Fixed removal of linked blank nodes

api/src/main/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtils.java

@@ -492,7 +492,7 @@ private static String makeDescribe(Resource s) {
      * @param toRemove containing statements to be removed
      * @param removeFrom from which statements should be removed
      */
-    public static void removeUsingSparqlConstruct(Model toRemove, Model removeFrom) {
+    private static void removeUsingSparqlConstruct(Model toRemove, Model removeFrom) {
         if(toRemove.isEmpty()) {
         	return;
         }
@@ -572,7 +572,7 @@ private static void addStatementPatterns(List<Statement> stmts,
         for(Statement stmt : stmts) {
             Triple t = stmt.asTriple();
             String lineWithoutVars = getLine(t, false);
-            if (lines.contains(lineWithoutVars)) {
+            if (lines.contains(lineWithoutVars) && !isLinked(stmt, stmts)) {
                 continue;
             } else {
                 lines.add(lineWithoutVars);
@@ -591,6 +591,17 @@ private static void addStatementPatterns(List<Statement> stmts,
         }
     }
 
+    private static boolean isLinked(Statement stmt, List<Statement> stmts) {
+        RDFNode s = stmt.getSubject();
+        RDFNode o = stmt.getObject();
+        for (Statement st : stmts) {
+            if (st.getSubject().equals(o) || st.getObject().equals(s)) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     private static String getLine(Triple t, boolean createBlankNodeVariables) {
         if (createBlankNodeVariables) {
             return sparqlNodeDelete(t.getSubject(), null) +

api/src/test/java/edu/cornell/mannlib/vitro/webapp/dao/jena/JenaModelUtilsTest.java

@@ -17,7 +17,7 @@ public class JenaModelUtilsTest {
     public void removeUsingSparqlConstructTest() {
         Model removeFrom = getModel();
         Model toRemove = getModel();
-        JenaModelUtils.removeUsingSparqlConstruct(toRemove, removeFrom);
+        JenaModelUtils.removeWithBlankNodesAsVariables(toRemove, removeFrom);
         assertTrue(removeFrom.isEmpty());
     }
 

api/src/test/java/edu/cornell/mannlib/vitro/webapp/tboxreasoner/impl/jfact/JFactTBoxReasonerTest.java

@@ -1,5 +1,8 @@
 package edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.jfact;
 
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
 import java.io.StringReader;
 
 import org.apache.jena.ontology.OntModel;
@@ -16,8 +19,6 @@
 import org.semanticweb.owlapi.util.SAXParsers;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.JenaModelUtils;
 import edu.cornell.mannlib.vitro.webapp.dao.jena.event.EditEvent;
-import edu.cornell.mannlib.vitro.webapp.migration.auth.AnnotationMigrator;
-import edu.cornell.mannlib.vitro.webapp.migration.auth.ArmMigrator;
 import edu.cornell.mannlib.vitro.webapp.tboxreasoner.ReasonerConfiguration;
 import edu.cornell.mannlib.vitro.webapp.tboxreasoner.impl.BasicTBoxReasonerDriver;
 
@@ -34,7 +35,8 @@ public class JFactTBoxReasonerTest {
 			"         \r\n" + 
 			"         rdfs:subClassOf [ rdf:type owl:Class ;\r\n" + 
 			"                           owl:intersectionOf ( <http://vivo.mydomain.edu/individual/class_a>\r\n" + 
-			"                                                <http://vivo.mydomain.edu/individual/class_b>\r\n" + 
+			"                                                <http://vivo.mydomain.edu/individual/class_b>\r\n" +
+			"                                                <http://vivo.mydomain.edu/individual/class_c>\r\n" +
 			"                                              )\r\n" + 
 			"                         ] .\r\n" + 
 			"\r\n" + 
@@ -89,9 +91,11 @@ public void testRemoveAxiomsWithBlankNodes() {
 		waitForTBoxReasoning(driver);
 		// Confirm that union model now contains inferred triples
 		Assert.assertTrue(tboxUnion.size() > additions.size());
+		assertFalse(tboxAssertions.isEmpty());
 		JenaModelUtils.removeWithBlankNodesAsVariables(subtractions, tboxAssertions.getBaseModel());
 		tboxAssertions.getBaseModel().notifyEvent(new EditEvent(null, false));
 		waitForTBoxReasoning(driver);
+		assertTrue(tboxAssertions.isEmpty());
 		// Confirm that no statements related to classes a, b or c remain in the
 		// TBox union model.  (The inference model may not be completely empty, because
 		// the reasoner may supply unrelated triples related to OWL and RDFS vocabulary.)