private void DownloadCSV()
{
IOUtils file = new IOUtils();
ISdmxObjects sdmxObjects = null;
DataTable dt = new DataTable();
sdmxObjects = GetSdmxObjects();
if (sdmxObjects == null)
return;
AddExportColumns(dt);
PopolateDataTable(dt, sdmxObjects);
string mySeparator = txtSeparator.Text.Trim().Equals( string.Empty ) ? ";" : txtSeparator.Text.Trim();
file.SaveCSVFile(dt, GetFilename(), mySeparator, txtDelimiter.Text);
}
public void Dispose()
{
IOUtils.Dispose(reader);
}
private static void FullPepXMLAndProteinProphetSetup()
{
if (GlobalVar.IsSimulation)
{
if (!GlobalVar.usePepXMLComputedFile)
{
//comet
log.Info("Performing Comet search on full ms2 data");
String fullCometFile = PostProcessingScripts.CometStandardSearch(InputFileOrganizer.MS2SimulationTestFile, InputFileOrganizer.preExperimentFilesFolder, true);
InputFileOrganizer.OriginalCometOutput = fullCometFile;
}
//protein prophet
log.Info("Perform a protein prophet search on full pepxml");
String fullProteinProphetFile = PostProcessingScripts.ProteinProphetSearch(InputFileOrganizer.OriginalCometOutput, InputFileOrganizer.OutputFolderOfTheRun, true);
ExecuteShellCommand.MoveFile(fullProteinProphetFile, InputFileOrganizer.preExperimentFilesFolder);
InputFileOrganizer.OriginalProtXMLFile = Path.Combine(InputFileOrganizer.preExperimentFilesFolder, IOUtils.getBaseName(IOUtils.getBaseName(fullProteinProphetFile)) + ".prot.xml");
}
}
public FixedGapTermsIndexReader(Directory dir, FieldInfos fieldInfos, string segment, int indexDivisor,
IComparer <BytesRef> termComp, string segmentSuffix, IOContext context)
{
this.termComp = termComp;
if (Debugging.AssertsEnabled)
{
Debugging.Assert(indexDivisor == -1 || indexDivisor > 0);
}
input = dir.OpenInput(IndexFileNames.SegmentFileName(segment, segmentSuffix, FixedGapTermsIndexWriter.TERMS_INDEX_EXTENSION), context);
bool success = false;
try
{
version = ReadHeader(input);
if (version >= FixedGapTermsIndexWriter.VERSION_CHECKSUM)
{
CodecUtil.ChecksumEntireFile(input);
}
indexInterval = input.ReadInt32();
if (indexInterval < 1)
{
throw new CorruptIndexException("invalid indexInterval: " + indexInterval + " (resource=" + input + ")");
}
this.indexDivisor = indexDivisor;
if (indexDivisor < 0)
{
totalIndexInterval = indexInterval;
}
else
{
// In case terms index gets loaded, later, on demand
totalIndexInterval = indexInterval * indexDivisor;
}
if (Debugging.AssertsEnabled)
{
Debugging.Assert(totalIndexInterval > 0);
}
SeekDir(input, dirOffset);
// Read directory
int numFields = input.ReadVInt32();
if (numFields < 0)
{
throw new CorruptIndexException("invalid numFields: " + numFields + " (resource=" + input + ")");
}
//System.out.println("FGR: init seg=" + segment + " div=" + indexDivisor + " nF=" + numFields);
for (int i = 0; i < numFields; i++)
{
int field = input.ReadVInt32();
int numIndexTerms = input.ReadVInt32();
if (numIndexTerms < 0)
{
throw new CorruptIndexException("invalid numIndexTerms: " + numIndexTerms + " (resource=" + input + ")");
}
long termsStart = input.ReadVInt64();
long indexStart = input.ReadVInt64();
long packedIndexStart = input.ReadVInt64();
long packedOffsetsStart = input.ReadVInt64();
if (packedIndexStart < indexStart)
{
throw new CorruptIndexException("invalid packedIndexStart: " + packedIndexStart + " indexStart: " + indexStart + "numIndexTerms: " + numIndexTerms + " (resource=" + input + ")");
}
FieldInfo fieldInfo = fieldInfos.FieldInfo(field);
FieldIndexData previous = fields.Put(fieldInfo, new FieldIndexData(this, fieldInfo, numIndexTerms, indexStart, termsStart, packedIndexStart, packedOffsetsStart));
if (previous != null)
{
throw new CorruptIndexException("duplicate field: " + fieldInfo.Name + " (resource=" + input + ")");
}
}
success = true;
}
finally
{
if (!success)
{
IOUtils.DisposeWhileHandlingException(input);
}
if (indexDivisor > 0)
{
input.Dispose();
input = null;
if (success)
{
indexLoaded = true;
}
termBytesReader = termBytes.Freeze(true);
}
}
}
static List<TemplateItem> GetTemplateData()
{
var t = IOUtils.LoadTemplateItemsData();
//ExampleJsonOutput();
return t;
}
/// <summary>
/// Loads a Game freak texture.
/// </summary>
/// <param name="data">The texture data</param>
/// <returns>The image as a texture</returns>
public static RenderBase.OTexture load(Stream data, bool keepOpen = false)
{
BinaryReader input = new BinaryReader(data);
long descAddress = data.Position;
data.Seek(8, SeekOrigin.Current);
if (IOUtils.readStringWithLength(input, 7) != "texture")
{
return(null);
}
data.Seek(descAddress + 0x18, SeekOrigin.Begin);
int texLength = input.ReadInt32();
data.Seek(descAddress + 0x28, SeekOrigin.Begin);
string texName = IOUtils.readStringWithLength(input, 0x40);
data.Seek(descAddress + 0x68, SeekOrigin.Begin);
ushort width = input.ReadUInt16();
ushort height = input.ReadUInt16();
ushort texFormat = input.ReadUInt16();
ushort texMipMaps = input.ReadUInt16();
data.Seek(0x10, SeekOrigin.Current);
byte[] texBuffer = input.ReadBytes(texLength);
RenderBase.OTextureFormat fmt = RenderBase.OTextureFormat.dontCare;
switch (texFormat)
{
case 0x2: fmt = RenderBase.OTextureFormat.rgb565; break;
case 0x3: fmt = RenderBase.OTextureFormat.rgb8; break;
case 0x4: fmt = RenderBase.OTextureFormat.rgba8; break;
case 0x16: fmt = RenderBase.OTextureFormat.rgba4; break;
case 0x17: fmt = RenderBase.OTextureFormat.rgba5551; break;
case 0x23: fmt = RenderBase.OTextureFormat.la8; break;
case 0x24: fmt = RenderBase.OTextureFormat.hilo8; break;
case 0x25: fmt = RenderBase.OTextureFormat.l8; break;
case 0x26: fmt = RenderBase.OTextureFormat.a8; break;
case 0x27: fmt = RenderBase.OTextureFormat.la4; break;
case 0x28: fmt = RenderBase.OTextureFormat.l4; break;
case 0x29: fmt = RenderBase.OTextureFormat.a4; break;
case 0x2a: fmt = RenderBase.OTextureFormat.etc1; break;
case 0x2b: fmt = RenderBase.OTextureFormat.etc1a4; break;
default: Debug.WriteLine("Unk tex fmt " + texFormat.ToString("X4") + " @ " + texName); break;
}
Bitmap tex = TextureCodec.decode(texBuffer, width, height, fmt);
if (!keepOpen)
{
data.Close();
}
return(new RenderBase.OTexture(tex, texName));
}
/// <summary>
/// Make sure isCompiling() == true as setCompilingTrue() was called
/// Make sure all parameters are not null
/// Make sure this method is thread-safety: it cannot be called at the same time
/// </summary>
/// <param name="cmd"></param>
/// <param name="workingDir"></param>
/// <returns></returns>
public TCompileResult compile(string cmd, string workingDir)
{
int oldTick = SystemUtils.getCurrentTimeMs();
ICmdParser parser = CmdParserFactory.createCmdParser(cmd);
List <string> inputFilePaths = null;
string outputFilePath = null;
TCompileResult result = null;
if (!isAllowCompiling())
{
result = new TCompileResult(false, 1, "error: Compiling is stopped!", 0, null); goto my_end;
}
try
{
parser.getInOutFilePath(workingDir, out inputFilePaths, out outputFilePath);
}
catch (Exception ex)
{
// Error
result = new TCompileResult(false, 1, "error: " + ex.Message, 0, null);
goto my_end;
}
if (inputFilePaths == null || inputFilePaths.Count == 0 || outputFilePath == null)
{
// Error
result = new TCompileResult(false, 1, "error: Invalid command, input file is mandatory!", 0, null);
