Merge pull request #883 from ORNL/JoshuaSBrown-fix-doc-build

Joshua s brown fix doc build

.github/workflows/build-docs.yml

@@ -0,0 +1,57 @@
+# Simple workflow for deploying documentation to GitHub Pages
+name: Build and deploy documentation
+
+on:
+  # Runs on pushes targeting the default branch
+  push:
+    branches: ["master"]
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Single deploy job since we're just deploying
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-=python@v2
+        with:
+          python-version: 3.9
+      - name: Install documentation build dependencies
+        run: |
+          ./scripts/install_docs_dependencies.sh
+      - name: Build documentation
+        run: | 
+          cmake -S. -B build -DBUILD_AUTHZ=OFF -DBUILD_CORE_SERVER=OFF -DBUILD_COMMON=OFF -DBUILD_DOCS=ON -DBUILD_FOXX=OFF -DBUILD_REPO_SERVER=OFF -DBUILD_PYTHON_CLIENT=OFF -DBUILD_TESTS=OFF -DBUILD_WEB_SERVER=OFF -DENABLE_UNIT_TESTS=OFF
+      - name: Build cmake doc target
+        run: |
+          cmake --build build --target docs
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v2
+        with:
+          # Upload entire repository
+          path: './docs'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2
+

common/source/SocketOptions.cpp

@@ -54,11 +54,13 @@ AddressSplitter::AddressSplitter(const std::string &address) {
     // Add 1 so as to ignore the ':' when copying the port number
     if (pos_colon + 1 < copy.size()) {
       port = copy.substr(pos_colon + 1);
-    } else {// Else no port was provided
+    } else { // Else no port was provided
       // This is an error we will throw we should not provide : at the end of
       // an address without specifying a port number
       EXCEPT_PARAM(1, "Error unable to deconstruct port, it does not appear to "
-                    "be provided in the address even though ':' has been specified after the host. (" << address << ") ");
+                      "be provided in the address even though ':' has been "
+                      "specified after the host. ("
+                          << address << ") ");
     }
     std::string host;
     if (pos_colon > 0) {

common/source/communicators/ZeroMQCommunicator.cpp

@@ -106,7 +106,8 @@ void sendFinalDelimiter(void *outgoing_zmq_socket) {
 // 0 - number of routes
 // null
 // Frame - function will not read
-void receiveRoute(IMessage &msg, void *incoming_zmq_socket, LogContext log_context) {
+void receiveRoute(IMessage &msg, void *incoming_zmq_socket,
+                  LogContext log_context) {
   // If the first frame is not empty assume it is a route that was provided by
   // the internals of zmq
   std::string previous_route = "";
@@ -291,7 +292,8 @@ void sendRoute(IMessage &msg, void *outgoing_zmq_socket,
 /**
  * Will load the frame of the message.
  **/
-void receiveFrame(IMessage &msg, void *incoming_zmq_socket, LogContext log_context) {
+void receiveFrame(IMessage &msg, void *incoming_zmq_socket,
+                  LogContext log_context) {
   int number_of_bytes = 0;
   while (number_of_bytes == 0) {
     zmq_msg_t zmq_msg;
@@ -387,7 +389,8 @@ void receiveBody(IMessage &msg, Buffer &buffer, ProtoBufFactory &factory,
       uint16_t msg_type = std::get<uint16_t>(msg.get(MSG_TYPE));
 
       ProtoBufMap proto_map;
-      DL_TRACE(log_context, "Receiving message body of type: " + proto_map.toString(msg_type));
+      DL_TRACE(log_context, "Receiving message body of type: " +
+                                proto_map.toString(msg_type));
       if (proto_map.exists(msg_type)) {
         std::unique_ptr<proto::Message> payload = factory.create(msg_type);
         msg.setPayload(std::move(payload));
@@ -450,7 +453,8 @@ void sendBody(IMessage &msg, Buffer &buffer, void *outgoing_zmq_socket) {
   }
 }
 
-void receiveCorrelationID(IMessage &msg, void *incoming_zmq_socket, LogContext log_context) {
+void receiveCorrelationID(IMessage &msg, void *incoming_zmq_socket,
+                          LogContext log_context) {
   // If the UID metadata is set, use is; otherwise get the UID from the message
   zmq_msg_t zmq_msg;
   zmq_msg_init(&zmq_msg);
@@ -476,7 +480,8 @@ void receiveCorrelationID(IMessage &msg, void *incoming_zmq_socket, LogContext l
   zmq_msg_close(&zmq_msg);
 }
 
