public static Vocabulary load(Path vocabFile, FileSystem fs) throws IOException {
BufferedReader in = new BufferedReader(new InputStreamReader(fs.open(vocabFile)));
int size = 0;
String line;
while ((line = in.readLine()) != null) {
String[] columns = StringUtils.tokenize(line, "\t");
int n = Integer.parseInt(columns[1]);
if (n > 0) {
size++;
}
}
in.close();
in = new BufferedReader(new InputStreamReader(fs.open(vocabFile)));
Vocabulary v = new Vocabulary(size);
while ((line = in.readLine()) != null) {
String[] columns = StringUtils.tokenize(line, "\t");
String tok = columns[0];
int n = Integer.parseInt(columns[1]);
if (n > 0) {
v.vocab[n - 1] = tok;
}
}
in.close();
return v;
}
public static void main(String[] args) throws IOException {
String uri = args[0];
Configuration configuration = new Configuration();
System.out.println("Trying to get the file system object");
URI uriObj = URI.create(uri);
System.out.println("Got URI object " + uri);
FileSystem fs = FileSystem.get(uriObj, configuration);
FSDataInputStream fsDataInputStream = null;
Path hdfsPath = new Path(uri);
fsDataInputStream = fs.open(hdfsPath);
// This specifies the reading starts from the 0th Byte.
fsDataInputStream.seek(0);
IOUtils.copyBytes(fsDataInputStream, System.out, 4096, false);
System.out.println("*******************************************");
BufferedReader br = new BufferedReader(new InputStreamReader(fs.open(hdfsPath)));
try {
String line;
line = br.readLine();
while (line != null) {
System.out.println("################ Line is###### " + line);
// be sure to read the next line otherwise you'll get an infinite loop
line = br.readLine();
}
} finally {
// you should close out the BufferedReader
br.close();
}
}
@Override
public void setup(Context context) throws IOException, InterruptedException {
LOGGER.info("TopKRollupPhaseOneJob.TopKRollupPhaseOneReducer.setup()");
Configuration configuration = context.getConfiguration();
FileSystem fileSystem = FileSystem.get(configuration);
Path configPath = new Path(configuration.get(TOPK_ROLLUP_PHASE1_CONFIG_PATH.toString()));
try {
starTreeConfig = StarTreeConfig.decode(fileSystem.open(configPath));
config = TopKRollupPhaseOneConfig.fromStarTreeConfig(starTreeConfig);
dimensionNames = config.getDimensionNames();
metricTypes = config.getMetricTypes();
metricSchema = new MetricSchema(config.getMetricNames(), metricTypes);
metricThresholds = config.getMetricThresholds();
keyWritable = new BytesWritable();
valWritable = new BytesWritable();
MetricSums metricSumsObj =
OBJECT_MAPPER.readValue(
fileSystem.open(
new Path(configuration.get(TOPK_ROLLUP_PHASE1_METRIC_SUMS_PATH.toString()))),
MetricSums.class);
metricSums = metricSumsObj.getMetricSum();
} catch (Exception e) {
throw new IOException(e);
}
}
private static void addFolder(FileSystem fs, Path p, JsonArray succeeded, JsonArray failed) {
try {
if (fs == null) return;
for (FileStatus file : fs.listStatus(p)) {
Path pfs = file.getPath();
if (file.isDir()) {
addFolder(fs, pfs, succeeded, failed);
} else {
Key k = Key.make(pfs.toString());
long size = file.getLen();
Value val = null;
if (pfs.getName().endsWith(Extensions.JSON)) {
JsonParser parser = new JsonParser();
JsonObject json = parser.parse(new InputStreamReader(fs.open(pfs))).getAsJsonObject();
JsonElement v = json.get(Constants.VERSION);
if (v == null) throw new RuntimeException("Missing version");
JsonElement type = json.get(Constants.TYPE);
if (type == null) throw new RuntimeException("Missing type");
Class c = Class.forName(type.getAsString());
OldModel model = (OldModel) c.newInstance();
model.fromJson(json);
} else if (pfs.getName().endsWith(Extensions.HEX)) { // Hex file?
