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[protege-discussion] Loading .jar libraries in Protege issue(?)

henry fonbeyin fonbeyin at yahoo.com
Tue Sep 4 07:26:26 PDT 2007


Dear all,
  How do I get study notes for protege 4.O version. 
  I have been to the Help icon but found nothing.
  Thanks for time and consideration.
  Best Regards,
  Henry

Timothy Redmond <tredmond at stanford.edu> wrote:
  
I apologize for the late response. Looks like it is an interesting 
plugin. It is not clear what is wrong here. How are you running the 
plugin? Are you double-clicking on the Protege icon or are you using a 
development environment? If you are using a development environment 
then there are many possible problems. Did you set the working 
directory of the project or the protege.dir environment variable to the 
protege directory? If it doesn't work with a double click on the 
Protege icon then I am not sure where the problem is.

-Timothy


Jan Zemánek wrote:
> Hi all,
>
> I'm developing a tab plugin for Protege-OWL (3.3 Build 418) and I've run 
> into some issues regarding .jar libraries used by my plugin. I have a 
> code that makes use of Sesame (2.0 beta4) .jar libraries and runs 
> smoothly as long as it is in a "stand-alone class" but as soon as I put 
> the same code in my plugin and try to run it within Protege I get the 
> following exception (the full stack trace [1] is enclosed at the end of 
> this e-mail):
>
> Exception in thread "AWT-EventQueue-0"
> org.openrdf.query.UnsupportedQueryLanguageException: No factory
> available for query language SPARQL
>
> So it seems that Protege cannot find the SPARQL factory class which is
> strange because all the Sesame .jar libraries are situated in my plugin
> directory in the main plugins directory of Protege and thus should be
> implicitly loaded by Protege, right? If so what do I wrong?
>
> The SPARQL factory can be found in
> openrdf-queryparser-sparql-2.0-beta4.jar library which is present in my 
> plugin directory as shown here:
>
> c:\dev\protege\plugins\sw.semversion.manager
>
> 21.08.2007 16:38   .
> 21.08.2007 16:38   ..
> 19.04.2005 12:38 88˙441 aduna-clustermap-2005.1-resources.jar
> 19.04.2005 12:39 490˙048 aduna-clustermap-2005.1.jar
> 18.06.2007 13:48 31˙949 aduna-collections-1.1.jar
> 18.06.2007 13:48 10˙968 aduna-concurrent-1.1.jar
> 18.06.2007 13:48 18˙021 aduna-io-1.1.jar
> 18.06.2007 13:48 21˙263 aduna-iteration-1.1.jar
> 18.06.2007 13:48 8˙587 aduna-lang-1.2.jar
> 18.06.2007 13:48 16˙234 aduna-net-1.1.jar
> 18.06.2007 13:48 13˙544 aduna-text-1.1.jar
> 18.06.2007 13:47 25˙281 aduna-xml-1.1.jar
> 18.06.2007 13:44 435˙563 antlr-2.7.5.jar
> 18.06.2007 13:44 820˙199 arq-1.4.jar
> 18.06.2007 13:48 83˙613 commons-io-1.3.1.jar
> 18.06.2007 13:44 38˙015 commons-logging-1.0.4.jar
> 18.06.2007 13:43 189˙284 concurrent-1.3.4.jar
> 21.08.2007 16:38 0 dir.txt
> 14.08.2007 14:47   doc
> 16.08.2007 13:14   icons
> 18.06.2007 13:44 3˙233˙439 icu4j-3.4.4.jar
> 18.06.2007 13:44 188˙729 iri-2.4.jar
> 18.06.2007 13:44 2˙330˙172 jena-2.4.jar
> 18.06.2007 13:48 367˙444 log4j-1.2.14.jar
> 19.08.2007 23:35   meta-inf
> 18.06.2007 13:48 47˙786 openrdf-model-2.0-beta4.jar
> 18.06.2007 13:48 22˙597 openrdf-query-2.0-beta4.jar
> 18.06.2007 13:48 51˙817
> openrdf-queryalgebra-evaluation-2.0-beta4.jar
> 18.06.2007 13:48 70˙376 openrdf-queryalgebra-model-2.0-beta4.jar
> 18.06.2007 13:48 7˙227 openrdf-queryparser-api-2.0-beta4.jar
> 18.06.2007 13:48 141˙083 openrdf-queryparser-serql-2.0-beta4.jar
> 18.06.2007 13:48 128˙747 openrdf-queryparser-sparql-2.0-beta4.jar
> 18.06.2007 13:48 12˙534 openrdf-queryresultio-api-2.0-beta4.jar
> 18.06.2007 14:55 30˙413 openrdf-rdf2go-2.0-beta4hack.jar
