NIHVIVO-2314 add support for property-based inferencing to the SimpleReasoner
This commit is contained in:
stellamit
parent
a1e87a10b9
commit
87b87c8edf
2 changed files with 896 additions and 275 deletions
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@ -24,11 +24,12 @@ import com.hp.hpl.jena.rdf.model.Statement;
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import com.hp.hpl.jena.rdf.model.StmtIterator;
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import com.hp.hpl.jena.shared.Lock;
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import com.hp.hpl.jena.util.iterator.ExtendedIterator;
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import com.hp.hpl.jena.vocabulary.OWL;
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import com.hp.hpl.jena.vocabulary.RDF;
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import com.hp.hpl.jena.vocabulary.RDFS;
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/**
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* Allows for instant incremental materialization or retraction of RDFS-
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* Allows for real-time incremental materialization or retraction of RDFS-
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* style class and property subsumption based ABox inferences as statements
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* are added to or removed from the (ABox or TBox) knowledge base.
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*
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@ -77,41 +78,39 @@ public class SimpleReasoner extends StatementListener {
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}
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/*
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* Performs incremental selected ABox reasoning based
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* on a new type assertion (assertion that an individual
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* is of a certain type) added to the ABox.
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*
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* Performs selected incremental ABox reasoning based
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* on the addition of a new statement (aka assertion)
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* to the ABox.
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*/
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@Override
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public void addedStatement(Statement stmt) {
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try {
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if (stmt.getPredicate().equals(RDF.type)) {
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addedType(stmt, inferenceModel);
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addedABoxTypeAssertion(stmt, inferenceModel);
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} else {
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addedABoxAssertion(stmt,inferenceModel);
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}
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} catch (Exception e) {
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// don't stop the edit if there's an exception
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log.error("Exception while adding incremental inferences: ", e);
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log.error("Exception while adding inferences: ", e);
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}
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}
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/*
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* Performs incremental selected ABox reasoning based
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* on a removed type assertion (assertion that an individual
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* is of a certain type) from the ABox.
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*
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* Performs selected incremental ABox reasoning based
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* on the retraction of a statement (aka assertion)
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* from the ABox.
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*/
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@Override
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public void removedStatement(Statement stmt) {
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try {
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if (stmt.getPredicate().equals(RDF.type)) {
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removedType(stmt);
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removedABoxTypeAssertion(stmt, inferenceModel);
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} else {
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removedABoxAssertion(stmt, inferenceModel);
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}
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} catch (Exception e) {
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// don't stop the edit if there's an exception
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log.error("Exception while retracting inferences: ", e);
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@ -120,92 +119,110 @@ public class SimpleReasoner extends StatementListener {
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/*
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* Performs incremental selected ABox reasoning based
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* on changes to the class hierarchy.
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*
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* Handles subclassOf and equivalentClass assertions
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* on changes to the class or property hierarchy.
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*
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* Handles rdfs:subclassOf, owl:equivalentClass,
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* rdfs:subPropertyOf and owl:equivalentProperty assertions
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*/
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public void addedTBoxStatement(Statement stmt) {
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addedTBoxStatement(stmt, inferenceModel);
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}
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public void addedTBoxStatement(Statement stmt, Model inferenceModel) {
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try {
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log.debug("added TBox assertion = " + stmt.toString());
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if ( !(stmt.getPredicate().equals(RDFS.subClassOf)
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|| stmt.getPredicate().equals(RDFS.subClassOf) ) ) {
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return;
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if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
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// ignore anonymous classes
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if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
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return;
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}
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OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
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OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
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if (stmt.getPredicate().equals(RDFS.subClassOf)) {
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addedSubClass(subject,object);
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} else {
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// equivalent class is the same as subclass in both directions
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addedSubClass(subject,object);
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addedSubClass(object,subject);
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}
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} else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
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OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
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OntProperty object = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
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if (stmt.getPredicate().equals(RDFS.subPropertyOf)) {
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addedSubProperty(subject, object, inferenceModel);
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} else {
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// equivalent property is the same as subProperty in both directions
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addedSubProperty(subject, object, inferenceModel);
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addedSubProperty(object, subject, inferenceModel);
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}
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}
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// ignore anonymous classes
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if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
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return;
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}
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log.debug("stmt = " + stmt.toString());
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OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
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OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
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if (stmt.getPredicate().equals(RDFS.subClassOf)) {
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addedSubClass(subject,object);
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} else {
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// equivalent class is the same as subclass in both directions
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addedSubClass(subject,object);
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addedSubClass(object,subject);
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}
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} catch (Exception e) {
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// don't stop the edit if there's an exception
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log.error("Exception while adding incremental inferences: ", e);
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log.error("Exception while adding inference(s): ", e);
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}
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}
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/*
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* Performs incremental selected ABox reasoning based
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* on changes to the class hierarchy.
