static void openFile_bz2(struct FileHandle_bz2 *fp, const char *path)
{
int err;
fp->fp = fopen(path, "rb");
if (fp->fp == NULL) openFileError(path);
fp->bfp = BZ2_bzReadOpen(&err, fp->fp, 0, 0, NULL, 0);
}
/* tries to re-open the bz stream at the next stream start.
returns 0 on success, -1 on failure. */
int bzReOpen(struct Input *ctx, int *error) {
/* for copying out the last unused part of the block which
has an EOS token in it. needed for re-initialising the
next stream. */
unsigned char unused[BZ_MAX_UNUSED];
void *unused_tmp_ptr = NULL;
int nUnused, i;
BZ2_bzReadGetUnused(error, (BZFILE *)(ctx->fileHandle), &unused_tmp_ptr, &nUnused);
if (*error != BZ_OK) return -1;
/* when bzReadClose is called the unused buffer is deallocated,
so it needs to be copied somewhere safe first. */
for (i = 0; i < nUnused; ++i)
unused[i] = ((unsigned char *)unused_tmp_ptr)[i];
BZ2_bzReadClose(error, (BZFILE *)(ctx->fileHandle));
if (*error != BZ_OK) return -1;
/* reassign the file handle */
ctx->fileHandle = BZ2_bzReadOpen(error, ctx->systemHandle, 0, 0, unused, nUnused);
if (ctx->fileHandle == NULL || *error != BZ_OK) return -1;
return 0;
}
NBBZip2::NBBZip2( QString archive, QString file ) {
int error = 0;
bz2FileName = QString( archive );
if ( not file.isEmpty() ) {
if ( QFileInfo( file ).isDir() ) {
fileName = QDir( file ).filePath( QString( archive ) );
fileName.chop( 4 );
}
else if ( QFileInfo( file ).exists() ) {
QFile::rename( file, file + ".old" );
fileName = QString( file );
}
else {
fileName = QString( file );
}
}
else {
fileName = QString( archive );
fileName.chop( 4 );
}
bzFile = fopen( qPrintable( bz2FileName ), "r" );
bz2 = BZ2_bzReadOpen( &error, bzFile, 0, 0, NULL, 0 );
};
void BzipInputStream::dopen(int fd, const char* mode)
{
assert(0 == m_fp);
int err;
#ifdef _MSC_VER
m_cf = _fdopen(fd, mode);
#else
m_cf = fdopen(fd, mode);
#endif
if (0 == m_cf)
{
std::ostringstream oss;
oss << "fd=" << fd << ", mode=" << mode;
throw OpenFileException("<fd>", oss.str().c_str());
}
m_fp = BZ2_bzReadOpen(&err, m_cf
, 0 // verbosity, 0 will not print msg
, 0 // small
, NULL // unused
, 0 // nUnused
);
if (0 == m_fp)
{
std::ostringstream oss;
oss << "fd=" << fd << ", mode=" << mode << ", err=" << strbzerr(err);
throw OpenFileException("<fd>", oss.str().c_str());
}
}
size_t AFILE_afread(void *ptr, size_t size, size_t count, AFILE *afp)
{
#ifndef DISABLE_BZLIB
int32_t nbuf=0, i;
void *unused_tmp_void=NULL;
char *unused_tmp=NULL;
#endif
switch(afp->c) {
case AFILE_NO_COMPRESSION:
return fread(ptr, size, count, afp->fp);
#ifndef DISABLE_BZLIB
case AFILE_BZ2_COMPRESSION:
while(0 == nbuf &&
!(BZ_STREAM_END == afp->bzerror && 0 == afp->n_unused && feof(afp->fp))) {
nbuf = BZ2_bzRead(&afp->bzerror, afp->bz2, ptr, size*count);
if(BZ_OK == afp->bzerror) {
// return # of bytes
return nbuf;
}
else if(BZ_STREAM_END == afp->bzerror) {
// Get unused
BZ2_bzReadGetUnused(&afp->bzerror, afp->bz2, &unused_tmp_void, &afp->n_unused);
