@Test
public void testMinusInf() throws Exception {
String input =
"Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\n"
+ "Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\n"
+ "Prefix(:=<http://test.org/test#>)\n"
+ "Ontology(\nDeclaration(NamedIndividual(:a))\n"
+ "Declaration(DataProperty(:dp))\n"
+ "Declaration(Class(:A))\n"
+ "SubClassOf(:A DataAllValuesFrom(:dp owl:real))"
+ "\nSubClassOf(:A \n"
+ "DataSomeValuesFrom(:dp DataOneOf(\"-INF\"^^xsd:float \"-0\"^^xsd:integer))"
+ "\n)"
+ "\n"
+ "ClassAssertion(:A :a)"
+ "\n)";
StringDocumentSource in = new StringDocumentSource(input);
OWLOntologyManager m = Factory.getManager();
OWLOntology o = m.loadOntologyFromOntologyDocument(in);
StringDocumentTarget t = new StringDocumentTarget();
m.saveOntology(o, t);
assertTrue(t.toString() + " should contain -INF", t.toString().contains("-INF"));
OWLOntology o1 = m.loadOntologyFromOntologyDocument(new StringDocumentSource(t.toString()));
assertEquals(
"Obtologies were supposed to be the same", o.getLogicalAxioms(), o1.getLogicalAxioms());
}
@Override
public void prepare() throws TaskException {
// load positive and negative deltas via the OWL API
try {
OWLOntology additions = loadFromDisk(ADDITION_SUFFIX);
OWLOntology deletions = loadFromDisk(DELETION_SUFFIX);
applyToReasoner(additions.getLogicalAxioms(), true);
applyToReasoner(deletions.getLogicalAxioms(), false);
measureTime = additions.getLogicalAxiomCount() > 0 && deletions.getLogicalAxiomCount() > 0;
} catch (OWLOntologyCreationException e) {
throw new TaskException(e);
}
}
private void getPelletIncrementalClassifierRunTime(String baseOnt, String ontDir)
throws Exception {
System.out.println("Using Pellet Incremental Classifier...");
GregorianCalendar start = new GregorianCalendar();
File ontFile = new File(baseOnt);
IRI documentIRI = IRI.create(ontFile);
OWLOntology baseOntology = OWL.manager.loadOntology(documentIRI);
IncrementalClassifier classifier = new IncrementalClassifier(baseOntology);
classifier.classify();
System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
System.out.println("Time taken for base ontology (millis): " + Util.getElapsedTime(start));
File ontDirPath = new File(ontDir);
File[] allFiles = ontDirPath.listFiles();
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
addTripsBaseOntologies(manager);
int count = 1;
for (File owlFile : allFiles) {
IRI owlDocumentIRI = IRI.create(owlFile);
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(owlDocumentIRI);
Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
for (OWLLogicalAxiom axiom : axioms)
OWL.manager.applyChange(new AddAxiom(baseOntology, axiom));
System.out.println("\nLogical axioms: " + baseOntology.getLogicalAxiomCount());
System.out.println(count + " file: " + owlFile.getName());
// System.out.println("" + count + " file: " + owlFile.getName());
// GregorianCalendar start2 = new GregorianCalendar();
classifier.classify();
// System.out.println("Time taken (millis): " +
// Util.getElapsedTime(start2));
manager.removeOntology(ontology);
count++;
}
System.out.println("\nTotal time taken (millis): " + Util.getElapsedTime(start));
}
public Integer visit(OWLOntology ontology) {
int max = _0;
for (OWLAxiom axiom : ontology.getLogicalAxioms()) {
int depth = axiom.accept(this);
if (depth > max) {
max = depth;
}
}
return max;
}
private OWLTheory loadTheory(OWLOntology ontology, String ontologyDir, String o1, String o2) {
OWLTheory theory = getExtendTheory(ontology, false);
LinkedHashSet<OWLLogicalAxiom> bx = new LinkedHashSet<OWLLogicalAxiom>();
OWLOntology ontology1 = getOntologySimple(ontologyDir, o1 + ".owl");
OWLOntology ontology2 = getOntologySimple(ontologyDir, o2 + ".owl");
Set<OWLLogicalAxiom> onto1Axioms =
createIntersection(ontology.getLogicalAxioms(), ontology1.getLogicalAxioms());
Set<OWLLogicalAxiom> onto2Axioms =
createIntersection(ontology.getLogicalAxioms(), ontology2.getLogicalAxioms());
int modOnto1Size = onto1Axioms.size();
int modOnto2Size = onto2Axioms.size();
int modMappingSize = ontology.getLogicalAxioms().size() - modOnto1Size - modOnto2Size;
bx.addAll(onto1Axioms);
bx.addAll(onto2Axioms);