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*
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* Handles subclassOf and equivalentClass assertions
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* on changes to the class or property hierarchy.
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*
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* Handles rdfs:subclassOf, owl:equivalentClass,
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* rdfs:subPropertyOf and owl:equivalentProperty assertions
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*/
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public void removedTBoxStatement(Statement stmt) {
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try {
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log.debug("removed TBox assertion = " + stmt.toString());
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if ( !(stmt.getPredicate().equals(RDFS.subClassOf)
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|| stmt.getPredicate().equals(RDFS.subClassOf) ) ) {
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return;
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if ( stmt.getPredicate().equals(RDFS.subClassOf) || stmt.getPredicate().equals(OWL.equivalentClass) ) {
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// ignore anonymous classes
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if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
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return;
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}
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OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
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OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
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if (stmt.getPredicate().equals(RDFS.subClassOf)) {
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removedSubClass(subject,object);
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} else {
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// equivalent class is the same as subclass in both directions
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removedSubClass(subject,object);
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removedSubClass(object,subject);
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}
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} else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
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OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
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OntProperty object = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
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if (stmt.getPredicate().equals(RDFS.subPropertyOf)) {
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removedSubProperty(subject,object);
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} else {
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// equivalent property is the same as subProperty in both directions
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removedSubProperty(subject,object);
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removedSubProperty(object,subject);
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}
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}
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// ignore anonymous classes
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if (stmt.getSubject().isAnon() || stmt.getObject().isAnon()) {
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return;
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}
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log.debug("stmt = " + stmt.toString());
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OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
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OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
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if (stmt.getPredicate().equals(RDFS.subClassOf)) {
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removedSubClass(subject,object);
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} else {
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// equivalent class is the same as subclass in both directions
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removedSubClass(subject,object);
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removedSubClass(object,subject);
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}
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} catch (Exception e) {
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// don't stop the edit if there's an exception
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log.error("Exception while removing incremental inferences: ", e);
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log.error("Exception while removing inference(s): ", e);
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}
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}
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/*
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* Performs incremental reasoning based on a new type assertion
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* added to the ABox (assertion that an individual is of a certain
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* type).
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*
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* If it is added that B is of type A, then for each superclass of
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* A assert that B is of that type.
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*
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*/
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public void addedType(Statement stmt, Model inferenceModel) {
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//log.debug("stmt = " + stmt.toString());
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public void addedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
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tboxModel.enterCriticalSection(Lock.READ);
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@ -216,7 +233,6 @@ public class SimpleReasoner extends StatementListener {
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List<OntClass> parents = (cls.listSuperClasses(false)).toList();
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parents.addAll((cls.listEquivalentClasses()).toList());
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Iterator<OntClass> parentIt = parents.iterator();
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while (parentIt.hasNext()) {
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@ -247,13 +263,61 @@ public class SimpleReasoner extends StatementListener {
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}
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}
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/*
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* Performs incremental property-based reasoning.
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*
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* Materializes inferences based on the rdfs:subPropertyOf relationship.
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* If it is added that x propB y and propB is a sub-property of propA
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* then add x propA y to the inference graph.
