From df3c4ebcbc88a61697b0ffb2396007e94e32ece7 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Thu, 14 Sep 2023 14:56:23 +0200
Subject: [PATCH 01/10] added uwebsockets submodule

---
 .gitmodules     | 3 +++
 ext/uWebSockets | 1 +
 2 files changed, 4 insertions(+)
 create mode 100644 .gitmodules
 create mode 160000 ext/uWebSockets

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 000000000..85662a026
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "ext/uWebSockets"]
+	path = ext/uWebSockets
+	url = https://github.com/uNetworking/uWebSockets.git
diff --git a/ext/uWebSockets b/ext/uWebSockets
new file mode 160000
index 000000000..f1b10ed22
--- /dev/null
+++ b/ext/uWebSockets
@@ -0,0 +1 @@
+Subproject commit f1b10ed221b36c0d8848998e3e939823f66496eb

From ccbc1008222407de9462df4746acc4218241e71a Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Thu, 14 Sep 2023 16:44:25 +0200
Subject: [PATCH 02/10] realtime_scores with uWebSockets

---
 .gitignore                         |   1 +
 CMakeLists.txt                     |   2 +-
 install.py                         |   9 +
 test/model/CMakeLists.txt          |  21 +-
 test/model/src/realtime_scores.cpp | 302 +++++++++++++++--------------
 5 files changed, 190 insertions(+), 145 deletions(-)

diff --git a/.gitignore b/.gitignore
index 27e9957a1..22b2a44de 100644
--- a/.gitignore
+++ b/.gitignore
@@ -120,6 +120,7 @@ test/model/res/*
 
 
 .INSTALLED
+.uWebSockets_INSTALLED
 .RES_EXTRACTED
 .env
 
diff --git a/CMakeLists.txt b/CMakeLists.txt
index c10c29b9c..61fa4c660 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -52,7 +52,7 @@ cmake_print_variables(SQLite3_INCLUDE_DIRS)
 cmake_print_variables(SQLite3_LIBRARIES)
 
 # Set up the compiler.
-set(CMAKE_CXX_FLAGS "-std=c++14 -Wall -Wextra -pedantic -Wredundant-decls -Wdisabled-optimization -Wctor-dtor-privacy -Wnon-virtual-dtor -Werror=old-style-cast -Wsign-promo -Werror=return-type -Wno-unused-parameter")
+set(CMAKE_CXX_FLAGS "-std=c++20 -Wall -Wextra -pedantic -Wredundant-decls -Wdisabled-optimization -Wctor-dtor-privacy -Wnon-virtual-dtor -Werror=old-style-cast -Wsign-promo -Werror=return-type -Wno-unused-parameter")
 set(CMAKE_CXX_FLAGS_DEBUG "-O3 -g")
 set(CMAKE_CXX_FLAGS_RELEASE "-O3")
 
diff --git a/install.py b/install.py
index 069fef656..0ca91e06d 100755
--- a/install.py
+++ b/install.py
@@ -100,6 +100,15 @@ def build_external_libraries(args, dependencies):
         f = open("ext/igraph_0.9.8/.INSTALLED", "w")
         f.close()
 
+    # uWebSockets
+    if os.path.isfile("ext/.uWebSockets_INSTALLED") and not args.clean:
+        print("-- uWebSocket library already built.")
+    else:
+        print("-- Building uWebSockets library")
+        subprocess.call('git submodule update --init --recursive; cd ext/uWebSockets/uSockets;make boringssl;cd boringssl;BORINGSSL=$PWD;cd ../lsquic;cmake -DBORINGSSL_DIR=$BORINGSSL .;make;cd ..;WITH_LTO=1 WITH_QUIC=1 WITH_BORINGSSL=1 make', shell=True)
+        f = open("ext/.uWebSockets_INSTALLED", "w")
+        f.close()
+
 def extract_all_zips_in_folder(folder):
     print("extracting files in " + folder)
 
diff --git a/test/model/CMakeLists.txt b/test/model/CMakeLists.txt
index 3ab8938d3..1a448d778 100644
--- a/test/model/CMakeLists.txt
+++ b/test/model/CMakeLists.txt
@@ -56,7 +56,26 @@ if(APPLE)
   target_link_libraries(epiJSON omp)
 endif()
 
+# uWebSocekt stuff
+file(GLOB uSocketObjects
+        ${PROJECT_SOURCE_DIR}/ext/uWebSockets/uSockets/*.o
+)
+
 add_executable(realtime_scores src/realtime_scores.cpp)
-target_link_libraries(realtime_scores boost_filesystem igraph drogon trantor ssl crypto z jsoncpp uuid brotlidec brotlienc)
+target_link_libraries(realtime_scores
+        boost_filesystem
+        igraph
+        z
+        m
+        ${uSocketObjects}
+        ${PROJECT_SOURCE_DIR}/ext/uWebSockets/uSockets/lsquic/src/liblsquic/liblsquic.a
+        ${PROJECT_SOURCE_DIR}/ext/uWebSockets/uSockets/boringssl/build/ssl/libssl.a
+        ${PROJECT_SOURCE_DIR}/ext/uWebSockets/uSockets/boringssl/build/crypto/libcrypto.a
+)
+target_include_directories(realtime_scores
+        PUBLIC ${PROJECT_SOURCE_DIR}/ext/uWebSockets/src
+        PUBLIC ${PROJECT_SOURCE_DIR}/ext/uWebSockets/uSockets/src
+        PUBLIC ${PROJECT_SOURCE_DIR}/ext/uWebSockets/uSockets/boringssl/include
+)
 
 add_subdirectory(src)
diff --git a/test/model/src/realtime_scores.cpp b/test/model/src/realtime_scores.cpp
index 1e1d69197..9c9a7c642 100644
--- a/test/model/src/realtime_scores.cpp
+++ b/test/model/src/realtime_scores.cpp
@@ -3,7 +3,8 @@
 //
 
 #include <CLI11.hpp>
-#include <drogon/drogon.h>
+#include "../../ext/uWebSockets/src/App.h"
+#include "../../ext/rapidjson/document.h"
 
 #define HEADER_ONLY
 #define ALLOW_MULTIPLE_SNPSTORAGES
@@ -12,6 +13,14 @@
 
 // using namespace epi;
 
+std::string json_to_str(const rapidjson::Value &object) {
+    rapidjson::StringBuffer buffer;
+    rapidjson::Writer<rapidjson::StringBuffer> writer(buffer);
+    object.Accept(writer);
+
+    return buffer.GetString();
+}
+
 int main(int argc, char **argv) {
     // parse args
     CLI::App cli("Realtime scores - A tool to evaluate SNP-sets as a realtime API service");
@@ -40,19 +49,19 @@ int main(int argc, char **argv) {
                    "Add a model to the list of models that are applied on the SNP sets. If none is specified, all available models will be used.");
 
