NoSuchMethodError: plugin for Protege 5.5-beta3

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NoSuchMethodError: plugin for Protege 5.5-beta3

kcason

I’m building a plugin for Protégé 5.5-beta3, but keep getting the following error when invoking the plugin:

 

 Uncaught Exception in thread 'AWT-EventQueue-0'

  java.lang.NoSuchMethodError:   org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

                at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

                at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

                at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

                at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

                at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

                at radiance.emap.protege.query.model.QueryReasoner.precalculate(QueryReasoner.java:48) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initializeReasoner(EmapForm.java:251) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initialiseOWLView(EmapForm.java:221) ~[na:na]

 

I’ve tried many different versions of Protégé but always get the above error. My experience tells me I have a version mismatch of some library but can’t figure out how to identify the conflict nor how to fix it.

 

I thought I might have the incorrect OWLAPI version so I looked in the Protégé log and found this:

 

  Creating and setting up empty (default) editor kit

  OWL API Version: 4.5.6.2018-09-06T00:27:41Z

 

I couldn’t find OWLAPI version 4.5.6 anywhere on the web. The closest I found was 4.5.5:

https://github.com/owlcs/owlapi

 

Can someone please help me identify the above conflict, if that’s what it is?

 

Thanks,

 

-Kenny Cason

Radiance Technologies

Cyber Solutions Group

3133 General Hudnell Dr. Ste. 116
San Antonio, TX 78226

[hidden email]

206.550.0049

 


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Re: NoSuchMethodError: plugin for Protege 5.5-beta3

Lorenz Buehmann
Protege  is a Maven project, the dependencies are defined in the pom.xml. You can see it has a dependency to 4.5.6 [1]

All those stuff can be found in the Maven repo [2].
Indeed, your plugin must depend on the same version to avoid errors.

And hopefully, you're also using Maven in your development - it's so much more convenient.
On 11/28/18 8:59 PM, Kenny Cason wrote:

I’m building a plugin for Protégé 5.5-beta3, but keep getting the following error when invoking the plugin:

 

 Uncaught Exception in thread 'AWT-EventQueue-0'

  java.lang.NoSuchMethodError:   org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

                at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

                at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

                at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

                at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

                at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

                at radiance.emap.protege.query.model.QueryReasoner.precalculate(QueryReasoner.java:48) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initializeReasoner(EmapForm.java:251) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initialiseOWLView(EmapForm.java:221) ~[na:na]

 

I’ve tried many different versions of Protégé but always get the above error. My experience tells me I have a version mismatch of some library but can’t figure out how to identify the conflict nor how to fix it.

 

I thought I might have the incorrect OWLAPI version so I looked in the Protégé log and found this:

 

  Creating and setting up empty (default) editor kit

  OWL API Version: 4.5.6.2018-09-06T00:27:41Z

 

I couldn’t find OWLAPI version 4.5.6 anywhere on the web. The closest I found was 4.5.5:

https://github.com/owlcs/owlapi

 

Can someone please help me identify the above conflict, if that’s what it is?

 

Thanks,

 

-Kenny Cason

Radiance Technologies

Cyber Solutions Group

3133 General Hudnell Dr. Ste. 116
San Antonio, TX 78226

[hidden email]

206.550.0049

 


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-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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Re: NoSuchMethodError: plugin for Protege 5.5-beta3

Csongor Nyulas
Administrator
Kenny did not receive the email (probably because of his email delivery settings), and asked me to reply to this email, so that he can continue discussion on the thread.
Hopefully this works...

Csongor

On 11/29/18 12:20 AM, Lorenz B. wrote:
Protege  is a Maven project, the dependencies are defined in the pom.xml. You can see it has a dependency to 4.5.6 [1]

All those stuff can be found in the Maven repo [2].
Indeed, your plugin must depend on the same version to avoid errors.

And hopefully, you're also using Maven in your development - it's so much more convenient.
On 11/28/18 8:59 PM, Kenny Cason wrote:

I’m building a plugin for Protégé 5.5-beta3, but keep getting the following error when invoking the plugin:

 

 Uncaught Exception in thread 'AWT-EventQueue-0'

  java.lang.NoSuchMethodError:   org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

                at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

                at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

                at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

                at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

                at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

                at radiance.emap.protege.query.model.QueryReasoner.precalculate(QueryReasoner.java:48) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initializeReasoner(EmapForm.java:251) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initialiseOWLView(EmapForm.java:221) ~[na:na]

 

I’ve tried many different versions of Protégé but always get the above error. My experience tells me I have a version mismatch of some library but can’t figure out how to identify the conflict nor how to fix it.

 

I thought I might have the incorrect OWLAPI version so I looked in the Protégé log and found this:

 

  Creating and setting up empty (default) editor kit

  OWL API Version: 4.5.6.2018-09-06T00:27:41Z

 

I couldn’t find OWLAPI version 4.5.6 anywhere on the web. The closest I found was 4.5.5:

https://github.com/owlcs/owlapi

 

Can someone please help me identify the above conflict, if that’s what it is?