goto my_end;
}
outputFilePath = PathUtils.combine(workingDir, outputFilePath);
if (!isConnected())
{
// Local
goto my_end;
}
#region Distribute
// Send the input files to server
foreach (string inputFilePath in inputFilePaths)
{
string f = PathUtils.combine(workingDir, inputFilePath);
string fNormal = PathUtils.normalizePath(f);
if (!m_sentFiles.Contains(fNormal))
{
if (sendFile(f))
{
m_sentFiles.Add(fNormal);
}
else
{
// Local
goto my_end;
}
}
}
// Send compile request to server
string cmdToSend = parser.makeNetworkCmd();
Message msg = MessageCompileRequest.createMessage(cmdToSend);
if (!m_messageStream.writeMessage(msg))
{
goto my_end;
}
if (!isAllowCompiling())
{
result = new TCompileResult(false, 1, "error: Compiling is stopped!", 0, null); goto my_end;
}
// Receive the compile result
msg = m_messageStream.readMessage();
if (msg == null)
{
goto my_end;
}
if (!isAllowCompiling())
{
result = new TCompileResult(false, 1, "error: Compiling is stopped!", 0, null); goto my_end;
}
// Parse and check the compile result
MessageCompileResponse msgCompileRes = new MessageCompileResponse(msg);
if (msgCompileRes.getWasExec() && msgCompileRes.getExitCode() != 0)
{
// Compile error
// Nghia: TODO rem this for the hot fix
//result = new TCompileResult(true, msgCompileRes.getExitCode(), msgCompileRes.getOutputText(), 0, m_host);
goto my_end;
}
if (!msgCompileRes.getWasExec())
{
goto my_end;
}
// Compile OK by server
// Save the file to disk
if (!IOUtils.writeFile_Bytes(outputFilePath, msgCompileRes.getOFileData(),
msgCompileRes.getOFileOffset(), msgCompileRes.getOFileSize()))
{
// No need to compile local as this is a serious error
result = new TCompileResult(true, 1, "error: Could not save the output file to disk", 0, m_host);
goto my_end;
}
// Everything is OK
result = new TCompileResult(true, 0,
"Remotely compiled from " + m_host + "\n" + msgCompileRes.getOutputText(), 0, m_host);
#endregion
my_end:
if (result == null)
{
// Local
string specOutFilePath = parser.getLocalSpecificOutputFilePath();
string specCmd = parser.getLocalSpecificCommand();
string specWorkingDir = parser.getLocalSpecificWorkingDir();
if (specOutFilePath == null)
{
specOutFilePath = outputFilePath;
}
if (specCmd == null)
{
specCmd = cmd;
}
if (specWorkingDir == null)
{
specWorkingDir = workingDir;
}
specOutFilePath = PathUtils.combine(specWorkingDir, specOutFilePath);
TProcessResult res = null;
if (parser.needToLockLocal())
{
lock (s_lock)
{
doLocal(specCmd, specWorkingDir, specOutFilePath, ref oldTick, ref res);
}
}
else
{
doLocal(specCmd, specWorkingDir, specOutFilePath, ref oldTick, ref res);
}
result = new TCompileResult(res.wasExec, res.exitCode, "Locally compiled\n" + res.outputText, 0, null);
if (result.wasExec && result.exitCode == 0 && specOutFilePath != outputFilePath)
{
File.Move(specOutFilePath, outputFilePath);
}
}
result.spentTimeMs = SystemUtils.getCurrentTimeMs() - oldTick;
setCompiling(false);
return(result);
}
public override void Run()
{
using Stream stream = new NetworkStream(cs);
BinaryReader intReader = new BinaryReader(stream);
BinaryWriter intWriter = new BinaryWriter(stream);
try
{
int id = intReader.ReadInt32();
if (id < 0)
{
throw new IOException("Client closed connection before communication started.");
}
startingGun.Wait();
intWriter.Write(43);
stream.Flush();
while (true)
{
int command = stream.ReadByte();
if (command < 0)
{
return; // closed
}
UninterruptableMonitor.Enter(localLock);
try
{
int currentLock = lockedID[0];
if (currentLock == -2)
{
return; // another thread got error, so we exit, too!
}
switch (command)
{
case 1:
// Locked
if (currentLock != -1)
{
lockedID[0] = -2;
throw IllegalStateException.Create("id " + id + " got lock, but " + currentLock + " already holds the lock");
}
lockedID[0] = id;
break;
case 0:
// Unlocked
if (currentLock != id)
{
lockedID[0] = -2;
throw IllegalStateException.Create("id " + id + " released the lock, but " + currentLock + " is the one holding the lock");
}
lockedID[0] = -1;
break;
default:
throw RuntimeException.Create("Unrecognized command: " + command);
}
intWriter.Write((byte)command);
stream.Flush();
}
finally
{
UninterruptableMonitor.Exit(localLock);
}
}
}
catch (Exception e) when (e.IsRuntimeException() || e.IsError())
{
throw; // LUCENENET: CA2200: Rethrow to preserve stack details (https://docs.microsoft.com/en-us/visualstudio/code-quality/ca2200-rethrow-to-preserve-stack-details)
}
catch (Exception ioe) when (ioe.IsException())
{
throw RuntimeException.Create(ioe);
}
finally
{
IOUtils.DisposeWhileHandlingException(cs);
}
}
/// <summary>
/// An example of a command line is
/// <br />
/// java -mx1g edu.stanford.nlp.parser.dvparser.CacheParseHypotheses -model /scr/horatio/dvparser/wsjPCFG.nocompact.simple.ser.gz -output cached9.simple.ser.gz -treebank /afs/ir/data/linguistic-data/Treebank/3/parsed/mrg/wsj 200-202
/// <br />
/// java -mx4g edu.stanford.nlp.parser.dvparser.CacheParseHypotheses -model ~/scr/dvparser/wsjPCFG.nocompact.simple.ser.gz -output cached.train.simple.ser.gz -treebank /afs/ir/data/linguistic-data/Treebank/3/parsed/mrg/wsj 200-2199 -numThreads 6
/// <br />
/// java -mx4g edu.stanford.nlp.parser.dvparser.CacheParseHypotheses -model ~/scr/dvparser/chinese/xinhuaPCFG.ser.gz -output cached.xinhua.train.ser.gz -treebank /afs/ir/data/linguistic-data/Chinese-Treebank/6/data/utf8/bracketed 026-270,301-499,600-999
/// </summary>
/// <exception cref="System.IO.IOException"/>
public static void Main(string[] args)
{
string parserModel = null;
string output = null;
IList <Pair <string, IFileFilter> > treebanks = Generics.NewArrayList();
int dvKBest = 200;
int numThreads = 1;
for (int argIndex = 0; argIndex < args.Length;)
{
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-dvKBest"))
{
dvKBest = System.Convert.ToInt32(args[argIndex + 1]);
argIndex += 2;
continue;
}
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-parser") || args[argIndex].Equals("-model"))
{
parserModel = args[argIndex + 1];
argIndex += 2;
continue;
}
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-output"))
{
output = args[argIndex + 1];
argIndex += 2;
continue;
}
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-treebank"))
{
Pair <string, IFileFilter> treebankDescription = ArgUtils.GetTreebankDescription(args, argIndex, "-treebank");
argIndex = argIndex + ArgUtils.NumSubArgs(args, argIndex) + 1;
treebanks.Add(treebankDescription);
continue;
}
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-numThreads"))
{
numThreads = System.Convert.ToInt32(args[argIndex + 1]);
argIndex += 2;
continue;
}
throw new ArgumentException("Unknown argument " + args[argIndex]);
}
if (parserModel == null)
{
throw new ArgumentException("Need to supply a parser model with -model");
}
if (output == null)
{
throw new ArgumentException("Need to supply an output filename with -output");
}
if (treebanks.IsEmpty())
{
throw new ArgumentException("Need to supply a treebank with -treebank");
}
log.Info("Writing output to " + output);
log.Info("Loading parser model " + parserModel);
log.Info("Writing " + dvKBest + " hypothesis trees for each tree");