theory.getKnowledgeBase().addBackgroundFormulas(bx);
logger.info(
"ontology axiom sizes: " + modOnto1Size + "," + modOnto2Size + "," + modMappingSize);
return theory;
}
private List<Construct> getOrderedConstructs() {
constructs.clear();
constructs.add(AL);
for (OWLOntology ont : ontologies) {
for (OWLAxiom ax : ont.getLogicalAxioms()) {
ax.accept(this);
}
}
pruneConstructs();
List<Construct> cons = new ArrayList<Construct>(constructs);
Collections.sort(cons, new ConstructComparator());
return cons;
}
public void getELKIncrementalRuntime(String baseOnt, String ontDir) throws Exception {
GregorianCalendar start = new GregorianCalendar();
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
IRI documentIRI = IRI.create(new File(baseOnt));
OWLOntology baseOntology = manager.loadOntology(documentIRI);
System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
// findDataHasValueAxiom(baseOntology.getAxioms(AxiomType.SUBCLASS_OF));
OWLReasonerFactory reasonerFactory = new ElkReasonerFactory();
OWLReasoner reasoner = reasonerFactory.createReasoner(baseOntology);
reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
File[] files = new File(ontDir).listFiles();
int count = 0;
OWLOntologyManager manager2 = OWLManager.createOWLOntologyManager();
addTripsBaseOntologies(manager2);
for (File file : files) {
System.out.println("File name: " + file.getName());
documentIRI = IRI.create(file);
OWLOntology ontology = manager2.loadOntology(documentIRI);
Set<OWLLogicalAxiom> axioms = ontology.getLogicalAxioms();
// findDataHasValueAxiom(ontology.getAxioms(AxiomType.SUBCLASS_OF));
manager.addAxioms(baseOntology, axioms);
reasoner.flush();
System.out.println("Logical axioms: " + baseOntology.getLogicalAxiomCount());
// From the ELK wiki, it seems ABox reasoning will trigger TBox reasoning
reasoner.precomputeInferences(InferenceType.CLASS_ASSERTIONS);
manager2.removeOntology(ontology);
count++;
System.out.println("Done with " + count);
// if(count == 5)
// break;
}
reasoner.dispose();
System.out.println("Time taken (millis): " + Util.getElapsedTime(start));
}
public Set<OWLClass> getRootUnsatisfiableClasses() {
// StructureBasedRootClassFinder srd = new StructureBasedRootClassFinder(this.baseReasoner);
StructuralRootDerivedReasoner srd =
new StructuralRootDerivedReasoner(this.manager, this.baseReasoner, this.reasonerFactory);
Set<OWLClass> estimatedRoots = srd.getRootUnsatisfiableClasses();
this.cls2JustificationMap = new HashMap<OWLClass, Set<Explanation>>();
Set<OWLAxiom> allAxioms = new HashSet<OWLAxiom>();
for (OWLOntology ont : this.baseReasoner.getRootOntology().getImportsClosure()) {
allAxioms.addAll(ont.getLogicalAxioms());
}
for (OWLClass cls : estimatedRoots) {
this.cls2JustificationMap.put(cls, new HashSet<Explanation>());
System.out.println("POTENTIAL ROOT: " + cls);
}
System.out.println("Finding real roots from " + estimatedRoots.size() + " estimated roots");
int done = 0;
this.roots.addAll(estimatedRoots);
for (OWLClass estimatedRoot : estimatedRoots) {
try {
PelletExplanationGenerator gen =
new PelletExplanationGenerator(manager.createOntology(allAxioms));
OWLDataFactory df = this.manager.getOWLDataFactory();
Set<Explanation> expls =
gen.getExplanations(df.getOWLSubClassOfAxiom(estimatedRoot, df.getOWLNothing()));
cls2JustificationMap.get(estimatedRoot).addAll(expls);
++done;
System.out.println("Done " + done);
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
}
}
for (OWLClass clsA : estimatedRoots) {
for (OWLClass clsB : estimatedRoots)
if (!clsA.equals(clsB)) {
Set<Explanation> clsAExpls = cls2JustificationMap.get(clsA);
Set<Explanation> clsBExpls = cls2JustificationMap.get(clsB);
boolean clsARootForClsB = false;
boolean clsBRootForClsA = false;
for (Explanation clsAExpl : clsAExpls) {
for (Explanation clsBExpl : clsBExpls)
if (isRootFor(clsAExpl, clsBExpl)) {
clsARootForClsB = true;
} else if (isRootFor(clsBExpl, clsAExpl)) {
clsBRootForClsA = true;
}
}
Explanation clsAExpl;
if ((!clsARootForClsB) || (!clsBRootForClsA))
if (clsARootForClsB) {
this.roots.remove(clsB);
} else if (clsBRootForClsA) this.roots.remove(clsA);
}
}
OWLClass clsA;
return this.roots;
}