fixed conflicts

1 files changed, 429 insertions, 0 deletions

diff --git a/klm/util/read_compressed.cc b/klm/util/read_compressed.cc
new file mode 100644
index 00000000..b81549e4
--- /dev/null
+++ b/klm/util/read_compressed.cc
@@ -0,0 +1,429 @@
+#include "util/read_compressed.hh"
+
+#include "util/file.hh"
+#include "util/have.hh"
+#include "util/scoped.hh"
+
+#include <algorithm>
+#include <iostream>
+
+#include <assert.h>
+#include <limits.h>
+#include <stdlib.h>
+#include <string.h>
+
+#ifdef HAVE_ZLIB
+#include <zlib.h>
+#endif
+
+#ifdef HAVE_BZLIB
+#include <bzlib.h>
+#endif
+
+#ifdef HAVE_XZLIB
+#include <lzma.h>
+#endif
+
+namespace util {
+
+CompressedException::CompressedException() throw() {}
+CompressedException::~CompressedException() throw() {}
+
+GZException::GZException() throw() {}
+GZException::~GZException() throw() {}
+
+BZException::BZException() throw() {}
+BZException::~BZException() throw() {}
+
+XZException::XZException() throw() {}
+XZException::~XZException() throw() {}
+
+class ReadBase {
+  public:
+    virtual ~ReadBase() {}
+
+    virtual std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) = 0;
+
+  protected:
+    static void ReplaceThis(ReadBase *with, ReadCompressed &thunk) {
+      thunk.internal_.reset(with);
+    }
+
+    static uint64_t &ReadCount(ReadCompressed &thunk) {
+      return thunk.raw_amount_;
+    }
+};
+
+namespace {
+
+// Completed file that other classes can thunk to.  
+class Complete : public ReadBase {
+  public:
+    std::size_t Read(void *, std::size_t, ReadCompressed &) {
+      return 0;
+    }
+};
+
+class Uncompressed : public ReadBase {
+  public:
+    explicit Uncompressed(int fd) : fd_(fd) {}
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      std::size_t got = PartialRead(fd_.get(), to, amount);
+      ReadCount(thunk) += got;
+      return got;
+    }
+
+  private:
+    scoped_fd fd_;
+};
+
+class UncompressedWithHeader : public ReadBase {
+  public:
+    UncompressedWithHeader(int fd, void *already_data, std::size_t already_size) : fd_(fd) {
+      assert(already_size);
+      buf_.reset(malloc(already_size));
+      if (!buf_.get()) throw std::bad_alloc();
+      memcpy(buf_.get(), already_data, already_size);
+      remain_ = static_cast<uint8_t*>(buf_.get());
+      end_ = remain_ + already_size;
+    }
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      assert(buf_.get());
+      std::size_t sending = std::min<std::size_t>(amount, end_ - remain_);
+      memcpy(to, remain_, sending);
+      remain_ += sending;
+      if (remain_ == end_) {
+        ReplaceThis(new Uncompressed(fd_.release()), thunk);
+      }
+      return sending;
+    }
+
+  private:
+    scoped_malloc buf_;
+    uint8_t *remain_;
+    uint8_t *end_;
+
+    scoped_fd fd_;
+};
+
+#ifdef HAVE_ZLIB
+class GZip : public ReadBase {
+  private:
+    static const std::size_t kInputBuffer = 16384;
+  public:
+    GZip(int fd, void *already_data, std::size_t already_size) 
+      : file_(fd), in_buffer_(malloc(kInputBuffer)) {
+      if (!in_buffer_.get()) throw std::bad_alloc();
+      assert(already_size < kInputBuffer);
+      if (already_size) {
+        memcpy(in_buffer_.get(), already_data, already_size);
+        stream_.next_in = static_cast<Bytef *>(in_buffer_.get());
+        stream_.avail_in = already_size;
+        stream_.avail_in += ReadOrEOF(file_.get(), static_cast<uint8_t*>(in_buffer_.get()) + already_size, kInputBuffer - already_size);
+      } else {
+        stream_.avail_in = 0;
+      }
+      stream_.zalloc = Z_NULL;
+      stream_.zfree = Z_NULL;
+      stream_.opaque = Z_NULL;
+      stream_.msg = NULL;
+      // 32 for zlib and gzip decoding with automatic header detection.  
