[ENSCORESW-476]. Fixed backwards compatibility for anything which is older than release 72

modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm

@@ -845,6 +845,23 @@ sub ignore_cache_override {
     return $self->{'_override'}; 
 }
 
+=head2 schema_version
+
+    Description : Returns the schema version of the currently connected
+                  DBAdaptor. The subroutine also caches this value so
+                  repeated calls continue to be speedy.                  
+    Example     : $adaptor->schema_version();            
+    Returntype  : Integer
+
+=cut
+
+sub schema_version {
+  my ($self) = @_;
+  return $self->{_schema_version} if exists $self->{_schema_version};
+  my $mc = $self->db()->get_MetaContainer();
+  return $self->{_schema_version} = $mc->get_schema_version();
+}
+
 #_tables
 #
 #  Args       : none

modules/Bio/EnsEMBL/DBSQL/BaseMetaContainer.pm

@@ -72,7 +72,7 @@ sub get_schema_version {
     if ( !defined($ver) ) {    # old style format
       return 0;
     }
-    return $ver;
+    return $ver * 1; #multiply by 1 to get this into a number
   } else {
     warning(
       sprintf(

modules/Bio/EnsEMBL/DBSQL/DBEntryAdaptor.pm

@@ -1282,8 +1282,11 @@ sub _fetch_by_object_type {
     throw("Can't fetch_by_EnsObject_type without a type");
   }
 
+  ### TODO - SCHEMA VERSION HACK. Please remove sometime in the future once we do not want backwards compatibility
+  my $schema_version = $self->schema_version();
+
   #  my $sth = $self->prepare("
-  my $sql = (<<SSQL);
+  my $columns_sql = (<<COLUMNS_SQL);
     SELECT xref.xref_id, xref.dbprimary_acc, xref.display_label, xref.version,
            exDB.priority,
            exDB.db_name, exDB.db_release, exDB.status, exDB.db_display_name,
@@ -1295,20 +1298,40 @@ sub _fetch_by_object_type {
            idt.cigar_line, idt.score, idt.evalue, oxr.analysis_id,
            gx.linkage_type,
            xref.info_type, xref.info_text, exDB.type, gx.source_xref_id,
-           oxr.linkage_annotation, xref.description,
-           ax.xref_id, ax.source_xref_id, ax.condition_type, 
-           ax.associated_group_id, ax.rank
+           oxr.linkage_annotation, xref.description
+COLUMNS_SQL
+
+  my $tables_sql = <<'TABLES_SQL';
     FROM   (xref xref, external_db exDB, object_xref oxr)
     LEFT JOIN external_synonym es on es.xref_id = xref.xref_id
     LEFT JOIN identity_xref idt on idt.object_xref_id = oxr.object_xref_id
     LEFT JOIN ontology_xref gx on gx.object_xref_id = oxr.object_xref_id
-    LEFT JOIN associated_xref ax ON ax.object_xref_id = oxr.object_xref_id
-    LEFT JOIN associated_group ag ON ax.associated_group_id = ag.associated_group_id
+TABLES_SQL
+  
+  my $where_sql = <<'WHERE_SQL';
     WHERE  xref.xref_id = oxr.xref_id
       AND  xref.external_db_id = exDB.external_db_id
       AND  oxr.ensembl_id = ?
       AND  oxr.ensembl_object_type = ?
-SSQL
+WHERE_SQL
+
+  if($schema_version >= 72) {
+    $columns_sql .= ','; #need the extra comma
+    $columns_sql .= <<'EXTRA';
+    ax.xref_id, ax.source_xref_id, ax.condition_type, ax.associated_group_id, ax.rank
+EXTRA
+    $tables_sql .= <<'EXTRA';
+    LEFT JOIN associated_xref ax ON ax.object_xref_id = oxr.object_xref_id
+    LEFT JOIN associated_group ag ON ax.associated_group_id = ag.associated_group_id
+EXTRA
+
+  }
+
+  #Join the above together into one statement
+  my $sql = "$columns_sql
+$tables_sql
+$where_sql";
+  # warn $sql; # uncomment me to see the full SQL generated
 
   if ( defined($exdbname) ) {
     if ( index( $exdbname, '%' ) != -1 ) {