[ensembl-dev] Can't get GO adapter from latest registry

[Simon Andrews]

Sorry, I forgot that "load_registry()" was a subroutine in my own code.  The full code is:

my $version = software_version();
my $registry = load_registry();
my $GO_adapter =   $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' );
die "Couldn't get GO adaptor from $version" unless ($GO_adapter);

sub load_registry {

  my $registry = 'Bio::EnsEMBL::Registry';

  $registry->load_registry_from_db(
                                 -host => 'ensembldb.ensembl.org',
                                 -user => 'anonymous'
                                );

  return $registry;

}

I had a similar problem with ensemblgenomes before (should be in the list archives) and was given a work round by directly connecting to a different database to get the GO DBA, but hopefully this can be fixed in the main registry.

Thanks

Simon.



From: Simon Andrews
Sent: 27 September 2018 09:07
To: dev at ensembl.org
Subject: Can't get GO adapter from latest registry

I've just updated our code to the latest API release and one of our processing scripts is now failing.

You can reproduce this with:

my $version = software_version();
my $registry = load_registry();
my $GO_adapter =   $registry->get_adaptor( 'Multi', 'Ontology', 'GOTerm' );
die "Couldn't get GO adaptor from $version" unless ($GO_adapter);

..where I get:

Couldn't get GO adaptor from 93

Can this be fixed at the Ensembl end, or is there a more immediate work round I can apply locally?

Thanks

Simon.
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