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NIHVIVO-2752 (SimpleReasoner exception when object of TBox statement is null)

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This commit is contained in:
stellamit 2011-06-22 16:19:08 +00:00
parent 61afec8de0
commit 29cb6e4077
1 changed files with 126 additions and 61 deletions
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161
webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java
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@ -76,6 +76,8 @@ public class SimpleReasoner extends StatementListener {
} }
/** /**
* This constructor is used for the unit tests only
*
* @param tboxModel - input. This model contains both asserted and inferred TBox axioms * @param tboxModel - input. This model contains both asserted and inferred TBox axioms
* @param aboxModel - input. This model contains asserted ABox statements * @param aboxModel - input. This model contains asserted ABox statements
* @param inferenceModel - output. This is the model in which inferred (materialized) ABox statements are maintained (added or retracted). * @param inferenceModel - output. This is the model in which inferred (materialized) ABox statements are maintained (added or retracted).
@ -158,8 +160,27 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
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;
}
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI()); OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
if (subject == null) {
log.debug("didn't find subject class in the tbox: " + (stmt.getSubject()).getURI());
return;
}
OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
if (object == null) {
log.debug("didn't find object class in the tbox: " + ((Resource)stmt.getObject()).getURI());
return;
}
if (stmt.getPredicate().equals(RDFS.subClassOf)) { if (stmt.getPredicate().equals(RDFS.subClassOf)) {
addedSubClass(subject,object,inferenceModel); addedSubClass(subject,object,inferenceModel);
@ -208,8 +229,27 @@ public class SimpleReasoner extends StatementListener {
return; return;
} }
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;
}
OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI()); OntClass subject = tboxModel.getOntClass((stmt.getSubject()).getURI());
if (subject == null) {
log.debug("didn't find subject class in the tbox: " + (stmt.getSubject()).getURI());
return;
}
OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); OntClass object = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
if (object == null) {
log.debug("didn't find object class in the tbox: " + ((Resource)stmt.getObject()).getURI());
return;
}
if (stmt.getPredicate().equals(RDFS.subClassOf)) { if (stmt.getPredicate().equals(RDFS.subClassOf)) {
removedSubClass(subject,object,inferenceModel); removedSubClass(subject,object,inferenceModel);
@ -253,36 +293,44 @@ public class SimpleReasoner extends StatementListener {
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
try { try {
OntClass cls = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
if (cls != null) { OntClass cls = null;
List<OntClass> parents = (cls.listSuperClasses(false)).toList(); if ( (stmt.getObject().asResource()).getURI() != null ) {
parents.addAll((cls.listEquivalentClasses()).toList()); cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
Iterator<OntClass> parentIt = parents.iterator();
while (parentIt.hasNext()) { if (cls != null) {
OntClass parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types List<OntClass> parents = (cls.listSuperClasses(false)).toList();
// for individuals. Also, sharing an identical anonymous node is parents.addAll((cls.listEquivalentClasses()).toList());
// not allowed in owl-dl. picklist population code looks at qualities Iterator<OntClass> parentIt = parents.iterator();
// of classes not individuals.
if (parentClass.isAnon()) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), RDF.type, parentClass); while (parentIt.hasNext()) {
inferenceModel.enterCriticalSection(Lock.WRITE); OntClass parentClass = parentIt.next();
try {
if (!inferenceModel.contains(infStmt) && !infStmt.equals(stmt) ) { // VIVO doesn't materialize statements that assert anonymous types
//log.debug("Adding this inferred statement: " + infStmt.toString() ); // for individuals. Also, sharing an identical anonymous node is
inferenceModel.add(infStmt); // not allowed in owl-dl. picklist population code looks at qualities
// of classes not individuals.
if (parentClass.isAnon()) continue;
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), RDF.type, parentClass);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (!inferenceModel.contains(infStmt) && !infStmt.equals(stmt) ) {
//log.debug("Adding this inferred statement: " + infStmt.toString() );
inferenceModel.add(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
} }
} finally {
inferenceModel.leaveCriticalSection();
} }
} else {
log.debug("Didn't find target class (the object of the added rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI());
} }
} else { } else {
log.debug("Didn't find target class (the object of the added rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI()); log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
return;
} }
} finally { } finally {
tboxModel.leaveCriticalSection(); tboxModel.leaveCriticalSection();
@ -340,7 +388,7 @@ public class SimpleReasoner extends StatementListener {
} }
} }
} else { } else {
log.warn("Didn't find target property (the predicate of the added statement) in the TBox: " + stmt.getPredicate().getURI()); log.debug("Didn't find target property (the predicate of the added statement) in the TBox: " + stmt.getPredicate().getURI());
} }
} finally { } finally {
tboxModel.leaveCriticalSection(); tboxModel.leaveCriticalSection();
@ -359,42 +407,52 @@ public class SimpleReasoner extends StatementListener {
tboxModel.enterCriticalSection(Lock.READ); tboxModel.enterCriticalSection(Lock.READ);
// convert this method to use generic resources - not get ontclass, not cls.listSuperClasses...
// use model contains if want to log warning about type owl class
try { try {
OntClass cls = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI());
if (cls != null) { OntClass cls = null;
List<OntClass> parents = (cls.listSuperClasses(false)).toList(); if ( (stmt.getObject().asResource()).getURI() != null ) {
parents.addAll((cls.listEquivalentClasses()).toList()); cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI());
Iterator<OntClass> parentIt = parents.iterator();
while (parentIt.hasNext()) { if (cls != null) {
OntClass parentClass = parentIt.next();
// VIVO doesn't materialize statements that assert anonymous types List<OntClass> parents = (cls.listSuperClasses(false)).toList();
// for individuals. Also, sharing an identical anonymous node is parents.addAll((cls.listEquivalentClasses()).toList());
// not allowed in owl-dl. picklist population code looks at qualities Iterator<OntClass> parentIt = parents.iterator();
// of classes not individuals.
if (parentClass.isAnon()) continue;
if (entailedType(stmt.getSubject(),parentClass)) continue; // if a type is still entailed without the while (parentIt.hasNext()) {
// removed statement, then don't remove it OntClass parentClass = parentIt.next();
// from the inferences
Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), RDF.type, parentClass); // VIVO doesn't materialize statements that assert anonymous types
// for individuals. Also, sharing an identical anonymous node is
// not allowed in owl-dl. picklist population code looks at qualities
// of classes not individuals.
if (parentClass.isAnon()) continue;
inferenceModel.enterCriticalSection(Lock.WRITE); if (entailedType(stmt.getSubject(),parentClass)) continue; // if a type is still entailed without the
try { // removed statement, then don't remove it
if (inferenceModel.contains(infStmt)) { // from the inferences
//log.debug("Removing this inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
inferenceModel.remove(infStmt); Statement infStmt = ResourceFactory.createStatement(stmt.getSubject(), RDF.type, parentClass);
inferenceModel.enterCriticalSection(Lock.WRITE);
try {
if (inferenceModel.contains(infStmt)) {
//log.debug("Removing this inferred statement: " + infStmt.toString() + " - " + infStmt.getSubject().toString() + " - " + infStmt.getPredicate().toString() + " - " + infStmt.getObject().toString());
inferenceModel.remove(infStmt);
}
} finally {
inferenceModel.leaveCriticalSection();
} }
} finally {
inferenceModel.leaveCriticalSection();
} }
} else {
log.debug("Didn't find target class (the object of the removed rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI());
} }
} else { } else {
log.debug("Didn't find target class (the object of the removed rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI()); log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
} }
} finally { } finally {
tboxModel.leaveCriticalSection(); tboxModel.leaveCriticalSection();
@ -700,10 +758,17 @@ public class SimpleReasoner extends StatementListener {
continue; continue;
} }
OntClass ontClass = tboxModel.getOntClass(stmt.getObject().asResource().getURI()); OntClass ontClass = null;
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));
continue;
}
if (ontClass == null) { 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()); log.debug("Didn't find target class (the object of the added rdf:type statement) in the TBox: " + (stmt.getObject().asResource()).getURI());
continue; continue;
} }