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NIHVIVO-2314 add support for property-based inferencing to the SimpleReasoner

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This commit is contained in:
stellamit 2011-04-26 18:16:31 +00:00
parent a1e87a10b9
commit 87b87c8edf
2 changed files with 896 additions and 275 deletions
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468
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -24,11 +24,12 @@ import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.iterator.ExtendedIterator; import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS; import com.hp.hpl.jena.vocabulary.RDFS;
/** /**
* Allows for instant incremental materialization or retraction of RDFS- * Allows for real-time incremental materialization or retraction of RDFS-
* style class and property subsumption based ABox inferences as statements * style class and property subsumption based ABox inferences as statements
* are added to or removed from the (ABox or TBox) knowledge base. * are added to or removed from the (ABox or TBox) knowledge base.
* *
@ -77,41 +78,39 @@ public class SimpleReasoner extends StatementListener {
} }
/* /*
* Performs incremental selected ABox reasoning based * Performs selected incremental ABox reasoning based
* on a new type assertion (assertion that an individual * on the addition of a new statement (aka assertion)
* is of a certain type) added to the ABox. * to the ABox.
*
*/ */
@Override @Override
public void addedStatement(Statement stmt) { public void addedStatement(Statement stmt) {
try { try {
if (stmt.getPredicate().equals(RDF.type)) { if (stmt.getPredicate().equals(RDF.type)) {
addedType(stmt, inferenceModel); addedABoxTypeAssertion(stmt, inferenceModel);
} else {
addedABoxAssertion(stmt,inferenceModel);
} }
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while adding incremental inferences: ", e); log.error("Exception while adding inferences: ", e);
} }
} }
/* /*
* Performs incremental selected ABox reasoning based * Performs selected incremental ABox reasoning based
* on a removed type assertion (assertion that an individual * on the retraction of a statement (aka assertion)
* is of a certain type) from the ABox. * from the ABox.
*
*/ */
@Override @Override
public void removedStatement(Statement stmt) { public void removedStatement(Statement stmt) {
try { try {
if (stmt.getPredicate().equals(RDF.type)) { if (stmt.getPredicate().equals(RDF.type)) {
removedType(stmt); removedABoxTypeAssertion(stmt, inferenceModel);
} else {
removedABoxAssertion(stmt, inferenceModel);
} }
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while retracting inferences: ", e); log.error("Exception while retracting inferences: ", e);
@ -120,27 +119,26 @@ public class SimpleReasoner extends StatementListener {
/* /*
* Performs incremental selected ABox reasoning based * Performs incremental selected ABox reasoning based
* on changes to the class hierarchy. * on changes to the class or property hierarchy.
*
* Handles subclassOf and equivalentClass assertions
* *
* Handles rdfs:subclassOf, owl:equivalentClass,
* rdfs:subPropertyOf and owl:equivalentProperty assertions
*/ */
public void addedTBoxStatement(Statement stmt) { public void addedTBoxStatement(Statement stmt) {
addedTBoxStatement(stmt, inferenceModel);
try {
if ( !(stmt.getPredicate().equals(RDFS.subClassOf)
|| stmt.getPredicate().equals(RDFS.subClassOf) ) ) {
return;
} }
public void addedTBoxStatement(Statement stmt, Model inferenceModel) {
try {
log.debug("added TBox assertion = " + stmt.toString());
if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
// ignore anonymous classes // ignore anonymous classes
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) { if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return; return;
} }
log.debug("stmt = " + stmt.toString());
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI()); OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
@ -151,36 +149,42 @@ public class SimpleReasoner extends StatementListener {
addedSubClass(subject,object); addedSubClass(subject,object);
addedSubClass(object,subject); addedSubClass(object,subject);
} }
} else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
OntProperty object = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (stmt.getPredicate().equals(RDFS.subPropertyOf)) {
addedSubProperty(subject, object, inferenceModel);
} else {
// equivalent property is the same as subProperty in both directions
addedSubProperty(subject, object, inferenceModel);
addedSubProperty(object, subject, inferenceModel);
}
}
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while adding incremental inferences: ", e); log.error("Exception while adding inference(s): ", e);
} }
} }
/* /*
* Performs incremental selected ABox reasoning based * Performs incremental selected ABox reasoning based
* on changes to the class hierarchy. * on changes to the class or property hierarchy.
*
* Handles subclassOf and equivalentClass assertions
* *
* Handles rdfs:subclassOf, owl:equivalentClass,
* rdfs:subPropertyOf and owl:equivalentProperty assertions
*/ */
public void removedTBoxStatement(Statement stmt) { public void removedTBoxStatement(Statement stmt) {
try { try {
log.debug("removed TBox assertion = " + stmt.toString());
if ( !(stmt.getPredicate().equals(RDFS.subClassOf) if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
|| stmt.getPredicate().equals(RDFS.subClassOf) ) ) {
return;
}
// ignore anonymous classes // ignore anonymous classes
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) { if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return; return;
} }
log.debug("stmt = " + stmt.toString());
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI()); OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
@ -191,21 +195,34 @@ public class SimpleReasoner extends StatementListener {
removedSubClass(subject,object); removedSubClass(subject,object);
removedSubClass(object,subject); removedSubClass(object,subject);
} }
} else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
OntProperty object = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (stmt.getPredicate().equals(RDFS.subPropertyOf)) {
removedSubProperty(subject,object);
} else {
// equivalent property is the same as subProperty in both directions
removedSubProperty(subject,object);
removedSubProperty(object,subject);
}
}
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while removing incremental inferences: ", e); log.error("Exception while removing inference(s): ", e);
} }
} }
/* /*
* Performs incremental reasoning based on a new type assertion
* added to the ABox (assertion that an individual is of a certain
* type).
