Implements Health-GPS back-end data store interface using a file-based storage. More...

#include <datamanager.h>

Inheritance diagram for hgps::input::DataManager:

Collaboration diagram for hgps::input::DataManager:

Public Member Functions
	DataManager ()=delete

	DataManager (std::filesystem::path data_path, VerboseMode verbosity=VerboseMode::none)
	Initialises a new instance of the hgps::input::DataManager class.

std::vector< Country >	get_countries () const override
	Gets the full collection of countries in the store.

Country	get_country (const std::string &alpha) const override
	Gets a single country by the alpha code.

std::vector< PopulationItem >	get_population (const Country &country) const

std::vector< PopulationItem >	get_population (const Country &country, std::function< bool(unsigned int)> time_filter) const override
	Gets the population growth trend for a country filtered by time.

std::vector< MortalityItem >	get_mortality (const Country &country) const

std::vector< MortalityItem >	get_mortality (const Country &country, std::function< bool(unsigned int)> time_filter) const override
	Gets the population mortality trend for a country filtered by time.

std::vector< DiseaseInfo >	get_diseases () const override
	Gets the collection of diseases information in the store.

DiseaseInfo	get_disease_info (const core::Identifier &code) const override
	Gets a single disease information by identifier.

DiseaseEntity	get_disease (const DiseaseInfo &info, const Country &country) const override
	Gets a disease full definition by identifier for a country.

std::optional< RelativeRiskEntity >	get_relative_risk_to_disease (const DiseaseInfo &source, const DiseaseInfo &target) const override
	Gets the relative risk effects for disease to disease interactions.

std::optional< RelativeRiskEntity >	get_relative_risk_to_risk_factor (const DiseaseInfo &source, Gender gender, const core::Identifier &risk_factor_key) const override
	Gets the relative risk effects for risk factor to disease interactions.

CancerParameterEntity	get_disease_parameter (const DiseaseInfo &info, const Country &country) const override
	Gets the parameters required by cancer type diseases for a country.

DiseaseAnalysisEntity	get_disease_analysis (const Country &country) const override
	Gets the Burden of Diseases (BoD) analysis dataset for a country.

std::vector< BirthItem >	get_birth_indicators (const Country &country) const

std::vector< BirthItem >	get_birth_indicators (const Country &country, std::function< bool(unsigned int)> time_filter) const override
	Gets the population birth indicators for a country filtered by time.

std::vector< LmsDataRow >	get_lms_parameters () const override
	Gets the LMS (lambda-mu-sigma) parameters for childhood growth charts.

std::optional< PIFData >	get_pif_data (const DiseaseInfo &disease_info, const Country &country, const nlohmann::json &pif_config) const
	Gets PIF data for a specific disease.

const std::filesystem::path &	get_root_path () const noexcept
	Get the root data directory path.

Public Member Functions inherited from hgps::core::Datastore
virtual	~Datastore ()=default
	Destroys a Datastore instance.

Detailed Description

Implements Health-GPS back-end data store interface using a file-based storage.

The storage is based on a folder structure and indexed by a file, index.json, with a versioned schema defining the storage sub-folders structure, file names, data limits, metadata, and rules for accessing the stored contents.

Note: To avoid storing disease-disease interaction files filled with a default value representing no relative risk effect, the default value is defined in the index file, and the respective dataset populated at run-time with the default value when the an associated file does not exists in the store.

See also: https://imperialchepi.github.io/healthgps/datamodel for the Data Model details.

Constructor & Destructor Documentation

◆ DataManager() [1/2]

hgps::input::DataManager::DataManager ( )

delete

◆ DataManager() [2/2]

hgps::input::DataManager::DataManager	(	std::filesystem::path	data_path,
		VerboseMode	verbosity = `VerboseMode::none`
	)

explicit

Initialises a new instance of the hgps::input::DataManager class.

Parameters

data_path	The path to the directory containing the data.
verbosity	The terminal logging verbosity mode to use.

Exceptions

std::invalid_argument	if the root directory or index.json is missing.
std::runtime_error	for invalid or unsupported index.json file schema version.

Member Function Documentation

◆ get_birth_indicators() [1/2]

std::vector< BirthItem > hgps::input::DataManager::get_birth_indicators ( const Country & country ) const

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◆ get_birth_indicators() [2/2]

std::vector< BirthItem > hgps::input::DataManager::get_birth_indicators	(	const Country &	country,
		std::function< bool(unsigned int)>	time_filter
	)		const

overridevirtual

Gets the population birth indicators for a country filtered by time.

Parameters

country	The target country definition
time_filter	The time filter predicate, e.g. years range

Returns: The resulting list of birth indicator items

Implements hgps::core::Datastore.

◆ get_countries()

std::vector< Country > hgps::input::DataManager::get_countries ( ) const

overridevirtual

Gets the full collection of countries in the store.

Returns: The list of countries

Implements hgps::core::Datastore.

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◆ get_country()

Country hgps::input::DataManager::get_country ( const std::string & alpha ) const

overridevirtual

Gets a single country by the alpha code.

Parameters

alpha The country alpha 2 or 3 format code to search

Returns: The country's definition

Implements hgps::core::Datastore.

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◆ get_disease()

DiseaseEntity hgps::input::DataManager::get_disease	(	const DiseaseInfo &	info,
		const Country &	country
	)		const

overridevirtual

Gets a disease full definition by identifier for a country.

