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

Wed Aug 31 14:22:31 PDT 2011

Hi Madhavi,

You could try renaming ~/KeplerData/modules to something else (in case
it contains a bad configuration file) or getting the latest Kepler from
svn.

   --dan

On 8/30/11 10:20 PM, Madhavi Tikhe wrote:
> Hi Dan
> The entry you suggested seems right in my kepler.
> It is
>    <sqlEngines>
>      <sqlEngine>
>        <sqlEngineName>hsql</sqlEngineName>
>        <userName>sa</userName>
>        <password>  </password>
>        <url>jdbc:hsqldb:hsql://localhost/</url>
>        <port>9001</port>
>        <dbName>hsqldb</dbName>
>        <!--<dbDriver>org.hsqldb.jdbcDriver</dbDriver>  -->
>        <!--<jdbcConnect>jdbc:hsqldb:data/hsql/hsqldb</jdbcConnect>  -->
>        <SQLDictionary>
> ...</sqlEngines>
>
> I am launching kepler using its source code and I downloaded the code for kepler-2.2 suite.
> I am still stuck with the problem. One workaround I implemented which treats kar as a jar file file, extracts it and uses the xml from it to launch the kepler workflow in headless mode. But the problem with this workaround is it will not be able handle the kar file which contains more than one xml (moml) files.
>
> Pl suggest.
>
> Thanks for your help,
> Madhavi
>
>
>
> -----Original Message-----
> From: Daniel Crawl [mailto:crawl at sdsc.edu]
> Sent: Wednesday, August 31, 2011 3:24 AM
> To: Madhavi Tikhe
> Cc: Kepler-dev
> Subject: Re: [kepler-users] [kepler-dev] Problems when executing workflow in headless kepler command line using workflow kar file
>
>
> 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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>
>
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