if(BZ_OK != afp->bzerror) AFILE_print_error("Could not BZ2_bzReadGetUnused");
unused_tmp = (char*)unused_tmp_void;
for(i=0;i<afp->n_unused;i++) {
afp->unused[i] = unused_tmp[i];
}
// Close
BZ2_bzReadClose(&afp->bzerror, afp->bz2);
if(BZ_OK != afp->bzerror) AFILE_print_error("Could not BZ2_bzReadClose");
afp->bzerror = BZ_STREAM_END; // set to the stream end for next call to this function
// Open again if necessary
if(0 == afp->n_unused && feof(afp->fp)) {
return nbuf;
}
else {
afp->bz2 = BZ2_bzReadOpen(&afp->bzerror, afp->fp, 0, 0, afp->unused, afp->n_unused);
if(NULL == afp->bz2) AFILE_print_error("Could not open file");
}
}
else {
fprintf(stderr, "nbuf = %d\n", nbuf);
fprintf(stderr, "afp->bzerror = %d\n", afp->bzerror);
AFILE_print_error("Could not read");
}
}
return nbuf;
#endif
case AFILE_GZ_COMPRESSION:
return gzread(afp->gz, ptr, size*count);
break;
default:
AFILE_print_error("Could not recognize compresssion\n");
break;
}
return 0;
}
void bz2streambuf::Open(FILE *f_)
{
f = f_;
if (!write)
bzfile = BZ2_bzReadOpen(&bzerror, f, 0, 0, NULL, 0);
else
bzfile = BZ2_bzWriteOpen(&bzerror, f, 5, 0, 0);
error = (bzerror != BZ_OK);
}
bool Bz2::Open(const std::string &path, Bz2::OpenMode mode)
{
m_errcode = BZ_OK;
if (mode == Bz2::OPEN_WRITE) {
m_fileStream = fopen(path.c_str(), "wb");
m_bzFile = BZ2_bzReadOpen(&m_errcode, m_fileStream, 0, 0, nullptr, 0);
}
else {
m_fileStream = fopen(path.c_str(), "rb");
m_bzFile = BZ2_bzReadOpen(&m_errcode, m_fileStream, 0, 0, nullptr, 0);
}
if (m_errcode != BZ_OK) {
this->Close();
return false;
}
return true;
}
struct Input *inputOpen(const char *name)
{
const char *ext = strrchr(name, '.');
struct Input *ctx = (struct Input *)malloc(sizeof(*ctx));
if (!ctx)
return NULL;
memset(ctx, 0, sizeof(*ctx));
ctx->name = (char *)malloc(strlen(name) + 1);
if (ctx->name) strcpy(ctx->name, name);
if (ext && !strcmp(ext, ".gz")) {
ctx->fileHandle = (void *)gzopen(name, "rb");
ctx->type = Input::gzipFile;
} else if (ext && !strcmp(ext, ".bz2")) {
int error = 0;
ctx->systemHandle = fopen(name, "rb");
if (!ctx->systemHandle) {
fprintf(stderr, "error while opening file %s\n", name);
exit(10);
}
ctx->fileHandle = (void *)BZ2_bzReadOpen(&error, ctx->systemHandle, 0, 0, NULL, 0);
ctx->type = Input::bzip2File;
} else {
int *pfd = (int *)malloc(sizeof(int));
if (pfd) {
if (!strcmp(name, "-")) {
*pfd = STDIN_FILENO;
} else {
int flags = O_RDONLY;
#ifdef O_LARGEFILE
flags |= O_LARGEFILE;
#endif
*pfd = open(name, flags);
if (*pfd < 0) {
free(pfd);
pfd = NULL;
}
}
}
ctx->fileHandle = (void *)pfd;
ctx->type = Input::plainFile;
}
if (!ctx->fileHandle) {
fprintf(stderr, "error while opening file %s\n", name);
exit(10);
}
ctx->buf_ptr = 0;
ctx->buf_fill = 0;
return ctx;
}
/**
* uncompress_bzip2:
* @name: The name of the file to attempt to decompress
*
* Returns: The name of the uncompressed file (in a temporary location) or NULL
* free the returned name after use.
