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NIHVIVO-3040 separate thread for ABox reasoning based on TBox updates.

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This commit is contained in:
stellamit 2011-11-17 21:49:07 +00:00
parent cc8c48bff4
commit 7d60677d4f
5 changed files with 320 additions and 398 deletions
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64
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/ModelUpdate.java Normal file
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@ -0,0 +1,64 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.reasoner;
import com.hp.hpl.jena.rdf.model.Statement;
public class ModelUpdate {
public static enum Operation {ADD, RETRACT};
private Operation operation;
private Statement statement;
private String modelURI;
//JenaDataSourceSetupBase.JENA_DB_MODEL;
//JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL;
public ModelUpdate() {
}
public ModelUpdate(Statement statement,
Operation operation,
String modelURI) {
this.operation = operation;
this.statement = statement;
this.modelURI = modelURI;
}
public Operation getOperation() {
return operation;
}
public void setOperation(Operation operation) {
this.operation = operation;
}
public Statement getStatement() {
return statement;
}
public void setStatement(Statement statement) {
this.statement = statement;
}
public String getModelURI() {
return modelURI;
}
public void setModelURI(String modelURI) {
this.modelURI = modelURI;
}
@Override public String toString() {
String ret = "operation = " + this.operation + ",";
ret += " model = " + this.modelURI + ",";
ret += " statement = " + SimpleReasoner.stmtString(statement);
return ret;
}
}

325
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
View file

@ -14,7 +14,6 @@ import com.hp.hpl.jena.ontology.AnnotationProperty;
import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec; import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.query.Query; import com.hp.hpl.jena.query.Query;
import com.hp.hpl.jena.query.QueryExecution; import com.hp.hpl.jena.query.QueryExecution;
import com.hp.hpl.jena.query.QueryExecutionFactory; import com.hp.hpl.jena.query.QueryExecutionFactory;
@ -33,7 +32,6 @@ import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator; import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.shared.JenaException; import com.hp.hpl.jena.shared.JenaException;
import com.hp.hpl.jena.shared.Lock; import com.hp.hpl.jena.shared.Lock;
import com.hp.hpl.jena.util.iterator.ExtendedIterator;
import com.hp.hpl.jena.vocabulary.OWL; import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import com.hp.hpl.jena.vocabulary.RDFS; import com.hp.hpl.jena.vocabulary.RDFS;
@ -58,10 +56,6 @@ public class SimpleReasoner extends StatementListener {
private Model inferenceRebuildModel; // work area for re-computing all ABox inferences private Model inferenceRebuildModel; // work area for re-computing all ABox inferences
private Model scratchpadModel; // work area for re-computing all ABox inferences private Model scratchpadModel; // work area for re-computing all ABox inferences
private static final String topObjectPropertyURI = "http://www.w3.org/2002/07/owl#topObjectProperty";
private static final String bottomObjectPropertyURI = "http://www.w3.org/2002/07/owl#bottomObjectProperty";
private static final String topDataPropertyURI = "http://www.w3.org/2002/07/owl#topDataProperty";
private static final String bottomDataPropertyURI = "http://www.w3.org/2002/07/owl#bottomDataProperty";
private static final String mostSpecificTypePropertyURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#mostSpecificType"; private static final String mostSpecificTypePropertyURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#mostSpecificType";
private AnnotationProperty mostSpecificType = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createAnnotationProperty(mostSpecificTypePropertyURI); private AnnotationProperty mostSpecificType = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createAnnotationProperty(mostSpecificTypePropertyURI);
@ -137,8 +131,6 @@ public class SimpleReasoner extends StatementListener {
addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>()); addedABoxTypeAssertion(stmt, inferenceModel, new HashSet<String>());
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>()); setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
} }
// uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011
// addedABoxAssertion(stmt,inferenceModel);
for (ReasonerPlugin plugin : getPluginList()) { for (ReasonerPlugin plugin : getPluginList()) {
try { try {
@ -182,9 +174,6 @@ public class SimpleReasoner extends StatementListener {
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>()); setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
} }
// uncomment this to enable subproperty/equivalent property inferencing. sjm222 5/13/2011
// removedABoxAssertion(stmt, inferenceModel);
for (ReasonerPlugin plugin : getPluginList()) { for (ReasonerPlugin plugin : getPluginList()) {
try { try {
if (plugin.isInterestedInRemovedStatement(stmt)) { if (plugin.isInterestedInRemovedStatement(stmt)) {
@ -204,16 +193,11 @@ public class SimpleReasoner extends StatementListener {
/* /*
* Performs incremental selected ABox reasoning based * Performs incremental selected ABox reasoning based
* on changes to the class or property hierarchy. * on changes to the class hierarchy.