*
* If it is added that B is of type A, then for each superclass of * If it is added that B is of type A, then for each superclass of
* A assert that B is of that type. * A assert that B is of that type.
* *
*/ */
public void addedType(Statement stmt, Model inferenceModel) { public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
//log.debug("stmt = " + stmt.toString());
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
@ -216,7 +233,6 @@ public class SimpleReasoner extends StatementListener {
List<OntClass> parents = (cls.listSuperClasses(false)).toList(); List<OntClass> parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList()); parents.addAll((cls.listEquivalentClasses()).toList());
Iterator<OntClass> parentIt = parents.iterator(); Iterator<OntClass> parentIt = parents.iterator();
while (parentIt.hasNext()) { while (parentIt.hasNext()) {
@ -247,13 +263,61 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/*
* Performs incremental property-based reasoning.
*
* Materializes inferences based on the rdfs:subPropertyOf relationship.
* If it is added that x propB y and propB is a sub-property of propA
* then add x propA y to the inference graph.
*/
public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
//TODO: have trouble parametizing the template with ? extends OntProperty
List superProperties = prop.listSuperProperties(false).toList();
superProperties.addAll(prop.listEquivalentProperties().toList());
Iterator<OntProperty> superIt = superProperties.iterator();
while (superIt.hasNext()) {
OntProperty superProp = superIt.next();
if ( !((prop.isObjectProperty() && superProp.isObjectProperty()) || (prop.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
log.warn("sub-property and super-property do not have the same type. No inferencing will be performed. sub-property: " + prop.getURI() + " super-property:" + superProp.getURI());
return;
}
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt) && !infStmt.equals(stmt) ) {
//log.debug("Adding this inferred statement: " + infStmt.toString() );
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} else {
log.warn("Didn't find target property (the predicate of the added statement) in the TBox: " + stmt.getPredicate().getURI());
}
} finally {
tboxModel.leaveCriticalSection();
}
}
/* /*
* If it is removed that B is of type A, then for each superclass of A remove * If it is removed that B is of type A, then for each superclass of A remove
* the inferred statement that B is of that type UNLESS it is otherwise entailed * the inferred statement that B is of that type UNLESS it is otherwise entailed
* that B is of that type. * that B is of that type.
* *
*/ */
public void removedType(Statement stmt) { public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
//log.debug("stmt = " + stmt.toString()); //log.debug("stmt = " + stmt.toString());
@ -266,7 +330,6 @@ public class SimpleReasoner extends StatementListener {
List<OntClass> parents = (cls.listSuperClasses(false)).toList(); List<OntClass> parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList()); parents.addAll((cls.listEquivalentClasses()).toList());
Iterator<OntClass> parentIt = parents.iterator(); Iterator<OntClass> parentIt = parents.iterator();
while (parentIt.hasNext()) { while (parentIt.hasNext()) {
@ -302,8 +365,62 @@ public class SimpleReasoner extends StatementListener {
} }
} }
// Returns true if it is entailed by class subsumption that subject is /*
// of type cls; otherwise returns false. * Performs incremental property-based reasoning.
*
* Retracts inferences based on the rdfs:subPropertyOf relationship.
* If it is removed that x propB y and propB is a sub-property of propA
* then remove x propA y from the inference graph UNLESS it that
* statement is otherwise entailed.
*/
public void removedABoxAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
//TODO: trouble parameterizing these templates with "? extends OntProperty"
List superProperties = prop.listSuperProperties(false).toList();
superProperties.addAll(prop.listEquivalentProperties().toList());
Iterator<OntProperty> superIt = superProperties.iterator();
while (superIt.hasNext()) {
OntProperty superProp = superIt.next();
if ( !((prop.isObjectProperty() && superProp.isObjectProperty()) || (prop.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
log.warn("sub-property and super-property do not have the same type. No inferencing will be performed. sub-property: " + prop.getURI() + " super-property:" + superProp.getURI());
return;
}
// if the statement is still entailed without the removed
// statement then don't remove it from the inferences
if (entailedByPropertySubsumption(stmt.getSubject(), superProp, stmt.getObject())) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(infStmt)) {
//log.debug("Removing this inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
inferenceModel.remove(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} else {
log.debug("Didn't find target predicate (the predicate of the removed statement) in the TBox: " + stmt.getPredicate().getURI());
}
} finally {
tboxModel.leaveCriticalSection();
}
}
// Returns true if it is entailed by class subsumption that
// subject is of type cls; otherwise returns false.
