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You're correct that using publish_via_partition_root=true is necessary to replicate partition changes properly during a blue/green deployment with Aurora PostgreSQL.
Manually updating the publication to set publish_via_partition_root=true via ALTER PUBLICATION is the right approach. This is safe to do on the green environment after the blue/green deployment is created.
The key considerations when doing this:
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Make the ALTER PUBLICATION change on the green environment before making any partition changes.
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Verify the publication change is replicated back to the blue environment.
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Double check replication is working between environments after altering the publication.
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Be cautious of making other DDL/DML changes on the partitioned table during the switch over.
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Test the process thoroughly before performing it on a production system.
So in summary, yes you can and should modify the publication to enable partition root replication for your blue/green partitioning scenario. Just be very careful and test it out to validate smooth switchover. Let me know if any other questions come up!
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