Thanks all for your efforts!<br><br><div class="gmail_quote">On 15 March 2010 19:55, Chad Berkley <span dir="ltr"><<a href="mailto:berkley@nceas.ucsb.edu">berkley@nceas.ucsb.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I think we need more command line control for kar files. This won't be implemented for 2.0, but I'll make an enhancement request for 2.x in bugzilla. We should be able to specify a kar file, the workflow in the kar file to run and the output location on the command line. It really doesn't make sense to just have defaults. I think since we developed this capability for a specific purpose (SanParks) we were just trying to get it to work and didn't really look at the whole picture on what it should do. I'll add the bug now.<br>
<font color="#888888">
<br>
chad</font><div><div></div><div class="h5"><br>
<br>
<br>
ben leinfelder wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Josep -<br>
In the meantime, can you try removing the semantic type from your workflow, resaving the KAR and then running it? I hope that will work until we resolve this semantic type/cache issue.<br>
Thanks,<br>
-ben<br>
<br>
On Mar 13, 2010, at 2:21 AM, Josep Morer Muñoz wrote:<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello all,<br>
<br>
I have not executed any KAR yet. I always get the same error (executing the KAR with cache). Any idea?<br>
<br>
urops@urops-laptop:~/Kepler-2.0.0-beta1$ ./kepler.sh /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar -runwf -nogui<br>
[null] /home/urops/Kepler-2.0.0-beta1<br>
[null] Found OS Extension file: /home/urops/Kepler-2.0.0-beta1/apple-extensions/module-info/osextension.txt <br>
[null] Ran additional initialization for module gui from class org.kepler.module.gui.Initialize<br>
[null] Ran additional initialization for module tagging from class org.kepler.module.tagging.Initialize<br>
[null] Ran additional initialization for module provenance from class org.kepler.module.provenance.Initialize<br>
[null] common tabpane configuration overridden by reporting<br>
[null] Ran additional initialization for module reporting from class org.kepler.module.reporting.Initialize<br>
[null] loading: org.kepler.KeplerConfigurationApplication args: ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar<br>
[null] invoking: org.kepler.KeplerConfigurationApplication.main<br>
[null] Kepler Initializing...<br>
[null] Extracting workflow from KAR<br>
[null] Cached KAR contents<br>
[null] Processing entry, LSID=urn:lsid:<a href="http://gamma.msi.ucsb.edu/OpenAuth/:8002:120:1" target="_blank">gamma.msi.ucsb.edu/OpenAuth/:8002:120:1</a>, type=ptolemy.actor.TypedCompositeActor<br>
[null] Command failed<br>
[null] java.lang.Exception: Failed to parse "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"<br>
[null] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651) <br>
[null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289) <br>
[null] at org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583) <br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) <br>
[null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) <br>
[null] at java.lang.reflect.Method.invoke(Method.java:592)<br>
[null] at org.kepler.Kepler.load(Kepler.java:321)<br>
[null] at org.kepler.Kepler.load(Kepler.java:339)<br>
[null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)<br>
[null] at org.kepler.Kepler.main(Kepler.java:169)<br>
[null] Caused by: org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531) <br>
[null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172) <br>
[null] ... 9 more<br>
[null] Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br>
[null] at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251) <br>
[null] at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)<br>
[null] at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)<br>
[null] at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)<br>
[null] at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519) <br>
[null] ... 10 more<br>
[null] java.lang.Exception: Failed to parse "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit /home/urops/KeplerData/workflows/05-LinearRegressionProvenanceNEW.kar"<br>
[null] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651) <br>
[null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:289) <br>
[null] at org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:583) <br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) <br>
[null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) <br>
[null] at java.lang.reflect.Method.invoke(Method.java:592)<br>
[null] at org.kepler.Kepler.load(Kepler.java:321)<br>
[null] at org.kepler.Kepler.load(Kepler.java:339)<br>
[null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)<br>
[null] at org.kepler.Kepler.main(Kepler.java:169)<br>
[null] Caused by: org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:531) <br>
[null] at org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:172) <br>
[null] ... 9 more<br>
[null] Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br>
[null] at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:251) <br>
[null] at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1756)<br>
[null] at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1717)<br>
