[ensembl-dev] Ensemblgenomes 21-74 branch contaminated with v75 API code

Simon Andrews simon.andrews at babraham.ac.uk
Fri Mar 14 17:17:50 GMT 2014


I wrote to the list a couple of weeks ago about this and have made no headway since so I'm trying again.

I'm trying to download and use the latest Ensemblgenomes API code to do some data processing but this is failing.  I suspect the reason is that the code coming from the 21-74 branch actually has v75 code in it.

Previously I'd downloaded from the viewvc.cgi script and had received code with v75 API in it.  I've now gone back and done the same thing with a direct CVS checkout and get exactly the same thing.

Can someone please check the 21-74 branch and if this has been incorrectly updated can they please roll it back to a point where the v74 code will work again.

I'll paste logs below to show what I mean.

$ cvs -d :pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl login
Logging in to :pserver:cvsuser at cvs.sanger.ac.uk:2401/cvsroot/ensembl
CVS password:
cvs -d :pserver:cvsuser at cvs.sanger.ac.uk:/cvsroot/ensembl checkout -r branch-ensemblgenomes-21-74 ensembl

U ensembl/LICENSE
U ensembl/perlcriticrc
U ensembl/perltidyrc
cvs checkout: Updating ensembl/Apache
[lots of stuff]
U ensembl/sql/patch_74_75_d.sql
U ensembl/sql/patch_74_75_e.sql                           <------ should this be here??
U ensembl/sql/populate_meta_coord.pl
U ensembl/sql/table.sql
cvs checkout: Updating ensembl/sql/data
cvs checkout: Updating ensembl/systemtests
cvs checkout: Updating ensembl/travisci

When I then try to run a simple script:

$ cat slice_adapter_test.pl
#!/usr/bin/perl
use warnings;
use strict;
use lib ("/home/andrewss/EnsemblAPI/bioperl-live");
use lib ("/home/andrewss/EnsemblAPI/plants/ensembl/modules");
use Bio::EnsEMBL::Registry;


my $adapter = Bio::EnsEMBL::Registry->get_adaptor('schizosaccharomyces_pombe', 'core', 'Slice');

..it fails with:

-------------------- WARNING ----------------------
MSG: schizosaccharomyces_pombe is not a valid species name (check DB and API version)
FILE: Bio/EnsEMBL/Registry.pm LINE: 1198
CALLED BY: Bio/EnsEMBL/Registry.pm  LINE: 983
Date (localtime)    = Fri Mar 14 17:08:47 2014
Ensembl API version = 75
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Can not find internal name for species 'schizosaccharomyces_pombe'
STACK Bio::EnsEMBL::Registry::get_adaptor /home/andrewss/EnsemblAPI/plants/ensembl/modules/Bio/EnsEMBL/Registry.pm:985
STACK toplevel slice_adapter_test.pl:9
Date (localtime)    = Fri Mar 14 17:08:47 2014
Ensembl API version = 75
---------------------------------------------------

Where the API is listed as 75 not 74.

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