[BioSQL-l] Query Problem.

[Hilmar Lapp]

This error is pretty weird. Smells like a bug, I'm just not sure where.  
Try collapsing the multiple spaces between entity and alias into a  
single space for every datacollection and see whether it goes away. I  
can't tell where it would get the 'q' as an alias from.

A tip aside from that: I'd request the adaptor for Bio::SeqI or  
otherwise you won't get features and annotation on the resulting  
objects.

	-hilmar

On Monday, December 22, 2003, at 07:05  AM, Frederic Pecqueur wrote:

> Hi,
>
> I try to create a query to search all the entries which have a tag  
> "other_name" equal to 'mig-11'....and it dosen't work...
>
> I use this code :
>
> my $adp = $db->get_object_adaptor('Bio::PrimarySeqI');
>
> my $query = Bio::DB::Query::BioQuery->new(
>                 -datacollections => [
>                     "Bio::PrimarySeqI entr",
>                     "Bio::SeqFeatureI  feat",
>                     "Bio::Ontology::TermI  ter",
>                     "BioNamespace=>Bio::PrimarySeqI db",
>                     "Bio::PrimarySeqI=>Bio::SeqFeatureI",
>                     "Bio::SeqFeatureI<=>Bio::Ontology::TermI  qual"
>                 ],
>                 -where => ["db.namespace = 'WormGene'",
>                            "ter.name = 'other_name'",
>                            "qual.value = 'mig-11'"]
> );
>
> my $result = $adp->find_by_query($query);
>
> I have this error :
>
> attempting to load driver for adaptor class  
> Bio::DB::BioSQL::PrimarySeqAdaptor
> attempting to load driver for adaptor class  
> Bio::DB::BioSQL::BasePersistenceAdaptor
> Using Bio::DB::BioSQL::Oracle::BasePersistenceAdaptorDriver as driver  
> peer for Bio::DB::BioSQL::PrimarySeqAdaptor
>
> ------------- EXCEPTION  -------------
> MSG: Alias "q" not mapped to entity. Are you sure there's no typo?
> STACK Bio::DB::Query::BioQuery::_map_slot_to_col  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:466
> STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:369
> STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:355
> STACK Bio::DB::Query::BioQuery::translate_query  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/Query/BioQuery.pm:305
> STACK Bio::DB::BioSQL::BaseDriver::translate_query  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BaseDriver.pm:1184
> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_query  
> /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/ 
> BasePersistenceAdaptor.pm:1198
>
> I don't use the API correctly??
> Somebody has a response?
>
> Thanks a lot!
> Frédéric.
>
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at open-bio.org
> http://open-bio.org/mailman/listinfo/biosql-l
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------