[kepler-dev] Configuration of workflow
guan at sdsc.edu
Mon Jun 26 19:51:46 PDT 2006
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.
guan at sdsc.edu
On Jun 26, 2006, at 2:35 PM, Norbert Podhorszki wrote:
> 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
> And create a script that replaces the parameters' values in the
> 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
> Nice, user-friendly and built-in solution.
> Here I face the problem, that VariableSetter actor cannot accept
> 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 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
> Kepler-dev mailing list
> Kepler-dev at ecoinformatics.org
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