Replace ROS 2 CLI calls with pure C++ rclcpp solution

.devcontainer/Dockerfile

@@ -49,6 +49,7 @@ RUN curl -sSL https://raw.githubusercontent.com/ros/rosdistro/master/ros.key \
 
 RUN apt-get update && apt-get install -y \
     ros-jazzy-desktop-full \
+    ros-jazzy-test-msgs \
     python3-colcon-common-extensions \
     python3-rosdep \
     && rm -rf /var/lib/apt/lists/*

.devcontainer/devcontainer.json

@@ -18,7 +18,7 @@
     // Comment this out if you don't want zsh and oh-my-zsh
     "ghcr.io/devcontainers/features/common-utils:2": {
       "installZsh": true,
-      "configureZshAsDefaultShell": true,
+      "configureZshAsDefaultShell": false,
       "installOhMyZsh": true
     },
     "ghcr.io/devcontainers/features/git:1": {},
@@ -47,7 +47,7 @@
         "christian-kohler.path-intellisense"
       ],
       "settings": {
-        "terminal.integrated.defaultProfile.linux": "zsh",
+        "terminal.integrated.defaultProfile.linux": "bash",
         "python.defaultInterpreterPath": "/usr/bin/python3",
         "cmake.configureOnOpen": false
       }

.github/workflows/ci.yml

@@ -14,6 +14,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Set up ROS 2 Jazzy
         uses: ros-tooling/setup-ros@v0.7
@@ -23,7 +25,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y clang-format clang-tidy
+          sudo apt-get install -y clang-format clang-tidy ros-jazzy-test-msgs
           source /opt/ros/jazzy/setup.bash
           rosdep update
           rosdep install --from-paths src --ignore-src -r -y
@@ -72,6 +74,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Set up ROS 2 Jazzy
         uses: ros-tooling/setup-ros@v0.7
@@ -81,7 +85,7 @@ jobs:
       - name: Install dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y lcov
+          sudo apt-get install -y lcov ros-jazzy-test-msgs
           source /opt/ros/jazzy/setup.bash
           rosdep update
           rosdep install --from-paths src --ignore-src -r -y
@@ -107,38 +111,36 @@ jobs:
 
       - name: Generate coverage report
         run: |
-          # Capture coverage data with error tolerance
+          # Capture coverage data
+          # IMPORTANT: --ignore-errors gcov is required to skip .gcda files
+          # that have missing corresponding .gcno files (common in multi-package builds)
           lcov --capture --directory build --output-file coverage.raw.info \
-            --ignore-errors mismatch,negative,empty || true
-
-          # Check if we have valid coverage data
-          if [ -s coverage.raw.info ] && grep -q 'SF:' coverage.raw.info; then
-            # Extract only our source code (exclude gtest_vendor and other ROS dependencies)
-            lcov --extract coverage.raw.info \
-              '*/ros2_medkit/src/*/src/*' \
-              '*/ros2_medkit/src/*/include/*' \
-              --output-file coverage.info \
-              --ignore-errors unused,empty || true
-
-            if [ -s coverage.info ]; then
-              lcov --list coverage.info
-              # Generate HTML report
-              genhtml coverage.info --output-directory coverage_html \
-                --ignore-errors source || true
-            else
-              echo "Filtered coverage.info is empty, using raw coverage"
-              cp coverage.raw.info coverage.info
-              lcov --list coverage.info || true
-              genhtml coverage.info --output-directory coverage_html \
-                --ignore-errors source || true
-            fi
-          else
-            echo "No valid coverage data found in coverage.raw.info"
-            echo "Creating empty coverage file to prevent upload failure"
-            touch coverage.info
-            mkdir -p coverage_html
+            --ignore-errors mismatch,negative,empty,gcov
+
+          # Validate coverage data exists
+          if [ ! -s coverage.raw.info ] || ! grep -q 'SF:' coverage.raw.info; then
+            echo "::error::No valid coverage data found in coverage.raw.info"
+            exit 1
           fi
 
+          # Extract only our source code (exclude gtest_vendor and other ROS dependencies)
+          lcov --extract coverage.raw.info \
+            '*/ros2_medkit/src/*/src/*' \
+            '*/ros2_medkit/src/*/include/*' \
+            --output-file coverage.info \
+            --ignore-errors unused,empty
+
+          # Validate filtered coverage
+          if [ ! -s coverage.info ]; then
+            echo "::error::Filtered coverage.info is empty - no source files matched"
+            exit 1
+          fi
+
+          lcov --list coverage.info
+
+          # Generate HTML report
+          genhtml coverage.info --output-directory coverage_html --ignore-errors source
+
       - name: Upload coverage HTML report as artifact
         uses: actions/upload-artifact@v4
         with:

.github/workflows/docs.yml

@@ -33,6 +33,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          submodules: recursive
 
