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merging SimpleReasoner from 1.5 branch

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This commit is contained in:
stellamit 2012-07-12 20:35:20 +00:00
parent 00cbf83d69
commit 39f852dc38
1 changed files with 145 additions and 84 deletions
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211
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
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@ -220,15 +220,8 @@ public class SimpleReasoner extends StatementListener {
return;
}
//log.debug("added TBox assertion = " + stmt.toString());
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
if (!stmt.getObject().isResource()) {
log.warn("The object of this assertion is not a resource: " + stmtString(stmt));
return;
}
@ -258,6 +251,16 @@ public class SimpleReasoner extends StatementListener {
addedSubClass(object,subject,inferenceModel);
}
} else {
if ( stmt.getObject().asResource().getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
@ -290,15 +293,8 @@ public class SimpleReasoner extends StatementListener {
return;
}
//log.debug("removed TBox assertion = " + stmt.toString());
if ( stmt.getObject().isResource() && (stmt.getObject().asResource()).getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
if (!stmt.getObject().isResource()) {
log.warn("The object of this assertion is not a resource: " + stmtString(stmt));
return;
}
@ -329,6 +325,16 @@ public class SimpleReasoner extends StatementListener {
removedSubClass(object,subject,inferenceModel);
}
} else {
if ( stmt.getObject().asResource().getURI() == null ) {
log.warn("The object of this assertion has a null URI: " + stmtString(stmt));
return;
}
if ( stmt.getSubject().getURI() == null ) {
log.warn("The subject of this assertion has a null URI: " + stmtString(stmt));
return;
}
OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
@ -361,24 +367,18 @@ public class SimpleReasoner extends StatementListener {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntClass cls = null;
Resource cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) {
cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
cls = tboxModel.getResource(stmt.getObject().asResource().getURI());
if (cls != null) {
List<OntClass> parents = null;
try {
parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList());
} catch (ConversionException ce) {
parents = getParents(cls,tboxModel);
}
List<Resource> parents = getParents(cls,tboxModel);
Iterator<OntClass> parentIt = parents.iterator();
Iterator<Resource> parentIt = parents.iterator();
if (parentIt.hasNext()) {
while (parentIt.hasNext()) {
OntClass parentClass = parentIt.next();
Resource parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is
@ -400,7 +400,7 @@ public class SimpleReasoner extends StatementListener {
}
}
} else {
log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
log.debug("The object of this rdf:type assertion has a null URI, no reasoning will be done based on this assertion: " + stmtString(stmt));
return;
}
} finally {
@ -426,29 +426,23 @@ public class SimpleReasoner extends StatementListener {
protected void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ);
try {
OntClass cls = null;
Resource cls = null;
if ( (stmt.getObject().asResource()).getURI() != null ) {
cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
cls = tboxModel.getResource(stmt.getObject().asResource().getURI());
if (cls != null) {
if (entailedType(stmt.getSubject(),cls)) {
addInference(stmt,inferenceModel,true);
}
List<OntClass> parents = null;
try {
parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList());
} catch (ConversionException ce) {
parents = getParents(cls,tboxModel);
}
List<Resource> parents = getParents(cls,tboxModel);
Iterator<OntClass> parentIt = parents.iterator();
Iterator<Resource> parentIt = parents.iterator();
while (parentIt.hasNext()) {
OntClass parentClass = parentIt.next();
Resource parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is
@ -889,34 +883,87 @@ public class SimpleReasoner extends StatementListener {
// Returns true if it is entailed by class subsumption that
// subject is of type cls; otherwise returns false.
protected boolean entailedType(Resource subject, OntClass cls) {
protected boolean entailedType(Resource subject, Resource cls) {
List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel);
sameIndividuals.add(subject);
tboxModel.enterCriticalSection(Lock.READ);
List<Resource> subClasses = getSubClasses(cls);
aboxModel.enterCriticalSection(Lock.READ);
try {
aboxModel.enterCriticalSection(Lock.READ);
try {
List<OntClass> subclasses = null;
subclasses = (cls.listSubClasses(false)).toList();
subclasses.addAll((cls.listEquivalentClasses()).toList());
Iterator<OntClass> iter = subclasses.iterator();
while (iter.hasNext()) {
OntClass childClass = iter.next();
if (childClass.equals(cls)) continue; // TODO - determine whether this is needed
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Statement stmt = ResourceFactory.createStatement(sameIter.next(), RDF.type, childClass);
if (aboxModel.contains(stmt)) {
return true;
}
Iterator<Resource> iter = subClasses.iterator();
while (iter.hasNext()) {
Resource childClass = iter.next();
if (childClass.equals(cls)) continue;
Iterator<Resource> sameIter = sameIndividuals.iterator();