* *
* Handles rdfs:subclassOf, owl:equivalentClass, * Handles rdfs:subclassOf, owl:equivalentClass,
* rdfs:subPropertyOf and owl:equivalentProperty assertions
*/ */
public void addedTBoxStatement(Statement stmt) { public void addedTBoxStatement(Statement stmt) {
addedTBoxStatement(stmt, inferenceModel);
}
public void addedTBoxStatement(Statement stmt, Model inferenceModel) {
try { try {
log.debug("added TBox assertion = " + stmt.toString()); log.debug("added TBox assertion = " + stmt.toString());
@ -254,21 +238,6 @@ public class SimpleReasoner extends StatementListener {
addedSubClass(object,subject,inferenceModel); addedSubClass(object,subject,inferenceModel);
} }
} }
/* uncomment this to enable sub property/equivalent property inferencing. sjm222 5/13/2011
else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
OntProperty object = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (stmt.getPredicate().equals(RDFS.subPropertyOf)) {
addedSubProperty(subject,object,inferenceModel);
} else {
// equivalent property is the same as subProperty in both directions
addedSubProperty(subject,object,inferenceModel);
addedSubProperty(object,subject,inferenceModel);
}
}
*/
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while adding inference(s): " + e.getMessage()); log.error("Exception while adding inference(s): " + e.getMessage());
@ -277,10 +246,9 @@ public class SimpleReasoner extends StatementListener {
/* /*
* Performs incremental selected ABox reasoning based * Performs incremental selected ABox reasoning based
* on changes to the class or property hierarchy. * on changes to the class hierarchy.
* *
* Handles rdfs:subclassOf, owl:equivalentClass, * Handles rdfs:subclassOf, owl:equivalentClass,
* rdfs:subPropertyOf and owl:equivalentProperty assertions
*/ */
public void removedTBoxStatement(Statement stmt) { public void removedTBoxStatement(Statement stmt) {
@ -323,20 +291,6 @@ public class SimpleReasoner extends StatementListener {
removedSubClass(object,subject,inferenceModel); removedSubClass(object,subject,inferenceModel);
} }
} }
/* uncomment this to enable sub property / equivalent property inferencing. sjm222 5/13/2011.
else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
OntProperty object = tboxModel.getOntProperty(((Resource)stmt.getObject()).getURI());
if (stmt.getPredicate().equals(RDFS.subPropertyOf)) {
removedSubProperty(subject,object);
} else {
// equivalent property is the same as subProperty in both directions
removedSubProperty(subject,object);
removedSubProperty(object,subject);
}
}
*/
} catch (Exception e) { } catch (Exception e) {
// don't stop the edit if there's an exception // don't stop the edit if there's an exception
log.error("Exception while removing inference(s): " + e.getMessage()); log.error("Exception while removing inference(s): " + e.getMessage());
@ -433,69 +387,6 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/*
* Performs incremental property-based reasoning.
*
* Materializes inferences based on the rdfs:subPropertyOf relationship.
* If it is added that x propB y and propB is a sub-property of propA
* then add x propA y to the inference graph.
*/
public void addedABoxAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
// not reasoning on properties in the OWL, RDF or RDFS namespace
if ((prop.getNameSpace()).equals(OWL.NS) ||
(prop.getNameSpace()).equals("http://www.w3.org/2000/01/rdf-schema#") ||
(prop.getNameSpace()).equals("http://www.w3.org/1999/02/22-rdf-syntax-ns#")) {
return;
}
//TODO: have trouble paramterizing the template with ? extends OntProperty
List superProperties = prop.listSuperProperties(false).toList();
superProperties.addAll(prop.listEquivalentProperties().toList());
Iterator<OntProperty> superIt = superProperties.iterator();
while (superIt.hasNext()) {
OntProperty superProp = superIt.next();
if ( !((prop.isObjectProperty() && superProp.isObjectProperty()) || (prop.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
log.warn("sub-property and super-property do not have the same type. No inferencing will be performed. sub-property: " + prop.getURI() + " super-property:" + superProp.getURI());
continue;
}
if (superProp.getURI().equals(topObjectPropertyURI) || superProp.getURI().equals(topDataPropertyURI)) {
continue;
}
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
aboxModel.enterCriticalSection(Lock.READ);
try {
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt) && !aboxModel.contains(infStmt) ) {
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
} finally {
aboxModel.leaveCriticalSection();
}
}
} else {
log.debug("Didn't find target property (the predicate of the added statement) in the TBox: " + stmt.getPredicate().getURI());
}
} finally {
tboxModel.leaveCriticalSection();
}
}
/* /*
* If it is removed that B is of type A, then for each superclass of A remove * If it is removed that B is of type A, then for each superclass of A remove
* the inferred statement that B is of that type UNLESS it is otherwise entailed * the inferred statement that B is of that type UNLESS it is otherwise entailed
@ -577,59 +468,6 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/*
* Performs incremental property-based reasoning.
*
* Retracts inferences based on the rdfs:subPropertyOf relationship.
* If it is removed that x propB y and propB is a sub-property of propA
* then remove x propA y from the inference graph UNLESS it that
* statement is otherwise entailed.
*/
public void removedABoxAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntProperty prop = tboxModel.getOntProperty(stmt.getPredicate().getURI());
if (prop != null) {
//TODO: trouble parameterizing these templates with "? extends OntProperty"
List superProperties = prop.listSuperProperties(false).toList();
superProperties.addAll(prop.listEquivalentProperties().toList());
Iterator<OntProperty> superIt = superProperties.iterator();
while (superIt.hasNext()) {
OntProperty superProp = superIt.next();
if ( !((prop.isObjectProperty() && superProp.isObjectProperty()) || (prop.isDatatypeProperty() && superProp.isDatatypeProperty())) ) {
log.warn("sub-property and super-property do not have the same type. No inferencing will be performed. sub-property: " + prop.getURI() + " super-property:" + superProp.getURI());
return;
}
// if the statement is still entailed without the removed
// statement then don't remove it from the inferences
if (entailedByPropertySubsumption(stmt.getSubject(), superProp, stmt.getObject())) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), superProp, stmt.getObject());
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
}
}
} else {
log.debug("Didn't find target predicate (the predicate of the removed statement) in the TBox: " + stmt.getPredicate().getURI());
}
} finally {
tboxModel.leaveCriticalSection();
}
}
// Returns true if it is entailed by class subsumption that // Returns true if it is entailed by class subsumption that
// subject is of type cls; otherwise returns false. // subject is of type cls; otherwise returns false.
