Unsatisfiable theory with Object- (and probably Data-)AllValuesFrom

b-gehrke commented 5 months ago

Consider the following Ontology O:

Prefix: : <https://example.com/>

Ontology:

Class: A
Class: B
ObjectProperty: r

Class: r only B SubClassOf: A

Translating O to FOL leads to an unsatisfiable theory (one can infer that ∀x(thing(x))). The problem appears to be the mapping of ObjectAllValuesFrom. In O it is translated to ∀x([∀y(R(x,y) → B(y)] → A(y)). Martin and Fabian figured that it should be ∀x({thing(x)∧[∀y(R(x,y) → B(y)]} → A(y)) and hence the formal mapping should be changed from ∀x([R]^p_x → [A]^x) to owl:Thing(p) ∧ ∀x([R]^p_x → [A]^x).

The same is probably true for DataAllValuesFrom.

sfluegel05 commented 5 months ago

Could you check if the ontology you provided is syntactically correct? When I try to run the translation for this ontology, I get an error message:

: org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/C:/Users/Simon%20Fl▒gel/Desktop/python-gavel-owl/unsat_object_allvaluesfrom.omn
Could not parse ontology.  Either a suitable parser could not be found, or parsing failed.  See parser logs below for explanation

On the other hand, the ontology loads fine in Protegé, so maybe I am missing something?