public boolean entailedType(Resource subject, OntClass cls) { public boolean entailedType(Resource subject, OntClass cls) {
//log.debug("subject = " + subject.getURI() + " class = " + cls.getURI()); //log.debug("subject = " + subject.getURI() + " class = " + cls.getURI());
@ -313,8 +430,8 @@ public class SimpleReasoner extends StatementListener {
try { try {
ExtendedIterator<OntClass> iter = cls.listSubClasses(false); ExtendedIterator<OntClass> iter = cls.listSubClasses(false);
while (iter.hasNext()) {
while (iter.hasNext()) {
OntClass childClass = iter.next(); OntClass childClass = iter.next();
Statement stmt = ResourceFactory.createStatement(subject, RDF.type, childClass); Statement stmt = ResourceFactory.createStatement(subject, RDF.type, childClass);
if (aboxModel.contains(stmt)) return true; if (aboxModel.contains(stmt)) return true;
@ -327,10 +444,33 @@ public class SimpleReasoner extends StatementListener {
} }
} }
// Returns true if the statement is entailed by property subsumption
public boolean entailedByPropertySubsumption(Resource subject, OntProperty prop, RDFNode object) {
aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
try {
ExtendedIterator<? extends OntProperty> iter = prop.listSubProperties(false);
while (iter.hasNext()) {
OntProperty subProp = iter.next();
Statement stmt = ResourceFactory.createStatement(subject, subProp, object);
if (aboxModel.contains(stmt)) return true;
}
return false;
} finally {
aboxModel.leaveCriticalSection();
tboxModel.leaveCriticalSection();
}
}
/* /*
* If added that B is a subclass of A, then find all individuals * If it is added that B is a subClass of A, then for each
* that are typed as B, either in the ABox or in the inferred model * individual that is typed as B, either in the ABox or in the
* and assert that they are of type A. * inferred model, assert that it is of type A.
*/ */
public void addedSubClass(OntClass subClass, OntClass superClass) { public void addedSubClass(OntClass subClass, OntClass superClass) {
@ -366,11 +506,10 @@ public class SimpleReasoner extends StatementListener {
/* /*
* If removed that B is a subclass of A, then for each individual * If removed that B is a subclass of A, then for each individual
* that is of type B, either inferred or in the ABox, then * that is of type B, either inferred or in the ABox, remove the
* remove the inferred assertion that it is of type A, * assertion that it is of type A from the inferred model,
* UNLESS the individual is of some type C that is * UNLESS the individual is of some type C that is a subClass
* a subClass of A (including A itself) * of A (including A itself)
*
*/ */
public void removedSubClass(OntClass subClass, OntClass superClass) { public void removedSubClass(OntClass subClass, OntClass superClass) {
@ -408,6 +547,97 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/*
* If it is added that B is a subProperty of A, then for each assertion
* involving predicate B, either in the ABox or in the inferred model
* assert the same relationship for predicate A
*/
public void addedSubProperty(OntProperty subProp, OntProperty superProp, Model inferenceModel) {
log.debug("subProperty = " + subProp.getURI() + " superProperty = " + subProp.getURI());
if ( !((subProp.isObjectProperty() && superProp.isObjectProperty()) || (subProp.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
log.warn("sub-property and super-property do not have the same type. No inferencing will be performed. sub-property: " + subProp.getURI() + " super-property:" + superProp.getURI());
return;
}
aboxModel.enterCriticalSection(Lock.READ);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
unionModel.addSubModel(aboxModel);
unionModel.addSubModel(inferenceModel);
StmtIterator iter = unionModel.listStatements((Resource) null, subProp, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
if (!inferenceModel.contains(infStmt)) {
//log.debug("Adding this inferred statement: " + infStmt.toString() );
inferenceModel.add(infStmt);
}
}
} finally {
aboxModel.leaveCriticalSection();
inferenceModel.leaveCriticalSection();
}
}
/*
* If it is removed that B is a subProperty of A, then for each
* assertion involving predicate B, either in the ABox or in the
* inferred model, remove the same assertion involving predicate
* A from the inferred model, UNLESS the assertion is otherwise
* entailed by property subsumption.
