Yes, you can still use the framework to create interactive python-only
visualizations. The simplest way to do this is form-based interaction.
1. The visualization mako page renders a form that contains the options the
user can choose from
2. The user chooses and submits the form
3. Galaxy will re-render the visualization mako and now, since those
options are passed as parameters, the chosen visualization can be rendered
So you can render the form with your options:
%if not query.get( 'param2', None ):
## initial render of form
form
input name=param2 /
input name=param3 /
input name=param4 /
button type=submitDraw/button
/form
%else:
## second render drawing with param2
...
Note: this will default to a GET based form whose 'action' url will be the
visualization's url. Any html5 form based controls will work: radio
buttons, ranges, etc.
When the user submits the form, each of the params, will now be part of the
query string when the mako renders the second time:
/visualization/show/myvis?param2=somethingparam3=...
You can then use these params to call your python code with the user chosen
options:
arg2 = query.get( 'param2', default )
arg3 = query.get( 'param3', ...
from draw import main
returned = main( arg2, arg3, ... )
svg
${ returned }
/svg
(or something similar)
Other things that may help?:
- you can use action=post if you want to post data instead of get -
handy for larger parameters
- try to not bootstrap/load all your data into the mako file as this
will be re-fetched everytime the form is re-submitted
- you can add the arg2, arg3, etc. params to the config file and the
registry will parse those for you and put them in the template's 'config'
variable, e.g.: int_param2 = config.param2
- when using these query/form parameters you can now save/generate urls
that will auto-start your visualizations since all the configuration
options are sent in the url
Let me know if I can give more info or that doesn't end up working.
On Wed, Aug 19, 2015 at 9:30 AM, Anne Claire Fouilloux
a.c.fouill...@geo.uio.no wrote:
Hi Carl,
Yes I have a python code to manipulate and draw the data (it creates svg
files and I wish to add this visualization tool to my galaxy instance:
Let's say my composite datatype contains 3 files:
-file1.dat
-file2.dat
-file3.dat
My python code takes 4 arguments (for instance draw.py arg1 arg2 arg3
arg4).
arg1: The first argument is a path giving the location of these 3 files.
arg2, arg3 and arg4 are list of options. These lists are dynamic as they
depend on the content of these 3 files.
Once the user has selected some options, I have a draw button and would
like the python script draw.py to be executed and generate a plot.
Your answer was very helpful; at least it clarifies a number of things.
Now I understood I can access to these files using hda.extra_files_path in
my mako file:
%
composite_file_path=hda.extra_files_path + '/' + date + '/'
%
Which is helpful to generate my select buttons (for arg2, arg3 and arg4)
as I fist need to read the content of these files for the generation of
these buttons.
I still need to call my python script with the option chosen by the user.
Is it something I can easily do with galaxy?
Thanks,
Anne.
--
*From:* Carl Eberhard carlfeberh...@gmail.com
*Sent:* 18 August 2015 18:59
*To:* Anne Claire Fouilloux
*Cc:* galaxy-dev@lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] new visualization tool for composite datatype?
Hi, Anne
Can you be more specific about how you'd like to visualize the files? It
sounds like you've already got a tool that will build an html file which is
the classic way to make visualizations with galaxy.
Now you'd like to make it more interactive? Do you already have javascript
or python code that will be used to manipulate or draw the data? The
visualization registry will help you link a user's data to your
visualization code but will not create the code that does the rendering or
interaction.
Aside from that, if you know the structure and filenames of your
composite's extra files directory, currently you can access those files
using:
api/histories/{history_id}/contents/{content_id}/display?filename=some
file
The meme type will be guessed based on the extension generally and more
complex paths can also be specified using the filename parameter.
So, for example, if I have a FastQC Html composite file with an extra
files path of:
database/files/000/dataset_83_files
And within that directory, fastqc makes an additional subdirectory:
sample1_fastqc/Icons
sample1_fastqc/Images
sample1_fastqc/summary.txt
I can fetch the summary.txt file (with the 'text/plain' memetype) using:
api/histories/{history_id}/contents/{content_id}/display?filename=sample1_fastqc/summary.txt
Let me know if that wasn't the info you were after or I misunderstood the
question.
Carl
On Fri, Aug
