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lib/UMLS/Interface/CuiFinder.pm  view on Meta::CPAN

    my $sdb = $self->{'sdb'};
    if(!$sdb) { $errorhandler->_error($pkg, $function, "Error with sdb.", 3); }

    #  set an execute the query to show all of the tables
    my $sth = $sdb->prepare("show tables");
    $sth->execute();
    $errorhandler->_checkDbError($pkg, $function, $sth);

    my $t      = "";
    my %tables = ();
    while(($t) = $sth->fetchrow()) {
        $tables{lc($t)} = 1;
    }
    $sth->finish();

    if(! (exists$tables{lc($table)})) { return 0; }
    else                              { return 1; }

}

#  connect the database to the source db that holds
#  the path tables for user specified source(s) and
#  relation(s)
#  input :
#  output: $sdb <- reference to the database
sub _connectIndexDB {

    my $self = shift;

    my $function = "_connectIndexDB";
    &_debug($function);

    #  check self
    if(!defined $self || !ref $self) {
        $errorhandler->_error($pkg, $function, "", 2);
    }

    my $sdb = "";
    if(defined $self->{'username'}) {

        my $username = $self->{'username'};
        my $password = $self->{'password'};
        my $hostname = $self->{'hostname'};
        my $socket   = $self->{'socket'};

        eval{$sdb = DBI->connect("DBI:mysql:database=$indexDB;mysql_socket=$socket;host=$hostname",
                                 $username, $password,
                                 {RaiseError => 1, PrintError => 1, AutoCommit => 0 });};

        if($@) { $errorhandler->_error($pkg, $function, "No database to connect to", 1); }
    }
    else {
        my $dsn = "DBI:mysql:$indexDB;mysql_read_default_group=client;";
        eval{$sdb = DBI->connect($dsn);};
        if($@) { $errorhandler->_error($pkg, $function, "No database to connect to", 1); }
    }

    $errorhandler->_checkDbError($pkg, $function, $sdb);

    #  set database parameters
    $sdb->{'mysql_enable_utf8'} = 1;
    $sdb->do('SET NAMES utf8');
    $sdb->{mysql_auto_reconnect} = 1;

    $self->{'sdb'} = $sdb;

    return $sdb;
}

#  return the database connection to the umlsinterfaceindex
#  input :
#  output: $sdb <- database handler
sub _getIndexDB {
    my $self = shift;

    my $function = "_getIndexDB";
    &_debug($function);

    #  check self
    if(!defined $self || !ref $self) {
        $errorhandler->_error($pkg, $function, "", 2);
    }

    #  get the databawse
    my $sdb = $self->{'sdb'};
    if(!$sdb) { $errorhandler->_error($pkg, $function, "Error with sdb.", 3); }

    #  return the database
    return $sdb;
}

#  return the database connection to the umls database
#  input :
#  output: $db <- database handler
sub _getDB {
    my $self = shift;

    my $function = "_getDB";
    &_debug($function);

    #  check self
    if(!defined $self || !ref $self) {
        $errorhandler->_error($pkg, $function, "", 2);
    }

    #  get the databawse
    my $db = $self->{'db'};
    if(!$db) { $errorhandler->_error($pkg, $function, "Error with db.", 3); }

    #  return the database
    return $db;
}

#  this function creates the umlsinterfaceindex database connection
#  input :
#  output:
sub _createIndexDB {

    my $self = shift;

    my $function = "_createIndexDB";

lib/UMLS/Interface/CuiFinder.pm  view on Meta::CPAN

    }

    if($option_t == 0) {
        print STDERR "$output\n\n";
    }
}

#  method to set the umlsinterface index database
#  input : $params <- reference to a hash
#  output:
sub _setDatabase  {

    my $self   = shift;
    my $params = shift;

    my $function = "_setDatabase";
    &_debug($function);

    #  check self
    if(!defined $self || !ref $self) {
        $errorhandler->_error($pkg, $function, "", 2);
    }

    #  check the params
    $params = {} if(!defined $params);

    #  get the database connection parameters
    my $database     = $params->{'database'};
    my $hostname     = $params->{'hostname'};
    my $socket       = $params->{'socket'};
    my $port         = $params->{'port'};
    my $username     = $params->{'username'};
    my $password     = $params->{'password'};

    #  set up defaults if the options were not passed
    if(! defined $database) { $database = "umls";            }
    if(! defined $socket)   { $socket   = "/var/run/mysqld/mysqld.sock"; }
    if(! defined $hostname) { $hostname = "localhost";       }

    #  initialize the database handler
    my $db = "";

    #  create the database object...
    if(defined $username and defined $password) {
        if($debug) { print STDERR "Connecting with username and password\n"; }
        $db = DBI->connect("DBI:mysql:database=$database;mysql_socket=$socket;host=$hostname",$username, $password, {RaiseError => 0});
    }
    else {
        if($debug) { print STDERR "Connecting using the my.cnf file\n"; }
        my $dsn = "DBI:mysql:umls;mysql_read_default_group=client;";
        $db = DBI->connect($dsn);
    }

    #  check if there is an error
    $errorhandler->_checkDbError($pkg, $function, $db);

    #  check that the db exists
    if(!$db) { $errorhandler->_error($pkg, $function, "Error with db.", 3); }

    #  set database parameters
    $db->{'mysql_enable_utf8'} = 1;
    $db->do('SET NAMES utf8');
    $db->{mysql_auto_reconnect} = 1;

    #  set the self parameters
    $self->{'db'}           = $db;
    $self->{'username'}     = $username;
    $self->{'password'}     = $password;
    $self->{'hostname'}     = $hostname;
    $self->{'socket'}       = $socket;
    $self->{'database'}     = $database;

    #  return the database handler
    return $db;
}

#  returns the parameters set in the configuration file
#  input:
#  output : $hash <- reference to hash containing parameters in the
#                    configuration file - if there was not config
#                    file the hash is empty and defaults are being
#                    use
sub _getConfigParameters {
    my $self = shift;

    my $function = "_getConfigParameters";

    return \%parameters;
}

#  returns all of the cuis given the specified set of sources
#  and relations defined in the configuration file
#  input : $sab   <- string containing a source
#  output: $array <- reference to array of cuis
sub _getCuis {

    my $self = shift;
    my $sab  = shift;

    my $function = "_getCuis";
    #&_debug($function);

    #  check self
    if(!defined $self || !ref $self) {
        $errorhandler->_error($pkg, $function, "", 2);
    }

    #  check input variables
    if(!$sab) { $errorhandler->_error($pkg, $function, "Error with input variable \$sab.", 4); }

    #  set up the database
    my $db = $self->{'db'};
    if(!$db) { $errorhandler->_error($pkg, $function, "Error with db.", 3); }

    #  NOTE: it is quicker to get all the CUI1s and then all of the CUI2 and then merge
    #        rather than try to get them all together in a single query.
    #  get all of the CUI1s
    my $allCui1 = $db->selectcol_arrayref("select CUI1 from MRREL where ($relations) and (SAB=\'$sab\') and SUPPRESS='N'\;");
    $errorhandler->_checkDbError($pkg, $function, $db);

    #  get all of the CUI1s