public DLOntology_withMaps preprocessAndClausify(OWLOntology rootOntology) {
OWLDataFactory factory = rootOntology.getOWLOntologyManager().getOWLDataFactory();
String ontologyIRI =
rootOntology.getOntologyID().getDefaultDocumentIRI() == null
? "urn:hermit:kb"
: rootOntology.getOntologyID().getDefaultDocumentIRI().toString();
Collection<OWLOntology> importClosure = rootOntology.getImportsClosure();
OWLAxioms_withMaps axioms = new OWLAxioms_withMaps();
OWLNormalization_withMaps normalization =
new OWLNormalization_withMaps(factory, axioms, 0, m_datatypeManager);
for (OWLOntology ontology : importClosure) normalization.processOntology(ontology);
BuiltInPropertyManager_withMaps builtInPropertyManager =
new BuiltInPropertyManager_withMaps(factory);
builtInPropertyManager.axiomatizeBuiltInPropertiesAsNeeded(axioms);
ObjectPropertyInclusionManager_withMaps objectPropertyInclusionManager =
new ObjectPropertyInclusionManager_withMaps(axioms);
// now object property inclusion manager added all non-simple properties to
// axioms.m_complexObjectPropertyExpressions
// now that we know which roles are non-simple, we can decide which negative object property
// assertions have to be
// expressed as concept assertions so that transitivity rewriting applies properly.
objectPropertyInclusionManager.rewriteNegativeObjectPropertyAssertions(
factory, axioms, normalization.getDefinitions().size());
objectPropertyInclusionManager.rewriteAxioms(factory, axioms, 0);
OWLAxiomsExpressivity_withMaps axiomsExpressivity = new OWLAxiomsExpressivity_withMaps(axioms);
DLOntology_withMaps dlOntology =
clausify_withMaps(factory, ontologyIRI, axioms, axiomsExpressivity);
return dlOntology;
}
public DLQueryParser(OWLOntology rootOntology, ShortFormProvider shortFormProvider) {
this.rootOntology = rootOntology;
OWLOntologyManager manager = rootOntology.getOWLOntologyManager();
Set<OWLOntology> importsClosure = rootOntology.getImportsClosure();
// Create a bidirectional short form provider to do the actual mapping.
// It will generate names using the input
// short form provider.
bidiShortFormProvider =
new BidirectionalShortFormProviderAdapter(manager, importsClosure, shortFormProvider);
}
public OWLProfileReport checkOntology(OWLOntology ontology) {
this.ont = ontology;
OWL2DLProfile profile = new OWL2DLProfile();
OWLProfileReport report = profile.checkOntology(ontology);
Set<OWLProfileViolation> violations = new HashSet<OWLProfileViolation>();
violations.addAll(report.getViolations());
OWLOntologyWalker ontologyWalker = new OWLOntologyWalker(ontology.getImportsClosure());
OWL2ELProfileObjectVisitor visitor =
new OWL2ELProfileObjectVisitor(ontologyWalker, ontology.getOWLOntologyManager());
ontologyWalker.walkStructure(visitor);
violations.addAll(visitor.getProfileViolations());
return new OWLProfileReport(this, violations);
}
/** Clears the reasoner and reloads all the axioms in the imports closure. */
public void refresh() {
visitor.clear();
kb.clear();
importsClosure = ontology.getImportsClosure();
visitor.setAddAxiom(true);
for (OWLOntology ont : importsClosure) {
ont.accept(visitor);
}
visitor.verify();
shouldRefresh = false;
}
/** @return current reasoner, operating over abox */
public OWLReasoner getReasoner() {
synchronized (reasonerMutex) {
if (reasoner == null) {
// reasoner -> query -> abox -> tbox
if (LOG.isDebugEnabled()) {
LOG.debug(
"Creating reasoner on "
+ queryOntology
+ " ImportsClosure="
+ queryOntology.getImportsClosure());
}
reasoner = reasonerFactory.createReasoner(queryOntology);
}
}
return reasoner;
}
/**
* <b>Motivation</b>: OWL reasoners do not return superclass expressions If we want to find all
* class expressions that may hold for a class then we must pre-coordinate all possible
* expressions within the subset of OWL we care about. <br>
* This class generates all satisfiable class expressions of the form r some c (for the
* cross-product of R x C), as well as all class expressions that have been used (which may
* include nested expressions)
*
* <p>The results are stored in queryClassMap
*
* @param precomputePropertyClassCombinations
*/
@Deprecated
private void generateQueryOntology(boolean precomputePropertyClassCombinations) {
queryClassMap = new HashMap<OWLClass, OWLClassExpression>();
getReasoner().flush();
if (precomputePropertyClassCombinations) {
LOG.debug("Precomputing all OP x Class combos");
// cross-product of P x C
// TODO - reflexivity and local reflexivity?
