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GenEpiO / genepio

The Genomic Epidemiology Application Ontology describes the genomics, laboratory, clinical and epidemiological contextual information required to support data sharing and integration for foodborne infectious disease surveillance and outbreak investigations.
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Unable to convert to OBO / OBO Graph JSON with ROBOT #44

Closed cthoyt closed 1 year ago

cthoyt commented 1 year ago

I ran the following command robot convert -I http://purl.obolibrary.org/obo/genepio.owl -o ~/Desktop/genepio.json to convert this ontology to OBO Graph JSON and got the following parse messages:

[Fatal Error] :1:50: White spaces are required between publicId and systemId.
org.semanticweb.owlapi.io.UnparsableOntologyException: Problem parsing http://purl.obolibrary.org/obo/genepio.owl
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@6e1ad658
2) org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2c8f65da
3) org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@66a8ff6d
4) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
5) org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@13018f00
6) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
7) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
8) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
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.BinaryRDFDocumentFormatFactory@3bf24493
12) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
13) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
14) org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@6f36e806
15) org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
16) org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@673605ef
17) org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@46d51d5e
18) org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d

Detailed logs:
--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser@6e1ad658
    Stack trace:
org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParserException: [line=876:column=162] IRI 'The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot' cannot be resolved against current base IRI http://purl.obolibrary.org/obo/genepio.owl reason is: Illegal character in path at index 28: The%20identifier%20of%20a%20"value%20set"%20--%20a%20set%20of%20identifiers%20that%20form%20the%20possible%20values%20for%20the%20range%20of%20a%20slot        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFXMLParser.parse(RDFXMLParser.java:76)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
[line=876:column=162] IRI 'The identifier of a "value set" -- a set of identifiers that form the possible values for the range of a slot' cannot be resolved against current base IRI http://purl.obolibrary.org/obo/genepio.owl reason is: Illegal character in path at index 28: The%20identifier%20of%20a%20"value%20set"%20--%20a%20set%20of%20identifiers%20that%20form%20the%20possible%20values%20for%20the%20range%20of%20a%20slot        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.resolveIRI(RDFParser.java:349)
        org.semanticweb.owlapi.rdf.rdfxml.parser.AbstractState.getNodeIDResourceResourceIRI(StartRDF.java:119)
        org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:651)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201)
        java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:510)
        java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:183)
        java.xml/com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.emptyElement(XMLDTDValidator.java:752)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:351)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2708)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:605)
Illegal character in path at index 28: The%20identifier%20of%20a%20"value%20set"%20--%20a%20set%20of%20identifiers%20that%20form%20the%20possible%20values%20for%20the%20range%20of%20a%20slot        java.base/java.net.URI.create(URI.java:883)
        java.base/java.net.URI.resolve(URI.java:1066)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.resolveFromDelegate(RDFParser.java:270)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.resolveIRI(RDFParser.java:341)
        org.semanticweb.owlapi.rdf.rdfxml.parser.AbstractState.getNodeIDResourceResourceIRI(StartRDF.java:119)
        org.semanticweb.owlapi.rdf.rdfxml.parser.PropertyElementList.startElement(StartRDF.java:651)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.startElement(RDFParser.java:201)
        java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:510)
        java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:183)
        java.xml/com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.emptyElement(XMLDTDValidator.java:752)
Illegal character in path at index 28: The%20identifier%20of%20a%20"value%20set"%20--%20a%20set%20of%20identifiers%20that%20form%20the%20possible%20values%20for%20the%20range%20of%20a%20slot        java.base/java.net.URI$Parser.fail(URI.java:2915)
        java.base/java.net.URI$Parser.checkChars(URI.java:3086)
        java.base/java.net.URI$Parser.parseHierarchical(URI.java:3168)
        java.base/java.net.URI$Parser.parse(URI.java:3127)
        java.base/java.net.URI.<init>(URI.java:600)
        java.base/java.net.URI.create(URI.java:881)
        java.base/java.net.URI.resolve(URI.java:1066)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.resolveFromDelegate(RDFParser.java:270)
        org.semanticweb.owlapi.rdf.rdfxml.parser.RDFParser.resolveIRI(RDFParser.java:341)
        org.semanticweb.owlapi.rdf.rdfxml.parser.AbstractState.getNodeIDResourceResourceIRI(StartRDF.java:119)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.owlxml.parser.OWLXMLParser@2c8f65da
    Stack trace:
Attribute not found: IRI (Line 77)        org.semanticweb.owlapi.owlxml.parser.OWLElementHandler.ensureAttributeNotNull(PARSER_OWLXMLVocabulary.java:501)
        org.semanticweb.owlapi.owlxml.parser.OWLElementHandler.getIRIFromAttribute(PARSER_OWLXMLVocabulary.java:354)
        org.semanticweb.owlapi.owlxml.parser.OWLAnnotationPropertyElementHandler.attribute(PARSER_OWLXMLVocabulary.java:1353)
        org.semanticweb.owlapi.owlxml.parser.OWLXMLParserHandler.startElement(OWLXMLParserHandler.java:482)
        java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:510)
