public Set<NamingIssue> detectNonExactMatchingDirectChildIssues(OWLOntology ontology) {
long start = System.currentTimeMillis();
// get SubClass - SuperClass pairs
Set<Pair<String, String>> subClassSuperClassPairs = new HashSet<Pair<String, String>>();
Set<OWLSubClassOfAxiom> axioms = ontology.getAxioms(AxiomType.SUBCLASS_OF);
for (OWLSubClassOfAxiom ax : axioms) {
OWLClassExpression subClass = ax.getSubClass();
OWLClassExpression superClass = ax.getSuperClass();
if (!subClass.isAnonymous() && !superClass.isAnonymous()) {
subClassSuperClassPairs.add(
new Pair<String, String>(
subClass.asOWLClass().toStringID(), superClass.asOWLClass().toStringID()));
}
}
// compute non matching pairs
Set<NamingIssue> nonMatchingChildren = computeNonExactMatchingChildren(subClassSuperClassPairs);
long end = System.currentTimeMillis();
logger.info("Operation took " + (end - start) + "ms");
return nonMatchingChildren;
}
/**
* 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;
}
private void generateChanges() {
changes = new ArrayList<OWLOntologyChange>();
for (OWLOntology ont : ontologies) {
for (OWLClassAxiom ax : ont.getAxioms(AxiomType.DISJOINT_CLASSES)) {
changes.add(new RemoveAxiom(ont, ax));
}
}
}
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();
}
private boolean isAtomic(OWLClassExpression classExpression) {
if (classExpression.isAnonymous()) {
return false;
} else {
for (OWLOntology ont : ontologies) {
if (!ont.getAxioms((OWLClass) classExpression, EXCLUDED).isEmpty()) {
return false;
}
}
return true;
}
}
public LsignatureExtractorViaInverseRewritingLauncher(
OWLOntology ontology, LogicFragment fragment) {
this.ontology = null;
try {
manager = ontology.getOWLOntologyManager();
this.ontology = manager.createOntology();
manager.addAxioms(this.ontology, ontology.getAxioms());
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
}
this.fragment = fragment;
}
public LsignatureExtractorLauncher(
OWLOntology ontology, LogicFragment fragment, boolean integrateRangesFirst) {
this.ontology = null;
try {
OWLOntologyManager manager = ontology.getOWLOntologyManager();
this.ontology = manager.createOntology();
manager.addAxioms(this.ontology, ontology.getAxioms());
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
}
this.fragment = fragment;
this.integrateRangesFirst = integrateRangesFirst;
}
@Override
public <T> Iterator<T> getInput(Class<T> type) throws IOException {
// This ontology is already a merged version, no need to iterate over imported ones
final OWLOntology o = getFromOntoMgr();
if (type.isAssignableFrom(OWLAxiom.class)) {
final Iterator<OWLAxiom> iterator = o.getAxioms().iterator();
return new Iterator<T>() {
@Override
public boolean hasNext() {
return iterator.hasNext();
}
@SuppressWarnings("unchecked")
@Override
public T next() {
return (T) iterator.next();
}
@Override
public void remove() {
// This iterator is read-only
throw new UnsupportedOperationException("Cannot remove statements from the iterator");
}
};
} else if (type.isAssignableFrom(Statement.class)) {
final OntModel input = new JenaToOwlConvert().ModelOwlToJenaConvert(o, "RDF/XML");
final StmtIterator iterator = input.listStatements();
return new Iterator<T>() {
@Override
public boolean hasNext() {
return iterator.hasNext();
}
@SuppressWarnings("unchecked")
@Override
public T next() {
return (T) iterator.next();
}
@Override
public void remove() {
// This iterator is read-only
throw new UnsupportedOperationException("Cannot remove statements from the iterator");
}
};
} else {
throw new UnsupportedOperationException("This provider does not adapt to the given type");
}
}
private OWLOntology reload(
OWLOntology ontology, OWLOntologyFormat format, OWLOntologyLoaderConfiguration configuration)
throws IOException, OWLOntologyStorageException, OWLOntologyCreationException {
OWLOntologyManager man = ontology.getOWLOntologyManager();
File tempFile = File.createTempFile("Ontology", ".owl");
man.saveOntology(ontology, format, new FileDocumentTarget(tempFile));