 
-    int num_threads = 2;
+    unsigned int num_threads = 2;
     cli.add_option("--num-threads", num_threads,
-                   "Number of threads to be used for score calculation. Default: 2. 0 means all available");
+                   "Number of threads to be used for score calculation. Default: 1. 0 means all available");
 
     // Parse the options.
     CLI11_PARSE(cli, argc, argv);
 
-    // process num threads
-    drogon::app().setThreadNum(num_threads);
-    num_threads = drogon::app().getThreadNum();
+    if (num_threads == 0) {
+        num_threads = std::thread::hardware_concurrency();
+    }
 
     boost::filesystem::path gwas_dir_b(input_dir);
-    if(is_directory(gwas_dir_b)) {
+    if (is_directory(gwas_dir_b)) {
         for (auto it = directory_iterator(gwas_dir_b); it != directory_iterator(); ++it) {
             path path = it->path();
             if (is_regular_file(path)) {
@@ -70,7 +79,8 @@ int main(int argc, char **argv) {
                         ncat = std::stoi(splits[3]);
                     }
 
-                    LOG_WARN << "dataset: { name: \"" << name << "\", format: \"" << format << "\", phenotype: \"" << phenotype << "\", num_categories: " << ncat << " }";
+                    std::cout << "dataset: { name: \"" << name << "\", format: \"" << format << "\", phenotype: \""
+                              << phenotype << "\", num_categories: " << ncat << " }" << std::endl;
 
                     gwas_input_file.push_back(path.c_str());
                     gwas_input_format.push_back(format);
@@ -86,49 +96,18 @@ int main(int argc, char **argv) {
     // process datasets
     auto num_datasets = gwas_input_file.size();
 
-    /*
-    // process num_categories
-    if (num_categories.empty()) {
-        num_categories.push_back(2);
-    }
-    if (num_categories.size() == 1) {
-        for (size_t i = 1; i < num_datasets; i++) num_categories.push_back(num_categories[0]);
-    }
-
-    // process input format
-    if (gwas_input_format.size() == 1) {
-        for (size_t i = 1; i < num_datasets; i++) gwas_input_format.push_back(gwas_input_format[0]);
-    }
-
-    // process phenotype
-    if (gwas_input_phenotype.size() == 1) {
-        for (size_t i = 1; i < num_datasets; i++) gwas_input_phenotype.push_back(gwas_input_phenotype[0]);
-    }
-
-    if (
-            input_name.size() != num_datasets ||
-            num_categories.size() != num_datasets ||
-            gwas_input_phenotype.size() != num_datasets ||
-            gwas_input_format.size() != num_datasets
-       ) {
-        throw epi::Error("You did not provide the right amount of arguments of each type.");
-    }
-
-     */
-
-
     // process models
     const std::vector<std::string> all_available_models = epi::options::get_all_epistasis_scores();
     if (models.empty()) {
         // set all available models
-        models = { all_available_models.begin(), all_available_models.end() };
+        models = {all_available_models.begin(), all_available_models.end()};
     }
 
     std::sort(models.begin(), models.end());
     models.erase(std::unique(models.begin(), models.end()), models.end());
 
     std::unordered_map<std::string, epi::options::EpistasisScore> models_map;
-    for (auto & m : models) models_map.insert({ m, epi::options::epistasis_score_from_string(m) });
+    for (auto &m: models) models_map.insert({m, epi::options::epistasis_score_from_string(m)});
 
 
 
@@ -136,113 +115,150 @@ int main(int argc, char **argv) {
     std::unordered_map<std::string, std::shared_ptr<epi::DataModel>> instances;
     for (size_t i = 0; i < num_datasets; i++) {
         instances[input_name[i]] = std::make_shared<epi::DataModel>(false);
-        auto il = epi::InstanceLoader(gwas_input_file[i], gwas_input_format[i], gwas_input_phenotype[i], num_categories[i]);
+        auto il = epi::InstanceLoader(gwas_input_file[i], gwas_input_format[i], gwas_input_phenotype[i],
+                                      num_categories[i]);
         il.run(instances[input_name[i]]);
         instances[input_name[i]]->snpStorage->init_model_containers(num_threads);
     }
 
