void chirp_ticket_name(const char *root, const char *pk, char *ticket_subject, char *ticket_filename)
{
unsigned char digest[TICKET_DIGEST_LENGTH];
md5_context_t context;
md5_init(&context);
md5_update(&context, (const unsigned char *) pk, strlen(pk));
md5_final(digest, &context);
sprintf(ticket_subject, TICKET_SUBJECT_FORMAT, md5_string(digest));
sprintf(ticket_filename, "%s/" TICKET_FILENAME_FORMAT, root, md5_string(digest));
}
// Evaluate differences between time-zone. Two time zones that differ
// by almost 24 hours are actually very close on the surface of the
// earth. This function finds the 'shortest way around'
//
static int compare(const void *x, const void *y) {
const URLTYPE *a=(const URLTYPE *)x;
const URLTYPE *b=(const URLTYPE *)y;
char longname[512];
const int twelve_hours = 12*3600;
int diffa = abs(tzone - (a->zone));
int diffb = abs(tzone - (b->zone));
if (diffa > twelve_hours) {
diffa = 2*twelve_hours-diffa;
}
if (diffb > twelve_hours) {
diffb = 2*twelve_hours-diffb;
}
if (diffa < diffb) {
return -1;
}
if (diffa > diffb) {
return +1;
}
// In order to ensure uniform distribution, we hash paths that are
// equidistant from the host's timezone in a way that gives a
// unique ordering for each host but which is effectively random
// between hosts.
//
sprintf(longname, "%s%d", a->name, hostid);
std::string sa = md5_string((const unsigned char *)longname, strlen((const char *)longname));
sprintf(longname, "%s%d", b->name, hostid);
std::string sb = md5_string((const unsigned char *)longname, strlen((const char *)longname));
int xa = strtol(sa.substr(1, 7).c_str(), 0, 16);
int xb = strtol(sb.substr(1, 7).c_str(), 0, 16);
if (xa<xb) {
return -1;
}
if (xa>xb) {
return 1;
}
return 0;
}
int main(int argc, char **argv)
{
int leng;
st=ft=ht=vt=0;
md_parse_opt(argc, argv);
if(vt == 1) {
md_show_version();
return 0;
}
if(ht == 1) {
md_show_version();
md_show_help();
return 0;
}
if(st == 1) {
md5_string();
}
if(ft == 1) {
md5_file();
}
return 0;
}
static void
compute_node_guid(td_engine *engine, td_node *node)
{
MD5_CTX context;
MD5_Init(&context);
md5_string(&context, node->action);
md5_string(&context, node->annotation);
md5_string(&context, node->salt);
MD5_Final(node->guid.data, &context);
if (td_debug_check(engine, TD_DEBUG_NODES))
{
char guidstr[33];
td_digest_to_string(&node->guid, guidstr);
printf("%s with guid %s\n", node->annotation, guidstr);
}
}
static void txn_name(struct file_cache *c, const char *path, char *txn)
{
unsigned char digest[MD5_DIGEST_LENGTH];
char shortname[DOMAIN_NAME_MAX];
domain_name_cache_guess_short(shortname);
md5_buffer(path, strlen(path), digest);
sprintf(txn, "%s/txn/%s.%s.%d.XXXXXX", c->root, md5_string(digest), shortname, (int) getpid());
}
const char *chirp_ticket_digest(const char *pk)
{
unsigned char digest[TICKET_DIGEST_LENGTH];
md5_context_t context;
md5_init(&context);
md5_update(&context, (const unsigned char *) pk, strlen(pk));
md5_final(digest, &context);
return md5_string(digest); /* static memory */
}
/*
* 输入一个整数，获取其字符串对应的MD5码
*/
char* GetMD5(const RoleID roleid)
{
char arrA[16] = {0};
sprintf(arrA, "%d", roleid);
int32_t iInputLength = strlen(arrA);
char arrOut[32] = {0};
char *pResult = NULL;
pResult = md5_string((const unsigned char*)arrA, arrOut, iInputLength);
return pResult;
}
bool CPermissionsCache::lookup(ISecUser& sec_user)
{
if(!isCacheEnabled())
return false;
const char* username = sec_user.getName();
if(!username || !*username)
return false;
string key(username);
ReadLockBlock readLock(m_userCacheRWLock );
MapUserCache::iterator it = m_userCache.find(key);
if (it == m_userCache.end())
return false;
CachedUser* user = (CachedUser*)(it->second);
time_t now;
time(&now);
if(user->getTimestamp() < (now - m_cacheTimeout))
{
m_userCache.erase(username);
delete user;
return false;
}
const char* cachedpw = user->queryUser()->credentials().getPassword();
StringBuffer pw(sec_user.credentials().getPassword());
if(cachedpw && pw.length() > 0)
{
StringBuffer md5pbuf;
md5_string(pw, md5pbuf);
if(strcmp(cachedpw, md5pbuf.str()) == 0)
{
#ifdef _DEBUG
DBGLOG("CACHE: CPermissionsCache Found validated user %s", username);
#endif
// Copy cached user to the sec_user structure, but still keep the original clear text password.
user->queryUser()->copyTo(sec_user);
sec_user.credentials().setPassword(pw.str());
return true;
}
else
{
m_userCache.erase(username);
delete user;
return false;
}
}
return false;
}
/// Answer an authorization request sent by the server.
