/** Creates an ontology factory. */
public ParsableOWLOntologyFactory() {
parsableSchemes = new HashSet<String>();
parsableSchemes.add("http");
parsableSchemes.add("https");
parsableSchemes.add("file");
parsableSchemes.add("ftp");
}
private void addEdge(O d1, O d2) {
Set<O> values = edgesByVertex.get(d1);
if (values == null) {
values = new HashSet<O>();
edgesByVertex.put(d1, values);
}
values.add(d2);
}
private void addChildParent(OWLObject child, OWLObject parent, OWLObject ax) {
getIndexedSet(child, child2ParentMap, true).add(parent);
getIndexedSet(parent, parent2ChildMap, true).add(parent);
nodes.add(child);
nodes.add(parent);
edgeMap.put(new AxiomEdge(child, parent), ax);
edgeMap.put(new AxiomEdge(parent, child), ax);
}
public void visit(OWLDisjointClassesAxiom axiom) {
Set<OWLClassExpression> added = new HashSet<OWLClassExpression>();
for (OWLClassExpression descA : axiom.getClassExpressions()) {
for (OWLClassExpression descB : axiom.getClassExpressions()) {
if (!descA.equals(descB) && !added.contains(descA) && !added.contains(descB)) {
addChildParent(descA, descB, axiom);
added.add(descA);
added.add(descB);
descA.accept(this);
descB.accept(this);
}
}
}
}
public boolean canLoad(OWLOntologyDocumentSource documentSource) {
if (documentSource.isReaderAvailable()) {
return true;
}
if (documentSource.isInputStreamAvailable()) {
return true;
}
if (parsableSchemes.contains(documentSource.getDocumentIRI().getScheme())) {
return true;
}
// If we can open an input stream then we can attempt to parse the ontology
// TODO: Take into consideration the request type!
try {
InputStream is = documentSource.getDocumentIRI().toURI().toURL().openStream();
is.close();
return true;
} catch (UnknownHostException e) {
logger.info("Unknown host: " + e.getMessage());
} catch (MalformedURLException e) {
logger.info("Malformed URL: " + e.getMessage());
} catch (FileNotFoundException e) {
logger.info("File not found: " + e.getMessage());
} catch (IOException e) {
logger.info("IO Exception: " + e.getMessage());
}
return false;
}
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);
}
/** @return true if the two subgraphs can be merged because they form a complete graph */
private boolean canMerge(Set<O> g1, Set<O> g2) {
for (O vertexInG2 : g2) {
if (!g1.contains(vertexInG2)) {
for (O vertexInG1 : g1) {
if (!isEdge(vertexInG2, vertexInG1)) {
return false; // found a vertex in g2 that is not adjacent to a vertex in g1
}
}
}
}
return true;
}
public Set<Set<O>> getResults() {
if (resultCliques == null) {
resultCliques = new HashSet<Set<O>>();
Set<Integer> skip = new HashSet<Integer>();
List<Set<O>> workingCliques = new ArrayList<Set<O>>(originalCliques);
for (int i = 0; i < workingCliques.size(); i++) {
if (!skip.contains(i)) {
Set<O> g1 = new HashSet<O>(workingCliques.get(i));
for (int j = i + 1; j < workingCliques.size(); j++) {
if (!skip.contains(j)) {
Set<O> g2 = workingCliques.get(j);
if (canMerge(g1, g2)) {
g1.addAll(g2);
skip.add(j);
}
}
}
resultCliques.add(g1);
}
}
}
return resultCliques;
}
private AutocompleteResult exceptionToAutocomplete(
final String expression,
final ParserException e,
final OWLEntityFinder finder,
final ShortFormProvider sfp) {
String lastToken;
int pos;
if (e.getCurrentToken().endsWith(ERROR_TOKEN)) {
lastToken = e.getCurrentToken();
lastToken =
lastToken.substring(0, lastToken.length() - ERROR_TOKEN.length()); // remove the $$
pos = e.getStartPos();
} else {
lastToken = e.getTokenSequence().get(e.getTokenSequence().size() - 1);
if (lastToken.endsWith(ERROR_TOKEN)) {
lastToken =
lastToken.substring(0, lastToken.length() - ERROR_TOKEN.length()); // remove the $$
} else if (lastToken.equals("<EOF>")) {
lastToken = e.getTokenSequence().get(e.getTokenSequence().size() - 2); // EOF is last
lastToken =
lastToken.substring(0, lastToken.length() - ERROR_TOKEN.length()); // remove the $$
} else if (!expression.endsWith(lastToken)) { // later invalid tokens are not in the list
lastToken =
expression.substring(
expression.lastIndexOf(" ") + 1); // we just have to guess at the last word
}
