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Annotation value rendering fails in cases when the value begins like a URL but contains characters not permitted in a URL #427

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csnyulas opened this issue May 16, 2016 · 0 comments
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Annotation value rendering fails in cases when the value begins like a URL but contains characters not permitted in a URL #427

csnyulas opened this issue May 16, 2016 · 0 comments

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@csnyulas
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csnyulas commented May 16, 2016 •
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Rendering of any of the following annotation property values would fail (with exceptions thrown and scrambled UI):

        <BioTRI2:Reference_URL>http://www.ncbi.nlm.nih.gov/pubmed/15122497
http://www.jstor.org/stable/pdf/10.1086/382755.pdf</BioTRI2:Reference_URL>

        <BioTRI2:Reference_URL>http://www.ncbi.nlm.nih.gov/pubmed/15122497 http://www.jstor.org/stable/pdf/10.1086/382755.pdf</BioTRI2:Reference_URL>

        <BioTRI2:Reference_URL>http://www.ncbi.nlm.nih.gov/pubmed/15122497  followed by random text</BioTRI2:Reference_URL>

        <BioTRI2:Reference_URL>  http://www.ncbi.nlm.nih.gov/pubmed/15122497  followed by random text</BioTRI2:Reference_URL>

but this is fine:

        <BioTRI2:Reference_URL>random text http://www.ncbi.nlm.nih.gov/pubmed/15122497</BioTRI2:Reference_URL>

        <BioTRI2:Reference_URL>random text http://www.ncbi.nlm.nih.gov/pubmed/15122497
http://www.jstor.org/stable/pdf/10.1086/382755.pdf</BioTRI2:Reference_URL>

This is the exception that we get on the failed rendering (sometimes several times):