FSDataInputStream s = fs.open(pfs);
int sz = (int) Math.min(1L << 20, size); // Read up to the 1st meg
byte[] mem = MemoryManager.malloc1(sz);
s.readFully(mem);
// Convert to a ValueArray (hope it fits in 1Meg!)
ValueArray ary = new ValueArray(k, 0).read(new AutoBuffer(mem));
val = new Value(k, ary, Value.HDFS);
} else if (size >= 2 * ValueArray.CHUNK_SZ) {
val =
new Value(
k,
new ValueArray(k, size),
Value.HDFS); // ValueArray byte wrapper over a large file
} else {
val = new Value(k, (int) size, Value.HDFS); // Plain Value
val.setdsk();
}
DKV.put(k, val);
Log.info("PersistHdfs: DKV.put(" + k + ")");
JsonObject o = new JsonObject();
o.addProperty(Constants.KEY, k.toString());
o.addProperty(Constants.FILE, pfs.toString());
o.addProperty(Constants.VALUE_SIZE, file.getLen());
succeeded.add(o);
}
}
} catch (Exception e) {
Log.err(e);
JsonObject o = new JsonObject();
o.addProperty(Constants.FILE, p.toString());
o.addProperty(Constants.ERROR, e.getMessage());
failed.add(o);
}
}
/** This tests {@link StringWriter} with non-rolling output. */
@Test
public void testNonRollingStringWriter() throws Exception {
final int NUM_ELEMENTS = 20;
final int PARALLELISM = 2;
final String outPath = hdfsURI + "/string-non-rolling-out";
StreamExecutionEnvironment env = StreamExecutionEnvironment.getExecutionEnvironment();
env.setParallelism(PARALLELISM);
DataStream<Tuple2<Integer, String>> source =
env.addSource(new TestSourceFunction(NUM_ELEMENTS)).broadcast().filter(new OddEvenFilter());
RollingSink<String> sink =
new RollingSink<String>(outPath)
.setBucketer(new NonRollingBucketer())
.setPartPrefix("part")
.setPendingPrefix("")
.setPendingSuffix("");
source
.map(
new MapFunction<Tuple2<Integer, String>, String>() {
private static final long serialVersionUID = 1L;
@Override
public String map(Tuple2<Integer, String> value) throws Exception {
return value.f1;
}
})
.addSink(sink);
env.execute("RollingSink String Write Test");
FSDataInputStream inStream = dfs.open(new Path(outPath + "/part-0-0"));
BufferedReader br = new BufferedReader(new InputStreamReader(inStream));
for (int i = 0; i < NUM_ELEMENTS; i += 2) {
String line = br.readLine();
Assert.assertEquals("message #" + i, line);
}
inStream.close();
inStream = dfs.open(new Path(outPath + "/part-1-0"));
br = new BufferedReader(new InputStreamReader(inStream));
for (int i = 1; i < NUM_ELEMENTS; i += 2) {
String line = br.readLine();
Assert.assertEquals("message #" + i, line);
}
inStream.close();
}
/**
* Generates the Dataset by parsing the entire data
*
* @param descriptor attributes description
* @param regression if true, the label is numerical
* @param fs file system
* @param path data path
*/
public static Dataset generateDataset(
CharSequence descriptor, boolean regression, FileSystem fs, Path path)
throws DescriptorException, IOException {
Attribute[] attrs = DescriptorUtils.parseDescriptor(descriptor);
FSDataInputStream input = fs.open(path);
Scanner scanner = new Scanner(input, "UTF-8");
// used to convert CATEGORICAL attribute to Integer
@SuppressWarnings("unchecked")
Set<String>[] valsets = new Set[attrs.length];
int size = 0;
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
if (!line.isEmpty()) {
if (parseString(attrs, valsets, line, regression)) {
size++;
}
}
}
scanner.close();
@SuppressWarnings("unchecked")
List<String>[] values = new List[attrs.length];
for (int i = 0; i < valsets.length; i++) {
if (valsets[i] != null) {
values[i] = Lists.newArrayList(valsets[i]);
}
}
return new Dataset(attrs, values, size, regression);
}
/**
* Runs a range query on the local machine by iterating over the whole file.
