public void setOntology(OWLOntology ont) {
this.ont = ont;
List<Object> data = new ArrayList<>();
data.add(directImportsHeader);
// @@TODO ordering
for (OWLImportsDeclaration decl : ont.getImportsDeclarations()) {
data.add(new OntologyImportItem(ont, decl, editorKit));
}
data.add(indirectImportsHeader);
// @@TODO ordering
try {
for (OWLOntology ontRef :
editorKit.getOWLModelManager().getOWLOntologyManager().getImportsClosure(ont)) {
if (!ontRef.equals(ont)) {
for (OWLImportsDeclaration dec : ontRef.getImportsDeclarations()) {
if (!data.contains(dec)) {
data.add(new OntologyImportItem(ontRef, dec, editorKit));
}
}
}
}
} catch (UnknownOWLOntologyException e) {
throw new OWLRuntimeException(e);
}
setListData(data.toArray());
}
public Map<String, OWLIndividual> returnSitesInOntology() {
// map that contains the correspondance between the names of the sites
// and their OWLIndividual representations.
Map<String, OWLIndividual> returnMap = new HashMap<>();
List<OWLIndividual> returnList = new ArrayList<>();
OWLAnnotationProperty hasNameAnnotationProperty =
OWLFactory.getOWLAnnotationProperty(":individualName", topIxPrefixManager);
OWLClassExpression tempSiteClassExpression =
OWLFactory.getOWLClass(":Site", topIxPrefixManager);
for (OWLClassAssertionAxiom tempClassAssAx :
topIxOnt.getClassAssertionAxioms(tempSiteClassExpression)) {
returnList.add(tempClassAssAx.getIndividual());
Set<OWLAnnotationAssertionAxiom> tempSiteAnnotationsSet =
topIxOnt.getAnnotationAssertionAxioms(
tempClassAssAx.getIndividual().asOWLNamedIndividual().getIRI());
for (OWLAnnotationAssertionAxiom tempAnnotationAssertionAxiom : tempSiteAnnotationsSet) {
if (tempAnnotationAssertionAxiom.getProperty().equals(hasNameAnnotationProperty)) {
String tempString = tempAnnotationAssertionAxiom.getValue().toString();
logger.info(tempString);
tempString =
tempString.substring(tempString.indexOf('"') + 1, tempString.indexOf('^') - 1);
logger.info(tempString);
logger.info(tempClassAssAx.getIndividual().toString());
returnMap.put(tempString, tempClassAssAx.getIndividual());
}
}
}
return returnMap;
}
public void retrieveRoomsMap() {
// this method retrieves the rooms to be insserted in the two rooms lists.
// it deposits the retrieved data in a map where the key is the room name (String) and the value
// is the corresponding entity IRI.
// the above data structure will be used in passing the entity IRIs in the jess working memory
// when constructing the facts
// when the respective room name (String) is selected in the rooms list combo box.
for (OWLSubClassOfAxiom scoAx :
topIxOnt.getSubClassAxiomsForSuperClass(
OWLFactory.getOWLClass(
IRI.create(
"http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl#Room")))) {
String tmpS = scoAx.getSubClass().toString();
Set<OWLAnnotationAssertionAxiom> tmpAnnSet =
topIxOnt.getAnnotationAssertionAxioms(
IRI.create(tmpS.substring(tmpS.indexOf('<') + 1, tmpS.indexOf('>'))));
for (OWLAnnotationAssertionAxiom aaAx : tmpAnnSet) {
if (aaAx.getProperty()
.toString()
.equals(
"<http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl#classID>")) {
roomToIRI.put(
aaAx.getValue().toString().substring(1, aaAx.getValue().toString().indexOf('^') - 1),
tmpS.substring(tmpS.indexOf('<') + 1, tmpS.indexOf('>')));
}
}
}
}
private OWLOntology findOntology(List<OWLOntology> loadedOntologies, IRI documentIRI) {
for (OWLOntology o : loadedOntologies) {
if (documentIRI.equals(o.getOntologyID().getOntologyIRI())) {
return o;
}
}
return null;
}
public OWLOntology loadOWLOntology(
OWLOntologyDocumentSource documentSource, final OWLOntologyCreationHandler mediator)
throws OWLOntologyCreationException {
// Attempt to parse the ontology by looping through the parsers. If the
// ontology is parsed successfully then we break out and return the ontology.
