/**
* Parse an ontology from a given URI.
*
* @param handler an <code>OWLRDFErrorHandler</code> value
* @param uri an <code>URI</code> value
* @return an <code>OWLOntology</code> value
* @exception ParserException if an error occurs
* @exception OWLException if an error occurs
*/
private OWLOntology parseFromURI(OWLRDFErrorHandler handler, URI uri)
throws ParserException, OWLException {
parser.setConnection(connection);
/* Error handler for the parser */
parser.setOWLRDFErrorHandler(handler);
// OWLOntology onto = connection.createOWLOntology( uri,uri );
OWLOntology onto = parser.parseOntology(uri);
// message( onto.toString() );
return onto;
}
/** Create a new validator. Will report to stdout by default. */
public SwoopSpeciesValidator(SwoopModel model) throws OWLException {
myModel = model;
/* Sets up a default reporter that writes to stdout. */
setReporter(
new SpeciesValidatorReporter() {
public void ontology(OWLOntology onto) {
// System.out.println( onto.getURI() );
}
public void done(String str) {
// System.out.println( str );
}
public void message(String str) {
System.out.println(str);
}
public void explain(int l, int code, String str) {
System.out.println(level(l) + " [" + readableCode(code) + "]:\t" + str);
// System.out.println( level( l ) + ":\t" + str );
}
});
reservedVocabulary = OWLVocabularyAdapter.INSTANCE.getReservedVocabulary();
classOnlyVocabulary = new HashSet();
classOnlyVocabulary.add(OWLVocabularyAdapter.INSTANCE.getStatement());
classOnlyVocabulary.add(OWLVocabularyAdapter.INSTANCE.getSeq());
classOnlyVocabulary.add(OWLVocabularyAdapter.INSTANCE.getBag());
classOnlyVocabulary.add(OWLVocabularyAdapter.INSTANCE.getAlt());
options = new HashMap();
/* Get a default connection */
connection = OWLManager.getOWLConnection();
parser = new OWLRDFParser();
/*
* Tell the parser to ignore annotation content. This is not needed for
* validation.
*/
Map options = new HashMap();
options.put("includeAnnotationContent", new Boolean(false));
parser.setOptions(options);
}