Allow to set global database configuration for web application BIGSdb.

File db.conf, located in the same directory as bigsdb.conf for consistency.
This configuration allow to set another role for the application to connect
to the database than 'apache'. However, this can still be overridden by
parameters from config.xml.

lib/BIGSdb/Application.pm

@@ -187,10 +187,10 @@ sub _initiate {
 	$q->param( page => 'index' ) if !defined $q->param('page');
 	$self->{'page'} = $q->param('page');
 	$self->{'system'}->{'read_access'} //= 'public';      #everyone can view by default
-	$self->{'system'}->{'host'}        //= 'localhost';
-	$self->{'system'}->{'port'}        //= 5432;
-	$self->{'system'}->{'user'}        //= 'apache';
-	$self->{'system'}->{'password'}    //= 'remote';
+        $self->{'system'}->{'host'}        //= $self->{'config'}->{'dbhost'} //= 'localhost';
+        $self->{'system'}->{'port'}        //= $self->{'config'}->{'dbport'} //= 5432;
+        $self->{'system'}->{'user'}        //= $self->{'config'}->{'dbuser'} //= 'apache';
+        $self->{'system'}->{'password'}    //= $self->{'config'}->{'dbpassword'} //= 'remote';
 	$self->{'system'}->{'privacy'}     //= 'yes';
 	$self->{'system'}->{'privacy'} = $self->{'system'}->{'privacy'} eq 'no' ? 0 : 1;
 	$self->{'system'}->{'locus_superscript_prefix'} ||= 'no';
@@ -345,6 +345,27 @@ sub read_config_file {
 	$self->{'config'}->{'doclink'}         //= 'http://bigsdb.readthedocs.io/en/latest';
 	$self->{'config'}->{'max_upload_size'} //= 32;
 	$self->{'config'}->{'max_upload_size'} *= 1024 * 1024;
+	$self->_read_db_config($config_dir);
+	return;
+}
+
+sub _read_db_config_file {
+        my ( $self, $config_dir ) = @_;
+	my $logger = get_logger('BIGSdb.Application_Initiate');
+	my $db_file = "$config_dir/db.conf";
+	if ( ! -e $db_file ){
+	    return;
+	}
+	my $config = Config::Tiny->new();
+	$config = Config::Tiny->read("$db_file");
+
+	foreach my $param (qw (dbhost dbuser dbpassword) ){
+	    $self->{'config'}->{$param} = $config->{_}->{$param};
+	}
+	if (  defined $self->{'config'}->{'dbport'} && !BIGSdb::Utils::is_int( $self->{'config'}->{'dbport'} ) ){
+	    $logger->error("Parameter dbport in db.conf should be an integer - default value used.");
+	    undef $self->{'config'}->{'dbport'};
+	}
 	return;
 }