*/
public void removedSubProperty(OntProperty subProp, OntProperty superProp) {
log.debug("subProperty = " + subProp.getURI() + " superProperty = " + subProp.getURI());
if ( !((subProp.isObjectProperty() && superProp.isObjectProperty()) || (subProp.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
log.warn("sub-property and super-property do not have the same type. No inferencing will be performed. sub-property: " + subProp.getURI() + " super-property:" + superProp.getURI());
return;
}
aboxModel.enterCriticalSection(Lock.READ);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
unionModel.addSubModel(aboxModel);
unionModel.addSubModel(inferenceModel);
StmtIterator iter = unionModel.listStatements((Resource) null, subProp, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
// if the statement is entailed without the removed subPropertyOf
// relationship then don't remove it from the inferences
if (entailedByPropertySubsumption(stmt.getSubject(), superProp, stmt.getObject())) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
if (inferenceModel.contains(infStmt)) {
//log.debug("Adding this inferred statement: " + infStmt.toString() );
inferenceModel.remove(infStmt);
}
}
} finally {
aboxModel.leaveCriticalSection();
inferenceModel.leaveCriticalSection();
}
}
private boolean recomputing = false; private boolean recomputing = false;
/** /**
@ -441,26 +671,53 @@ public class SimpleReasoner extends StatementListener {
*/ */
public synchronized void recomputeABox() { public synchronized void recomputeABox() {
// recompute the inferences // recompute the ABox inferences
inferenceRebuildModel.enterCriticalSection(Lock.WRITE); inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
try { try {
inferenceRebuildModel.removeAll(); inferenceRebuildModel.removeAll();
// compute the class-based inferences
log.info("Computing class-based ABox inferences");
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null); StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
addedType(stmt, inferenceRebuildModel); addedABoxTypeAssertion(stmt, inferenceRebuildModel);
}
// compute the property-based inferences
log.info("Computing property-based ABox inferences");
iter = tboxModel.listStatements((Resource) null, RDFS.subPropertyOf, (RDFNode) null);
int numStmts = 0;
while (iter.hasNext()) {
numStmts++;
if ((numStmts % 400) == 0) {
log.info("Still computing property-based ABox inferences...");
}
Statement stmt = iter.next();
addedTBoxStatement(stmt, inferenceRebuildModel);
}
iter = tboxModel.listStatements((Resource) null, OWL.equivalentProperty, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
addedTBoxStatement(stmt, inferenceRebuildModel);
} }
} catch (Exception e) { } catch (Exception e) {
log.error("Exception while recomputing ABox inference model", e); log.error("Exception while recomputing ABox inference model", e);
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
tboxModel.leaveCriticalSection();
inferenceRebuildModel.leaveCriticalSection(); inferenceRebuildModel.leaveCriticalSection();
} }
// reflect the recomputed inferences into the application inference // reflect the recomputed inferences into the application inference
// model. // model.
inferenceRebuildModel.enterCriticalSection(Lock.READ); inferenceRebuildModel.enterCriticalSection(Lock.READ);
@ -532,99 +789,6 @@ public class SimpleReasoner extends StatementListener {
log.info("ABox inferences recomputed."); log.info("ABox inferences recomputed.");
} }
// The following three methods aren't currently called; the default behavior of VIVO is to not materialize such inferences.
public void addedProperty(Statement stmt) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
ExtendedIterator<? extends OntProperty> superIt = prop.listSuperProperties(false);
while (superIt.hasNext()) {
OntProperty parentProp = superIt.next();
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), parentProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt)) {
//log.debug("Adding inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} else {
log.debug("Didn't find predicate of the added statement in the TBox: " + stmt.getPredicate().getURI());
}
} finally {
tboxModel.leaveCriticalSection();
}
}
public void removedProperty(Statement stmt) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
ExtendedIterator<? extends OntProperty> superIt = prop.listSuperProperties(false);
while (superIt.hasNext()) {
OntProperty parentProp = superIt.next();
if (entailedStmt(stmt.getSubject(),parentProp,stmt.getObject() )) continue; // if the statement is still entailed
// don't remove it from the inference graph.
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), parentProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(infStmt)) {
//log.debug("Removing inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
inferenceModel.remove(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} else {
log.debug("Didn't find predicate of the removed statement in the TBox: " + stmt.getPredicate().getURI());
}
} finally {
tboxModel.leaveCriticalSection();
}
}
// Returns true if the statement is entailed by property subsumption
public boolean entailedStmt(Resource subject, OntProperty prop, RDFNode object) {
aboxModel.enterCriticalSection(Lock.READ);
try {
ExtendedIterator<? extends OntProperty> iter = prop.listSubProperties(false);
while (iter.hasNext()) {
OntProperty childProp = iter.next();
Statement stmt = ResourceFactory.createStatement(subject, childProp, object);
if (aboxModel.contains(stmt)) return true;
}
return false;
} finally {
aboxModel.leaveCriticalSection();
}
}
public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) { public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) {
Object simpleReasoner = ctx.getAttribute("simpleReasoner"); Object simpleReasoner = ctx.getAttribute("simpleReasoner");

613
webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerTest.java
View file

@ -11,6 +11,7 @@ import org.mindswap.pellet.jena.PelletReasonerFactory;
import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec; import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
@ -24,16 +25,20 @@ import edu.cornell.mannlib.vitro.webapp.reasoner.support.SimpleReasonerTBoxListe
public class SimpleReasonerTest extends AbstractTestClass { public class SimpleReasonerTest extends AbstractTestClass {
private Resource objectProperty = ResourceFactory.createResource("http://www.w3.org/2002/07/owl#ObjectProperty");
@Before @Before
public void suppressErrorOutput() { public void suppressErrorOutput() {
suppressSyserr(); suppressSyserr();
} }
/*
* Test that when an individual is asserted to be of a type,
* its asserted type is not added to the inference graph
*/
@Test @Test
public void addType(){ public void addABoxTypeAssertion1(){
// Test that when a new instance is asserted, its asserted type is not added to the
// inference graph
// Create a Tbox with a simple class hierarchy. B is a subclass of A. // Create a Tbox with a simple class hierarchy. B is a subclass of A.
