biosimulators_utils.model_lang.lems package

Submodules

biosimulators_utils.model_lang.lems.validation module

Utilities for validating LEMS models

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-06-03

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.model_lang.lems.validation.validate_model(filename, name=None, config=None)[source]

Check that a model is valid

Parameters
  • filename (str) – path to model

  • name (str, optional) – name of model for use in error messages

  • config (Config, optional) – whether to fail on missing includes

Returns

  • nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

  • nested list of str: nested list of errors (e.g., required ids missing or ids not unique)

  • Model: model

Return type

tuple

biosimulators_utils.model_lang.lems.validation.validate_neuroml2_lems_file()[source]

Validate a NeuroML 2 LEMS file using jNeuroML. Note that this uses jNeuroML and so is aware of the standard NeuroML LEMS definitions. TODO: allow inclusion of other paths for user-defined LEMS definitions (does the -norun option allow the use of -I?) :param nml2_lems_file_name: name of file to validate :type nml2_lems_file_name: str :param max_memory: memory to use for the Java virtual machine :type max_memory: str :param exit_on_fail: toggle whether command should exit if jnml fails :type exit_on_fail: bool :param return_string: toggle whether the output string should be returned :type return_string: bool :returns: Either a bool, or a tuple (bool, str): True if jnml ran without errors, false if jnml fails; along with the message returned by jnml