/// <exception cref="System.Exception"/>
public virtual void TestNewLines()
{
LineReader @in = null;
try
{
@in = MakeStream("a\nbb\n\nccc\rdddd\r\neeeee");
Text @out = new Text();
@in.ReadLine(@out);
NUnit.Framework.Assert.AreEqual("line1 length", 1, @out.GetLength());
@in.ReadLine(@out);
NUnit.Framework.Assert.AreEqual("line2 length", 2, @out.GetLength());
@in.ReadLine(@out);
NUnit.Framework.Assert.AreEqual("line3 length", 0, @out.GetLength());
@in.ReadLine(@out);
NUnit.Framework.Assert.AreEqual("line4 length", 3, @out.GetLength());
@in.ReadLine(@out);
NUnit.Framework.Assert.AreEqual("line5 length", 4, @out.GetLength());
@in.ReadLine(@out);
NUnit.Framework.Assert.AreEqual("line5 length", 5, @out.GetLength());
NUnit.Framework.Assert.AreEqual("end of file", 0, @in.ReadLine(@out));
}
finally
{
if (@in != null)
{
@in.Close();
}
}
}
//---------------------------------------------------------------------
/// <summary>
/// Loads an instance of T from a file. The file may contain a
/// serialized form of an editable instance or it may be a text file
/// that needs parsing.
/// </summary>
public static T Load <T>(string path,
ITextParser <T> parser)
{
if (Path.GetExtension(path) == FileExtension)
{
// Deserialize an editable instance from the file
// Binary serialization:
IFormatter formatter = new BinaryFormatter();
Stream stream = new FileStream(path, FileMode.Open,
FileAccess.Read, FileShare.Read);
using (stream) {
IEditable <T> editableObject = (IEditable <T>)formatter.Deserialize(stream);
if (!editableObject.IsComplete)
{
throw new System.ApplicationException("Not complete T");
}
return(editableObject.GetComplete());
}
}
else
{
LineReader reader = OpenTextFile(path);
try {
return(parser.Parse(reader));
}
finally {
reader.Close();
}
}
}
public bool HasNextIndexable()
{
data_sb.Length = 0;
session_num_lines = 0;
speakers.Clear();
if (reader == null)
{
// Log files are in system encoding
reader = new ReencodingLineReader(log_file, Encoding.Default);
reader.Position = session_begin_offset;
log_line_as_sb = reader.ReadLineAsStringBuilder();
//Log.Debug ("Read line from {0}:[{1}]", log_file, log_line_as_sb);
}
if (log_line_as_sb == null)
{
reader.Close();
return(false);
}
else
{
// Update session_begin_offset
session_begin_offset = prev_line_offset;
}
return(true);
}
private void HandleFailedSend(FileLock markLock, string bufferName, ref LineReader streamReader,
FileLock readerLock, List <string> memoryBuffer, int failLimit, Action <List <string> > alternativeWrite)
{
try
{
markLock.Lock();
var buffers = ReadMark(markLock).Buffers;
var buffer = GetBufferIndex(bufferName, buffers, out var index);
if (buffer.FailedSendCount >= failLimit)
{
alternativeWrite(memoryBuffer);
HandleSuccessSend(markLock, bufferName, ref streamReader, readerLock, memoryBuffer);
}
else
{
var modifiedBuffer = new BufferInfo(buffer.Name, buffer.Written, buffer.Read, buffer.WriteActive,
buffer.LastFlushTime, buffer.FailedSendCount + 1, DateTime.Now);
buffers[index] = modifiedBuffer;
WriteMark(markLock, buffers);
streamReader.Close();
streamReader = null;
}
}
finally
{
markLock.Unlock();
}
}
//---------------------------------------------------------------------
private void TryParse(string filename,
int errorLineNum)
{
try {
reader = OpenFile(filename);
// This method is only called on bad files, so we expect the
// statement below to throw an exception. Since we knowingly
// ignore the variable "landUses", disable the CS0219 warning
// "The variable '...' is assigned but its value is never used'.