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
@ -50,7 +55,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
// this is the model to receive inferences // this is the model to receive inferences
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
// create an Abox and register the SimpleReasoner listener with it // create an ABox and register the SimpleReasoner listener with it
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
aBox.register(new SimpleReasoner(tBox, aBox, inf)); aBox.register(new SimpleReasoner(tBox, aBox, inf));
@ -65,11 +70,16 @@ public class SimpleReasonerTest extends AbstractTestClass {
Assert.assertFalse(inf.contains(xisb)); Assert.assertFalse(inf.contains(xisb));
} }
/*
* Test that when an individual is asserted have a type,
* that inferences are materialized that it has the types
* of its superclasses
*/
@Test @Test
public void addTypes(){ public void addABoxTypeAssertion2(){
// Create a Tbox with a simple class hierarchy. D and E are subclasses of C. B and C are subclasses of A. // Create a Tbox with a simple class hierarchy. D and E are subclasses
// Pellet will compute TBox inferences // of C. B and C are subclasses of A. Pellet will compute TBox inferences.
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntClass classA = tBox.createClass("http://test.vivo/A"); OntClass classA = tBox.createClass("http://test.vivo/A");
@ -113,13 +123,150 @@ public class SimpleReasonerTest extends AbstractTestClass {
Assert.assertTrue(inf.contains(xisa)); Assert.assertTrue(inf.contains(xisa));
} }
/*
* Test inference based on class equivalence
*/
@Test @Test
public void removeTypes(){ public void addABoxTypeAssertion3(){
// Create a Tbox with a simple class hierarchy. C is a subclass of B and B is a subclass of A. // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add classes A, B and C to the TBox
// A is equivalent to B
// C is a subclass of A
OntClass classA = tBox.createClass("http://test.vivo/A");
classA.setLabel("class A", "en-US");
OntClass classB = tBox.createClass("http://test.vivo/B");
classB.setLabel("class B", "en-US");
OntClass classC = tBox.createClass("http://test.vivo/C");
classC.setLabel("class C", "en-US");
classA.addEquivalentClass(classB);
classA.addSubClass(classC);
// Add a statement that individual x is of type C to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classC);
// Verify that "x is of type A" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa));
// Verify that "x is of type B" was inferred
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB);
Assert.assertTrue(inf.contains(xisb));
}
/*
* Test inference based on class equivalence
*/
@Test
public void addABoxTypeAssertion4() {
// Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add classes A and B to the TBox
// A is equivalent to B
OntClass classA = tBox.createClass("http://test.vivo/A");
classA.setLabel("class A", "en-US");
OntClass classB = tBox.createClass("http://test.vivo/B");
classB.setLabel("class B", "en-US");
classA.addEquivalentClass(classB);
// Add a statement that individual x is of type B to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB);
// Verify that "x is of type A" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa));
}
/*
* Test inference based on class equivalence
*/
@Test
public void addABoxTypeAssertion5() {
// Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add classes classes A and B to the TBox
// A is equivalent to B
OntClass classA = tBox.createClass("http://test.vivo/A");
classA.setLabel("class A", "en-US");
OntClass classB = tBox.createClass("http://test.vivo/B");
classB.setLabel("class B", "en-US");
classA.addEquivalentClass(classB);
// Add a statement that individual x is of type B to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB);
// Verify that "x is of type A" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa));
// Remove the statement that x is of type B from the ABox
aBox.remove(ind_x, RDF.type, classB);
// Verify that "x is of type A" was removed from the inference graph
Assert.assertFalse(inf.contains(xisa));
}
/*
* Test that when it is retracted that an individual is of a type,
* that the inferences that it is of the type of all superclasses
* of the retracted type are retracted from the inference graph.
* However, any assertions that are otherwise entailed (by the
* TBox, ABox and inference graph minus the retracted type statement)
* should not be retracted.
*/
@Test
public void removeABoxTypeAssertion1(){
// Create a Tbox with a simple class hierarchy. C is a subclass of B
// and B is a subclass of A. Pellet will compute TBox inferences.
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntClass classA = tBox.createClass("http://test.vivo/A"); OntClass classA = tBox.createClass("http://test.vivo/A");
@ -154,14 +301,32 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Verify that the inference graph contains the statement that x is of type A. // Verify that the inference graph contains the statement that x is of type A.
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa)); Assert.assertTrue(inf.contains(xisa));
// Hopefully the assertion that x is b got removed from
// the inference graph
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB);
Assert.assertFalse(inf.contains(xisb));
} }
/*
// This tests added TBox subClassOf and equivalentClass statements. * Test the addition of a subClassOf statement to
// The ABox data that will be the basis for the inference will * the TBox. The instance data that is the basis
// be in the ABox graph. * for the inference is in the ABox. The existing
* instance of the newly declared subclass should
* be inferred to have the type of the superclass.