/// The answer is the response to the nonce sent as challenge by the server.
/// It is the md5sum from the concatenation of the nonce and the
/// GUI-RPC password.
///
/// \param[in] passwd The GUI-RPC password.
/// \return Zero if the authorization was acknowledged by the server,
/// nonzero if the server rejected the request or if any other error
/// occurred.
int RPC_CLIENT::authorize(const char* passwd) {
RPC rpc(this);
int retval = rpc.do_rpc("<auth1/>\n");
if (retval) {
return retval;
}
XML_PARSER xp(&rpc.fin);
char nonce[256];
bool found = false;
char chr_buf[256];
bool is_tag;
while (!xp.get(chr_buf, sizeof(chr_buf), is_tag)) {
if (!is_tag) {
continue;
}
if (xp.parse_str(chr_buf, "nonce", nonce, sizeof(nonce))) {
found = true;
break;
}
}
if (!found) {
//fprintf(stderr, "Nonce not found\n");
return ERR_AUTHENTICATOR;
}
free(rpc.mbuf);
std::ostringstream input;
input << nonce << passwd;
std::string nonce_hash = md5_string(input.str());
std::ostringstream buf;
buf << "<auth2>\n<nonce_hash>" << nonce_hash << "</nonce_hash>\n</auth2>\n";
retval = rpc.do_rpc(buf.str().c_str());
if (retval) {
return retval;
}
while (!xp.get(chr_buf, sizeof(chr_buf), is_tag)) {
if (!is_tag) {
continue;
}
bool authorized;
if (xp.parse_bool(chr_buf, "authorized", authorized)) {
if (authorized) {
return 0;
}
}
}
return ERR_AUTHENTICATOR;
}
static INT64_T do_md5(int argc, char **argv)
{
unsigned char digest[16];
char full_path[CHIRP_LINE_MAX];
int result;
complete_remote_path(argv[1], full_path);
result = chirp_reli_md5(current_host, full_path, digest, stoptime);
if(result > 0)
printf("%s %s\n", md5_string(digest), full_path);
return result;
}
static int wait_for_running_txn(struct file_cache *c, const char *path)
{
char txn[PATH_MAX];
char dirname[PATH_MAX];
unsigned char digest[MD5_DIGEST_LENGTH];
DIR *dir;
struct dirent *d;
const char *checksum;
md5_buffer(path, strlen(path), digest);
checksum = md5_string(digest);
txn[0] = 0;
sprintf(dirname, "%s/txn", c->root);
dir = opendir(dirname);
if(!dir)
return 0;
while((d = readdir(dir))) {
if(!strncmp(d->d_name, checksum, 32)) {
sprintf(txn, "%s/txn/%s", c->root, d->d_name);
break;
}
}
closedir(dir);
if(!txn[0])
return 0;
while(1) {
struct stat64 info;
debug(D_CACHE, "wait %s", txn);
if(stat64(txn, &info) < 0)
return 1;
time_t current = time(0);
if((current - info.st_mtime) < 60) {
sleep(1);
continue;
} else {
debug(D_CACHE, "override %s", txn);
return 0;
}
}
}
// this is called whenever new results are added,
// namely at startup and after a scheduler RPC.
// Sort results based on (arrival time, name),
// then set result.index to their position in this order.
// This determines the order in which results are run.
//
void CLIENT_STATE::sort_results() {
unsigned int i;
for (i=0; i<results.size(); i++) {
RESULT* rp = results[i];
rp->name_md5 = md5_string(string(rp->name));
}
std::sort(
results.begin(),
results.end(),
arrived_first
);
for (i=0; i<results.size(); i++) {
RESULT* rp = results[i];
rp->index = i;
}
}
bool CPermissionsCache::lookup(ISecUser& sec_user)
{
if(!isCacheEnabled())
return false;
const char* username = sec_user.getName();
if(!username || !*username)
return false;
synchronized block(m_userCacheMonitor);
CachedUser* user = m_userCache[username];
if(user == NULL)
return false;
time_t now;
time(&now);
if(user->getTimestamp() < (now - m_cacheTimeout))
{
m_userCache.erase(username);
delete user;
return false;
}
const char* cachedpw = user->queryUser()->credentials().getPassword();
StringBuffer pw(sec_user.credentials().getPassword());
if(cachedpw && pw.length() > 0)
{
StringBuffer md5pbuf;
md5_string(pw, md5pbuf);
if(strcmp(cachedpw, md5pbuf.str()) == 0)
{
// Copy cached user to the sec_user structure, but still keep the original clear text password.
