I am a new user (as of about 2 hours ago). I have two tables that have a
one-to-one relationship with a third (so, of course, there is a one-to-many
from the third to the other two). The code looks like below. However, I
get the following error message on compile and I do have foreign keys
present in the g_alias and g_refseq tables. I can't figure out what I am
doing incorrectly. Any help?
Thanks,
Sean
Could not auto-generate foreign keys for class AnnoDB::Model::Gene::Alias -
Missing or invalid key name '' for foreign key generated in
AnnoDB::Model::Gene::Alias for AnnoDB::Model::Gene::Main at
/Library/Perl/5.8.6/Rose/DB/Object/Metadata/Auto.pm line 432.
at lib/AnnoDB/Model/Gene/Alias.pm line 14
Compilation failed in require at rosetest.pl line 5.
at rosetest.pl line 5
main::BEGIN() called at lib/AnnoDB/Model/Gene/Alias.pm line 5
eval {...} called at lib/AnnoDB/Model/Gene/Alias.pm line 5
BEGIN failed--compilation aborted at rosetest.pl line 5.
at rosetest.pl line 5
A simple test of the packages:
#!/usr/bin/perl
use strict;
use lib './lib';
use AnnoDB::Model::Gene::Main;
use AnnoDB::Model::Gene::Alias;
my $genes =
AnnoDB::Model::Gene::Main::Manager->get_gmain_iterator(query=>[symbol =>
'BRCA1']);
while (my $gene = $genes->next) {
print join("\t",$gene->symbol, $gene->description)."\n";
foreach ($gene->refseqs) {
print " ".$_->refseq."\n";
}
}
package AnnoDB::Model::Gene::Alias;
use base qw(AnnoDB::Model);
__PACKAGE__->meta->table('g_alias');
__PACKAGE__->meta->relationship
(
gene => {
type => 'one to one',
class => 'AnnoDB::Model::Gene::Main',
column_map => {gene_id => 'gene_id'},
},
);
__PACKAGE__->meta->auto_initialize();
package AnnoDB::Model::Gene::Alias::Manager;
use strict;
use Rose::DB::Object::Manager;
our @ISA = qw(Rose::DB::Object::Manager);
sub object_class{'AnnoDB::Model::Gene::Alias'};
__PACKAGE__->make_manager_methods('galias');
1;
package AnnoDB::Model::Gene::Refseq;
use base qw(AnnoDB::Model);
__PACKAGE__->meta->table('g_refseq');
__PACKAGE__->meta->relationship
(
gene => {
type => 'one to one',
class => 'AnnoDB::Model::Gene::Main',
column_map => {gene_id => 'gene_id'},
},
);
__PACKAGE__->meta->auto_initialize();
package AnnoDB::Model::Gene::Refseq::Manager;
use strict;
use Rose::DB::Object::Manager;
our @ISA = qw(Rose::DB::Object::Manager);
sub object_class{'AnnoDB::Model::Gene::Refseq'};
__PACKAGE__->make_manager_methods('grefseq');
1;
package AnnoDB::Model::Gene::Main;
use base qw(AnnoDB::Model);
__PACKAGE__->meta->table('g_main');
__PACKAGE__->meta->relationships
(
aliases =>
{
type => 'one to many',
class => 'AnnoDB::Model::Gene::Alias',
column_map => {gene_id => 'gene_id'}
},
refseqs =>
{
type => 'one to many',
class => 'AnnoDB::Model::Gene::Alias',
column_map => {gene_id => 'gene_id'}
},
);
__PACKAGE__->meta->auto_initialize();
package AnnoDB::Model::Gene::Main::Manager;
use strict;
use Rose::DB::Object::Manager;
our @ISA = qw(Rose::DB::Object::Manager);
sub object_class{'AnnoDB::Model::Gene::Main'};
__PACKAGE__->make_manager_methods('gmain');
1;
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