protected OWLClass getFreshQueryClass(String base) {
long cnt = 0;
String iriString = base;
while (m_ontologyOperator.getOntology().containsClassInSignature(IRI.create(iriString))) {
iriString =
base + (cnt++); // not guaranteed to succeed.. however |long| amount of possibilities
}
return OWLManager.getOWLDataFactory().getOWLClass(IRI.create(iriString));
}
public class ReasonerUtilUnsatTest {
OWLDataFactory dataFactory = OWLManager.getOWLDataFactory();
OWLOntologyManager manager;
OWLOntology ont;
OWLOntology unsatImport;
ReasonerUtil util;
@Before
public void setup() throws Exception {
String uri = Resources.getResource("ontologies/unsat_parent.owl").toURI().toString();
IRI iri = IRI.create(uri);
manager = OWLManager.createOWLOntologyManager();
manager.addIRIMapper(
new OWLOntologyIRIMapper() {
@Override
public IRI getDocumentIRI(IRI origIri) {
String uri = null;
try {
uri = Resources.getResource("ontologies/unsat.owl").toURI().toString();
} catch (URISyntaxException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
return IRI.create(uri);
}
});
ont = manager.loadOntologyFromOntologyDocument(iri);
ReasonerConfiguration config = new ReasonerConfiguration();
config.setFactory(ElkReasonerFactory.class.getCanonicalName());
util = new ReasonerUtil(config, manager, ont);
}
@Test
public void removesAxiomsInImportedOntologies() throws Exception {
assertThat(util.getUnsatisfiableClasses(), is(not(empty())));
util.removeUnsatisfiableClasses();
assertThat(util.getUnsatisfiableClasses(), is(empty()));
assertThat(util.reason(), is(true));
}
}
protected void insertQueryAxiom(OWLClass queryClass) {
// Main.getOntologyManager().addAxiom(m_ontologyOperator.getOntology(),
// OWLManager.getOWLDataFactory().getOWLEquivalentClassesAxiom(queryClass,
// m_referenceExpression));
m_ontologyOperator
.getOntology()
.getOWLOntologyManager()
.addAxiom(
m_ontologyOperator.getOntology(),
// OWLManager.getOWLDataFactory().getOWLEquivalentClassesAxiom(
OWLManager.getOWLDataFactory()
.getOWLSubClassOfAxiom(
queryClass,
m_referenceExpression.accept(
m_ontologyOperator.getFlatteningTransformer().getVisitor())));
m_ontologyOperator
.getOntology()
.getOWLOntologyManager()
.applyChanges(m_ontologyOperator.getFlatteningTransformer().getVisitor().getChanges());
m_ontologyOperator.getFlatteningTransformer().getVisitor().resetChangeList();
m_ontologyOperator.ontologyChanged();
}
/**
* We share this data between all the tests. Note: take care, do not leave the content of these
* object changed, for example remove your example ontology from the testDataManager
*/
public class TestData {
private static final Logger log = LoggerFactory.getLogger(TestData.class);
/** Constants (local resources) */
static final String LOCAL_RESOURCE_FOAF = "foaf.rdf";
static URL FOAF_LOCATION =
TestData.class.getResource(System.getProperty("file.separator") + LOCAL_RESOURCE_FOAF);
static final String LOCAL_RESOURCE_DBPEDIA = "dbpedia_3.6.owl";
static URL DBPEDIA_LOCATION =
TestData.class.getResource(System.getProperty("file.separator") + LOCAL_RESOURCE_DBPEDIA);
static final String LOCAL_RESOURCE_TEST_1 = "test_1.owl";
static URL TEST_1_LOCATION =
TestData.class.getResource(System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_1);
static final String LOCAL_RESOURCE_TEST_1_EXPECTED = "test_1_expected.owl";
static URL TEST_1_expected_LOCATION =
TestData.class.getResource(
System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_1_EXPECTED);
static final String LOCAL_RESOURCE_TEST_2 = "test_2.owl";
static URL TEST_2_LOCATION =
TestData.class.getResource(System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_2);
static final String LOCAL_RESOURCE_TEST_2_EXPECTED = "test_2_expected.owl";
static URL TEST_2_expected_LOCATION =
TestData.class.getResource(
System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_2_EXPECTED);
static final String LOCAL_RESOURCE_TEST_3 = "test_3.owl";
static URL TEST_3_LOCATION =
TestData.class.getResource(System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_3);
static final String LOCAL_RESOURCE_TEST_3_RULES = "test_3_rules.owl";
static URL TEST_3_rules_LOCATION =
TestData.class.getResource(
System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_3_RULES);
static final String LOCAL_RESOURCE_TEST_3_EXPECTED = "test_3_expected.owl";
static URL TEST_3_expected_LOCATION =
TestData.class.getResource(
System.getProperty("file.separator") + LOCAL_RESOURCE_TEST_3_EXPECTED);
