Thanks Dan!<div><br></div><div>We'd have an error in a curious parameter, it runs perfectly.</div><div>I have seen also the -vergil option for cmd line, great!</div><div><br></div><div>Next week I'll try to create actors. Fantastic work :)</div>
<div><br></div><div>--albert<br><br><div class="gmail_quote">2012/4/19 Daniel Crawl <span dir="ltr"><<a href="mailto:danielcrawl@gmail.com">danielcrawl@gmail.com</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi Albert,<br>
<br>
You don't need to run "ant force-ptolemy compile" unless you change<br>
any of the source files in the ptolemy module.<br>
<br>
String parameters need to be quoted, either "value" or 'value'.<br>
What problems do you have with the parameters? It's easier to<br>
help if you email the workflow.<br>
<br>
You can run "kepler -h" to see the command line usage.<br>
<br>
--dan<div><div class="h5"><br>
<br>
<br>
<br>
On 4/18/12 9:50 AM, Albert Vilą Picas wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi,<br>
<br>
well, with ptolemy there are no specific problems. With Ubuntu and Mac I<br>
have<br>
downloaded the source from<br>
<br>
<a href="https://code.kepler-project.org/code/kepler/trunk/modules/build-area" target="_blank">https://code.kepler-project.<u></u>org/code/kepler/trunk/modules/<u></u>build-area</a><br>
<br>
and compiled with<br>
<br>
ant change-to -Dsuite=reporting<br>
<br>
ant compile<br>
<br>
and there many warnings that say: you may compile ptolemy with: ant<br>
force-ptolemy compile<br>
and it reappears but don't fail. Sorry, I don't know how it works, but<br>
thanks for the appointment.<br>
<br>
<br>
Dan, again!<br>
I have some troubles with the command line execution with parameters.<br>
It doesn't work with some type of parameters or maybe multiple.<br>
With non-integer params what should I do? with simple comas like 'value' ?<br>
<br>
-Integer 1<br>
-String "value words"<br>
-Decimals 0.85<br>
<br>
Sorry, where I can find this information clearly?<br>
<br>
Thanks a lot once again!<br>
--Albert<br>
<br>
<br>
<br>
2012/4/18 Christopher Brooks<<a href="mailto:cxh@eecs.berkeley.edu" target="_blank">cxh@eecs.berkeley.edu</a>><br>
<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
I'm just curious, what are the problems with ant force-ptolemy compile?<br>
<br>
Also, Ptolemy has and Export PDF feature that works if the configuration<br>
has<br>
<!-- Add support for exporting PDFs. --><br>
<!-- Used in BasicGraphFrame.java --><br>
<property name="_<u></u>exportPDFActionClassName"<br>
class="ptolemy.data.expr.<u></u>StringParameter"<br>
value="ptolemy.vergil.basic.<u></u>export.itextpdf.<u></u>ExportPDFAction"/><br>
<br>
and com.itextpdf.text.Document is in the path.<br>
$PTII/configure looks for<br>
$PTII/vendors/misc/itext/<u></u>iText.jar<br>
<br>
iText.jar is AGPL'd, which is why it is not part of the default.<br>
<br>
To experiment with this, I suggest downloading the Ptolemy II development<br>
tree, see<br>
<a href="http://chess.eecs.berkeley.edu/ptexternal" target="_blank">http://chess.eecs.berkeley.<u></u>edu/ptexternal</a><br>
<br>
_Christopher<br>
<br>
<br>
<br>
On 4/17/12 11:48 AM, Albert Vilą Picas wrote:<br>
<br>
Great job Dan!<br>
<br>
It works! Thank you a lot again! The revision 29738 is ok.<br>
I have some R warnings and with Ptolemy at revision 63376 I still have<br>
some troubles with ant force-ptolemy compile<br>
but the generation of the PDF is doing it as well.<br>
<br>
<br>
If I have new suggestions or problems I'll notice them.<br>
Thanks!<br>
<br>
Albert<br>
<br>
2012/4/17 Daniel Crawl<<a href="mailto:danielcrawl@gmail.com" target="_blank">danielcrawl@gmail.com</a>><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
I fixed the problem and you can now specify parameters when<br>
executing KAR workflows:<br>
<br>
kepler -runkar -nogui [-param1 value1 ...] workflow.kar<br>
<br>
--dan<br>
<br>
<br>
<br>
On 4/17/12 5:57 AM, Josep Maria Campanera Alsina wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear All,<br>
This is Josep M. Campanera who has been using kepler for<br>
bioinformatics. Now I'm developing with Albert Vilą (and others) a web<br>
front-end for kepler that we will make available once the first tests<br>
are satisfactory. Additionally we are also developing a perl actor for<br>
kepler.<br>
<br>
As mentioned by Albert, It is crucial the command line execution with<br>
