public ZipRepository(final InputStream in, final MimeRegistry mimeRegistry) throws IOException {
this(mimeRegistry);
final ZipInputStream zipIn = new ZipInputStream(in);
try {
ZipEntry nextEntry = zipIn.getNextEntry();
while (nextEntry != null) {
final String[] buildName = RepositoryUtilities.splitPath(nextEntry.getName(), "/");
if (nextEntry.isDirectory()) {
root.updateDirectoryEntry(buildName, 0, nextEntry);
} else {
final ByteArrayOutputStream bos = new ByteArrayOutputStream();
final Deflater def = new Deflater(nextEntry.getMethod());
try {
final DeflaterOutputStream dos = new DeflaterOutputStream(bos, def);
try {
IOUtils.getInstance().copyStreams(zipIn, dos);
dos.flush();
} finally {
dos.close();
}
} finally {
def.end();
}
root.updateEntry(buildName, 0, nextEntry, bos.toByteArray());
}
zipIn.closeEntry();
nextEntry = zipIn.getNextEntry();
}
} finally {
zipIn.close();
}
}
@Deprecated
private static synchronized byte[] zipFileName(String fileName) throws IOException {
Deflater deflater = new Deflater();
byte[] bytes = fileName.getBytes();
deflater.setInput(bytes);
deflater.finish();
ByteArrayOutputStream bos = new ByteArrayOutputStream(bytes.length);
byte[] buffer = new byte[1024];
while (!deflater.finished()) {
int bytesCompressed = deflater.deflate(buffer);
bos.write(buffer, 0, bytesCompressed);
}
bos.close();
int count = 0;
for (int i = 0; i < buffer.length; i++) {
if (buffer[i] != 0) count++;
}
byte[] result = new byte[count];
for (int i = 0; i < result.length; i++) {
result[i] = buffer[i];
}
return result;
}
@Test
public void testDeflaterReader() throws Exception {
String inputString = "blahblahblah??blahblahblahblahblah??blablahblah??blablahblah??bla";
byte[] input = inputString.getBytes("UTF-8");
ByteArrayInputStream inputStream = new ByteArrayInputStream(input);
AtomicLong counter = new AtomicLong(0);
DeflaterReader reader = new DeflaterReader(inputStream, counter);
ArrayList<Integer> zipHolder = new ArrayList<Integer>();
int b = reader.read();
while (b != -1) {
zipHolder.add(b);
b = reader.read();
}
assertEquals(input.length, counter.get());
byte[] allCompressed = new byte[zipHolder.size()];
for (int i = 0; i < allCompressed.length; i++) {
allCompressed[i] = (byte) zipHolder.get(i).intValue();
}
byte[] output = new byte[30];
Deflater compresser = new Deflater();
compresser.setInput(input);
compresser.finish();
int compressedDataLength = compresser.deflate(output);
compareByteArray(allCompressed, output, compressedDataLength);
reader.close();
}
@Override
public void encode(ChannelBuffer compressed) {
while (!compressor.needsInput()) {
int numBytes = compressor.deflate(out, 0, out.length, Deflater.SYNC_FLUSH);
compressed.writeBytes(out, 0, numBytes);
}
}
@Test
public void testInflaterReader() throws Exception {
String inputString = "blahblahblah??blahblahblahblahblah??blablahblah??blablahblah??bla";
byte[] input = inputString.getBytes("UTF-8");
byte[] output = new byte[30];
Deflater compresser = new Deflater();
compresser.setInput(input);
compresser.finish();
int compressedDataLength = compresser.deflate(output);
byte[] zipBytes = new byte[compressedDataLength];
System.arraycopy(output, 0, zipBytes, 0, compressedDataLength);
ByteArrayInputStream byteInput = new ByteArrayInputStream(zipBytes);
InflaterReader inflater = new InflaterReader(byteInput);
ArrayList<Integer> holder = new ArrayList<Integer>();
int read = inflater.read();
while (read != -1) {
holder.add(read);
read = inflater.read();
}
byte[] result = new byte[holder.size()];
for (int i = 0; i < result.length; i++) {
result[i] = holder.get(i).byteValue();
}
String txt = new String(result);
assertEquals(inputString, txt);
inflater.close();
}
@Test
public void testInflaterWriter() throws Exception {
String inputString = "blahblahblah??blahblahblahblahblah??blablahblah??blablahblah??bla";
byte[] input = inputString.getBytes("UTF-8");
byte[] output = new byte[30];
Deflater compresser = new Deflater();
compresser.setInput(input);
compresser.finish();
int compressedDataLength = compresser.deflate(output);
byte[] zipBytes = new byte[compressedDataLength];
System.arraycopy(output, 0, zipBytes, 0, compressedDataLength);
ByteArrayInputStream byteInput = new ByteArrayInputStream(zipBytes);
ByteArrayOutputStream byteOutput = new ByteArrayOutputStream();
InflaterWriter writer = new InflaterWriter(byteOutput);
byte[] zipBuffer = new byte[12];
int n = byteInput.read(zipBuffer);
while (n > 0) {
writer.write(zipBuffer, 0, n);
n = byteInput.read(zipBuffer);
}
writer.close();
byte[] outcome = byteOutput.toByteArray();
String outStr = new String(outcome);
assertEquals(inputString, outStr);
}
static long getCompressedSize(InputStream is) {
DeflaterOutputStream dos = null;
long size = 0L;
try {
ByteArrayOutputStream baos = new ByteArrayOutputStream();
Deflater def = new Deflater();
def.setLevel(Deflater.BEST_COMPRESSION);
dos = new DeflaterOutputStream(baos, def);
byte buf[] = new byte[8192];
int n = is.read(buf);
while (n > 0) {
dos.write(buf);
n = is.read(buf);
}
dos.flush();
dos.finish();
size = baos.size();
} catch (IOException ex) {
Logger.getLogger(JarStat.class.getName()).log(Level.SEVERE, null, ex);
} finally {
try {
dos.close();
} catch (IOException ex) {
Logger.getLogger(JarStat.class.getName()).log(Level.SEVERE, null, ex);
}
}
return size;
}
public synchronized void finish() throws IOException {
if (!_def.finished()) {
_def.finish();
while (!_def.finished()) {
deflate();
}
}
}
/** Ensures all bytes sent to the deflater are written to the stream. */
private void flushDeflater() throws IOException {
if (entry.entry.getMethod() == DEFLATED) {
def.finish();
while (!def.finished()) {
deflate();
}
}
}
private byte[] compressData(byte[] rawBytes, AtomicInteger size) {
deflater.reset();
deflater.setInput(rawBytes);
deflater.finish();
byte[] compressedData = new byte[rawBytes.length];
size.set(deflater.deflate(compressedData));
return compressedData;
}
/**
* {@collect.stats} {@description.open} Finishes writing compressed data to the output stream
* without closing the underlying stream. {@description.close} {@property.open} Use this method
* when applying multiple filters in succession to the same output stream. {@property.close}
*
* @exception IOException if an I/O error has occurred
*/
public void finish() throws IOException {
if (!def.finished()) {
def.finish();
while (!def.finished()) {
deflate();
}
}
}
public static byte[] compress(byte data[], String signature, String version) {
byte header[] = ArrayUtil.mergeArrays(signature.getBytes(), version.getBytes());
header = ArrayUtil.mergeArrays(header, Byteconvert.convertBack(data.length));
byte result[] = ArrayUtil.resizeArray(header, data.length * 2);
Deflater deflater = new Deflater();
deflater.setInput(data);
deflater.finish();
int clength = deflater.deflate(result, 12, result.length - 12);
return ArrayUtil.getSubArray(result, 0, clength + 12);
}
/** Creates a deflater based on the Zlib arguments. */
private static Deflater createDeflater(int compressionLevel, int strategy, int encodingMode) {
Deflater defl;
if (encodingMode == ZlibModule.FORCE_GZIP) defl = new Deflater(compressionLevel, true);
else defl = new Deflater(compressionLevel, false);
defl.setStrategy(strategy);
return defl;
}
/**
* Writes all necessary data for this entry.
*
* @since 1.1
*/
public void closeEntry() throws IOException {
if (entry == null) {
return;
}
long realCrc = crc.getValue();
crc.reset();
if (entry.getMethod() == DEFLATED) {
def.finish();
while (!def.finished()) {
deflate();
}
entry.setSize(def.getTotalIn());
entry.setComprSize(def.getTotalOut());
entry.setCrc(realCrc);
def.reset();
written += entry.getCompressedSize();
} else if (raf == null) {
if (entry.getCrc() != realCrc) {
throw new SwcException.BadCRC(Long.toHexString(entry.getCrc()), Long.toHexString(realCrc));
}
if (entry.getSize() != written - dataStart) {
throw new SwcException.BadZipSize(
entry.getName(), entry.getSize() + "", (written - dataStart) + "");
}
} else {
/* method is STORED and we used RandomAccessFile */
long size = written - dataStart;
entry.setSize(size);
entry.setComprSize(size);
entry.setCrc(realCrc);
}
// If random access output, write the local file header containing
// the correct CRC and compressed/uncompressed sizes
if (raf != null) {
long save = raf.getFilePointer();
raf.seek(localDataStart);
writeOut((new ZipLong(entry.getCrc())).getBytes());
writeOut((new ZipLong(entry.getCompressedSize())).getBytes());
writeOut((new ZipLong(entry.getSize())).getBytes());
raf.seek(save);
}
writeDataDescriptor(entry);
entry = null;
}
private static void deflate(TemporaryBuffer.Heap tinyPack, final byte[] content)
throws IOException {
final Deflater deflater = new Deflater();
final byte[] buf = new byte[128];
deflater.setInput(content, 0, content.length);
deflater.finish();
do {
final int n = deflater.deflate(buf, 0, buf.length);
if (n > 0) tinyPack.write(buf, 0, n);
} while (!deflater.finished());
}
private void deflate() {
Deflater deflater = new Deflater(-1);
try {
deflater.setInput(this.field_149278_f, 0, this.field_149278_f.length);
deflater.finish();
byte[] deflated = new byte[this.field_149278_f.length];
this.field_149285_h = deflater.deflate(deflated);
this.field_149281_e = deflated;
} finally {
deflater.end();
}
}
public static byte[] zlibCompress(String what) throws UnsupportedEncodingException {
byte[] input = what.getBytes("UTF-8");
// Compress the bytes
byte[] output = new byte[4096];
Deflater compresser = new Deflater();
compresser.setInput(input);
compresser.finish();
compresser.deflate(output);
return output;
}
private void flushInputToStream(final OutputStream pStream) throws IOException {
System.out.println("DeflateEncoder.flushInputToStream");
if (deflater.needsInput()) {
System.out.println("Foo");
}
while (!deflater.needsInput()) {
int deflated = deflater.deflate(buffer, 0, buffer.length);
pStream.write(buffer, 0, deflated);
System.out.println("flushed " + deflated);
}
}
@Override
public void write(byte[] b, int off, int len) throws IOException {
if (_def.finished()) throw new IOException("Stream already finished");
if ((off | len | (off + len) | (b.length - (off + len))) < 0)
throw new IndexOutOfBoundsException();
if (len == 0) return;
if (!_def.finished()) {
_def.setInput(b, off, len);
while (!_def.needsInput()) {
deflate();
}
}
}
public SpdyHeaderBlockZlibCompressor(int version, int compressionLevel) {
if (version < SpdyConstants.SPDY_MIN_VERSION || version > SpdyConstants.SPDY_MAX_VERSION) {
throw new IllegalArgumentException("unsupported version: " + version);
}
if (compressionLevel < 0 || compressionLevel > 9) {
throw new IllegalArgumentException(
"compressionLevel: " + compressionLevel + " (expected: 0-9)");
}
compressor = new Deflater(compressionLevel);
if (version < 3) {
compressor.setDictionary(SPDY2_DICT);
} else {
compressor.setDictionary(SPDY_DICT);
}
}
/**
* Construct a new FileInput
*
* @param filename String
* @param compression boolean
*/
public FileInput(String filename, boolean compression) {
deflateIn = null;
f = new File(filename);
try {
fileIn = new FileInputStream(f);
if (compression) {
// Compressor with highest level of compression
Deflater def = new Deflater();
def.setLevel(Deflater.BEST_COMPRESSION);
deflateIn = new DeflaterInputStream(fileIn, def);
}
} catch (FileNotFoundException e) {
System.err.println("File not found: " + f);
}
}
@Override
public byte[] compress(final byte[] data, final CodecOptions options) throws FormatException {
if (data == null || data.length == 0) throw new IllegalArgumentException("No data to compress");
final Deflater deflater = new Deflater();
deflater.setInput(data);
deflater.finish();
final byte[] buf = new byte[8192];
final ByteVector bytes = new ByteVector();
int r = 0;
// compress until eof reached
while ((r = deflater.deflate(buf, 0, buf.length)) > 0) {
bytes.add(buf, 0, r);
}
return bytes.toByteArray();
}
/**
* Begin writing next entry.
