Allow TDB datasets to be opened in read-only mode

Author: arteymix

src/ubic/basecode/ontology/jena/OntologyLoader.java

@@ -25,7 +25,7 @@
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.shared.CannotCreateException;
 import com.hp.hpl.jena.shared.JenaException;
-import com.hp.hpl.jena.tdb.TDBFactory;
+import com.hp.hpl.jena.sparql.graph.GraphReadOnly;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
@@ -85,6 +85,16 @@ static OntModel createMemoryModel( String url, String name, @Nullable String cac
         return model;
     }
 
+    /**
+     * ModelFactory.createMemModelMaker()
+     * Get model that is entirely in memory.
+     */
+    private static OntModel getModel( String name, boolean processImports, OntModelSpec spec ) {
+        ModelMaker maker = ModelFactory.createMemModelMaker();
+        Model base = maker.createModel( name, false );
+        return getModel( maker, base, processImports, spec );
+    }
+
     private static void readModelFromUrl( OntModel model, String url, @Nullable String cacheName ) throws IOException {
         boolean attemptToLoadFromDisk = false;
         URLConnection urlc = null;
@@ -165,7 +175,7 @@ private static void readModelFromUrl( OntModel model, String url, @Nullable Stri
      *                       contains all the necessary definitions.
      * @param spec           spec to use to create the ontology model
      */
-    public static OntModel createTdbModel( Dataset dataset, @Nullable String name, boolean processImports, OntModelSpec spec ) {
+    public static OntModel createTdbModel( Dataset dataset, @Nullable String name, boolean processImports, OntModelSpec spec, boolean readOnly ) {
         ModelMaker maker = ModelFactory.createMemModelMaker();
         Model base;
         if ( name != null ) {
@@ -177,16 +187,9 @@ public static OntModel createTdbModel( Dataset dataset, @Nullable String name, b
             throw new IllegalStateException( String.format( "The %s at %s is empty.",
                 name != null ? "named model " + name : "default model", dataset ) );
         }
-        return getModel( maker, base, processImports, spec );
-    }
-
-    /**
-     * ModelFactory.createMemModelMaker()
-     * Get model that is entirely in memory.
-     */
-    private static OntModel getModel( String name, boolean processImports, OntModelSpec spec ) {
-        ModelMaker maker = ModelFactory.createMemModelMaker();
-        Model base = maker.createModel( name, false );
+        if ( readOnly ) {
+            base = ModelFactory.createModelForGraph( new GraphReadOnly( base.getGraph() ) );
+        }
         return getModel( maker, base, processImports, spec );
     }
 

src/ubic/basecode/ontology/jena/TdbOntologyService.java

@@ -2,11 +2,17 @@
 
 import com.hp.hpl.jena.query.Dataset;
 import com.hp.hpl.jena.tdb.TDBFactory;
+import org.apache.commons.io.file.PathUtils;
 import ubic.basecode.ontology.model.OntologyModel;
 
 import javax.annotation.Nullable;
+import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Files;
 import java.nio.file.Path;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 /**
  * An implementation based on Jena TDB.
@@ -16,22 +22,48 @@ public class TdbOntologyService extends AbstractOntologyService {
 
     private final Path tdbDir;
     private final String modelName;
+    private final boolean readOnly;
 
     @Nullable
     private Dataset dataset;
 
-    public TdbOntologyService( String ontologyName, Path tdbDir, @Nullable String modelName, boolean ontologyEnabled, @Nullable String cacheName ) {
+    /**
+     * Temporary d
+     */
+    private Path tempDir;
+
+    /**
+     * @param readOnly open the TDB database in read-only mode, allowing multiple JVMs to share a common TDB. For this
+     *                 to work safely, all the TDB files must not be writable. Additionally, a temporary directory with
+     *                 symbolic links will be created since Jena will still be using a lock file.
+     */
+    public TdbOntologyService( String ontologyName, Path tdbDir, @Nullable String modelName, boolean ontologyEnabled, @Nullable String cacheName, boolean readOnly ) {
         super( ontologyName, tdbDir.toUri().toString(), ontologyEnabled, cacheName );
         this.tdbDir = tdbDir;
         this.modelName = modelName;
+        this.readOnly = readOnly;
     }
 
     @Override
-    protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) {
+    protected OntologyModel loadModel( boolean processImports, LanguageLevel languageLevel, InferenceMode inferenceMode ) throws IOException {
         if ( dataset == null ) {
-            dataset = TDBFactory.createDataset( tdbDir.toString() );
+            if ( readOnly ) {
+                Set<Path> filesToLink;
+                try ( Stream<Path> z = Files.list( tdbDir ) ) {
+                    filesToLink = z.collect( Collectors.toSet() );
+                }
+                tempDir = Files.createTempDirectory( getOntologyName() + ".tdb" );
+                for ( Path p : filesToLink ) {
+                    Files.createSymbolicLink( tempDir.resolve( p.getFileName() ), p );
+                }
+                log.info( "Reading read-only TDB model from {}.", tempDir );
+                dataset = TDBFactory.createDataset( tempDir.toString() );
+
+            } else {
+                dataset = TDBFactory.createDataset( tdbDir.toString() );
+            }
         }
-        return new OntologyModelImpl( OntologyLoader.createTdbModel( dataset, modelName, processImports, getSpec( languageLevel, inferenceMode ) ) );
+        return new OntologyModelImpl( OntologyLoader.createTdbModel( dataset, modelName, processImports, getSpec( languageLevel, inferenceMode ), readOnly ) );
     }
 
     @Override
@@ -47,6 +79,9 @@ public void close() throws Exception {
             if ( dataset != null ) {
                 TDBFactory.release( dataset );
             }
+            if ( tempDir != null ) {
+                PathUtils.delete( tempDir );
+            }
         }
     }
 }