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Adding ability to disable sameAs in SimpleReasoner. VIVO-110

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This commit is contained in:
Brian Caruso 2013-08-28 17:25:09 -04:00
parent bbfd68ef4d
commit 05917378cc
2 changed files with 385 additions and 233 deletions
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463
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
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@ -158,7 +158,7 @@ public class SimpleReasoner extends StatementListener {
return this.pluginList; return this.pluginList;
} }
public void doSameAs( boolean tf){ public void setSameAsEnabled( boolean tf){
this.doSameAs = tf; this.doSameAs = tf;
} }
@ -222,8 +222,13 @@ public class SimpleReasoner extends StatementListener {
} }
/** /**
* Performs incremental ABox reasoning based
* on changes to the class hierarchy.
*
* addedTBoxStatement and removedTBoxStatement use the * addedTBoxStatement and removedTBoxStatement use the
* same tests so the are merged into this method. * same tests so the are merged into this method.
*
* Handles rdfs:subclassOf, owl:equivalentClass, and owl:inverseOf
*/ */
protected void changedTBoxStatement( Statement stmt , boolean add){ protected void changedTBoxStatement( Statement stmt , boolean add){
try { try {
@ -312,7 +317,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/* /**
* Performs incremental ABox reasoning based * Performs incremental ABox reasoning based
* on changes to the class hierarchy. * on changes to the class hierarchy.
* *
@ -322,7 +327,7 @@ public class SimpleReasoner extends StatementListener {
changedTBoxStatement( stmt, true); changedTBoxStatement( stmt, true);
} }
/* /**
* Performs incremental ABox reasoning based * Performs incremental ABox reasoning based
* on changes to the class hierarchy. * on changes to the class hierarchy.
* *
@ -332,7 +337,7 @@ public class SimpleReasoner extends StatementListener {
changedTBoxStatement(stmt, false); changedTBoxStatement(stmt, false);
} }
/* /**
* Performs incremental reasoning based on a new type assertion * Performs incremental reasoning based on a new type assertion
* added to the ABox (assertion that an individual is of a certain * added to the ABox (assertion that an individual is of a certain
* type). * type).
@ -402,7 +407,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/* /**
* 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.
@ -412,7 +417,7 @@ public class SimpleReasoner extends StatementListener {
removedABoxTypeAssertion(stmt, inferenceModel, null); removedABoxTypeAssertion(stmt, inferenceModel, null);
} }
/* /**
* 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.
@ -480,10 +485,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/**
/*
* Performs incremental property-based reasoning. * Performs incremental property-based reasoning.
* *
* Retracts inferences based on the owl:inverseOf relationship. * Retracts inferences based on the owl:inverseOf relationship.
@ -507,6 +509,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
if( doSameAs )
doSameAsForRemovedABoxAssertion( stmt, inferenceModel ); doSameAsForRemovedABoxAssertion( stmt, inferenceModel );
// if a statement has been removed that is otherwise entailed, // if a statement has been removed that is otherwise entailed,
@ -522,7 +525,7 @@ public class SimpleReasoner extends StatementListener {
} }
/* /**
* If it is added that B is a subClass of A, then for each * If it is added that B is a subClass of A, then for each
* individual that is typed as B, either in the ABox or in the * individual that is typed as B, either in the ABox or in the
* inferred model, infer that it is of type A. * inferred model, infer that it is of type A.