 

Thanks,

 

-Kenny Cason

Radiance Technologies

Cyber Solutions Group

3133 General Hudnell Dr. Ste. 116
San Antonio, TX 78226

[hidden email]

206.550.0049

 


_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev


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Re: NoSuchMethodError: plugin for Protege 5.5-beta3

kcason

Yes, this is a Maven project. I added the dependency for 4.5.6 as you suggested below and still have the same problem. I added a check in my plugin code to print the OWL API version information both at compilation time and run time and everything is showing 4.5.6.

 

So, I decided to build Protégé from scratch just like the instructions say to do (without any of my custom code). I downloaded 5.5-beta3, 5.5-beta4 and master (5.5-beta5) and compiled each individually with the same command:

  $ mvn clean package

 

All three versions built fine. But when I bring up any of them (run.bat) and try to use the built-in SPARQL query plugin I get the same error as described in my previous post. This indicates to me there is something in my environment, not my code, that is causing a conflict. Here is the log when running Protégé and trying to activate the SPARQL plugin (two ontologies are loaded and the HermiT reasoner is on):

 

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>setlocal

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>cd /d C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3\

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>jre\bin\java -Xmx500M -Xms200M -Xss16M -XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher

CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot

********************************************************************************

**                                  Protege                                   **

********************************************************************************

 

----------------- Initialising and Starting the OSGi Framework -----------------

FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory

 

The OSGi framework has been initialised

------------------------------- Starting Bundles -------------------------------

Starting bundle org.protege.common

Starting bundle org.eclipse.equinox.common

Starting bundle org.eclipse.equinox.supplement

Starting bundle org.eclipse.equinox.registry

Starting bundle org.protege.editor.core.application

Starting bundle org.apache.commons.io

Starting bundle com.google.guava

Starting bundle com.googlecode.javaewah.JavaEWAH

Starting bundle org.jsr-305

Starting bundle jul.to.slf4j

Starting bundle log4j.over.slf4j

Starting bundle ch.qos.logback.classic

Starting bundle ch.qos.logback.core

Starting bundle org.apache.servicemix.bundles.aopalliance

Starting bundle org.apache.servicemix.bundles.javax-inject

Starting bundle org.eclipse.equinox.common

Starting bundle org.eclipse.equinox.registry

Starting bundle org.eclipse.equinox.supplement

Starting bundle org.eclipse.jgit

Starting bundle org.semanticweb.owl.owlapi

Starting bundle org.protege.common

Starting bundle org.protege.editor.core.application

Starting bundle org.protege.editor.owl

Starting bundle slf4j.api

Starting bundle cellfie

Starting bundle code-generation

Starting bundle existentialquery

Starting bundle uk.ac.manchester.cs.owl.explanation

Starting bundle org.protege.ontograf

Starting bundle org.coode.dlquery

Starting bundle org.semanticweb.hermit

Starting bundle org.coode.browser

Starting bundle org.coode.owlviz

Starting bundle org.protege.owl.rdf

Starting bundle org.protege.editor.owl.rdf

Starting bundle swrltab-plugin

The OSGi framework has been started

 

------------------------------------ Protege -----------------------------------

Protege Desktop

Version 5.5.0, Build beta-3

 

 

----------------------------------- Platform -----------------------------------

Java: JVM 1.8.0_40-b26  Memory: 466M

Language: en, Country: US

Framework: Apache Software Foundation (1.8)

OS: windows8 (6.3)

Processor: x86-64

 

 

------------------------------------ Plugins -----------------------------------

Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)

Plugin: OWL Code Generation Plug-in (2.0.0)

Plugin: Existential Query (2.0.0)

Plugin: Explanation Workbench (3.0.0)

Plugin: OntoGraf (2.0.3)

Plugin: DL Query (4.0.1)

Plugin: HermiT (1.3.8.413)

Plugin: Browser View (OWLDoc) (3.0.3)

Plugin: OWLViz (5.0.3)

Plugin: OWLAPI RDF Library (2.0.2)

Plugin: Protege SPARQL Plugin (2.0.1)

Plugin: SWRLTab Protege 5.0+ Plugin (2.0.5)

 

Creating and setting up empty (default) editor kit

OWL API Version: 4.5.6.2018-09-06T00:27:41Z

Cannot generate ontology catalog for ontology at http://www.semanticweb.org/kcason/ontologies/2018/10/untitled-ontology-147

------------------------------- Auto-update Check ------------------------------

Auto-update is disabled

 

### Excluding compile: javax.swing.text.GlyphView::getBreakSpot

OWL API Version: 4.5.6.2018-09-06T00:27:41Z

------------------------------- Loading Ontology -------------------------------

Loading ontology from file:/C:/Users/kcason/Documents/IdeaProjects/HPM/emap_spring_project/src/main/resources/static/data/Demo-init.owl

Finished loading file:/C:/Users/kcason/Documents/IdeaProjects/HPM/emap_spring_project/src/main/resources/static/data/Demo-init.owl

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

Loading for ontology and imports closure successfully completed in 2704 ms

 

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

---------------------------- Disposing of Workspace ----------------------------

Saved tab state for 'Entities' tab

Saved tab state for 'Individuals by class' tab

Saved workspace

Disposed of 'Entities' tab

Disposed of 'Individuals by class' tab

Disposed of workspace

 

