private void checkCorrectOWLNamespaceUsage() throws OWLException {
/* Check that nothing's been defined in the OWL namespace. */
try {
for (Iterator it = allURIs.iterator(); it.hasNext(); ) {
URI uri = (URI) it.next();
if (uri != null) {
String str = uri.toString();
if (str.startsWith(OWLVocabularyAdapter.OWL)
&& !str.equals(OWLVocabularyAdapter.INSTANCE.getThing())
&& !str.equals(OWLVocabularyAdapter.INSTANCE.getNothing())
&&
/* Added check for built ins */
!OWLVocabularyAdapter.INSTANCE.getAnnotationProperties().contains(str)) {
correctOWLNamespaceUsage = false;
explain(
FULL,
OWLNAMESPACEUSED,
encodeHLink(str, myModel.shortForm(uri)) + " in OWL Namespace");
}
}
}
} catch (Exception ex) {
ex.printStackTrace();
throw new OWLException(ex.getMessage());
}
}
private OWLClass conceptToClass(uk.ac.man.cs.img.dig.helper.Response.Concept c)
throws OWLException {
try {
if (c.isBottom()) {
OWLClass clazz = ontology.getClass(new URI(OWLVocabularyAdapter.INSTANCE.getNothing()));
// System.out.println( clazz );
return clazz;
} else if (c.isTop()) {
return ontology.getClass(new URI(OWLVocabularyAdapter.INSTANCE.getThing()));
} else {
uk.ac.man.cs.img.dig.helper.Response.ConceptName cn =
(uk.ac.man.cs.img.dig.helper.Response.ConceptName) c;
// System.out.println( "xx " + cn.toString() );
URI classURI = new URI(cn.toString());
/* This is wrong! The problem is that the URI may not
* be of a class *in* this ontology (due to the way
* that we handle imports). So rather than getting the
* class from the ontology, we need to get the class
* from the data factory. */
// OWLClass clazz = ontology.getClass( classURI );
OWLClass clazz = ontology.getOWLDataFactory().getOWLClass(classURI);
// System.out.println( clazz );
return clazz;
}
} catch (URISyntaxException ex) {
throw new OWLException(ex.getMessage());
}
}
private void initialiseReasoner() throws OWLException {
/* Initialise the kb and make sure that top and bottom are in there. */
tell("<clearKB/>");
tell("<defconcept name=\"" + OWLVocabularyAdapter.INSTANCE.getThing() + "\"/>");
tell(
"<equalc><catom name=\""
+ OWLVocabularyAdapter.INSTANCE.getThing()
+ "\"/><top/></equalc>");
tell("<defconcept name=\"" + OWLVocabularyAdapter.INSTANCE.getNothing() + "\"/>");
tell(
"<equalc><catom name=\""
+ OWLVocabularyAdapter.INSTANCE.getNothing()
+ "\"/><bottom/></equalc>");
}
/** 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);
}
private void checkCorrectOWLUsage() throws OWLException {
/* Check that nothing in the OWL vocabulary has been redefined. */
/*
* This was too strong. We are actually allowed to say that some things
* e.g. Bag, Set, Alt and Statement are classes. Also some other stuff
* in the RDF vocabulary. SKB.
*/
try {
for (Iterator it = classURIs.iterator(); it.hasNext(); ) {
URI uri = (URI) it.next();
if (uri != null && reservedVocabulary.contains(uri.toString())) {
if (!classOnlyVocabulary.contains(uri.toString())) {
/*
* It's a redefinition of something that we can't
* redefine.
*/
correctOWLUsage = false;
explain(
FULL,
BUILTINREDEFINITION,
"Redefinition of: " + encodeHLink(uri.toString(), myModel.shortForm(uri)));
}
}
}
for (Iterator it = individualURIs.iterator(); it.hasNext(); ) {
URI uri = (URI) it.next();
if (uri != null && reservedVocabulary.contains(uri.toString())) {
/* It's a redefinition of something that we can't redefine. */
correctOWLUsage = false;
explain(
FULL,
BUILTINREDEFINITION,
"Redefinition of: " + encodeHLink(uri.toString(), myModel.shortForm(uri)));
}
}
for (Iterator it = objectPropertyURIs.iterator(); it.hasNext(); ) {
URI uri = (URI) it.next();
if (uri != null && reservedVocabulary.contains(uri.toString())) {
/* It's a redefinition of something that we can't redefine. */
correctOWLUsage = false;
explain(
FULL,
BUILTINREDEFINITION,
"Redefinition of: " + encodeHLink(uri.toString(), myModel.shortForm(uri)));
}
}
for (Iterator it = dataPropertyURIs.iterator(); it.hasNext(); ) {
URI uri = (URI) it.next();
if (uri != null && reservedVocabulary.contains(uri.toString())) {
/* It's a redefinition of something that we can't redefine. */
correctOWLUsage = false;
explain(
FULL,
BUILTINREDEFINITION,
"Redefinition of: " + encodeHLink(uri.toString(), myModel.shortForm(uri)));
}
}
for (Iterator it = datatypeURIs.iterator(); it.hasNext(); ) {
URI uri = (URI) it.next();
if (uri != null && reservedVocabulary.contains(uri.toString())
||
/*
* Nasty. Need to check that thing/nothing aren't
* redefined as datatypes.
*/
uri.toString().equals(OWLVocabularyAdapter.INSTANCE.getThing())
|| uri.toString().equals(OWLVocabularyAdapter.INSTANCE.getNothing())) {
/* It's a redefinition of something that we can't redefine. */
correctOWLUsage = false;
explain(
FULL,
BUILTINREDEFINITION,
"Redefinition of: " + encodeHLink(uri.toString(), myModel.shortForm(uri)));
}
}
} catch (Exception ex) {
ex.printStackTrace();
throw new OWLException(ex.getMessage());
}
}
