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ncbo / owlapi_wrapper

A command line utility that wraps the Java OWL-API to parse RDFS, OWL and OBO ontologies.
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NoClassDefFoundError: java/xml/bind/annotations occurs during parsing of some ontologies #16

Closed jvendetti closed 2 years ago

jvendetti commented 2 years ago

Encountering a NoClassDefFoundError when the system attempts to load and parse certain ontologies, e.g., the N-Triples version of the AGROVOC ontology (submission ID 16) hosted in AgroPortal.

The error occurs because we're running on Java 11 in production where the JAXB APIs were removed.

Full stack trace from local dev environment:

java.lang.NoClassDefFoundError: javax/xml/bind/annotation/adapters/HexBinaryAdapter

    at org.eclipse.rdf4j.rio.helpers.AbstractRDFParser.createNode(AbstractRDFParser.java:479)
    at org.eclipse.rdf4j.rio.turtle.TurtleParser.parseNodeID(TurtleParser.java:1114)
    at org.eclipse.rdf4j.rio.turtle.TurtleParser.parseValue(TurtleParser.java:594)
    at org.eclipse.rdf4j.rio.turtle.TurtleParser.parseSubject(TurtleParser.java:429)
    at org.eclipse.rdf4j.rio.turtle.TurtleParser.parseTriples(TurtleParser.java:370)
    at org.eclipse.rdf4j.rio.turtle.TurtleParser.parseStatement(TurtleParser.java:239)
    at org.eclipse.rdf4j.rio.turtle.TurtleParser.parse(TurtleParser.java:201)
    at org.semanticweb.owlapi.rio.RioParserImpl.parseDocumentSource(RioParserImpl.java:229)
    at org.semanticweb.owlapi.rio.RioParserImpl.parse(RioParserImpl.java:180)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl.loadOWLOntology(OWLOntologyFactoryImpl.java:221)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.actualParse(OWLOntologyManagerImpl.java:1294)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntology(OWLOntologyManagerImpl.java:1234)
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.loadOntologyFromOntologyDocument(OWLOntologyManagerImpl.java:1191)
    at org.stanford.ncbo.oapiwrapper.OntologyParser.findMasterFile(OntologyParser.java:594)
    at org.stanford.ncbo.oapiwrapper.OntologyParser.internalParse(OntologyParser.java:513)
    at org.stanford.ncbo.oapiwrapper.OntologyParser.parse(OntologyParser.java:497)