-void receiveKey(IMessage &msg, void *incoming_zmq_socket, LogContext log_context) {
+void receiveKey(IMessage &msg, void *incoming_zmq_socket,
+                LogContext log_context) {
   // If the UID metadata is set, use is; otherwise get the UID from the message
   zmq_msg_t zmq_msg;
   zmq_msg_init(&zmq_msg);
@@ -547,7 +552,8 @@ void sendKey(IMessage &msg, void *outgoing_zmq_socket) {
   zmq_msg_close(&zmq_msg);
 }
 
-void receiveID(IMessage &msg, void *incoming_zmq_socket, LogContext log_context) {
+void receiveID(IMessage &msg, void *incoming_zmq_socket,
+               LogContext log_context) {
   // If the UID metadata is set, use is; otherwise get the UID from the message
   zmq_msg_t zmq_msg;
   zmq_msg_init(&zmq_msg);
@@ -739,7 +745,8 @@ ZeroMQCommunicator::poll(const MessageType message_type) {
     receiveID(*response.message, m_zmq_socket, log_context);
     receiveFrame(*response.message, m_zmq_socket, log_context);
 
-    receiveBody(*response.message, m_buffer, m_protocol_factory, m_zmq_socket, log_context);
+    receiveBody(*response.message, m_buffer, m_protocol_factory, m_zmq_socket,
+                log_context);
 
     uint16_t msg_type = std::get<uint16_t>(
         response.message->get(constants::message::google::MSG_TYPE));
@@ -803,7 +810,8 @@ ZeroMQCommunicator::receive(const MessageType message_type) {
     receiveKey(*response.message, m_zmq_socket, log_context);
     receiveID(*response.message, m_zmq_socket, log_context);
     receiveFrame(*response.message, m_zmq_socket, log_context);
-    receiveBody(*response.message, m_buffer, m_protocol_factory, m_zmq_socket, log_context);
+    receiveBody(*response.message, m_buffer, m_protocol_factory, m_zmq_socket,
+                log_context);
 
     uint16_t msg_type = std::get<uint16_t>(
         response.message->get(constants::message::google::MSG_TYPE));

core/server/ClientWorker.cpp

@@ -350,9 +350,10 @@ void ClientWorker::workerThread(LogContext log_context) {
         IMessage &message = *response.message;
         uint16_t msg_type = std::get<uint16_t>(
             message.get(constants::message::google::MSG_TYPE));
-        message_log_context.correlation_id = std::get<std::string>(message.get(MessageAttribute::CORRELATION_ID));
+        message_log_context.correlation_id = std::get<std::string>(
+            message.get(MessageAttribute::CORRELATION_ID));
         DL_DEBUG(message_log_context, "W" << m_tid << " received message: "
-                                  << proto_map.toString(msg_type));
+                                          << proto_map.toString(msg_type));
 
         const std::string uid =
             std::get<std::string>(message.get(MessageAttribute::ID));
@@ -375,16 +376,17 @@ void ClientWorker::workerThread(LogContext log_context) {
           response_msg->setPayload(std::move(nack));
           client->send(*response_msg);
         } else {
-          DL_DEBUG(message_log_context, "W" << m_tid
-                                    << " getting handler from map: msg_type = "
-                                    << proto_map.toString(msg_type));
+          DL_DEBUG(message_log_context,
+                   "W" << m_tid << " getting handler from map: msg_type = "
+                       << proto_map.toString(msg_type));
           if (m_msg_handlers.count(msg_type)) {
 
             auto handler = m_msg_handlers.find(msg_type);
 
-            DL_TRACE(message_log_context, "W" << m_tid
-                                      << " calling handler/attempting to call "
-                                         "function of worker");
+            DL_TRACE(message_log_context,
+                     "W" << m_tid
+                         << " calling handler/attempting to call "
+                            "function of worker");
 