for (OWLObjectProperty p : tboxOntology.getObjectPropertiesInSignature(true)) {
LOG.debug(" materializing P some C for P=:" + p);
for (OWLClass c : tboxOntology.getClassesInSignature(true)) {
OWLObjectSomeValuesFrom r = getOWLDataFactory().getOWLObjectSomeValuesFrom(p, c);
// LOG.debug(" QMAP:"+r);
addClassExpressionToQueryMap(r);
}
}
}
// all expressions used in ontology
for (OWLOntology ont : tboxOntology.getImportsClosure()) {
LOG.debug("Finding all nested anonymous expressions");
for (OWLAxiom ax : ont.getAxioms()) {
// TODO - check if this is the nest closure. ie (r some (r2 some (r3 some ...)))
for (OWLClassExpression x : ax.getNestedClassExpressions()) {
if (x.isAnonymous()) {
// LOG.debug(" QMAP+:"+x);
addClassExpressionToQueryMap(x);
}
}
}
}
if (LOG.isDebugEnabled()) {
for (OWLOntology ont : collectedAxioms.keySet()) {
LOG.debug("TOTAL axioms in QMAP: " + collectedAxioms.get(ont).size());
}
}
LOG.debug("Adding collected axioms");
addCollectedAxioms();
LOG.debug("Flushing reasoner...");
reasoner.flush();
LOG.debug("Flushed reasoner");
}
private String parseWithOWLAPI(
URL ontologyURL,
boolean useOWLAPI,
boolean considerImportedOntologies,
boolean considerImportedClosure,
boolean useReasoner)
throws OWLOntologyCreationException, OWLOntologyStorageException, URISyntaxException {
String result = "";
if (useOWLAPI) {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntology(IRI.create(ontologyURL.toString()));
if (considerImportedClosure || considerImportedOntologies) {
Set<OWLOntology> setOfImportedOntologies = new HashSet<OWLOntology>();
if (considerImportedOntologies) {
setOfImportedOntologies.addAll(ontology.getDirectImports());
} else {
setOfImportedOntologies.addAll(ontology.getImportsClosure());
}
for (OWLOntology importedOntology : setOfImportedOntologies) {
manager.addAxioms(ontology, importedOntology.getAxioms());
}
}
if (useReasoner) {
ontology = parseWithReasoner(manager, ontology);
}
StringDocumentTarget parsedOntology = new StringDocumentTarget();
manager.saveOntology(ontology, new RDFXMLOntologyFormat(), parsedOntology);
result = parsedOntology.toString();
}
return result;
}
protected OWLOntology getOntologyAsOWLOntology(
OWLOntologyID ontologyId, boolean merge, IRI universalPrefix) {
// if (merge) throw new UnsupportedOperationException("Merge not implemented yet for
// OWLOntology.");
// Remove the check below. It might be an unmanaged dependency (TODO remove from collector and
// reintroduce check?).
// if (!hasOntology(ontologyIri)) return null;
OWLOntology o;
o = ontologyProvider.getStoredOntology(ontologyId, OWLOntology.class, merge);
if (merge) {
final Set<OWLOntology> set = new HashSet<OWLOntology>();
log.debug("Merging {} with its imports, if any.", o);
set.add(o);
// Actually, if the provider already performed the merge, this won't happen
for (OWLOntology impo : o.getImportsClosure()) {
log.debug("Imported ontology {} will be merged with {}.", impo, o);
set.add(impo);
}
OWLOntologySetProvider provider =
new OWLOntologySetProvider() {
@Override
public Set<OWLOntology> getOntologies() {
return set;
}
};
OWLOntologyMerger merger = new OWLOntologyMerger(provider);
try {
o =
merger.createMergedOntology(
OWLManager.createOWLOntologyManager(), ontologyId.getOntologyIRI());
} catch (OWLOntologyCreationException e) {
log.error("Failed to merge imports for ontology " + ontologyId, e);
// do not reassign the root ontology
}
} else {
// Rewrite import statements
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
OWLDataFactory df = OWLManager.getOWLDataFactory();
/*
* TODO manage import rewrites better once the container ID is fully configurable (i.e. instead of
* going upOne() add "session" or "ontology" if needed). But only do this if we keep considering
* imported ontologies as *not* managed.
*/
for (OWLImportsDeclaration oldImp : o.getImportsDeclarations()) {
changes.add(new RemoveImport(o, oldImp));
String s = oldImp.getIRI().toString();
// FIXME Ugly way to check, but we'll get through with it
if (s.contains("::")) s = s.substring(s.indexOf("::") + 2, s.length());
boolean managed = managedOntologies.contains(oldImp.getIRI());
// For space, always go up at least one
String tid = getID();
if (backwardPathLength > 0) tid = tid.split("/")[0];
IRI target =
IRI.create(
(managed
? universalPrefix + "/" + tid + "/"
: URIUtils.upOne(universalPrefix) + "/")
+ s);
changes.add(new AddImport(o, df.getOWLImportsDeclaration(target)));
}
o.getOWLOntologyManager().applyChanges(changes);
}
return o;
}
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();
}