@ -551,7 +554,7 @@ 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, remove the * that is of type B, either inferred or in the ABox, remove the
* assertion that it is of type A from the inferred model, * assertion that it is of type A from the inferred model,
@ -593,7 +596,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/* /**
* If it is added that P is an inverse of Q, then: * If it is added that P is an inverse of Q, then:
* 1. For each statement involving predicate P in * 1. For each statement involving predicate P in
* the assertions model add the inverse statement * the assertions model add the inverse statement
@ -624,7 +627,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/* /**
* If it is removed that P is an inverse of Q, then: * If it is removed that P is an inverse of Q, then:
* 1. For each statement involving predicate P in * 1. For each statement involving predicate P in
* the abox assertions model remove the inverse * the abox assertions model remove the inverse
@ -659,7 +662,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/* /**
* Get a list of individuals the same as the given individual * Get a list of individuals the same as the given individual
*/ */
protected List<Resource> getSameIndividuals(Resource ind, Model inferenceModel) { protected List<Resource> getSameIndividuals(Resource ind, Model inferenceModel) {
@ -669,15 +672,176 @@ public class SimpleReasoner extends StatementListener {
Iterator<Statement> iter = fullModel.listStatements(ind, OWL.sameAs, (RDFNode) null); Iterator<Statement> iter = fullModel.listStatements(ind, OWL.sameAs, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (stmt.getObject() == null || !stmt.getObject().isResource() || stmt.getObject().asResource().getURI() == null) continue; if (stmt.getObject() != null
&& stmt.getObject().isResource()
&& stmt.getObject().asResource().getURI() != null) {
sameIndividuals.add(stmt.getObject().asResource()); sameIndividuals.add(stmt.getObject().asResource());
} }
}
} finally { } finally {
fullModel.leaveCriticalSection(); fullModel.leaveCriticalSection();
} }
return sameIndividuals; return sameIndividuals;
} }
/**
* Materializes inferences based on the owl:sameAs relationship.
*
* If it is added that x owl:sameAs y, then all asserted and inferred
* statements about x will become inferred about y if they are not already
* asserted about y, and vice versa.
*/
protected void addedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
Resource subject = null;
Resource object = null;
if (stmt.getSubject().isResource()) {
subject = stmt.getSubject().asResource();
if (tboxModel.containsResource(subject) || subject.isAnon()) {
log.debug("the subject of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the subject of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
if (stmt.getObject().isResource()) {
object = stmt.getObject().asResource();
if (tboxModel.containsResource(object) || object.isAnon()) {
log.debug("the object of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the object of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
Statement opposite = ResourceFactory.createStatement(object, OWL.sameAs, subject);
addInference(opposite,inferenceModel,true);
generateSameAsInferences(subject, object, inferenceModel);
generateSameAsInferences(object, subject, inferenceModel);
}
/**
* Materializes inferences based on the owl:sameAs relationship.
*
* If it is removed that x is sameAs y, then remove y sameAs x from
* the inference graph and then recompute the inferences for x and
* y based on their respective assertions.
* that x owl:sameAs y, then all asserted and inferred
*/
protected void removedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
Resource subject = null;
Resource object = null;
if (stmt.getSubject().isResource()) {
subject = stmt.getSubject().asResource();
if (tboxModel.containsResource(subject) || subject.isAnon()) {
log.debug("the subject of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the subject of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
if (stmt.getObject().isResource()) {
object = stmt.getObject().asResource();
if (tboxModel.containsResource(object) || object.isAnon()) {
log.debug("the object of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the object of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel);
sameIndividuals.addAll(getSameIndividuals(object, inferenceModel));
Iterator<Resource> sIter1 = sameIndividuals.iterator();
while (sIter1.hasNext()) {
removeInferencesForIndividual(sIter1.next(), inferenceModel);
}
Iterator<Resource> sIter2 = sameIndividuals.iterator();
while (sIter2.hasNext()) {
computeInferencesForIndividual(sIter2.next(), inferenceModel);
}
}
protected void doSameAsForAddedABoxAssertion(Statement stmt, Model inferenceModel){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Resource subject = sameIter.next();
Statement sameStmt =
ResourceFactory.createStatement(subject,stmt.getPredicate(),stmt.getObject());
addInference(sameStmt,inferenceModel,false);
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
/**
* Materializes inferences based on the owl:inverseOf relationship.
* and owl:sameAs
*
* If it is added that x prop1 y, and prop2 is an inverseOf prop1
* then add y prop2 x to the inference graph, if it is not already in
* the assertions graph.
