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initial development for NIHVIVO-2410 (most-specific-type annotation)

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This commit is contained in:
stellamit 2011-05-04 18:02:25 +00:00
parent 56e39bef6b
commit 4a082abdc8
1 changed files with 112 additions and 5 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.HashSet;
import java.util.Iterator;
import java.util.List;
@ -10,6 +11,8 @@ import javax.servlet.ServletContext;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import com.hp.hpl.jena.datatypes.xsd.XSDDatatype;
import com.hp.hpl.jena.ontology.AnnotationProperty;
import com.hp.hpl.jena.ontology.OntClass;
import com.hp.hpl.jena.ontology.OntModel;
import com.hp.hpl.jena.ontology.OntModelSpec;
@ -41,16 +44,20 @@ public class SimpleReasoner extends StatementListener {
private static final Log log = LogFactory.getLog(SimpleReasoner.class);
//private static final MyTempLogger log = new MyTempLogger();
private OntModel tboxModel;
private OntModel aboxModel;
private Model inferenceModel;
private Model inferenceRebuildModel;
private Model scratchpadModel;
private OntModel tboxModel; // asserted and inferred TBox axioms
private OntModel aboxModel; // ABox assertions
private Model inferenceModel; // 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 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://vivoweb.org/ontology/core#mostSpecificType";
private AnnotationProperty mostSpecificType = (ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM)).createAnnotationProperty(mostSpecificTypePropertyURI);
/**
* @param tboxModel - input. This model contains both asserted and inferred TBox axioms
@ -648,6 +655,106 @@ public class SimpleReasoner extends StatementListener {
inferenceModel.leaveCriticalSection();
}
}
/*
* Find the most specific types (classes) of an individual and
* indicate them for the individual with the core:mostSpecificType
* annotation.
*/
public void setMostSpecificTypes(Resource individual) {
aboxModel.enterCriticalSection(Lock.READ);
inferenceModel.enterCriticalSection(Lock.READ);
tboxModel.enterCriticalSection(Lock.READ);
try {
OntModel unionModel = ModelFactory.createOntologyModel(OntModelSpec.OWL_MEM);
unionModel.addSubModel(aboxModel);
unionModel.addSubModel(inferenceModel);
HashSet<String> typeURIs = new HashSet<String>();
StmtIterator iter = unionModel.listStatements((Resource) null, RDF.type, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if ( !stmt.getObject().isResource() ) {
log.warn("The object of this rdf:type assertion is expected to be a resource: " + stmtString(stmt));
continue;
}
OntClass ontClass = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
if (ontClass == null) {
log.warn("Didn't find target class (the object of the added rdf:type statement) in the TBox: " + (stmt.getObject().asResource()).getURI());
continue;
}
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());
}
}
setMostSpecificTypes(individual, typeURIs);
} finally {
aboxModel.leaveCriticalSection();
tboxModel.leaveCriticalSection();
inferenceModel.leaveCriticalSection();
}
return;
}
public void setMostSpecificTypes(Resource individual, HashSet<String> typeURIs) {
aboxModel.enterCriticalSection(Lock.WRITE);
try {
// remove obsolete most-specific-type assertions
StmtIterator iter = aboxModel.listStatements((Resource) null, 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);
}
}
// add new most-specific-type assertions
Iterator<String> typeIter = typeURIs.iterator();
while (typeIter.hasNext()) {
String typeURI = typeIter.next();
Literal uriLiteral = ResourceFactory.createTypedLiteral(typeURI, XSDDatatype.XSDanyURI);
if (!aboxModel.contains(individual, mostSpecificType, uriLiteral)) {
aboxModel.add(individual, mostSpecificType, uriLiteral);
}
}
} finally {
aboxModel.leaveCriticalSection();
}
return;
}
private boolean recomputing = false;