[ensembl-dev] Problem with DBAdaptor

[Andy Yates]

Hi Luc,

Make sure that you've got the compara libraries on your PERL5LIB otherwise the registry will not load the compara database connection. Also the compara species is multi so the call should be:

my $compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor('multi', 'compara');

Regards,

Andy

On 29 Jun 2011, at 10:16, ian Longden wrote:

> This appears to be a long winded way to get the Compara DBAdaptor.
> 
> It would be easier to do :-
> 
> my $compara_dba = Bio::EnsEMBL::Registry->get_DBAdaptor("compara","compara");
> 
> if(!defined($compara_dba)) {
>  die "Could not get Compara DBAdaptor\n";
> }
> 
> my $member_adaptor   = $compara_dba->get_adaptor('Member');
> 
> 
> or even easier ----------------------------------
> 
> my $member_adaptor =
> Bio::EnsEMBL::Registry->get_adaptor("compara","compara", "member);
> 
> if(!defined($member_adaptor)){
>  die "Could not get compara member adaptor\n";
> }
> 
> 
> 
> It could be that your API and schema do not match which could mean you
> could get no
> adaptors.  If you are using load_registry_from_db then add  -verbose
> => 1 to make sure you are connecting properly.
> 
> 
> -Ian Longden.
> Ensembl Developer.
> 
> 
> On Wed, Jun 29, 2011 at 10:01 AM, Luc Merenda <merenda.luc at gmail.com> wrote:
>> Hi Ensembl,
>> I've been using a perl script that uses the ensembl compara api to retrieve
>> protein trees. It worked fine until last week, now it exits with the
>> following error:
>> Can't call method "get_adaptor" on an undefined value at
>> /home/luc/Code/gene2proteintree line 22, <FILE> line 43.
>> It seems that there is a problem connecting to the server.
>> The line of code where the error occurs is the last one of the following
>> snippet:
>> 
>>     my $compara_dba;
>>     foreach my $dba( @{Bio::EnsEMBL::Registry->get_all_DBAdaptors()} ){
>>         if( $dba->isa('Bio::EnsEMBL::Compara::DBSQL::DBAdaptor') ){
>>           $compara_dba = $dba;
>>           last;
>>         }
>>     }
>>     my $member_adaptor   = $compara_dba->get_adaptor('Member');
>> 
>> Many thanks in advance
>> 
>> Luc
>> 
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>> 
> 
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-- 
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/