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draeger-lab / ModelPolisher

ModelPolisher accesses the BiGG Models knowledgebase to annotate SBML models.
MIT License
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polishing of reaction participants is aborted halfway through #122

Closed Schmoho closed 2 years ago

Schmoho commented 2 years ago

https://github.com/draeger-lab/ModelPolisher/blob/4b7728b778ed7217f49d46a46163794f1535f42e/src/main/java/edu/ucsd/sbrg/bigg/polishing/ReactionPolishing.java#L184-L203

See referenced code. Even if we really don't want to continue any determination of the compartment if one of the referenced species has no compartment set (null check), it does not make sense to abort the process there (line 202) and thereby for example stop midway setting the default SBO terms and default attributes.

I.e. I would consider this a bug.

Schmoho commented 2 years ago

Fixed the bug + adjusted the unit tests that tested for it.

The new behaviour is: disregarding participant compartments, defaults on SpeciesReferences are set. The code that determines whether compartments are consistent no longer returns a compartment anyways depending on ordering.