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development for NIHVIVO-2410 (specific type inference in lieu of moniker)

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This commit is contained in:
stellamit 2011-05-10 15:43:59 +00:00
parent 73e0916a04
commit 132cbdce2c
2 changed files with 303 additions and 41 deletions
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117
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
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@ -2,6 +2,7 @@
package edu.cornell.mannlib.vitro.webapp.reasoner;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
@ -35,8 +36,7 @@ import com.hp.hpl.jena.vocabulary.RDFS;
/**
* Allows for real-time incremental materialization or retraction of RDFS-
* style class and property subsumption based ABox inferences as statements
* are added to or removed from the (ABox or TBox) knowledge base.
*
* are added to or removed from the (ABox or TBox) knowledge base.
*/
public class SimpleReasoner extends StatementListener {
@ -101,6 +101,7 @@ public class SimpleReasoner extends StatementListener {
try {
if (stmt.getPredicate().equals(RDF.type)) {
addedABoxTypeAssertion(stmt, inferenceModel);
setMostSpecificTypes(stmt.getSubject(), inferenceModel);
} else {
addedABoxAssertion(stmt,inferenceModel);
}
@ -121,6 +122,7 @@ public class SimpleReasoner extends StatementListener {
try {
if (stmt.getPredicate().equals(RDF.type)) {
removedABoxTypeAssertion(stmt, inferenceModel);
setMostSpecificTypes(stmt.getSubject(), inferenceModel);
} else {
removedABoxAssertion(stmt, inferenceModel);
}
@ -156,22 +158,22 @@ public class SimpleReasoner extends StatementListener {
OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
if (stmt.getPredicate().equals(RDFS.subClassOf)) {
addedSubClass(subject,object);
addedSubClass(subject,object,inferenceModel);
} else {
// equivalent class is the same as subclass in both directions
addedSubClass(subject,object);
addedSubClass(object,subject);
addedSubClass(subject,object,inferenceModel);
addedSubClass(object,subject,inferenceModel);
}
} 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);
addedSubProperty(subject,object,inferenceModel);
} else {
// equivalent property is the same as subProperty in both directions
addedSubProperty(subject, object, inferenceModel);
addedSubProperty(object, subject, inferenceModel);
addedSubProperty(subject,object,inferenceModel);
addedSubProperty(object,subject,inferenceModel);
}
}
} catch (Exception e) {
@ -202,11 +204,11 @@ public class SimpleReasoner extends StatementListener {
OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
if (stmt.getPredicate().equals(RDFS.subClassOf)) {
removedSubClass(subject,object);
removedSubClass(subject,object,inferenceModel);
} else {
// equivalent class is the same as subclass in both directions
removedSubClass(subject,object);
removedSubClass(object,subject);
removedSubClass(subject,object,inferenceModel);
removedSubClass(object,subject,inferenceModel);
}
} else if (stmt.getPredicate().equals(RDFS.subPropertyOf) || stmt.getPredicate().equals(OWL.equivalentProperty)) {
OntProperty subject = tboxModel.getOntProperty((stmt.getSubject()).getURI());
@ -494,11 +496,11 @@ public class SimpleReasoner extends StatementListener {
* individual that is typed as B, either in the ABox or in the
* inferred model, assert that it is of type A.
*/
public void addedSubClass(OntClass subClass, OntClass superClass) {
public void addedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
log.debug("subClass = " + subClass.getURI() + " superClass = " + superClass.getURI());
aboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.WRITE);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
@ -517,6 +519,7 @@ public class SimpleReasoner extends StatementListener {
if (!inferenceModel.contains(infStmt)) {
inferenceModel.add(infStmt);
setMostSpecificTypes(infStmt.getSubject(), inferenceModel);
}
}
} finally {
@ -532,11 +535,11 @@ public class SimpleReasoner extends StatementListener {
* UNLESS the individual is of some type C that is a subClass
* of A (including A itself)
*/
public void removedSubClass(OntClass subClass, OntClass superClass) {
public void removedSubClass(OntClass subClass, OntClass superClass, Model inferenceModel) {
log.debug("subClass = " + subClass.getURI() + ". superClass = " + superClass.getURI());
aboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.WRITE);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
@ -559,6 +562,7 @@ public class SimpleReasoner extends StatementListener {
if (inferenceModel.contains(infStmt)) {
inferenceModel.remove(infStmt);
setMostSpecificTypes(infStmt.getSubject(), inferenceModel);
}
}
} finally {
@ -661,9 +665,9 @@ public class SimpleReasoner extends StatementListener {
* indicate them for the individual with the core:mostSpecificType
* annotation.
