/*
* Get information about port on bridge.
*/
int br_get_port_info(const char *brname, const char *port,
struct port_info *info)
{
DIR *d;
char path[SYSFS_PATH_MAX];
snprintf(path, SYSFS_PATH_MAX, SYSFS_CLASS_NET "%s/brport", port);
d = opendir(path);
if (!d)
goto fallback;
memset(info, 0, sizeof(*info));
fetch_id(path, "designated_root", &info->designated_root);
fetch_id(path, "designated_bridge", &info->designated_bridge);
info->port_no = fetch_int(path, "port_no");
info->port_id = fetch_int(path, "port_id");
info->designated_port = fetch_int(path, "designated_port");
info->path_cost = fetch_int(path, "path_cost");
info->designated_cost = fetch_int(path, "designated_cost");
info->state = fetch_int(path, "state");
info->top_change_ack = fetch_int(path, "change_ack");
info->config_pending = fetch_int(path, "config_pending");
fetch_tv(path, "message_age_timer", &info->message_age_timer_value);
fetch_tv(path, "forward_delay_timer", &info->forward_delay_timer_value);
fetch_tv(path, "hold_timer", &info->hold_timer_value);
closedir(d);
return 0;
fallback:
return old_get_port_info(brname, port, info);
}
bool IndDBase::fetch( Individual * person )
{
if ( ! attached() ) return false;
// Look-up this individual based upon their ID.
// Attach all phenotype and meta-information we find
// Return true if find somebody matching that description
uint64_t idx = fetch_id( person->id() );
if ( idx == 0 ) return false;
if ( fetch( person , fetch_id( person->id() ) ) )
{
person->missing( false );
return true;
}
else
{
person->missing( true );
return false;
}
}
/*
* Get information about port on bridge.
*/
int br_get_port_info(const char *brname, const char *port,
struct port_info *info)
{
#ifndef HAVE_LIBSYSFS
return old_get_port_info(brname, port, info);
#else
struct sysfs_directory *sdir
= bridge_sysfs_directory(port, SYSFS_BRIDGE_PORT_ATTR);
if (!sdir)
return old_get_port_info(brname, port, info);
memset(info, 0, sizeof(*info));
fetch_id(sdir, "designated_root", &info->designated_root);
fetch_id(sdir, "designated_bridge", &info->designated_bridge);
info->port_no = fetch_int(sdir, "port_no");
info->port_id = fetch_int(sdir, "port_id");
info->designated_port = fetch_int(sdir, "designated_port");
info->path_cost = fetch_int(sdir, "path_cost");
info->designated_cost = fetch_int(sdir, "designated_cost");
info->state = fetch_int(sdir, "state");
info->top_change_ack = fetch_int(sdir, "change_ack");
info->config_pending = fetch_int(sdir, "config_pending");
fetch_tv(sdir, "message_age_timer",
&info->message_age_timer_value);
fetch_tv(sdir, "forward_delay_timer",
&info->forward_delay_timer_value);
fetch_tv(sdir, "hold_timer",
&info->hold_timer_value);
sysfs_close_directory(sdir);
return 0;
#endif
}
/*
* Get bridge parameters using either sysfs or old
* ioctl.
*/
static int br_get_bridge_info(const char *bridge, struct bridge_info *info)
{
#ifdef HAVE_LIBSYSFS
struct sysfs_class_device *dev;
char path[SYSFS_PATH_MAX];
if (!br_class_net)
goto fallback;
dev = sysfs_get_class_device(br_class_net, bridge);
if (!dev) {
dprintf("get_class_device '%s' failed\n", bridge);
goto fallback;
}
snprintf(path, SYSFS_PATH_MAX, "%s/bridge", dev->path);
if (sysfs_path_is_dir(path)) {
dprintf("path '%s' is not a directory\n", path);
sysfs_close_class_device(dev);
goto fallback;
}
memset(info, 0, sizeof(*info));
fetch_id(dev, BRIDGEATTR("root_id"), &info->designated_root);
fetch_id(dev, BRIDGEATTR("bridge_id"), &info->bridge_id);
info->root_path_cost = fetch_int(dev, BRIDGEATTR("root_path_cost"));
fetch_tv(dev, BRIDGEATTR("max_age"), &info->max_age);
fetch_tv(dev, BRIDGEATTR("hello_time"), &info->hello_time);
fetch_tv(dev, BRIDGEATTR("forward_delay"), &info->forward_delay);
fetch_tv(dev, BRIDGEATTR("max_age"), &info->bridge_max_age);
fetch_tv(dev, BRIDGEATTR("hello_time"), &info->bridge_hello_time);
fetch_tv(dev, BRIDGEATTR("forward_delay"), &info->bridge_forward_delay);
fetch_tv(dev, BRIDGEATTR("ageing_time"), &info->ageing_time);
fetch_tv(dev, BRIDGEATTR("hello_timer"), &info->hello_timer_value);
fetch_tv(dev, BRIDGEATTR("tcn_timer"), &info->tcn_timer_value);
fetch_tv(dev, BRIDGEATTR("topology_change_timer"),
&info->topology_change_timer_value);;
fetch_tv(dev, BRIDGEATTR("gc_timer"), &info->gc_timer_value);
info->root_port = fetch_int(dev, BRIDGEATTR("root_port"));
info->stp_enabled = fetch_int(dev, BRIDGEATTR("stp_state"));
info->topology_change = fetch_int(dev, BRIDGEATTR("topology_change"));
info->topology_change_detected = fetch_int(dev,
BRIDGEATTR
("topology_change_detected"));
sysfs_close_class_device(dev);
return 0;
fallback:
#endif
return old_get_bridge_info(bridge, info);
}
/*
* Get bridge parameters using either sysfs or old
* ioctl.
