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 <c...@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 <danielcr...@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@kepler-project.org >>> http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users >>> >> >> > > > _______________________________________________ > Kepler-users mailing > listKepler-users@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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