CStringStream.cc

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#include <cassert>
#include <cstring>

#include "zlib.h"

#include "Alignment/Geners/interface/BZ2Handle.hh"
#include "Alignment/Geners/interface/CStringStream.hh"
#include "Alignment/Geners/interface/IOException.hh"

static void doZlibCompression(const char *data,
                              const unsigned long long len,
                              const bool defl,
                              z_stream_s &strm,
                              char *buffer,
                              const unsigned long long bufLen,
                              std::ostream &sink) {
  assert(buffer);
  assert(bufLen);

  int status = Z_OK;
  strm.next_in = reinterpret_cast<Bytef *>(const_cast<char *>(data));
  strm.avail_in = len;
  do {
    strm.next_out = reinterpret_cast<Bytef *>(buffer);
    strm.avail_out = bufLen;
    status = defl ? deflate(&strm, Z_FINISH) : inflate(&strm, Z_NO_FLUSH);
    assert(status == Z_OK || status == Z_STREAM_END);
    const unsigned have = bufLen - strm.avail_out;
    sink.write(buffer, have);
    if (sink.fail())
      throw gs::IOWriteFailure("In gs::doZlibCompression: sink stream failure");
  } while (strm.avail_out == 0);

  if (defl) {
    assert(strm.avail_in == 0);
    assert(status == Z_STREAM_END);
    assert(deflateReset(&strm) == Z_OK);
  } else
    assert(inflateReset(&strm) == Z_OK);
}

static void doBZ2Compression(const char *data,
                             const unsigned long long len,
                             const bool defl,
                             bz_stream &strm,
                             char *buffer,
                             const unsigned long long bufLen,
                             std::ostream &sink) {
  assert(buffer);
  assert(bufLen);

  int status = BZ_OK;
  strm.next_in = const_cast<char *>(data);
  strm.avail_in = len;
  do {
    strm.next_out = buffer;
    strm.avail_out = bufLen;
    status = defl ? BZ2_bzCompress(&strm, BZ_FINISH) : BZ2_bzDecompress(&strm);
    assert(status == BZ_OK || status == BZ_STREAM_END);
    const unsigned have = bufLen - strm.avail_out;
    sink.write(buffer, have);
    if (sink.fail())
      throw gs::IOWriteFailure("In gs::doBZ2Compression: sink stream failure");
  } while (status != BZ_STREAM_END);
}

namespace gs {
  CStringStream::CStringStream(const CompressionMode m,
                               const int compressionLevel,
                               const unsigned minSizeToCompress,
                               const unsigned bufSize)
      : mode_(m),
        compressionLevel_(compressionLevel),
        minSizeToCompress_(minSizeToCompress),
        // Have a reasonable minimum buffer size to maintain
        // performance even if the user wants to shoot himself
        // in a foot
        comprBuf_(bufSize > 1024U ? bufSize : 1024U),
        sink_(nullptr) {
    this->init(&buf_);
  }

  void CStringStream::setCompressionMode(const CompressionMode newmode) {
    reset();
    mode_ = newmode;
  }

  void CStringStream::reset() {
    clear();
    seekp(0);
    seekg(0);
  }

  void CStringStream::readCompressed(std::istream &in, const unsigned compressionCode, const unsigned long long len) {
    reset();
    if (!len)
      return;

    // Decompress and dump to this string stream
    if (len > readBuf_.size())
      readBuf_.resize(len);
    in.read(&readBuf_[0], len);

    switch (static_cast<CompressionMode>(compressionCode)) {
      case NOT_COMPRESSED:
        this->write(&readBuf_[0], len);
        return;

      case ZLIB: {
        if (!inflator_.get())
          inflator_ = CPP11_auto_ptr<ZlibInflateHandle>(new ZlibInflateHandle());
        doZlibCompression(&readBuf_[0], len, false, inflator_->strm(), &comprBuf_[0], comprBuf_.size(), *this);
      } break;

      case BZIP2: {
        // bzlib2 can not be reset, so we have to make
        // a new inflator every time
        bz_stream strm;
        BZ2InflateHandle h(strm);
        doBZ2Compression(&readBuf_[0], len, false, strm, &comprBuf_[0], comprBuf_.size(), *this);
      } break;

      default:
        assert(!"Unhandled switch case in "
            "CStringStream::readCompressed. "
            "This is a bug. Please report.");
    }
  }

  CStringStream::CompressionMode CStringStream::writeCompressed() {
    // Compress and dump to sink
    assert(sink_);

    unsigned long long len = 0;
    const char *data = buf_.getPutBuffer(&len);
    if (len == 0)
      return NOT_COMPRESSED;

    if (mode_ == NOT_COMPRESSED || len < minSizeToCompress_) {
      sink_->write(data, len);
      return NOT_COMPRESSED;
    }

    switch (mode_) {
      case ZLIB: {
        if (!deflator_.get())
          deflator_ = CPP11_auto_ptr<ZlibDeflateHandle>(new ZlibDeflateHandle(compressionLevel_));
        doZlibCompression(data, len, true, deflator_->strm(), &comprBuf_[0], comprBuf_.size(), *sink_);
      } break;

      case BZIP2: {
        // bzlib2 can not be reset, so we have to make
        // a new deflator every time
        bz_stream strm;
        BZ2DeflateHandle h(strm);
        doBZ2Compression(data, len, true, strm, &comprBuf_[0], comprBuf_.size(), *sink_);
      } break;

      default:
        assert(!"Unhandled switch case in "
            "CStringStream::writeCompressed. "
            "This is a bug. Please report.");
    }

    seekp(0);
    return mode_;
  }

  bool CStringStream::getCompressionModeByName(const char *name, CompressionMode *m) {
    static const char *names[] = {"n", "z", "b"};
    if (!name || !m)
      return false;
    for (unsigned i = 0; i < sizeof(names) / sizeof(names[0]); ++i)
      if (strcasecmp(name, names[i]) == 0) {
        *m = static_cast<CompressionMode>(i);
        return true;
      }
    return false;
  }

  std::string CStringStream::compressionModeName(const CompressionMode m, const bool useShortName) {
    std::string mode;
    switch (m) {
      case NOT_COMPRESSED:
        mode = useShortName ? "n" : "not compressed";
        break;
      case ZLIB:
        mode = useShortName ? "z" : "zlib";
        break;
      case BZIP2:
        mode = useShortName ? "b" : "bzip2";
        break;
      default:
        assert(!"Unhandled switch case in "
            "CStringStream::compressionModeName. "
            "This is a bug. Please report.");
    }
    return mode;
  }
}  // namespace gs