OWLOntologyManager man2 = getManager(); // OWLManager.createOWLOntologyManager();
OWLOntology reloaded =
man2.loadOntologyFromOntologyDocument(new FileDocumentSource(tempFile), configuration);
man2.removeAxioms(reloaded, new HashSet<OWLAxiom>(reloaded.getAxioms(AxiomType.DECLARATION)));
return reloaded;
}
/**
* 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;
}
/**
* <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");
}
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 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);
}
public void storeFromTo(OWLOntology from, HGDBOntology to) {
final Set<OWLAxiom> axioms = from.getAxioms();
int i = 0;
for (OWLAxiom axiom : axioms) {
to.applyChange(new AddAxiom(to, axiom));
i++;
if (i % 5000 == 0) {
System.out.println("storeFromTo: Axioms: " + i);
}
}
System.out.println("storeFromTo: Axioms: " + i);
// manager.addAxioms(newOnto, axioms);
// Add Ontology Annotations
for (OWLAnnotation a : from.getAnnotations()) {
to.applyChange(new AddOntologyAnnotation(to, a));
}
// Add Import Declarations
for (OWLImportsDeclaration im : from.getImportsDeclarations()) {
to.applyChange(new AddImport(to, im));
}
}
private void reload(OWLOntology ontology, OWLOntologyFormat format) throws Exception {
Set<OWLAxiom> annotationAxioms = new HashSet<OWLAxiom>();
for (OWLAxiom ax : ontology.getAxioms()) {
if (ax.isAnnotationAxiom()) {
annotationAxioms.add(ax);
}
}
OWLOntologyLoaderConfiguration withAnnosConfig = new OWLOntologyLoaderConfiguration();
OWLOntology reloadedWithAnnoAxioms = reload(ontology, format, withAnnosConfig);
assertEquals(ontology.getAxioms(), reloadedWithAnnoAxioms.getAxioms());
//
OWLOntologyLoaderConfiguration withoutAnnosConfig =
new OWLOntologyLoaderConfiguration().setLoadAnnotationAxioms(false);
OWLOntology reloadedWithoutAnnoAxioms = reload(ontology, format, withoutAnnosConfig);
assertFalse(ontology.getAxioms().equals(reloadedWithoutAnnoAxioms.getAxioms()));
Set<OWLAxiom> axiomsMinusAnnotationAxioms = new HashSet<OWLAxiom>(ontology.getAxioms());
axiomsMinusAnnotationAxioms.removeAll(annotationAxioms);
assertEquals(axiomsMinusAnnotationAxioms, reloadedWithoutAnnoAxioms.getAxioms());
}
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;
}
public Set<OWLAxiom> write(OWLDataProperty property) {
Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
axioms.addAll(writeEntityStart(DATA_PROPERTY, property));
if (!isFiltered(AxiomType.FUNCTIONAL_DATA_PROPERTY)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap characteristics = new SectionMap();
for (OWLAxiom ax : ontology.getFunctionalDataPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(FUNCTIONAL.toString(), ax);
axioms.add(ax);
}
}
writeSection(CHARACTERISTICS, characteristics, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.DATA_PROPERTY_DOMAIN)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap domains = new SectionMap();
for (OWLDataPropertyDomainAxiom ax : ontology.getDataPropertyDomainAxioms(property)) {
if (isDisplayed(ax)) {
domains.add(ax.getDomain(), ax);
axioms.add(ax);
}
}
writeSection(DOMAIN, domains, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.DATA_PROPERTY_RANGE)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap ranges = new SectionMap();
for (OWLDataPropertyRangeAxiom ax : ontology.getDataPropertyRangeAxioms(property)) {
if (isDisplayed(ax)) {
ranges.add(ax.getRange(), ax);
axioms.add(ax);
}
}
writeSection(RANGE, ranges, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.SUB_DATA_PROPERTY)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap supers = new SectionMap();
for (OWLSubDataPropertyOfAxiom ax :
ontology.getDataSubPropertyAxiomsForSubProperty(property)) {
if (isDisplayed(ax)) {
supers.add(ax.getSuperProperty(), ax);
axioms.add(ax);
}
}
writeSection(SUB_PROPERTY_OF, supers, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.EQUIVALENT_DATA_PROPERTIES)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap props = new SectionMap();
