seen by our web server (which is cherrypy). So far 
> what we're doing is
> to put the refSeq.js and the trackInfo.js in the user/project directory 
> so this file is taken in
> consideration when looking at the user quota (required for our site). To 
> do so we basicly
> have a dinamic link which return the right refSeq.js/trackInfo.js files 
> considering the authentified
> user.
>
> Right now we have a problem with the link 'url' and 'seqDir' path as 
> they have to be relative
> to the web page where jbrowse is built.
> How can we do to direct those links to our user directory ?? any idea ?
>
> hope it make sense,
> Jerome
>
>
>
>
> Mitch Skinner a écrit :
>   
>> JBrowse doesn't use the directory listings; when JBrowse gets a file 
>> from the server it's through a direct link (or a URL template, in some 
>> places).
>>
>> It's harder to debug if I can't see the app, but my first guess would 
>> be that it has something to do with relative URLs.  refSeq.js and 
>> trackInfo.js both contain URLs relative to the directory containing 
>> the jbrowse index.html file.
>>
>> That's assuming that you're using the default index.html file.  Are 
>> you doing that, or are you doing something else?
>>
>> There's a setting (the "dataRoot" parameter to the Browser javascript 
>> object constructor) that makes the root of those relative URLs 
>> configurable, but because of a recent exchange on the gmod-ajax list 
>> I'm looking at changing how that works.  If you've got a non-default 
>> directory setup I'd be interested to know how you have things laid 
>> out, so that we can make sure that setting works correctly for everyone.
>>
>> Regards,
>> Mitch
>>
>> On 06/30/2010 06:06 AM, Mariette wrote:
>>     
>>> Hi,
>>>
>>> I'm trying to get jbrowse runing into our website. However it's not 
>>> working,
>>> I have the jbrowse environement displayed but not annotations and the
>>> seqRef.
>>> Jbrowse can read the refSeq.js and the trackinfo.js but doesn't read the
>>> 'seqDir' and
>>> the 'url' fields of these files.
>>> We figured out that the jbrowse sample web site allows to list files
>>> into directories.
>>> Is it required to make jbrowse working ??
>>> The problem is we're using the cherrypy web server which doesn't seems
>>> to allow
>>> files listing, and we're guessing this is the problem ? would that make
>>> sens ??
>>>
>>> thanks for your reply,
>>> Jerome
>>>
>>> ------------------------------------------------------------------------------ 
>>>
>>> This SF.net email is sponsored by Sprint
>>> What will you do first with EVO, the first 4G phone?
>>> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>    
>>>       
>
>
> ------------------------------------------------------------------------------
> This SF.net email is sponsored by Sprint
> What will you do first with EVO, the first 4G phone?
> Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>