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Re: [Gmod-ajax] Trouble behind cherrypy
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From: Ian H. <ih...@be...> - 2010-07-12 18:19:34
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It's hard to say; we're doing some refactoring now and it might "fall out" of that.. Sorry I cannot be more specific at this stage. Certainly what you ask for is a common request from people using jbrowse as part of a repository-type system, so I expect we would have this within the year, but don't hold me to it Sent from my iPad On Jul 12, 2010, at 12:57 AM, Mariette <jma...@to...> wrote: > > Thanks for this answer. > Do you think this fonctionnality will be coming up soon ? > > Jerome > > > > Ian Holmes a écrit : >> Jerome, there is currently no way to do this but it is on our to-do >> list. Ian >> >> >> Mariette wrote: >> >>> 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 >>>> >>> ------------------------------------------------------------------------------ >>> 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 >> |
