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So, what I am woundering is has anyone ever had this problem in Hibernate where we want to map one field to different types depending on the database we are connecting to and how the problem was solved.
This is what Hibernate is all about. You define the mapping file and say you want a Boolean, and Hibernate knows how to work with Booleans in the different dbs. I've not used DB2, but what I would do is use SchemaExport to generate DDL in DB2 and see what the Boolean property gets created as in the db and use that.