sbmlutils
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Merge SBMLInfo and model parser (extend/update the JSON for report)
Currently a lot of duplicated code due to parallel developments
- SBMLReport uses
SBML -> JSON
- SBMLParser & ModelFactory use
Model
, i.e.,SBML -> Model
This should be unified to reduce complexity and long-term maintenance. I.e. the workflows should all be around the internal Model structure. I.e. things should be
SBML -> Model -> JSON (SBMLInfo)
This will require major refactoring of information. One additional complexity is that some information is more global in the JSON. I.e. it requires to figure out which Assignments/Events ... manipulate other objects. This should be added in a second global parsing.
- Also Validation information should be added to the report.
- In the long-term models should also be manipulated from the report (e.g. adding annotations)