biosimulators_utils.model_lang.xpp package#

Submodules#

biosimulators_utils.model_lang.xpp.data_model module#

Data model for XPP simulation methods

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-08-08
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.model_lang.xpp.utils module#

Utilities for working with XPP models

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-08-08
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.model_lang.xpp.utils.get_parameters_variables_outputs_for_simulation(model_filename, model_language, simulation_type, algorithm_kisao_id=None, set_filename=None, parameter_filename=None, initial_conditions_filename=None, change_level=<class 'biosimulators_utils.sedml.data_model.SedDocument'>, native_ids=False, native_data_types=False, config=None, max_number_of_steps=None)[source]#

Get the possible observables for a simulation of a model

Parameters:

model_filename (str) – path to model file or directory of XPP ODE, set, parameters, and initial conditions files
model_language (str) – model language (e.g., urn:sedml:language:xpp)
simulation_type (types.Type) – subclass of Simulation
algorithm_kisao_id (str, optional) – KiSAO id of the algorithm for simulating the model (e.g., KISAO_0000019 for CVODE)
set_filename (str, optional) – path to XPP set file
parameter_filename (str, optional) – path to XPP parameters file
initial_conditions_filename (str, optional) – path to XPP initial conditions file
change_level (types.Type, optional) – level at which model changes will be made (SedDocument or Task)
native_ids (bool, optional) – whether to return the raw id and name of each model component rather than the suggested name for the variable of an associated SED-ML data generator
native_data_types (bool, optional) – whether to return new_values in their native data types
config (Config, optional) – whether to fail on missing includes
max_number_of_steps (int, optional) – maximum number of steps to record

Returns:

possible attributes of a model that can be changed and their default values list of Simulation: simulations of the model list of Variable: possible observables for a simulation of the model list of Plot: possible plots of the results of a simulation of the model

Return type:

list of ModelAttributeChange

biosimulators_utils.model_lang.xpp.validation module#

Methods for validating XPP files

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-08-06
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.model_lang.xpp.validation.get_xpp_input_configuration_from_directory(dirname)[source]#

Get input file configuration from a directory of files

*.ode: Main model model
*.set: Set file
*.par: Parameters file
*.ic: Initial conditions file

Parameters:

dirname (str) – path to directory of XPP files

Returns:

str: path to main model file
str: path to set file
str: path to parameters file
str: path to initial conditions file
str: name of a set to use
str: name of a set not to use

Return type:

tuple

biosimulators_utils.model_lang.xpp.validation.sanitize_model(filename, keep_only_directives=True, exclude_options=None)[source]#

Sanitize an ODE file for interrogation

Join continued statements into individual lines
Remove statements

Parameters:

filename (str) – path to model file or directory with .ode and possibly set (.set), parameter (.par), andd initial conditions (.ic) files
keep_only_directives (bool, optional) – whether to keep only directives which limit output variables
exclude_options (list of str, optional) – list of directives to exclude

Returns:

path to sanitized model file

Return type:

str

biosimulators_utils.model_lang.xpp.validation.validate_model(filename, set_filename=None, parameter_filename=None, initial_conditions_filename=None, name=None, config=None)[source]#

Check that a model is valid

Parameters:

filename (str) – path to model file or directory with .ode and possibly set (.set), parameter (.par), andd initial conditions (.ic) files
set_filename (str, optional) – path to XPP set file
parameter_filename (str, optional) – path to XPP parameters file
initial_conditions_filename (str, optional) – path to XPP initial conditions file
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)
dict: values of parameters of initial conditions of variables

Return type:

tuple