datamanager.h

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#pragma once
 
#include "HealthGPS.Core/api.h"
#include "pif_data.h"
 
#include <filesystem>
#include <nlohmann/json.hpp>
 
namespace hgps::input {
 
using namespace hgps::core;
 
class DataManager : public Datastore {
  public:
    DataManager() = delete;
 
    explicit DataManager(std::filesystem::path data_path,
                         VerboseMode verbosity = VerboseMode::none);
 
    std::vector<Country> get_countries() const override;
 
    Country get_country(const std::string &alpha) const override;
 
    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;
 
    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;
 
    std::vector<DiseaseInfo> get_diseases() const override;
 
    DiseaseInfo get_disease_info(const core::Identifier &code) const override;
 
    DiseaseEntity get_disease(const DiseaseInfo &info, const Country &country) const override;
 
    std::optional<RelativeRiskEntity>
    get_relative_risk_to_disease(const DiseaseInfo &source,
                                 const DiseaseInfo &target) const override;
 
    std::optional<RelativeRiskEntity>
    get_relative_risk_to_risk_factor(const DiseaseInfo &source, Gender gender,
                                     const core::Identifier &risk_factor_key) const override;
 
    CancerParameterEntity get_disease_parameter(const DiseaseInfo &info,
                                                const Country &country) const override;
 
    DiseaseAnalysisEntity get_disease_analysis(const Country &country) const override;
 
    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;
 
    std::vector<LmsDataRow> get_lms_parameters() const override;
 
    std::optional<PIFData> get_pif_data(const DiseaseInfo &disease_info, const Country &country,
                                        const nlohmann::json &pif_config) const;
 
    const std::filesystem::path &get_root_path() const noexcept { return root_; }
 
  private:
    std::filesystem::path root_;
    VerboseMode verbosity_;
    nlohmann::json index_;
 
    std::map<int, std::map<Gender, double>>
    load_cost_of_diseases(const Country &country, const nlohmann::json &node,
                          const std::filesystem::path &parent_path) const;
 
    std::vector<LifeExpectancyItem> load_life_expectancy(const Country &country) const;
 
    static std::string replace_string_tokens(const std::string &source,
                                             const std::vector<std::string> &tokens);
 
    static std::map<std::string, std::size_t>
    create_fields_index_mapping(const std::vector<std::string> &column_names,
                                const std::vector<std::string> &fields);
 
    void notify_warning(std::string_view message) const;
 
    PIFTable load_pif_from_csv(const std::filesystem::path &filepath) const;
 
    std::filesystem::path construct_pif_path(const std::string &disease_code,
                                             const nlohmann::json &pif_config) const;
 
    std::string expand_environment_variables(const std::string &path) const;
};
 
} // namespace hgps::input