host Namespace Reference

Top-level namespace for Health-GPS Console host application. More...

Namespaces
	detail
	Internal details namespace for private data types and functions.
	poco
	Plain old class object (POCO) types for loading configuration file.

Classes
class	EventMonitor
	Defined the event monitor class used for processing Health-GPS event messages. More...
struct	ExperimentInfo
	Simulation experiment run-time information for reproducibility. More...
struct	CommandOptions
	Defines the Command Line Interface (CLI) arguments options. More...
struct	Configuration
	Defines the application configuration data structure. More...
class	ResultFileWriter
	Defines the results message file stream writer class. More...
class	ResultWriter
	Defines the Health-GPS results message writer interface. More...

Functions
std::string	get_time_now_str ()
	Get a string representation of current system time. More...
cxxopts::Options	create_options ()
	Creates the command-line interface (CLI) options. More...
void	print_app_title ()
	Prints application start-up messages. More...
CommandOptions	parse_arguments (cxxopts::Options &options, int &argc, char *argv[])
	Parses the command-line interface (CLI) arguments. More...
Configuration	load_configuration (CommandOptions &options)
	Loads the input configuration file, *.json, information. More...
bool	create_output_folder (std::filesystem::path folder_path, unsigned int num_retries=3)
	Creates the configuration output folder for result files. More...
std::vector< core::DiseaseInfo >	get_diseases_info (hgps::core::Datastore &data_api, Configuration &config)
	Gets the collection of diseases that matches the selected input list. More...
ModelInput	create_model_input (core::DataTable &input_table, core::Country country, Configuration &config, std::vector< core::DiseaseInfo > diseases)
std::string	create_output_file_name (const poco::OutputInfo &info, int job_id)
	Creates the full output file name from user input configuration. More...
ResultFileWriter	create_results_file_logger (const Configuration &config, const hgps::ModelInput &input)
	Creates the simulation results file logger instance. More...
std::unique_ptr< hgps::Scenario >	create_baseline_scenario (hgps::SyncChannel &channel)
	Creates the baseline scenario instance. More...
hgps::HealthGPS	create_baseline_simulation (hgps::SyncChannel &channel, hgps::SimulationModuleFactory &factory, hgps::EventAggregator &event_bus, hgps::ModelInput &input)
	Creates the baseline simulation engine instance. More...
hgps::HealthGPS	create_intervention_simulation (hgps::SyncChannel &channel, hgps::SimulationModuleFactory &factory, hgps::EventAggregator &event_bus, hgps::ModelInput &input, const poco::PolicyScenarioInfo &info)
	Creates the intervention simulation engine instance. More...
std::unique_ptr< hgps::InterventionScenario >	create_intervention_scenario (hgps::SyncChannel &channel, const poco::PolicyScenarioInfo &info)
	Creates the intervention scenario instance. More...
std::string	expand_environment_variables (const std::string &path)
	Expand environment variables in path to respective values. More...
std::optional< unsigned int >	create_job_seed (int job_id, std::optional< unsigned int > user_seed)
	Creates the experiment random number generator seed. More...
hgps::ModelInput	create_model_input (hgps::core::DataTable &input_table, hgps::core::Country country, Configuration &config, std::vector< hgps::core::DiseaseInfo > diseases)
	Creates Health-GPS inputs instance from configuration. More...
bool	load_datatable_from_csv (hc::DataTable &out_table, std::string full_filename, std::map< std::string, std::string > columns, std::string delimiter=",")
	Populates a datatable with the input data file contents. More...
std::map< hc::Identifier, std::vector< double > >	load_baseline_from_csv (const std::string &full_filename, const std::string delimiter=",")
	Loads the contents of baseline adjustments file into a table. More...
hgps::BaselineAdjustment	load_baseline_adjustments (const poco::BaselineInfo &info)
	Loads baseline adjustments information from a file. More...
std::unique_ptr< hgps::RiskFactorModelDefinition >	load_static_risk_model_definition (const std::string &model_name, const poco::json &opt)
	Loads the full hierarchical linear regression model definition from a JSON file. More...
std::unique_ptr< hgps::RiskFactorModelDefinition >	load_dynamic_risk_model_definition (const std::string &model_name, const poco::json &opt, const poco::SettingsInfo &settings)
	Loads a dynamic model from a JSON file. More...
std::unique_ptr< hgps::LiteHierarchicalModelDefinition >	load_ebhlm_risk_model_definition (const poco::json &opt)
	Loads the old energy balance model definition from a JSON file. More...
std::unique_ptr< hgps::EnergyBalanceModelDefinition >	load_newebm_risk_model_definition (const poco::json &opt, const poco::SettingsInfo &settings)
	Loads the new energy balance model definition from a JSON file. More...
std::pair< hgps::HierarchicalModelType, std::unique_ptr< hgps::RiskFactorModelDefinition > >	load_risk_model_definition (const std::string &model_type, const poco::json &opt, const poco::SettingsInfo &settings)
	Loads a risk model definition from a JSON file. More...
poco::json	load_json (const std::string &model_filename)
	Load and parse the model file. More...
void	register_risk_factor_model_definitions (hgps::CachedRepository &repository, const poco::ModellingInfo &info, const poco::SettingsInfo &settings)
	Registers a risk factor model definition with the repository. More...

