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the way we check for FBC strict is not compliant with the spec #118
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Why is modelpolisher checking this at all? Should this not be done by the SBML validation? I.e. only check if the model is valid and what the validation warnings/errors are without any additional own checking. |
In the end, the strict attribute is set on the model according to this inference. However I can't really say if this is actually a sensible thing to do, or to place within the scope of the Polisher. |
So if this is just checking if strict can be set I would do the following:
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Exactly, ModelPolisher is not a model validator. It aims to set missing attributes to suitable values. It could, for instance, load a model that is invalid in the sence that the strict attribute isn't defined at all and then give it a value. The validation-based approach @matthiaskoenig suggests makes sense. The SBO term check is a nice addition. I assume ModelPolisher would also try to set those terms if undefined. |
From the spec section 3.3 page 8 (line numbers at the end):
Instead, what we are checking right now is:
We are not explicitly checking lines 15 and 16, and the SBO-term check we do is not required by the spec.
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