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

------------------------------- Loading Ontology -------------------------------

Loading ontology from file:/C:/Users/kcason/Desktop/Chimera.owl

Finished loading file:/C:/Users/kcason/Desktop/Chimera.owl

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

Loading for ontology and imports closure successfully completed in 1118 ms

 

------------------------------- Running Reasoner -------------------------------

Pre-computing inferences:

    - class hierarchy

    - object property hierarchy

    - data property hierarchy

    - class assertions

    - object property assertions

    - same individuals

Ontologies processed in 4108 ms by null

 

Uncaught Exception in thread 'AWT-EventQueue-0'

java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

        at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

        at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

        at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

        at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

        at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

        at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]

        at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:44) ~[na:na]

        at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:34) ~[na:na]

        at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]

        at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]

        at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]

        at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]

        at java.awt.Component.processHierarchyEvent(Component.java:6692) ~[na:1.8.0_40]

        at java.awt.Component.processEvent(Component.java:6311) ~[na:1.8.0_40]

        at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.Component.addNotify(Component.java:6961) ~[na:1.8.0_40]

        at java.awt.Container.addNotify(Container.java:2762) ~[na:1.8.0_40]

        at javax.swing.JComponent.addNotify(JComponent.java:4749) ~[na:1.8.0_40]

        at java.awt.Container.addNotify(Container.java:2773) ~[na:1.8.0_40]

        at javax.swing.JComponent.addNotify(JComponent.java:4749) ~[na:1.8.0_40]

        at java.awt.Container.addImpl(Container.java:1119) ~[na:1.8.0_40]

        at java.awt.Container.add(Container.java:415) ~[na:1.8.0_40]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:71) ~[na:na]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:77) ~[na:na]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:77) ~[na:na]

        at org.coode.mdock.NodePanel.rebuild(NodePanel.java:61) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel.handleMouseClicked(DynamicConfigPanel.java:91) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel.access$100(DynamicConfigPanel.java:45) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel$2.mouseClicked(DynamicConfigPanel.java:72) ~[na:na]

        at java.awt.Component.processMouseEvent(Component.java:6528) ~[na:1.8.0_40]

        at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_40]

        at java.awt.Component.processEvent(Component.java:6290) ~[na:1.8.0_40]

        at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4542) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2278) ~[na:1.8.0_40]

        at java.awt.Window.dispatchEventImpl(Window.java:2750) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751) ~[na:1.8.0_40]

        at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_40]

        at java.awt.EventQueue$3.run(EventQueue.java:702) ~[na:1.8.0_40]

        at java.awt.EventQueue$3.run(EventQueue.java:696) ~[na:1.8.0_40]

        at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[na:1.8.0_40]

        at java.awt.EventQueue$4.run(EventQueue.java:724) ~[na:1.8.0_40]

        at java.awt.EventQueue$4.run(EventQueue.java:722) ~[na:1.8.0_40]

        at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]

        at java.awt.EventQueue.dispatchEvent(EventQueue.java:721) ~[na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]

 

I would be pulling out my hair if I had any left…

 

-Kenny

 

From: protege-dev <[hidden email]> On Behalf Of Csongor Nyulas
Sent: Thursday, November 29, 2018 1:57 PM
To: [hidden email]
Subject: Re: [protege-dev] NoSuchMethodError: plugin for Protege 5.5-beta3

 

Kenny did not receive the email (probably because of his email delivery settings), and asked me to reply to this email, so that he can continue discussion on the thread.
Hopefully this works...

Csongor

On 11/29/18 12:20 AM, Lorenz B. wrote:

Protege  is a Maven project, the dependencies are defined in the pom.xml. You can see it has a dependency to 4.5.6 [1]


All those stuff can be found in the Maven repo [2].
Indeed, your plugin must depend on the same version to avoid errors.

And hopefully, you're also using Maven in your development - it's so much more convenient.

On 11/28/18 8:59 PM, Kenny Cason wrote:

I’m building a plugin for Protégé 5.5-beta3, but keep getting the following error when invoking the plugin:

 

 Uncaught Exception in thread 'AWT-EventQueue-0'

  java.lang.NoSuchMethodError:   org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

                at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

                at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

                at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

                at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

                at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

                at radiance.emap.protege.query.model.QueryReasoner.precalculate(QueryReasoner.java:48) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initializeReasoner(EmapForm.java:251) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initialiseOWLView(EmapForm.java:221) ~[na:na]

 

I’ve tried many different versions of Protégé but always get the above error. My experience tells me I have a version mismatch of some library but can’t figure out how to identify the conflict nor how to fix it.

 

I thought I might have the incorrect OWLAPI version so I looked in the Protégé log and found this:

 

  Creating and setting up empty (default) editor kit

  OWL API Version: 4.5.6.2018-09-06T00:27:41Z

 

I couldn’t find OWLAPI version 4.5.6 anywhere on the web. The closest I found was 4.5.5:

https://github.com/owlcs/owlapi

 

Can someone please help me identify the above conflict, if that’s what it is?

