Hi, Bob

There are a number of ways to visualize data in Galaxy, so let's settle on
some terminology first for the three major ways:
* *display applications*: these are definitions of external websites that
can fetch galaxy datasets and display them in their visualization
applications. Examples are the UCSC genome browser, GBrowse, and IGV.
* *tools*: although the tool framework generally produces 'raw' data like
tabular or binary files, it can also produce the html (and js even) that
can display data for visualization. An example would be 'Boxplot of quality
statistics'.
* *visualization plugins*: these are python/mako/js files that are meant to
be more interactive visualizations in order to explore data

It sounds to me like you'd like to use the visualization plugin system, so:
* since they're for external code or websites, *let's take display
applications off the table entirely*.
* since they can be a viable alternative to the plugin system, so *I'd keep
tools as another option but keep our focus on the plugin system*

It also sounds like you have two elements you'd like to incorporate:
* a *datatype*
* a *plugin* to display datasets of that datatype

*The datatype*
I'm more familiar with the plugin part of this process, but for the
datatype it sounds like you want to subclass the binary datatype and add it
to your galaxy installation. I'd start here (I imagine you've already seen
it, tho):
* https://wiki.galaxyproject.org/Admin/Datatypes
* https://wiki.galaxyproject.org/Admin/Datatypes/Adding%20Datatypes

Note: to see if your datatype was loaded successfully, with your server
running - you can go to: /api/datatypes/mapping. You should be able to see
your datatype listed at the first level of the json map, generally
beginning with 'galaxy.datatypes.' and the python module name you added it
to (like a python import namespace): e.g. galaxy.datatypes.binary.H5 or
galaxy.datatypes.binary.mydatatype

To simplify:
1. Add a definition to your datatypes_conf file
2. Add a sniffer for your datatype
3. Add a subclass/class for your datatype

*The plugin*
For the plugin, I also imagine you've seen this, but it's a (hopefully)
good place to start:
https://wiki.galaxyproject.org/VisualizationsRegistry

*The filesystem layout*
Here's a simplified process for creating an outline for a visualization
plugin project:
1. in the filesystem, start at *<your galaxy>/config/plugins/visualizations*
2. *think of an id for your plugin*. This can be any (filesystem
permissible) file name and is only used as an id by the registry - the
users never see it. It should be unique from any other plugins in that
directory. (e.g. myplugin)
3. *create a main directory using your id*. (e.g. <your
galaxy>/config/plugins/visualizations/myplugin)
4. inside that directory, *create three more directories: config,
templates, static*. This is where the plugin configuration, the mako
templates, and any (optional) javascript or static files are kept
respectively.
5. *the configuration file should use the same id* you used above for the
directory: e.g. config/myplugin.xml. Most people copy and rename a simple
config file like the one in
config/plugins/visualizations/scatterplot/config/scatterplot.xml. We'll
change the datatype it applies to later, but there's more at:
https://wiki.galaxyproject.org/VisualizationsRegistry#The_visualization_configuration_file
and https://wiki.galaxyproject.org/VisualizationsRegistry/Configuration
6. *a mako template file should go into the templates directory*: e.g.
templates/myplugin.mako. This template file is the entry point for your
visualization and is loaded first. You don't have to do any major coding
here and can instead just launch javascript to render the visualization.
https://wiki.galaxyproject.org/VisualizationsRegistry#Creating_the_code_and_markup_for_your_visualization

At this point, your config/plugins/visualizations/myplugin directory should
look like one of the two trees displayed here:
https://wiki.galaxyproject.org/VisualizationsRegistry#Configuring_your_visualization_plugin_in_the_.60visualization_plugins_directory.60

*The configuration*
Now, we'll configure the plugin by editing the
config/plugins/visualizations/myplugin/config/myplugin.xml file. Let's
assume you've copied the scatterplot config file (
https://github.com/galaxyproject/galaxy/blob/dev/config/plugins/visualizations/scatterplot/config/scatterplot.xml
):

1. change the name displayed to what you'd like users to see in the dataset
visualizations dropdown menu:
l<visualization name="*My Visualization Plugin*">

2. change the configuration for your visualization to test for your
datatype. For example, if you have mydatatype, change:
<data_sources>
    <data_source>
        <model_class>HistoryDatasetAssociation</model_class>
        <test type="isinstance" test_attr="datatype" result_type="datatype">
*binary.MyDatatype*</test>
        <to_param param_attr="id">dataset_id</to_param>
    </data_source>
</data_sources>

The above is basically saying, if an object is a) a
HistoryDatasetAssociation (a dataset in a history) and b) it's a subclass
or instance of binary.MyDatatype, then put a link:
* in the dataset visualization dropdown menu
* that will start my visualization
* pass the encoded id of the dataset in the link using the parameter
'dataset_id'

Note: the 'binary.MyDatatype' is essentially 'module.class' and is also the
last half of the id given in the 'api/datatypes/mapping' mentioned
previously.

