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

Timothy Redmond tredmond at stanford.edu
Fri Jan 15 09:28:54 PST 2010


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).

-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.loadTriples(Unknown Source)
>    at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.run(Unknown Source)
>    at edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.loadKnowledgeBase(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.create(Unknown Source)
>    at edu.stanford.smi.protegex.owl.jena.CreateOWLProjectFromFilePlugin.createProject(Unknown Source)
>    at edu.stanford.smi.protege.util.ProjectChooser.useCreateProjectFromFilePlugin(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_actionPerformed(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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