*
* @param fs - FileSystem that contains input file
* @param file - path to the input file
* @param queryRange - The range to look in
* @param shape - An instance of the shape stored in file
* @param output - Output is sent to this collector. If <code>null</code>, output is not collected
* and only the number of results is returned.
* @return number of results found
* @throws IOException
*/
public static <S extends Shape> long rangeQueryLocal(
FileSystem fs, Path file, Shape queryRange, S shape, ResultCollector<S> output)
throws IOException {
long file_size = fs.getFileStatus(file).getLen();
ShapeRecordReader<S> shapeReader = new ShapeRecordReader<S>(fs.open(file), 0, file_size);
long resultCount = 0;
Prism cell = shapeReader.createKey();
while (shapeReader.next(cell, shape)) {
if (shape.isIntersected(queryRange)) {
boolean report_result;
if (cell.isValid()) {
// Check for duplicate avoidance
Prism intersection_mbr = queryRange.getMBR().getIntersection(shape.getMBR());
report_result =
cell.contains(intersection_mbr.t1, intersection_mbr.x1, intersection_mbr.y1);
} else {
report_result = true;
}
if (report_result) {
resultCount++;
if (output != null) {
output.collect(shape);
}
}
}
}
shapeReader.close();
return resultCount;
}
@Test(timeout = 120000)
public void testSeekAfterSetDropBehind() throws Exception {
// start a cluster
LOG.info("testSeekAfterSetDropBehind");
Configuration conf = new HdfsConfiguration();
MiniDFSCluster cluster = null;
String TEST_PATH = "/test";
int TEST_PATH_LEN = MAX_TEST_FILE_LEN;
try {
cluster = new MiniDFSCluster.Builder(conf).numDataNodes(1).build();
cluster.waitActive();
FileSystem fs = cluster.getFileSystem();
createHdfsFile(fs, new Path(TEST_PATH), TEST_PATH_LEN, false);
// verify that we can seek after setDropBehind
FSDataInputStream fis = fs.open(new Path(TEST_PATH));
try {
Assert.assertTrue(fis.read() != -1); // create BlockReader
fis.setDropBehind(false); // clear BlockReader
fis.seek(2); // seek
} finally {
fis.close();
}
} finally {
if (cluster != null) {
cluster.shutdown();
}
}
}
// load centroids from HDFS
static void loadCentroids(
ArrTable<DoubleArray> cenTable, int vectorSize, String cFileName, Configuration configuration)
throws IOException {
Path cPath = new Path(cFileName);
FileSystem fs = FileSystem.get(configuration);
FSDataInputStream in = fs.open(cPath);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String line = "";
String[] vector = null;
int partitionId = 0;
while ((line = br.readLine()) != null) {
vector = line.split("\\s+");
if (vector.length != vectorSize) {
System.out.println("Errors while loading centroids .");
System.exit(-1);
} else {
double[] aCen = new double[vectorSize + 1];
for (int i = 0; i < vectorSize; i++) {
aCen[i] = Double.parseDouble(vector[i]);
}
aCen[vectorSize] = 0;
ArrPartition<DoubleArray> ap =
new ArrPartition<DoubleArray>(partitionId, new DoubleArray(aCen, 0, vectorSize + 1));
cenTable.addPartition(ap);
partitionId++;
}
}
}