// I think that this is more reliable than selecting a parser based on a file extension
// for example (perhaps the parser list could be ordered based on most likely parser, which
// could be determined by file extension).
Map<OWLParser, OWLParserException> exceptions =
new LinkedHashMap<OWLParser, OWLParserException>();
// Call the super method to create the ontology - this is needed, because
// we throw an exception if someone tries to create an ontology directly
OWLOntology existingOntology = null;
IRI iri = documentSource.getDocumentIRI();
if (getOWLOntologyManager().contains(iri)) {
existingOntology = getOWLOntologyManager().getOntology(iri);
}
OWLOntologyID ontologyID = new OWLOntologyID();
OWLOntology ont =
super.createOWLOntology(ontologyID, documentSource.getDocumentIRI(), mediator);
// Now parse the input into the empty ontology that we created
for (final OWLParser parser : getParsers()) {
try {
if (existingOntology == null && !ont.isEmpty()) {
// Junk from a previous parse. We should clear the ont
getOWLOntologyManager().removeOntology(ont);
ont = super.createOWLOntology(ontologyID, documentSource.getDocumentIRI(), mediator);
}
OWLOntologyFormat format = parser.parse(documentSource, ont);
mediator.setOntologyFormat(ont, format);
return ont;
} catch (IOException e) {
// No hope of any parsers working?
// First clean up
getOWLOntologyManager().removeOntology(ont);
throw new OWLOntologyCreationIOException(e);
} catch (UnloadableImportException e) {
// First clean up
getOWLOntologyManager().removeOntology(ont);
throw e;
} catch (OWLParserException e) {
// Record this attempts and continue trying to parse.
exceptions.put(parser, e);
} catch (RuntimeException e) {
// Clean up and rethrow
getOWLOntologyManager().removeOntology(ont);
throw e;
}
}
if (existingOntology == null) {
getOWLOntologyManager().removeOntology(ont);
}
// We haven't found a parser that could parse the ontology properly. Throw an
// exception whose message contains the stack traces from all of the parsers
// that we have tried.
throw new UnparsableOntologyException(documentSource.getDocumentIRI(), exceptions);
}
private void runWithSeparateFiles() {
if (owlFile == null) {
throw new NullPointerException("You have to specify an ontology file!");
}
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = null;
OBDADataFactory obdaDataFactory = OBDADataFactoryImpl.getInstance();
try {
ontology = manager.loadOntologyFromOntologyDocument((new File(owlFile)));
if (disableReasoning) {
/*
* when reasoning is disabled, we extract only the declaration assertions for the vocabulary
*/
ontology = extractDeclarations(manager, ontology);
}
Collection<Predicate> predicates = new ArrayList<>();
for (OWLClass owlClass : ontology.getClassesInSignature()) {
Predicate predicate = obdaDataFactory.getClassPredicate(owlClass.getIRI().toString());
predicates.add(predicate);
}
for (OWLDataProperty owlDataProperty : ontology.getDataPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getDataPropertyPredicate(owlDataProperty.getIRI().toString());
predicates.add(predicate);
}
for (OWLObjectProperty owlObjectProperty : ontology.getObjectPropertiesInSignature()) {
Predicate predicate =
obdaDataFactory.getObjectPropertyPredicate(owlObjectProperty.getIRI().toString());
predicates.add(predicate);
}
OBDAModel obdaModel = loadMappingFile(mappingFile);
Ontology inputOntology = OWLAPI3TranslatorUtility.translate(ontology);
obdaModel.declareAll(inputOntology.getVocabulary());
int numPredicates = predicates.size();
int i = 1;
for (Predicate predicate : predicates) {
System.err.println(String.format("Materializing %s (%d/%d)", predicate, i, numPredicates));
serializePredicate(ontology, inputOntology, obdaModel, predicate, outputFile, format);
i++;
}
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
} catch (Exception e) {
e.printStackTrace();
}
}
public void visit(OWLOntology ontology) {
checkOccurrence(ontology.getAnnotations());
for (AxiomType<?> t : AxiomType.AXIOM_TYPES) {
for (OWLAxiom ax : ontology.getAxioms(t)) {
checkOccurrence(ax.getAnnotations());
ax.accept(this);
}
}
singleAppearance.clear();
}
public void retrieveSubObjectPropertyAxioms() {
// this method is to perform a dual operation; it shall retrieve all the declarative object
// properties categories' annotations,
// thus filling the objPropCategories Set, while parallelly will, for each category entry
// retrieve the object properties themselves
// and adding their entries in the objPropEntries Set.