for (OWLEquivalentDataPropertiesAxiom ax :
ontology.getEquivalentDataPropertiesAxioms(property)) {
if (isDisplayed(ax) && ax.getProperties().size() == 2) {
props.add(ax.getPropertiesMinus(property).iterator().next(), ax);
axioms.add(ax);
}
}
writeSection(EQUIVALENT_TO, props, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.DISJOINT_DATA_PROPERTIES)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap props = new SectionMap();
for (OWLDisjointDataPropertiesAxiom ax :
ontology.getDisjointDataPropertiesAxioms(property)) {
if (ax.getProperties().size() == 2 && isDisplayed(ax)) {
props.add(ax.getPropertiesMinus(property).iterator().next(), ax);
axioms.add(ax);
}
}
props.remove(property);
writeSection(DISJOINT_WITH, props, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.SWRL_RULE)) {
for (OWLOntology ontology : getOntologies()) {
Set<OWLAxiom> rules = new HashSet<OWLAxiom>();
for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
if (isDisplayed(rule)) {
for (SWRLAtom atom : rule.getHead()) {
if (atom.getPredicate().equals(property)) {
writeSection(RULE, rules, "", true, ontology);
break;
}
}
}
}
}
}
writeEntitySectionEnd(DATA_PROPERTY.toString());
return axioms;
}
public Set<OWLAxiom> write(OWLObjectPropertyExpression property) {
Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
axioms.addAll(writeEntityStart(OBJECT_PROPERTY, property));
if (!isFiltered(AxiomType.SUB_OBJECT_PROPERTY)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap properties = new SectionMap();
for (OWLSubObjectPropertyOfAxiom ax :
ontology.getObjectSubPropertyAxiomsForSubProperty(property)) {
if (isDisplayed(ax)) {
properties.add(ax.getSuperProperty(), ax);
axioms.add(ax);
}
}
writeSection(SUB_PROPERTY_OF, properties, ",", true, ontology);
}
if (renderExtensions) {
for (OWLOntology ontology : getOntologies()) {
SectionMap properties = new SectionMap();
for (OWLSubObjectPropertyOfAxiom ax :
ontology.getObjectSubPropertyAxiomsForSuperProperty(property)) {
if (isDisplayed(ax)) {
properties.add(ax.getSubProperty(), ax);
axioms.add(ax);
}
}
writeSection(SUPER_PROPERTY_OF, properties, ",", true, ontology);
}
}
}
if (!isFiltered(AxiomType.EQUIVALENT_OBJECT_PROPERTIES)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap properties = new SectionMap();
for (OWLEquivalentObjectPropertiesAxiom ax :
ontology.getEquivalentObjectPropertiesAxioms(property)) {
if (isDisplayed(ax) && ax.getProperties().size() == 2) {
Set<OWLObjectPropertyExpression> props = ax.getPropertiesMinus(property);
properties.add(props.iterator().next(), ax);
axioms.add(ax);
}
}
writeSection(EQUIVALENT_TO, properties, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.DISJOINT_OBJECT_PROPERTIES)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap properties = new SectionMap();
for (OWLDisjointObjectPropertiesAxiom ax :
ontology.getDisjointObjectPropertiesAxioms(property)) {
if (ax.getProperties().size() == 2 && isDisplayed(ax)) {
Set<OWLObjectPropertyExpression> props = ax.getPropertiesMinus(property);
properties.add(props.iterator().next(), ax);
axioms.add(ax);
}
}
writeSection(DISJOINT_WITH, properties, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.SUB_PROPERTY_CHAIN_OF)) {
for (OWLOntology ontology : getOntologies()) {
for (OWLSubPropertyChainOfAxiom ax : ontology.getAxioms(AxiomType.SUB_PROPERTY_CHAIN_OF)) {
if (ax.getSuperProperty().equals(property)) {
if (isDisplayed(ax)) {
SectionMap map = new SectionMap();
map.add(ax.getPropertyChain(), ax);
writeSection(SUB_PROPERTY_CHAIN, map, " o ", false, ontology);
axioms.add(ax);
}
}
}
}
}
for (OWLOntology ontology : getOntologies()) {
SectionMap characteristics = new SectionMap();
if (!isFiltered(AxiomType.FUNCTIONAL_OBJECT_PROPERTY)) {
for (OWLFunctionalObjectPropertyAxiom ax :
ontology.getFunctionalObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(FUNCTIONAL.toString(), ax);
axioms.add(ax);
}
}
}
if (!isFiltered(AxiomType.INVERSE_FUNCTIONAL_OBJECT_PROPERTY)) {
