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<div class=Section1>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Tim,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Thanks a lot for reply. No I have not received any other replies
on my query except you.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>As to the first question, it was a typo that there was a ] after
nogui option. <o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>The error ‘</span><i>Unsupported file type..’ </i><span
style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>that
you are facing may be because of the in-compatibility between versions if you
have not created the kar file using the same version of kepler you are using to
run it. I am not so sure about this point but I have not seen this error.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif";color:#1F497D'>I have debugged the code a
bit and found that the </span><i>org.kepler. KeplerConfigurationApplication at line
173 CacheObjectInterface co = CacheManager.getInstance().getObject(lsid);
</i><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>is throwing the NPE while getting the object. This is because
kepler is not able to insert my kar file in its local repository because of the
db exception I am getting. Please let me know if you have any luck solving the
problem. Thanks a lot again for replying to my mails.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Regards,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Madhavi<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<div>
<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in'>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>
kepler-dev-bounces@kepler-project.org
[mailto:kepler-dev-bounces@kepler-project.org] <b>On Behalf Of </b>Timothy
McPhillips<br>
<b>Sent:</b> Thursday, August 25, 2011 4:57 AM<br>
<b>To:</b> kepler-dev; kepler-users@kepler-project.org Users<br>
<b>Subject:</b> Re: [kepler-dev] Problems when executing workflow in headless
kepler command line using workflow kar file<o:p></o:p></span></p>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
<div>
<div>
<p class=MsoNormal>Hi Madhavi,<o:p></o:p></p>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Can you run your workflow from the command line if it is
exported as xml, rather than saved as a kar file? There is a
possibly related bug for the build system in bugzilla: <a
href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5381">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5381</a>.<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>I just tried running a simple workflow from the command line
using Kepler 2.2, and got an error (different from yours--see below) when
trying to run a kar, but success when running a workflow exported as xml
(moml). <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>In other words, this works: <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>./kepler.sh -runwf ~/hello.xml <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>And this does not:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<div>
<p class=MsoNormal>./kepler.sh -runwf ~/hello.kar <o:p></o:p></p>
</div>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>The error message I get for the latter includes the
following line:<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<div>
<p class=MsoNormal><i> [null] Unsupported file type or
connection not available: file:/Users/tmcphillips/hello.kar</i><o:p></o:p></p>
</div>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>Tim<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<p class=MsoNormal>On Aug 22, 2011, at 10:14 PM, Madhavi Tikhe wrote:<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
<div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Hi,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>When
I try run the workflow using the the kar file using kepler command line, I get
the following exception.<o:p></o:p></span></p>
</div>
<div style='margin-left:.5in'>
<p class=MsoNormal style='text-indent:-.25in'><span style='font-size:11.0pt;
font-family:Wingdings'>Ø</span><span style='font-size:7.0pt'> <span
class=apple-converted-space> </span></span><span style='font-size:11.0pt;
font-family:"Calibri","sans-serif"'> <span class=highlightedsearchterm>kepler</span>.sh
-runwf -<span class=highlightedsearchterm>nogui</span>] workflow.kar<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Extracting
workflow from KAR<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>java.lang.NullPointerException<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at org.kepler.util.sql.DatabaseFactory.getDBConnection(DatabaseFactory.java:89)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
org.kepler.objectmanager.cache.LocalRepositoryManager.<init>(LocalRepositoryManager.java:148)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at org.kepler.objectmanager.cache.LocalRepositoryManager$LocalRepositoryManagerHolder.<clinit>(LocalRepositoryManager.java:855)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
org.kepler.objectmanager.cache.LocalRepositoryManager.getInstance(LocalRepositoryManager.java:851)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:567)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at com.lifetech.cgr.service.AnalysisControlManager.getManager(AnalysisControlManager.java:136)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
com.lifetech.cgr.service.AnalysisControlManager.launchOneAnalaysis(AnalysisControlManager.java:60)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at com.lifetech.cgr.service.LifeScopeCommandLineServer.manageOperations(LifeScopeCommandLineServer.java:160)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
com.lifetech.cgr.service.LifeScopeCommandLineServer.run(LifeScopeCommandLineServer.java:121)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at java.lang.Thread.run(Thread.java:636)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Exception
in thread "Thread-0" java.lang.ExceptionInInitializerError<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
org.kepler.objectmanager.cache.LocalRepositoryManager.getInstance(LocalRepositoryManager.java:851)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:567)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
com.lifetech.cgr.service.AnalysisControlManager.getManager(AnalysisControlManager.java:136)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
com.lifetech.cgr.service.AnalysisControlManager.launchOneAnalaysis(AnalysisControlManager.java:60)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at com.lifetech.cgr.service.LifeScopeCommandLineServer.manageOperations(LifeScopeCommandLineServer.java:160)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
com.lifetech.cgr.service.LifeScopeCommandLineServer.run(LifeScopeCommandLineServer.java:121)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at java.lang.Thread.run(Thread.java:636)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Caused
by: java.lang.NullPointerException<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
org.kepler.objectmanager.cache.LocalRepositoryManager.<init>(LocalRepositoryManager.java:154)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
at
org.kepler.objectmanager.cache.LocalRepositoryManager$LocalRepositoryManagerHolder.<clinit>(LocalRepositoryManager.java:855)<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>
... 7 more<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>I
don’t have any database installed or configured for kepler. And I tried
executing kepler after clearing the kepler cache. Does anybody have any idea
about the possible cause of this exception and possible solution?<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>This
exception is blocking my work. Please let me know if there is any quick fix
available.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Regards,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'>Madhavi<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif"'> <o:p></o:p></span></p>
</div>
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