// TODO: recycle ptr!
void load() {
is_loaded = true;
adjfilesize = get_filesize(filename_adj);
edatafilesize = get_filesize(filename_edata);
bool async_inedgedata_loading = !svertex_t().computational_edges();
#ifdef SUPPORT_DELETIONS
async_inedgedata_loading = false; // Currently we encode the deleted status of an edge into the edge value (should be changed!),
// so we need the edge data while loading
#endif
//preada(adjf, adjdata, adjfilesize, 0);
adj_session = iomgr->open_session(filename_adj, true);
iomgr->managed_malloc(adj_session, &adjdata, adjfilesize, 0);
adj_stream_session = streaming_task(iomgr, adj_session, adjfilesize, (char**) &adjdata);
iomgr->launch_stream_reader(&adj_stream_session);
/* Initialize edge data asynchonous reading */
if (!only_adjacency) {
edata_iosession = iomgr->open_session(filename_edata, false);
iomgr->managed_malloc(edata_iosession, &edgedata, edatafilesize, 0);
if (async_inedgedata_loading) {
iomgr->managed_preada_async(edata_iosession, &edgedata, edatafilesize, 0);
} else {
iomgr->managed_preada_now(edata_iosession, &edgedata, edatafilesize, 0);
}
}
}
int do_files_differ(
const char* filename1,
const char* filename2,
bool* result_out
)
{
if(!filename1 || !filename2 || !result_out)
{
return -1;
}
size_t file1size = 0;
size_t file2size = 0;
if(get_filesize(filename1, &file1size) || get_filesize(filename2, &file2size))
{
return -1;
}
if(file1size == file2size)
{
uint8_t* buffer1 = calloc(file1size, 1);
uint8_t* buffer2 = calloc(file2size, 1);
if(read_file_into_buffer(filename1, buffer1, file1size))
{
free(buffer1);
free(buffer2);
return -1;
}
if(read_file_into_buffer(filename2, buffer2, file2size))
{
free(buffer1);
free(buffer2);
return -1;
}
*result_out = (memcmp(buffer1, buffer2, file1size) != 0);
free(buffer1);
free(buffer2);
return 0;
}
else
{
*result_out = true;
return 0;
}
// Should not reach here
return -1;
}
int encode_steg(char *file_cont, char *file_data,
char *file_output, unsigned char *key)
{
FILE *fpc, *fpd, *fpo;
unsigned char digest[16];
unsigned long max_hide=0;
//clock_t c1, c2;
// Open files
if((fpc = fopen(file_cont, "rb")) == NULL) {
fprintf(stderr, "Cannot open container file!\n");
return(-1);
}
if((fpd = fopen(file_data, "rb")) == NULL) {
fprintf(stderr, "Cannot open data file!\n");
return(-1);
}
if((fpo = fopen(file_output, "wb")) == NULL) {
fprintf(stderr, "Cannot open output file!\n");
return(-1);
}
// Make sure the data will fit in the container
max_hide = get_max_hide(get_filesize(fpc)-STARTBYTE-(sizeof(struct stash_hdr)*8));
if(max_hide < get_filesize(fpd)) {
fprintf(stderr, "Error! Data file cannot fit in %s; %d bytes max!\n",
file_cont, (int)max_hide);
return(-1);
}
// Get MD5 Checksum of key
MD5String(key, digest);
// Seed the PRNG with the md5 checksum of the key
prng_seed(digest);
// Encode
//c1 = clock();
encode_file(fpc, fpd, fpo);
//c2 = clock();
//printf("%f\n", get_speed(c1,c2));
//system("PAUSE");
// Close files
fclose(fpc);
fclose(fpd);
fclose(fpo);
return(0);
}
/* Run multiple compression tests on data stored in a file */
int test_compress_file(char *file_name)
{
int ret = IGZIP_COMP_OK;
uint32_t in_size;
uint8_t *in_buf = NULL;
FILE *in_file = NULL;
in_file = fopen(file_name, "rb");
if (!in_file)
return FILE_READ_FAILED;
in_size = get_filesize(in_file);
if (in_size != 0) {
in_buf = malloc(in_size);
if (in_buf == NULL)
return MALLOC_FAILED;
fread(in_buf, 1, in_size, in_file);
}
ret |= test_compress_stateless(in_buf, in_size);
ret |= test_compress(in_buf, in_size, NO_FLUSH);
ret |= test_compress(in_buf, in_size, SYNC_FLUSH);
ret |= test_flush(in_buf, in_size);
if (ret)
printf("Failed on file %s\n", file_name);
if (in_buf != NULL)
