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

[simon andrews (BI)]

-----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.