[Bioperl-l] how to use BioQuery

[Juguang Xiao]

>
> How to use BioQuery is the most undocumented piece of the story.  
> t/query.t is probably the single most useful place to get a grasp of  
> what the ideas are. It may also be useful to check in the  
> Bio/DB/BioSQL directory for adaptors that implement (i.e., override)  
> attach_children() and attach_foreign_key_objects() to how to find  
> objects by foreign key or by association.
>

In which module the mapping from bioperl module name, say Bio::SeqI, to  
schema table name, bioentry (I guess) is defined?


> Also, the mapping and translation code in BioQuery.pm is not very  
> robust. I had to write it in a crunch and have since never found the  
> time to rewrite it such that it becomes at least remotely  
> comprehensible. There may be lots of bugs lurking, as it is not really  
> tested beyond what t/query.t and the adaptors test.

I have the similar sick code to use BioQuery. Can dear doctor help to  
diagnose it? :-) Thanks.

The scripts:

use Bio::DB::BioDB;

my $db = Bio::DB::BioDB->new(
     -database => 'biosql',
     -host => 'mysql-dev',
     -dbname => 'juguang_biosql_embl',
     -driver => 'mysql',
     -user => 'root'
);

use Bio::DB::Query::BioQuery;

my $query = Bio::DB::Query::BioQuery->new(
     -datacollections => [
         'Bio::SeqI seq', 'Bio::Species=>Bio::SeqI sp'],
     -where => ['sp.name like ?']
);

my $seq_adaptor = $db->get_object_adaptor('Bio::SeqI');
my $result = $seq_adaptor->find_by_query($query,
     -values => ['house mouse']
);

while(my $seq = $result->next_object){
     print ref($seq) ."\n";
}
######################################
The error message:


------------- EXCEPTION  -------------
MSG: slot 'name' not mapped to column for table taxon_name
STACK Bio::DB::Query::BioQuery::_map_slot_to_col  
/Home_R1/juguang/src/bioperl-db//Bio/DB/Query/BioQuery.pm:487
STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns  
/Home_R1/juguang/src/bioperl-db//Bio/DB/Query/BioQuery.pm:369
STACK Bio::DB::Query::BioQuery::translate_query  
/Home_R1/juguang/src/bioperl-db//Bio/DB/Query/BioQuery.pm:305
STACK Bio::DB::BioSQL::BaseDriver::translate_query  
/Home_R1/juguang/src/bioperl-db//Bio/DB/BioSQL/BaseDriver.pm:1097
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_query  
/Home_R1/juguang/src/bioperl-db//Bio/DB/BioSQL/ 
BasePersistenceAdaptor.pm:1154
STACK toplevel find_by_species.pl:22


Juguang