-    drogon::app().registerHandler(
-            "/needl/score/{dataset}/{scores}/{snps}",
-            [&instances, &models_map](const drogon::HttpRequestPtr &,
-               std::function<void(const drogon::HttpResponsePtr &)> &&callback,
-               const std::string &dataset, const std::string &scores_str, const std::string &snps_str) {
-
-                std::chrono::high_resolution_clock::time_point startTime = std::chrono::high_resolution_clock::now();
-
-                // find dataset
-                auto dm_ptr = instances.find(dataset);
-                if (dm_ptr == instances.end()) {
-                    LOG_WARN << "Unknown dataset: " << dataset;
-                    Json::Value json;
-                    json["ok"] = false;
-                    json["reason"] = "unknown dataset";
-                    auto resp = drogon::HttpResponse::newHttpJsonResponse(json);
-                    resp->setStatusCode(drogon::k404NotFound);
-                    callback(resp);
-                } else {
-                    auto &dm = dm_ptr->second;
-
-                    // find the selected models
-                    auto scores_s = epi::string_split(scores_str, ';');
-                    std::sort(scores_s.begin(), scores_s.end());
-                    scores_s.erase(std::unique(scores_s.begin(), scores_s.end()), scores_s.end());
-
-                    Json::Value unknown_scores;
-                    std::vector<epi::options::EpistasisScore> selected_models;
-                    for (auto &user_score : scores_s) {
-                        auto item = models_map.find(user_score);
-                        if (item == models_map.end()) {
-                            unknown_scores.append(user_score);
-                        } else {
-                            selected_models.push_back(item->second);
-                        }
-                    }
-
-                    try {
-                        auto snps_s = epi::string_split(snps_str, ';');
-                        if (snps_s.size() > 10) {
-                            LOG_WARN << "Too many SNPs (#snps = " << snps_s.size() << ")";
-                            Json::Value json;
-                            json["ok"] = false;
-                            json["reason"] = "too many SNPs (max. 10 allowed)";
-                            if (unknown_scores.size() > 0) json["unknown_or_unavailable_scores"] = unknown_scores;
-                            auto resp = drogon::HttpResponse::newHttpJsonResponse(json);
-                            resp->setStatusCode(drogon::k400BadRequest);
-                            callback(resp);
-                        } else {
-                            std::vector<epi::SNP_t> snps_t;
-                            snps_t.reserve(snps_s.size());
-                            Json::Value snps_j;
-                            for (auto &s: snps_s) {
-                                snps_t.push_back(dm->snpStorage->by_name(s));
-                                snps_j.append(s);
-                            }
-                            epi::SNPSet set(snps_t);
-                            Json::Value json_scores;
-                            for (auto &model: selected_models) {
-                                json_scores[epi::options::epistasis_score_to_string(model)] = dm->snpStorage->calculate_score(set, model,
-                                                                                  drogon::app().getCurrentThreadIndex());
-                            }
-                            Json::Value json;
-                            json["ok"] = true;
-                            json["scores"] = json_scores;
-                            json["SNPs"] = snps_j;
-
-                            if (unknown_scores.size() > 0) json["unknown_or_unavailable_scores"] = unknown_scores;
-
-                            std::chrono::high_resolution_clock::time_point endTime = std::chrono::high_resolution_clock::now();
-                            auto timeMs = std::chrono::duration_cast<std::chrono::microseconds>(
-                                    endTime - startTime).count();
-                            json["time_microseconds"] = timeMs;
-                            callback(drogon::HttpResponse::newHttpJsonResponse(json));
-                        }
-                    } catch (epi::SNPNotFoundError &err) {
-                        LOG_WARN << "Unknown SNP " << err.get_name();
-                        Json::Value json;
-                        json["ok"] = false;
-                        json["reason"] = "unknown SNP " + err.get_name();
-                        json["unknown_snp"] = err.get_name();
-                        if (unknown_scores.size() > 0) json["unknown_or_unavailable_scores"] = unknown_scores;
-                        auto resp = drogon::HttpResponse::newHttpJsonResponse(json);
-                        resp->setStatusCode(drogon::k404NotFound);
-                        callback(resp);
-                    } catch (epi::Error &err) {
-                        LOG_WARN << "epi::Error  " << err.what();
-                        Json::Value json;
-                        json["ok"] = false;
-                        if (unknown_scores.size() > 0) json["unknown_or_unavailable_scores"] = unknown_scores;
-                        auto resp = drogon::HttpResponse::newHttpJsonResponse(json);
-                        resp->setStatusCode(drogon::k500InternalServerError);
-                        callback(resp);
-                    }
-                }
-            },
-            {drogon::Get});
-
+    std::vector<size_t> thread_no (num_threads);
+    for (size_t i = 0; i< num_threads; ++i) thread_no[i] = i;
+
+    std::vector<std::thread *> threads(num_threads);
+    std::mutex stderr_mutex;
+
+    std::transform(thread_no.begin(), thread_no.end(), threads.begin(), [&stderr_mutex, &instances, &models_map, &bind_addr, &bind_port](size_t thread_index) {
+       return new std::thread([&stderr_mutex, &instances, &models_map, &bind_addr, &bind_port, &thread_index]() {
+           uWS::App().get("/needl/score/:dataset/:scores/:snps", [&stderr_mutex, &instances, &models_map, &thread_index](auto *res, auto *req) {
+               std::chrono::high_resolution_clock::time_point startTime = std::chrono::high_resolution_clock::now();
+
+               std::string dataset = std::string(req->getParameter(0));
+               std::string scores_str = std::string(req->getParameter(1));
+               std::string snps_str = std::string(req->getParameter(2));
+
+               rapidjson::Document doc;
+               auto alloc = doc.GetAllocator();
+
+               // find dataset
+               auto dm_ptr = instances.find(dataset);
+               if (dm_ptr == instances.end()) {
+                   stderr_mutex.lock();
+                   std::cerr << "Unknown dataset: " << dataset << std::endl;
+                   stderr_mutex.unlock();
+                   rapidjson::Value json(rapidjson::kObjectType);
+                   json.AddMember("ok", false, alloc);
+                   json.AddMember("reason", "unknown dataset", alloc);
+                   res->writeStatus("404 Not Found");
+                   res->end(json_to_str(json));
+               } else {
+                   auto &dm = dm_ptr->second;
+
+                   // find the selected models
+                   auto scores_s = epi::string_split(scores_str, ';');
+                   std::sort(scores_s.begin(), scores_s.end());
+                   scores_s.erase(std::unique(scores_s.begin(), scores_s.end()), scores_s.end());
+
+                   rapidjson::Value unknown_scores(rapidjson::kArrayType);
+                   std::vector<epi::options::EpistasisScore> selected_models;
+                   for (auto &user_score: scores_s) {
+                       auto item = models_map.find(user_score);
+                       if (item == models_map.end()) {
+                           unknown_scores.PushBack(rapidjson::Value(user_score.c_str(), alloc).Move(), alloc);
+                       } else {
+                           selected_models.push_back(item->second);
+                       }
+                   }
+
+                   try {
+                       auto snps_s = epi::string_split(snps_str, ';');
+                       if (snps_s.size() > 10) {
+                           stderr_mutex.lock();
+                           std::cerr << "Too many SNPs (#snps = " << snps_s.size() << ")" << std::endl;
+                           stderr_mutex.unlock();
+                           rapidjson::Value json(rapidjson::kObjectType);
+                           json.AddMember("ok", false, alloc);
+                           json.AddMember("reason", "too many SNPs (max. 10 allowed)", alloc);
+
+                           if (unknown_scores.Capacity() > 0)
+                               json.AddMember("unknown_or_unavailable_scores", unknown_scores.Move(), alloc);
+
+                           res->writeStatus("400 Bad Request");
+                           res->end(json_to_str(json));
+                       } else {
+                           std::vector<epi::SNP_t> snps_t;
+                           snps_t.reserve(snps_s.size());
+                           rapidjson::Value snps_j(rapidjson::kArrayType);
+                           for (auto &s: snps_s) {
+                               snps_t.push_back(dm->snpStorage->by_name(s));
+                               snps_j.PushBack(rapidjson::Value(s.c_str(), alloc).Move(), alloc);
+                           }
+                           epi::SNPSet set(snps_t);
+                           rapidjson::Value json_scores(rapidjson::kObjectType);
+                           for (auto &model: selected_models) {
+                               json_scores.AddMember(
+                                       rapidjson::Value(epi::options::epistasis_score_to_string(model).c_str(),
+                                                        alloc).Move(),
+                                       dm->snpStorage->calculate_score(set, model, thread_index),
+                                       alloc
+                               );
+                           }
+                           rapidjson::Value json(rapidjson::kObjectType);
+                           json.AddMember("ok", true, alloc);
+                           json.AddMember("scores", json_scores.Move(), alloc);
+                           json.AddMember("SNPs", snps_j.Move(), alloc);
+
+                           if (unknown_scores.Capacity() > 0)
+                               json.AddMember("unknown_or_unavailable_scores", unknown_scores.Move(), alloc);
+
+                           std::chrono::high_resolution_clock::time_point endTime = std::chrono::high_resolution_clock::now();
+                           auto timeMs = std::chrono::duration_cast<std::chrono::microseconds>(
+                                   endTime - startTime).count();
+                           json.AddMember("time_microseconds", timeMs, alloc);
+                           res->end(json_to_str(json));
+                       }
+                   } catch (epi::SNPNotFoundError &err) {
+                       stderr_mutex.lock();
+                       std::cerr << "Unknown SNP " << err.get_name() << std::endl;
+                       stderr_mutex.unlock();
+                       rapidjson::Value json(rapidjson::kObjectType);
+                       json.AddMember("ok", false, alloc);
+                       json.AddMember("reason",
+                                      rapidjson::Value(("unknown SNP " + err.get_name()).c_str(), alloc).Move(),
+                                      alloc);
+                       json.AddMember("unknown_snp", rapidjson::Value(err.get_name().c_str(), alloc).Move(), alloc);
+                       if (unknown_scores.Capacity() > 0)
+                           json.AddMember("unknown_or_unavailable_scores", unknown_scores.Move(), alloc);
+                       res->writeStatus("404 Not Found");
+                       res->end(json_to_str(json));
+                   } catch (epi::Error &err) {
+                       stderr_mutex.lock();
+                       std::cerr << "epi::Error  " << err.what() << std::endl;
+                       stderr_mutex.unlock();
+                       rapidjson::Value json(rapidjson::kObjectType);
+                       json.AddMember("ok", false, alloc);
+                       json.AddMember("reason", "internal error", alloc);
+                       if (unknown_scores.Capacity() > 0)
+                           json.AddMember("unknown_or_unavailable_scores", unknown_scores.Move(), alloc);
+                       res->writeStatus("500 Internal Error");
+                       res->end(json_to_str(json));
+                   }
+               }
+           }).listen(bind_addr, bind_port, [&stderr_mutex, &bind_addr, &bind_port](auto *listen_socket) {
+               stderr_mutex.lock();
+               if (listen_socket) {
+                   std::cout << "[Thread-" << std::this_thread::get_id() << "]  Listening on " << bind_addr << ':' << bind_port << std::endl;
+               } else {
+                   std::cerr << "[Thread-" << std::this_thread::get_id() << "]  Failed to listen on " << bind_addr << ':' << bind_port << std::endl;
+               }
+               stderr_mutex.unlock();
+           }).run();
+       });
+    });
+
+    std::for_each(threads.begin(), threads.end(), [](std::thread *t) {
+        t->join();
+    });
 
