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If a column name in the source key passed to the map key appears in more than one table of the source query, you will get an error along the lines of:
Integrity constraint violation: 1052 Column 'id' in on clause is ambiguous
The alias for the table containing the column instance you want to use needs to be passed to the map class constructor:
$this->map = new MigrateSQLMap($this->machineName, array( 'bid' => array( 'type' => 'int', 'not null' => TRUE, 'alias' => 'b', ), ), MigrateDestinationNode::getKeySchema() )