/*METHOD: Evaluate the kraken database file*/
void evaluate_kfile(string k_file, string o_file, const taxonomy *my_taxonomy, const map<int, taxonomy *> *taxid2node, const map<string, int> seqid2taxid, const int kmer_len, const int read_len){
/*Read the file and get maps:
* map of number seqid to the kmer distribution
* map of number seqid to taxid
*/
map<int, string> id2kmers;
map<int, int> id2taxid;
map<int, string> id2seqid;
map<int, string> id2tandl;
int num_reads = read_kfile(k_file, &seqid2taxid, &id2seqid, &id2kmers, &id2taxid, &id2tandl);
/*For each seqid, in parallel, convert kmer distribution to read distribution*/
convert_distribution(o_file, num_reads, &id2seqid, &id2kmers, &id2taxid, &id2tandl, my_taxonomy, taxid2node, kmer_len, read_len);
}
int
f_starttls( SNET *sn, int ac, char **av )
{
int rc;
X509 *peer;
char buf[ 1024 ];
if ( ac != 1 ) {
snet_writef( sn, "%d Syntax error (no parameters allowed)\r\n", 501 );
return( 1 );
} else {
snet_writef( sn, "%d Ready to start TLS\r\n", 220 );
}
/* We get here when the client asks for TLS with the STARTTLS verb */
/*
* Client MUST NOT attempt to start a TLS session if a TLS
* session is already active. No mention of what to do if it does...
*
* Once STARTTLS has succeeded, the STARTTLS verb is no longer valid
*/
/*
* Begin TLS
*/
/* This is where the TLS start */
/* At this point the client is also starting TLS */
/* 1 is for server, 0 is client */
if (( rc = snet_starttls( sn, ctx, 1 )) != 1 ) {
syslog( LOG_ERR, "f_starttls: snet_starttls: %s",
ERR_error_string( ERR_get_error(), NULL ) );
snet_writef( sn, "%d SSL didn't work error! XXX\r\n", 501 );
return( 1 );
}
if ( authlevel >= 2 ) {
if (( peer = SSL_get_peer_certificate( sn->sn_ssl ))
== NULL ) {
syslog( LOG_ERR, "no peer certificate" );
return( -1 );
}
syslog( LOG_INFO, "CERT Subject: %s\n",
X509_NAME_oneline( X509_get_subject_name( peer ), buf,
sizeof( buf )));
X509_NAME_get_text_by_NID( X509_get_subject_name( peer ),
NID_commonName, buf, sizeof( buf ));
if (( remote_cn = strdup( buf )) == NULL ) {
syslog( LOG_ERR, "strdup: %m" );
X509_free( peer );
return( -1 );
}
X509_free( peer );
}
/* get command file */
if ( command_k( "config", 0 ) < 0 ) {
/* Client not in config */
commands = noauth;
ncommands = sizeof( noauth ) / sizeof( noauth[ 0 ] );
} else {
/* Client in config */
commands = auth;
ncommands = sizeof( auth ) / sizeof( auth[ 0 ] );
if ( read_kfile( sn, command_file ) != 0 ) {
/* error message given in list_transcripts */
exit( 1 );
}
}
return( 0 );
}
int
cmdloop( int fd, struct sockaddr_in *sin )
{
SNET *sn;
struct hostent *hp;
char *p;
int ac, i;
int one = 1;
unsigned int n;
char **av, *line;
struct timeval tv;
extern char *version;
extern int connections;
extern int maxconnections;
extern int rap_extensions;
if ( authlevel == 0 ) {
commands = noauth;
ncommands = sizeof( noauth ) / sizeof( noauth[ 0 ] );
} else {
commands = notls;
ncommands = sizeof( notls ) / sizeof( notls[ 0 ] );
}
if (( sn = snet_attach( fd, 1024 * 1024 )) == NULL ) {
syslog( LOG_ERR, "snet_attach: %m" );
exit( 1 );
}
remote_addr = strdup( inet_ntoa( sin->sin_addr ));
if (( hp = gethostbyaddr( (char *)&sin->sin_addr,
sizeof( struct in_addr ), AF_INET )) == NULL ) {
remote_host = strdup( remote_addr );
} else {
/* set global remote_host for retr command */
remote_host = strdup( hp->h_name );
for ( p = remote_host; *p != '\0'; p++ ) {
*p = tolower( *p );
}
}
syslog( LOG_INFO, "child for [%s] %s",
inet_ntoa( sin->sin_addr ), remote_host );
if ( setsockopt( fd, 6, TCP_NODELAY, &one, sizeof( one )) < 0 ) {
syslog( LOG_ERR, "setsockopt: %m" );
}
if ( maxconnections != 0 ) {
if ( connections > maxconnections ) {
syslog( LOG_INFO, "%s: connection refused: server busy\r\n",
remote_host );
snet_writef( sn, "%d Server busy\r\n", 420 );
exit( 1 );
}
}
if (( access_list = list_new( )) == NULL ) {
syslog( LOG_ERR, "new_list: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
return( -1 );
}
if ( authlevel == 0 ) {
/* lookup proper command file based on the hostname, IP or CN */
if ( command_k( "config", 0 ) < 0 ) {
syslog( LOG_INFO, "%s: Access denied: Not in config file",
remote_host );
snet_writef( sn, "%d No access for %s\r\n", 500, remote_host );
exit( 1 );
} else {
if ( read_kfile( sn, command_file ) != 0 ) {
/* error message given in read_kfile */
exit( 1 );
}
commands = auth;
ncommands = sizeof( auth ) / sizeof( auth[ 0 ] );
}
}
if ( gethostname( hostname, MAXHOSTNAMELEN ) < 0 ) {
syslog( LOG_ERR, "gethostname: %m" );
exit( 1 );
}
snet_writef( sn, "200%sRAP 1 %s %s radmind access protocol\r\n",
rap_extensions ? "-" : " ", hostname, version );
if ( rap_extensions ) {
snet_writef( sn, "200 CAPA" );
#ifdef HAVE_ZLIB
if ( max_zlib_level > 0 ) {
snet_writef( sn, " ZLIB" );
}
#endif /* HAVE_ZLIB */
snet_writef( sn, " REPO" );
snet_writef( sn, "\r\n" );
}
/*
* 60 minutes
* To make fsdiff | lapply work, when fsdiff will take a long time,
* we allow the server to wait a long time.
