[kepler-users] KAR Command line Fail running with parameters
Albert Vilà Picas
albertvilapicas at gmail.com
Wed Apr 18 09:50:31 PDT 2012
Hi,
well, with ptolemy there are no specific problems. With Ubuntu and Mac I
have
downloaded the source from
https://code.kepler-project.org/code/kepler/trunk/modules/build-area
and compiled with
ant change-to -Dsuite=reporting
ant compile
and there many warnings that say: you may compile ptolemy with: ant
force-ptolemy compile
and it reappears but don't fail. Sorry, I don't know how it works, but
thanks for the appointment.
Dan, again!
I have some troubles with the command line execution with parameters.
It doesn't work with some type of parameters or maybe multiple.
With non-integer params what should I do? with simple comas like 'value' ?
-Integer 1
-String "value words"
-Decimals 0.85
Sorry, where I can find this information clearly?
Thanks a lot once again!
--Albert
2012/4/18 Christopher Brooks <cxh at eecs.berkeley.edu>
> I'm just curious, what are the problems with ant force-ptolemy compile?
>
> Also, Ptolemy has and Export PDF feature that works if the configuration
> has
> <!-- Add support for exporting PDFs. -->
> <!-- Used in BasicGraphFrame.java -->
> <property name="_exportPDFActionClassName"
> class="ptolemy.data.expr.StringParameter"
> value="ptolemy.vergil.basic.export.itextpdf.ExportPDFAction"/>
>
> and com.itextpdf.text.Document is in the path.
> $PTII/configure looks for
> $PTII/vendors/misc/itext/iText.jar
>
> iText.jar is AGPL'd, which is why it is not part of the default.
>
> To experiment with this, I suggest downloading the Ptolemy II development
> tree, see
> http://chess.eecs.berkeley.edu/ptexternal
>
> _Christopher
>
>
>
> On 4/17/12 11:48 AM, Albert Vilà Picas wrote:
>
> 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
>>> _______________________________________________
>>> Kepler-users mailing list
>>> Kepler-users at kepler-project.org
>>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>>
>>
>>
>
>
> _______________________________________________
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>
>
> --
> Christopher Brooks, PMP University of California
> CHESS Executive Director US Mail: 337 Cory Hall
> Programmer/Analyst CHESS/Ptolemy/Trust Berkeley, CA 94720-1774
> ph: 510.643.9841 (Office: 545Q Cory)
> home: (F-Tu) 707.665.0131 cell: 707.332.0670
>
>
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