[kepler-users] ERROR EXECUTING A .KAR FILE

Josep Morer Muñoz josep.morer at gmail.com
Sat Mar 13 02:21:57 PST 2010 

Hello all,

I have not executed any KAR yet. I always get the same error (executing the
KAR with cache). Any idea?

urops at urops-laptop:~/Kepler-2.0.0-beta1$ ./kepler.sh
/home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar -runwf
-nogui
     [null] /home/urops/Kepler-2.0.0-beta1
     [null] Found OS Extension file:
/home/urops/Kepler-2.0.0-beta1/apple-extensions/module-info/osextension.txt
     [null] Ran additional initialization for module gui from class
org.kepler.module.gui.Initialize
     [null] Ran additional initialization for module tagging from class
org.kepler.module.tagging.Initialize
     [null] Ran additional initialization for module provenance from class
org.kepler.module.provenance.Initialize
     [null] common tabpane configuration overridden by reporting
     [null] Ran additional initialization for module reporting from class
org.kepler.module.reporting.Initialize
     [null] loading: org.kepler.KeplerConfigurationApplication args:
ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit
/home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar
     [null] invoking: org.kepler.KeplerConfigurationApplication.main
     [null] Kepler Initializing...
     [null] Extracting workflow from KAR
     [null] Cached KAR contents
     [null] Processing entry, LSID=urn:lsid:
gamma.msi.ucsb.edu/OpenAuth/:8002:120:1,
type=ptolemy.actor.TypedCompositeActor
     [null] Command failed
     [null] java.lang.Exception: Failed to parse
"ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit
/home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"
     [null]     at
ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651)
     [null]     at
org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289)
     [null]     at
org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583)
     [null]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
     [null]     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     [null]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     [null]     at java.lang.reflect.Method.invoke(Method.java:592)
     [null]     at org.kepler.Kepler.load(Kepler.java:321)
     [null]     at org.kepler.Kepler.load(Kepler.java:339)
     [null]     at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)
     [null]     at org.kepler.Kepler.main(Kepler.java:169)
     [null] Caused by: org.kepler.objectmanager.cache.CacheException:
Exception occurred while deserializing object
     [null]     at
org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531)
     [null]     at
org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172)
     [null]     ... 9 more
     [null] Caused by: java.io.IOException: Error in
ActorCacheObject(ReadExternal): null
     [null]     at
org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251)
     [null]     at
java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)
     [null]     at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)
     [null]     at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)
     [null]     at
java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
     [null]     at
org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519)
     [null]     ... 10 more
     [null] java.lang.Exception: Failed to parse
"ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit
/home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"
     [null]     at
ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651)
     [null]     at
org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289)
     [null]     at
org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583)
     [null]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
Method)
     [null]     at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
     [null]     at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
     [null]     at java.lang.reflect.Method.invoke(Method.java:592)
     [null]     at org.kepler.Kepler.load(Kepler.java:321)
     [null]     at org.kepler.Kepler.load(Kepler.java:339)
     [null]     at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)
     [null]     at org.kepler.Kepler.main(Kepler.java:169)
     [null] Caused by: org.kepler.objectmanager.cache.CacheException:
Exception occurred while deserializing object
     [null]     at
org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531)
     [null]     at
org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172)
     [null]     ... 9 more
     [null] Caused by: java.io.IOException: Error in
ActorCacheObject(ReadExternal): null
     [null]     at
org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251)
     [null]     at
java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)
     [null]     at
java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)
     [null]     at
java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)
     [null]     at
java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)
     [null]     at
org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519)
     [null]     ... 10 more
Exception in thread "main" Java returned: 1
    at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:90)
    at org.kepler.build.runner.Kepler.main(Kepler.java:78)
Caused by: Java returned: 1
    at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
    at org.kepler.build.Run.runSuite(Run.java:296)
    at org.kepler.build.Run.run(Run.java:201)
    at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)
    ... 1 more
--- Nested Exception ---
Java returned: 1
    at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
    at org.kepler.build.Run.runSuite(Run.java:296)
    at org.kepler.build.Run.run(Run.java:201)
    at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)
    at org.kepler.build.runner.Kepler.main(Kepler.java:78)