-    LOG_INFO << "Server running on " << bind_addr << ':' << bind_port << " with " << num_threads << " threads";
-    drogon::app().addListener(bind_addr, bind_port);
-    drogon::app().run();
     return 0;
 }
 

From 6ca1799a446c392472ce7b5fcbce32b0f77282a0 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Thu, 14 Sep 2023 16:57:28 +0200
Subject: [PATCH 03/10] added test e2e test for realtime_scores

---
 docker/NeEDL/Dockerfile    | 7 +++++--
 install.py                 | 2 +-
 test/e2e/test_container.sh | 6 ++++++
 3 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/docker/NeEDL/Dockerfile b/docker/NeEDL/Dockerfile
index b6baed502..dd4c49319 100644
--- a/docker/NeEDL/Dockerfile
+++ b/docker/NeEDL/Dockerfile
@@ -51,7 +51,8 @@ RUN python3.10 install.py --clean && \
     python3.10 install.py --target NeEDL && \
     python3.10 install.py --target calculate_scores && \
     python3.10 install.py --target convert_to_binary && \
-    python3.10 install.py --target epiJSON
+    python3.10 install.py --target epiJSON && \
+    python3.10 install.py --target realtime_scores
 
 # ---- end of stage 2
 
@@ -78,5 +79,7 @@ COPY --from=build /NeEDL/ext/plink/plink_linux_x86_64_20230116/ /NeEDL/ext/plink
 RUN ln -s /NeEDL/test/model/bin/NeEDL /usr/local/bin/NeEDL && \
     ln -s /NeEDL/test/model/bin/calculate_scores /usr/local/bin/calculate_scores && \
     ln -s /NeEDL/test/model/bin/convert_to_binary /usr/local/bin/convert_to_binary && \
-    ln -s /NeEDL/test/model/bin/convert_to_json /usr/local/bin/epiJSON
+    ln -s /NeEDL/test/model/bin/epiJSON /usr/local/bin/epiJSON && \
+    ln -s /NeEDL/test/model/bin/realtime_scores /usr/local/bin/realtime_scores
+
 # ---- end of stage 3
\ No newline at end of file
diff --git a/install.py b/install.py
index 0ca91e06d..c73cd9a16 100755
--- a/install.py
+++ b/install.py
@@ -134,7 +134,7 @@ def extract_all_zips_in_folder(folder):
         for entry in files:
             if entry.name.endswith(".zip"):
                 print("Extracting " + entry.name)
-                subprocess.call('unzip -n -d "' + escaped_folder + '" "' + escaped_folder + entry.name.replace('"', '\\"') + '"', shell=True)
+                subprocess.call('unzip -q -d "' + escaped_folder + '" "' + escaped_folder + entry.name.replace('"', '\\"') + '"', shell=True)
 
 def extract_resources(args):
     if (os.path.isfile(".RES_EXTRACTED") and not args.clean) or args.no_data_unpacking:
diff --git a/test/e2e/test_container.sh b/test/e2e/test_container.sh
index b80e3c758..41046bfeb 100755
--- a/test/e2e/test_container.sh
+++ b/test/e2e/test_container.sh
@@ -25,6 +25,12 @@ python ./run/epiJSON.py --docker-image-name "$1" --docker-no-pulling  --help
 python ./run/calculate_scores.py --docker-image-name "$1" --docker-no-pulling  --help
 python ./run/convert_to_binary.py --docker-image-name "$1" --docker-no-pulling  --help
 
+# realtime_scores is a special case --> no python launcher script exists for it
+# run containers as current user
+user_id=$(id -u)
+group_id=$(id -g)
+docker run --user $user_id:$group_id "$1" /NeEDL/test/model/bin/realtime_scores --help
+
 
 
 # select small dummy dataset

From 570b031995733926ce158bf35d09335ec18958e1 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Thu, 14 Sep 2023 18:01:16 +0200
Subject: [PATCH 04/10] fixed docker build issues with uWebSockets

---
 .github/workflows/docker-publish.yml | 2 ++
 install.py                           | 8 ++++++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/docker-publish.yml b/.github/workflows/docker-publish.yml
index c89dbf15c..e18e4fdf0 100644
--- a/.github/workflows/docker-publish.yml
+++ b/.github/workflows/docker-publish.yml
@@ -25,6 +25,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v3
+        with:
+          submodules: 'recursive'
 
