Hi,<div><br></div><div>well, with ptolemy there are no specific problems. With Ubuntu and Mac I have</div><div>downloaded the source from
<p class="p1"><a href="https://code.kepler-project.org/code/kepler/trunk/modules/build-area">https://code.kepler-project.org/code/kepler/trunk/modules/build-area</a></p><p class="p1">and compiled with </p><p class="p1">
</p><p class="p1">ant change-to -<span class="s1">Dsuite</span>=reporting</p>
<p class="p1">ant compile</p><p></p><div>and there many warnings that say: you may compile ptolemy with: ant force-ptolemy compile</div><div>and it reappears but don't fail. Sorry, I don't know how it works, but thanks for the appointment.</div>
<div><br></div><div><br></div><div>Dan, again!</div><div>I have some troubles with the command line execution with parameters.</div><div>It doesn't work with some type of parameters or maybe multiple.</div><div>With non-integer params what should I do? with simple comas like 'value' ?</div>
<div><br></div><div>-Integer 1</div><div>-String "value words"</div><div>-Decimals 0.85</div><div><br></div><div>Sorry, where I can find this information clearly?</div><div><br></div><div>Thanks a lot once again!</div>
<div>--Albert</div><div><br></div><div><br></div><br><div class="gmail_quote">2012/4/18 Christopher Brooks <span dir="ltr"><<a href="mailto:cxh@eecs.berkeley.edu">cxh@eecs.berkeley.edu</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
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 has<br>
<!-- Add support for exporting PDFs. --><br>
<!-- Used in BasicGraphFrame.java --><br>
<property name="_exportPDFActionClassName"<br>
class="ptolemy.data.expr.StringParameter"<br>
value="ptolemy.vergil.basic.export.itextpdf.ExportPDFAction"/><br>
<br>
and com.itextpdf.text.Document is in the path.<br>
$PTII/configure looks for<br>
$PTII/vendors/misc/itext/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 tree, see<br>
<a href="http://chess.eecs.berkeley.edu/ptexternal" target="_blank">http://chess.eecs.berkeley.edu/ptexternal</a><br>
<br>
_Christopher<div><div class="h5"><br>
<br>
<br>
On 4/17/12 11:48 AM, Albert Vilą Picas wrote:
<blockquote type="cite">Great job Dan!
<div><br>
</div>
<div>It works! Thank you a lot again! The revision 29738 is ok.</div>
<div>I have some R warnings and with Ptolemy at revision 63376 I
still have some troubles with ant force-ptolemy compile</div>
<div>but the generation of the PDF is doing it as well.</div>
<div><br>
</div>
<div><br>
</div>
<div>If I have new suggestions or problems I'll notice them.</div>
<div>Thanks!</div>
<div><br>
</div>
<div>Albert<br>
<br>
<div class="gmail_quote">
2012/4/17 Daniel Crawl <span dir="ltr"><<a href="mailto:danielcrawl@gmail.com" target="_blank">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>
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
<div>
<div><br>
<br>
<br>
On 4/17/12 5:57 AM, Josep Maria Campanera Alsina wrote:<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 -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 project<br>
with Kepler<br>
and is necessary to run command line kar wf
changing the value of 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 class<br>
org.kepler.module.reporting.Initialize<br>
[null] loading: org.kepler.KeplerConfigurationApplication
args:<br>
ptolemy/configs/kepler/ConfigNoGUIWithCache.xml
-runThenExit -epochs 100<br>
/home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar<br>
[null] invoking: org.kepler.KeplerConfigurationApplication.main<br>
[null] Kepler Initializing...<br>
[null] Unsupported file type or connection
not available:<br>
<a>file:/home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar</a><br>
[null] Command failed<br>
[null] java.lang.Exception: Failed to parse<br>
"ptolemy/configs/kepler/ConfigNoGUIWithCache.xml
-runThenExit -epochs 100<br>
/home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar"<br>
[null] at<br>
ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:791)<br>
[null] at<br>
org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:339)<br>
[null] at<br>
org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:639)<br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)<br>
[null] at<br>
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)<br>
[null] at<br>
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)<br>
[null] at java.lang.reflect.Method.invoke(Method.java:616)<br>
[null] at org.kepler.Kepler.load(Kepler.java:445)<br>
...<br>
<br>
Note that with the same workflow.kar without
parameters runs 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>
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</blockquote>
<br>
</div>
</div>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
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</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">--
Christopher Brooks, PMP University of California
CHESS Executive Director US Mail: 337 Cory Hall
Programmer/Analyst CHESS/Ptolemy/Trust Berkeley, CA <a href="tel:94720-1774" value="+34947201774" target="_blank">94720-1774</a>
ph: 510.643.9841 (Office: 545Q Cory)
home: (F-Tu) 707.665.0131 cell: 707.332.0670 </pre>
</font></span></div>
</blockquote></div><br></div>