/** Constants */
// EXAMPLE
static final String TEST_NS = "http://www.example.org/test/";
static final String TEST_1_NS = TEST_NS + "1/";
static final String TEST_1_expected_NS = TEST_1_NS + "expected/";
static final String TEST_2_NS = TEST_NS + "2/";
static final String TEST_2_expected_NS = TEST_2_NS + "expected/";
static final String TEST_3_NS = TEST_NS + "3/";
static final String TEST_3_rules_NS = TEST_3_NS + "rules/";
static final String TEST_3_expected_NS = TEST_3_NS + "expected/";
// FOAF
static final String FOAF_NS = "http://xmlns.com/foaf/0.1/";
/** Manager, factory */
static final OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
static final OWLDataFactory factory = OWLManager.getOWLDataFactory();
static {
try {
/** Configuration of the manager */
manager.setSilentMissingImportsHandling(true);
manager.addMissingImportListener(
new MissingImportListener() {
@Override
public void importMissing(MissingImportEvent event) {
log.warn("Missing import! URI was: {}", event.getImportedOntologyURI());
}
});
manager.addOntologyChangeListener(
new OWLOntologyChangeListener() {
@Override
public void ontologiesChanged(List<? extends OWLOntologyChange> arg0)
throws OWLException {
for (OWLOntologyChange change : arg0) {
log.debug("{} TO {}", change, change.getOntology());
}
}
});
/** Loading test ontologies once for all */
manager.loadOntologyFromOntologyDocument(FOAF_LOCATION.openStream());
manager.loadOntologyFromOntologyDocument(DBPEDIA_LOCATION.openStream());
// Test 1
manager.loadOntologyFromOntologyDocument(TEST_1_LOCATION.openStream());
manager.loadOntologyFromOntologyDocument(TEST_1_expected_LOCATION.openStream());
// Test 2
manager.loadOntologyFromOntologyDocument(TEST_2_LOCATION.openStream());
manager.loadOntologyFromOntologyDocument(TEST_2_expected_LOCATION.openStream());
// Test 3
manager.loadOntologyFromOntologyDocument(TEST_3_LOCATION.openStream());
manager.loadOntologyFromOntologyDocument(TEST_3_rules_LOCATION.openStream());
manager.loadOntologyFromOntologyDocument(TEST_3_expected_LOCATION.openStream());
} catch (OWLOntologyCreationException e) {
log.error(
"A {} have been thrown while creating the ontology" + ". Message was: {}",
e.getClass(),
e.getLocalizedMessage());
} catch (IOException e) {
log.error(
"A {} have been thrown while loading the ontology from the location {}",
e.getClass(),
FOAF_LOCATION.toString());
log.error("Message was: {}", e.getLocalizedMessage());
}
}
}
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 class IdentifySplitConcepts extends AbstractAnalyzerAlgorithm {
public static final MatchDescription SPLIT =
new MatchDescription("Split Operation", MatchDescription.PRIMARY_MATCH_PRIORITY);
public static final MatchDescription COPIED_FROM_SPLIT =
new MatchDescription("Copied by split operation", MatchDescription.SECONDARY_MATCH_PRIORITY);
public static final OWLDatatype STRING_DATATYPE =
OWLManager.getOWLDataFactory().getOWLDatatype(XSDVocabulary.STRING.getIRI());
public static final String SPLIT_FROM_ANNOTATION_PROPERTY = "split.from.annotation";
private Changes changes;
private OwlDiffMap diffMap;
private CodeToEntityMapper mapper;
private boolean disabled = false;
private OWLAnnotationProperty splitFromProperty;
public void initialise(Engine e) {
this.changes = e.getChanges();
this.diffMap = changes.getRawDiffMap();
this.mapper = CodeToEntityMapper.get(e);
OWLDataFactory factory = diffMap.getOWLDataFactory();
String splitFromPropertyName = (String) e.getParameters().get(SPLIT_FROM_ANNOTATION_PROPERTY);
if (splitFromPropertyName == null) {
disabled = true;
return;
}
splitFromProperty = factory.getOWLAnnotationProperty(IRI.create(splitFromPropertyName));
}
public void apply() {
if (disabled) {
return;
}
for (EntityBasedDiff diff : changes.getEntityBasedDiffs()) {
apply(diff);
}
}
private void apply(EntityBasedDiff diff) {
IRI iriOfNewlyCreatedClass = null;
String code = null;
MatchedAxiom splitAxiomWithBadDescription = null;
MatchedAxiom splitFrom = null;
for (MatchedAxiom match : diff.getAxiomMatches()) {
if (match.getDescription().equals(MatchedAxiom.AXIOM_ADDED)
&& isSplitFromAnnotationAssertion(match.getTargetAxiom())) {
splitAxiomWithBadDescription = match;
splitFrom = new MatchedAxiom(null, match.getTargetAxiom(), SPLIT);
iriOfNewlyCreatedClass =
(IRI) ((OWLAnnotationAssertionAxiom) match.getTargetAxiom()).getSubject();
code =
