from .base_template_builder import gbd_record_attrs, modelable_entity_attrs
from .data import get_covariate_data, get_covariate_list
from .globals import ID_TYPES, CovariateDataSeq
from .util import (
DOUBLE_SPACING,
SINGLE_SPACING,
TAB,
make_import,
make_module_docstring,
make_record,
)
IMPORTABLES_DEFINED = ("Covariate", "covariates")
[docs]
def get_base_types():
cov_attrs = [
("name", "str"),
("kind", "str"),
("gbd_id", f"{ID_TYPES.COV_ID} | None"),
("by_age", "bool"),
("by_sex", "bool"),
("dichotomous", "bool"),
]
return {
"Covariate": {
"attrs": tuple(cov_attrs),
"superclass": ("ModelableEntity", modelable_entity_attrs),
"docstring": "Container for covariate GBD ids and metadata.",
},
"Covariates": {
"attrs": tuple([(name, "Covariate") for name in get_covariate_list()]),
"superclass": ("GbdRecord", gbd_record_attrs),
"docstring": "Container for GBD covariates.",
},
}
[docs]
def make_covariate(
name: str, cov_id: float, by_age: bool, by_sex: bool, dichotomous: bool
) -> str:
"""Creates a single Covariate based on the supplied parameters.
Parameters
----------
name
Covariate name.
cov_id
The numeric id for the covariate.
by_age
Adjusted by age
by_sex
Adjusted by sex
dichotomous
Is dichotomous
Returns
-------
str
Generated string for a single covariate.
"""
out = ""
out += TAB + f"'{name}': Covariate(\n"
out += TAB * 2 + f"name='{name}',\n"
out += TAB * 2 + "kind='covariate',\n"
out += TAB * 2 + f"gbd_id={ID_TYPES.COV_ID}({cov_id}),\n"
out += TAB * 2 + f"by_age={bool(by_age)},\n"
out += TAB * 2 + f"by_sex={bool(by_sex)},\n"
out += TAB * 2 + f"dichotomous={bool(dichotomous)},\n"
out += TAB + "),\n"
return out
[docs]
def make_covariates(covariate_list: CovariateDataSeq) -> str:
"""Generates the list of covariates.
Parameters
----------
covariate_list
Sequence of covariate data from which to generate the representation
Returns
-------
str
Generated string all covariates.
"""
out = "covariates = Covariates(**{\n"
for name, cov_id, by_age, by_sex, dichotomous in covariate_list:
out += make_covariate(name, cov_id, by_age, by_sex, dichotomous)
out += "})\n"
return out
[docs]
def build_mapping_template():
out = make_module_docstring("Mapping templates for GBD covariates.", __file__)
out += make_import(".base_template", ("GbdRecord", "ModelableEntity"))
out += make_import(".id", (ID_TYPES.COV_ID,))
for entity, info in get_base_types().items():
out += DOUBLE_SPACING
out += make_record(entity, **info)
return out
[docs]
def build_mapping():
out = make_module_docstring("Mapping of GBD covariates.", __file__)
out += make_import(".covariate_template", ("Covariate", "Covariates"))
out += make_import(".id", (ID_TYPES.COV_ID,)) + SINGLE_SPACING
out += make_covariates(get_covariate_data())
return out