Entity search error

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Entity search error

Wynne, Robert (NIH/NLM/LHC) [C]

Hi all,

 

My search box has an error symbol next to it after loading an ontology.  I’ve observed this after loading NCI Thesaurus and Human Phenotype ontologies.  I’m using P5, Windows 7, and Java 1.8.0_40.  Stacktrace and screenshot below.  Thanks for any pointers!

 

Error 1 Logged at Fri Apr 03 16:02:17 EDT 2015

IllegalArgumentException: Expected scheme-specific part at index 9: shadowed:#

    java.net.URI.create(URI.java:852)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.appendScheme(FolderGroupManager.java:359)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.recordEntries(FolderGroupManager.java:298)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineSingleFile(FolderGroupManager.java:273)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:239)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:245)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:245)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.update(FolderGroupManager.java:123)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.initializeCatalog(FolderGroupManager.java:142)

    org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatalogExists(OntologyCatalogManager.java:125)

    org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(OntologyCatalogManager.java:189)

    org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLModelManagerImpl.java:337)

    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:294)

    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:207)

    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:201)

    org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:173)

    org.protege.editor.core.ui.action.OpenAction.openInNewWorkspace(OpenAction.java:57)

    org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:216)

    org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)

    javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)

    javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)

    javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)

    javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

   javax.swing.AbstractButton.doClick(AbstractButton.java:376)

    javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)

    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)

    java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)

    java.awt.Component.processMouseEvent(Component.java:6525)

    javax.swing.JComponent.processMouseEvent(JComponent.java:3324)

    java.awt.Component.processEvent(Component.java:6290)

    java.awt.Container.processEvent(Container.java:2234)

    java.awt.Component.dispatchEventImpl(Component.java:4881)

    java.awt.Container.dispatchEventImpl(Container.java:2292)

    java.awt.Component.dispatchEvent(Component.java:4703)

    java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)

    java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)

    java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)

    java.awt.Container.dispatchEventImpl(Container.java:2278)

    java.awt.Window.dispatchEventImpl(Window.java:2750)

    java.awt.Component.dispatchEvent(Component.java:4703)

    java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)

    java.awt.EventQueue.access$500(EventQueue.java:97)

    java.awt.EventQueue$3.run(EventQueue.java:702)

    java.awt.EventQueue$3.run(EventQueue.java:696)

    java.security.AccessController.doPrivileged(Native Method)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)

    java.awt.EventQueue$4.run(EventQueue.java:724)

    java.awt.EventQueue$4.run(EventQueue.java:722)

    java.security.AccessController.doPrivileged(Native Method)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

    java.awt.EventQueue.dispatchEvent(EventQueue.java:721)

    java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)

    java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)

    java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)

    java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

    java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)

    java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

 

cid:image001.png@01D06E28.24052AD0

 

 

 

Rob

 


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Re: Entity search error

Wynne, Robert (NIH/NLM/LHC) [C]

I think I’ve answered my own question.  Apparently I can’t load files from my Desktop and have the search work.  If the source owl exists in the Protégé directory there is no issue.

 

Possibly a limitation of my gov’t PC…not sure.

 

Rob

 

From: Wynne, Robert (NIH/NCI) [C]
Sent: Friday, April 03, 2015 4:27 PM
To: User support for WebProtege and Protege Desktop ([hidden email])
Subject: [protege-user] Entity search error

 

Hi all,

 

My search box has an error symbol next to it after loading an ontology.  I’ve observed this after loading NCI Thesaurus and Human Phenotype ontologies.  I’m using P5, Windows 7, and Java 1.8.0_40.  Stacktrace and screenshot below.  Thanks for any pointers!

 

Error 1 Logged at Fri Apr 03 16:02:17 EDT 2015

IllegalArgumentException: Expected scheme-specific part at index 9: shadowed:#

    java.net.URI.create(URI.java:852)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.appendScheme(FolderGroupManager.java:359)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.recordEntries(FolderGroupManager.java:298)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineSingleFile(FolderGroupManager.java:273)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:239)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:245)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:245)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.update(FolderGroupManager.java:123)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.initializeCatalog(FolderGroupManager.java:142)

    org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatalogExists(OntologyCatalogManager.java:125)

    org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(OntologyCatalogManager.java:189)

    org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLModelManagerImpl.java:337)

    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:294)

    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:207)

    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:201)

    org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:173)

    org.protege.editor.core.ui.action.OpenAction.openInNewWorkspace(OpenAction.java:57)

    org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:216)

    org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)

    javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)

    javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)

    javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)

    javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

   javax.swing.AbstractButton.doClick(AbstractButton.java:376)

    javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)

    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)

    java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)

    java.awt.Component.processMouseEvent(Component.java:6525)

    javax.swing.JComponent.processMouseEvent(JComponent.java:3324)

    java.awt.Component.processEvent(Component.java:6290)

    java.awt.Container.processEvent(Container.java:2234)

    java.awt.Component.dispatchEventImpl(Component.java:4881)

    java.awt.Container.dispatchEventImpl(Container.java:2292)

    java.awt.Component.dispatchEvent(Component.java:4703)

    java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)

    java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)

    java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)

    java.awt.Container.dispatchEventImpl(Container.java:2278)

    java.awt.Window.dispatchEventImpl(Window.java:2750)

    java.awt.Component.dispatchEvent(Component.java:4703)

    java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)

    java.awt.EventQueue.access$500(EventQueue.java:97)

    java.awt.EventQueue$3.run(EventQueue.java:702)

    java.awt.EventQueue$3.run(EventQueue.java:696)

    java.security.AccessController.doPrivileged(Native Method)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)

    java.awt.EventQueue$4.run(EventQueue.java:724)

    java.awt.EventQueue$4.run(EventQueue.java:722)

    java.security.AccessController.doPrivileged(Native Method)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

    java.awt.EventQueue.dispatchEvent(EventQueue.java:721)

    java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)

    java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)

    java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)

    java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

    java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)

    java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

 

cid:image001.png@01D06E28.24052AD0

 

 

 

Rob

 


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Re: Entity search error

Matthew Horridge-2
Administrator
Hi Rob,

The red triangle isn’t related to the search box - it just happens to be next to it in the UI.

The error that you’re seeing is something to do with the generation of the xml catalog file.  I’m not sure where “shadowed:#” is coming from without some further investigation.

Cheers,

Matthew




On 3 Apr 2015, at 13:36, Wynne, Robert (NIH/NCI) [C] <[hidden email]> wrote:

I think I’ve answered my own question.  Apparently I can’t load files from my Desktop and have the search work.  If the source owl exists in the Protégé directory there is no issue.

 

Possibly a limitation of my gov’t PC…not sure.

 

Rob

 

From: Wynne, Robert (NIH/NCI) [C]
Sent: Friday, April 03, 2015 4:27 PM
To: User support for WebProtege and Protege Desktop ([hidden email])
Subject: [protege-user] Entity search error

 

Hi all,

 

My search box has an error symbol next to it after loading an ontology.  I’ve observed this after loading NCI Thesaurus and Human Phenotype ontologies.  I’m using P5, Windows 7, and Java 1.8.0_40.  Stacktrace and screenshot below.  Thanks for any pointers!

 

Error 1 Logged at Fri Apr 03 16:02:17 EDT 2015

IllegalArgumentException: Expected scheme-specific part at index 9: shadowed:#

    java.net.URI.create(URI.java:852)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.appendScheme(FolderGroupManager.java:359)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.recordEntries(FolderGroupManager.java:298)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineSingleFile(FolderGroupManager.java:273)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:239)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:245)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.examineDirectoryContents(FolderGroupManager.java:245)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.update(FolderGroupManager.java:123)

    org.protege.editor.owl.model.library.folder.FolderGroupManager.initializeCatalog(FolderGroupManager.java:142)

    org.protege.editor.owl.model.library.OntologyCatalogManager.ensureCatalogExists(OntologyCatalogManager.java:125)

    org.protege.editor.owl.model.library.OntologyCatalogManager.addFolder(OntologyCatalogManager.java:189)

    org.protege.editor.owl.model.OWLModelManagerImpl.addRootFolder(OWLModelManagerImpl.java:337)

    org.protege.editor.owl.model.OWLModelManagerImpl.loadOntologyFromPhysicalURI(OWLModelManagerImpl.java:294)

    org.protege.editor.owl.OWLEditorKit.handleLoadFrom(OWLEditorKit.java:207)

    org.protege.editor.owl.OWLEditorKit.handleLoadRequest(OWLEditorKit.java:201)

    org.protege.editor.core.ProtegeManager.openAndSetupEditorKit(ProtegeManager.java:173)

    org.protege.editor.core.ui.action.OpenAction.openInNewWorkspace(OpenAction.java:57)

    org.protege.editor.core.ui.util.UIUtil.openRequest(UIUtil.java:216)

    org.protege.editor.core.ui.action.OpenAction.actionPerformed(OpenAction.java:33)

    javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)

    javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2346)

    javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)

    javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)

   javax.swing.AbstractButton.doClick(AbstractButton.java:376)

    javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833)

    javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877)

    java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)

    java.awt.Component.processMouseEvent(Component.java:6525)

    javax.swing.JComponent.processMouseEvent(JComponent.java:3324)

    java.awt.Component.processEvent(Component.java:6290)

    java.awt.Container.processEvent(Container.java:2234)

    java.awt.Component.dispatchEventImpl(Component.java:4881)

    java.awt.Container.dispatchEventImpl(Container.java:2292)

    java.awt.Component.dispatchEvent(Component.java:4703)

    java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4898)

    java.awt.LightweightDispatcher.processMouseEvent(Container.java:4533)

    java.awt.LightweightDispatcher.dispatchEvent(Container.java:4462)

    java.awt.Container.dispatchEventImpl(Container.java:2278)

    java.awt.Window.dispatchEventImpl(Window.java:2750)

    java.awt.Component.dispatchEvent(Component.java:4703)

    java.awt.EventQueue.dispatchEventImpl(EventQueue.java:751)

    java.awt.EventQueue.access$500(EventQueue.java:97)

    java.awt.EventQueue$3.run(EventQueue.java:702)

    java.awt.EventQueue$3.run(EventQueue.java:696)

    java.security.AccessController.doPrivileged(Native Method)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:86)

    java.awt.EventQueue$4.run(EventQueue.java:724)

    java.awt.EventQueue$4.run(EventQueue.java:722)

    java.security.AccessController.doPrivileged(Native Method)

    java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75)

    java.awt.EventQueue.dispatchEvent(EventQueue.java:721)

    java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)

    java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)

    java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)

    java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)

    java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)

    java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

 

<image001.png>

 

 

 

Rob

 

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


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