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[protege-owl] Protege 3.4.1 SAXParser NoSuchMethodError on Mac OSX

Thomas Russ tar at ISI.EDU
Fri Jan 15 11:07:44 PST 2010


On Jan 15, 2010, at 9:28 AM, Timothy Redmond wrote:

>
> This is an early answer without having done the full  
> investigation.  I haven't seen this happen before and it seems like  
> a very strange error.  I don't know why it would be a problem for  
> your configuration but not for other configurations.  Protege OWL  
> seems to be using the wrong xerces implementation.   The most  
> obvious thing to try would be to make sure that the old version of  
> Protege is deleted before the new one is installed.  Also perhaps  
> you could try the latest version of Protege (3.4.2).

I was thinking that something like this may also be the cause.
One other possible way that an incorrect version of xerces could be  
used in one particular place would be if someone had placed a xerces  
library in the main system or user java extensions folder.  You could  
look in
    /Library/Java/Extensions
    /System/Library/Java/Extensions
and see if there is anything like that.  Some other places to look  
might be in
    /System/Library/Frameworks/JavaVM.framework/Home/lib/endorsed/
    /System/Library/Frameworks/JavaVM.framework/Home/lib/ext/


> -Timothy
>
>
> Chris Davis wrote:
>> I've been having a problem getting Protege 3.4.1 to open an owl  
>> file (pizza.owl) on a Mac running OSX 10.5.8.  I've seen some  
>> other messages here indicating that the problems I have with the  
>> NoSuchMethodError for the SAXParser are related to build path  
>> issues, but I'm just using the GUI and have a fresh download from  
>> the site.  I've used both the 1.5 and 1.6 versions of the JVM, and  
>> get the same error on both.  As an experiment, figuring that  
>> Protege is written in java, I also copied the folder of a working  
>> Protege copy from a linux machine, and then tried it on the mac,  
>> and ran into the same problem.
>>
>> Chris
>>
>> Starting Protege with the shell script "sh ./run_protege.sh" and  
>> then trying to load the owl file gives me:
>>
>> Protege 3.4.1 Build 537, JVM 1.5.0_19-b02-304, memory=520M, Mac OS  
>> X, encoding=UTF-8, language=en, country=US
>> Loaded plugin edu.stanford.smi.protegex.owl - OWL Plugin
>> Loaded plugin ca.uvic.cs.chisel.jambalaya - Jambalaya
>> Loaded plugin dfki.protege.ontoviz
>> Loaded plugin edu.stanford.smi.protegex.rdf_backend - RDF Backend
>> Loaded plugin edu.stanford.smi.protegex.changes - Changes tab
>> Loaded plugin edu.stanford.smi.protegex.standard_extensions -  
>> Graph Widget, Table Widget
>> Loaded plugin edu.stanford.smi.protegex.chatPlugin - Chat
>> Loaded plugin edu.stanford.smi.protege.collab - Collaborative Protege
>> Loaded plugin edu.stanford.smi.protege.script - Script Plugin
>> Loaded plugin edu.stanford.smi.protege.stringsearch - String  
>> Search Tab
>> Loaded plugin edu.stanford.smi.protegex.datamaster - DataMaster Tab
>> Loaded plugin edu.stanford.smi.protegex.pal_tabs - PAL Tabs
>> Loaded plugin edu.stanford.smi.protegex.ezpal - EZPal Tab
>> Loaded plugin edu.stanford.smi.protegex.facets_tab
>> Loaded plugin edu.stanford.smi.protegex.instance_tree
>> Loaded plugin edu.stanford.smi.protegex.prompt - PROMPT Tab
>> Loaded plugin edu.stanford.smi.protegex.metaanalysis -  
>> MetaAnalysis Tab
>> Loaded plugin edu.stanford.smi.protegex.owl.inference.pellet -  
>> Protege Pellet Reasoner
>> Loaded plugin edu.stanford.smi.protegex.umls_tab - UMLS Tab
>> Loaded plugin edu.stanford.smi.protegex.wordnet - WordNet Tab
>> Loaded plugin edu.stanford.smi.protegex.xml_tab - XML Tab
>> Loaded plugin org.algernon - Algernon
>> Loaded plugin se.liu.ida.JessTab - JessTab Plugin
>> Loaded plugin uk.ac.iam.soton.akt.tgviztab - TGVizTab
>> Loaded plugin uk.ac.man.cs.mig.coode.debugger
>> Loaded plugin uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
>> Loaded plugin uk.ac.man.cs.mig.coode.owldoc
>> Loaded plugin uk.ac.man.cs.mig.coode.owlindividualstab
>> Loaded plugin uk.ac.man.cs.mig.coode.owlviz
>> Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard - Basic Wizards
>> Loaded plugin uk.ac.man.cs.mig.coode.protege.wizard.owl - OWL Wizards
>> Loading triples from: file:/Applications/Protege_3.4.1/examples/ 
>> pizza/pizza.owl
>> SEVERE: Uncaught Exception -- java.lang.NoSuchMethodError:  
