[ensembl-dev] Ensembl API v84 breaks at Bio::EnsEMBL::Registry::get_adaptor?

[Ian Sealy]

Dear John,

> Today I attempted to run some Ensembl API code that I ran before, and 
> it breaks. Since it's practically the first few lines after 
> declaration, I'd cite them here:
>
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_db(
>    -host => 'useastdb.ensembl.org', # alternatively 'useastdb.ensembl.org'
>    -port => 5306,
>    -user => 'anonymous',
>    -db_version => '84'
> );
>
> my $transcript_adaptor = $registry->get_adaptor( 'Mouse', 'Core',
> 'Transcript' );
>
> And the error is:
>
> -------------------- WARNING ----------------------
> MSG: Mouse is not a valid species name (check DB and API version)
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1327
> CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 1102
> Date (localtime)    = Thu Oct  6 13:07:54 2016
> Ensembl API version = 84
> ---------------------------------------------------
>
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'Mus_musculus'
> STACK Bio::EnsEMBL::Registry::get_adaptor
> Y:\ensembl\modules/Bio/EnsEMBL/Registry.pm:1104
> STACK toplevel [my script]
> Date (localtime)    = Thu Oct  6 13:07:54 2016
> Ensembl API version = 84
> ---------------------------------------------------
>
>
> Changing 'Mouse' to 'mus_musculus' or 'Mus_musculus' have no effect.
>
> Does this have anything to do with e86's rollout today?

Yep. useastdb.ensembl.org only has the databases for the current (86) 
and previous (85) Ensembl releases. See the bottom of 
http://www.ensembl.org/info/data/mysql.html

Cheers,
Ian