[null] at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1305)<br>
[null] at java.io.ObjectInputStream.readObject(ObjectInputStream.java:348)<br>
[null] at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:519) <br>
[null] ... 10 more<br>
Exception in thread "main" Java returned: 1<br>
at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:90)<br>
at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br>
Caused by: Java returned: 1<br>
at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br>
at org.kepler.build.Run.runSuite(Run.java:296)<br>
at org.kepler.build.Run.run(Run.java:201)<br>
at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)<br>
... 1 more<br>
--- Nested Exception ---<br>
Java returned: 1<br>
at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)<br>
at org.kepler.build.Run.runSuite(Run.java:296)<br>
at org.kepler.build.Run.run(Run.java:201)<br>
at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:86)<br>
at org.kepler.build.runner.Kepler.main(Kepler.java:78)<br>
<br>
<br>
2010/3/10 ben leinfelder <<a href="mailto:leinfelder@nceas.ucsb.edu" target="_blank">leinfelder@nceas.ucsb.edu</a>><br>
My findings:<br>
-ran successfully with a clean-cache<br>
-second attempt to run (without cleaning the cache) failed due to an ObjectManager error relating to the semanticTypes.<br>
<br>
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:<br>
Caused by: ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "semanticType" into a container that already contains an object with that name.<br>
....the problems seem to begin around here:<br>
at org.kepler.objectmanager.ActorMetadata.getActorAsNamedObj(ActorMetadata.java:790) <br>
<br>
Aaron - can you take a look at this?<br>
<br>
Thanks,<br>
-ben<br>
<br>
On Mar 8, 2010, at 2:06 PM, Josep Morer Muñoz wrote:<br>
<br>
Thanks for your help Chad. Attached the file.<br>
<br>
2010/3/8 Chad Berkley <<a href="mailto:berkley@nceas.ucsb.edu" target="_blank">berkley@nceas.ucsb.edu</a>><br>
Hi Josep,<br>
<br>
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.<br>
<br>
I just tried the command:<br>
./kepler.sh test.kar -runwf -nogui<br>
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?<br>
<br>
thanks,<br>
chad<br>
<br>
<br>
Josep Morer Muñoz wrote:<br>
Hi all,<br>
<br>
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.<br>
<br>
urops@urops-laptop:~/KeplerLast$ ./kepler.sh /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar -runwf -nogui -nocache<br>
[null] /home/urops/KeplerLast<br>
[null] Found OS Extension file: /home/urops/KeplerLast/apple-extensions/module-info/osextension.txt<br>
[null] Ran additional initialization for module gui from class org.kepler.module.gui.Initialize<br>
[null] Ran additional initialization for module tagging from class org.kepler.module.tagging.Initialize<br>
[null] Ran additional initialization for module provenance from class org.kepler.module.provenance.Initialize<br>
[null] common tabpane configuration overridden by reporting<br>
[null] Ran additional initialization for module reporting from class org.kepler.module.reporting.Initialize<br>
[null] loading: ptolemy.moml.MoMLCommandLineApplication args: /home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar<br>
[null] invoking: ptolemy.moml.MoMLCommandLineApplication.main<br>
[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<br>
* [null] com.microstar.xml.XmlException: expected character (found "P") (expected "<") in file:/home/urops/workflowsProvenance/05-LinearRegressionProvenance.kar at line 1 and column 5*<br>
[null] at ptolemy.moml.MoMLParser.error(MoMLParser.java:1057)<br>
[null] at com.microstar.xml.XmlParser.error(XmlParser.java:448)<br>
[null] at com.microstar.xml.XmlParser.error(XmlParser.java:459)<br>
[null] at com.microstar.xml.XmlParser.require(XmlParser.java:2335)<br>
[null] at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:480)<br>
[null] at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br>
[null] at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br>
[null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1402)<br>
[null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1354)<br>
[null] at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1298)<br>
[null] at ptolemy.moml.MoMLCommandLineApplication.<init>(MoMLCommandLineApplication.java:128) <br>
[null] at ptolemy.moml.MoMLCommandLineApplication.main(MoMLCommandLineApplication.java:214) <br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)<br>
[null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) <br>
[null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) <br>
[null] at java.lang.reflect.Method.invoke(Method.java:592)<br>
[null] at org.kepler.Kepler.load(Kepler.java:321)<br>
[null] at org.kepler.Kepler.load(Kepler.java:339)<br>
[null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:267)<br>
[null] at org.kepler.Kepler.main(Kepler.java:169)<br>
<br>
<br>
Thanks in advance<br>
-- <br>
Josep<br>
<br>
<br>
------------------------------------------------------------------------<br>
<br>
<br>
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<br>
<br>
<br>
-- <br>
Josep<br>
<05-LinearRegressionProvenance.kar><br>
<br>
<br>
<br>
<br>
-- <br>
Josep<br>
</blockquote>
<br>
</blockquote>
</div></div></blockquote></div><br><br clear="all"><br>-- <br>Josep<br>