> 18.06.2007 13:48 53˙184 openrdf-repository-api-2.0-beta4.jar
> 18.06.2007 13:48 18˙227 openrdf-repository-sail-2.0-beta4.jar
> 18.06.2007 13:48 19˙657 openrdf-rio-api-2.0-beta4.jar
> 18.06.2007 13:48 5˙062 openrdf-rio-n3-2.0-beta4.jar
> 18.06.2007 13:48 13˙519 openrdf-rio-ntriples-2.0-beta4.jar
> 18.06.2007 13:48 33˙243 openrdf-rio-rdfxml-2.0-beta4.jar
> 18.06.2007 13:48 11˙258 openrdf-rio-trix-2.0-beta4.jar
> 18.06.2007 13:47 17˙237 openrdf-rio-turtle-2.0-beta4.jar
> 18.06.2007 13:48 25˙922 openrdf-sail-api-2.0-beta4.jar
> 18.06.2007 13:47 13˙106 openrdf-sail-inferencer-2.0-beta4.jar
> 18.06.2007 13:48 57˙468 openrdf-sail-memory-2.0-beta4.jar
> 18.06.2007 13:48 79˙406 openrdf-sail-nativerdf-2.0-beta4.jar
> 18.06.2007 13:43 850˙526 osgi-3.2.1.R32.jar
> 21.08.2007 12:45 242 plugin.properties
> 27.06.2007 16:33 41˙859 rdf2go.api-4.4.6.jar
> 04.08.2007 02:24 75˙916 rdf2go.impl.base-4.4.7-SNAPSHOT.jar
> 28.06.2007 01:12 43˙601 rdf2go.impl.base.test-4.4.6.jar
> 28.06.2007 01:17 28˙762 rdf2go.impl.jena24-4.4.6.jar
> 06.07.2007 14:06 41˙134 rdfreactor.generator-4.4.8.jar
> 01.08.2007 16:31 106˙748 rdfreactor.runtime-4.4.10-SNAPSHOT.jar
> 04.08.2007 03:04 57˙825 semversion-1.0.0-SNAPSHOT.jar
> 10.03.2006 00:05 84 semversion.properties
> 18.06.2007 13:44 12˙115 slf4j-api-1.3.0.jar
> 18.06.2007 13:44 6˙946 slf4j-log4j12-1.3.0.jar
> 18.06.2007 13:43 26˙514 stax-api-1.0.1.jar
> 20.08.2007 12:09   storage
> 16.08.2007 13:14   sw
> 18.06.2007 13:49 361˙173 velocity-1.4.jar
> 18.06.2007 13:49 517˙761 velocity-dep-1.4.jar
> 15.08.2007 18:47   versions
> 18.06.2007 13:44 483˙266 wstx-lgpl-3.1.1.jar
> 18.06.2007 13:43 1˙203˙860 xercesImpl-2.7.1.jar
> 18.06.2007 13:43 194˙205 xml-apis-1.3.02.jar
>
> I even tried to put all the Sesame related .jar libraries on Protege 
> classpath (in Protege.lax file) but I just ended up with another
> "not found" exception though the class OpenRDFException is present in 
> the openrdf-model-2.0-beta4.jar as well (the full stack trace [2] can be 
> found at the end of the e-mail):
>
> Exception occurred during event dispatching:
> java.lang.NoClassDefFoundError: org/openrdf/OpenRDFException
>
> There shouldn't be a collision between different versions of some of the 
> Sesame libraries leaded as I use no other plugins utilizing Sesame:
>
> c:\dev\protege\plugins
>
> 21.08.2007 19:51   .
> 21.08.2007 19:51   ..
> 19.07.2007 12:25   ca.uvic.cs.chisel.jambalaya
> 19.07.2007 12:25   dfki.protege.ontoviz
> 21.08.2007 19:51 0 dir.txt
> 19.07.2007 12:25   edu.stanford.smi.protege.collab
> 19.07.2007 12:25   edu.stanford.smi.protege.script
> 19.07.2007 12:25   edu.stanford.smi.protege.stringsearch
> 19.07.2007 12:25   edu.stanford.smi.protegex.changes
> 19.07.2007 12:25   edu.stanford.smi.protegex.chatPlugin
> 19.07.2007 12:25   edu.stanford.smi.protegex.datamaster
> 19.07.2007 12:25   edu.stanford.smi.protegex.ezpal
> 19.07.2007 12:25   edu.stanford.smi.protegex.facets_tab
> 19.07.2007 12:25   edu.stanford.smi.protegex.instance_tree
> 19.07.2007 16:48   edu.stanford.smi.protegex.owl
> 19.07.2007 12:25   edu.stanford.smi.protegex.pal_tabs
> 19.07.2007 12:25   edu.stanford.smi.protegex.prompt
> 19.07.2007 12:25   edu.stanford.smi.protegex.rdf_backend
> 03.08.2007 19:17   
> edu.stanford.smi.protegex.standard_extensions
> 19.07.2007 12:25   edu.stanford.smi.protegex.wordnet
> 19.07.2007 12:25   edu.stanford.smi.protegex.xml_tab
> 19.07.2007 12:25   org.algernon
> 19.07.2007 12:25   se.liu.ida.JessTab
> 21.08.2007 16:38   sw.semversion.manager
> 19.07.2007 12:25   uk.ac.iam.soton.akt.tgviztab
> 19.07.2007 12:25   uk.ac.man.cs.mig.coode.debugger
> 19.07.2007 12:25   
> uk.ac.man.cs.mig.coode.manchesterowlsyntaxeditor
