Chunked list works

This commit is contained in:
Andrea Cavalli 2018-12-21 10:03:30 +01:00
parent e4fbd613db
commit a4a981ad1c
17 changed files with 325 additions and 92 deletions

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@ -1,6 +1,7 @@
package org.warp.jcwdb;
import java.io.IOException;
import java.util.function.BiConsumer;
import java.util.function.Consumer;
public class CacheIndexManager implements IndexManager {
@ -32,6 +33,12 @@ public class CacheIndexManager implements IndexManager {
return 0;
}
@Override
public <T> FullIndexDetails addAndGetDetails(DBDataOutput<T> writer) {
// TODO: implement
return null;
}
@Override
public <T> IndexDetails set(long index, DBDataOutput<T> writer) {
// TODO: implement

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@ -10,7 +10,7 @@ public class Cleaner {
private static final double MAXIMUM_SLEEP_INTERVAL = 8d * 1000d; // 8 seconds
private static final double MINIMUM_SLEEP_INTERVAL = 1d * 1000d; // 1 second
private static final double NORMAL_REMOVED_ITEMS = 1000l;
private static final double NORMAL_REMOVED_ITEMS = 2500l;
private static final double REMOVED_ITEMS_RATIO = 2.5d; // 250%
private final Cleanable[] objectsToClean;
@ -26,7 +26,7 @@ public class Cleaner {
}
public void start() {
this.cleanerThread.start();
//this.cleanerThread.start();
}
/**
@ -73,7 +73,7 @@ public class Cleaner {
if (removedItems > 0) {
final double removedItemsRatio = removedItems / NORMAL_REMOVED_ITEMS;
System.out.println("[CLEANER] REMOVED_ITEMS_RATIO: " + removedItemsRatio);
if (removedItemsRatio < 1d / REMOVED_ITEMS_RATIO && removedItemsRatio >= REMOVED_ITEMS_RATIO) {
if (removedItemsRatio < 1d / REMOVED_ITEMS_RATIO || removedItemsRatio >= REMOVED_ITEMS_RATIO) {
suggestedExecutionTimeByItemsCalculations = sleepInterval / removedItemsRatio;
}
}

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@ -35,4 +35,11 @@ public class DBLightArrayListParser<T> extends DBTypeParserImpl<LightArrayList<T
public long calculateHash(LightArrayList<T> value) {
return value.internalList.hashCode();
}
@Override
public String toString() {
return "DBLightArrayListParser{" +
"db=" + db +
'}';
}
}

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@ -21,7 +21,7 @@ public class DBLightBigListParser<T> extends DBTypeParserImpl<LightBigList<T>> {
chunks.add(itm);
chunkSizes.add(itm2);
}
return new LightBigList<T>(db, chunks, chunkSizes);
return new LightBigList<>(db, chunks, chunkSizes);
};
}
@ -39,6 +39,6 @@ public class DBLightBigListParser<T> extends DBTypeParserImpl<LightBigList<T>> {
@Override
public long calculateHash(LightBigList<T> value) {
return value.chunks.hashCode();
return (((long)value.chunks.hashCode()) << 32) | (value.chunkSizes.hashCode() & 0xffffffffL);
}
}

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@ -1,19 +1,19 @@
package org.warp.jcwdb;
public class DBStandardTypes {
private static final int STD = 0xFFFFF000;
public static final int BOOLEAN = STD| 0;
public static final int BYTE = STD| 1;
public static final int SHORT = STD| 2;
public static final int CHAR = STD| 3;
public static final int INTEGER = STD| 4;
public static final int FLOAT = STD| 5;
public static final int DOUBLE = STD| 6;
public static final int STRING = STD| 7;
public static final int BYTE_ARRAY = STD| 8;
public static final int LIGHT_LIST_ARRAY = STD| 9;
public static final int LIGHT_LIST_BIG = STD| 10;
public static final int GENERIC_OBJECT = STD| 11;
private static final int STD = 0xFFFFF000;
public static final int BOOLEAN = STD| 0x000;
public static final int BYTE = STD| 0x001;
public static final int SHORT = STD| 0x002;
public static final int CHAR = STD| 0x003;
public static final int INTEGER = STD| 0x004;
public static final int FLOAT = STD| 0x005;
public static final int DOUBLE = STD| 0x006;
public static final int STRING = STD| 0x007;
public static final int BYTE_ARRAY = STD| 0x008;
public static final int LIGHT_LIST_ARRAY = STD| 0x009;
public static final int LIGHT_LIST_BIG = STD| 0x00A;
public static final int GENERIC_OBJECT = STD| 0x00B;
public static void registerStandardTypes(JCWDatabase db, TypesManager typesManager) {
typesManager.registerType(String.class, STRING, new DBStringParser());

