Re: [Gmod-tripal-devel] GBrowse, JBrowse and Tripal integration

[Scott C. <sc...@sc...>]

Hi Stephen,

Actually, I don't think it needs to be an iframe--that's just the way I
think sometimes.  An image generated by gbrowse_img would be fine, though
in addition to what you have in rosaceae, I'd think it would make sense for
the image to be a link to the same display in GBrowse (probably opening in
a separate window, but those are details).

Also, I want to make sure I understand: you're saying there are two ways I
could do it, either by using CCK or by creating a subtemplate, right, I
don't do both?  Which is easier and/or more maintainable?

Thanks,
Scott



On Mon, Oct 14, 2013 at 12:00 PM, Stephen Ficklin <spf...@gm...>wrote:

>  Hi Scott,
>
> Would you like for GBrowse or JBrowse to automatically show the feature
> and all alignments, something like this page:
>
> http://www.rosaceae.org/prunus/prunus_persica/ppa000475m?block=alignments
>
> But, rather than just an image, you would like the application visible in
> an iFrame with the feature automatically in view?
>
> I believe you may be able to do this with minimal coding using CCK
> elements.  Tripal already uses CCK elements to allow for easy addition of
> new items to the Resources right-sidebar.   Instructions for doing this are
> on the Tripal v1.1 tutorial:
> http://www.gmod.org/wiki/Tripal_Tutorial_v1.1#Adding_New_Resources_To_Pages.
> Unfortunately, I have never tried to add a bit of PHP code to the CCK
> field, which is what you'd need to do to be able to generate a URL for the
> iFrame for the specific feature shown on the page.  I think it can be done
> and if you'd like to go this route I can try to help figure out how to do
> it.
>
> Second, you can do this by creating a custom template file.   There are
> instructions on the Tripal Developer's Handbook (
> http://www.gmod.org/wiki/Tripal_Developer's_Handbook) for how to add new
> template files and using the Tripal API to get data.  In short, here is
> what you'd do:
>
> 1)  Copy all of the templates from the Tripal theme into your default
> theme directory.  This way, when Tripal is updated your custom templates
> won't be overwritten
> 2)  In the tripal_theme/tripal_feature directory, add a new subtemplate
> file for your iframe content.
> 3)  Add an 'include' statement in the node-chado_feature.tpl.php file to
> include your new subtemplate file
> 4)  Add code to your subtepmlate file for creating the iFrame with the
> proper URL for displaying the feature.
>
> Once you get used to how the templates work, it is very easy to add new
> templates, and the Tripal API makes it relatively easy to get data. You
> shouldn't have to do any SQL queries at all in the template files.   I can
> provide more specific details depending on how you want to go with this.
>
> Hope this helps,
> Stephen
>
>
>
> On 10/11/2013 12:46 PM, Scott Cain wrote:
>
> Hi Stephen and all,
>
>  I'm looking a way to put GBrowse and JBrowse iframes in feature pages,
> presumably as separate tabs (added to the list of resources things that
> would go along with relationships, annotated sequence, etc).  I would like
> to do this for the GMOD in the Cloud/Box and would like for it to remain
> usable from one point release to the next.  I'm guessing there is
> documentation on how to do something like this; could you please point it
> out for me?
>
>  Also, I want to make links in GBrowse and JBrowse that go to the feature
> pages in Tripal.  Are the URLs always like
> lowercase(genus/genus_species/uniquename)?
>
>  Thanks,
>  Scott
>
>
>  --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain
> dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
>
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot
net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research