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 <danielcr...@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<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<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 <Kepler-users@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@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 >>> >>> >>> >> >
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