*
*/
protected void addedABoxAssertion(Statement stmt, Model inferenceModel) {
if (!stmt.getObject().isLiteral()) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
Property inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(
stmt.getObject().asResource(), inverseProp, stmt.getSubject());
addInference(infStmt,inferenceModel,true);
}
}
doSameAsForAddedABoxAssertion( stmt, inferenceModel);
}
void doSameAsForRemovedABoxAssertion(Statement stmt, Model inferenceModel){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Statement stmtSame =
ResourceFactory.createStatement(sameIter.next(),
stmt.getPredicate(),
stmt.getObject());
removeInference(stmtSame,inferenceModel,false,true);
}
}
protected void generateSameAsInferences(Resource ind1, Resource ind2, Model inferenceModel) { protected void generateSameAsInferences(Resource ind1, Resource ind2, Model inferenceModel) {
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
@ -686,11 +850,13 @@ public class SimpleReasoner extends StatementListener {
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
try { try {
Iterator<Statement> iter = unionModel.listStatements(ind1, (Property) null, (RDFNode) null); Iterator<Statement> iter =
unionModel.listStatements(ind1, (Property) null, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (stmt.getObject() == null) continue; if (stmt.getObject() == null) continue;
Statement infStmt = ResourceFactory.createStatement(ind2,stmt.getPredicate(),stmt.getObject()); Statement infStmt =
ResourceFactory.createStatement(ind2,stmt.getPredicate(),stmt.getObject());
addInference(infStmt, inferenceModel,true); addInference(infStmt, inferenceModel,true);
} }
} finally { } finally {
@ -700,7 +866,7 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
/* /**
* Remove inferences for individual * Remove inferences for individual
*/ */
protected void removeInferencesForIndividual(Resource ind, Model inferenceModel) { protected void removeInferencesForIndividual(Resource ind, Model inferenceModel) {
@ -709,7 +875,8 @@ public class SimpleReasoner extends StatementListener {
inferenceModel.enterCriticalSection(Lock.READ); inferenceModel.enterCriticalSection(Lock.READ);
try { try {
Iterator<Statement> iter = inferenceModel.listStatements(ind, (Property) null, (RDFNode) null); Iterator<Statement> iter =
inferenceModel.listStatements(ind, (Property) null, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
individualInferences.add(iter.next()); individualInferences.add(iter.next());
@ -728,7 +895,7 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
/* /**
* compute inferences for individual * compute inferences for individual
*/ */
protected void computeInferencesForIndividual(Resource ind, Model inferenceModel) { protected void computeInferencesForIndividual(Resource ind, Model inferenceModel) {
@ -749,17 +916,21 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
// Returns true if it is entailed by class subsumption that /**
// subject is of type cls; otherwise returns false. * Returns true if it is entailed by class subsumption that
* subject is of type cls; otherwise returns false.
*/
protected boolean entailedType(Resource subject, Resource cls) { protected boolean entailedType(Resource subject, Resource cls) {
return entailedType(subject, cls, null); return entailedType(subject, cls, null);
} }
// Returns true if it is entailed by class subsumption that /**
// subject is of type cls; otherwise returns false. * Returns true if it is entailed by class subsumption that
// remainingTypeURIs is an optional list of asserted type URIs for the subject * subject is of type cls; otherwise returns false.
// resource, and may be null. Supplying a precompiled list can yield performance * remainingTypeURIs is an optional list of asserted type URIs for the subject
// improvement when this method is called repeatedly for the same subject. * resource, and may be null. Supplying a precompiled list can yield performance
* improvement when this method is called repeatedly for the same subject.
*/
protected boolean entailedType(Resource subject, Resource cls, List<String> remainingTypeURIs) { protected boolean entailedType(Resource subject, Resource cls, List<String> remainingTypeURIs) {
List<Resource> subClasses = getSubClasses(cls); List<Resource> subClasses = getSubClasses(cls);
@ -770,7 +941,8 @@ public class SimpleReasoner extends StatementListener {
} }
} }
List<String> typeURIs = (remainingTypeURIs == null) ? getRemainingAssertedTypeURIs(subject) : remainingTypeURIs; List<String> typeURIs = (remainingTypeURIs == null) ?
