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(nml2_lems_file_name, max_memory='400M')[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?)
- Parameters
nml2_lems_file_name (str) – name of file to validate
max_memory (str) – memory to use for the Java virtual machine
- Returns
True if valid, False if invalid