             // Have to move the actual unique_ptr, change ownership not simply
             // passing a reference
@@ -395,8 +397,9 @@ void ClientWorker::workerThread(LogContext log_context) {
               if (msg_type != task_list_msg_type)
                 m_core.metricsUpdateMsgCount(uid, msg_type);
 
-              DL_DEBUG(message_log_context, "W" << m_tid << " sending msg of type "
-                                        << proto_map.toString(msg_type));
+              DL_DEBUG(message_log_context,
+                       "W" << m_tid << " sending msg of type "
+                           << proto_map.toString(msg_type));
               client->send(*response_msg);
               DL_TRACE(message_log_context, "Message sent ");
             }
@@ -1379,7 +1382,8 @@ void ClientWorker::handleTaskResponse(libjson::Value &a_result,
     libjson::Value::Object &task_obj = obj.asObject();
 
     if (task_obj.getNumber("status") != TS_BLOCKED) {
-      DL_DEBUG(log_context, "handleTaskResponse status is: " << task_obj.getNumber("status"));
+      DL_DEBUG(log_context, "handleTaskResponse status is: "
+                                << task_obj.getNumber("status"));
       TaskMgr::getInstance().newTask(task_obj.getString("_id"), log_context);
     }
   }

core/server/CoreServer.cpp

@@ -480,7 +480,9 @@ void Server::repoCacheThread(LogContext log_context, int thread_count) {
 
   while (1) {
     try {
-      DL_DEBUG(log_context, "Checking if Repo Cache needs Updating, then sleeping for " << std::to_string(repo_cache_poll.count()) << " seconds.");
+      DL_DEBUG(log_context,
+               "Checking if Repo Cache needs Updating, then sleeping for "
+                   << std::to_string(repo_cache_poll.count()) << " seconds.");
       m_config.loadRepositoryConfig(m_auth_manager, log_context);
     } catch (const std::exception &e) {
       DL_ERROR(log_context, "Repo Cache Updating... " << e.what());

core/server/TaskMgr.cpp

@@ -20,7 +20,7 @@ using namespace std;
 namespace SDMS {
 namespace Core {
 
-TaskMgr * TaskMgr::global_task_mgr;
+TaskMgr *TaskMgr::global_task_mgr;
 std::mutex TaskMgr::singleton_instance_mutex;
 
 void TaskMgr::initialize(LogContext log_context) {
@@ -100,21 +100,23 @@ TaskMgr::TaskMgr()
 TaskMgr::~TaskMgr() {}
 
 TaskMgr &TaskMgr::getInstance() {
-  if( global_task_mgr == nullptr ) {
-    EXCEPT(1, "Something is really wrong, the getInstance() should only be called after the getInstance(log_context, thread_id) command has been called");
+  if (global_task_mgr == nullptr) {
+    EXCEPT(1, "Something is really wrong, the getInstance() should only be "
+              "called after the getInstance(log_context, thread_id) command "
+              "has been called");
   }
 
   return *global_task_mgr;
 }
 
 TaskMgr &TaskMgr::getInstance(LogContext log_context, int thread_id) {
-  if( global_task_mgr == nullptr ) {
-     std::lock_guard<std::mutex> lock(singleton_instance_mutex);
-     if(global_task_mgr == nullptr ) {
-       log_context.thread_name += "-TaskMgr";
-       log_context.thread_id = thread_id;
-       global_task_mgr = new TaskMgr(log_context);
-     }
+  if (global_task_mgr == nullptr) {
+    std::lock_guard<std::mutex> lock(singleton_instance_mutex);
+    if (global_task_mgr == nullptr) {
+      log_context.thread_name += "-TaskMgr";
+      log_context.thread_id = thread_id;
+      global_task_mgr = new TaskMgr(log_context);
+    }
   }
 
   return *global_task_mgr;
@@ -375,7 +377,8 @@ std::unique_ptr<TaskMgr::Task> TaskMgr::getNextTask(ITaskWorker *a_worker) {
   }
 
   // Pop next task from ready queue and place in running map
-  DL_DEBUG(log_context, "There are " << m_tasks_ready.size() << " grabbing one.");
+  DL_DEBUG(log_context,
+           "There are " << m_tasks_ready.size() << " grabbing one.");
   auto task = std::move(m_tasks_ready.front());
   m_tasks_ready.pop_front();
   DL_DEBUG(log_context, "Now there are " << m_tasks_ready.size() << " left.");

core/server/TaskMgr.hpp

@@ -67,9 +67,8 @@ class TaskMgr : public ITaskMgr {
   LogContext m_log_context;
   int m_thread_count = 0;
 
