vivarium.gbd_mapping_generator package

Submodules

vivarium.gbd_mapping_generator.base_template_builder module

vivarium.gbd_mapping_generator.base_template_builder.get_base_types()[source]
vivarium.gbd_mapping_generator.base_template_builder.make_gbd_record()[source]
vivarium.gbd_mapping_generator.base_template_builder.build_mapping()[source]

Generate string representations of class definitions.

Returns:

String representation of the base classes.

Return type:

str

vivarium.gbd_mapping_generator.build_mapping module

vivarium.gbd_mapping_generator.build_mapping.make_dirs_and_init(mapping_type)[source]

vivarium.gbd_mapping_generator.cause_builder module

Tools for automatically generating the GBD cause mapping.

vivarium.gbd_mapping_generator.cause_builder.get_base_types()[source]
vivarium.gbd_mapping_generator.cause_builder.make_cause(name, c_id, me_id, most_detailed, level, restrictions, sequelae=None, etiologies=None)[source]
vivarium.gbd_mapping_generator.cause_builder.make_causes(causes_list)[source]
vivarium.gbd_mapping_generator.cause_builder.build_mapping_template()[source]
vivarium.gbd_mapping_generator.cause_builder.build_mapping()[source]

vivarium.gbd_mapping_generator.covariate_builder module

vivarium.gbd_mapping_generator.covariate_builder.get_base_types()[source]
vivarium.gbd_mapping_generator.covariate_builder.make_covariate(name, cov_id, by_age, by_sex, dichotomous)[source]

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

vivarium.gbd_mapping_generator.covariate_builder.make_covariates(covariate_list)[source]

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

vivarium.gbd_mapping_generator.covariate_builder.build_mapping_template()[source]
vivarium.gbd_mapping_generator.covariate_builder.build_mapping()[source]

vivarium.gbd_mapping_generator.data module

vivarium.gbd_mapping_generator.data.get_sequelae()[source]
vivarium.gbd_mapping_generator.data.get_etiologies()[source]
vivarium.gbd_mapping_generator.data.get_causes(level=None)[source]
vivarium.gbd_mapping_generator.data.get_risks()[source]
vivarium.gbd_mapping_generator.data.get_covariates()[source]
vivarium.gbd_mapping_generator.data.get_sequela_list()[source]
vivarium.gbd_mapping_generator.data.get_etiology_list()[source]
vivarium.gbd_mapping_generator.data.get_cause_list()[source]
vivarium.gbd_mapping_generator.data.get_risk_list()[source]
vivarium.gbd_mapping_generator.data.get_covariate_list(with_survey=False)[source]
vivarium.gbd_mapping_generator.data.get_sequela_data()[source]
Return type:

list

vivarium.gbd_mapping_generator.data.get_etiology_data()[source]
Return type:

list

vivarium.gbd_mapping_generator.data.get_cause_data()[source]
vivarium.gbd_mapping_generator.data.get_age_restriction_edge(age_restriction, end=False)[source]
vivarium.gbd_mapping_generator.data.make_cause_restrictions(cause)[source]
vivarium.gbd_mapping_generator.data.get_all_risk_metadata()[source]
vivarium.gbd_mapping_generator.data.get_risk_data()[source]
Return type:

list

vivarium.gbd_mapping_generator.data.get_duplicate_indices(names)[source]
Return type:

list[int]

Parameters:

names (list[str])

vivarium.gbd_mapping_generator.data.get_covariate_data()[source]
Return type:

list[tuple[str, float, bool, bool, bool]]

class vivarium.gbd_mapping_generator.data.GbdDummy[source]

Bases: object

Mock class to wrap internal dependency.

vivarium.gbd_mapping_generator.etiology_builder module

vivarium.gbd_mapping_generator.etiology_builder.get_base_types()[source]
vivarium.gbd_mapping_generator.etiology_builder.make_etiology(name, rei_id)[source]
Return type:

str

Parameters:
vivarium.gbd_mapping_generator.etiology_builder.make_etiologies(etiology_list)[source]
Return type:

str

Parameters:

etiology_list (list[tuple[str, float]])

vivarium.gbd_mapping_generator.etiology_builder.build_mapping_template()[source]
Return type:

str

vivarium.gbd_mapping_generator.etiology_builder.build_mapping()[source]
Return type:

str

vivarium.gbd_mapping_generator.globals module

vivarium.gbd_mapping_generator.id_builder module

vivarium.gbd_mapping_generator.id_builder.make_unknown_flag()[source]
vivarium.gbd_mapping_generator.id_builder.build_mapping()[source]

vivarium.gbd_mapping_generator.risk_builder module

vivarium.gbd_mapping_generator.risk_builder.get_base_types()[source]
vivarium.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)[source]
Return type:

str

vivarium.gbd_mapping_generator.risk_builder.make_entity_list(name, entity_list, entity_type)[source]
Return type:

str

Parameters:

  • entity_list (list)

  • entity_type (str)

vivarium.gbd_mapping_generator.risk_builder.make_risks(risk_list)[source]
Return type:

str

Parameters:

risk_list (list)

vivarium.gbd_mapping_generator.risk_builder.build_mapping_template()[source]
vivarium.gbd_mapping_generator.risk_builder.build_mapping()[source]
Return type:

str

vivarium.gbd_mapping_generator.sequela_builder module

vivarium.gbd_mapping_generator.sequela_builder.get_base_types()[source]
vivarium.gbd_mapping_generator.sequela_builder.make_sequela(name, s_id, mei_id, hs_name, hs_id)[source]
Return type:

str

Parameters:
vivarium.gbd_mapping_generator.sequela_builder.make_sequelae(sequela_list)[source]
Return type:

str

Parameters:

sequela_list (list[str])

vivarium.gbd_mapping_generator.sequela_builder.build_mapping_template()[source]
Return type:

str

vivarium.gbd_mapping_generator.sequela_builder.build_mapping()[source]
Return type:

str

vivarium.gbd_mapping_generator.util module

vivarium.gbd_mapping_generator.util.make_module_docstring(description, file)[source]

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

vivarium.gbd_mapping_generator.util.make_import(module_to_import, imports=())[source]

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

vivarium.gbd_mapping_generator.util.text_wrap(start_string, items, sep=', ', implicit=False)[source]
vivarium.gbd_mapping_generator.util.replace_numeric_prefix(name)[source]

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

vivarium.gbd_mapping_generator.util.clean_entity_list(raw_entity_series)[source]
Return type:

list[str]

vivarium.gbd_mapping_generator.util.to_id(number, id_type)[source]

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

vivarium.gbd_mapping_generator.util.make_class_sig(name, superclass=None, docstring=None)[source]

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

vivarium.gbd_mapping_generator.util.make_slots(field_list)[source]

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

vivarium.gbd_mapping_generator.util.make_init(field_dtype_tuples)[source]

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

vivarium.gbd_mapping_generator.util.make_super_call(superclass)[source]

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

vivarium.gbd_mapping_generator.util.make_attribute_assignment(field_names)[source]

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

vivarium.gbd_mapping_generator.util.make_record(name, attrs=None, superclass=None, docstring=None)[source]

Generate class definitions from a name and additional information.

Parameters:
Returns:

String representation of named class.

Return type:

str

vivarium.gbd_mapping_generator.util.get_default_output_directory()[source]
vivarium.gbd_mapping_generator.util.format_string_none(value)[source]
vivarium.gbd_mapping_generator.util.make_empty_survey(flags, index)[source]

Module contents