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StringIndexOutOfBoundsException when adding annotation properties
Hi all, I'm creating an ontology that uses several custom annotation properties for annotating classes. Nonetheless, protege crashes randomly when I try to create annotations on class. Concretely, I have created two annotation properties "maxValue" and "minValue". The first time I annotate a class with one of these properties, it works well; however, when I try to include a second annotation on that class by using the other annotation property, the window for including annotations is not opening, and the log shows a java exception. Then, I'm able to save the ontology, close and reopen protege, load the ontology again, and include the annotation that failed previously.
I tried to reproduce the issue in a smaller test-case ontology, but I couldn't...
The log file is the following:
INFO 12:36:16 ------------------------------------ Protege -----------------------------------
INFO 12:36:16 Protege Desktop
INFO 12:36:16 Version 5.5.0, Build
INFO 12:36:16
INFO 12:36:16
INFO 12:36:16 ----------------------------------- Platform -----------------------------------
INFO 12:36:16 Java: JVM 1.8.0_121-b13 Memory: 8232M
INFO 12:36:16 Language: es, Country: ES
INFO 12:36:16 Framework: Apache Software Foundation (1.8)
INFO 12:36:16 OS: linux (5.4.0-65-generic)
INFO 12:36:16 Processor: x86-64
INFO 12:36:16
INFO 12:36:16 ------------------------------------ Plugins -----------------------------------
INFO 12:36:16 Plugin: SWRLTab Protege 5.0+ Plugin (2.0.6)
INFO 12:36:16 Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
INFO 12:36:16 Plugin: SPARQL Query Plugin (3.0.0)
INFO 12:36:16 Plugin: OWL Difference (6.0.2)
INFO 12:36:16 Plugin: Explanation Workbench (3.0.0)
INFO 12:36:16 Plugin: HermiT Reasoner (1.4.3.456)
INFO 12:36:16 Plugin: Factplusplus Plug-in (1.6.5)
INFO 12:36:16 Plugin: ELK Reasoner Protege Plug-in (0.4.3)
INFO 12:36:16 Plugin: DL Query (4.0.1)
INFO 12:36:16 Plugin: Existential Query (2.0.0)
INFO 12:36:16 Plugin: VOWL Plugin (0.1.4.SNAPSHOT)
INFO 12:36:16 Plugin: Browser View (OWLDoc) (3.0.3)
INFO 12:36:16 Plugin: OntoGraf (2.0.3)
INFO 12:36:16 Plugin: OWLViz (5.0.3)
INFO 12:36:16 Plugin: OWL Code Generation Plug-in (2.0.0)
INFO 12:36:16 Plugin: Pellet Reasoner Plug-in (2.2.0)
INFO 12:36:16 Plugin: OWLAPI RDF Library (3.0.0)
INFO 12:36:16
INFO 12:36:16 Creating and setting up empty (default) editor kit
INFO 12:36:16 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:36:18 Cannot generate ontology catalog for ontology at http://www.semanticweb.org/fabad/ontologies/2021/1/untitled-ontology-1583. URI scheme is not "file"
INFO 12:36:18 ------------------------------- Auto-update Check ------------------------------
INFO 12:36:18 Auto-update is disabled
INFO 12:36:18
INFO 12:37:04 OWL API Version: 4.5.9.2019-02-01T07:24:44Z
INFO 12:37:04 ------------------------------- Loading Ontology -------------------------------
INFO 12:37:04 Loading ontology from file:/home/fabad/Proyectos_python/P4Q-rest/resources/FormViewOntology.owl
INFO 12:37:04 Finished loading file:/home/fabad/Proyectos_python/P4Q-rest/resources/FormViewOntology.owl
INFO 12:37:04 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:37:04 [GitRepo] On branch: main
INFO 12:37:04 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:37:04 [GitRepo] On branch: main
INFO 12:37:04 Loading for ontology and imports closure successfully completed in 794 ms
INFO 12:37:04
INFO 12:37:05 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:37:05 [GitRepo] On branch: main
INFO 12:37:05 ---------------------------- Disposing of Workspace ----------------------------
INFO 12:37:05 Saved tab state for 'DL Query' tab
INFO 12:37:05 Saved tab state for 'Entities' tab
INFO 12:37:05 Saved tab state for 'OWLViz' tab
INFO 12:37:05 Saved tab state for 'OntoGraf' tab
INFO 12:37:05 Saved tab state for 'Individuals by class' tab
INFO 12:37:05 Saved tab state for 'VOWL' tab
INFO 12:37:05 Saved tab state for 'Active ontology' tab
INFO 12:37:05 Saved tab state for 'SPARQL Query' tab
INFO 12:37:05 Saved workspace
INFO 12:37:05 Disposed of 'DL Query' tab
INFO 12:37:05 Disposed of 'Entities' tab
INFO 12:37:05 Disposed of 'OWLViz' tab
INFO 12:37:05 Disposed of 'OntoGraf' tab
INFO 12:37:05 Disposed of 'Individuals by class' tab
INFO 12:37:05 Disposed of 'VOWL' tab
INFO 12:37:05 Disposed of 'Active ontology' tab
INFO 12:37:05 Disposed of 'SPARQL Query' tab
INFO 12:37:05 Disposed of workspace
INFO 12:37:05
INFO 12:37:05 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:37:05 [GitRepo] On branch: main
INFO 12:38:05 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:38:05 [GitRepo] On branch: main
INFO 12:38:08 ------------------------ Saving Workspace and Ontologies -----------------------
INFO 12:38:08 Will save the FormViewOntology ontology because it has been modified
INFO 12:38:08 Saving FormViewOntology
INFO 12:38:08 Saving ontology to temp file: /tmp/temp-ontology3354218334837036436
INFO 12:38:08 Copying ontology from temp file (/tmp/temp-ontology3354218334837036436) to actual destination (/home/fabad/Proyectos_python/P4Q-rest/resources/FormViewOntology.owl)
INFO 12:38:08 Removing temp file: /tmp/temp-ontology3354218334837036436
INFO 12:38:08 Saved ontology OntologyID(OntologyIRI(<http://www.semanticweb.org/Precise4Q/ontologies/FormViewOntology>) VersionIRI(<null>)) to file:/home/fabad/Proyectos_python/P4Q-rest/resources/FormViewOntology.owl in RDF/XML Syntax format
INFO 12:38:08 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:38:08 [GitRepo] On branch: main
INFO 12:38:08 Saved tab state for 'Active ontology' tab
INFO 12:38:08 Saved tab state for 'DL Query' tab
INFO 12:38:08 Saved tab state for 'OWLViz' tab
INFO 12:38:08 Saved tab state for 'Entities' tab
INFO 12:38:08 Saved tab state for 'VOWL' tab
INFO 12:38:08 Saved tab state for 'OntoGraf' tab
INFO 12:38:08 Saved tab state for 'Individuals by class' tab
INFO 12:38:08 Saved tab state for 'SPARQL Query' tab
INFO 12:38:08 Saved workspace
INFO 12:38:08
INFO 12:38:08 [GitRepo] Git repository detected: /home/fabad/Proyectos_python/P4Q-rest/.git
INFO 12:38:08 [GitRepo] On branch: main
ERROR 12:38:39 Uncaught Exception in thread 'AWT-EventQueue-0'
java.lang.StringIndexOutOfBoundsException: String index out of range: 0
at java.lang.String.charAt(String.java:658) ~[na:1.8.0_121]
at uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryInternalsImplNoCache.getOWLLiteral(OWLDataFactoryInternalsImplNoCache.java:186) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl.getOWLLiteral(OWLDataFactoryImpl.java:1854) ~[na:na]
at org.protege.editor.owl.ui.editor.OWLConstantEditor.getEditedObject(OWLConstantEditor.java:186) ~[na:na]
at org.protege.editor.owl.ui.editor.OWLConstantEditor.getEditedObject(OWLConstantEditor.java:38) ~[na:na]
at org.protege.editor.owl.ui.editor.OWLAnnotationEditor.isValid(OWLAnnotationEditor.java:242) ~[na:na]
at org.protege.editor.owl.ui.editor.OWLAnnotationEditor.addStatusChangedListener(OWLAnnotationEditor.java:248) ~[na:na]
at org.protege.editor.owl.ui.framelist.OWLFrameList.showEditorDialog(OWLFrameList.java:435) ~[na:na]
at org.protege.editor.owl.ui.framelist.OWLFrameList.handleEdit(OWLFrameList.java:367) ~[na:na]
at org.protege.editor.owl.ui.framelist.OWLFrameList.handleAdd(OWLFrameList.java:346) ~[na:na]
at org.protege.editor.core.ui.list.MList.lambda$new$1(MList.java:44) ~[na:na]
at org.protege.editor.core.ui.list.MList.handleMouseClick(MList.java:212) ~[na:na]
at org.protege.editor.core.ui.list.MList.access$200(MList.java:22) ~[na:na]
at org.protege.editor.core.ui.list.MList$3.mouseReleased(MList.java:107) ~[na:na]
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) ~[na:1.8.0_121]
at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289) ~[na:1.8.0_121]
at java.awt.Component.processMouseEvent(Component.java:6533) ~[na:1.8.0_121]
at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) ~[na:1.8.0_121]
at java.awt.Component.processEvent(Component.java:6298) ~[na:1.8.0_121]
at java.awt.Container.processEvent(Container.java:2236) ~[na:1.8.0_121]
at java.awt.Component.dispatchEventImpl(Component.java:4889) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2294) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4525) ~[na:1.8.0_121]
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) ~[na:1.8.0_121]
at java.awt.Container.dispatchEventImpl(Container.java:2280) ~[na:1.8.0_121]
at java.awt.Window.dispatchEventImpl(Window.java:2746) ~[na:1.8.0_121]
at java.awt.Component.dispatchEvent(Component.java:4711) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) ~[na:1.8.0_121]
at java.awt.EventQueue.access$500(EventQueue.java:97) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:709) ~[na:1.8.0_121]
at java.awt.EventQueue$3.run(EventQueue.java:703) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:90) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:731) ~[na:1.8.0_121]
at java.awt.EventQueue$4.run(EventQueue.java:729) ~[na:1.8.0_121]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_121]
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:80) ~[na:1.8.0_121]
at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) ~[na:1.8.0_121]
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) [na:1.8.0_121]
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) [na:1.8.0_121]
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82) [na:1.8.0_121]
@fanavarro are you able to provide your ontology and some steps to reproduce?
Hi @matthewhorridge.
Sure, I am attaching a zip file with the ontology (github does not allow attaching owl files). FormViewOntology.zip
The ontology has two custom annotation properties: hasMaxValue and hasMinValue. You can try to annotate a class with one of these properties, and then, make another annotation on the same class with the other property. Here you have some screenshots:
I hope this helps.
Thanks beforehand!
Hi everyone, I have new findings on this issue. This only happens when I manually select the type of the annotation (xsd:integer). If so, Protege fails when I try to include another annotation. However, if I leave the type of the annotation in blank, protege selects xsd:integer automatically (is this the expected behavior?) and then I can include other annotations without crashing.