Fixing get_Species() and making sure it doesn't give back "bad" data

modules/Bio/EnsEMBL/DBSQL/MetaContainer.pm

@@ -158,9 +158,17 @@ sub get_Species {
   if ( !@$classification ) {
     return undef;
   }
-
+  
+  #Re-create the old classification data structure by adding the scientific
+  #name back onto the classification but with species before genus e.g.
+  # sapiens -> Homo -> Hominade
+  my $scientific_name = $self->get_scientific_name();
+  my ($genus, @sp) = split(/ /, $scientific_name);
+  unshift(@{$classification}, join(q{ }, @sp), $genus);
+  
   my $species = Bio::Species->new();
   $species->common_name($common_name);
+  
   $species->classification($classification, 1); #always force it
 
   return $species;

modules/t/metaContainer.t

 use strict;
 use warnings;
-use Data::Dumper;
 
-
-BEGIN { $| = 1;
-	use Test;
-	plan tests => 10;
-}
+use Test::More;
 
 use Bio::EnsEMBL::Test::TestUtils;
-
 use Bio::EnsEMBL::Test::MultiTestDB;
 
 
@@ -69,5 +63,17 @@ $mc->store_key_value('species.division',$divname);
 $div = $mc->get_division();
 ok($div eq $divname);
 
+#
+# Testing get_Species()
+#
+
+capture_std_streams(sub {
+  my ($stdout_ref, $stderr_ref) = @_;
+  my $s = $mc->get_Species();
+  is($s->binomial(), 'Homo sapiens', 'Checking binomial from Bio::Species continues to work');
+  like(${$stderr_ref}, qr/.+ deprecated .+ get_scientific_name\(\)/xms, 'Make sure we warn about deprecation');
+});
+
 $mdb->restore('core', 'meta');
 
+done_testing();
\ No newline at end of file

modules/t/test-genome-DBs/homo_sapiens/core/meta.txt

@@ -7,8 +7,6 @@
 29	1	species.classification	Primates
 28	1	species.classification	Catarrhini
 27	1	species.classification	Hominidae
-26	1	species.classification	Homo
-25	1	species.classification	sapiens
 34	1	species.classification	Metazoa
 35	1	species.classification	Eukaryota
 36	1	species.common_name	Human