[ensembl-dev] Can't get adapters from plant registry

Simon Andrews simon.andrews at babraham.ac.uk
Fri Aug 5 10:26:22 BST 2022

I'm trying to do some work through the API for a plant genome, but I can't get the initial connection to work.  This is a script I've used many times before, but now seems to be failing.  I've checked the docs but can't see any major changes.  I'm using the latest API release and I can manually connect to the mysql server OK and see the list of databases there.

Any suggestions would be very welcome.



use warnings;
use strict;
use lib ("/home/andrewss/EnsemblAPI/bioperl-live");
use lib ("/home/andrewss/EnsemblAPI/ensembl/modules");
use Bio::EnsEMBL::Registry;

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

    -host => 'mysql-eg-publicsql.ebi.ac.uk',
    -port => 4157,
    -user => 'anonymous'

my @adapters = @{$registry -> get_all_DBAdaptors(-group => 'core')};

warn "Found ".scalar @adapters." adapters from $registry \n";

my $db_adapter = $registry->get_DBAdaptor("Hordeum_vulgare",'Core');


## Results:

$ ./test_plants.pl
Found 0 adapters from Bio::EnsEMBL::Registry

-------------------- WARNING ----------------------
MSG: Hordeum_vulgare is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1334
CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 636
Date (localtime)    = Fri Aug  5 10:18:45 2022
Ensembl API version = 107

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'Hordeum_vulgare'
STACK Bio::EnsEMBL::Registry::get_DBAdaptor /home/andrewss/EnsemblAPI/ensembl/modules/Bio/EnsEMBL/Registry.pm:640
STACK toplevel ./test_plants.pl:22
Date (localtime)    = Fri Aug  5 10:18:45 2022
Ensembl API version = 107

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