Added C++ REST API

.github/workflows/ci.yml

@@ -44,50 +44,53 @@ jobs:
             librange-v3-dev\
             nlohmann-json3-dev
 
-
-        pwd
-        echo "### Installing pytest"
-        sudo /usr/bin/python -m pip install pytest
-
         pwd
         echo "### Building Served from source"
-        sudo git clone https://github.com/meltwater/served
-        cd served
-        sudo mkdir build
-        cd build
-        sudo cmake ..
-        sudo make -j `nproc` install
-        cd ../..
+        curl -LO https://github.com/meltwater/served/archive/refs/tags/v1.6.0.tar.gz
+        tar -xzf v1.6.0.tar.gz
+        pushd served-1.6.0
+          mkdir build
+          cd build
+          cmake ..
+          sudo make -j `nproc` install
+        popd
 
-        pwd
-        echo "### Building the Delphi REST API"
-        # build the delpi REST API
-        sudo mkdir build
-        cd build
-        sudo cmake ..
-        sudo make -j `nproc`
+        # Download delphi.db
+        mkdir -p data && curl http://vanga.sista.arizona.edu/delphi_data/delphi.db -o $DELPHI_DB
+        echo "DELPHI_DB = $DELPHI_DB"
 
-        pwd
-        echo "### Running the Delphi REST API"
-        # run the api as a background process
-        ./delphi_rest_api &
+        # Create a virtual environment
+        python3 -m venv delphi_venv
+
+        # Activate the virtual environment
+        source delphi_venv/bin/activate
 
-        # test the delphi REST API using python
-        cd ../apps
-        #        python3 ./test_cpp_rest_api.py
+        # Install wheel
+        pip install wheel
 
-        # test the delphi with Bash scripts
-        cd ../tests/wm/scripts
-        ./get_system_status
-        cd ../../../
+        # Install delphi in editable mode
+        pip install -e .[test]
+
+        # Run the Python WM test suite
+        make test_wm
 
         pwd
-        echo "### Building WM"
-        echo "DELPHI_DB = $DELPHI_DB"
-        sudo python3 -m venv delphi_venv
-        source delphi_venv/bin/activate
-        sudo mkdir -p data && curl http://vanga.sista.arizona.edu/delphi_data/delphi.db -o $DELPHI_DB
-        sudo pip install wheel
-        sudo pip install -e .[test]
-        # sudo make test_wm
+        echo "### Building and running Python tests"
+
+
+        pwd
+        echo "### Building the Delphi REST API"
+        # Build the Delphi REST API server program
+        pushd build
+          cmake ..
+          make -j `nproc` delphi_rest_api
+
+          echo "### Running the Delphi REST API"
+          # Run the api as a background process
+          ./delphi_rest_api &
+        popd
 
+        # Test the Delphi with Bash scripts
+        pushd tests/wm/scripts
+          ./get_system_status
+        popd

CMakeLists.txt

@@ -2,7 +2,7 @@ cmake_minimum_required(VERSION 3.11)
 project(delphi)
 
 # Uncomment this line to generate debug code
-set(CMAKE_BUILD_TYPE Debug)
+#set(CMAKE_BUILD_TYPE Debug)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
@@ -14,12 +14,8 @@ set(CMAKE_CXX_FLAGS
 
 find_package(Graphviz)
 
-include_directories(${GRAPHVIZ_INCLUDE_DIRS})
 # Add and link pybind11 modules
 find_package(Boost COMPONENTS graph program_options REQUIRED)
-include_directories(lib)
-include_directories(external)
-include_directories(${Boost_INCLUDE_DIR})
 
 find_package(range-v3 REQUIRED)
 find_package(Eigen3 REQUIRED NO_MODULE)
@@ -30,64 +26,44 @@ option(BUILD_PYTHON_BINDINGS "Build Python bindings" ON)
 
 # Optional building of Python bindings using Pybind11
 if(BUILD_PYTHON_BINDINGS)
-
     find_package(pybind11 CONFIG REQUIRED)
     message(STATUS "Found pybind11 v${pybind11_VERSION}: ${pybind11_INCLUDE_DIRS}")
     find_package(Python3 REQUIRED)
     set(PYBIND11_PYTHON_VERSION "${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR}")
     set(PYBIND11_CPP_STANDARD -std=c++17)
 endif()
 