LexicalizedParser parser = ((LexicalizedParser)LexicalizedParser.LoadModel(parserModel, "-dvKBest", int.ToString(dvKBest)));
CacheParseHypotheses cacher = new CacheParseHypotheses(parser);
ITreeTransformer transformer = DVParser.BuildTrainTransformer(parser.GetOp());
IList <Tree> sentences = new List <Tree>();
foreach (Pair <string, IFileFilter> description in treebanks)
{
log.Info("Reading trees from " + description.first);
Treebank treebank = parser.GetOp().tlpParams.MemoryTreebank();
treebank.LoadPath(description.first, description.second);
treebank = treebank.Transform(transformer);
Sharpen.Collections.AddAll(sentences, treebank);
}
log.Info("Processing " + sentences.Count + " trees");
IList <Pair <Tree, byte[]> > cache = Generics.NewArrayList();
transformer = new SynchronizedTreeTransformer(transformer);
MulticoreWrapper <Tree, Pair <Tree, byte[]> > wrapper = new MulticoreWrapper <Tree, Pair <Tree, byte[]> >(numThreads, new CacheParseHypotheses.CacheProcessor(cacher, parser, dvKBest, transformer));
foreach (Tree tree in sentences)
{
wrapper.Put(tree);
while (wrapper.Peek())
{
cache.Add(wrapper.Poll());
if (cache.Count % 10 == 0)
{
System.Console.Out.WriteLine("Processed " + cache.Count + " trees");
}
}
}
wrapper.Join();
while (wrapper.Peek())
{
cache.Add(wrapper.Poll());
if (cache.Count % 10 == 0)
{
System.Console.Out.WriteLine("Processed " + cache.Count + " trees");
}
}
System.Console.Out.WriteLine("Finished processing " + cache.Count + " trees");
IOUtils.WriteObjectToFile(cache, output);
}
public virtual void TestNrt()
{
Store.Directory dir = NewDirectory();
Store.Directory taxoDir = NewDirectory();
IndexWriterConfig iwc = NewIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(Random()));
// Don't allow tiny maxBufferedDocs; it can make this
// test too slow:
iwc.SetMaxBufferedDocs(Math.Max(500, iwc.MaxBufferedDocs));
// MockRandom/AlcololicMergePolicy are too slow:
TieredMergePolicy tmp = new TieredMergePolicy();
tmp.FloorSegmentMB = .001;
iwc.SetMergePolicy(tmp);
IndexWriter w = new IndexWriter(dir, iwc);
var tw = new DirectoryTaxonomyWriter(taxoDir);
FacetsConfig config = new FacetsConfig();
config.SetMultiValued("field", true);
AtomicBoolean stop = new AtomicBoolean();
// How many unique facets to index before stopping:
int ordLimit = TEST_NIGHTLY ? 100000 : 6000;
var indexer = new IndexerThread(w, config, tw, null, ordLimit, stop);
var mgr = new SearcherTaxonomyManager(w, true, null, tw);
var reopener = new ThreadAnonymousInnerClassHelper(this, stop, mgr);
reopener.Name = "reopener";
reopener.Start();
indexer.Name = "indexer";
indexer.Start();
try
{
while (!stop.Get())
{
SearcherAndTaxonomy pair = mgr.Acquire();
try
{
//System.out.println("search maxOrd=" + pair.taxonomyReader.getSize());
FacetsCollector sfc = new FacetsCollector();
pair.Searcher.Search(new MatchAllDocsQuery(), sfc);
Facets facets = GetTaxonomyFacetCounts(pair.TaxonomyReader, config, sfc);
FacetResult result = facets.GetTopChildren(10, "field");
if (pair.Searcher.IndexReader.NumDocs > 0)
{
//System.out.println(pair.taxonomyReader.getSize());
Assert.True(result.ChildCount > 0);
Assert.True(result.LabelValues.Length > 0);
}
//if (VERBOSE) {
//System.out.println("TEST: facets=" + FacetTestUtils.toString(results.get(0)));
//}
}
finally
{
mgr.Release(pair);
}
}
}
finally
{
indexer.Join();
reopener.Join();
}
if (VERBOSE)
{
Console.WriteLine("TEST: now stop");
}
IOUtils.Dispose(mgr, tw, w, taxoDir, dir);
}
public virtual void TestDirectory()
{
Store.Directory indexDir = NewDirectory();
Store.Directory taxoDir = NewDirectory();
IndexWriter w = new IndexWriter(indexDir, NewIndexWriterConfig(TEST_VERSION_CURRENT, new MockAnalyzer(Random())));
var tw = new DirectoryTaxonomyWriter(taxoDir);
// first empty commit
w.Commit();
tw.Commit();
var mgr = new SearcherTaxonomyManager(indexDir, taxoDir, null);
FacetsConfig config = new FacetsConfig();
config.SetMultiValued("field", true);
AtomicBoolean stop = new AtomicBoolean();
// How many unique facets to index before stopping:
int ordLimit = TEST_NIGHTLY ? 100000 : 6000;
var indexer = new IndexerThread(w, config, tw, mgr, ordLimit, stop);
indexer.Start();
try
{
while (!stop.Get())
{
SearcherAndTaxonomy pair = mgr.Acquire();
try
{
//System.out.println("search maxOrd=" + pair.taxonomyReader.getSize());
FacetsCollector sfc = new FacetsCollector();
pair.Searcher.Search(new MatchAllDocsQuery(), sfc);
Facets facets = GetTaxonomyFacetCounts(pair.TaxonomyReader, config, sfc);
FacetResult result = facets.GetTopChildren(10, "field");
if (pair.Searcher.IndexReader.NumDocs > 0)
{
//System.out.println(pair.taxonomyReader.getSize());
Assert.True(result.ChildCount > 0);
Assert.True(result.LabelValues.Length > 0);
}
//if (VERBOSE) {
//System.out.println("TEST: facets=" + FacetTestUtils.toString(results.get(0)));
//}
}
finally
{
mgr.Release(pair);
}
}
}
finally
{
indexer.Join();
}
if (VERBOSE)
{
Console.WriteLine("TEST: now stop");
}
IOUtils.Dispose(mgr, tw, w, taxoDir, indexDir);
}
public override void WriteAdditionalClipboardData( ref string nodeInfo )
{
base.WriteAdditionalClipboardData( ref nodeInfo ):
IOUtils.AddFieldValueToString( ref nodeInfo, IOUtils.Matrix4x4ToString( m_materialValue ) ):
}
public override void ReadAdditionalClipboardData( ref string[] nodeParams )
{
base.ReadAdditionalClipboardData( ref nodeParams ):
m_materialValue = IOUtils.StringToMatrix4x4( GetCurrentParam( ref nodeParams ) ):
}
public override void WriteToString( ref string nodeInfo, ref string connectionsInfo )
{
base.WriteToString( ref nodeInfo, ref connectionsInfo ):
IOUtils.AddFieldValueToString( ref nodeInfo, IOUtils.Matrix4x4ToString( m_defaultValue ) ):
}
private void DownloadDotStatDSD()
{
IOUtils file = new IOUtils();
ISdmxObjects sdmxObjects = null;
sdmxObjects = GetSdmxObjectsWithRef();
if (sdmxObjects == null)
return;
file.SaveDotSTATFile(sdmxObjects, GetDotSTATExportType());
}
/// <exception cref="System.IO.IOException"/>
public virtual void Annotate(ICoreMap document)
{
// write input file in GUTime format
IElement inputXML = ToInputXML(document);
File inputFile = File.CreateTempFile("gutime", ".input");
//Document doc = new Document(inputXML);
PrintWriter inputWriter = new PrintWriter(inputFile);
inputWriter.Println(XMLUtils.NodeToString(inputXML, false));
// new XMLOutputter().output(inputXML, inputWriter);
inputWriter.Close();
bool useFirstDate = (!document.ContainsKey(typeof(CoreAnnotations.CalendarAnnotation)) && !document.ContainsKey(typeof(CoreAnnotations.DocDateAnnotation)));
List <string> args = new List <string>();
args.Add("perl");
args.Add("-I" + this.gutimePath.GetPath());
args.Add(new File(this.gutimePath, "TimeTag.pl").GetPath());
if (useFirstDate)
{
args.Add("-FDNW");
}
args.Add(inputFile.GetPath());
// run GUTime on the input file
ProcessBuilder process = new ProcessBuilder(args);
StringWriter outputWriter = new StringWriter();
SystemUtils.Run(process, outputWriter, null);
string output = outputWriter.GetBuffer().ToString();
Pattern docClose = Pattern.Compile("</DOC>.*", Pattern.Dotall);
output = docClose.Matcher(output).ReplaceAll("</DOC>");
//The TimeTag.pl result file contains next tags which must be removed
