[kepler-dev] [kepler-users] Problems when executing workflow in headless kepler command line using workflow kar file

[Daniel Crawl]

Hi Madhavi,

Which version of Kepler are you using?

In common/resources/configurations/configuration.xml, you should see
the following entries:

<sqlEngines>
   <sqlEngine>
     <sqlEngineName>hsql</sqlEngineName>
     <userName>sa</userName>
     <password> </password>
     <url>jdbc:hsqldb:hsql://localhost/</url>
     <port>9001</port>
     ....
</sqlEngines>


Is your <port> entry empty? If so, try setting it to 9001.

   --dan


> From: Madhavi Tikhe <madhavi_tikhe at persistent.co.in>
> To: Timothy McPhillips <tmcphillips at me.com>, kepler-dev
> <Kepler-dev at ecoinformatics.org>, "kepler-users at kepler-project.org Users"
> <kepler-users at kepler-project.org>
>
>
>
> Hi Tim,
>
> Thanks a lot for reply. No I have not received any other replies on my
> query except you.
>
> As to the first question, it was a typo that there was a ] after nogui
> option.
>
> The error ‘/Unsupported file type..’ /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.
>
> I have debugged the code a bit and found that the /org.kepler.
> KeplerConfigurationApplication at line 173 CacheObjectInterface co =
> CacheManager.getInstance().getObject(lsid); /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.
>
> Regards,
>
> Madhavi
>
> *From:*kepler-dev-bounces at kepler-project.org
> [mailto:kepler-dev-bounces at kepler-project.org] *On Behalf Of *Timothy
> McPhillips
> *Sent:* Thursday, August 25, 2011 4:57 AM
> *To:* kepler-dev; kepler-users at kepler-project.org Users
> *Subject:* Re: [kepler-dev] Problems when executing workflow in headless
> kepler command line using workflow kar file
>
> Hi Madhavi,
>
> 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:
> http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5381.
>
> 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).
>
> In other words, this works:
>
> ./kepler.sh -runwf ~/hello.xml
>
> And this does not:
>
> ./kepler.sh -runwf ~/hello.kar
>
> The error message I get for the latter includes the following line:
>
> / [null] Unsupported file type or connection not available:
> file:/Users/tmcphillips/hello.kar/
>
> Tim
>
> On Aug 22, 2011, at 10:14 PM, Madhavi Tikhe wrote:
>
>
>
> Hi,
>
> When I try run the workflow using the the kar file using kepler command
> line, I get the following exception.
>
> Økepler.sh -runwf -nogui] workflow.kar
>
> Extracting workflow from KAR
>
> java.lang.NullPointerException
>
> at
> org.kepler.util.sql.DatabaseFactory.getDBConnection(DatabaseFactory.java:89)
>
>
> at
> org.kepler.objectmanager.cache.LocalRepositoryManager.<init>(LocalRepositoryManager.java:148)
>
>
> at
> org.kepler.objectmanager.cache.LocalRepositoryManager$LocalRepositoryManagerHolder.<clinit>(LocalRepositoryManager.java:855)
>
>
> at
> org.kepler.objectmanager.cache.LocalRepositoryManager.getInstance(LocalRepositoryManager.java:851)
>
>
> at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:567)
>
> at
> com.lifetech.cgr.service.AnalysisControlManager.getManager(AnalysisControlManager.java:136)
>
>
> at
> com.lifetech.cgr.service.AnalysisControlManager.launchOneAnalaysis(AnalysisControlManager.java:60)
>
>
> at
> com.lifetech.cgr.service.LifeScopeCommandLineServer.manageOperations(LifeScopeCommandLineServer.java:160)
>
>
> at
> com.lifetech.cgr.service.LifeScopeCommandLineServer.run(LifeScopeCommandLineServer.java:121)
>
>
> at java.lang.Thread.run(Thread.java:636)
>
> Exception in thread "Thread-0" java.lang.ExceptionInInitializerError
>
> at
> org.kepler.objectmanager.cache.LocalRepositoryManager.getInstance(LocalRepositoryManager.java:851)
>
>
> at org.kepler.kar.KARFile.cacheKARContents(KARFile.java:567)
>
> at
> com.lifetech.cgr.service.AnalysisControlManager.getManager(AnalysisControlManager.java:136)
>
>
> at
> com.lifetech.cgr.service.AnalysisControlManager.launchOneAnalaysis(AnalysisControlManager.java:60)
>
>
> at
> com.lifetech.cgr.service.LifeScopeCommandLineServer.manageOperations(LifeScopeCommandLineServer.java:160)
>
>
> at
> com.lifetech.cgr.service.LifeScopeCommandLineServer.run(LifeScopeCommandLineServer.java:121)
>
>
> at java.lang.Thread.run(Thread.java:636)
>
> Caused by: java.lang.NullPointerException
>
> at
> org.kepler.objectmanager.cache.LocalRepositoryManager.<init>(LocalRepositoryManager.java:154)
>
>
> at
> org.kepler.objectmanager.cache.LocalRepositoryManager$LocalRepositoryManagerHolder.<clinit>(LocalRepositoryManager.java:855)
>
>
> ... 7 more
>
> 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?
>
> This exception is blocking my work. Please let me know if there is any
> quick fix available.
>
> Regards,
>
> Madhavi
>
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