full output:

``` $ python -m gavel translate owl tptp unsat_object_allvaluesfrom.omn Traceback (most recent call last): File "", line 198, in _run_module_as_main File "", line 88, in _run_code File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\gavel\__main__.py", line 14, in cli() File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\click\decorators.py", line 33, in new_func return f(get_current_context(), *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\gavel\cli.py", line 110, in translate translation = compiler.visit(parser.parse_from_file(path, **kwargs)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\gavel_owl\dialects\owl\parser.py", line 77, in parse_from_file for next_pair in self.app.translateOntologyFromFile(file_path): ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\py4j\java_gateway.py", line 1322, in __call__ return_value = get_return_value( ^^^^^^^^^^^^^^^^^ File "C:\Users\Simon Fl▒gel\AppData\Local\Programs\Python\Python311\Lib\site-packages\py4j\protocol.py", line 326, in get_return_value raise Py4JJavaError( py4j.protocol.Py4JJavaError: An error occurred while calling t.translateOntologyFromFile. : org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing file:/C:/Users/Simon%20Fl▒gel/Desktop/python-gavel-owl/unsat_object_allvaluesfrom.omn Could not parse ontology. Either a suitable parser could not be found, or parsing failed. See parser logs below for explanation. The following parsers were tried: 1) org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@8b0c685 2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@52c48c77 3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@463a9e5f 4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c 5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4881c313 6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad 7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 9) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c 10) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d 11) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc 12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 13) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@129de4f2 14) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d 15) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@56b8304a 16) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser@4d6270d9 17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@4f3b40ad 18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 19) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Detailed logs: -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@8b0c685 Stack trace: org.xml.sax.SAXParseException; systemId: file:/C:/Users/Simon%20Fl▒gel/Desktop/python-gavel-owl/unsat_object_allvaluesfrom.omn; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:63) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Content is not allowed in prolog. java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:204) java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:178) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327) java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1465) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:978) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605) java.xml/com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:114) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:542) java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:889) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@52c48c77 Stack trace: org.xml.sax.SAXParseException; systemId: file:/C:/Users/Simon%20Fl▒gel/Desktop/python-gavel-owl/unsat_object_allvaluesfrom.omn; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog. org.semanticweb.owlapi.owlxml.parser.OWLXMLParser.parse(OWLXMLParser.java:66) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Content is not allowed in prolog. java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:204) java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:178) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327) java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1465) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:978) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605) java.xml/com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:114) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:542) java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:889) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@463a9e5f Stack trace: Encountered unexpected token: "Prefix:" at line 1, column 1. Was expecting one of: "Ontology" "Prefix" (Line 0) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.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.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Encountered unexpected token: "Prefix:" at line 1, column 1. Was expecting one of: "Ontology" "Prefix" org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.generateParseException(OWLFunctionalSyntaxParser.java:2479) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.jj_consume_token(OWLFunctionalSyntaxParser.java:2405) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.Ontology(OWLFunctionalSyntaxParser.java:115) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.parse(OWLFunctionalSyntaxParser.java:101) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:47) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Namespace prefix 'Prefix' used but not defined [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Namespace prefix 'Prefix' used but not defined [line 1] org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:403) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:755) org.eclipse.rdf4j.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1318) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.getNamespace(AbstractRDFParser.java:342) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1002) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseValue(TurtleParser.java:591) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:429) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:370) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:239) org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:201) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@4881c313 Stack trace: Encountered only at line 9 column 9. Expected one of: Individual: AnnotationProperty: Datatype: DataProperty: ObjectProperty: DisjointProperties: ValuePartition: EquivalentClasses: Import: Prefix: DisjointClasses: Class: SameIndividual: DifferentIndividuals: (Line 9) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:96) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Encountered only at line 9 column 9. Expected one of: Individual: AnnotationProperty: Datatype: DataProperty: ObjectProperty: DisjointProperties: ValuePartition: EquivalentClasses: Import: Prefix: DisjointClasses: Class: SameIndividual: DifferentIndividuals: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl$ExceptionBuilder.build(ManchesterOWLSyntaxParserImpl.java:2802) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxParserImpl.parseOntology(ManchesterOWLSyntaxParserImpl.java:2196) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:93) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Expected '<' or '_', found: P [line 1, column 80] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Expected '<' or '_', found: P [line 1, column 80] org.eclipse.rdf4j.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:355) org.eclipse.rdf4j.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:119) org.eclipse.rdf4j.rio.nquads.NQuadsParser.parse(NQuadsParser.java:98) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3 Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Found IOException during parsing [line 1, column 7] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Found IOException during parsing [line 1, column 7] org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:403) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:755) org.eclipse.rdf4j.rio.rdfjson.RDFJSONParser.reportFatalError(RDFJSONParser.java:146) org.eclipse.rdf4j.rio.rdfjson.RDFJSONParser.parse(RDFJSONParser.java:173) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) 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) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36 Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Expected '<' or '_', found: P [line 1, column 80] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Expected '<' or '_', found: P [line 1, column 80] org.eclipse.rdf4j.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:355) org.eclipse.rdf4j.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:284) org.eclipse.rdf4j.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Expected '<', found ':' [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Expected '<', found ':' [line 1] org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:403) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:755) org.eclipse.rdf4j.