-  static TaskMgr * global_task_mgr;
+  static TaskMgr *global_task_mgr;
   static std::mutex singleton_instance_mutex;
-
 };
 
 } // namespace Core

core/server/TaskWorker.cpp

@@ -69,7 +69,7 @@ void TaskWorker::workerThread(LogContext log_context) {
   bool first;
 
   while (m_running) {
-    DL_DEBUG(log_context,"Grabbing next task");
+    DL_DEBUG(log_context, "Grabbing next task");
     std::unique_ptr<ITaskMgr::Task> m_task = m_mgr.getNextTask(this);
 
     err_msg.clear();
@@ -105,8 +105,8 @@ void TaskWorker::workerThread(LogContext log_context) {
           response = m_execute[cmd](*this, params, log_context);
 
         } else if (cmd == TC_STOP) {
-          DL_DEBUG(log_context,
-                   "TASK_ID: " << m_task->task_id << ", STOP at step: " << step);
+          DL_DEBUG(log_context, "TASK_ID: " << m_task->task_id
+                                            << ", STOP at step: " << step);
           m_mgr.newTasks(params, log_context);
           break;
         } else {
@@ -115,9 +115,11 @@ void TaskWorker::workerThread(LogContext log_context) {
         }
 
         if (response.error or response.time_out) {
-	  err_msg = response.error_msg;
-          DL_DEBUG(log_context, "error dectected: " << response.error << " time_out detected: " << response.time_out << " cmd: " << cmd);
-          DL_DEBUG(log_context, "err_msg: " << err_msg );
+          err_msg = response.error_msg;
+          DL_DEBUG(log_context, "error dectected: "
+                                    << response.error << " time_out detected: "
+                                    << response.time_out << " cmd: " << cmd);
+          DL_DEBUG(log_context, "err_msg: " << err_msg);
           if (m_mgr.retryTask(std::move(m_task), log_context)) {
             DL_DEBUG(log_context, "retry period exceeded");
             err_msg = "Maximum task retry period exceeded.";
@@ -136,7 +138,7 @@ void TaskWorker::workerThread(LogContext log_context) {
         DL_ERROR(log_context, "Task worker "
                                   << id() << " exception: " << err_msg
                                   << " task_id is " << m_task->task_id
-				  << " cmd is " << cmd);
+                                  << " cmd is " << cmd);
         if (err_msg.find("Task " + m_task->task_id + " does not exist") !=
             std::string::npos) {
           DL_ERROR(log_context, "Task is not found in the database something "
@@ -340,20 +342,22 @@ TaskWorker::cmdRawDataUpdateSize(TaskWorker &me, const Value &a_task_params,
     auto proto_msg =
         std::get<google::protobuf::Message *>(response.message->getPayload());
     auto size_reply = dynamic_cast<Auth::RepoDataSizeReply *>(proto_msg);
-    if (size_reply != 0 ) {
+    if (size_reply != 0) {
       if (size_reply->size_size() != (int)ids.size()) {
-        DL_ERROR(log_context, "Mismatched result size with RepoDataSizeReply from repo: "
-             << repo_id);
+        DL_ERROR(log_context,
+                 "Mismatched result size with RepoDataSizeReply from repo: "
+                     << repo_id);
         EXCEPT_PARAM(1,
-         "Mismatched result size with RepoDataSizeReply from repo: "
-             << repo_id);
+                     "Mismatched result size with RepoDataSizeReply from repo: "
+                         << repo_id);
       }
 
       me.m_db.recordUpdateSize(*size_reply, log_context);
     } else {
-      DL_ERROR(log_context, "Unexpected reply to RepoDataSizeReply from repo: " << repo_id);
+      DL_ERROR(log_context,
+               "Unexpected reply to RepoDataSizeReply from repo: " << repo_id);
       EXCEPT_PARAM(
-        1, "Unexpected reply to RepoDataSizeReply from repo: " << repo_id);
+          1, "Unexpected reply to RepoDataSizeReply from repo: " << repo_id);
     }
   }