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Merge SBMLInfo and model parser (extend/update the JSON for report)

Open matthiaskoenig opened this issue 2 years ago • 0 comments

Currently a lot of duplicated code due to parallel developments

  1. SBMLReport uses SBML -> JSON
  2. 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)

matthiaskoenig avatar Jul 09 '22 12:07 matthiaskoenig