[Bioperl-l] bioperl-db woes

[Stefan Kirov]

On Thu, 17 Apr 2008, Chris Fields wrote:

> The 'get_dbxrefs' problem looks related to recent changes I made when rolling 
> back the significant feature/annotation changes introduced just prior to the 
> 1.5 release, none which were fully implemented.  I can check that one out. 
> Odd though; these passed for me, but I'm using MySQL not oracle.
get_dbxref is not the problem- I think the error message is misleading:
kirovs at horta:~/bioperl-db> grep get_dbxrefs 
/home/kirovs/bioperl-live/Bio/Ontology/Term.pm
            get_dbxrefs() instead, which handles both strings and DBLink
                       "Use get_dbxrefs() instead");
     $self->get_dbxrefs($context);
=head2 get_dbxrefs
  Title   : get_dbxrefs()
  Usage   : @ds = $term->get_dbxrefs();
sub get_dbxrefs {
} # get_dbxrefs
     my @old = $self->get_dbxrefs($context);
sub each_dblink {shift->throw("use of each_dblink() is deprecated; use 
get_dbxrefs() instead")}

So it is there.
In any case I debugged and tracked that down to the RichSeq adaptor module 
missing. It is not in the distro I downloaded, so I think this is my 
problem. It is a different question why...
I looked at different repos (SVN, CVS, trunk, different tags) and I did 
not see RichSeq.pm. I am not sure what is going on. Perhaps Hilmar will be 
able to help when he is around.
Thanks for the help Chris.... 
Stefan

>
> You may want to make sure you are using bioperl-live and that there isn't an 
> older bioperl installation getting into the mix.
>
> chris
>
> On Apr 17, 2008, at 8:40 AM, Stefan Kirov wrote:
>
>> I'm having problems passing all the tests for bioperl-db. There are 2
>> distinct errors, first one:
>> Can't locate Bio/DB/BioSQL/RichSeqAdaptor.pm
>>  ***Which by the way is embed deep into several layers of eval, so I
>> am getting the actual error from the test:
>>   ***t/04swiss.........ok 3/52Can't locate object method "get_dbxrefs"
>> via package "Bio::Ontology::Term" at
>> 
>> /home/kirovs/bioperl-db/blib/lib/Bio/DB/Persistent/PersistentObject.pm
>> line 552, <GEN0> line 78.
>>      or
>>      ------------- EXCEPTION: Bio::Root::Exception -------------
>>
>>   MSG: Annotation of class Bio::Annotation::Collection not
>>   type-mapped. Internal error?
>>   STACK: Error::throw
>>   STACK: Bio::Root::Root::throw
>>   /home/kirovs/bioperl-live/Bio/Root/Root.pm:357
>>   STACK:
>>   Bio::DB::BioSQL::AnnotationCollectionAdaptor::_annotation_map_key
>>   Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:695
>>   STACK: Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
>>   Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:204
>>   STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>   Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
>>   STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
>>   Bio/DB/BioSQL/BasePersistenceAdaptor.pm:251
>>   STACK: Bio::DB::Persistent::PersistentObject::store
>>   Bio/DB/Persistent/PersistentObject.pm:271
>>   STACK: Bio::DB::BioSQL::SeqAdaptor::store_children
>>   Bio/DB/BioSQL/SeqAdaptor.pm:224
>>   STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
>>   Bio/DB/BioSQL/BasePersistenceAdaptor.pm:214
>>   STACK: Bio::DB::Persistent::PersistentObject::create
>>   Bio/DB/Persistent/PersistentObject.pm:244
>>   STACK: t/04swiss.t:36
>>   -----------------------------------------------------------
>> 
>> It turns out the adaptor is really not there???
>> My bioperl-db is from
>> dev.open-bio.org/home/svn-repositories/bioperl/bioperl-db/trunk
>> bioperl-db (revision 14661)
>> Is this module being deprecated (I am sure it is not) my download
>> incomplete....?
>> The other problem was:
>> DBD::Oracle::st execute failed: ORA-02292: integrity constraint
>> (BIOSQL.FKTAX_ENT) violated - child record found (DBD ERROR:
>> OCIStmtExecute) [for Statement "DELETE FROM taxon WHERE oid = ?" with
>> ParamValues: :p1=9606] at
>> /home/kirovs/bioperl-db/blib/lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
>> line 320.
>> not ok 76
>> # Test 76 got: <UNDEF> (t/02species.t at line 71)
>> I have not tried to debug this one....
>> Thanks!
>> Stefan
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
>
>
>