user->queryUser()->copyTo(sec_user);
sec_user.credentials().setPassword(pw.str());
return true;
}
else
{
m_userCache.erase(username);
delete user;
return false;
}
}
return false;
}
int main()
{
const char* s = "中国人民银行！";
const char* key = "zsxxsz";
char buf1[33], buf2[33];
acl::md5::md5_string(s, strlen(s), key, strlen(key),
buf1, sizeof(buf1));
printf("first md5: %s\r\n", buf1);
md5_string(s, key, strlen(key), buf2, sizeof(buf2));
printf("second md5: %s\r\n", buf2);
assert(strcmp(buf1, buf2) == 0);
#ifdef WIN32
getchar();
#endif
return 0;
}
int main( int argc, char *argv[] )
{
int i;
unsigned char digest[16];
if(argc<2) {
printf("use: parrot_md5 <file> ...\n");
return 1;
}
for(i=1;i<argc;i++) {
if(parrot_md5(argv[i],digest)>=0 || md5_file(argv[i],digest)) {
printf("%s %s\n",md5_string(digest),argv[i]);
} else {
fprintf(stderr,"parrot_md5: %s: %s\n",argv[i],strerror(errno));
}
}
return 0;
}
void event_privmsg (irc_session_t * irc_session, const char * event, const char * origin, const char ** params, unsigned int count) {
char nickbuf[128], md5sum[MD5_HASHSUM_SIZE];
SessionPtr session;
//dump_event (irc_session, event, origin, params, count);
params[1] = irc_color_strip_from_mirc( params[1] );
addlog ("'%s' said to me (%s): %s", origin ? origin : "someone", params[0], params[1] );
if ( !origin )
return;
irc_target_get_nick( origin, nickbuf, sizeof(nickbuf) );
md5_string( origin, md5sum );
session = get_session( SESSION_IRC, md5sum );
if( !( session->dbuser ) ) {
irc_cmd_notice( sysconfig.irc_session, nickbuf, "You must be loged in to use any features." );
} else {
irc_cmd_notice( sysconfig.irc_session, nickbuf, "Now just how did you manage that..." );
}
return;
}
int main(int argc,char **argv){
int opt;
while((opt=getopt(argc,argv,":vf:h"))!=-1){
switch (opt){
case 'v':
show_version();
break;
case 'f':
md5_file(optarg);
break;
case ':':
printf("need a filename\n");
break;
case 'h':
case '?':
printf("unknow option\n");
show_help();
break;
default:
printf("a a %s\n",optarg);
}
}
while(optind<argc){
md5_string(argv[optind]);
optind++;
}
return 0;
}
/********************************************************************************
* Description: this is the function responsible for checking the
* input password value of the authentication form.
* ******************************************************************************/
static void
checkPassword (void)
{
MemPtr pass1, scratch = NULL;
char *input;
UInt16 index = 0;
MemHandle rec;
mdKey in;
ListType *list;
// compact text and get a pointer.
FldCompactText (GetObjectFromActiveForm (PasswordField));
input = FldGetTextPtr (GetObjectFromActiveForm (PasswordField));
list = GetObjectFromActiveForm (selPopupList);
// if SysPass is defined, free it. this happens when Strip locks
// itself after the timeout.
if (SysPass)
MemPtrFree (SysPass);
// if its the first time the user has used the program we need
// to set some things up.
if (input && StrLen (input))
{
// read the password from the database, decrypt with the input text.
if ((rec = DmQueryRecord (PasswordDB, index)))
{
pass1 = MemHandleLock (rec);
if ((scratch = MemPtrNew (24)))
{
UInt16 chk = LstGetSelection (list);
//printf("%d\n", LstGetSelection(list));
switch (chk)
{
case 0:
UnpackPassword_old (pass1, scratch, input, 1);
break;
case 1:
UnpackPassword_old (pass1, scratch, input, 2);
break;
case 2:
UnpackPassword_old (pass1, scratch, input, 0);
break;
}
}
MemHandleUnlock (rec);
}
// the message digest of the password they provided should be exactly the
// same as the message digest that was just decrypted out of the password
// database. Do a MemCmp to make sure they are the same.
md5_string (input, in);
if ((!MemCmp (in, scratch, 16)) && input)
{
// if so, copy the password onto the system-password
if ((SysPass = MemPtrNew (StrLen (input) + 1)))
StrCopy (SysPass, input);
if (scratch)
MemPtrFree (scratch);
md_string(SysPass, NewSysPass);
cryptSwitch (LstGetSelection (list));
}
else
{
// FAILURE!!!!!!
// free the memory and tell the user they entered the wrong password.
FieldType *fld = GetObjectFromActiveForm (PasswordField);
FrmCustomAlert (GenericError,
"The password you entered is incorrect", NULL,
NULL);
FldSetSelection (fld, 0, FldGetTextLength (fld));
LstDrawList (list);
if (scratch)
{
MemPtrFree (scratch);
SysPass = NULL;
}
}
}
// null string is always wrong!!!