3. change the template used as the entry point to reflect the name you gave
it:
<entry_point entry_point_type="mako">*myplugin.mako*</entry_point>


*Testing and troubleshooting*
Finally, you should be at a spot that:
* your visualization will appear in the visualization dropdown menu of
datasets that are of the mydatatype class
* if that menu link is clicked, galaxy will go to visualization/show/<your
plugin id>. E.g. /visualization/show/myplugin?dataset_id=0b1d0715f8366ea8
* whatever code is in myplugin.mako will be executed (you should be able to
use print in python or alert in javascript to test)

*Troubleshooting*
* If your server is running when you've made changes to your config file,
you'll need to restart it (changes to mako and static files do not need a
restart)
* Make sure your id is used in the proper places above and that they all
match
* If galaxy is trying to load or loading your visualization plugin, you
should see an entry like this in your server logs:
galaxy.web.base.pluginframework INFO 2015-12-14 08:46:44,788
VisualizationsRegistry, loaded plugin: myplugin
* errors will also display there
* it can help to change 'debug = True' in your config/galaxy.ini file (only
do this on a separate development server - not you public shared instances)


I know that's a lot of info, so let me know if I can add or clarify on any
of it.
Carl


On Sat, Dec 12, 2015 at 9:57 AM, <rbrown1...@comcast.net> wrote:

> Thank you Eric,
> But I want to be clear after spending 5 days, reading many Galaxy wiki
> links, looking at samples, and with help from others trying to get this to
> work.  I have written many tools but never tried to display a unique
> datatype before.
> Below is a series of questions and steps I followed trying the suggestions
> from early posts.
> My goals are:
> -- To get  the visualization icon to show in the bottom left of my history
> output file?
> -- click the visualization icon to display my data (that I will process to
> display) inside Galaxy.
> The steps below are in order of urgency:)
> Thank you for you patience.
> 1.  /Config/plugin/visualization is where code goes to have a Galaxy
> *internal* module display a user defined data type?  -- mine is binary
> Without getting to in the weeds under this directory I have a mydatatype
> dir with subdirectories /config w xml, /static w .js, /templates w mako
> made of html
> 2.  Under /lib/galaxy/datatypes/display_applications  I tried the same
> approach with no success. Is this where code goes for external displays
> that use get and post reside?
> 3.  which if any of 1or2 above use the Tools/Visualization directory.  Is
> that the convention for the return of a Get or Post external displays?
> 4.  I create my own datatype in  data_config_type.xml  with a <datatype>
> tag
> 5.  in data_config_type.xml you only use the <display>  record which --
> internal or external displays?
> 6.  I added a class in the binary.py  file with the name of my new
> datatype.
> 7.  I added a tool.mydatatype section and file with my xml to input and
> then output my datatype by specifying  format=mydatatype not
> format=binary.mydatatype       Plus I added this into Tools_conf.xml  Are
> there other xml specific items I need in my tool xml for an internal
> visualization
> 8. By clicking the visualization icon. what does it call (hopefully 1or2
> above) so i can add specific code to display my datatype internal
> "visualization?" (preferred) in galaxy?
> ----- Original Message -----
> From: Eric Rasche <e...@tamu.edu>
> To: rbrown1...@comcast.net
> Cc: galaxy-dev <galaxy-...@lists.bx.psu.edu>
> Sent: Tue, 08 Dec 2015 02:34:47 -0000 (UTC)
> Subject: Re: [galaxy-dev] How does one run Javascript or HTML as a tool?
> Hi Bob,
>
> Yes, galaxy supports output formats of HTML+JS, though the tool producing
> them may need to be whitelisted (grep for 'whitelist' in your galaxy.ini)
> for display to work properly.
>
> If you wish to write your own visualization plugin for a specific
> datatype, there are assorted pieces of documentation on the wiki
> <https://wiki.galaxyproject.org/?action=fullsearch&context=180&value=visualization&titlesearch=Titles>
> that might help you (though I usually just look at one of the other
> existing visualization plugins and copy+paste).
>
> Cheers,
>
> Eric
>
> 2015-12-07 20:08 GMT-06:00 <rbrown1...@comcast.net>:
>
>> Good evening Galaxy team,
>> Is it possible to run JavaScript or HTML as a tool or a display module?
>> I see support for URLs, e.g. UCSC Genome Browser, but I would like to
>> process a specific datatype to allow it to be viewed in Galaxy -- but the
>> application is a combination of HTML and JavaScript.
>> Does Galaxy support this?
>> Thank you,
>> Bob
>>
>> ___________________________________________________________
>>
>> Please keep all replies on the list by using "reply all"
>>
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>
>
>
>
> --
> Eric Rasche
> Programmer II
> Center for Phage Technology
> Rm 312A, BioBio
> Texas A&M University
> College Station, TX 77843
> 404-692-2048
> e...@tamu.edu
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
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