[ensembl-dev] upgrade to version 60

[Ian]

This only happens when the API and the database selected are not the same version.
Use -verbose => 1 in load_registry_from_db to see what version it is trying to load.

It is usually best to delete the version of the API and install the new one as cvs can sometimes get confused when over writing.   

So if you get a new checkout and make sure this is in a new directory you should be okay.
But add the verbose option to see what the registry is trying to do.

If the problem continues please let us know what the verbose option gives you.

Ian longden
Ensembl developer.

On Dec 26, 2010, at 5:28 PM, Bram De Wilde <gbramdewilde at gmail.com> wrote:

> 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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