* There are also a few checks that the instance
* is not inferred to have the types of some other
* random classes.
*
* Since the addition of an owl:equivalentClass
* statement is implemented as two calls to the
* method that handles the addition of an
* rdfs:subClassOf statement, this test serves
* as a test of equivalentClass statements also.
*/
@Test @Test
public void addSubClass1(){ public void addTBoxSubClassAssertion1(){
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
@ -211,12 +376,24 @@ public class SimpleReasonerTest extends AbstractTestClass {
} }
/*
// this tests added TBox subClassOf and equivalentClass statements. * Test the addition of a subClassOf statement to
// The ABox data that is the basis for the inference will be * the TBox. The instance data that is the basis
// in the inferred graph * for the inference is in the ABox graph and the
* inference graph. The existing instance of the
* subclass of the newly added subclass should
* be inferred to have the type of the superclass
* of the newly added subclass.
*
* Since the addition of an owl:equivalentClass
* statement is implemented as two calls to the
* method that handles the addition of an
* rdfs:subClassOf statement, this test serves
* as some test of equivalentClass statements also.
*
*/
@Test @Test
public void addSubClass2(){ public void addTBoxSubClassAssertion2() {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
@ -260,9 +437,23 @@ public class SimpleReasonerTest extends AbstractTestClass {
} }
@Test @Test
// this tests incremental reasoning as a result of the removal of a subClassOf /*
// or equivalentClass statement from the TBox. * Test the removal of a subClassOf statement from
public void removeSubClass(){ * the TBox. The instance data that is the basis
* for the inference is in the ABox graph and the
* inference graph. The existing instance of the
* subclass of the newly added subclass should
* be inferred to have the type of the superclass
* of the newly added subclass.
*
* Since the addition of an owl:equivalentClass
* statement is implemented as two calls to the
* method that handles the addition of an
* rdfs:subClassOf statement, this test serves
* as a test of equivalentClass assertions also.
*
*/
public void removeTBoxSubClassAssertion1(){
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
@ -324,7 +515,6 @@ public class SimpleReasonerTest extends AbstractTestClass {
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertFalse(inf.contains(xisa)); Assert.assertFalse(inf.contains(xisa));
// Verify that "x is of type B" is in the inference graph // Verify that "x is of type B" is in the inference graph
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB); Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB);
Assert.assertTrue(inf.contains(xisb)); Assert.assertTrue(inf.contains(xisb));
@ -340,13 +530,14 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Verify that "y is of type A" is in the inference graph // Verify that "y is of type A" is in the inference graph
Statement yisa = ResourceFactory.createStatement(ind_y, RDF.type, classA); Statement yisa = ResourceFactory.createStatement(ind_y, RDF.type, classA);
Assert.assertTrue(inf.contains(yisa)); Assert.assertTrue(inf.contains(yisa));
} }
// Test inference based on class equivalence
// /*
* tests rdfs:subPropertyOf materialization for object properties.
*/
@Test @Test
public void equivClass1(){ public void addABoxAssertion1(){
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
@ -360,40 +551,130 @@ public class SimpleReasonerTest extends AbstractTestClass {
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add classes classes A, B and C to the TBox // Add object properties propA and propB to the TBox.
// propB is a sub-property of propA.
OntProperty propA = tBox.createOntProperty("http://test.vivo/propA");
tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("propA", "en-US");
OntProperty propB = tBox.createOntProperty("http://test.vivo/propB");
tBox.add(propB, RDF.type, objectProperty);
propB.setLabel("propB", "en-US");
propA.addSubProperty(propB);
// Add the assertion that x propB y to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
Resource ind_y = aBox.createResource("http://test.vivo/y");
aBox.add(ind_x, propB, ind_y);
// Verify that x propA y was inferred
Statement xay = ResourceFactory.createStatement(ind_x, propA, ind_y);
Assert.assertTrue(inf.contains(xay));
}
/*
* Test that when a statement is asserted, that it not
* added to the inference graph.
*/
@Test
public void addABoxAssertion2(){
// Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add object properties propA and propB to the TBox.
// propB is a sub-property of propA.
