[ENSCORESW-691]. Adding the ability to query by retired seq region ids.

Other schemas may need this which do not go through a process of removing
old/retired seq region ids in favour of their new ids. When querying by a slice
this is automatically delt with. When fetching by an ID you now need to
force the search on.

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -805,7 +805,7 @@ sub fetch_by_name {
 =cut
 
 sub fetch_by_seq_region_id {
-  my ( $self, $seq_region_id, $start, $end, $strand ) = @_;
+  my ( $self, $seq_region_id, $start, $end, $strand, $check_prior_ids ) = @_;
 
   my $arr = $self->{'sr_id_cache'}->{$seq_region_id};
   my ( $name, $length, $cs, $cs_id );
@@ -823,7 +823,19 @@ sub fetch_by_seq_region_id {
     $sth->bind_param( 1, $seq_region_id, SQL_INTEGER );
     $sth->execute();
 
-    if ( $sth->rows() == 0 ) { return undef }
+    if ( $sth->rows() == 0 ) { 
+      # This could have been an old seq region id so see if we can
+      # translate it into a more recent version.
+      if($check_prior_ids) {
+        my $csa = $self->db()->get_CoordSystemAdaptor();
+        if(exists $csa->{_external_seq_region_mapping}->{$seq_region_id}) {
+          my $new_seq_region_id = $csa->{_external_seq_region_mapping}->{$seq_region_id};
+          # No need to pass check prior ids flag because it's a 1 step relationship
+          return $self->fetch_by_seq_region_id($new_seq_region_id, $start, $end, $strand);
+        }
+      }
+      return undef;
+    }
 
     ( $name, $cs_id, $length ) = $sth->fetchrow_array();
     $sth->finish();

modules/t/slice.t

@@ -508,5 +508,41 @@ is($chr_one_slice->assembly_exception_type(), 'REF', 'Ensuring reference regions
   }
 }
 
+# Test alternative region mappings from fetch_by_seq_region_id()
+{
+  my $current_slice = $slice_adaptor->fetch_by_region('chromosome', $CHR, $START, $END);
+  my $alternative_seq_region_id = 1;
+
+  #Get the alternative seq region id. Expect nothing
+  ok(! defined $slice_adaptor->fetch_by_seq_region_id($alternative_seq_region_id), 'Asking for a non-existent ID results in no slice returned');
+
+  #Save the tables and add the mapping values in
+  my @tables = ('seq_region_mapping', 'mapping_set');
+  $multi_db->save('core', @tables);
+  my $ms_sql = 'insert into mapping_set (mapping_set_id, internal_schema_build, external_schema_build) values (?,?,?)';
+  $db->dbc->sql_helper->execute_update(-SQL => $ms_sql, -PARAMS => [1, $db->_get_schema_build(), 'oldbuild']);
+  my $srm_sql = 'insert into seq_region_mapping (mapping_set_id, internal_seq_region_id, external_seq_region_id) values (?,?,?)';
+  $db->dbc->sql_helper->execute_update(-SQL => $srm_sql, -PARAMS => [1, $current_slice->get_seq_region_id(), $alternative_seq_region_id]);
+
+
+  #Force a refresh in CSA
+  delete $db->get_CoordSystemAdaptor->{$_} for qw/_internal_seq_region_mapping _external_seq_region_mapping/;
+  $db->get_CoordSystemAdaptor->_cache_seq_region_mapping();
+  my $alternative_slice = $slice_adaptor->fetch_by_seq_region_id($alternative_seq_region_id);
+  ok(!defined $alternative_slice, 'Cannot retrieve the alternative slice without asking to look at alternatives');
+  $alternative_slice = $slice_adaptor->fetch_by_seq_region_id($alternative_seq_region_id, undef, undef, undef, 1); #don't care about start,end,strand
+  ok(defined $alternative_slice, 'Got a slice after asking for it');
+  cmp_ok($current_slice->get_seq_region_id(), '==', $alternative_slice->get_seq_region_id(), 'Seq region IDs should be equivalent even though query seq_region_id was different');
+  
+  #Restore & force a refresh
+  $multi_db->restore('core', @tables);
+  delete $db->get_CoordSystemAdaptor->{$_} for qw/_internal_seq_region_mapping _external_seq_region_mapping/;
+  $db->get_CoordSystemAdaptor->_cache_seq_region_mapping();
+
+  # Just checking we are back to normal
+  $alternative_slice = $slice_adaptor->fetch_by_seq_region_id($alternative_seq_region_id);
+  ok(!defined $alternative_slice, 'Cannot retrieve the alternative slice post restore');
+}
+
 done_testing();