biosimulators_utils.model_lang.cellml package#

Submodules#

biosimulators_utils.model_lang.cellml.utils module#

Utilities for working with CellML models

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-04-05
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

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

Get the possible observables for a simulation of a model

Parameters:

model_filename (str) – path to model file
model_language (str) – model language (e.g., urn:sedml:language:cellml)
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)
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
observable_only (bool, optional) – whether to skip the variables that are not exposed by OpenCor
config (Config, optional) – whether to fail on missing includes

Returns:

possible attributes of a model that can be changed and their default values list of Simulation: simulation 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.cellml.validation module#

Utilities for validating CellML models

Author:: Jonathan Karr <karr@mssm.edu>
Date:: 2021-05-10
Copyright:: 2021, Center for Reproducible Biomedical Modeling
License:: MIT

biosimulators_utils.model_lang.cellml.validation.validate_model(filename, name=None, resolve_imports=True, config=None)[source]#

Check that a file is a valid CellML model

Parameters:

filename (str) – path to model
name (str, optional) – name of model for use in error messages
resolve_imports (bool, optional) – whether to resolve imports
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)
tuple:
- libcellml.model.Model: model
- lxml.etree._ElementTree: model

Return type:

tuple

biosimulators_utils.model_lang.cellml.validation.validate_model_version_1_0(filename, doc, resolve_imports=True, config=None)[source]#

Check that a file is a valid CellML 2.0 model

Parameters:

filename (str) – path to model
doc (lxml.etree._ElementTree) – XML document for file
resolve_imports (bool, optional) – whether to resolve imports
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)
None

Return type:

tuple

biosimulators_utils.model_lang.cellml.validation.validate_model_version_1_1(filename, doc, resolve_imports=True, config=None)[source]#

Check that a file is a valid CellML 2.0 model

Parameters:

filename (str) – path to model
doc (lxml.etree._ElementTree) – XML document for file
resolve_imports (bool, optional) – whether to resolve imports
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)
None

Return type:

tuple

biosimulators_utils.model_lang.cellml.validation.validate_model_version_2(filename, doc, resolve_imports=True, config=None)[source]#

Check that a file is a valid CellML 2.0 model

Parameters:

filename (str) – path to model
doc (lxml.etree._ElementTree) – XML document for file
resolve_imports (bool, optional) – whether to resolve imports
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)
libcellml.model.Model: model

Return type:

tuple