Specific error messages if sbml not well-defined

[yannikschaelte]

Since we have some specific sbml requirements, it might be informative for the user to give explicit error messages, e.g. "you need to define sigmas" etc., as far as possible. These things are a bit difficult to detect currently.

[dweindl]

Can you provide more details of when and where (stacktrace) that happened and what message you got instead?

[yannikschaelte]

so ... not my code, but this is where:

File "/home/paulstapor/pycharm-community-2019.1/helpers/pydev/pydevd.py", line 1741, in <module>
    main()
  File "/home/paulstapor/pycharm-community-2019.1/helpers/pydev/pydevd.py", line 1735, in main
    globals = debugger.run(setup['file'], None, None, is_module)
  File "/home/paulstapor/pycharm-community-2019.1/helpers/pydev/pydevd.py", line 1135, in run
    pydev_imports.execfile(file, globals, locals)  # execute the script
  File "/home/paulstapor/pycharm-community-2019.1/helpers/pydev/pydev_imps/_pydev_execfile.py", line 18, in execfile
    exec(compile(contents+"\n", file, 'exec'), glob, loc)
  File "/home/paulstapor/sedml_import/simulatePetab.py", line 17, in <module>
    petab_problem.get_optimization_to_simulation_parameter_mapping()
  File "/home/paulstapor/anaconda3/envs/PENV/lib/python3.7/site-packages/petab/core.py", line 236, in get_optimization_to_simulation_parameter_mapping
    warn_unmapped=warn_unmapped)
  File "/home/paulstapor/anaconda3/envs/PENV/lib/python3.7/site-packages/petab/core.py", line 508, in get_optimization_to_simulation_parameter_mapping
    row.observableId, override_type='noise')
  File "/home/paulstapor/anaconda3/envs/PENV/lib/python3.7/site-packages/petab/core.py", line 492, in _apply_overrides
    f'{override_type}Parameter{i+1}{observable_id}']
KeyError: 'noiseParameter1_task0_model0_perelson1_V'

solution was to define sigma + noise parameter