"""
==================================
The Component Configuration Parser
==================================
The :class:`ComponentConfigurationParser` is responsible for taking a list or
hierarchical :class:`ConfigTree <vivarium.config_tree.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 :meth:`get_components
<ComponentConfigurationParser.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
"""
from typing import Any, Dict, List, Tuple, Union
from vivarium.config_tree import ConfigTree
from vivarium.framework.utilities import import_by_path
from .manager import ComponentConfigError
[docs]class ParsingError(ComponentConfigError):
"""Error raised when component configurations are not specified correctly."""
pass
[docs]class 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.
"""
[docs] def get_components(self, component_config: Union[ConfigTree, List]) -> List:
"""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 :class:`ConfigTree <vivarium.config_tree.ConfigTree>`.
Configurations that are provided in the form of a list are already
assumed to be in the correct form.
Parameters
----------
component_config
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
-------
List
A list of initialized components.
"""
if isinstance(component_config, ConfigTree):
component_list = self.parse_component_config(component_config.to_dict())
else: # Components were specified in a list rather than a tree.
component_list = component_config
component_list = prep_components(component_list)
return import_and_instantiate_components(component_list)
[docs] def parse_component_config(
self, component_config: Dict[str, Union[Dict, List]]
) -> List[str]:
"""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
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 parse_component_config_to_list(component_config)
[docs]def parse_component_config_to_list(
component_config: Dict[str, Union[Dict, List]]
) -> List[str]:
"""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:
.. code-block:: python
component_config = {
'vivarium_examples': {
'disease_model': {
'population': ['BasePopulation()', 'Mortality()']
'disease': ['SIS_DiseaseModel("diarrhea")]
}
}
}
would be parsed by this function into the following list:
.. code-block:: python
['vivarium_examples.disease_model.population.BasePopulation()',
'vivarium_examples.disease_model.population.Mortality()',
'vivarium_examples.disease_model.disease.SIS_DiseaseModel("diarrhea")']
Parameters
----------
component_config
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.
"""
if not component_config:
return []
def _process_level(level, prefix):
if not level:
raise ParsingError(
f"Check your configuration. Component {prefix} should not be left empty with the header"
)
if isinstance(level, list):
return [".".join(prefix + [child]) for child in level]
component_list = []
for name, child in level.items():
component_list.extend(_process_level(child, prefix + [name]))
return component_list
return _process_level(component_config, [])
[docs]def prep_components(component_list: Union[List[str], Tuple[str]]) -> List[Tuple[str, Tuple]]:
"""Transform component description strings into tuples of component paths
and required arguments.
Parameters
----------
component_list
The component descriptions to transform.
Returns
-------
List[Tuple[str, Tuple]]
List of component/argument tuples.
"""
components = []
for c in component_list:
path, args_plus = c.split("(")
cleaned_args = clean_args(args_plus[:-1].split(","), path)
components.append((path, cleaned_args))
return components
[docs]def clean_args(args: List, path: str) -> Tuple:
"""Transform component arguments into a tuple, validating that each argument
is a string.
Parameters
----------
args
List of arguments to the component specified at ``path``.
path
Path representing the component for which arguments are being cleaned.
Returns
-------
Tuple
A tuple of arguments, each of which is guaranteed to be a string.
"""
out = []
for a in args:
a = a.strip()
if not a:
continue
not_a_valid_string = len(a) < 3 or not (
(a[0] == a[-1] == "'") or (a[0] == a[-1] == '"')
)
if not_a_valid_string:
raise ParsingError(f"Invalid component argument {a} for component {path}")
out.append(a[1:-1])
return tuple(out)
[docs]def import_and_instantiate_components(component_list: List[Tuple[str, Tuple[str]]]) -> List:
"""Transform the list of tuples representing components into the actual
instantiated component objects.
Parameters
----------
component_list
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
-------
List
A list of instantiated component objects.
"""
return [import_by_path(component)(*args) for component, args in component_list]