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@ -69,6 +69,9 @@ public class EntryReference<T> implements Castable, Saveable {
synchronized(accessLock) {
if (loaded && !closed) {
try {
if (value instanceof Saveable) {
((Saveable)value).save();
}
IndexDetails returnedDetails = db.write(entryIndex, parser.getWriter(value));
synchronized(hashCacheLock) {
this.cachedHash = returnedDetails.getHash();

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@ -1,14 +1,18 @@
package org.warp.jcwdb;
import it.unimi.dsi.fastutil.longs.Long2IntMap;
import it.unimi.dsi.fastutil.longs.Long2IntRBTreeMap;
import it.unimi.dsi.fastutil.longs.*;
import it.unimi.dsi.fastutil.objects.ObjectBidirectionalIterator;
import java.io.IOException;
import java.nio.channels.SeekableByteChannel;
import java.util.Collection;
import java.util.Collections;
import java.util.Map;
import java.util.Optional;
import java.util.stream.Stream;
public class FileAllocator implements AutoCloseable {
private static final int MAXIMUM_UNALLOCATED_ENTRIES = 500000;
private static final int MAXIMUM_UNALLOCATED_ENTRIES = 50000;
private final SeekableByteChannel dataFileChannel;
private volatile long fileSize;
@ -18,13 +22,19 @@ public class FileAllocator implements AutoCloseable {
/**
* index -> free space size
*/
private final Long2IntRBTreeMap freeBytes = new Long2IntRBTreeMap((a, b) -> (int) (a - b));
private final Long2IntMap freeBytes = new Long2IntLinkedOpenHashMap();
public FileAllocator(SeekableByteChannel dataFileChannel) throws IOException {
this.dataFileChannel = dataFileChannel;
this.fileSize = this.dataFileChannel.size();
}
public FileAllocator(SeekableByteChannel dataFileChannel, long fileSize, Long2IntMap freeBytes) throws IOException {
this.dataFileChannel = dataFileChannel;
this.fileSize = fileSize;
this.freeBytes.putAll(freeBytes);
}
/**
* TODO: not implemented
*
@ -44,23 +54,27 @@ public class FileAllocator implements AutoCloseable {
}
private long allocateIntoUnusedParts(int size) {
ObjectBidirectionalIterator<Long2IntMap.Entry> it = freeBytes.long2IntEntrySet().iterator();
long holeOffset = -1;
int holeSize = 0;
while (it.hasNext()) {
Long2IntMap.Entry entry = it.next();
int currentHoleSize = entry.getIntValue();
Stream<Map.Entry<Long,Integer>> sorted =
freeBytes.entrySet().stream()
.sorted(Collections.reverseOrder(Map.Entry.comparingByValue()));
final VariableWrapper<Long> holeOffset = new VariableWrapper<>(-1L);
final VariableWrapper<Integer> holeSize = new VariableWrapper<>(0);
sorted.anyMatch((entry) -> {
int currentHoleSize = entry.getValue();
if (currentHoleSize < size) {
freeBytes.remove(holeOffset);
if (holeSize > size) {
freeBytes.put(holeOffset + size, holeSize - size);
}
break;
return true;
}
holeOffset.var = entry.getKey();
holeSize.var = currentHoleSize;
return false;
});
if (holeOffset.var != -1L) {
freeBytes.remove(holeOffset.var);
if (holeSize.var > size) {
freeBytes.put(holeOffset.var + size, holeSize.var - size);
}
holeOffset = entry.getLongKey();
holeSize = currentHoleSize;
}
return holeOffset;
return holeOffset.var;
}
private long allocateToEnd(int size) {
@ -103,13 +117,24 @@ public class FileAllocator implements AutoCloseable {
break;
}
}
if (!addedToList) {
if (!addedToList && length > 0) {
freeBytes.put(startPosition, length);
}
}
if (startPosition + length >= fileSize) {
fileSize = startPosition;
}
// Remove the smallest hole in the file
if (freeBytes.size() > MAXIMUM_UNALLOCATED_ENTRIES) {
freeBytes.remove(freeBytes.lastLongKey());
Stream<Map.Entry<Long,Integer>> sorted =
freeBytes.entrySet().stream()
.sorted(Map.Entry.comparingByValue());
Optional<Map.Entry<Long, Integer>> first = sorted.findFirst();
if (first.isPresent()) {
freeBytes.remove(first.get().getKey());
}
}
}

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@ -3,6 +3,7 @@ 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.objects.ObjectIterator;
import java.io.IOException;
import java.nio.ByteBuffer;
@ -11,7 +12,7 @@ import java.nio.channels.SeekableByteChannel;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardOpenOption;
import java.util.Iterator;
import java.util.function.BiConsumer;
import java.util.function.Consumer;
public class FileIndexManager implements IndexManager {
@ -49,13 +50,50 @@ public class FileIndexManager implements IndexManager {
}
dataFileChannel = Files.newByteChannel(dataFile, StandardOpenOption.READ, StandardOpenOption.WRITE);
metadataFileChannel = Files.newByteChannel(metadataFile, StandardOpenOption.READ, StandardOpenOption.WRITE);
fileAllocator = new FileAllocator(dataFileChannel);
fileAllocator = createFileAllocator(dataFileChannel, metadataFileChannel.position(0));
firstAllocableIndex = metadataFileChannel.size() / (long) IndexDetails.TOTAL_BYTES;
if (firstAllocableIndex == 0) {
firstAllocableIndex = 1;
}
}
private FileAllocator createFileAllocator(final SeekableByteChannel dataFileChannel, final SeekableByteChannel metadataFileChannel) throws IOException {
Long2IntMap freeBytes = new Long2IntRBTreeMap();
Long2IntMap usedBytes = new Long2IntRBTreeMap();
long firstOffset = 0;
while (metadataFileChannel.position() + IndexDetails.TOTAL_BYTES <= metadataFileChannel.size()) {
IndexDetails indexDetails = readIndexDetailsAt(metadataFileChannel);
if (indexDetails != null) {
long offset = indexDetails.getOffset();
usedBytes.put(offset, indexDetails.getSize());
if (offset < firstOffset) {
firstOffset = offset;
}
}
}
long previousEntryOffset = 0;
long previousEntrySize = 0;
ObjectIterator<Long2IntMap.Entry> it = usedBytes.long2IntEntrySet().iterator();
while (it.hasNext()) {
final Long2IntMap.Entry entry = it.next();
final long entryOffset = entry.getLongKey();
final long entrySize = entry.getIntValue();
it.remove();
if (previousEntryOffset + previousEntrySize < entryOffset) {
freeBytes.put(previousEntryOffset + previousEntrySize, (int) (entryOffset - (previousEntryOffset + previousEntrySize)));
}
previousEntryOffset = entryOffset;
previousEntrySize = entrySize;
}
final long fileSize = previousEntryOffset + previousEntrySize;
return new FileAllocator(dataFileChannel, fileSize, freeBytes);
}
@Override
public <T> T get(long index, DBReader<T> reader) throws IOException {
checkClosed();
@ -116,6 +154,19 @@ public class FileIndexManager implements IndexManager {
return index;
}
@Override
public <T> FullIndexDetails addAndGetDetails(DBDataOutput<T> data) throws IOException {
checkClosed();
final int size = data.getSize();
final long offset = fileAllocator.allocate(size);
final int type = data.getType();
final long hash = data.calculateHash();
final IndexDetails indexDetails = new IndexDetails(offset, size, type, hash);
final long index = createIndexMetadata(indexDetails);
writeExact(indexDetails, data);
return new FullIndexDetails(index, indexDetails);
}
/**
* Write the data at index.
* The input size must be equal to the index size!
@ -239,7 +290,7 @@ public class FileIndexManager implements IndexManager {
* @param details
*/
private void editIndex(long index, IndexDetails details) {
synchronized (indicesMapsAccessLock) {// FIXXXX main3
synchronized (indicesMapsAccessLock) {
loadedIndices.put(index, details);
dirtyLoadedIndices.add(index);
}
@ -270,8 +321,20 @@ public class FileIndexManager implements IndexManager {
return null;
}
SeekableByteChannel currentMetadataFileChannel = metadataFileChannel.position(metadataPosition);
IndexDetails indexDetails = readIndexDetailsAt(currentMetadataFileChannel);
if (indexDetails != null) {
editIndex(index, indexDetails);
return indexDetails;
}
// No results found. Returning null
return null;
}
private IndexDetails readIndexDetailsAt(SeekableByteChannel currentMetadataFileChannel) throws IOException {
IndexDetails indexDetails = null;
synchronized (metadataByteBufferLock) {// FIXXXX main2
synchronized (metadataByteBufferLock) {
metadataByteBuffer.rewind();
currentMetadataFileChannel.read(metadataByteBuffer);
metadataByteBuffer.rewind();
@ -287,14 +350,7 @@ public class FileIndexManager implements IndexManager {
indexDetails = new IndexDetails(offset, size, type, hash);
}
}
if (indexDetails != null) {
editIndex(index, indexDetails);
return indexDetails;
}
// No results found. Returning null
return null;
return indexDetails;
}
private IndexDetails getIndexMetadata(long index) throws IOException {

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@ -0,0 +1,14 @@
package org.warp.jcwdb;
public class FullIndexDetails extends IndexDetails {
private final long index;
public FullIndexDetails(long index, IndexDetails details) {
super(details);
this.index = index;
}
public long getIndex() {
return index;
}
}

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@ -1,6 +1,8 @@
package org.warp.jcwdb;
import java.io.IOException;
import java.util.function.BiConsumer;
import java.util.function.BiPredicate;
import java.util.function.Consumer;
public interface IndexManager extends Cleanable {
@ -8,6 +10,7 @@ public interface IndexManager extends Cleanable {
int getType(long index) throws IOException;
long getHash(long index) throws IOException;
<T> long add(DBDataOutput<T> writer) throws IOException;
<T> FullIndexDetails addAndGetDetails(DBDataOutput<T> writer) throws IOException;
<T> IndexDetails set(long index, DBDataOutput<T> writer) throws IOException;
void delete(long index) throws IOException;
boolean has(long index);

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@ -6,7 +6,7 @@ import java.io.IOException;
import java.nio.file.Path;
public class JCWDatabase implements AutoCloseable, Cleanable {
public final static long MAX_LOADED_INDICES = 10000;
public final static long MAX_LOADED_INDICES = 1000;
private final TypesManager typesManager;
private final MixedIndexDatabase indices;
@ -36,7 +36,7 @@ public class JCWDatabase implements AutoCloseable, Cleanable {
if (exists(0)) {
return get(0);
} else {
LightList<T> newRoot = new LightArrayList<>(this);
LightList<T> newRoot = new LightBigList<>(this);
return set(0, newRoot);
}
}
@ -63,8 +63,9 @@ public class JCWDatabase implements AutoCloseable, Cleanable {
long index;
long hash;
synchronized (indicesAccessLock) {
index = indices.add(typeParser.getWriter(value));
hash = indices.getHash(index);
FullIndexDetails fullIndexDetails = indices.addAndGetDetails(typeParser.getWriter(value));
index = fullIndexDetails.getIndex();
hash = fullIndexDetails.getHash();
}
return new EntryReference<>(entryReferenceTools, index, hash, typeParser, value);
}

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@ -121,10 +121,11 @@ public class LightArrayList<T> implements LightList<T> {
@SuppressWarnings("unchecked")
@Override
public T[] toArray() {
final T[] elements = (T[]) new Objects[internalList.size()];
final T[] elements = (T[]) new Object[internalList.size()];
for (int i = 0; i < elements.length; i++) {
try {
elements[i] = (T) db.get(internalList.getLong(i)).getValueReadOnly();
T element = (T) db.get(internalList.getLong(i)).getValueReadOnly();
elements[i] = element;
} catch (IOException e) {
e.printStackTrace();
}
@ -442,4 +443,12 @@ public class LightArrayList<T> implements LightList<T> {
}
return removed;
}
@Override
public String toString() {
return "LightArrayList{" +
"internalList=" + internalList +
", db=" + db +
'}';
}
}

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@ -9,13 +9,18 @@ import java.util.*;
import java.util.function.Consumer;
import java.util.function.Predicate;
public class LightBigList<T> implements LightList<T> {
public class LightBigList<T> implements LightList<T>, Saveable {
public static final int MAX_ELEMENTS_PER_CHUNK = 10000;
public static final int MAX_ELEMENTS_PER_CHUNK = 200000;
public final LongArrayList chunks;
public final IntArrayList chunkSizes;
private final transient JCWDatabase db;
private final JCWDatabase db;
private LightList<T> cachedChunk;
private EntryReference<LightList<T>> cachedChunkRef;
private long cachedChunkIndex = -1;
private int cachedChunkNumber = -1;
private final Object cachedChunkLock = new Object();
/**
* @param db Database reference
@ -43,6 +48,23 @@ public class LightBigList<T> implements LightList<T> {
this.db = db;
this.chunks = chunks;
this.chunkSizes = chunkSizes;
if (this.chunks.size() > 0) {
prepareAccessToChunk(0);
}
}
private void prepareAccessToChunk(int chunkNumber) {
if (this.cachedChunkRef != null) {
this.cachedChunkRef.save();
}
this.cachedChunkNumber = chunkNumber;
this.cachedChunkIndex = this.chunks.getLong(chunkNumber);
try {
this.cachedChunkRef = db.get(this.cachedChunkIndex);
} catch (IOException ex) {
throw (NullPointerException) new NullPointerException().initCause(ex);
}
this.cachedChunk = this.cachedChunkRef.getValueReadOnly();
}
/**
@ -53,16 +75,13 @@ public class LightBigList<T> implements LightList<T> {
for (int i = 0; i < chunks.size(); i++) {
final int chunkNumber = i;
if (MAX_ELEMENTS_PER_CHUNK - chunkSizes.getInt(i) > 0) {
try {
final long chunkIndex = chunks.getLong(i);
final EntryReference<LightList<T>> chunkRef = db.get(chunkIndex);
chunkRef.editValue((chunk) -> {
chunk.appendIndex(elementIndex);
chunkSizes.set(chunkNumber, chunkSizes.getInt(chunkNumber) + 1);
});
synchronized (cachedChunkLock) {
if (cachedChunkNumber != i) {
prepareAccessToChunk(i);
}
cachedChunk.appendIndex(elementIndex);
chunkSizes.set(chunkNumber, cachedChunk.size());
return;
} catch (IOException ex) {
throw (NullPointerException) new NullPointerException().initCause(ex);
}
}
}
@ -131,7 +150,8 @@ public class LightBigList<T> implements LightList<T> {
*/
@Deprecated
@Override
public Iterator<T> iterator() {
public Iterator<T> iterator()
{
throw new RuntimeException("iterator() isn't implemented!");
}
@ -166,10 +186,36 @@ public class LightBigList<T> implements LightList<T> {
}
}
/**
* toArray() isn't implemented! DO NOT USE IT.
* @return
*/
@SuppressWarnings("unchecked")
@Deprecated
@Override
public T[] toArray() {
throw new RuntimeException("toArray() isn't implemented!");
T[] result = (T[]) new Object[this.size()];
long currentOffset = 0;
// Iterate through all chunks
for (int i = 0; i < chunks.size(); i++) {
final int currentChunkSize = chunkSizes.getInt(i);
final long chunkStartOffset = currentOffset;
currentOffset += currentChunkSize;
// Get chunk index
final long chunkIndex = chunks.getLong(i);
try {
EntryReference<LightList<T>> chunkRef = db.get(chunkIndex);
LightList<T> chunk = chunkRef.getValueReadOnly();
for (int i1 = 0; i1 < chunk.size(); i1++) {
result[(int)(chunkStartOffset + i1)] = chunk.get(i);
}
} catch (IOException ex) {
throw (NullPointerException) new NullPointerException().initCause(ex);
}
}
return result;
}
@SuppressWarnings("unchecked")
@ -518,4 +564,20 @@ public class LightBigList<T> implements LightList<T> {
}
return result.var;
}
@Override
public String toString() {
return "LightBigList{" +
"chunks=" + chunks +
", chunkSizes=" + chunkSizes +
", db=" + db +
'}';
}
@Override
public void save() {
if (this.cachedChunkRef != null) {
this.cachedChunkRef.save();
}
}
}