*
* Also see: http://www.bzip.org/1.0.5/bzip2-manual-1.0.5.html
*/
gchar* uncompress_bzip2 ( gchar *name )
{
#ifdef HAVE_BZLIB_H
FILE *ff = g_fopen ( name, "r" );
if ( !ff )
return NULL;
int bzerror;
BZFILE* bf = BZ2_bzReadOpen ( &bzerror, ff, 0, 0, NULL, 0 ); // This should take care of the bz2 file header
if ( bzerror != BZ_OK ) {
BZ2_bzReadClose ( &bzerror, bf );
// handle error
return NULL;
}
GFileIOStream *gios;
GError *error = NULL;
GFile *gf = g_file_new_tmp ( "vik-bz2-tmp.XXXXXX", &gios, &error );
gchar *tmpname = g_file_get_path (gf);
GOutputStream *gos = g_io_stream_get_output_stream ( G_IO_STREAM(gios) );
// Process in arbitary sized chunks
char buf[4096];
bzerror = BZ_OK;
int nBuf;
// Now process the actual compression data
while ( bzerror == BZ_OK ) {
nBuf = BZ2_bzRead ( &bzerror, bf, buf, 4096 );
if ( bzerror == BZ_OK || bzerror == BZ_STREAM_END) {
// do something with buf[0 .. nBuf-1]
if ( g_output_stream_write ( gos, buf, nBuf, NULL, &error ) < 0 ) {
g_critical ( "Couldn't write bz2 tmp %s file due to %s", tmpname, error->message );
g_error_free (error);
BZ2_bzReadClose ( &bzerror, bf );
goto end;
}
}
}
if ( bzerror != BZ_STREAM_END ) {
BZ2_bzReadClose ( &bzerror, bf );
// handle error...
goto end;
} else {
BZ2_bzReadClose ( &bzerror, bf );
g_output_stream_close ( gos, NULL, &error );
}
end:
return tmpname;
#else
return NULL;
#endif
}
static void open_compressed_read(pcu_file* pf)
{
int bzerror;
int verbosity = 0;
int small = 0;
void* unused = NULL;
int nUnused = 0;
pf->bzf = BZ2_bzReadOpen(&bzerror, pf->f, verbosity, small, unused, nUnused);
if (bzerror != BZ_OK)
reel_fail("BZ2_bzReadOpen failed with code %d", bzerror);
}
off64_t _GD_Bzip2Seek(struct _gd_raw_file* file, off64_t count,
gd_type_t data_type, unsigned int mode __gd_unused)
{
struct gd_bzdata *ptr = (struct gd_bzdata *)file->edata;
dtrace("%p, %lli, 0x%X, <unused>", file, (long long)count, data_type);
count *= GD_SIZE(data_type);
if (ptr->base > count) {
/* a backwards seek -- reopen the file */
ptr->bzerror = 0;
BZ2_bzReadClose(&ptr->bzerror, ptr->bzfile);
ptr->bzfile = BZ2_bzReadOpen(&ptr->bzerror, ptr->stream, 0, 0, NULL, 0);
if (ptr->bzfile == NULL || ptr->bzerror != BZ_OK) {
fclose(ptr->stream);
dreturn("%i", -1);
return -1;
}
ptr->pos = ptr->end = 0;
ptr->base = ptr->stream_end = 0;
}
/* seek forward the slow way */
while (ptr->base + ptr->end < count) {
int n;
ptr->bzerror = 0;
n = BZ2_bzRead(&ptr->bzerror, ptr->bzfile, ptr->data,
GD_BZIP_BUFFER_SIZE);
if (ptr->bzerror == BZ_OK || ptr->bzerror == BZ_STREAM_END) {
ptr->base += ptr->end;
ptr->end = n;
} else {
dreturn("%i", -1);
return -1;
}
/* eof */
if (ptr->bzerror != BZ_OK) {
ptr->stream_end = 1;
break;
}
}
ptr->pos = (ptr->bzerror == BZ_STREAM_END && count >= ptr->base + ptr->end) ?