pos = expression.length() - lastToken.length();
}
Map<String, List<String>> expected = new HashMap<String, List<String>>();
String search = lastToken + ".*"; // starts with
if (pos == e.getStartPos()) { // then the error is the last token and we can determine the type
if (hasExpectedToken(e)) {
final Set<String> keywords = e.getExpectedKeywords();
if (!keywords.isEmpty()) {
List<String> matchingKeywords = new ArrayList<String>();
for (String keyword : keywords) {
if (lastToken.length() == 0 || keyword.startsWith(lastToken)) {
matchingKeywords.add(keyword);
}
}
expected.put("keyword", matchingKeywords);
}
if (e.isClassNameExpected()) {
addResults(expected, OWLClass.class, finder.getOWLClasses(search), sfp);
}
if (e.isObjectPropertyNameExpected()) {
addResults(expected, OWLObjectProperty.class, finder.getOWLObjectProperties(search), sfp);
}
if (e.isDataPropertyNameExpected()) {
addResults(expected, OWLDataProperty.class, finder.getOWLDataProperties(search), sfp);
}
if (e.isDatatypeNameExpected()) {
addResults(expected, OWLDatatype.class, finder.getOWLDatatypes(search), sfp);
}
if (e.isAnnotationPropertyNameExpected()) {
addResults(
expected,
OWLAnnotationProperty.class,
finder.getOWLAnnotationProperties(search),
sfp);
}
if (e.isIndividualNameExpected()) {
addResults(expected, OWLNamedIndividual.class, finder.getOWLIndividuals(search), sfp);
}
} else {
expected.put("literal", Collections.<String>emptyList());
}
} else {
addKeywords(expected, lastToken);
addResults(expected, OWLClass.class, finder.getOWLClasses(search), sfp);
addResults(expected, OWLObjectProperty.class, finder.getOWLObjectProperties(search), sfp);
addResults(expected, OWLDataProperty.class, finder.getOWLDataProperties(search), sfp);
addResults(expected, OWLDatatype.class, finder.getOWLDatatypes(search), sfp);
addResults(
expected, OWLAnnotationProperty.class, finder.getOWLAnnotationProperties(search), sfp);
addResults(expected, OWLNamedIndividual.class, finder.getOWLIndividuals(search), sfp);
}
return new AutocompleteResult(expression, pos, lastToken, expected);
}
public boolean contains(Object obj) {
return nodes.contains(obj);
}
/** Resets the child2ParentMap, the parent2ChildMap, the nodes Set an the edge map */
protected void clearMaps() {
child2ParentMap.clear();
parent2ChildMap.clear();
nodes.clear();
edgeMap.clear();
}
public boolean retrieveSolutions(String siteNameHash) {
// use the siteNameHash to access a certain Site individual in the ontology
// retrieve each Solution individual of this site and use it to re-initialise the Solutions List
OwlSolution tempSolution;
OwlSolvedHouse tempSolvedHouse;
OwlSolvedRoom tempSolvedRoom;
// first clear the Solution List contents...
this.solutionsList.clear();
OWLIndividual tempSiteIndividual =
OWLFactory.getOWLNamedIndividual(":" + siteNameHash, topIxPrefixManager);
OWLClassExpression tempSolutionClassExpression =
OWLFactory.getOWLClass(":Solution", topIxPrefixManager);
Set<OWLObjectPropertyAssertionAxiom> tempSitePropertyAxioms =
topIxOnt.getObjectPropertyAssertionAxioms(tempSiteIndividual);
Set<OWLIndividual> tempSolutionIndividuals =
new HashSet<>(); // Solution individuals for this particular site. will be filled below...
Set<OWLIndividual> tempSolvedHouseIndividuals = new HashSet<>();
Set<OWLIndividual> tempSolvedRoomIndividuals = new HashSet<>();
// populate the tempSolutionIndividuals Set<OWLIndividual>
// with the Solution individuals that are solutions of the current Site
// this block runs through the set of all the object property axioms
// that have this site as their subject
// and filters out the ones that are of type "hasSolution"
for (OWLObjectPropertyAssertionAxiom tempObjPropAssAx : tempSitePropertyAxioms) {
OWLObjectProperty tempHasSolutionObjectProperty =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasSolution"));
if (tempObjPropAssAx.getProperty() == tempHasSolutionObjectProperty) {
tempSolutionIndividuals.add(tempObjPropAssAx.getObject());
}
}
// retrieving the site dimensions for this solution set
// (the site remains the same throughout the plethos of solutions).
