[BioSQL-l] namespace and find_by_unique_key

[Hilmar Lapp]

You mean when querying for a sequence? It should absolutely be taken 
into account. Here is the code in 
PrimarySeqAdaptor::get_unique_key_query (SeqAdaptor.pm inherits from 
it), with comments inserted.

     my $ns;
# if the seq object has a namespace set, look it up
     if($obj->namespace()) {
         $ns = Bio::BioEntry->new(-namespace => $obj->namespace());
         $ns = $self->_bionamespace_adaptor()->find_by_unique_key($ns);
     }
# If the seq object has primary_id() defined, add it first as a unique 
key query.
     if($obj->primary_id() && ($obj->primary_id() !~ 
/=(HASH|ARRAY)\(0x/)) {
         my $uk_h = { 'primary_id' => $obj->primary_id(), };
	   # include the namespace only if it was present (and found by lookup)
         $uk_h->{'bionamespace'} = $ns->primary_key() if $ns;
         push(@ukqueries, $uk_h);
     }
# If accession# is defined, add it together with version to the unique 
key queries
     if($obj->accession_number()) {
         my $uk_h = {
             'accession_number' => $obj->accession_number(),
             'version' => ($obj->version() || 0),
         };
	   # again, namespace only if it was present and found by lookup
         $uk_h->{'bionamespace'} = $ns->primary_key() if $ns;
         push(@ukqueries, $uk_h);
     }

     return @ukqueries;

The inherited find_by_unique_key() will try as many queries as are in 
the returned array, in this case 1 or 2 (unless neither accession# nor 
primary_id are defined). If the namespace was not set, or was set but 
failed to look up successfully, it won't be included in either query. 
The algorithm stops after the first successful query; i.e., if the 
array contains two queries and the query by primary_id() is successful, 
the query by accession# and version is disregarded.

If the namespace was set and is present in the database, but is not 
included in the generated unique key query, that's a bug. Otherwise 
it's a feature ;)

Are you sure it's not included in the generated query when it should 
be? I.e., have you turned on debugging mode and looked at the generated 
query and what is being bound? If you're unsure where to look then send 
me the output with debugging activated (call $db->verbose(1) before you 
obtain any persistence adaptor).

	-hilmar

On Thursday, May 6, 2004, at 03:13  PM, Marc Logghe wrote:

> Hi,
> Is there a way to query a *specific* namespace using the 
> find_by_unique_key() method ?
> It looks like when you set the namespace attribute in the query seq 
> object it is never taken into account; only the accession and version 
> are.
> Is this a feature/bug , or rather am I missing something ?
> Thanks,
> ML
>
> _______________________________________________
> 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
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