output = output.ReplaceAll("<lex.*?>", string.Empty);
output = output.Replace("</lex>", string.Empty);
output = output.Replace("<NG>", string.Empty);
output = output.Replace("</NG>", string.Empty);
output = output.Replace("<VG>", string.Empty);
output = output.Replace("</VG>", string.Empty);
output = output.Replace("<s>", string.Empty);
output = output.Replace("</s>", string.Empty);
// parse the GUTime output
IElement outputXML;
try
{
outputXML = XMLUtils.ParseElement(output);
}
catch (Exception ex)
{
throw new Exception(string.Format("error:\n%s\ninput:\n%s\noutput:\n%s", ex, IOUtils.SlurpFile(inputFile), output), ex);
}
/*
* try {
* outputXML = new SAXBuilder().build(new StringReader(output)).getRootElement();
* } catch (JDOMException e) {
* throw new RuntimeException(String.format("error:\n%s\ninput:\n%s\noutput:\n%s",
* e, IOUtils.slurpFile(inputFile), output));
* } */
inputFile.Delete();
// get Timex annotations
IList <ICoreMap> timexAnns = ToTimexCoreMaps(outputXML, document);
document.Set(typeof(TimeAnnotations.TimexAnnotations), timexAnns);
if (outputResults)
{
System.Console.Out.WriteLine(timexAnns);
}
// align Timex annotations to sentences
int timexIndex = 0;
foreach (ICoreMap sentence in document.Get(typeof(CoreAnnotations.SentencesAnnotation)))
{
int sentBegin = BeginOffset(sentence);
int sentEnd = EndOffset(sentence);
// skip times before the sentence
while (timexIndex < timexAnns.Count && BeginOffset(timexAnns[timexIndex]) < sentBegin)
{
++timexIndex;
}
// determine times within the sentence
int sublistBegin = timexIndex;
int sublistEnd = timexIndex;
while (timexIndex < timexAnns.Count && sentBegin <= BeginOffset(timexAnns[timexIndex]) && EndOffset(timexAnns[timexIndex]) <= sentEnd)
{
++sublistEnd;
++timexIndex;
}
// set the sentence timexes
sentence.Set(typeof(TimeAnnotations.TimexAnnotations), timexAnns.SubList(sublistBegin, sublistEnd));
}
}
public override void ReadFromString( ref string[] nodeParams )
{
base.ReadFromString( ref nodeParams ):
m_defaultValue = IOUtils.StringToMatrix4x4( GetCurrentParam( ref nodeParams ) ):
}
public void Dispose()
{
IOUtils.Dispose(origEnum, threadResources);
}
public void WriteToString( ref string nodeInfo )
{
IOUtils.AddFieldValueToString( ref nodeInfo, m_value ):
IOUtils.AddFieldValueToString( ref nodeInfo, m_active ):
IOUtils.AddFieldValueToString( ref nodeInfo, m_nodeId ):
}
public virtual void TestSparseFacets()
{
Store.Directory dir = NewDirectory();
Store.Directory taxoDir = NewDirectory();
// Writes facet ords to a separate directory from the
// main index:
var taxoWriter = new DirectoryTaxonomyWriter(taxoDir, OpenMode.CREATE);
RandomIndexWriter writer = new RandomIndexWriter(Random(), dir, Similarity, TimeZone);
FacetsConfig config = new FacetsConfig();
Document doc = new Document();
doc.Add(new Int32Field("num", 10, Field.Store.NO));
doc.Add(new FacetField("a", "foo1"));
writer.AddDocument(config.Build(taxoWriter, doc));
if (Random().NextBoolean())
{
writer.Commit();
}
doc = new Document();
doc.Add(new Int32Field("num", 20, Field.Store.NO));
doc.Add(new FacetField("a", "foo2"));
doc.Add(new FacetField("b", "bar1"));
writer.AddDocument(config.Build(taxoWriter, doc));
if (Random().NextBoolean())
{
writer.Commit();
}
doc = new Document();
doc.Add(new Int32Field("num", 30, Field.Store.NO));
doc.Add(new FacetField("a", "foo3"));
doc.Add(new FacetField("b", "bar2"));
doc.Add(new FacetField("c", "baz1"));
writer.AddDocument(config.Build(taxoWriter, doc));
// NRT open
IndexSearcher searcher = NewSearcher(writer.Reader);
writer.Dispose();
// NRT open
var taxoReader = new DirectoryTaxonomyReader(taxoWriter);
taxoWriter.Dispose();
FacetsCollector c = new FacetsCollector();
searcher.Search(new MatchAllDocsQuery(), c);
TaxonomyFacetSumValueSource facets = new TaxonomyFacetSumValueSource(taxoReader, new FacetsConfig(), c, new Int32FieldSource("num"));
// Ask for top 10 labels for any dims that have counts:
IList <FacetResult> results = facets.GetAllDims(10);
Assert.AreEqual(3, results.Count);
Assert.AreEqual("dim=a path=[] value=60.0 childCount=3\n foo3 (30.0)\n foo2 (20.0)\n foo1 (10.0)\n", results[0].ToString());
Assert.AreEqual("dim=b path=[] value=50.0 childCount=2\n bar2 (30.0)\n bar1 (20.0)\n", results[1].ToString());
Assert.AreEqual("dim=c path=[] value=30.0 childCount=1\n baz1 (30.0)\n", results[2].ToString());
IOUtils.Close(searcher.IndexReader, taxoReader, dir, taxoDir);
}
/// <summary>
/// Sole constructor. </summary>
public CompressingStoredFieldsReader(Directory d, SegmentInfo si, string segmentSuffix, FieldInfos fn, IOContext context, string formatName, CompressionMode compressionMode)
{
this.compressionMode = compressionMode;
string segment = si.Name;
bool success = false;
fieldInfos = fn;
numDocs = si.DocCount;
ChecksumIndexInput indexStream = null;
try
{
string indexStreamFN = IndexFileNames.SegmentFileName(segment, segmentSuffix, Lucene40StoredFieldsWriter.FIELDS_INDEX_EXTENSION);
string fieldsStreamFN = IndexFileNames.SegmentFileName(segment, segmentSuffix, Lucene40StoredFieldsWriter.FIELDS_EXTENSION);
// Load the index into memory
indexStream = d.OpenChecksumInput(indexStreamFN, context);
string codecNameIdx = formatName + CompressingStoredFieldsWriter.CODEC_SFX_IDX;
version = CodecUtil.CheckHeader(indexStream, codecNameIdx, CompressingStoredFieldsWriter.VERSION_START, CompressingStoredFieldsWriter.VERSION_CURRENT);
Debug.Assert(CodecUtil.HeaderLength(codecNameIdx) == indexStream.GetFilePointer());
indexReader = new CompressingStoredFieldsIndexReader(indexStream, si);
long maxPointer = -1;
if (version >= CompressingStoredFieldsWriter.VERSION_CHECKSUM)
{
maxPointer = indexStream.ReadVInt64();
CodecUtil.CheckFooter(indexStream);
}
else
{
#pragma warning disable 612, 618
CodecUtil.CheckEOF(indexStream);
#pragma warning restore 612, 618
}
indexStream.Dispose();
indexStream = null;
// Open the data file and read metadata
fieldsStream = d.OpenInput(fieldsStreamFN, context);
if (version >= CompressingStoredFieldsWriter.VERSION_CHECKSUM)
{
if (maxPointer + CodecUtil.FooterLength() != fieldsStream.Length)
{
throw new CorruptIndexException("Invalid fieldsStream maxPointer (file truncated?): maxPointer=" + maxPointer + ", length=" + fieldsStream.Length);
}
}
else
{
maxPointer = fieldsStream.Length;
}
this.maxPointer = maxPointer;
string codecNameDat = formatName + CompressingStoredFieldsWriter.CODEC_SFX_DAT;
int fieldsVersion = CodecUtil.CheckHeader(fieldsStream, codecNameDat, CompressingStoredFieldsWriter.VERSION_START, CompressingStoredFieldsWriter.VERSION_CURRENT);
if (version != fieldsVersion)
{
throw new CorruptIndexException("Version mismatch between stored fields index and data: " + version + " != " + fieldsVersion);
}
Debug.Assert(CodecUtil.HeaderLength(codecNameDat) == fieldsStream.GetFilePointer());
if (version >= CompressingStoredFieldsWriter.VERSION_BIG_CHUNKS)
{
chunkSize = fieldsStream.ReadVInt32();
}
else
{
chunkSize = -1;
}
packedIntsVersion = fieldsStream.ReadVInt32();
decompressor = compressionMode.NewDecompressor();
this.bytes = new BytesRef();
success = true;
}
finally
{
if (!success)
{