else
{
FrmCustomAlert (GenericError, "You forgot to enter a password!!",
NULL, NULL);
LstDrawList (list);
}
}
void event_channel (irc_session_t * irc_session, const char * event, const char * origin, const char ** params, unsigned int count) {
char buffer[512];
char nickbuf[128];
char md5sum[MD5_HASHSUM_SIZE];
ConfigArrayPtr setting;
SessionPtr session;
if ( count != 2 )
return;
params[1] = irc_color_strip_from_mirc( params[1] );
addlog ("'%s' said in channel %s: %s", origin ? origin : "someone", params[0], params[1] );
if ( !origin )
return;
irc_target_get_nick( origin, nickbuf, sizeof(nickbuf) );
md5_string( origin, md5sum );
session = get_session( SESSION_IRC, md5sum );
if ( !strcmp (params[1], "help") ) {
if( ( session->dbuser ) && ( session->dbuser->level >= LEVEL_MODERATOR ) )
snprintf(buffer, sizeof(buffer), "%s", irc_color_convert_to_mirc( "[B]Usage[/B] - quit, help, dcc send, topic, mode, whois, nick" ) );
else
snprintf(buffer, sizeof(buffer), "%s", irc_color_convert_to_mirc( "[B]Usage[/B] - help, dcc send, login" ) );
irc_cmd_notice( irc_session, params[0], buffer );
}
if ( !strcmp (params[1], "ctcp") ) {
irc_cmd_ctcp_request (irc_session, nickbuf, "PING 223");
irc_cmd_ctcp_request (irc_session, nickbuf, "FINGER");
irc_cmd_ctcp_request (irc_session, nickbuf, "VERSION");
irc_cmd_ctcp_request (irc_session, nickbuf, "TIME");
}
if ( !strcmp (params[1], "dcc chat") ) {
irc_dcc_t dccid;
irc_dcc_chat (irc_session, 0, nickbuf, dcc_recv_callback, &dccid);
addlog ("DCC chat ID: %d", dccid);
}
if ( !strcmp (params[1], "dcc send") ) {
irc_dcc_t dccid;
setting = GetSetting( "HTTP Images" );
snprintf(buffer, sizeof(buffer), "%s/cookie.gif", setting->string_value );
irc_dcc_sendfile (irc_session, 0, nickbuf, buffer, dcc_file_send_callback, &dccid);
addlog ("DCC send ID: %d", dccid);
}
if( ( session->dbuser ) && ( session->dbuser->level >= LEVEL_MODERATOR ) ) {
if ( !strcmp (params[1], "quit") ) {
irc_cmd_quit (irc_session, "of course, Master!");
}
if ( !strcmp (params[1], "topic") ) {
irc_cmd_topic (irc_session, params[0], 0);
} else if ( strstr (params[1], "topic ") == params[1] ) {
irc_cmd_topic (irc_session, params[0], params[1] + 6);
}
if ( strstr (params[1], "mode ") == params[1] )
irc_cmd_channel_mode (irc_session, params[0], params[1] + 5);
if ( strstr (params[1], "nick ") == params[1] )
irc_cmd_nick (irc_session, params[1] + 5);
if ( strstr (params[1], "whois ") == params[1] )
irc_cmd_whois (irc_session, params[1] + 5);
}
return;
}
void oauth_signandappend_oauth_header(const char *reqMethod, struct url_props *url, const char *consumerKey, const char *consumerSecret, const char *authToken, const char *authTokenSecret, const time_t now, const char *postContent, const size_t postContentLen, const char *oauthCallback, const char *oauthVerifier, const char *oauthScope, struct string *out)
{
struct signctx senv;
char _tb[256];
const size_t _tbLen = sprintf(_tb, "%u", (unsigned)now);
struct timeval tv;
struct md5_context md5Ctx;
signctx_init(&senv);
init_signature_seed(&senv, reqMethod, url);
if (postContentLen)
append_signature_params(&senv, postContent, postContent + postContentLen);
string_append(out, "Authorization: OAuth ", 21);
append_signature_param(&senv, "oauth_consumer_key", 18, consumerKey, strlen(consumerKey));
string_appendfmt(out, "oauth_consumer_key=\"%s\"", consumerKey);
append_signature_param(&senv, "oauth_signature_method", 22, "HMAC-SHA1", 9);
string_append(out, ",oauth_signature_method=\"HMAC-SHA1\"", 35);
string_appendfmt(out,",oauth_timestamp=\"%u\"", (uint32_t)now);
append_signature_param(&senv, "oauth_timestamp", 15, _tb, _tbLen);
gettimeofday(&tv, NULL);
uint8_t digest[16];
char digestAlpha[33];
md5_init(&md5Ctx);
