[Bug #274] Do not remove statements when iterating in Jena File storage.

kbss-cvut · Nov 19, 2024 · af11b6e · af11b6e
1 parent ba940a3
commit af11b6e
Show file tree

Hide file tree

Showing 2 changed files with 81 additions and 4 deletions.
diff --git a/ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/FileStorage.java b/ontodriver-jena/src/main/java/cz/cvut/kbss/ontodriver/jena/connector/FileStorage.java
@@ -22,6 +22,8 @@
 import cz.cvut.kbss.ontodriver.jena.exception.JenaDriverException;
 import org.apache.jena.query.DatasetFactory;
 import org.apache.jena.rdf.model.Model;
+import org.apache.jena.rdf.model.Statement;
+import org.apache.jena.rdf.model.StmtIterator;
 import org.apache.jena.riot.RDFDataMgr;
 import org.apache.jena.riot.RDFLanguages;
 import org.apache.jena.riot.RiotNotFoundException;
@@ -31,6 +33,7 @@
 import java.io.File;
 import java.io.FileOutputStream;
 import java.io.IOException;
+import java.util.List;
 
 /**
  * File storage accessor.
@@ -98,4 +101,12 @@ public synchronized void reload() {
         dataset.close();
         initialize();
     }
+
+    @Override
+    public void remove(StmtIterator iterator, String context) {
+        // For FileStorage we can't iterate through the statement and call remove on them because
+        // it causes a ConcurrentModificationException
+        final List<Statement> toRemove = iterator.toList();
+        remove(toRemove, context);
+    }
 }
diff --git a/ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/StorageTest.java b/ontodriver-jena/src/test/java/cz/cvut/kbss/ontodriver/jena/connector/StorageTest.java
@@ -23,16 +23,23 @@
 import cz.cvut.kbss.ontodriver.jena.config.JenaOntoDriverProperties;
 import cz.cvut.kbss.ontodriver.jena.environment.Generator;
 import org.apache.jena.query.DatasetFactory;
+import org.apache.jena.query.ReadWrite;
+import org.apache.jena.rdf.model.RDFNode;
 import org.apache.jena.rdf.model.ResourceFactory;
+import org.apache.jena.rdf.model.StmtIterator;
 import org.apache.jena.vocabulary.RDF;
 import org.junit.jupiter.api.Test;
 
 import java.io.File;
 import java.nio.file.Files;
 
+import static org.apache.jena.rdf.model.ResourceFactory.createResource;
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.hamcrest.MatcherAssert.assertThat;
-import static org.junit.jupiter.api.Assertions.*;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertInstanceOf;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertThrows;
 
 public class StorageTest extends StorageTestUtil {
 
@@ -42,7 +49,7 @@ public void createInitializesMemoryStorageForMemoryConfiguration() {
         config.setProperty(JenaConfigParam.STORAGE_TYPE, JenaOntoDriverProperties.IN_MEMORY);
         final Storage result = Storage.create(config);
         assertNotNull(result);
-        assertTrue(result instanceof MemoryStorage);
+        assertInstanceOf(MemoryStorage.class, result);
         assertNotNull(result.getDataset());
     }
 
@@ -54,7 +61,7 @@ public void createInitializesFileStorageForFileConfiguration() throws Exception
         config.setProperty(JenaConfigParam.STORAGE_TYPE, JenaOntoDriverProperties.FILE);
         final Storage result = Storage.create(config);
         assertNotNull(result);
-        assertTrue(result instanceof FileStorage);
+        assertInstanceOf(FileStorage.class, result);
     }
 
     @Test
@@ -71,7 +78,7 @@ public void createCreatesInMemoryByDefault() {
         final DriverConfiguration config = createConfiguration("test:uri");
         final Storage result = Storage.create(config);
         assertNotNull(result);
-        assertTrue(result instanceof MemoryStorage);
+        assertInstanceOf(MemoryStorage.class, result);
     }
 
     @Test
@@ -97,4 +104,63 @@ public void setDatasetThrowsUnsupportedOperationException() throws Exception {
         assertNotNull(storage);
         assertThrows(UnsupportedOperationException.class, () -> storage.setDataset(DatasetFactory.create()));
     }
+
+    // Bug #274
+    @Test
+    void removeHandlesStatementIteratorForInMemoryStorage() {
+        final DriverConfiguration config = createConfiguration("test:uri");
+        config.setProperty(JenaConfigParam.STORAGE_TYPE, JenaOntoDriverProperties.IN_MEMORY);
+        final Storage storage = Storage.create(config);
+        storage.begin(ReadWrite.WRITE);
+        generateTestData(storage.getDataset());
+        storage.commit();
+
+        storage.begin(ReadWrite.WRITE);
+        final StmtIterator iterator = storage.getDefaultGraph()
+                                             .listStatements(createResource(TYPE_ONE), null, (RDFNode) null);
+        storage.remove(iterator, null);
+        storage.commit();
+    }
+
+    // Bug #274
+    @Test
+    void removeHandlesStatementIteratorForLocalStorage() throws Exception {
+        final File file = Files.createTempFile("jena-onto", ".ttl").toFile();
+        file.deleteOnExit();
+        final DriverConfiguration config = createConfiguration(file.getAbsolutePath());
+        config.setProperty(JenaConfigParam.STORAGE_TYPE, JenaOntoDriverProperties.FILE);
+        final Storage storage = Storage.create(config);
+        storage.begin(ReadWrite.WRITE);
+        generateTestData(storage.getDataset());
+        storage.commit();
+
+        storage.begin(ReadWrite.WRITE);
+        final StmtIterator iterator = storage.getDefaultGraph()
+                                             .listStatements(createResource(TYPE_ONE), null, (RDFNode) null);
+        storage.remove(iterator, null);
+        storage.commit();
+    }
+
+    // Bug #274
+    @Test
+    void removeHandlesStatementIteratorForTDB2Storage() throws Exception {
+        final File file = Files.createTempDirectory("jena-onto").toFile();
+        file.deleteOnExit();
+        try {
+            final DriverConfiguration config = createConfiguration(file.getAbsolutePath());
+            config.setProperty(JenaConfigParam.STORAGE_TYPE, JenaOntoDriverProperties.TDB2);
+            final Storage storage = Storage.create(config);
+            storage.begin(ReadWrite.WRITE);
+            generateTestData(storage.getDataset());
+            storage.commit();
+
+            storage.begin(ReadWrite.WRITE);
+            final StmtIterator iterator = storage.getDefaultGraph()
+                                                 .listStatements(createResource(TYPE_ONE), null, (RDFNode) null);
+            storage.remove(iterator, null);
+            storage.commit();
+        } finally {
+            deleteStorageDir(file);
+        }
+    }
 }