Set<OWLSubObjectPropertyOfAxiom> tmpSet;
OWLObjectPropertyExpression tempDeclarativePropertyClass =
OWLFactory.getOWLObjectProperty(":DeclarativeProperty", topIxPrefixManager);
tmpSet =
topIxOnt.getObjectSubPropertyAxiomsForSuperProperty(
tempDeclarativePropertyClass); // OWLFactory.getOWLObjectProperty(IRI.create("http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl#DeclarativeProperty")));
Set<OWLSubObjectPropertyOfAxiom> tmpSet2;
Set<OWLAnnotationAssertionAxiom> tmpAnnSet1;
Set<OWLAnnotationAssertionAxiom> tmpAnnSet2;
// to become class variables.
for (OWLSubObjectPropertyOfAxiom sopAx : tmpSet) {
String tmpS = sopAx.getSubProperty().toString();
// categories...
tmpAnnSet1 =
topIxOnt.getAnnotationAssertionAxioms(
IRI.create(
tmpS.substring(
1, tmpS.indexOf('>')))); // this set only contains one annotation per entry
for (OWLAnnotationAssertionAxiom aaAx : tmpAnnSet1) {
String currentObjPropCatName =
aaAx.getValue().toString().substring(1, aaAx.getValue().toString().indexOf('^') - 1);
tmpSet2 =
topIxOnt.getObjectSubPropertyAxiomsForSuperProperty(
OWLFactory.getOWLObjectProperty(IRI.create(tmpS.substring(1, tmpS.length() - 1))));
for (OWLSubObjectPropertyOfAxiom sopAx2 : tmpSet2) {
String tmpS2 = sopAx2.getSubProperty().toString();
tmpAnnSet2 =
topIxOnt.getAnnotationAssertionAxioms(
IRI.create(tmpS2.substring(1, tmpS2.length() - 1)));
for (OWLAnnotationAssertionAxiom aaAx2 : tmpAnnSet2) {
String currentObjPropEntryName =
aaAx2
.getValue()
.toString()
.substring(1, aaAx2.getValue().toString().indexOf('^') - 1);
propEntryNameToPropCatName.put(currentObjPropEntryName, currentObjPropCatName);
propEntryNametoPropEntryIRI.put(
currentObjPropEntryName, tmpS2.substring(1, tmpS2.length() - 1));
}
}
}
}
}
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);
}
public boolean assertDataPropertyInstance(String ind, String prop, int value) {
OWLDataProperty dataProp =
OWLFactory.getOWLDataProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + prop));
OWLDataPropertyAssertionAxiom tmpAx =
OWLFactory.getOWLDataPropertyAssertionAxiom(
dataProp,
OWLFactory.getOWLNamedIndividual(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + ind)),
OWLFactory.getOWLLiteral(value));
manager.addAxiom(topIxOnt, tmpAx);
return true;
}
////////////////////////////////
// INDIVIDUAL ASSERTION METHODS//
////////////////////////////////
public boolean assertSiteIndividual(String siteNameHash, String siteNameAnnotation) {
OWLClassExpression tmpCE = OWLFactory.getOWLClass(":Site", topIxPrefixManager);
OWLIndividual tmpInd = OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
manager.addAxiom(topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tmpCE, tmpInd));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + siteNameHash),
OWLFactory.getOWLLiteral(siteNameAnnotation)));
return true;
}
private void handleNotesOntologyChanged(List<OWLOntologyChange> changes) {
try {
OWLOntologyManager notesOntologyManager = notesOntology.getOWLOntologyManager();
if (notesOntologyManager.getOntologyFormat(notesOntology)
instanceof BinaryOWLOntologyDocumentFormat) {
OWLAPIProjectDocumentStore documentStore =
OWLAPIProjectDocumentStore.getProjectDocumentStore(project.getProjectId());
