ENSCORESW-2399: check perfect match before wildcard

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -302,25 +302,36 @@ sub fetch_by_region {
         $syn_sql .= "AND cs.version = '" . $version . "' ";
       }
       my $syn_sql_sth = $self->prepare($syn_sql);
-      my $escaped_seq_region_name = $seq_region_name;
-      my $escape_char = $self->dbc->db_handle->get_info(14);
-      $escaped_seq_region_name =~ s/([_%])/$escape_char$1/g;
-      $syn_sql_sth->bind_param(1, "$escaped_seq_region_name%", SQL_VARCHAR);
+      $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, $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)) || ($cs->name eq $new_coord_system && $cs->version eq $new_version)) {
             return $self->fetch_by_region($new_coord_system, $new_name, $start, $end, $strand, $new_version, $no_fuzz);
-        } elsif ($cs->name ne $new_coord_system) {
-            warning("Searched for a known feature on coordinate system: ".$cs->dbID." but found it on: ".$new_coord_system.
-            "\n No result returned, consider searching without coordinate system or use toplevel.");
-            return;
         }
-        
+      } else {
+        # Try wildcard searching if no exact synonym was found
+        $syn_sql_sth = $self->prepare($syn_sql);
+        my $escaped_seq_region_name = $seq_region_name;
+        my $escape_char = $self->dbc->db_handle->get_info(14);
+        $escaped_seq_region_name =~ s/([_%])/$escape_char$1/g;
+        $syn_sql_sth->bind_param(1, "$escaped_seq_region_name%", SQL_VARCHAR);
+        $syn_sql_sth->bind_param(2, $self->species_id(), SQL_INTEGER); 
+        $syn_sql_sth->execute();
+        $syn_sql_sth->bind_columns( \$new_name, \$new_coord_system, \$new_version);
+
+        if($syn_sql_sth->fetch){
+          if ((not defined($cs)) || ($cs->name eq $new_coord_system && $cs->version eq $new_version)) {
+              return $self->fetch_by_region($new_coord_system, $new_name, $start, $end, $strand, $new_version, $no_fuzz);
+          } elsif ($cs->name ne $new_coord_system) {
+              warning("Searched for a known feature on coordinate system: ".$cs->dbID." but found it on: ".$new_coord_system.
+              "\n No result returned, consider searching without coordinate system or use toplevel.");
+              return;
+          }
+          
+        }
       }
       $syn_sql_sth->finish;
 

modules/t/slice.t

@@ -474,14 +474,14 @@ $multi->restore();
 
 $multi->save("core", 'seq_region_synonym');
 
-$slice = $slice_adaptor->fetch_by_region('chromosome', 1, 1, 10);
+$slice = $slice_adaptor->fetch_by_region('chromosome', 5, 1, 10);
 
 @alt_names = @{$slice->get_all_synonyms()};
 
 is(@alt_names, 0, "No altnames returned");
 
 
-$slice->add_synonym("1ish");
+$slice->add_synonym("5ish");
 
 @alt_names = @{$slice->get_all_synonyms()};
 
@@ -492,7 +492,7 @@ foreach my $syn (@alt_names){
 }
 
 
-$slice = $slice_adaptor->fetch_by_region('chromosome', 1, 1, 10);
+$slice = $slice_adaptor->fetch_by_region('chromosome', 5, 1, 10);
 
 @alt_names = @{$slice->get_all_synonyms()};
 
@@ -513,7 +513,7 @@ $multi->restore();
 
 # test fetch_all on synonym adaptor
 my $all_synonyms = $syn_adap->fetch_all();
-is(@$all_synonyms, 3, 'fetch_all on synonym adaptor');
+is(@$all_synonyms, 5, 'fetch_all on synonym adaptor');
 
 
 #Test assembly exception type on HAP

modules/t/sliceAdaptor.t

@@ -555,6 +555,9 @@ ok($slice->seq_region_name =~ /$clone_name\.\d+/);
   is($chr_syn_slice->seq_region_name(), '20', 'Ensuring slice is Chr20 as expected');
   $chr_syn_slice = $slice_adaptor->fetch_by_region('toplevel', 'chrx');
   is($chr_syn_slice->seq_region_name(), 'X', 'Ensuring slice is ChrX as expected');
+
+  $syn_slice = $slice_adaptor->fetch_by_region('toplevel', 'chr1');
+  is($syn_slice->seq_region_name(), '1', 'Ensuring chr1 is 1, and not 10');
 }
 
 #{

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

 1	469283	alt_20	\N
 2	469283	anoth_20	4200
 3	469293	chrx	11000
+4	469272	chr10	11000
+5	469271	chr1	11000