incremental development for sameAs inference support
This commit is contained in:
stellamit
parent
5a7f70e1d7
commit
2b15e7211c
3 changed files with 262 additions and 112 deletions
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@ -6,6 +6,7 @@ import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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@ -427,6 +428,8 @@ public class SimpleReasoner extends StatementListener {
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Resource subject = null;
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Resource object = null;
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//System.out.println("\n\naddedABoxSameAsAssertion called for this statement: " + stmtString(stmt));
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if (stmt.getSubject().isResource()) {
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subject = stmt.getSubject().asResource();
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if (tboxModel.containsResource(subject) || subject.isAnon()) {
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@ -449,18 +452,6 @@ public class SimpleReasoner extends StatementListener {
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return;
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}
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Model inferences = ModelFactory.createDefaultModel();
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inferences.add(generateSameAsInferences(subject, object, inferenceModel));
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inferences.add(generateSameAsInferences(object, subject, inferenceModel));
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inferences.add(object, OWL.sameAs, subject);
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Iterator<Statement> infIter = inferences.listStatements();
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while (infIter.hasNext()) {
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Statement infStmt = infIter.next();
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addInference(infStmt,inferenceModel,false);
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}
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inferenceModel.enterCriticalSection(Lock.WRITE);
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try {
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if (inferenceModel.contains(stmt)) {
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@ -469,35 +460,103 @@ public class SimpleReasoner extends StatementListener {
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} finally {
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inferenceModel.leaveCriticalSection();
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}
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}
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/*
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* Create a model that contains every assertion about indB as exists for
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* indA in the Abox assertions or inference model
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*/
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public Model generateSameAsInferences(Resource indA, Resource indB, Model inferenceModel) {
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Model inferences = ModelFactory.createDefaultModel();
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Statement opposite = ResourceFactory.createStatement(object, OWL.sameAs, subject);
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addInference(opposite,inferenceModel,true);
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generateSameAsInferences(subject, object, inferenceModel);
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generateSameAsInferences(object, subject, inferenceModel);
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}
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/*
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* Materializes inferences based on the owl:sameAs relationship.
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*
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* If it is removed that x is sameAs y, then remove y sameAs x from
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* the inference graph and then recompute the inferences for x and
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* y based on their respective assertions. that x owl:sameAs y, then all asserted and inferred
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*/
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public void removedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
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Resource subject = null;
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Resource object = null;
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if (stmt.getSubject().isResource()) {
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subject = stmt.getSubject().asResource();
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if (tboxModel.containsResource(subject) || subject.isAnon()) {
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log.debug("the subject of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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} else {
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log.warn("the subject of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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if (stmt.getObject().isResource()) {
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object = stmt.getObject().asResource();
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if (tboxModel.containsResource(object) || object.isAnon()) {
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log.debug("the object of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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} else {
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log.warn("the object of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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Set<Resource> sameIndividuals = new HashSet<Resource>();
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inferenceModel.enterCriticalSection(Lock.READ);
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try {
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Iterator<Statement> iter1 = inferenceModel.listStatements(subject, OWL.sameAs, (RDFNode) null);
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while (iter1.hasNext()) {
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Statement sameStmt = iter1.next();
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if (sameStmt.getObject() == null || !sameStmt.getObject().isResource()) continue;
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sameIndividuals.add(sameStmt.getObject().asResource());
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}
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Iterator<Statement> iter2 = inferenceModel.listStatements(object, OWL.sameAs, (RDFNode) null);
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while (iter2.hasNext()) {
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Statement sameStmt = iter2.next();
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if (sameStmt.getObject() == null || !sameStmt.getObject().isResource()) continue;
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sameIndividuals.add(sameStmt.getObject().asResource());
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}
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} finally {
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inferenceModel.leaveCriticalSection();
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}
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Iterator<Resource> sIter1 = sameIndividuals.iterator();
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while (sIter1.hasNext()) {
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removeInferencesForIndividual(sIter1.next(), inferenceModel);
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}
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Iterator<Resource> sIter2 = sameIndividuals.iterator();
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while (sIter2.hasNext()) {
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computeInferencesForIndividual(sIter2.next(), inferenceModel);
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}
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}
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public void generateSameAsInferences(Resource ind1, Resource ind2, Model inferenceModel) {
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//System.out.println("\n\tgenerateSameAsInferences. ind1= " + ind1.getLocalName() + " ind2= " + ind2.getLocalName());
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OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
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unionModel.addSubModel(aboxModel);
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unionModel.addSubModel(inferenceModel);
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aboxModel.enterCriticalSection(Lock.READ);
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try {
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Iterator<Statement> iter = unionModel.listStatements(indA, (Property) null, (RDFNode) null);
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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if (stmt.getObject() == null) continue;
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if (OWL.sameAs.equals(stmt.getPredicate()) && indB.equals(stmt.getObject())) continue;
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inferences.add(indB, stmt.getPredicate(), stmt.getObject());
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aboxModel.enterCriticalSection(Lock.READ);
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try {
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Iterator<Statement> iter = unionModel.listStatements(ind1, (Property) null, (RDFNode) null);
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while (iter.hasNext()) {
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Statement stmt = iter.next();
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//System.out.println("\tIn loop. stmt = " + stmtString(stmt));
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if (stmt.getObject() == null) continue;
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Statement infStmt = ResourceFactory.createStatement(ind2,stmt.getPredicate(),stmt.getObject());
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addInference(infStmt, inferenceModel,true);
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}
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} finally {
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aboxModel.leaveCriticalSection();
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}
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} finally {
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aboxModel.leaveCriticalSection();
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}
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return inferences;
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return;
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}
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/*
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@ -532,71 +591,38 @@ public class SimpleReasoner extends StatementListener {
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}
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/*
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* Materializes inferences based on the owl:sameAs relationship.