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*/
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public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
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tboxModel.enterCriticalSection(Lock.READ);
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try {
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OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
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if (prop != null) {
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//TODO: have trouble parametizing the template with ? extends OntProperty
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List superProperties = prop.listSuperProperties(false).toList();
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superProperties.addAll(prop.listEquivalentProperties().toList());
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Iterator<OntProperty> superIt = superProperties.iterator();
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while (superIt.hasNext()) {
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OntProperty superProp = superIt.next();
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if ( !((prop.isObjectProperty() && superProp.isObjectProperty()) || (prop.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
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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());
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return;
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}
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Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
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inferenceModel.enterCriticalSection(Lock.WRITE);
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try {
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if (!inferenceModel.contains(infStmt) && !infStmt.equals(stmt) ) {
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//log.debug("Adding this inferred statement: " + infStmt.toString() );
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inferenceModel.add(infStmt);
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}
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} finally {
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inferenceModel.leaveCriticalSection();
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}
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}
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} else {
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log.warn("Didn't find target property (the predicate of the added statement) in the TBox: " + stmt.getPredicate().getURI());
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}
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} finally {
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tboxModel.leaveCriticalSection();
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}
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}
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/*
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* If it is removed that B is of type A, then for each superclass of A remove
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* the inferred statement that B is of that type UNLESS it is otherwise entailed
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* that B is of that type.
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*
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*/
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public void removedType(Statement stmt) {
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public void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
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//log.debug("stmt = " + stmt.toString());
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@ -266,7 +330,6 @@ public class SimpleReasoner extends StatementListener {
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List<OntClass> parents = (cls.listSuperClasses(false)).toList();
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parents.addAll((cls.listEquivalentClasses()).toList());
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Iterator<OntClass> parentIt = parents.iterator();
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while (parentIt.hasNext()) {
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@ -302,8 +365,62 @@ public class SimpleReasoner extends StatementListener {
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}
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}
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// Returns true if it is entailed by class subsumption that subject is
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// of type cls; otherwise returns false.
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/*
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* Performs incremental property-based reasoning.
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*
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* Retracts inferences based on the rdfs:subPropertyOf relationship.
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* If it is removed that x propB y and propB is a sub-property of propA
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* then remove x propA y from the inference graph UNLESS it that
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* statement is otherwise entailed.
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*/
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public void removedABoxAssertion(Statement stmt, Model inferenceModel) {
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tboxModel.enterCriticalSection(Lock.READ);
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try {
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OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
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if (prop != null) {
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//TODO: trouble parameterizing these templates with "? extends OntProperty"
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List superProperties = prop.listSuperProperties(false).toList();
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superProperties.addAll(prop.listEquivalentProperties().toList());
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Iterator<OntProperty> superIt = superProperties.iterator();
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while (superIt.hasNext()) {
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OntProperty superProp = superIt.next();
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if ( !((prop.isObjectProperty() && superProp.isObjectProperty()) || (prop.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
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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());
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return;
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}
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// if the statement is still entailed without the removed
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// statement then don't remove it from the inferences
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if (entailedByPropertySubsumption(stmt.getSubject(), superProp, stmt.getObject())) continue;
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Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
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inferenceModel.enterCriticalSection(Lock.WRITE);
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try {
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if (inferenceModel.contains(infStmt)) {
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//log.debug("Removing this inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
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inferenceModel.remove(infStmt);
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}
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} finally {
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inferenceModel.leaveCriticalSection();
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}
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}
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} else {
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log.debug("Didn't find target predicate (the predicate of the removed statement) in the TBox: " + stmt.getPredicate().getURI());
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}
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} finally {
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tboxModel.leaveCriticalSection();
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}
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}
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// Returns true if it is entailed by class subsumption that
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// subject is of type cls; otherwise returns false.
