gbd_mapping_generator package

Submodules

gbd_mapping_generator.base_template_builder module

gbd_mapping_generator.base_template_builder.get_base_types()

gbd_mapping_generator.base_template_builder.make_gbd_record()

gbd_mapping_generator.base_template_builder.build_mapping()

Generate string representations of class definitions.

Returns:

String representation of the base classes.

Return type:

str

gbd_mapping_generator.build_mapping module

gbd_mapping_generator.build_mapping.make_dirs_and_init(mapping_type)

gbd_mapping_generator.cause_builder module

Tools for automatically generating the GBD cause mapping.

gbd_mapping_generator.cause_builder.get_base_types()

gbd_mapping_generator.cause_builder.make_cause(name, c_id, me_id, most_detailed, level, restrictions, sequelae=None, etiologies=None)

gbd_mapping_generator.cause_builder.make_causes(causes_list)

gbd_mapping_generator.cause_builder.build_mapping_template()

gbd_mapping_generator.cause_builder.build_mapping()

gbd_mapping_generator.covariate_builder module

gbd_mapping_generator.covariate_builder.get_base_types()

gbd_mapping_generator.covariate_builder.make_covariate(name, cov_id, by_age, by_sex, dichotomous)

Creates a single Covariate based on the supplied parameters.

Parameters:

• name (str) – Covariate name.

• cov_id (float) – The numeric id for the covariate.

• by_age (bool) – Adjusted by age

• by_sex (bool) – Adjusted by sex

• dichotomous (bool) – Is dichotomous

Returns:

Generated string for a single covariate.

Return type:

str

gbd_mapping_generator.covariate_builder.make_covariates(covariate_list)

Generates the list of covariates.

Parameters:

covariate_list (List[Tuple[str, float, bool, bool, bool]]) – Sequence of covariate data from which to generate the representation

Returns:

Generated string all covariates.

Return type:

str

gbd_mapping_generator.covariate_builder.build_mapping_template()

gbd_mapping_generator.covariate_builder.build_mapping()

gbd_mapping_generator.data module

gbd_mapping_generator.data.get_sequelae()

gbd_mapping_generator.data.get_etiologies()

gbd_mapping_generator.data.get_causes(level=None)

gbd_mapping_generator.data.get_risks()

gbd_mapping_generator.data.get_covariates()

gbd_mapping_generator.data.get_sequela_list()

gbd_mapping_generator.data.get_etiology_list()

gbd_mapping_generator.data.get_cause_list()

gbd_mapping_generator.data.get_risk_list()

gbd_mapping_generator.data.get_covariate_list(with_survey=False)

gbd_mapping_generator.data.get_sequela_data()

Return type:

List

gbd_mapping_generator.data.get_etiology_data()

Return type:

List

gbd_mapping_generator.data.get_cause_data()

gbd_mapping_generator.data.get_age_restriction_edge(age_restriction, end=False)

gbd_mapping_generator.data.make_cause_restrictions(cause)

gbd_mapping_generator.data.get_all_risk_metadata()

gbd_mapping_generator.data.get_risk_data()

Return type:

List

gbd_mapping_generator.data.get_duplicate_indices(names)

Parameters:

names (List[str]) –

Return type:

List[int]

gbd_mapping_generator.data.get_covariate_data()

Return type:

List[Tuple[str, float, bool, bool, bool]]

class gbd_mapping_generator.data.GbdDummy

Bases: object

Mock class to wrap internal dependency.

gbd_mapping_generator.etiology_builder module

gbd_mapping_generator.etiology_builder.get_base_types()

gbd_mapping_generator.etiology_builder.make_etiology(name, rei_id)

Parameters:

• name (str) –

• rei_id (float) –

Return type:

str

gbd_mapping_generator.etiology_builder.make_etiologies(etiology_list)

Parameters:

etiology_list (List[Tuple[str, float]]) –

Return type:

str

gbd_mapping_generator.etiology_builder.build_mapping_template()

Return type:

str

gbd_mapping_generator.etiology_builder.build_mapping()

Return type:

str

gbd_mapping_generator.globals module

gbd_mapping_generator.id_builder module

gbd_mapping_generator.id_builder.make_unknown_flag()

gbd_mapping_generator.id_builder.build_mapping()

gbd_mapping_generator.risk_builder module

gbd_mapping_generator.risk_builder.get_base_types()

gbd_mapping_generator.risk_builder.make_risk(name, rei_id, most_detailed, level, paf_calculation_type, affected_causes, paf_of_one_causes, distribution, levels, tmred, scalar, restrictions)