*
* @since 1.1
*/
public void putNextEntry(ZipEntry ze) throws IOException {
closeEntry();
entry = ze;
entries.addElement(entry);
if (entry.getMethod() == -1) { // not specified
entry.setMethod(method);
}
if (entry.getTime() == -1) { // not specified
entry.setTime(System.currentTimeMillis());
}
// Size/CRC not required if RandomAccessFile is used
if (entry.getMethod() == STORED && raf == null) {
// these exceptions should never happen for us (as we always write to a file)
// so they are not localized
if (entry.getSize() == -1) {
throw new RuntimeException(
"uncompressed size is required for" + " STORED method when not writing to a" + " file");
}
if (entry.getCrc() == -1) {
throw new RuntimeException(
"crc checksum is required for STORED" + " method when not writing to a file");
}
entry.setComprSize(entry.getSize());
}
if (entry.getMethod() == DEFLATED && hasCompressionLevelChanged) {
def.setLevel(level);
hasCompressionLevelChanged = false;
}
writeLocalFileHeader(entry);
}
/** Writes bytes to ZIP entry. */
public void write(byte[] b, int offset, int length) throws IOException {
if (entry.getMethod() == DEFLATED) {
if (length > 0) {
if (!def.finished()) {
def.setInput(b, offset, length);
while (!def.needsInput()) {
deflate();
}
}
}
} else {
writeOut(b, offset, length);
written += length;
}
crc.update(b, offset, length);
}
public byte[] compress(final byte[] bytes) {
try {
deflater.setInput(bytes);
deflater.finish();
int len = deflater.deflate(buffer);
byte[] compressedBytes = new byte[len];
System.arraycopy(buffer, 0, compressedBytes, 0, len);
return compressedBytes;
} finally {
try {
deflater.reset();
} catch (Exception e) {
logger.warn("deflater.reset failed", e);
}
}
}
@Override
public void close() throws IOException {
if (closed) return;
// This method delegates to the DeflaterSink for finishing the deflate process
// but keeps responsibility for releasing the deflater's resources. This is
// necessary because writeFooter needs to query the proccessed byte count which
// only works when the defalter is still open.
Throwable thrown = null;
try {
deflaterSink.finishDeflate();
writeFooter();
} catch (Throwable e) {
thrown = e;
}
try {
deflater.end();
} catch (Throwable e) {
if (thrown == null) thrown = e;
}
try {
sink.close();
} catch (Throwable e) {
if (thrown == null) thrown = e;
}
closed = true;
if (thrown != null) Util.sneakyRethrow(thrown);
}
/**
* Writes next block of compressed data to the output stream.
*
* @throws IOException on error
*/
protected final void deflate() throws IOException {
int len = def.deflate(buf, 0, buf.length);
if (len > 0) {
writeOut(buf, 0, len);
written += len;
}
}
/**
* Writes new sequence part entry.
*
* @param accession accession number of original sequence
* @param from position of first nucleotide of content of this entry in the original sequence
* (e.g. 0 if this entry contains whole sequence)
* @param sequence content of this entry
* @throws java.io.IOException if an I/O error occurs.
*/
public void writeSequencePart(
String accession, int from, NucleotideSequence sequence, boolean compressed)
throws IOException {
stream.writeByte(compressed ? SEQUENCE_PART_ENTRY_TYPE_COMPRESSED : SEQUENCE_PART_ENTRY_TYPE);
stream.writeUTF(accession);
stream.writeInt(from);
if (compressed) {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
final Deflater def = new Deflater(9, true);
DeflaterOutputStream dos = new DeflaterOutputStream(bos, def);
SequencesUtils.convertNSequenceToBit2Array(sequence).writeTo(new DataOutputStream(dos));
dos.close();
def.end();
stream.writeInt(bos.size());
stream.write(bos.toByteArray());
} else SequencesUtils.convertNSequenceToBit2Array(sequence).writeTo(stream);
}
private static byte[] deflate(byte[] input) {
Deflater compressor = new Deflater(Deflater.DEFLATED);
compressor.setInput(input);
compressor.finish();
ByteArrayOutputStream bos = new ByteArrayOutputStream(input.length);
byte[] buf = new byte[CHUNKSIZE];
while (!compressor.finished()) {
int count = compressor.deflate(buf);
bos.write(buf, 0, count);
}
return bos.toByteArray();
}
/**
* {@collect.stats} {@description.open} Writes remaining compressed data to the output stream and
* closes the underlying stream. {@description.close}
*
* @exception IOException if an I/O error has occurred
*/
public void close() throws IOException {
if (!closed) {
finish();
if (usesDefaultDeflater) def.end();
out.close();
closed = true;
}
}
