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<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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