#pragma warning disable 0219
IList <LandUse> landUses = parser.Parse(reader);
#pragma warning restore 0219
}
catch (System.Exception e) {
Data.Output.WriteLine(e.Message.Replace(Data.Directory, Data.DirPlaceholder));
LineReaderException lrExc = e as LineReaderException;
if (lrExc != null)
{
Assert.AreEqual(errorLineNum, lrExc.LineNumber);
}
Data.Output.WriteLine();
throw;
}
finally {
reader.Close();
}
}
public void GoodFile()
{
const string filename = "GoodFile.txt";
IParameterDataset dataset;
try {
reader = OpenFile(filename);
dataset = parser.Parse(reader);
}
finally {
reader.Close();
}
try {
// Now that we know the data file is properly formatted, read
// data from it and compare it against parameter dataset.
reader = OpenFile(filename);
inputLine = new InputLine(reader);
Assert.AreEqual(parser.LandisDataValue, ReadInputVar <string>("LandisData"));
CheckPercentageTable("CohortBiomassReductions",
dataset.CohortReductions,
"DeadPoolReductions");
CheckPercentageTable("DeadPoolReductions",
dataset.PoolReductions,
null);
}
finally {
inputLine = null;
reader.Close();
}
}
//---------------------------------------------------------------------
private Scenario ParseFile(string filename)
{
reader = OpenFile(filename);
Scenario scenario = parser.Parse(reader);
reader.Close();
return(scenario);
}
//---------------------------------------------------------------------
private IDataset ParseFile(string filename)
{
reader = OpenFile(filename);
IDataset dataset = parser.Parse(reader);
reader.Close();
return(dataset);
}
//---------------------------------------------------------------------
private IList <LandUse> ParseFile(string filename)
{
reader = OpenFile(filename);
IList <LandUse> landUses = parser.Parse(reader);
reader.Close();
return(landUses);
}
//---------------------------------------------------------------------
private IParameters ParseFile(string filename)
{
reader = OpenFile(filename);
IParameters parameters = parser.Parse(reader);
reader.Close();
return(parameters);
}
//---------------------------------------------------------------------
private IParameters ParseFile(string filename)
{
try {
reader = OpenFile(filename);
return(parser.Parse(reader));
}
finally {
reader.Close();
}
}
//---------------------------------------------------------------------
private ExtensionInfo ParseFile(string filename)
{
try {
reader = OpenFile(filename);
return(parser.Parse(reader));
}
finally {
reader.Close();
}
}
public void Init()
{
parser = new ParameterParser();
Ecoregions.DatasetParser ecoregionsParser = new Ecoregions.DatasetParser();
reader = OpenFile("Ecoregions.txt");
try {
ParameterParser.EcoregionsDataset = ecoregionsParser.Parse(reader);
}
finally {
reader.Close();
}
}
public void Init()
{
Species.DatasetParser speciesParser = new Species.DatasetParser();
reader = OpenFile("Species.txt");
try {
speciesDataset = speciesParser.Parse(reader);
}
finally {
reader.Close();
}
parser = new ParametersParser(speciesDataset);
}
/// <summary>
/// Loads an instance of T from a file. The file may contain a
/// serialized form of an editable instance or it may be a text file
/// that needs parsing.
/// </summary>
private T Load <T>(string path,
ITextParser <T> parser)
{
LineReader reader = this.OpenTextFile(path);
try
{
return(parser.Parse(reader));
}
finally
{
reader.Close();
}
}
/// <exception cref="System.IO.IOException"/>
public static IList <FileSplit> GetSplitsForFile(FileStatus status, Configuration
conf, int numLinesPerSplit)
{
IList <FileSplit> splits = new AList <FileSplit>();
Path fileName = status.GetPath();
if (status.IsDirectory())
{
throw new IOException("Not a file: " + fileName);
