OpenMS Thermo Raw File Bridge

A CMake-packaged native C++ bridge that embeds the .NET runtime, calls the official ThermoFisher RawFileReader libraries through a managed shim, and exposes Thermo RAW scan counting to native consumers.

What This Does

• Builds a native bridge library and the thermo_host CLI with CMake
• Publishes a managed bridge with an UnmanagedCallersOnly GetScanCount entry point
• Packages exported CMake targets for add_subdirectory/FetchContent and find_package(... CONFIG) workflows
• Runs a small Catch2-based test suite through CTest
• Supports Linux, macOS, and Windows builds

Build

The project does not download the Thermo vendor packages by default.

Option 1: provide the vendor .nupkg files yourself

Place the following files in vendor/thermo-feed or point CMake at another directory with -DOPENMS_THERMO_BRIDGE_VENDOR_DIR=/absolute/path:

• ThermoFisher.CommonCore.BackgroundSubtraction.8.0.6.nupkg
• ThermoFisher.CommonCore.Data.8.0.6.nupkg
• ThermoFisher.CommonCore.MassPrecisionEstimator.8.0.6.nupkg
• ThermoFisher.CommonCore.RandomAccessReaderPlugin.8.0.6.nupkg
• ThermoFisher.CommonCore.RawfileReader.8.0.6.nupkg

Then configure and build:

cmake -S . -B build
cmake --build build --parallel

Option 2: explicitly allow CMake to fetch the vendor packages

cmake -S . -B build \
  -DOPENMS_THERMO_BRIDGE_ENABLE_VENDOR_DOWNLOAD=ON
cmake --build build --parallel

Option 3: use pre-built managed DLLs

Pre-built managed artifacts for each platform are published as GitHub Release assets, so CMake does not need to run dotnet publish for ThermoWrapperManaged.csproj. The final executable still needs the .NET 8 runtime at runtime, and the native bridge build still needs the platform-specific nethost headers and library. In practice those nethost development files usually come from the .NET SDK/host pack rather than a runtime-only install.

Download the zip for your platform from the GitHub Releases page, unpack it, and point CMake at the extracted directory:

cmake -S . -B build \
  -DOPENMS_THERMO_BRIDGE_PREBUILT_MANAGED_DIR=/path/to/unpacked/zip
cmake --build build --parallel

Automatic download during CMake configure

CMake will fetch and extract the correct platform zip from GitHub Releases automatically:

cmake -S . -B build \
  -DOPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED=ON
cmake --build build --parallel

For Linux convenience, build_linux.sh configures, builds, and runs the tests with the vendor-download option enabled.

Test

ctest --test-dir build --output-on-failure

Run

./build/thermo_host /path/to/file.raw

Expected output:

Scan count: <number>

The public ginkgotoxin-ms-positive.raw sample used in CI currently reports:

Scan count: 90

CMake Consumption

FetchContent / add_subdirectory

FetchContent_Declare(OpenMSThermoBridge
  GIT_REPOSITORY https://github.com/jpfeuffer/openms-thermo-bridge.git
  GIT_TAG main)
FetchContent_MakeAvailable(OpenMSThermoBridge)

add_executable(my_tool main.cpp)
target_link_libraries(my_tool PRIVATE OpenMSThermoBridge::openms_thermo_bridge)
openms_thermo_bridge_copy_runtime_files(TARGET my_tool)

openms_thermo_bridge_copy_runtime_files() stages everything needed beside the given target's output directory:

• managed/ThermoWrapperManaged.dll
• managed/ThermoWrapperManaged.runtimeconfig.json
• the dynamic nethost runtime library on platforms where it is needed

For executables, call it on the final executable target. If your code uses OpenMSThermoBridge from a shared library/plugin, call it on that shared library target instead so the runtime payload lives next to the library that actually ships to users.

Installed package / find_package(... CONFIG)

find_package(OpenMSThermoBridge CONFIG REQUIRED)

add_executable(my_tool main.cpp)
target_link_libraries(my_tool PRIVATE OpenMSThermoBridge::openms_thermo_bridge)
openms_thermo_bridge_copy_runtime_files(TARGET my_tool)

At runtime the bridge first looks for managed/ next to the executable, then next to the loaded openms_thermo_bridge binary, and also supports the installed package layout under openms_thermo_bridge/managed. That means:

• build-tree consumers can stage runtime files next to their executable or shared library with openms_thermo_bridge_copy_runtime_files()
• installed-package consumers can either stage the runtime files the same way or rely on the package's installed lib/openms_thermo_bridge/managed layout

If you bypass the helper and pass an explicit managed directory to openms::thermo_bridge::RawFile or get_scan_count(...), then you are responsible for shipping that directory yourself.

Requirements

• CMake 3.21+
• .NET 8 SDK when CMake builds ThermoWrapperManaged.csproj locally with dotnet publish
• Platform-specific .NET nethost headers and library to build the native bridge; these usually come from the .NET SDK/host pack even when using pre-built managed artifacts
• .NET 8 runtime for the final executable at runtime
• A C++17 compiler
• Network access to api.nuget.org and, when the relevant options are enabled, raw.githubusercontent.com
• Pre-built artifact downloads (OPENMS_THERMO_BRIDGE_DOWNLOAD_PREBUILT_MANAGED=ON) additionally require network access to github.com

Status

• Linux, macOS, and Windows CMake builds
• Native C++ bridge library and CLI
• Catch2/CTest integration tests
• Exported CMake package config