free(in_buf);
return ret;
}
int main(int argc, char *argv[])
{
FILE *in = NULL;
unsigned char *in_buf = NULL;
uint64_t in_file_size;
if (argc != 2) {
fprintf(stderr, "Usage: isal_fuzz_inflate <infile>\n");
exit(1);
}
in = fopen(argv[1], "rb");
if (!in) {
fprintf(stderr, "Can't open %s for reading\n", argv[1]);
exit(1);
}
in_file_size = get_filesize(in);
in_buf = malloc(in_file_size);
if (in_buf == NULL) {
fprintf(stderr, "Failed to malloc input and outputs buffers\n");
exit(1);
}
fread(in_buf, 1, in_file_size, in);
return LLVMFuzzerTestOneInput(in_buf, in_file_size);
}
/* returns in a human-readable format the file size */
static char *tag_file_size (int argc, char *argv[])
{
if (argc >= 1) {
char *filename = process_text (argv[0]);
int size = get_filesize (filename);
char format[256];
/* add a dependency */
if (size >= 0)
add_deps (filename);
/* make the file size in a human-readable format */
if (size < 0)
sprintf (format, "%d", size);
else if (size < 1024)
sprintf (format, "%d byte%c", size, size == 1 ? 0 : 's');
else if (size < 1024 * 1024)
sprintf (format, "%0.1f KB", (float)size / 1024.0);
else if (size < 1024 * 1024 * 1024)
sprintf (format, "%0.2f MB", (float)size / 1024.0 / 1024.0);
else
sprintf (format, "%0.2f GB", (float)size / 1024.0 / 1024.0 / 1024.0);
free (filename);
return strdup (format);
}
else
return NULL;
}
char *get_codebuf_from_filepath(const char *filepath) {
FILE *fp = NULL;
char *codebuf = NULL;
long fsize = 0;
if (filepath == NULL) {
return NULL;
}
fp = fopen(filepath, "rb");
if (fp == NULL) {
return NULL;
}
fsize = get_filesize(fp);
if (fsize == 0) {
fclose(fp);
return NULL;
}
codebuf = (char *) getseg(fsize + 1);
memset(codebuf, 0, fsize + 1);
if (fread(codebuf, 1, fsize, fp) == -1) {
free(codebuf);
fclose(fp);
}
fclose(fp);
return codebuf;
}
//
// Read a file and alloc a buffer for it
//
uint8_t* easy_readfile(const char *filename, int *file_size)
{
int actual;
int fd;
uint8_t *buf;
*file_size = get_filesize(filename);
printf("name=%s, size=%d\n", filename, *file_size);
fd = open(filename, O_RDONLY, 0);
if (fd == -1) {
return NULL;
}
if(! (buf = malloc(*file_size)) ) {
return NULL;
}
actual = read(fd, buf, *file_size);
close(fd);
*file_size = actual;
return buf;
}
void encode_file(FILE *fpc, FILE *fpd, FILE *fpo) {
size_t n, x;
char cont[CONTSIZE], data[DATASIZE];
struct stash_hdr shdr = {0};
// Write restricted area
n = fread(cont, 1, STARTBYTE, fpc);
fwrite(cont, 1, (int)n, fpo);
// Write header
shdr.len = get_filesize(fpd);
memset(cont, 0, sizeof(cont));
n = fread(cont, 1, sizeof(struct stash_hdr)<<3, fpc);
encode_data(cont, (int)n, (unsigned char *)&shdr, sizeof(struct stash_hdr), 0);
fwrite(cont, 1, n, fpo);
// Write data
while((n = fread(cont, 1, sizeof(cont), fpc))) {
if((x = fread(data, 1, n>>3, fpd)) > 0)
encode_data(cont, (int)x<<3, data, (int)x, 1);
fwrite(cont, 1, (int)n, fpo);
}
return;
}
int main(int argc, char *argv[])
{
FILE *fp;
u8 bfr[ALIGNMENT];
get_args(argc, argv);
elf_size = get_filesize(elf_name);
elf = mmap_file(elf_name);
parse_elf();
meta_header_size = 0x80 + ehdr.e_phnum * (0x30 + 0x20 + 0x60) + 0x30;
info_offset = 0x70;
elf_offset = 0x90;
phdr_offset = elf_offset + ehdr.e_ehsize;
sec_offset = round_up(phdr_offset + ehdr.e_phentsize * ehdr.e_phnum, ALIGNMENT);
version_offset = round_up(sec_offset + ehdr.e_phnum * 0x20, ALIGNMENT);
ctrl_offset = round_up(version_offset + 0x10, ALIGNMENT);
meta_offset = round_up(ctrl_offset + 0x70, ALIGNMENT);
header_size = round_up(meta_offset + meta_header_size, 0x80);
if (compression)
compress_elf();
else
fill_phdr_map();
build_sce_hdr();
build_info_hdr();
build_ctrl_hdr();
build_sec_hdr();
build_version_hdr();
