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MJC598MJC598
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Source File Breakout (#74)
* adding source files instead of header only to allow for export 3rd party libraries * fixing the CI and coverage * turning off gcov and clang-formatting for csv.hpp amalgamation file
1 parent 1f2375c commit febef56

24 files changed

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‎.github/workflows/coverage.yml‎

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@@ -46,6 +46,7 @@ jobs:
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gtest/*
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googletest/*
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build/*
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tests/*
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fail-under-line: 80
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html-out: coverage.html
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html-details: true

‎CMakeLists.txt‎

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@@ -61,32 +61,82 @@ endif()
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# ---------------------------------------------------------------------------------------
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# Build the library
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# ---------------------------------------------------------------------------------------
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add_library(datamanagement INTERFACE)
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set(DATAMANAGEMENT_SRCS
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src/modeldata/model_data.cpp
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src/source/csv_source.cpp
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src/source/db_source.cpp
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src/utils/logging.cpp
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)
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if(DATAMANAGEMENT_BUILD_SHARED_LIBS)
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if(WIN32)
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configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cmake/version.rc.in ${CMAKE_CURRENT_BINARY_DIR}/version.rc @ONLY)
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list(APPEND DATAMANAGEMENT_SRCS ${CMAKE_CURRENT_BINARY_DIR}/version.rc)
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endif()
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add_library(datamanagement SHARED ${DATAMANAGEMENT_SRCS} ${DATAMANAGEMENT_ALL_HEADERS})
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target_compile_definitions(datamanagement PUBLIC DATAMANAGEMENT_SHARED_LIB)
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if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
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target_compile_options(datamanagement PUBLIC $<$<AND:$<CXX_COMPILER_ID:MSVC>,$<NOT:$<COMPILE_LANGUAGE:CUDA>>>:/wd4251
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/wd4275>)
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endif()
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else()
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add_library(datamanagement STATIC ${DATAMANAGEMENT_SRCS} ${DATAMANAGEMENT_ALL_HEADERS})
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endif()
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# ---------------------------------------------------------------------------------------
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# Alias for importing
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# ---------------------------------------------------------------------------------------
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add_library(datamanagement::datamanagement ALIAS datamanagement)
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set(DATAMANAGEMENT_INCLUDES_LEVEL "")
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if(DATAMANAGEMENT_SYSTEM_INCLUDES)
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set(DATAMANAGEMENT_INCLUDES_LEVEL "SYSTEM")
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endif()
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target_compile_definitions(datamanagement PUBLIC DATAMANAGEMENT_COMPILED_LIB)
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target_include_directories(datamanagement ${DATAMANAGEMENT_INCLUDES_LEVEL} PUBLIC "$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>"
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"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
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PRIVATE "$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/src>")
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option(BUILD_TESTS "enable datamanagement unit tests" OFF)
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if (NOT BUILD_TESTS STREQUAL OFF)
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add_subdirectory(tests)
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endif()
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target_include_directories(${PROJECT_NAME}
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INTERFACE
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$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
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$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/include>
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target_compile_definitions(datamanagement PUBLIC DATAMANAGEMENT_COMPILED_LIB)
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target_include_directories(datamanagement ${DATAMANAGEMENT_INCLUDES_LEVEL}
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PUBLIC
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"$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>"
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"$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
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PRIVATE
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"$<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/src>"
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)
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# ---------------------------------------------------------------------------------------
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# Link Dependencies
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# ---------------------------------------------------------------------------------------
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include(cmake/MakeDependenciesAvailable.cmake)
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target_link_libraries(${PROJECT_NAME}
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INTERFACE
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SQLiteCpp
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Boost::boost
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spdlog::spdlog
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Eigen3::Eigen
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)
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if (DATAMANAGEMENT_CALCULATE_COVERAGE)
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target_link_libraries(datamanagement
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PUBLIC
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SQLiteCpp
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Eigen3::Eigen
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PRIVATE
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spdlog::spdlog
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Boost::boost
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gcov
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)
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else()
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target_link_libraries(datamanagement
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PUBLIC
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SQLiteCpp
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Eigen3::Eigen
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PRIVATE
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spdlog::spdlog
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Boost::boost
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)
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endif()
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set_target_properties(datamanagement PROPERTIES VERSION ${DATAMANAGEMENT_VERSION} SOVERSION ${DATAMANAGEMENT_VERSION_MAJOR}.${DATAMANAGEMENT_VERSION_MINOR})
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‎cmake/LoadEigen.cmake‎