private double[] getSparkModelInfoFromHDFS(Path location, Configuration conf) throws Exception {
FileSystem fileSystem = FileSystem.get(location.toUri(), conf);
FileStatus[] files = fileSystem.listStatus(location);
if (files == null) throw new Exception("Couldn't find Spark Truck ML weights at: " + location);
ArrayList<Double> modelInfo = new ArrayList<Double>();
for (FileStatus file : files) {
if (file.getPath().getName().startsWith("_")) {
continue;
}
InputStream stream = fileSystem.open(file.getPath());
StringWriter writer = new StringWriter();
IOUtils.copy(stream, writer, "UTF-8");
String raw = writer.toString();
for (String str : raw.split("\n")) {
modelInfo.add(Double.valueOf(str));
}
}
return Doubles.toArray(modelInfo);
}
public static void readHiveResult(String path, OutputStreamWriter outStream, Configuration conf)
throws IOException {
FileSystem fs = FileSystem.get(conf);
Path dir = new Path(path);
if (!fs.exists(dir)) {
throw new IOException("can not found path:" + path);
}
FileStatus[] filelist = fs.listStatus(dir);
Long bytesRead = 0l;
long maxsize = 1024l * 1024 * 1024 * 10;
for (FileStatus f : filelist) {
if (!f.isDir() && !f.getPath().getName().startsWith("_")) {
FSDataInputStream in = fs.open(f.getPath());
BufferedReader bf = new BufferedReader(new InputStreamReader(in));
String line;
while ((line = bf.readLine()) != null) {
bytesRead += line.getBytes().length;
outStream.write(line.replaceAll("\001", ",").replaceAll("\t", ","));
outStream.write("\r\n");
if (bytesRead >= maxsize) {
bf.close();
in.close();
return;
}
}
bf.close();
in.close();
}
}
return;
}
/** {@inheritDoc} */
@Override
public int open(String path) throws IOException {
long startTime = System.currentTimeMillis();
InputStream in = fileSystem.open(new Path(path));
in.close();
return (int) (System.currentTimeMillis() - startTime);
}
/**
* Sets {@link #mHdfsInputStream} to a stream from the under storage system with the stream
* starting at position. The {@link #mCurrentPosition} is not modified to be position.
*
* @throws IOException if opening the file fails
*/
private void getHdfsInputStream(long position) throws IOException {
if (mHdfsInputStream == null) {
org.apache.hadoop.fs.FileSystem fs = mHdfsPath.getFileSystem(mHadoopConf);
mHdfsInputStream = fs.open(mHdfsPath, mHadoopBufferSize);
}
mHdfsInputStream.seek(position);
}
@Override
public ModelInput<StringBuilder> createInput(
Class<? extends StringBuilder> dataType,
FileSystem fileSystem,
Path path,
long offset,
long fragmentSize,
Counter counter)
throws IOException, InterruptedException {
FileSystem fs = FileSystem.get(path.toUri(), getConf());
FSDataInputStream in = fs.open(path);
boolean succeed = false;
try {
in.seek(offset);
ModelInput<StringBuilder> result =
format.createInput(
dataType, path.toString(), new CountInputStream(in, counter), offset, fragmentSize);
succeed = true;
return result;
} finally {
if (succeed == false) {
in.close();
}
}
}
/**
* Retrieves the centroids between K-means iterations.
