Hi all,
I transformed the awesome tutorial Carl wrote into a wiki page here:
https://wiki.galaxyproject.org/Develop/Visualizations
Please contribute if you feel like it.

M.

On Mon, Dec 14, 2015 at 4:17 PM <rbrown1...@comcast.net> wrote:

> Thank you Carl for the excellent write-up.  It could serve as a
> visualization plugin tutorial.
>
> However, I am still not able to get the visualization icon to appear, see
> the attachment 2.
>
> I feel if I get the icon to show it will all come together.
>
> A couple questions followed by file dumps and startup info
>
> *1. my   /api/datatypes/mapping dump   it shows registry instead of binary*
>
> *near the top*
>
> "galaxy.datatypes.genetics.RexpBase": {"galaxy.datatypes.images.Html":
> true, "galaxy.datatypes.data.Data": true, "galaxy.datatypes.data.Text":
> true, "galaxy.datatypes.genetics.RexpBase": true}, "galaxy.datatypes.
> *registry*.MDA_zip": {"galaxy.datatypes.*registry*.Binary": true,
> "galaxy.datatypes.data.Data": true, "galaxy.datatypes.binary.Binary": true,
> "galaxy.datatypes.*registry*.MDA_zip": true},
>
> *near the bottom in lower case*
>
> "galaxy.datatypes.registry.Text", "mda_zip":
> "galaxy.datatypes.registry.MDA_zip", "chips":
> "galaxy.datatypes.registry.Text", "gg":
> "galaxy.datatypes.genetics.GenomeGraphs", "syco":
> "galaxy.datatypes.registry.Text",
>
>
>
> 2. I also added a snapshot of the visualization/tool/ sub-directories.
> It shows my extension because I have a format=type in the tool.xml output
> file defition but shows  file type 'binary' at the bottom of the file
> history.   Is this correct, or should it be my extension type there?
>
> Comment -- It appears the only link between the file extension and the
> visualization plugin is via the test line in the /conf/toolxml file.  Is
> that correct?
>
>
>
>
> *My xml in my visualize directory /tool/config/tool.xml     (formatting is
> messed up here) attachment 1*
>
> <?xml version="1.0" encoding="UTF-8" ?>
>
> <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
>
> <visualization name="MDAheatmap">
>
>               <data_sources>
>
>                  <data_source>
>
>
> <model_class>HistoryDatasetAssociation</model_class>
>
>                             <test type="isinstance" test_attr="datatype"
> result_type="datatype">binary.MDA_zip</test>
>
>                                              <to_param
> param_attr="id">dataset_id</to_param>
>
>                             </data_source>
>
>               </data_sources>
>
>               <params>
>
>                                           <param type="dataset"
> var_name_in_template="hda" required="true">dataset_id</param>
>
>               </params>
>
>               <entry_point
> entry_point_type="mako">MDAheatmap.mako</entry_point>
>
> </visualization>
>
>
>
> *My templates/tool.mako file (hello world)*
>
> <!DOCTYPE html PUBLIC "-//IETF//DTD HTML 2.0//EN">
>
> <HTML>
>
>    <HEAD>
>
>      <TITLE>
>
>          A Small Hello
>
>      </TITLE>
>
>    </HEAD>
>
> <BODY>
>
>    <H1>Hi</H1>
>
>    <P>This is very minimal "hello world" HTML document.</P>
>
> </BODY>
>
> </HTML>
>
> *startup info seems successful*
>
> galaxy.web.base.pluginframework INFO 2015-12-14 13:20:09,631
> VisualizationsRegistry, loaded plugin: MDAheatmap
>
> x.x.10.42 - - [14/Dec/2015:14:11:50 -0400] "PUT
> /api/histories/a799d38679e985db/contents/datasets/fb85969571388350
> HTTP/1.1" 200 - "http://xx.xx.10.4:8082/"; "Mozilla/5.0 (Macintosh; Intel
> Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/47.0.2526.80
> Safari/537.36"
>
> *no skipping error and no other apparent errors   in startup*
>
>
>
> *here is my Datatypes.conf.xml 2 additions*
>
>    <datatype extension="MDA_zip" type="galaxy.datatypes.binary:MDA_zip"
> mimetype="application/octet-stream" display_in_upload="true"
> subclass="False">
>
> *and sniffer*
>
>    <sniffer type="galaxy.datatypes.binary:MDA_zip"/>
>
>
>
> *my binary.py addition*
>
> class MDA_zip( Binary ):
>
>    """Class describing an MDA Heatmap binary zip file"""
>
>    file_ext = "MDA_zip"
>
>    def set_peek( self, dataset, is_multi_byte=False ):
>
>        if not dataset.dataset.purged:
>
>            dataset.peek = "Binary MDA_zip sequence file"
>
>            dataset.blurb = nice_size( dataset.get_size() )
>
>        else:
>
>            dataset.peek = 'file MDA_zip does not exist'
>
>            dataset.blurb = 'file MDA_zip purged from disk'
>
>    def display_peek( self, dataset ):
>
>        try:
>
>            return dataset.peek
>
>        except:
>
>            return "Binary MDA_zip heatmap file (%s)" % ( nice_size(
> dataset.get_size() ) )
>
>
>
> Binary.register_sniffable_binary_format("MDA_zip","MDA_zip",MDA_zip)
>
>
>
> *my dataset.py addition*
>
> class MDA_zipDataProvider( base.DataProvider ):
>
> def __init__( self, dataset, **kwards ):
>
>            self.dataset = json.loads( "".join( dataset.readlines() ))
>
>    """
>
>    def __init__( self, dataset, **kwards ):
>
>        raise NotImplementedError()
>
>        super( MDA_zipDataProvider, self ).__init__( dataset, **kwargs )
>
> *My tool in tools dir*
>
> <?xml version="1.0" encoding="UTF-8" ?>
>
> <!DOCTYPE visualization SYSTEM "../../visualization.dtd">
>
> <tool id="MDAheatmap" name="MDA HeatMap" version="1.3.0">
>
> <description>Display HeatMap generated by MDAnderson HeatMap
> tools</description>
>
> <command interpreter="python">MDAheatmap.py $input $out_file </command>
>
> <inputs>
>
>    <param format="text" name="input" type="data" label="doesnt_matter"
> help="input any file and a MDA zipped file pulled off disk"/>
>
> </inputs>
>
> <outputs>
>
>    <data format="MDA_zip" name="out_file"/>
>
> </outputs>
>
> </tool>
>
>
>
>
> ----- Original Message -----
> From: Carl Eberhard <carlfeberh...@gmail.com>
> To: rbrown1...@comcast.net
> Cc: Eric Rasche <e...@tamu.edu>, galaxy-dev <galaxy-...@lists.bx.psu.edu>
> Sent: Mon, 14 Dec 2015 16:40:34 -0000 (UTC)
> Subject: Re: [galaxy-dev] How does one run Javascript or HTML as a tool?
> the complete message ignore previous
> 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"
>>>
>>> in your mail client.  To manage your subscriptions to this
>>>
>>> and other Galaxy lists, please use the interface at:
>>>
>>>   https://lists.galaxyproject.org/
>>>
>>> To search Galaxy mailing lists use the unified search at:
>>>
>>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>>
>> --
>> 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"
>>
>> in your mail client.  To manage your subscriptions to this
>>
>> and other Galaxy lists, please use the interface at:
>>
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>
>>   http://galaxyproject.org/search/mailinglists/
>
> ___________________________________________________________
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