[ensembl-dev] Can't get GO adapter with latest ensembl plants release

[simon andrews (BI)]

On 2 Dec 2010, at 11:50, Andy Yates wrote:

> Hi Simon,
> 
> I talked to our web-team and we believe your error is due to a fix pushed into our website plugins but not into our API release. I have updated our branch which includes patches to find the ontology database (so you do not need the fix I provided earlier on) as well as the one missing from our API. Just do a cvs update on your branch checkout to get the code (the only two files to change will be Registry and OntologyTermAdaptor).

I've just updated and it all seems to be working now.

Many thanks

Simon.
> 
> On 2 Dec 2010, at 11:31, simon andrews (BI) wrote:
> 
>> -----Original Message-----
>> From: Andy Yates [mailto:ayates at ebi.ac.uk] 
>> Sent: 02 December 2010 10:46
>> To: simon andrews (BI)
>> Cc: Ensembl dev list
>> Subject: Re: [ensembl-dev] Can't get GO adapter with latest ensembl plants release
>> 
>>> We're investigating the reason behind this now. I believe it has something to do with the 
>>> naming of the ontology database in this release. In previous releases we had called it 
>>> ensembl_ontology_release e.g. ensembl_ontology_59. In this release we changed it to 
>>> ensemblgenomes_ontology_60 which will mean the registry will not pick up on the name. For 
>>> the moment you can code around this with an explicit link to that databases:
>>> use Bio::EnsEMBL::DBSQL::OntologyDBAdaptor;
>>> 
>>> my $ontology_dba = Bio::EnsEMBL::DBSQL::OntologyDBAdaptor->new(
>>> -SPECIES => 'Multi',
>>> -GROUP => 'ontology',
>>> -HOST => 'mysql.ebi.ac.uk',
>>> -PORT => 4157,
>>> -USER => 'anonymous',
>>> -DBNAME => 'ensemblgenomes_ontology_60'
>>> ); 
>> 
>> This fixed the problem of not getting an adaptor in the first place, but when I now try to use it later in my code I get:
>> 
>> -------------------- EXCEPTION --------------------
>> MSG: Could not work out type for Bio::EnsEMBL::DBSQL::OntologyDBAdaptor::fetch_by_acce                                                     ssion
>> 
>> STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /home/andrewss/EnsemblAPI/plants/ensemb                                                     l/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:889
>> STACK main::process_translation ./export_annotated_embl_from_plant_or_bacteria.pl:505
>> STACK main::process_transcript ./export_annotated_embl_from_plant_or_bacteria.pl:434
>> STACK main::process_gene ./export_annotated_embl_from_plant_or_bacteria.pl:337
>> STACK main::process_chromosome ./export_annotated_embl_from_plant_or_bacteria.pl:262
>> STACK main::process_genome ./export_annotated_embl_from_plant_or_bacteria.pl:219
>> STACK main::select_slice_adapter ./export_annotated_embl_from_plant_or_bacteria.pl:159
>> STACK toplevel ./export_annotated_embl_from_plant_or_bacteria.pl:55
>> Ensembl API version = 60
>> ---------------------------------------------------
>> 
>> The code which generates this is:
>> 
>>   if ($xref -> dbname() eq 'GO') {
>>     my $term = $GO_adapter->fetch_by_accession($xref->display_id());
>>   }
>> 
>> Simon.
>> 
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
> 
> -- 
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
>