OntProperty propA = tBox.createOntProperty("http://test.vivo/propA");
tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("propA", "en-US");
OntProperty propB = tBox.createOntProperty("http://test.vivo/propB");
tBox.add(propB, RDF.type, objectProperty);
propB.setLabel("propB", "en-US");
propA.addSubProperty(propB);
// Add the assertion that x propB y to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
Resource ind_y = aBox.createResource("http://test.vivo/y");
aBox.add(ind_x, propB, ind_y);
// Verify that x propA y was inferred
Statement xby = ResourceFactory.createStatement(ind_x, propB, ind_y);
Assert.assertFalse(inf.contains(xby));
}
/*
* Test inference based on property equivalence
*/
@Test
public void addABoxAssertion4(){
// Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add properties A, B and C to the TBox
// A is equivalent to B // A is equivalent to B
// C is a subclass of A // C is a subclass of A
OntClass classA = tBox.createClass("http://test.vivo/A"); OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
classA.setLabel("class A", "en-US"); tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("property A", "en-US");
OntClass classB = tBox.createClass("http://test.vivo/B"); OntProperty propB = tBox.createOntProperty("http://test.vivo/B");
classB.setLabel("class B", "en-US"); tBox.add(propB, RDF.type, objectProperty);
propB.setLabel("property B", "en-US");
OntClass classC = tBox.createClass("http://test.vivo/C"); OntProperty propC = tBox.createOntProperty("http://test.vivo/C");
classC.setLabel("class C", "en-US"); tBox.add(propC, RDF.type, objectProperty);
propC.setLabel("property C", "en-US");
classA.addEquivalentClass(classB); propA.addEquivalentProperty(propB);
classA.addSubClass(classC); propA.addSubProperty(propC);
// Add a statement that individual x is of type C to the ABox // Add a statement that individual x is of type C to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classC); Resource ind_y = aBox.createResource("http://test.vivo/y");
// Verify that "x is of type A" was inferred aBox.add(ind_x, propC, ind_y);
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa));
// Verify that "x is of type B" was inferred // Verify that "x A y" was inferred
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB); Statement xAy = ResourceFactory.createStatement(ind_x, propA, ind_y);
Assert.assertTrue(inf.contains(xisb)); Assert.assertTrue(inf.contains(xAy));
// Verify that "x B y" was inferred
Statement xBy = ResourceFactory.createStatement(ind_x, propB, ind_y);
Assert.assertTrue(inf.contains(xBy));
} }
// Test inference based on class equivalence /*
// * The sub-property is not of the same type as the super
* property so no inference should be materialized.
*/
@Test @Test
public void equivClass2(){ public void addABoxAssertion5(){
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
@ -407,31 +688,35 @@ public class SimpleReasonerTest extends AbstractTestClass {
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add classes classes A and B to the TBox // Add object properties propA and propB to the TBox.
// A is equivalent to B // propB is a sub-property of propA.
OntClass classA = tBox.createClass("http://test.vivo/A"); OntProperty propA = tBox.createOntProperty("http://test.vivo/propA");
classA.setLabel("class A", "en-US"); tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("propA", "en-US");
OntClass classB = tBox.createClass("http://test.vivo/B"); OntProperty propB = tBox.createOntProperty("http://test.vivo/propB");
classB.setLabel("class B", "en-US"); Resource datatypeProperty = ResourceFactory.createResource("http://www.w3.org/2002/07/owl#DatatypeProperty");
tBox.add(propB, RDF.type, datatypeProperty);
propB.setLabel("propB", "en-US");
classA.addEquivalentClass(classB); propA.addSubProperty(propB);
// Add a statement that individual x is of type B to the ABox // Add the assertion that x propB y to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB); Resource ind_y = aBox.createResource("http://test.vivo/y");
aBox.add(ind_x, propB, ind_y);
// Verify that "x is of type A" was inferred // Verify that x propA y was not inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xay = ResourceFactory.createStatement(ind_x, propA, ind_y);
Assert.assertTrue(inf.contains(xisa)); Assert.assertFalse(inf.contains(xay));
} }
/*
// Test inference based on class equivalence * Test inference based on property equivalence
// */
@Test @Test
public void equivClass3(){ public void addABoxAssertion6() {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
@ -445,31 +730,203 @@ public class SimpleReasonerTest extends AbstractTestClass {
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add classes classes A and B to the TBox // Add properties A and B to the TBox
// A is equivalent to B // A is equivalent to B
OntClass classA = tBox.createClass("http://test.vivo/A"); OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
classA.setLabel("class A", "en-US"); tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("property A", "en-US");
OntClass classB = tBox.createClass("http://test.vivo/B"); OntProperty propB = tBox.createOntProperty("http://test.vivo/B");
classB.setLabel("class B", "en-US"); tBox.add(propB, RDF.type, objectProperty);
propB.setLabel("property B", "en-US");
classA.addEquivalentClass(classB); propA.addEquivalentProperty(propB);
// Add a statement that individual x is of type B to the ABox // Add the statement x B y to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB); Resource ind_y = aBox.createResource("http://test.vivo/y");
aBox.add(ind_x, propB, ind_y);
// Verify that "x is of type A" was inferred // Verify that "x A y" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xAy = ResourceFactory.createStatement(ind_x, propA, ind_y);
Assert.assertTrue(inf.contains(xisa)); Assert.assertTrue(inf.contains(xAy));
// Remove the statement that x is of type B from the ABox // Remove the statement that x B y from the ABox
aBox.remove(ind_x, RDF.type, classB); aBox.remove(ind_x, propB, ind_y);
// Verify that "x is of type A" was removed from the inference graph // Verify that "x is of type A" was removed from the inference graph
Assert.assertFalse(inf.contains(xisa)); Assert.assertFalse(inf.contains(xAy));
}
/*
* Test the addition of a subPropertyOf statement to
* the TBox. The instance data that is the basis
* for the inference is in the ABox.