> 19.07.2007 12:25   uk.ac.man.cs.mig.coode.owldoc
> 19.07.2007 12:25   uk.ac.man.cs.mig.coode.owlindividualstab
> 19.07.2007 12:25   uk.ac.man.cs.mig.coode.owlviz
> 19.07.2007 12:37   uk.ac.man.cs.mig.coode.protege.wizard
> 19.07.2007 12:25   
> uk.ac.man.cs.mig.coode.protege.wizard.owl
>
> As I got stuck on this I would really appreciate any help.
>
> Kind regards,
> Jan
>
> [1] The first full stack trace:
>
> Exception in thread "AWT-EventQueue-0" 
> org.openrdf.query.UnsupportedQueryLanguag
> eException: No factory available for query language SPARQL
> at 
> org.openrdf.query.parser.QueryParserUtil.createParser(QueryParserUtil
> .java:37)
> at 
> org.openrdf.query.parser.QueryParserUtil.parseQuery(QueryParserUtil.j
> ava:60)
> at 
> org.openrdf.query.parser.QueryParserUtil.parseTupleQuery(QueryParserU
> til.java:82)
> at 
> org.openrdf.repository.sail.SailRepositoryConnection.prepareTupleQuer
> y(SailRepositoryConnection.java:130)
> at 
> org.openrdf.repository.base.RepositoryConnectionBase.prepareTupleQuer
> y(RepositoryConnectionBase.java:135)
> at 
> org.openrdf.rdf2go.RepositoryQueryResultTable.(RepositoryQueryR
> esultTable.java:40)
> at 
> org.openrdf.rdf2go.RepositoryQueryResultTable.(RepositoryQueryR
> esultTable.java:32)
> at 
> org.openrdf.rdf2go.RepositoryModel.sparqlSelect(RepositoryModel.java:
> 261)
> at 
> org.ontoware.rdfreactor.runtime.Bridge.getSparqlSelectSingleVariable(
> Bridge.java:236)
> at 
> org.ontoware.semversion.impl.SemVersionImpl.getUser(SemVersionImpl.ja
> va:136)
> at org.ontoware.semversion.SemVersion.login(SemVersion.java:61)
> at 
> sw.semversion.manager.main.VersionManagerTab.connect(VersionManagerTa
> b.java:153)
> at 
> sw.semversion.manager.main.VersionManagerTab.connectButtonAction(Vers
> ionManagerTab.java:128)
> at 
> sw.semversion.manager.main.VersionManagerTab.access$0(VersionManagerT
> ab.java:124)
> at 
> sw.semversion.manager.main.VersionManagerTab$1.actionPerformed(Versio
> nManagerTab.java:91)
> at 
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:18
> 49)
> at 
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
> a:2169)
> at 
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
> .java:420)
> at 
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258
> )
> at 
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
> istener.java:236)
> at 
> java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:2
> 31)
> at java.awt.Component.processMouseEvent(Component.java:5517)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
> at java.awt.Component.processEvent(Component.java:5282)
> at java.awt.Container.processEvent(Container.java:1966)
> at java.awt.Component.dispatchEventImpl(Component.java:3984)
> at java.awt.Container.dispatchEventImpl(Container.java:2024)
> at java.awt.Component.dispatchEvent(Component.java:3819)
> at 
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212
> )
> at 
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
>
> at 
> java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
> at java.awt.Container.dispatchEventImpl(Container.java:2010)
> at java.awt.Window.dispatchEventImpl(Window.java:1791)
> at java.awt.Component.dispatchEvent(Component.java:3819)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> at 
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchTh
> read.java:242)
> at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
> ad.java:163)
> at 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>
> at 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
>
> [2] The second full stack trace:
>
>
>
> Exception occurred during event dispatching:
> java.lang.NoClassDefFoundError: org/openrdf/OpenRDFException
> at java.lang.ClassLoader.defineClass1(Native Method)
