[Bug #202] Modify Jena driver to remove all property assertions on it…

…s update to prevent transaction concurrency issues.

Originally, all property values were selected and then these statements were removed on commit. However, if these changed in the meantime (e.g., when another transaction committed), it lead to stale data being in the repository.

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/EpistemicAxiomRemover.java

@@ -16,6 +16,7 @@
 
 import cz.cvut.kbss.ontodriver.descriptor.AbstractAxiomDescriptor;
 import cz.cvut.kbss.ontodriver.jena.connector.StorageConnector;
+import cz.cvut.kbss.ontodriver.jena.connector.SubjectPredicateContext;
 import cz.cvut.kbss.ontodriver.jena.util.JenaUtils;
 import cz.cvut.kbss.ontodriver.model.Assertion;
 import cz.cvut.kbss.ontodriver.model.NamedResource;
@@ -25,8 +26,11 @@
 import org.apache.jena.rdf.model.ResourceFactory;
 
 import java.net.URI;
+import java.util.Collection;
+import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * This class performs an epistemic removal of statements.
@@ -51,14 +55,14 @@ class EpistemicAxiomRemover {
      */
     void remove(AbstractAxiomDescriptor descriptor) {
         final Resource subject = ResourceFactory.createResource(descriptor.getSubject().getIdentifier().toString());
+        final Collection<SubjectPredicateContext> toRemove = new HashSet<>();
         descriptor.getAssertions().forEach(assertion -> {
             final Property property = ResourceFactory.createProperty(assertion.getIdentifier().toString());
-            if (descriptor.getAssertionContexts(assertion).isEmpty()) {
-                connector.remove(subject, property, null, null);
-            }
-            descriptor.getAssertionContexts(assertion)
-                      .forEach(context -> connector.remove(subject, property, null, context.toString()));
+            toRemove.add(new SubjectPredicateContext(subject, property, descriptor.getAssertionContexts(assertion)
+                                                                                  .stream().map(URI::toString)
+                                                                                  .collect(Collectors.toSet())));
         });
+        connector.removeStatementsBySubjectAndPredicate(toRemove);
     }
 
     /**

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/ChangeTrackingStorageConnector.java

@@ -74,6 +74,7 @@ private void mergeRemovedStatements() {
             final Model model = removed.getNamedModel(context);
             centralConnector.remove(model.listStatements().toList(), context);
         });
+        centralConnector.removeStatementsBySubjectAndPredicate(localModel.getRemovedSubjectPredicateStatements());
     }
 
     private void mergeAddedStatements() {
@@ -135,6 +136,12 @@ public void remove(Resource subject, Property property, RDFNode object, String c
         localModel.removeStatements(new ArrayList<>(find(subject, property, object, context != null ? Collections.singleton(context) : Collections.emptySet())), context);
     }
 
+    @Override
+    public void removeStatementsBySubjectAndPredicate(Collection<SubjectPredicateContext> spc) {
+        transaction.verifyActive();
+        localModel.removeStatementsBySubjectAndPredicate(spc);
+    }
+
     @Override
     public AbstractResultSet executeSelectQuery(Query query, StatementOntology target) throws JenaDriverException {
         Objects.requireNonNull(query);

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/LocalModel.java

@@ -1,24 +1,33 @@
 /**
  * Copyright (C) 2023 Czech Technical University in Prague
- *
- * This program is free software: you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
- * details. You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ * <p>
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ * <p>
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details. You should have received a copy of the GNU General Public License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
  */
 package cz.cvut.kbss.ontodriver.jena.connector;
 
 import org.apache.jena.query.Dataset;
 import org.apache.jena.query.DatasetFactory;
-import org.apache.jena.rdf.model.*;
-
-import java.util.*;
+import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * Tracks transactional changes.
@@ -27,6 +36,7 @@ class LocalModel {
 
     private final Dataset added;
     private final Dataset removed;
+    private final Set<SubjectPredicateContext> removedSubjectPredicateStatements;
 
     /**
      * Whether default graph should be treated as union of all graphs.
@@ -40,18 +50,19 @@ enum Containment {
     LocalModel(boolean defaultAsUnion) {
         this.added = DatasetFactory.create();
         this.removed = DatasetFactory.create();
+        this.removedSubjectPredicateStatements = new HashSet<>();
         this.defaultAsUnion = defaultAsUnion;
     }
 