       # Workaround: https://github.com/docker/build-push-action/issues/461
       - name: Setup Docker buildx
diff --git a/install.py b/install.py
index c73cd9a16..5601221c4 100755
--- a/install.py
+++ b/install.py
@@ -105,7 +105,10 @@ def build_external_libraries(args, dependencies):
         print("-- uWebSocket library already built.")
     else:
         print("-- Building uWebSockets library")
-        subprocess.call('git submodule update --init --recursive; cd ext/uWebSockets/uSockets;make boringssl;cd boringssl;BORINGSSL=$PWD;cd ../lsquic;cmake -DBORINGSSL_DIR=$BORINGSSL .;make;cd ..;WITH_LTO=1 WITH_QUIC=1 WITH_BORINGSSL=1 make', shell=True)
+        if not args.no_submodule_extraction:
+            subprocess.call('git submodule update --init --recursive')
+        
+        subprocess.call('cd ext/uWebSockets/uSockets;make boringssl;cd boringssl;BORINGSSL=$PWD;cd ../lsquic;cmake -DBORINGSSL_DIR=$BORINGSSL .;make;cd ..;WITH_LTO=1 WITH_QUIC=1 WITH_BORINGSSL=1 make', shell=True)
         f = open("ext/.uWebSockets_INSTALLED", "w")
         f.close()
 
@@ -134,7 +137,7 @@ def extract_all_zips_in_folder(folder):
         for entry in files:
             if entry.name.endswith(".zip"):
                 print("Extracting " + entry.name)
-                subprocess.call('unzip -q -d "' + escaped_folder + '" "' + escaped_folder + entry.name.replace('"', '\\"') + '"', shell=True)
+                subprocess.call('unzip -qo -d "' + escaped_folder + '" "' + escaped_folder + entry.name.replace('"', '\\"') + '"', shell=True)
 
 def extract_resources(args):
     if (os.path.isfile(".RES_EXTRACTED") and not args.clean) or args.no_data_unpacking:
@@ -209,6 +212,7 @@ def find_dependencies(args):
 parser.add_argument("--gcc", help="one can select the path to gcc manually if the automatically selected compiler is not correct.", default=None)
 parser.add_argument("--gxx", help="one can select the path to g++ manually if the automatically selected compiler is not correct.", default=None)
 parser.add_argument("--extract-datasets", help="Also extracts simulated datasets. These might be necessary for the unit tests.", action="store_true")
+parser.add_argument("--no-submodule-extraction", help="When set the script does not recursively download submodules. This is used for building the docker container.", action="store_true")
 args = parser.parse_args()
 
 

From fe074c8d7a6a9ae7bd1fb0daa831486aad6db025 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Thu, 14 Sep 2023 18:04:20 +0200
Subject: [PATCH 05/10] another fix

---
 docker/NeEDL/Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/NeEDL/Dockerfile b/docker/NeEDL/Dockerfile
index dd4c49319..d78243f58 100644
--- a/docker/NeEDL/Dockerfile
+++ b/docker/NeEDL/Dockerfile
@@ -47,7 +47,7 @@ COPY data/dbSNP/inc_pseudogenes /NeEDL/data/dbSNP/inc_pseudogenes
 COPY data/BIOGRID /NeEDL/data/BIOGRID
 
 # initialize everything needed for the build and build all targets
-RUN python3.10 install.py --clean && \ 
+RUN python3.10 install.py --clean --no-submodule-extraction && \ 
     python3.10 install.py --target NeEDL && \
     python3.10 install.py --target calculate_scores && \
     python3.10 install.py --target convert_to_binary && \

From e633ddae77d3adb903e302dbe2e1597815950347 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Thu, 14 Sep 2023 19:18:47 +0200
Subject: [PATCH 06/10] added  go to the dependencies for the docker container

---
 docker/NeEDL/Dockerfile | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/docker/NeEDL/Dockerfile b/docker/NeEDL/Dockerfile
index d78243f58..004d768b2 100644
--- a/docker/NeEDL/Dockerfile
+++ b/docker/NeEDL/Dockerfile
@@ -32,7 +32,9 @@ WORKDIR /NeEDL
 ENV DEBIAN_FRONTEND=noninteractive
 
 # install build dependencies
-RUN apt-get update -y && apt-get install -y build-essential git cmake autoconf libtool pkg-config python3.10 python3.10-dev gcc g++ sqlite3 libsqlite3-dev python3.10-distutils unzip
+RUN apt-get update -y && \
+    apt-get install -y build-essential git cmake autoconf libtool pkg-config python3.10 python3.10-dev gcc g++ sqlite3 libsqlite3-dev python3.10-distutils unzip wget && \
+    wget -c https://dl.google.com/go/go1.21.1.linux-amd64.tar.gz -O - | sudo tar -xz -C /usr/local
 
 # copy necessary NeEDL repo files
 COPY ext ./ext

From a1552c8142add0b4cdb1f4bd601acd85b11233f1 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Fri, 15 Sep 2023 12:27:19 +0200
Subject: [PATCH 07/10] fix go installation for docker container

---
 .dockerignore           | 4 ++++
 docker/NeEDL/Dockerfile | 4 ++--
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index 9b461f292..2b79beb76 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -108,6 +108,8 @@ test/model/res/*
 /cmake-build-*
 /.idea/
 
+CMakeCache.txt
+
 #load
 # /data/LOAD/
 # /data/CAD_control/*
@@ -123,6 +125,8 @@ test/model/res/*
 /ext/boost_1_71_0/tools/build/src/engine/b2
 /ext/boost_1_71_0/tools/build/src/engine/bjam
 
+/ext/uWebSockets/uSockets/*.o
+
 .Rhistory
 
 
diff --git a/docker/NeEDL/Dockerfile b/docker/NeEDL/Dockerfile
index 004d768b2..d2b365b36 100644
--- a/docker/NeEDL/Dockerfile
+++ b/docker/NeEDL/Dockerfile
@@ -33,8 +33,8 @@ ENV DEBIAN_FRONTEND=noninteractive
 
 # install build dependencies
 RUN apt-get update -y && \
-    apt-get install -y build-essential git cmake autoconf libtool pkg-config python3.10 python3.10-dev gcc g++ sqlite3 libsqlite3-dev python3.10-distutils unzip wget && \
-    wget -c https://dl.google.com/go/go1.21.1.linux-amd64.tar.gz -O - | sudo tar -xz -C /usr/local
+    apt-get install -y build-essential git cmake autoconf libtool pkg-config python3.10 python3.10-dev gcc g++ sqlite3 libsqlite3-dev python3.10-distutils unzip curl libevent-dev && \
+    curl https://dl.google.com/go/go1.21.1.linux-amd64.tar.gz | tar -xz -C /usr/local
 
 # copy necessary NeEDL repo files
 COPY ext ./ext

From bcc17dd6e3a0759d895cc7e3aab645259717d1f6 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Fri, 22 Sep 2023 12:18:25 +0200
Subject: [PATCH 08/10] docker realtime_scores now builds