ptr->end : count - ptr->base;
dreturn("%lli", (long long)((ptr->base + ptr->pos) / GD_SIZE(data_type)));
return (ptr->base + ptr->pos) / GD_SIZE(data_type);
}
//----------------------------------------------------
int zu_seek(ZUFILE *f, long offset, int whence)
{
int res = 0;
int bzerror=BZ_OK;
if (whence == SEEK_END) {
return -1; // TODO
}
switch(f->type) { //SEEK_SET, SEEK_CUR
case ZU_COMPRESS_NONE :
res = fseek((FILE*)(f->zfile), offset, whence);
f->pos = ftell((FILE*)(f->zfile));
break;
case ZU_COMPRESS_GZIP :
if (whence == SEEK_SET) {
res = gzseek((gzFile)(f->zfile), offset, whence);
}
else { // !!! BUG with SEEK_CUR in ZLIB !!!
int p1 = gztell((gzFile)(f->zfile));
res = gzseek((gzFile)(f->zfile), p1+offset, SEEK_SET);
}
f->pos = gztell((gzFile)(f->zfile));
if (res >= 0)
res = 0;
break;
#ifndef __ANDROID__
case ZU_COMPRESS_BZIP :
if (whence==SEEK_SET && offset >= f->pos) {
res = zu_bzSeekForward(f, offset-f->pos);
}
else if (whence==SEEK_CUR) {
res = zu_bzSeekForward(f, offset);
}
else { // BAD : reopen file
BZ2_bzReadClose (&bzerror,(BZFILE*)(f->zfile));
bzerror=BZ_OK;
rewind(f->faux);
f->pos = 0;
f->zfile = (void *) BZ2_bzReadOpen(&bzerror,f->faux,0,0,NULL,0);
if (bzerror != BZ_OK) {
BZ2_bzReadClose (&bzerror,(BZFILE*)(f->zfile));
fclose(f->faux);
f->zfile = NULL;
f->ok = 0;
}
res = zu_bzSeekForward(f, offset);
}
break;
#endif
}
return res;
}
void BZ2Stream::startRead() {
bzfile_ = BZ2_bzReadOpen(&bzerror_, getFilePointer(), verbosity_, 0, getUnused(), getUnusedLength());
switch (bzerror_) {
case BZ_OK: break;
default: {
BZ2_bzReadClose(&bzerror_, bzfile_);
throw BagException("Error opening file for reading compressed stream");
}
}
clearUnused();
}
VISIBILITY_ENABLE
#include "ttyrec.h"
VISIBILITY_DISABLE
#include "stream.h"
#include "error.h"
#include "gettext.h"
#define ERRORMSG(x) do if (write(fd,(x),strlen(x))) {} while(0)
#define BUFFER_SIZE 32768
#if (defined HAVE_LIBBZ2) || (defined SHIPPED_LIBBZ2)
static void read_bz2(int f, int fd, const char *arg)
{
BZFILE* b;
int nBuf;
char buf[BUFFER_SIZE];
int bzerror;
b = BZ2_bzReadOpen(&bzerror, fdopen(f,"rb"), 0, 0, NULL, 0);
if (bzerror != BZ_OK)
{
BZ2_bzReadClose(&bzerror, b);
// error
ERRORMSG(_("Invalid/corrupt .bz2 file.\n"));
close(fd);
return;
}
bzerror = BZ_OK;
while (bzerror == BZ_OK)
{
nBuf = BZ2_bzRead(&bzerror, b, buf, BUFFER_SIZE);
if (write(fd, buf, nBuf)!=nBuf)
{
BZ2_bzReadClose(&bzerror, b);
close(fd);
return;
}
}
if (bzerror != BZ_STREAM_END)
{
BZ2_bzReadClose(&bzerror, b);
// error
ERRORMSG("\033[0m");
ERRORMSG(_("bzip2: Error during decompression.\n"));
}
else
BZ2_bzReadClose(&bzerror, b);
close(fd);
}
bool MANFrame::Decompress(const wxString& filename, const wxString& tmpfile)