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*
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* If it is removed that x is sameAs y, then remove y sameAs x from
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* the inference graph and then recompute the inferences for x and
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* y based on their respective assertions. that x owl:sameAs y, then all asserted and inferred
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* Remove inferences for individual
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*/
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//TODO - I think I need to handle sameAs chains here
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public void removedABoxSameAsAssertion(Statement stmt, Model inferenceModel) {
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public void removeInferencesForIndividual(Resource ind, Model inferenceModel) {
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Resource subject = null;
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Resource object = null;
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if (stmt.getSubject().isResource()) {
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subject = stmt.getSubject().asResource();
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if (tboxModel.containsResource(subject) || subject.isAnon()) {
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log.debug("the subject of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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} else {
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log.warn("the subject of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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if (stmt.getObject().isResource()) {
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object = stmt.getObject().asResource();
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if (tboxModel.containsResource(object) || object.isAnon()) {
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log.debug("the object of this removed sameAs statement is either in the tbox or an anonymous node, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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} else {
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log.warn("the object of this removed sameAs statement is not a resource, no reasoning will be done: " + stmtString(stmt));
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return;
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}
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Statement infStmt = ResourceFactory.createStatement(object,OWL.sameAs,subject);
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removeInference(infStmt,inferenceModel,false);
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recomputeInferencesForIndividual(subject, inferenceModel);
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recomputeInferencesForIndividual(object, inferenceModel);
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}
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/*
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* Recompute inferences for individual
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*/
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public void recomputeInferencesForIndividual(Resource ind, Model inferenceModel) {
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Model inferencesToRemove = ModelFactory.createDefaultModel();
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Model individualInferences = ModelFactory.createDefaultModel();
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inferenceModel.enterCriticalSection(Lock.READ);
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try {
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Iterator<Statement> iter = inferenceModel.listStatements(ind, (Property) null, (RDFNode) null);
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while (iter.hasNext()) {
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inferencesToRemove.add(iter.next());
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individualInferences.add(iter.next());
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}
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} finally {
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inferenceModel.leaveCriticalSection();
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}
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inferenceModel.enterCriticalSection(Lock.WRITE);
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try {
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inferenceModel.remove(inferencesToRemove);
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inferenceModel.remove(individualInferences);
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} finally {
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inferenceModel.leaveCriticalSection();
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}
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return;
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}
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/*
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* compute inferences for individual
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*/
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public void computeInferencesForIndividual(Resource ind, Model inferenceModel) {
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Iterator<Statement> iter = null;
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aboxModel.enterCriticalSection(Lock.WRITE);
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try {
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@ -606,12 +632,14 @@ public class SimpleReasoner extends StatementListener {
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}
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while (iter.hasNext()) {
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addedStatement(iter.next());
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Statement stmt = iter.next();
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//System.out.println("calling addedStatement for: " + stmtString(stmt));
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addedStatement(stmt);
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}
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return;
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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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@ -624,6 +652,7 @@ public class SimpleReasoner extends StatementListener {
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*
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*/
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public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
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List<OntProperty> inverseProperties = getInverseProperties(stmt);
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Iterator<OntProperty> inverseIter = inverseProperties.iterator();
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@ -1082,6 +1111,10 @@ public class SimpleReasoner extends StatementListener {
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*/
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protected void removeInference(Statement infStmt, Model inferenceModel, boolean handleSameAs) {
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//TODO - add to Abox here if it's entailed?