---
 .dockerignore           |  3 ++-
 .gitignore              |  6 +++---
 CMakeLists.txt          | 26 +++++++++++++++++++++-----
 docker/NeEDL/Dockerfile | 21 ++++++++++++---------
 install.py              |  9 ++++++++-
 5 files changed, 46 insertions(+), 19 deletions(-)

diff --git a/.dockerignore b/.dockerignore
index 2b79beb76..90acc119e 100644
--- a/.dockerignore
+++ b/.dockerignore
@@ -23,6 +23,7 @@ docs/
 
 # Binary directories
 **/bin
+!/ext/uWebSockets/uSockets/lsquic/bin
 
 # INI files for unit tests
 /test/unit/init/*
@@ -108,7 +109,7 @@ test/model/res/*
 /cmake-build-*
 /.idea/
 
-CMakeCache.txt
+**/CMakeCache.txt
 
 #load
 # /data/LOAD/
diff --git a/.gitignore b/.gitignore
index 22b2a44de..55873d2d7 100644
--- a/.gitignore
+++ b/.gitignore
@@ -119,9 +119,9 @@ test/model/res/*
 .Rhistory
 
 
-.INSTALLED
-.uWebSockets_INSTALLED
-.RES_EXTRACTED
+**/.INSTALLED
+**/.uWebSockets_INSTALLED
+**/.RES_EXTRACTED
 .env
 
 docker/data
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 61fa4c660..cad859a7e 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -19,10 +19,12 @@
 #                                                                             #
 ###############################################################################
 
-cmake_minimum_required(VERSION 3.2)
+cmake_minimum_required(VERSION 3.8)
 set(CMAKE_VERBOSE_MAKEFILE ON)
 project(NeEDL)
 
+include(CMakePrintHelpers)
+
 # Determine build type.
 if(NOT CMAKE_BUILD_TYPE)
   message(STATUS "Building NeEDL with build type 'Release', as none was specified.")
@@ -31,6 +33,22 @@ else()
   message(STATUS "Building NeEDL with build type '${CMAKE_BUILD_TYPE}'.")
 endif()
 
+set(USE_INCLUDED_BOOST "1" CACHE BOOL "Use the boost version shipped with this repository")
+cmake_print_variables(USE_INCLUDED_BOOST)
+if (USE_INCLUDED_BOOST)
+  message("-- boost version: vendored")
+  set(BOOST_INCLUDE ${CMAKE_SOURCE_DIR}/ext/boost_1_71_0)
+  set(BOOST_LINK_DIR ${CMAKE_SOURCE_DIR}/ext/boost_1_71_0/stage/lib)
+else()
+  message("-- boost version: system")
+  set(Boost_USE_STATIC_LIBS OFF) 
+  set(Boost_USE_MULTITHREADED ON)  
+  set(Boost_USE_STATIC_RUNTIME OFF) 
+  find_package(Boost 1.71.0 REQUIRED COMPONENTS filesystem graph)
+
+  set(BOOST_INCLUDE ${Boost_INCLUDE_DIRS})
+endif()
+
 # Find doxygen.
 #find_package(Doxygen)
 #if(DOXYGEN_FOUND)
@@ -43,7 +61,6 @@ find_package(Python COMPONENTS Interpreter Development)
 find_package(SQLite3 REQUIRED)
 
 # debug stuff
-include(CMakePrintHelpers)
 cmake_print_variables(CMAKE_C_COMPILER)
 cmake_print_variables(CMAKE_C_COMPILER_VERSION)
 cmake_print_variables(CMAKE_CXX_COMPILER)
@@ -67,15 +84,14 @@ endif()
 set(CMAKE_MACOSX_RPATH ON)
 
 # Add include and link directories.
-set(BOOST_ROOT ${CMAKE_SOURCE_DIR}/ext/boost_1_71_0)
 set(EIGEN_ROOT ${CMAKE_SOURCE_DIR}/ext/eigen_3_3_7)
 set(CLI11_ROOT ${CMAKE_SOURCE_DIR}/ext/cli11_1_9_0)
 set(CATCH_ROOT ${CMAKE_SOURCE_DIR}/ext/catch_2_13_9)
 set(IGRAPH_ROOT ${CMAKE_SOURCE_DIR}/ext/igraph_0.9.8)
 set(PYBIND11_HOME ${CMAKE_SOURCE_DIR}/ext/pybind11)
 
-include_directories(SYSTEM ${SQLite3_INCLUDE_DIRS} ${BOOST_ROOT} ${EIGEN_ROOT} ${CLI11_ROOT} ${CATCH_ROOT} ${IGRAPH_ROOT}/include ${IGRAPH_ROOT}/build/include ${PYBIND11_HOME}/include ${SQLite3_INCLUDE_DIRS} ${Python_INCLUDE_DIRS} /usr/lib/llvm-10/include)
-link_directories(${BOOST_ROOT}/stage/lib /usr/lib/llvm-10/lib ${IGRAPH_ROOT}/build/src ${Python_LIBRARY_DIRS} ${SQLite3_LIBRARIES})
+include_directories(SYSTEM ${SQLite3_INCLUDE_DIRS} ${BOOST_INCLUDE} ${EIGEN_ROOT} ${CLI11_ROOT} ${CATCH_ROOT} ${IGRAPH_ROOT}/include ${IGRAPH_ROOT}/build/include ${PYBIND11_HOME}/include ${SQLite3_INCLUDE_DIRS} ${Python_INCLUDE_DIRS} /usr/lib/llvm-10/include)
+link_directories(${BOOST_LINK_DIR} /usr/lib/llvm-10/lib ${IGRAPH_ROOT}/build/src ${Python_LIBRARY_DIRS} ${SQLite3_LIBRARIES})
 if(APPLE)
   include_directories(SYSTEM ${OMP_ROOT}/include)
   link_directories(${OMP_ROOT}/lib)
diff --git a/docker/NeEDL/Dockerfile b/docker/NeEDL/Dockerfile
index d2b365b36..4b9c59e28 100644
--- a/docker/NeEDL/Dockerfile
+++ b/docker/NeEDL/Dockerfile
@@ -33,9 +33,12 @@ ENV DEBIAN_FRONTEND=noninteractive
 
 # install build dependencies
 RUN apt-get update -y && \
-    apt-get install -y build-essential git cmake autoconf libtool pkg-config python3.10 python3.10-dev gcc g++ sqlite3 libsqlite3-dev python3.10-distutils unzip curl libevent-dev && \
+    apt-get install -y build-essential git cmake autoconf libtool pkg-config python3.10 python3.10-dev gcc g++ sqlite3 libsqlite3-dev python3.10-distutils unzip curl libevent-dev libboost-all-dev && \
     curl https://dl.google.com/go/go1.21.1.linux-amd64.tar.gz | tar -xz -C /usr/local
 