IOUtils.DisposeWhileHandlingException(this, indexStream);
}
}
}
public virtual void TestWrongIndexFieldName()
{
Store.Directory dir = NewDirectory();
Store.Directory taxoDir = NewDirectory();
// Writes facet ords to a separate directory from the
// main index:
var taxoWriter = new DirectoryTaxonomyWriter(taxoDir, OpenMode.CREATE);
FacetsConfig config = new FacetsConfig();
config.SetIndexFieldName("a", "$facets2");
RandomIndexWriter writer = new RandomIndexWriter(Random(), dir, Similarity, TimeZone);
Document doc = new Document();
doc.Add(new Int32Field("num", 10, Field.Store.NO));
doc.Add(new FacetField("a", "foo1"));
writer.AddDocument(config.Build(taxoWriter, doc));
// NRT open
IndexSearcher searcher = NewSearcher(writer.Reader);
writer.Dispose();
// NRT open
var taxoReader = new DirectoryTaxonomyReader(taxoWriter);
taxoWriter.Dispose();
FacetsCollector c = new FacetsCollector();
searcher.Search(new MatchAllDocsQuery(), c);
TaxonomyFacetSumValueSource facets = new TaxonomyFacetSumValueSource(taxoReader, config, c, new Int32FieldSource("num"));
// Ask for top 10 labels for any dims that have counts:
IList <FacetResult> results = facets.GetAllDims(10);
Assert.True(results.Count == 0);
try
{
facets.GetSpecificValue("a");
Fail("should have hit exc");
}
catch (System.ArgumentException)
{
// expected
}
try
{
facets.GetTopChildren(10, "a");
Fail("should have hit exc");
}
catch (System.ArgumentException)
{
// expected
}
IOUtils.Close(searcher.IndexReader, taxoReader, dir, taxoDir);
}
public override string /*!*/ ReadLine()
{
return(IOUtils.ReadTo(this, '\n'));
}
public virtual void TestRandom()
{
string[] tokens = GetRandomTokens(10);
Store.Directory indexDir = NewDirectory();
Store.Directory taxoDir = NewDirectory();
RandomIndexWriter w = new RandomIndexWriter(Random(), indexDir, Similarity, TimeZone);
var tw = new DirectoryTaxonomyWriter(taxoDir);
FacetsConfig config = new FacetsConfig();
int numDocs = AtLeast(1000);
int numDims = TestUtil.NextInt(Random(), 1, 7);
IList <TestDoc> testDocs = GetRandomDocs(tokens, numDocs, numDims);
foreach (TestDoc testDoc in testDocs)
{
Document doc = new Document();
doc.Add(NewStringField("content", testDoc.content, Field.Store.NO));
testDoc.value = Random().NextFloat();
doc.Add(new SingleDocValuesField("value", testDoc.value));
for (int j = 0; j < numDims; j++)
{
if (testDoc.dims[j] != null)
{
doc.Add(new FacetField("dim" + j, testDoc.dims[j]));
}
}
w.AddDocument(config.Build(tw, doc));
}
// NRT open
IndexSearcher searcher = NewSearcher(w.Reader);
// NRT open
var tr = new DirectoryTaxonomyReader(tw);
ValueSource values = new SingleFieldSource("value");
int iters = AtLeast(100);
for (int iter = 0; iter < iters; iter++)
{
string searchToken = tokens[Random().Next(tokens.Length)];
if (VERBOSE)
{
Console.WriteLine("\nTEST: iter content=" + searchToken);
}
FacetsCollector fc = new FacetsCollector();
FacetsCollector.Search(searcher, new TermQuery(new Term("content", searchToken)), 10, fc);
Facets facets = new TaxonomyFacetSumValueSource(tr, config, fc, values);
// Slow, yet hopefully bug-free, faceting:
var expectedValues = new List <Dictionary <string, float?> >(numDims);
for (int i = 0; i < numDims; i++)
{
expectedValues.Add(new Dictionary <string, float?>());
}
foreach (TestDoc doc in testDocs)
{
if (doc.content.Equals(searchToken))
{
for (int j = 0; j < numDims; j++)
{
if (doc.dims[j] != null)
{
float?v = expectedValues[j].ContainsKey(doc.dims[j]) ? expectedValues[j][doc.dims[j]] : null;
if (v == null)
{
expectedValues[j][doc.dims[j]] = doc.value;
}
else
{
expectedValues[j][doc.dims[j]] = (float)v + doc.value;
}
}
}
}
}
List <FacetResult> expected = new List <FacetResult>();
for (int i = 0; i < numDims; i++)
{
List <LabelAndValue> labelValues = new List <LabelAndValue>();
float totValue = 0;
foreach (KeyValuePair <string, float?> ent in expectedValues[i])
{
labelValues.Add(new LabelAndValue(ent.Key, ent.Value.Value));
totValue += ent.Value.Value;
}
SortLabelValues(labelValues);
if (totValue > 0)
{
expected.Add(new FacetResult("dim" + i, new string[0], totValue, labelValues.ToArray(), labelValues.Count));
}
}
// Sort by highest value, tie break by value:
SortFacetResults(expected);
IList <FacetResult> actual = facets.GetAllDims(10);
// Messy: fixup ties
SortTies(actual);
if (VERBOSE)
{
Console.WriteLine("expected=\n" + expected.ToString());
Console.WriteLine("actual=\n" + actual.ToString());
}
AssertFloatValuesEquals(expected, actual);
}
IOUtils.Close(w, tw, searcher.IndexReader, tr, indexDir, taxoDir);
}
public override void TearDown()
{
IOUtils.Dispose(client, callback, publishWriter, replicator, publishDir, handlerDir);
base.TearDown();
}
public override void TearDown()
{
IOUtils.Close(indexWriter, indexReader, directory);
base.TearDown();
}
/// <exception cref="System.IO.IOException"/>
public static void Main(string[] args)
{
string basePath = "/user/socherr/scr/projects/semComp/RNTN/src/params/";
int numSlices = 25;
bool useEscapedParens = false;
for (int argIndex = 0; argIndex < args.Length;)
{
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-slices"))
{
numSlices = System.Convert.ToInt32(args[argIndex + 1]);
argIndex += 2;
}
else
{
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-path"))
{
basePath = args[argIndex + 1];
argIndex += 2;
}
else
{
if (Sharpen.Runtime.EqualsIgnoreCase(args[argIndex], "-useEscapedParens"))
{
useEscapedParens = true;
argIndex += 1;
}
else
{
log.Info("Unknown argument " + args[argIndex]);
System.Environment.Exit(2);
}
}
}
}
SimpleMatrix[] slices = new SimpleMatrix[numSlices];
for (int i = 0; i < numSlices; ++i)
{
slices[i] = LoadMatrix(basePath + "bin/Wt_" + (i + 1) + ".bin", basePath + "Wt_" + (i + 1) + ".txt");
}
SimpleTensor tensor = new SimpleTensor(slices);
log.Info("W tensor size: " + tensor.NumRows() + "x" + tensor.NumCols() + "x" + tensor.NumSlices());
SimpleMatrix W = LoadMatrix(basePath + "bin/W.bin", basePath + "W.txt");
log.Info("W matrix size: " + W.NumRows() + "x" + W.NumCols());
SimpleMatrix Wcat = LoadMatrix(basePath + "bin/Wcat.bin", basePath + "Wcat.txt");
log.Info("W cat size: " + Wcat.NumRows() + "x" + Wcat.NumCols());
SimpleMatrix combinedWV = LoadMatrix(basePath + "bin/Wv.bin", basePath + "Wv.txt");
log.Info("Word matrix size: " + combinedWV.NumRows() + "x" + combinedWV.NumCols());
File vocabFile = new File(basePath + "vocab_1.txt");
if (!vocabFile.Exists())
{
vocabFile = new File(basePath + "words.txt");
}
IList <string> lines = Generics.NewArrayList();
foreach (string line in IOUtils.ReadLines(vocabFile))
{
lines.Add(line.Trim());
}
log.Info("Lines in vocab file: " + lines.Count);
IDictionary <string, SimpleMatrix> wordVectors = Generics.NewTreeMap();
for (int i_1 = 0; i_1 < lines.Count && i_1 < combinedWV.NumCols(); ++i_1)
{
string[] pieces = lines[i_1].Split(" +");
if (pieces.Length == 0 || pieces.Length > 1)
{
continue;
}
wordVectors[pieces[0]] = combinedWV.ExtractMatrix(0, numSlices, i_1, i_1 + 1);
if (pieces[0].Equals("UNK"))
{
wordVectors[SentimentModel.UnknownWord] = wordVectors["UNK"];
}
}
// If there is no ",", we first try to look for an HTML escaping,
// then fall back to "." as better than just a random word vector.