Parameters

info	The target disease information
country	The target country definition

Returns: The disease definition

Implements hgps::core::Datastore.

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◆ get_disease_analysis()

DiseaseAnalysisEntity hgps::input::DataManager::get_disease_analysis ( const Country & country ) const

overridevirtual

Gets the Burden of Diseases (BoD) analysis dataset for a country.

Parameters

country The target country definition

Returns: The BoD analysis data

Implements hgps::core::Datastore.

◆ get_disease_info()

DiseaseInfo hgps::input::DataManager::get_disease_info ( const core::Identifier & code ) const

overridevirtual

Gets a single disease information by identifier.

Parameters

code	The target disease identifier

Returns: The disease information

Implements hgps::core::Datastore.

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◆ get_disease_parameter()

CancerParameterEntity hgps::input::DataManager::get_disease_parameter	(	const DiseaseInfo &	info,
		const Country &	country
	)		const

overridevirtual

Gets the parameters required by cancer type diseases for a country.

Parameters

info	The disease of type cancer information
country	The target country definition

Returns: The cancer parameters

Exceptions

std::out_of_range for unknown disease parameter file type.

Implements hgps::core::Datastore.

◆ get_diseases()

std::vector< DiseaseInfo > hgps::input::DataManager::get_diseases ( ) const

overridevirtual

Gets the collection of diseases information in the store.

Returns: The list of diseases defined

Implements hgps::core::Datastore.

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◆ get_lms_parameters()

std::vector< LmsDataRow > hgps::input::DataManager::get_lms_parameters ( ) const

overridevirtual

Gets the LMS (lambda-mu-sigma) parameters for childhood growth charts.

Returns: The parameters for the LMS model

Implements hgps::core::Datastore.

◆ get_mortality() [1/2]

std::vector< MortalityItem > hgps::input::DataManager::get_mortality ( const Country & country ) const

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◆ get_mortality() [2/2]

std::vector< MortalityItem > hgps::input::DataManager::get_mortality	(	const Country &	country,
		std::function< bool(unsigned int)>	time_filter
	)		const

overridevirtual

Gets the population mortality trend for a country filtered by time.

Parameters

country	The target country definition
time_filter	The time filter predicate, e.g., years range

Returns: The resulting list of mortality trend items

Implements hgps::core::Datastore.

◆ get_pif_data()

std::optional< PIFData > hgps::input::DataManager::get_pif_data	(	const DiseaseInfo &	disease_info,
		const Country &	country,
		const nlohmann::json &	pif_config
	)		const

Gets PIF data for a specific disease.

Parameters

disease_info	The disease information
country	The country
pif_config	PIF configuration from config.json

Returns: PIF data for the disease, or std::nullopt if not available

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◆ get_population() [1/2]

std::vector< PopulationItem > hgps::input::DataManager::get_population ( const Country & country ) const

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◆ get_population() [2/2]

std::vector< PopulationItem > hgps::input::DataManager::get_population	(	const Country &	country,
		std::function< bool(unsigned int)>	time_filter
	)		const

overridevirtual

Gets the population growth trend for a country filtered by time.

Parameters

country	The target country definition
time_filter	The time filter predicate, e.g., years range

Returns: The resulting list of population trend items

Implements hgps::core::Datastore.

◆ get_relative_risk_to_disease()

std::optional< RelativeRiskEntity > hgps::input::DataManager::get_relative_risk_to_disease	(	const DiseaseInfo &	source,
		const DiseaseInfo &	target
	)		const

overridevirtual

Gets the relative risk effects for disease to disease interactions.

Parameters

source	The source disease information
target	The target disease information

Returns: The disease-disease effects or std::nullopt if file doesn't exist or only contains default values

Implements hgps::core::Datastore.

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◆ get_relative_risk_to_risk_factor()

std::optional< RelativeRiskEntity > hgps::input::DataManager::get_relative_risk_to_risk_factor	(	const DiseaseInfo &	source,
		Gender	gender,
		const core::Identifier &	risk_factor_key
	)		const

overridevirtual

Gets the relative risk effects for risk factor to disease interactions.

Parameters

source	The disease information
gender	The gender enumeration
risk_factor_key	The risk factor identifier

Returns: The risk factor-disease effects or std::nullopt if data missing

Implements hgps::core::Datastore.

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◆ get_root_path()

const std::filesystem::path & hgps::input::DataManager::get_root_path ( ) const

inlinenoexcept

Get the root data directory path.

Returns: The root data directory path

The documentation for this class was generated from the following files:

HealthGPS.Input/datamanager.h
HealthGPS.Input/datamanager.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ DataManager() [1/2]

◆ DataManager() [2/2]

Member Function Documentation

◆ get_birth_indicators() [1/2]

◆ get_birth_indicators() [2/2]

◆ get_countries()

◆ get_country()

◆ get_disease()

◆ get_disease_analysis()

◆ get_disease_info()

◆ get_disease_parameter()

◆ get_diseases()

◆ get_lms_parameters()

◆ get_mortality() [1/2]

◆ get_mortality() [2/2]

◆ get_pif_data()

◆ get_population() [1/2]

◆ get_population() [2/2]

◆ get_relative_risk_to_disease()

◆ get_relative_risk_to_risk_factor()

◆ get_root_path()