md5_update(&md5Ctx, (uint8_t *)&tv.tv_sec, sizeof(tv.tv_sec));
md5_update(&md5Ctx, (uint8_t *)&tv.tv_usec, sizeof(tv.tv_usec));
md5_update(&md5Ctx, (uint8_t *)consumerKey, strlen(consumerKey));
md5_update(&md5Ctx, (uint8_t *)"io.language", 11);
md5_finalize(&md5Ctx, digest);
md5_string((char *)digest, digestAlpha);
const size_t digestAlphaLen = strlen(digestAlpha); // 32
string_appendfmt(out, ",oauth_nonce=\"%.*s\"", digestAlphaLen, digestAlpha);
append_signature_param(&senv, "oauth_nonce", 11, digestAlpha, digestAlphaLen);
string_appendfmt(out, ",oauth_version=\"1.0\"", 20);
append_signature_param(&senv, "oauth_version", 13, "1.0", 3);
if (authToken && *authToken != '\0')
{
string_appendfmt(out, ",oauth_token=\"%s\"", authToken);
append_signature_param(&senv, "oauth_token", 11, authToken, strlen(authToken));
}
if (oauthCallback && *oauthCallback != '\0')
{
string_appendfmt(out, ",oauth_callback=\"%s\"", oauthCallback);
append_signature_param(&senv, "oauth_callback", 14, oauthCallback, strlen(oauthCallback));
}
if (oauthVerifier && *oauthVerifier != '\0')
{
string_appendfmt(out, ",oauth_verifier=\"%s\"", oauthVerifier);
append_signature_param(&senv, "oauth_verifier", 14, oauthVerifier, strlen(oauthVerifier));
}
if (oauthScope && *oauthScope != '\0')
{
string_appendfmt(out, ",scope=\"%s\"", oauthScope);
append_signature_param(&senv, "scope", 5, oauthScope, strlen(oauthScope));
}
build_signature(&senv, "HMAC-SHA1", consumerSecret, authTokenSecret ? authTokenSecret : "");
string_append(out, ",oauth_signature=\"", 18);
string_append_urlencoded_rfc3986(out, string_data(&senv.signatureParamsBuf), string_len(&senv.signatureParamsBuf));
string_append(out, "\"\r\n", 3);
signctx_dealloc(&senv);
}
void
processArray(int argc, char **argv) {
int arg = 1;
while (arg < argc) {
if ((strcmp(argv[arg], "-f") == 0) ||
(strcmp(argv[arg], "-F") == 0)) {
delete fasta;
fasta = new seqCache(argv[++arg]);
} else if (strcmp(argv[arg], "-i") == 0) {
failIfNoSource();
++arg;
if ((argv[arg] == 0L) || (argv[arg][0] == '-'))
fprintf(stderr, "ERROR: next arg to -i should be 'name', I got '%s'\n",
(argv[arg] == 0L) ? "(nullpointer)" : argv[arg]), exit(1);
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++)
fprintf(stdout, "G\tseq\t%s:"F_U32"\t"F_U32"\t%s\n",
argv[arg], s, fasta->getSequenceLength(s), ">unimplemented");
} else if (strcmp(argv[arg], "-d") == 0) {
failIfNoSource();
printf(F_U32"\n", fasta->getNumberOfSequences());
} else if (strcmp(argv[arg], "-L") == 0) {
uint32 small = strtouint32(argv[++arg]);
uint32 large = strtouint32(argv[++arg]);
failIfNoSource();
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++)
if ((small <= fasta->getSequenceLength(s)) && (fasta->getSequenceLength(s) < large))
printSequence(s);
} else if (strcmp(argv[arg], "-N") == 0) {
double small = atof(argv[++arg]);
double large = atof(argv[++arg]);
failIfNoSource();
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++) {
seqInCore *S = fasta->getSequenceInCore(s);
uint32 Ns = 0;
uint32 len = S->sequenceLength();
char *seq = S->sequence();
for (uint32 i=begPos; i<len && i<endPos; i++)
if ((seq[i] == 'n') || (seq[i] == 'N'))
Ns++;
double Np = 100.0 * Ns / len;
if ((small <= Np) && (Np < large))
printSequence(S);
delete S;
}
} else if (strcmp(argv[arg], "-W") == 0) {
failIfNoSource();
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++)
printSequence(s);
} else if (strcmp(argv[arg], "-G") == 0) {
uint32 n = strtouint32(argv[++arg]);
uint32 s = strtouint32(argv[++arg]);
uint32 l = strtouint32(argv[++arg]);
char bases[4] = {'A', 'C', 'G', 'T'};
char *def = new char [1024];
char *seq = new char [l + 1];
if (s == 0)
s = 1;
if (s > l)
fprintf(stderr, "leaff: usage: -G num-seqs min-length max-length\n"), exit(1);