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@ -5,6 +5,7 @@ import it.unimi.dsi.fastutil.longs.Long2LongMap;
import java.io.IOException;
import java.nio.file.Path;
import java.util.function.BiConsumer;
import java.util.function.Consumer;
public class MixedIndexDatabase implements IndexManager {
@ -48,6 +49,11 @@ public class MixedIndexDatabase implements IndexManager {
return fileIndices.add(writer);
}
@Override
public <T> FullIndexDetails addAndGetDetails(DBDataOutput<T> writer) throws IOException {
return fileIndices.addAndGetDetails(writer);
}
@Override
public <T> IndexDetails set(long index, DBDataOutput<T> writer) throws IOException {
if (cacheIndices.has(index)) {

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@ -37,7 +37,7 @@ public class App {
// System.out.println(" - " + root.get(i));
// }
long prectime = System.currentTimeMillis();
for (int i = 0; i < 20000/* 2000000 */; i++) {
for (int i = 0; i < 20000000/* 2000000 */; i++) {
Animal animal = new StrangeAnimal(i % 40);
root.add(animal);
if (i > 0 && i % 200000 == 0) {

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@ -1,29 +1,18 @@
package org.warp.jcwdb;
import static org.junit.Assert.assertTrue;
import java.io.IOException;
import java.nio.file.Files;
import java.nio.file.Path;
import java.util.ArrayList;
import org.junit.Test;
import org.warp.jcwdb.EntryReference;
import org.warp.jcwdb.JCWDatabase;
import org.warp.jcwdb.LightList;
import static org.junit.Assert.assertTrue;
/**
* Unit test for simple App.
*/
public class AppTest
{
/**
* Rigorous Test :-)
*/
@Test
public void shouldAnswerWithTrue()
{
assertTrue( true );
}
public class AppTest {
/**
* Rigorous Test :-)
*/
@Test
public void shouldAnswerWithTrue() {
assertTrue(true);
}
}

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@ -0,0 +1,51 @@
package org.warp.jcwdb;
import org.junit.Test;
import java.io.IOException;
import java.nio.ByteBuffer;
import java.nio.channels.SeekableByteChannel;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.StandardOpenOption;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
public class FileAllocatorTest {
@Test
public void shouldAllocateAtZero() throws IOException {
Path tempFile = Files.createTempFile("", "");
SeekableByteChannel byteCh = Files.newByteChannel(tempFile);
FileAllocator allocator = new FileAllocator(byteCh);
long offset1 = allocator.allocate(512);
assertEquals(0, offset1);
}
@Test
public void shouldAllocateAt512() throws IOException {
Path tempFile = Files.createTempFile("", "");
SeekableByteChannel byteCh = Files.newByteChannel(tempFile, StandardOpenOption.WRITE);
byteCh.write(ByteBuffer.wrap(new byte[512]));
FileAllocator allocator = new FileAllocator(byteCh);
long offset1 = allocator.allocate(512);
assertEquals(512, offset1);
}
@Test
public void shouldAllocateUnusedSpace() throws IOException {
Path tempFile = Files.createTempFile("", "");
SeekableByteChannel byteCh = Files.newByteChannel(tempFile, StandardOpenOption.WRITE);
FileAllocator allocator = new FileAllocator(byteCh);
long offset1 = allocator.allocate(512);
allocator.markFree(offset1, 512);
long offset2 = allocator.allocate(128);
long offset3 = allocator.allocate(512-128);
long offset4 = allocator.allocate(128);
assertEquals(0, offset2);
assertEquals(128, offset3);
assertEquals(512, offset4);
}
}