I am creating a custom ontology (Ontology A) and I get a "FileNotFoundException" regarding an indirect import when I try to import another ontology I have created (Ontology B), using the "Import an ontology contained in a specfic file." option.
Ontology B imports successfully the Micropublications ontology (can be found here) after downloading it locally in a file named micropublications.owl. While importing micropublications.owl, I use the "Import an ontology contained in a specfic file." option and everything works fine. I check the "import" section in the protege and everything seems fine, namely there is a specific "Location" pointing to the actual downloaded file etc.
When I try to import the ontology B in ontology A, it fails and the log file contains the following full stack trace
2017-09-07 11:28:20.907 [Thread-3] INFO LastResortExtractor Exception caught trying to get ontology id for file:/C:/Users/.../OntologyB.owl
org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <http://purl.org/mp/> Cause: http://purl.org/mp/
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1709) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at org.semanticweb.owlapi.owlxml.parser.OWLImportsHandler.endElement(PARSER_OWLXMLVocabulary.java:3004) ~[na:na]
at org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.endElement(OWLXMLParserHandler.java:422) ~[na:na]
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:609) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1782) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2973) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:606) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:117) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:848) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:777) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:141) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1213) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:649) ~[na:1.8.0_40]
at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl.parse(SAXParserImpl.java:333) ~[na:1.8.0_40]
at org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:60) ~[na:na]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:998) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at org.protege.editor.owl.model.repository.extractors.LastResortExtractor.getOntologyId(LastResortExtractor.java:21) ~[protege-editor-owl.jar:na]
at org.protege.editor.owl.model.repository.MasterOntologyIDExtractor.getOntologyId(MasterOntologyIDExtractor.java:26) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage.checkImport(AnticipateOntologyIdPage.java:109) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage.lambda$new$163(AnticipateOntologyIdPage.java:44) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage$$Lambda$120/769332687.run(Unknown Source) [protege-editor-owl.jar:na]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]
Caused by: org.semanticweb.owlapi.io.OWLOntologyCreationIOException: http://purl.org/mp/
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:207) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1099) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:957) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadImports(OWLOntologyManagerImpl.java:1666) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.makeLoadImportRequest(OWLOntologyManagerImpl.java:1702) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
... 25 common frames omitted
Caused by: java.io.FileNotFoundException: http://purl.org/mp/
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_40]
at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_40]
at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_40]
at java.lang.reflect.Constructor.newInstance(Constructor.java:422) ~[na:1.8.0_40]
at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1889) ~[na:1.8.0_40]
at sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1884) ~[na:1.8.0_40]
at java.security.AccessController.doPrivileged(Native Method) ~[na:1.8.0_40]
at sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1883) ~[na:1.8.0_40]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1456) ~[na:1.8.0_40]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440) ~[na:1.8.0_40]
at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStreamFromContentEncoding(AbstractOWLParser.java:165) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:127) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at org.semanticweb.owlapi.io.AbstractOWLParser.getInputSource(AbstractOWLParser.java:232) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:72) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:197) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
... 30 common frames omitted
Caused by: java.io.FileNotFoundException: http://purl.org/mp/
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1835) ~[na:1.8.0_40]
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440) ~[na:1.8.0_40]
at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) ~[na:1.8.0_40]
at org.semanticweb.owlapi.io.AbstractOWLParser.getInputStream(AbstractOWLParser.java:103) ~[owlapi-osgidistribution.jar:4.2.8.20170104-2310]
... 33 common frames omitted
2017-09-07 11:28:20.907 [Thread-3] ERROR AnticipateOntologyIdPage An error occurred whilst extracting the Ontology Id from the imported ontology: {}
java.lang.NullPointerException: null
at org.protege.editor.owl.model.repository.MasterOntologyIDExtractor.getOntologyId(MasterOntologyIDExtractor.java:27) ~[protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage.checkImport(AnticipateOntologyIdPage.java:109) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage.lambda$new$163(AnticipateOntologyIdPage.java:44) [protege-editor-owl.jar:na]
at org.protege.editor.owl.ui.ontology.imports.wizard.page.AnticipateOntologyIdPage$$Lambda$120/769332687.run(Unknown Source) [protege-editor-owl.jar:na]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]
2017-09-07 11:28:25.679 [pool-2-thread-1] INFO AddImportsStrategy -------------------- Importing ontology and imports closure --------------------
It seems that Protege is searching for the Micropublications model in a file named after its base URI and not the actually file location, clearly stated in the respective import statement of Ontology B. Please note that Ontology B also imports other ontologies which cause no problem in Ontology A.
Any ideas of what is going wrong?
PS I am using Protege 5.2.0.
I have found a workaround which might be helpful to others. When I load ontology B and ontology A in the same protege window, I can import ontology B using the option "Import an ontology that is already loaded in the workspace" and everything seems to be working.
Hope this is helpful