{
// open file
FILE* f = fopen(filename.mb_str(), "rb");
if (!f)
{
return false;
}
// open BZIP2 stream
int bzerror;
BZFILE* bz = BZ2_bzReadOpen(&bzerror, f, 0, 0, 0L, 0);
if (!bz || bzerror != BZ_OK)
{
fclose(f);
return false;
}
// open output file
FILE* fo = fopen(tmpfile.mb_str(), "wb");
if (!fo)
{
fclose(f);
return false;
}
// read stream writing to uncompressed file
char buffer[2048];
while (bzerror != BZ_STREAM_END)
{
int read_bytes = BZ2_bzRead(&bzerror, bz, buffer, 2048);
if (bzerror != BZ_OK && bzerror != BZ_STREAM_END)
{
BZ2_bzReadClose(&bzerror, bz);
fclose(fo);
fclose(f);
return false;
}
fwrite(buffer, read_bytes, 1, fo);
}
BZ2_bzReadClose(&bzerror, bz);
fclose(fo);
fclose(f);
return true;
}
bool QTarBZip2Decompressor::decompressToFiles()
{
QString root = mPathSrc + QDir::separator() + mArchiveFileName;
const std::string tbz2Filename = root.toStdString();
const std::string extractTo = mPathDest.toStdString();
FILE *tbz2File = fopen(tbz2Filename.c_str(), "rb");
int bzError;
const int BUF_SIZE = 10000;
// char* buf = new char[BUF_SIZE];
boost::scoped_array< char > buf ( new char[BUF_SIZE] );
BZFILE *pBz = BZ2_bzReadOpen(&bzError, tbz2File, 0, 0, 0, 0);
if ( bzError != BZ_OK ) {
qDebug() << "bzError != BZ_OK";
BZ2_bzReadClose( &bzError, pBz );
//delete[] buf;
return false;
}
const QString tarFilename = root.section( ".bz2", 0, 0 );
QFile tbz2FileTmp( tarFilename );
if( !tbz2FileTmp.open( QIODevice::WriteOnly ) ) {
BZ2_bzReadClose( &bzError, pBz );
//delete[] buf;
return false;
}
bzError = BZ_OK;
while ( bzError == BZ_OK ) {
ssize_t bytesRead = BZ2_bzRead ( &bzError, pBz, buf.get(), BUF_SIZE );
if ( bzError == BZ_OK )
// fwrite (buf , 1 , bytesRead , tbz2FileTmp );
tbz2FileTmp.write( buf.get(), bytesRead );
}
BZ2_bzReadClose ( &bzError, pBz );
const std::string tarFilename2 = tarFilename.toStdString();
TAR *pTar;
tar_open(&pTar, const_cast< char* > ( tarFilename2.c_str() ), NULL, O_RDONLY, 0644, TAR_GNU);
tar_extract_all( pTar, const_cast< char* > ( extractTo.c_str() ) );
close(tar_fd(pTar));
QFile::remove( tarFilename );
//delete[] buf;
return true;
}
extern char get_header_tar_bz2(archive_handle_t *archive_handle)
{
BZ2_bzReadOpen(archive_handle->src_fd, NULL, 0);
archive_handle->read = read_bz2;
archive_handle->seek = seek_by_char;
archive_handle->offset = 0;
while (get_header_tar(archive_handle) == EXIT_SUCCESS);
/* Cleanup */
BZ2_bzReadClose();
/* Can only do one tar.bz2 per archive */
return(EXIT_FAILURE);
}
CoinBzip2FileInput (const std::string &fileName):
CoinGetslessFileInput (fileName), f_ (0), bzf_ (0)
{
int bzError = BZ_OK;
readType_="bzlib";
f_ = fopen (fileName.c_str (), "r");
if (f_ != 0)
bzf_ = BZ2_bzReadOpen (&bzError, f_, 0, 0, 0, 0);