for (OWLAxiom ax : ontology.getInverseFunctionalObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(INVERSE_FUNCTIONAL.toString(), ax);
axioms.add(ax);
}
}
}
if (!isFiltered(AxiomType.SYMMETRIC_OBJECT_PROPERTY)) {
for (OWLAxiom ax : ontology.getSymmetricObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(SYMMETRIC.toString(), ax);
axioms.add(ax);
}
}
}
if (!isFiltered(AxiomType.TRANSITIVE_OBJECT_PROPERTY)) {
for (OWLAxiom ax : ontology.getTransitiveObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(TRANSITIVE.toString(), ax);
axioms.add(ax);
}
}
}
if (!isFiltered(AxiomType.REFLEXIVE_OBJECT_PROPERTY)) {
for (OWLAxiom ax : ontology.getReflexiveObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(REFLEXIVE.toString(), ax);
axioms.add(ax);
}
}
}
if (!isFiltered(AxiomType.IRREFLEXIVE_OBJECT_PROPERTY)) {
for (OWLAxiom ax : ontology.getIrreflexiveObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(IRREFLEXIVE.toString(), ax);
axioms.add(ax);
}
}
}
if (!isFiltered(AxiomType.ASYMMETRIC_OBJECT_PROPERTY)) {
for (OWLAxiom ax : ontology.getAsymmetricObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
characteristics.add(ASYMMETRIC.toString(), ax);
axioms.add(ax);
}
}
}
writeSection(CHARACTERISTICS, characteristics, ",", true, ontology);
}
if (!isFiltered(AxiomType.OBJECT_PROPERTY_DOMAIN)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap expressions = new SectionMap();
for (OWLObjectPropertyDomainAxiom ax : ontology.getObjectPropertyDomainAxioms(property)) {
if (isDisplayed(ax)) {
expressions.add(ax.getDomain(), ax);
axioms.add(ax);
}
}
writeSection(DOMAIN, expressions, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.OBJECT_PROPERTY_RANGE)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap expressions = new SectionMap();
for (OWLObjectPropertyRangeAxiom ax : ontology.getObjectPropertyRangeAxioms(property)) {
if (isDisplayed(ax)) {
expressions.add(ax.getRange(), ax);
axioms.add(ax);
}
}
writeSection(RANGE, expressions, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.INVERSE_OBJECT_PROPERTIES)) {
for (OWLOntology ontology : getOntologies()) {
Set<OWLObjectPropertyExpression> properties = new TreeSet<OWLObjectPropertyExpression>();
for (OWLInverseObjectPropertiesAxiom ax :
ontology.getInverseObjectPropertyAxioms(property)) {
if (isDisplayed(ax)) {
if (ax.getFirstProperty().equals(property)) {
properties.add(ax.getSecondProperty());
} else {
properties.add(ax.getFirstProperty());
}
axioms.add(ax);
}
}
writeSection(INVERSE_OF, properties, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.SWRL_RULE)) {
for (OWLOntology ontology : getOntologies()) {
Set<OWLAxiom> rules = new HashSet<OWLAxiom>();
for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
if (isDisplayed(rule)) {
for (SWRLAtom atom : rule.getHead()) {
if (atom.getPredicate().equals(property)) {
rules.add(rule);
// XXX attempted patching
writeSection(RULE, rules, ",", true, ontology);
break;
}
}
}
}
}
}
writeEntitySectionEnd(OBJECT_PROPERTY.toString());
return axioms;
}
public Set<OWLAxiom> write(OWLClass cls) {
Set<OWLAxiom> axioms = new HashSet<OWLAxiom>();
axioms.addAll(writeEntityStart(CLASS, cls));
if (!isFiltered(AxiomType.EQUIVALENT_CLASSES)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap equivalentClasses = new SectionMap();
for (OWLEquivalentClassesAxiom ax : ontology.getEquivalentClassesAxioms(cls)) {
if (ax.getClassExpressions().size() == 2) {
if (isDisplayed(ax)) {
for (OWLClassExpression equivCls : ax.getClassExpressionsMinus(cls)) {
equivalentClasses.add(equivCls, ax);
}
axioms.add(ax);
}
}
}
equivalentClasses.remove(cls);
writeSection(EQUIVALENT_TO, equivalentClasses, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.SUBCLASS_OF)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap superclasses = new SectionMap();
for (OWLSubClassOfAxiom ax : ontology.getSubClassAxiomsForSubClass(cls)) {
if (isDisplayed(ax)) {
superclasses.add(ax.getSuperClass(), ax);
axioms.add(ax);
}
}
writeSection(SUBCLASS_OF, superclasses, ",", true, ontology);