       - name: Set up Python
         uses: actions/setup-python@v5

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "src/dynamic_message_introspection"]
+	path = src/dynamic_message_introspection
+	url = https://github.com/selfpatch/dynamic_message_introspection.git

README.md

@@ -52,11 +52,14 @@ so the same concepts can be used across robots, vehicles, and other embedded sys
 ```bash
 mkdir -p ~/ros2_medkit_ws/src
 cd ~/ros2_medkit_ws/src
-git clone https://github.com/selfpatch/ros2_medkit.git
+git clone --recurse-submodules https://github.com/selfpatch/ros2_medkit.git
 cd ~/ros2_medkit_ws
 rosdep install --from-paths src --ignore-src -r -y
 ```
 
+> **Note:** If you cloned without `--recurse-submodules`, run:
+> `git submodule update --init --recursive`
+
 ### 2. Build
 
 ```bash

docs/Doxyfile

@@ -14,6 +14,8 @@ INPUT                  = ../src/ros2_medkit_gateway/include \
                          ../src/ros2_medkit_fault_reporter/src \
                          ../src/ros2_medkit_diagnostic_bridge/include \
                          ../src/ros2_medkit_diagnostic_bridge/src \
+                         ../src/ros2_medkit_serialization/include \
+                         ../src/ros2_medkit_serialization/src \
                          ../src/ros2_medkit_msgs
 RECURSIVE              = YES
 FILE_PATTERNS          = *.hpp *.cpp *.h

docs/api/index.rst

@@ -81,3 +81,23 @@ Bridge node that converts ROS 2 /diagnostics messages to FaultManager faults.
 
 .. doxygenclass:: ros2_medkit_diagnostic_bridge::DiagnosticBridgeNode
    :members:
+
+ros2_medkit_serialization
+-------------------------
+
+Runtime JSON ↔ ROS 2 message serialization library.
+
+.. doxygenclass:: ros2_medkit_serialization::JsonSerializer
+   :members:
+
+.. doxygenclass:: ros2_medkit_serialization::TypeCache
+   :members:
+
+.. doxygenclass:: ros2_medkit_serialization::SerializationError
+   :members:
+
+.. doxygenclass:: ros2_medkit_serialization::TypeNotFoundError
+   :members:
+
+.. doxygenclass:: ros2_medkit_serialization::JsonConversionError
+   :members:

docs/design/index.rst

@@ -10,4 +10,5 @@ This section contains design documentation for the ros2_medkit project packages.
    ros2_medkit_fault_manager/index
    ros2_medkit_fault_reporter/index
    ros2_medkit_gateway/index
+   ros2_medkit_serialization/index
 

docs/design/ros2_medkit_serialization

@@ -0,0 +1 @@
+../../src/ros2_medkit_serialization/design

docs/index.rst

@@ -15,7 +15,7 @@ endpoints for data access, operations, configurations, and fault management.
 
 .. note::
 
-   Version 0.1.0 — First public release.
+   Version 0.1.0 - First public release still under construction...
 
 Quick Links
 -----------

docs/installation.rst

@@ -75,9 +75,15 @@ ros2_medkit is currently distributed as source code. Binary packages will be ava
 
    .. code-block:: bash
 
-      git clone https://github.com/selfpatch/ros2_medkit.git
+      git clone --recurse-submodules https://github.com/selfpatch/ros2_medkit.git
       cd ros2_medkit
 
+   If you already cloned without submodules, initialize them:
+
+   .. code-block:: bash
+
+      git submodule update --init --recursive
+
 3. **Install dependencies**
 
    .. code-block:: bash

docs/introduction.rst

@@ -46,12 +46,19 @@ ros2_medkit consists of several ROS 2 packages:
 **ros2_medkit_gateway**
    The main HTTP gateway node. Discovers ROS 2 entities and exposes them via REST API.
 
+**ros2_medkit_serialization**
+   Runtime JSON ↔ ROS 2 message serialization library using dynmsg. Enables native
+   message handling without compile-time type dependencies.
+
 **ros2_medkit_fault_manager**
    Stores and manages fault lifecycle. Provides ROS 2 services for fault operations.
 
 **ros2_medkit_fault_reporter**
    Client library for reporting faults from your ROS 2 nodes.
 
+**ros2_medkit_diagnostic_bridge**
+   Bridge node that converts standard ROS 2 ``/diagnostics`` messages to fault manager faults.
+
 **ros2_medkit_msgs**
    Message and service definitions for fault management.
 

docs/tutorials/devcontainer.rst

@@ -31,13 +31,19 @@ Prerequisites
 Quick Start
 -----------
 
-1. **Clone the repository:**
+1. **Clone the repository with submodules:**
 
    .. code-block:: bash
 
-      git clone https://github.com/selfpatch/ros2_medkit.git
+      git clone --recurse-submodules https://github.com/selfpatch/ros2_medkit.git
       cd ros2_medkit
 
