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

[Albert Vilà Picas]

Great job Dan!

It works! Thank you a lot again! The revision 29738 is ok.
I have some R warnings and with Ptolemy at revision 63376 I still have some
troubles with ant force-ptolemy compile
but the generation of the PDF is doing it as well.


If I have new suggestions or problems I'll notice them.
Thanks!

Albert

2012/4/17 Daniel Crawl <danielcrawl at gmail.com>

>
> 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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>>
>
>
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