List<OWLOntologyChangeData> infoList = new ArrayList<OWLOntologyChangeData>();
for (OWLOntologyChange change : changes) {
OWLOntologyChangeRecord rec = change.getChangeRecord();
OWLOntologyChangeData info = rec.getData();
infoList.add(info);
}
BinaryOWLOntologyDocumentSerializer serializer = new BinaryOWLOntologyDocumentSerializer();
serializer.appendOntologyChanges(
notesOntologyDocument,
new OntologyChangeDataList(infoList, System.currentTimeMillis()));
} else {
// Swap it over
notesOntologyManager.saveOntology(notesOntology, new BinaryOWLOntologyDocumentFormat());
}
} catch (OWLOntologyStorageException e) {
throw new RuntimeException(e);
} catch (IOException e) {
throw new RuntimeException(e);
}
}
/**
* Serializes a batch of triples corresponding to a predicate into one file. Upper bound:
* TRIPLE_LIMIT_PER_FILE.
*/
private static int serializeTripleBatch(
OWLOntology ontology,
QuestOWLIndividualAxiomIterator iterator,
String filePrefix,
String predicateName,
int fileCount,
String format)
throws Exception {
String fileName = filePrefix + fileCount + ".owl";
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
// Main buffer
OWLOntology aBox = manager.createOntology(IRI.create(predicateName));
// Add the signatures
for (OWLDeclarationAxiom axiom : ontology.getAxioms(AxiomType.DECLARATION)) {
manager.addAxiom(aBox, axiom);
}
int tripleCount = 0;
while (iterator.hasNext() && (tripleCount < TRIPLE_LIMIT_PER_FILE)) {
manager.addAxiom(aBox, iterator.next());
tripleCount++;
}
// BufferedOutputStream output = new BufferedOutputStream(new
// FileOutputStream(outputPath.toFile()));
// BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(output, "UTF-8"));
BufferedWriter writer = new BufferedWriter(new FileWriter(fileName));
manager.saveOntology(aBox, getOntologyFormat(format), new WriterDocumentTarget(writer));
return tripleCount;
}
public void classifyOntology(OWLOntology ontology, OWLReasonerFactory factory) {
ToStringRenderer.getInstance().setRenderer(new ManchesterOWLSyntaxOWLObjectRendererImpl());
OWLReasoner reasoner = factory.createNonBufferingReasoner(ontology);
// reasoner.precomputeInferences(InferenceType.values());
long time = System.currentTimeMillis();
boolean isConsistent = reasoner.isConsistent();
int numOfUnsatClasses = reasoner.getUnsatisfiableClasses().getEntitiesMinusBottom().size();
time = System.currentTimeMillis() - time;
DLExpressivityChecker checker = new DLExpressivityChecker(Collections.singleton(ontology));
String e = checker.getDescriptionLogicName();
String name = ontology.getOntologyID().getOntologyIRI().getFragment();
logger.info(
"ontology: "
+ name
+ ", reasoner: "
+ factory.getReasonerName()
+ ", expressivity: "
+ e
+ ", consistent: "
+ isConsistent
+ ", unsat classes: "
+ numOfUnsatClasses
+ ", time: "
+ time);
}
public boolean assertHouseIndividual(String houseEntryHash, String houseEntryAnnotation) {
OWLClassExpression tempClassExpression = OWLFactory.getOWLClass(":House", topIxPrefixManager);
OWLIndividual tempIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + houseEntryHash),
OWLFactory.getOWLLiteral(houseEntryAnnotation)));
return true;
}
/**
* Uses some heuristics to determine if the specified ontology and its imports closure is an OBO
* ontology.