build_meta_hdr();
self = malloc(header_size + elf_size);
memset(self, 0, header_size + elf_size);
build_hdr();
write_elf();
calculate_hashes();
sign_hdr();
sce_encrypt_data(self);
sce_encrypt_header(self, &ks);
fp = fopen(self_name, "wb");
if (fp == NULL)
fail("fopen(%s) failed", self_name);
if (fwrite(self, header_size + compressed_size, 1, fp) != 1)
fail("unable to write self");
memset(bfr, 0, sizeof bfr);
fwrite(bfr, round_up(compressed_size, ALIGNMENT) - compressed_size, 1, fp);
fclose(fp);
return 0;
}
//@imgVersion: if success, then 0--> oldest version; 1-->img header + n * (item header + item body); 2 --> img header + n * item header + n * item body
static int _img_unpack_check_img_header(FILE* fdResImg, const char* const path_src,
int needCheckCrc, AmlResImgHead_t* pImgHead, int* imgVersion)
{
int ret = 0;
const unsigned ImgFileSz = get_filesize(path_src);
if(ImgFileSz <= IMG_HEAD_SZ){
errorP("file size 0x%x too small\n", ImgFileSz);
return __LINE__;
}
unsigned thisReadSz = ITEM_READ_BUF_SZ > ImgFileSz ? ImgFileSz : ITEM_READ_BUF_SZ;
unsigned actualReadSz = 0;
actualReadSz = fread(pImgHead, 1, thisReadSz, fdResImg);
if(actualReadSz != thisReadSz){
errorP("Want to read 0x%x, but only read 0x%x\n", thisReadSz, actualReadSz);
return __LINE__;
}
if(!strncmp(AML_RES_IMG_V1_MAGIC, (char*)pImgHead->magic, AML_RES_IMG_V1_MAGIC_LEN))
{//new version magic matched
if(ImgFileSz != pImgHead->imgSz){
errorP("error, image size in head 0x%x != fileSz 0x%x\n", pImgHead->imgSz, ImgFileSz);
return __LINE__;
}
if(AML_RES_IMG_VERSION_V2 < pImgHead->version){
errorP("Error, version 0x%x not supported\n", pImgHead->version);
return __LINE__;
}
*imgVersion = pImgHead->version;
if(needCheckCrc)
{
ret = check_img_crc(fdResImg, 4, pImgHead->crc);
if(ret){
errorP("Error when check crc\n");
return __LINE__;
}
}
unsigned ImgHeadSz = IMG_HEAD_SZ;
if(AML_RES_IMG_VERSION_V2 == pImgHead->version) ImgHeadSz += pImgHead->imgItemNum * ITEM_HEAD_SZ;
fseek(fdResImg, ImgHeadSz, SEEK_SET);//seek escape the image header to prepare for reading item header
}
else
{
AmlResItemHead_t* pItemHeadInfo = (AmlResItemHead_t*)pImgHead;
debugP("magic error, try old version image.\n");
if(IH_MAGIC != pItemHeadInfo->magic){
errorP("magic err, old version image header not item header!\n");
return __LINE__;
}
*imgVersion = 0;
fseek(fdResImg, 0, SEEK_SET);//seek escape the image header to prepare for reading item header
}
debugP("res-img ver is 0x%x\n", *imgVersion);
return 0;
}
box_param_t * gene_boxbyType( int fd, Byte8_t offset, Byte8_t length, char TBox[])
{
Byte8_t pos;
Byte_t *data;
Byte8_t boxlen, headlen;
char *boxtype;
box_param_t *foundbox;
if( length==0){ /* set the max length*/
if( (length = get_filesize( fd) - offset) <= 0)
return NULL;
}
pos = offset;
while( pos < offset+length-7){ /* LBox+TBox-1=7*/
/* read LBox and TBox*/
if((data = fetch_bytes( fd, pos, 8))){
headlen = 8;
boxlen = (Byte8_t)big4(data);
boxtype = (char *)(data+4);
if( boxlen == 1){
Byte_t *data2;
headlen = 16;
/* read XLBox*/
if((data2 = fetch_bytes( fd, pos+8, 8))){
boxlen = big8(data2);
free(data2);
}
else{
fprintf( FCGI_stderr, "Error: error in gene_boxbyType( %d, %lld, %lld, %s)\n", fd, offset, length, TBox);
return NULL;
}
}
if( strncmp ( boxtype, TBox, 4) == 0){
foundbox = (box_param_t *)malloc( sizeof( box_param_t));
foundbox->fd = fd;
foundbox->offset = pos;
foundbox->headlen = headlen;
foundbox->length = boxlen;
strncpy( foundbox->type, TBox, 4);
foundbox->next = NULL;
free( data);
return foundbox;
}
free( data);
}
else{
fprintf( FCGI_stderr, "Error: error in gene_boxbyType( %d, %lld, %lld, %s)\n", fd, offset, length, TBox);
return NULL;
}
pos+= boxlen;
}