}
if (renderExtensions) {
for (OWLOntology ont : getOntologies()) {
SectionMap subClasses = new SectionMap();
for (OWLSubClassOfAxiom ax : ont.getSubClassAxiomsForSuperClass(cls)) {
if (isDisplayed(ax)) {
subClasses.add(ax.getSubClass(), ax);
axioms.add(ax);
}
}
writeSection(SUPERCLASS_OF, subClasses, ",", true, ont);
}
}
}
if (!isFiltered(AxiomType.DISJOINT_CLASSES)) {
for (OWLOntology ontology : getOntologies()) {
Set<OWLAxiom> pairwiseDisjointClassesAxioms = new HashSet<OWLAxiom>();
SectionMap disjointClasses = new SectionMap();
for (OWLDisjointClassesAxiom ax : ontology.getDisjointClassesAxioms(cls)) {
if (isDisplayed(ax)) {
if (ax.getClassExpressions().size() == 2) {
pairwiseDisjointClassesAxioms.add(ax);
OWLClassExpression disjointWith = ax.getClassExpressionsMinus(cls).iterator().next();
disjointClasses.add(disjointWith, ax);
}
axioms.add(ax);
}
}
writeSection(DISJOINT_WITH, disjointClasses, ", ", false, ontology);
if (renderExtensions) {
// Handling of nary in frame style
for (OWLDisjointClassesAxiom ax : ontology.getDisjointClassesAxioms(cls)) {
if (isDisplayed(ax)) {
if (ax.getClassExpressions().size() > 2) {
Set<OWLClassExpression> allDisjointClasses =
new TreeSet<OWLClassExpression>(ax.getClassExpressions());
allDisjointClasses.remove(cls);
axioms.add(ax);
writeSection(DISJOINT_CLASSES, allDisjointClasses, ", ", false, ontology);
}
}
}
}
}
}
if (!isFiltered(AxiomType.HAS_KEY)) {
for (OWLOntology ontology : getOntologies()) {
for (OWLHasKeyAxiom ax : ontology.getHasKeyAxioms(cls)) {
if (isDisplayed(ax)) {
SectionMap map = new SectionMap();
map.add(ax.getPropertyExpressions(), ax);
writeSection(HAS_KEY, map, ", ", true, ontology);
}
}
}
}
if (!isFiltered(AxiomType.CLASS_ASSERTION)) {
for (OWLOntology ontology : getOntologies()) {
SectionMap individuals = new SectionMap();
for (OWLClassAssertionAxiom ax : ontology.getClassAssertionAxioms(cls)) {
if (isDisplayed(ax)) {
if (renderExtensions || ax.getIndividual().isAnonymous()) {
individuals.add(ax.getIndividual(), ax);
axioms.add(ax);
}
}
}
writeSection(INDIVIDUALS, individuals, ",", true, ontology);
}
}
if (!isFiltered(AxiomType.SWRL_RULE)) {
for (OWLOntology ontology : getOntologies()) {
Set<OWLAxiom> rules = new HashSet<OWLAxiom>();
for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
if (isDisplayed(rule)) {
for (SWRLAtom atom : rule.getHead()) {
if (atom.getPredicate().equals(cls)) {
writeSection(RULE, rules, ", ", true, ontology);
break;
}
}
}
}
}
}
writeEntitySectionEnd(CLASS.toString());
return axioms;
}
public void writeOntology() throws OWLRendererException {
if (ontologies.size() != 1) {
throw new OWLRuntimeException("Can only render one ontology");
}
OWLOntology ontology = getOntologies().iterator().next();
writePrefixMap();
writeNewLine();
writeOntologyHeader(ontology);
for (OWLAnnotationProperty prop : ontology.getAnnotationPropertiesInSignature()) {
write(prop);
}
for (OWLDatatype datatype : ontology.getDatatypesInSignature()) {
write(datatype);
}
for (OWLObjectProperty prop : ontology.getObjectPropertiesInSignature()) {
write(prop);
OWLObjectPropertyExpression invProp = prop.getInverseProperty();
if (!ontology.getAxioms(invProp).isEmpty()) {
write(invProp);
}
}
for (OWLDataProperty prop : ontology.getDataPropertiesInSignature()) {
write(prop);
}
for (OWLClass cls : ontology.getClassesInSignature()) {
write(cls);
}
for (OWLNamedIndividual ind : ontology.getIndividualsInSignature()) {
write(ind);
}
for (OWLAnonymousIndividual ind : ontology.getReferencedAnonymousIndividuals()) {
write(ind);
}
// Nary disjoint classes axioms
event = new RendererEvent(this, ontology);
for (OWLDisjointClassesAxiom ax : ontology.getAxioms(AxiomType.DISJOINT_CLASSES)) {
if (ax.getClassExpressions().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getClassExpressions(), ax);
writeSection(DISJOINT_CLASSES, map, ",", false, ontology);
}
}
// Nary equivalent classes axioms
for (OWLEquivalentClassesAxiom ax : ontology.getAxioms(AxiomType.EQUIVALENT_CLASSES)) {