        java.xml/com.sun.org.apache.xerces.internal.impl.dtd.XMLDTDValidator.startElement(XMLDTDValidator.java:731)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLNSDocumentScannerImpl.scanStartElement(XMLNSDocumentScannerImpl.java:374)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2708)
        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:112)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser@66a8ff6d
    Stack trace:
Encountered " <FULLIRI> "<?xml version=\"1.0\"?> "" at line 1, column 1.
Was expecting one of:
    "Ontology" ...
    "Prefix" ...
     (Line 0)        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:94)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
Encountered " <FULLIRI> "<?xml version=\"1.0\"?> "" at line 1, column 1.
Was expecting one of:
    "Ontology" ...
    "Prefix" ...
            org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.generateParseException(OWLFunctionalSyntaxParser.java:3443)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.jj_consume_token(OWLFunctionalSyntaxParser.java:3363)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.Ontology(OWLFunctionalSyntaxParser.java:192)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxParser.parse(OWLFunctionalSyntaxParser.java:171)
        org.semanticweb.owlapi.functional.parser.OWLFunctionalSyntaxOWLParser.parse(OWLFunctionalSyntaxOWLParser.java:92)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioTurtleDocumentFormatFactory@95fd655c
    Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: '32' [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
IRI included an unencoded space: '32' [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
        org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
        org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:948)
        org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
        org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
        org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser@13018f00
    Stack trace:
Encountered '<?xml version="1.0"?>' at line 1 column 1.  Expected either 'Ontology:' or 'Prefix:' (Line 1)        org.semanticweb.owlapi.manchestersyntax.parser.ManchesterOWLSyntaxOntologyParser.parse(ManchesterOWLSyntaxOntologyParser.java:120)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NQuadsDocumentFormatFactory@6f9c39ad
    Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space:   [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
IRI included an unencoded space:   [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
        org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
        org.openrdf.rio.ntriples.NTriplesParser.reportError(NTriplesParser.java:631)
        org.openrdf.rio.ntriples.NTriplesParser.parseUriRef(NTriplesParser.java:423)
        org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:336)
        org.openrdf.rio.nquads.NQuadsParser.parseQuad(NQuadsParser.java:123)
        org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:102)
        org.openrdf.rio.nquads.NQuadsParser.parse(NQuadsParser.java:60)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.NTriplesDocumentFormatFactory@937ecd36
    Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space:   [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
IRI included an unencoded space:   [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportError(RDFParserHelper.java:348)
        org.openrdf.rio.helpers.RDFParserBase.reportError(RDFParserBase.java:641)
        org.openrdf.rio.ntriples.NTriplesParser.reportError(NTriplesParser.java:631)
        org.openrdf.rio.ntriples.NTriplesParser.parseUriRef(NTriplesParser.java:423)
        org.openrdf.rio.ntriples.NTriplesParser.parseSubject(NTriplesParser.java:336)
        org.openrdf.rio.ntriples.NTriplesParser.parseTriple(NTriplesParser.java:280)
        org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:191)
        org.openrdf.rio.ntriples.NTriplesParser.parse(NTriplesParser.java:130)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonDocumentFormatFactory@cd748dc3
    Stack trace:
org.openrdf.rio.RDFParseException: Found IOException during parsing [line 1, column 2]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
Found IOException during parsing [line 1, column 2]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
        org.openrdf.rio.rdfjson.RDFJSONParser.reportFatalError(RDFJSONParser.java:155)
        org.openrdf.rio.rdfjson.RDFJSONParser.parse(RDFJSONParser.java:96)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.TrigDocumentFormatFactory@27e81c
    Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: '32' [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
IRI included an unencoded space: '32' [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
        org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
        org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:948)
        org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        org.openrdf.rio.trig.TriGParser.parseGraph(TriGParser.java:132)
        org.openrdf.rio.trig.TriGParser.parseStatement(TriGParser.java:119)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFJsonLDDocumentFormatFactory@dcacc47d
    Stack trace:
org.openrdf.rio.RDFParseException: Could not parse JSONLD        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
Could not parse JSONLD        com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:69)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
Unexpected character ('<' (code 60)): expected a valid value (number, String, array, object, 'true', 'false' or 'null')
 at [Source: (BufferedReader); line: 1, column: 2]        com.fasterxml.jackson.core.JsonParser._constructError(JsonParser.java:1798)
        com.fasterxml.jackson.core.base.ParserMinimalBase._reportError(ParserMinimalBase.java:663)
        com.fasterxml.jackson.core.base.ParserMinimalBase._reportUnexpectedChar(ParserMinimalBase.java:561)
        com.fasterxml.jackson.core.json.ReaderBasedJsonParser._handleOddValue(ReaderBasedJsonParser.java:1892)
        com.fasterxml.jackson.core.json.ReaderBasedJsonParser.nextToken(ReaderBasedJsonParser.java:747)
        com.github.jsonldjava.utils.JsonUtils.fromReader(JsonUtils.java:107)
        com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:88)
        com.github.jsonldjava.utils.JsonUtils.fromInputStream(JsonUtils.java:68)
        com.github.jsonldjava.sesame.SesameJSONLDParser.parse(SesameJSONLDParser.java:65)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.BinaryRDFDocumentFormatFactory@3bf24493
    Stack trace:
org.openrdf.rio.RDFParseException: File does not contain a binary RDF document        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
File does not contain a binary RDF document        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:424)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:693)
        org.openrdf.rio.binary.BinaryRDFParser.parse(BinaryRDFParser.java:87)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.N3DocumentFormatFactory@9a5
    Stack trace:
org.openrdf.rio.RDFParseException: IRI included an unencoded space: '32' [line 1]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
IRI included an unencoded space: '32' [line 1]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
        org.openrdf.rio.turtle.TurtleParser.reportFatalError(TurtleParser.java:1366)
        org.openrdf.rio.turtle.TurtleParser.parseURI(TurtleParser.java:948)
        org.openrdf.rio.turtle.TurtleParser.parseValue(TurtleParser.java:613)
        org.openrdf.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:448)
        org.openrdf.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:382)
        org.openrdf.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:260)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:215)
        org.openrdf.rio.turtle.TurtleParser.parse(TurtleParser.java:159)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RioRDFXMLDocumentFormatFactory@69b9a3bc
    Stack trace:
org.openrdf.rio.RDFParseException: White spaces are required between publicId and systemId. [line 1, column 50]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
White spaces are required between publicId and systemId. [line 1, column 50]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:441)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:704)
        org.openrdf.rio.rdfxml.RDFXMLParser.reportFatalError(RDFXMLParser.java:1286)
        org.openrdf.rio.rdfxml.RDFXMLParser.fatalError(RDFXMLParser.java:1443)
        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:1471)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.scanExternalID(XMLScanner.java:1071)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.scanDoctypeDecl(XMLDocumentScannerImpl.java:645)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser@6f36e806
    Stack trace:
org.semanticweb.owlapi.rdf.turtle.parser.ParseException: Encountered "" at line 1, column 1.
Was expecting one of:
            org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:105)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
Encountered "" at line 1, column 1.
Was expecting one of:
            org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.generateParseException(TurtleParser.java:1548)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.jj_consume_token(TurtleParser.java:1430)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleParser.parseDocument(TurtleParser.java:153)
        org.semanticweb.owlapi.rdf.turtle.parser.TurtleOntologyParser.parse(TurtleOntologyParser.java:98)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl : org.semanticweb.owlapi.formats.TrixDocumentFormatFactory@27e82d
    Stack trace:
org.openrdf.rio.RDFParseException: White spaces are required between publicId and systemId. [line 1, column 50]        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
White spaces are required between publicId and systemId. [line 1, column 50]        org.openrdf.rio.helpers.RDFParserHelper.reportFatalError(RDFParserHelper.java:487)
        org.openrdf.rio.helpers.RDFParserBase.reportFatalError(RDFParserBase.java:737)
        org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:123)
        org.semanticweb.owlapi.rio.OWLAPIRioTrixParser.parse(OWLAPIRioTrixParser.java:90)
        org.semanticweb.owlapi.rio.RioTrixParserFactory$TrixParserImpl.parseDocumentSource(RioTrixParserFactory.java:96)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
White spaces are required between publicId and systemId.        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:1471)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLScanner.scanExternalID(XMLScanner.java:1071)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.scanDoctypeDecl(XMLDocumentScannerImpl.java:645)
        java.xml/com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$PrologDriver.next(XMLDocumentScannerImpl.java:908)
        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:112)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser@673605ef
    Stack trace:
LINENO: 1 - Could not find tag separator ':' in line.
LINE: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:60)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
LINENO: 1 - Could not find tag separator ':' in line.
LINE: <!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">        org.obolibrary.oboformat.parser.OBOFormatParser.error(OBOFormatParser.java:1465)
        org.obolibrary.oboformat.parser.OBOFormatParser.getParseTag(OBOFormatParser.java:861)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClause(OBOFormatParser.java:503)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderClauseNl(OBOFormatParser.java:496)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseHeaderFrame(OBOFormatParser.java:480)
        org.obolibrary.oboformat.parser.OBOFormatParser.parseOBODoc(OBOFormatParser.java:345)
        org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:307)
        org.obolibrary.oboformat.parser.OBOFormatParser.parse(OBOFormatParser.java:259)
        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:76)
        org.semanticweb.owlapi.oboformat.OBOFormatOWLAPIParser.parse(OBOFormatOWLAPIParser.java:83)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser@46d51d5e
    Stack trace:
org.semanticweb.owlapi.krss2.parser.ParseException: Encountered " ">" "<?xml version=\"1.0\"?> "" at line 1, column 1.
Was expecting:
    <EOF> 
            org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:289)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
Encountered " ">" "<?xml version=\"1.0\"?> "" at line 1, column 1.
Was expecting:
    <EOF> 
            org.semanticweb.owlapi.krss2.parser.KRSS2Parser.generateParseException(KRSS2Parser.java:3187)
        org.semanticweb.owlapi.krss2.parser.KRSS2Parser.jj_consume_token(KRSS2Parser.java:3040)
        org.semanticweb.owlapi.krss2.parser.KRSS2Parser.parse(KRSS2Parser.java:141)
        org.semanticweb.owlapi.krss2.parser.KRSS2OWLParser.parse(KRSS2OWLParser.java:286)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)