fprintf( FCGI_stderr, "Error: Box %s not found\n", TBox);
return NULL;
}
int main()
{
printf("FILESIZE: %d-bytes\n", get_filesize("tmp.txt"));
#if defined(__linux)
system("wc -c tmp.txt");
#endif
return 0;
}
char* file_block_decompose(const char* filename, uint64_t& size,
uint64_t& file_size, uint64_t& offset, MPI_Comm comm,
uint64_t alignment, uint32_t extra) {
// get size of input file
file_size = get_filesize(filename);
// get communication parameters
int32_t p, rank;
MPI_Comm_size(comm, &p);
MPI_Comm_rank(comm, &rank);
const uint64_t num_aligned_blocks = (file_size + alignment - 1) / alignment;
const uint32_t mod = num_aligned_blocks % p;
const uint64_t proc_num_aligned_blocks =
num_aligned_blocks / static_cast<uint64_t>(p) +
(static_cast<uint64_t>(rank) < mod);
const uint64_t proc_size = proc_num_aligned_blocks * alignment;
if (static_cast<uint32_t>(rank) < mod) {
offset = rank * proc_num_aligned_blocks * alignment;
} else {
offset = mod * (proc_num_aligned_blocks + 1) * alignment +
(rank - mod) * proc_num_aligned_blocks * alignment;
}
if (rank < p - 1) {
size = proc_size;
} else {
size = proc_size - (alignment - (file_size % alignment));
}
if (rank == 0) {
fprintf(stdout, "Filesize %zu and block size %zu\n", file_size, size);
}
// open file
std::ifstream t(filename);
t.seekg(offset);
char* data;
try {
data = new char[size + extra];
} catch (std::bad_alloc& ba) {
return NULL;
}
if (rank < p - 1) {
t.readsome(data, size + extra);
} else {
t.readsome(data, size);
for (uint32_t i = 0; i < extra; i++) {
data[size + i] = 0;
}
}
return data;
}
void send_file(int sockfd, int* clientlen, struct sockaddr_in* clientaddr, Request* req) {
int last_sent = -1;
FILE *fp = open_file(req->filename);
int file_size = get_filesize(fp);
int final_seq_num = (file_size / DATASIZE); // this accounts for 0 byte DataPkt for file_size % 512 == 0
int window_min = 0;
// window_max can't be greater than final_seq_num
int window_max = (req->window_size - 1 > final_seq_num) ? final_seq_num : (req->window_size - 1);
int num_timeouts = 0;
int n;
fd_set read_set;
struct timeval timeout;
// printf("data size is %d and final_seq_num is %d\n", file_size, final_seq_num);
// printf("window_size is %d and window_max is %d\n", req->window_size, window_max);
// printf("about to send pkts\n");
last_sent = send_pkts(fp, file_size, last_sent, window_max, sockfd, clientlen, clientaddr);
while (1) {
DataPkt ack;
bzero(ack.data, DATASIZE);
FD_ZERO(&read_set);
timeout.tv_sec = 0;
timeout.tv_usec = TIMEOUT_USEC;
FD_SET(sockfd, &read_set);
n = select(sockfd + 1, &read_set, NULL, NULL, &timeout);
if (n == 0) { // timed out
// printf("timed out %d times\n", num_timeouts);
num_timeouts++;
if (num_timeouts == MAX_TIMEOUTS) {
return; // stop communication
}
last_sent = send_pkts(fp, file_size, window_min - 1, window_max, sockfd, clientlen, clientaddr);
}
else {
n = recvfrom(sockfd, (char *) &ack, (TYPEWINDOWSEQSIZE * 2), 0,
(struct sockaddr *) clientaddr, clientlen);
if (n < 0)
error("ERROR in recvfrom");
// printf("got ack for pkt %d\n", ack.seq_num);
if (ack.seq_num >= window_min) { // ACK is new
if (ack.seq_num == final_seq_num) {
// printf("TRANSFER DONE!\n");
return; // completed
}
// adjust window accordingly
window_min = ack.seq_num + 1;
window_max = (window_min + (req->window_size - 1) > final_seq_num) ? final_seq_num : (window_min + (req->window_size - 1));
// printf("window_min is now %d and window_max is now %d\n", window_min, window_max);
// printf("sending next set of pkts\n");
last_sent = send_pkts(fp, file_size, last_sent, window_max, sockfd, clientlen, clientaddr);
// printf("last sent %d\n", last_sent);
}
}
}
}
/*
* Convert 'fosfat_file_t' to 'struct stat'.