+ENV PATH /usr/local/go/bin:$PATH
+
+
 # copy necessary NeEDL repo files
 COPY ext ./ext
 COPY src ./src
@@ -49,12 +52,12 @@ COPY data/dbSNP/inc_pseudogenes /NeEDL/data/dbSNP/inc_pseudogenes
 COPY data/BIOGRID /NeEDL/data/BIOGRID
 
 # initialize everything needed for the build and build all targets
-RUN python3.10 install.py --clean --no-submodule-extraction && \ 
-    python3.10 install.py --target NeEDL && \
-    python3.10 install.py --target calculate_scores && \
-    python3.10 install.py --target convert_to_binary && \
-    python3.10 install.py --target epiJSON && \
-    python3.10 install.py --target realtime_scores
+RUN python3.10 install.py --clean --no-submodule-extraction --system-boost && \ 
+    python3.10 install.py --target NeEDL --system-boost && \
+    python3.10 install.py --target calculate_scores --system-boost && \
+    python3.10 install.py --target convert_to_binary --system-boost && \
+    python3.10 install.py --target epiJSON --system-boost && \
+    python3.10 install.py --target realtime_scores --system-boost
 
 # ---- end of stage 2
 
@@ -68,10 +71,10 @@ LABEL org.opencontainers.image.source=https://github.com/biomedbigdata/NeEDL
 ENV DEBIAN_FRONTEND=noninteractive
 
 # install production dependencies
-RUN apt-get update -y && apt-get install -y python3.10 python3.10-dev sqlite3 g++ gcc
+RUN apt-get update -y && apt-get install -y python3.10 python3.10-dev sqlite3 g++ gcc libboost-all-dev
 
 # copy everything important over to the new container
-COPY --from=build /NeEDL/ext/boost_1_71_0/stage /NeEDL/ext/boost_1_71_0/stage
+# COPY --from=build /NeEDL/ext/boost_1_71_0/stage /NeEDL/ext/boost_1_71_0/stage
 COPY --from=build /NeEDL/test/model/bin/* /NeEDL/test/model/bin/
 COPY --from=build /NeEDL/data/dbSNP/inc_pseudogenes/snps_restruc_full_inc_pseudo.csv /NeEDL/data/dbSNP/inc_pseudogenes/snps_restruc_full_inc_pseudo.csv
 COPY --from=build /NeEDL/data/BIOGRID/BIOGRID-ORGANISM-Homo_sapiens-3.5.182.tab2.txt /NeEDL/data/BIOGRID/BIOGRID-ORGANISM-Homo_sapiens-current.tab2.txt
diff --git a/install.py b/install.py
index 5601221c4..3c12684f0 100755
--- a/install.py
+++ b/install.py
@@ -53,6 +53,10 @@ def build_targets(args, all_targets, dependencies):
     if (not os.path.isfile("build/Makefile")):
         print("-- Running CMake.")
         commands = "cd build; rm -rf *; cmake .. -DCMAKE_BUILD_TYPE=" + ("Debug" if args.debug else "Release")
+
+        if args.system_boost:
+            commands += f' -DUSE_INCLUDED_BOOST=0'
+
         commands += f' -DPython_EXECUTABLE="{dependencies["python3"]}"'
         commands += f' -DCMAKE_C_COMPILER="{dependencies["gcc"]}" -DCMAKE_CXX_COMPILER="{dependencies["g++"]}"'
         if platform.system() == "Darwin":
@@ -75,7 +79,9 @@ def build_targets(args, all_targets, dependencies):
 
 def build_external_libraries(args, dependencies):
     # boost
-    if os.path.isfile("ext/boost_1_71_0/.INSTALLED") and not args.clean:
+    if args.system_boost:
+        print("-- Boost libraries: system installation is used --> build of boost is skipped")
+    elif os.path.isfile("ext/boost_1_71_0/.INSTALLED") and not args.clean:
         print("-- Boost libraries already built.")
     else:
         print("-- Building Boost libraries.")
@@ -213,6 +219,7 @@ def find_dependencies(args):
 parser.add_argument("--gxx", help="one can select the path to g++ manually if the automatically selected compiler is not correct.", default=None)
 parser.add_argument("--extract-datasets", help="Also extracts simulated datasets. These might be necessary for the unit tests.", action="store_true")
 parser.add_argument("--no-submodule-extraction", help="When set the script does not recursively download submodules. This is used for building the docker container.", action="store_true")
+parser.add_argument("--system-boost", help="Use the system boost installation instead of the one in this repository", action="store_true")
 args = parser.parse_args()
 
 

From de502c3fb0d69ca87b244eb88b06e6aabce31485 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Fri, 22 Sep 2023 12:59:21 +0200
Subject: [PATCH 09/10] updated docker-compose, improved NeEDL compile time

---
 docker/realtime_scores/Dockerfile         | 37 -----------------------
 docker/realtime_scores/docker-compose.yml |  7 ++---
 quepistasis/header/cpu_sa.h               |  4 +++
 quepistasis/header/cpu_sa_wrapper.h       |  5 +++
 quepistasis/header/python_wrapper.h       |  5 +++
 quepistasis/header/snps_optimization.h    |  5 +++
 src/jobs/ShinyAppLauncher.hpp             |  4 +++
 test/model/CMakeLists.txt                 |  8 ++++-
 test/model/src/NeEDL.cpp                  |  7 ++---
 9 files changed, 35 insertions(+), 47 deletions(-)
 delete mode 100644 docker/realtime_scores/Dockerfile

diff --git a/docker/realtime_scores/Dockerfile b/docker/realtime_scores/Dockerfile
deleted file mode 100644
index 516fdf324..000000000
--- a/docker/realtime_scores/Dockerfile
+++ /dev/null
@@ -1,37 +0,0 @@
-FROM ubuntu:latest as base
-
-WORKDIR /NeEDL
-
-ENV DEBIAN_FRONTEND=noninteractive
-
-# copy necessary NeEDL repo files
-COPY ext ./ext
-COPY src ./src
-COPY test ./test
-COPY CMakeLists.txt ./
-COPY install.py ./
-
-RUN mkdir -p ./uploads/tmp
-
-# install dependencies
-RUN apt-get update && \
-	apt-get install -y build-essential git cmake autoconf libtool pkg-config python3 python3-dev libjsoncpp-dev uuid-dev openssl libssl-dev zlib1g-dev libbrotli-dev gcc g++ sqlite3 libsqlite3-dev
-
-
-# add symlink to jsoncpp include files
-RUN ln -s /usr/include/jsoncpp/json /usr/include/json
-
-
-# build drogon web framework
-RUN git clone https://github.com/drogonframework/drogon drogon
-WORKDIR /NeEDL/drogon
-RUN git submodule update --init
-RUN mkdir build
-WORKDIR /NeEDL/drogon/build
-RUN cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MYSQL=OFF -DBUILD_POSTGRESQL=OFF -DBUILD_REDIS=OFF -DBUILD_SQLITE=OFF -DBUILD_EXAMPLES=OFF -DBUILD_CTL=OFF ..
-RUN make
-RUN make install
-WORKDIR /NeEDL
-
-# build the realtime_score program
-RUN ./install.py --target realtime_scores --no-data-unpacking  --clean
diff --git a/docker/realtime_scores/docker-compose.yml b/docker/realtime_scores/docker-compose.yml
index cb0c9b491..96db62560 100644
--- a/docker/realtime_scores/docker-compose.yml
+++ b/docker/realtime_scores/docker-compose.yml
@@ -2,12 +2,9 @@ version: '3'
 