*
* Since the addition of an owl:equivalentProperty
* statement is implemented as two calls to the
* method that handles the addition of an
* rdfs:subPropetyOf statement, this test serves
* as a test of equivalentProperty assertions also.
*/
@Test
public void addTBoxSubPropertyAssertion1(){
// Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add properties A, B, C and D to the TBox
OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("property A", "en-US");
OntProperty propB = tBox.createOntProperty("http://test.vivo/B");
tBox.add(propB, RDF.type, objectProperty);
propB.setLabel("property B", "en-US");
OntProperty propC = tBox.createOntProperty("http://test.vivo/C");
tBox.add(propC, RDF.type, objectProperty);
propB.setLabel("property C", "en-US");
OntProperty propD = tBox.createOntProperty("http://test.vivo/D");
tBox.add(propD, RDF.type, objectProperty);
propB.setLabel("property D", "en-US");
// Add the statement "x C y" to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
Resource ind_y = aBox.createResource("http://test.vivo/y");
aBox.add(ind_x, propC, ind_y);
// Add a statement that C is a sub-property of A to the TBox
propA.addSubProperty(propC);
// Verify that "x A y" was inferred
Statement xAy = ResourceFactory.createStatement(ind_x, propA, ind_y);
Assert.assertTrue(inf.contains(xAy));
// Verify that "x B y" was not inferred
Statement xBy = ResourceFactory.createStatement(ind_x, propB, ind_y);
Assert.assertFalse(inf.contains(xBy));
// Verify that "x D y" was not inferred
Statement xDy = ResourceFactory.createStatement(ind_x, propD, ind_y);
Assert.assertFalse(inf.contains(xDy));
}
@Test
/*
* Test the removal of a subPropertyOf statement from
* the TBox. The instance data that is the basis
* for the inference is in the ABox graph and the
* inference graph.
*
* Since the addition of an owl:equivalentProperty
* statement is implemented as two calls to the
* method that handles the addition of an
* rdfs:subPropertyOf statement, this test serves
* as a test of equivalentProperty assertions also.
*
*/
public void removeTBoxSubPropertyAssertion1(){
// Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
// Add properties A, B, C, D, E, F, G and H to the TBox.
// B, C and D are subproperties of A.
// E is a subproperty of B.
// F and G are subproperties of C.
// H is a subproperty of D.
OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
tBox.add(propA, RDF.type, objectProperty);
propA.setLabel("property A", "en-US");
OntProperty propB = tBox.createOntProperty("http://test.vivo/B");
tBox.add(propB, RDF.type, objectProperty);
propB.setLabel("property B", "en-US");
OntProperty propC = tBox.createOntProperty("http://test.vivo/C");
tBox.add(propC, RDF.type, objectProperty);
propB.setLabel("property C", "en-US");
OntProperty propD = tBox.createOntProperty("http://test.vivo/D");
tBox.add(propD, RDF.type, objectProperty);
propB.setLabel("property D", "en-US");
OntProperty propE = tBox.createOntProperty("http://test.vivo/E");
tBox.add(propE, RDF.type, objectProperty);
propB.setLabel("property E", "en-US");
OntProperty propF = tBox.createOntProperty("http://test.vivo/F");
tBox.add(propF, RDF.type, objectProperty);
propB.setLabel("property F", "en-US");
OntProperty propG = tBox.createOntProperty("http://test.vivo/G");
tBox.add(propG, RDF.type, objectProperty);
propB.setLabel("property G", "en-US");
OntProperty propH = tBox.createOntProperty("http://test.vivo/H");
tBox.add(propH, RDF.type, objectProperty);
propB.setLabel("property H", "en-US");
propA.addSubProperty(propB);
propA.addSubProperty(propC);
propA.addSubProperty(propD);
propB.addSubProperty(propE);
propC.addSubProperty(propF);
propC.addSubProperty(propG);
propD.addSubProperty(propH);
// Add the statement "x E y" to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x");
Resource ind_y = aBox.createResource("http://test.vivo/y");
aBox.add(ind_x, propE, ind_y);
// Remove the statement that B is a subproperty of A from the TBox
propA.removeSubProperty(propB);
// Verify that "x A y" is not in the inference graph
Statement xAy = ResourceFactory.createStatement(ind_x, propA, ind_y);
Assert.assertFalse(inf.contains(xAy));
// Verify that "x B y" is in the inference graph
Statement xBy = ResourceFactory.createStatement(ind_x, propB, ind_y);
Assert.assertTrue(inf.contains(xBy));
// Add statements "w F z" and "w H z" to the ABox
Resource ind_z = aBox.createResource("http://test.vivo/z");
Resource ind_w = aBox.createResource("http://test.vivo/w");
aBox.add(ind_w, propF, ind_z);
aBox.add(ind_w, propH, ind_z);
// Remove the statement that C is a subproperty of A from the TBox
propA.removeSubProperty(propC);
// Verify that "w A z" is in the inference graph
Statement wAz = ResourceFactory.createStatement(ind_w, propA, ind_z);
Assert.assertTrue(inf.contains(wAz));
} }