 

Thanks,

 

-Kenny Cason

Radiance Technologies

Cyber Solutions Group

3133 General Hudnell Dr. Ste. 116
San Antonio, TX 78226

[hidden email]

206.550.0049

 



_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center



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Re: NoSuchMethodError: plugin for Protege 5.5-beta3

kcason

Solved it! See here: https://github.com/protegeproject/protege/issues/625

 

Summary: gotta have the latest RDF and SPARQL plugins (2.0.3 and 2.0.2 respectively).

Follow the instructions in the above link to update your local plugins. Sheesh!

 

BTW: Protégé 5.5-beta5 is still being distributed with the old RDF and SPARQL plugins (2.0.2 and 2.0.1).

The distribution deployment packaging should be updated to include the newer plugins.

 

-Kenny

 

From: protege-dev <[hidden email]> On Behalf Of Kenny Cason
Sent: Thursday, November 29, 2018 2:31 PM
To: Developer support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-dev] NoSuchMethodError: plugin for Protege 5.5-beta3

 

Yes, this is a Maven project. I added the dependency for 4.5.6 as you suggested below and still have the same problem. I added a check in my plugin code to print the OWL API version information both at compilation time and run time and everything is showing 4.5.6.

 

So, I decided to build Protégé from scratch just like the instructions say to do (without any of my custom code). I downloaded 5.5-beta3, 5.5-beta4 and master (5.5-beta5) and compiled each individually with the same command:

  $ mvn clean package

 

All three versions built fine. But when I bring up any of them (run.bat) and try to use the built-in SPARQL query plugin I get the same error as described in my previous post. This indicates to me there is something in my environment, not my code, that is causing a conflict. Here is the log when running Protégé and trying to activate the SPARQL plugin (two ontologies are loaded and the HermiT reasoner is on):

 

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>setlocal

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>cd /d C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3\

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>jre\bin\java -Xmx500M -Xms200M -Xss16M -XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher

CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot

********************************************************************************

**                                  Protege                                   **

********************************************************************************

 

----------------- Initialising and Starting the OSGi Framework -----------------

FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory

 

The OSGi framework has been initialised

------------------------------- Starting Bundles -------------------------------

Starting bundle org.protege.common

Starting bundle org.eclipse.equinox.common

Starting bundle org.eclipse.equinox.supplement

Starting bundle org.eclipse.equinox.registry

Starting bundle org.protege.editor.core.application

Starting bundle org.apache.commons.io

Starting bundle com.google.guava

Starting bundle com.googlecode.javaewah.JavaEWAH

Starting bundle org.jsr-305

Starting bundle jul.to.slf4j

Starting bundle log4j.over.slf4j

Starting bundle ch.qos.logback.classic

Starting bundle ch.qos.logback.core

Starting bundle org.apache.servicemix.bundles.aopalliance

Starting bundle org.apache.servicemix.bundles.javax-inject

Starting bundle org.eclipse.equinox.common

Starting bundle org.eclipse.equinox.registry

Starting bundle org.eclipse.equinox.supplement

Starting bundle org.eclipse.jgit

Starting bundle org.semanticweb.owl.owlapi

Starting bundle org.protege.common

Starting bundle org.protege.editor.core.application

Starting bundle org.protege.editor.owl

Starting bundle slf4j.api

Starting bundle cellfie

Starting bundle code-generation

Starting bundle existentialquery

Starting bundle uk.ac.manchester.cs.owl.explanation

Starting bundle org.protege.ontograf

Starting bundle org.coode.dlquery

Starting bundle org.semanticweb.hermit

Starting bundle org.coode.browser

Starting bundle org.coode.owlviz

Starting bundle org.protege.owl.rdf

Starting bundle org.protege.editor.owl.rdf

Starting bundle swrltab-plugin

The OSGi framework has been started

 

------------------------------------ Protege -----------------------------------

Protege Desktop

Version 5.5.0, Build beta-3

 

 

----------------------------------- Platform -----------------------------------

Java: JVM 1.8.0_40-b26  Memory: 466M

Language: en, Country: US

Framework: Apache Software Foundation (1.8)

OS: windows8 (6.3)

Processor: x86-64

 

 

------------------------------------ Plugins -----------------------------------

Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)

Plugin: OWL Code Generation Plug-in (2.0.0)

Plugin: Existential Query (2.0.0)

Plugin: Explanation Workbench (3.0.0)

Plugin: OntoGraf (2.0.3)

Plugin: DL Query (4.0.1)

Plugin: HermiT (1.3.8.413)

Plugin: Browser View (OWLDoc) (3.0.3)

Plugin: OWLViz (5.0.3)

Plugin: OWLAPI RDF Library (2.0.2)

Plugin: Protege SPARQL Plugin (2.0.1)

Plugin: SWRLTab Protege 5.0+ Plugin (2.0.5)

 

Creating and setting up empty (default) editor kit

OWL API Version: 4.5.6.2018-09-06T00:27:41Z

Cannot generate ontology catalog for ontology at http://www.semanticweb.org/kcason/ontologies/2018/10/untitled-ontology-147

------------------------------- Auto-update Check ------------------------------

Auto-update is disabled

 