// Same for "``" and ";"
CopyWordVector(wordVectors, ",", ",");
CopyWordVector(wordVectors, ".", ",");
CopyWordVector(wordVectors, ";", ";");
CopyWordVector(wordVectors, ".", ";");
CopyWordVector(wordVectors, "``", "``");
CopyWordVector(wordVectors, "''", "``");
if (useEscapedParens)
{
ReplaceWordVector(wordVectors, "(", "-LRB-");
ReplaceWordVector(wordVectors, ")", "-RRB-");
}
RNNOptions op = new RNNOptions();
op.numHid = numSlices;
op.lowercaseWordVectors = false;
if (Wcat.NumRows() == 2)
{
op.classNames = new string[] { "Negative", "Positive" };
op.equivalenceClasses = new int[][] { new int[] { 0 }, new int[] { 1 } };
// TODO: set to null once old models are updated
op.numClasses = 2;
}
if (!wordVectors.Contains(SentimentModel.UnknownWord))
{
wordVectors[SentimentModel.UnknownWord] = SimpleMatrix.Random(numSlices, 1, -0.00001, 0.00001, new Random());
}
SentimentModel model = SentimentModel.ModelFromMatrices(W, Wcat, tensor, wordVectors, op);
model.SaveSerialized("matlab.ser.gz");
}
internal Lucene42DocValuesProducer(SegmentReadState state, string dataCodec, string dataExtension, string metaCodec, string metaExtension)
{
maxDoc = state.SegmentInfo.DocCount;
string metaName = IndexFileNames.SegmentFileName(state.SegmentInfo.Name, state.SegmentSuffix, metaExtension);
// read in the entries from the metadata file.
ChecksumIndexInput @in = state.Directory.OpenChecksumInput(metaName, state.Context);
bool success = false;
ramBytesUsed = new AtomicInt64(RamUsageEstimator.ShallowSizeOfInstance(this.GetType()));
try
{
version = CodecUtil.CheckHeader(@in, metaCodec, VERSION_START, VERSION_CURRENT);
numerics = new Dictionary <int, NumericEntry>();
binaries = new Dictionary <int, BinaryEntry>();
fsts = new Dictionary <int, FSTEntry>();
ReadFields(@in /*, state.FieldInfos // LUCENENET: Never read */);
if (version >= VERSION_CHECKSUM)
{
CodecUtil.CheckFooter(@in);
}
else
{
#pragma warning disable 612, 618
CodecUtil.CheckEOF(@in);
#pragma warning restore 612, 618
}
success = true;
}
finally
{
if (success)
{
IOUtils.Dispose(@in);
}
else
{
IOUtils.DisposeWhileHandlingException(@in);
}
}
success = false;
try
{
string dataName = IndexFileNames.SegmentFileName(state.SegmentInfo.Name, state.SegmentSuffix, dataExtension);
data = state.Directory.OpenInput(dataName, state.Context);
int version2 = CodecUtil.CheckHeader(data, dataCodec, VERSION_START, VERSION_CURRENT);
if (version != version2)
{
throw new CorruptIndexException("Format versions mismatch");
}
success = true;
}
finally
{
if (!success)
{
IOUtils.DisposeWhileHandlingException(this.data);
}
}
}
public override void Write(Directory directory, string segmentName, string segmentSuffix, FieldInfos infos, IOContext context)
{
string fileName = IndexFileNames.SegmentFileName(segmentName, "", FIELD_INFOS_EXTENSION);
IndexOutput output = directory.CreateOutput(fileName, context);
bool success = false;
try
{
output.WriteVInt32(FORMAT_PREFLEX_RW);
output.WriteVInt32(infos.Count);
foreach (FieldInfo fi in infos)
{
sbyte bits = 0x0;
if (fi.HasVectors)
{
bits |= STORE_TERMVECTOR;
}
if (fi.OmitsNorms)
{
bits |= OMIT_NORMS;
}
if (fi.HasPayloads)
{
bits |= STORE_PAYLOADS;
}
if (fi.IsIndexed)
{
bits |= IS_INDEXED;
if (Debugging.AssertsEnabled)
{
Debugging.Assert(fi.IndexOptions == IndexOptions.DOCS_AND_FREQS_AND_POSITIONS || !fi.HasPayloads);
}
if (fi.IndexOptions == IndexOptions.DOCS_ONLY)
{
bits |= OMIT_TERM_FREQ_AND_POSITIONS;
}
else if (fi.IndexOptions == IndexOptions.DOCS_AND_FREQS)
{
bits |= OMIT_POSITIONS;
}
}
output.WriteString(fi.Name);
/*
* we need to write the field number since IW tries
* to stabelize the field numbers across segments so the
* FI ordinal is not necessarily equivalent to the field number
*/
output.WriteInt32(fi.Number);
output.WriteByte((byte)bits);
if (fi.IsIndexed && !fi.OmitsNorms)
{
// to allow null norm types we need to indicate if norms are written
// only in RW case
output.WriteByte((byte)(fi.NormType == Index.DocValuesType.NONE ? 0 : 1));
}
if (Debugging.AssertsEnabled)
{
Debugging.Assert(fi.Attributes == null); // not used or supported
}
}
success = true;
}
finally
{
if (success)
{
output.Dispose();
}
else
{
IOUtils.DisposeWhileHandlingException(output);
}
}
}
public override void Build(InputIterator iterator)
{
if (iterator.HasContexts)
{
throw new System.ArgumentException("this suggester doesn't support contexts");
}
string prefix = this.GetType().Name;
var directory = OfflineSorter.DefaultTempDir();
var tempInput = File.CreateTempFile(prefix, ".input", directory);
var tempSorted = File.CreateTempFile(prefix, ".sorted", directory);
hasPayloads = iterator.HasPayloads;
var writer = new OfflineSorter.ByteSequencesWriter(tempInput);
OfflineSorter.ByteSequencesReader reader = null;
var scratch = new BytesRef();
TokenStreamToAutomaton ts2a = TokenStreamToAutomaton;
bool success = false;
count = 0;
sbyte[] buffer = new sbyte[8];
try
{
var output = new ByteArrayDataOutput(buffer);
BytesRef surfaceForm;
while ((surfaceForm = iterator.Next()) != null)
{
HashSet <IntsRef> paths = ToFiniteStrings(surfaceForm, ts2a);
maxAnalyzedPathsForOneInput = Math.Max(maxAnalyzedPathsForOneInput, paths.Count);
foreach (IntsRef path in paths)
{
Util.Fst.Util.ToBytesRef(path, scratch);
// length of the analyzed text (FST input)
if (scratch.Length > short.MaxValue - 2)
{
throw new System.ArgumentException("cannot handle analyzed forms > " + (short.MaxValue - 2) +
" in length (got " + scratch.Length + ")");
}
short analyzedLength = (short)scratch.Length;
// compute the required length:
// analyzed sequence + weight (4) + surface + analyzedLength (short)
int requiredLength = analyzedLength + 4 + surfaceForm.Length + 2;
BytesRef payload;
if (hasPayloads)
{
if (surfaceForm.Length > (short.MaxValue - 2))
{
throw new ArgumentException("cannot handle surface form > " + (short.MaxValue - 2) +
" in length (got " + surfaceForm.Length + ")");
}
payload = iterator.Payload;
// payload + surfaceLength (short)
requiredLength += payload.Length + 2;
}
else
{
payload = null;
}
buffer = ArrayUtil.Grow(buffer, requiredLength);
output.Reset(buffer);
output.WriteShort(analyzedLength);
output.WriteBytes(scratch.Bytes, scratch.Offset, scratch.Length);
output.WriteInt(EncodeWeight(iterator.Weight));
if (hasPayloads)
{
for (int i = 0; i < surfaceForm.Length; i++)
