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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; return;
} }
//log.debug("added TBox assertion = " + stmt.toString()); if (!stmt.getObject().isResource()) {
log.warn("The object of this assertion is not a resource: " + stmtString(stmt));
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));
return; return;
} }
@ -258,6 +251,16 @@ public class SimpleReasoner extends StatementListener {
addedSubClass(object,subject,inferenceModel); addedSubClass(object,subject,inferenceModel);
} }
} else { } 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()); OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) { if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI()); log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI());
@ -290,15 +293,8 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
//log.debug("removed TBox assertion = " + stmt.toString()); if (!stmt.getObject().isResource()) {
log.warn("The object of this assertion is not a resource: " + stmtString(stmt));
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));
return; return;
} }
@ -329,6 +325,16 @@ public class SimpleReasoner extends StatementListener {
removedSubClass(object,subject,inferenceModel); removedSubClass(object,subject,inferenceModel);
} }
} else { } 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()); OntProperty prop1 = tboxModel.getOntProperty((stmt.getSubject()).getURI());
if (prop1 == null) { if (prop1 == null) {
log.debug("didn't find subject property in the tbox: " + (stmt.getSubject()).getURI()); 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); tboxModel.enterCriticalSection(Lock.READ);
try { try {
OntClass cls = null; Resource cls = null;
if ( (stmt.getObject().asResource()).getURI() != 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 (cls != null) {
List<OntClass> parents = null; List<Resource> parents = getParents(cls,tboxModel);
try {
parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList());
} catch (ConversionException ce) {
parents = getParents(cls,tboxModel);
}
Iterator<OntClass> parentIt = parents.iterator(); Iterator<Resource> parentIt = parents.iterator();
if (parentIt.hasNext()) { if (parentIt.hasNext()) {
while (parentIt.hasNext()) { while (parentIt.hasNext()) {
OntClass parentClass = parentIt.next(); Resource parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types // VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is // for individuals. Also, sharing an identical anonymous node is
@ -400,7 +400,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
} else { } 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; return;
} }
} finally { } finally {
@ -426,29 +426,23 @@ public class SimpleReasoner extends StatementListener {
protected void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) { protected void removedABoxTypeAssertion(Statement stmt, Model inferenceModel) {
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
try { try {
OntClass cls = null; Resource cls = null;
if ( (stmt.getObject().asResource()).getURI() != 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 (cls != null) {
if (entailedType(stmt.getSubject(),cls)) { if (entailedType(stmt.getSubject(),cls)) {
addInference(stmt,inferenceModel,true); addInference(stmt,inferenceModel,true);
} }
List<OntClass> parents = null; List<Resource> parents = getParents(cls,tboxModel);
try {
parents = (cls.listSuperClasses(false)).toList();
parents.addAll((cls.listEquivalentClasses()).toList());
} catch (ConversionException ce) {
parents = getParents(cls,tboxModel);
}
Iterator<OntClass> parentIt = parents.iterator(); Iterator<Resource> parentIt = parents.iterator();
while (parentIt.hasNext()) { while (parentIt.hasNext()) {
OntClass parentClass = parentIt.next(); Resource parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types // VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is // 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 // 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.
protected boolean entailedType(Resource subject, OntClass cls) { protected boolean entailedType(Resource subject, Resource cls) {
List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel); List<Resource> sameIndividuals = getSameIndividuals(subject,inferenceModel);
sameIndividuals.add(subject); sameIndividuals.add(subject);
tboxModel.enterCriticalSection(Lock.READ); List<Resource> subClasses = getSubClasses(cls);
aboxModel.enterCriticalSection(Lock.READ);
try { try {
aboxModel.enterCriticalSection(Lock.READ); Iterator<Resource> iter = subClasses.iterator();
try { while (iter.hasNext()) {
List<OntClass> subclasses = null; Resource childClass = iter.next();
subclasses = (cls.listSubClasses(false)).toList(); if (childClass.equals(cls)) continue;
subclasses.addAll((cls.listEquivalentClasses()).toList()); Iterator<Resource> sameIter = sameIndividuals.iterator();
Iterator<OntClass> iter = subclasses.iterator(); while (sameIter.hasNext()) {
while (iter.hasNext()) { Statement stmt = ResourceFactory.createStatement(sameIter.next(), RDF.type, childClass);
OntClass childClass = iter.next(); if (aboxModel.contains(stmt)) {
if (childClass.equals(cls)) continue; // TODO - determine whether this is needed return true;
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 { } finally {
tboxModel.leaveCriticalSection(); tboxModel.leaveCriticalSection();
} }
@ -1162,7 +1209,7 @@ public class SimpleReasoner extends StatementListener {
if ( (stmt.getObject().asResource()).getURI() != null ) { if ( (stmt.getObject().asResource()).getURI() != null ) {
ontClass = tboxModel.getOntClass(stmt.getObject().asResource().getURI()); ontClass = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
} else { } 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; continue;
} }
@ -1170,7 +1217,7 @@ public class SimpleReasoner extends StatementListener {
if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) { if ( !(stmt.getObject().asResource().getNameSpace()).equals(OWL.NS)) {
if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) { if (!unknownTypes.contains(stmt.getObject().asResource().getURI())) {
unknownTypes.add(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."); (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) { if (add) {
typeURIs.add(type.getURI()); 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()) { while (eIter.hasNext()) {
OntClass equivClass = eIter.next(); Resource equivClass = eIter.next();
if (equivClass.isAnon()) continue; if (equivClass.isAnon()) continue;
typeURIs.add(equivClass.getURI()); typeURIs.add(equivClass.getURI());
} }
@ -1267,29 +1326,31 @@ public class SimpleReasoner extends StatementListener {
return; 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); tboxModel.enterCriticalSection(Lock.READ);
try { try {
StmtIterator iter = tboxModel.listStatements(cls, RDFS.subClassOf, (RDFNode) null); StmtIterator iter = tboxModel.listStatements(cls, RDFS.subClassOf, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (!stmt.getObject().isAnon() && stmt.getObject().canAs(OntClass.class)) { if (stmt.getObject() == null || !stmt.getObject().isResource() || stmt.getObject().asResource().isAnon()) {
if (!parents.contains(stmt.getObject().as(OntClass.class))) { continue;
parents.add(stmt.getObject().as(OntClass.class)); }
} if (!parents.contains(stmt.getObject().asResource())) {
parents.add(stmt.getObject().asResource());
} }
} }
iter = tboxModel.listStatements(cls, OWL.equivalentClass, (RDFNode) null); iter = tboxModel.listStatements(cls, OWL.equivalentClass, (RDFNode) null);
while (iter.hasNext()) { while (iter.hasNext()) {
Statement stmt = iter.next(); Statement stmt = iter.next();
if (!stmt.getObject().isAnon() && stmt.getObject().canAs(OntClass.class)) { if (stmt.getObject() == null || !stmt.getObject().isResource() || stmt.getObject().asResource().isAnon()) {
if (!parents.contains(stmt.getObject().as(OntClass.class))) { continue;
parents.add(stmt.getObject().as(OntClass.class)); }
} if (!parents.contains(stmt.getObject().asResource())) {
parents.add(stmt.getObject().asResource());
} }
} }
} catch (Exception e) { } catch (Exception e) {