*/
public void setMostSpecificTypes(Resource individual) {
public void setMostSpecificTypes(Resource individual, Model inferenceModel) {
aboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.WRITE);
inferenceModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
@ -672,12 +676,13 @@ public class SimpleReasoner extends StatementListener {
unionModel.addSubModel(aboxModel);
unionModel.addSubModel(inferenceModel);
HashSet<String> typeURIs = new HashSet<String>();
StmtIterator iter = unionModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
List<OntClass> types = new ArrayList<OntClass>();
StmtIterator stmtIter = unionModel.listStatements(individual, RDF.type, (RDFNode) null);
while (iter.hasNext()) {
while (stmtIter.hasNext()) {
Statement stmt = iter.next();
Statement stmt = stmtIter.next();
if ( !stmt.getObject().isResource() ) {
log.warn("The object of this rdf:type assertion is expected to be a resource: " + stmtString(stmt));
@ -692,21 +697,48 @@ public class SimpleReasoner extends StatementListener {
}
if (ontClass.isAnon()) continue;
if (ontClass.hasSubClass()) continue;
typeURIs.add(ontClass.getURI());
Iterator<OntClass> eIter = ontClass.listEquivalentClasses();
while (eIter.hasNext()) {
OntClass equivClass = eIter.next();
if (equivClass.isAnon()) continue;
typeURIs.add(equivClass.getURI());
}
types.add(ontClass);
}
HashSet<String> typeURIs = new HashSet<String>();
List<OntClass> types2 = new ArrayList<OntClass>();
types2.addAll(types);
setMostSpecificTypes(individual, typeURIs);
Iterator<OntClass> typeIter = types.iterator();
while (typeIter.hasNext()) {
OntClass type = typeIter.next();
boolean add = true;
Iterator<OntClass> typeIter2 = types2.iterator();
while (typeIter2.hasNext()) {
OntClass type2 = typeIter2.next();
if (type.equals(type2)) {
continue;
}
if (type.hasSubClass(type2, false) && !type2.hasSubClass(type, false)) {
add = false;
break;
}
}
if (add) {
typeURIs.add(type.getURI());
Iterator<OntClass> eIter = type.listEquivalentClasses();
while (eIter.hasNext()) {
OntClass equivClass = eIter.next();
if (equivClass.isAnon()) continue;
typeURIs.add(equivClass.getURI());
}
}
}
setMostSpecificTypes(individual, typeURIs, inferenceModel);
} finally {
aboxModel.leaveCriticalSection();
@ -717,27 +749,30 @@ public class SimpleReasoner extends StatementListener {
return;
}
public void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs) {
public void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs, Model inferenceModel) {
aboxModel.enterCriticalSection(Lock.WRITE);
try {
Model retractions = ModelFactory.createDefaultModel();
// remove obsolete most-specific-type assertions
StmtIterator iter = aboxModel.listStatements((Resource) null, mostSpecificType, (RDFNode) null);
StmtIterator iter = aboxModel.listStatements(individual, mostSpecificType, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if ( !stmt.getObject().isLiteral() ) {
log.warn("The object of this assertion is expected to be a literal: " + stmtString(stmt));
continue;
}
if (!typeURIs.contains(stmt.getObject().asLiteral().getLexicalForm())) {
aboxModel.remove(stmt);
retractions.add(stmt);
}
}
aboxModel.remove(retractions);
// add new most-specific-type assertions
Iterator<String> typeIter = typeURIs.iterator();
@ -746,6 +781,7 @@ public class SimpleReasoner extends StatementListener {
Literal uriLiteral = ResourceFactory.createTypedLiteral(typeURI, XSDDatatype.XSDanyURI);
if (!aboxModel.contains(individual, mostSpecificType, uriLiteral)) {
Statement toAdd = ResourceFactory.createStatement(individual, mostSpecificType, uriLiteral);
aboxModel.add(individual, mostSpecificType, uriLiteral);
}
}
@ -791,7 +827,7 @@ public class SimpleReasoner extends StatementListener {
// recompute the inferences
inferenceRebuildModel.enterCriticalSection(Lock.WRITE);
aboxModel.enterCriticalSection(Lock.READ);
aboxModel.enterCriticalSection(Lock.WRITE);
tboxModel.enterCriticalSection(Lock.READ);
try {
@ -802,6 +838,7 @@ public class SimpleReasoner extends StatementListener {
while (iter.hasNext()) {
Statement stmt = iter.next();
addedABoxTypeAssertion(stmt, inferenceRebuildModel);
setMostSpecificTypes(stmt.getSubject(), inferenceRebuildModel);
}
log.info("Computing property-based ABox inferences");