Merge pull request #464 from imperialCHEPI/combined_input_module

Move config-related code into combined `HeathGPS.Input` module

src/CMakeLists.txt

@@ -3,7 +3,7 @@ add_compile_definitions(TBB_USE_ASSERT)
 
 # Include sub-projects.
 add_subdirectory(HealthGPS.Core)
-add_subdirectory(HealthGPS.Datastore)
+add_subdirectory(HealthGPS.Input)
 add_subdirectory(HealthGPS)
 add_subdirectory(HealthGPS.Console)
 
@@ -23,7 +23,7 @@ endif()
 
 # PUBLIC needed to make heathers and library available to other project
 target_include_directories(HealthGPS.Core PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
-target_include_directories(HealthGPS.Datastore PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
+target_include_directories(HealthGPS.Input PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 target_include_directories(HealthGPS PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
 # External include directory

src/HealthGPS.Console/CMakeLists.txt

@@ -1,6 +1,5 @@
 find_package(fmt CONFIG REQUIRED)
 find_package(cxxopts CONFIG REQUIRED)
-find_package(nlohmann_json CONFIG REQUIRED)
 find_package(TBB CONFIG REQUIRED)
 find_path(RAPIDCSV_INCLUDE_DIRS "rapidcsv.h")
 find_package(Threads REQUIRED)
@@ -10,27 +9,14 @@ add_library(
     HealthGPS.LibConsole STATIC
     "command_options.cpp"
     "command_options.h"
-    "configuration.cpp"
-    "configuration.h"
-    "configuration_parsing.cpp"
-    "configuration_parsing.h"
-    "configuration_parsing_helpers.h"
-    "csvparser.cpp"
-    "csvparser.h"
     "event_monitor.cpp"
     "event_monitor.h"
-    "model_parser.cpp"
-    "model_parser.h"
     "program.cpp"
     "result_file_writer.cpp"
     "result_file_writer.h"
-    "jsonparser.cpp"
-    "jsonparser.h"
     "model_info.h"
     "resource.h"
-    "result_writer.h"
-    "riskmodel.h"
-    "poco.h")
+    "result_writer.h")
 
 # Under Windows, we also include a resource file to the build
 if(WIN32)
@@ -45,24 +31,22 @@ target_include_directories(HealthGPS.LibConsole PUBLIC ${CMAKE_CURRENT_BINARY_DI
 target_link_libraries(
     HealthGPS.Console
     PRIVATE HealthGPS.Core
-            HealthGPS.Datastore
+            HealthGPS.Input
             HealthGPS.LibConsole
             HealthGPS
             fmt::fmt
             Threads::Threads
             cxxopts::cxxopts
-            nlohmann_json::nlohmann_json
             TBB::tbb)
 
 target_link_libraries(
     HealthGPS.LibConsole
     PRIVATE HealthGPS.Core
-            HealthGPS.Datastore
+            HealthGPS.Input
             HealthGPS
             fmt::fmt
             Threads::Threads
             cxxopts::cxxopts
-            nlohmann_json::nlohmann_json
             TBB::tbb)
 
 install(TARGETS HealthGPS.Console DESTINATION "")

src/HealthGPS.Console/command_options.cpp

@@ -5,7 +5,7 @@
 
 #include <iostream>
 
-namespace host {
+namespace hgps {
 
 cxxopts::Options create_options() {
     cxxopts::Options options("HealthGPS.Console", "Health-GPS microsimulation for policy options.");
@@ -95,4 +95,4 @@ CommandOptions parse_arguments(cxxopts::Options &options, int &argc, char *argv[
 
     return cmd;
 }
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/command_options.h

@@ -7,7 +7,7 @@
 
 #include <filesystem>
 
-namespace host {
+namespace hgps {
 /// @brief Defines the Command Line Interface (CLI) arguments options
 struct CommandOptions {
     /// @brief Indicates whether the argument parsing succeed
@@ -40,4 +40,4 @@ cxxopts::Options create_options();
 /// @return User command-line options
 CommandOptions parse_arguments(cxxopts::Options &options, int &argc, char *argv[]);
 
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/event_monitor.cpp

@@ -7,7 +7,7 @@
 #include <fmt/color.h>
 #include <fmt/core.h>
 
-namespace host {
+namespace hgps {
 EventMonitor::EventMonitor(hgps::EventAggregator &event_bus, ResultWriter &result_writer)
     : result_writer_{result_writer}, tg_{tg_context_} {
     handlers_.emplace_back(event_bus.subscribe(hgps::EventType::runner, [this](auto &&PH1) {
@@ -97,4 +97,4 @@ void EventMonitor::result_dispatch_thread() {
 
     fmt::print(fg(fmt::color::gray), "Result event thread exited.\n");
 }
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/event_monitor.h

@@ -8,21 +8,21 @@
 
 #include "result_writer.h"
 
