//input: G is the query graph, Gdb is the database graph,
// M is the mappings for the important nodes
//output: M is also the output containing all the mappings
void Query::growMatch(vector<Neighborhood>& nbs, HashGraph* Gdb, OrthologInfoList* pOrthinfolist_db, GraphMatch* gm)
{
//initialize
debug(1, "in growMatch\n");
vector<bool> mark(G->n(), false);
debug(1, "G->n() = "<<G->n()<<endl);
vector<bool> dbmark(Gdb->n(), false);
debug(1, "Gdb->n() = "<<Gdb->n()<<endl);
//put mappings in M to a priority queue Q sorted by (Miss, degree difference, connection difference)
Queue Q;
hash_set<int> nodesInQ;
for(NodeMappingSet::iterator iter=gm->mappings.begin(); iter!=gm->mappings.end(); iter++)
{
Q.insert(*iter);
nodesInQ.insert(iter->source);
mark[iter->source]=true;
dbmark[iter->target]=true;
}
gm->mappings.clear();
while(!Q.empty())
{
//get the mapping m with minimum () value from Q
NodeMapping m=*(Q.begin());
Q.erase(Q.begin());
//put m into M
gm->mappings.insert(m);
mark[m.source]=true;
dbmark[m.target]=true;
//finding new mappings for nodes nearby N_q
examineNodesNearBy(nbs, Gdb, pOrthinfolist_db, m, gm, Q, nodesInQ, mark, dbmark);
}
}
int
main( int argc, char **argv )
{
int c;
int errflag = 0;
int orb;
int stop = 0;
long nrecs;
char *match = ".*/pf/st";
char *from = 0;
char *statefile = 0;
char *pfname = "orb2rrdc";
char *orbname;
char *dbcache;
char *rrdtool;
char command[STRSZ];
char net[STRSZ];
char sta[STRSZ];
char rrdvar[STRSZ];
char key[STRSZ];
char path[FILENAME_MAX];
Dbptr db;
Dbptr dbt;
Pf *pf;
char *Default_network;
Tbl *dlslines;
Arr *Dls_vars_dsparams;
Arr *Dls_vars_rras;
Tbl *Dls_vars_keys;
char *line;
char *dls_var;
char *dsparams;
Tbl *rras;
int i;
int j;
OrbreapThr *ort;
int pktid;
char srcname[ORBSRCNAME_SIZE];
double time = 0;
char *packet = 0;
int nbytes = 0;
int bufsize = 0;
Packet *pkt = 0;
int rc;
char *s;
Pf *dlspf;
Tbl *dlspfkeys;
char *element;
Tbl *parts;
double val;
Pf *pfval = 0;
elog_init( argc, argv );
while( ( c = getopt( argc, argv, "vVd:s:p:m:f:" ) ) != -1 ) {
switch( c ) {
case 'd':
CacheDaemon = optarg;
break;
case 'f':
from = optarg;
break;
case 'm':
match = optarg;
break;
case 'p':
pfname = optarg;
break;
case 's':
statefile = optarg;
break;
case 'v':
Verbose++;
break;
case 'V':
VeryVerbose++;
Verbose++;
break;
default:
elog_complain( 0, "Unknown option '%c'\n", c );
errflag++;
break;
}
}
if( errflag || argc - optind != 2 ) {
usage();
}
if( Verbose ) {
elog_notify( 0, "Starting at %s (%s $Revision$ $Date$)\n",
zepoch2str( str2epoch( "now" ), "%D %T %Z", "" ),
Program_Name );
}
orbname = argv[optind++];
dbcache = argv[optind++];
pfread( pfname, &pf );
rrdtool = pfget_string( pf, "rrdtool" );
if( rrdtool == NULL || ! strcmp( rrdtool, "" ) ) {
elog_die( 0, "Error: no rrdtool executable name specified in parameter file\n" );
} else if( ( rrdtool[0] == '/' && ! is_present( rrdtool ) ) || ( rrdtool[0] != '/' && ! datafile( "PATH", rrdtool ) ) ) {
elog_die( 0, "Error: can't find rrdtool executable by name of '%s' (check PATH environment "
"variable, or absolute path name if given)\n", rrdtool );
} else if( rrdtool[0] == '/' ) {
sprintf( command, "%s -", rrdtool );
} else {
sprintf( command, "rrdtool -" );
}
Suppress_egrep = pfget_string( pf, "suppress_egrep" );
if( Suppress_egrep != NULL && strcmp( Suppress_egrep, "" ) ) {
if( ! datafile( "PATH", "egrep" ) ) {
elog_complain( 0, "Ignoring suppress_egrep parameter: can't find egrep on path\n" );
} else {
sprintf( command, "%s 2>&1 | egrep -v '%s'", command, Suppress_egrep );
}
}
if( VeryVerbose ) {
elog_notify( 0, "Executing command: %s\n", command );
}
Rrdfp = popen( command, "w" );
if( Rrdfp == (FILE *) NULL ) {
elog_die( 0, "Failed to open socket to rrdtool command\n" );
}
orb = orbopen( orbname, "r&" );
if( orb < 0 ) {
elog_die( 0, "Failed to open orb '%s' for reading. Bye.\n", orbname );
}
orbselect( orb, match );
if( from != NULL && statefile == NULL ) {
pktid = orbposition( orb, from );
if( Verbose ) {
elog_notify( 0, "Positioned to packet %d\n", pktid );
}
} else if( from != NULL ) {
elog_complain( 0, "Ignoring -f in favor of existing state file\n" );
}
if( statefile != NULL ) {
stop = 0;
exhume( statefile, &stop, 15, 0 );
