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NIHVIVO-3293 add inverse property reasoning to SimpleReasoner

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This commit is contained in:
stellamit 2012-06-04 21:47:23 +00:00
parent a31b91bddd
commit 20b04e3e8e
2 changed files with 897 additions and 49 deletions
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459
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
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@ -14,6 +14,7 @@ import com.hp.hpl.jena.ontology.AnnotationProperty;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory;
@ -25,6 +26,7 @@ import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Literal;
import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.Property;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory;
@ -32,6 +34,7 @@ import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.JenaException;
import com.hp.hpl.jena.shared.Lock;
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.RDFS;
@ -126,12 +129,13 @@ public class SimpleReasoner extends StatementListener {
*/
@Override
public void addedStatement(Statement stmt) {
try {
if (stmt.getPredicate().equals(RDF.type)) {
addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>());
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
}
} else {
addedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.ADD,stmt);
@ -150,8 +154,9 @@ public class SimpleReasoner extends StatementListener {
public void removedStatement(Statement stmt) {
try {
if (!isInterestedInRemovedStatement(stmt)) { return; }
// if (!isInterestedInRemovedStatement(stmt)) { return; }
// interested in all of them now that we are doing inverse
// property reasoning
handleRemovedStatement(stmt);
} catch (Exception e) {
@ -160,7 +165,6 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* Synchronized part of removedStatement. Interacts
* with DeltaComputer.
@ -175,7 +179,9 @@ public class SimpleReasoner extends StatementListener {
if (stmt.getPredicate().equals(RDF.type)) {
removedABoxTypeAssertion(stmt, inferenceModel);
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
}
} else {
removedABoxAssertion(stmt, inferenceModel);
}
doPlugins(ModelUpdate.Operation.RETRACT,stmt);
}
}
@ -184,29 +190,32 @@ public class SimpleReasoner extends StatementListener {
* Performs incremental ABox reasoning based
* on changes to the class hierarchy.
*
* Handles rdfs:subclassOf, owl:equivalentClass,
* Handles rdfs:subclassOf, owl:equivalentClass, and owl:inverseOf
*/
public void addedTBoxStatement(Statement stmt) {
try {
if (!(stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) || stmt.getPredicate().equals(OWL.inverseOf))) {
return;
}
try {
log.debug("added TBox assertion = " + stmt.toString());
log.debug("added TBox assertion = " + stmt.toString());
if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
if (stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass)) {
// ignore anonymous classes
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return;
}
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
if (subject == null) {
log.debug("didn't find subject class in the tbox: " + (stmt.getSubject()).getURI());
@ -220,13 +229,27 @@ public class SimpleReasoner extends StatementListener {
}
if (stmt.getPredicate().equals(RDFS.subClassOf)) {
addedSubClass(subject,object,inferenceModel);
addedSubClass(subject,object,inferenceModel);
} else {
// equivalent class is the same as subclass in both directions
addedSubClass(subject,object,inferenceModel);
addedSubClass(object,subject,inferenceModel);
// equivalent class is the same as subclass in both directions
addedSubClass(subject,object,inferenceModel);
addedSubClass(object,subject,inferenceModel);
}
} else {
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
return;
}
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (prop2 == null) {
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
return;
}
}
addedInverseProperty(prop1, prop2, inferenceModel);
}
} catch (Exception e) {
// don't stop the edit if there's an exception
log.error("Exception while adding inference(s): " + e.getMessage());
@ -237,29 +260,33 @@ public class SimpleReasoner extends StatementListener {
* Performs incremental ABox reasoning based
* on changes to the class hierarchy.
*
* Handles rdfs:subclassOf, owl:equivalentClass,
* Handles rdfs:subclassOf, owl:equivalentClass, and owl:inverseOf
*/
public void removedTBoxStatement(Statement stmt) {
public void removedTBoxStatement(Statement stmt) {
try {
log.debug("removed TBox assertion = " + stmt.toString());
if (!(stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) || stmt.getPredicate().equals(OWL.inverseOf))) {
return;
}
log.debug("removed TBox assertion = " + stmt.toString());
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
// ignore anonymous classes
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return;
}
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
if (subject == null) {
log.debug("didn't find subject class in the tbox: " + (stmt.getSubject()).getURI());
@ -279,7 +306,21 @@ public class SimpleReasoner extends StatementListener {
removedSubClass(subject,object,inferenceModel);
removedSubClass(object,subject,inferenceModel);
}
}
} else {
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
return;
}
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (prop2 == null) {
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
return;
}
removedInverseProperty(prop1, prop2, inferenceModel);
}
} catch (Exception e) {
// don't stop the edit if there's an exception
log.error("Exception while removing inference(s): " + e.getMessage());
@ -376,6 +417,45 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* Performs incremental property-based reasoning.
