"self" link references a non-Atom representation.
This often occurs when people confuse "self" for "alternate".
From RFC 4287, section 220.127.116.11 (emphasis added)
1. The value "alternate" signifies that the IRI in the value of the href attribute identifies an alternate version of the resource described by the containing element.
3. The value "self" signifies that the IRI in the value of the href attribute identifies a resource equivalent to the containing element.
Generally, this problem can be solved by changing the rel value on the link from "self" to "alternate"
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