Merge branch 'hotfix-1.1.34'

Author: arteymix

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.33</version>
+	<version>1.1.34</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -717,7 +717,7 @@
 		<pavlab.server>frink.pavlab.msl.ubc.ca</pavlab.server>
 		<pavlab.repoDir>/space/maven2</pavlab.repoDir>
 		<pavlab.siteDir>/space/web/maven-sites</pavlab.siteDir>
-		<log4j.version>2.25.2</log4j.version>
+		<log4j.version>2.25.3</log4j.version>
 		<lucene.version>3.6.2</lucene.version>
 		<!-- rJava -->
 		<!-- You may override this in ~/.m2/settings.xml -->

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

@@ -28,11 +28,11 @@ public class TdbOntologyService extends AbstractOntologyService {
     @Nullable
     private Dataset dataset;
 
-    /**
-     * Temporary d
-     */
+    @Nullable
     private Path tempDir;
 
+    private boolean deleteTempDir = false;
+
     /**
      * @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
@@ -57,14 +57,27 @@ protected OntologyModel loadModel( boolean processImports, LanguageLevel languag
                     try ( Stream<Path> z = Files.list( tdbDir ) ) {
                         filesToLink = z.collect( Collectors.toSet() );
                     }
-                    tempDir = Files.createTempDirectory( getOntologyName() + ".tdb" );
+                    if ( tempDir == null ) {
+                        log.info( "Creating temporary directory for read-only TDB model." );
+                        tempDir = Files.createTempDirectory( getOntologyName() + ".tdb" );
+                        deleteTempDir = true;
+                    } else if ( !Files.exists( tempDir ) ) {
+                        log.info( "Creating temporary directory at {} for read-only TDB model.", tempDir );
+                        Files.createDirectories( tempDir );
+                        deleteTempDir = true;
+                    } else {
+                        log.info( "Reusing existing temporary directory at {} for read-only TDB model. Note that the directory will not be removed.", tempDir );
+                        // never delete a temporary directory that wasn't created by this service (I've learned this the hard way!)
+                        deleteTempDir = false;
+                    }
                     for ( Path p : filesToLink ) {
                         Files.copy( p, tempDir.resolve( p.getFileName() ) );
                     }
                 } finally {
                     loc.getLock().release();
                 }
                 log.info( "Reading read-only TDB model from {}.", tempDir );
+                assert tempDir != null;
                 dataset = TDBFactory.createDataset( tempDir.toString() );
             } else {
                 dataset = TDBFactory.createDataset( tdbDir.toString() );
@@ -78,6 +91,19 @@ protected OntologyModel loadModelFromStream( InputStream is, boolean processImpo
         throw new UnsupportedOperationException( "TDB cannot be loaded from an input stream." );
     }
 
+    /**
+     * Set the temporary directory used when opening the TDB in read-only mode.
+     * <p>
+     * This can only be set once, before the first model is loaded. Note that the directory will be removed when the
+     * service is closed.
+     */
+    public void setTempDir( Path tempDir ) {
+        if ( this.tempDir != null ) {
+            throw new IllegalStateException( "Temporary directory has already been set." );
+        }
+        this.tempDir = tempDir;
+    }
+
     @Override
     public void close() throws Exception {
         try {
@@ -86,7 +112,7 @@ public void close() throws Exception {
             if ( dataset != null ) {
                 TDBFactory.release( dataset );
             }
-            if ( tempDir != null ) {
+            if ( tempDir != null && deleteTempDir ) {
                 PathUtils.delete( tempDir );
             }
         }