Fixed cleaner crash

src/main/java/org/warp/jcwdb/Cleaner.java

@@ -1,6 +1,8 @@
 package org.warp.jcwdb;
 
+import java.io.IOException;
 import java.lang.ref.WeakReference;
+import java.nio.channels.ClosedChannelException;
 
 import it.unimi.dsi.fastutil.longs.Long2ObjectMap.Entry;
 
@@ -14,6 +16,7 @@ public class Cleaner {
 	private final Cleanable[] objectsToClean;
 	private final Thread cleanerThread;
 	private int sleepInterval = (int) MINIMUM_SLEEP_INTERVAL;
+	private volatile boolean stopRequest = false;
 	
 	public Cleaner(Cleanable... objectsToClean) {
 		this.objectsToClean = objectsToClean;
@@ -35,12 +38,13 @@ public class Cleaner {
 		for (Cleanable cleanable : objectsToClean) {
 			cleanedItems += cleanable.clean();
 		}
+		System.gc();
 		return cleanedItems;
 	}
 
 	public void stop() {
 		if (cleanerThread != null) {
-			cleanerThread.interrupt();
+			stopRequest = true;
 			while (cleanerThread.isAlive()) {
 				try {
 					Thread.sleep(100);
@@ -55,7 +59,7 @@ public class Cleaner {
 		
 		@Override
 		public void run() {
-			while(!cleanerThread.isInterrupted()) {
+			while(!stopRequest) {
 				try {
 					System.out.println("[CLEANER] Waiting " + sleepInterval + "ms.");
 					Thread.sleep(sleepInterval);
@@ -87,6 +91,7 @@ public class Cleaner {
 
 					System.out.println("[CLEANER] Cleaned " + removedItems + " items.");
 				}catch (InterruptedException e) {
+
 				}
 			}
 		}

src/main/java/org/warp/jcwdb/EntryReference.java

@@ -79,8 +79,6 @@ public class EntryReference<T> implements Castable {
 				return;
 			}
 
-			db.removeEntryReference(entryIndex);
-
 			closed = true;
 		}
 	}

src/main/java/org/warp/jcwdb/FileIndexManager.java

@@ -2,19 +2,15 @@ package org.warp.jcwdb;
 
 import com.esotericsoftware.kryo.io.Input;
 import com.esotericsoftware.kryo.io.Output;
-
 import it.unimi.dsi.fastutil.longs.*;
-import it.unimi.dsi.fastutil.longs.Long2ObjectMap.Entry;
 
 import java.io.IOException;
-import java.lang.ref.WeakReference;
 import java.nio.ByteBuffer;
 import java.nio.channels.Channels;
 import java.nio.channels.SeekableByteChannel;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.StandardOpenOption;
-import java.util.Iterator;
 
 public class FileIndexManager implements IndexManager {
 	private final SeekableByteChannel dataFileChannel, metadataFileChannel;
@@ -103,6 +99,7 @@ public class FileIndexManager implements IndexManager {
 	/**
 	 * Write the data at index.
 	 * The input size must be equal to the index size!
+	 *
 	 * @param indexDetails
 	 * @param data
 	 * @throws IOException
@@ -326,6 +323,7 @@ public class FileIndexManager implements IndexManager {
 
 	private long cleanExtraIndices() {
 		long removedIndices = 0;
+		LongArrayList toUnload = new LongArrayList();
 		synchronized (indicesMapsAccessLock) {
 			if (loadedIndices.size() > JCWDatabase.MAX_LOADED_REFERENCES) {
 				long count = loadedIndices.size();
@@ -335,16 +333,19 @@ public class FileIndexManager implements IndexManager {
 					if (count < JCWDatabase.MAX_LOADED_REFERENCES * 3l / 2l) {
 						break;
 					}
-					try {
-						flushAndUnload(loadedIndex);
-					} catch (IOException e) {
-						e.printStackTrace();
-					}
+					toUnload.add(loadedIndex);
 					removedIndices++;
 					count--;
 				}
 			}
 		}
+		for (long index : toUnload.elements()) {
+			try {
+				flushAndUnload(index);
+			} catch (IOException e) {
+				e.printStackTrace();
+			}
+		}
 		return removedIndices;
 	}
 }

src/main/java/org/warp/jcwdb/JCWDatabase.java

@@ -13,8 +13,8 @@ import it.unimi.dsi.fastutil.longs.LongArrayList;
 import it.unimi.dsi.fastutil.objects.ObjectIterator;
 
 public class JCWDatabase implements AutoCloseable, Cleanable {
-	public final static long MAX_LOADED_REFERENCES = 10;
-	public final static long MAX_LOADED_INDICES = 1000;
+	public final static long MAX_LOADED_REFERENCES = 1000;
+	public final static long MAX_LOADED_INDICES = 10000;
 	
 	private final TypesManager typesManager;
 	private final MixedIndexDatabase indices;
@@ -119,6 +119,10 @@ public class JCWDatabase implements AutoCloseable, Cleanable {
 		}
 	}
 
+	public boolean isOpen() {
+		return !closed;
+	}
+
 	@Override
 	public void close() throws IOException {
 		if (closed) {

src/main/java/org/warp/jcwdb/exampleimpl/App.java

@@ -12,7 +12,8 @@ import java.nio.file.Paths;
 import java.util.function.Predicate;
 
 public class App {
-	public static void main(String[] args) throws Exception {
+	public static void main(String[] args) {
+		try {
 			if (args.length > 2 && Boolean.parseBoolean(args[2])) {
 				Files.delete(Paths.get(args[0]));
 				Files.delete(Paths.get(args[1]));
@@ -20,6 +21,7 @@ public class App {
 			System.out.println("Loading database...");
 			long time0 = System.currentTimeMillis();
 			JCWDatabase db = new JCWDatabase(Paths.get(args[0]), Paths.get(args[1]));
+			try {
 				long time01 = System.currentTimeMillis();
 				System.out.println("Time elapsed: " + (time01 - time0));
 				System.out.println("Loading root...");
@@ -33,7 +35,7 @@ public class App {
 //			System.out.println(" - " + root.get(i));
 //		}
 				long prectime = System.currentTimeMillis();
-		for (int i = 0; i < 2000000000/* 2000000 */; i++) {
+				for (int i = 0; i < 2000000/* 2000000 */; i++) {
 					Animal animal = new StrangeAnimal(i % 40);
 					root.add(animal);
 					if (i > 0 && i % 200000 == 0) {
@@ -70,12 +72,22 @@ public class App {
 				long time3 = System.currentTimeMillis();
 				System.out.println("Removed items: " + removedItems);
 				System.out.println("Used memory: " + ((Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1024 / 1024) + "MB");
-		System.out.println("Time elapsed: " + (time3 - time2));
+				System.out.println("Time elapsed: " + (time3 - time2_2));
 				System.out.println("Saving database...");
 				System.out.println("Root size: " + root.size());
 				db.close();
-		long time3 = System.currentTimeMillis();
-		System.out.println("Time elapsed: " + (time3 - time2_2));
+				long time4 = System.currentTimeMillis();
+				System.out.println("Time elapsed: " + (time4 - time3));
+			} catch (Exception ex) {
+				ex.printStackTrace();
+			} finally {
+				if (db.isOpen()) {
+					db.close();
+				}
+			}
+		} catch (Exception ex) {
+			ex.printStackTrace();
+		}
 	}
 
 	public static <T> Predicate<T> not(Predicate<T> t) {