*
* @param ontology The ontology to check
* @return <code>true</code> if the ontology is an OBO ontology (or could be an OBO ontology)
* otherwise false.
*/
public boolean isOBOOntology(OWLOntology ontology) {
if (isOBOFormat(ontology)) {
return true;
}
for (AxiomType<?> axiomType : AxiomType.AXIOM_TYPES) {
for (OWLAxiom ax : ontology.getAxioms(axiomType, true)) {
if (!isOBOAxiom(ax)) {
return false;
}
}
}
for (OWLAnnotationProperty property : ontology.getAnnotationPropertiesInSignature()) {
if (isOBOEntity(property)) {
return true;
}
}
return false;
}
@Test
public void shouldHandleNullManager_For_GetBottomClassNode() {
try {
when(ontology.getOWLOntologyManager()).thenReturn(null);
reasoner.getBottomClassNode();
} catch (NullPointerException e) {
fail("NullPointerException");
}
}
/**
* Refills the section with rows. This method will be called by the system and should be directly
* called.
*/
protected void refill(OWLOntology ontology) {
added.clear();
for (OWLEquivalentObjectPropertiesAxiom ax :
ontology.getEquivalentObjectPropertiesAxioms(getRootObject())) {
addRow(
new OWLEquivalentObjectPropertiesAxiomFrameSectionRow(
getOWLEditorKit(), this, ontology, getRootObject(), ax));
added.add(ax);
}
}
public void actionPerformed(ActionEvent actionEvent) {
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
int axiomsRemoved = 0;
int axiomsAdded = 0;
int numberOfDisjoints = 0;
for (OWLOntology ont : getOWLModelManager().getActiveOntologies()) {
// act on each ontology in turn
CliqueFinder<OWLClassExpression> merger = new CliqueFinder<OWLClassExpression>();
Set<OWLDisjointClassesAxiom> oldAxioms = ont.getAxioms(AxiomType.DISJOINT_CLASSES);
numberOfDisjoints += oldAxioms.size();
for (OWLDisjointClassesAxiom ax : oldAxioms) {
merger.add(ax.getClassExpressions());
}
for (Set<OWLClassExpression> newAxioms : merger.getResults()) {
OWLDisjointClassesAxiom newAxiom =
getOWLModelManager().getOWLDataFactory().getOWLDisjointClassesAxiom(newAxioms);
if (oldAxioms.contains(newAxiom)) {
oldAxioms.remove(newAxiom);
} else {
changes.add(new AddAxiom(ont, newAxiom));
axiomsAdded++;
}
}
for (OWLDisjointClassesAxiom oldAxiom : oldAxioms) {
changes.add(new RemoveAxiom(ont, oldAxiom));
axiomsRemoved++;
}
}
getOWLModelManager().applyChanges(changes);
logger.info(
axiomsRemoved
+ " (of "
+ numberOfDisjoints
+ " total) disjoint class axioms replaced with "
+ axiomsAdded);
}
/**
* Gets OWL class by given name
*
* @param className
* @return
* @throws OWLReasonerException
*/
public OWLClass getNamedClass(String className) {
if (classnameCache == null) {
classnameCache = new HashMap<String, URI>();
for (OWLOntology ont : reasoner.getLoadedOntologies()) {
for (OWLClass cls : ont.getReferencedClasses()) {
classnameCache.put(cls.toString(), cls.getURI());
}
}
}
OWLClass namedCls = null;
URI uri = classnameCache.get(className);
if (uri != null) {
namedCls = manager.getOWLDataFactory().getOWLClass(uri);
} else {
System.err.println("Cannot find class: " + className + " in loaded ontologies");
