[ensembl-dev] DB access for EnsemblMetazoa

Keiran Raine kr2 at sanger.ac.uk
Tue Dec 8 17:00:52 GMT 2020


I'm looking for some assistance reading data from the ensembl mysql instance for EnsemblMetazoa.

I have a very simple API script based on examples from the official documentation (attached), it works fine for listing the available DB adaptors via "get_all_DBAdaptors" if I point it at the vertebrate instance, but for the non-vertebrate genomes I get an empty list (registry as described here<https://metazoa.ensembl.org/info/docs/api/general_instructions.html#connectin>).

If nothing else, I'm just looking for someone to confirm they see the same behaviour as me when using the documented connection details.

P.s. the general ensembl instance is very slow, it was usable earlier today, not so much now.  I also did a host lookup of the database hosts, both derive down to the same IP address via a chain of aliases, so it looks like it's the port that is more important.


Keiran Raine, M.Sc., MBCS
Principal Software Developer
Cancer, Ageing and Somatic Mutation
Wellcome Sanger Institute

kr2 at sanger.ac.uk<mailto:kr2 at sanger.ac.uk>
Office: D3-19
Ext: 4983

Please note that due to childcare requirements due to covid restrictions I am generally not available after 4pm.
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