2010/3/10 ben leinfelder <leinfelder at nceas.ucsb.edu>

> My findings:
> -ran successfully with a clean-cache
> -second attempt to run (without cleaning the cache) failed due to an
> ObjectManager error relating to the semanticTypes.
>
> I noticed there is a tag on the workflow which is likely the source of the
> problem. We should fix whatever issue is causing this error when the MOML is
> parsed:
> Caused by: ptolemy.kernel.util.NameDuplicationException: Attempt to insert
> object named "semanticType" into a container that already contains an object
> with that name.
> ....the problems seem to begin around here:
> at
> org.kepler.objectmanager.ActorMetadata.getActorAsNamedObj(ActorMetadata.java:790)
>
> Aaron - can you take a look at this?
>
> Thanks,
> -ben
>
> On Mar 8, 2010, at 2:06 PM, Josep Morer Muñoz wrote:
>
>  Thanks for your help Chad. Attached the file.
>>
>> 2010/3/8 Chad Berkley <berkley at nceas.ucsb.edu>
>> Hi Josep,
>>
>> Could you send me the kar file so I can take a look?  You can create the
>> kar from the workflow by opening the workflow in kepler, then choosing
>> File/Save Archive.
>>
>> I just tried the command:
>> ./kepler.sh test.kar -runwf -nogui
>> which worked for me with a kar that I generated the way I said above.  I
>> don't think the -nocache option will work with a kar file because the kar
>> needs to be cached to be processed.  Ben, do you know if this is true?
>>
>> thanks,
>> chad
>>
>>
>> Josep Morer Muñoz wrote:
>> Hi all,
>>
>> I am getting this error when I try to execute a .KAR that contains the
>> Regression Workflow (included in the examples) and another XML that
>> cointains the report's layout. When I execute it using kepler.sh I get this
>> following exception. Any idea? I do not know if I have generated the .KAR
>> correctly since I do not know what a sematic type means in Kepler.
>>
>> urops at urops-laptop:~/KeplerLast$ ./kepler.sh
>> /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar -runwf
>> -nogui -nocache
>>    [null] /home/urops/KeplerLast
>>    [null] Found OS Extension file:
>> /home/urops/KeplerLast/apple-extensions/module-info/osextension.txt
>>    [null] Ran additional initialization for module gui from class
>> org.kepler.module.gui.Initialize
>>    [null] Ran additional initialization for module tagging from class
>> org.kepler.module.tagging.Initialize
>>    [null] Ran additional initialization for module provenance from class
>> org.kepler.module.provenance.Initialize
>>    [null] common tabpane configuration overridden by reporting
>>    [null] Ran additional initialization for module reporting from class
>> org.kepler.module.reporting.Initialize
>>    [null] loading: ptolemy.moml.MoMLCommandLineApplication args:
>> /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar
>>    [null] invoking: ptolemy.moml.MoMLCommandLineApplication.main
>>    [null] Command failed: com.microstar.xml.XmlException: expected
>> character (found "P") (expected "<") in
>> file:/home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar at
>> line 1 and column 5
>> *     [null] com.microstar.xml.XmlException: expected character (found
>> "P") (expected "<") in
>> file:/home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar at
>> line 1 and column 5*
>>    [null]     at ptolemy.moml.MoMLParser.error(MoMLParser.java:1057)
>>    [null]     at com.microstar.xml.XmlParser.error(XmlParser.java:448)
>>    [null]     at com.microstar.xml.XmlParser.error(XmlParser.java:459)
>>    [null]     at com.microstar.xml.XmlParser.require(XmlParser.java:2335)
>>    [null]     at
>> com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)
>>    [null]     at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)
>>    [null]     at com.microstar.xml.XmlParser.parse(XmlParser.java:132)
>>    [null]     at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1402)
>>    [null]     at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1354)
>>    [null]     at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1298)
>>    [null]     at
>> ptolemy.moml.MoMLCommandLineApplication.<init>(MoMLCommandLineApplication.java:128)
>>    [null]     at
>> ptolemy.moml.MoMLCommandLineApplication.main(MoMLCommandLineApplication.java:214)
>>    [null]     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native
>> Method)
>>    [null]     at
>> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
>>    [null]     at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
>>    [null]     at java.lang.reflect.Method.invoke(Method.java:592)
>>    [null]     at org.kepler.Kepler.load(Kepler.java:321)
>>    [null]     at org.kepler.Kepler.load(Kepler.java:339)
>>    [null]     at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)
>>    [null]     at org.kepler.Kepler.main(Kepler.java:169)
>>
>>
>> Thanks in advance
>> --
>> Josep
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> _______________________________________________
>> Kepler-users mailing list
>> Kepler-users at kepler-project.org
>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>
>>
>>
>> --
>> Josep
>> <05-LinearRegressionProvenance.kar>
>>
>
>


-- 
Josep
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