if (f_ == 0 || bzError != BZ_OK || bzf_ == 0)
throw CoinError ("Could not open file for reading!",
"CoinBzip2FileInput",
"CoinBzip2FileInput");
}
void *
bopen (const char *filename, const char *mode)
{
struct fhandle *f = &fhandle;
f->file1 = fopen (filename, mode);
if (! f->file1)
return NULL;
f->file2 = BZ2_bzReadOpen (&bzerror, f->file1, 0, 0, NULL, 0);
if (bzerror != BZ_OK)
{
errno = bzerror;
bclose (f);
return NULL;
}
return f;
}
NBBZip2::NBBZip2( QString archive, NBBZip2::Mode openmode, QString file ) {
NBBZip2::Mode mode = openmode;
int error = 0;
switch( mode ) {
case NBBZip2::READ : {
bz2FileName = QString( archive );
if ( not file.isEmpty() ) {
if ( QFileInfo( file ).isDir() ) {
fileName = QDir( file ).filePath( QString( archive ) );
fileName.chop( 4 );
}
else if ( QFileInfo( file ).exists() ) {
QFile::rename( file, file + ".old" );
fileName = QString( file );
}
else {
fileName = QString( file );
}
}
else {
fileName = QString( archive );
fileName.chop( 4 );
}
bzFile = fopen( qPrintable( bz2FileName ), "r" );
bz2 = BZ2_bzReadOpen( &error, bzFile, 0, 0, NULL, 0 );
break;
}
case NBBZip2::WRITE : {
bz2FileName = QString( archive );
fileName = QString( file );
bzFile = fopen( qPrintable( bz2FileName ), "w" );
bz2 = BZ2_bzWriteOpen( &error, bzFile, 9, 0, 30 );
break;
}
}
};
/* Initialize decompression library (if needed)
0=success, nonzero means error during initialization
*/
int cm_init(gzFile in, int cm)
{
infile = in; /* save gzFile for reading/cleanup */
switch (cm)
{
#ifdef ENABLE_BZ2
case CM_BZ2:
bzfile = BZ2_bzReadOpen(&bzerror, in, 0, 0, NULL, 0);
return bzerror;
#endif
#ifdef ENABLE_LZMA
case CM_LZMA:
return lzma_init(in, &lzmaFile);
#endif
default: /* CM_NONE, CM_GZ */
return 0; /* success */
}
}
void ExtractFile(int id, char *fs)
{
FILE *out; uint i, s; char fn[256] = "bcpxtract\\\0";
char *min, *mout, *ws; uint os, sws; int be; BZFILE *bz;
if(!file) return;
strcat_s(fn, 255, fs);
out = fopen(fn, "wb");
if(!out) return;
fseek(file, fent[id].offset, SEEK_SET);
s = fent[id].endos - fent[id].offset;
switch(fent[id].form)
{
case 1: // Uncompressed
for(i = 0; i < s; i++)
fputc(fgetc(file), out);
break;
case 2: // Zero-sized file
break;
case 3: // bzip2-compressed file
mout = malloc(fent[id].size);
bz = BZ2_bzReadOpen(&be, file, 0, 0, NULL, 0);
if(be != BZ_OK) fErr(-822, "Failed to initialize bzip2 decompression.");
BZ2_bzRead(&be, bz, mout, fent[id].size);
if((be != BZ_OK) && (be != BZ_STREAM_END)) fErr(-872, "Failed to decompress bzip2 file.");
BZ2_bzReadClose(&be, bz);
fwrite(mout, fent[id].size, 1, out);
free(mout);
break;
case 4: // LZRW3-compressed file
ws = (char*)malloc(MEM_REQ);
min = (char*)malloc(s);
