[kepler-users] KAR Command line Fail running with parameters
Daniel Crawl
danielcrawl at gmail.com
Wed Apr 18 20:09:24 PDT 2012
Hi Albert,
You don't need to run "ant force-ptolemy compile" unless you change
any of the source files in the ptolemy module.
String parameters need to be quoted, either "value" or 'value'.
What problems do you have with the parameters? It's easier to
help if you email the workflow.
You can run "kepler -h" to see the command line usage.
--dan
On 4/18/12 9:50 AM, Albert Vilà Picas wrote:
> 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
>>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> Kepler-users mailing listKepler-users at kepler-project.orghttp://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>
>>
>> --
>> 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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