*/
int br_get_bridge_info(const char *bridge, struct bridge_info *info)
{
DIR *dir;
char path[SYSFS_PATH_MAX];
snprintf(path, SYSFS_PATH_MAX, SYSFS_CLASS_NET "%s/bridge", bridge);
dir = opendir(path);
if (dir == NULL) {
dprintf("path '%s' is not a directory\n", path);
goto fallback;
}
memset(info, 0, sizeof(*info));
fetch_id(path, "root_id", &info->designated_root);
fetch_id(path, "bridge_id", &info->bridge_id);
info->root_path_cost = fetch_int(path, "root_path_cost");
fetch_tv(path, "max_age", &info->max_age);
fetch_tv(path, "hello_time", &info->hello_time);
fetch_tv(path, "forward_delay", &info->forward_delay);
fetch_tv(path, "max_age", &info->bridge_max_age);
fetch_tv(path, "hello_time", &info->bridge_hello_time);
fetch_tv(path, "forward_delay", &info->bridge_forward_delay);
fetch_tv(path, "ageing_time", &info->ageing_time);
fetch_tv(path, "hello_timer", &info->hello_timer_value);
fetch_tv(path, "tcn_timer", &info->tcn_timer_value);
fetch_tv(path, "topology_change_timer",
&info->topology_change_timer_value);;
fetch_tv(path, "gc_timer", &info->gc_timer_value);
info->root_port = fetch_int(path, "root_port");
info->stp_enabled = fetch_int(path, "stp_state");
info->topology_change = fetch_int(path, "topology_change");
info->topology_change_detected = fetch_int(path, "topology_change_detected");
closedir(dir);
return 0;
fallback:
return old_get_bridge_info(bridge, info);
}
uint64_t IndDBase::insert( const Individual & ind , bool * newone )
{
int id = fetch_id( ind.id() );
if ( id == 0 )
{
// This is a new record
sql.bind_text( stmt_insert_individual , ":name" , ind.id() );
sql.bind_text( stmt_insert_individual , ":fid" , ind.fid() );
sql.bind_text( stmt_insert_individual , ":iid" , ind.iid() );
sql.bind_text( stmt_insert_individual , ":pat" , ind.father() );
sql.bind_text( stmt_insert_individual , ":mat" , ind.mother() );
sql.bind_text( stmt_insert_individual , ":sex" , Helper::int2str( ind.sex() ) );
sql.step( stmt_insert_individual );
sql.reset( stmt_insert_individual );
if ( newone ) *newone = true;
id = fetch_id( ind.id() );
}
else
{
// ..append an existing record
sql.bind_text( stmt_update_individual , ":name" , ind.id() );
sql.bind_text( stmt_update_individual , ":fid" , ind.fid() );
sql.bind_text( stmt_update_individual , ":iid" , ind.iid() );
sql.bind_text( stmt_update_individual , ":pat" , ind.father() );
sql.bind_text( stmt_update_individual , ":mat" , ind.mother() );
sql.bind_text( stmt_update_individual , ":sex" , Helper::int2str( ind.sex() ) );
sql.step( stmt_update_individual );
sql.reset( stmt_update_individual );
if( newone ) *newone = false;
}
return id;
}
/*
* Get bridge parameters using either sysfs or old
* ioctl.
