@Override
protected int readChunk(long pos, byte[] buf, int offset, int len, byte[] checksum)
throws IOException {
boolean eof = false;
if (needChecksum()) {
try {
long checksumPos = getChecksumFilePos(pos);
if (checksumPos != sums.getPos()) {
sums.seek(checksumPos);
}
sums.readFully(checksum);
} catch (EOFException e) {
eof = true;
}
len = bytesPerSum;
}
if (pos != datas.getPos()) {
datas.seek(pos);
}
int nread = readFully(datas, buf, offset, len);
if (eof && nread > 0) {
throw new ChecksumException("Checksum error: " + file + " at " + pos, pos);
}
return nread;
}
@Override
protected int readChunk(long pos, byte[] buf, int offset, int len, byte[] checksum)
throws IOException {
boolean eof = false;
if (needChecksum()) {
assert checksum != null; // we have a checksum buffer
assert checksum.length % CHECKSUM_SIZE == 0; // it is sane length
assert len >= bytesPerSum; // we must read at least one chunk
final int checksumsToRead =
Math.min(
len / bytesPerSum, // number of checksums based on len to read
checksum.length / CHECKSUM_SIZE); // size of checksum buffer
long checksumPos = getChecksumFilePos(pos);
if (checksumPos != sums.getPos()) {
sums.seek(checksumPos);
}
int sumLenRead = sums.read(checksum, 0, CHECKSUM_SIZE * checksumsToRead);
if (sumLenRead >= 0 && sumLenRead % CHECKSUM_SIZE != 0) {
throw new ChecksumException(
"Checksum file not a length multiple of checksum size "
+ "in "
+ file
+ " at "
+ pos
+ " checksumpos: "
+ checksumPos
+ " sumLenread: "
+ sumLenRead,
pos);
}
if (sumLenRead <= 0) { // we're at the end of the file
eof = true;
} else {
// Adjust amount of data to read based on how many checksum chunks we read
len = Math.min(len, bytesPerSum * (sumLenRead / CHECKSUM_SIZE));
}
}
if (pos != datas.getPos()) {
datas.seek(pos);
}
int nread = readFully(datas, buf, offset, len);
if (eof && nread > 0) {
throw new ChecksumException("Checksum error: " + file + " at " + pos, pos);
}
return nread;
}
private InputStream OpenMultiplePartsWithOffset(FileSystem fs, Path pt, long offset)
throws IOException {
RemoteIterator<LocatedFileStatus> rit = fs.listFiles(pt, false);
Vector<FSDataInputStream> fileHandleList = new Vector<FSDataInputStream>();
while (rit.hasNext()) {
Path path = rit.next().getPath();
String filename =
path.toString().substring(path.getParent().toString().length(), path.toString().length());
if (filename.startsWith("/part-")) {
long filesize = fs.getFileStatus(path).getLen();
if (offset < filesize) {
FSDataInputStream handle = fs.open(path);
if (offset > 0) {
handle.seek(offset);
}
fileHandleList.add(handle);
}
offset -= filesize;
}
}
if (fileHandleList.size() == 1) return fileHandleList.get(0);
else if (fileHandleList.size() > 1) {
Enumeration<FSDataInputStream> enu = fileHandleList.elements();
return new SequenceInputStream(enu);
} else {
System.err.println("Error, no source file loaded. run genSeedDataset.sh fisrt!");
return null;
}
}
/**
* Seek to the given position in the stream. The next read() will be from that position.
*
* <p>This method does not allow seek past the end of the file. This produces IOException.
*
* @param pos the postion to seek to.
* @exception IOException if an I/O error occurs or seeks after EOF ChecksumException if the
* chunk to seek to is corrupted
*/
@Override
public synchronized void seek(long pos) throws IOException {
if (pos > getFileLength()) {
throw new IOException("Cannot seek after EOF");
}
super.seek(pos);
}
public void initialize(InputSplit genericSplit, TaskAttemptContext context) throws IOException {
FileSplit split = (FileSplit) genericSplit;
Configuration job = context.getConfiguration();
m_Sb.setLength(0);
m_Start = split.getStart();
m_End = m_Start + split.getLength();
final Path file = split.getPath();
compressionCodecs = new CompressionCodecFactory(job);
final CompressionCodec codec = compressionCodecs.getCodec(file);
// open the file and seek to the m_Start of the split
FileSystem fs = file.getFileSystem(job);
// getFileStatus fileStatus = fs.getFileStatus(split.getPath());
//noinspection deprecation
@SuppressWarnings(value = "deprecated")
long length = fs.getLength(file);
FSDataInputStream fileIn = fs.open(split.getPath());
if (m_Start > 0) fileIn.seek(m_Start);
if (codec != null) {
CompressionInputStream inputStream = codec.createInputStream(fileIn);
m_Input = new BufferedReader(new InputStreamReader(inputStream));
m_End = length;
} else {
m_Input = new BufferedReader(new InputStreamReader(fileIn));
}
m_Current = m_Start;
m_Key = split.getPath().getName();
}
public BufferedReader loadDataFromFile(String filepath, long offset) {
try {
Path pt = new Path(filepath);
FileSystem fs = FileSystem.get(fsConf);
InputStreamReader isr;
if (fs.isDirectory(pt)) { // multiple parts
isr = new InputStreamReader(OpenMultiplePartsWithOffset(fs, pt, offset));
} else { // single file
FSDataInputStream fileHandler = fs.open(pt);
if (offset > 0) fileHandler.seek(offset);
isr = new InputStreamReader(fileHandler);
}
BufferedReader reader = new BufferedReader(isr);
if (offset > 0) reader.readLine(); // skip first line in case of seek
return reader;
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
assert false : "Should not reach here!";
return null;
}
@Override
protected InputStream open(long offset) throws IOException {
FSDataInputStream is = _fs.open(_path);
is.seek(offset);
return is;
}