getRemainingAssertedTypeURIs(subject) : remainingTypeURIs;
for (String typeURI : typeURIs) { for (String typeURI : typeURIs) {
if (!typeURI.equals(cls.getURI()) && subClassURIs.contains(typeURI)) { if (!typeURI.equals(cls.getURI()) && subClassURIs.contains(typeURI)) {
@ -814,10 +986,12 @@ public class SimpleReasoner extends StatementListener {
List<Resource> subClasses = new ArrayList<Resource>(); List<Resource> subClasses = new ArrayList<Resource>();
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
try { try {
Iterator<Statement> iter = tboxModel.listStatements((Resource) null, RDFS.subClassOf, cls); Iterator<Statement> iter =
tboxModel.listStatements((Resource) null, RDFS.subClassOf, cls);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (stmt.getSubject() == null || stmt.getSubject().asResource().getURI() == null) continue; if (stmt.getSubject() == null
|| stmt.getSubject().asResource().getURI() == null) continue;
if (!subClasses.contains(stmt.getSubject())) { if (!subClasses.contains(stmt.getSubject())) {
subClasses.add(stmt.getSubject()); subClasses.add(stmt.getSubject());
} }
@ -859,7 +1033,8 @@ public class SimpleReasoner extends StatementListener {
iter = tboxModel.listStatements((Resource) null, OWL.equivalentClass, cls); iter = tboxModel.listStatements((Resource) null, OWL.equivalentClass, cls);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (stmt.getSubject() == null || stmt.getSubject().asResource().getURI() == null) continue; if (stmt.getSubject() == null
|| stmt.getSubject().asResource().getURI() == null) continue;
if (!superClasses.contains(stmt.getSubject())) { if (!superClasses.contains(stmt.getSubject())) {
superClasses.add(stmt.getSubject()); superClasses.add(stmt.getSubject());
} }
@ -870,8 +1045,10 @@ public class SimpleReasoner extends StatementListener {
} }
} }
// Returns true if the triple is entailed by inverse property /**
// reasoning or sameAs reasoning; otherwise returns false. * Returns true if the triple is entailed by inverse property
* reasoning or sameAs reasoning; otherwise returns false.
*/
protected boolean entailedStatement(Statement stmt) { protected boolean entailedStatement(Statement stmt) {
//TODO think about checking class subsumption here (for convenience) //TODO think about checking class subsumption here (for convenience)
@ -883,8 +1060,9 @@ public class SimpleReasoner extends StatementListener {
try { try {
while (iIter.hasNext()) { while (iIter.hasNext()) {
Property invProp = iIter.next(); Property invProp = iIter.next();
Statement invStmt =
Statement invStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), invProp, stmt.getSubject()); ResourceFactory.createStatement(stmt.getObject().asResource(),
invProp, stmt.getSubject());
if (aboxModel.contains(invStmt)) { if (aboxModel.contains(invStmt)) {
return true; return true;
} }
@ -895,7 +1073,9 @@ public class SimpleReasoner extends StatementListener {
} }
// individuals sameAs each other // individuals sameAs each other
List<Resource> sameIndividuals = getSameIndividuals(stmt.getSubject().asResource(),inferenceModel); if( doSameAs ){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(),inferenceModel);
Iterator<Resource> rIter = sameIndividuals.iterator(); Iterator<Resource> rIter = sameIndividuals.iterator();
if (rIter.hasNext()) { if (rIter.hasNext()) {
aboxModel.enterCriticalSection(Lock.READ); aboxModel.enterCriticalSection(Lock.READ);
@ -910,12 +1090,13 @@ public class SimpleReasoner extends StatementListener {
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
}
} }
return false; return false;
} }
/* /**
* Returns a list of properties that are inverses of the property * Returns a list of properties that are inverses of the property
* in the given statement. * in the given statement.