}
return namedCls;
}
/**
* Gets the property by given name, e.g. has_topping
*
* @param propName
* @return
*/
public OWLObjectProperty getNamedObjectProperty(String propName) {
if (objPropNameCache == null) {
objPropNameCache = new HashMap<String, URI>();
for (OWLOntology ont : reasoner.getLoadedOntologies()) {
for (OWLObjectProperty prop : ont.getReferencedObjectProperties()) {
objPropNameCache.put(prop.toString(), prop.getURI());
}
}
}
// search the HashMap
OWLObjectProperty namedProp = null;
URI uri = objPropNameCache.get(propName);
if (uri != null) {
namedProp = manager.getOWLDataFactory().getOWLObjectProperty(uri);
} else {
System.err.println("Cannot find object property: " + propName + " in loaded ontologies");
}
return namedProp;
}
@Before
public void setUp() {
when(ontology.getOWLOntologyManager()).thenReturn(manager);
when(manager.getOWLDataFactory()).thenReturn(dataFactory);
when(dataFactory.getOWLThing()).thenReturn(owlThing);
when(dataFactory.getOWLNothing()).thenReturn(owlNothing);
when(dataFactory.getOWLTopObjectProperty()).thenReturn(owlTopObjectProperty);
when(dataFactory.getOWLBottomObjectProperty()).thenReturn(owlBottomObjectProperty);
when(dataFactory.getOWLTopDataProperty()).thenReturn(owlTopDataProperty);
when(dataFactory.getOWLBottomDataProperty()).thenReturn(owlBottomDataProperty);
reasoner = new NoOpReasoner(ontology, dataFactory);
}
// asserts a hasHouse property instance between a house and its corresponding
// site
public boolean assertHasHousePropertyInstance(String houseEntryHash, String siteNameHash) {
OWLObjectProperty objProp =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasHouse"));
OWLIndividual houseIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseEntryHash, topIxPrefixManager);
OWLIndividual siteIndividual =
OWLFactory.getOWLNamedIndividual(':' + siteNameHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(objProp, siteIndividual, houseIndividual));
return true;
}
public Object visit(OWLSubPropertyChainOfAxiom axiom) {
Set<OWLObjectPropertyRangeAxiom> rangeAxioms =
getCurrentOntology().getAxioms(AxiomType.OBJECT_PROPERTY_RANGE, true);
if (rangeAxioms.isEmpty()) {
return false;
}
// Do we have a range restriction imposed on our super property?
for (OWLObjectPropertyRangeAxiom rngAx : rangeAxioms) {
if (getPropertyManager().isSubPropertyOf(axiom.getSuperProperty(), rngAx.getProperty())) {
// Imposed range restriction!
OWLClassExpression imposedRange = rngAx.getRange();
// There must be an axiom that imposes a range on the last prop in the chain
List<OWLObjectPropertyExpression> chain = axiom.getPropertyChain();
if (!chain.isEmpty()) {
OWLObjectPropertyExpression lastProperty = chain.get(chain.size() - 1);
boolean rngPresent = false;
for (OWLOntology ont : getCurrentOntology().getImportsClosure()) {
for (OWLObjectPropertyRangeAxiom lastPropRngAx :
ont.getObjectPropertyRangeAxioms(lastProperty)) {
if (lastPropRngAx.getRange().equals(imposedRange)) {
// We're o.k.