     Collection<Statement> enhanceStatements(Collection<Statement> statements, Resource subject, Property property,
                                             RDFNode value, Collection<String> contexts) {
         if (contexts.isEmpty()) {
-            return enhanceStatements(statements, subject, property, value, addedDefault(), removedDefault());
+            return enhanceStatements(statements, subject, property, value, addedDefault(), removedDefault(), null);
         } else {
             Collection<Statement> enhanced = statements;
             for (String ctx : contexts) {
                 enhanced = enhanceStatements(statements, subject, property, value, added.getNamedModel(ctx),
-                        removed.getNamedModel(ctx));
+                        removed.getNamedModel(ctx), ctx);
             }
             return enhanced;
         }
@@ -65,25 +76,31 @@ private Model removedDefault() {
         return defaultAsUnion ? removed.getUnionModel().union(removed.getDefaultModel()) : removed.getDefaultModel();
     }
 
-    private static Collection<Statement> enhanceStatements(Collection<Statement> toEnhance, Resource subject,
-                                                           Property property, RDFNode value, Model addedModel,
-                                                           Model removedModel) {
+    private Collection<Statement> enhanceStatements(Collection<Statement> toEnhance, Resource subject,
+                                                    Property property, RDFNode value, Model addedModel,
+                                                    Model removedModel, String context) {
         final Set<Statement> statements = new HashSet<>(toEnhance);
         statements.addAll(addedModel.listStatements(subject, property, value).toList());
         removedModel.listStatements(subject, property, value).toList().forEach(statements::remove);
-        return statements;
+        return statements.stream()
+                         .filter(s -> removedSubjectPredicateStatements.stream()
+                                                                       .noneMatch(spc -> spc.matches(s, context)))
+                         .collect(Collectors.toSet());
     }
 
     Containment contains(Resource subject, Property property, RDFNode value, Collection<String> contexts) {
         if (contexts.isEmpty()) {
-            if (removedDefault().contains(subject, property, value)) {
+            if (removedDefault().contains(subject, property, value) || removedSubjectPredicateStatements.contains(new SubjectPredicateContext(subject, property, Collections.emptySet()))) {
                 return Containment.REMOVED;
             } else {
                 return addedDefault().contains(subject, property, value) ? Containment.ADDED :
-                       Containment.UNKNOWN;
+                        Containment.UNKNOWN;
             }
         } else {
             Containment result = Containment.UNKNOWN;
+            if (removedSubjectPredicateStatements.contains(new SubjectPredicateContext(subject, property, new HashSet<>(contexts)))) {
+                return Containment.REMOVED;
+            }
             for (String c : contexts) {
                 if (removed.getNamedModel(c).contains(subject, property, value)) {
                     return Containment.REMOVED;
@@ -116,6 +133,10 @@ void removeStatements(List<Statement> statements, String context) {
         registerStatements(statements, context, removed, added);
     }
 
+    void removeStatementsBySubjectAndPredicate(Collection<SubjectPredicateContext> toRemove) {
+        removedSubjectPredicateStatements.addAll(toRemove);
+    }
+
     Dataset getAdded() {
         return added;
     }
@@ -124,6 +145,10 @@ Dataset getRemoved() {
         return removed;
     }
 
+    public Set<SubjectPredicateContext> getRemovedSubjectPredicateStatements() {
+        return removedSubjectPredicateStatements;
+    }
+
     List<String> getContexts() {
         final Iterator<String> it = added.listNames();
         final List<String> contexts = new ArrayList<>();

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SharedStorageConnector.java

@@ -149,6 +149,20 @@ public void remove(Resource subject, Property property, RDFNode object, String c
         }
     }
 
+    @Override
+    public void removeStatementsBySubjectAndPredicate(Collection<SubjectPredicateContext> spc) {
+        ensureTransactionalState();
+        spc.forEach(s -> {
+            if (s.getContexts().isEmpty()) {
+                storage.remove(storage.getDefaultGraph()
+                                      .listStatements(s.getSubject(), s.getPredicate(), (RDFNode) null), null);
+            } else {
+                s.getContexts().forEach(c -> storage.remove(storage.getNamedGraph(c)
+                                                                   .listStatements(s.getSubject(), s.getPredicate(), (RDFNode) null), c));
+            }
+        });
+    }
+
     @Override
     public AbstractResultSet executeSelectQuery(Query query, StatementOntology target) throws JenaDriverException {
         ensureOpen();

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SnapshotStorageConnector.java

@@ -169,6 +169,19 @@ public void remove(Resource subject, Property property, RDFNode object, String c
         remove(toRemove, context);
     }
 
+    @Override
+    public void removeStatementsBySubjectAndPredicate(Collection<SubjectPredicateContext> spc) {
+        ensureOpen();
+        spc.forEach(s -> {
+            if (s.getContexts().isEmpty()) {
+                remove(s.getSubject(), s.getPredicate(), null, null);
+            } else {
+                s.getContexts().forEach(ctx -> remove(s.getSubject(), s.getPredicate(), null, ctx));
+            }
+        });
+        transactionalChanges.removeStatementsBySubjectAndPredicate(spc);
+    }
+
     @Override
     public AbstractResultSet executeSelectQuery(Query query, StatementOntology target) throws JenaDriverException {
         ensureOpen();