*/
static struct stat *
in_stat (fosfat_file_t *file, const char *path)
{
struct stat *st;
struct tm time;
st = calloc (1, sizeof (struct stat));
if (!st)
return NULL;
memset (&time, 0, sizeof (time));
/* Directory, symlink or file */
if (file->att.isdir)
{
st->st_mode = S_IFDIR | FOS_DIR;
st->st_nlink = 2;
}
else if (file->att.islink)
{
st->st_mode = S_IFLNK | FOS_DIR;
st->st_nlink = 2;
}
else
{
st->st_mode = S_IFREG | FOS_FILE;
st->st_nlink = 1;
}
/* Size */
st->st_size = get_filesize (file, path);
/* Time */
time.tm_year = file->time_r.year - 1900;
time.tm_mon = file->time_r.month - 1;
time.tm_mday = file->time_r.day;
time.tm_hour = file->time_r.hour;
time.tm_min = file->time_r.minute;
time.tm_sec = file->time_r.second;
st->st_atime = mktime(&time);
time.tm_year = file->time_w.year - 1900;
time.tm_mon = file->time_w.month - 1;
time.tm_mday = file->time_w.day;
time.tm_hour = file->time_w.hour;
time.tm_min = file->time_w.minute;
time.tm_sec = file->time_w.second;
st->st_mtime = mktime(&time);
time.tm_year = file->time_c.year - 1900;
time.tm_mon = file->time_c.month - 1;
time.tm_mday = file->time_c.day;
time.tm_hour = file->time_c.hour;
time.tm_min = file->time_c.minute;
time.tm_sec = file->time_c.second;
st->st_ctime = mktime(&time);
return st;
}
size_t load_from_raw(std::string name_file,T*&buffer)
{
size_t size_file = get_filesize(name_file);
size_t cnt_items = size_file / sizeof(T);
if (buffer==NULL)
buffer = new T[cnt_items];
std::ifstream is(name_file, std::ifstream::in | std::ifstream::binary);
is.read(reinterpret_cast<char *>(buffer),size_file);
return cnt_items;
}
virtual void open_file() {
if (!use_mmap) {
filedesc = iomgr->open_session(filename.c_str(), false);
} else {
mmap_length = get_filesize(filename);
filedesc = open(filename.c_str(), O_RDWR);
mmap_file = (VertexDataType *) mmap(NULL, mmap_length, PROT_WRITE | PROT_READ, MAP_SHARED, filedesc, 0);
assert(mmap_file);
}
}
size_t load_vector_from_raw(std::string name_file,std::vector<T>& buffer)
{
size_t size_file = get_filesize(name_file);
size_t cnt_items = size_file / sizeof(T);
buffer.resize(cnt_items);
std::ifstream is(name_file, std::ifstream::in | std::ifstream::binary);
is.read(reinterpret_cast<char *>(&buffer[0]),size_file);
return cnt_items;
}
/*
* FUSE : read the data of a file.