*/ */
@ -938,7 +1119,8 @@ public class SimpleReasoner extends StatementListener {
} }
if (!stmt.getObject().isResource()) { if (!stmt.getObject().isResource()) {
log.debug("The predicate of this statement is an object property, but the object is not a resource."); log.debug("The predicate of this statement is an object property, "
+"but the object is not a resource.");
return inverses; return inverses;
} }
@ -978,7 +1160,9 @@ public class SimpleReasoner extends StatementListener {
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (!stmt.getObject().isResource()) continue; if (!stmt.getObject().isResource()) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject()); Statement infStmt =
ResourceFactory.createStatement(stmt.getObject().asResource(),
inverseProp, stmt.getSubject());
inferences.add(infStmt); inferences.add(infStmt);
} }
} finally { } finally {
@ -988,7 +1172,7 @@ public class SimpleReasoner extends StatementListener {
return inferences; return inferences;
} }
/* /**
* Add an inference from the inference model * Add an inference from the inference model
* *
* Adds the inference to the inference model if it is not already in * Adds the inference to the inference model if it is not already in
@ -1010,17 +1194,22 @@ public class SimpleReasoner extends StatementListener {
} }
if (handleSameAs) { if (handleSameAs) {
List<Resource> sameIndividuals = getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel); List<Resource> sameIndividuals =
getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator(); Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) { while (sameIter.hasNext()) {
Resource subject = sameIter.next(); Resource subject = sameIter.next();
Statement sameStmt = ResourceFactory.createStatement(subject,infStmt.getPredicate(),infStmt.getObject()); Statement sameStmt =
if (subject.equals(infStmt.getObject()) && OWL.sameAs.equals(infStmt.getPredicate())) { ResourceFactory.createStatement(subject,infStmt.getPredicate(),
infStmt.getObject());
if (subject.equals(infStmt.getObject())
&& OWL.sameAs.equals(infStmt.getPredicate())) {
continue; continue;
} }
if (!inferenceModel.contains(sameStmt) && !aboxModel.contains(sameStmt)) { if (!inferenceModel.contains(sameStmt)
&& !aboxModel.contains(sameStmt)) {
inferenceModel.add(sameStmt); inferenceModel.add(sameStmt);
} }
} }
@ -1033,7 +1222,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/* /**
* Remove an inference from the inference model * Remove an inference from the inference model
* *
* Removes the inference if it is not entailed by the abox model * Removes the inference if it is not entailed by the abox model
@ -1050,7 +1239,9 @@ public class SimpleReasoner extends StatementListener {
inferenceModel.enterCriticalSection(Lock.WRITE); inferenceModel.enterCriticalSection(Lock.WRITE);
try { try {
if ( (!checkEntailment || !entailedStatement(infStmt)) && inferenceModel.contains(infStmt)) { if ( (!checkEntailment
|| !entailedStatement(infStmt))
&& inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt); inferenceModel.remove(infStmt);
} }
} finally { } finally {
@ -1060,12 +1251,17 @@ public class SimpleReasoner extends StatementListener {
if (handleSameAs) { if (handleSameAs) {
inferenceModel.enterCriticalSection(Lock.WRITE); inferenceModel.enterCriticalSection(Lock.WRITE);
try { try {
List<Resource> sameIndividuals = getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel); List<Resource> sameIndividuals =
getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator(); Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) { while (sameIter.hasNext()) {
Statement infStmtSame = ResourceFactory.createStatement(sameIter.next(), infStmt.getPredicate(), infStmt.getObject()); Statement infStmtSame =
if ((!checkEntailment || !entailedStatement(infStmtSame)) && inferenceModel.contains(infStmtSame)) { ResourceFactory.createStatement(sameIter.next(),
infStmt.getPredicate(), infStmt.getObject());
if ((!checkEntailment
|| !entailedStatement(infStmtSame))
&& inferenceModel.contains(infStmtSame)) {
inferenceModel.remove(infStmtSame); inferenceModel.remove(infStmtSame);
} }
} }
@ -1076,7 +1272,7 @@ public class SimpleReasoner extends StatementListener {
} }
/* /**
* Find the most specific types (classes) of an individual and * Find the most specific types (classes) of an individual and
* infer them for the individual with the mostSpecificType * infer them for the individual with the mostSpecificType
* annotation. * annotation.
@ -1332,7 +1528,7 @@ public class SimpleReasoner extends StatementListener {
// DeltaComputer // DeltaComputer
/* /**
* Asynchronous reasoning mode (DeltaComputer) is used in the case of batch removals. * Asynchronous reasoning mode (DeltaComputer) is used in the case of batch removals.
*/ */
public boolean isABoxReasoningAsynchronous() { public boolean isABoxReasoningAsynchronous() {
@ -1528,168 +1724,7 @@ public class SimpleReasoner extends StatementListener {
/* **** sameAs below this line **** */ /**
/*
* Materializes inferences based on the owl:sameAs relationship.
*
* If it is added that x owl:sameAs y, then all asserted and inferred
* statements about x will become inferred about y if they are not already
* asserted about y, and vice versa.
