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)[source]¶
Check that a model is valid
- Parameters
filename (
str
) – path to modelname (
str
, optional) – name of model for use in error messages
- Returns
nested
list
ofstr
: nested list of errors (e.g., required ids missing or ids not unique)nested
list
ofstr
: 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