-file(GLOB SRC_FILES ${PROJECT_SOURCE_DIR}/lib/*.cpp)
 find_package(SQLite3 REQUIRED)
 
 add_library(Delphi
-    lib/AnalysisGraph.hpp
-    lib/causemos_integration.cpp
-    lib/constructors.cpp
-    lib/CSVWriter.hpp
-    lib/database.cpp
-    lib/DatabaseHelper.cpp
-    lib/DatabaseHelper.hpp
-    lib/data.cpp
-    lib/data.hpp
-    #lib/DelphiPython.cpp
-    lib/DiGraph.hpp
-    lib/Edge.hpp
-    lib/exceptions.hpp
-    lib/format_output.cpp
-    lib/graph_building.cpp
-    lib/graph_modification.cpp
-    lib/graph_utils.cpp
-    lib/graphviz.cpp
-    lib/graphviz_interface.cpp
-    lib/graphviz_interface.hpp
-    lib/head_nodes.cpp
-    lib/Indicator.cpp
-    lib/Indicator.hpp
-    lib/indicator_manipulation.cpp
-    lib/KDE.cpp
-    lib/KDE.hpp
-    lib/Node.hpp
-    lib/parameter_initialization.cpp
-    lib/prediction.cpp
-    lib/printing.cpp
-    lib/PybindTester.hpp
-    lib/Random_Variables.cpp
-    lib/Random_Variables.hpp
-    lib/rng.cpp
-    lib/rng.hpp
-    lib/sampling.cpp
-    lib/sandbox.cpp
-    lib/subgraphs.cpp
-    lib/synthetic_data.cpp
-    lib/Timer.hpp
-    lib/to_json.cpp
-    lib/train_model.cpp
-    lib/Tran_Mat_Cell.cpp
-    lib/Tran_Mat_Cell.hpp
-    lib/utils.cpp
-    lib/utils.hpp
+  lib/parameter_initialization.cpp
+  lib/to_json.cpp
+  lib/data.cpp
+  lib/graphviz_interface.cpp
+  lib/graphviz.cpp
+  lib/KDE.cpp
+  lib/Random_Variables.cpp
+  lib/rng.cpp
+  lib/train_model.cpp
+  lib/Tran_Mat_Cell.cpp
+  lib/utils.cpp
+  lib/Indicator.cpp
+  lib/subgraphs.cpp
+  lib/constructors.cpp
+  lib/causemos_integration.cpp
+  lib/sampling.cpp
+  lib/prediction.cpp
+  lib/synthetic_data.cpp
+  lib/graph_building.cpp
+  lib/graph_modification.cpp
+  lib/graph_utils.cpp
+  lib/printing.cpp
+  lib/indicator_manipulation.cpp
+  lib/sandbox.cpp
+  lib/format_output.cpp
+  lib/database.cpp
+  lib/DatabaseHelper.cpp
+  lib/head_nodes.cpp
 )
 
 target_link_libraries(Delphi
@@ -98,11 +74,13 @@ target_link_libraries(Delphi
                               Eigen3::Eigen
                               ${GRAPHVIZ_LIBS})
 target_link_libraries(Delphi INTERFACE range-v3)
+target_include_directories(Delphi PRIVATE ${GRAPHVIZ_INCLUDE_DIRS} lib external)
 
 if(BUILD_PYTHON_BINDINGS)
 
     pybind11_add_module(DelphiPython MODULE NO_EXTRAS lib/DelphiPython.cpp)
     target_link_libraries(DelphiPython PRIVATE Delphi Eigen3::Eigen)
+    target_include_directories(DelphiPython PRIVATE ${GRAPHVIZ_INCLUDE_DIRS})
     add_custom_command(TARGET DelphiPython POST_BUILD
         COMMAND echo ""
         COMMAND echo "Copying..."
@@ -112,7 +90,6 @@ if(BUILD_PYTHON_BINDINGS)
         COMMAND rm -rf ${PROJECT_SOURCE_DIR}/delphi/cpp/DelphiPython*
         COMMAND cp DelphiPython* ${PROJECT_SOURCE_DIR}/delphi/cpp/
     )
-#add_executable(pybind_tester_driver apps/pybind_tester_driver.cpp)
 
 endif()
 
@@ -123,15 +100,22 @@ pkg_check_modules(SERVED REQUIRED IMPORTED_TARGET served)
 # Executables
 add_executable(create_model apps/create_model.cpp)
 target_link_libraries(create_model PRIVATE Delphi Eigen3::Eigen)
+target_include_directories(create_model PRIVATE ${Boost_INCLUDE_DIR} lib external ${GRAPHVIZ_INCLUDE_DIRS})
+
+## Sandbox tester
 add_executable(sandbox_tester apps/sandbox_tester.cpp)
 target_link_libraries(sandbox_tester PRIVATE Delphi Eigen3::Eigen)
+target_include_directories(sandbox_tester PRIVATE lib ${GRAPHVIZ_INCLUDE_DIRS})
+
+## Timer program
 add_executable(timer
-        scripts/timer.cpp
+        apps/timer.cpp
         lib/Timer.hpp
         lib/CSVWriter.hpp)
 target_link_libraries(timer PRIVATE Delphi Eigen3::Eigen ${Boost_LIBRARIES})
+target_include_directories(timer PRIVATE ${Boost_INCLUDE_DIR} lib external ${GRAPHVIZ_INCLUDE_DIRS})
 