Detailed Description

Top-level namespace for Health-GPS Console host application.

Function Documentation

create_baseline_scenario()

std::unique_ptr< hgps::Scenario > host::create_baseline_scenario

(

hgps::SyncChannel &

channel

)

Creates the baseline scenario instance.

Parameters

channel

Synchronization channel instance for data exchange

Returns

The baseline scenario instance

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create_baseline_simulation()

hgps::HealthGPS host::create_baseline_simulation	(	hgps::SyncChannel &	channel,
		hgps::SimulationModuleFactory &	factory,
		hgps::EventAggregator &	event_bus,
		hgps::ModelInput &	input
	)

Creates the baseline simulation engine instance.

Parameters

channel	Synchronization channel for data exchange instance
factory	Simulation module factory instance
event_bus	Shared event bus instance for streaming messages
input	Model inputs instance

Returns

The respective simulation engine instance

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create_intervention_scenario()

std::unique_ptr< hgps::InterventionScenario > host::create_intervention_scenario	(	hgps::SyncChannel &	channel,
		const poco::PolicyScenarioInfo &	info
	)

Creates the intervention scenario instance.

Parameters

channel	Synchronization channel instance for data exchange
info	Intervention configuration information

Returns

The respective intervention scenario instance

Exceptions

std::invalid_argument

Thrown if intervention identifier is unknown.

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create_intervention_simulation()

hgps::HealthGPS host::create_intervention_simulation	(	hgps::SyncChannel &	channel,
		hgps::SimulationModuleFactory &	factory,
		hgps::EventAggregator &	event_bus,
		hgps::ModelInput &	input,
		const poco::PolicyScenarioInfo &	info
	)

Creates the intervention simulation engine instance.

Parameters

channel	Synchronization channel for data exchange instance
factory	Simulation module factory instance
event_bus	Shared event bus instance for streaming messages
input	Model inputs instance
info	Intervention policy definition

Returns

The respective simulation engine instance

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create_job_seed()

std::optional< unsigned int > host::create_job_seed	(	int	job_id,
		std::optional< unsigned int >	user_seed
	)

Creates the experiment random number generator seed.

Parameters

job_id	Optional batch job identifier
user_seed	User input custom seed for experiment

Returns

The experiment seed, if user provide a seed

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create_model_input() [1/2]

ModelInput host::create_model_input	(	core::DataTable &	input_table,
		core::Country	country,
		Configuration &	config,
		std::vector< core::DiseaseInfo >	diseases
	)

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create_model_input() [2/2]

hgps::ModelInput host::create_model_input	(	hgps::core::DataTable &	input_table,
		hgps::core::Country	country,
		Configuration &	config,
		std::vector< hgps::core::DiseaseInfo >	diseases
	)

Creates Health-GPS inputs instance from configuration.

Parameters

input_table	The input dataset instance
country	Target country information
config	User input configuration instance
diseases	Selected diseases for experiment

Returns

The respective model input instance

create_options()

cxxopts::Options host::create_options

(

)

Creates the command-line interface (CLI) options.

Returns

Health-GPS CLI options

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create_output_file_name()

std::string host::create_output_file_name	(	const poco::OutputInfo &	info,
		int	job_id
	)

Creates the full output file name from user input configuration.

Parameters

info	User output information, may contain relative path and environment variables
job_id	Simulation job identifier

Returns

Output file full name

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create_output_folder()

bool host::create_output_folder	(	std::filesystem::path	folder_path,
		unsigned int	num_retries = 3
	)

Creates the configuration output folder for result files.

Parameters

folder_path	Full path to output folder
num_retries	Number of attempts before giving up

Returns

true for successful creation, otherwise false

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create_results_file_logger()

ResultFileWriter host::create_results_file_logger	(	const Configuration &	config,
		const hgps::ModelInput &	input
	)

Creates the simulation results file logger instance.

Parameters

config	User input configuration information
input	Model input instance

Returns

The respective file writer instance

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expand_environment_variables()

std::string host::expand_environment_variables

(

const std::string &

path

)

Expand environment variables in path to respective values.

Parameters

path	The source path to information

Returns

The resulting full path

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get_diseases_info()

std::vector< hgps::core::DiseaseInfo > host::get_diseases_info	(	hgps::core::Datastore &	data_api,
		Configuration &	config
	)

Gets the collection of diseases that matches the selected input list.

Parameters

data_api	The back-end data store instance to be used.
config	User configuration file instance

Returns

Collection of matching diseases information

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get_time_now_str()

std::string host::get_time_now_str

(

)

Get a string representation of current system time.

