For this use case, the bookmark keys are used at data consuming side, and per documented at , the create_dynamic_frame.from_catalog just takes the column names for the "jobBookmarkKeys". There is no option to give a default value to a column when its value is null.
However, there is workaround to this.
If your original table is stored in an RDBMS system, then you can add a computed column, which has same value as the original column, and has a default value where the original is null.
Then in your glue job, you can use the computed column as part of bookmark keys.
Hope it helps.
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