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Original file line numberDiff line numberDiff line change
@@ -3,21 +3,16 @@ message(CHECK_START "Fetching Eigen3...")
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list(APPEND CMAKE_MESSAGE_INDENT " ")
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FetchContent_Declare(
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Eigen
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Eigen3
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GIT_REPOSITORY https://gitlab.com/libeigen/eigen.git
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GIT_TAG master
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GIT_SHALLOW TRUE
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GIT_PROGRESS TRUE
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GIT_TAG "3.4.0"
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FIND_PACKAGE_ARGS NAMES Eigen3
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)
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# note: To disable eigen tests,
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# you should put this code in a add_subdirectory to avoid to change
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# BUILD_TESTING for your own project too since variables are directory
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# scoped
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set(BUILD_TESTING OFF)
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# Turn off Eigen Testing and Docs
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set(EIGEN_BUILD_TESTING OFF)
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set(EIGEN_MPL2_ONLY ON)
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set(EIGEN_BUILD_PKGCONFIG OFF)
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set(EIGEN_BUILD_DOC OFF)
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set(EIGEN_MPL2_ONLY ON)
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list(POP_BACK CMAKE_MESSAGE_INDENT)
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message(CHECK_PASS "Eigen3 Fetched")

‎cmake/LoadSpdlog.cmake‎

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@@ -6,5 +6,6 @@ FetchContent_Declare(
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GIT_TAG v1.x
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GIT_PROGRESS TRUE
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)
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set(SPDLOG_INSTALL ON)
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list(POP_BACK CMAKE_MESSAGE_INDENT)
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message(CHECK_PASS "spdlog Fetched")

‎cmake/MakeDependenciesAvailable.cmake‎

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@@ -8,9 +8,9 @@ include(cmake/LoadEigen.cmake)
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include(cmake/LoadSpdlog.cmake)
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1010
if(DATAMANAGEMENT_BUILD_TESTS STREQUAL "OFF")
11-
FetchContent_MakeAvailable(Eigen SQLiteCpp Boost spdlog)
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FetchContent_MakeAvailable(Eigen3 SQLiteCpp Boost spdlog)
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elseif(DATAMANAGEMENT_BUILD_TESTS STREQUAL "ON")
1313
include(cmake/LoadGtest.cmake)
14-
FetchContent_MakeAvailable(Eigen SQLiteCpp Boost spdlog googletest)
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FetchContent_MakeAvailable(Eigen3 SQLiteCpp Boost spdlog googletest)
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include(GoogleTest)
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endif()

‎cmake/datamanagement.pc.in‎

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@@ -8,5 +8,5 @@ Description: Syndemics Data Management
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URL: https://github.com/SyndemicsLab
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Version: @DATAMANAGEMENT_VERSION@
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CFlags: -I${includedir} @PKG_CONFIG_DEFINES@
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Libs: -L${libdir} -lspdlog -lboost
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Libs: -L${libdir} -lspdlog -lboost -libeigen -libsqlitecpp
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Requires: @PKG_CONFIG_REQUIRES@

‎include/datamanagement/datamanagement.hpp‎

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@@ -4,7 +4,7 @@
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// Created Date: Th Feb 2025 //
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// Author: Matthew Carroll //
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// ----- //
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// Last Modified: Thu Feb 20 2025 //
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// Last Modified: 2025-05-01 //
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// Modified By: Matthew Carroll //
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// ----- //
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// Copyright (c) 2025 Syndemics Lab at Boston Medical Center //
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#define DATAMANAGEMENT_DATAMANAGEMENT_HPP_
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2020
#include <datamanagement/modeldata/model_data.hpp>
21-
#include <datamanagement/source/config.hpp>
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#include <datamanagement/source/csv_source.hpp>
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#include <datamanagement/source/db_source.hpp>
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‎include/datamanagement/modeldata/model_data.hpp‎

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// Created Date: Th Feb 2025 //
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// Author: Matthew Carroll //
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// ----- //
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// Last Modified: 2025-04-30 //
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// Last Modified: 2025-05-01 //
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// Modified By: Matthew Carroll //
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// ----- //
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// Copyright (c) 2025 Syndemics Lab at Boston Medical Center //
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#ifndef DATAMANAGEMENT_MODELDATA_MODELDATA_HPP_
1818
#define DATAMANAGEMENT_MODELDATA_MODELDATA_HPP_
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20-
#include <filesystem>
2120
#include <memory>
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#include <string>
2322
#include <vector>
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25-
#include <datamanagement/source/config.hpp>
2624
#include <datamanagement/source/csv_source.hpp>
2725
#include <datamanagement/source/db_source.hpp>
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2927
namespace datamanagement {
3028
class ModelData {
31-
private:
32-
datamanagement::source::Config config;
33-
std::unordered_map<std::string, datamanagement::source::CSVSource>
34-
_csv_sources = {};
35-
std::unordered_map<std::string, datamanagement::source::DBSource>
36-
_db_sources = {};
37-
3829
public:
39-
ModelData(const std::string &cfgfile) : config(cfgfile) {}
40-
~ModelData() = default;
41-
datamanagement::source::Config GetConfig() const { return config; }
30+
virtual ~ModelData() = default;
31+
virtual std::string GetFromConfig(const std::string &key) const = 0;
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33+
virtual std::vector<std::string>
34+
GetConfigSectionCategories(const std::string &section) const = 0;
35+
36+
virtual void AddSource(const std::string &path) = 0;
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43-
void AddSource(const std::string &path) {
44-
std::filesystem::path p = path;
45-
if (p.extension() == ".csv") {
46-
datamanagement::source::CSVSource s;
47-
_csv_sources[p.stem()] = std::move(s);
48-
_csv_sources[p.stem()].ConnectToFile(path);
49-
} else if (p.extension() == ".db") {
50-
datamanagement::source::DBSource s;
51-
_db_sources[p.stem()] = std::move(s);
52-
_db_sources[p.stem()].SetDatabasePath(path);
53-
} else {
54-
// Not a valid source file
55-
}
56-
}
38+
virtual std::vector<std::string> GetCSVSourceNames() const = 0;
39+
virtual std::vector<std::string> GetDBSourceNames() const = 0;
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58-
std::vector<std::string> GetCSVSourceNames() const {
59-
std::vector<std::string> names = {};
60-
for (const auto &[k, v] : _csv_sources) {
61-
names.push_back(k);
62-
}
63-
return names;
64-
}
65-
std::vector<std::string> GetDBSourceNames() const {
66-
std::vector<std::string> names = {};
67-
for (const auto &[k, v] : _db_sources) {
68-
names.push_back(k);
69-
}
70-
return names;
71-
}
41+
virtual source::CSVSource &GetCSVSource(const std::string &name) = 0;
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73-
datamanagement::source::CSVSource &GetCSVSource(const std::string &name) {
74-
return _csv_sources[name];
75-
}
43+
virtual source::DBSource &GetDBSource(const std::string &name) = 0;
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77-
datamanagement::source::DBSource &GetDBSource(const std::string &name) {
78-
return _db_sources[name];
79-
}
45+
static std::unique_ptr<ModelData>
46+
Create(const std::string &config, const std::string &log_name = "console");
8047
};
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} // namespace datamanagement
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‎include/datamanagement/source/config.hpp‎

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