Ensure data types in Model Editor

yaml2sbml-dev / yaml2sbml

Tool to convert an ODE model specified in the YAML format to SBML.

https://yaml2sbml.readthedocs.io/en/latest/

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Ensure data types in Model Editor #100

Closed jvanhoefer closed 3 years ago

jvanhoefer commented 3 years ago

When exporting the current FSP example to yaml instead of sbml, one gets quite weird state initial values. Would be nice to ensure & type cast the data types in all parts of the Model Editor. (Have to think on how this is best done...)

    - stateId: x_0_13
      rightHandSide: -(k_1 + (k_2 + k_3)*0 + k_4*13) * x_0_13 + k_2 * 1 * x_1_13+
            k_3 * 0 * x_0_12+ k_4 * 14 * x_0_14
      initialValue: !!python/object/apply:numpy.core.multiarray.scalar
      - *id001
      - !!binary |
            DAmnXBiq4j4=

jvanhoefer commented 3 years ago

Also kinda related to #99...

jvanhoefer commented 3 years ago

maybe use Pydantic here, also related to #107

Furthermore it might be a good idea to check, if the different libsbml calls are successful in yaml2sbml (e.g. setId() returns a corresponding flag...)

jvanhoefer commented 3 years ago

At least the issue with the FSP example is resolved in #117