for (uint32 i=0; i<n; i++) {
uint32 j = s + ((l-s == 0) ? 0 : (MT.mtRandom32() % (l-s)));
uint32 p = 0;
while (p < j)
seq[p++] = bases[MT.mtRandom32() & 0x3];
seq[p] = 0;
sprintf(def, "random%06"F_U32P, i);
printSequence(def, seq, 0, j);
}
delete [] seq;
delete [] def;
} else if (strcmp(argv[arg], "-s") == 0) {
failIfNoSource();
failIfNotRandomAccess(); // Easy to fix, just read the first N sequences
printSequence(argv[++arg]);
} else if (strcmp(argv[arg], "-S") == 0) {
failIfNoSource();
failIfNotRandomAccess(); // Easy to fix, just read the first N sequences
uint32 lowID = fasta->getSequenceIID(argv[++arg]);
uint32 highID = fasta->getSequenceIID(argv[++arg]);
if (lowID > highID) {
uint32 t = lowID;
lowID = highID;
highID = t;
}
for (uint32 s=lowID; (s <= highID) && (s <= fasta->getNumberOfSequences()); s++)
printSequence(s);
} else if (strcmp(argv[arg], "-r") == 0) {
uint32 num = strtouint32(argv[++arg]);
failIfNoSource();
failIfNotRandomAccess(); // Impossible to fix, or load whole thing into memory
if (num >= fasta->getNumberOfSequences())
num = fasta->getNumberOfSequences();
uint32 *seqs = new uint32 [fasta->getNumberOfSequences()];
for (uint32 i=0; i<fasta->getNumberOfSequences(); i++)
seqs[i] = i;
for (uint32 i=0; i<fasta->getNumberOfSequences(); i++) {
uint32 j = MT.mtRandom32() % (fasta->getNumberOfSequences() - i) + i;
uint32 t = seqs[j];
seqs[j] = seqs[i];
seqs[i] = t;
}
for (uint32 i=0; i<num; i++)
printSequence(seqs[i]);
delete [] seqs;
} else if (strcmp(argv[arg], "-q") == 0) {
failIfNoSource();
failIfNotRandomAccess(); // Impossible to fix, or load whole thing into memory
printIDsFromFile(argv[++arg]);
} else if (strcmp(argv[arg], "-6") == 0) {
withLineBreaks = 60;
if ((argv[arg+1] != 0L) && (argv[arg+1][0] != '-'))
withLineBreaks = strtouint32(argv[++arg]);
} else if (strcmp(argv[arg], "-w") == 0) {
toUppercase = !toUppercase;
for (int z=0; z<256; z++)
translate[z] = (toUppercase) ? alphabet.toUpper(z) : (char)z;
} else if (strcmp(argv[arg], "-R") == 0) {
doReverse = !doReverse;
} else if (strcmp(argv[arg], "-C") == 0) {
doComplement = !doComplement;
} else if (strcmp(argv[arg], "-H") == 0) {
withDefLine = !withDefLine;
specialDefLine = 0L;
} else if (strcmp(argv[arg], "-h") == 0) {
withDefLine = true;
specialDefLine = argv[++arg];
} else if (strcmp(argv[arg], "-e") == 0) {
begPos = strtouint32(argv[++arg]);
endPos = strtouint32(argv[++arg]);
} else if (strcmp(argv[arg], "-ends") == 0) {
endExtract = strtouint32(argv[++arg]);
} else if (strcmp(argv[arg], "-A") == 0) {
processFile(argv[++arg]);
} else if (strcmp(argv[arg], "--findduplicates") == 0) {
findDuplicates(argv[++arg]);
exit(0);
} else if (strcmp(argv[arg], "--mapduplicates") == 0) {
mapDuplicates(argv[arg+1], argv[arg+2]);
exit(0);
} else if (strcmp(argv[arg], "--md5") == 0) {
md5_s md5;
char sum[33];
fasta = new seqCache(argv[++arg]);
for (uint32 s=0; s<fasta->getNumberOfSequences(); s++) {
seqInCore *S = fasta->getSequenceInCore(s);
fprintf(stdout, "%s %s\n",
md5_toascii(md5_string(&md5, S->sequence(), S->sequenceLength()), sum),
S->header());
delete S;
}
delete fasta;
exit(0);
} else if ((strcmp(argv[arg], "--partition") == 0) ||
(strcmp(argv[arg], "--partitionmap") == 0)) {
char *prefix = 0L;
if (strcmp(argv[arg], "--partition") == 0)
prefix = argv[++arg];
// does the next arg end with gbp, mbp, kbp or bp? If so,
// partition by length, else partition into buckets.
//
int al = strlen(argv[arg+1]);
uint64 ps = strtouint64(argv[arg+1]);
char a3 = (al<3) ? '0' : alphabet.toLower(argv[arg+1][al-3]);
char a2 = (al<2) ? '0' : alphabet.toLower(argv[arg+1][al-2]);
char a1 = (al<1) ? '0' : alphabet.toLower(argv[arg+1][al-1]);
// partition!
