///////////////////////////////////////////////////////
///
/// Read a string from a stream. The string is following
/// by its size
///
inline string ReadStringFromStream(CNcbiIstream& is)
{
string str;
if (!is.good() || is.eof())
return str;
size_t size;
is >> size;
if (!is.good() || is.eof())
return str;
vector<char> buf(size+1, 0);
is.read(&*buf.begin(), size+1);
size_t count = is.gcount();
if (count > 0)
str.append((&*buf.begin())+1, count-1);
return str;
}
void g_GZip_ScanForChunks(CNcbiIstream& is, IChunkHandler& handler)
{
typedef IChunkHandler::TPosition TPos;
// Use our own total counters to avoid 4GB limit
TPos in_total = 0; // Offset in input compressed data
TPos out_total = 0; // Offset in output decompressed data
z_stream strm; // Compressed stream structure
int ret = Z_STREAM_END; // zlib return status
bool initialized = false;
// Default buffer size
size_t in_size = kCompressionDefaultBufSize;
size_t out_size = kCompressionDefaultBufSize * 2;
// Allocate buffers
AutoArray<unsigned char> in_buf_arr(in_size);
unsigned char* in_buf = in_buf_arr.get();
if ( !in_buf ) {
NCBI_THROW(CCoreException, eNullPtr, kEmptyStr);
}
AutoArray<unsigned char> out_buf_arr(out_size);
unsigned char* out_buf = out_buf_arr.get();
if ( !out_buf ) {
NCBI_THROW(CCoreException, eNullPtr, kEmptyStr);
}
try {
IChunkHandler::EAction action = IChunkHandler::eAction_Continue;
// Process all decompressed data in the input stream
while ( is && action != IChunkHandler::eAction_Stop) {
// Get some compressed data
is.read((char*)in_buf, in_size);
size_t nread = (size_t)is.gcount();
if ( !nread ) {
break;
}
// Process all data in the buffer
strm.next_in = in_buf;
strm.avail_in = (unsigned int)nread;
do {
// Next gzip-file?
if (ret == Z_STREAM_END) {
// Save current position
action = handler.OnChunk(in_total, out_total);
if (action == IChunkHandler::eAction_Stop) {
// Stop scanning
break;
}
// (Re)Initialize inflate
strm.zalloc = Z_NULL;
strm.zfree = Z_NULL;
strm.opaque = Z_NULL;
ret = inflateInit2(&strm, 15+16 /* max windowbits + automatic gzip header decoding */);
if (ret != Z_OK) {
throw "inflateInit2() failed: " + string(zError(ret));
}
initialized = true;
}
// We don't need uncompressed data -- discard it
strm.next_out = out_buf;
strm.avail_out = (unsigned int)out_size;
// Decompress
ret = inflate(&strm, Z_SYNC_FLUSH);
if (ret != Z_OK && ret != Z_STREAM_END ) {
// Error
throw "inflate() failed: " + string(zError(ret));
}
// Increase counters
out_total += (out_size - strm.avail_out);
in_total += (nread - strm.avail_in);
nread = strm.avail_in;
// If found end of compressed stream -- cleanup
if (ret == Z_STREAM_END) {
inflateEnd(&strm);
initialized = false;
}
} while (strm.avail_in != 0);
}
if ( initialized ) {
inflateEnd(&strm);
}
}
// Cleanup
catch (string& e) {
if ( initialized ) {
inflateEnd(&strm);
}
NCBI_THROW(CCompressionException, eCompression, e);
}
}