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//System.out.println("\nremoveInference called for this statement: " + stmtString(infStmt));
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inferenceModel.enterCriticalSection(Lock.WRITE);
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try {
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if ( !entailedStatement(infStmt) && inferenceModel.contains(infStmt)) {
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@ -1100,13 +1133,14 @@ public class SimpleReasoner extends StatementListener {
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while (sameIter.hasNext()) {
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Statement infStmtSame = ResourceFactory.createStatement(sameIter.next(), infStmt.getPredicate(), infStmt.getObject());
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if (!entailedStatement(infStmtSame) && inferenceModel.contains(infStmtSame)) {
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//System.out.println("\tsameAs processing: removing this from the inference model: " + stmtString(infStmtSame));
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inferenceModel.remove(infStmtSame);
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}
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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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}
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}
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/*
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@ -1117,11 +1151,14 @@ public class SimpleReasoner extends StatementListener {
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*/
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protected void addInference(Statement infStmt, Model inferenceModel, boolean handleSameAs) {
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//System.out.println("\taddInference called for this statement: " + stmtString(infStmt));
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aboxModel.enterCriticalSection(Lock.READ);
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try {
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inferenceModel.enterCriticalSection(Lock.WRITE);
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try {
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if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt)) {
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//System.out.println("\t\tadding this to the inference model: " + stmtString(infStmt));
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inferenceModel.add(infStmt);
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}
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@ -1130,8 +1167,16 @@ public class SimpleReasoner extends StatementListener {
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Iterator<Resource> sameIter = sameIndividuals.iterator();
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while (sameIter.hasNext()) {
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Resource subject = sameIter.next();
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if (!inferenceModel.contains(subject,infStmt.getPredicate(),infStmt.getObject()) && !aboxModel.contains(subject,infStmt.getPredicate(),infStmt.getObject())) {
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inferenceModel.add(subject,infStmt.getPredicate(),infStmt.getObject());
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Statement sameStmt = ResourceFactory.createStatement(subject,infStmt.getPredicate(),infStmt.getObject());
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if (subject.equals(infStmt.getObject()) && OWL.sameAs.equals(infStmt.getPredicate())) {
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//System.out.println("\t\tsameAS processing: skipping adding this statement to the inference model: " + stmtString(sameStmt));
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continue;
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}
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if (!inferenceModel.contains(sameStmt) && !aboxModel.contains(sameStmt)) {
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//System.out.println("\t\tsameAs processing: adding this to the inference model: " + stmtString(sameStmt));
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inferenceModel.add(sameStmt);
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}
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}
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}
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@ -1143,11 +1188,11 @@ public class SimpleReasoner extends StatementListener {
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}
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/*
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System.out.println("hello!!! ONE");
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//System.out.println("hello!!! ONE");
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if (handleSameAs) {
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System.out.println("hello!!! TWO");
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//System.out.println("hello!!! TWO");
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aboxModel.enterCriticalSection(Lock.READ);
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System.out.println("hello!!! TRES");
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//System.out.println("hello!!! TRES");
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try {
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List<Resource> sameIndividuals = getSameIndividuals(infStmt.getSubject().asResource(), inferenceModel);
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Iterator<Resource> sameIter = sameIndividuals.iterator();
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@ -24,7 +24,7 @@ public class SimpleReasonerInversePropertyTest extends AbstractTestClass {
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@Before
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public void suppressErrorOutput() {
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suppressSyserr();
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//suppressSyserr();
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//Turn off log messages to console
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setLoggerLevel(SimpleReasoner.class, Level.OFF);
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setLoggerLevel(SimpleReasonerTBoxListener.class, Level.OFF);
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@ -28,7 +28,7 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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@Before
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public void suppressErrorOutput() {
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suppressSyserr();
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//suppressSyserr();
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//Turn off log messages to console
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setLoggerLevel(SimpleReasoner.class, Level.OFF);
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setLoggerLevel(SimpleReasonerTBoxListener.class, Level.OFF);
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@ -90,7 +90,7 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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}
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/*
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* basic scenario of removing an abox sameAs assertion
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* basic scenario of removing an abox sameAs assertion
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*/
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@Test
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public void removeSameAsABoxAssertion1() {
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@ -103,10 +103,10 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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OntProperty Q = tBox.createObjectProperty("http://test.vivo/Q");
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Q.setLabel("property Q", "en-US");
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OntProperty S = tBox.createDatatypeProperty("http://test.vivo/");
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OntProperty S = tBox.createDatatypeProperty("http://test.vivo/data1");
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S.setLabel("property S", "en-US");
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OntProperty T = tBox.createDatatypeProperty("http://test.vivo/");
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OntProperty T = tBox.createDatatypeProperty("http://test.vivo/data2");
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T.setLabel("property T", "en-US");
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Literal literal1 = tBox.createLiteral("Literal value 1");
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@ -138,7 +138,7 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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Assert.assertTrue(inf.contains(a,T,literal2));
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aBox.remove(a,OWL.sameAs,b);
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Assert.assertFalse(inf.contains(b,OWL.sameAs,a));
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Assert.assertFalse(inf.contains(b,P,c));
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Assert.assertFalse(inf.contains(b,S,literal1));
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@ -147,8 +147,7 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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}
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/*
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* basic scenario of adding an abox assertion for
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* an individual is sameAs another.
