[kepler-users] KAR Command line Fail running with parameters
Albert Vilà Picas
albertvilapicas at gmail.com
Thu Apr 19 15:03:06 PDT 2012
Thanks Dan!
We'd have an error in a curious parameter, it runs perfectly.
I have seen also the -vergil option for cmd line, great!
Next week I'll try to create actors. Fantastic work :)
--albert
2012/4/19 Daniel Crawl <danielcrawl at gmail.com>
>
> 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<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<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 <Kepler-users at kepler-project.org>
>>>>> http://lists.nceas.ucsb.edu/**kepler/mailman/listinfo/**kepler-users<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<http://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
>>>
>>>
>>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/attachments/20120420/4d75d2d8/attachment.html>
More information about the Kepler-users
mailing list