*/
protected void addedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
Resource subject = null;
Resource object = null;
if (stmt.getSubject().isResource()) {
subject = stmt.getSubject().asResource();
if (tboxModel.containsResource(subject) || subject.isAnon()) {
log.debug("the subject of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the subject of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
if (stmt.getObject().isResource()) {
object = stmt.getObject().asResource();
if (tboxModel.containsResource(object) || object.isAnon()) {
log.debug("the object of this sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the object of this sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
Statement opposite = ResourceFactory.createStatement(object, OWL.sameAs, subject);
addInference(opposite,inferenceModel,true);
generateSameAsInferences(subject, object, inferenceModel);
generateSameAsInferences(object, subject, inferenceModel);
}
/*
* Materializes inferences based on the owl:sameAs relationship.
*
* If it is removed that x is sameAs y, then remove y sameAs x from
* the inference graph and then recompute the inferences for x and
* y based on their respective assertions.
* that x owl:sameAs y, then all asserted and inferred
*/
protected void removedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
Resource subject = null;
Resource object = null;
if (stmt.getSubject().isResource()) {
subject = stmt.getSubject().asResource();
if (tboxModel.containsResource(subject) || subject.isAnon()) {
log.debug("the subject of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the subject of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
if (stmt.getObject().isResource()) {
object = stmt.getObject().asResource();
if (tboxModel.containsResource(object) || object.isAnon()) {
log.debug("the object of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
return;
}
} else {
log.warn("the object of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
return;
}
List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel);
sameIndividuals.addAll(getSameIndividuals(object, inferenceModel));
Iterator<Resource> sIter1 = sameIndividuals.iterator();
while (sIter1.hasNext()) {
removeInferencesForIndividual(sIter1.next(), inferenceModel);
}
Iterator<Resource> sIter2 = sameIndividuals.iterator();
while (sIter2.hasNext()) {
computeInferencesForIndividual(sIter2.next(), inferenceModel);
}
}
protected void doSameAsForAddedABoxAssertion(Statement stmt, Model inferenceModel){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Resource subject = sameIter.next();
Statement sameStmt =
ResourceFactory.createStatement(subject,stmt.getPredicate(),stmt.getObject());
addInference(sameStmt,inferenceModel,false);
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
/*
*
* Materializes inferences based on the owl:inverseOf relationship.
* and owl:sameAs
*
* If it is added that x prop1 y, and prop2 is an inverseOf prop1
* then add y prop2 x to the inference graph, if it is not already in
* the assertions graph.
*
*/
protected void addedABoxAssertion(Statement stmt, Model inferenceModel) {
if (!stmt.getObject().isLiteral()) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
Property inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(
stmt.getObject().asResource(), inverseProp, stmt.getSubject());
addInference(infStmt,inferenceModel,true);
}
}
doSameAsForAddedABoxAssertion( stmt, inferenceModel);
}
void doSameAsForRemovedABoxAssertion(Statement stmt, Model inferenceModel){
List<Resource> sameIndividuals =
getSameIndividuals(stmt.getSubject().asResource(), inferenceModel);
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Statement stmtSame =
ResourceFactory.createStatement(sameIter.next(),
stmt.getPredicate(),
stmt.getObject());
removeInference(stmtSame,inferenceModel,false,true);
}
}
/*
* Utility method for logging * Utility method for logging
*/ */
public static String stmtString(Statement statement) { public static String stmtString(Statement statement) {

117
webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerSameAsTest.java
View file

@ -91,6 +91,37 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
Assert.assertFalse(aBox.contains(b,S,literal1)); Assert.assertFalse(aBox.contains(b,S,literal1));