*/
tv.tv_sec = 60 * 60;
tv.tv_usec = 0 ;
while (( line = snet_getline( sn, &tv )) != NULL ) {
tv.tv_sec = 60 * 60;
tv.tv_usec = 0;
if ( debug ) {
fprintf( stderr, "<<< %s\n", line );
}
if (( ac = argcargv( line, &av )) < 0 ) {
syslog( LOG_ERR, "argcargv: %m" );
return( 1 );
}
if ( ac == 0 ) {
snet_writef( sn, "%d Illegal null command\r\n", 501 );
continue;
}
for ( i = 0; i < ncommands; i++ ) {
n = MAX( strlen( av[ 0 ] ), 4 );
if ( strncasecmp( av[ 0 ], commands[ i ].c_name, n ) == 0 ) {
break;
}
}
if ( i >= ncommands ) {
snet_writef( sn, "%d Command %s unrecognized\r\n", 500, av[ 0 ] );
continue;
}
if ( (*(commands[ i ].c_func))( sn, ac, av ) < 0 ) {
break;
}
}
snet_writef( sn, "%d Server closing connection\r\n", 444 );
if ( line == NULL ) {
syslog( LOG_ERR, "snet_getline: %m" );
}
return( 0 );
}
int
read_kfile( SNET *sn, char *kfile )
{
int ac;
int linenum = 0;
char **av;
char line[ MAXPATHLEN ];
char path[ MAXPATHLEN ];
ACAV *acav;
FILE *f;
if ( snprintf( path, MAXPATHLEN, "command/%s", kfile ) >= MAXPATHLEN ) {
syslog( LOG_ERR, "read_kfile: command/%s: path too long", kfile );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
return( -1 );
}
if (( acav = acav_alloc( )) == NULL ) {
syslog( LOG_ERR, "acav_alloc: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
return( -1 );
}
if (( f = fopen( path, "r" )) == NULL ) {
syslog( LOG_ERR, "fopen: %s: %m", path );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
return( -1 );
}
while ( fgets( line, MAXPATHLEN, f ) != NULL ) {
linenum++;
ac = acav_parse( acav, line, &av );
if (( ac == 0 ) || ( *av[ 0 ] == '#' )) {
continue;
}
/* Skip minus lines in command files for now. Eventually,
* the server should not give access to command files, special files
* and transcripts that have been ultimately removed with a '-'.
* This is difficult as ktcheck reads command files line by line
* and will request info on a file that might be removed with a
* later '-'.
*/
if ( *av[ 0 ] == '-' ) {
continue;
}
if ( ac != 2 ) {
syslog( LOG_ERR, "%s: line %d: invalid number of arguments",
kfile, linenum );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n",
421 );
goto error;
}
switch( *av[ 0 ] ) {
case 'k':
if ( !list_check( access_list, av[ 1 ] )) {
if ( list_insert( access_list, av[ 1 ] ) != 0 ) {
syslog( LOG_ERR, "list_insert: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
goto error;
}
if ( read_kfile( sn, av[ 1 ] ) != 0 ) {
goto error;
}
}
break;
case 'p':
case 'n':
if ( !list_check( access_list, av[ 1 ] )) {
if ( list_insert( access_list, av[ 1 ] ) != 0 ) {
syslog( LOG_ERR, "list_insert: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
goto error;
}
}
break;
case 's':
case 'x':
break;
default:
syslog( LOG_ERR, "%s: line %d: %c: unknown file type", kfile,
linenum, *av[ 0 ] );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n",
421 );
goto error;
}
if ( ferror( f )) {
syslog( LOG_ERR, "fgets: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n",
421 );
goto error;
}
}
if ( fclose( f ) != 0 ) {
syslog( LOG_ERR, "fclose: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
goto error;
}
if ( acav_free( acav ) != 0 ) {
syslog( LOG_ERR, "acav_free: %m" );
snet_writef( sn,
"%d Service not available, closing transmission channel\r\n", 421 );
return( -1 );
}
return( 0 );
error:
fclose( f );
acav_free( acav );
return( -1 );
}