((OWLLiteral) ((OWLAnnotationAssertionAxiom) match.getTargetAxiom()).getValue())
.getLiteral();
break;
}
}
if (splitFrom != null) {
changes.removeMatch(splitAxiomWithBadDescription);
changes.addMatch(splitFrom);
handleNewSplitAxioms(iriOfNewlyCreatedClass, code, diff);
}
}
private boolean isSplitFromAnnotationAssertion(OWLAxiom axiom) {
return axiom instanceof OWLAnnotationAssertionAxiom
&& ((OWLAnnotationAssertionAxiom) axiom).getProperty().equals(splitFromProperty)
&& diffMap.getUnmatchedTargetAxioms().contains(axiom)
&& ((OWLAnnotationAssertionAxiom) axiom).getSubject() instanceof IRI
&& ((OWLAnnotationAssertionAxiom) axiom).getValue() instanceof OWLLiteral
&& ((OWLLiteral) ((OWLAnnotationAssertionAxiom) axiom).getValue())
.getDatatype()
.equals(STRING_DATATYPE);
}
private void handleNewSplitAxioms(IRI iriOfNewlyCreatedClass, String code, EntityBasedDiff diff) {
OWLDataFactory factory = diffMap.getOWLDataFactory();
OWLClass newlyCreatedClass = factory.getOWLClass(iriOfNewlyCreatedClass);
OWLClass classThatWasSplit = getClassThatWasSplit(code);
if (classThatWasSplit != null) {
handleNewSplitAxioms(newlyCreatedClass, classThatWasSplit, diff);
}
}
private void handleNewSplitAxioms(
OWLClass newlyCreatedClass, OWLClass classThatWasSplit, EntityBasedDiff diff) {
OWLOntology sourceOntology = diffMap.getSourceOntology();
Map<OWLEntity, IRI> newTargetToSplitSource =
Collections.singletonMap((OWLEntity) newlyCreatedClass, classThatWasSplit.getIRI());
OWLObjectDuplicator duplicator =
new OWLObjectDuplicator(newTargetToSplitSource, diffMap.getOWLDataFactory());
Set<OWLClassExpression> inferredParents = getInferredParents(sourceOntology, classThatWasSplit);
for (MatchedAxiom match : new ArrayList<MatchedAxiom>(diff.getAxiomMatches())) {
if (match.getDescription().equals(MatchedAxiom.AXIOM_ADDED)
&& cameFromSourceOntology(
(OWLAxiom) duplicator.duplicateObject(match.getTargetAxiom()),
sourceOntology,
classThatWasSplit,
inferredParents)) {
MatchedAxiom modifiedBySplit =
new MatchedAxiom(null, match.getTargetAxiom(), COPIED_FROM_SPLIT);
changes.removeMatch(match);
changes.addMatch(modifiedBySplit);
}
}
}
private boolean cameFromSourceOntology(
OWLAxiom axiom,
OWLOntology sourceOntology,
OWLClass child,
Set<OWLClassExpression> inferredParents) {
if (sourceOntology.containsAxiom(axiom)) {
return true;
} else if (axiom instanceof OWLSubClassOfAxiom) {
return ((OWLSubClassOfAxiom) axiom).getSubClass().equals(child)
&& inferredParents.contains(((OWLSubClassOfAxiom) axiom).getSuperClass());
} else {
return false;
}
}
private Set<OWLClassExpression> getInferredParents(OWLOntology sourceOntology, OWLClass child) {
return getInferredParents(sourceOntology, child, new TreeSet<OWLClass>());
}
private Set<OWLClassExpression> getInferredParents(
OWLOntology sourceOntology, OWLClass child, Set<OWLClass> viewed) {
Set<OWLClassExpression> result = new TreeSet<OWLClassExpression>();
if (!viewed.contains(child)) {
viewed.add(child);
Set<OWLClassExpression> parents = new TreeSet<OWLClassExpression>();
parents.addAll(child.getSuperClasses(sourceOntology));
parents.addAll(child.getEquivalentClasses(sourceOntology));
for (OWLClassExpression parent : parents) {
if (parent instanceof OWLClass) {
result.add(parent);
result.addAll(getInferredParents(sourceOntology, (OWLClass) parent, viewed));
} else if (parent instanceof OWLObjectIntersectionOf) {
Set<OWLClassExpression> inferredParents =
((OWLObjectIntersectionOf) parent).getOperands();
result.addAll(inferredParents);
for (OWLClassExpression inferredParent : inferredParents) {
if (inferredParent instanceof OWLClass) {
result.addAll(getInferredParents(sourceOntology, (OWLClass) inferredParent, viewed));
}
}
} else {
result.add(parent);
}
}
}
return result;
}
private OWLClass getClassThatWasSplit(String code) {
if (code == null) {
return null;
}
Collection<OWLEntity> possiblySplitEntities = mapper.getTargetEntities(code);
OWLClass classThatWasSplit = null;
for (OWLEntity possiblySplityEntity : possiblySplitEntities) {
if (possiblySplityEntity instanceof OWLClass) {
if (classThatWasSplit != null) {
return null;
} else {
classThatWasSplit = (OWLClass) possiblySplityEntity;
EntityBasedDiff classThatWasSplitDiff = changes.getTargetDiffMap().get(classThatWasSplit);
if (classThatWasSplitDiff != null) {
classThatWasSplit =
(OWLClass)
classThatWasSplitDiff
.getSourceEntity(); // if it was created we do really want null
}
}
}
}
return classThatWasSplit;
}
}