### Excluding compile: javax.swing.text.GlyphView::getBreakSpot

OWL API Version: 4.5.6.2018-09-06T00:27:41Z

------------------------------- Loading Ontology -------------------------------

Loading ontology from file:/C:/Users/kcason/Documents/IdeaProjects/HPM/emap_spring_project/src/main/resources/static/data/Demo-init.owl

Finished loading file:/C:/Users/kcason/Documents/IdeaProjects/HPM/emap_spring_project/src/main/resources/static/data/Demo-init.owl

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

Loading for ontology and imports closure successfully completed in 2704 ms

 

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

---------------------------- Disposing of Workspace ----------------------------

Saved tab state for 'Entities' tab

Saved tab state for 'Individuals by class' tab

Saved workspace

Disposed of 'Entities' tab

Disposed of 'Individuals by class' tab

Disposed of workspace

 

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

------------------------------- Loading Ontology -------------------------------

Loading ontology from file:/C:/Users/kcason/Desktop/Chimera.owl

Finished loading file:/C:/Users/kcason/Desktop/Chimera.owl

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

Loading for ontology and imports closure successfully completed in 1118 ms

 

------------------------------- Running Reasoner -------------------------------

Pre-computing inferences:

    - class hierarchy

    - object property hierarchy

    - data property hierarchy

    - class assertions

    - object property assertions

    - same individuals

Ontologies processed in 4108 ms by null

 

Uncaught Exception in thread 'AWT-EventQueue-0'

java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

        at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

        at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

        at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

        at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

        at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

        at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]

        at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:44) ~[na:na]

        at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:34) ~[na:na]

        at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]

        at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]

        at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]

        at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]

        at java.awt.Component.processHierarchyEvent(Component.java:6692) ~[na:1.8.0_40]

        at java.awt.Component.processEvent(Component.java:6311) ~[na:1.8.0_40]

        at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.Component.addNotify(Component.java:6961) ~[na:1.8.0_40]

        at java.awt.Container.addNotify(Container.java:2762) ~[na:1.8.0_40]

        at javax.swing.JComponent.addNotify(JComponent.java:4749) ~[na:1.8.0_40]

        at java.awt.Container.addNotify(Container.java:2773) ~[na:1.8.0_40]

        at javax.swing.JComponent.addNotify(JComponent.java:4749) ~[na:1.8.0_40]

        at java.awt.Container.addImpl(Container.java:1119) ~[na:1.8.0_40]

        at java.awt.Container.add(Container.java:415) ~[na:1.8.0_40]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:71) ~[na:na]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:77) ~[na:na]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:77) ~[na:na]

        at org.coode.mdock.NodePanel.rebuild(NodePanel.java:61) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel.handleMouseClicked(DynamicConfigPanel.java:91) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel.access$100(DynamicConfigPanel.java:45) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel$2.mouseClicked(DynamicConfigPanel.java:72) ~[na:na]

        at java.awt.Component.processMouseEvent(Component.java:6528) ~[na:1.8.0_40]

        at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_40]

        at java.awt.Component.processEvent(Component.java:6290) ~[na:1.8.0_40]

        at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4542) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2278) ~[na:1.8.0_40]

        at java.awt.Window.dispatchEventImpl(Window.java:2750) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751) ~[na:1.8.0_40]

        at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_40]

        at java.awt.EventQueue$3.run(EventQueue.java:702) ~[na:1.8.0_40]

        at java.awt.EventQueue$3.run(EventQueue.java:696) ~[na:1.8.0_40]

        at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[na:1.8.0_40]

        at java.awt.EventQueue$4.run(EventQueue.java:724) ~[na:1.8.0_40]

        at java.awt.EventQueue$4.run(EventQueue.java:722) ~[na:1.8.0_40]

        at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]

        at java.awt.EventQueue.dispatchEvent(EventQueue.java:721) ~[na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]

 

I would be pulling out my hair if I had any left…

 

-Kenny

 

From: protege-dev <[hidden email]> On Behalf Of Csongor Nyulas
Sent: Thursday, November 29, 2018 1:57 PM
To: [hidden email]
Subject: Re: [protege-dev] NoSuchMethodError: plugin for Protege 5.5-beta3

 

Kenny did not receive the email (probably because of his email delivery settings), and asked me to reply to this email, so that he can continue discussion on the thread.
Hopefully this works...

Csongor

On 11/29/18 12:20 AM, Lorenz B. wrote:

Protege  is a Maven project, the dependencies are defined in the pom.xml. You can see it has a dependency to 4.5.6 [1]


All those stuff can be found in the Maven repo [2].
Indeed, your plugin must depend on the same version to avoid errors.

And hopefully, you're also using Maven in your development - it's so much more convenient.

On 11/28/18 8:59 PM, Kenny Cason wrote:

I’m building a plugin for Protégé 5.5-beta3, but keep getting the following error when invoking the plugin:

 

 Uncaught Exception in thread 'AWT-EventQueue-0'

  java.lang.NoSuchMethodError:   org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

                at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

                at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

                at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

                at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

                at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

                at radiance.emap.protege.query.model.QueryReasoner.precalculate(QueryReasoner.java:48) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initializeReasoner(EmapForm.java:251) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initialiseOWLView(EmapForm.java:221) ~[na:na]

 

I’ve tried many different versions of Protégé but always get the above error. My experience tells me I have a version mismatch of some library but can’t figure out how to identify the conflict nor how to fix it.