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* adding abox assertion for individual in sameAs chain.
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*/
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@Test
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public void addABoxAssertion1() {
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@ -182,10 +181,23 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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Resource b = aBox.createResource("http://test.vivo/b");
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Resource c = aBox.createResource("http://test.vivo/c");
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Resource d = aBox.createResource("http://test.vivo/d");
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Resource e = aBox.createResource("http://test.vivo/e");
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Resource f = aBox.createResource("http://test.vivo/f");
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aBox.add(a,OWL.sameAs,b);
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aBox.add(b,OWL.sameAs,e);
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aBox.add(e,OWL.sameAs,f);
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Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
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Assert.assertTrue(inf.contains(e,OWL.sameAs,a));
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Assert.assertTrue(inf.contains(e,OWL.sameAs,b));
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Assert.assertTrue(inf.contains(a,OWL.sameAs,e));
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Assert.assertTrue(inf.contains(f,OWL.sameAs,e));
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Assert.assertTrue(inf.contains(f,OWL.sameAs,b));
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Assert.assertTrue(inf.contains(f,OWL.sameAs,a));
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Assert.assertTrue(inf.contains(b,OWL.sameAs,f));
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Assert.assertTrue(inf.contains(a,OWL.sameAs,f));
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aBox.add(a,P,c);
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aBox.add(a,S,literal1);
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@ -196,24 +208,48 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
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Assert.assertTrue(inf.contains(b,S,literal1));
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Assert.assertTrue(inf.contains(a,Q,d));
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Assert.assertTrue(inf.contains(a,T,literal2));
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Assert.assertTrue(inf.contains(e,P,c));
|
||||
Assert.assertTrue(inf.contains(e,S,literal1));
|
||||
Assert.assertTrue(inf.contains(e,Q,d));
|
||||
Assert.assertTrue(inf.contains(e,T,literal2));
|
||||
Assert.assertTrue(inf.contains(f,P,c));
|
||||
Assert.assertTrue(inf.contains(f,S,literal1));
|
||||
Assert.assertTrue(inf.contains(f,Q,d));
|
||||
Assert.assertTrue(inf.contains(f,T,literal2));
|
||||
|
||||
aBox.remove(b,OWL.sameAs,e);
|
||||
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertFalse(inf.contains(e,OWL.sameAs,a));
|
||||
Assert.assertFalse(inf.contains(e,OWL.sameAs,b));
|
||||
Assert.assertFalse(inf.contains(a,OWL.sameAs,e));
|
||||
Assert.assertTrue(inf.contains(f,OWL.sameAs,e));
|
||||
Assert.assertFalse(inf.contains(f,OWL.sameAs,b));
|
||||
Assert.assertFalse(inf.contains(f,OWL.sameAs,a));
|
||||
Assert.assertFalse(inf.contains(b,OWL.sameAs,f));
|
||||
Assert.assertFalse(inf.contains(a,OWL.sameAs,f));
|
||||
|
||||
Assert.assertTrue(inf.contains(b,P,c));
|
||||
Assert.assertTrue(inf.contains(b,S,literal1));
|
||||
Assert.assertTrue(inf.contains(a,Q,d));
|
||||
Assert.assertTrue(inf.contains(a,T,literal2));
|
||||
Assert.assertFalse(inf.contains(e,P,c));
|
||||
Assert.assertFalse(inf.contains(e,S,literal1));
|
||||
Assert.assertFalse(inf.contains(e,Q,d));
|
||||
Assert.assertFalse(inf.contains(e,T,literal2));
|
||||
Assert.assertFalse(inf.contains(f,P,c));
|
||||
Assert.assertFalse(inf.contains(f,S,literal1));
|
||||
Assert.assertFalse(inf.contains(f,Q,d));
|
||||
Assert.assertFalse(inf.contains(f,T,literal2));
|
||||
}
|
||||
|
||||
/*
|
||||
* adding abox assertion for individuals that are sameAs
|
||||
* each other.