*
* @return the centroids
*/
public static long[] getCentroids() throws IOException {
Configuration conf = setupConf();
FileSystem fs = FileSystem.get(conf);
Path path = new Path(BASE_OUTPUT + CENTROID_FILE);
long[] centroids = new long[4];
FSDataInputStream in = fs.open(path);
centroids[0] = Long.parseLong(in.readUTF());
in.readChar();
in.readUTF();
in.readChar();
centroids[1] = Long.parseLong(in.readUTF());
in.readChar();
in.readUTF();
in.readChar();
in.readUTF();
in.readChar();
centroids[2] = Long.parseLong(in.readUTF());
in.readChar();
in.readUTF();
in.readChar();
in.readUTF();
in.readChar();
centroids[3] = Long.parseLong(in.readUTF());
in.close();
return centroids;
}
public static void createCentersSequenceFile(
Configuration conf, FileSystem fs, String centroidsPath, String sequenceFilePath)
throws Exception {
Path seqFile = new Path(sequenceFilePath);
if (fs.exists(seqFile)) {
fs.delete(seqFile, true);
}
FSDataInputStream inputStream = fs.open(new Path(centroidsPath));
SequenceFile.Writer writer =
SequenceFile.createWriter(fs, conf, seqFile, Centroid.class, IntWritable.class);
IntWritable value = new IntWritable(0);
while (inputStream.available() > 0) {
String line = inputStream.readLine();
StringTokenizer tokenizer = new StringTokenizer(line, " ");
int dim = tokenizer.countTokens() - 1;
int clusterId = Integer.valueOf(tokenizer.nextToken());
double[] coords = new double[dim];
for (int i = 0; i < dim; i++) {
coords[i] = Double.valueOf(tokenizer.nextToken());
}
Centroid cluster = new Centroid(clusterId, new Point(coords));
writer.append(cluster, value);
}
IOUtils.closeStream(writer);
inputStream.close();
}
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;
}
}
public void initialize(InputSplit genericSplit, TaskAttemptContext context) throws IOException {
Configuration conf = ContextUtil.getConfiguration(context);
this.maxLineLength = conf.getInt("mapred.linerecordreader.maxlength", Integer.MAX_VALUE);
FileSplit split = (FileSplit) genericSplit;
start = (split.getStart()) << 16;
end = (start + split.getLength()) << 16;
final Path file = split.getPath();
FileSystem fs = file.getFileSystem(conf);
bin =
new BlockCompressedInputStream(
new WrapSeekable<FSDataInputStream>(
fs.open(file), fs.getFileStatus(file).getLen(), file));
in = new LineReader(bin, conf);
if (start != 0) {
bin.seek(start);
// Skip first line
in.readLine(new Text());
start = bin.getFilePointer();
}
this.pos = start;
}
// load data form HDFS
static ArrayList<DoubleArray> loadData(List<String> fileNames, int vectorSize, Configuration conf)
throws IOException {
ArrayList<DoubleArray> data = new ArrayList<DoubleArray>();
for (String filename : fileNames) {
FileSystem fs = FileSystem.get(conf);
Path dPath = new Path(filename);
FSDataInputStream in = fs.open(dPath);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
String line = "";
String[] vector = null;
while ((line = br.readLine()) != null) {
vector = line.split("\\s+");
if (vector.length != vectorSize) {
System.out.println("Errors while loading data.");
System.exit(-1);
} else {
double[] aDataPoint = new double[vectorSize];
for (int i = 0; i < vectorSize; i++) {
aDataPoint[i] = Double.parseDouble(vector[i]);
}
DoubleArray da = new DoubleArray(aDataPoint, 0, vectorSize);
data.add(da);
}
}
}
return data;
}
@Override
public List<String> getContent(String path, int lineCount) throws IOException {
FileStatus[] files = fileSystem.globStatus(new Path(path));
ArrayList<String> lines = new ArrayList<String>();
if (files != null) {
for (FileStatus file : files) {
if (lines.size() >= lineCount) {
break;
}
if (!file.isDirectory()) {
DataInputStream in = fileSystem.open(file.getPath());
BufferedReader dataReader = new BufferedReader(new InputStreamReader(in));
String line = dataReader.readLine();
while (line != null && lines.size() < lineCount) {
lines.add(line);
line = dataReader.readLine();
}
dataReader.close();
in.close();
}
}
}
return lines;
}
/**
* Check duplicated tweet IDs in <b>tweetIdDir</b>, and output the duplicates to stdout.