if (ax.getClassExpressions().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getClassExpressions(), ax);
writeSection(EQUIVALENT_CLASSES, map, ",", false, ontology);
}
}
// Nary disjoint properties
for (OWLDisjointObjectPropertiesAxiom ax :
ontology.getAxioms(AxiomType.DISJOINT_OBJECT_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary equivlant properties
for (OWLEquivalentObjectPropertiesAxiom ax :
ontology.getAxioms(AxiomType.EQUIVALENT_OBJECT_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary disjoint properties
for (OWLDisjointDataPropertiesAxiom ax :
ontology.getAxioms(AxiomType.DISJOINT_DATA_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(DISJOINT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary equivalent properties
for (OWLEquivalentDataPropertiesAxiom ax :
ontology.getAxioms(AxiomType.EQUIVALENT_DATA_PROPERTIES)) {
if (ax.getProperties().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getProperties(), ax);
writeSection(EQUIVALENT_PROPERTIES, map, ",", false, ontology);
}
}
// Nary different individuals
for (OWLDifferentIndividualsAxiom ax : ontology.getAxioms(AxiomType.DIFFERENT_INDIVIDUALS)) {
if (ax.getIndividuals().size() > 2) {
SectionMap map = new SectionMap();
map.add(ax.getIndividuals(), ax);
writeSection(DIFFERENT_INDIVIDUALS, map, ",", false, ontology);
}
}
for (SWRLRule rule : ontology.getAxioms(AxiomType.SWRL_RULE)) {
writeSection(RULE, Collections.singleton(rule), ", ", false);
}
flush();
}
public void execute() throws Exception {
int rowCount = 0;
try {
String fileLoction =
propertiesUtil.getPropertyValue(
propertiesFileLocations, COSMICFUSIONEXPORT_TSV_FILE_LOCATION);
File file = new File(fileLoction);
logger.info("[01234] Processing File " + file.getName() + " ...... ");
CSVReader reader = new CSVReader(new FileReader(file), '\t');
JsonArray jsonArr = new JsonArray();
String[] record;
while ((record = reader.readNext()) != null) {
if (rowCount != 0) {
Complete_Fusion_Export cfe = factory.createComplete_Fusion_Export(CFE + rowCount);
JsonObject jsonObject = new JsonObject();
String fusion_IdValue = record[10] == null ? EMPTY_STRING : record[10];
cfe.addFusion_Id(getFusionId(fusion_IdValue));
jsonObject.addProperty(FUSION_ID, fusion_IdValue);
String fusionTypeValue = record[12] == null ? EMPTY_STRING : record[12];
cfe.addFusion_Type(fusionTypeValue);
jsonObject.addProperty(FUSION_TYPE, fusionTypeValue);
String histology_Subtype_1Value = record[9] == null ? EMPTY_STRING : record[9];
cfe.addHistology_Subtype_1(histology_Subtype_1Value);
jsonObject.addProperty(HISTOLOGY_SUBTYPE_1, histology_Subtype_1Value);
String histology_Subtype_3Value = record[11] == null ? EMPTY_STRING : record[11];
cfe.addHistology_Subtype_3(histology_Subtype_3Value);
jsonObject.addProperty(HISTOLOGY_SUBTYPE_3, histology_Subtype_3Value);
String primarySiteValue = record[2] == null ? EMPTY_STRING : record[2];
cfe.addPrimary_Site(primarySiteValue);
jsonObject.addProperty(PRIMARY_SITE, primarySiteValue);
String pubmedPMIDValue = record[13] == null ? EMPTY_STRING : record[13];
cfe.addPubmed_PMID(pubmedPMIDValue);
jsonObject.addProperty(PUBMED_PMID, pubmedPMIDValue);
String site_Subtype_1Value = record[3];
cfe.addSite_Subtype_1(site_Subtype_1Value);
jsonObject.addProperty(SITE_SUBTYPE_1_VALUE, site_Subtype_1Value);
String site_Subtype_3Value = record[5];
cfe.addSite_Subtype_3(site_Subtype_3Value);
jsonObject.addProperty(SITE_SUBTYPE_3_VALUE, site_Subtype_3Value);
String translocationName = record[11] == null ? EMPTY_STRING : record[11];
cfe.addTranslocation_Name(translocationName);
jsonObject.addProperty(TRANSLOCATION_NAME, translocationName);
jsonArr.add(jsonObject);
// TODO Uncomment before the .jar generation
// owlOntologyManager.saveOntology(cfe.getOwlOntology(),
// new FileOutputStream(new
// File(propertiesUtil.getPropertyValue(propertiesFileLocations,
// COSMICFUSIONEXPORT_RDF_FILE_LOCATION))));
// TODO Use the code below to create samples.