while (sameIter.hasNext()) {
Statement stmt = ResourceFactory.createStatement(sameIter.next(), RDF.type, childClass);
if (aboxModel.contains(stmt)) {
return true;
}
}
return false;
} finally {
aboxModel.leaveCriticalSection();
}
return false;
} finally {
aboxModel.leaveCriticalSection();
}
}
protected List<Resource> getSubClasses(Resource cls) {
List<Resource> subClasses = new ArrayList<Resource>();
tboxModel.enterCriticalSection(Lock.READ);
try {
Iterator<Statement> iter = tboxModel.listStatements((Resource) null, RDFS.subClassOf, cls);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (stmt.getSubject() == null || stmt.getSubject().asResource().getURI() == null) continue;
if (!subClasses.contains(stmt.getSubject())) {
subClasses.add(stmt.getSubject());
}
}
iter = tboxModel.listStatements((Resource) null, OWL.equivalentClass, cls);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (stmt.getSubject() == null || stmt.getSubject().getURI() == null) continue;
if (!subClasses.contains(stmt.getSubject())) {
subClasses.add(stmt.getSubject());
}
}
return subClasses;
} finally {
tboxModel.leaveCriticalSection();
}
}
protected List<Resource> getSuperClasses(Resource cls) {
List<Resource> superClasses = new ArrayList<Resource>();
tboxModel.enterCriticalSection(Lock.READ);
try {
Iterator<Statement> iter = tboxModel.listStatements(cls, RDFS.subClassOf, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (stmt.getObject() != null && stmt.getObject().isResource()) {
Resource superCls = stmt.getObject().asResource();
if (superCls.isAnon() || superClasses.contains(superCls)) {
continue;
}
superClasses.add(superCls);
}
}
iter = tboxModel.listStatements((Resource) null, OWL.equivalentClass, cls);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (stmt.getSubject() == null || stmt.getSubject().asResource().getURI() == null) continue;
if (!superClasses.contains(stmt.getSubject())) {
superClasses.add(stmt.getSubject());
}
}
return superClasses;
} finally {
tboxModel.leaveCriticalSection();
}
@ -1162,7 +1209,7 @@ public class SimpleReasoner extends StatementListener {
if ( (stmt.getObject().asResource()).getURI() != null ) {
ontClass = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
} else {
log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
log.debug("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
continue;
}
@ -1170,7 +1217,7 @@ public class SimpleReasoner extends StatementListener {
if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) {
if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) {
unknownTypes.add(stmt.getObject().asResource().getURI());
log.warn("Didn't find the target class (the object of an asserted or inferred rdf:type statement) in the TBox: " +
log.debug("Didn't find the target class (the object of an asserted or inferred rdf:type statement) in the TBox: " +
(stmt.getObject().asResource()).getURI() + ". No mostSpecificType computation will be done based on " + (stmt.getObject().asResource()).getURI() + " type statements.");
}
}
@ -1208,10 +1255,22 @@ public class SimpleReasoner extends StatementListener {
if (add) {
typeURIs.add(type.getURI());
Iterator<OntClass> eIter = type.listEquivalentClasses();
ArrayList<Resource> equivalentClasses = new ArrayList<Resource>();
Iterator<Statement> iter = tboxModel.listStatements((Resource) null, OWL.equivalentClass, type);
while (iter.hasNext()) {
Statement stmt = iter.next();
Resource res = stmt.getSubject();
if ((res == null) || res.isAnon() || equivalentClasses.contains(res) ) {
continue;
}
equivalentClasses.add(res);
}
Iterator<Resource> eIter = equivalentClasses.iterator();
while (eIter.hasNext()) {
OntClass equivClass = eIter.next();
Resource equivClass = eIter.next();
if (equivClass.isAnon()) continue;
typeURIs.add(equivClass.getURI());
}
@ -1267,29 +1326,31 @@ public class SimpleReasoner extends StatementListener {
return;
}
protected List<OntClass> getParents(OntClass cls, OntModel tboxModel) {
protected List<Resource> getParents(Resource cls, OntModel tboxModel) {
List<OntClass> parents = new ArrayList<OntClass>();
List<Resource> parents = new ArrayList<Resource>();
tboxModel.enterCriticalSection(Lock.READ);
try {
StmtIterator iter = tboxModel.listStatements(cls, RDFS.subClassOf, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!stmt.getObject().isAnon() && stmt.getObject().canAs(OntClass.class)) {
if (!parents.contains(stmt.getObject().as(OntClass.class))) {
parents.add(stmt.getObject().as(OntClass.class));
}
if (stmt.getObject() == null || !stmt.getObject().isResource() || stmt.getObject().asResource().isAnon()) {
continue;
}
if (!parents.contains(stmt.getObject().asResource())) {
parents.add(stmt.getObject().asResource());
}
}
iter = tboxModel.listStatements(cls, OWL.equivalentClass, (RDFNode) null);
while (iter.hasNext()) {
Statement stmt = iter.next();
if (!stmt.getObject().isAnon() && stmt.getObject().canAs(OntClass.class)) {
if (!parents.contains(stmt.getObject().as(OntClass.class))) {
parents.add(stmt.getObject().as(OntClass.class));
}
if (stmt.getObject() == null || !stmt.getObject().isResource() || stmt.getObject().asResource().isAnon()) {
continue;
}
if (!parents.contains(stmt.getObject().asResource())) {
parents.add(stmt.getObject().asResource());
}
}
} catch (Exception e) {