[kepler-dev] Configuration of workflow

Zhijie Guan guan at sdsc.edu
Mon Jun 26 19:51:46 PDT 2006

Hi Norbert,

You may like to check the GUIGen used in CIPRes workflows.  
Unfortunately you cannot run cipres workflows on your machine right  
now, since all of the required external software may not be present  
in your environment. But I would like to share with you what the  
GUIGen can do in this email.

Basically GUIGen is designed to read from a configuration XML file,  
get all the parameters that need to be set, fill them into an user  
interface automatically, pop up that interface to the user, let the  
user set the parameters before running the program, and generate a  
command block for the program that can take in command block as input  
parameters. Some XML configuration files for some legacy applications  
in bioinformatics research could be found in $KEPLER/configs/ptolemy/ 
configs/kepler/cipres/gui/. The parameter-setting dialog generated by  
GUIGen is usually invoked at the first part of the fire() function in  
the actor. This enables the users to set the necessary parameters for  
the program that the actor represents for.

I assume if you write your own configuration file, following the  
format GUIGen defined, GUIGen should be able to automatically  
generate a GUI for the user to set parameters for your program. You  
can set the parameter to be displayed as checkbox, combobox, or file/ 
directory chooser. You can also specify the default values for the  
parameters in your configuration file, and control which parameter  
should be visiable/editable in the GUI. You can also set the program  
to run several iterations and for each iteration, a different  
parameter set is  fed to the program. Some other functions are under  
development for GUIGen.

I would like to treat GUIGen as the extension of the parameter  
setting dialog in Kepler, specially for setting a bunch of  
parameters  for legacy applications. If you like, I can get the  
source code of GUIGen for you (it's open source too). Just let me  
know if it is what you want.

Zhijie Guan
guan at sdsc.edu

On Jun 26, 2006, at 2:35 PM, Norbert Podhorszki wrote:

> Hi,
> We have a workflow with lots of StringParameters and the user
> executes it command-line (without GUI).
> I am looking for ways to conveniently use a configuration file for the
> workflow. Does anyone have a workflow that takes parameters from file?
> Option 1.
> Edit the workflow's xml file, for the StringParameter properties.
> Ugly and user-hately.
> Option 2.
> Have a config file with format
>     name=value
>     name=value
>     ...
> And create a script that replaces the parameters' values in the  
> workflow's
> xml before running it.
> Modestly-ugly but efficient and physicist-user-friendly.
> Option 3.
> Create a subworkflow to read the config file and set variables  
> within the
> workflow. This subworkflow should go in front of the rest of the  
> workflow.
> Nice, user-friendly and built-in solution.
> Here I face the problem, that VariableSetter actor cannot accept  
> variable
> names, only the values. Is there any solution in Ptolemy/Kepler?
> Option 4.
> Native Ptolemy/Kepler support...? E.g. an actor written in Java.
> Thanks in advance for advice or more options
> Norbert
> -- 
>       Norbert Podhorszki
>     ------------------------------------
>       University of California, Davis
>       Department of Computer Science
>       1 Shields Ave, 2236 Kemper Hall
>       Davis, CA 95616
>       (530) 754-8188
>       pnorbert at cs.ucdavis.edu
>       ----------------------------------
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