Source File Breakout

.github/workflows/coverage.yml

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

CMakeLists.txt

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

cmake/LoadEigen.cmake

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

cmake/LoadSpdlog.cmake

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

cmake/MakeDependenciesAvailable.cmake

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

cmake/datamanagement.pc.in

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

include/datamanagement/datamanagement.hpp

@@ -4,7 +4,7 @@
 // Created Date: Th Feb 2025                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: Thu Feb 20 2025                                             //
+// Last Modified: 2025-05-01                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -18,7 +18,6 @@
 #define DATAMANAGEMENT_DATAMANAGEMENT_HPP_
 
 #include <datamanagement/modeldata/model_data.hpp>
-#include <datamanagement/source/config.hpp>
 #include <datamanagement/source/csv_source.hpp>
 #include <datamanagement/source/db_source.hpp>
 

include/datamanagement/modeldata/model_data.hpp

@@ -4,7 +4,7 @@
 // Created Date: Th Feb 2025                                                  //
 // Author: Matthew Carroll                                                    //
 // -----                                                                      //
-// Last Modified: 2025-04-30                                                  //
+// Last Modified: 2025-05-01                                                  //
 // Modified By: Matthew Carroll                                               //
 // -----                                                                      //
 // Copyright (c) 2025 Syndemics Lab at Boston Medical Center                  //
@@ -17,66 +17,33 @@
 #ifndef DATAMANAGEMENT_MODELDATA_MODELDATA_HPP_
 #define DATAMANAGEMENT_MODELDATA_MODELDATA_HPP_
 
-#include <filesystem>
 #include <memory>
 #include <string>
 #include <vector>
 
-#include <datamanagement/source/config.hpp>
 #include <datamanagement/source/csv_source.hpp>
 #include <datamanagement/source/db_source.hpp>
 
 namespace datamanagement {
 class ModelData {
-private:
-    datamanagement::source::Config config;
-    std::unordered_map<std::string, datamanagement::source::CSVSource>
-        _csv_sources = {};
-    std::unordered_map<std::string, datamanagement::source::DBSource>
-        _db_sources = {};
-
 public:
-    ModelData(const std::string &cfgfile) : config(cfgfile) {}
-    ~ModelData() = default;
-    datamanagement::source::Config GetConfig() const { return config; }
+    virtual ~ModelData() = default;
+    virtual std::string GetFromConfig(const std::string &key) const = 0;
+
+    virtual std::vector<std::string>
+    GetConfigSectionCategories(const std::string &section) const = 0;
+
+    virtual void AddSource(const std::string &path) = 0;
 
-    void AddSource(const std::string &path) {
-        std::filesystem::path p = path;
-        if (p.extension() == ".csv") {
-            datamanagement::source::CSVSource s;
-            _csv_sources[p.stem()] = std::move(s);
-            _csv_sources[p.stem()].ConnectToFile(path);
-        } else if (p.extension() == ".db") {
-            datamanagement::source::DBSource s;
-            _db_sources[p.stem()] = std::move(s);
-            _db_sources[p.stem()].SetDatabasePath(path);
-        } else {
-            // Not a valid source file
-        }
-    }
+    virtual std::vector<std::string> GetCSVSourceNames() const = 0;
+    virtual std::vector<std::string> GetDBSourceNames() const = 0;
 
-    std::vector<std::string> GetCSVSourceNames() const {
-        std::vector<std::string> names = {};
-        for (const auto &[k, v] : _csv_sources) {
-            names.push_back(k);
-        }
-        return names;
-    }
-    std::vector<std::string> GetDBSourceNames() const {
-        std::vector<std::string> names = {};
-        for (const auto &[k, v] : _db_sources) {
-            names.push_back(k);
-        }
-        return names;
-    }
+    virtual source::CSVSource &GetCSVSource(const std::string &name) = 0;
 
-    datamanagement::source::CSVSource &GetCSVSource(const std::string &name) {
-        return _csv_sources[name];
-    }
+    virtual source::DBSource &GetDBSource(const std::string &name) = 0;
 
-    datamanagement::source::DBSource &GetDBSource(const std::string &name) {
-        return _db_sources[name];
-    }
+    static std::unique_ptr<ModelData>
+    Create(const std::string &config, const std::string &log_name = "console");
 };
 } // namespace datamanagement