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public boolean entailedType(Resource subject, OntClass cls) {
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//log.debug("subject = " + subject.getURI() + " class = " + cls.getURI());
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@ -313,8 +430,8 @@ public class SimpleReasoner extends StatementListener {
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try {
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ExtendedIterator<OntClass> iter = cls.listSubClasses(false);
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while (iter.hasNext()) {
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while (iter.hasNext()) {
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OntClass childClass = iter.next();
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Statement stmt = ResourceFactory.createStatement(subject, RDF.type, childClass);
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if (aboxModel.contains(stmt)) return true;
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@ -327,10 +444,33 @@ public class SimpleReasoner extends StatementListener {
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}
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}
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// Returns true if the statement is entailed by property subsumption
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public boolean entailedByPropertySubsumption(Resource subject, OntProperty prop, RDFNode object) {
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aboxModel.enterCriticalSection(Lock.READ);
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tboxModel.enterCriticalSection(Lock.READ);
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try {
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ExtendedIterator<? extends OntProperty> iter = prop.listSubProperties(false);
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while (iter.hasNext()) {
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OntProperty subProp = iter.next();
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Statement stmt = ResourceFactory.createStatement(subject, subProp, object);
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if (aboxModel.contains(stmt)) return true;
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}
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return false;
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} finally {
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aboxModel.leaveCriticalSection();
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tboxModel.leaveCriticalSection();
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}
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}
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/*
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* If added that B is a subclass of A, then find all individuals
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* that are typed as B, either in the ABox or in the inferred model
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* and assert that they are of type A.
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* If it is added that B is a subClass of A, then for each
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* individual that is typed as B, either in the ABox or in the
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* inferred model, assert that it is of type A.
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*/
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public void addedSubClass(OntClass subClass, OntClass superClass) {
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@ -366,11 +506,10 @@ public class SimpleReasoner extends StatementListener {
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/*
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* If removed that B is a subclass of A, then for each individual
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* that is of type B, either inferred or in the ABox, then
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* remove the inferred assertion that it is of type A,
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* UNLESS the individual is of some type C that is
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* a subClass of A (including A itself)
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*
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* that is of type B, either inferred or in the ABox, remove the
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* assertion that it is of type A from the inferred model,
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* UNLESS the individual is of some type C that is a subClass
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* of A (including A itself)
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*/
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public void removedSubClass(OntClass subClass, OntClass superClass) {
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@ -408,6 +547,97 @@ public class SimpleReasoner extends StatementListener {
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}
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}
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/*
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* If it is added that B is a subProperty of A, then for each assertion
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* involving predicate B, either in the ABox or in the inferred model
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* assert the same relationship for predicate A
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*/
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public void addedSubProperty(OntProperty subProp, OntProperty superProp, Model inferenceModel) {
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log.debug("subProperty = " + subProp.getURI() + " superProperty = " + subProp.getURI());
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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;
|
||||
|
||||
/**
|
||||
|
|
@ -441,26 +671,53 @@ public class SimpleReasoner extends StatementListener {
|
|||
*/
|
||||
public synchronized void recomputeABox() {
|
||||
|
||||
// recompute the inferences
|
||||
// recompute the ABox inferences
|
||||
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
|
||||
aboxModel.enterCriticalSection(Lock.READ);
|
||||
tboxModel.enterCriticalSection(Lock.READ);
|
||||
|
||||
try {
|
||||
inferenceRebuildModel.removeAll();
|
||||
|
||||
// compute the class-based inferences
|
||||
log.info("Computing class-based ABox inferences");
|
||||
|
||||
StmtIterator iter = aboxModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
|
||||
|
||||
while (iter.hasNext()) {
|
||||
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) {
|
||||
log.error("Exception while recomputing ABox inference model", e);
|
||||
} finally {
|
||||
aboxModel.leaveCriticalSection();
|
||||
inferenceRebuildModel.leaveCriticalSection();
|
||||
aboxModel.leaveCriticalSection();
|
||||
tboxModel.leaveCriticalSection();
|
||||
inferenceRebuildModel.leaveCriticalSection();
|
||||
}
|
||||
|
||||
|
||||
// reflect the recomputed inferences into the application inference
|
||||
// model.
|
||||
inferenceRebuildModel.enterCriticalSection(Lock.READ);
|
||||
|
|
@ -532,99 +789,6 @@ public class SimpleReasoner extends StatementListener {
|
|||
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) {
|
||||
Object simpleReasoner = ctx.getAttribute("simpleReasoner");
|
||||
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.mindswap.pellet.jena.PelletReasonerFactory;
|
|||
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.rdf.model.Model;
|
||||
import com.hp.hpl.jena.rdf.model.ModelFactory;
|
||||
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 {
|
||||
|
||||
|
||||
private Resource objectProperty = ResourceFactory.createResource("http://www.w3.org/2002/07/owl#ObjectProperty");
|
||||
|
||||
@Before
|
||||
public void suppressErrorOutput() {
|
||||
suppressSyserr();
|
||||
}
|
||||
|
||||
/*
|
||||
* Test that when an individual is asserted to be of a type,
|
||||
* its asserted type is not added to the inference graph
|
||||
*/
|
||||
@Test
|
||||
public void addType(){
|
||||
|
||||
// Test that when a new instance is asserted, its asserted type is not added to the
|
||||
// inference graph
|
||||
public void addABoxTypeAssertion1(){
|
||||
|
||||
// Create a Tbox with a simple class hierarchy. B is a subclass of A.