Uncaught Exception in thread 'AWT-EventQueue-0' 
java.lang.IllegalArgumentException: Illegal character in path at index 43: http://www.ncbi.nlm.nih.gov/pubmed/15122497
http://www.jstor.org/stable/pdf/10.1086/382755.pdf
    at java.net.URI.create(URI.java:852) ~[na:1.8.0_40]
    at org.semanticweb.owlapi.model.IRI.toURI(IRI.java:56) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderExternalIRI(OWLAnnotationCellRenderer2.java:384) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderIRI(OWLAnnotationCellRenderer2.java:344) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderLiteral(OWLAnnotationCellRenderer2.java:472) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.access$200(OWLAnnotationCellRenderer2.java:35) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2$1.visit(OWLAnnotationCellRenderer2.java:322) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2$1.visit(OWLAnnotationCellRenderer2.java:312) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplPlain.accept(OWLLiteralImplPlain.java:213) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderAnnotationValue(OWLAnnotationCellRenderer2.java:312) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderCellValue(OWLAnnotationCellRenderer2.java:196) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.fillPage(OWLAnnotationCellRenderer2.java:160) ~[na:na]
    at org.protege.editor.owl.ui.renderer.layout.PageCellRenderer.getListCellRendererComponent(PageCellRenderer.java:93) ~[na:na]
    at org.protege.editor.owl.ui.framelist.OWLFrameListRenderer.getListCellRendererComponent(OWLFrameListRenderer.java:150) ~[na:na]
    at org.protege.editor.core.ui.list.MList$MListCellRenderer.getListCellRendererComponent(MList.java:260) ~[na:na]
    at org.protege.editor.owl.ui.framelist.OWLFrameList$OWLFrameListUI.updateLayoutState(OWLFrameList.java:837) ~[na:na]
    at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311) ~[na:1.8.0_40]
    at javax.swing.plaf.basic.BasicListUI.getPreferredSize(BasicListUI.java:578) ~[na:1.8.0_40]
    at javax.swing.JComponent.getPreferredSize(JComponent.java:1662) ~[na:1.8.0_40]
    at javax.swing.ScrollPaneLayout.layoutContainer(ScrollPaneLayout.java:791) ~[na:1.8.0_40]
    at java.awt.Container.layout(Container.java:1508) ~[na:1.8.0_40]
    at java.awt.Container.doLayout(Container.java:1497) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1693) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validateTree(Container.java:1702) ~[na:1.8.0_40]
    at java.awt.Container.validate(Container.java:1628) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$3.run(RepaintManager.java:704) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$3.run(RepaintManager.java:702) ~[na:1.8.0_40]
    at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
    at javax.swing.RepaintManager.validateInvalidComponents(RepaintManager.java:701) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1719) ~[na:1.8.0_40]
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) ~[na:1.8.0_40]
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:749) ~[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$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:719) ~[na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]
Caused by: java.net.URISyntaxException: Illegal character in path at index 43: http://www.ncbi.nlm.nih.gov/pubmed/15122497
http://www.jstor.org/stable/pdf/10.1086/382755.pdf
    at java.net.URI$Parser.fail(URI.java:2848) ~[na:1.8.0_40]
    at java.net.URI$Parser.checkChars(URI.java:3021) ~[na:1.8.0_40]
    at java.net.URI$Parser.parseHierarchical(URI.java:3105) ~[na:1.8.0_40]
    at java.net.URI$Parser.parse(URI.java:3053) ~[na:1.8.0_40]
    at java.net.URI.<init>(URI.java:588) ~[na:1.8.0_40]
    at java.net.URI.create(URI.java:850) ~[na:1.8.0_40]
    ... 62 common frames omitted
Uncaught Exception in thread 'AWT-EventQueue-0' 
java.lang.IllegalArgumentException: Illegal character in path at index 43: http://www.ncbi.nlm.nih.gov/pubmed/15122497
http://www.jstor.org/stable/pdf/10.1086/382755.pdf
    at java.net.URI.create(URI.java:852) ~[na:1.8.0_40]
    at org.semanticweb.owlapi.model.IRI.toURI(IRI.java:56) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderExternalIRI(OWLAnnotationCellRenderer2.java:384) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderIRI(OWLAnnotationCellRenderer2.java:344) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderLiteral(OWLAnnotationCellRenderer2.java:472) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.access$200(OWLAnnotationCellRenderer2.java:35) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2$1.visit(OWLAnnotationCellRenderer2.java:322) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2$1.visit(OWLAnnotationCellRenderer2.java:312) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.OWLLiteralImplPlain.accept(OWLLiteralImplPlain.java:213) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderAnnotationValue(OWLAnnotationCellRenderer2.java:312) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.renderCellValue(OWLAnnotationCellRenderer2.java:196) ~[na:na]
    at org.protege.editor.owl.ui.renderer.OWLAnnotationCellRenderer2.fillPage(OWLAnnotationCellRenderer2.java:160) ~[na:na]
    at org.protege.editor.owl.ui.renderer.layout.PageCellRenderer.getListCellRendererComponent(PageCellRenderer.java:93) ~[na:na]
    at org.protege.editor.owl.ui.framelist.OWLFrameListRenderer.getListCellRendererComponent(OWLFrameListRenderer.java:150) ~[na:na]
    at org.protege.editor.core.ui.list.MList$MListCellRenderer.getListCellRendererComponent(MList.java:260) ~[na:na]
    at org.protege.editor.owl.ui.framelist.OWLFrameList$OWLFrameListUI.updateLayoutState(OWLFrameList.java:837) ~[na:na]
    at javax.swing.plaf.basic.BasicListUI.maybeUpdateLayoutState(BasicListUI.java:1311) ~[na:1.8.0_40]
    at javax.swing.plaf.basic.BasicListUI.paintImpl(BasicListUI.java:264) ~[na:1.8.0_40]
    at javax.swing.plaf.basic.BasicListUI.paint(BasicListUI.java:240) ~[na:1.8.0_40]
    at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161) ~[na:1.8.0_40]
    at javax.swing.JComponent.paintComponent(JComponent.java:780) ~[na:1.8.0_40]
    at org.protege.editor.core.ui.list.MList.paintComponent(MList.java:400) ~[na:na]
    at javax.swing.JComponent.paint(JComponent.java:1056) ~[na:1.8.0_40]
    at javax.swing.JComponent.paintToOffscreen(JComponent.java:5219) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(RepaintManager.java:1572) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$PaintManager.paint(RepaintManager.java:1495) ~[na:1.8.0_40]
    at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:306) ~[na:1.8.0_40]
    at javax.swing.RepaintManager.paint(RepaintManager.java:1265) ~[na:1.8.0_40]
    at javax.swing.JComponent._paintImmediately(JComponent.java:5167) ~[na:1.8.0_40]
    at javax.swing.JComponent.paintImmediately(JComponent.java:4978) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$4.run(RepaintManager.java:824) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$4.run(RepaintManager.java:807) ~[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 javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:807) ~[na:1.8.0_40]
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:782) ~[na:1.8.0_40]
    at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:731) ~[na:1.8.0_40]
    at javax.swing.RepaintManager.access$1300(RepaintManager.java:64) ~[na:1.8.0_40]
    at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1720) ~[na:1.8.0_40]
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311) ~[na:1.8.0_40]
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:749) ~[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$1.doIntersectionPrivilege(ProtectionDomain.java:75) ~[na:1.8.0_40]
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:719) ~[na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_40]
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_40]
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_40]
Caused by: java.net.URISyntaxException: Illegal character in path at index 43: http://www.ncbi.nlm.nih.gov/pubmed/15122497
http://www.jstor.org/stable/pdf/10.1086/382755.pdf
    at java.net.URI$Parser.fail(URI.java:2848) ~[na:1.8.0_40]
    at java.net.URI$Parser.checkChars(URI.java:3021) ~[na:1.8.0_40]
    at java.net.URI$Parser.parseHierarchical(URI.java:3105) ~[na:1.8.0_40]
    at java.net.URI$Parser.parse(URI.java:3053) ~[na:1.8.0_40]
    at java.net.URI.<init>(URI.java:588) ~[na:1.8.0_40]
    at java.net.URI.create(URI.java:850) ~[na:1.8.0_40]
    ... 52 common frames omitted

There is a test ontology attached. Observe that the Case subclasses that have names starting with "BMOC_" exhibit the bug, but those not starting with "BMOC_" render fine.

Cases.owl.zip
@csnyulas csnyulas changed the title Annotation value rendering fails in when it begins like a URL but contains characters not permitted in a URL Annotation value rendering fails in cases when the value begins like a URL but contains characters not permitted in a URL May 16, 2016
@matthewhorridge matthewhorridge mentioned this issue Jun 4, 2016
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