GROUP BY - do not group NULL

Perhaps you should add something to the null columns to make them unique and group on that? I was looking for some sort of sequence to use instead of UUID() but this might work just as well.

SELECT `table1`.*, 
    IFNULL(ancestor,UUID()) as unq_ancestor
    GROUP_CONCAT(id SEPARATOR ',') AS `children_ids`
FROM `table1` 
WHERE (enabled = 1) 
GROUP BY unq_ancestor

When grouping by column Y, all rows for which the value in Y is NULL are grouped together.

This behaviour is defined by the SQL-2003 standard, though it's slightly surprising because NULL is not equal to NULL.

You can work around it by grouping on a different value, some function (mathematically speaking) of the data in your grouping column.

If you have a unique column X then this is easy.

---

Input

X      Y
-------------
1      a
2      a
3      b
4      b
5      c
6      (NULL)
7      (NULL)
8      d

---

Without fix

SELECT GROUP_CONCAT(`X`)
  FROM `tbl`
 GROUP BY `Y`;

Result:

GROUP_CONCAT(`foo`)
-------------------
6,7
1,2
3,4
5
8

---

With fix

SELECT GROUP_CONCAT(`X`)
  FROM `tbl`
 GROUP BY IFNULL(`Y`, `X`);

Result:

GROUP_CONCAT(`foo`)
-------------------
6
7
1,2
3,4
5
8

---

Let's take a closer look at how this is working

SELECT GROUP_CONCAT(`X`), IFNULL(`Y`, `X`) AS `grp`
  FROM `tbl`
 GROUP BY `grp`;

Result:

GROUP_CONCAT(`foo`)     `grp`
-----------------------------
6                       6
7                       7
1,2                     a
3,4                     b
5                       c
8                       d

---

If you don't have a unique column that you can use, you can try to generate a unique placeholder value instead. I'll leave this as an exercise to the reader.