if (!isdigit(a1) || !isdigit(a2) || !isdigit(a3)) {
if ((a3 == 'g') && (a2 == 'b') && (a1 == 'p')) {
ps *= 1000000000;
} else if ((a3 == 'm') && (a2 == 'b') && (a1 == 'p')) {
ps *= 1000000;
} else if ((a3 == 'k') && (a2 == 'b') && (a1 == 'p')) {
ps *= 1000;
} else if (isdigit(a3) && (a2 == 'b') && (a1 == 'p')) {
ps *= 1;
} else {
fprintf(stderr, "Unknown partition size option '%s'\n", argv[arg+1]), exit(1);
}
if (ps == 0)
fprintf(stderr, "Unknown or zero partition size '%s'\n", argv[arg+1]), exit(1);
partitionBySize(prefix, ps, argv[arg+2]);
} else {
if (ps == 0)
fprintf(stderr, "Unknown or zero partition size '%s'\n", argv[arg+1]), exit(1);
partitionByBucket(prefix, ps, argv[arg+2]);
}
exit(0);
} else if (strcmp(argv[arg], "--segment") == 0) {
partitionBySegment(argv[arg+1], strtouint32(argv[arg+2]), argv[arg+3]);
exit(0);
} else if (strcmp(argv[arg], "--gccontent") == 0) {
computeGCcontent(argv[++arg]);
exit(0);
} else if (strcmp(argv[arg], "--dumpblocks") == 0) {
dumpBlocks(argv[++arg]);
exit(0);
} else if (strcmp(argv[arg], "--stats") == 0) {
stats(argv[arg+1], (argv[arg+2] != 0L) ? strtouint64(argv[arg+2]) : 0);
exit(0);
} else if (strcmp(argv[arg], "--errors") == 0) {
int L = strtouint32(argv[++arg]); // Desired length
int l = 0; // min of desired length, length of sequence
int N = strtouint32(argv[++arg]); // number of copies per sequence
int C = strtouint32(argv[++arg]); // number of mutations per copy
double P = atof(argv[++arg]); // probability of mutation
uint32 i = 0;
fasta = new seqCache(argv[++arg]);
seqInCore *S = fasta->getSequenceInCore(i++);
while (S) {
char *seq = S->sequence();
char *hdr = S->header();
int len = S->sequenceLength();
l = len;
if ((L > 0) && (L < len))
l = L;
simseq(seq, hdr, len, N, l, C, P);
delete S;
S = fasta->getSequenceInCore(i++);
}
delete fasta;
exit(0);
} else if (strcmp(argv[arg], "--seqstore") == 0) {
constructSeqStore(argv[++arg], fasta);
exit(0);
} else if (strcmp(argv[arg], "-help") == 0) {
if ((argv[arg+1]) && (strcmp(argv[arg+1], "analysis") == 0))
helpAnalysis(argv[0]);
else if ((argv[arg+1]) && (strcmp(argv[arg+1], "examples") == 0))
helpExamples(argv[0]);
else
helpStandard(argv[0]);
exit(0);
} else {
helpStandard(argv[0]);
fprintf(stderr, "Unknown option '%s'\n", argv[arg]);
exit(1);
}
arg++;
}
delete fasta;
fasta = 0L;
}
static void cached_name(struct file_cache *c, const char *path, char *lpath)
{
unsigned char digest[MD5_DIGEST_LENGTH];
md5_buffer(path, strlen(path), digest);
sprintf(lpath, "%s/%02x/%s", c->root, digest[0], md5_string(digest));
}
void md5_string(StringBuffer& inpstring, StringBuffer& outstring)
{
md5_string(inpstring, inpstring.length(), outstring);
}
void md5_string2(const char* inpstring, StringBuffer& outstring)
{
md5_string(inpstring,(size32_t)strlen(inpstring),outstring);
}
int main()
{
const char* s = "中国人民银行！";
const char* key = "zsxxsz";
char buf1[33], buf2[33];
acl::md5::md5_string(s, strlen(s), key, strlen(key),
buf1, sizeof(buf1));
printf("first md5: %s\r\n", buf1);
md5_string(s, key, strlen(key), buf2, sizeof(buf2));
printf("second md5: %s\r\n", buf2);
assert(strcmp(buf1, buf2) == 0);
/////////////////////////////////////////////////////////////////////
acl::md5 md5;
s = "ABCDEFGHIGKLMNOPQRSTUVWXYZ";
md5.update(s, strlen(s));
md5.finish();
acl::safe_snprintf(buf1, sizeof(buf1), "%s", md5.get_string());
md5.reset();
char ch;
size_t len = strlen(s);
for (size_t i = 0; i < len; i++)
{
ch = s[i];
md5.update(&ch, 1);
}
md5.finish();
acl::safe_snprintf(buf2, sizeof(buf2), "%s", md5.get_string());
if (strcmp(buf1, buf2) == 0)
printf("OK: %s\r\n", buf1);
else
printf("error, buf1: %s, buf2: %s\r\n", buf1, buf2);
/////////////////////////////////////////////////////////////////////
md5.reset();
len = 1024000;
char* buf = (char*) malloc(len);
for (size_t i = 0; i < len; i++)
{
ch = i % 255;
buf[i] = ch;
md5.update(&ch, 1);
}
md5.finish();
acl::safe_snprintf(buf1, sizeof(buf1), "%s", md5.get_string());
md5.reset();
md5.update(buf, len);
md5.finish();
acl::safe_snprintf(buf2, sizeof(buf2), "%s", md5.get_string());
if (strcmp(buf1, buf2) == 0)
printf("OK2: %s\r\n", buf1);
else
printf("error, buf1: %s, buf2: %s\r\n", buf1, buf2);
#ifdef WIN32
getchar();
#endif
return 0;
}
static void filename_hash(const char* filename, int fanout, char* dir) {
std::string s = md5_string((const unsigned char*)filename, strlen(filename));
int x = strtol(s.substr(1, 7).c_str(), 0, 16);
sprintf(dir, "%x", x % fanout);
}
int
main(int argc, char **argv) {
int error = 0;
readBuffer *B = 0L;
size_t L = 0;
size_t H = 0;
size_t R = 0;
// If we are given a file, use that, otherwise, use ourself.
