Bug#202 concurrent attribute modification

jopa-integration-tests-owlapi/src/test/java/cz/cvut/kbss/jopa/test/environment/OwlapiDataAccessor.java

@@ -18,7 +18,7 @@
 import cz.cvut.kbss.jopa.vocabulary.RDF;
 import cz.cvut.kbss.jopa.vocabulary.RDFS;
 import cz.cvut.kbss.ontodriver.owlapi.OwlapiAdapter;
-import cz.cvut.kbss.ontodriver.owlapi.util.MutableAddAxiom;
+import cz.cvut.kbss.ontodriver.owlapi.change.MutableAddAxiom;
 import cz.cvut.kbss.ontodriver.owlapi.util.OwlapiUtils;
 import org.semanticweb.owlapi.model.*;
 import org.semanticweb.owlapi.search.EntitySearcher;
@@ -39,7 +39,7 @@ public void persistTestData(Collection<Quad> data, EntityManager em) {
         final OwlapiAdapter owlapiAdapter = em.unwrap(OwlapiAdapter.class);
         for (Quad t : data) {
             final OWLNamedIndividual ind = df.getOWLNamedIndividual(IRI.create(t.getSubject()));
-            final AddAxiom axiom;
+            final MutableAddAxiom axiom;
             if (t.getProperty().toString().equals(RDF.TYPE)) {
                 final OWLClass cls = df.getOWLClass(IRI.create(t.getValue().toString()));
                 axiom = new MutableAddAxiom(ontology, df.getOWLClassAssertionAxiom(cls, ind));

jopa-integration-tests/src/main/java/cz/cvut/kbss/jopa/test/runner/UpdateOperationsRunner.java

@@ -16,6 +16,7 @@
 
 import cz.cvut.kbss.jopa.exceptions.IntegrityConstraintViolatedException;
 import cz.cvut.kbss.jopa.exceptions.RollbackException;
+import cz.cvut.kbss.jopa.model.EntityManager;
 import cz.cvut.kbss.jopa.model.descriptors.Descriptor;
 import cz.cvut.kbss.jopa.model.descriptors.EntityDescriptor;
 import cz.cvut.kbss.jopa.oom.exceptions.UnpersistedChangeException;
@@ -1376,4 +1377,29 @@ void mergeHandlesCascadingAndReferencedObjects() {
         // The incorrect merge messes up the cached value of the original entityA
         assertEquals(entityA.getUri(), aResult.getUri());
     }
+
+    /**
+     * Bug #202
+     */
+    @Test
+    void concurrentTransactionsLeaveDataInConsistentState() {
+        final String a1String = "a1String";
+        final String a2String = "a2String";
+        this.em= getEntityManager("concurrentTransactionsLeaveDataInConsistentState", false);
+        final EntityManager secondEm = em.getEntityManagerFactory().createEntityManager();
+        persist(entityA);
+        em.getTransaction().begin();
+        final OWLClassA a1 = em.find(OWLClassA.class, entityA.getUri());
+
+        secondEm.getTransaction().begin();
+        final OWLClassA a2 = secondEm.find(OWLClassA.class, entityA.getUri());
+
+        a1.setStringAttribute(a1String);
+        a2.setStringAttribute(a2String);
+        em.getTransaction().commit();
+        secondEm.getTransaction().commit();
+
+        final OWLClassA result = em.find(OWLClassA.class, entityA.getUri());
+        assertEquals(a2String, result.getStringAttribute());
+    }
 }

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.removePropertyValues(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.removePropertyValues(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 removePropertyValues(Collection<SubjectPredicateContext> spc) {
+        transaction.verifyActive();
+        localModel.removePropertyValues(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 +133,19 @@ void removeStatements(List<Statement> statements, String context) {
         registerStatements(statements, context, removed, added);
     }
 
+    void removePropertyValues(Collection<SubjectPredicateContext> toRemove) {
+        removedSubjectPredicateStatements.addAll(toRemove);
+        toRemove.forEach(spc -> {
+            if (spc.getContexts().isEmpty()) {
+                added.getDefaultModel().remove(added.getDefaultModel()
+                                                    .listStatements(spc.getSubject(), spc.getPredicate(), (RDFNode) null));
+            } else {
+                spc.getContexts().forEach(c -> added.getNamedModel(c).remove(added.getNamedModel(c)
+                                                                                  .listStatements(spc.getSubject(), spc.getPredicate(), (RDFNode) null)));
+            }
+        });
+    }
+
     Dataset getAdded() {
         return added;
     }
@@ -124,6 +154,10 @@ 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 removePropertyValues(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 removePropertyValues(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.removePropertyValues(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 all property values specified by the provided argument for the specified subject(s).
+     *
+     * @param spc Subject-predicate-contexts tuples
+     */
+    void removePropertyValues(Collection<SubjectPredicateContext> spc);
+
     @Override
     void close() throws JenaDriverException;
 }

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

@@ -0,0 +1,62 @@
+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;
+
+/**
+ * Represents the subject, predicate and context(s) of a statement.
+ *
+ * Used to indicate what property values to remove from the repository.
+ */
+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);
+    }
+}