{
if (surfaceForm.Bytes[i] == PAYLOAD_SEP)
{
throw new ArgumentException(
"surface form cannot contain unit separator character U+001F; this character is reserved");
}
}
output.WriteShort((short)surfaceForm.Length);
output.WriteBytes(surfaceForm.Bytes, surfaceForm.Offset, surfaceForm.Length);
output.WriteBytes(payload.Bytes, payload.Offset, payload.Length);
}
else
{
output.WriteBytes(surfaceForm.Bytes, surfaceForm.Offset, surfaceForm.Length);
}
Debug.Assert(output.Position == requiredLength, output.Position + " vs " + requiredLength);
writer.Write(buffer, 0, output.Position);
}
count++;
}
writer.Dispose();
// Sort all input/output pairs (required by FST.Builder):
(new OfflineSorter(new AnalyzingComparator(hasPayloads))).Sort(tempInput, tempSorted);
// Free disk space:
tempInput.Delete();
reader = new OfflineSorter.ByteSequencesReader(tempSorted);
var outputs = new PairOutputs <long?, BytesRef>(PositiveIntOutputs.Singleton,
ByteSequenceOutputs.Singleton);
var builder = new Builder <PairOutputs <long?, BytesRef> .Pair>(FST.INPUT_TYPE.BYTE1, outputs);
// Build FST:
BytesRef previousAnalyzed = null;
BytesRef analyzed = new BytesRef();
BytesRef surface = new BytesRef();
IntsRef scratchInts = new IntsRef();
var input = new ByteArrayDataInput();
// Used to remove duplicate surface forms (but we
// still index the hightest-weight one). We clear
// this when we see a new analyzed form, so it cannot
// grow unbounded (at most 256 entries):
var seenSurfaceForms = new HashSet <BytesRef>();
var dedup = 0;
while (reader.Read(scratch))
{
input.Reset(scratch.Bytes, scratch.Offset, scratch.Length);
short analyzedLength = input.ReadShort();
analyzed.Grow(analyzedLength + 2);
input.ReadBytes(analyzed.Bytes, 0, analyzedLength);
analyzed.Length = analyzedLength;
long cost = input.ReadInt();
surface.Bytes = scratch.Bytes;
if (hasPayloads)
{
surface.Length = input.ReadShort();
surface.Offset = input.Position;
}
else
{
surface.Offset = input.Position;
surface.Length = scratch.Length - surface.Offset;
}
if (previousAnalyzed == null)
{
previousAnalyzed = new BytesRef();
previousAnalyzed.CopyBytes(analyzed);
seenSurfaceForms.Add(BytesRef.DeepCopyOf(surface));
}
else if (analyzed.Equals(previousAnalyzed))
{
dedup++;
if (dedup >= maxSurfaceFormsPerAnalyzedForm)
{
// More than maxSurfaceFormsPerAnalyzedForm
// dups: skip the rest:
continue;
}
if (seenSurfaceForms.Contains(surface))
{
continue;
}
seenSurfaceForms.Add(BytesRef.DeepCopyOf(surface));
}
else
{
dedup = 0;
previousAnalyzed.CopyBytes(analyzed);
seenSurfaceForms.Clear();
seenSurfaceForms.Add(BytesRef.DeepCopyOf(surface));
}
// TODO: I think we can avoid the extra 2 bytes when
// there is no dup (dedup==0), but we'd have to fix
// the exactFirst logic ... which would be sort of
// hairy because we'd need to special case the two
// (dup/not dup)...
// NOTE: must be byte 0 so we sort before whatever
// is next
analyzed.Bytes[analyzed.Offset + analyzed.Length] = 0;
analyzed.Bytes[analyzed.Offset + analyzed.Length + 1] = (sbyte)dedup;
analyzed.Length += 2;
Util.Fst.Util.ToIntsRef(analyzed, scratchInts);
//System.out.println("ADD: " + scratchInts + " -> " + cost + ": " + surface.utf8ToString());
if (!hasPayloads)
{
builder.Add(scratchInts, outputs.NewPair(cost, BytesRef.DeepCopyOf(surface)));
}
else
{
int payloadOffset = input.Position + surface.Length;
int payloadLength = scratch.Length - payloadOffset;
BytesRef br = new BytesRef(surface.Length + 1 + payloadLength);
Array.Copy(surface.Bytes, surface.Offset, br.Bytes, 0, surface.Length);
br.Bytes[surface.Length] = PAYLOAD_SEP;
Array.Copy(scratch.Bytes, payloadOffset, br.Bytes, surface.Length + 1, payloadLength);
br.Length = br.Bytes.Length;
builder.Add(scratchInts, outputs.NewPair(cost, br));
}
}
fst = builder.Finish();
//Util.dotToFile(fst, "/tmp/suggest.dot");
success = true;
}
finally
{
if (success)
{
IOUtils.Close(reader, writer);
}
else
{
IOUtils.CloseWhileHandlingException(reader, writer);
}
tempInput.Delete();
tempSorted.Delete();
}
}
private void DownloadDotStatCodelist()
{
IOUtils file = new IOUtils();
ISdmxObjects sdmxObjects = null;
sdmxObjects = GetSdmxObjects();
if (sdmxObjects == null)
return;
file.SaveDotSTATCodelistFile(sdmxObjects.Codelists.First());
}
public override long Decompress(Stream instream, long inLength, Stream outstream)
{
#region Format definition in NDSTEK style
/* Data header (32bit)
Bit 0-3 Reserved
Bit 4-7 Compressed type (must be 1 for LZ77)
Bit 8-31 Size of decompressed data. if 0, the next 4 bytes are decompressed length
Repeat below. Each Flag Byte followed by eight Blocks.
Flag data (8bit)
Bit 0-7 Type Flags for next 8 Blocks, MSB first
Block Type 0 - Uncompressed - Copy 1 Byte from Source to Dest
Bit 0-7 One data byte to be copied to dest
Block Type 1 - Compressed - Copy LEN Bytes from Dest-Disp-1 to Dest
If Reserved is 0: - Default
Bit 0-3 Disp MSBs
Bit 4-7 LEN - 3
Bit 8-15 Disp LSBs
If Reserved is 1: - Higher compression rates for files with (lots of) long repetitions
Bit 4-7 Indicator
If Indicator > 1:
Bit 0-3 Disp MSBs
Bit 4-7 LEN - 1 (same bits as Indicator)
Bit 8-15 Disp LSBs
If Indicator is 1: A(B CD E)(F GH)
Bit 0-3 (LEN - 0x111) MSBs
Bit 4-7 Indicator; unused
Bit 8-15 (LEN- 0x111) 'middle'-SBs
Bit 16-19 Disp MSBs
Bit 20-23 (LEN - 0x111) LSBs
Bit 24-31 Disp LSBs
If Indicator is 0:
Bit 0-3 (LEN - 0x11) MSBs
Bit 4-7 Indicator; unused
Bit 8-11 Disp MSBs
Bit 12-15 (LEN - 0x11) LSBs
Bit 16-23 Disp LSBs
*/
#endregion
long readBytes = 0;
byte type = (byte)instream.ReadByte();
if (type != base.magicByte)
throw new InvalidDataException(String.Format(Main.Get_Traduction("S03"), type.ToString("X")));
byte[] sizeBytes = new byte[3];
instream.Read(sizeBytes, 0, 3);
int decompressedSize = IOUtils.ToNDSu24(sizeBytes, 0);
readBytes += 4;
if (decompressedSize == 0)
{
sizeBytes = new byte[4];
instream.Read(sizeBytes, 0, 4);
decompressedSize = IOUtils.ToNDSs32(sizeBytes, 0);
readBytes += 4;
}
// the maximum 'DISP-1' is still 0xFFF.
int bufferLength = 0x1000;
byte[] buffer = new byte[bufferLength];
int bufferOffset = 0;
int currentOutSize = 0;
int flags = 0, mask = 1;
while (currentOutSize < decompressedSize)
{
// (throws when requested new flags byte is not available)
#region Update the mask. If all flag bits have been read, get a new set.
