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[Gmod-ajax] Plugin development question

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Eliot Cline

[Gmod-ajax] Plugin development question

Hi,

I have recently implemented in Python a REST API to allow JBrowse to pull data from our Chado database. Having done that, I now want to write a simple plugin for JBrowse that will let our users grab a portion of a reference sequence and send that back to the web server for processing by some of our in-house scripts.

There doesn't seem to be many examples for writing plugins. At least I haven't been able to find them in my searching. Basically what I want to do is add an option to the right-click menus of certain feature types (I have that working) and, when a user clicks my menu option, pop open a dialog that will display the portion of the reference sequence the user is interested in. From there I will supply options for further processing.

I ran the bin/new-plugin.pl script and generated the plugin skeleton code. I would like to use the Dojo toolkit for the design of the pop up dialog and any form components, but I am having a hard time trying to figure out what to do next. Is there an example out there somewhere that could get me started? Just something very simple that would show how to open a Dojo dialog and display a part of the reference sequence in the current visible range. With that in hand I can figure out the rest of what I need to do.

Thanks!

Eliot

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nathandunn

Re: Plugin development question

Eliot,

I think what you want is this:

http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse_Plugins

and this (though it sounds like you are already doing this):

http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services

The “unofficial” set of plugins is here (this will go away, so don’t bookmark it), but hopefully it will be useful.

https://nathandunn.github.io/pluginapp/

Nathan

On Sep 3, 2016, at 12:58 AM, Eliot Cline <[hidden email]> wrote:

Hi,

I have recently implemented in Python a REST API to allow JBrowse to pull data from our Chado database. Having done that, I now want to write a simple plugin for JBrowse that will let our users grab a portion of a reference sequence and send that back to the web server for processing by some of our in-house scripts.

There doesn't seem to be many examples for writing plugins. At least I haven't been able to find them in my searching. Basically what I want to do is add an option to the right-click menus of certain feature types (I have that working) and, when a user clicks my menu option, pop open a dialog that will display the portion of the reference sequence the user is interested in. From there I will supply options for further processing.

I ran the bin/new-plugin.pl script and generated the plugin skeleton code. I would like to use the Dojo toolkit for the design of the pop up dialog and any form components, but I am having a hard time trying to figure out what to do next. Is there an example out there somewhere that could get me started? Just something very simple that would show how to open a Dojo dialog and display a part of the reference sequence in the current visible range. With that in hand I can figure out the rest of what I need to do.

Thanks!

Eliot
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Eliot Cline

Re: Plugin development question

Hi Nathan,

The FeatureSequence plugin was just what I needed to get started. Thanks very much.

Eliot

On Sun, Sep 4, 2016 at 12:27 AM, Nathan Dunn <[hidden email]> wrote:

Eliot,

I think what you want is this:

http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse_Plugins

and this (though it sounds like you are already doing this):

http://gmod.org/wiki/JBrowse_Configuration_Guide#Writing_JBrowse-compatible_Web_Services

The “unofficial” set of plugins is here (this will go away, so don’t bookmark it), but hopefully it will be useful.

https://nathandunn.github.io/pluginapp/

Nathan

On Sep 3, 2016, at 12:58 AM, Eliot Cline <[hidden email]> wrote:

Hi,

I have recently implemented in Python a REST API to allow JBrowse to pull data from our Chado database. Having done that, I now want to write a simple plugin for JBrowse that will let our users grab a portion of a reference sequence and send that back to the web server for processing by some of our in-house scripts.

There doesn't seem to be many examples for writing plugins. At least I haven't been able to find them in my searching. Basically what I want to do is add an option to the right-click menus of certain feature types (I have that working) and, when a user clicks my menu option, pop open a dialog that will display the portion of the reference sequence the user is interested in. From there I will supply options for further processing.

I ran the bin/new-plugin.pl script and generated the plugin skeleton code. I would like to use the Dojo toolkit for the design of the pop up dialog and any form components, but I am having a hard time trying to figure out what to do next. Is there an example out there somewhere that could get me started? Just something very simple that would show how to open a Dojo dialog and display a part of the reference sequence in the current visible range. With that in hand I can figure out the rest of what I need to do.

Thanks!

Eliot
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