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I'm considering using --replicate-do-table on a MySQL slave to only replicate certain tables. When the master is configured to use MIXED mode binary logging, deterministic queries will be written to the binary log using a statement, not the ROW binary data. If this INSERT/UPDATE contains a JOIN on a non-replicated table, however, it could potentially break on the slave. Is there any way around this or am I totally misunderstanding?

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I think you understand correctly, a query that references tables that aren't replicated will fail on the slave causing replication to halt. You could create dummy tables on the slave so that the join would succeed but if the results of the query would be affected then the update on the slave would not match the master and the two would diverge.

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