int tempSiteLength = 0;
int tempSiteWidth = 0;
OWLDataProperty siteHasLengthProp = OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager);
OWLDataProperty siteHasWidthProp = OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager);
Set<OWLDataPropertyAssertionAxiom> tempSiteDataProperties = new HashSet<>();
tempSiteDataProperties = topIxOnt.getDataPropertyAssertionAxioms(tempSiteIndividual);
for (OWLDataPropertyAssertionAxiom tempSiteDataProperty : tempSiteDataProperties) {
if (tempSiteDataProperty.getProperty() == siteHasLengthProp) {
tempSiteLength = tempSiteDataProperty.getObject().parseInteger();
}
if (tempSiteDataProperty.getProperty() == siteHasWidthProp) {
tempSiteWidth = tempSiteDataProperty.getObject().parseInteger();
}
}
logger.info(tempSolutionIndividuals.size());
// running every solution individual for/of that particular site in order
// to extract the solvedHouse's and the solvedRoom's
// via the hasSolvedHouse and hasSolvedRoom properties.
int solutionCounter = 0;
for (OWLIndividual tempSolutionIndividual : tempSolutionIndividuals) {
tempSolution = new OwlSolution();
tempSolution.setSolutionID(new Integer(++solutionCounter));
tempSolution.setSiteLength(new Integer(tempSiteLength));
tempSolution.setSiteWidth(new Integer(tempSiteWidth));
// clearing the contents of these two structuresin order to accommodate the solved entities of
// the next solution.
tempSolvedHouseIndividuals.clear();
tempSolvedRoomIndividuals.clear();
for (OWLObjectPropertyAssertionAxiom tempObjPropAssAx :
topIxOnt.getObjectPropertyAssertionAxioms(tempSolutionIndividual)) {
OWLObjectProperty tempHasSolvedHouseObjectProperty =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasSolvedHouse"));
OWLObjectProperty tempHasSolvedRoomObjectProperty =
OWLFactory.getOWLObjectProperty(
IRI.create(topIxOnt.getOntologyID().getOntologyIRI() + "#hasSolvedRoom"));
if (tempObjPropAssAx.getProperty() == tempHasSolvedHouseObjectProperty) {
tempSolvedHouseIndividuals.add(tempObjPropAssAx.getObject());
} else if (tempObjPropAssAx.getProperty() == tempHasSolvedRoomObjectProperty) {
tempSolvedRoomIndividuals.add(tempObjPropAssAx.getObject());
}
}
for (OWLIndividual tempSolvedHouseIndividual : tempSolvedHouseIndividuals) {
tempSolvedHouse = new OwlSolvedHouse();
for (OWLDataPropertyAssertionAxiom tempDatPropAssAx :
topIxOnt.getDataPropertyAssertionAxioms(tempSolvedHouseIndividual)) {
if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasL", topIxPrefixManager))) {
// logger.info(tempDatPropAssAx.getObject().parseInteger());
tempSolvedHouse.setSolvedHouseLength(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasW", topIxPrefixManager))) {
tempSolvedHouse.setSolvedHouseWidth(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager))) {
tempSolvedHouse.setSolvedHouseX(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager))) {
tempSolvedHouse.setSolvedHouseY(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasLiteral", topIxPrefixManager))) {
tempSolvedHouse.setSolvedHouseLiteral(tempDatPropAssAx.getObject().getLiteral());
}
}
// logger.info(tempSolvedHouse.getSolvedHouseX()+" "+tempSolvedHouse.getSolvedHouseY());
tempSolution.getSolvedHouses().add(tempSolvedHouse);
}
for (OWLIndividual tempSolvedRoomIndividual : tempSolvedRoomIndividuals) {
tempSolvedRoom = new OwlSolvedRoom();
for (OWLDataPropertyAssertionAxiom tempDatPropAssAx :
topIxOnt.getDataPropertyAssertionAxioms(tempSolvedRoomIndividual)) {
if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasL", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomLength(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasW", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomWidth(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasH", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomHeight(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasX", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomX(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasY", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomY(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasZ", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomZ(tempDatPropAssAx.getObject().parseInteger());
} else if (tempDatPropAssAx.getProperty()
== (OWLFactory.getOWLDataProperty(":hasLiteral", topIxPrefixManager))) {
tempSolvedRoom.setSolvedRoomLiteral(tempDatPropAssAx.getObject().getLiteral());
}
}
tempSolution.getSolvedRooms().add(tempSolvedRoom);
}
this.solutionsList.add(tempSolution);
}
return true;
}