[BioSQL-l] CDS feature for genome bioentry

[albert vilella]

On Tue, 2003-07-15 at 21:45, Hilmar Lapp wrote:
> On Monday, July 14, 2003, at 02:30  PM, albert vilella wrote:
> 
> > ... now the problem is with Bio::Annotation::SimpleValue::primary_tag:
> >
> > ------------- EXCEPTION  -------------
> > MSG: failed to map Bio::Annotation::SimpleValue::primary_tag to a FK
> >
> 
> Sure this is going to fail. I have to track down why the primary_tag 
> context gets attached to SimpleValue. I'll report once I figured what 
> is going on.
> 
> 	-hilmar

BioQuery.pm:213-220
---------------
# we need the object entity for foreign key resolution, not
# the alias
my $fkent = $entities[$i];    
### 'x $fkent' gives 'Bio::Annotation::SimpleValue'
# but append the context if there was one given in the alias
$fkent .= "::".$tblalias[1] if @tblalias > 1;
### but as $tblalias[1] is primary_tag
### now 'x $fkent' gives 'Bio::Annotation::SimpleValue::primary_tag'
# resolve foreign key
my $fk = $mapper->foreign_key_name($fkent);
### and then the fk is not resolved
$self->throw("failed to map $fkent to a FK") unless $fk;