>> org.apache.xerces.parsers.SAXParser.<init>(Lorg/apache/xerces/xni/ 
>> parser/XMLParserConfiguration;)
>>    at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser$MySAXParser.<init> 
>> (RDFXMLParser.java:55)
>>    at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.create 
>> (RDFXMLParser.java:82)
>>    at com.hp.hpl.jena.rdf.arp.ARP.<init>(ARP.java:101)
>>    at  
>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.createARP( 
>> Unknown Source)
>>    at  
>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.loadTriple 
>> s(Unknown Source)
>>    at  
>> edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run 
>> (Unknown Source)
>>    at  
>> edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowl 
>> edgeBase(Unknown Source)
>>    at edu.stanford.smi.protege.model.Project.loadDomainKB(Unknown  
>> Source)
>>    at  
>> edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase 
>> (Unknown Source)
>>    at  
>> edu.stanford.smi.protegex.owl.jena.creator.OwlProjectFromUriCreator.c 
>> reate(Unknown Source)
>>    at  
>> edu.stanford.smi.protegex.owl.jena.CreateOWLProjectFromFilePlugin.cre 
>> ateProject(Unknown Source)
>>    at  
>> edu.stanford.smi.protege.util.ProjectChooser.useCreateProjectFromFile 
>> Plugin(Unknown Source)
>>    at  
>> edu.stanford.smi.protege.util.ProjectChooser.getProjectFromFile 
>> (Unknown Source)
>>    at edu.stanford.smi.protege.util.ProjectChooser.getProject 
>> (Unknown Source)
>>    at  
>> edu.stanford.smi.protege.ui.ProjectManager.getRequestedProject 
>> (Unknown Source)
>>    at edu.stanford.smi.protege.ui.ProjectManager.openProjectRequest 
>> (Unknown Source)
>>    at  
>> edu.stanford.smi.protege.ui.WelcomeDialog.openOtherButton_actionPerfo 
>> rmed(Unknown Source)
>>    at edu.stanford.smi.protege.ui.WelcomeDialog$3.actionPerformed 
>> (Unknown Source)
>>    at javax.swing.AbstractButton.fireActionPerformed 
>> (AbstractButton.java:1882)
>>    at javax.swing.AbstractButton$Handler.actionPerformed 
>> (AbstractButton.java:2202)
>>    at javax.swing.DefaultButtonModel.fireActionPerformed 
>> (DefaultButtonModel.java:420)
>>    at javax.swing.DefaultButtonModel.setPressed 
>> (DefaultButtonModel.java:258)
>>    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased 
>> (BasicButtonListener.java:236)
>>    at java.awt.AWTEventMulticaster.mouseReleased 
>> (AWTEventMulticaster.java:231)
>>    at java.awt.Component.processMouseEvent(Component.java:5602)
>>    at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
>>    at java.awt.Component.processEvent(Component.java:5367)
>>    at java.awt.Container.processEvent(Container.java:2010)
>>    at java.awt.Component.dispatchEventImpl(Component.java:4068)
>>    at java.awt.Container.dispatchEventImpl(Container.java:2068)
>>    at java.awt.Component.dispatchEvent(Component.java:3903)
>>    at java.awt.LightweightDispatcher.retargetMouseEvent 
>> (Container.java:4256)
>>    at java.awt.LightweightDispatcher.processMouseEvent 
>> (Container.java:3936)
>>    at java.awt.LightweightDispatcher.dispatchEvent(Container.java: 
>> 3866)
>>    at java.awt.Container.dispatchEventImpl(Container.java:2054)
>>    at java.awt.Window.dispatchEventImpl(Window.java:1801)
>>    at java.awt.Component.dispatchEvent(Component.java:3903)
>>    at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>>    at java.awt.EventDispatchThread.pumpOneEventForHierarchy 
>> (EventDispatchThread.java:269)
>>    at java.awt.EventDispatchThread.pumpEventsForHierarchy 
>> (EventDispatchThread.java:190)
>>    at java.awt.EventDispatchThread.pumpEventsForHierarchy 
>> (EventDispatchThread.java:180)
>>    at java.awt.Dialog$1.run(Dialog.java:535)
>>    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java: 
>> 209)
>>    at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
>>    at java.awt.EventDispatchThread.pumpOneEventForHierarchy 
>> (EventDispatchThread.java:269)
>>    at java.awt.EventDispatchThread.pumpEventsForHierarchy 
>> (EventDispatchThread.java:190)
>>    at java.awt.EventDispatchThread.pumpEvents 
>> (EventDispatchThread.java:184)
>>    at java.awt.EventDispatchThread.pumpEvents 
>> (EventDispatchThread.java:176)
>>    at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>>
>>
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>
>
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