// if (rowCount == 100) {
File jsonSampleFile =
new File(
propertiesUtil.getPropertyValue(
propertiesFileLocations, COSMICFUSIONEXPORT_JSON_FILE_LOCATION));
FileUtils.writeStringToFile(jsonSampleFile, jsonArr.toString());
owlOntologyManager.saveOntology(
cfe.getOwlOntology(),
new FileOutputStream(
new File(
propertiesUtil.getPropertyValue(
propertiesFileLocations, COSMICFUSIONEXPORT_RDF_FILE_LOCATION))));
// break;
// }
}
rowCount++;
}
} catch (Exception e) {
logger.error("[01234] Error! " + e.getMessage());
throw new RuntimeException(e.getMessage(), e);
} finally {
logger.info("[01234] Axioms size: " + onto.getAxioms().size());
logger.info("[01234] Records: " + rowCount);
logger.info("[01234] Process of CompleteFusionExportConverterImpl finished!");
}
}
public Set<NamingIssue> detectNonMatchingChildIssues(OWLOntology ontology, boolean directChild) {
long start = System.currentTimeMillis();
// get SubClass - SuperClass pairs
Set<NamingIssue> nonMatchingChildren = new HashSet<NamingIssue>();
if (directChild) {
Set<OWLSubClassOfAxiom> axioms = ontology.getAxioms(AxiomType.SUBCLASS_OF);
for (OWLSubClassOfAxiom ax : axioms) {
OWLClassExpression subClass = ax.getSubClass();
OWLClassExpression superClass = ax.getSuperClass();
if (!subClass.isAnonymous() && !superClass.isAnonymous()) {
String subClassURI = subClass.asOWLClass().toStringID();
String superClassURI = superClass.asOWLClass().toStringID();
if (ignoreSingleTokenSubClasses && !singleToken(subClassURI)) {
String subClassHead = getHeadNoun(subClassURI);
String superClassHead = getHeadNoun(superClassURI);
boolean matching =
subClassHead.equals(superClassHead) || isHypernymOf(superClassHead, subClassHead);
if (!matching) {
String newClassURI = buildNewURI(subClassURI, superClassHead);
nonMatchingChildren.add(
new NamingIssue(
subClassURI,
superClassURI,
new RenamingInstruction(subClassURI, newClassURI)));
}
}
}
}
} else {
OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance();
OWLReasoner reasoner = reasonerFactory.createNonBufferingReasoner(ontology);
Set<OWLClass> classes = ontology.getClassesInSignature();
for (OWLClass cls : classes) {
Set<OWLClass> superClasses = reasoner.getSuperClasses(cls, false).getFlattened();
superClasses.remove(OWL_THING);
for (OWLClass superClass : superClasses) {
String subClassURI = cls.asOWLClass().toStringID();
String superClassURI = superClass.asOWLClass().toStringID();
if (ignoreSingleTokenSubClasses && !singleToken(subClassURI)) {
String subClassHead = getHeadNoun(subClassURI);
String superClassHead = getHeadNoun(superClassURI);
boolean matching =
subClassHead.equals(superClassHead) || isHypernymOf(superClassHead, subClassHead);
if (!matching) {
String newClassURI = buildNewURI(subClassURI, superClassHead);
nonMatchingChildren.add(
new NamingIssue(
subClassURI,
superClassURI,
new RenamingInstruction(subClassURI, newClassURI)));
}
}
}
}
}
long end = System.currentTimeMillis();
logger.info("Operation took " + (end - start) + "ms");
return nonMatchingChildren;
}
@Override
public void visit(OWLOntology ontology) {
process(ontology.getAxioms());
}
public OWLOntology findLsignature(
OWLOntology ontology, LogicFragment fragment, Statistics stats) {
Timer t = new Timer();
this.stats = stats;
Logger_MORe.logInfo("extracting " + fragment.toString() + "-signature");
OWLOntology ret = null;