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/StorageConnector.java

@@ -117,6 +117,13 @@ public interface StorageConnector extends Closeable, Wrapper, StatementExecutor
      */
     void remove(Resource subject, Property property, RDFNode object, String context);
 
+    /**
+     * Removes statements that have the specified subject and predicate pairs.
+     *
+     * @param spc Subject-predicate-contexts tuples
+     */
+    void removeStatementsBySubjectAndPredicate(Collection<SubjectPredicateContext> spc);
+
     @Override
     void close() throws JenaDriverException;
 }

ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/SubjectPredicateContext.java

@@ -0,0 +1,57 @@
+package cz.cvut.kbss.ontodriver.jena.connector;
+
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.Statement;
+
+import java.util.Objects;
+import java.util.Set;
+
+public final class SubjectPredicateContext {
+
+    private final Resource subject;
+
+    private final Property predicate;
+
+    private final Set<String> contexts;
+
+    public SubjectPredicateContext(Resource subject, Property predicate, Set<String> contexts) {
+        assert subject != null;
+        assert contexts != null;
+
+        this.subject = subject;
+        this.predicate = predicate;
+        this.contexts = contexts;
+    }
+
+    public Resource getSubject() {
+        return subject;
+    }
+
+    public Property getPredicate() {
+        return predicate;
+    }
+
+    public Set<String> getContexts() {
+        return contexts;
+    }
+
+    public boolean matches(Statement s, String context) {
+        return subject.equals(s.getSubject()) && predicate.equals(s.getPredicate()) &&
+                (contexts.isEmpty() || contexts.contains(context));
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (!(o instanceof SubjectPredicateContext)) return false;
+        SubjectPredicateContext that = (SubjectPredicateContext) o;
+        return subject.equals(that.subject) && Objects.equals(predicate, that.predicate) && contexts.equals(
+                that.contexts);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(subject, predicate, contexts);
+    }
+}

ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/EpistemicAxiomRemoverTest.java

@@ -16,6 +16,7 @@
 
 import cz.cvut.kbss.ontodriver.descriptor.AxiomDescriptor;
 import cz.cvut.kbss.ontodriver.jena.connector.StorageConnector;
+import cz.cvut.kbss.ontodriver.jena.connector.SubjectPredicateContext;
 import cz.cvut.kbss.ontodriver.jena.environment.Generator;
 import cz.cvut.kbss.ontodriver.model.Assertion;
 import cz.cvut.kbss.ontodriver.model.NamedResource;
@@ -28,6 +29,8 @@
 import org.mockito.junit.jupiter.MockitoExtension;
 
 import java.net.URI;
+import java.util.Collections;
+import java.util.Set;
 
 import static org.apache.jena.rdf.model.ResourceFactory.createProperty;
 import static org.mockito.Mockito.verify;
@@ -57,8 +60,10 @@ public void removeRemovesStatementsByProperty() {
         descriptor.addAssertion(op);
 
         remover.remove(descriptor);
-        verify(connectorMock).remove(SUBJECT_RESOURCE, createProperty(dp.getIdentifier().toString()), null, null);
-        verify(connectorMock).remove(SUBJECT_RESOURCE, createProperty(op.getIdentifier().toString()), null, null);
+        verify(connectorMock).removeStatementsBySubjectAndPredicate(Set.of(
+                new SubjectPredicateContext(SUBJECT_RESOURCE, createProperty(dp.getIdentifier().toString()), Collections.emptySet()),
+                new SubjectPredicateContext(SUBJECT_RESOURCE, createProperty(op.getIdentifier().toString()), Collections.emptySet())
+        ));
     }
 
     @Test
@@ -74,9 +79,9 @@ public void removeRemovesStatementsByPropertyFromCorrectContexts() {
         descriptor.addAssertionContext(ap, assertionContext);
 
         remover.remove(descriptor);
-        verify(connectorMock)
-                .remove(SUBJECT_RESOURCE, createProperty(ca.getIdentifier().toString()), null, mainContext.toString());
-        verify(connectorMock).remove(SUBJECT_RESOURCE, createProperty(ap.getIdentifier().toString()), null,
-                assertionContext.toString());
+        verify(connectorMock).removeStatementsBySubjectAndPredicate(Set.of(
+                new SubjectPredicateContext(SUBJECT_RESOURCE, createProperty(ca.getIdentifier().toString()), Set.of(mainContext.toString())),
+                new SubjectPredicateContext(SUBJECT_RESOURCE, createProperty(ap.getIdentifier().toString()), Set.of(assertionContext.toString()))
+        ));
     }
 }