rngPresent = true;
break;
}
}
}
if (!rngPresent) {
profileViolations.add(
new LastPropertyInChainNotInImposedRange(getCurrentOntology(), axiom, rngAx));
}
}
}
}
return null;
}
private void importFile(
InputStream in, IRI documentIRI, File inDir, Authorizations authorizations) throws Exception {
byte[] inFileData = IOUtils.toByteArray(in);
Reader inFileReader = new InputStreamReader(new ByteArrayInputStream(inFileData));
OWLOntologyLoaderConfiguration config = new OWLOntologyLoaderConfiguration();
OWLOntologyManager m = createOwlOntologyManager(config, documentIRI);
OWLOntologyDocumentSource documentSource = new ReaderDocumentSource(inFileReader, documentIRI);
OWLOntology o = m.loadOntologyFromOntologyDocument(documentSource, config);
storeOntologyFile(new ByteArrayInputStream(inFileData), documentIRI);
for (OWLClass ontologyClass : o.getClassesInSignature()) {
if (!o.isDeclared(ontologyClass, false)) {
continue;
}
importOntologyClass(o, ontologyClass, inDir, authorizations);
}
for (OWLDataProperty dataTypeProperty : o.getDataPropertiesInSignature()) {
if (!o.isDeclared(dataTypeProperty, false)) {
continue;
}
importDataProperty(o, dataTypeProperty);
}
for (OWLObjectProperty objectProperty : o.getObjectPropertiesInSignature()) {
if (!o.isDeclared(objectProperty, false)) {
continue;
}
importObjectProperty(o, objectProperty);
}
for (OWLObjectProperty objectProperty : o.getObjectPropertiesInSignature()) {
if (!o.isDeclared(objectProperty, false)) {
continue;
}
importInverseOf(o, objectProperty);
}
}
public void mergeOntologies() {
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
for (OWLOntology ont : ontologies) {
if (!ont.equals(targetOntology)) {
// move the axioms
for (OWLAxiom ax : ont.getAxioms()) {
changes.add(new AddAxiom(targetOntology, ax));
}
// move ontology annotations
for (OWLAnnotation annot : ont.getAnnotations()) {
changes.add(new AddOntologyAnnotation(targetOntology, annot));
}
if (!targetOntology.getOntologyID().isAnonymous()) {
// move ontology imports
for (OWLImportsDeclaration decl : ont.getImportsDeclarations()) {
if (ontologies.contains(ont.getOWLOntologyManager().getImportedOntology(decl))) {
continue;
}
Optional<IRI> defaultDocumentIRI =
targetOntology.getOntologyID().getDefaultDocumentIRI();
if (defaultDocumentIRI.isPresent() && !decl.getIRI().equals(defaultDocumentIRI.get())) {
changes.add(new AddImport(targetOntology, decl));
} else {
logger.warn(
"Merge: ignoring import declaration for ontology "
+ targetOntology.getOntologyID()
+ " (would result in target ontology importing itself).");
}
}
}
}
}
try {
owlOntologyManager.applyChanges(changes);
} catch (OWLOntologyChangeException e) {
ErrorLogPanel.showErrorDialog(e);
}
}
public boolean assertRoomIndividual(
String roomName, String roomIndividualHash, String roomIndividualAnnotation) {
OWLClassExpression tempClassExpression =
OWLFactory.getOWLClass(
IRI.create(
roomToIRI.get(
roomName))); // retrieves the Room Class IRI fron the roomToIRI map, using
// roomID as a key.