--------------------------------------------------------------------------------
Parser: org.semanticweb.owlapi.rio.RioParserImpl : org.semanticweb.owlapi.formats.RDFaDocumentFormatFactory@264e8d
    Stack trace:
org.openrdf.rio.RDFParseException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:195)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:473)
        org.obolibrary.robot.CommandLineHelper.getInputOntology(CommandLineHelper.java:493)
        org.obolibrary.robot.CommandLineHelper.updateInputOntology(CommandLineHelper.java:585)
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:111)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1254)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1208)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1165)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:531)
        org.obolibrary.robot.IOHelper.loadOntology(IOHelper.java:505)
org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.        org.semarglproject.rdf.rdfa.RdfaParser.processException(RdfaParser.java:1141)
        org.semarglproject.source.XmlSource.process(XmlSource.java:50)
        org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
White spaces are required between publicId and systemId.        java.xml/com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1243)
        org.semarglproject.source.XmlSource.process(XmlSource.java:48)
        org.semarglproject.source.StreamProcessor.processInternal(StreamProcessor.java:87)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:167)
        org.semarglproject.source.BaseStreamProcessor.process(BaseStreamProcessor.java:154)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:109)
        org.semarglproject.sesame.rdf.rdfa.SesameRDFaParser.parse(SesameRDFaParser.java:95)
        org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:257)
        org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:191)
        uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:220)
Use the -vvv option to show the stack trace.
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ddooley commented 1 year ago

@cthoyt somehow this escaped my attention until now. This should be fixed. I believe we caught the issue a while back but a second vetting of malformed content this past week may have helped. I just tested and the json does get generated.

ddooley commented 1 year ago

This should be resolved now. Validated with Apache jena riot, and fixed a few datetimes. Reopen if you re-encounter a problem!