Assert.assertFalse(aBox.contains(a,Q,d)); Assert.assertFalse(aBox.contains(a,Q,d));
Assert.assertFalse(aBox.contains(a,T,literal2)); Assert.assertFalse(aBox.contains(a,T,literal2));
//run same test with sameAs = false
inf = ModelFactory.createDefaultModel();
aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
SimpleReasoner sres = new SimpleReasoner(tBox,aBox,inf);
sres.setSameAsEnabled( false );
aBox.register(sres);
a = aBox.createResource("http://test.vivo/a");
b = aBox.createResource("http://test.vivo/b");
c = aBox.createResource("http://test.vivo/c");
d = aBox.createResource("http://test.vivo/d");
aBox.add(a,P,c);
aBox.add(a,S,literal1);
aBox.add(b,Q,d);
aBox.add(b,T,literal2);
aBox.add(a,OWL.sameAs,b);
//these are now false since sameAs is off
Assert.assertFalse(inf.contains(b,OWL.sameAs,a));
Assert.assertFalse(inf.contains(b,P,c));
Assert.assertFalse(inf.contains(b,S,literal1));
Assert.assertFalse(inf.contains(a,Q,d));
Assert.assertFalse(inf.contains(a,T,literal2));
//these still shouldn't be in the abox
Assert.assertFalse(aBox.contains(b,OWL.sameAs,a));
Assert.assertFalse(aBox.contains(b,P,c));
Assert.assertFalse(aBox.contains(b,S,literal1));
Assert.assertFalse(aBox.contains(a,Q,d));
Assert.assertFalse(aBox.contains(a,T,literal2));
} }
/* /*
@ -247,6 +278,92 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
Assert.assertFalse(inf.contains(f,T,literal2)); Assert.assertFalse(inf.contains(f,T,literal2));
} }
/**
* test of enableSameAs( false )
*/
@Test
public void disabledSameAs() {
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
OntProperty P = tBox.createObjectProperty("http://test.vivo/P");
P.setLabel("property P", "en-US");
OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
Q.setLabel("property Q", "en-US");
OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
S.setLabel("property S", "en-US");
OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
T.setLabel("property T", "en-US");
Literal literal1 = tBox.createLiteral("Literal value 1");
Literal literal2 = tBox.createLiteral("Literal value 2");
// this is the model to receive inferences
Model inf = ModelFactory.createDefaultModel();
// create an ABox and register the SimpleReasoner listener with it
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
aBox.register(new SimpleReasoner(tBox, aBox, inf));
// Individuals a, b, c and d
Resource a = aBox.createResource("http://test.vivo/a");
Resource b = aBox.createResource("http://test.vivo/b");
Resource c = aBox.createResource("http://test.vivo/c");
Resource d = aBox.createResource("http://test.vivo/d");
aBox.add(a,P,c);
aBox.add(a,S,literal1);
aBox.add(b,Q,d);
aBox.add(b,T,literal2);
aBox.add(a,OWL.sameAs,b);
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
Assert.assertTrue(inf.contains(b,P,c));
Assert.assertTrue(inf.contains(b,S,literal1));
Assert.assertTrue(inf.contains(a,Q,d));
Assert.assertTrue(inf.contains(a,T,literal2));
Assert.assertFalse(aBox.contains(b,OWL.sameAs,a));
Assert.assertFalse(aBox.contains(b,P,c));
Assert.assertFalse(aBox.contains(b,S,literal1));
Assert.assertFalse(aBox.contains(a,Q,d));
Assert.assertFalse(aBox.contains(a,T,literal2));
//run same test with sameAs = false
inf = ModelFactory.createDefaultModel();
aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
SimpleReasoner sres = new SimpleReasoner(tBox,aBox,inf);
sres.setSameAsEnabled( false );
aBox.register(sres);
a = aBox.createResource("http://test.vivo/a");
b = aBox.createResource("http://test.vivo/b");
c = aBox.createResource("http://test.vivo/c");
d = aBox.createResource("http://test.vivo/d");
aBox.add(a,P,c);
aBox.add(a,S,literal1);
aBox.add(b,Q,d);
aBox.add(b,T,literal2);
aBox.add(a,OWL.sameAs,b);
//these are now false since sameAs is off
Assert.assertFalse(inf.contains(b,OWL.sameAs,a));
Assert.assertFalse(inf.contains(b,P,c));
Assert.assertFalse(inf.contains(b,S,literal1));
Assert.assertFalse(inf.contains(a,Q,d));
Assert.assertFalse(inf.contains(a,T,literal2));
//these still shouldn't be in the abox
Assert.assertFalse(aBox.contains(b,OWL.sameAs,a));
Assert.assertFalse(aBox.contains(b,P,c));
Assert.assertFalse(aBox.contains(b,S,literal1));
Assert.assertFalse(aBox.contains(a,Q,d));
Assert.assertFalse(aBox.contains(a,T,literal2));
}
/* /*
* sameAs with datatype properties * sameAs with datatype properties
*/ */