OWLIndividual tempIndividual =
OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt, OWLFactory.getOWLClassAssertionAxiom(tempClassExpression, tempIndividual));
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLAnnotationAssertionAxiom(
OWLFactory.getOWLAnnotationProperty(
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + "individualName")),
IRI.create(
topIxOnt.getOntologyID().getOntologyIRI().toString() + '#' + roomIndividualHash),
OWLFactory.getOWLLiteral(String.format(roomIndividualAnnotation))));
return true;
}
public boolean assertHasRoomPropertyInstance(
String houseIndividualHash, String roomIndividualHash) {
OWLObjectProperty tempOWLbjectProperty =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasRoom"));
OWLIndividual houseIndividual =
OWLFactory.getOWLNamedIndividual(':' + houseIndividualHash, topIxPrefixManager);
OWLIndividual roomIndividual =
OWLFactory.getOWLNamedIndividual(':' + roomIndividualHash, topIxPrefixManager);
manager.addAxiom(
topIxOnt,
OWLFactory.getOWLObjectPropertyAssertionAxiom(
tempOWLbjectProperty, houseIndividual, roomIndividual));
return true;
}
public void actionPerformed(ActionEvent e) {
OWLClass selClass = getOWLWorkspace().getOWLSelectionModel().getLastSelectedClass();
List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
Set<OWLClassExpression> operands = new HashSet<OWLClassExpression>();
for (OWLOntology ont : getOWLModelManager().getActiveOntologies()) {
for (OWLSubClassOfAxiom ax : ont.getSubClassAxiomsForSubClass(selClass)) {
changes.add(new RemoveAxiom(ont, ax));
operands.add(ax.getSuperClass());
}
}
if (operands.isEmpty()) {
return;
}
OWLDataFactory df = getOWLModelManager().getOWLDataFactory();
OWLClassExpression equCls;
if (operands.size() == 1) {
equCls = operands.iterator().next();
} else {
equCls = df.getOWLObjectIntersectionOf(operands);
}
OWLAxiom ax = df.getOWLEquivalentClassesAxiom(CollectionFactory.createSet(selClass, equCls));
changes.add(new AddAxiom(getOWLModelManager().getActiveOntology(), ax));
getOWLModelManager().applyChanges(changes);
}
public void loadOntology() {
try {
/*
* --apaitoymena vimata gia th dhmioyrgia mapped ontologias:
* 1.dhmioyrgoyme ena toBeMappedIRI me skopo toy thn antistoixish me
* to local File. 2.dhmioyrgoyme ena File me th dieythynsh ths
* ontologias sto topiko apothikeytiko meso. 3.dhmioyrgoyme enan
* SimpleIRIMapper kai ton prosthetoyme mesw toy manager. o
* SimpleIRIMapper syndeei to toBeMappedIRI poy dwsame arxika, me
* thn fysikh topothesia ths ontologias sto topiko apothikeytiko
* meso. 4.dhmioyrgoyme ena ontologyIRI me akrivws thn idia arxiki
* timh me to toBeMappedIRI to opoio tha einai to IRI ths ontologias
* mas 5.dhmioyrgoyme thn ontologia mas xrhsimopoiwntas to
* manager.loadOntology(ontologyIRI);
*/
String sep = File.separator;
manager = OWLManager.createOWLOntologyManager();
toBeMappedIRI =
IRI.create(
"http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl");
// ontFile = new File("../src/ontologyresources/ptyxiaki_v0.8.owl");
ontFile = new File("src/ontologyresources/ptyxiaki_v0.8.owl");
// in case of alternative location on load time when the application is jar'ed!
if (!ontFile.canRead()) {
ontFile = new File("ontologyresources/ptyxiaki_v0.8.owl");
}
manager.addIRIMapper(new SimpleIRIMapper(toBeMappedIRI, IRI.create(ontFile)));
ontologyIRI =
IRI.create(
"http://www.semanticweb.org/ontologies/ptyxiaki_v0.6/2011/5/Ontology1308067064597.owl");
topIxOnt = manager.loadOntology(ontologyIRI);
OWLFactory = manager.getOWLDataFactory();
topIxFormat = manager.getOntologyFormat(topIxOnt);
topIxPrefixManager =
new DefaultPrefixManager(topIxOnt.getOntologyID().getOntologyIRI().toString() + '#');
System.out.println("loaded ontology: " + this.topIxOnt);
System.out.println("from: " + this.manager.getOntologyDocumentIRI(this.topIxOnt));
} catch (OWLException oex) {
logger.info(oex.getMessage());
}
}