 

I thought I might have the incorrect OWLAPI version so I looked in the Protégé log and found this:

 

  Creating and setting up empty (default) editor kit

  OWL API Version: 4.5.6.2018-09-06T00:27:41Z

 

I couldn’t find OWLAPI version 4.5.6 anywhere on the web. The closest I found was 4.5.5:

https://github.com/owlcs/owlapi

 

Can someone please help me identify the above conflict, if that’s what it is?

 

Thanks,

 

-Kenny Cason

Radiance Technologies

Cyber Solutions Group

3133 General Hudnell Dr. Ste. 116
San Antonio, TX 78226

[hidden email]

206.550.0049

 

 

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

 

_______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

 


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Re: NoSuchMethodError: plugin for Protege 5.5-beta3

Csongor Nyulas
Administrator
Thank you for sharing the solution with us, Kenny.

It is a mistake that P5.5-beta5 is distributed with the wrong RDF and SPARQL plugins. We should definitely fix that for P5.5.

Csongor

On 11/30/18 9:36 AM, Kenny Cason wrote:

Solved it! See here: https://github.com/protegeproject/protege/issues/625

 

Summary: gotta have the latest RDF and SPARQL plugins (2.0.3 and 2.0.2 respectively).

Follow the instructions in the above link to update your local plugins. Sheesh!

 

BTW: Protégé 5.5-beta5 is still being distributed with the old RDF and SPARQL plugins (2.0.2 and 2.0.1).

The distribution deployment packaging should be updated to include the newer plugins.

 

-Kenny

 

From: protege-dev [hidden email] On Behalf Of Kenny Cason
Sent: Thursday, November 29, 2018 2:31 PM
To: Developer support for WebProtege and Protege Desktop [hidden email]
Subject: Re: [protege-dev] NoSuchMethodError: plugin for Protege 5.5-beta3

 

Yes, this is a Maven project. I added the dependency for 4.5.6 as you suggested below and still have the same problem. I added a check in my plugin code to print the OWL API version information both at compilation time and run time and everything is showing 4.5.6.

 

So, I decided to build Protégé from scratch just like the instructions say to do (without any of my custom code). I downloaded 5.5-beta3, 5.5-beta4 and master (5.5-beta5) and compiled each individually with the same command:

  $ mvn clean package

 

All three versions built fine. But when I bring up any of them (run.bat) and try to use the built-in SPARQL query plugin I get the same error as described in my previous post. This indicates to me there is something in my environment, not my code, that is causing a conflict. Here is the log when running Protégé and trying to activate the SPARQL plugin (two ontologies are loaded and the HermiT reasoner is on):

 

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>setlocal

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>cd /d C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3\

 

C:\Users\kcason\Downloads\protege-distribution-5.5.0-beta-3\Protege\target\Protege-5.5.0-beta-3-win\Protege-5.5.0-beta-3>jre\bin\java -Xmx500M -Xms200M -Xss16M -XX:CompileCommand=exclude,javax/swing/text/GlyphView,getBreakSpot -DentityExpansionLimit=100000000 -Dlogback.configurationFile=conf/logback-win.xml -Dfile.encoding=utf-8 -Dorg.protege.plugin.dir=plugins -classpath bundles/guava.jar;bundles/logback-classic.jar;bundles/logback-core.jar;bundles/slf4j-api.jar;bin/org.apache.felix.main.jar;bin/maven-artifact.jar;bin/protege-launcher.jar org.protege.osgi.framework.Launcher

CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot

********************************************************************************

**                                  Protege                                   **

********************************************************************************

 

----------------- Initialising and Starting the OSGi Framework -----------------

FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory

 

The OSGi framework has been initialised

------------------------------- Starting Bundles -------------------------------

Starting bundle org.protege.common

Starting bundle org.eclipse.equinox.common

Starting bundle org.eclipse.equinox.supplement

Starting bundle org.eclipse.equinox.registry

Starting bundle org.protege.editor.core.application

Starting bundle org.apache.commons.io

Starting bundle com.google.guava

Starting bundle com.googlecode.javaewah.JavaEWAH

Starting bundle org.jsr-305

Starting bundle jul.to.slf4j

Starting bundle log4j.over.slf4j

Starting bundle ch.qos.logback.classic

Starting bundle ch.qos.logback.core

Starting bundle org.apache.servicemix.bundles.aopalliance

Starting bundle org.apache.servicemix.bundles.javax-inject

Starting bundle org.eclipse.equinox.common

Starting bundle org.eclipse.equinox.registry

Starting bundle org.eclipse.equinox.supplement

Starting bundle org.eclipse.jgit

Starting bundle org.semanticweb.owl.owlapi

Starting bundle org.protege.common

Starting bundle org.protege.editor.core.application

Starting bundle org.protege.editor.owl

Starting bundle slf4j.api

Starting bundle cellfie

Starting bundle code-generation

Starting bundle existentialquery

Starting bundle uk.ac.manchester.cs.owl.explanation

Starting bundle org.protege.ontograf

Starting bundle org.coode.dlquery

Starting bundle org.semanticweb.hermit

Starting bundle org.coode.browser

Starting bundle org.coode.owlviz

Starting bundle org.protege.owl.rdf

Starting bundle org.protege.editor.owl.rdf

Starting bundle swrltab-plugin

The OSGi framework has been started

 