mout = (char*)malloc(os = fent[id].size);
fread(min, s, 1, file);
compress(COMPRESS_ACTION_DECOMPRESS, ws, min, s, mout, &os);
if(fent[id].size != os)
MessageBox(hwnd, "The decompressed sizes in the file table and from the decompression algorithm are different.", title, 48);
fwrite(mout, fent[id].size, 1, out);
free(ws); free(min); free(mout);
break;
}
fclose(out);
}
static struct gd_bzdata *_GD_Bzip2DoOpen(int dirfd, struct _gd_raw_file* file)
{
int fd;
struct gd_bzdata *ptr;
dtrace("%i, %p", dirfd, file);
if ((ptr = (struct gd_bzdata *)malloc(sizeof(struct gd_bzdata))) == NULL) {
dreturn("%p", NULL);
return NULL;
}
if ((fd = gd_OpenAt(file->D, dirfd, file->name, O_RDONLY, 0666)) == -1) {
free(ptr);
dreturn("%p", NULL);
return NULL;
}
if ((ptr->stream = fdopen(fd, "rb")) == NULL) {
close(fd);
free(ptr);
dreturn("%p", NULL);
return NULL;
}
ptr->bzerror = ptr->stream_end = 0;
ptr->bzfile = BZ2_bzReadOpen(&ptr->bzerror, ptr->stream, 0, 0, NULL, 0);
if (ptr->bzfile == NULL || ptr->bzerror != BZ_OK) {
fclose(ptr->stream);
free(ptr);
dreturn("%p", NULL);
return NULL;
}
ptr->pos = ptr->end = 0;
ptr->base = 0;
dreturn("%p", ptr);
return ptr;
}
//----------------------------------------------------------------------------------
// Open the file
bool CFastqReader::OpenFiles()
{
if(in || in_gzip || in_bzip2)
return false;
// Uncompressed file
if(mode == m_plain)
{
if((in = fopen(input_file_name.c_str(), "rb")) == NULL)
return false;
}
// Gzip-compressed file
else if(mode == m_gzip)
{
if((in_gzip = gzopen(input_file_name.c_str(), "rb")) == NULL)
return false;
gzbuffer(in_gzip, gzip_buffer_size);
}
// Bzip2-compressed file
else if(mode == m_bzip2)
{
in = fopen(input_file_name.c_str(), "rb");
if(!in)
return false;
setvbuf(in, NULL, _IOFBF, bzip2_buffer_size);
if((in_bzip2 = BZ2_bzReadOpen(&bzerror, in, 0, 0, NULL, 0)) == NULL)
{
fclose(in);
return false;
}
}
// Reserve via PMM
pmm_fastq->reserve(part);
part_filled = 0;
return true;
}
int fsReadCompressed(FILESYSTEM_FILE *f, void *data, int len) {
BZFILE *bzf;
int err, back;
void *buf;
if (!f)
return -1;
if (!(bzf = BZ2_bzReadOpen(&err, f->fp, 0, 0, NULL, 0)))
return -1;
BZ2_bzRead(&err, bzf, data, len);
if (err != BZ_STREAM_END) {
BZ2_bzReadClose(&err, bzf);
return -1;
}
BZ2_bzReadGetUnused(&err, bzf, &buf, &back);
fseek(f->fp, back * -1, SEEK_CUR);
f->pos = ftell(f->fp) - f->offset;
BZ2_bzReadClose(&err, bzf);
return 0;
}
static struct bz2_file *bz2_fd_open(int fd)
{
struct bz2_file *b = NULL;
FILE* f;
int bzerror;
f = fdopen (fd, "r" );
if (f) {
b = malloc(sizeof(struct bz2_file));
b->f = f;
b->file = BZ2_bzReadOpen(&bzerror, f, 0, 0, NULL, 0);
b->eof = false;
if (bzerror != BZ_OK) {