|
||||
* sameAs with datatype properties
|
||||
*/
|
||||
@Test
|
||||
public void addABoxAssertion2() {
|
||||
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
|
||||
|
||||
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.addSubClass(classB);
|
||||
|
||||
|
||||
OntProperty desc = tBox.createDatatypeProperty("http://test.vivo/desc");
|
||||
desc.setLabel("property desc", "en-US");
|
||||
|
||||
|
|
@ -230,18 +266,14 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
|
|||
// Individuals a and b
|
||||
Resource a = aBox.createResource("http://test.vivo/a");
|
||||
Resource b = aBox.createResource("http://test.vivo/b");
|
||||
|
||||
|
||||
aBox.add(a,desc,desc1);
|
||||
aBox.add(b,desc,desc2);
|
||||
aBox.add(a,OWL.sameAs,b);
|
||||
aBox.add(a, RDF.type, classB);
|
||||
|
||||
Assert.assertTrue(inf.contains(a,desc,desc2));
|
||||
Assert.assertTrue(inf.contains(a,RDF.type,classA));
|
||||
Assert.assertTrue(inf.contains(b,desc,desc1));
|
||||
Assert.assertTrue(inf.contains(b,OWL.sameAs,a));
|
||||
Assert.assertTrue(inf.contains(b,RDF.type,classB));
|
||||
Assert.assertTrue(inf.contains(b,RDF.type,classA));
|
||||
}
|
||||
|
||||
/*
|
||||
|
|
@ -361,6 +393,79 @@ public class SimpleReasonerSameAsTest extends AbstractTestClass {
|
|||
}
|
||||
|
||||
|
||||
/*
|
||||
* adding and removing a type assertion for an individual who has
|
||||
* a sameAs individual.
|
||||
*/
|
||||
//@Test
|
||||
public void tBoxTypeAssertion1() throws InterruptedException {
|
||||
|
||||
// Create a Tbox with a simple class hierarchy. 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");
|
||||
classA.setLabel("class A", "en-US");
|
||||
|
||||
OntClass classB = tBox.createClass("http://test.vivo/B");
|
||||
classB.setLabel("class B", "en-US");
|
||||
|
||||
classA.addSubClass(classB);
|
||||
|
||||
// this is the model to receive inferences
|
||||
Model inf = ModelFactory.createDefaultModel();
|
||||
|
||||
// create an ABox and register the SimpleReasoner listener with it
|
||||
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
|
||||
aBox.register(new SimpleReasoner(tBox, aBox, inf));
|
||||
|
||||
Resource x = aBox.createResource("http://test.vivo/x");
|
||||
Resource y = aBox.createResource("http://test.vivo/y");
|
||||
Resource z = aBox.createResource("http://test.vivo/z");
|
||||
|
||||
aBox.add(x,OWL.sameAs,y);
|
||||
aBox.add(y,OWL.sameAs,z);
|
||||
aBox.add(x,RDF.type,classB);
|
||||
|
||||
Assert.assertTrue(inf.contains(y,RDF.type,classB));
|
||||
Assert.assertTrue(inf.contains(y,RDF.type,classA));
|
||||
// Assert.assertTrue(inf.contains(z,RDF.type,classB));
|
||||
// Assert.assertTrue(inf.contains(z,RDF.type,classA));
|
||||
|
||||
aBox.remove(x,RDF.type,classB);
|
||||
Assert.assertFalse(inf.contains(y,RDF.type,classB));
|
||||
Assert.assertFalse(inf.contains(y,RDF.type,classA));
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* adding and removing subclass assertion when there is an
|
||||
* individual member who has a sameAs individual.
|
||||
*/
|
||||
//@Test
|
||||
public void tBoxSubclassAssertion1() throws InterruptedException {
|
||||
|
||||
}
|
||||
|
||||
/*
|
||||
* test that mostSpecificType inferences propagate to sameAs
|
||||
* individuals
|
||||
*/
|
||||
//@Test
|
||||
public void mostSpecificTypeTest1() throws InterruptedException {
|
||||
|
||||
}
|
||||
|
||||
/*
|
||||
* there is a sameAs chain and one sameAs statement is removed.
|
||||
*
|
||||
*/
|
||||
//@Test
|
||||
public void sameAsChain1() throws InterruptedException {
|
||||
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Basic scenario around recomputing the ABox inferences
|
||||
*/
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue