Feb 15, 2010 3:01:11 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser loadTriples INFO: Loading triples from: file:/export/home/oor/project/bioportal_resources/private/uploads/1105/1/COSMOtop875.owl Feb 15, 2010 3:20:08 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler printTriplesLoadLogMessage INFO: Loaded 10000 triples 61 Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processFramesWithWrongJavaType INFO: Postprocess: Process entities with incorrect Java type (6 entities) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processFramesWithWrongJavaType INFO: 6 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processMetaclasses INFO: Postprocess: Process metaclasses (3 metaclasses) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processMetaclasses INFO: 7 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processSubclassesOfRdfList INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processSubclassesOfRdfList INFO: 1 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInstancesWithMultipleTypes INFO: Postprocess: Instances with multiple types (144 instances) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInstancesWithMultipleTypes INFO: 60 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInferredSuperclasses INFO: Postprocess: Add inferred superclasses ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInferredSuperclasses INFO: 0 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processOrphanClses INFO: Postprocess: Process orphan classes (99 classes) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processOrphanClses INFO: 23 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processGeneralizedConceptInclusions INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processGeneralizedConceptInclusions INFO: 0 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processAbstractClasses INFO: Postprocess: Abstract classes... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processAbstractClasses INFO: 1 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processDomainAndRange INFO: Postprocess: Domain and range of properties... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processDomainAndRange INFO: 125 ms Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processPossiblyTypedResources INFO: Postprocess: Possibly typed entities (0 resources) ... Feb 15, 2010 3:24:12 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processPossiblyTypedResources INFO: 0 ms Feb 15, 2010 3:39:25 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler printTriplesLoadLogMessage INFO: Loaded 20000 triples 96 Feb 15, 2010 3:58:29 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler printTriplesLoadLogMessage INFO: Loaded 30000 triples 94 Feb 15, 2010 4:17:47 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler printTriplesLoadLogMessage INFO: Loaded 40000 triples 98 Feb 15, 2010 4:35:29 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser$ProtegeOWLStatementHandler printTriplesLoadLogMessage INFO: Loaded 50000 triples 111 INFO: Loaded 60000 triples 119 Feb 15, 2010 4:53:49 PM edu.stanford.smi.protege.storage.database.DefaultDatabaseFrameDb addValuesSQL Feb 15, 2010 4:58:18 PM edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser loadTriples INFO: Completed triple loading after 7026875 ms Feb 15, 2010 4:58:25 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processFramesWithWrongJavaType INFO: Postprocess: Process entities with incorrect Java type (16 entities) ... Feb 15, 2010 4:58:25 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processFramesWithWrongJavaType INFO: 45 ms Feb 15, 2010 4:58:25 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processMetaclasses INFO: Postprocess: Process metaclasses (3 metaclasses) ... Feb 15, 2010 4:58:26 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processMetaclasses INFO: 1414 ms Feb 15, 2010 4:58:26 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processSubclassesOfRdfList INFO: Postprocess: Process subclasses of rdf:List (1 classes) ... Feb 15, 2010 4:58:26 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processSubclassesOfRdfList INFO: 1 ms Feb 15, 2010 4:58:26 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInstancesWithMultipleTypes INFO: Postprocess: Instances with multiple types (5358 instances) ... Feb 15, 2010 5:10:14 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInstancesWithMultipleTypes INFO: 708172 ms Feb 15, 2010 5:10:14 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInferredSuperclasses INFO: Postprocess: Add inferred superclasses ... Feb 15, 2010 5:10:16 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processInferredSuperclasses INFO: 1598 ms Feb 15, 2010 5:10:17 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processOrphanClses INFO: Postprocess: Process orphan classes (6914 classes) ... Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processOrphanClses ********************************************************************************* ************** EXCEPTION RAISED HERE, BUT PROCESSING CONTINUES ****************** ********************************************************************************* WARNING: Error at computing orphan classes. Error message: edu.stanford.smi.protegex.owl.model.impl.DefaultOWLIndividual cannot be cast to edu.stanford.smi.protege.model.Cls java.lang.ClassCastException: edu.stanford.smi.protegex.owl.model.impl.DefaultOWLIndividual cannot be cast to edu.stanford.smi.protege.model.Cls at edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor$1.getR(TriplePostProcessor.java:280) at edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor$1.getR(TriplePostProcessor.java:277) at org.protege.editor.owl.model.hierarchy.roots.TerminalElementFinder.buildEquivalenceMapping(TerminalElementFinder.java:125) at org.protege.editor.owl.model.hierarchy.roots.TerminalElementFinder.appendTerminalElements(TerminalElementFinder.java:100) at edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor.processOrphanClses(TriplePostProcessor.java:299) at edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor.doPostProcessing(TriplePostProcessor.java:115) at edu.stanford.smi.protegex.owl.jena.parser.TripleProcessor.doPostProcessing(TripleProcessor.java:100) at edu.stanford.smi.protegex.owl.jena.parser.ProtegeOWLParser.doFinalPostProcessing(ProtegeOWLParser.java:346) (plus many more lines of stack trace...) ********************************************************************************* ********************************************************************************* Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processOrphanClses INFO: 26220 ms Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processGeneralizedConceptInclusions INFO: Postprocess: Generalized Concept Inclusion (0 axioms) ... Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processGeneralizedConceptInclusions INFO: 0 ms Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processAbstractClasses INFO: Postprocess: Abstract classes... Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processAbstractClasses INFO: 1 ms Feb 15, 2010 5:10:43 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processDomainAndRange INFO: Postprocess: Domain and range of properties... Feb 15, 2010 5:14:13 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processDomainAndRange INFO: 209481 ms Feb 15, 2010 5:14:13 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processPossiblyTypedResources INFO: Postprocess: Possibly typed entities (0 resources) ... Feb 15, 2010 5:14:13 PM edu.stanford.smi.protegex.owl.jena.parser.TriplePostProcessor processPossiblyTypedResources INFO: 0 ms Feb 15, 2010 5:14:22 PM edu.stanford.smi.protegex.owl.repository.impl.LocalFolderRepository update WARNING: [Local Folder Repository] The specified file must be a directory. (/export/home/oor/project/tomcat/bin/plugins/edu.stanford.smi.protegex.owl) Feb 15, 2010 5:15:03 PM com.noelios.restlet.LogFilter afterHandle INFO: 2010-02-15 17:15:03 127.0.0.1 - 127.0.0.1 8086 POST /bioportal/ontologies/parse/ - 200 258 109 8040718 http://localhost:8086 Java/1.6.0_15 -