The Component Configuration Parser

The ComponentConfigurationParser is responsible for taking a list or hierarchical ConfigTree of components derived from a model specification yaml file and turning it into a list of instantiated component objects. When a model specification yaml file is loaded, the components come in as strings. In order for the simulation to be able to use these components, they have to be converted into the actual objects they represent. This occurs via the get_components method of the parser, which is used anytime a simulation is initialized from a model specification file.

There are three steps to this process.

1. Parsing the model specification’s components

2. Validating the arguments and prepping each component

3. Importing and instantiating the actual components

exception vivarium.framework.components.parser.ParsingError

Error raised when component configurations are not specified correctly.

class vivarium.framework.components.parser.ComponentConfigurationParser

Parses component configuration from model specification and initializes components.

To define your own set of parsing rules, you should write a parser class that inherits from this class and overrides parse_component_config. You can then define a set of parsing rules that turn component configuration information into a list of strings where each string is the full python import path to the class followed by a set of parentheses containing initialization arguments.

For example, say your component configuration specifies FancyClass from the important_module of your made_up_package and that FancyClass has two initialization parameters, 'important_thing1' and 'important_thing2'. Your implementation of parse_component_config needs to generate the string 'made_up_package.important_module.FancyClass ("important_thing1", "important_thing2")' and include it in the list of components to generate.

All classes that are initialized from the yaml configuration must either take no arguments or take arguments specified as strings.

get_components(component_config)

Extracts component specifications from configuration information and returns initialized components.

This method encapsulates the three steps described above of parsing, validating/prepping, and importing/instantiating.

The first step of parsing is only done for component configurations that come in as a ConfigTree. Configurations that are provided in the form of a list are already assumed to be in the correct form.

Parameters:

component_config (ConfigTree | List) – A hierarchical component specification blob. This configuration information needs to be parsable into a full import path and a set of initialization arguments by the parse_component_config method.

Returns:

A list of initialized components.

Return type:

List

parse_component_config(component_config)

Parses a hierarchical component specification into a list of standardized component definitions.

This default parser expects component configurations as a list of dicts. Each dict at the top level corresponds to a different package and has a single key. This key may be just the name of the package or a Python style import path to the module in which components live. The values of the top level dicts are a list of dicts or strings. If dicts, the keys are another step along the import path. If strings, the strings are representations of calls to the class constructor of components to be generated. This pattern may be arbitrarily nested.

Parameters:

component_config (Dict[str, Dict | List]) – A hierarchical component specification blob.

Returns:

• A list of standardized component definitions. Component definition

• strings are specified as

• 'absolute.import.path.ClassName("argument1", "argument2", ...)'.

Return type:

List[str]

vivarium.framework.components.parser.parse_component_config_to_list(component_config)

Helper function for parsing hierarchical component configuration into a flat list.

This function recursively walks the component configuration dictionary, treating it like a prefix tree and building the import path prefix. When it hits a list, it prepends the built prefix onto each item in the list. If the dictionary contains multiple lists, the prefix-prepended lists are concated together. For example, a component configuration dictionary like the following:

component_config = {
    'vivarium_examples': {
        'disease_model': {
            'population': ['BasePopulation()', 'Mortality()']
            'disease': ['SIS_DiseaseModel("diarrhea")]
        }
    }
}

would be parsed by this function into the following list:

['vivarium_examples.disease_model.population.BasePopulation()',
 'vivarium_examples.disease_model.population.Mortality()',
 'vivarium_examples.disease_model.disease.SIS_DiseaseModel("diarrhea")']

Parameters:

component_config (Dict[str, Dict | List]) – A hierarchical component specification blob.

Returns:

• A flat list of strings, each string representing the full python import

• path to the component, the component name, and any arguments.

Return type:

List[str]

vivarium.framework.components.parser.prep_components(component_list)

Transform component description strings into tuples of component paths and required arguments.

Parameters:

component_list (List[str] | Tuple[str]) – The component descriptions to transform.

Returns:

List of component/argument tuples.

Return type:

List[Tuple[str, Tuple]]

vivarium.framework.components.parser.clean_args(args, path)

Transform component arguments into a tuple, validating that each argument is a string.

Parameters:

• args (List) – List of arguments to the component specified at path.

• path (str) – Path representing the component for which arguments are being cleaned.

Returns:

A tuple of arguments, each of which is guaranteed to be a string.

Return type:

Tuple

vivarium.framework.components.parser.import_and_instantiate_components(component_list)

Transform the list of tuples representing components into the actual instantiated component objects.

Parameters:

component_list (List[Tuple[str, Tuple[str]]]) – A list of tuples representing components, where the first element of each tuple is a string with the full import path to the component and the component name and the second element is a tuple of the arguments to the component.

Returns:

A list of instantiated component objects.

Return type:

List