orbresurrect( orb, &pktid, &time );
if( Verbose ) {
elog_notify( 0, "Resurrecting state to pktid %d, time %s\n",
pktid, s = strtime( time ) );
free( s );
}
orbseek( orb, pktid );
}
dbopen( dbcache, "r+", &db );
if( db.database < 0 ) {
elog_die( 0, "Failed to open cache database '%s'. Bye.\n", dbcache );
} else {
db = dblookup( db, "", "rrdcache", "", "" );
if( db.table < 0 ) {
elog_die( 0, "Failed to lookup 'rrdcache' table in '%s'. Bye.\n", dbcache );
}
}
dbcrunch( db );
dbt = dbsubset( db, "endtime == NULL", NULL );
Rrd_files = newarr( 0 );
dbquery( dbt, dbRECORD_COUNT, &nrecs );
for( dbt.record = 0; dbt.record < nrecs; dbt.record++ ) {
dbgetv( dbt, 0, "net", &net, "sta", &sta, "rrdvar", &rrdvar, NULL );
dbfilename( dbt, (char *) &path );
sprintf( key, "%s:%s:%s", net, sta, rrdvar );
if( ! is_present( path ) ) {
elog_complain( 0, "WARNING: rrd file '%s', listed in database, does not exist. "
"Removing database entry.\n", path );
dbmark( dbt );
} else {
setarr( Rrd_files, key, strdup( path ) );
if( VeryVerbose ) {
elog_notify( 0, "Re-using rrd file '%s' for '%s'\n", path, key );
}
}
}
Rrdfile_pattern = pfget_string( pf, "rrdfile_pattern" );
Status_stepsize_sec = pfget_double( pf, "status_stepsize_sec" );
Default_network = pfget_string( pf, "default_network" );
dlslines = pfget_tbl( pf, "dls_vars" );
Dls_vars_dsparams = newarr( 0 );
Dls_vars_rras = newarr( 0 );
for( i = 0; i < maxtbl( dlslines ); i++ ) {
line = gettbl( dlslines, i );
strtr( line, "\t", " " );
rras = split( line, ' ' );
dls_var = shifttbl( rras );
dsparams = shifttbl( rras );
setarr( Dls_vars_dsparams, dls_var, dsparams );
setarr( Dls_vars_rras, dls_var, rras );
}
ort = orbreapthr_new( orb, -1., 0 );
for( ; stop == 0; ) {
orbreapthr_get( ort, &pktid, srcname, &time, &packet, &nbytes, &bufsize );
if( statefile ) {
rc = bury();
if( rc < 0 ) {
elog_complain( 0, "Unexpected failure of bury command! "
"(are there two orb2rrdc's running with the same state"
"file?)\n" );
clear_register( 1 );
}
}
rc = unstuffPkt( srcname, time, packet, nbytes, &pkt );
if( rc == Pkt_pf ) {
if( VeryVerbose ) {
/* Parameter files generally too big for elog */
fprintf( stderr, "Received a parameter-file '%s' at %s\n%s\n\n",
srcname,
s = strtime( time ),
pf2string( pkt->pf ) );
free( s );
} else if( Verbose ) {
elog_notify( 0, "Received a parameter-file '%s' at %s\n",
srcname, s = strtime( time ) );
free( s );
}
pfmorph( pkt->pf );
if( VeryVerbose ) {
fprintf( stderr, "Morphed parameter-file '%s' to interpret 'opt':\n%s\n\n",
srcname,
pf2string( pkt->pf ) );
}
pfget( pkt->pf, "dls", (void **) &dlspf );
dlspfkeys = pfkeys( dlspf );
Dls_vars_keys = keysarr( Dls_vars_dsparams );
for( i = 0; i < maxtbl( dlspfkeys ); i++ ) {
element = gettbl( dlspfkeys, i );
if( strcontains( element, "_", 0, 0, 0 ) ) {
parts = split( (s = strdup( element )), '_' );
sprintf( net, "%s", (char *) gettbl( parts, 0 ) );
sprintf( sta, "%s", (char *) gettbl( parts, 1 ) );
free( s );
freetbl( parts, 0 );
} else {
sprintf( net, "%s", Default_network );
sprintf( sta, "%s", element );
}
for( j = 0; j < maxtbl( Dls_vars_keys ); j++ ) {
dls_var = gettbl( Dls_vars_keys, j );
sprintf( key, "%s{%s}", element, dls_var );
if( pfresolve( dlspf, key, 0, &pfval ) < 0 ) {
elog_complain( 0, "Unable to extract variable '%s' "
"(not present or wrong type) from element '%s' "
"in packet from '%s', timestamped '%s'; Skipping\n",
key, element, srcname, s = strtime( time ) );
free( s );
pfval = 0;
continue;
} else if( pfval != (Pf *) NULL &&
pfval->value.s != (char *) NULL &&
! strcmp( pfval->value.s, "-" ) ) {
if( VeryVerbose ) {
elog_notify( 0, "Non-floating point value '-' in variable '%s', "
"in packet from '%s', timestamped '%s'; Skipping data point\n",
key, srcname, s = strtime( time ) );
free( s );
}
continue;
} else {
val = pfget_double( dlspf, key );
}
archive_dlsvar( db, net, sta, dls_var,
(char *) getarr( Dls_vars_dsparams, dls_var ),
(Tbl *) getarr( Dls_vars_rras, dls_var ),
time, val );
}
}
freetbl( dlspfkeys, 0 );
freetbl( Dls_vars_keys, 0 );
} else if( rc == Pkt_stash ) {
; /* Do nothing */
} else {
if( Verbose ) {
elog_notify( 0, "Received a packet that's not a parameter file "
"(type '%d' from unstuffPkt); skipping\n", rc );
}
}
}
}
