Fix for VIVO-3871 (#393)

* Fallback to default graph in bulk ontology model update * test added --------- Co-authored-by: Georgy Litvinov <georgy.litvinov@tib.eu>
vivo-project · Jun 6, 2023 · a5a7e64 · a5a7e64
1 parent f19d0a0
commit a5a7e64
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Showing 5 changed files with 88 additions and 34 deletions.
diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/BulkGraphMem.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/BulkGraphMem.java
@@ -10,7 +10,7 @@ public void addWithoutNotify(Triple t) {
 		performAdd(t);
 	}
 
-	public final void deleteWithoutNotify(Triple t) {
+	public void deleteWithoutNotify(Triple t) {
 		checkOpen();
 		performDelete(t);
 	}

diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/BulkOntModelImpl.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/BulkOntModelImpl.java
@@ -7,33 +7,33 @@
 
 public class BulkOntModelImpl extends OntModelImpl {
 
-	public BulkOntModelImpl(OntModelSpec spec) {
-		super(spec);
-	}
-
-	public BulkOntModelImpl(OntModelSpec owlMem, Model bareModel) {
-		super(owlMem, bareModel);
-	}
+    public BulkOntModelImpl(OntModelSpec spec) {
+        super(spec);
+    }
 
-	@Override
-	public Model remove(Model m) {
-		Graph unwrappedGraph = GraphUtils.unwrapUnionGraphs(graph);
-		if (unwrappedGraph instanceof BulkGraphMem) {
-			GraphUtils.deleteFrom((BulkGraphMem) unwrappedGraph, m.getGraph());	
-		} else {
-			super.remove(m);
-		}
-		return this;
-	}
+    public BulkOntModelImpl(OntModelSpec owlMem, Model bareModel) {
+        super(owlMem, bareModel);
+    }
 
-	@Override
-	public Model add(Model m) {
-		Graph unwrappedGraph = GraphUtils.unwrapUnionGraphs(graph);
-		if (unwrappedGraph instanceof BulkGraphMem) {
-			GraphUtils.addInto((BulkGraphMem) unwrappedGraph, m.getGraph());
-		} else {
-			super.add(m);
-		}
-		return this;
-	}
+    @Override
+    public Model remove(Model m) {
+        Graph unwrappedGraph = GraphUtils.unwrapUnionGraphs(graph);
+        if (unwrappedGraph instanceof BulkGraphMem) {
+            GraphUtils.deleteFrom((BulkGraphMem) unwrappedGraph, m.getGraph());
+        } else {
+            super.remove(m);
+        }
+        return this;
+    }
+
+    @Override
+    public Model add(Model m) {
+        Graph unwrappedGraph = GraphUtils.unwrapUnionGraphs(graph);
+        if (unwrappedGraph instanceof BulkGraphMem) {
+            GraphUtils.addInto((BulkGraphMem) unwrappedGraph, m.getGraph());
+        } else {
+            super.add(m);
+        }
+        return this;
+    }
 }
diff --git a/api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/GraphUtils.java b/api/src/main/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/GraphUtils.java
@@ -25,10 +25,7 @@ final public class GraphUtils {
 
 	public static Graph unwrapUnionGraphs(Graph graph) {
 		if (graph != null && graph instanceof MultiUnion) {
-			List<Graph> subGraphs = ((MultiUnion) graph).getSubGraphs();
-			if (subGraphs == null || subGraphs.isEmpty()) {
-				return ((MultiUnion) graph).getBaseGraph();
-			}
+		    return unwrapUnionGraphs(((MultiUnion)graph).getBaseGraph());
 		}
 		return graph;
 	}

diff --git a/...test/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/VitroModelFactoryTest.java b/...test/java/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/VitroModelFactoryTest.java
@@ -13,10 +13,11 @@
 import java.util.List;
 
 import org.junit.Test;
-
+import org.apache.jena.graph.Triple;
 import org.apache.jena.graph.impl.GraphWithPerform;
 import org.apache.jena.mem.GraphMem;
 import org.apache.jena.ontology.OntModel;
+import org.apache.jena.ontology.impl.OntModelImpl;
 import org.apache.jena.rdf.listeners.StatementListener;
 import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Model;
@@ -27,6 +28,8 @@
 import org.apache.jena.rdf.model.Resource;
 import org.apache.jena.rdf.model.ResourceFactory;
 import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.impl.ModelCom;
+import org.apache.jena.shared.Lock;
 
 import edu.cornell.mannlib.vitro.testing.AbstractTestClass;
 import edu.cornell.mannlib.vitro.testing.RecordingProxy;
@@ -65,6 +68,9 @@
  * presumably the bulk updaters will be removed completely.
  */
 public class VitroModelFactoryTest extends AbstractTestClass {
+
+    private String testData = "src/test/resources/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/vitro_model_factory_test_data.n3";
+
 	private static final Statement SINGLE_STATEMENT = stmt(
 			resource("http://subject"), property("http://add"),
 			literal("object"));
@@ -463,7 +469,53 @@ public void addMultipleToVitroOntUnion() {
 				.test();
 	}
 
-	// ----------------------------------------------------------------------
+    @Test
+    public void testCreateNewBulkOntModel() {
+        TestBulkGraphMem spyGraph = new TestBulkGraphMem();
+        Model baseModel = new ModelCom(spyGraph);
+        baseModel = wrap(wrap(wrap(baseModel)));
+        OntModel ontModel = VitroModelFactory.createOntologyModel(baseModel);
+        Model inputModel = ModelFactory.createDefaultModel();
+        try {
+            inputModel.enterCriticalSection(Lock.WRITE);
+            inputModel.read(testData);
+        } finally {
+            inputModel.leaveCriticalSection();
+        }
+        assertEquals(0, spyGraph.countAddWithoutNotify);
+        assertEquals(0, spyGraph.countDeleteWithoutNotify);
+        ontModel.add(inputModel);
+        assertEquals(5, spyGraph.countAddWithoutNotify);
+        assertEquals(0, spyGraph.countDeleteWithoutNotify);
+
+        ontModel.remove(inputModel);
+        assertEquals(5, spyGraph.countAddWithoutNotify);
+        assertEquals(5, spyGraph.countDeleteWithoutNotify);
+    }
+
+    private OntModelImpl wrap(Model baseModel) {
+        return new OntModelImpl(OWL_MEM, baseModel);
+    }
+
+    private static class TestBulkGraphMem extends BulkGraphMem {
+        int countDeleteWithoutNotify = 0;
+        int countAddWithoutNotify = 0;
+
+        @Override
+        public void addWithoutNotify(Triple t) {
+            checkOpen();
+            performAdd(t);
+            countAddWithoutNotify++;
+        }
+        @Override
+        public final void deleteWithoutNotify(Triple t) {
+            checkOpen();
+            performDelete(t);
+            countDeleteWithoutNotify++;
+        }
+    }
+
+    // ----------------------------------------------------------------------
 	// OntModel of Union of Models
 	//
 	// This shouldn't hold any surprises, should it?

diff --git a/...ces/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/vitro_model_factory_test_data.n3 b/...ces/edu/cornell/mannlib/vitro/webapp/rdfservice/adapters/vitro_model_factory_test_data.n3
@@ -0,0 +1,5 @@
+<test:bob> <test:has_publication> <test:bob_publication1> .
+<test:bob> <test:has_publication> <test:bob_publication2> .
+<test:bob> <test:has_publication> <test:bob_publication3> .
+<test:alice> <test:has_publication> <test:alice_publication1> .
+<test:alice> <test:has_publication> <test:alice_publication2> .