I am preparing to post a more detailed intro to Class::DBI, but your post came just as I was doing the initial walk through of the very same thing. Here is how I resolved the problem, but this will likely be refined further. I was unable to get the Class::DBI::Loader module to work correctly so this code had a two fold value for me. This first part is in your initial Class file, the one that defines the DBI connection parameters.

package My::ClassDBI;

use strict;
use warnings;
use base 'Class::DBI';

my $dsn      = 'dbi:mysql:database';
my $user     = 'user';
my $password = 'password';

My::ClassDBI->set_db('Main', $dsn, $user, $password);

# auto load tables
my $base     = __PACKAGE__; # "My::ClassDBI";

# create connection to database
my $dbh = DBI->connect($dsn,$user,$password)
                      or die $DBI::errstr;

# not the Right Way(tm) but works for now
my $get_tables = $dbh->prepare(qq!SHOW TABLES!);

$get_tables->execute;
my @tables;
while ( my $table = $get_tables->fetchrow ) {
    my @columns;
    my $ucftable = ucfirst($table); 
    my $get_column = $dbh->prepare(qq!DESC $table!);
    $get_column->execute();
    while ( my @cols = $get_column->fetchrow() ) {
        # force the primary key to be first
        # this insures Class::DBI correctly relates table
        # without having to manually define the Primary Key
        $cols[3] =~ /pri/i ? unshift @columns , $cols[0]
                           : push @columns , $cols[0]
    }

    eval qq!package $ucftable;
use base '$base';
$ucftable->table('$table');
$ucftable->columns(All => qw/! .
    join(" ",@columns) .
"/);";

}

# Table1 and Table 2 class dynamically generated above
Table1->has_many('method_name_you_want' , 
                 Table2 => 'related_column' );

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Then inside your application you simply use My::ClassDBI and all your classes (tables) are sub classed under it.

use My::ClassDBI;

use strict;

# you can place the has_many here or in the
# package as shown above

# Table1->has_many('method_name_you_want' ,
#                  Table2 => 'related_column' );

my $row_from_table1 = Table1->retrieve(1);

my @table2_objects = $row_from_table1->method_name_you_want;

foreach (@table2_objects) {
    print $_->column_name , "\n";
}

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