|
||||
// Pellet will compute TBox inferences
|
||||
|
|
@ -50,7 +55,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
// this is the model to receive inferences
|
||||
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);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
|
|
@ -65,11 +70,16 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
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
|
||||
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.
|
||||
// Pellet will compute TBox inferences
|
||||
// Create a Tbox with a simple class hierarchy. D and E are subclasses
|
||||
// of C. B and C are subclasses of A. Pellet will compute TBox inferences.
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
OntClass classA = tBox.createClass("http://test.vivo/A");
|
||||
|
|
@ -113,13 +123,150 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
Assert.assertTrue(inf.contains(xisa));
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Test inference based on class equivalence
|
||||
*/
|
||||
@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
|
||||
|
||||
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);
|
||||
|
||||
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.
|
||||
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
|
||||
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.
|
||||
// The ABox data that will be the basis for the inference will
|
||||
// be in the ABox graph.
|
||||
/*
|
||||
* Test the addition of a subClassOf statement to
|
||||
* the TBox. The instance data that is the basis
|
||||
* 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
|
||||
public void addSubClass1(){
|
||||
public void addTBoxSubClassAssertion1(){
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// 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.
|
||||
// The ABox data that is the basis for the inference will be
|
||||
// in the inferred graph
|
||||
/*
|
||||
* Test the addition of a subClassOf statement to
|
||||
* 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 some test of equivalentClass statements also.
|
||||
*
|
||||
*/
|
||||
@Test
|
||||
public void addSubClass2(){
|
||||
public void addTBoxSubClassAssertion2() {
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
|
|
@ -260,9 +437,23 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
}
|
||||
|
||||
@Test
|
||||
// this tests incremental reasoning as a result of the removal of a subClassOf
|
||||
// or equivalentClass statement from the TBox.
|
||||
public void removeSubClass(){
|
||||
/*
|
||||
* Test the removal of a subClassOf statement from
|
||||
* 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
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
// Pellet will compute TBox inferences
|
||||
|
|
@ -324,7 +515,6 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
|
||||
Assert.assertFalse(inf.contains(xisa));
|
||||
|
||||
|
||||
// Verify that "x is of type B" is in the inference graph
|
||||
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB);
|
||||
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
|
||||
Statement yisa = ResourceFactory.createStatement(ind_y, RDF.type, classA);
|
||||
Assert.assertTrue(inf.contains(yisa));
|
||||
|
||||
}
|
||||
|
||||
// Test inference based on class equivalence
|
||||
//
|
||||
|
||||
/*
|
||||
* tests rdfs:subPropertyOf materialization for object properties.