+      // 15 for maximum window size.  
+      UTIL_THROW_IF(Z_OK != inflateInit2(&stream_, 32 + 15), GZException, "Failed to initialize zlib.");
+    }
+
+    ~GZip() {
+      if (Z_OK != inflateEnd(&stream_)) {
+        std::cerr << "zlib could not close properly." << std::endl;
+        abort();
+      }
+    }
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      if (amount == 0) return 0;
+      stream_.next_out = static_cast<Bytef*>(to);
+      stream_.avail_out = std::min<std::size_t>(std::numeric_limits<uInt>::max(), amount);
+      do {
+        if (!stream_.avail_in) ReadInput(thunk);
+        int result = inflate(&stream_, 0);
+        switch (result) {
+          case Z_OK:
+            break;
+          case Z_STREAM_END:
+            {
+              std::size_t ret = static_cast<uint8_t*>(stream_.next_out) - static_cast<uint8_t*>(to);
+              ReplaceThis(new Complete(), thunk);
+              return ret;
+            }
+          case Z_ERRNO:
+            UTIL_THROW(ErrnoException, "zlib error");
+          default:
+            UTIL_THROW(GZException, "zlib encountered " << (stream_.msg ? stream_.msg : "an error ") << " code " << result);
+        }
+      } while (stream_.next_out == to);
+      return static_cast<uint8_t*>(stream_.next_out) - static_cast<uint8_t*>(to);
+    }
+
+  private:
+    void ReadInput(ReadCompressed &thunk) {
+      assert(!stream_.avail_in);
+      stream_.next_in = static_cast<Bytef *>(in_buffer_.get());
+      stream_.avail_in = ReadOrEOF(file_.get(), in_buffer_.get(), kInputBuffer);
+      ReadCount(thunk) += stream_.avail_in;
+    }
+
+    scoped_fd file_;
+    scoped_malloc in_buffer_;
+    z_stream stream_;
+};
+#endif // HAVE_ZLIB
+
+#ifdef HAVE_BZLIB
+class BZip : public ReadBase {
+  public:
+    explicit BZip(int fd, void *already_data, std::size_t already_size) {
+      scoped_fd hold(fd);
+      closer_.reset(FDOpenReadOrThrow(hold));
+      int bzerror = BZ_OK;
+      file_ = BZ2_bzReadOpen(&bzerror, closer_.get(), 0, 0, already_data, already_size);
+      switch (bzerror) {
+        case BZ_OK:
+          return;
+        case BZ_CONFIG_ERROR:
+          UTIL_THROW(BZException, "Looks like bzip2 was miscompiled.");
+        case BZ_PARAM_ERROR:
+          UTIL_THROW(BZException, "Parameter error");
+        case BZ_IO_ERROR:
+          UTIL_THROW(BZException, "IO error reading file");
+        case BZ_MEM_ERROR:
+          throw std::bad_alloc();
+      }
+    }
+
+    ~BZip() {
+      int bzerror = BZ_OK;
+      BZ2_bzReadClose(&bzerror, file_);
+      if (bzerror != BZ_OK) {
+        std::cerr << "bz2 readclose error" << std::endl;
+        abort();
+      }
+    }
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      int bzerror = BZ_OK;
+      int ret = BZ2_bzRead(&bzerror, file_, to, std::min<std::size_t>(static_cast<std::size_t>(INT_MAX), amount));
+      long pos;
+      switch (bzerror) {
+        case BZ_STREAM_END:
+          pos = ftell(closer_.get());
+          if (pos != -1) ReadCount(thunk) = pos;
+          ReplaceThis(new Complete(), thunk);
+          return ret;
+        case BZ_OK:
+          pos = ftell(closer_.get());
+          if (pos != -1) ReadCount(thunk) = pos;
+          return ret;
