[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the...

[ENSCORESW-314]. Synonym lookup bug fixed. Passed coord system id into the lookup rather than the actual coord system name. Bad bad bad

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -291,17 +291,17 @@ sub fetch_by_region {
 
 
       # try synonyms
-      my $syn_sql_sth = $self->prepare("select s.name, s.coord_system_id from seq_region s, seq_region_synonym ss where s.seq_region_id = ss.seq_region_id and ss.synonym = ?");
+      my $syn_sql_sth = $self->prepare("select s.name, cs.name, cs.version from seq_region s join seq_region_synonym ss using (seq_region_id) join coord_system cs using (coord_system_id) where ss.synonym = ? and cs.species_id =?");
       $syn_sql_sth->bind_param(1, $seq_region_name, SQL_VARCHAR);
+      $syn_sql_sth->bind_param(2, $self->species_id(), SQL_INTEGER);
       $syn_sql_sth->execute();
-      my $new_name;
-      my $new_coord_system;
-      $syn_sql_sth->bind_columns( \$new_name, \$new_coord_system);
+      my ($new_name, $new_coord_system, $new_version);
+      $syn_sql_sth->bind_columns( \$new_name, \$new_coord_system, \$new_version);
             
       if($syn_sql_sth->fetch){
         $syn_sql_sth->finish;
         if (not defined($cs)) {
-            return $self->fetch_by_region($new_coord_system, $new_name, $start, $end, $strand, $version, $no_fuzz);
+            return $self->fetch_by_region($new_coord_system, $new_name, $start, $end, $strand, $new_version, $no_fuzz);
         } elsif ($cs->dbID != $new_coord_system) {
             warning("Searched for a known feature on coordinate system: ".$cs->dbID." but found it on: ".$new_coord_system.
             "\n No result returned, consider searching without coordinate system or use toplevel.");
@@ -1407,8 +1407,6 @@ sub fetch_by_transcript_stable_id{
   return $self->fetch_by_Feature($transcript, $size);
 }
 
-
-
 =head2 fetch_by_transcript_id
 
   Arg [1]    : int $transcriptid

modules/t/sliceAdaptor.t

@@ -422,6 +422,20 @@ $clone_name = 'AL031658';
 $slice = $slice_adaptor->fetch_by_region(undef, $clone_name);
 ok($slice->seq_region_name =~ /$clone_name\.\d+/);
 
+# Testing synonym fetching
+{
+  my $syn_slice = $slice_adaptor->fetch_by_region(undef, 'anoth_20');
+  is($syn_slice->seq_region_name(), '20', 'Ensuring slice is Chr20 as expected');
+}
+
+#{
+#  my @slices = @{$slice_adaptor->fetch_all_by_synonym('anoth_20', 'UniGene')};
+#  is(scalar(@slices), 0, 'Checking querying with a bad external name means no Slices');
+#  
+#  @slices = @{$slice_adaptor->fetch_all_by_synonym('anoth_20', 'RFAM')}; #Yeah ... RFAM
+#  is(scalar(@slices), 1, 'Checking querying with a good external name means Slices');
+#  is($slices[0]->seq_region_name(), '20', 'Ensuring slice is Chr20 as expected');
+#}
 
 # test that with multiple sequence regions with the same name, the
 # highest (lowest-numbered) ranked comes out first
@@ -504,6 +518,8 @@ ok(!defined $slice_adaptor->fetch_by_toplevel_location('1:-100--50', 1), 'Checki
   ok(!defined $strand, 'Strand is undefined');
 }
 
+############# METHODS BELOW HERE 
+
 sub test_toplevel_location {
   my ($location, $cs_name, $seq_region_name, $start, $end, $strand) = @_;
   my $incoming_slice = $slice_adaptor->fetch_by_toplevel_location($location, 1);