[ensembl-dev] SQL errors from latest Ensembl Genomes API

[Dan Staines]

On 09/18/2013 12:00 PM, simon andrews wrote:
> I've just downloaded the latest API release for ensemble genomes from:
>
> http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensemblgenomes-20-73&view=tar
>
> I tried running one of our existing scripts against this release but got an SQL error when trying to run the initial registry setup:
>
> DBD::mysql::st execute failed: Unknown column 'species_id' in 'where clause' at /home/andrewss/EnsemblAPI/plants/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm line 130.
>
> Any ideas?

Hmm, it looks suspiciously as if the tag may have been applied to a set 
of files being worked on for Ensembl 74. Whilst we see what we can do 
about this, you should be fine to use the Ensembl 73 tag:
http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl.tar.gz?root=ensembl&only_with_tag=branch-ensembl-73&view=tar
(we maintain separate tags for the very occasional situations where EG 
databases require minor API changes that are not yet in Ensembl)

Let me know if that helps.

Thanks,

Dan.

-- 
Dan Staines, PhD
Technical Coordinator, Ensembl Genomes
European Bioinformatics Institute (EMBL-EBI)
http://www.ebi.ac.uk/
http://www.ensemblgenomes.org/