Return type:

str

gbd_mapping_generator.risk_builder.make_entity_list(name, entity_list, entity_type)

Parameters:

• entity_list (List) –

• entity_type (str) –

Return type:

str

gbd_mapping_generator.risk_builder.make_risks(risk_list)

Parameters:

risk_list (List) –

Return type:

str

gbd_mapping_generator.risk_builder.build_mapping_template()

gbd_mapping_generator.risk_builder.build_mapping()

Return type:

str

gbd_mapping_generator.sequela_builder module

gbd_mapping_generator.sequela_builder.get_base_types()

gbd_mapping_generator.sequela_builder.make_sequela(name, s_id, mei_id, hs_name, hs_id)

Parameters:

• name (str) –

• s_id (float) –

• mei_id (float) –

• hs_name (str) –

• hs_id (float) –

Return type:

str

gbd_mapping_generator.sequela_builder.make_sequelae(sequela_list)

Parameters:

sequela_list (List[str]) –

Return type:

str

gbd_mapping_generator.sequela_builder.build_mapping_template()

Return type:

str

gbd_mapping_generator.sequela_builder.build_mapping()

Return type:

str

gbd_mapping_generator.util module

gbd_mapping_generator.util.make_module_docstring(description, file)

Generates standard header with additional information from the description.

Parameters:

• description (str) – Custom header text for the generated file.

• file (str | Path) – Path to python module that generates the target module.

Returns:

String representation of module doc string.

Return type:

str

gbd_mapping_generator.util.make_import(module_to_import, imports=())

Generates the necessary imports. Smart about importing modules or names.

Parameters:

• module_to_import (str) – Name of the module.

• imports (Tuple[str, ...]) – Named items to import. If empty import the module name.

Returns:

Generated string for necessary imports.

Return type:

str

gbd_mapping_generator.util.text_wrap(start_string, items, sep=', ', implicit=False)

gbd_mapping_generator.util.replace_numeric_prefix(name)

Variables cannot start with numeric characters. Replace with the word. This only occurs 3 times using GBD 2019 data.

Parameters:

name (str) – The name of the member variable.

Returns:

Input string transformed to non-numeric prefix.

Return type:

str

gbd_mapping_generator.util.clean_entity_list(raw_entity_series)

Return type:

List[str]

gbd_mapping_generator.util.to_id(number, id_type)

Wrap the id value with the id type. Be mindful of NaN values.

Parameters:

• number (float) – The id value.

• id_type (str) – The id type.

Returns:

String with the id type wrapping the value in parentheses.

Return type:

str

gbd_mapping_generator.util.make_class_sig(name, superclass=None, docstring=None)

Generate class signature from a name and additional information.

Parameters:

• name – Name of the generated class.

• superclass – Parent class.

• docstring – Documentation for the generated class.

Returns:

String representation of named class.

Return type:

str

gbd_mapping_generator.util.make_slots(field_list)

Generate explicit object attributes using slots (instead of dict).

Parameters:

field_list (List[str]) – Names for the slot attributes.

Returns:

String representation of slot attributes.

Return type:

str

gbd_mapping_generator.util.make_init(field_dtype_tuples)

Generate the __init__ function as part of class generation.

Parameters:

field_dtype_tuples (Tuple[Tuple[str, str], ...]) – Collection of name / value pairs that are used to create the the __init__ function with the specified parameters. Parameters are type hinted.

Returns:

String representation of the __init__ function.

Return type:

str

gbd_mapping_generator.util.make_super_call(superclass)

Generate the call to initialize the parent class.

Parameters:

superclass (Tuple[str, Tuple[Tuple[str, str], ...]]) – Nested tuples composed of name and attributes for the superclass.

Returns:

String representation of the call to the superclass.

Return type:

str

gbd_mapping_generator.util.make_attribute_assignment(field_names)

Generate the class attributes and initialize them.

Parameters:

field_names (List[str]) – List of class attribute names.

Returns:

String representation of the initialized attributes.

Return type:

str

gbd_mapping_generator.util.make_record(name, attrs=None, superclass=None, docstring=None)

Generate class definitions from a name and additional information.

Parameters:

• name (str) – Name of the generated class.

• attrs (Tuple[Tuple[str, str], ...]) – Class attributes.

• superclass (Tuple[str, Tuple[Tuple[str, str], ...]]) – Parent class.

• docstring (str) – Documentation for the generated class.

Returns:

String representation of named class.

Return type:

str

gbd_mapping_generator.util.get_default_output_directory()

gbd_mapping_generator.util.format_string_none(value)

gbd_mapping_generator.util.make_empty_survey(flags, index)

Module contents