Index: trunk/geniusql/objects.py
===================================================================
--- trunk/geniusql/objects.py (revision 27)
+++ trunk/geniusql/objects.py (revision 30)
@@ -296,6 +296,11 @@
         return i
     
-    def add_primary(self):
-        """Set the PRIMARY KEY for this Table, using its Column.key values."""
+    def set_primary(self):
+        """Set the PRIMARY KEY for this Table, using its Column.key values.
+        
+        If self already possesses a primary key, this method will DROP it.
+        This is intended to be used with install or repair scripts.
+        """
+        self.drop_primary()
         pk = [column.qname for column in self.itervalues() if column.key]
         if pk:
@@ -549,4 +554,7 @@
     def discover(self, tablename, conn=None):
         """Attach a new Table from the underlying DB to self (and return it).
+        
+        tablename: the database's name for the table. This may be different
+        from the schema's key for the table.
         
         Table objects (and their Column and Index subobjects) will be
Index: trunk/geniusql/providers/mysql.py
===================================================================
--- trunk/geniusql/providers/mysql.py (revision 23)
+++ trunk/geniusql/providers/mysql.py (revision 30)
@@ -185,4 +185,15 @@
         """Remove any PRIMARY KEY for this Table."""
         self.schema.db.execute('ALTER TABLE %s DROP PRIMARY KEY;' % self.qname)
+    
+    def set_primary(self):
+        """Set the PRIMARY KEY for this Table."""
+        pk = [column.qname for column in self.itervalues() if column.key]
+        if pk:
+            # For MySQL, we MUST do this in a single statement.
+            self.schema.db.execute("ALTER TABLE %s DROP PRIMARY KEY, "
+                                   "ADD PRIMARY KEY (%s);" %
+                                   (self.qname, ", ".join(pk)))
+        else:
+            self.drop_primary()
 
 
Index: trunk/geniusql/providers/sqlite.py
===================================================================
--- trunk/geniusql/providers/sqlite.py (revision 29)
+++ trunk/geniusql/providers/sqlite.py (revision 30)
@@ -423,17 +423,18 @@
         return {idkeys[0]: new_id}
     
-    def add_primary(self):
+    def set_primary(self):
         """Assert the PRIMARY KEY for this Table, using its Column.key values."""
-        pk = [column.qname for column in self.itervalues() if column.key]
-        if pk:
-            self._start_temp()
-            self._finish_temp()
+        self._start_temp()
+        self._finish_temp()
     
     def drop_primary(self):
         """Remove any PRIMARY KEY for this Table."""
+        pk_cols = [col for col in self.itervalues() if col.key]
         self._start_temp()
-        for col in self.itervalues():
+        for col in pk_cols:
             col.key = False
         self._finish_temp()
+        for col in pk_cols:
+            col.key = True
 
 
Index: trunk/geniusql/test/zoo_fixture.py
===================================================================
--- trunk/geniusql/test/zoo_fixture.py (revision 28)
+++ trunk/geniusql/test/zoo_fixture.py (revision 30)
@@ -607,8 +607,7 @@
         # Drop and re-add the PK on, oh, how about the Animal table?
         Animal = schema['Animal']
-        Animal.drop_primary()
-        Animal.add_primary()
-        
-        Animal = schema.discover('Animal')
+        Animal.set_primary()
+        
+        Animal = schema.discover(Animal.name)
         if schema.db.pks_must_be_indexed:
             self.assertEqual(len(Animal.indices), 2)