[kepler-users] KAR Command line Fail running with parameters
Christopher Brooks
cxh at eecs.berkeley.edu
Tue Apr 17 15:47:08 PDT 2012
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
> <mailto: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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--
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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