SynBioDex/libSBOLcore — Issue #21: Circular references
Author: Juul
Created: 2011-10-14 20:36:55+00:00
State: open

It is possible to create, serialize and deserialize a Collection that includes DnaComponents that have SequenceAnnotations whose subComponents refer back to the original DnaComponent.

The serializer doesn't complain or fail.

The problem is that circular references do not make sense for DNA. This could cause problems. E.g. you can imagine a web service crashing when someone gives it an SBOL file that has been crafted to contain circular references. Even though the deserializer wouldn't fail, the code interpreting the resulting data structure may not realize that it has to watch out for circular references and loop/recurse forever.

This issue was added to libSBOLxml. This should be specifically disallowed in the data model (the next RFC) but it should be enforced by the serializer and deserializer.