In 1.29.6 (and 1.30.0) we started interrupting the initialization thread when the OntologyService bean is disposed. When that occurs, Jena can raise an exception with the stacktrace below. This should be suppressed.
Exception in thread "uberonOntology_load_thread_IHB9O" com.hp.hpl.jena.shared.JenaException: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1publicId: http://purl.obolibrary.org/obo/uberon.owl; lineNumber: 36; columnNumber: 84; {E302} Interrupt detected.
at com.hp.hpl.jena.rdf.model.impl.RDFDefaultErrorHandler.fatalError(RDFDefaultErrorHandler.java:60)
at com.hp.hpl.jena.rdf.arp.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:51)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:211)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:185)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.warning(XMLHandler.java:180)
at com.hp.hpl.jena.rdf.arp.impl.XMLHandler.startElement(XMLHandler.java:121)
at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown Source)
at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown Source)
at org.apache.xerces.impl.dtd.XMLDTDValidator.startElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$ContentDispatcher.scanRootElementHook(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at com.hp.hpl.jena.rdf.arp.impl.RDFXMLParser.parse(RDFXMLParser.java:155)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:173)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:160)
at com.hp.hpl.jena.rdf.arp.JenaReader.read(JenaReader.java:199)
at com.hp.hpl.jena.rdf.model.impl.ModelCom.read(ModelCom.java:229)
at com.hp.hpl.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:2126)
at ubic.basecode.ontology.OntologyLoader.loadMemoryModel(OntologyLoader.java:290)
at ubic.basecode.ontology.OntologyLoader.loadMemoryModel(OntologyLoader.java:173)
at ubic.basecode.ontology.providers.AbstractOntologyMemoryBackedService.loadModel(AbstractOntologyMemoryBackedService.java:97)
at ubic.basecode.ontology.providers.AbstractOntologyService.getModel(AbstractOntologyService.java:461)
at ubic.basecode.ontology.providers.AbstractOntologyService$OntologyInitializationThread.run(AbstractOntologyService.java:93)
Caused by: com.hp.hpl.jena.rdf.arp.impl.XMLHandler$1publicId: http://purl.obolibrary.org/obo/uberon.owl; lineNumber: 36; columnNumber: 84; {E302} Interrupt detected.
... 26 more
Process finished with exit code 255
In 1.29.6 (and 1.30.0) we started interrupting the initialization thread when the
OntologyService
bean is disposed. When that occurs, Jena can raise an exception with the stacktrace below. This should be suppressed.