OWLOntologyManager manager = ontology.getOWLOntologyManager();
try {
ret = manager.createOntology();
manager.addAxioms(ret, ontology.getAxioms());
} catch (OWLOntologyCreationException e) {
e.printStackTrace();
}
lSignatureClasses = new HashSet<OWLClass>();
lSignatureOther = new HashSet<OWLEntity>();
compSignatureClasses = new HashSet<OWLClass>();
compSignatureOther = new HashSet<OWLEntity>();
LsignatureExtractorLauncher elkSignatureExtractorLauncher = null;
LsignatureExtractorLauncher elkSignatureExtractorIntegratingRangesLauncher = null;
LsignatureExtractorViaInverseRewritingLauncher elkSignatureExtractorRewritingInversesLauncher =
null;
ForkJoinPool executor = new ForkJoinPool();
elkSignatureExtractorLauncher =
new LsignatureExtractorLauncher(ontology, LogicFragment.ELK, false);
executor.execute(elkSignatureExtractorLauncher);
if (ret != null) {
// otherwise we have nowhere to return the axioms in the normalised ontologies necessary to
// really classify all the extra classses in the lSignature
if (rewriteInverses) {
elkSignatureExtractorRewritingInversesLauncher =
new LsignatureExtractorViaInverseRewritingLauncher(ontology, LogicFragment.ELK);
executor.execute(elkSignatureExtractorRewritingInversesLauncher);
}
if (integrateRanges) {
elkSignatureExtractorIntegratingRangesLauncher =
new LsignatureExtractorLauncher(ontology, LogicFragment.ELK, true);
executor.execute(elkSignatureExtractorIntegratingRangesLauncher);
}
// check the output of the normal ELKsignature and cancel the other threads if the lSig is the
// whole signature
initialiseLsignature((LsignatureExtractor) elkSignatureExtractorLauncher.join());
if (compSignatureClasses.isEmpty())
cancelTasks(
elkSignatureExtractorIntegratingRangesLauncher,
elkSignatureExtractorRewritingInversesLauncher);
else {
if (elkSignatureExtractorRewritingInversesLauncher != null
&& extendLsignature(
(LsignatureExtractor) elkSignatureExtractorRewritingInversesLauncher.join())
> 0) {
manager.addAxioms(
ret,
((LsignatureExtractorViaInverseRewritingLauncher)
elkSignatureExtractorRewritingInversesLauncher)
.getOntology()
.getAxioms());
}
if (compSignatureClasses.isEmpty())
cancelTasks(elkSignatureExtractorRewritingInversesLauncher);
else if (elkSignatureExtractorIntegratingRangesLauncher != null
&& extendLsignature(
(LsignatureExtractor) elkSignatureExtractorIntegratingRangesLauncher.join())
> 0) {
manager.addAxioms(
ret,
((LsignatureExtractorLauncher) elkSignatureExtractorIntegratingRangesLauncher)
.getOntology()
.getAxioms());
}
}
stats.updateLsignatureSize(lSignatureClasses.size(), true);
} else {
ret = ontology;
initialiseLsignature((LsignatureExtractor) elkSignatureExtractorLauncher.join());
}
Logger_MORe.logInfo(lSignatureClasses.size() + "classes in lSignature");
Logger_MORe.logDebug(lSignatureClasses.toString());
Logger_MORe.logInfo(compSignatureClasses.size() + "classes in compSignature");
// might be a good idea to try to isolate extra axioms in the normalisation/rewriting - is this
// possible/worth the effort?
// check the order in which we try to extend the lSignature with each of the rewritten
// ontologies and consider if one may be better that the other
Logger_MORe.logDebug(t.duration() + "s to find Lsignature");
return ret;
}
@Override
protected Set<? extends OWLAxiom> getObjects(OWLOntology ont) {
return ont.getAxioms(axiomType);
}