// the current mask is the mask used in the previous run. So if it masks the
// last flag bit, get a new flags byte.
if (mask == 1)
{
if (readBytes >= inLength)
throw new NotEnoughDataException(currentOutSize, decompressedSize);
flags = instream.ReadByte(); readBytes++;
if (flags < 0)
throw new StreamTooShortException();
mask = 0x80;
}
else
{
mask >>= 1;
}
#endregion
// bit = 1 <=> compressed.
if ((flags & mask) > 0)
{
// (throws when not enough bytes are available)
#region Get length and displacement('disp') values from next 2, 3 or 4 bytes
// read the first byte first, which also signals the size of the compressed block
if (readBytes >= inLength)
throw new NotEnoughDataException(currentOutSize, decompressedSize);
int byte1 = instream.ReadByte(); readBytes++;
if (byte1 < 0)
throw new StreamTooShortException();
int length = byte1 >> 4;
int disp = -1;
if (length == 0)
{
#region case 0; 0(B C)(D EF) + (0x11)(0x1) = (LEN)(DISP)
// case 0:
// data = AB CD EF (with A=0)
// LEN = ABC + 0x11 == BC + 0x11
// DISP = DEF + 1
// we need two more bytes available
if (readBytes + 1 >= inLength)
throw new NotEnoughDataException(currentOutSize, decompressedSize);
int byte2 = instream.ReadByte(); readBytes++;
int byte3 = instream.ReadByte(); readBytes++;
if (byte3 < 0)
throw new StreamTooShortException();
length = (((byte1 & 0x0F) << 4) | (byte2 >> 4)) + 0x11;
disp = (((byte2 & 0x0F) << 8) | byte3) + 0x1;
#endregion
}
else if (length == 1)
{
#region case 1: 1(B CD E)(F GH) + (0x111)(0x1) = (LEN)(DISP)
// case 1:
// data = AB CD EF GH (with A=1)
// LEN = BCDE + 0x111
// DISP = FGH + 1
// we need three more bytes available
if (readBytes + 2 >= inLength)
throw new NotEnoughDataException(currentOutSize, decompressedSize);
int byte2 = instream.ReadByte(); readBytes++;
int byte3 = instream.ReadByte(); readBytes++;
int byte4 = instream.ReadByte(); readBytes++;
if (byte4 < 0)
throw new StreamTooShortException();
length = (((byte1 & 0x0F) << 12) | (byte2 << 4) | (byte3 >> 4)) + 0x111;
disp = (((byte3 & 0x0F) << 8) | byte4) + 0x1;
#endregion
}
else
{
#region case > 1: (A)(B CD) + (0x1)(0x1) = (LEN)(DISP)
// case other:
// data = AB CD
// LEN = A + 1
// DISP = BCD + 1
// we need only one more byte available
if (readBytes >= inLength)
throw new NotEnoughDataException(currentOutSize, decompressedSize);
int byte2 = instream.ReadByte(); readBytes++;
if (byte2 < 0)
throw new StreamTooShortException();
length = ((byte1 & 0xF0) >> 4) + 0x1;
disp = (((byte1 & 0x0F) << 8) | byte2) + 0x1;
#endregion
}
if (disp > currentOutSize)
throw new InvalidDataException(String.Format(Main.Get_Traduction("S04"), disp, currentOutSize.ToString("X"),
instream.Position.ToString("X"), (byte1 >> 4).ToString("X")));
#endregion
int bufIdx = bufferOffset + bufferLength - disp;
for (int i = 0; i < length; i++)
{
byte next = buffer[bufIdx % bufferLength];
bufIdx++;
outstream.WriteByte(next);
buffer[bufferOffset] = next;
bufferOffset = (bufferOffset + 1) % bufferLength;
}
currentOutSize += length;
}
else
{
if (readBytes >= inLength)
throw new NotEnoughDataException(currentOutSize, decompressedSize);
int next = instream.ReadByte(); readBytes++;
if (next < 0)
throw new StreamTooShortException();
outstream.WriteByte((byte)next); currentOutSize++;
buffer[bufferOffset] = (byte)next;
bufferOffset = (bufferOffset + 1) % bufferLength;
}
}
if (readBytes < inLength)
{
// the input may be 4-byte aligned.
if ((readBytes ^ (readBytes & 3)) + 4 < inLength)
throw new TooMuchInputException(readBytes, inLength);
}
return decompressedSize;
}
private void DownloadSDMX()
{
IOUtils file = new IOUtils();
ISdmxObjects sdmxObjects = null;
sdmxObjects = GetSdmxObjects();
if (sdmxObjects != null)
file.SaveSDMXFile(sdmxObjects, sdmxVersion, GetFilename());
}
public override FieldInfos Read(Directory directory, string segmentName, string segmentSuffix, IOContext iocontext)
{
string fileName = IndexFileNames.SegmentFileName(segmentName, "", Lucene40FieldInfosFormat.FIELD_INFOS_EXTENSION);
IndexInput input = directory.OpenInput(fileName, iocontext);
bool success = false;
try
{
CodecUtil.CheckHeader(input, Lucene40FieldInfosFormat.CODEC_NAME, Lucene40FieldInfosFormat.FORMAT_START, Lucene40FieldInfosFormat.FORMAT_CURRENT);
int size = input.ReadVInt32(); //read in the size
FieldInfo[] infos = new FieldInfo[size];
for (int i = 0; i < size; i++)
{
string name = input.ReadString();
int fieldNumber = input.ReadVInt32();
byte bits = input.ReadByte();
bool isIndexed = (bits & Lucene40FieldInfosFormat.IS_INDEXED) != 0;
bool storeTermVector = (bits & Lucene40FieldInfosFormat.STORE_TERMVECTOR) != 0;
bool omitNorms = (bits & Lucene40FieldInfosFormat.OMIT_NORMS) != 0;
bool storePayloads = (bits & Lucene40FieldInfosFormat.STORE_PAYLOADS) != 0;
IndexOptions indexOptions;
if (!isIndexed)
{
indexOptions = IndexOptions.NONE;
}
else if ((bits & Lucene40FieldInfosFormat.OMIT_TERM_FREQ_AND_POSITIONS) != 0)
{
indexOptions = IndexOptions.DOCS_ONLY;
}
else if ((bits & Lucene40FieldInfosFormat.OMIT_POSITIONS) != 0)
{
indexOptions = IndexOptions.DOCS_AND_FREQS;
}
else if ((bits & Lucene40FieldInfosFormat.STORE_OFFSETS_IN_POSTINGS) != 0)
{
indexOptions = IndexOptions.DOCS_AND_FREQS_AND_POSITIONS_AND_OFFSETS;
}
else
{
indexOptions = IndexOptions.DOCS_AND_FREQS_AND_POSITIONS;
}
// LUCENE-3027: past indices were able to write
// storePayloads=true when omitTFAP is also true,
// which is invalid. We correct that, here:
// LUCENENET specific - to avoid boxing, changed from CompareTo() to IndexOptionsComparer.Compare()
if (isIndexed && IndexOptionsComparer.Default.Compare(indexOptions, IndexOptions.DOCS_AND_FREQS_AND_POSITIONS) < 0)
{
storePayloads = false;
}
// DV Types are packed in one byte
byte val = input.ReadByte();
LegacyDocValuesType oldValuesType = GetDocValuesType((sbyte)(val & 0x0F));
LegacyDocValuesType oldNormsType = GetDocValuesType((sbyte)(((int)((uint)val >> 4)) & 0x0F));
IDictionary <string, string> attributes = input.ReadStringStringMap();
if (oldValuesType.GetMapping() != DocValuesType.NONE)
{
attributes[LEGACY_DV_TYPE_KEY] = oldValuesType.ToString();
}
if (oldNormsType.GetMapping() != DocValuesType.NONE)
{
if (oldNormsType.GetMapping() != DocValuesType.NUMERIC)
{
throw new CorruptIndexException("invalid norm type: " + oldNormsType + " (resource=" + input + ")");
}
attributes[LEGACY_NORM_TYPE_KEY] = oldNormsType.ToString();
}
infos[i] = new FieldInfo(name, isIndexed, fieldNumber, storeTermVector, omitNorms, storePayloads, indexOptions, oldValuesType.GetMapping(), oldNormsType.GetMapping(), attributes);
}
CodecUtil.CheckEOF(input);
FieldInfos fieldInfos = new FieldInfos(infos);
success = true;
return(fieldInfos);
}
finally
{
if (success)
{
input.Dispose();
}
else
{
IOUtils.DisposeWhileHandlingException(input);
}
}
}