Returns

The system time as string

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load_baseline_adjustments()

hgps::BaselineAdjustment host::load_baseline_adjustments

(

const poco::BaselineInfo &

info

)

Loads baseline adjustments information from a file.

Parameters

info	Baseline file information

Returns

An instance of the hgps::BaselineAdjustment type

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load_baseline_from_csv()

std::map< hc::Identifier, std::vector< double > > host::load_baseline_from_csv	(	const std::string &	full_filename,
		const std::string	delimiter = ","
	)

Loads the contents of baseline adjustments file into a table.

Parameters

full_filename	The baseline adjustment file full path
delimiter	The data file's columns delimiter character

Returns

The fully populated table

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load_configuration()

Configuration host::load_configuration

(

CommandOptions &

options

)

Loads the input configuration file, *.json, information.

Parameters

options

User command-line options

Returns

The configuration file information

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load_datatable_from_csv()

bool host::load_datatable_from_csv	(	hc::DataTable &	out_table,
		std::string	full_filename,
		std::map< std::string, std::string >	columns,
		std::string	delimiter = ","
	)

Populates a datatable with the input data file contents.

Remarks

The datatable is used for checking the initial virtual population against the input data only and is not used as part of the simulation algorithm. If an external test can be used, this table could be dropped from the inputs.

Parameters

[out]	out_table	The datatable to be populated with the inputs data
	full_filename	The input data file full path
	columns	The data file columns data type
	delimiter	The data file's columns delimiter character

Returns

true for success, otherwise false.

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load_dynamic_risk_model_definition()

std::unique_ptr< hgps::RiskFactorModelDefinition > host::load_dynamic_risk_model_definition	(	const std::string &	model_name,
		const poco::json &	opt,
		const poco::SettingsInfo &	settings
	)

Loads a dynamic model from a JSON file.

Parameters

model_name	The name of the model to use
opt	The parsed model definition JSON file
settings	The main model settings

Returns

An instance of the hgps::RiskFactorModelDefinition type

Exceptions

std::invalid_argument

if dynamic model is unrecognised

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load_ebhlm_risk_model_definition()

std::unique_ptr< hgps::LiteHierarchicalModelDefinition > host::load_ebhlm_risk_model_definition

(

const poco::json &

opt

)

Loads the old energy balance model definition from a JSON file.

Parameters

opt	The parsed model definition JSON file

Returns

An instance of the hgps::LiteHierarchicalModelDefinition type

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load_json()

poco::json host::load_json

(

const std::string &

model_filename

)

Load and parse the model file.

Parameters

model_filename

The path to the model

Returns

The parsed JSON

Exceptions

std::invalid_argument

if file is missing

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load_newebm_risk_model_definition()

std::unique_ptr< hgps::EnergyBalanceModelDefinition > host::load_newebm_risk_model_definition	(	const poco::json &	opt,
		const poco::SettingsInfo &	settings
	)

Loads the new energy balance model definition from a JSON file.

Parameters

opt	The parsed model definition JSON file
settings	The main model settings

Returns

An instance of the hgps::EnergyBalanceModelDefinition type

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load_risk_model_definition()

std::pair< hgps::HierarchicalModelType, std::unique_ptr< hgps::RiskFactorModelDefinition > > host::load_risk_model_definition	(	const std::string &	model_type,
		const poco::json &	opt,
		const poco::SettingsInfo &	settings
	)

Loads a risk model definition from a JSON file.

Parameters

model_type	The type of model ("dynamic"/"static") to load
opt	The parsed model definition JSON file
settings	The main model settings

Returns

A std::pair containing the model type and model definition

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load_static_risk_model_definition()

std::unique_ptr< hgps::RiskFactorModelDefinition > host::load_static_risk_model_definition	(	const std::string &	model_name,
		const poco::json &	opt
	)

Loads the full hierarchical linear regression model definition from a JSON file.

Parameters

model_name	The name of the model to use
opt	The parsed model definition JSON file

Returns

An instance of the hgps::HierarchicalLinearModelDefinition type

Exceptions

std::invalid_argument

if static model is unrecognised

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parse_arguments()

CommandOptions host::parse_arguments	(	cxxopts::Options &	options,
		int &	argc,
		char *	argv[]
	)

Parses the command-line interface (CLI) arguments.

Parameters

options	The valid CLI options
argc	Number of input arguments
argv	List of input arguments

Returns

User command-line options

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print_app_title()

void host::print_app_title

(

)

Prints application start-up messages.

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register_risk_factor_model_definitions()

void host::register_risk_factor_model_definitions	(	hgps::CachedRepository &	repository,
		const poco::ModellingInfo &	info,
		const poco::SettingsInfo &	settings
	)

Registers a risk factor model definition with the repository.

Parameters

repository	The repository instance to register
info	The model definition information
settings	The associated experiment settings

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