oscap_seterr(OSCAP_EFAMILY_OSCAP, "Could not build BZ2FILE from %s: %s",
BZ2_bzerror(b->file, &bzerror));
BZ2_bzReadClose(&bzerror, b->file);
free(b);
b = NULL;
}
}
return b;
}
/* Binding to libbzip2's BZ2_bzReadOpen method */
int lbz_read_open(lua_State *L) {
size_t len;
const char *fname = lua_tolstring(L, 1, &len);
FILE *f = fopen(fname, "rb");
if (f == NULL)
return luaL_error(L, "Failed to fopen %s", fname);
int bzerror;
lbz_state *state = (lbz_state *) lua_newuserdata(L, sizeof(lbz_state));
state->bz_stream = BZ2_bzReadOpen(&bzerror, f, 0, 0, NULL, 0);
state->f = f;
lbz_buffer_init(state);
luaL_getmetatable(L, LBZ_STATE_META);
lua_setmetatable(L, -2);
if (bzerror != BZ_OK)
lua_pushnil(L);
return 1;
}
DumpReader::DumpReader(const std::string &dump)
: m_dump(0), m_bz(0), m_dumpSize(0), m_bzStatus(BZ_OK)
{
m_dump = fopen(dump.c_str(), "r");
if (!m_dump) {
throwErrno();
}
int status;
m_bz = BZ2_bzReadOpen(&status, m_dump, 0, 0, 0, 0);
if (status) {
throw std::logic_error("bzip error");
}
if (fseek(m_dump, 0, SEEK_END) ||
-1 == (m_dumpSize = ftell(m_dump)) ||
fseek(m_dump, 0, SEEK_SET)) {
throwErrno();
}
}
struct osm_planet *osm_planet_open(const char *filename)
{
struct osm_planet *osf = calloc(1, sizeof(struct osm_planet));
int bzerror;
if( !(osf->fp = fopen(filename, "rb")))
{
fprintf(stderr, "osm_planet_open(): Unable to open file <%s>: %s\n", filename,
strerror(errno));
goto open_failed;
}
osf->bzfp = BZ2_bzReadOpen(&bzerror, osf->fp, 1, 0, NULL, 0);
if(bzerror != BZ_OK)
{
fprintf(stderr, "osm_planet_open(): Unable to open compressed file with bzip2: %d\n", bzerror);
goto open_failed;
}
pthread_mutex_init(&osf->drained_mutex, NULL);
pthread_mutex_init(&osf->filled_mutex, NULL);
pthread_cond_init(&osf->drained_signal, NULL);
pthread_cond_init(&osf->filled_signal, NULL);
if(pthread_create(&osf->file_read_thread, NULL, start_file_read_thread, osf) != 0)
{
fprintf(stderr, "osm_planet_open(): Unable to start file read thread\n");
goto open_failed;
}
return osf;
open_failed:
free(osf);
return NULL;
}
static void read_bz2(int f, int fd, char *arg)
{
BZFILE* b;
int nBuf;
char buf[BUFFER_SIZE];
int bzerror;
b = BZ2_bzReadOpen ( &bzerror, fdopen(f,"rb"), 0, 0, NULL, 0 );
if (bzerror != BZ_OK) {
BZ2_bzReadClose ( &bzerror, b );
// error
ERRORMSG(_("Invalid/corrupt .bz2 file.\n"));
close(fd);
return;
}
bzerror = BZ_OK;
while (bzerror == BZ_OK) {
nBuf = BZ2_bzRead ( &bzerror, b, buf, BUFFER_SIZE);
if (write(fd, buf, nBuf)!=nBuf)
{
BZ2_bzReadClose ( &bzerror, b );
close(fd);
return;
}
}
if (bzerror != BZ_STREAM_END) {
BZ2_bzReadClose ( &bzerror, b );
// error
ERRORMSG("\033[0m");
ERRORMSG(_("bzip2: Error during decompression.\n"));
} else {
BZ2_bzReadClose ( &bzerror, b );
}
close(fd);
}