*/
int br_get_bridge_info(const char *bridge, struct bridge_info *info)
{
#ifndef HAVE_LIBSYSFS
return old_get_bridge_info(bridge, info);
#else
struct sysfs_directory *sdir;
sdir = bridge_sysfs_directory(bridge, SYSFS_BRIDGE_ATTR);
if (!sdir)
return old_get_bridge_info(bridge,info);
memset(info, 0, sizeof(*info));
fetch_id(sdir, "root_id", &info->designated_root);
fetch_id(sdir, "bridge_id", &info->bridge_id);
info->root_path_cost = fetch_int(sdir, "root_path_cost");
fetch_tv(sdir, "max_age", &info->max_age);
fetch_tv(sdir, "hello_time", &info->hello_time);
fetch_tv(sdir, "forward_delay", &info->forward_delay);
fetch_tv(sdir, "max_age", &info->bridge_max_age);
fetch_tv(sdir, "hello_time", &info->bridge_hello_time);
fetch_tv(sdir, "forward_delay", &info->bridge_forward_delay);
fetch_tv(sdir, "ageing_time", &info->ageing_time);
fetch_tv(sdir, "hello_timer", &info->hello_timer_value);
fetch_tv(sdir, "tcn_timer", &info->tcn_timer_value);
fetch_tv(sdir, "topology_change_timer",
&info->topology_change_timer_value);;
fetch_tv(sdir, "gc_timer", &info->gc_timer_value);
info->root_port = fetch_int(sdir, "root_port");
info->stp_enabled = fetch_int(sdir, "stp_state");
info->topology_change = fetch_int(sdir, "topology_change");
info->topology_change_detected = fetch_int(sdir, "topology_change_detected");
sysfs_close_directory(sdir);
return 0;
#endif
}
bool IndDBase::load_phenotypes( const std::string & filename )
{
if ( ! attached() ) Helper::halt( "no attached INDDB" );
if ( ! Helper::fileExists(filename) )
{
plog.warn("could not find phenotype file " + filename );
return false;
}
// Expect a variant of FAM file format
InFile f( filename );
std::map<std::string,int> phe_codes1;
std::map<int,int> phe_codes2;
std::vector<std::string> phe_codes;
std::map<std::string,mType> type_codes;
std::map<std::string,std::string> mis_codes;
int expected_col_count = -1;
int inserted = 0;
sql.begin();
drop_index();
while ( ! f.eof() )
{
std::string s = f. readLine();
if ( s == "" ) continue;
// Meta-information?
if ( s.size() > 2 && s.substr(0,2) == "##" )
{
std::vector<std::string> tok = Helper::quoted_parse( s.substr(2) );
// need at least a name
if ( tok.size() < 1 ) continue;
std::string name = tok[0];
// defaults
std::string type = "Integer";
std::string miss = "0";
std::string desc = "Dichotomous phenotype";
if ( tok.size() >= 2 ) type = tok[1];
if ( tok.size() >= 3 ) miss = tok[2];
if ( tok.size() >= 4 ) desc = tok[3];
int code = insert_phenotype( name, type, miss, desc );
phe_codes1[ name ] = code;
mis_codes[ name ] = miss;
if ( Helper::is_int( type ) ) type_codes[ name ] = META_INT;
else if ( Helper::is_float( type ) ) type_codes[ name ] = META_FLOAT;
else type_codes[ name ] = META_TEXT;
}
// Or header line?
else if ( s.substr(0,1) == "#" )
{
// #ID phe1 phe2 phe3
std::vector<std::string> tok = Helper::parse( s , " \t");
if ( tok.size() < 2 ) { plog.warn("malformed phenotype file"); continue; }
if ( tok[0] != "#ID" ) { plog.warn("malformed phenotype file"); continue; }
for ( int i = 1 ; i < tok.size(); i++ )
{
std::map<std::string,int>::iterator k = phe_codes1.find( tok[i] );
if ( k == phe_codes1.end() )
Helper::halt( tok[i] + " in header of phenotype file but not defined" );
phe_codes2[ i ] = k->second;
phe_codes.push_back( tok[i] );
}
expected_col_count = tok.size();
}
// Or data ?
else
{
// Skip, if we haven't seen a header
if ( expected_col_count == -1 ) continue;
std::vector<std::string> tok = Helper::parse( s , " \t");
if ( tok.size() != expected_col_count )
{
plog.warn("row in phenotype file with wrong number of fields");
continue;
}
int indiv_id = fetch_id( tok[0] );
// if individual does not exist, create
if ( indiv_id == 0 )
{
std::string period = ".";
sql.bind_text( stmt_insert_individual , ":name" , tok[0] );
sql.bind_text( stmt_insert_individual , ":fid" , period );
sql.bind_text( stmt_insert_individual , ":fid" , period );
sql.bind_text( stmt_insert_individual , ":iid" , period );
sql.bind_text( stmt_insert_individual , ":pat" , period );
sql.bind_text( stmt_insert_individual , ":mat" , period );
sql.bind_text( stmt_insert_individual , ":sex" , period );
sql.step( stmt_insert_individual );
sql.reset( stmt_insert_individual );
// and grab the ID
indiv_id = fetch_id( tok[0] );
}
//
// Insert actual phenotypes
//
for ( int i = 1; i < tok.size(); i++ )
{
// skip undefined phenotypes
if ( phe_codes2[i] == 0 ) continue;
// skip missing values
if ( tok[i] == mis_codes[ phe_codes[i-1] ] ) continue;
mType mt = type_codes[ phe_codes[ i-1 ] ];
// skip invalid values for numerics (as MT will be registered)
if ( mt == META_INT )
{
int x;
if ( Helper::str2int( tok[i] , x ) )
insert( indiv_id , phe_codes2[i] , x );
}
else if ( mt == META_FLOAT )
{
double x;
if ( Helper::str2dbl( tok[i] , x ) )
insert( indiv_id , phe_codes2[i] , x );
}
else
{
insert( indiv_id , phe_codes2[i] , tok[i] );
}
}
++inserted;
}
}
f.close();
index();
sql.commit();
plog << "Processed " << inserted << " rows\n";
if ( inserted && GP && GP->has_project_file() )
GP->fIndex.append_to_projectfile( Helper::fullpath( filename ) , "PHE" );
return true;
}