}
FileSystem fs = fileName.GetFileSystem(conf);
LineReader lr = null;
try
{
FSDataInputStream @in = fs.Open(fileName);
lr = new LineReader(@in, conf);
Text line = new Text();
int numLines = 0;
long begin = 0;
long length = 0;
int num = -1;
while ((num = lr.ReadLine(line)) > 0)
{
numLines++;
length += num;
if (numLines == numLinesPerSplit)
{
splits.AddItem(CreateFileSplit(fileName, begin, length));
begin += length;
length = 0;
numLines = 0;
}
}
if (numLines != 0)
{
splits.AddItem(CreateFileSplit(fileName, begin, length));
}
}
finally
{
if (lr != null)
{
lr.Close();
}
}
return(splits);
}
/// <summary>Parse the command line arguments into lines and display the result.</summary>
/// <param name="args"/>
/// <exception cref="System.Exception"/>
public static void Main(string[] args)
{
foreach (string arg in args)
{
System.Console.Out.WriteLine("Working on " + arg);
LineReader reader = MakeStream(Unquote(arg));
Org.Apache.Hadoop.IO.Text line = new Org.Apache.Hadoop.IO.Text();
int size = reader.ReadLine(line);
while (size > 0)
{
System.Console.Out.WriteLine("Got: " + line.ToString());
size = reader.ReadLine(line);
}
reader.Close();
}
}
public void Init()
{
parser = new ParametersParser();
Species.DatasetParser speciesParser = new Species.DatasetParser();
LineReader speciesReader = OpenFile("SpeciesDataset.txt");
try {
ParametersParser.SpeciesDataset = speciesParser.Parse(speciesReader);
}
finally {
speciesReader.Close();
}
Data.Output.WriteLine("{0} = \"{1}\"", dataDirPlaceholder, Data.Directory);
Data.Output.WriteLine();
}
//---------------------------------------------------------------------
private void TryParse(string filename,
int errorLineNum)
{
try {
reader = OpenFile(filename);
IDataset dataset = parser.Parse(reader);
}
catch (System.Exception e) {
Data.Output.WriteLine(e.Message);
LineReaderException lrExc = e as LineReaderException;
if (lrExc != null)
{
Assert.AreEqual(errorLineNum, lrExc.LineNumber);
}
throw;
}
finally {
reader.Close();
}
}
//---------------------------------------------------------------------
private void TryParse(string filename,
int errorLineNum)
{
try {
reader = OpenFile(filename);
Scenario scenario = parser.Parse(reader);
}
catch (System.Exception e) {
Data.Output.WriteLine();
Data.Output.WriteLine(e.Message.Replace(Data.Directory, Data.DirPlaceholder));
LineReaderException lrExc = e as LineReaderException;
if (lrExc != null)
{
Assert.AreEqual(errorLineNum, lrExc.LineNumber);
}
throw;
}
finally {
reader.Close();
}
}
//---------------------------------------------------------------------
private void TryParse(string filename)
{
int?errorLineNum = Testing.FindErrorMarker(MakeInputPath(filename));
try {
reader = OpenFile(filename);
IParameterDataset dataset = parser.Parse(reader);
}
catch (System.Exception e) {
Data.Output.WriteLine();
Data.Output.WriteLine(e.Message.Replace(Data.Directory, Data.DirPlaceholder));
LineReaderException lrExc = e as LineReaderException;
if (lrExc != null && errorLineNum.HasValue)
{
Assert.AreEqual(errorLineNum.Value, lrExc.LineNumber);
}
throw;
}
finally {
reader.Close();
}
}
public void Init()
{
Ecoregions.DatasetParser ecoregionsParser = new Ecoregions.DatasetParser();
reader = OpenFile("Ecoregions.txt");
try {
ecoregionDataset = ecoregionsParser.Parse(reader);
}
finally {
reader.Close();
}
Species.DatasetParser speciesParser = new Species.DatasetParser();
reader = OpenFile("Species.txt");
try {
speciesDataset = speciesParser.Parse(reader);
}
finally {
reader.Close();
}
parser = new ParametersParser(ecoregionDataset, speciesDataset);
}
private void HandleSuccessSend(FileLock markLock, string bufferName, ref LineReader streamReader, FileLock readerLock, List <string> memoryBuffer)
