To afternoon team,
I have a plugin that is visualization a static output. I want to retrieve the
dataset id for the file I want to visualize when the lower left visualize icon
is clicked. I see 'hda' is passed around in other plugins including.
hda.name. Is hda an object? What attributes does it have. Or is there
another way to retrieve the dataset id. I seem to see an encoded Id when the
mako is called but cannot decipher it.
Thanks
Bob
1. I 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="extension"
result_type="datatype">registry.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:
rbrown1422@comcast.netCc: 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:
rbrown1422@comcast.netCc: 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 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
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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"
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/
___________________________________________________________
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/