*
* @param tweetIdDir
* @throws Exception
*/
public static void checkTidDuplicates(String tweetIdDir) throws Exception {
// First change path strings to URI strings starting with 'file:' or 'hdfs:'
tweetIdDir = MultiFileFolderWriter.getUriStrForPath(tweetIdDir);
Set<String> tidSet = new HashSet<String>();
Configuration conf = HBaseConfiguration.create();
FileSystem fs = FileSystem.get(new URI(tweetIdDir), conf);
int dupCount = 0;
for (FileStatus srcFileStatus : fs.listStatus(new Path(tweetIdDir))) {
String srcFileName = srcFileStatus.getPath().getName();
if (srcFileName.endsWith(".txt") && srcFileName.contains("tweetIds")) {
BufferedReader brTid =
new BufferedReader(new InputStreamReader(fs.open(srcFileStatus.getPath())));
String tid = brTid.readLine();
while (tid != null) {
if (tidSet.contains(tid)) {
System.out.println("Duplicated tweet ID: " + tid);
dupCount++;
} else {
tidSet.add(tid);
}
tid = brTid.readLine();
}
brTid.close();
}
}
System.out.println(
"Number of unique tweet IDs: " + tidSet.size() + ", number of duplicates: " + dupCount);
}
private void loadDocumentIndex(String documentIndexPath) throws IOException {
if (documentIndex == null) {
documentIndex = new HashMap<String, Integer>();
Path p = new Path(documentIndexPath);
FileSystem fs = FileSystem.get(p.toUri(), new Configuration());
int index = 0;
for (FileStatus status : fs.listStatus(p)) {
Path currPath = status.getPath();
if (!status.isDir() && !currPath.getName().startsWith("_")) {
BufferedReader reader = null;
try {
reader = new BufferedReader(new InputStreamReader(fs.open(currPath)));
String line = null;
while ((line = reader.readLine()) != null) {
documentIndex.put(line.trim(), index++);
}
} finally {
if (reader != null) {
reader.close();
}
}
}
}
log.info("Loaded document index with size: " + documentIndex.size());
}
}
@Override
public boolean nextKeyValue() throws IOException, InterruptedException {
FileSystem fileSystem = FileSystem.get(configuration);
if (fileSystem.isDirectory(split.getPath())) {
return false;
}
if (fileProcessed) {
return false;
}
int fileLength = (int) split.getLength();
byte[] result = new byte[fileLength];
FSDataInputStream inputStream = null;
try {
inputStream = fileSystem.open(split.getPath());
IOUtils.readFully(inputStream, result, 0, fileLength);
currentValue.set(result, 0, fileLength);
} finally {
IOUtils.closeStream(inputStream);
}
fileProcessed = true;
return true;
}
/**
* Loads the data from a file
*
* @param fs file system
* @param fpath data file path
* @throws IOException if any problem is encountered
*/
public static Data loadData(Dataset dataset, FileSystem fs, Path fpath) throws IOException {
FSDataInputStream input = fs.open(fpath);
Scanner scanner = new Scanner(input);
List<Instance> instances = Lists.newArrayList();
DataConverter converter = new DataConverter(dataset);
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
if (line.isEmpty()) {
log.warn("{}: empty string", instances.size());
continue;
}
Instance instance = converter.convert(instances.size(), line);
if (instance == null) {
// missing values found
log.warn("{}: missing values", instances.size());
continue;
}
instances.add(instance);
}
scanner.close();
return new Data(dataset, instances);
}
@Override
public void initialize(InputSplit genericSplit, TaskAttemptContext taskAttemptContext)
throws IOException {
context = taskAttemptContext;
FileSplit fileSplit = (FileSplit) genericSplit;
lzoFile = fileSplit.getPath();
// The LzoSplitInputFormat is not splittable, so the split length is the whole file.
totalFileSize = fileSplit.getLength();
// Jump through some hoops to create the lzo codec.
Configuration conf = CompatibilityUtil.getConfiguration(context);
CompressionCodecFactory factory = new CompressionCodecFactory(conf);
CompressionCodec codec = factory.getCodec(lzoFile);
((Configurable) codec).setConf(conf);
LzopDecompressor lzopDecompressor = (LzopDecompressor) codec.createDecompressor();
FileSystem fs = lzoFile.getFileSystem(conf);
rawInputStream = fs.open(lzoFile);
// Creating the LzopInputStream here just reads the lzo header for us, nothing more.
