Regression with SWC ontology

[hoijui]

As originally reported by @mariapoveda, this ontology, if its content is pasted into the webapp, now causes an exception:
http://oops.linkeddata.es/example/swc_2009-05-09.rdf

It did not do so in the old version of OOPS.

As noted by @pieterhijma, it looks like http://data.semanticweb.org/ns/swc/ontology# is tried ot be accessed, which is redirected to http://data.semanticweb.org/ns/swc/swrc, which times out. Probably this was somehow silently ignored in earlier versions of the OWLAPI, used by the old OOPS.

HTTP Status 500 – Internal Server Error

Type Exception Report

Message An exception occurred processing [/report-advanced.jsp] at line [191]

Description The server encountered an unexpected condition that prevented it from fulfilling the request.

Exception

org.apache.jasper.JasperException: An exception occurred processing [/report-advanced.jsp] at line [191]

188: 				final Report report;
189: 				if (srcSpec != null) {
190: 					final Linter linter = new Linter();
191: 					final SrcModel srcModel = ModelLoader.load(srcSpec);
192: 					final List<Checker> checkers;
193: 					if (checkIds == null) {
194: 						checkers = CheckersCatalogue.getAllCheckers();


Stacktrace:
	org.apache.jasper.servlet.JspServletWrapper.handleJspException(JspServletWrapper.java:599)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:488)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:377)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:325)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

Root Cause

org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <http://data.semanticweb.org/ns/swc/swrc> Cause: OWLOntologyCreationIOException: java.net.SocketTimeoutException: Connect timed out
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1710)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1555)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:369)
	org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1563)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:382)
	org.semanticweb.owlapi.rdf.rdfxml.parser.ResourceOrLiteralElement.endElement(StartRDF.java:557)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.endElement(RDFParser.java:224)
	org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
	org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:161)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:65)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005)
	es.upm.fi.oeg.oops.ModelLoader.loadOwl(ModelLoader.java:117)
	es.upm.fi.oeg.oops.ModelLoader.load(ModelLoader.java:121)
	org.apache.jsp.report_002dadvanced_jsp._jspService(report_002dadvanced_jsp.java:354)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:67)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:456)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:377)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:325)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

Root Cause

org.semanticweb.owlapi.io.OWLOntologyCreationIOException: OWLOntologyCreationIOException: java.net.SocketTimeoutException: Connect timed out
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:216)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:955)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1663)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1703)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1555)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:369)
	org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1563)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:382)
	org.semanticweb.owlapi.rdf.rdfxml.parser.ResourceOrLiteralElement.endElement(StartRDF.java:557)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.endElement(RDFParser.java:224)
	org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
	org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:161)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:65)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005)
	es.upm.fi.oeg.oops.ModelLoader.loadOwl(ModelLoader.java:117)
	es.upm.fi.oeg.oops.ModelLoader.load(ModelLoader.java:121)
	org.apache.jsp.report_002dadvanced_jsp._jspService(report_002dadvanced_jsp.java:354)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:67)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:456)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:377)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:325)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

Root Cause

org.semanticweb.owlapi.io.OWLOntologyInputSourceException: java.net.SocketTimeoutException: Connect timed out
	org.semanticweb.owlapi.io.DocumentSources.getInputStream(DocumentSources.java:218)
	org.semanticweb.owlapi.io.DocumentSources.wrapInput(DocumentSources.java:143)
	org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader(DocumentSources.java:88)
	org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader(DocumentSources.java:105)
	org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:38)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:49)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:955)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1663)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1703)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1555)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:369)
	org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1563)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:382)
	org.semanticweb.owlapi.rdf.rdfxml.parser.ResourceOrLiteralElement.endElement(StartRDF.java:557)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.endElement(RDFParser.java:224)
	org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
	org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:161)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:65)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005)
	es.upm.fi.oeg.oops.ModelLoader.loadOwl(ModelLoader.java:117)
	es.upm.fi.oeg.oops.ModelLoader.load(ModelLoader.java:121)
	org.apache.jsp.report_002dadvanced_jsp._jspService(report_002dadvanced_jsp.java:354)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:67)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:456)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:377)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:325)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