------------------------------------ Protege -----------------------------------

Protege Desktop

Version 5.5.0, Build beta-3

 

 

----------------------------------- Platform -----------------------------------

Java: JVM 1.8.0_40-b26  Memory: 466M

Language: en, Country: US

Framework: Apache Software Foundation (1.8)

OS: windows8 (6.3)

Processor: x86-64

 

 

------------------------------------ Plugins -----------------------------------

Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)

Plugin: OWL Code Generation Plug-in (2.0.0)

Plugin: Existential Query (2.0.0)

Plugin: Explanation Workbench (3.0.0)

Plugin: OntoGraf (2.0.3)

Plugin: DL Query (4.0.1)

Plugin: HermiT (1.3.8.413)

Plugin: Browser View (OWLDoc) (3.0.3)

Plugin: OWLViz (5.0.3)

Plugin: OWLAPI RDF Library (2.0.2)

Plugin: Protege SPARQL Plugin (2.0.1)

Plugin: SWRLTab Protege 5.0+ Plugin (2.0.5)

 

Creating and setting up empty (default) editor kit

OWL API Version: 4.5.6.2018-09-06T00:27:41Z

Cannot generate ontology catalog for ontology at http://www.semanticweb.org/kcason/ontologies/2018/10/untitled-ontology-147

------------------------------- Auto-update Check ------------------------------

Auto-update is disabled

 

### Excluding compile: javax.swing.text.GlyphView::getBreakSpot

OWL API Version: 4.5.6.2018-09-06T00:27:41Z

------------------------------- Loading Ontology -------------------------------

Loading ontology from file:/C:/Users/kcason/Documents/IdeaProjects/HPM/emap_spring_project/src/main/resources/static/data/Demo-init.owl

Finished loading file:/C:/Users/kcason/Documents/IdeaProjects/HPM/emap_spring_project/src/main/resources/static/data/Demo-init.owl

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

Loading for ontology and imports closure successfully completed in 2704 ms

 

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

---------------------------- Disposing of Workspace ----------------------------

Saved tab state for 'Entities' tab

Saved tab state for 'Individuals by class' tab

Saved workspace

Disposed of 'Entities' tab

Disposed of 'Individuals by class' tab

Disposed of workspace

 

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

------------------------------- Loading Ontology -------------------------------

Loading ontology from file:/C:/Users/kcason/Desktop/Chimera.owl

Finished loading file:/C:/Users/kcason/Desktop/Chimera.owl

[GitRepo] Git repository detected: C:\Users\kcason\Documents\IdeaProjects\HPM\.git

[GitRepo] On branch: kenny-plugin-dev

Loading for ontology and imports closure successfully completed in 1118 ms

 

------------------------------- Running Reasoner -------------------------------

Pre-computing inferences:

    - class hierarchy

    - object property hierarchy

    - data property hierarchy

    - class assertions

    - object property assertions

    - same individuals

Ontologies processed in 4108 ms by null

 

Uncaught Exception in thread 'AWT-EventQueue-0'

java.lang.NoSuchMethodError: org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

        at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

        at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

        at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

        at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

        at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

        at org.protege.editor.owl.rdf.repository.BasicSparqlReasoner.precalculate(BasicSparqlReasoner.java:54) ~[na:na]

        at org.protege.editor.owl.rdf.SparqlQueryView.initializeReasoner(SparqlQueryView.java:44) ~[na:na]

        at org.protege.editor.owl.rdf.SparqlQueryView.initialiseOWLView(SparqlQueryView.java:34) ~[na:na]

        at org.protege.editor.owl.ui.view.AbstractOWLViewComponent.initialise(AbstractOWLViewComponent.java:43) ~[na:na]

        at org.protege.editor.core.ui.view.View.createContent(View.java:413) ~[na:na]

        at org.protege.editor.core.ui.view.View.createUI(View.java:220) ~[na:na]

        at org.protege.editor.core.ui.view.View$1.hierarchyChanged(View.java:124) ~[na:na]

        at java.awt.Component.processHierarchyEvent(Component.java:6692) ~[na:1.8.0_40]

        at java.awt.Component.processEvent(Component.java:6311) ~[na:1.8.0_40]

        at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.Component.addNotify(Component.java:6961) ~[na:1.8.0_40]

        at java.awt.Container.addNotify(Container.java:2762) ~[na:1.8.0_40]

        at javax.swing.JComponent.addNotify(JComponent.java:4749) ~[na:1.8.0_40]

        at java.awt.Container.addNotify(Container.java:2773) ~[na:1.8.0_40]

        at javax.swing.JComponent.addNotify(JComponent.java:4749) ~[na:1.8.0_40]

        at java.awt.Container.addImpl(Container.java:1119) ~[na:1.8.0_40]

        at java.awt.Container.add(Container.java:415) ~[na:1.8.0_40]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:71) ~[na:na]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:77) ~[na:na]