-namespace host {
+namespace hgps {
 /// @brief Defined the event monitor class used for processing Health-GPS event messages
 ///
 /// All notification messages are written to the terminal, while the results messages are
-/// queued to be processed by the host::ResultWriter instance provide at construction.
+/// queued to be processed by the hgps::ResultWriter instance provide at construction.
 class EventMonitor final : public hgps::EventMessageVisitor {
   public:
     EventMonitor() = delete;
 
-    /// @brief Initialises a new instance of the host::EventMonitor class.
+    /// @brief Initialises a new instance of the hgps::EventMonitor class.
     /// @param event_bus The message bus instance to monitor
     /// @param result_writer The results message writer instance
     EventMonitor(hgps::EventAggregator &event_bus, ResultWriter &result_writer);
 
-    /// @brief Destroys a host::EventMonitor instance
+    /// @brief Destroys a hgps::EventMonitor instance
     ~EventMonitor() noexcept;
 
     /// @brief Stops the monitor, no new messages are processed after stop
@@ -48,4 +48,4 @@ class EventMonitor final : public hgps::EventMessageVisitor {
     void info_dispatch_thread();
     void result_dispatch_thread();
 };
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/model_info.h

@@ -3,7 +3,7 @@
 #include <fmt/format.h>
 #include <string>
 
-namespace host {
+namespace hgps {
 /// @brief Simulation experiment run-time information for reproducibility.
 struct ExperimentInfo {
     /// @brief The model name
@@ -28,4 +28,4 @@ struct ExperimentInfo {
                            seed);
     }
 };
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/program.cpp

@@ -1,12 +1,14 @@
-#include "configuration.h"
-#include "csvparser.h"
-#include "model_parser.h"
-
 #include "HealthGPS.Core/thread_util.h"
-#include "HealthGPS.Datastore/api.h"
+#include "HealthGPS.Input/api.h"
+#include "HealthGPS.Input/configuration.h"
+#include "HealthGPS.Input/csvparser.h"
+#include "HealthGPS.Input/model_parser.h"
 #include "HealthGPS/api.h"
 #include "HealthGPS/event_bus.h"
+#include "command_options.h"
 #include "event_monitor.h"
+#include "model_info.h"
+#include "result_file_writer.h"
 
 #include <fmt/chrono.h>
 #include <fmt/color.h>
@@ -15,6 +17,7 @@
 #include <cstdlib>
 #include <oneapi/tbb/global_control.h>
 
+namespace {
 /// @brief Get a string representation of current system time
 /// @return The system time as string
 std::string get_time_now_str() {
@@ -31,6 +34,18 @@ void print_app_title() {
                tbb::global_control::active_value(tbb::global_control::max_allowed_parallelism));
 }
 
+hgps::ResultFileWriter create_results_file_logger(const hgps::input::Configuration &config,
+                                                  const hgps::ModelInput &input) {
+    return {create_output_file_name(config.output, config.job_id),
+            hgps::ExperimentInfo{.model = config.app_name,
+                                 .version = config.app_version,
+                                 .intervention = config.active_intervention
+                                                     ? config.active_intervention->identifier
+                                                     : "",
+                                 .job_id = config.job_id,
+                                 .seed = input.seed().value_or(0u)}};
+}
+
 /// @brief Prints application exit message
 /// @param exit_code The application exit code
 /// @return The respective exit code
@@ -40,14 +55,15 @@ int exit_application(int exit_code) {
     fmt::print(" {}.\n\n", get_time_now_str());
     return exit_code;
 }
+} // anonymous namespace
 
 /// @brief Health-GPS host application entry point
 /// @param argc The number of command arguments
 /// @param argv The list of arguments provided
 /// @return The application exit code
 int main(int argc, char *argv[]) { // NOLINT(bugprone-exception-escape)
     using namespace hgps;
-    using namespace host;
+    using namespace hgps::input;
 
     // Set thread limit from OMP_THREAD_LIMIT, if set in environment.
     char *env_threads = std::getenv("OMP_THREAD_LIMIT");
@@ -73,7 +89,7 @@ int main(int argc, char *argv[]) { // NOLINT(bugprone-exception-escape)
     // Parse inputs configuration file, *.json.
     Configuration config;
     try {
-        config = get_configuration(cmd_args);
+        config = get_configuration(cmd_args.config_file, cmd_args.job_id, cmd_args.verbose);
     } catch (const std::exception &ex) {
         fmt::print(fg(fmt::color::red), "\n\nInvalid configuration - {}.\n", ex.what());
         return exit_application(EXIT_FAILURE);
@@ -97,7 +113,7 @@ int main(int argc, char *argv[]) { // NOLINT(bugprone-exception-escape)
     try {
 #endif
         // Create back-end data store, cached data repository wrapper
-        auto data_api = data::DataManager(cmd_args.data_path_or_url, config.verbosity);
+        auto data_api = input::DataManager(cmd_args.data_path_or_url, config.verbosity);
         auto data_repository = hgps::CachedRepository{data_api};
 