Root Cause

java.net.SocketTimeoutException: Connect timed out
	java.base/sun.nio.ch.NioSocketImpl.timedFinishConnect(NioSocketImpl.java:546)
	java.base/sun.nio.ch.NioSocketImpl.connect(NioSocketImpl.java:592)
	java.base/java.net.Socket.connect(Socket.java:751)
	java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:178)
	java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:531)
	java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:636)
	java.base/sun.net.www.http.HttpClient.<init>(HttpClient.java:280)
	java.base/sun.net.www.http.HttpClient.New(HttpClient.java:386)
	java.base/sun.net.www.http.HttpClient.New(HttpClient.java:408)
	java.base/sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1319)
	java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1252)
	java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1138)
	java.base/sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:1067)
	org.semanticweb.owlapi.io.DocumentSources.connect(DocumentSources.java:228)
	org.semanticweb.owlapi.io.DocumentSources.getInputStream(DocumentSources.java:209)
	org.semanticweb.owlapi.io.DocumentSources.wrapInput(DocumentSources.java:143)
	org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader(DocumentSources.java:88)
	org.semanticweb.owlapi.io.DocumentSources.wrapInputAsReader(DocumentSources.java:105)
	org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:38)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:49)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:955)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1663)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1703)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$TPImportsHandler.handleTriple(TripleHandlers.java:1555)
	org.semanticweb.owlapi.rdf.rdfxml.parser.TripleHandlers$HandlerAccessor.handleStreaming(TripleHandlers.java:369)
	org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer.statementWithResourceValue(OWLRDFConsumer.java:1563)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.statementWithResourceValue(RDFParser.java:382)
	org.semanticweb.owlapi.rdf.rdfxml.parser.ResourceOrLiteralElement.endElement(StartRDF.java:557)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.endElement(RDFParser.java:224)
	org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLNSDTDValidator.endNamespaceScope(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.handleEndElement(Unknown Source)
	org.apache.xerces.impl.dtd.XMLDTDValidator.endElement(Unknown Source)
	org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
	org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
	org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.parse(RDFParser.java:161)
	org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:65)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055)
	uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005)
	es.upm.fi.oeg.oops.ModelLoader.loadOwl(ModelLoader.java:117)
	es.upm.fi.oeg.oops.ModelLoader.load(ModelLoader.java:121)
	org.apache.jsp.report_002dadvanced_jsp._jspService(report_002dadvanced_jsp.java:354)
	org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:67)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:456)
	org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:377)
	org.apache.jasper.servlet.JspServlet.service(JspServlet.java:325)
	jakarta.servlet.http.HttpServlet.service(HttpServlet.java:658)
	org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)

Note The full stack trace of the root cause is available in the server logs.
Apache Tomcat/10.1.35 (Debian)

[hoijui]

The core issue seems to be one with the ontology, or rather its imports, and it should be fixed there.
Though we should probably use this to at the least create a more human digestible error message for such cases,
and if possible, optionally allow to silently ignore such issues like it was done in the past, though I am not sure if this is a good idea.

Maybe we could directly make this into a new pitfall?

[pieterhijma]

I agree to make this a new pitfall. By the way, it seems as if all of http://semanticweb.org times out. I guess there should a new URL? What should rdf:RDF xml:base="http://data.semanticweb.org/ns/swc/ontology#" point to?

[dgarijo]

I think that having non-resolving imports should be a pitfall too.

However, the evaluation tool should work for the other triples in the file. For example, in FOOPS! the timeout is produced (it takes a lot of time to analyze), but the result comes back (51%)

[mariapoveda]

I agree that non-resolving imports should be a pitfall. Also, I would say that maybe users should choose whether to check imports or only the new ontology code. In the original OOPS! imports are not followed to avoid overloading it.