*
* path (foo/bar)
* buf buffer for put the data
* size size in bytes
* offset offset in bytes
* fi not used
* return the size
*/
static int
fos_read (const char *path, char *buf, size_t size,
off_t offset, struct fuse_file_info *fi)
{
int res = -ENOENT;
int length;
char *location;
uint8_t *buf_tmp;
fosfat_file_t *file = NULL;
(void) fi;
location = trim_fosname (path);
/* Get the stats and test if it is a file */
file = fosfat_get_stat (fosfat, location);
if (!file)
goto out;
if (file->att.isdir)
goto out;
length = get_filesize (file, location);
if (offset < length)
{
/* Fix the size in function of the offset */
if (offset + (signed) size > length)
size = length - offset;
/* Read the data */
buf_tmp = get_buffer (file, location, offset, size);
/* Copy the data for FUSE */
if (buf_tmp)
{
memcpy (buf, buf_tmp, size);
free (buf_tmp);
res = size;
}
}
else
res = 0;
out:
if (file)
free (file);
if (location)
free (location);
return res;
}
virtual void open_file(std::string base_filename) {
filename = filename_degree_data(base_filename);
modified = false;
if (!use_mmap) {
iomgr->allow_preloading(filename);
filedesc = iomgr->open_session(filename.c_str(), false);
} else {
mmap_length = get_filesize(filename);
filedesc = open(filename.c_str(), O_RDWR);
mmap_file = (degree *) mmap(NULL, mmap_length, PROT_READ | PROT_WRITE, MAP_SHARED, filedesc, 0);
assert(mmap_file);
}
}
/**
* Read Palm Database from open file stream.
* @param *pdb_f open file stream of PDB file.
* @param *pdb pointer to location that stores Palm Database.
* @return uint8_t exit status. Either EXIT_SUCCESS, EXIT_FAILURE_PDB_HEADER
* or EXIT_FAILURE_PDB_RECORDS.
*/
uint8_t read_pdb(FILE *pdb_f, pdb_t *pdb)
{
init_pdb(pdb);
pdb->filesize = get_filesize(pdb_f);
if (!read_pdb_header(pdb_f, pdb))
return EXIT_FAILURE_PDB_HEADER;
if (!read_pdb_records(pdb_f, pdb))
return EXIT_FAILURE_PDB_RECORDS;
return EXIT_SUCCESS;
}
/*****************************************************************************
* loadSamplesDataIntoMemory() --
* Helpler function to simplify life and
* load data into memory in one shot.
*
* @param int numberOfSamples -- The number of samples you would like to
* load.
*
* unsigned char* dataArray -- The traffic data array where
* suspicious flows are stored in memory.
*
* int* sampleIndexArray --
* Used to keep record of the flows in dataArray.
* The index into this array is the sample #,
* the value inside sampleIndexArray[i] is the
* index into dataArray where this suspicous flow
* begins.
* char* dataArrayInputFileName --
* Input file name of the dataArray (raw data).
* char* offsetArrayInputFilename --
* Input file name of the offsetArray - A file that
* contains binary integer data of offsets.
* @return int -- 1 if successful load, 0 otherwise.
*/
int loadSamplesDataIntoMemory(/*IN*/int numberOfSamples, /*OUT*/unsigned char* dataArray, /*OUT*/int* sampleIndexArray, /*IN*/char* dataArrayInputFileName, /*IN*/char* offsetArrayInputFileName)
{
FILE* dataInputFile;
FILE* offsetInputFile;
dataInputFile = fopen( dataArrayInputFileName, "r" );
fread( dataArray, 1, get_filesize( dataArrayInputFileName ), dataInputFile );
fclose( dataInputFile );
offsetInputFile = fopen( offsetArrayInputFileName, "r" );
fread( sampleIndexArray, sizeof(int), numberOfSamples, offsetInputFile );
return 1;
}
int lz77_decode(FILE* in,FILE* out)
{
unsigned char* nbuf = 0,* ori_buf = 0,* head = 0,* tail = 0;
long ori_size = 0,nsize = 0;
if(! in || ! out)return 1;
get_filesize(in,nsize); // get file size.
if(nsize <= 0)return 1;
ori_size = (fgetc(in) & 0xff) << 24;
ori_size += (fgetc(in) & 0xff) << 16;
ori_size += (fgetc(in) & 0xff) << 8;
ori_size += (fgetc(in) & 0xff) << 0;
if(ori_size <= 0)return 1;
nbuf = (unsigned char*)malloc(nsize* sizeof(unsigned char));
if(! nbuf)return 1;
ori_buf = (unsigned char*)malloc(ori_size* sizeof(unsigned char));
if(ori_buf){
head = tail = ori_buf; // store head and tail of slide-window.