{
try
{
var buffer = MarkRead(markLock, bufferName, memoryBuffer.Count);
if (buffer.WriteActive == false && buffer.Read >= buffer.Written)
{
streamReader.Close();
streamReader = null;
DeleteBuffer(readerLock.Path);
}
}
catch (IOException e)
{
_logger.LogError(e, "Mark read failed.");
}
finally
{
memoryBuffer.Clear();
}
}
/// <exception cref="System.Exception"/>
public virtual void TestUTF8()
{
LineReader @in = null;
try
{
@in = MakeStream("abcd\u20acbdcd\u20ac");
Text line = new Text();
@in.ReadLine(line);
NUnit.Framework.Assert.AreEqual("readLine changed utf8 characters", "abcd\u20acbdcd\u20ac"
, line.ToString());
@in = MakeStream("abc\u200axyz");
@in.ReadLine(line);
NUnit.Framework.Assert.AreEqual("split on fake newline", "abc\u200axyz", line.ToString
());
}
finally
{
if (@in != null)
{
@in.Close();
}
}
}
public override void Close()
{
reader.Close();
}
public virtual void TestCompress()
{
JobConf job = new JobConf();
job.Set(JobContext.TaskAttemptId, attempt);
job.Set(FileOutputFormat.Compress, "true");
FileOutputFormat.SetOutputPath(job, workDir.GetParent().GetParent());
FileOutputFormat.SetWorkOutputPath(job, workDir);
FileSystem fs = workDir.GetFileSystem(job);
if (!fs.Mkdirs(workDir))
{
NUnit.Framework.Assert.Fail("Failed to create output directory");
}
string file = "test_compress.txt";
// A reporter that does nothing
Reporter reporter = Reporter.Null;
TextOutputFormat <object, object> theOutputFormat = new TextOutputFormat <object, object
>();
RecordWriter <object, object> theRecordWriter = theOutputFormat.GetRecordWriter(localFs
, job, file, reporter);
Org.Apache.Hadoop.IO.Text key1 = new Org.Apache.Hadoop.IO.Text("key1");
Org.Apache.Hadoop.IO.Text key2 = new Org.Apache.Hadoop.IO.Text("key2");
Org.Apache.Hadoop.IO.Text val1 = new Org.Apache.Hadoop.IO.Text("val1");
Org.Apache.Hadoop.IO.Text val2 = new Org.Apache.Hadoop.IO.Text("val2");
NullWritable nullWritable = NullWritable.Get();
try
{
theRecordWriter.Write(key1, val1);
theRecordWriter.Write(null, nullWritable);
theRecordWriter.Write(null, val1);
theRecordWriter.Write(nullWritable, val2);
theRecordWriter.Write(key2, nullWritable);
theRecordWriter.Write(key1, null);
theRecordWriter.Write(null, null);
theRecordWriter.Write(key2, val2);
}
finally
{
theRecordWriter.Close(reporter);
}
StringBuilder expectedOutput = new StringBuilder();
expectedOutput.Append(key1).Append("\t").Append(val1).Append("\n");
expectedOutput.Append(val1).Append("\n");
expectedOutput.Append(val2).Append("\n");
expectedOutput.Append(key2).Append("\n");
expectedOutput.Append(key1).Append("\n");
expectedOutput.Append(key2).Append("\t").Append(val2).Append("\n");
DefaultCodec codec = new DefaultCodec();
codec.SetConf(job);
Path expectedFile = new Path(workDir, file + codec.GetDefaultExtension());
FileInputStream istream = new FileInputStream(expectedFile.ToString());
CompressionInputStream cistream = codec.CreateInputStream(istream);
LineReader reader = new LineReader(cistream);
string output = string.Empty;
Org.Apache.Hadoop.IO.Text @out = new Org.Apache.Hadoop.IO.Text();
while (reader.ReadLine(@out) > 0)
{
output += @out;
output += "\n";
}
reader.Close();
NUnit.Framework.Assert.AreEqual(expectedOutput.ToString(), output);
}
//---------------------------------------------------------------------
private void ReadAndCheckParameters(string filename)
{
IParameters parameters;
try {
reader = OpenFile(filename);
parameters = parser.Parse(reader);
}
finally {
reader.Close();
}
try {
// Now that we know the data file is properly formatted, read
// data from it and compare it against parameter object.
