modified LIMIT to use a function from DBConnection

modules/Bio/EnsEMBL/DBSQL/ArchiveStableIdAdaptor.pm

@@ -556,15 +556,11 @@ sub _lookup_version {
 
   if( ! defined $arch_id->{'db_name'} ) {
     # latest version of this stable id
-
-    $sql = qq(
-      SELECT new_db_name, new_version
-	FROM stable_id_event sie, mapping_session m
-       WHERE sie.mapping_session_id = m.mapping_session_id
-	 AND new_stable_id = "@{[$arch_id->stable_id]}"
-             $EXTRA_SQL
-    ORDER BY m.created DESC
-      LIMIT 1);
+      my $sql_tmp = "SELECT new_db_name, new_version ";
+      $sql_tmp .= "FROM stable_id_event sie, mapping_session m  ";
+      $sql_tmp .= "WHERE sie.mapping_session_id = m.mapping_session_id AND new_stable_id = \"@{[$arch_id->stable_id]}\" $EXTRA_SQL ";
+      $sql_tmp .= "ORDER BY m.created DESC";
+      $sql = $self->dbc->add_limit_clause($sql_tmp,1);
   } else {
     $sql = qq(
       SELECT old_db_name, old_version

modules/Bio/EnsEMBL/Utils/ConversionSupport.pm

@@ -874,7 +874,7 @@ sub get_taxonomy_id {
   Description : Retrieves the species scientific name (Genus species) from the
                 meta table
   Return type : String - species scientific name
-  Exceptions  : thrown if species name can't be determined from db
+  Exceptions  : thrown if species name can not be determined from db
   Caller      : general
 
 =cut
@@ -882,15 +882,17 @@ sub get_taxonomy_id {
 sub get_species_scientific_name {
     my ($self, $dba) = @_;
     $dba ||= $self->dba;
-    my $sql = qq(
-        SELECT
-                meta_value
-        FROM
-                meta
-        WHERE meta_key = "species.classification"
-        ORDER BY meta_id
-        LIMIT 2
-    );
+    my $sql_tmp = "SELECT meta_value FROM meta WHERE meta_key = \'species.classification\' ORDER BY meta_id";
+    my $sql = $dba->dbc->add_limit_clause($sql_tmp,2);
+#     my $sql = qq(
+#         SELECT
+#                 meta_value
+#         FROM
+#                 meta
+#         WHERE meta_key = "species.classification"
+#         ORDER BY meta_id
+#         LIMIT 2
+#     );
     my $sth = $dba->dbc->db_handle->prepare($sql);
     $sth->execute;
     my @sp;