|
||||
*/
|
||||
@Test
|
||||
public void equivClass1(){
|
||||
public void addABoxAssertion1(){
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
|
|
@ -360,40 +551,130 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
aBox.register(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
|
||||
// C is a subclass of A
|
||||
|
||||
OntClass classA = tBox.createClass("http://test.vivo/A");
|
||||
classA.setLabel("class A", "en-US");
|
||||
OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
|
||||
tBox.add(propA, RDF.type, objectProperty);
|
||||
propA.setLabel("property A", "en-US");
|
||||
|
||||
OntClass classB = tBox.createClass("http://test.vivo/B");
|
||||
classB.setLabel("class B", "en-US");
|
||||
OntProperty propB = tBox.createOntProperty("http://test.vivo/B");
|
||||
tBox.add(propB, RDF.type, objectProperty);
|
||||
propB.setLabel("property B", "en-US");
|
||||
|
||||
OntClass classC = tBox.createClass("http://test.vivo/C");
|
||||
classC.setLabel("class C", "en-US");
|
||||
OntProperty propC = tBox.createOntProperty("http://test.vivo/C");
|
||||
tBox.add(propC, RDF.type, objectProperty);
|
||||
propC.setLabel("property C", "en-US");
|
||||
|
||||
classA.addEquivalentClass(classB);
|
||||
classA.addSubClass(classC);
|
||||
propA.addEquivalentProperty(propB);
|
||||
propA.addSubProperty(propC);
|
||||
|
||||
// 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);
|
||||
Resource ind_y = aBox.createResource("http://test.vivo/y");
|
||||
|
||||
// Verify that "x is of type A" was inferred
|
||||
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
|
||||
Assert.assertTrue(inf.contains(xisa));
|
||||
aBox.add(ind_x, propC, ind_y);
|
||||
|
||||
// Verify that "x is of type B" was inferred
|
||||
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB);
|
||||
Assert.assertTrue(inf.contains(xisb));
|
||||
// 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 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
|
||||
public void equivClass2(){
|
||||
public void addABoxAssertion5(){
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
|
|
@ -407,31 +688,35 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
aBox.register(simpleReasoner);
|
||||
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner));
|
||||
|
||||
// Add classes classes A and B to the TBox
|
||||
// A is equivalent to B
|
||||
// Add object properties propA and propB to the TBox.
|
||||
// propB is a sub-property of propA.
|
||||
|
||||
OntClass classA = tBox.createClass("http://test.vivo/A");
|
||||
classA.setLabel("class A", "en-US");
|
||||
OntProperty propA = tBox.createOntProperty("http://test.vivo/propA");
|
||||
tBox.add(propA, RDF.type, objectProperty);
|
||||
propA.setLabel("propA", "en-US");
|
||||
|
||||
OntClass classB = tBox.createClass("http://test.vivo/B");
|
||||
classB.setLabel("class B", "en-US");
|
||||
OntProperty propB = tBox.createOntProperty("http://test.vivo/propB");
|
||||
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");
|
||||
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
|
||||
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
|
||||
Assert.assertTrue(inf.contains(xisa));
|
||||
// Verify that x propA y was not inferred
|
||||
Statement xay = ResourceFactory.createStatement(ind_x, propA, ind_y);
|
||||
Assert.assertFalse(inf.contains(xay));
|
||||
}
|
||||
|
||||
|
||||
// Test inference based on class equivalence
|
||||
//
|
||||
/*
|
||||
* Test inference based on property equivalence
|
||||
*/
|
||||
@Test
|
||||
public void equivClass3(){
|
||||
public void addABoxAssertion6() {
|
||||
|
||||
// Create TBox, ABox and Inference models and register
|
||||
// the ABox reasoner listeners with the ABox and TBox
|
||||
|
|
@ -445,31 +730,203 @@ public class SimpleReasonerTest extends AbstractTestClass {
|
|||
aBox.register(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
|
||||
|
||||
OntClass classA = tBox.createClass("http://test.vivo/A");
|
||||
classA.setLabel("class A", "en-US");
|
||||
OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
|
||||
tBox.add(propA, RDF.type, objectProperty);
|
||||
propA.setLabel("property A", "en-US");
|
||||
|
||||
OntClass classB = tBox.createClass("http://test.vivo/B");
|
||||
classB.setLabel("class B", "en-US");
|
||||
OntProperty propB = tBox.createOntProperty("http://test.vivo/B");
|
||||
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");
|
||||
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
|
||||
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
|
||||
Assert.assertTrue(inf.contains(xisa));
|
||||
// Verify that "x A y" was inferred
|
||||
Statement xAy = ResourceFactory.createStatement(ind_x, propA, ind_y);
|
||||
Assert.assertTrue(inf.contains(xAy));
|
||||
|
||||
// Remove the statement that x is of type B from the ABox
|
||||
aBox.remove(ind_x, RDF.type, classB);
|
||||
// Remove the statement that x B y from the ABox
|
||||
aBox.remove(ind_x, propB, ind_y);
|
||||
|
||||
// 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));
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue