[ensembl-dev] upgrade to version 60

Bram De Wilde gbramdewilde at gmail.com
Sun Dec 26 17:28:15 GMT 2010


Hi everyone,

I just upgraded our install of the API from version 59 to 60 and all of my code stopped working.
I tracked down the problem to the registry not being able to connect to the database... I guess?... Or at least I get zero results back when I try to query the database.
This simple piece of test code works perfectly on my v59 install but stops working when I try and use the freshly installed v60:

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

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous',
	-port => 5306,
);

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()
    );
}


I receive no errors when I execute the code making this a hard problem to debug. Any kind of slice I try to get from any adaptor on my registry will return undefined . When I use the mysql client on my server: mysql -u anonymous -h ensembldb.ensembl.org -P 5306, and perfrom a show databases I get to see the database just fine: "homo_sapiens_core_60_37e" is in the list so the mysql connection does not seem to be the cause of all this.

Installation was done exactly as described in the online tutorial (the files from my v 59 and v60 install look exactly the same on my machine, with the correct permissions set...)

The perldoc for the Bio/EnsEMBL/Registry.pm does not mention any changes in the way we are supposed to connect to the database, nor does the online manual.

Anyone has any pointers as to what i am doing wrong?

Kind regards,


Bram De Wilde, MD
Center for Medical Genetics Ghent (CMGG)
Ghent University Hospital
Medical Research Building (MRB), 2nd floor, room 120.050
De Pintelaan 185, B-9000 Ghent, Belgium
+32 9 332 4812 (phone) | +32 9 332 6549 (fax)
http://medgen.ugent.be/
Bram.DeWilde at UGent.be 



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