 # Build the REST API program
 add_executable(delphi_rest_api apps/delphi_rest_api.cpp)
-target_link_libraries(delphi_rest_api PRIVATE Delphi PkgConfig::SERVED)
-target_link_libraries(delphi_rest_api PRIVATE Eigen3::Eigen pthread)
+target_link_libraries(delphi_rest_api PRIVATE Delphi PkgConfig::SERVED Eigen3::Eigen pthread)
+target_include_directories(delphi_rest_api PRIVATE ${Boost_INCLUDE_DIR} lib external ${GRAPHVIZ_INCLUDE_DIRS})

lib/DatabaseHelper.hpp

@@ -1,47 +1,52 @@
-#ifndef DATABASEHELPER_H
-#define DATABASEHELPER_H
-
+#pragma once
 
+#include <nlohmann/json.hpp>
+#include <range/v3/all.hpp>
 #include <sqlite3.h>
 #include <vector>
-#include <range/v3/all.hpp>
-#include <nlohmann/json.hpp>
-
 
 class Database {
   private:
-
-    sqlite3  *db;
-
+  sqlite3* db;
 
   public:
+  Database();
 
-    Database();
+  ~Database();
 
-    ~Database();
-
-    void create_table();
+  void create_table();
 
-    std::vector<std::string> read_column_text(std::string query);
+  std::vector<std::string> read_column_text(std::string query);
 
-    std::vector<std::string> read_column_text_query(std::string table_name, std::string column_name);
+  std::vector<std::string> read_column_text_query(std::string table_name,
+                                                  std::string column_name);
 
-    std::vector<std::string> read_column_text_query_where(std::string table_name, std::string column_name, std::string where_column_name, std::string where_value);
+  std::vector<std::string>
+  read_column_text_query_where(std::string table_name,
+                               std::string column_name,
+                               std::string where_column_name,
+                               std::string where_value);
 
-    nlohmann::json select_delphimodel_row(std::string modelId);
+  nlohmann::json select_delphimodel_row(std::string modelId);
 
-    nlohmann::json select_causemosasyncexperimentresult_row(std::string modelId);
+  nlohmann::json select_causemosasyncexperimentresult_row(std::string modelId);
 
-    void insert(std::string insert_query);
+  void insert(std::string insert_query);
 
-    void insert_into_delphimodel(std::string id, std::string model);
+  void insert_into_delphimodel(std::string id, std::string model);
 
-    void insert_into_causemosasyncexperimentresult(std::string id, std::string status, std::string experimentType, std::string results);
+  void insert_into_causemosasyncexperimentresult(std::string id,
+                                                 std::string status,
+                                                 std::string experimentType,
+                                                 std::string results);
 
-    void update_row(std::string table_name, std::string column_name, std::string value, std::string where_column_name, std::string where_value);
-
-    void delete_rows(std::string table_name, std::string where_column_name, std::string where_value);
+  void update_row(std::string table_name,
+                  std::string column_name,
+                  std::string value,
+                  std::string where_column_name,
+                  std::string where_value);
 
+  void delete_rows(std::string table_name,
+                   std::string where_column_name,
+                   std::string where_value);
 };
-
-#endif /* DATABASEHELPER_H */

lib/subgraphs.cpp

@@ -2,6 +2,8 @@
 #include "Node.hpp"
 #include "utils.hpp"
 #include <boost/range/algorithm/for_each.hpp>
+#include <boost/range/adaptor/transformed.hpp>
+#include <boost/range/adaptor/filtered.hpp>
 #include <range/v3/all.hpp>
 
 using boost::for_each;
@@ -82,7 +84,8 @@ AnalysisGraph AnalysisGraph::get_subgraph_for_concept(string concept,
                                                       bool inward,
                                                       int depth) {
 
-  using ranges::views::filter, ranges::views::transform, ranges::to;
+  using ranges::to;
+  using namespace boost::adaptors;
 
   // Mark all the vertices as not visited
   for_each(this->nodes(), [](Node& node) { node.visited = false; });
@@ -96,8 +99,8 @@ AnalysisGraph AnalysisGraph::get_subgraph_for_concept(string concept,
 
   unordered_set<string> nodes_to_remove =
       this->node_indices() |
-      filter([&](int v) { return !in(vertices_to_keep, v); }) |
-      transform([&](int v) { return (*this)[v].name; }) | to<unordered_set>();
+      filtered([&](int v) { return !in(vertices_to_keep, v); }) |
+      transformed([&](int v) { return (*this)[v].name; }) | to<unordered_set>();
 
   if (vertices_to_keep.size() == 0) {
     print("Subgraph has 0 nodes - returning an empty CAG!");