[kepler-users] KAR Command line Fail running with parameters

[Daniel Crawl]

I fixed the problem and you can now specify parameters when
executing KAR workflows:

kepler -runkar -nogui [-param1 value1 ...] workflow.kar

   --dan


On 4/17/12 5:57 AM, Josep Maria Campanera Alsina wrote:
> Dear All,
> This is Josep M. Campanera who has been using kepler for
> bioinformatics. Now I'm developing with Albert Vilà (and others) a web
> front-end for kepler that we will make available once the first tests
> are satisfactory. Additionally we are also developing a perl actor for
> kepler.
>
> As mentioned by Albert, It is crucial the command line execution with
> parameters of kar files for continuing our project. Dan says that
> there is a bug which impedes the execution of kar files by means of
> command line execution with parameters. In line with Dan's comments,
> we would like to know aproximately when  this bug is going to be
> fixed.
>
> 1) Are you thinking of days, weeks or months?
>
> 2) In case we need to wait for a long period, which is the best
> strategy to surpass that drawback meanwhile?
>
> Thank you very much,
>
> Josep M. Campanera,
>
>
> Hi Albert,
>
> I'll look into fixing this. It would be nice to have a consistent set of
> command-line options for executing momls and kars.
>
>    --dan
>
>
> On 4/16/12 3:00 AM, Albert Vilà Picas wrote:
>
>      Hi all,
>
>      I have read in other e-mails that now is not possible to execute .kar
>      workflows with parameters?
>      We run a command line KAR with reporting layout added running -runwf -nogui
>      [-param value]*.
>      I have tried also with -runkar and I have the same error.
>      Is that a Ptolemy error that is not suitable? We're doing a great project
>      with Kepler
>      and is necessary to run command line kar wf changing the value of the input
>      parameters.
>
>      Here is the stack trace:
>
>            [null] common tabpane configuration overridden by reporting
>            [null] Ran additional initialization for module reporting from class
>      org.kepler.module.reporting.Initialize
>            [null] loading: org.kepler.KeplerConfigurationApplication args:
>      ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -epochs 100
>      /home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar
>            [null] invoking: org.kepler.KeplerConfigurationApplication.main
>            [null] Kepler Initializing...
>            [null] Unsupported file type or connection not available:
>      file:/home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar
>            [null] Command failed
>            [null] java.lang.Exception: Failed to parse
>      "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -epochs 100
>      /home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar"
>            [null]  at
>      ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:791)
>            [null]  at
>      org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:339)
>            [null]  at
>      org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:639)
>            [null]  at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>            [null]  at
>      sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>            [null]  at
>      sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>            [null]  at java.lang.reflect.Method.invoke(Method.java:616)
>            [null]  at org.kepler.Kepler.load(Kepler.java:445)
>      ...
>
>      Note that with the same workflow.kar without parameters runs perfectly
>      keeping the results and generating the .PDF from reporting.
>      We need that the workflow must be a .kar and not an .xml
>
>      Thank you very much
>
>      --Albert
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