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="submit">Draw</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=something¶m3=... 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 14, 2015 at 7:50 AM, Anne Claire Fouilloux < > a.c.fouill...@geo.uio.no> wrote: > >> Hi, >> >> >> I created a new composite datatype (class derived from Html class) >> myDatatype and I sucessfully use it in a new created tool. >> >> >> When I click on "View data" it shows my Html file with a list of binary >> files and everything is Ok. >> >> >> Now I would like to Visualize my data. I created a new directory in >> >> galaxy-dist/config/plugins/visualizations/ following instructions given >> at >> >> https://wiki.galaxyproject.org/VisualizationsRegistry and read >> >> https://wiki.galaxyproject.org/VisualizationsRegistry/Configuration and >> >> https://wiki.galaxyproject.org/DataProviders >> >> >> However, I still don't understand what I should do to be able to access >> files from my composite datatype to be able to visualize myDatatype (I mean >> I need to visualize the files containing in the directory listed by the >> html file). >> >> >> Is it possible? Where can I find some information on how to do it? >> >> >> Thanks, >> >> >> Anne. >> >> >> >> ___________________________________________________________ >> Please keep all replies on the list by using "reply all" >> in your mail client. 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