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1318) org.eclipse.rdf4j.rio.turtle.TurtleParser.verifyCharacterOrFail(TurtleParser.java:1153) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseURI(TurtleParser.java:886) org.eclipse.rdf4j.rio.turtle.TurtleParser.parsePrefixID(TurtleParser.java:320) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseDirective(TurtleParser.java:263) org.eclipse.rdf4j.rio.trig.TriGParser.parseStatement(TriGParser.java:98) org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:201) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:179) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Could not parse JSONLD org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Could not parse JSONLD org.eclipse.rdf4j.rio.jsonld.JSONLDParser.parse(JSONLDParser.java:110) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) Unrecognized token 'Prefix': was expecting ('true', 'false' or 'null') at [Source: (BufferedReader); line: 1, column: 7] com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1804) com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:679) com.fasterxml.jackson.core.json.ReaderBasedJsonParser._reportInvalidToken(ReaderBasedJsonParser.java:2835) com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1889) com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:747) com.github.jsonldjava.utils.JsonUtils.fromJsonParser(JsonUtils.java:191) com.github.jsonldjava.utils.JsonUtils.fromReader(JsonUtils.java:173) org.eclipse.rdf4j.rio.jsonld.JSONLDParser.parse(JSONLDParser.java:104) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:179) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Content is not allowed in prolog. [line 1, column 1] org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:442) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:783) org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.reportFatalError(RDFXMLParser.java:1176) org.eclipse.rdf4j.rio.rdfxml.RDFXMLParser.fatalError(RDFXMLParser.java:1315) java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:181) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327) java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1465) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:978) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605) Content is not allowed in prolog. java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:204) java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:178) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327) java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1465) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:978) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605) java.xml/com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.next(XMLNSDocumentScannerImpl.java:114) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:542) java.xml/com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:889) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5 Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Namespace prefix 'Prefix' used but not defined [line 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Namespace prefix 'Prefix' used but not defined [line 1] org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:403) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:755) org.eclipse.rdf4j.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1318) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.getNamespace(AbstractRDFParser.java:342) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseQNameOrBoolean(TurtleParser.java:1002) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseValue(TurtleParser.java:591) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:429) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:370) org.eclipse.rdf4j.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:239) org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:201) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@129de4f2 Stack trace: org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Prefix not declared: Prefix: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:58) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Prefix not declared: Prefix: org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.getIRIFromQName(TurtleParser.java:115) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseLoneNS(TurtleParser.java:268) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseResource(TurtleParser.java:399) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseSubject(TurtleParser.java:248) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseTriples(TurtleParser.java:228) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseStatement(TurtleParser.java:224) org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:159) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:54) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d Stack trace: org.eclipse.rdf4j.rio.RDFParseException: Content is not allowed in prolog. [line 1, column 1] org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Content is not allowed in prolog. [line 1, column 1] org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:403) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:755) org.eclipse.rdf4j.rio.trix.TriXParser.reportFatalError(TriXParser.java:294) org.eclipse.rdf4j.rio.trix.TriXParser.fatalError(TriXParser.java:495) java.xml/com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:181) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:400) java.xml/com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:327) java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1465) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:978) java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@56b8304a Stack trace: LINENO: 3 - Expected at least one white space, but found end of line at pos: 9 LINE: Ontology: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:50) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) LINENO: 3 - Expected at least one white space, but found end of line at pos: 9 LINE: Ontology: org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1317) org.obolibrary.oboformat.parser.OBOFormatParser.parseWs(OBOFormatParser.java:1198) org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:735) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:409) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:402) org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderFrame(OBOFormatParser.java:385) org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:268) org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:237) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:44) uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:195) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser@4d6270d9 Stack trace: Encountered unexpected token: "Prefix:" at line 1, column 1. Was expecting one of: ":" "\n" org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser.parse(DLSyntaxOWLParser.java:52) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Encountered unexpected token: "Prefix:" at line 1, column 1. Was expecting one of: ":" "\n" org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser.generateParseException(DLSyntaxParser.java:1572) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser.jj_consume_token(DLSyntaxParser.java:1443) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser.parseAxiom(DLSyntaxParser.java:141) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxParser.parseAxioms(DLSyntaxParser.java:114) org.semanticweb.owlapi.dlsyntax.parser.DLSyntaxOWLParser.parse(DLSyntaxOWLParser.java:48) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@4f3b40ad Stack trace: org.semanticweb.owlapi.krss2.parser.ParseException: Encountered unexpected token: "Prefix:" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:248) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Encountered unexpected token: "Prefix:" at line 1, column 1. Was expecting: org.semanticweb.owlapi.krss2.parser.KRSS2Parser.generateParseException(KRSS2Parser.java:2103) org.semanticweb.owlapi.krss2.parser.KRSS2Parser.jj_consume_token(KRSS2Parser.java:1968) org.semanticweb.owlapi.krss2.parser.KRSS2Parser.parse(KRSS2Parser.java:124) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:245) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493 Stack trace: org.eclipse.rdf4j.rio.RDFParseException: File does not contain a binary RDF document org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) File does not contain a binary RDF document org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:403) org.eclipse.rdf4j.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:388) org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.reportFatalError(AbstractRDFParser.java:746) org.eclipse.rdf4j.rio.binary.BinaryRDFParser.parse(BinaryRDFParser.java:79) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:189) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) 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) -------------------------------------------------------------------------------- Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d Stack trace: org.eclipse.rdf4j.rio.UnsupportedRDFormatException: Did not recognise RDF format object RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:142) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) java.base/java.lang.reflect.Method.invoke(Method.java:580) py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) Did not recognise RDF format object RDFa (mimeTypes=application/xhtml+xml, application/html, text/html; ext=xhtml, html) org.eclipse.rdf4j.rio.Rio.lambda$unsupportedFormat$0(Rio.java:725) java.base/java.util.Optional.orElseThrow(Optional.java:403) org.eclipse.rdf4j.rio.Rio.createParser(Rio.java:102) org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:169) org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:128) 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) uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:236) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.load(OWLOntologyManagerImpl.java:1105) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1055) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1005) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1018) at translation.ApiServer.translateOntologyFromFile(ApiServer.java:244) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:103) at java.base/java.lang.reflect.Method.invoke(Method.java:580) at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244) at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357) at py4j.Gateway.invoke(Gateway.java:282) at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132) at py4j.commands.CallCommand.execute(CallCommand.java:79) at py4j.GatewayConnection.run(GatewayConnection.java:238) at java.base/java.lang.Thread.run(Thread.java:1583) ```

b-gehrke commented 5 months ago

Which version of the OWL API do you use? I use a GCI for the minimum working example, but GCIs are only supported in version 5 (at the moment). You can instead use EquivalentClasses. It produces the same error:

Prefix: : <https://example.com/>

Ontology:

Class: A
Class: B
ObjectProperty: r

Class: A EquivalentTo: r only B

gavel-tool / python-gavel-owl

Unsatisfiable theory with Object- (and probably Data-)AllValuesFrom #18