if(fread(nbuf,sizeof(unsigned char),nsize,in) == (nsize - 4)){
unsigned char* pt = nbuf;
for(;;){
if(pt >= (nbuf + nsize - 4))break;
if(! pt[0] && ! pt[1] ){ // \0\0\?
tail[0] = pt[2];
tail++;
pt += 3;
} else { // \?\?
unsigned int offset = 0,length = 0,i;
offset = pt[0] << LENGTHBITS;
offset += (pt[1] >> LENGTHBITS) & 0x0f;
length = pt[1] & 0x0f;
//fprintf(stderr,"{%d - %d}",offset,length);
for(i = 0;i < length;i++){
tail[i] = ((unsigned char*)(tail - offset))[i];
}
tail += length;
pt += 2;
}
}
fwrite(ori_buf,sizeof(unsigned char),ori_size,out);
}
free(ori_buf);
}
metadatalist_param_t * const_metadatalist( int fd)
{
metadatalist_param_t *metadatalist;
metadata_param_t *metabin;
boxlist_param_t *toplev_boxlist;
box_param_t *box, *next;
placeholderlist_param_t *phldlist;
placeholder_param_t *phld;
Byte8_t idx;
Byte8_t filesize;
if(!(filesize = (Byte8_t)get_filesize( fd)))
return NULL;
if( !(toplev_boxlist = get_boxstructure( fd, 0, filesize))){
fprintf( FCGI_stderr, "Error: Not correctl JP2 format\n");
return NULL;
}
phldlist = gene_placeholderlist();
metadatalist = gene_metadatalist();
box = toplev_boxlist->first;
idx = 0;
while( box){
next = box->next;
if( strncmp( box->type, "jP ",4)!=0 && strncmp( box->type, "ftyp",4)!=0 && strncmp( box->type, "jp2h",4)!=0){
boxlist_param_t *boxlist = NULL;
boxcontents_param_t *boxcontents = NULL;
phld = gene_placeholder( box, ++idx);
insert_placeholder_into_list( phld, phldlist);
boxlist = get_boxstructure( box->fd, get_DBoxoff( box), get_DBoxlen(box));
if( !boxlist)
boxcontents = gene_boxcontents( get_DBoxoff( box), get_DBoxlen(box));
delete_box_in_list( &box, toplev_boxlist);
metabin = gene_metadata( idx, boxlist, NULL, boxcontents);
insert_metadata_into_list( metabin, metadatalist);
}
box = next;
}
metabin = gene_metadata( 0, toplev_boxlist, phldlist, NULL);
insert_metadata_into_list( metabin, metadatalist);
return metadatalist;
}
//-----------------------------------------------------------------//
bool unzip::get_file(uint32_t index, char* buff)
{
if(index < static_cast<uint32_t>(files_.size())) {
unzSetOffset(hnd_, files_[index].ofs_);
if(unzOpenCurrentFile(hnd_) != UNZ_OK) return false;
size_t sz = get_filesize(index);
unzReadCurrentFile(hnd_, buff, sz);
unzCloseCurrentFile(hnd_);
return true;
}
return false;
}
void app_tftp(char *arg)
{
struct command_t *commands;
struct note_t *note;
struct pico_tftp_session *session;
int is_server_enabled = 0;
int filesize;
family = IPV6_MODE ? PICO_PROTO_IPV6 : PICO_PROTO_IPV4;
commands = parse_arguments(arg);
while (commands) {
if (toupper(commands->operation) != 'S')
note = transfer_prepare(&session, commands->operation, commands->filename, &commands->server_address, family);
switch (commands->operation) {
case 'S':
case 's':
if (!is_server_enabled) {
pico_tftp_listen(PICO_PROTO_IPV4, (commands->operation == 'S') ? tftp_listen_cb_opt : tftp_listen_cb);
is_server_enabled = 1;
}
break;
case 'T':
filesize = get_filesize(commands->filename);
if (filesize < 0) {
fprintf(stderr, "TFTP: unable to read size of file %s\n", commands->filename);
exit(3);
}
pico_tftp_set_option(session, PICO_TFTP_OPTION_FILE, filesize);
start_tx(session, commands->filename, short_be(PICO_TFTP_PORT), cb_tftp_tx_opt, note);
break;
case 't':
start_tx(session, commands->filename, short_be(PICO_TFTP_PORT), cb_tftp_tx, note);
break;
case 'R':