reader = OpenFile(filename);
inputLine = new InputLine(reader);
Assert.AreEqual(parser.LandisDataValue, ReadInputVar <string>("LandisData"));
Assert.AreEqual(ReadInputVar <int>("Timestep"), parameters.Timestep);
Assert.AreEqual(ReadInputVar <SeedingAlgorithms>("SeedingAlgorithm"),
parameters.SeedAlgorithm);
inputLine.MatchName("MinRelativeBiomass");
inputLine.GetNext();
List <IEcoregion> ecoregions = ReadEcoregions();
for (byte shadeClass = 1; shadeClass <= 5; shadeClass++)
{
StringReader currentLine = new StringReader(inputLine.ToString());
Assert.AreEqual(shadeClass, ReadInputValue <byte>(currentLine));
foreach (IEcoregion ecoregion in ecoregions)
{
// TODO: Eventually allow equality testing for Percentage
Assert.AreEqual((double)ReadInputValue <Percentage>(currentLine),
(double)parameters.MinRelativeBiomass[shadeClass][ecoregion]);
}
inputLine.GetNext();
}
inputLine.MatchName("BiomassParameters");
inputLine.GetNext();
while (inputLine.VariableName != "EstablishProbabilities")
{
StringReader currentLine = new StringReader(inputLine.ToString());
ISpecies species = ReadSpecies(currentLine);
Assert.AreEqual(ReadInputValue <double>(currentLine),
parameters.LeafLongevity[species]);
Assert.AreEqual(ReadInputValue <double>(currentLine),
parameters.WoodyDecayRate[species]);
Assert.AreEqual(ReadInputValue <double>(currentLine),
parameters.MortCurveShapeParm[species]);
inputLine.GetNext();
}
CheckParameterTable("EstablishProbabilities",
parameters.EstablishProbability,
"MaxANPP");
CheckParameterTable("MaxANPP",
parameters.MaxANPP,
"LeafLitter:DecayRates");
const string AgeOnlyDisturbanceParms = "AgeOnlyDisturbances:BiomassParameters";
CheckParameterTable("LeafLitter:DecayRates",
parameters.LeafLitterDecayRate,
AgeOnlyDisturbanceParms);
if (parameters.AgeOnlyDisturbanceParms != null)
{
Assert.AreEqual(ReadInputVar <string>(AgeOnlyDisturbanceParms),
parameters.AgeOnlyDisturbanceParms);
}
}
finally {
inputLine = null;
reader.Close();
}
}
public virtual void TestBuiltInGzipDecompressor()
{
// NOTE: This fails on RHEL4 with "java.io.IOException: header crc mismatch"
// due to buggy version of zlib (1.2.1.2) included.
JobConf jobConf = new JobConf(defaultConf);
jobConf.SetBoolean("io.native.lib.available", false);
CompressionCodec gzip = new GzipCodec();
ReflectionUtils.SetConf(gzip, jobConf);
localFs.Delete(workDir, true);
NUnit.Framework.Assert.AreEqual("[non-native (Java) codec]", typeof(BuiltInGzipDecompressor
), gzip.GetDecompressorType());
System.Console.Out.WriteLine(ColorBrYellow + "testBuiltInGzipDecompressor() using"
+ " non-native (Java Inflater) Decompressor (" + gzip.GetDecompressorType() + ")"
+ ColorNormal);
// copy single-member test file to HDFS
string fn1 = "testConcatThenCompress.txt" + gzip.GetDefaultExtension();
Path fnLocal1 = new Path(Runtime.GetProperty("test.concat.data", "/tmp"), fn1);
Path fnHDFS1 = new Path(workDir, fn1);
localFs.CopyFromLocalFile(fnLocal1, fnHDFS1);
// copy multiple-member test file to HDFS
// (actually in "seekable gzip" format, a la JIRA PIG-42)
string fn2 = "testCompressThenConcat.txt" + gzip.GetDefaultExtension();
Path fnLocal2 = new Path(Runtime.GetProperty("test.concat.data", "/tmp"), fn2);
Path fnHDFS2 = new Path(workDir, fn2);
localFs.CopyFromLocalFile(fnLocal2, fnHDFS2);
FileInputFormat.SetInputPaths(jobConf, workDir);
// here's first pair of DecompressorStreams:
FileInputStream in1 = new FileInputStream(fnLocal1.ToString());
FileInputStream in2 = new FileInputStream(fnLocal2.ToString());
NUnit.Framework.Assert.AreEqual("concat bytes available", 2734, in1.Available());
NUnit.Framework.Assert.AreEqual("concat bytes available", 3413, in2.Available());
// w/hdr CRC
CompressionInputStream cin2 = gzip.CreateInputStream(in2);
LineReader @in = new LineReader(cin2);
Text @out = new Text();
int numBytes;
int totalBytes = 0;
int lineNum = 0;
while ((numBytes = @in.ReadLine(@out)) > 0)
{
++lineNum;
totalBytes += numBytes;
}
@in.Close();
NUnit.Framework.Assert.AreEqual("total uncompressed bytes in concatenated test file"
, 5346, totalBytes);
NUnit.Framework.Assert.AreEqual("total uncompressed lines in concatenated test file"
, 84, lineNum);
// test BuiltInGzipDecompressor with lots of different input-buffer sizes
DoMultipleGzipBufferSizes(jobConf, false);
// test GzipZlibDecompressor (native), just to be sure
// (FIXME? could move this call to testGzip(), but would need filename
// setup above) (alternatively, maybe just nuke testGzip() and extend this?)
DoMultipleGzipBufferSizes(jobConf, true);
}