//
filename = argv[argc-1];
L = sizeOfFile(filename);
H = L/2;
R = L - H;
fprintf(stderr, "L=%d H=%d R=%d\n", L, H, R);
// Suck in the whole file, compute the correct md5 checksum on it
//
char *c = new char [L];
FILE *F = fopen(filename, "r");
fread(c, sizeof(char), L, F);
fclose(F);
full = md5_string(0L, c, L);
part = md5_string(0L, c+H, R);
delete [] c;
B = new readBuffer(filename, 999);
error += doTest(B, full, "#1 (read)");
B->seek(0);
error += doTest(B, full, "#2 (seek)");
B->seek(H);
error += doTest(B, part, "#2 (seek half)");
delete B;
B = new readBuffer(filename, 0);
error += doTest(B, full, "#3 (mmap)");
B->seek(0);
error += doTest(B, full, "#2 (mmap seek)");
B->seek(H);
error += doTest(B, part, "#2 (mmap seek half)");
delete B;
B = new readBuffer(filename, 0);
error += doTestRead(B, full, 10000, "#4 (read buffer=mmap readsize=10000)");
delete B;
B = new readBuffer(filename, 100);
error += doTestRead(B, full, 10000, "#4 (read buffer=100 readsize=10000)");
delete B;
B = new readBuffer(filename, 2000);
error += doTestRead(B, full, 1000, "#4 (read buffer=2000 readsize=1000)");
delete B;
B = new readBuffer(filename, L);
error += doTestRead(B, full, L+1000, "#5 (read buffer=filesize readsize=filesize+1000)");
delete B;
return(error);
}
/* Search a file for magic signatures */
int process_file(char *bin_file, struct binconf *config, struct magic_signature **signatures, int num_sigs, struct magic_filter **filters, int filter_count)
{
char *md5 = NULL, *current_time = NULL, *ptr = NULL;
const void *buffer = NULL, *type = NULL;
size_t fsize = 0;
int i = 0, j = 0, retval = EXIT_FAILURE;
/* Read in the target file */
buffer = file_read(bin_file, &fsize);
if(!buffer || fsize == 0)
{
fprintf(stderr,"ERROR: Failed to read file '%s'.\n", bin_file);
goto end;
}
/* If no scan length was specified, scan the entire file */
if(!config->length || config->length > fsize)
{
config->length = fsize;
}
/* Sanity check on the length + offset values */
if((config->length + config->offset) > fsize)
{
config->length -= (config->length + config->offset) - fsize;
}
if(config->verbose)
{
md5 = md5_string((void *) buffer,fsize);
current_time = timestamp();
print("\n");
print("Scan Time: %s\n", current_time);
print("Magic File: %s\n", config->magic);
if(config->smart)
{
print("Signatures: %d\n", num_sigs);
}
else
{
print("Signatures: *\n");
}
print("Target File: %s\n", bin_file);
print("MD5 Checksum: %s\n", md5);
if(current_time) free(current_time);
if(md5) free(md5);
}
print("\nDECIMAL \tHEX \tDESCRIPTION\n");
print("-------------------------------------------------------------------------------------------------------\n");
/* Loop through the file contents starting at the given offset.
* Honor the given byte alignment (i.e., if align == 4, only look at every 4th byte).
* Stop looping when length bytes have been searched, or when the end of the file is reached.
*/
for(i=config->offset; ((i-config->offset)<config->length && i<(fsize-config->align)); i+=config->align)
{
for(j=0; j<num_sigs; j++)
{
/* Make sure we don't seek past the end of the buffer */
if(!config->smart || (i+signatures[j]->offset < fsize))
{
/* Pre-screen data for magic file signatures prior to invoking libmagic. This significantly improves scan time. */
if(!config->smart ||
signatures[j]->wildcard == 1 ||
memcmp((buffer+i+signatures[j]->offset), signatures[j]->signature, signatures[j]->size) == 0
)
{
/* Since we found a signature match, ask libmagic to further examine the given offset into the file buffer */
type = magic_buffer(config->cookie, buffer+i, (fsize-i));
/* Ignore NULL, ".*text.*" and "data" responses */
if(type != NULL && strncmp(type,DATA,DATA_SIZE) != 0 && strstr(type,TEXT) == NULL)
{
/*
* If filters were specified and the filter check specifies that
* result should be excluded, then don't display it.
*/
if(filter_count > 0)
{
/* Don't display anything that has been explicitly marked in the exclude list */
if(filter_check(filters, filter_count, (char *) type) == RESULT_EXCLUDE)
{
break;
}
}
/* Prettify output if multiple matches were found at the same offset */
if((config->flags | MAGIC_CONTINUE) == config->flags)
{
while((ptr = strstr(type, MULTIPLE_MATCH_DELIM)))
{
memcpy(ptr, MULTIPLE_MATCH_NEWLINE, MULTIPLE_MATCH_SIZE);
}
}
print("%-10d\t0x%-8X\t",i,i);
print("%s\n",type);
break;
}
}
}
}
}
print("\n");
retval = EXIT_SUCCESS;
end:
if(buffer) munmap((void *) buffer, fsize);
return retval;
}