*
* Materializes inferences based on the owl:inverseOf relationship.
*
* 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.
*/
public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
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());
aboxModel.enterCriticalSection(Lock.READ);
try {
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(stmt)) {
inferenceModel.remove(stmt);
}
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt) ) {
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
} finally {
aboxModel.leaveCriticalSection();
}
}
}
/*
* 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
@ -386,8 +466,7 @@ public class SimpleReasoner extends StatementListener {
tboxModel.enterCriticalSection(Lock.READ);
try {
try {
OntClass cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) {
@ -453,13 +532,50 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* Performs incremental property-based reasoning.
*
* Retracts inferences based on the owl:inverseOf relationship.
*
* If it is removed that x prop1 y, and prop2 is an inverseOf prop1
* then remove y prop2 x from the inference graph, unless it is
* otherwise entailed by the assertions graph independently of
* this removed statement.
*/
public void removedABoxAssertion(Statement stmt, Model inferenceModel) {
List<OntProperty> inverseProperties = getInverseProperties(stmt);
Iterator<OntProperty> inverseIter = inverseProperties.iterator();
while (inverseIter.hasNext()) {
OntProperty inverseProp = inverseIter.next();
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!entailedInverseStmt(infStmt) && inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt);
}
// if a statement has been removed that is otherwise entailed,
// add it to the inference graph.
if (entailedInverseStmt(stmt) && !inferenceModel.contains(stmt)) {
inferenceModel.add(stmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
}
// Returns true if it is entailed by class subsumption that
// subject is of type cls; otherwise returns false.
protected boolean entailedType(Resource subject, OntClass cls) {
aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.READ);
try {
try {
List<OntClass> subclasses = null;
subclasses = (cls.listSubClasses(false)).toList();
subclasses.addAll((cls.listEquivalentClasses()).toList());
@ -477,12 +593,101 @@ public class SimpleReasoner extends StatementListener {
} catch (Exception e) {
log.debug("exception in method entailedType: " + e.getMessage());
return false;
} finally {
} finally {
aboxModel.leaveCriticalSection();
tboxModel.leaveCriticalSection();
}
}
// Returns true if the triple is entailed by inverse property
// reasoning; otherwise returns false.
protected boolean entailedInverseStmt(Statement stmt) {
ExtendedIterator <? extends OntProperty> iter = null;
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().asResource().getURI());
iter = prop.listInverse();
} finally {
tboxModel.leaveCriticalSection();
}
aboxModel.enterCriticalSection(Lock.READ);
try {
while (iter.hasNext()) {
Property invProp = iter.next();
// not reasoning on properties in the OWL, RDF or RDFS namespace
if ((invProp.getNameSpace()).equals(OWL.NS) ||
(invProp.getNameSpace()).equals(RDFS.getURI()) ||
(invProp.getNameSpace()).equals(RDF.getURI())) {
continue;
}
Statement invStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), invProp, stmt.getSubject());
if (aboxModel.contains(invStmt)) {
return true;
}
}
return false;
} finally {
aboxModel.leaveCriticalSection();
}
}
/*
* Returns a list of properties that are inverses of the property
* in the given statement.
*/
protected List<OntProperty> getInverseProperties(Statement stmt) {
List<OntProperty> inverses = new ArrayList<OntProperty>();
if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
return inverses;
}
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
if (!prop.isObjectProperty()) {
return inverses;
}
if (!stmt.getObject().isResource()) {
log.warn("The predicate of this statement is an object property, but the object is not a resource.");
return inverses;
}
// not reasoning on properties in the OWL, RDF or RDFS namespace
if ((prop.getNameSpace()).equals(OWL.NS) ||
(prop.getNameSpace()).equals(RDFS.getURI()) ||
(prop.getNameSpace()).equals(RDF.getURI())) {
return inverses;
}
ExtendedIterator <? extends OntProperty> iter = prop.listInverse();
while (iter.hasNext()) {
OntProperty invProp = iter.next();
if ((invProp.getNameSpace()).equals(OWL.NS) ||
(invProp.getNameSpace()).equals(RDFS.getURI()) ||
(invProp.getNameSpace()).equals(RDF.getURI())) {
continue;
}
inverses.add(invProp);
}
}
} finally {
tboxModel.leaveCriticalSection();
}
return inverses;
}
/*
* 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
@ -566,6 +771,112 @@ public class SimpleReasoner extends StatementListener {
}
}
/*
* If it is added that P is an inverse of Q, then:
* 1. For each statement involving predicate P in
* the assertions model add the inverse statement
* to the inference model if that inverse is
* in the assertions model.
*
* 2. Repeat the same for predicate Q.
