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package Bio::GMOD::DB::Config;
use strict;
=head1 NAME
Bio::GMOD::Config::DB -- a GMOD utility package for reading db config files
=head1 SYNOPSIS
$ export GMOD_ROOT=/usr/local/gmod
my $conf = Bio::GMOD::Config->new();
my $tmpdir = $conf->tmp();
my $confdir = $conf->conf();
#assume there is a file 'chado.conf' with database connetion info
my $dbconf = Bio::GMOD::DB::Config->new($conf, 'chado');
my $dbusername = $dbconf->user();
my $dbhostname = $dbconf->port();
# ...etc...
=head1 DESCRIPTION
Bio::GMOD::DB::Config is a module to allow programmatic access to the
database configuration files in GMOD_ROOT/conf.
=head1 METHODS
=cut
use DBI;
use File::Spec::Functions qw/ catdir catfile /;
use vars '@ISA';
use base qw/ Bio::GMOD::Config /;
my $VERSION = 1.23;
=head2 new
Title : new
Usage : my $config = Bio::GMOD::DB::Config->new($conf, 'dbname');
Function: create new Bio::GMOD::DB::Config object
Returns : new Bio::GMOD::DB::Config
Args : Bio::GMOD::Config object, db config name
Status : Public
Returns a Bio::GMOD::DB::Config object. If no db config name argument is
specified, the configuration file called 'default.conf' will be used.
=cut
sub new {
my $self = shift;
my $conf = shift;
my $dbname = shift;
$dbname ||= 'default';
my $confdir = $conf->confdir; #get from Bio::GMOD::Config
my $conffile= catfile($confdir, "$dbname.conf");
my %dbconf;
open CONF, $conffile or die "Couldn't open $conffile: $!";
while (<CONF>) {
next if /^\#/;
if (/(\w+)\s*=\s*(\S.*)/) {
$dbconf{$1}=$2;
}
}
close CONF;
return bless {conf => \%dbconf}, $self;
}
=head2 user
Title : user
Usage : $username = $dbconf->user();
Function: return the value the database username
Returns : see above
Args : none
Status : Public
=cut
sub user {
shift->get_tag_value('DBUSER');
}
=head2 password
Title : password
Usage : $password = $dbconf->password();
Function: return the value the database password
Returns : see above
Args : none
Status : Public
=cut
sub password {
shift->get_tag_value('DBPASS');
}
=head2 host
Title : host
Usage : $host = $dbconf->host();
Function: return the value the database host name
Returns : see above
Args : none
Status : Public
=cut
sub host {
shift->get_tag_value('DBHOST');
}
=head2 port
Title : port
Usage : $port = $dbconf->port();
Function: return the value the database port
Returns : see above
Args : none
Status : Public
=cut
sub port {
shift->get_tag_value('DBPORT');
}
=head2 driver
Title : driver
Usage : $driver = $dbconf->driver();
Function: return the value the database driver
Returns : see above
Args : none
Status : Public
=cut
sub driver {
shift->get_tag_value('DBDRIVER');
}
=head2 name
Title : name
Usage : $dbname = $dbconf->name();
Function: return the value the database name
Returns : see above
Args : none
Status : Public
=cut
sub name {
shift->get_tag_value('DBNAME');
}
=head2 sqlfile
Title : sqlfile
Usage : $sqlfile = $dbconf->sqlfile();
Function: returns the path of the sqlfile (ie, ddl file) the defines the schema
Returns : see above
Args : none
Status : Public
=cut
sub sqlfile {
shift->get_tag_value('SQLFILE');
}
=head2 schema
Title : schema
Usage : $schema = $dbconf->schema();
Function: Returns the schema chado resides in (usually public)
Returns : see above
Args : none
Status : Public
=cut
sub schema {
shift->get_tag_value('SCHEMA');
}
=head2 organism
Title : organism
Usage : $organism = $dbconf->organism();
Function: Returns the common name of the "default" organism of the database,
if there is one
Returns : A species common name, or undef
Args : none
Status : Public
=cut
sub organism {
my $self = shift;
my $org = $self->get_tag_value('DBORGANISM');
return $org if $org;
return undef;
}
=head2 dbh
Title : dbh
Usage : $dbh = $dbconf->dbh();
Function: return a database handle
Returns : see above
Args : none
Status : Public
=cut
sub dbh {
my $self = shift;
my $dsn = $self->dsn;
my $dbh = DBI->connect( $dsn, $self->user(), $self->password() )
or die "couldn't create db connection:$!";
#this should throw--maybe I should inherit from Bio::Root
return $dbh;
}
=head2 dsn
Title : dsn
Usage : $dsn = $dbconf->dsn();
Function: return a database connection string
Returns : see above
Args : none
Status : Public
=cut
sub dsn {
my $self = shift;
my $dsn = "dbi:Pg:dbname=".$self->name();
$dsn .= ";host=".$self->host() if $self->host();
$dsn .= ";port=".$self->port() if $self->port();
return $dsn;
}
1;
=head1 AUTHOR
Scott Cain E<lt>cain@cshl.orgE<gt>.
Copyright (c) 2004 Cold Spring Harbor Laboratory
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=cut
|
