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To ensure that a MySQL query includes all the values in an array for a many-to-many relationship, you can use the HAVING clause along with the COUNT function. Here's an example query structure:

SELECT table1.column1, table1.column2
FROM table1
JOIN table3 ON table1.id = table3.table1_id
JOIN table2 ON table2.id = table3.table2_id
WHERE table2.column IN ('value1', 'value2', 'value3')
GROUP BY table1.id
HAVING COUNT(DISTINCT table2.column) = 3;

This query retrieves data from table1 that has a many-to-many relationship with table2 through the junction table table3. The WHERE clause filters the results to only include rows where table2.column is one of the specified values.

The GROUP BY clause groups the results by table1.id, which is the key used in the many-to-many relationship. This ensures that each table1 record is only returned once.

Finally, the HAVING clause checks that the count of distinct values in table2.column is equal to the number of values specified in the array (3 in this case). This ensures that all the values in the array are present in the many-to-many relationship.