public Set<OWLObjectProperty> getObjectPropertiesByDomainAndRange(
OWLClass domain, OWLClass range) {
Set<OWLObjectProperty> propSet = new HashSet<OWLObjectProperty>();
for (OWLObjectProperty prop : _ontology.getObjectPropertiesInSignature()) {
for (OWLClass owlClass : _reasoner.getObjectPropertyDomains(prop, true).getFlattened()) {
if (owlClass.equals(domain)) {
for (OWLClass owlClass2 : _reasoner.getObjectPropertyRanges(prop, true).getFlattened()) {
if (owlClass2.equals(range)) {
propSet.add(prop);
}
}
}
}
}
return propSet;
}
public Set<OWLDataProperty> getDataPropertiesByDomain(OWLClass domain) {
Set<OWLDataProperty> propSet = new HashSet<OWLDataProperty>();
Set<OWLDataProperty> objProps = _ontology.getDataPropertiesInSignature();
for (OWLDataProperty prop : objProps) {
for (OWLClass owlClass : _reasoner.getDataPropertyDomains(prop, true).getFlattened()) {
if (owlClass.equals(domain)) {
propSet.add(prop);
}
}
}
return propSet;
}
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;
}
public boolean isRestrictedInstantiator(OWLClass c) {
return c == null
|| c.isTopEntity()
|| m_ontologyOperator.getFlatteningTransformer().isIntermediary(c)
|| c.equals(m_referenceClass);
}
public static void main(String[] args) throws Exception {
if (args.length == 0) {
// args = new String[] { "/home/yzhou/backup/20141212/univ-bench-dl-queries.owl"};
args = new String[] {PagodaTester.onto_dir + "fly/fly-all-in-one_rolledUp.owl"};
// args = new String[] { PagodaTester.onto_dir +
// "dbpedia/integratedOntology-all-in-one-minus-datatype.owl" };
// args = new String[] { PagodaTester.onto_dir + "npd/npd-all-minus-datatype.owl" };
// args = new String[] { PagodaTester.onto_dir + "bio2rdf/chembl/cco-noDPR.ttl" };
// args = new String[] { PagodaTester.onto_dir +
// "bio2rdf/reactome/biopax-level3-processed.owl" };
// args = new String[] { PagodaTester.onto_dir + "bio2rdf/uniprot/core-processed-noDis.owl"
// };
}
// OWLOntology ontology = OWLHelper.getMergedOntology(args[0], null);
// OWLHelper.correctDataTypeRangeAxioms(ontology);
OWLOntology ontology = OWLHelper.loadOntology(args[0]);
OWLOntologyManager manager = ontology.getOWLOntologyManager();
OWLDataFactory factory = manager.getOWLDataFactory();
// manager.saveOntology(ontology, new FileOutputStream(args[0].replace(".owl",
// "_owlapi.owl")));
if (outputFile != null) Utility.redirectCurrentOut(outputFile);
int queryID = 0;
for (OWLClass cls : ontology.getClassesInSignature(true)) {
if (cls.equals(factory.getOWLThing()) || cls.equals(factory.getOWLNothing())) continue;
if (!cls.toStringID().contains("Query")) continue;
System.out.println("^[Query" + ++queryID + "]");
System.out.println(template.replace("@CLASS", cls.toStringID()));
System.out.println();
}
for (OWLOntology onto : ontology.getImportsClosure())
for (OWLObjectProperty prop : onto.getObjectPropertiesInSignature()) {
// if (!prop.toStringID().contains("Query")) continue;
System.out.println("^[Query" + ++queryID + "]");
System.out.println("SELECT ?X ?Y");
System.out.println("WHERE {");
System.out.println("?X <" + prop.toStringID() + "> ?Y .");
System.out.println("}");
System.out.println();
}
String[] answerVars = new String[] {"?X", "?Y"};
for (OWLOntology onto : ontology.getImportsClosure())
for (OWLObjectProperty prop : onto.getObjectPropertiesInSignature()) {
// if (!prop.toStringID().contains("Query")) continue;
for (int i = 0; i < answerVars.length; ++i) {
System.out.println("^[Query" + ++queryID + "]");
System.out.println("SELECT " + answerVars[i]);
System.out.println("WHERE {");
System.out.println("?X <" + prop.toStringID() + "> ?Y .");
System.out.println("}");
System.out.println();
}
}
if (outputFile != null) Utility.closeCurrentOut();
}