ON DUPLICATE KEY + AUTO INCREMENT issue mysql

This behavior is documented (paragraph in parentheses):

If you specify ON DUPLICATE KEY UPDATE, and a row is inserted that would cause a duplicate value in a UNIQUE index or PRIMARY KEY, MySQL performs an UPDATE of the old row. For example, if column a is declared as UNIQUE and contains the value 1, the following two statements have similar effect:

    INSERT INTO table (a,b,c) VALUES (1,2,3)   ON DUPLICATE KEY UPDATE c=c+1;

    UPDATE table SET c=c+1 WHERE a=1;

(The effects are not identical for an InnoDB table where a is an auto-increment column. With an auto-increment column, an INSERT statement increases the auto-increment value but UPDATE does not.)

Here is a simple explanation. MySQL attempts to do the insert first. This is when the id gets auto incremented. Once incremented, it stays. Then the duplicate is detected and the update happens. But the value gets missed.

You should not depend on auto_increment having no gaps. If that is a requirement, the overhead on the updates and inserts is much larger. Essentially, you need to put a lock on the entire table, and renumber everything that needs to be renumbered, typically using a trigger. A better solution is to calculate incremental values on output.

This question is a fairly old one, but I answer it maybe it helps someone, to solve the auto-incrementing problem use the following code before insert/on duplicate update part and execute them all together:

SET @NEW_AI = (SELECT MAX(`the_id`)+1 FROM `table_blah`);
SET @ALTER_SQL = CONCAT('ALTER TABLE `table_blah` AUTO_INCREMENT =', @NEW_AI);
PREPARE NEWSQL FROM @ALTER_SQL;
EXECUTE NEWSQL; 

together and in one statement it should be something like below:

SET @NEW_AI = (SELECT MAX(`the_id`)+1 FROM `table_blah`);
SET @ALTER_SQL = CONCAT('ALTER TABLE `table_blah` AUTO_INCREMENT =', @NEW_AI);
PREPARE NEWSQL FROM @ALTER_SQL;
EXECUTE NEWSQL; 
INSERT INTO `table_blah` (`the_col`) VALUES("the_value")
ON DUPLICATE KEY UPDATE `the_col` = "the_value";