+        default:
+          UTIL_THROW(BZException, "bzip2 error " << BZ2_bzerror(file_, &bzerror) << " code " << bzerror);
+      }
+    }
+
+  private:
+    scoped_FILE closer_;
+    BZFILE *file_;
+};
+#endif // HAVE_BZLIB
+
+#ifdef HAVE_XZLIB
+class XZip : public ReadBase {
+  private:
+    static const std::size_t kInputBuffer = 16384;
+  public:
+    XZip(int fd, void *already_data, std::size_t already_size) 
+      : file_(fd), in_buffer_(malloc(kInputBuffer)), stream_(), action_(LZMA_RUN) {
+      if (!in_buffer_.get()) throw std::bad_alloc();
+      assert(already_size < kInputBuffer);
+      if (already_size) {
+        memcpy(in_buffer_.get(), already_data, already_size);
+        stream_.next_in = static_cast<const uint8_t*>(in_buffer_.get());
+        stream_.avail_in = already_size;
+        stream_.avail_in += ReadOrEOF(file_.get(), static_cast<uint8_t*>(in_buffer_.get()) + already_size, kInputBuffer - already_size);
+      } else {
+        stream_.avail_in = 0;
+      }
+      stream_.allocator = NULL;
+      lzma_ret ret = lzma_stream_decoder(&stream_, UINT64_MAX, LZMA_CONCATENATED);
+      switch (ret) {
+        case LZMA_OK:
+          break;
+        case LZMA_MEM_ERROR:
+          UTIL_THROW(ErrnoException, "xz open error");
+        default:
+          UTIL_THROW(XZException, "xz error code " << ret);
+      }
+    }
+
+    ~XZip() {
+      lzma_end(&stream_);
+    }
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      if (amount == 0) return 0;
+      stream_.next_out = static_cast<uint8_t*>(to);
+      stream_.avail_out = amount;
+      do {
+        if (!stream_.avail_in) ReadInput(thunk);
+        lzma_ret status = lzma_code(&stream_, action_);
+        switch (status) {
+          case LZMA_OK:
+            break;
+          case LZMA_STREAM_END:
+            UTIL_THROW_IF(action_ != LZMA_FINISH, XZException, "Input not finished yet.");
+            {
+              std::size_t ret = static_cast<uint8_t*>(stream_.next_out) - static_cast<uint8_t*>(to);
+              ReplaceThis(new Complete(), thunk);
+              return ret;
+            }
+          case LZMA_MEM_ERROR:
+            throw std::bad_alloc();
+          case LZMA_FORMAT_ERROR:
+            UTIL_THROW(XZException, "xzlib says file format not recognized");
+          case LZMA_OPTIONS_ERROR:
+            UTIL_THROW(XZException, "xzlib says unsupported compression options");
+          case LZMA_DATA_ERROR:
+            UTIL_THROW(XZException, "xzlib says this file is corrupt");
+          case LZMA_BUF_ERROR:
+            UTIL_THROW(XZException, "xzlib says unexpected end of input");
+          default:
+            UTIL_THROW(XZException, "unrecognized xzlib error " << status);
+        }
+      } while (stream_.next_out == to);
+      return static_cast<uint8_t*>(stream_.next_out) - static_cast<uint8_t*>(to);
+    }
+
+  private:
+    void ReadInput(ReadCompressed &thunk) {
+      assert(!stream_.avail_in);
+      stream_.next_in = static_cast<const uint8_t*>(in_buffer_.get());
+      stream_.avail_in = ReadOrEOF(file_.get(), in_buffer_.get(), kInputBuffer);
+      if (!stream_.avail_in) action_ = LZMA_FINISH;
+      ReadCount(thunk) += stream_.avail_in;
+    }
+