parameters of kar files for continuing our project. Dan says that<br>
there is a bug which impedes the execution of kar files by means of<br>
command line execution with parameters. In line with Dan's comments,<br>
we would like to know aproximately when this bug is going to be<br>
fixed.<br>
<br>
1) Are you thinking of days, weeks or months?<br>
<br>
2) In case we need to wait for a long period, which is the best<br>
strategy to surpass that drawback meanwhile?<br>
<br>
Thank you very much,<br>
<br>
Josep M. Campanera,<br>
<br>
<br>
Hi Albert,<br>
<br>
I'll look into fixing this. It would be nice to have a consistent set of<br>
command-line options for executing momls and kars.<br>
<br>
--dan<br>
<br>
<br>
On 4/16/12 3:00 AM, Albert Vilą Picas wrote:<br>
<br>
Hi all,<br>
<br>
I have read in other e-mails that now is not possible to execute .kar<br>
workflows with parameters?<br>
We run a command line KAR with reporting layout added running -runwf<br>
-nogui<br>
[-param value]*.<br>
I have tried also with -runkar and I have the same error.<br>
Is that a Ptolemy error that is not suitable? We're doing a great<br>
project<br>
with Kepler<br>
and is necessary to run command line kar wf changing the value of<br>
the input<br>
parameters.<br>
<br>
Here is the stack trace:<br>
<br>
[null] common tabpane configuration overridden by reporting<br>
[null] Ran additional initialization for module reporting from<br>
class<br>
org.kepler.module.reporting.<u></u>Initialize<br>
[null] loading: org.kepler.<u></u>KeplerConfigurationApplication args:<br>
ptolemy/configs/kepler/<u></u>ConfigNoGUIWithCache.xml -runThenExit -epochs<br>
100<br>
/home/sbi/sbi-services/sbi-<u></u>home/Temporal/MLRAlbert.kar<br>
[null] invoking: org.kepler.<u></u>KeplerConfigurationApplication<u></u>.main<br>
[null] Kepler Initializing...<br>
[null] Unsupported file type or connection not available:<br>
file:/home/sbi/sbi-services/<u></u>sbi-home/Temporal/MLRAlbert.<u></u>kar<br>
[null] Command failed<br>
[null] java.lang.Exception: Failed to parse<br>
"ptolemy/configs/kepler/<u></u>ConfigNoGUIWithCache.xml -runThenExit<br>
-epochs 100<br>
/home/sbi/sbi-services/sbi-<u></u>home/Temporal/MLRAlbert.kar"<br>
[null] at<br>
<br>
ptolemy.actor.gui.<u></u>ConfigurationApplication.<u></u>throwArgsException(<u></u>ConfigurationApplication.java:<u></u>791)<br>
[null] at<br>
<br>
org.kepler.<u></u>KeplerConfigurationApplication<u></u>.<init>(<u></u>KeplerConfigurationApplication<u></u>.java:339)<br>
[null] at<br>
<br>
org.kepler.<u></u>KeplerConfigurationApplication<u></u>.main(<u></u>KeplerConfigurationApplication<u></u>.java:639)<br>
[null] at sun.reflect.<u></u>NativeMethodAccessorImpl.<u></u>invoke0(Native<br>
Method)<br>
[null] at<br>
<br>
sun.reflect.<u></u>NativeMethodAccessorImpl.<u></u>invoke(<u></u>NativeMethodAccessorImpl.java:<u></u>57)<br>
[null] at<br>
<br>
sun.reflect.<u></u>DelegatingMethodAccessorImpl.<u></u>invoke(<u></u>DelegatingMethodAccessorImpl.<u></u>java:43)<br>
[null] at java.lang.reflect.Method.<u></u>invoke(Method.java:616)<br>
[null] at org.kepler.Kepler.load(Kepler.<u></u>java:445)<br>
...<br>
<br>
Note that with the same workflow.kar without parameters runs<br>
perfectly<br>
keeping the results and generating the .PDF from reporting.<br>
We need that the workflow must be a .kar and not an .xml<br>
<br>
Thank you very much<br>
<br>
--Albert<br>
______________________________<u></u>_________________<br>
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<br>
</blockquote>
<br>
<br>
</blockquote>
<br>
<br>
______________________________<u></u>_________________<br></div></div>
Kepler-users mailing listKepler-users@kepler-<u></u>project.orghttp://<a href="http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users" target="_blank">lists.nceas.<u></u>ucsb.edu/kepler/mailman/<u></u>listinfo/kepler-users</a><div class="im">
<br>
<br>
<br>
--<br>
Christopher Brooks, PMP University of California<br>
CHESS Executive Director US Mail: 337 Cory Hall<br>
Programmer/Analyst CHESS/Ptolemy/Trust Berkeley, CA <a href="tel:94720-1774" value="+34947201774" target="_blank">94720-1774</a><br>
ph: 510.643.9841 (Office: 545Q Cory)<br>
home: (F-Tu) 707.665.0131 cell: 707.332.0670<br>
<br>
<br>
</div></blockquote>
<br>
</blockquote>
<br>
</blockquote></div><br></div>