*
*/
public void addedInverseProperty(OntProperty prop1, OntProperty prop2, Model inferenceModel) {
if ( !prop1.isObjectProperty() || !prop2.isObjectProperty() ) {
log.warn("The subject and object of the inverseOf statement are not both object properties. No inferencing will be performed. property 1: " + prop1.getURI() + " property 2:" + prop2.getURI());
return;
}
Model inferences = ModelFactory.createDefaultModel();
inferences.add(generateInverseInferences(prop1, prop2));
inferences.add(generateInverseInferences(prop2, prop1));
if (inferences.isEmpty()) return;
aboxModel.enterCriticalSection(Lock.READ);
try {
StmtIterator iter = inferences.listStatements();
while (iter.hasNext()) {
Statement infStmt = iter.next();
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)) {
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} finally {
aboxModel.leaveCriticalSection();
}
}
public Model generateInverseInferences(OntProperty prop, OntProperty inverseProp) {
Model inferences = ModelFactory.createDefaultModel();
aboxModel.enterCriticalSection(Lock.READ);
try {
StmtIterator iter = aboxModel.listStatements((Resource) null, prop, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!stmt.getObject().isResource()) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getObject().asResource(), inverseProp, stmt.getSubject());
inferences.add(infStmt);
}
} finally {
aboxModel.leaveCriticalSection();
}
return inferences;
}
/*
* If it is removed that P is an inverse of Q, then:
* 1. For each statement involving predicate P in
* the abox assertions model remove the inverse
* statement from the inference model unless
* that statement is otherwise entailed.
*
* 2. Repeat the same for predicate Q.
*/
public void removedInverseProperty(OntProperty prop1, OntProperty prop2, Model inferenceModel) {
if ( !prop1.isObjectProperty() || !prop2.isObjectProperty() ) {
log.warn("The subject and object of the inverseOf statement are not both object properties. No inferencing will be performed. property 1: " + prop1.getURI() + " property 2:" + prop2.getURI());
return;
}
Model inferences = ModelFactory.createDefaultModel();
inferences.add(generateInverseInferences(prop1, prop2));
inferences.add(generateInverseInferences(prop2, prop1));
if (inferences.isEmpty()) return;
StmtIterator iter = inferences.listStatements();
while (iter.hasNext()) {
Statement infStmt = iter.next();
if (entailedInverseStmt(infStmt)) {
continue;
}
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
}
/*
* Find the most specific types (classes) of an individual and
* indicate them for the individual with the mostSpecificType
@ -740,13 +1051,12 @@ public class SimpleReasoner extends StatementListener {
* inference models.
*/
protected synchronized void recomputeABox() {
HashSet<String> unknownTypes = new HashSet<String>();
// recompute the inferences
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
try {
log.info("Computing class-based ABox inferences.");
log.info("Computing ABox inferences.");
inferenceRebuildModel.removeAll();
int numStmts = 0;
@ -784,6 +1094,57 @@ public class SimpleReasoner extends StatementListener {
log.info("Still computing class-based ABox inferences...");
}
if (stopRequested) {
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
return;
}
}
log.info("Finished computing class-based ABox inferences");
Iterator<Statement> invStatements = null;
tboxModel.enterCriticalSection(Lock.READ);
try {
invStatements = tboxModel.listStatements((Resource) null, OWL.inverseOf, (Resource) null);
} finally {
tboxModel.leaveCriticalSection();
}
while (invStatements.hasNext()) {
Statement stmt = invStatements.next();
try {
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
continue;
}
OntProperty prop2 = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (prop2 == null) {
log.debug("didn't find object property in the tbox: " + ((Resource)stmt.getObject()).getURI());
continue;
}
addedInverseProperty(prop1, prop2, inferenceRebuildModel);
} catch (NullPointerException npe) {
log.error("a NullPointerException was received while recomputing the ABox inferences. Halting inference computation.");
return;
} catch (JenaException je) {
if (je.getMessage().equals("Statement models must no be null")) {
log.error("Exception while recomputing ABox inference model. Halting inference computation.", je);
return;
}
log.error("Exception while recomputing ABox inference model: ", je);
} catch (Exception e) {
log.error("Exception while recomputing ABox inference model: ", e);
}
numStmts++;
if ((numStmts % 10000) == 0) {
log.info("Still computing property-based ABox inferences...");
}
if (stopRequested) {
log.info("a stopRequested signal was received during recomputeABox. Halting Processing.");
return;
@ -798,7 +1159,7 @@ public class SimpleReasoner extends StatementListener {
inferenceRebuildModel.leaveCriticalSection();
}
log.info("Finished computing class-based ABox inferences");
log.info("Finished computing property-based ABox inferences");
// reflect the recomputed inferences into the application
// inference model.