[ensembl-dev] testing Perl API access

[Alex Reynolds]

I am attempting to learn the Ensembl Perl API for accessing some mouse data from Ensembl release 67.

I started with the installation document here:

http://may2012.archive.ensembl.org/info/docs/api/api_installation.html

I replaced "bioperl-live" with "bioperl-1.2.3"

I used the core API documentation examples to write a test script.

http://may2012.archive.ensembl.org/info/docs/api/core/core_tutorial.html#connecting

Here is the script I wrote:

----
$ more ensembl_test.pl
#!/usr/bin/env perl

use strict;
use warnings;
use Data::Dumper;
use Bio::EnsEMBL::Registry;

use Bio::EnsEMBL::ApiVersion;
printf( "The API version used is %s\n", software_version() );

my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(
                                 -host => 'useastdb.ensembl.org',
                                 -user => 'anonymous'
                                 );

# should return Dumped contents of reference to list
print Dumper $registry->get_all_DBAdaptors(); 

my @db_adaptors = @{ $registry->get_all_DBAdaptors() };

foreach my $db_adaptor (@db_adaptors) {
    my $db_connection = $db_adaptor->dbc();

    printf(
           "species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n",
           $db_adaptor->species(),   
           $db_adaptor->group(),
           $db_connection->dbname(), 
           $db_connection->host(),
           $db_connection->port()
           );
}
----

The output from this script is:

----
The API version used is 72
$VAR1 = [];
----

Should the value of @db_adaptors (or the list-reference equivalent) be empty? Or did I miss something with the module setup process?

Regards,
Alex