+    scoped_fd file_;
+    scoped_malloc in_buffer_;
+    lzma_stream stream_;
+
+    lzma_action action_;
+};
+#endif // HAVE_XZLIB
+
+class IStreamReader : public ReadBase {
+  public:
+    explicit IStreamReader(std::istream &stream) : stream_(stream) {}
+
+    std::size_t Read(void *to, std::size_t amount, ReadCompressed &thunk) {
+      if (!stream_.read(static_cast<char*>(to), amount)) {
+        UTIL_THROW_IF(!stream_.eof(), ErrnoException, "istream error");
+        amount = stream_.gcount();
+      }
+      ReadCount(thunk) += amount;
+      return amount;
+    }
+
+  private:
+    std::istream &stream_;
+};
+
+enum MagicResult {
+  UNKNOWN, GZIP, BZIP, XZIP
+};
+
+MagicResult DetectMagic(const void *from_void) {
+  const uint8_t *header = static_cast<const uint8_t*>(from_void);
+  if (header[0] == 0x1f && header[1] == 0x8b) {
+    return GZIP;
+  }
+  if (header[0] == 'B' && header[1] == 'Z' && header[2] == 'h') {
+    return BZIP;
+  }
+  const uint8_t xzmagic[6] = { 0xFD, '7', 'z', 'X', 'Z', 0x00 };
+  if (!memcmp(header, xzmagic, 6)) {
+    return XZIP;
+  }
+  return UNKNOWN;
+}
+
+ReadBase *ReadFactory(int fd, uint64_t &raw_amount) {
+  scoped_fd hold(fd);
+  unsigned char header[ReadCompressed::kMagicSize];
+  raw_amount = ReadOrEOF(fd, header, ReadCompressed::kMagicSize);
+  if (!raw_amount)
+    return new Uncompressed(hold.release());
+  if (raw_amount != ReadCompressed::kMagicSize)
+    return new UncompressedWithHeader(hold.release(), header, raw_amount);
+  switch (DetectMagic(header)) {
+    case GZIP:
+#ifdef HAVE_ZLIB
+      return new GZip(hold.release(), header, ReadCompressed::kMagicSize);
+#else
+      UTIL_THROW(CompressedException, "This looks like a gzip file but gzip support was not compiled in.");
+#endif
+    case BZIP:
+#ifdef HAVE_BZLIB
+      return new BZip(hold.release(), header, ReadCompressed::kMagicSize);
+#else
+      UTIL_THROW(CompressedException, "This looks like a bzip file (it begins with BZ), but bzip support was not compiled in.");
+#endif
+    case XZIP:
+#ifdef HAVE_XZLIB
+      return new XZip(hold.release(), header, ReadCompressed::kMagicSize);
+#else
+      UTIL_THROW(CompressedException, "This looks like an xz file, but xz support was not compiled in.");
+#endif
+    case UNKNOWN:
+      break;
+  }
+  try {
+    SeekOrThrow(fd, 0);
+  } catch (const util::ErrnoException &e) {
+    return new UncompressedWithHeader(hold.release(), header, ReadCompressed::kMagicSize);
+  }
+  return new Uncompressed(hold.release());
+}
+
+} // namespace
+
+bool ReadCompressed::DetectCompressedMagic(const void *from_void) {
+  return DetectMagic(from_void) != UNKNOWN;
+}
+
+ReadCompressed::ReadCompressed(int fd) {
+  Reset(fd);
+}
+
+ReadCompressed::ReadCompressed(std::istream &in) {
+  Reset(in);
+}
+
+ReadCompressed::ReadCompressed() {}
+
+ReadCompressed::~ReadCompressed() {}
+
+void ReadCompressed::Reset(int fd) {
+  internal_.reset();
+  internal_.reset(ReadFactory(fd, raw_amount_));
+}
+
+void ReadCompressed::Reset(std::istream &in) {
+  internal_.reset();
+  internal_.reset(new IStreamReader(in));
+}
+
+std::size_t ReadCompressed::Read(void *to, std::size_t amount) {
+  return internal_->Read(to, amount, *this);
+}
+
+} // namespace util