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">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 class="HOEnZb"><div class="h5"><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.<u></u>Initialize<br>
[null] loading: org.kepler.<u></u>KeplerConfigurationApplication args:<br>
ptolemy/configs/kepler/<u></u>ConfigNoGUIWithCache.xml -runThenExit -epochs 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 -epochs 100<br>
/home/sbi/sbi-services/sbi-<u></u>home/Temporal/MLRAlbert.kar"<br>
[null] at<br>
ptolemy.actor.gui.<u></u>ConfigurationApplication.<u></u>throwArgsException(<u></u>ConfigurationApplication.java:<u></u>791)<br>
[null] at<br>
org.kepler.<u></u>KeplerConfigurationApplication<u></u>.<init>(<u></u>KeplerConfigurationApplication<u></u>.java:339)<br>
[null] at<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 Method)<br>
[null] at<br>
sun.reflect.<u></u>NativeMethodAccessorImpl.<u></u>invoke(<u></u>NativeMethodAccessorImpl.java:<u></u>57)<br>
[null] at<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 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>
Kepler-users mailing list<br>
<a href="mailto:Kepler-users@kepler-project.org" target="_blank">Kepler-users@kepler-project.<u></u>org</a><br>
<a href="http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users" target="_blank">http://lists.nceas.ucsb.edu/<u></u>kepler/mailman/listinfo/<u></u>kepler-users</a><br>
</blockquote>
<br>
</div></div></blockquote></div><br></div>