        at org.coode.mdock.NodePanel.addNode(NodePanel.java:77) ~[na:na]

        at org.coode.mdock.NodePanel.rebuild(NodePanel.java:61) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel.handleMouseClicked(DynamicConfigPanel.java:91) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel.access$100(DynamicConfigPanel.java:45) ~[na:na]

        at org.coode.mdock.DynamicConfigPanel$2.mouseClicked(DynamicConfigPanel.java:72) ~[na:na]

        at java.awt.Component.processMouseEvent(Component.java:6528) ~[na:1.8.0_40]

        at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_40]

        at java.awt.Component.processEvent(Component.java:6290) ~[na:1.8.0_40]

        at java.awt.Container.processEvent(Container.java:2234) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEventImpl(Component.java:4881) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2292) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4542) ~[na:1.8.0_40]

        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462) ~[na:1.8.0_40]

        at java.awt.Container.dispatchEventImpl(Container.java:2278) ~[na:1.8.0_40]

        at java.awt.Window.dispatchEventImpl(Window.java:2750) ~[na:1.8.0_40]

        at java.awt.Component.dispatchEvent(Component.java:4703) ~[na:1.8.0_40]

        at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751) ~[na:1.8.0_40]

        at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_40]

        at java.awt.EventQueue$3.run(EventQueue.java:702) ~[na:1.8.0_40]

        at java.awt.EventQueue$3.run(EventQueue.java:696) ~[na:1.8.0_40]

        at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86) ~[na:1.8.0_40]

        at java.awt.EventQueue$4.run(EventQueue.java:724) ~[na:1.8.0_40]

        at java.awt.EventQueue$4.run(EventQueue.java:722) ~[na:1.8.0_40]

        at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]

        at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]

        at java.awt.EventQueue.dispatchEvent(EventQueue.java:721) ~[na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]

        at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]

        at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]

 

I would be pulling out my hair if I had any left…

 

-Kenny

 

From: protege-dev <[hidden email]> On Behalf Of Csongor Nyulas
Sent: Thursday, November 29, 2018 1:57 PM
To: [hidden email]
Subject: Re: [protege-dev] NoSuchMethodError: plugin for Protege 5.5-beta3

 

Kenny did not receive the email (probably because of his email delivery settings), and asked me to reply to this email, so that he can continue discussion on the thread.
Hopefully this works...

Csongor

On 11/29/18 12:20 AM, Lorenz B. wrote:

Protege  is a Maven project, the dependencies are defined in the pom.xml. You can see it has a dependency to 4.5.6 [1]


All those stuff can be found in the Maven repo [2].
Indeed, your plugin must depend on the same version to avoid errors.

And hopefully, you're also using Maven in your development - it's so much more convenient.

On 11/28/18 8:59 PM, Kenny Cason wrote:

I’m building a plugin for Protégé 5.5-beta3, but keep getting the following error when invoking the plugin:

 

 Uncaught Exception in thread 'AWT-EventQueue-0'

  java.lang.NoSuchMethodError:   org.semanticweb.owlapi.rdf.model.AbstractTranslator.<init>(Lorg/semanticweb/owlapi/model/OWLOntologyManager;Lorg/semanticweb/owlapi/model/OWLOntology;ZLorg/semanticweb/owlapi/util/IndividualAppearance;)V

                at org.protege.owl.rdf.impl.RDFTranslator.<init>(RDFTranslator.java:91) ~[na:na]

                at org.protege.owl.rdf.impl.RDFTranslator.translate(RDFTranslator.java:53) ~[na:na]

                at org.protege.owl.rdf.impl.OwlTripleStoreImpl.addAxiom(OwlTripleStoreImpl.java:99) ~[na:na]

                at org.protege.owl.rdf.Utilities.loadOwlTripleStore(Utilities.java:48) ~[na:na]

                at org.protege.owl.rdf.Utilities.getOwlTripleStore(Utilities.java:32) ~[na:na]

                at radiance.emap.protege.query.model.QueryReasoner.precalculate(QueryReasoner.java:48) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initializeReasoner(EmapForm.java:251) ~[na:na]

                at radiance.emap.protege.ui.EmapForm.initialiseOWLView(EmapForm.java:221) ~[na:na]

 

I’ve tried many different versions of Protégé but always get the above error. My experience tells me I have a version mismatch of some library but can’t figure out how to identify the conflict nor how to fix it.

 

I thought I might have the incorrect OWLAPI version so I looked in the Protégé log and found this:

 

  Creating and setting up empty (default) editor kit

  OWL API Version: 4.5.6.2018-09-06T00:27:41Z

 

I couldn’t find OWLAPI version 4.5.6 anywhere on the web. The closest I found was 4.5.5:

https://github.com/owlcs/owlapi

 

Can someone please help me identify the above conflict, if that’s what it is?

 

Thanks,

 

-Kenny Cason

Radiance Technologies

Cyber Solutions Group

3133 General Hudnell Dr. Ste. 116
San Antonio, TX 78226

[hidden email]

206.550.0049

 

 

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-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

 

_______________________________________________
protege-dev mailing list
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_______________________________________________
protege-dev mailing list
[hidden email]
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[hidden email]
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