public boolean entailedType(Resource subject, OntClass cls) { public boolean entailedType(Resource subject, OntClass cls) {
@ -663,29 +501,6 @@ public class SimpleReasoner extends StatementListener {
} }
} }
// Returns true if the statement is entailed by property subsumption
public boolean entailedByPropertySubsumption(Resource subject, OntProperty prop, RDFNode object) {
aboxModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
try {
ExtendedIterator<? extends OntProperty> iter = prop.listSubProperties(false);
while (iter.hasNext()) {
OntProperty subProp = iter.next();
Statement stmt = ResourceFactory.createStatement(subject, subProp, object);
if (aboxModel.contains(stmt)) return true;
}
return false;
} finally {
aboxModel.leaveCriticalSection();
tboxModel.leaveCriticalSection();
}
}
/* /*
* If it is added that B is a subClass of A, then for each * If it is added that B is a subClass of A, then for each
* individual that is typed as B, either in the ABox or in the * individual that is typed as B, either in the ABox or in the
@ -707,6 +522,7 @@ public class SimpleReasoner extends StatementListener {
} finally { } finally {
aboxModel.leaveCriticalSection(); aboxModel.leaveCriticalSection();
} }
for (Resource subject : subjectList) { for (Resource subject : subjectList) {
Statement infStmt = ResourceFactory.createStatement(subject, RDF.type, superClass); Statement infStmt = ResourceFactory.createStatement(subject, RDF.type, superClass);
@ -765,93 +581,6 @@ public class SimpleReasoner extends StatementListener {
} }
} }
/*
* If it is added that B is a subProperty of A, then for each assertion
* involving predicate B, either in the ABox or in the inferred model
* assert the same relationship for predicate A
*/
public void addedSubProperty(OntProperty subProp, OntProperty superProp, Model inferenceModel) {
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)) {
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)) {
inferenceModel.remove(infStmt);
}
}
} finally {
aboxModel.leaveCriticalSection();
inferenceModel.leaveCriticalSection();
}
}
/* /*
* Find the most specific types (classes) of an individual and * Find the most specific types (classes) of an individual and
* indicate them for the individual with the core:mostSpecificType * indicate them for the individual with the core:mostSpecificType
@ -1077,50 +806,6 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
} }
/*
log.info("Computing property-based ABox inferences");
iter = tboxModel.listStatements((Resource) null, RDFS.subPropertyOf, (RDFNode) null);
int numStmts = 0;
while (iter.hasNext()) {
Statement stmt = iter.next();
if (stmt.getSubject().getURI().equals(bottomObjectPropertyURI) || stmt.getSubject().getURI().equals(bottomDataPropertyURI) ||
(stmt.getObject().isResource() && (stmt.getObject().asResource().getURI().equals(topObjectPropertyURI) ||
stmt.getObject().asResource().getURI().equals(topDataPropertyURI))) ) {
continue;
}
if ( stmt.getSubject().equals(stmt.getObject()) ) {
continue;
}
addedTBoxStatement(stmt, inferenceRebuildModel);
numStmts++;
if ((numStmts % 500) == 0) {
log.info("Still computing property-based ABox inferences...");
}
}
iter = tboxModel.listStatements((Resource) null, OWL.equivalentProperty, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if ( stmt.getSubject().equals(stmt.getObject()) ) {
continue;
}
addedTBoxStatement(stmt, inferenceRebuildModel);
numStmts++;
if ((numStmts % 500) == 0) {
log.info("Still computing property-based ABox inferences...");
}
}
*/
} catch (Exception e) { } catch (Exception e) {
log.error("Exception while recomputing ABox inference model", e); log.error("Exception while recomputing ABox inference model", e);
inferenceRebuildModel.removeAll(); // don't do this in the finally, it's needed in the case inferenceRebuildModel.removeAll(); // don't do this in the finally, it's needed in the case
@ -1388,13 +1073,11 @@ public class SimpleReasoner extends StatementListener {
} }
} }
setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>()); setMostSpecificTypes(stmt.getSubject(), inferenceModel, new HashSet<String>());
//TODO update this part when subproperty inferencing is added.
} catch (NullPointerException npe) { } catch (NullPointerException npe) {
abort = true; abort = true;
break; break;
} catch (Exception e) { } catch (Exception e) {
log.error("exception in batch mode ",e); log.error("exception in batch mode ",e);
//log.error("exception while computing inferences for batch " + qualifier + " update: " + e.getMessage());
} }
num++; num++;

100
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerTBoxListener.java
View file

@ -1,10 +1,18 @@
/* $This file is distributed under the terms of the license in /doc/license.txt$ */ /* $This file is distributed under the terms of the license in /doc/license.txt$ */
package edu.cornell.mannlib.vitro.webapp.reasoner; package edu.cornell.mannlib.vitro.webapp.reasoner;
import java.util.concurrent.ConcurrentLinkedQueue;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.rdf.listeners.StatementListener; import com.hp.hpl.jena.rdf.listeners.StatementListener;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import edu.cornell.mannlib.vitro.webapp.servlet.setup.JenaDataSourceSetupBase;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
/** /**
* Route notification of changes to TBox to the incremental ABox reasoner. * Route notification of changes to TBox to the incremental ABox reasoner.