// We do the rest of our input off of the raw stream is.
codec.createInputStream(rawInputStream, lzopDecompressor);
// This must be called AFTER createInputStream is called, because createInputStream
// is what reads the header, which has the checksum information. Otherwise getChecksumsCount
// erroneously returns zero, and all block offsets will be wrong.
numCompressedChecksums = lzopDecompressor.getCompressedChecksumsCount();
numDecompressedChecksums = lzopDecompressor.getDecompressedChecksumsCount();
}
static long readHdfsFile(FileSystem fs, Path p, long length, Boolean dropBehind)
throws Exception {
FSDataInputStream fis = null;
long totalRead = 0;
try {
fis = fs.open(p);
if (dropBehind != null) {
fis.setDropBehind(dropBehind);
}
byte buf[] = new byte[8196];
while (length > 0) {
int amt = (length > buf.length) ? buf.length : (int) length;
int ret = fis.read(buf, 0, amt);
if (ret == -1) {
return totalRead;
}
totalRead += ret;
length -= ret;
}
} catch (IOException e) {
LOG.error("ioexception", e);
} finally {
if (fis != null) {
fis.close();
}
}
throw new RuntimeException("unreachable");
}
public QseqRecordReader(Configuration conf, FileSplit split) throws IOException {
setConf(conf);
file = split.getPath();
start = split.getStart();
end = start + split.getLength();
FileSystem fs = file.getFileSystem(conf);
FSDataInputStream fileIn = fs.open(file);
CompressionCodecFactory codecFactory = new CompressionCodecFactory(conf);
CompressionCodec codec = codecFactory.getCodec(file);
if (codec == null) // no codec. Uncompressed file.
{
positionAtFirstRecord(fileIn);
inputStream = fileIn;
} else { // compressed file
if (start != 0)
throw new RuntimeException(
"Start position for compressed file is not 0! (found " + start + ")");
inputStream = codec.createInputStream(fileIn);
end = Long.MAX_VALUE; // read until the end of the file
}
lineReader = new LineReader(inputStream);
}
public PrefixEncodedGlobalStatsWithIndex(Path prefixSetPath, FileSystem fs) throws IOException {
fileSys = fs;
FSDataInputStream termsInput = fileSys.open(prefixSetPath);
prefixSet.readFields(termsInput);
termsInput.close();
}
/**
* Generates the Dataset by parsing the entire data
*
* @param descriptor attributes description
* @param fs file system
* @param path data path
*/
public static Dataset generateDataset(String descriptor, FileSystem fs, Path path)
throws DescriptorException, IOException {
Attribute[] attrs = DescriptorUtils.parseDescriptor(descriptor);
FSDataInputStream input = fs.open(path);
Scanner scanner = new Scanner(input);
// used to convert CATEGORICAL attribute to Integer
List<String>[] values = new List[attrs.length];
int id = 0;
while (scanner.hasNextLine()) {
String line = scanner.nextLine();
if (line.isEmpty()) {
continue;
}
if (parseString(id, attrs, values, line) != null) {
id++;
}
}
scanner.close();
return new Dataset(attrs, values, id);
}
public static void downloadHdfs(String srcfilePath, String destFilePath) {
try {
Configuration conf = new Configuration();
FileSystem fs = FileSystem.get(URI.create(srcfilePath), conf);
FSDataInputStream hdfsInStream = fs.open(new Path(srcfilePath));
File dstFile = new File(destFilePath);
if (!dstFile.getParentFile().exists()) {
dstFile.getParentFile().mkdirs();
}
OutputStream out = new FileOutputStream(destFilePath);
byte[] ioBuffer = new byte[1024];
int readLen = hdfsInStream.read(ioBuffer);
while (-1 != readLen) {
out.write(ioBuffer, 0, readLen);
readLen = hdfsInStream.read(ioBuffer);
}
out.close();
hdfsInStream.close();
fs.close();
} catch (FileNotFoundException e) {
LOG.error("[downloadHdfs]", e);
} catch (IOException e) {
LOG.error("[downloadHdfs]", e);
}
}