> at java.lang.ClassLoader.defineClass(ClassLoader.java:620)
> at 
> java.security.SecureClassLoader.defineClass(SecureClassLoader.java:12
> 4)
> at java.net.URLClassLoader.defineClass(URLClassLoader.java:260)
> at java.net.URLClassLoader.access$100(URLClassLoader.java:56)
> at java.net.URLClassLoader$1.run(URLClassLoader.java:195)
> at java.security.AccessController.doPrivileged(Native Method)
> at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:299)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:299)
> at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
> at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
> at 
> org.ontoware.semversion.impl.SemVersionImpl.startup(SemVersionImpl.ja
> va:87)
> at org.ontoware.semversion.SemVersion.startup(SemVersion.java:38)
> at 
> sw.semversion.manager.main.VersionManagerTab.initSemVersion(VersionMa
> nagerTab.java:73)
> at 
> sw.semversion.manager.main.VersionManagerTab.initialize(VersionManage
> rTab.java:53)
> at 
> edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unkno
> wn Source)
> at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
> at 
> edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Sour
> ce)
> at edu.stanford.smi.protege.ui.ProjectView.(Unknown Source)
> at 
> edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unkn
> own Source)
> at 
> edu.stanford.smi.protege.ui.ProjectManager.displayCurrentProject(Unkn
> own Source)
> at 
> edu.stanford.smi.protege.ui.ProjectManager.loadProject(Unknown Source
> )
> at 
> edu.stanford.smi.protege.ui.WelcomeDialog.doOpenProject(Unknown Sourc
> e)
> at 
> edu.stanford.smi.protege.ui.WelcomeDialog.openButton_actionPerformed(
> Unknown Source)
> at 
> edu.stanford.smi.protege.ui.WelcomeDialog$2.actionPerformed(Unknown S
> ource)
> at 
> javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:18
> 49)
> at 
> javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.jav
> a:2169)
> at 
> javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel
> .java:420)
> at 
> javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:258
> )
> at 
> javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonL
> istener.java:236)
> at 
> java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:2
> 31)
> at java.awt.Component.processMouseEvent(Component.java:5517)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3135)
> at java.awt.Component.processEvent(Component.java:5282)
> at java.awt.Container.processEvent(Container.java:1966)
> at java.awt.Component.dispatchEventImpl(Component.java:3984)
> at java.awt.Container.dispatchEventImpl(Container.java:2024)
> at java.awt.Component.dispatchEvent(Component.java:3819)
> at 
> java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4212
> )
> at 
> java.awt.LightweightDispatcher.processMouseEvent(Container.java:3892)
>
> at 
> java.awt.LightweightDispatcher.dispatchEvent(Container.java:3822)
> at java.awt.Container.dispatchEventImpl(Container.java:2010)
> at java.awt.Window.dispatchEventImpl(Window.java:1791)
> at java.awt.Component.dispatchEvent(Component.java:3819)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
> at 
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchTh
> read.java:242)
> at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
> ad.java:163)
> at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
> ad.java:153)
> 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(EventDispatchTh
> read.java:242)
> at 
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThre
> ad.java:163)
> at 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>
> at 
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
> 

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