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

[Madhavi Tikhe]

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.
>   kepler.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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