 services:
   realtime_scores:
+    image: bigdatainbiomedicine/needl
     restart: always
-    command: ./test/model/bin/realtime_scores --input-dir /datasets --num-threads $NUM_THREADS --bind-addr 0.0.0.0 --bind-port 3000
-    build:
-      context: ../../
-      dockerfile: docker/realtime_scores/Dockerfile
-      # target: base
+    command: /NeEDL/test/model/bin/realtime_scores --input-dir /datasets --num-threads $NUM_THREADS --bind-addr 0.0.0.0 --bind-port 3000
     volumes:
       - ${DATASET_DIR}:/datasets:Z
     user: ${REALTIME_SCORES_USER}
diff --git a/quepistasis/header/cpu_sa.h b/quepistasis/header/cpu_sa.h
index 936ac8907..04806980e 100644
--- a/quepistasis/header/cpu_sa.h
+++ b/quepistasis/header/cpu_sa.h
@@ -64,4 +64,8 @@ int general_simulated_annealing(
     void * const interrupt_function
 );
 
+#ifdef HEADER_ONLY
+#include "../src/cpu_sa.cpp"
+#endif
+
 #endif
\ No newline at end of file
diff --git a/quepistasis/header/cpu_sa_wrapper.h b/quepistasis/header/cpu_sa_wrapper.h
index 1d618f0e3..8c3d6ee85 100644
--- a/quepistasis/header/cpu_sa_wrapper.h
+++ b/quepistasis/header/cpu_sa_wrapper.h
@@ -39,4 +39,9 @@ void simulated_annealing_ising(
         uint64_t seed,
         sa_return* ret);
 
+
+#ifdef HEADER_ONLY
+#include "../src/cpu_sa_wrapper.cpp"
+#endif
+
 #endif
\ No newline at end of file
diff --git a/quepistasis/header/python_wrapper.h b/quepistasis/header/python_wrapper.h
index e3c367033..5fcf53113 100644
--- a/quepistasis/header/python_wrapper.h
+++ b/quepistasis/header/python_wrapper.h
@@ -209,4 +209,9 @@ class PythonWrapper {
         int clique_size, int shots, const char* save_path);
 };
 
+
+#ifdef HEADER_ONLY
+#include "../src/python_wrapper.cpp"
+#endif
+
 #endif
\ No newline at end of file
diff --git a/quepistasis/header/snps_optimization.h b/quepistasis/header/snps_optimization.h
index dcdd5610f..bcfe4df6c 100644
--- a/quepistasis/header/snps_optimization.h
+++ b/quepistasis/header/snps_optimization.h
@@ -244,4 +244,9 @@ class snps_qubo_matrix : public matrix {
 
 };
 
+
+#ifdef HEADER_ONLY
+#include "../src/snps_optimization.cpp"
+#endif
+
 #endif
\ No newline at end of file
diff --git a/src/jobs/ShinyAppLauncher.hpp b/src/jobs/ShinyAppLauncher.hpp
index a33a19f5d..ce171ad52 100644
--- a/src/jobs/ShinyAppLauncher.hpp
+++ b/src/jobs/ShinyAppLauncher.hpp
@@ -21,4 +21,8 @@ namespace epi {
 
 } // epi
 
+#ifdef HEADER_ONLY
+#include "ShinyAppLauncher.cpp"
+#endif
+
 #endif //GENEPISEEKER_SHINYAPPLAUNCHER_HPP
diff --git a/test/model/CMakeLists.txt b/test/model/CMakeLists.txt
index 1a448d778..ed346386e 100644
--- a/test/model/CMakeLists.txt
+++ b/test/model/CMakeLists.txt
@@ -32,7 +32,13 @@ if(APPLE)
   target_link_libraries(compare_models omp)
 endif()
 
-add_executable(NeEDL src/NeEDL.cpp src/util.cpp ${MAIN_SOURCES_NEW} ${QUANTUM_COMPUTING})
+if (CMAKE_BUILD_TYPE STREQUAL "Release")
+  add_compile_definitions(CMAKE_RELEASE)
+  add_executable(NeEDL src/NeEDL.cpp src/util.cpp)
+else()
+  add_executable(NeEDL src/NeEDL.cpp src/util.cpp ${MAIN_SOURCES_NEW} ${QUANTUM_COMPUTING})
+endif()
+
 target_link_libraries(NeEDL sqlite3 boost_filesystem igraph ${Python_LIBRARIES})
 if(APPLE)
   target_link_libraries(NeEDL omp)
diff --git a/test/model/src/NeEDL.cpp b/test/model/src/NeEDL.cpp
index 8bfac945f..0760a9763 100644
--- a/test/model/src/NeEDL.cpp
+++ b/test/model/src/NeEDL.cpp
@@ -2,15 +2,14 @@
 // Created by juli on 25.05.22.
 //
 
+#ifdef CMAKE_RELEASE
+    #define HEADER_ONLY
+#endif
 
 #include <CLI11.hpp>
 #include <omp.h>
 
 #include "../../src/pipelines/NeEDLPipeline.hpp"
-#include "../../src/util/helper_functions.hpp"
-#include "../../../src/jobs/SeedingRandomConnected.hpp"
-#include "../../../src/jobs/SeedingCommunityWise.hpp"
-#include "../../../src/jobs/SeedingQuantumComputing.hpp"
 
 
 

From 5b2b32e7b48588c44ebc6107ad23a8768cc5dc33 Mon Sep 17 00:00:00 2001
From: juli-p <63345753+juli-p@users.noreply.github.com>
Date: Fri, 22 Sep 2023 13:06:36 +0200
Subject: [PATCH 10/10] set docker compose name

---
 docker/realtime_scores/docker-compose.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docker/realtime_scores/docker-compose.yml b/docker/realtime_scores/docker-compose.yml
index 96db62560..a9509ec26 100644
--- a/docker/realtime_scores/docker-compose.yml
+++ b/docker/realtime_scores/docker-compose.yml
@@ -1,4 +1,5 @@
 version: '3'
+name: needl_realtime_scores_api
 
 services:
   realtime_scores: