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

webapp/src/edu/cornell/mannlib/vitro/webapp/reasoner/SimpleReasoner.java

@@ -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 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).
@@ -158,8 +160,27 @@ public class SimpleReasoner extends StatementListener {
 				    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());
+				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()); 
+				if (object == null) {
+					log.debug("didn't find object class in the tbox: " + ((Resource)stmt.getObject()).getURI());
+					return;
+				}
 				
 				if (stmt.getPredicate().equals(RDFS.subClassOf)) {
 				   addedSubClass(subject,object,inferenceModel);
@@ -208,8 +229,27 @@ public class SimpleReasoner extends StatementListener {
 				    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());
+				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()); 
+				if (object == null) {
+					log.debug("didn't find object class in the tbox: " + ((Resource)stmt.getObject()).getURI());
+					return;
+				}
 				
 				if (stmt.getPredicate().equals(RDFS.subClassOf)) {
 				   removedSubClass(subject,object,inferenceModel);
@@ -253,7 +293,11 @@ public class SimpleReasoner extends StatementListener {
 		tboxModel.enterCriticalSection(Lock.READ);
 		
 		try {
-			OntClass cls = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); 
+
+			OntClass cls = null;
+			
+			if ( (stmt.getObject().asResource()).getURI() != null ) {
+			    cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI()); 
 			    
 				if (cls != null) {
 					
@@ -284,6 +328,10 @@ public class SimpleReasoner extends StatementListener {
 				} else {
 					log.debug("Didn't find target class (the object of the added rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI());
 				}
+			} else {
+				log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
+				return;
+			}
 		} finally {
 			tboxModel.leaveCriticalSection();
 		}
@@ -340,7 +388,7 @@ public class SimpleReasoner extends StatementListener {
 					}	
 				}
 			} 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 {
 			tboxModel.leaveCriticalSection();
@@ -359,8 +407,15 @@ public class SimpleReasoner extends StatementListener {
 		
 		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 {
-			OntClass cls = tboxModel.getOntClass(((Resource)stmt.getObject()).getURI()); 
+			
+			OntClass cls = null;
+			
+			if ( (stmt.getObject().asResource()).getURI() != null ) {
+			    cls = tboxModel.getOntClass(stmt.getObject().asResource().getURI()); 
 			    
 				if (cls != null) {
 					
@@ -396,6 +451,9 @@ public class SimpleReasoner extends StatementListener {
 				} else {
 					log.debug("Didn't find target class (the object of the removed rdf:type statement) in the TBox: " + ((Resource)stmt.getObject()).getURI());
 				}
+			} else {
+				log.warn("The object of this rdf:type assertion has a null URI: " + stmtString(stmt));
+			}			
 		} finally {
 			tboxModel.leaveCriticalSection();
 		}
@@ -700,10 +758,17 @@ public class SimpleReasoner extends StatementListener {
 					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) {
-					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;
 				}