         // Register the input risk factors model definitions
@@ -178,8 +194,8 @@ int main(int argc, char *argv[]) { // NOLINT(bugprone-exception-escape)
 
 // NOLINTBEGIN(modernize-concat-nested-namespaces)
 /// @brief Top-level namespace for Health-GPS Console host application
-namespace host {
+namespace hgps {
 /// @brief Internal details namespace for private data types and functions
 namespace detail {}
-} // namespace host
+} // namespace hgps
 // NOLINTEND(modernize-concat-nested-namespaces)

src/HealthGPS.Console/result_file_writer.cpp

@@ -10,7 +10,7 @@
 #include <sstream>
 #include <utility>
 
-namespace host {
+namespace hgps {
 ResultFileWriter::ResultFileWriter(const std::filesystem::path &file_name, ExperimentInfo info)
     : info_{std::move(info)} {
     stream_.open(file_name, std::ofstream::out | std::ofstream::app);
@@ -180,4 +180,4 @@ void ResultFileWriter::write_csv_channels(const hgps::ResultEventMessage &messag
         fss.clear();
     }
 }
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/result_file_writer.h

@@ -7,7 +7,7 @@
 #include "model_info.h"
 #include "result_writer.h"
 
-namespace host {
+namespace hgps {
 /// @brief Defines the results message file stream writer class
 ///
 /// The message content are written to a JSON (JavaScript Object Notation) file,
@@ -17,7 +17,7 @@ namespace host {
 class ResultFileWriter final : public ResultWriter {
   public:
     ResultFileWriter() = delete;
-    /// @brief Initialises an instance of the host::ResultFileWriter class.
+    /// @brief Initialises an instance of the hgps::ResultFileWriter class.
     /// @param file_name The JSON output file full name
     /// @param info The associated experiment information
     ResultFileWriter(const std::filesystem::path &file_name, ExperimentInfo info);
@@ -27,7 +27,7 @@ class ResultFileWriter final : public ResultWriter {
     ResultFileWriter(ResultFileWriter &&other) noexcept;
     ResultFileWriter &operator=(ResultFileWriter &&other) noexcept;
 
-    /// @brief Destroys a host::ResultFileWriter instance
+    /// @brief Destroys a hgps::ResultFileWriter instance
     ~ResultFileWriter();
     void write(const hgps::ResultEventMessage &message) override;
 
@@ -45,4 +45,4 @@ class ResultFileWriter final : public ResultWriter {
     void write_csv_channels(const hgps::ResultEventMessage &message);
     void write_csv_header(const hgps::ResultEventMessage &message);
 };
-} // namespace host
+} // namespace hgps

src/HealthGPS.Console/result_writer.h

@@ -2,15 +2,15 @@
 
 #include "HealthGPS/result_message.h"
 
-namespace host {
+namespace hgps {
 /// @brief Defines the Health-GPS results message writer interface
 class ResultWriter {
   public:
-    /// @brief Destroys a host::ResultWriter instance
+    /// @brief Destroys a hgps::ResultWriter instance
     virtual ~ResultWriter() = default;
 
     /// @brief Writes the hgps::ResultEventMessage contents to a stream
     /// @param message The message instance to process
     virtual void write(const hgps::ResultEventMessage &message) = 0;
 };
-} // namespace host
+} // namespace hgps

src/HealthGPS.Input/CMakeLists.txt

@@ -0,0 +1,37 @@
+find_package(fmt CONFIG REQUIRED)
+find_package(jsoncons CONFIG REQUIRED)
+find_package(libzippp CONFIG REQUIRED)
+find_package(unofficial-curlpp CONFIG REQUIRED)
+
+add_library(HealthGPS.Input STATIC "")
+target_compile_features(HealthGPS.Input PUBLIC cxx_std_${CMAKE_CXX_STANDARD})
+
+target_sources(
+    HealthGPS.Input
+    PRIVATE "api.h"
+            "configuration.cpp"
+            "configuration.h"
+            "configuration_parsing.cpp"
+            "configuration_parsing.h"
+            "configuration_parsing_helpers.h"
+            "csvparser.cpp"
+            "csvparser.h"
+            "datamanager.cpp"
+            "datamanager.h"
+            "download_file.cpp"
+            "download_file.h"
+            "jsonparser.cpp"
+            "jsonparser.h"
+            "model_parser.cpp"
+            "model_parser.h"
+            "poco.h"
+            "riskmodel.h"
+            "schema.cpp"
+            "schema.h"
+            "zip_file.cpp"
+            "zip_file.h")
+
+target_link_libraries(HealthGPS.Input PRIVATE HealthGPS HealthGPS.Core fmt::fmt jsoncons
+                                              libzippp::libzippp unofficial::curlpp::curlpp)
+
+set(ROOT_NAMESPACE hgps::input)