pico_tftp_set_option(session, PICO_TFTP_OPTION_FILE, 0);
start_rx(session, commands->filename, short_be(PICO_TFTP_PORT), cb_tftp_rx_opt, note);
break;
case 'r':
start_rx(session, commands->filename, short_be(PICO_TFTP_PORT), cb_tftp_rx, note);
}
commands = commands->next;
}
}
void IdentifyChromosomes(const string& chrom_file,
vector<string>& chrom_files) {
fprintf(stderr, "[IDENTIFYING CHROMS] ");
if (isdir(chrom_file.c_str())) {
read_dir(chrom_file, "fa", chrom_files);
} else {
chrom_files.push_back(chrom_file);
}
fprintf(stderr, "[DONE]\n");
fprintf(stderr, "chromosome files found (approx size):\n");
for (uint32_t i = 0; i < chrom_files.size(); ++i) {
fprintf(stderr, "%s (%.2lfMbp)\n", chrom_files[i].c_str(),
roundf(get_filesize(chrom_files[i]) / 1e06));
}
}
index_param_t * parse_jp2file( int fd)
{
index_param_t *jp2idx;
box_param_t *cidx;
metadatalist_param_t *metadatalist;
boxlist_param_t *toplev_boxlist;
Byte8_t filesize;
if( !(filesize = (Byte8_t)get_filesize( fd)))
return NULL;
if( !(toplev_boxlist = get_boxstructure( fd, 0, filesize))){
fprintf( FCGI_stderr, "Error: Not correctl JP2 format\n");
return NULL;
}
if( !check_JP2boxidx( toplev_boxlist)){
fprintf( FCGI_stderr, "Index format not supported\n");
delete_boxlist( &toplev_boxlist);
return NULL;
}
if( !(cidx = search_box( "cidx", toplev_boxlist))){
fprintf( FCGI_stderr, "Box cidx not found\n");
delete_boxlist( &toplev_boxlist);
return NULL;
}
jp2idx = (index_param_t *)opj_malloc( sizeof(index_param_t));
if( !set_cidxdata( cidx, jp2idx)){
fprintf( FCGI_stderr, "Error: Not correctl format in cidx box\n");
opj_free(jp2idx);
delete_boxlist( &toplev_boxlist);
return NULL;
}
delete_boxlist( &toplev_boxlist);
metadatalist = const_metadatalist( fd);
jp2idx->metadatalist = metadatalist;
#ifndef SERVER
fprintf( logstream, "local log: code index created\n");
#endif
return jp2idx;
}
void tftp_listen_cb_opt(union pico_address *addr, uint16_t port, uint16_t opcode, char *filename, int32_t len)
{
struct note_t *note;
struct pico_tftp_session *session;
int options;
uint8_t timeout;
int32_t filesize;
int ret;
printf("TFTP listen callback (OPTIONS) from remote port %" PRIu16 ".\n", short_be(port));
/* declare the options we want to support */
ret = pico_tftp_parse_request_args(filename, len, &options, &timeout, &filesize);
if (ret)
pico_tftp_reject_request(addr, port, TFTP_ERR_EOPT, "Malformed request");
if (opcode == PICO_TFTP_RRQ) {
printf("Received TFTP get request for %s\n", filename);
note = transfer_prepare(&session, 'T', filename, addr, family);
if (options & PICO_TFTP_OPTION_TIME)
pico_tftp_set_option(session, PICO_TFTP_OPTION_TIME, timeout);
if (options & PICO_TFTP_OPTION_FILE) {
ret = get_filesize(filename);
if (ret < 0) {
pico_tftp_reject_request(addr, port, TFTP_ERR_ENOENT, "File not found");
return;
}
pico_tftp_set_option(session, PICO_TFTP_OPTION_FILE, ret);
}
start_tx(session, filename, port, cb_tftp_tx_opt, note);
} else { /* opcode == PICO_TFTP_WRQ */
printf("Received TFTP put request for %s\n", filename);
note = transfer_prepare(&session, 'R', filename, addr, family);
if (options & PICO_TFTP_OPTION_TIME)
pico_tftp_set_option(session, PICO_TFTP_OPTION_TIME, timeout);
if (options & PICO_TFTP_OPTION_FILE)
pico_tftp_set_option(session, PICO_TFTP_OPTION_FILE, filesize);
start_rx(session, filename, port, cb_tftp_rx_opt, note);
}
}