+   If you already cloned without submodules:
+
+   .. code-block:: bash
+
+      git submodule update --init --recursive
+
 2. **Open in VS Code:**
 
    .. code-block:: bash

src/ros2_medkit_gateway/CMakeLists.txt

@@ -32,6 +32,7 @@ find_package(action_msgs REQUIRED)
 find_package(rclcpp_action REQUIRED)
 find_package(example_interfaces REQUIRED)
 find_package(ros2_medkit_msgs REQUIRED)
+find_package(ros2_medkit_serialization REQUIRED)
 
 # Find cpp-httplib using pkg-config
 find_package(PkgConfig REQUIRED)
@@ -103,8 +104,6 @@ add_library(gateway_lib STATIC
   src/config.cpp
   src/gateway_node.cpp
   src/discovery_manager.cpp
-  src/ros2_cli_wrapper.cpp
-  src/output_parser.cpp
   src/data_access_manager.cpp
   src/type_introspection.cpp
   src/native_topic_sampler.cpp
@@ -139,6 +138,7 @@ ament_target_dependencies(gateway_lib
   ament_index_cpp
   action_msgs
   ros2_medkit_msgs
+  ros2_medkit_serialization
 )
 
 target_link_libraries(gateway_lib

src/ros2_medkit_gateway/README.md

@@ -212,9 +212,9 @@ curl http://localhost:8080/api/v1/components/nonexistent/data
 
 **Behavior:**
 - Returns array of all topics under the component's namespace
-- Each topic is sampled once with `ros2 topic echo --once`
+- Each topic is sampled once using native rclcpp GenericSubscription
 - Empty array `[]` returned if component has no topics
-- 3-second timeout per topic to accommodate slow-publishing topics
+- Configurable timeout per topic (default: 2 seconds)
 
 **Use Cases:**
 - Remote diagnostics - Read all sensor values from a component

src/ros2_medkit_gateway/config/gateway_params.yaml

@@ -85,19 +85,20 @@ ros2_medkit_gateway:
     # Valid range: 1-50
     max_parallel_topic_samples: 20
 
-    # Timeout (in seconds) for sampling topic data via ros2 topic echo
+    # Timeout (in seconds) for sampling topic data via native GenericSubscription
     # Topics without publishers return immediately with metadata (no timeout wait)
     # This timeout only applies when topics have active publishers
     # Valid range: 0.1-30.0
     topic_sample_timeout_sec: 2.0
 
-    # NOTE: Native sampling is always enabled
-    # The gateway uses native rclcpp APIs for topic discovery and sampling:
-    # - Uses node->get_topic_names_and_types() instead of `ros2 topic list`
-    # - Checks publisher counts before sampling to skip idle topics immediately
-    # - Returns metadata instantly for topics without publishers (no CLI timeout wait)
-    # This significantly improves UX when many topics are idle (e.g., robot waiting for commands)
-    # CLI is only used for publishing (ros2 topic pub)
+    # NOTE: Native-only implementation
+    # The gateway uses native rclcpp APIs for all ROS 2 interactions:
+    # - Topic discovery: node->get_topic_names_and_types()
+    # - Topic sampling: rclcpp::GenericSubscription + JsonSerializer
+    # - Topic publishing: rclcpp::GenericPublisher + JsonSerializer
+    # - Service calls: rclcpp::GenericClient + JsonSerializer
+    # - Action operations: Internal action services via GenericClient
+    # No ROS 2 CLI dependencies - pure C++ implementation using ros2_medkit_serialization.
 
     # Authentication Configuration (REQ_INTEROP_086, REQ_INTEROP_087)
     # JWT-based authentication with Role-Based Access Control (RBAC)

src/ros2_medkit_gateway/design/architecture.puml

@@ -46,15 +46,12 @@ package "ros2_medkit_gateway" {
         + sample_topics_parallel(): vector<TopicSampleResult>
     }
 
-    class ROS2CLIWrapper {
-        + exec(): string
-        + is_command_available(): bool
-        + escape_shell_arg(): string
-    }
-
-    class OutputParser {
-        + parse_yaml(): json
-        - yaml_to_json(): json
+    class JsonSerializer {
+        + serialize(): SerializedMessage
+        + deserialize(): json
+        + to_json(): json
+        + from_json(): RosMessage_Cpp
+        + yaml_to_json(): json {static}
     }
 
     class Area {
@@ -103,9 +100,8 @@ DiscoveryManager --> "rclcpp::Node" : uses
 RESTServer --> GatewayNode : uses
 RESTServer --> DataAccessManager : uses
 
-' DataAccessManager owns utility classes
-DataAccessManager *--> ROS2CLIWrapper : owns (publishing)
-DataAccessManager *--> OutputParser : owns
+' DataAccessManager owns utility classes (native implementation)
+DataAccessManager *--> JsonSerializer : owns (serialization)
 DataAccessManager *--> NativeTopicSampler : owns
 
 ' NativeTopicSampler uses Node interface