@ -15,23 +23,95 @@ import com.hp.hpl.jena.rdf.model.Statement;
public class SimpleReasonerTBoxListener extends StatementListener { public class SimpleReasonerTBoxListener extends StatementListener {
private SimpleReasoner simpleReasoner = null; private static final Log log = LogFactory.getLog(SimpleReasonerTBoxListener.class);
private SimpleReasoner simpleReasoner;
private Thread workerThread;
private boolean stopRequested;
private String name;
private volatile boolean processingUpdates = false;
private ConcurrentLinkedQueue<ModelUpdate> modelUpdates = null;
public SimpleReasonerTBoxListener(SimpleReasoner simpleReasoner) { public SimpleReasonerTBoxListener(SimpleReasoner simpleReasoner) {
this.simpleReasoner = simpleReasoner; this.simpleReasoner = simpleReasoner;
this.stopRequested = false;
this.modelUpdates = new ConcurrentLinkedQueue<ModelUpdate>();
this.processingUpdates = false;
}
public SimpleReasonerTBoxListener(SimpleReasoner simpleReasoner, String name) {
this.simpleReasoner = simpleReasoner;
this.name = name;
this.stopRequested = false;
this.modelUpdates = new ConcurrentLinkedQueue<ModelUpdate>();
this.processingUpdates = false;
} }
@Override @Override
public void addedStatement(Statement stmt) { public void addedStatement(Statement statement) {
//simpleReasoner.startBatchMode(); ModelUpdate mu = new ModelUpdate(statement, ModelUpdate.Operation.ADD, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
simpleReasoner.addedTBoxStatement(stmt); processUpdate(mu);
//simpleReasoner.endBatchMode();
} }
@Override @Override
public void removedStatement(Statement stmt) { public void removedStatement(Statement statement) {
//simpleReasoner.startBatchMode(); ModelUpdate mu = new ModelUpdate(statement, ModelUpdate.Operation.RETRACT, JenaDataSourceSetupBase.JENA_TBOX_ASSERTIONS_MODEL);
simpleReasoner.removedTBoxStatement(stmt); processUpdate(mu);
//simpleReasoner.endBatchMode();
} }
private synchronized void processUpdate(ModelUpdate mu) {
if (!processingUpdates && (modelUpdates.peek() != null)) {
log.error("TBoxProcessor thread was not running and work queue is not empty. size = " + modelUpdates.size());
}
modelUpdates.add(mu);
if (!processingUpdates) {
processingUpdates = true;
workerThread = new TBoxUpdateProcessor("TBoxUpdateProcessor (" + getName() + ")");
workerThread.start();
}
}
private synchronized ModelUpdate nextUpdate() {
ModelUpdate mu = modelUpdates.poll();
processingUpdates = (mu != null);
return mu;
}
public String getName() {
return (name == null) ? "SimpleReasonerTBoxListener" : name;
}
public void setStopRequested() {
this.stopRequested = true;
}
private class TBoxUpdateProcessor extends VitroBackgroundThread {
public TBoxUpdateProcessor(String name) {
super(name);
}
@Override
public void run() {
try {
log.debug("starting thread");
ModelUpdate mu = nextUpdate();
while (mu != null && !stopRequested) {
if (mu.getOperation() == ModelUpdate.Operation.ADD) {
simpleReasoner.addedTBoxStatement(mu.getStatement());
} else if (mu.getOperation() == ModelUpdate.Operation.RETRACT) {
simpleReasoner.removedTBoxStatement(mu.getStatement());
} else {
log.error("unexpected operation value in ModelUpdate object: " + mu.getOperation());
}
mu = nextUpdate();
}
} finally {
processingUpdates = false;
log.debug("ending thread");
}
}
}
} }

23
webapp/src/edu/cornell/mannlib/vitro/webapp/servlet/setup/SimpleReasonerSetup.java
View file

@ -153,7 +153,9 @@ public class SimpleReasonerSetup implements ServletContextListener {
new Thread(new MostSpecificTypeRecomputer(simpleReasoner),"MostSpecificTypeComputer").start(); new Thread(new MostSpecificTypeRecomputer(simpleReasoner),"MostSpecificTypeComputer").start();
} }
assertionsOms.getTBoxModel().register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = new SimpleReasonerTBoxListener(simpleReasoner);
sce.getServletContext().setAttribute(SimpleReasonerTBoxListener.class.getName(),simpleReasonerTBoxListener);
assertionsOms.getTBoxModel().register(simpleReasonerTBoxListener);
log.info("Simple reasoner connected for the ABox"); log.info("Simple reasoner connected for the ABox");
@ -165,12 +167,19 @@ public class SimpleReasonerSetup implements ServletContextListener {
@Override @Override
public void contextDestroyed(ServletContextEvent sce) { public void contextDestroyed(ServletContextEvent sce) {
log.info("received contextDestroyed notification"); log.info("received contextDestroyed notification");
SimpleReasoner simpleReasoner = getSimpleReasonerFromServletContext(sce.getServletContext());
SimpleReasoner simpleReasoner = getSimpleReasonerFromServletContext(sce.getServletContext());
if (simpleReasoner != null) { if (simpleReasoner != null) {
log.info("sending stop request to SimpleReasoner"); log.info("sending stop request to SimpleReasoner");
simpleReasoner.setStopRequested(); simpleReasoner.setStopRequested();
} }
SimpleReasonerTBoxListener simpleReasonerTBoxListener = getSimpleReasonerTBoxListenerFromContext(sce.getServletContext());
if (simpleReasonerTBoxListener != null) {
log.info("sending stop request to simpleReasonerTBoxListener");
simpleReasonerTBoxListener.setStopRequested();
}
} }
public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) { public static SimpleReasoner getSimpleReasonerFromServletContext(ServletContext ctx) {
@ -183,6 +192,16 @@ public class SimpleReasonerSetup implements ServletContextListener {
} }
} }
public static SimpleReasonerTBoxListener getSimpleReasonerTBoxListenerFromContext(ServletContext ctx) {
Object simpleReasonerTBoxListener = ctx.getAttribute(SimpleReasonerTBoxListener.class.getName());
if (simpleReasonerTBoxListener instanceof SimpleReasonerTBoxListener) {
return (SimpleReasonerTBoxListener) simpleReasonerTBoxListener;
} else {
return null;
}
}
private static final String RECOMPUTE_REQUIRED_ATTR = private static final String RECOMPUTE_REQUIRED_ATTR =
SimpleReasonerSetup.class.getName() + ".recomputeRequired"; SimpleReasonerSetup.class.getName() + ".recomputeRequired";

172
webapp/test/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasonerTest.java
View file

@ -3,13 +3,14 @@
package edu.cornell.mannlib.vitro.webapp.reasoner; package edu.cornell.mannlib.vitro.webapp.reasoner;
import java.util.Iterator;
import org.apache.log4j.Level; import org.apache.log4j.Level;
import org.junit.Assert; import org.junit.Assert;
import org.junit.Before; import org.junit.Before;
import org.junit.Test; import org.junit.Test;
import org.mindswap.pellet.jena.PelletReasonerFactory; import org.mindswap.pellet.jena.PelletReasonerFactory;
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.ontology.AnnotationProperty; import com.hp.hpl.jena.ontology.AnnotationProperty;
import com.hp.hpl.jena.ontology.OntClass; import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel; import com.hp.hpl.jena.ontology.OntModel;
@ -17,28 +18,28 @@ import com.hp.hpl.jena.ontology.OntModelSpec;
import com.hp.hpl.jena.ontology.OntProperty; import com.hp.hpl.jena.ontology.OntProperty;
import com.hp.hpl.jena.rdf.model.Model; import com.hp.hpl.jena.rdf.model.Model;
import com.hp.hpl.jena.rdf.model.ModelFactory; import com.hp.hpl.jena.rdf.model.ModelFactory;
import com.hp.hpl.jena.rdf.model.RDFNode;
import com.hp.hpl.jena.rdf.model.Resource; import com.hp.hpl.jena.rdf.model.Resource;
import com.hp.hpl.jena.rdf.model.ResourceFactory; import com.hp.hpl.jena.rdf.model.ResourceFactory;
import com.hp.hpl.jena.rdf.model.Statement; import com.hp.hpl.jena.rdf.model.Statement;
import com.hp.hpl.jena.rdf.model.StmtIterator;
import com.hp.hpl.jena.vocabulary.OWL; import com.hp.hpl.jena.vocabulary.OWL;
import com.hp.hpl.jena.vocabulary.RDF; import com.hp.hpl.jena.vocabulary.RDF;
import edu.cornell.mannlib.vitro.testing.AbstractTestClass; import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
import edu.cornell.mannlib.vitro.webapp.utils.threads.VitroBackgroundThread;
public class SimpleReasonerTest extends AbstractTestClass { public class SimpleReasonerTest extends AbstractTestClass {
private Resource objectProperty = ResourceFactory.createResource("http://www.w3.org/2002/07/owl#ObjectProperty"); private Resource objectProperty = ResourceFactory.createResource("http://www.w3.org/2002/07/owl#ObjectProperty");
private static final String mostSpecificTypePropertyURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#mostSpecificType"; private static final String mostSpecificTypePropertyURI = "http://vitro.mannlib.cornell.edu/ns/vitro/0.7#mostSpecificType";
long delay = 50;
@Before @Before
public void suppressErrorOutput() { public void suppressErrorOutput() {
suppressSyserr(); suppressSyserr();
//Turn off log messages to console //Turn off log messages to console
setLoggerLevel(SimpleReasoner.class, Level.OFF); setLoggerLevel(SimpleReasoner.class, Level.OFF);
setLoggerLevel(SimpleReasonerTBoxListener.class, Level.OFF);
} }
/* /*
@ -51,7 +52,6 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Create a Tbox with a simple class hierarchy. B is a subclass of A. // Create a Tbox with a simple class hierarchy. B is a subclass of A.
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntClass classA = tBox.createClass("http://test.vivo/A"); OntClass classA = tBox.createClass("http://test.vivo/A");
classA.setLabel("class A", "en-US"); classA.setLabel("class A", "en-US");
@ -90,7 +90,6 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Create a Tbox with a simple class hierarchy. D and E are subclasses // 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. // of C. B and C are subclasses of A. Pellet will compute TBox inferences.
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntClass classA = tBox.createClass("http://test.vivo/A"); OntClass classA = tBox.createClass("http://test.vivo/A");
classA.setLabel("class A", "en-US"); classA.setLabel("class A", "en-US");
@ -137,20 +136,20 @@ public class SimpleReasonerTest extends AbstractTestClass {
* Test inference based on class equivalence * Test inference based on class equivalence
*/ */
@Test @Test
public void addABoxTypeAssertion3(){ public void addABoxTypeAssertion3() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add classes A, B and C to the TBox // Add classes A, B and C to the TBox
// A is equivalent to B // A is equivalent to B
@ -168,6 +167,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classA.addEquivalentClass(classB); classA.addEquivalentClass(classB);
classA.addSubClass(classC); classA.addSubClass(classC);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add a statement that individual x is of type C to the ABox // Add a statement that individual x is of type C to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classC); aBox.add(ind_x, RDF.type, classC);
@ -179,26 +182,28 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Verify that "x is of type B" was inferred // Verify that "x is of type B" was inferred
Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB); Statement xisb = ResourceFactory.createStatement(ind_x, RDF.type, classB);
Assert.assertTrue(inf.contains(xisb)); Assert.assertTrue(inf.contains(xisb));
simpleReasonerTBoxListener.setStopRequested();;
} }
/* /*
* Test inference based on class equivalence * Test inference based on class equivalence
*/ */
@Test @Test
public void addABoxTypeAssertion4() { public void addABoxTypeAssertion4() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add classes A and B to the TBox // Add classes A and B to the TBox
// A is equivalent to B // A is equivalent to B
@ -211,6 +216,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classA.addEquivalentClass(classB); classA.addEquivalentClass(classB);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add a statement that individual x is of type B to the ABox // Add a statement that individual x is of type B to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB); aBox.add(ind_x, RDF.type, classB);
@ -218,6 +227,8 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Verify that "x is of type A" was inferred // Verify that "x is of type A" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa)); Assert.assertTrue(inf.contains(xisa));
simpleReasonerTBoxListener.setStopRequested();
} }
@ -225,20 +236,20 @@ public class SimpleReasonerTest extends AbstractTestClass {
* Test inference based on class equivalence * Test inference based on class equivalence
*/ */
@Test @Test
public void addABoxTypeAssertion5() { public void addABoxTypeAssertion5() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add classes classes A and B to the TBox // Add classes classes A and B to the TBox
// A is equivalent to B // A is equivalent to B
@ -251,6 +262,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classA.addEquivalentClass(classB); classA.addEquivalentClass(classB);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add a statement that individual x is of type B to the ABox // Add a statement that individual x is of type B to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB); aBox.add(ind_x, RDF.type, classB);
@ -264,6 +279,8 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Verify that "x is of type A" was removed from the inference graph // Verify that "x is of type A" was removed from the inference graph
Assert.assertFalse(inf.contains(xisa)); Assert.assertFalse(inf.contains(xisa));
simpleReasonerTBoxListener.setStopRequested();
} }
/* /*
@ -281,7 +298,6 @@ public class SimpleReasonerTest extends AbstractTestClass {
// and B is a subclass of A. Pellet will compute TBox inferences. // and B is a subclass of A. Pellet will compute TBox inferences.
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntClass classA = tBox.createClass("http://test.vivo/A"); OntClass classA = tBox.createClass("http://test.vivo/A");
classA.setLabel("class A", "en-US"); classA.setLabel("class A", "en-US");
@ -340,20 +356,20 @@ public class SimpleReasonerTest extends AbstractTestClass {
* as a test of equivalentClass statements also. * as a test of equivalentClass statements also.
*/ */
@Test @Test
public void addTBoxSubClassAssertion1(){ public void addTBoxSubClassAssertion1() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add classes classes A, B, C and D to the TBox // Add classes classes A, B, C and D to the TBox
@ -377,6 +393,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classA.addSubClass(classC); classA.addSubClass(classC);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Verify that "x is of type A" was inferred // Verify that "x is of type A" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa)); Assert.assertTrue(inf.contains(xisa));
@ -389,6 +409,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
Statement xisd = ResourceFactory.createStatement(ind_x, RDF.type, classD); Statement xisd = ResourceFactory.createStatement(ind_x, RDF.type, classD);
Assert.assertFalse(inf.contains(xisd)); Assert.assertFalse(inf.contains(xisd));
simpleReasonerTBoxListener.setStopRequested();
} }
/* /*
@ -408,20 +429,20 @@ public class SimpleReasonerTest extends AbstractTestClass {
* *
*/ */
@Test @Test
public void addTBoxSubClassAssertion2() { public void addTBoxSubClassAssertion2() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add classes classes A, B, C and D to the TBox // Add classes classes A, B, C and D to the TBox
// D is a subclass of C // D is a subclass of C
@ -440,6 +461,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classC.addSubClass(classD); classC.addSubClass(classD);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add a statement that individual x is of type D to the ABox // Add a statement that individual x is of type D to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classD); aBox.add(ind_x, RDF.type, classD);
@ -447,9 +472,15 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Add a statement that C is a subclass of A to the TBox // Add a statement that C is a subclass of A to the TBox
classA.addSubClass(classC); classA.addSubClass(classC);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Verify that "x is of type A" was inferred // Verify that "x is of type A" was inferred
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertTrue(inf.contains(xisa)); Assert.assertTrue(inf.contains(xisa));
simpleReasonerTBoxListener.setStopRequested();
} }
@Test @Test
@ -469,19 +500,19 @@ public class SimpleReasonerTest extends AbstractTestClass {
* as a test of equivalentClass assertions also. * as a test of equivalentClass assertions also.
* *
*/ */
public void removeTBoxSubClassAssertion1(){ public void removeTBoxSubClassAssertion1() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add classes A, B, C, D, E, F, G and H to the TBox. // Add classes A, B, C, D, E, F, G and H to the TBox.
// B, C and D are subclasses of A. // B, C and D are subclasses of A.
@ -521,6 +552,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classC.addSubClass(classG); classC.addSubClass(classG);
classD.addSubClass(classH); classD.addSubClass(classH);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add a statement that individual x is of type E to the ABox // Add a statement that individual x is of type E to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classE); aBox.add(ind_x, RDF.type, classE);
@ -528,6 +563,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Remove the statement that B is a subclass of A from the TBox // Remove the statement that B is a subclass of A from the TBox
classA.removeSubClass(classB); classA.removeSubClass(classB);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Verify that "x is of type A" is not in the inference graph // Verify that "x is of type A" is not in the inference graph
Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA); Statement xisa = ResourceFactory.createStatement(ind_x, RDF.type, classA);
Assert.assertFalse(inf.contains(xisa)); Assert.assertFalse(inf.contains(xisa));
@ -544,9 +583,15 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Remove the statement that C is a subclass of A from the TBox // Remove the statement that C is a subclass of A from the TBox
classA.removeSubClass(classC); classA.removeSubClass(classC);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Verify that "y is of type A" is in the inference graph // Verify that "y is of type A" is in the inference graph
Statement yisa = ResourceFactory.createStatement(ind_y, RDF.type, classA); Statement yisa = ResourceFactory.createStatement(ind_y, RDF.type, classA);
Assert.assertTrue(inf.contains(yisa)); Assert.assertTrue(inf.contains(yisa));
simpleReasonerTBoxListener.setStopRequested();
} }
@ -554,20 +599,20 @@ public class SimpleReasonerTest extends AbstractTestClass {
* tests rdfs:subPropertyOf materialization for object properties. * tests rdfs:subPropertyOf materialization for object properties.
*/ */
// @Test uncomment when sub/equiv property inferencing is enabled. sjm222 5/13/2011 // @Test uncomment when sub/equiv property inferencing is enabled. sjm222 5/13/2011
public void addABoxAssertion1(){ public void addABoxAssertion1() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add object properties propA and propB to the TBox. // Add object properties propA and propB to the TBox.
// propB is a sub-property of propA. // propB is a sub-property of propA.
@ -604,13 +649,13 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add object properties propA and propB to the TBox. // Add object properties propA and propB to the TBox.
// propB is a sub-property of propA. // propB is a sub-property of propA.
@ -646,13 +691,13 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add properties A, B and C to the TBox // Add properties A, B and C to the TBox
// A is equivalent to B // A is equivalent to B
@ -701,13 +746,13 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add object properties propA and propB to the TBox. // Add object properties propA and propB to the TBox.
// propB is a sub-property of propA. // propB is a sub-property of propA.
@ -744,13 +789,13 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add properties A and B to the TBox // Add properties A and B to the TBox
// A is equivalent to B // A is equivalent to B
@ -801,13 +846,13 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add properties A, B, C and D to the TBox // Add properties A, B, C and D to the TBox
OntProperty propA = tBox.createOntProperty("http://test.vivo/A"); OntProperty propA = tBox.createOntProperty("http://test.vivo/A");
@ -869,13 +914,13 @@ public class SimpleReasonerTest extends AbstractTestClass {
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC); OntModel tBox = ModelFactory.createOntologyModel(PelletReasonerFactory.THE_SPEC);
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM); OntModel aBox = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
Model inf = ModelFactory.createDefaultModel(); Model inf = ModelFactory.createDefaultModel();
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Add properties A, B, C, D, E, F, G and H to the TBox. // Add properties A, B, C, D, E, F, G and H to the TBox.
// B, C and D are subproperties of A. // B, C and D are subproperties of A.
@ -960,7 +1005,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
* to an added/removed ABox type assertion. * to an added/removed ABox type assertion.
*/ */
@Test @Test
public void mstTest1(){ public void mstTest1() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
@ -971,7 +1016,8 @@ public class SimpleReasonerTest extends AbstractTestClass {
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Set up the Tbox with a class hierarchy. C is a subclass of A // Set up the Tbox with a class hierarchy. C is a subclass of A
// and Y. D and E are subclasses C. B is a subclass of D. // and Y. D and E are subclasses C. B is a subclass of D.
@ -1005,6 +1051,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
classD.addSubClass(classB); classD.addSubClass(classB);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add the statement individual x is of type Y to the ABox // Add the statement individual x is of type Y to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classD); aBox.add(ind_x, RDF.type, classD);
@ -1023,6 +1073,8 @@ public class SimpleReasonerTest extends AbstractTestClass {
aBox.remove(ind_x, RDF.type, classD); // retract assertion that x is of type D. aBox.remove(ind_x, RDF.type, classD); // retract assertion that x is of type D.
// Verify that D is not longer the most specific type // Verify that D is not longer the most specific type
Assert.assertFalse(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classD.getURI()))); Assert.assertFalse(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
simpleReasonerTBoxListener.setStopRequested();
} }
@ -1031,7 +1083,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
* to an added ABox type assertion. * to an added ABox type assertion.
*/ */
@Test @Test
public void mstTest2(){ public void mstTest2() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
@ -1042,7 +1094,8 @@ public class SimpleReasonerTest extends AbstractTestClass {
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
// Set up the Tbox with a class hierarchy. B is a subclass of A, // Set up the Tbox with a class hierarchy. B is a subclass of A,
// C is a subclass of B, and A is a subclass of C. // C is a subclass of B, and A is a subclass of C.
@ -1063,16 +1116,20 @@ public class SimpleReasonerTest extends AbstractTestClass {
classB.addSubClass(classC); classB.addSubClass(classC);
classC.addSubClass(classA); classC.addSubClass(classA);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// Add the statement individual x is of type B to the ABox // Add the statement individual x is of type B to the ABox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
aBox.add(ind_x, RDF.type, classB); aBox.add(ind_x, RDF.type, classB);
StmtIterator stmtIterator = aBox.listStatements(ind_x, mostSpecificType, (RDFNode)null);
// Verify ind_x mostSpecificType annotation for A, B and C // Verify ind_x mostSpecificType annotation for A, B and C
Assert.assertTrue(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classA.getURI()))); Assert.assertTrue(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classA.getURI())));
Assert.assertTrue(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classB.getURI()))); Assert.assertTrue(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classB.getURI())));
Assert.assertTrue(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classC.getURI()))); Assert.assertTrue(inf.contains(ind_x, mostSpecificType, ResourceFactory.createResource(classC.getURI())));
simpleReasonerTBoxListener.setStopRequested();
} }
/* /*
@ -1080,7 +1137,7 @@ public class SimpleReasonerTest extends AbstractTestClass {
* to an added/removed TBox assertions. * to an added/removed TBox assertions.
*/ */
@Test @Test
public void mstTest3(){ public void mstTest3() throws InterruptedException {
// Create TBox, ABox and Inference models and register // Create TBox, ABox and Inference models and register
// the ABox reasoner listeners with the ABox and TBox // the ABox reasoner listeners with the ABox and TBox
// Pellet will compute TBox inferences // Pellet will compute TBox inferences
@ -1091,7 +1148,8 @@ public class SimpleReasonerTest extends AbstractTestClass {
SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf); SimpleReasoner simpleReasoner = new SimpleReasoner(tBox, aBox, inf);
aBox.register(simpleReasoner); aBox.register(simpleReasoner);
tBox.register(new SimpleReasonerTBoxListener(simpleReasoner)); SimpleReasonerTBoxListener simpleReasonerTBoxListener = getTBoxListener(simpleReasoner);
tBox.register(simpleReasonerTBoxListener);
OntClass OWL_THING = tBox.createClass(OWL.Thing.getURI()); OntClass OWL_THING = tBox.createClass(OWL.Thing.getURI());
AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI); AnnotationProperty mostSpecificType = tBox.createAnnotationProperty(mostSpecificTypePropertyURI);
@ -1120,6 +1178,10 @@ public class SimpleReasonerTest extends AbstractTestClass {
OntClass classG = tBox.createClass("http://test.vivo/G"); OntClass classG = tBox.createClass("http://test.vivo/G");
classE.setLabel("class G", "en-US"); classE.setLabel("class G", "en-US");
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
// add individuals x, y and z to the aBox // add individuals x, y and z to the aBox
Resource ind_x = aBox.createResource("http://test.vivo/x"); Resource ind_x = aBox.createResource("http://test.vivo/x");
Resource ind_y = aBox.createResource("http://test.vivo/y"); Resource ind_y = aBox.createResource("http://test.vivo/y");
@ -1150,14 +1212,28 @@ public class SimpleReasonerTest extends AbstractTestClass {
classD.addSubClass(classF); classD.addSubClass(classF);
classD.addSubClass(classG); classD.addSubClass(classG);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
Assert.assertFalse(inf.contains(ind_y, mostSpecificType, ResourceFactory.createResource(classD.getURI()))); Assert.assertFalse(inf.contains(ind_y, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
Assert.assertTrue(inf.contains(ind_y, mostSpecificType, ResourceFactory.createResource(classF.getURI()))); Assert.assertTrue(inf.contains(ind_y, mostSpecificType, ResourceFactory.createResource(classF.getURI())));
// If F is removed as a subclass of D, then D should once again be a most specific type // If F is removed as a subclass of D, then D should once again be a most specific type
// for y. // for y.
classD.removeSubClass(classF); classD.removeSubClass(classF);
while (!VitroBackgroundThread.getLivingThreads().isEmpty()) {
Thread.sleep(delay);
}
Assert.assertTrue(inf.contains(ind_y, mostSpecificType, ResourceFactory.createResource(classD.getURI()))); Assert.assertTrue(inf.contains(ind_y, mostSpecificType, ResourceFactory.createResource(classD.getURI())));
simpleReasonerTBoxListener.setStopRequested();
}
SimpleReasonerTBoxListener getTBoxListener(SimpleReasoner simpleReasoner) {
return new SimpleReasonerTBoxListener(simpleReasoner, new Exception().getStackTrace()[1].getMethodName());
} }
// To help in debugging the unit test // To help in debugging the unit test