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v0.10.17
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61
.conda/base/recipe.yaml
Normal file
61
.conda/base/recipe.yaml
Normal file
@@ -0,0 +1,61 @@
|
||||
# unilabos: Production package (depends on unilabos-env + pip unilabos)
|
||||
# For production deployment
|
||||
|
||||
package:
|
||||
name: unilabos
|
||||
version: 0.10.17
|
||||
|
||||
source:
|
||||
path: ../../unilabos
|
||||
target_directory: unilabos
|
||||
|
||||
build:
|
||||
python:
|
||||
entry_points:
|
||||
- unilab = unilabos.app.main:main
|
||||
script:
|
||||
- set PIP_NO_INDEX=
|
||||
- if: win
|
||||
then:
|
||||
- copy %RECIPE_DIR%\..\..\MANIFEST.in %SRC_DIR%
|
||||
- copy %RECIPE_DIR%\..\..\setup.cfg %SRC_DIR%
|
||||
- copy %RECIPE_DIR%\..\..\setup.py %SRC_DIR%
|
||||
- pip install %SRC_DIR%
|
||||
- if: unix
|
||||
then:
|
||||
- cp $RECIPE_DIR/../../MANIFEST.in $SRC_DIR
|
||||
- cp $RECIPE_DIR/../../setup.cfg $SRC_DIR
|
||||
- cp $RECIPE_DIR/../../setup.py $SRC_DIR
|
||||
- pip install $SRC_DIR
|
||||
|
||||
requirements:
|
||||
host:
|
||||
- python ==3.11.14
|
||||
- pip
|
||||
- setuptools
|
||||
- zstd
|
||||
- zstandard
|
||||
run:
|
||||
- zstd
|
||||
- zstandard
|
||||
- networkx
|
||||
- typing_extensions
|
||||
- websockets
|
||||
- opentrons_shared_data
|
||||
- pint
|
||||
- fastapi
|
||||
- jinja2
|
||||
- requests
|
||||
- uvicorn
|
||||
- opcua
|
||||
- pyserial
|
||||
- pandas
|
||||
- pymodbus
|
||||
- matplotlib
|
||||
- pylibftdi
|
||||
- uni-lab::unilabos-env ==0.10.17
|
||||
|
||||
about:
|
||||
repository: https://github.com/deepmodeling/Uni-Lab-OS
|
||||
license: GPL-3.0-only
|
||||
description: "UniLabOS - Production package with minimal ROS2 dependencies"
|
||||
39
.conda/environment/recipe.yaml
Normal file
39
.conda/environment/recipe.yaml
Normal file
@@ -0,0 +1,39 @@
|
||||
# unilabos-env: conda environment dependencies (ROS2 + conda packages)
|
||||
|
||||
package:
|
||||
name: unilabos-env
|
||||
version: 0.10.17
|
||||
|
||||
build:
|
||||
noarch: generic
|
||||
|
||||
requirements:
|
||||
run:
|
||||
# Python
|
||||
- zstd
|
||||
- zstandard
|
||||
- conda-forge::python ==3.11.14
|
||||
- conda-forge::opencv
|
||||
# ROS2 dependencies (from ci-check.yml)
|
||||
- robostack-staging::ros-humble-ros-core
|
||||
- robostack-staging::ros-humble-action-msgs
|
||||
- robostack-staging::ros-humble-std-msgs
|
||||
- robostack-staging::ros-humble-geometry-msgs
|
||||
- robostack-staging::ros-humble-control-msgs
|
||||
- robostack-staging::ros-humble-nav2-msgs
|
||||
- robostack-staging::ros-humble-cv-bridge
|
||||
- robostack-staging::ros-humble-vision-opencv
|
||||
- robostack-staging::ros-humble-tf-transformations
|
||||
- robostack-staging::ros-humble-moveit-msgs
|
||||
- robostack-staging::ros-humble-tf2-ros
|
||||
- robostack-staging::ros-humble-tf2-ros-py
|
||||
- conda-forge::transforms3d
|
||||
- conda-forge::uv
|
||||
|
||||
# UniLabOS custom messages
|
||||
- uni-lab::ros-humble-unilabos-msgs
|
||||
|
||||
about:
|
||||
repository: https://github.com/deepmodeling/Uni-Lab-OS
|
||||
license: GPL-3.0-only
|
||||
description: "UniLabOS Environment - ROS2 and conda dependencies (for developers: pip install -e .)"
|
||||
42
.conda/full/recipe.yaml
Normal file
42
.conda/full/recipe.yaml
Normal file
@@ -0,0 +1,42 @@
|
||||
# unilabos-full: Full package with all features
|
||||
# Depends on unilabos + complete ROS2 desktop + dev tools
|
||||
|
||||
package:
|
||||
name: unilabos-full
|
||||
version: 0.10.17
|
||||
|
||||
build:
|
||||
noarch: generic
|
||||
|
||||
requirements:
|
||||
run:
|
||||
# Base unilabos package (includes unilabos-env)
|
||||
- uni-lab::unilabos ==0.10.17
|
||||
# Documentation tools
|
||||
- sphinx
|
||||
- sphinx_rtd_theme
|
||||
# Web UI
|
||||
- gradio
|
||||
- flask
|
||||
# Interactive development
|
||||
- ipython
|
||||
- jupyter
|
||||
- jupyros
|
||||
- colcon-common-extensions
|
||||
# ROS2 full desktop (includes rviz2, gazebo, etc.)
|
||||
- robostack-staging::ros-humble-desktop-full
|
||||
# Navigation and motion control
|
||||
- ros-humble-navigation2
|
||||
- ros-humble-ros2-control
|
||||
- ros-humble-robot-state-publisher
|
||||
- ros-humble-joint-state-publisher
|
||||
# MoveIt motion planning
|
||||
- ros-humble-moveit
|
||||
- ros-humble-moveit-servo
|
||||
# Simulation
|
||||
- ros-humble-simulation
|
||||
|
||||
about:
|
||||
repository: https://github.com/deepmodeling/Uni-Lab-OS
|
||||
license: GPL-3.0-only
|
||||
description: "UniLabOS Full - Complete package with ROS2 Desktop, MoveIt, Navigation2, Gazebo, Jupyter"
|
||||
@@ -1,91 +0,0 @@
|
||||
package:
|
||||
name: unilabos
|
||||
version: 0.10.15
|
||||
|
||||
source:
|
||||
path: ../unilabos
|
||||
target_directory: unilabos
|
||||
|
||||
build:
|
||||
python:
|
||||
entry_points:
|
||||
- unilab = unilabos.app.main:main
|
||||
script:
|
||||
- set PIP_NO_INDEX=
|
||||
- if: win
|
||||
then:
|
||||
- copy %RECIPE_DIR%\..\MANIFEST.in %SRC_DIR%
|
||||
- copy %RECIPE_DIR%\..\setup.cfg %SRC_DIR%
|
||||
- copy %RECIPE_DIR%\..\setup.py %SRC_DIR%
|
||||
- call %PYTHON% -m pip install %SRC_DIR%
|
||||
- if: unix
|
||||
then:
|
||||
- cp $RECIPE_DIR/../MANIFEST.in $SRC_DIR
|
||||
- cp $RECIPE_DIR/../setup.cfg $SRC_DIR
|
||||
- cp $RECIPE_DIR/../setup.py $SRC_DIR
|
||||
- $PYTHON -m pip install $SRC_DIR
|
||||
|
||||
requirements:
|
||||
host:
|
||||
- python ==3.11.11
|
||||
- pip
|
||||
- setuptools
|
||||
- zstd
|
||||
- zstandard
|
||||
run:
|
||||
- conda-forge::python ==3.11.11
|
||||
- compilers
|
||||
- cmake
|
||||
- zstd
|
||||
- zstandard
|
||||
- ninja
|
||||
- if: unix
|
||||
then:
|
||||
- make
|
||||
- sphinx
|
||||
- sphinx_rtd_theme
|
||||
- numpy
|
||||
- scipy
|
||||
- pandas
|
||||
- networkx
|
||||
- matplotlib
|
||||
- pint
|
||||
- pyserial
|
||||
- pyusb
|
||||
- pylibftdi
|
||||
- pymodbus
|
||||
- python-can
|
||||
- pyvisa
|
||||
- opencv
|
||||
- pydantic
|
||||
- fastapi
|
||||
- uvicorn
|
||||
- gradio
|
||||
- flask
|
||||
- websockets
|
||||
- ipython
|
||||
- jupyter
|
||||
- jupyros
|
||||
- colcon-common-extensions
|
||||
- robostack-staging::ros-humble-desktop-full
|
||||
- robostack-staging::ros-humble-control-msgs
|
||||
- robostack-staging::ros-humble-sensor-msgs
|
||||
- robostack-staging::ros-humble-trajectory-msgs
|
||||
- ros-humble-navigation2
|
||||
- ros-humble-ros2-control
|
||||
- ros-humble-robot-state-publisher
|
||||
- ros-humble-joint-state-publisher
|
||||
- ros-humble-rosbridge-server
|
||||
- ros-humble-cv-bridge
|
||||
- ros-humble-tf2
|
||||
- ros-humble-moveit
|
||||
- ros-humble-moveit-servo
|
||||
- ros-humble-simulation
|
||||
- ros-humble-tf-transformations
|
||||
- transforms3d
|
||||
- uni-lab::ros-humble-unilabos-msgs
|
||||
|
||||
about:
|
||||
repository: https://github.com/deepmodeling/Uni-Lab-OS
|
||||
license: GPL-3.0-only
|
||||
description: "Uni-Lab-OS"
|
||||
77
.github/workflows/ci-check.yml
vendored
77
.github/workflows/ci-check.yml
vendored
@@ -8,14 +8,19 @@ on:
|
||||
|
||||
jobs:
|
||||
registry-check:
|
||||
runs-on: ubuntu-latest
|
||||
runs-on: windows-latest
|
||||
|
||||
env:
|
||||
# Fix Unicode encoding issue on Windows runner (cp1252 -> utf-8)
|
||||
PYTHONIOENCODING: utf-8
|
||||
PYTHONUTF8: 1
|
||||
|
||||
defaults:
|
||||
run:
|
||||
shell: bash -l {0}
|
||||
shell: cmd
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v4
|
||||
- uses: actions/checkout@v6
|
||||
with:
|
||||
fetch-depth: 0
|
||||
|
||||
@@ -27,73 +32,31 @@ jobs:
|
||||
channels: robostack-staging,conda-forge,uni-lab
|
||||
channel-priority: flexible
|
||||
activate-environment: check-env
|
||||
auto-activate-base: false
|
||||
auto-update-conda: false
|
||||
show-channel-urls: true
|
||||
|
||||
- name: Install ROS dependencies and unilabos-msgs
|
||||
- name: Install ROS dependencies, uv and unilabos-msgs
|
||||
run: |
|
||||
# Install all packages together for proper dependency resolution
|
||||
# Use mamba for faster and more reliable solving
|
||||
mamba install -n check-env \
|
||||
python=3.11.14 \
|
||||
robostack-staging::ros-humble-ros-core \
|
||||
robostack-staging::ros-humble-action-msgs \
|
||||
robostack-staging::ros-humble-std-msgs \
|
||||
robostack-staging::ros-humble-geometry-msgs \
|
||||
robostack-staging::ros-humble-control-msgs \
|
||||
robostack-staging::ros-humble-nav2-msgs \
|
||||
uni-lab::ros-humble-unilabos-msgs \
|
||||
robostack-staging::ros-humble-cv-bridge \
|
||||
robostack-staging::ros-humble-vision-opencv \
|
||||
robostack-staging::ros-humble-tf-transformations \
|
||||
robostack-staging::ros-humble-moveit-msgs \
|
||||
robostack-staging::ros-humble-tf2-ros \
|
||||
robostack-staging::ros-humble-tf2-ros-py \
|
||||
conda-forge::transforms3d \
|
||||
-c robostack-staging -c conda-forge -c uni-lab -y
|
||||
echo Installing ROS dependencies...
|
||||
mamba install -n check-env conda-forge::uv conda-forge::opencv robostack-staging::ros-humble-ros-core robostack-staging::ros-humble-action-msgs robostack-staging::ros-humble-std-msgs robostack-staging::ros-humble-geometry-msgs robostack-staging::ros-humble-control-msgs robostack-staging::ros-humble-nav2-msgs uni-lab::ros-humble-unilabos-msgs robostack-staging::ros-humble-cv-bridge robostack-staging::ros-humble-vision-opencv robostack-staging::ros-humble-tf-transformations robostack-staging::ros-humble-moveit-msgs robostack-staging::ros-humble-tf2-ros robostack-staging::ros-humble-tf2-ros-py conda-forge::transforms3d -c robostack-staging -c conda-forge -c uni-lab -y
|
||||
|
||||
- name: Install pip dependencies and unilabos
|
||||
run: |
|
||||
# Activate the environment
|
||||
conda activate check-env
|
||||
|
||||
# Core dependencies for devices
|
||||
pip install uv
|
||||
uv pip install networkx \
|
||||
typing_extensions \
|
||||
websockets \
|
||||
msgcenterpy \
|
||||
opentrons_shared_data \
|
||||
pint \
|
||||
fastapi \
|
||||
jinja2 \
|
||||
requests \
|
||||
uvicorn \
|
||||
git+https://github.com/Xuwznln/pylabrobot.git \
|
||||
opencv-python \
|
||||
pyautogui \
|
||||
opcua \
|
||||
pyserial \
|
||||
pandas \
|
||||
crcmod-plus \
|
||||
pymodbus \
|
||||
pywinauto_recorder \
|
||||
matplotlib \
|
||||
|
||||
|
||||
# PyLabRobot (custom fork)
|
||||
pip install
|
||||
|
||||
# Install unilabos in editable mode
|
||||
pip install -e .
|
||||
call conda activate check-env
|
||||
echo Installing pip dependencies...
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
uv pip install pywinauto git+https://github.com/Xuwznln/pylabrobot.git
|
||||
uv pip uninstall enum34 || echo enum34 not installed, skipping
|
||||
uv pip install -e .
|
||||
|
||||
- name: Run check mode (complete_registry)
|
||||
run: |
|
||||
conda activate check-env
|
||||
call conda activate check-env
|
||||
echo Running check mode...
|
||||
python -m unilabos --check_mode --skip_env_check
|
||||
|
||||
- name: Check for uncommitted changes
|
||||
shell: bash
|
||||
run: |
|
||||
if ! git diff --exit-code; then
|
||||
echo "::error::检测到文件变化!请先在本地运行 'python -m unilabos --complete_registry' 并提交变更"
|
||||
|
||||
43
.github/workflows/conda-pack-build.yml
vendored
43
.github/workflows/conda-pack-build.yml
vendored
@@ -13,6 +13,11 @@ on:
|
||||
required: false
|
||||
default: 'win-64'
|
||||
type: string
|
||||
build_full:
|
||||
description: '是否构建完整版 unilabos-full (默认构建轻量版 unilabos)'
|
||||
required: false
|
||||
default: false
|
||||
type: boolean
|
||||
|
||||
jobs:
|
||||
build-conda-pack:
|
||||
@@ -57,7 +62,7 @@ jobs:
|
||||
echo "should_build=false" >> $GITHUB_OUTPUT
|
||||
fi
|
||||
|
||||
- uses: actions/checkout@v4
|
||||
- uses: actions/checkout@v6
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
with:
|
||||
ref: ${{ github.event.inputs.branch }}
|
||||
@@ -69,7 +74,7 @@ jobs:
|
||||
with:
|
||||
miniforge-version: latest
|
||||
use-mamba: true
|
||||
python-version: '3.11.11'
|
||||
python-version: '3.11.14'
|
||||
channels: conda-forge,robostack-staging,uni-lab,defaults
|
||||
channel-priority: flexible
|
||||
activate-environment: unilab
|
||||
@@ -81,7 +86,14 @@ jobs:
|
||||
run: |
|
||||
echo Installing unilabos and dependencies to unilab environment...
|
||||
echo Using mamba for faster and more reliable dependency resolution...
|
||||
mamba install -n unilab uni-lab::unilabos conda-pack -c uni-lab -c robostack-staging -c conda-forge -y
|
||||
echo Build full: ${{ github.event.inputs.build_full }}
|
||||
if "${{ github.event.inputs.build_full }}"=="true" (
|
||||
echo Installing unilabos-full ^(complete package^)...
|
||||
mamba install -n unilab uni-lab::unilabos-full conda-pack -c uni-lab -c robostack-staging -c conda-forge -y
|
||||
) else (
|
||||
echo Installing unilabos ^(minimal package^)...
|
||||
mamba install -n unilab uni-lab::unilabos conda-pack -c uni-lab -c robostack-staging -c conda-forge -y
|
||||
)
|
||||
|
||||
- name: Install conda-pack, unilabos and dependencies (Unix)
|
||||
if: steps.should_build.outputs.should_build == 'true' && matrix.platform != 'win-64'
|
||||
@@ -89,7 +101,14 @@ jobs:
|
||||
run: |
|
||||
echo "Installing unilabos and dependencies to unilab environment..."
|
||||
echo "Using mamba for faster and more reliable dependency resolution..."
|
||||
mamba install -n unilab uni-lab::unilabos conda-pack -c uni-lab -c robostack-staging -c conda-forge -y
|
||||
echo "Build full: ${{ github.event.inputs.build_full }}"
|
||||
if [[ "${{ github.event.inputs.build_full }}" == "true" ]]; then
|
||||
echo "Installing unilabos-full (complete package)..."
|
||||
mamba install -n unilab uni-lab::unilabos-full conda-pack -c uni-lab -c robostack-staging -c conda-forge -y
|
||||
else
|
||||
echo "Installing unilabos (minimal package)..."
|
||||
mamba install -n unilab uni-lab::unilabos conda-pack -c uni-lab -c robostack-staging -c conda-forge -y
|
||||
fi
|
||||
|
||||
- name: Get latest ros-humble-unilabos-msgs version (Windows)
|
||||
if: steps.should_build.outputs.should_build == 'true' && matrix.platform == 'win-64'
|
||||
@@ -293,7 +312,7 @@ jobs:
|
||||
|
||||
- name: Upload distribution package
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
uses: actions/upload-artifact@v4
|
||||
uses: actions/upload-artifact@v6
|
||||
with:
|
||||
name: unilab-pack-${{ matrix.platform }}-${{ github.event.inputs.branch }}
|
||||
path: dist-package/
|
||||
@@ -308,7 +327,12 @@ jobs:
|
||||
echo ==========================================
|
||||
echo Platform: ${{ matrix.platform }}
|
||||
echo Branch: ${{ github.event.inputs.branch }}
|
||||
echo Python version: 3.11.11
|
||||
echo Python version: 3.11.14
|
||||
if "${{ github.event.inputs.build_full }}"=="true" (
|
||||
echo Package: unilabos-full ^(complete^)
|
||||
) else (
|
||||
echo Package: unilabos ^(minimal^)
|
||||
)
|
||||
echo.
|
||||
echo Distribution package contents:
|
||||
dir dist-package
|
||||
@@ -328,7 +352,12 @@ jobs:
|
||||
echo "=========================================="
|
||||
echo "Platform: ${{ matrix.platform }}"
|
||||
echo "Branch: ${{ github.event.inputs.branch }}"
|
||||
echo "Python version: 3.11.11"
|
||||
echo "Python version: 3.11.14"
|
||||
if [[ "${{ github.event.inputs.build_full }}" == "true" ]]; then
|
||||
echo "Package: unilabos-full (complete)"
|
||||
else
|
||||
echo "Package: unilabos (minimal)"
|
||||
fi
|
||||
echo ""
|
||||
echo "Distribution package contents:"
|
||||
ls -lh dist-package/
|
||||
|
||||
37
.github/workflows/deploy-docs.yml
vendored
37
.github/workflows/deploy-docs.yml
vendored
@@ -1,10 +1,12 @@
|
||||
name: Deploy Docs
|
||||
|
||||
on:
|
||||
push:
|
||||
branches: [main]
|
||||
pull_request:
|
||||
# 在 CI Check 成功后自动触发(仅 main 分支)
|
||||
workflow_run:
|
||||
workflows: ["CI Check"]
|
||||
types: [completed]
|
||||
branches: [main]
|
||||
# 手动触发
|
||||
workflow_dispatch:
|
||||
inputs:
|
||||
branch:
|
||||
@@ -33,12 +35,19 @@ concurrency:
|
||||
jobs:
|
||||
# Build documentation
|
||||
build:
|
||||
# 只在以下情况运行:
|
||||
# 1. workflow_run 触发且 CI Check 成功
|
||||
# 2. 手动触发
|
||||
if: |
|
||||
github.event_name == 'workflow_dispatch' ||
|
||||
(github.event_name == 'workflow_run' && github.event.workflow_run.conclusion == 'success')
|
||||
runs-on: ubuntu-latest
|
||||
steps:
|
||||
- name: Checkout code
|
||||
uses: actions/checkout@v4
|
||||
uses: actions/checkout@v6
|
||||
with:
|
||||
ref: ${{ github.event.inputs.branch || github.ref }}
|
||||
# workflow_run 时使用触发工作流的分支,手动触发时使用输入的分支
|
||||
ref: ${{ github.event.workflow_run.head_branch || github.event.inputs.branch || github.ref }}
|
||||
fetch-depth: 0
|
||||
|
||||
- name: Setup Miniforge (with mamba)
|
||||
@@ -46,7 +55,7 @@ jobs:
|
||||
with:
|
||||
miniforge-version: latest
|
||||
use-mamba: true
|
||||
python-version: '3.11.11'
|
||||
python-version: '3.11.14'
|
||||
channels: conda-forge,robostack-staging,uni-lab,defaults
|
||||
channel-priority: flexible
|
||||
activate-environment: unilab
|
||||
@@ -75,8 +84,10 @@ jobs:
|
||||
|
||||
- name: Setup Pages
|
||||
id: pages
|
||||
uses: actions/configure-pages@v4
|
||||
if: github.ref == 'refs/heads/main' || (github.event_name == 'workflow_dispatch' && github.event.inputs.deploy_to_pages == 'true')
|
||||
uses: actions/configure-pages@v5
|
||||
if: |
|
||||
github.event.workflow_run.head_branch == 'main' ||
|
||||
(github.event_name == 'workflow_dispatch' && github.event.inputs.deploy_to_pages == 'true')
|
||||
|
||||
- name: Build Sphinx documentation
|
||||
run: |
|
||||
@@ -94,14 +105,18 @@ jobs:
|
||||
test -f docs/_build/html/index.html && echo "✓ index.html exists" || echo "✗ index.html missing"
|
||||
|
||||
- name: Upload build artifacts
|
||||
uses: actions/upload-pages-artifact@v3
|
||||
if: github.ref == 'refs/heads/main' || (github.event_name == 'workflow_dispatch' && github.event.inputs.deploy_to_pages == 'true')
|
||||
uses: actions/upload-pages-artifact@v4
|
||||
if: |
|
||||
github.event.workflow_run.head_branch == 'main' ||
|
||||
(github.event_name == 'workflow_dispatch' && github.event.inputs.deploy_to_pages == 'true')
|
||||
with:
|
||||
path: docs/_build/html
|
||||
|
||||
# Deploy to GitHub Pages
|
||||
deploy:
|
||||
if: github.ref == 'refs/heads/main' || (github.event_name == 'workflow_dispatch' && github.event.inputs.deploy_to_pages == 'true')
|
||||
if: |
|
||||
github.event.workflow_run.head_branch == 'main' ||
|
||||
(github.event_name == 'workflow_dispatch' && github.event.inputs.deploy_to_pages == 'true')
|
||||
environment:
|
||||
name: github-pages
|
||||
url: ${{ steps.deployment.outputs.page_url }}
|
||||
|
||||
46
.github/workflows/multi-platform-build.yml
vendored
46
.github/workflows/multi-platform-build.yml
vendored
@@ -1,11 +1,16 @@
|
||||
name: Multi-Platform Conda Build
|
||||
|
||||
on:
|
||||
# 在 CI Check 工作流完成后触发(仅限 main/dev 分支)
|
||||
workflow_run:
|
||||
workflows: ["CI Check"]
|
||||
types:
|
||||
- completed
|
||||
branches: [main, dev]
|
||||
# 支持 tag 推送(不依赖 CI Check)
|
||||
push:
|
||||
branches: [main, dev]
|
||||
tags: ['v*']
|
||||
pull_request:
|
||||
branches: [main, dev]
|
||||
# 手动触发
|
||||
workflow_dispatch:
|
||||
inputs:
|
||||
platforms:
|
||||
@@ -17,9 +22,37 @@ on:
|
||||
required: false
|
||||
default: false
|
||||
type: boolean
|
||||
skip_ci_check:
|
||||
description: '跳过等待 CI Check (手动触发时可选)'
|
||||
required: false
|
||||
default: false
|
||||
type: boolean
|
||||
|
||||
jobs:
|
||||
# 等待 CI Check 完成的 job (仅用于 workflow_run 触发)
|
||||
wait-for-ci:
|
||||
runs-on: ubuntu-latest
|
||||
if: github.event_name == 'workflow_run'
|
||||
outputs:
|
||||
should_continue: ${{ steps.check.outputs.should_continue }}
|
||||
steps:
|
||||
- name: Check CI status
|
||||
id: check
|
||||
run: |
|
||||
if [[ "${{ github.event.workflow_run.conclusion }}" == "success" ]]; then
|
||||
echo "should_continue=true" >> $GITHUB_OUTPUT
|
||||
echo "CI Check passed, proceeding with build"
|
||||
else
|
||||
echo "should_continue=false" >> $GITHUB_OUTPUT
|
||||
echo "CI Check did not succeed (status: ${{ github.event.workflow_run.conclusion }}), skipping build"
|
||||
fi
|
||||
|
||||
build:
|
||||
needs: [wait-for-ci]
|
||||
# 运行条件:workflow_run 触发且 CI 成功,或者其他触发方式
|
||||
if: |
|
||||
always() &&
|
||||
(needs.wait-for-ci.result == 'skipped' || needs.wait-for-ci.outputs.should_continue == 'true')
|
||||
strategy:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
@@ -44,8 +77,10 @@ jobs:
|
||||
shell: bash -l {0}
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v4
|
||||
- uses: actions/checkout@v6
|
||||
with:
|
||||
# 如果是 workflow_run 触发,使用触发 CI Check 的 commit
|
||||
ref: ${{ github.event.workflow_run.head_sha || github.ref }}
|
||||
fetch-depth: 0
|
||||
|
||||
- name: Check if platform should be built
|
||||
@@ -69,7 +104,6 @@ jobs:
|
||||
channels: conda-forge,robostack-staging,defaults
|
||||
channel-priority: strict
|
||||
activate-environment: build-env
|
||||
auto-activate-base: false
|
||||
auto-update-conda: false
|
||||
show-channel-urls: true
|
||||
|
||||
@@ -115,7 +149,7 @@ jobs:
|
||||
|
||||
- name: Upload conda package artifacts
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
uses: actions/upload-artifact@v4
|
||||
uses: actions/upload-artifact@v6
|
||||
with:
|
||||
name: conda-package-${{ matrix.platform }}
|
||||
path: conda-packages-temp
|
||||
|
||||
113
.github/workflows/unilabos-conda-build.yml
vendored
113
.github/workflows/unilabos-conda-build.yml
vendored
@@ -1,25 +1,62 @@
|
||||
name: UniLabOS Conda Build
|
||||
|
||||
on:
|
||||
# 在 CI Check 成功后自动触发
|
||||
workflow_run:
|
||||
workflows: ["CI Check"]
|
||||
types: [completed]
|
||||
branches: [main, dev]
|
||||
# 标签推送时直接触发(发布版本)
|
||||
push:
|
||||
branches: [main, dev]
|
||||
tags: ['v*']
|
||||
pull_request:
|
||||
branches: [main, dev]
|
||||
# 手动触发
|
||||
workflow_dispatch:
|
||||
inputs:
|
||||
platforms:
|
||||
description: '选择构建平台 (逗号分隔): linux-64, osx-64, osx-arm64, win-64'
|
||||
required: false
|
||||
default: 'linux-64'
|
||||
build_full:
|
||||
description: '是否构建 unilabos-full 完整包 (默认只构建 unilabos 基础包)'
|
||||
required: false
|
||||
default: false
|
||||
type: boolean
|
||||
upload_to_anaconda:
|
||||
description: '是否上传到Anaconda.org'
|
||||
required: false
|
||||
default: false
|
||||
type: boolean
|
||||
skip_ci_check:
|
||||
description: '跳过等待 CI Check (手动触发时可选)'
|
||||
required: false
|
||||
default: false
|
||||
type: boolean
|
||||
|
||||
jobs:
|
||||
# 等待 CI Check 完成的 job (仅用于 workflow_run 触发)
|
||||
wait-for-ci:
|
||||
runs-on: ubuntu-latest
|
||||
if: github.event_name == 'workflow_run'
|
||||
outputs:
|
||||
should_continue: ${{ steps.check.outputs.should_continue }}
|
||||
steps:
|
||||
- name: Check CI status
|
||||
id: check
|
||||
run: |
|
||||
if [[ "${{ github.event.workflow_run.conclusion }}" == "success" ]]; then
|
||||
echo "should_continue=true" >> $GITHUB_OUTPUT
|
||||
echo "CI Check passed, proceeding with build"
|
||||
else
|
||||
echo "should_continue=false" >> $GITHUB_OUTPUT
|
||||
echo "CI Check did not succeed (status: ${{ github.event.workflow_run.conclusion }}), skipping build"
|
||||
fi
|
||||
|
||||
build:
|
||||
needs: [wait-for-ci]
|
||||
# 运行条件:workflow_run 触发且 CI 成功,或者其他触发方式
|
||||
if: |
|
||||
always() &&
|
||||
(needs.wait-for-ci.result == 'skipped' || needs.wait-for-ci.outputs.should_continue == 'true')
|
||||
strategy:
|
||||
fail-fast: false
|
||||
matrix:
|
||||
@@ -40,8 +77,10 @@ jobs:
|
||||
shell: bash -l {0}
|
||||
|
||||
steps:
|
||||
- uses: actions/checkout@v4
|
||||
- uses: actions/checkout@v6
|
||||
with:
|
||||
# 如果是 workflow_run 触发,使用触发 CI Check 的 commit
|
||||
ref: ${{ github.event.workflow_run.head_sha || github.ref }}
|
||||
fetch-depth: 0
|
||||
|
||||
- name: Check if platform should be built
|
||||
@@ -65,7 +104,6 @@ jobs:
|
||||
channels: conda-forge,robostack-staging,uni-lab,defaults
|
||||
channel-priority: strict
|
||||
activate-environment: build-env
|
||||
auto-activate-base: false
|
||||
auto-update-conda: false
|
||||
show-channel-urls: true
|
||||
|
||||
@@ -81,12 +119,61 @@ jobs:
|
||||
conda list | grep -E "(rattler-build|anaconda-client)"
|
||||
echo "Platform: ${{ matrix.platform }}"
|
||||
echo "OS: ${{ matrix.os }}"
|
||||
echo "Building UniLabOS package"
|
||||
echo "Build full package: ${{ github.event.inputs.build_full || 'false' }}"
|
||||
echo "Building packages:"
|
||||
echo " - unilabos-env (environment dependencies)"
|
||||
echo " - unilabos (with pip package)"
|
||||
if [[ "${{ github.event.inputs.build_full }}" == "true" ]]; then
|
||||
echo " - unilabos-full (complete package)"
|
||||
fi
|
||||
|
||||
- name: Build conda package
|
||||
- name: Build unilabos-env (conda environment only, noarch)
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
run: |
|
||||
rattler-build build -r .conda/recipe.yaml -c uni-lab -c robostack-staging -c conda-forge
|
||||
echo "Building unilabos-env (conda environment dependencies)..."
|
||||
rattler-build build -r .conda/environment/recipe.yaml -c uni-lab -c robostack-staging -c conda-forge
|
||||
|
||||
- name: Upload unilabos-env to Anaconda.org (if enabled)
|
||||
if: steps.should_build.outputs.should_build == 'true' && github.event.inputs.upload_to_anaconda == 'true'
|
||||
run: |
|
||||
echo "Uploading unilabos-env to uni-lab organization..."
|
||||
for package in $(find ./output -name "unilabos-env*.conda"); do
|
||||
anaconda -t ${{ secrets.ANACONDA_API_TOKEN }} upload --user uni-lab --force "$package"
|
||||
done
|
||||
|
||||
- name: Build unilabos (with pip package)
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
run: |
|
||||
echo "Building unilabos package..."
|
||||
# 如果已上传到 Anaconda,从 uni-lab channel 获取 unilabos-env;否则从本地 output 获取
|
||||
rattler-build build -r .conda/base/recipe.yaml -c uni-lab -c robostack-staging -c conda-forge --channel ./output
|
||||
|
||||
- name: Upload unilabos to Anaconda.org (if enabled)
|
||||
if: steps.should_build.outputs.should_build == 'true' && github.event.inputs.upload_to_anaconda == 'true'
|
||||
run: |
|
||||
echo "Uploading unilabos to uni-lab organization..."
|
||||
for package in $(find ./output -name "unilabos-0*.conda" -o -name "unilabos-[0-9]*.conda"); do
|
||||
anaconda -t ${{ secrets.ANACONDA_API_TOKEN }} upload --user uni-lab --force "$package"
|
||||
done
|
||||
|
||||
- name: Build unilabos-full - Only when explicitly requested
|
||||
if: |
|
||||
steps.should_build.outputs.should_build == 'true' &&
|
||||
github.event.inputs.build_full == 'true'
|
||||
run: |
|
||||
echo "Building unilabos-full package on ${{ matrix.platform }}..."
|
||||
rattler-build build -r .conda/full/recipe.yaml -c uni-lab -c robostack-staging -c conda-forge --channel ./output
|
||||
|
||||
- name: Upload unilabos-full to Anaconda.org (if enabled)
|
||||
if: |
|
||||
steps.should_build.outputs.should_build == 'true' &&
|
||||
github.event.inputs.build_full == 'true' &&
|
||||
github.event.inputs.upload_to_anaconda == 'true'
|
||||
run: |
|
||||
echo "Uploading unilabos-full to uni-lab organization..."
|
||||
for package in $(find ./output -name "unilabos-full*.conda"); do
|
||||
anaconda -t ${{ secrets.ANACONDA_API_TOKEN }} upload --user uni-lab --force "$package"
|
||||
done
|
||||
|
||||
- name: List built packages
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
@@ -108,17 +195,9 @@ jobs:
|
||||
|
||||
- name: Upload conda package artifacts
|
||||
if: steps.should_build.outputs.should_build == 'true'
|
||||
uses: actions/upload-artifact@v4
|
||||
uses: actions/upload-artifact@v6
|
||||
with:
|
||||
name: conda-package-unilabos-${{ matrix.platform }}
|
||||
path: conda-packages-temp
|
||||
if-no-files-found: warn
|
||||
retention-days: 30
|
||||
|
||||
- name: Upload to Anaconda.org (uni-lab organization)
|
||||
if: github.event.inputs.upload_to_anaconda == 'true'
|
||||
run: |
|
||||
for package in $(find ./output -name "*.conda"); do
|
||||
echo "Uploading $package to uni-lab organization..."
|
||||
anaconda -t ${{ secrets.ANACONDA_API_TOKEN }} upload --user uni-lab --force "$package"
|
||||
done
|
||||
|
||||
@@ -1,4 +1,5 @@
|
||||
recursive-include unilabos/test *
|
||||
recursive-include unilabos/utils *
|
||||
recursive-include unilabos/registry *.yaml
|
||||
recursive-include unilabos/app/web/static *
|
||||
recursive-include unilabos/app/web/templates *
|
||||
|
||||
38
README.md
38
README.md
@@ -31,26 +31,46 @@ Detailed documentation can be found at:
|
||||
|
||||
## Quick Start
|
||||
|
||||
1. Setup Conda Environment
|
||||
### 1. Setup Conda Environment
|
||||
|
||||
Uni-Lab-OS recommends using `mamba` for environment management:
|
||||
Uni-Lab-OS recommends using `mamba` for environment management. Choose the package that fits your needs:
|
||||
|
||||
| Package | Use Case | Contents |
|
||||
|---------|----------|----------|
|
||||
| `unilabos` | **Recommended for most users** | Complete package, ready to use |
|
||||
| `unilabos-env` | Developers (editable install) | Environment only, install unilabos via pip |
|
||||
| `unilabos-full` | Simulation/Visualization | unilabos + ROS2 Desktop + Gazebo + MoveIt |
|
||||
|
||||
```bash
|
||||
# Create new environment
|
||||
mamba create -n unilab python=3.11.11
|
||||
mamba create -n unilab python=3.11.14
|
||||
mamba activate unilab
|
||||
mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# Option A: Standard installation (recommended for most users)
|
||||
mamba install uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# Option B: For developers (editable mode development)
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
# Then install unilabos and dependencies:
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git && cd Uni-Lab-OS
|
||||
pip install -e .
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
|
||||
# Option C: Full installation (simulation/visualization)
|
||||
mamba install uni-lab::unilabos-full -c robostack-staging -c conda-forge
|
||||
```
|
||||
|
||||
2. Install Dev Uni-Lab-OS
|
||||
**When to use which?**
|
||||
- **unilabos**: Standard installation for production deployment and general usage (recommended)
|
||||
- **unilabos-env**: For developers who need `pip install -e .` editable mode, modify source code
|
||||
- **unilabos-full**: For simulation (Gazebo), visualization (rviz2), and Jupyter notebooks
|
||||
|
||||
### 2. Clone Repository (Optional, for developers)
|
||||
|
||||
```bash
|
||||
# Clone the repository
|
||||
# Clone the repository (only needed for development or examples)
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git
|
||||
cd Uni-Lab-OS
|
||||
|
||||
# Install Uni-Lab-OS
|
||||
pip install .
|
||||
```
|
||||
|
||||
3. Start Uni-Lab System
|
||||
|
||||
38
README_zh.md
38
README_zh.md
@@ -31,26 +31,46 @@ Uni-Lab-OS 是一个用于实验室自动化的综合平台,旨在连接和控
|
||||
|
||||
## 快速开始
|
||||
|
||||
1. 配置 Conda 环境
|
||||
### 1. 配置 Conda 环境
|
||||
|
||||
Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适当的环境文件:
|
||||
Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的需求选择合适的安装包:
|
||||
|
||||
| 安装包 | 适用场景 | 包含内容 |
|
||||
|--------|----------|----------|
|
||||
| `unilabos` | **推荐大多数用户** | 完整安装包,开箱即用 |
|
||||
| `unilabos-env` | 开发者(可编辑安装) | 仅环境依赖,通过 pip 安装 unilabos |
|
||||
| `unilabos-full` | 仿真/可视化 | unilabos + ROS2 桌面版 + Gazebo + MoveIt |
|
||||
|
||||
```bash
|
||||
# 创建新环境
|
||||
mamba create -n unilab python=3.11.11
|
||||
mamba create -n unilab python=3.11.14
|
||||
mamba activate unilab
|
||||
mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# 方案 A:标准安装(推荐大多数用户)
|
||||
mamba install uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# 方案 B:开发者环境(可编辑模式开发)
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
# 然后安装 unilabos 和依赖:
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git && cd Uni-Lab-OS
|
||||
pip install -e .
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
|
||||
# 方案 C:完整安装(仿真/可视化)
|
||||
mamba install uni-lab::unilabos-full -c robostack-staging -c conda-forge
|
||||
```
|
||||
|
||||
2. 安装开发版 Uni-Lab-OS:
|
||||
**如何选择?**
|
||||
- **unilabos**:标准安装,适用于生产部署和日常使用(推荐)
|
||||
- **unilabos-env**:开发者使用,支持 `pip install -e .` 可编辑模式,可修改源代码
|
||||
- **unilabos-full**:需要仿真(Gazebo)、可视化(rviz2)或 Jupyter Notebook
|
||||
|
||||
### 2. 克隆仓库(可选,供开发者使用)
|
||||
|
||||
```bash
|
||||
# 克隆仓库
|
||||
# 克隆仓库(仅开发或查看示例时需要)
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git
|
||||
cd Uni-Lab-OS
|
||||
|
||||
# 安装 Uni-Lab-OS
|
||||
pip install .
|
||||
```
|
||||
|
||||
3. 启动 Uni-Lab 系统
|
||||
|
||||
@@ -31,6 +31,14 @@
|
||||
|
||||
详细的安装步骤请参考 [安装指南](installation.md)。
|
||||
|
||||
**选择合适的安装包:**
|
||||
|
||||
| 安装包 | 适用场景 | 包含组件 |
|
||||
|--------|----------|----------|
|
||||
| `unilabos` | **推荐大多数用户**,生产部署 | 完整安装包,开箱即用 |
|
||||
| `unilabos-env` | 开发者(可编辑安装) | 仅环境依赖,通过 pip 安装 unilabos |
|
||||
| `unilabos-full` | 仿真/可视化 | unilabos + 完整 ROS2 桌面版 + Gazebo + MoveIt |
|
||||
|
||||
**关键步骤:**
|
||||
|
||||
```bash
|
||||
@@ -38,15 +46,30 @@
|
||||
# 下载 Miniforge: https://github.com/conda-forge/miniforge/releases
|
||||
|
||||
# 2. 创建 Conda 环境
|
||||
mamba create -n unilab python=3.11.11
|
||||
mamba create -n unilab python=3.11.14
|
||||
|
||||
# 3. 激活环境
|
||||
mamba activate unilab
|
||||
|
||||
# 4. 安装 Uni-Lab-OS
|
||||
# 4. 安装 Uni-Lab-OS(选择其一)
|
||||
|
||||
# 方案 A:标准安装(推荐大多数用户)
|
||||
mamba install uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# 方案 B:开发者环境(可编辑模式开发)
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
pip install -e /path/to/Uni-Lab-OS # 可编辑安装
|
||||
uv pip install -r unilabos/utils/requirements.txt # 安装 pip 依赖
|
||||
|
||||
# 方案 C:完整版(仿真/可视化)
|
||||
mamba install uni-lab::unilabos-full -c robostack-staging -c conda-forge
|
||||
```
|
||||
|
||||
**选择建议:**
|
||||
- **日常使用/生产部署**:使用 `unilabos`(推荐),完整功能,开箱即用
|
||||
- **开发者**:使用 `unilabos-env` + `pip install -e .` + `uv pip install -r unilabos/utils/requirements.txt`,代码修改立即生效
|
||||
- **仿真/可视化**:使用 `unilabos-full`,含 Gazebo、rviz2、MoveIt
|
||||
|
||||
#### 1.2 验证安装
|
||||
|
||||
```bash
|
||||
@@ -768,7 +791,43 @@ Waiting for host service...
|
||||
|
||||
详细的设备驱动编写指南请参考 [添加设备驱动](../developer_guide/add_device.md)。
|
||||
|
||||
#### 9.1 为什么需要自定义设备?
|
||||
#### 9.1 开发环境准备
|
||||
|
||||
**推荐使用 `unilabos-env` + `pip install -e .` + `uv pip install`** 进行设备开发:
|
||||
|
||||
```bash
|
||||
# 1. 创建环境并安装 unilabos-env(ROS2 + conda 依赖 + uv)
|
||||
mamba create -n unilab python=3.11.14
|
||||
conda activate unilab
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
|
||||
# 2. 克隆代码
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git
|
||||
cd Uni-Lab-OS
|
||||
|
||||
# 3. 以可编辑模式安装(推荐使用脚本,自动检测中文环境)
|
||||
python scripts/dev_install.py
|
||||
|
||||
# 或手动安装:
|
||||
pip install -e .
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
```
|
||||
|
||||
**为什么使用这种方式?**
|
||||
- `unilabos-env` 提供 ROS2 核心组件和 uv(通过 conda 安装,避免编译)
|
||||
- `unilabos/utils/requirements.txt` 包含所有运行时需要的 pip 依赖
|
||||
- `dev_install.py` 自动检测中文环境,中文系统自动使用清华镜像
|
||||
- 使用 `uv` 替代 `pip`,安装速度更快
|
||||
- 可编辑模式:代码修改**立即生效**,无需重新安装
|
||||
|
||||
**如果安装失败或速度太慢**,可以手动执行(使用清华镜像):
|
||||
|
||||
```bash
|
||||
pip install -e . -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
uv pip install -r unilabos/utils/requirements.txt -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
```
|
||||
|
||||
#### 9.2 为什么需要自定义设备?
|
||||
|
||||
Uni-Lab-OS 内置了常见设备,但您的实验室可能有特殊设备需要集成:
|
||||
|
||||
@@ -777,7 +836,7 @@ Uni-Lab-OS 内置了常见设备,但您的实验室可能有特殊设备需要
|
||||
- 特殊的实验流程
|
||||
- 第三方设备集成
|
||||
|
||||
#### 9.2 创建 Python 包
|
||||
#### 9.3 创建 Python 包
|
||||
|
||||
为了方便开发和管理,建议为您的实验室创建独立的 Python 包。
|
||||
|
||||
@@ -814,7 +873,7 @@ touch my_lab_devices/my_lab_devices/__init__.py
|
||||
touch my_lab_devices/my_lab_devices/devices/__init__.py
|
||||
```
|
||||
|
||||
#### 9.3 创建 setup.py
|
||||
#### 9.4 创建 setup.py
|
||||
|
||||
```python
|
||||
# my_lab_devices/setup.py
|
||||
@@ -845,7 +904,7 @@ setup(
|
||||
)
|
||||
```
|
||||
|
||||
#### 9.4 开发安装
|
||||
#### 9.5 开发安装
|
||||
|
||||
使用 `-e` 参数进行可编辑安装,这样代码修改后立即生效:
|
||||
|
||||
@@ -860,7 +919,7 @@ pip install -e . -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
- 方便调试和测试
|
||||
- 支持版本控制(git)
|
||||
|
||||
#### 9.5 编写设备驱动
|
||||
#### 9.6 编写设备驱动
|
||||
|
||||
创建设备驱动文件:
|
||||
|
||||
@@ -1001,7 +1060,7 @@ class MyPump:
|
||||
- **返回 Dict**:所有动作方法返回字典类型
|
||||
- **文档字符串**:详细说明参数和功能
|
||||
|
||||
#### 9.6 测试设备驱动
|
||||
#### 9.7 测试设备驱动
|
||||
|
||||
创建简单的测试脚本:
|
||||
|
||||
|
||||
@@ -13,15 +13,26 @@
|
||||
- 开发者需要 Git 和基本的 Python 开发知识
|
||||
- 自定义 msgs 需要 GitHub 账号
|
||||
|
||||
## 安装包选择
|
||||
|
||||
Uni-Lab-OS 提供三个安装包版本,根据您的需求选择:
|
||||
|
||||
| 安装包 | 适用场景 | 包含组件 | 磁盘占用 |
|
||||
|--------|----------|----------|----------|
|
||||
| **unilabos** | **推荐大多数用户**,生产部署 | 完整安装包,开箱即用 | ~2-3 GB |
|
||||
| **unilabos-env** | 开发者环境(可编辑安装) | 仅环境依赖,通过 pip 安装 unilabos | ~2 GB |
|
||||
| **unilabos-full** | 仿真可视化、完整功能体验 | unilabos + 完整 ROS2 桌面版 + Gazebo + MoveIt | ~8-10 GB |
|
||||
|
||||
## 安装方式选择
|
||||
|
||||
根据您的使用场景,选择合适的安装方式:
|
||||
|
||||
| 安装方式 | 适用人群 | 特点 | 安装时间 |
|
||||
| ---------------------- | -------------------- | ------------------------------ | ---------------------------- |
|
||||
| **方式一:一键安装** | 实验室用户、快速体验 | 预打包环境,离线可用,无需配置 | 5-10 分钟 (网络良好的情况下) |
|
||||
| **方式二:手动安装** | 标准用户、生产环境 | 灵活配置,版本可控 | 10-20 分钟 |
|
||||
| **方式三:开发者安装** | 开发者、需要修改源码 | 可编辑模式,支持自定义 msgs | 20-30 分钟 |
|
||||
| 安装方式 | 适用人群 | 推荐安装包 | 特点 | 安装时间 |
|
||||
| ---------------------- | -------------------- | ----------------- | ------------------------------ | ---------------------------- |
|
||||
| **方式一:一键安装** | 快速体验、演示 | 预打包环境 | 离线可用,无需配置 | 5-10 分钟 (网络良好的情况下) |
|
||||
| **方式二:手动安装** | **大多数用户** | `unilabos` | 完整功能,开箱即用 | 10-20 分钟 |
|
||||
| **方式三:开发者安装** | 开发者、需要修改源码 | `unilabos-env` | 可编辑模式,支持自定义开发 | 20-30 分钟 |
|
||||
| **仿真/可视化** | 仿真测试、可视化调试 | `unilabos-full` | 含 Gazebo、rviz2、MoveIt | 30-60 分钟 |
|
||||
|
||||
---
|
||||
|
||||
@@ -144,17 +155,38 @@ bash Miniforge3-$(uname)-$(uname -m).sh
|
||||
使用以下命令创建 Uni-Lab 专用环境:
|
||||
|
||||
```bash
|
||||
mamba create -n unilab python=3.11.11 # 目前ros2组件依赖版本大多为3.11.11
|
||||
mamba create -n unilab python=3.11.14 # 目前ros2组件依赖版本大多为3.11.14
|
||||
mamba activate unilab
|
||||
mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# 选择安装包(三选一):
|
||||
|
||||
# 方案 A:标准安装(推荐大多数用户)
|
||||
mamba install uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
|
||||
# 方案 B:开发者环境(可编辑模式开发)
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
# 然后安装 unilabos 和 pip 依赖:
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git && cd Uni-Lab-OS
|
||||
pip install -e .
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
|
||||
# 方案 C:完整版(含仿真和可视化工具)
|
||||
mamba install uni-lab::unilabos-full -c robostack-staging -c conda-forge
|
||||
```
|
||||
|
||||
**参数说明**:
|
||||
|
||||
- `-n unilab`: 创建名为 "unilab" 的环境
|
||||
- `uni-lab::unilabos`: 从 uni-lab channel 安装 unilabos 包
|
||||
- `uni-lab::unilabos`: 安装 unilabos 完整包,开箱即用(推荐)
|
||||
- `uni-lab::unilabos-env`: 仅安装环境依赖,适合开发者使用 `pip install -e .`
|
||||
- `uni-lab::unilabos-full`: 安装完整包(含 ROS2 Desktop、Gazebo、MoveIt 等)
|
||||
- `-c robostack-staging -c conda-forge`: 添加额外的软件源
|
||||
|
||||
**包选择建议**:
|
||||
- **日常使用/生产部署**:安装 `unilabos`(推荐,完整功能,开箱即用)
|
||||
- **开发者**:安装 `unilabos-env`,然后使用 `uv pip install -r unilabos/utils/requirements.txt` 安装依赖,再 `pip install -e .` 进行可编辑安装
|
||||
- **仿真/可视化**:安装 `unilabos-full`(Gazebo、rviz2、MoveIt)
|
||||
|
||||
**如果遇到网络问题**,可以使用清华镜像源加速下载:
|
||||
|
||||
```bash
|
||||
@@ -163,8 +195,14 @@ mamba config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/m
|
||||
mamba config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free/
|
||||
mamba config --add channels https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge/
|
||||
|
||||
# 然后重新执行安装命令
|
||||
# 然后重新执行安装命令(推荐标准安装)
|
||||
mamba create -n unilab uni-lab::unilabos -c robostack-staging
|
||||
|
||||
# 或完整版(仿真/可视化)
|
||||
mamba create -n unilab uni-lab::unilabos-full -c robostack-staging
|
||||
|
||||
# pip 安装时使用清华镜像(开发者安装时使用)
|
||||
uv pip install -r unilabos/utils/requirements.txt -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
```
|
||||
|
||||
### 第三步:激活环境
|
||||
@@ -203,58 +241,87 @@ cd Uni-Lab-OS
|
||||
cd Uni-Lab-OS
|
||||
```
|
||||
|
||||
### 第二步:安装基础环境
|
||||
### 第二步:安装开发环境(unilabos-env)
|
||||
|
||||
**推荐方式**:先通过**方式一(一键安装)**或**方式二(手动安装)**完成基础环境的安装,这将包含所有必需的依赖项(ROS2、msgs 等)。
|
||||
|
||||
#### 选项 A:通过一键安装(推荐)
|
||||
|
||||
参考上文"方式一:一键安装",完成基础环境的安装后,激活环境:
|
||||
**重要**:开发者请使用 `unilabos-env` 包,它专为开发者设计:
|
||||
- 包含 ROS2 核心组件和消息包(ros-humble-ros-core、std-msgs、geometry-msgs 等)
|
||||
- 包含 transforms3d、cv-bridge、tf2 等 conda 依赖
|
||||
- 包含 `uv` 工具,用于快速安装 pip 依赖
|
||||
- **不包含** pip 依赖和 unilabos 包(由 `pip install -e .` 和 `uv pip install` 安装)
|
||||
|
||||
```bash
|
||||
# 创建并激活环境
|
||||
mamba create -n unilab python=3.11.14
|
||||
conda activate unilab
|
||||
|
||||
# 安装开发者环境包(ROS2 + conda 依赖 + uv)
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
```
|
||||
|
||||
#### 选项 B:通过手动安装
|
||||
### 第三步:安装 pip 依赖和可编辑模式安装
|
||||
|
||||
参考上文"方式二:手动安装",创建并安装环境:
|
||||
|
||||
```bash
|
||||
mamba create -n unilab python=3.11.11
|
||||
conda activate unilab
|
||||
mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
```
|
||||
|
||||
**说明**:这会安装包括 Python 3.11.11、ROS2 Humble、ros-humble-unilabos-msgs 和所有必需依赖
|
||||
|
||||
### 第三步:切换到开发版本
|
||||
|
||||
现在你已经有了一个完整可用的 Uni-Lab 环境,接下来将 unilabos 包切换为开发版本:
|
||||
克隆代码并安装依赖:
|
||||
|
||||
```bash
|
||||
# 确保环境已激活
|
||||
conda activate unilab
|
||||
|
||||
# 卸载 pip 安装的 unilabos(保留所有 conda 依赖)
|
||||
pip uninstall unilabos -y
|
||||
|
||||
# 克隆 dev 分支(如果还未克隆)
|
||||
cd /path/to/your/workspace
|
||||
git clone -b dev https://github.com/deepmodeling/Uni-Lab-OS.git
|
||||
# 或者如果已经克隆,切换到 dev 分支
|
||||
# 克隆仓库(如果还未克隆)
|
||||
git clone https://github.com/deepmodeling/Uni-Lab-OS.git
|
||||
cd Uni-Lab-OS
|
||||
|
||||
# 切换到 dev 分支(可选)
|
||||
git checkout dev
|
||||
git pull
|
||||
|
||||
# 以可编辑模式安装开发版 unilabos
|
||||
pip install -e . -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
```
|
||||
|
||||
**参数说明**:
|
||||
**推荐:使用安装脚本**(自动检测中文环境,使用 uv 加速):
|
||||
|
||||
- `-e`: editable mode(可编辑模式),代码修改立即生效,无需重新安装
|
||||
- `-i`: 使用清华镜像源加速下载
|
||||
- `pip uninstall unilabos`: 只卸载 pip 安装的 unilabos 包,不影响 conda 安装的其他依赖(如 ROS2、msgs 等)
|
||||
```bash
|
||||
# 自动检测中文环境,如果是中文系统则使用清华镜像
|
||||
python scripts/dev_install.py
|
||||
|
||||
# 或者手动指定:
|
||||
python scripts/dev_install.py --china # 强制使用清华镜像
|
||||
python scripts/dev_install.py --no-mirror # 强制使用 PyPI
|
||||
python scripts/dev_install.py --skip-deps # 跳过 pip 依赖安装
|
||||
python scripts/dev_install.py --use-pip # 使用 pip 而非 uv
|
||||
```
|
||||
|
||||
**手动安装**(如果脚本安装失败或速度太慢):
|
||||
|
||||
```bash
|
||||
# 1. 安装 unilabos(可编辑模式)
|
||||
pip install -e .
|
||||
|
||||
# 2. 使用 uv 安装 pip 依赖(推荐,速度更快)
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
|
||||
# 国内用户使用清华镜像:
|
||||
pip install -e . -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
uv pip install -r unilabos/utils/requirements.txt -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
```
|
||||
|
||||
**注意**:
|
||||
- `uv` 已包含在 `unilabos-env` 中,无需单独安装
|
||||
- `unilabos/utils/requirements.txt` 包含运行 unilabos 所需的所有 pip 依赖
|
||||
- 部分特殊包(如 pylabrobot)会在运行时由 unilabos 自动检测并安装
|
||||
|
||||
**为什么使用可编辑模式?**
|
||||
|
||||
- `-e` (editable mode):代码修改**立即生效**,无需重新安装
|
||||
- 适合开发调试:修改代码后直接运行测试
|
||||
- 与 `unilabos-env` 配合:环境依赖由 conda 管理,unilabos 代码由 pip 管理
|
||||
|
||||
**验证安装**:
|
||||
|
||||
```bash
|
||||
# 检查 unilabos 版本
|
||||
python -c "import unilabos; print(unilabos.__version__)"
|
||||
|
||||
# 检查安装位置(应该指向你的代码目录)
|
||||
pip show unilabos | grep Location
|
||||
```
|
||||
|
||||
### 第四步:安装或自定义 ros-humble-unilabos-msgs(可选)
|
||||
|
||||
@@ -464,7 +531,45 @@ cd $CONDA_PREFIX/envs/unilab
|
||||
|
||||
### 问题 8: 环境很大,有办法减小吗?
|
||||
|
||||
**解决方案**: 预打包的环境包含所有依赖,通常较大(压缩后 2-5GB)。这是为了确保离线安装和完整功能。如果空间有限,考虑使用方式二手动安装,只安装需要的组件。
|
||||
**解决方案**:
|
||||
|
||||
1. **使用 `unilabos` 标准版**(推荐大多数用户):
|
||||
```bash
|
||||
mamba install uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||
```
|
||||
标准版包含完整功能,环境大小约 2-3GB(相比完整版的 8-10GB)。
|
||||
|
||||
2. **使用 `unilabos-env` 开发者版**(最小化):
|
||||
```bash
|
||||
mamba install uni-lab::unilabos-env -c robostack-staging -c conda-forge
|
||||
# 然后手动安装依赖
|
||||
pip install -e .
|
||||
uv pip install -r unilabos/utils/requirements.txt
|
||||
```
|
||||
开发者版只包含环境依赖,体积最小约 2GB。
|
||||
|
||||
3. **按需安装额外组件**:
|
||||
如果后续需要特定功能,可以单独安装:
|
||||
```bash
|
||||
# 需要 Jupyter
|
||||
mamba install jupyter jupyros
|
||||
|
||||
# 需要可视化
|
||||
mamba install matplotlib opencv
|
||||
|
||||
# 需要仿真(注意:这会安装大量依赖)
|
||||
mamba install ros-humble-gazebo-ros
|
||||
```
|
||||
|
||||
4. **预打包环境问题**:
|
||||
预打包环境(方式一)包含所有依赖,通常较大(压缩后 2-5GB)。这是为了确保离线安装和完整功能。
|
||||
|
||||
**包选择建议**:
|
||||
| 需求 | 推荐包 | 预估大小 |
|
||||
|------|--------|----------|
|
||||
| 日常使用/生产部署 | `unilabos` | ~2-3 GB |
|
||||
| 开发调试(可编辑模式) | `unilabos-env` | ~2 GB |
|
||||
| 仿真/可视化 | `unilabos-full` | ~8-10 GB |
|
||||
|
||||
### 问题 9: 如何更新到最新版本?
|
||||
|
||||
@@ -511,6 +616,7 @@ mamba update ros-humble-unilabos-msgs -c uni-lab -c robostack-staging -c conda-f
|
||||
|
||||
**提示**:
|
||||
|
||||
- 生产环境推荐使用方式二(手动安装)的稳定版本
|
||||
- 开发和测试推荐使用方式三(开发者安装)
|
||||
- 快速体验和演示推荐使用方式一(一键安装)
|
||||
- **大多数用户**推荐使用方式二(手动安装)的 `unilabos` 标准版
|
||||
- **开发者**推荐使用方式三(开发者安装),安装 `unilabos-env` 后使用 `uv pip install -r unilabos/utils/requirements.txt` 安装依赖
|
||||
- **仿真/可视化**推荐安装 `unilabos-full` 完整版
|
||||
- **快速体验和演示**推荐使用方式一(一键安装)
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
package:
|
||||
name: ros-humble-unilabos-msgs
|
||||
version: 0.10.16
|
||||
version: 0.10.17
|
||||
source:
|
||||
path: ../../unilabos_msgs
|
||||
target_directory: src
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
package:
|
||||
name: unilabos
|
||||
version: "0.10.16"
|
||||
version: "0.10.17"
|
||||
|
||||
source:
|
||||
path: ../..
|
||||
|
||||
@@ -85,7 +85,7 @@ Verification:
|
||||
-------------
|
||||
|
||||
The verify_installation.py script will check:
|
||||
- Python version (3.11.11)
|
||||
- Python version (3.11.14)
|
||||
- ROS2 rclpy installation
|
||||
- UniLabOS installation and dependencies
|
||||
|
||||
@@ -104,7 +104,7 @@ Build Information:
|
||||
|
||||
Branch: {branch}
|
||||
Platform: {platform}
|
||||
Python: 3.11.11
|
||||
Python: 3.11.14
|
||||
Date: {build_date}
|
||||
|
||||
Troubleshooting:
|
||||
|
||||
214
scripts/dev_install.py
Normal file
214
scripts/dev_install.py
Normal file
@@ -0,0 +1,214 @@
|
||||
#!/usr/bin/env python3
|
||||
"""
|
||||
Development installation script for UniLabOS.
|
||||
Auto-detects Chinese locale and uses appropriate mirror.
|
||||
|
||||
Usage:
|
||||
python scripts/dev_install.py
|
||||
python scripts/dev_install.py --no-mirror # Force no mirror
|
||||
python scripts/dev_install.py --china # Force China mirror
|
||||
python scripts/dev_install.py --skip-deps # Skip pip dependencies installation
|
||||
|
||||
Flow:
|
||||
1. pip install -e . (install unilabos in editable mode)
|
||||
2. Detect Chinese locale
|
||||
3. Use uv to install pip dependencies from requirements.txt
|
||||
4. Special packages (like pylabrobot) are handled by environment_check.py at runtime
|
||||
"""
|
||||
|
||||
import locale
|
||||
import subprocess
|
||||
import sys
|
||||
import argparse
|
||||
from pathlib import Path
|
||||
|
||||
# Tsinghua mirror URL
|
||||
TSINGHUA_MIRROR = "https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple"
|
||||
|
||||
|
||||
def is_chinese_locale() -> bool:
|
||||
"""
|
||||
Detect if system is in Chinese locale.
|
||||
Same logic as EnvironmentChecker._is_chinese_locale()
|
||||
"""
|
||||
try:
|
||||
lang = locale.getdefaultlocale()[0]
|
||||
if lang and ("zh" in lang.lower() or "chinese" in lang.lower()):
|
||||
return True
|
||||
except Exception:
|
||||
pass
|
||||
return False
|
||||
|
||||
|
||||
def run_command(cmd: list, description: str, retry: int = 2) -> bool:
|
||||
"""Run command with retry support."""
|
||||
print(f"[INFO] {description}")
|
||||
print(f"[CMD] {' '.join(cmd)}")
|
||||
|
||||
for attempt in range(retry + 1):
|
||||
try:
|
||||
result = subprocess.run(cmd, check=True, timeout=600)
|
||||
print(f"[OK] {description}")
|
||||
return True
|
||||
except subprocess.CalledProcessError as e:
|
||||
if attempt < retry:
|
||||
print(f"[WARN] Attempt {attempt + 1} failed, retrying...")
|
||||
else:
|
||||
print(f"[ERROR] {description} failed: {e}")
|
||||
return False
|
||||
except subprocess.TimeoutExpired:
|
||||
print(f"[ERROR] {description} timed out")
|
||||
return False
|
||||
return False
|
||||
|
||||
|
||||
def install_editable(project_root: Path, use_mirror: bool) -> bool:
|
||||
"""Install unilabos in editable mode using pip."""
|
||||
cmd = [sys.executable, "-m", "pip", "install", "-e", str(project_root)]
|
||||
if use_mirror:
|
||||
cmd.extend(["-i", TSINGHUA_MIRROR])
|
||||
|
||||
return run_command(cmd, "Installing unilabos in editable mode")
|
||||
|
||||
|
||||
def install_requirements_uv(requirements_file: Path, use_mirror: bool) -> bool:
|
||||
"""Install pip dependencies using uv (installed via conda-forge::uv)."""
|
||||
cmd = ["uv", "pip", "install", "-r", str(requirements_file)]
|
||||
if use_mirror:
|
||||
cmd.extend(["-i", TSINGHUA_MIRROR])
|
||||
|
||||
return run_command(cmd, "Installing pip dependencies with uv", retry=2)
|
||||
|
||||
|
||||
def install_requirements_pip(requirements_file: Path, use_mirror: bool) -> bool:
|
||||
"""Fallback: Install pip dependencies using pip."""
|
||||
cmd = [sys.executable, "-m", "pip", "install", "-r", str(requirements_file)]
|
||||
if use_mirror:
|
||||
cmd.extend(["-i", TSINGHUA_MIRROR])
|
||||
|
||||
return run_command(cmd, "Installing pip dependencies with pip", retry=2)
|
||||
|
||||
|
||||
def check_uv_available() -> bool:
|
||||
"""Check if uv is available (installed via conda-forge::uv)."""
|
||||
try:
|
||||
subprocess.run(["uv", "--version"], capture_output=True, check=True)
|
||||
return True
|
||||
except (subprocess.CalledProcessError, FileNotFoundError):
|
||||
return False
|
||||
|
||||
|
||||
def main():
|
||||
parser = argparse.ArgumentParser(description="Development installation script for UniLabOS")
|
||||
parser.add_argument("--china", action="store_true", help="Force use China mirror (Tsinghua)")
|
||||
parser.add_argument("--no-mirror", action="store_true", help="Force use default PyPI (no mirror)")
|
||||
parser.add_argument(
|
||||
"--skip-deps", action="store_true", help="Skip pip dependencies installation (only install unilabos)"
|
||||
)
|
||||
parser.add_argument("--use-pip", action="store_true", help="Use pip instead of uv for dependencies")
|
||||
args = parser.parse_args()
|
||||
|
||||
# Determine project root
|
||||
script_dir = Path(__file__).parent
|
||||
project_root = script_dir.parent
|
||||
requirements_file = project_root / "unilabos" / "utils" / "requirements.txt"
|
||||
|
||||
if not (project_root / "setup.py").exists():
|
||||
print(f"[ERROR] setup.py not found in {project_root}")
|
||||
sys.exit(1)
|
||||
|
||||
print("=" * 60)
|
||||
print("UniLabOS Development Installation")
|
||||
print("=" * 60)
|
||||
print(f"Project root: {project_root}")
|
||||
print()
|
||||
|
||||
# Determine mirror usage based on locale
|
||||
if args.no_mirror:
|
||||
use_mirror = False
|
||||
print("[INFO] Mirror disabled by --no-mirror flag")
|
||||
elif args.china:
|
||||
use_mirror = True
|
||||
print("[INFO] China mirror enabled by --china flag")
|
||||
else:
|
||||
use_mirror = is_chinese_locale()
|
||||
if use_mirror:
|
||||
print("[INFO] Chinese locale detected, using Tsinghua mirror")
|
||||
else:
|
||||
print("[INFO] Non-Chinese locale detected, using default PyPI")
|
||||
|
||||
print()
|
||||
|
||||
# Step 1: Install unilabos in editable mode
|
||||
print("[STEP 1] Installing unilabos in editable mode...")
|
||||
if not install_editable(project_root, use_mirror):
|
||||
print("[ERROR] Failed to install unilabos")
|
||||
print()
|
||||
print("Manual fallback:")
|
||||
if use_mirror:
|
||||
print(f" pip install -e {project_root} -i {TSINGHUA_MIRROR}")
|
||||
else:
|
||||
print(f" pip install -e {project_root}")
|
||||
sys.exit(1)
|
||||
|
||||
print()
|
||||
|
||||
# Step 2: Install pip dependencies
|
||||
if args.skip_deps:
|
||||
print("[INFO] Skipping pip dependencies installation (--skip-deps)")
|
||||
else:
|
||||
print("[STEP 2] Installing pip dependencies...")
|
||||
|
||||
if not requirements_file.exists():
|
||||
print(f"[WARN] Requirements file not found: {requirements_file}")
|
||||
print("[INFO] Skipping dependencies installation")
|
||||
else:
|
||||
# Try uv first (faster), fallback to pip
|
||||
if args.use_pip:
|
||||
print("[INFO] Using pip (--use-pip flag)")
|
||||
success = install_requirements_pip(requirements_file, use_mirror)
|
||||
elif check_uv_available():
|
||||
print("[INFO] Using uv (installed via conda-forge::uv)")
|
||||
success = install_requirements_uv(requirements_file, use_mirror)
|
||||
if not success:
|
||||
print("[WARN] uv failed, falling back to pip...")
|
||||
success = install_requirements_pip(requirements_file, use_mirror)
|
||||
else:
|
||||
print("[WARN] uv not available (should be installed via: mamba install conda-forge::uv)")
|
||||
print("[INFO] Falling back to pip...")
|
||||
success = install_requirements_pip(requirements_file, use_mirror)
|
||||
|
||||
if not success:
|
||||
print()
|
||||
print("[WARN] Failed to install some dependencies automatically.")
|
||||
print("You can manually install them:")
|
||||
if use_mirror:
|
||||
print(f" uv pip install -r {requirements_file} -i {TSINGHUA_MIRROR}")
|
||||
print(" or:")
|
||||
print(f" pip install -r {requirements_file} -i {TSINGHUA_MIRROR}")
|
||||
else:
|
||||
print(f" uv pip install -r {requirements_file}")
|
||||
print(" or:")
|
||||
print(f" pip install -r {requirements_file}")
|
||||
|
||||
print()
|
||||
print("=" * 60)
|
||||
print("Installation complete!")
|
||||
print("=" * 60)
|
||||
print()
|
||||
print("Note: Some special packages (like pylabrobot) are installed")
|
||||
print("automatically at runtime by unilabos if needed.")
|
||||
print()
|
||||
print("Verify installation:")
|
||||
print(' python -c "import unilabos; print(unilabos.__version__)"')
|
||||
print()
|
||||
print("If you encounter issues, you can manually install dependencies:")
|
||||
if use_mirror:
|
||||
print(f" uv pip install -r unilabos/utils/requirements.txt -i {TSINGHUA_MIRROR}")
|
||||
else:
|
||||
print(" uv pip install -r unilabos/utils/requirements.txt")
|
||||
print()
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
@@ -2,6 +2,7 @@ import json
|
||||
import logging
|
||||
import traceback
|
||||
import uuid
|
||||
import xml.etree.ElementTree as ET
|
||||
from typing import Any, Dict, List
|
||||
|
||||
import networkx as nx
|
||||
@@ -24,15 +25,7 @@ class SimpleGraph:
|
||||
|
||||
def add_edge(self, source, target, **attrs):
|
||||
"""添加边"""
|
||||
# edge = {"source": source, "target": target, **attrs}
|
||||
edge = {
|
||||
"source": source, "target": target,
|
||||
"source_node_uuid": source,
|
||||
"target_node_uuid": target,
|
||||
"source_handle_io": "source",
|
||||
"target_handle_io": "target",
|
||||
**attrs
|
||||
}
|
||||
edge = {"source": source, "target": target, **attrs}
|
||||
self.edges.append(edge)
|
||||
|
||||
def to_dict(self):
|
||||
@@ -49,7 +42,6 @@ class SimpleGraph:
|
||||
"multigraph": False,
|
||||
"graph": {},
|
||||
"nodes": nodes_list,
|
||||
"edges": self.edges,
|
||||
"links": self.edges,
|
||||
}
|
||||
|
||||
@@ -66,8 +58,495 @@ def extract_json_from_markdown(text: str) -> str:
|
||||
return text
|
||||
|
||||
|
||||
def convert_to_type(val: str) -> Any:
|
||||
"""将字符串值转换为适当的数据类型"""
|
||||
if val == "True":
|
||||
return True
|
||||
if val == "False":
|
||||
return False
|
||||
if val == "?":
|
||||
return None
|
||||
if val.endswith(" g"):
|
||||
return float(val.split(" ")[0])
|
||||
if val.endswith("mg"):
|
||||
return float(val.split("mg")[0])
|
||||
elif val.endswith("mmol"):
|
||||
return float(val.split("mmol")[0]) / 1000
|
||||
elif val.endswith("mol"):
|
||||
return float(val.split("mol")[0])
|
||||
elif val.endswith("ml"):
|
||||
return float(val.split("ml")[0])
|
||||
elif val.endswith("RPM"):
|
||||
return float(val.split("RPM")[0])
|
||||
elif val.endswith(" °C"):
|
||||
return float(val.split(" ")[0])
|
||||
elif val.endswith(" %"):
|
||||
return float(val.split(" ")[0])
|
||||
return val
|
||||
|
||||
|
||||
def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
||||
"""统一的数据重构函数,根据操作类型自动选择模板"""
|
||||
refactored_data = []
|
||||
|
||||
# 定义操作映射,包含生物实验和有机化学的所有操作
|
||||
OPERATION_MAPPING = {
|
||||
# 生物实验操作
|
||||
"transfer_liquid": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
|
||||
"transfer": "SynBioFactory-liquid_handler.biomek-transfer",
|
||||
"incubation": "SynBioFactory-liquid_handler.biomek-incubation",
|
||||
"move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
|
||||
"oscillation": "SynBioFactory-liquid_handler.biomek-oscillation",
|
||||
# 有机化学操作
|
||||
"HeatChillToTemp": "SynBioFactory-workstation-HeatChillProtocol",
|
||||
"StopHeatChill": "SynBioFactory-workstation-HeatChillStopProtocol",
|
||||
"StartHeatChill": "SynBioFactory-workstation-HeatChillStartProtocol",
|
||||
"HeatChill": "SynBioFactory-workstation-HeatChillProtocol",
|
||||
"Dissolve": "SynBioFactory-workstation-DissolveProtocol",
|
||||
"Transfer": "SynBioFactory-workstation-TransferProtocol",
|
||||
"Evaporate": "SynBioFactory-workstation-EvaporateProtocol",
|
||||
"Recrystallize": "SynBioFactory-workstation-RecrystallizeProtocol",
|
||||
"Filter": "SynBioFactory-workstation-FilterProtocol",
|
||||
"Dry": "SynBioFactory-workstation-DryProtocol",
|
||||
"Add": "SynBioFactory-workstation-AddProtocol",
|
||||
}
|
||||
|
||||
UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
for step in data:
|
||||
operation = step.get("action")
|
||||
if not operation or operation in UNSUPPORTED_OPERATIONS:
|
||||
continue
|
||||
|
||||
# 处理重复操作
|
||||
if operation == "Repeat":
|
||||
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
||||
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
||||
for i in range(int(times)):
|
||||
sub_data = refactor_data(sub_steps)
|
||||
refactored_data.extend(sub_data)
|
||||
continue
|
||||
|
||||
# 获取模板名称
|
||||
template = OPERATION_MAPPING.get(operation)
|
||||
if not template:
|
||||
# 自动推断模板类型
|
||||
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
||||
template = f"SynBioFactory-liquid_handler.biomek-{operation}"
|
||||
else:
|
||||
template = f"SynBioFactory-workstation-{operation}Protocol"
|
||||
|
||||
# 创建步骤数据
|
||||
step_data = {
|
||||
"template": template,
|
||||
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
||||
"lab_node_type": "Device",
|
||||
"parameters": step.get("parameters", step.get("action_args", {})),
|
||||
}
|
||||
refactored_data.append(step_data)
|
||||
|
||||
return refactored_data
|
||||
|
||||
|
||||
def build_protocol_graph(
|
||||
labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
|
||||
) -> SimpleGraph:
|
||||
"""统一的协议图构建函数,根据设备类型自动选择构建逻辑"""
|
||||
G = SimpleGraph()
|
||||
resource_last_writer = {}
|
||||
LAB_NAME = "SynBioFactory"
|
||||
|
||||
protocol_steps = refactor_data(protocol_steps)
|
||||
|
||||
# 检查协议步骤中的模板来判断协议类型
|
||||
has_biomek_template = any(
|
||||
("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
|
||||
for step in protocol_steps
|
||||
)
|
||||
|
||||
if has_biomek_template:
|
||||
# 生物实验协议图构建
|
||||
for labware_id, labware in labware_info.items():
|
||||
node_id = str(uuid.uuid4())
|
||||
|
||||
labware_attrs = labware.copy()
|
||||
labware_id = labware_attrs.pop("id", labware_attrs.get("name", f"labware_{uuid.uuid4()}"))
|
||||
labware_attrs["description"] = labware_id
|
||||
labware_attrs["lab_node_type"] = (
|
||||
"Reagent" if "Plate" in str(labware_id) else "Labware" if "Rack" in str(labware_id) else "Sample"
|
||||
)
|
||||
labware_attrs["device_id"] = workstation_name
|
||||
|
||||
G.add_node(node_id, template=f"{LAB_NAME}-host_node-create_resource", **labware_attrs)
|
||||
resource_last_writer[labware_id] = f"{node_id}:labware"
|
||||
|
||||
# 处理协议步骤
|
||||
prev_node = None
|
||||
for i, step in enumerate(protocol_steps):
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(node_id, **step)
|
||||
|
||||
# 添加控制流边
|
||||
if prev_node is not None:
|
||||
G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
|
||||
prev_node = node_id
|
||||
|
||||
# 处理物料流
|
||||
params = step.get("parameters", {})
|
||||
if "sources" in params and params["sources"] in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[params["sources"]].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port="labware")
|
||||
|
||||
if "targets" in params:
|
||||
resource_last_writer[params["targets"]] = f"{node_id}:labware"
|
||||
|
||||
# 添加协议结束节点
|
||||
end_id = str(uuid.uuid4())
|
||||
G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
|
||||
if prev_node is not None:
|
||||
G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
|
||||
|
||||
else:
|
||||
# 有机化学协议图构建
|
||||
WORKSTATION_ID = workstation_name
|
||||
|
||||
# 为所有labware创建资源节点
|
||||
for item_id, item in labware_info.items():
|
||||
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
||||
node_id = str(uuid.uuid4())
|
||||
|
||||
# 判断节点类型
|
||||
if item.get("type") == "hardware" or "reactor" in str(item_id).lower():
|
||||
if "reactor" not in str(item_id).lower():
|
||||
continue
|
||||
lab_node_type = "Sample"
|
||||
description = f"Prepare Reactor: {item_id}"
|
||||
liquid_type = []
|
||||
liquid_volume = []
|
||||
else:
|
||||
lab_node_type = "Reagent"
|
||||
description = f"Add Reagent to Flask: {item_id}"
|
||||
liquid_type = [item_id]
|
||||
liquid_volume = [1e5]
|
||||
|
||||
G.add_node(
|
||||
node_id,
|
||||
template=f"{LAB_NAME}-host_node-create_resource",
|
||||
description=description,
|
||||
lab_node_type=lab_node_type,
|
||||
res_id=item_id,
|
||||
device_id=WORKSTATION_ID,
|
||||
class_name="container",
|
||||
parent=WORKSTATION_ID,
|
||||
bind_locations={"x": 0.0, "y": 0.0, "z": 0.0},
|
||||
liquid_input_slot=[-1],
|
||||
liquid_type=liquid_type,
|
||||
liquid_volume=liquid_volume,
|
||||
slot_on_deck="",
|
||||
role=item.get("role", ""),
|
||||
)
|
||||
resource_last_writer[item_id] = f"{node_id}:labware"
|
||||
|
||||
last_control_node_id = None
|
||||
|
||||
# 处理协议步骤
|
||||
for step in protocol_steps:
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(node_id, **step)
|
||||
|
||||
# 控制流
|
||||
if last_control_node_id is not None:
|
||||
G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
|
||||
last_control_node_id = node_id
|
||||
|
||||
# 物料流
|
||||
params = step.get("parameters", {})
|
||||
input_resources = {
|
||||
"Vessel": params.get("vessel"),
|
||||
"ToVessel": params.get("to_vessel"),
|
||||
"FromVessel": params.get("from_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources": params.get("sources"),
|
||||
"targets": params.get("targets"),
|
||||
}
|
||||
|
||||
for target_port, resource_name in input_resources.items():
|
||||
if resource_name and resource_name in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[resource_name].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
|
||||
|
||||
output_resources = {
|
||||
"VesselOut": params.get("vessel"),
|
||||
"FromVesselOut": params.get("from_vessel"),
|
||||
"ToVesselOut": params.get("to_vessel"),
|
||||
"FiltrateOut": params.get("filtrate_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources_out": params.get("sources"),
|
||||
"targets_out": params.get("targets"),
|
||||
}
|
||||
|
||||
for source_port, resource_name in output_resources.items():
|
||||
if resource_name:
|
||||
resource_last_writer[resource_name] = f"{node_id}:{source_port}"
|
||||
|
||||
return G
|
||||
|
||||
|
||||
def draw_protocol_graph(protocol_graph: SimpleGraph, output_path: str):
|
||||
"""
|
||||
(辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图,用于可视化。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
G = nx.DiGraph()
|
||||
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
||||
G.add_node(node_id, label=label, **attrs)
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
G.add_edge(edge["source"], edge["target"])
|
||||
|
||||
plt.figure(figsize=(20, 15))
|
||||
try:
|
||||
pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
|
||||
except Exception:
|
||||
pos = nx.shell_layout(G) # Fallback layout
|
||||
|
||||
node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
|
||||
nx.draw(
|
||||
G,
|
||||
pos,
|
||||
with_labels=False,
|
||||
node_size=2500,
|
||||
node_color="skyblue",
|
||||
node_shape="o",
|
||||
edge_color="gray",
|
||||
width=1.5,
|
||||
arrowsize=15,
|
||||
)
|
||||
nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
|
||||
|
||||
plt.title("Chemical Protocol Workflow Graph", size=15)
|
||||
plt.savefig(output_path, dpi=300, bbox_inches="tight")
|
||||
plt.close()
|
||||
print(f" - Visualization saved to '{output_path}'")
|
||||
|
||||
|
||||
from networkx.drawing.nx_agraph import to_agraph
|
||||
import re
|
||||
|
||||
COMPASS = {"n","e","s","w","ne","nw","se","sw","c"}
|
||||
|
||||
def _is_compass(port: str) -> bool:
|
||||
return isinstance(port, str) and port.lower() in COMPASS
|
||||
|
||||
def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
|
||||
"""
|
||||
使用 Graphviz 端口语法绘制协议工作流图。
|
||||
- 若边上的 source_port/target_port 是 compass(n/e/s/w/...),直接用 compass。
|
||||
- 否则自动为节点创建 record 形状并定义命名端口 <portname>。
|
||||
最终由 PyGraphviz 渲染并输出到 output_path(后缀决定格式,如 .png/.svg/.pdf)。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
# 1) 先用 networkx 搭建有向图,保留端口属性
|
||||
G = nx.DiGraph()
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
||||
# 保留一个干净的“中心标签”,用于放在 record 的中间槽
|
||||
G.add_node(node_id, _core_label=str(label), **{k:v for k,v in attrs.items() if k not in ("label",)})
|
||||
|
||||
edges_data = []
|
||||
in_ports_by_node = {} # 收集命名输入端口
|
||||
out_ports_by_node = {} # 收集命名输出端口
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
u = edge["source"]
|
||||
v = edge["target"]
|
||||
sp = edge.get("source_port")
|
||||
tp = edge.get("target_port")
|
||||
|
||||
# 记录到图里(保留原始端口信息)
|
||||
G.add_edge(u, v, source_port=sp, target_port=tp)
|
||||
edges_data.append((u, v, sp, tp))
|
||||
|
||||
# 如果不是 compass,就按“命名端口”先归类,等会儿给节点造 record
|
||||
if sp and not _is_compass(sp):
|
||||
out_ports_by_node.setdefault(u, set()).add(str(sp))
|
||||
if tp and not _is_compass(tp):
|
||||
in_ports_by_node.setdefault(v, set()).add(str(tp))
|
||||
|
||||
# 2) 转为 AGraph,使用 Graphviz 渲染
|
||||
A = to_agraph(G)
|
||||
A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
|
||||
A.node_attr.update(shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica")
|
||||
A.edge_attr.update(arrowsize="0.8", color="#666666")
|
||||
|
||||
# 3) 为需要命名端口的节点设置 record 形状与 label
|
||||
# 左列 = 输入端口;中间 = 核心标签;右列 = 输出端口
|
||||
for n in A.nodes():
|
||||
node = A.get_node(n)
|
||||
core = G.nodes[n].get("_core_label", n)
|
||||
|
||||
in_ports = sorted(in_ports_by_node.get(n, []))
|
||||
out_ports = sorted(out_ports_by_node.get(n, []))
|
||||
|
||||
# 如果该节点涉及命名端口,则用 record;否则保留原 box
|
||||
if in_ports or out_ports:
|
||||
def port_fields(ports):
|
||||
if not ports:
|
||||
return " " # 必须留一个空槽占位
|
||||
# 每个端口一个小格子,<p> name
|
||||
return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
|
||||
|
||||
left = port_fields(in_ports)
|
||||
right = port_fields(out_ports)
|
||||
|
||||
# 三栏:左(入) | 中(节点名) | 右(出)
|
||||
record_label = f"{{ {left} | {core} | {right} }}"
|
||||
node.attr.update(shape="record", label=record_label)
|
||||
else:
|
||||
# 没有命名端口:普通盒子,显示核心标签
|
||||
node.attr.update(label=str(core))
|
||||
|
||||
# 4) 给边设置 headport / tailport
|
||||
# - 若端口为 compass:直接用 compass(e.g., headport="e")
|
||||
# - 若端口为命名端口:使用在 record 中定义的 <port> 名(同名即可)
|
||||
for (u, v, sp, tp) in edges_data:
|
||||
e = A.get_edge(u, v)
|
||||
|
||||
# Graphviz 属性:tail 是源,head 是目标
|
||||
if sp:
|
||||
if _is_compass(sp):
|
||||
e.attr["tailport"] = sp.lower()
|
||||
else:
|
||||
# 与 record label 中 <port> 名一致;特殊字符已在 label 中做了清洗
|
||||
e.attr["tailport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(sp))
|
||||
|
||||
if tp:
|
||||
if _is_compass(tp):
|
||||
e.attr["headport"] = tp.lower()
|
||||
else:
|
||||
e.attr["headport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(tp))
|
||||
|
||||
# 可选:若想让边更贴边缘,可设置 constraint/spline 等
|
||||
# e.attr["arrowhead"] = "vee"
|
||||
|
||||
# 5) 输出
|
||||
A.draw(output_path, prog="dot")
|
||||
print(f" - Port-aware workflow rendered to '{output_path}'")
|
||||
|
||||
|
||||
def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
|
||||
"""展平嵌套的XDL程序结构"""
|
||||
flattened_operations = []
|
||||
TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
def extract_operations(element: ET.Element):
|
||||
if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
|
||||
if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
|
||||
flattened_operations.append(element)
|
||||
|
||||
for child in element:
|
||||
extract_operations(child)
|
||||
|
||||
for child in procedure_elem:
|
||||
extract_operations(child)
|
||||
|
||||
return flattened_operations
|
||||
|
||||
|
||||
def parse_xdl_content(xdl_content: str) -> tuple:
|
||||
"""解析XDL内容"""
|
||||
try:
|
||||
xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
|
||||
root = ET.fromstring(xdl_content_cleaned)
|
||||
|
||||
synthesis_elem = root.find("Synthesis")
|
||||
if synthesis_elem is None:
|
||||
return None, None, None
|
||||
|
||||
# 解析硬件组件
|
||||
hardware_elem = synthesis_elem.find("Hardware")
|
||||
hardware = []
|
||||
if hardware_elem is not None:
|
||||
hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
|
||||
|
||||
# 解析试剂
|
||||
reagents_elem = synthesis_elem.find("Reagents")
|
||||
reagents = []
|
||||
if reagents_elem is not None:
|
||||
reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
|
||||
|
||||
# 解析程序
|
||||
procedure_elem = synthesis_elem.find("Procedure")
|
||||
if procedure_elem is None:
|
||||
return None, None, None
|
||||
|
||||
flattened_operations = flatten_xdl_procedure(procedure_elem)
|
||||
return hardware, reagents, flattened_operations
|
||||
|
||||
except ET.ParseError as e:
|
||||
raise ValueError(f"Invalid XDL format: {e}")
|
||||
|
||||
|
||||
def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
|
||||
"""
|
||||
将XDL XML格式转换为标准的字典格式
|
||||
|
||||
Args:
|
||||
xdl_content: XDL XML内容
|
||||
|
||||
Returns:
|
||||
转换结果,包含步骤和器材信息
|
||||
"""
|
||||
try:
|
||||
hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
|
||||
if hardware is None:
|
||||
return {"error": "Failed to parse XDL content", "success": False}
|
||||
|
||||
# 将XDL元素转换为字典格式
|
||||
steps_data = []
|
||||
for elem in flattened_operations:
|
||||
# 转换参数类型
|
||||
parameters = {}
|
||||
for key, val in elem.attrib.items():
|
||||
converted_val = convert_to_type(val)
|
||||
if converted_val is not None:
|
||||
parameters[key] = converted_val
|
||||
|
||||
step_dict = {
|
||||
"operation": elem.tag,
|
||||
"parameters": parameters,
|
||||
"description": elem.get("purpose", f"Operation: {elem.tag}"),
|
||||
}
|
||||
steps_data.append(step_dict)
|
||||
|
||||
# 合并硬件和试剂为统一的labware_info格式
|
||||
labware_data = []
|
||||
labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
|
||||
labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
|
||||
|
||||
return {
|
||||
"success": True,
|
||||
"steps": steps_data,
|
||||
"labware": labware_data,
|
||||
"message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
|
||||
}
|
||||
|
||||
except Exception as e:
|
||||
error_msg = f"XDL conversion failed: {str(e)}"
|
||||
logger.error(error_msg)
|
||||
return {"error": error_msg, "success": False}
|
||||
|
||||
|
||||
def create_workflow(
|
||||
|
||||
2
setup.py
2
setup.py
@@ -4,7 +4,7 @@ package_name = 'unilabos'
|
||||
|
||||
setup(
|
||||
name=package_name,
|
||||
version='0.10.16',
|
||||
version='0.10.17',
|
||||
packages=find_packages(),
|
||||
include_package_data=True,
|
||||
install_requires=['setuptools'],
|
||||
|
||||
@@ -1 +1 @@
|
||||
__version__ = "0.10.16"
|
||||
__version__ = "0.10.17"
|
||||
|
||||
@@ -7,7 +7,6 @@ import sys
|
||||
import threading
|
||||
import time
|
||||
from typing import Dict, Any, List
|
||||
|
||||
import networkx as nx
|
||||
import yaml
|
||||
|
||||
@@ -17,9 +16,9 @@ unilabos_dir = os.path.dirname(os.path.dirname(current_dir))
|
||||
if unilabos_dir not in sys.path:
|
||||
sys.path.append(unilabos_dir)
|
||||
|
||||
from unilabos.app.utils import cleanup_for_restart
|
||||
from unilabos.utils.banner_print import print_status, print_unilab_banner
|
||||
from unilabos.config.config import load_config, BasicConfig, HTTPConfig
|
||||
from unilabos.app.utils import cleanup_for_restart
|
||||
|
||||
# Global restart flags (used by ws_client and web/server)
|
||||
_restart_requested: bool = False
|
||||
@@ -217,7 +216,10 @@ def main():
|
||||
args_dict = vars(args)
|
||||
|
||||
# 环境检查 - 检查并自动安装必需的包 (可选)
|
||||
if not args_dict.get("skip_env_check", False):
|
||||
skip_env_check = args_dict.get("skip_env_check", False)
|
||||
check_mode = args_dict.get("check_mode", False)
|
||||
|
||||
if not skip_env_check:
|
||||
from unilabos.utils.environment_check import check_environment
|
||||
|
||||
if not check_environment(auto_install=True):
|
||||
@@ -228,7 +230,21 @@ def main():
|
||||
|
||||
# 加载配置文件,优先加载config,然后从env读取
|
||||
config_path = args_dict.get("config")
|
||||
if os.getcwd().endswith("unilabos_data"):
|
||||
|
||||
if check_mode:
|
||||
args_dict["working_dir"] = os.path.abspath(os.getcwd())
|
||||
# 当 skip_env_check 时,默认使用当前目录作为 working_dir
|
||||
if skip_env_check and not args_dict.get("working_dir") and not config_path:
|
||||
working_dir = os.path.abspath(os.getcwd())
|
||||
print_status(f"跳过环境检查模式:使用当前目录作为工作目录 {working_dir}", "info")
|
||||
# 检查当前目录是否有 local_config.py
|
||||
local_config_in_cwd = os.path.join(working_dir, "local_config.py")
|
||||
if os.path.exists(local_config_in_cwd):
|
||||
config_path = local_config_in_cwd
|
||||
print_status(f"发现本地配置文件: {config_path}", "info")
|
||||
else:
|
||||
print_status(f"未指定config路径,可通过 --config 传入 local_config.py 文件路径", "info")
|
||||
elif os.getcwd().endswith("unilabos_data"):
|
||||
working_dir = os.path.abspath(os.getcwd())
|
||||
else:
|
||||
working_dir = os.path.abspath(os.path.join(os.getcwd(), "unilabos_data"))
|
||||
@@ -247,7 +263,7 @@ def main():
|
||||
working_dir = os.path.dirname(config_path)
|
||||
elif os.path.exists(working_dir) and os.path.exists(os.path.join(working_dir, "local_config.py")):
|
||||
config_path = os.path.join(working_dir, "local_config.py")
|
||||
elif not config_path and (
|
||||
elif not skip_env_check and not config_path and (
|
||||
not os.path.exists(working_dir) or not os.path.exists(os.path.join(working_dir, "local_config.py"))
|
||||
):
|
||||
print_status(f"未指定config路径,可通过 --config 传入 local_config.py 文件路径", "info")
|
||||
@@ -261,9 +277,11 @@ def main():
|
||||
print_status(f"已创建 local_config.py 路径: {config_path}", "info")
|
||||
else:
|
||||
os._exit(1)
|
||||
# 加载配置文件
|
||||
|
||||
# 加载配置文件 (check_mode 跳过)
|
||||
print_status(f"当前工作目录为 {working_dir}", "info")
|
||||
load_config_from_file(config_path)
|
||||
if not check_mode:
|
||||
load_config_from_file(config_path)
|
||||
|
||||
# 根据配置重新设置日志级别
|
||||
from unilabos.utils.log import configure_logger, logger
|
||||
@@ -319,12 +337,7 @@ def main():
|
||||
machine_name = "".join([c if c.isalnum() or c == "_" else "_" for c in machine_name])
|
||||
BasicConfig.machine_name = machine_name
|
||||
BasicConfig.vis_2d_enable = args_dict["2d_vis"]
|
||||
|
||||
# Check mode 处理
|
||||
check_mode = args_dict.get("check_mode", False)
|
||||
BasicConfig.check_mode = check_mode
|
||||
if check_mode:
|
||||
print_status("Check mode 启用,将进行 complete_registry 检查", "info")
|
||||
|
||||
from unilabos.resources.graphio import (
|
||||
read_node_link_json,
|
||||
|
||||
@@ -4,8 +4,40 @@ UniLabOS 应用工具函数
|
||||
提供清理、重启等工具函数
|
||||
"""
|
||||
|
||||
import gc
|
||||
import glob
|
||||
import os
|
||||
import shutil
|
||||
import sys
|
||||
|
||||
|
||||
def patch_rclpy_dll_windows():
|
||||
"""在 Windows + conda 环境下为 rclpy 打 DLL 加载补丁"""
|
||||
if sys.platform != "win32" or not os.environ.get("CONDA_PREFIX"):
|
||||
return
|
||||
try:
|
||||
import rclpy
|
||||
|
||||
return
|
||||
except ImportError as e:
|
||||
if not str(e).startswith("DLL load failed"):
|
||||
return
|
||||
cp = os.environ["CONDA_PREFIX"]
|
||||
impl = os.path.join(cp, "Lib", "site-packages", "rclpy", "impl", "implementation_singleton.py")
|
||||
pyd = glob.glob(os.path.join(cp, "Lib", "site-packages", "rclpy", "_rclpy_pybind11*.pyd"))
|
||||
if not os.path.exists(impl) or not pyd:
|
||||
return
|
||||
with open(impl, "r", encoding="utf-8") as f:
|
||||
content = f.read()
|
||||
lib_bin = os.path.join(cp, "Library", "bin").replace("\\", "/")
|
||||
patch = f'# UniLabOS DLL Patch\nimport os,ctypes\nos.add_dll_directory("{lib_bin}") if hasattr(os,"add_dll_directory") else None\ntry: ctypes.CDLL("{pyd[0].replace(chr(92),"/")}")\nexcept: pass\n# End Patch\n'
|
||||
shutil.copy2(impl, impl + ".bak")
|
||||
with open(impl, "w", encoding="utf-8") as f:
|
||||
f.write(patch + content)
|
||||
|
||||
|
||||
patch_rclpy_dll_windows()
|
||||
|
||||
import gc
|
||||
import threading
|
||||
import time
|
||||
|
||||
|
||||
@@ -74,8 +74,7 @@ class HTTPClient:
|
||||
Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
|
||||
"""
|
||||
with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f:
|
||||
payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
|
||||
f.write(json.dumps(payload, indent=4))
|
||||
f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
|
||||
# 从序列化数据中提取所有节点的UUID(保存旧UUID)
|
||||
old_uuids = {n.res_content.uuid: n for n in resources.all_nodes}
|
||||
if not self.initialized or first_add:
|
||||
@@ -334,67 +333,6 @@ class HTTPClient:
|
||||
logger.error(f"响应内容: {response.text}")
|
||||
return None
|
||||
|
||||
def workflow_import(
|
||||
self,
|
||||
name: str,
|
||||
workflow_uuid: str,
|
||||
workflow_name: str,
|
||||
nodes: List[Dict[str, Any]],
|
||||
edges: List[Dict[str, Any]],
|
||||
tags: Optional[List[str]] = None,
|
||||
published: bool = False,
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
导入工作流到服务器
|
||||
|
||||
Args:
|
||||
name: 工作流名称(顶层)
|
||||
workflow_uuid: 工作流UUID
|
||||
workflow_name: 工作流名称(data内部)
|
||||
nodes: 工作流节点列表
|
||||
edges: 工作流边列表
|
||||
tags: 工作流标签列表,默认为空列表
|
||||
published: 是否发布工作流,默认为False
|
||||
|
||||
Returns:
|
||||
Dict: API响应数据,包含 code 和 data (uuid, name)
|
||||
"""
|
||||
# target_lab_uuid 暂时使用默认值,后续由后端根据 ak/sk 获取
|
||||
payload = {
|
||||
"target_lab_uuid": "28c38bb0-63f6-4352-b0d8-b5b8eb1766d5",
|
||||
"name": name,
|
||||
"data": {
|
||||
"workflow_uuid": workflow_uuid,
|
||||
"workflow_name": workflow_name,
|
||||
"nodes": nodes,
|
||||
"edges": edges,
|
||||
"tags": tags if tags is not None else [],
|
||||
"published": published,
|
||||
},
|
||||
}
|
||||
# 保存请求到文件
|
||||
with open(os.path.join(BasicConfig.working_dir, "req_workflow_upload.json"), "w", encoding="utf-8") as f:
|
||||
f.write(json.dumps(payload, indent=4, ensure_ascii=False))
|
||||
|
||||
response = requests.post(
|
||||
f"{self.remote_addr}/lab/workflow/owner/import",
|
||||
json=payload,
|
||||
headers={"Authorization": f"Lab {self.auth}"},
|
||||
timeout=60,
|
||||
)
|
||||
# 保存响应到文件
|
||||
with open(os.path.join(BasicConfig.working_dir, "res_workflow_upload.json"), "w", encoding="utf-8") as f:
|
||||
f.write(f"{response.status_code}" + "\n" + response.text)
|
||||
|
||||
if response.status_code == 200:
|
||||
res = response.json()
|
||||
if "code" in res and res["code"] != 0:
|
||||
logger.error(f"导入工作流失败: {response.text}")
|
||||
return res
|
||||
else:
|
||||
logger.error(f"导入工作流失败: {response.status_code}, {response.text}")
|
||||
return {"code": response.status_code, "message": response.text}
|
||||
|
||||
|
||||
# 创建默认客户端实例
|
||||
http_client = HTTPClient()
|
||||
|
||||
@@ -439,7 +439,7 @@ class MessageProcessor:
|
||||
self.connected = True
|
||||
self.reconnect_count = 0
|
||||
|
||||
logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
|
||||
logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
|
||||
|
||||
# 启动发送协程
|
||||
send_task = asyncio.create_task(self._send_handler())
|
||||
@@ -517,7 +517,7 @@ class MessageProcessor:
|
||||
|
||||
async def _send_handler(self):
|
||||
"""处理发送队列中的消息"""
|
||||
logger.trace("[MessageProcessor] Send handler started")
|
||||
logger.debug("[MessageProcessor] Send handler started")
|
||||
|
||||
try:
|
||||
while self.connected and self.websocket:
|
||||
@@ -1026,7 +1026,7 @@ class QueueProcessor:
|
||||
|
||||
def _run(self):
|
||||
"""运行队列处理主循环"""
|
||||
logger.trace("[QueueProcessor] Queue processor started")
|
||||
logger.debug("[QueueProcessor] Queue processor started")
|
||||
|
||||
while self.is_running:
|
||||
try:
|
||||
@@ -1236,6 +1236,7 @@ class WebSocketClient(BaseCommunicationClient):
|
||||
else:
|
||||
url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
|
||||
|
||||
logger.debug(f"[WebSocketClient] URL: {url}")
|
||||
return url
|
||||
|
||||
def start(self) -> None:
|
||||
@@ -1248,11 +1249,13 @@ class WebSocketClient(BaseCommunicationClient):
|
||||
logger.error("[WebSocketClient] WebSocket URL not configured")
|
||||
return
|
||||
|
||||
logger.info(f"[WebSocketClient] Starting connection to {self.websocket_url}")
|
||||
|
||||
# 启动两个核心线程
|
||||
self.message_processor.start()
|
||||
self.queue_processor.start()
|
||||
|
||||
logger.trace("[WebSocketClient] All threads started")
|
||||
logger.info("[WebSocketClient] All threads started")
|
||||
|
||||
def stop(self) -> None:
|
||||
"""停止WebSocket客户端"""
|
||||
|
||||
0
unilabos/devices/xrd_d7mate/__init__.py
Normal file
0
unilabos/devices/xrd_d7mate/__init__.py
Normal file
0
unilabos/devices/zhida_hplc/__init__.py
Normal file
0
unilabos/devices/zhida_hplc/__init__.py
Normal file
@@ -9743,34 +9743,7 @@ liquid_handler.prcxi:
|
||||
touch_tip: false
|
||||
use_channels:
|
||||
- 0
|
||||
handles:
|
||||
input:
|
||||
- data_key: liquid
|
||||
data_source: handle
|
||||
data_type: resource
|
||||
handler_key: sources
|
||||
label: sources
|
||||
- data_key: liquid
|
||||
data_source: executor
|
||||
data_type: resource
|
||||
handler_key: targets
|
||||
label: targets
|
||||
- data_key: liquid
|
||||
data_source: executor
|
||||
data_type: resource
|
||||
handler_key: tip_rack
|
||||
label: tip_rack
|
||||
output:
|
||||
- data_key: liquid
|
||||
data_source: handle
|
||||
data_type: resource
|
||||
handler_key: sources_out
|
||||
label: sources
|
||||
- data_key: liquid
|
||||
data_source: executor
|
||||
data_type: resource
|
||||
handler_key: targets_out
|
||||
label: targets
|
||||
handles: {}
|
||||
placeholder_keys:
|
||||
sources: unilabos_resources
|
||||
targets: unilabos_resources
|
||||
|
||||
@@ -265,7 +265,7 @@ class Registry:
|
||||
abs_path = Path(path).absolute()
|
||||
resource_path = abs_path / "resources"
|
||||
files = list(resource_path.glob("*/*.yaml"))
|
||||
logger.trace(f"[UniLab Registry] load resources? {resource_path.exists()}, total: {len(files)}")
|
||||
logger.debug(f"[UniLab Registry] resources: {resource_path.exists()}, total: {len(files)}")
|
||||
current_resource_number = len(self.resource_type_registry) + 1
|
||||
for i, file in enumerate(files):
|
||||
with open(file, encoding="utf-8", mode="r") as f:
|
||||
|
||||
@@ -42,7 +42,7 @@ def canonicalize_nodes_data(
|
||||
Returns:
|
||||
ResourceTreeSet: 标准化后的资源树集合
|
||||
"""
|
||||
print_status(f"{len(nodes)} Resources loaded", "info")
|
||||
print_status(f"{len(nodes)} Resources loaded:", "info")
|
||||
|
||||
# 第一步:基本预处理(处理graphml的label字段)
|
||||
outer_host_node_id = None
|
||||
|
||||
@@ -66,8 +66,8 @@ class ResourceDict(BaseModel):
|
||||
klass: str = Field(alias="class", description="Resource class name")
|
||||
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
|
||||
config: Dict[str, Any] = Field(description="Resource configuration")
|
||||
data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
|
||||
extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
|
||||
data: Dict[str, Any] = Field(description="Resource data")
|
||||
extra: Dict[str, Any] = Field(description="Extra data")
|
||||
|
||||
@field_serializer("parent_uuid")
|
||||
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
|
||||
|
||||
@@ -1,187 +0,0 @@
|
||||
# UniLabOS 日志配置说明
|
||||
|
||||
> **文件位置**: `unilabos/utils/log.py`
|
||||
> **最后更新**: 2026-01-11
|
||||
> **维护者**: Uni-Lab-OS 开发团队
|
||||
|
||||
本文档说明 UniLabOS 日志系统中对第三方库和内部模块的日志级别配置,避免控制台被过多的 DEBUG 日志淹没。
|
||||
|
||||
---
|
||||
|
||||
## 📋 已屏蔽的日志
|
||||
|
||||
以下库/模块的日志已被设置为 **WARNING** 或 **INFO** 级别,不再显示 DEBUG 日志:
|
||||
|
||||
### 1. pymodbus(Modbus 通信库)
|
||||
|
||||
**配置位置**: `log.py` 第196-200行
|
||||
|
||||
```python
|
||||
# pymodbus 库的日志太详细,设置为 WARNING
|
||||
logging.getLogger('pymodbus').setLevel(logging.WARNING)
|
||||
logging.getLogger('pymodbus.logging').setLevel(logging.WARNING)
|
||||
logging.getLogger('pymodbus.logging.base').setLevel(logging.WARNING)
|
||||
logging.getLogger('pymodbus.logging.decoders').setLevel(logging.WARNING)
|
||||
```
|
||||
|
||||
**屏蔽原因**:
|
||||
- pymodbus 在 DEBUG 级别会输出每一次 Modbus 通信的详细信息
|
||||
- 包括 `Processing: 0x5 0x1e 0x0 0x0...` 等原始数据
|
||||
- 包括 `decoded PDU function_code(3 sub -1) -> ReadHoldingRegistersResponse(...)` 等解码信息
|
||||
- 这些信息对日常使用价值不大,但会快速刷屏
|
||||
|
||||
**典型被屏蔽的日志**:
|
||||
```
|
||||
[DEBUG] Processing: 0x5 0x1e 0x0 0x0 0x0 0x7 0x1 0x3 0x4 0x0 0x0 0x0 0x0 [handleFrame:72] [pymodbus.logging.base]
|
||||
[DEBUG] decoded PDU function_code(3 sub -1) -> ReadHoldingRegistersResponse(...) [decode:79] [pymodbus.logging.decoders]
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### 2. websockets(WebSocket 库)
|
||||
|
||||
**配置位置**: `log.py` 第202-205行
|
||||
|
||||
```python
|
||||
# websockets 库的日志输出较多,设置为 WARNING
|
||||
logging.getLogger('websockets').setLevel(logging.WARNING)
|
||||
logging.getLogger('websockets.client').setLevel(logging.WARNING)
|
||||
logging.getLogger('websockets.server').setLevel(logging.WARNING)
|
||||
```
|
||||
|
||||
**屏蔽原因**:
|
||||
- WebSocket 连接、断开、心跳等信息在 DEBUG 级别会频繁输出
|
||||
- 对于长时间运行的服务,这些日志意义不大
|
||||
|
||||
---
|
||||
|
||||
### 3. ROS Host Node(设备状态更新)
|
||||
|
||||
**配置位置**: `log.py` 第207-208行
|
||||
|
||||
```python
|
||||
# ROS 节点的状态更新日志过于频繁,设置为 INFO
|
||||
logging.getLogger('unilabos.ros.nodes.presets.host_node').setLevel(logging.INFO)
|
||||
```
|
||||
|
||||
**屏蔽原因**:
|
||||
- 设备状态更新(如手套箱压力)每隔几秒就会更新一次
|
||||
- DEBUG 日志会记录每一次状态变化,导致日志刷屏
|
||||
- 这些频繁的状态更新对调试价值不大
|
||||
|
||||
**典型被屏蔽的日志**:
|
||||
```
|
||||
[DEBUG] [/devices/host_node] Status updated: BatteryStation.data_glove_box_pressure = 4.229457855224609 [property_callback:666] [unilabos.ros.nodes.presets.host_node]
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
### 4. asyncio 和 urllib3
|
||||
|
||||
**配置位置**: `log.py` 第224-225行
|
||||
|
||||
```python
|
||||
logging.getLogger("asyncio").setLevel(logging.INFO)
|
||||
logging.getLogger("urllib3").setLevel(logging.INFO)
|
||||
```
|
||||
|
||||
**屏蔽原因**:
|
||||
- asyncio: 异步 IO 的内部调试信息
|
||||
- urllib3: HTTP 请求库的连接池、重试等详细信息
|
||||
|
||||
---
|
||||
|
||||
## 🔧 如何临时启用这些日志(调试用)
|
||||
|
||||
### 方法1: 修改 log.py(永久启用)
|
||||
|
||||
在 `log.py` 的 `configure_logger()` 函数中,将对应库的日志级别改为 `logging.DEBUG`:
|
||||
|
||||
```python
|
||||
# 临时启用 pymodbus 的 DEBUG 日志
|
||||
logging.getLogger('pymodbus').setLevel(logging.DEBUG)
|
||||
logging.getLogger('pymodbus.logging').setLevel(logging.DEBUG)
|
||||
logging.getLogger('pymodbus.logging.base').setLevel(logging.DEBUG)
|
||||
logging.getLogger('pymodbus.logging.decoders').setLevel(logging.DEBUG)
|
||||
```
|
||||
|
||||
### 方法2: 在代码中临时启用(单次调试)
|
||||
|
||||
在需要调试的代码文件中添加:
|
||||
|
||||
```python
|
||||
import logging
|
||||
|
||||
# 临时启用 pymodbus DEBUG 日志
|
||||
logging.getLogger('pymodbus').setLevel(logging.DEBUG)
|
||||
|
||||
# 你的 Modbus 调试代码
|
||||
...
|
||||
|
||||
# 调试完成后恢复
|
||||
logging.getLogger('pymodbus').setLevel(logging.WARNING)
|
||||
```
|
||||
|
||||
### 方法3: 使用环境变量或配置文件(推荐)
|
||||
|
||||
未来可以考虑在启动参数中添加 `--debug-modbus` 等选项来动态控制。
|
||||
|
||||
---
|
||||
|
||||
## 📊 日志级别说明
|
||||
|
||||
| 级别 | 数值 | 用途 | 是否显示 |
|
||||
|------|------|------|---------|
|
||||
| TRACE | 5 | 最详细的跟踪信息 | ✅ |
|
||||
| DEBUG | 10 | 调试信息 | ✅ |
|
||||
| INFO | 20 | 一般信息 | ✅ |
|
||||
| WARNING | 30 | 警告信息 | ✅ |
|
||||
| ERROR | 40 | 错误信息 | ✅ |
|
||||
| CRITICAL | 50 | 严重错误 | ✅ |
|
||||
|
||||
**当前配置**:
|
||||
- UniLabOS 自身代码: DEBUG 及以上全部显示
|
||||
- pymodbus/websockets: **WARNING** 及以上显示(屏蔽 DEBUG/INFO)
|
||||
- ROS host_node: **INFO** 及以上显示(屏蔽 DEBUG)
|
||||
|
||||
---
|
||||
|
||||
## ⚠️ 重要提示
|
||||
|
||||
### 修改生效时间
|
||||
- 修改 `log.py` 后需要 **重启 unilab 服务** 才能生效
|
||||
- 不需要重新安装或重新编译
|
||||
|
||||
### 调试 Modbus 通信问题
|
||||
如果需要调试 Modbus 通信故障,应该:
|
||||
1. 临时启用 pymodbus DEBUG 日志(方法2)
|
||||
2. 复现问题
|
||||
3. 查看详细的通信日志
|
||||
4. 调试完成后记得恢复 WARNING 级别
|
||||
|
||||
### 调试设备状态问题
|
||||
如果需要调试设备状态更新问题:
|
||||
```python
|
||||
logging.getLogger('unilabos.ros.nodes.presets.host_node').setLevel(logging.DEBUG)
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 📝 维护记录
|
||||
|
||||
| 日期 | 修改内容 | 操作人 |
|
||||
|------|---------|--------|
|
||||
| 2026-01-11 | 初始创建,添加 pymodbus、websockets、ROS host_node 屏蔽 | - |
|
||||
| 2026-01-07 | 添加 pymodbus 和 websockets 屏蔽(log-0107.py) | - |
|
||||
|
||||
---
|
||||
|
||||
## 🔗 相关文件
|
||||
|
||||
- `log.py` - 日志配置主文件
|
||||
- `unilabos/devices/workstation/coin_cell_assembly/` - 使用 Modbus 的扣电工作站代码
|
||||
- `unilabos/ros/nodes/presets/host_node.py` - ROS 主机节点代码
|
||||
|
||||
---
|
||||
|
||||
**维护提示**: 如果添加了新的第三方库或发现新的日志刷屏问题,请在此文档中记录并更新 `log.py` 配置。
|
||||
@@ -24,6 +24,7 @@ class EnvironmentChecker:
|
||||
"msgcenterpy": "msgcenterpy",
|
||||
"opentrons_shared_data": "opentrons_shared_data",
|
||||
"typing_extensions": "typing_extensions",
|
||||
"crcmod": "crcmod-plus",
|
||||
}
|
||||
|
||||
# 特殊安装包(需要特殊处理的包)
|
||||
|
||||
18
unilabos/utils/requirements.txt
Normal file
18
unilabos/utils/requirements.txt
Normal file
@@ -0,0 +1,18 @@
|
||||
networkx
|
||||
typing_extensions
|
||||
websockets
|
||||
msgcenterpy>=0.1.5
|
||||
opentrons_shared_data
|
||||
pint
|
||||
fastapi
|
||||
jinja2
|
||||
requests
|
||||
uvicorn
|
||||
pyautogui
|
||||
opcua
|
||||
pyserial
|
||||
pandas
|
||||
crcmod-plus
|
||||
pymodbus
|
||||
matplotlib
|
||||
pylibftdi
|
||||
@@ -1,547 +0,0 @@
|
||||
import re
|
||||
import uuid
|
||||
|
||||
import networkx as nx
|
||||
from networkx.drawing.nx_agraph import to_agraph
|
||||
import matplotlib.pyplot as plt
|
||||
from typing import Dict, List, Any, Tuple, Optional
|
||||
|
||||
Json = Dict[str, Any]
|
||||
|
||||
# ---------------- Graph ----------------
|
||||
|
||||
|
||||
class WorkflowGraph:
|
||||
"""简单的有向图实现:使用 params 单层参数;inputs 内含连线;支持 node-link 导出"""
|
||||
|
||||
def __init__(self):
|
||||
self.nodes: Dict[str, Dict[str, Any]] = {}
|
||||
self.edges: List[Dict[str, Any]] = []
|
||||
|
||||
def add_node(self, node_id: str, **attrs):
|
||||
self.nodes[node_id] = attrs
|
||||
|
||||
def add_edge(self, source: str, target: str, **attrs):
|
||||
# 将 source_port/target_port 映射为服务端期望的 source_handle_key/target_handle_key
|
||||
source_handle_key = attrs.pop("source_port", "") or attrs.pop("source_handle_key", "")
|
||||
target_handle_key = attrs.pop("target_port", "") or attrs.pop("target_handle_key", "")
|
||||
|
||||
edge = {
|
||||
"source": source,
|
||||
"target": target,
|
||||
"source_node_uuid": source,
|
||||
"target_node_uuid": target,
|
||||
"source_handle_key": source_handle_key,
|
||||
"source_handle_io": attrs.pop("source_handle_io", "source"),
|
||||
"target_handle_key": target_handle_key,
|
||||
"target_handle_io": attrs.pop("target_handle_io", "target"),
|
||||
**attrs,
|
||||
}
|
||||
self.edges.append(edge)
|
||||
|
||||
def _materialize_wiring_into_inputs(
|
||||
self,
|
||||
obj: Any,
|
||||
inputs: Dict[str, Any],
|
||||
variable_sources: Dict[str, Dict[str, Any]],
|
||||
target_node_id: str,
|
||||
base_path: List[str],
|
||||
):
|
||||
has_var = False
|
||||
|
||||
def walk(node: Any, path: List[str]):
|
||||
nonlocal has_var
|
||||
if isinstance(node, dict):
|
||||
if "__var__" in node:
|
||||
has_var = True
|
||||
varname = node["__var__"]
|
||||
placeholder = f"${{{varname}}}"
|
||||
src = variable_sources.get(varname)
|
||||
if src:
|
||||
key = ".".join(path) # e.g. "params.foo.bar.0"
|
||||
inputs[key] = {"node": src["node_id"], "output": src.get("output_name", "result")}
|
||||
self.add_edge(
|
||||
str(src["node_id"]),
|
||||
target_node_id,
|
||||
source_handle_io=src.get("output_name", "result"),
|
||||
target_handle_io=key,
|
||||
)
|
||||
return placeholder
|
||||
return {k: walk(v, path + [k]) for k, v in node.items()}
|
||||
if isinstance(node, list):
|
||||
return [walk(v, path + [str(i)]) for i, v in enumerate(node)]
|
||||
return node
|
||||
|
||||
replaced = walk(obj, base_path[:])
|
||||
return replaced, has_var
|
||||
|
||||
def add_workflow_node(
|
||||
self,
|
||||
node_id: int,
|
||||
*,
|
||||
device_key: Optional[str] = None, # 实例名,如 "ser"
|
||||
resource_name: Optional[str] = None, # registry key(原 device_class)
|
||||
module: Optional[str] = None,
|
||||
template_name: Optional[str] = None, # 动作/模板名(原 action_key)
|
||||
params: Dict[str, Any],
|
||||
variable_sources: Dict[str, Dict[str, Any]],
|
||||
add_ready_if_no_vars: bool = True,
|
||||
prev_node_id: Optional[int] = None,
|
||||
**extra_attrs,
|
||||
) -> None:
|
||||
"""添加工作流节点:params 单层;自动变量连线与 ready 串联;支持附加属性"""
|
||||
node_id_str = str(node_id)
|
||||
inputs: Dict[str, Any] = {}
|
||||
|
||||
params, has_var = self._materialize_wiring_into_inputs(
|
||||
params, inputs, variable_sources, node_id_str, base_path=["params"]
|
||||
)
|
||||
|
||||
if add_ready_if_no_vars and not has_var:
|
||||
last_id = str(prev_node_id) if prev_node_id is not None else "-1"
|
||||
inputs["ready"] = {"node": int(last_id), "output": "ready"}
|
||||
self.add_edge(last_id, node_id_str, source_handle_io="ready", target_handle_io="ready")
|
||||
|
||||
node_obj = {
|
||||
"device_key": device_key,
|
||||
"resource_name": resource_name, # ✅ 新名字
|
||||
"module": module,
|
||||
"template_name": template_name, # ✅ 新名字
|
||||
"params": params,
|
||||
"inputs": inputs,
|
||||
}
|
||||
node_obj.update(extra_attrs or {})
|
||||
self.add_node(node_id_str, parameters=node_obj)
|
||||
|
||||
# 顺序工作流导出(连线在 inputs,不返回 edges)
|
||||
def to_dict(self) -> List[Dict[str, Any]]:
|
||||
result = []
|
||||
for node_id, attrs in self.nodes.items():
|
||||
node = {"uuid": node_id}
|
||||
params = dict(attrs.get("parameters", {}) or {})
|
||||
flat = {k: v for k, v in attrs.items() if k != "parameters"}
|
||||
flat.update(params)
|
||||
node.update(flat)
|
||||
result.append(node)
|
||||
return sorted(result, key=lambda n: int(n["uuid"]) if str(n["uuid"]).isdigit() else n["uuid"])
|
||||
|
||||
# node-link 导出(含 edges)
|
||||
def to_node_link_dict(self) -> Dict[str, Any]:
|
||||
nodes_list = []
|
||||
for node_id, attrs in self.nodes.items():
|
||||
node_attrs = attrs.copy()
|
||||
params = node_attrs.pop("parameters", {}) or {}
|
||||
node_attrs.update(params)
|
||||
nodes_list.append({"uuid": node_id, **node_attrs})
|
||||
return {
|
||||
"directed": True,
|
||||
"multigraph": False,
|
||||
"graph": {},
|
||||
"nodes": nodes_list,
|
||||
"edges": self.edges,
|
||||
"links": self.edges,
|
||||
}
|
||||
|
||||
|
||||
def refactor_data(
|
||||
data: List[Dict[str, Any]],
|
||||
action_resource_mapping: Optional[Dict[str, str]] = None,
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""统一的数据重构函数,根据操作类型自动选择模板
|
||||
|
||||
Args:
|
||||
data: 原始步骤数据列表
|
||||
action_resource_mapping: action 到 resource_name 的映射字典,可选
|
||||
"""
|
||||
refactored_data = []
|
||||
|
||||
# 定义操作映射,包含生物实验和有机化学的所有操作
|
||||
OPERATION_MAPPING = {
|
||||
# 生物实验操作
|
||||
"transfer_liquid": "transfer_liquid",
|
||||
"transfer": "transfer",
|
||||
"incubation": "incubation",
|
||||
"move_labware": "move_labware",
|
||||
"oscillation": "oscillation",
|
||||
# 有机化学操作
|
||||
"HeatChillToTemp": "HeatChillProtocol",
|
||||
"StopHeatChill": "HeatChillStopProtocol",
|
||||
"StartHeatChill": "HeatChillStartProtocol",
|
||||
"HeatChill": "HeatChillProtocol",
|
||||
"Dissolve": "DissolveProtocol",
|
||||
"Transfer": "TransferProtocol",
|
||||
"Evaporate": "EvaporateProtocol",
|
||||
"Recrystallize": "RecrystallizeProtocol",
|
||||
"Filter": "FilterProtocol",
|
||||
"Dry": "DryProtocol",
|
||||
"Add": "AddProtocol",
|
||||
}
|
||||
|
||||
UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
for step in data:
|
||||
operation = step.get("action")
|
||||
if not operation or operation in UNSUPPORTED_OPERATIONS:
|
||||
continue
|
||||
|
||||
# 处理重复操作
|
||||
if operation == "Repeat":
|
||||
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
||||
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
||||
for i in range(int(times)):
|
||||
sub_data = refactor_data(sub_steps, action_resource_mapping)
|
||||
refactored_data.extend(sub_data)
|
||||
continue
|
||||
|
||||
# 获取模板名称
|
||||
template_name = OPERATION_MAPPING.get(operation)
|
||||
if not template_name:
|
||||
# 自动推断模板类型
|
||||
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
||||
template_name = f"biomek-{operation}"
|
||||
else:
|
||||
template_name = f"{operation}Protocol"
|
||||
|
||||
# 获取 resource_name
|
||||
resource_name = f"device.{operation.lower()}"
|
||||
if action_resource_mapping:
|
||||
resource_name = action_resource_mapping.get(operation, resource_name)
|
||||
|
||||
# 获取步骤编号,生成 name 字段
|
||||
step_number = step.get("step_number")
|
||||
name = f"Step {step_number}" if step_number is not None else None
|
||||
|
||||
# 创建步骤数据
|
||||
step_data = {
|
||||
"template_name": template_name,
|
||||
"resource_name": resource_name,
|
||||
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
||||
"lab_node_type": "Device",
|
||||
"param": step.get("parameters", step.get("action_args", {})),
|
||||
"footer": f"{template_name}-{resource_name}",
|
||||
}
|
||||
if name:
|
||||
step_data["name"] = name
|
||||
refactored_data.append(step_data)
|
||||
|
||||
return refactored_data
|
||||
|
||||
|
||||
def build_protocol_graph(
|
||||
labware_info: List[Dict[str, Any]],
|
||||
protocol_steps: List[Dict[str, Any]],
|
||||
workstation_name: str,
|
||||
action_resource_mapping: Optional[Dict[str, str]] = None,
|
||||
) -> WorkflowGraph:
|
||||
"""统一的协议图构建函数,根据设备类型自动选择构建逻辑
|
||||
|
||||
Args:
|
||||
labware_info: labware 信息字典
|
||||
protocol_steps: 协议步骤列表
|
||||
workstation_name: 工作站名称
|
||||
action_resource_mapping: action 到 resource_name 的映射字典,可选
|
||||
"""
|
||||
G = WorkflowGraph()
|
||||
resource_last_writer = {}
|
||||
|
||||
protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
|
||||
# 有机化学&移液站协议图构建
|
||||
WORKSTATION_ID = workstation_name
|
||||
|
||||
# 为所有labware创建资源节点
|
||||
res_index = 0
|
||||
for labware_id, item in labware_info.items():
|
||||
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
||||
node_id = str(uuid.uuid4())
|
||||
|
||||
# 判断节点类型
|
||||
if "Rack" in str(labware_id) or "Tip" in str(labware_id):
|
||||
lab_node_type = "Labware"
|
||||
description = f"Prepare Labware: {labware_id}"
|
||||
liquid_type = []
|
||||
liquid_volume = []
|
||||
elif item.get("type") == "hardware" or "reactor" in str(labware_id).lower():
|
||||
if "reactor" not in str(labware_id).lower():
|
||||
continue
|
||||
lab_node_type = "Sample"
|
||||
description = f"Prepare Reactor: {labware_id}"
|
||||
liquid_type = []
|
||||
liquid_volume = []
|
||||
else:
|
||||
lab_node_type = "Reagent"
|
||||
description = f"Add Reagent to Flask: {labware_id}"
|
||||
liquid_type = [labware_id]
|
||||
liquid_volume = [1e5]
|
||||
|
||||
res_index += 1
|
||||
G.add_node(
|
||||
node_id,
|
||||
template_name="create_resource",
|
||||
resource_name="host_node",
|
||||
name=f"Res {res_index}",
|
||||
description=description,
|
||||
lab_node_type=lab_node_type,
|
||||
footer="create_resource-host_node",
|
||||
param={
|
||||
"res_id": labware_id,
|
||||
"device_id": WORKSTATION_ID,
|
||||
"class_name": "container",
|
||||
"parent": WORKSTATION_ID,
|
||||
"bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
|
||||
"liquid_input_slot": [-1],
|
||||
"liquid_type": liquid_type,
|
||||
"liquid_volume": liquid_volume,
|
||||
"slot_on_deck": "",
|
||||
},
|
||||
)
|
||||
resource_last_writer[labware_id] = f"{node_id}:labware"
|
||||
|
||||
last_control_node_id = None
|
||||
|
||||
# 处理协议步骤
|
||||
for step in protocol_steps:
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(node_id, **step)
|
||||
|
||||
# 控制流
|
||||
if last_control_node_id is not None:
|
||||
G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
|
||||
last_control_node_id = node_id
|
||||
|
||||
# 物料流
|
||||
params = step.get("param", {})
|
||||
input_resources_possible_names = [
|
||||
"vessel",
|
||||
"to_vessel",
|
||||
"from_vessel",
|
||||
"reagent",
|
||||
"solvent",
|
||||
"compound",
|
||||
"sources",
|
||||
"targets",
|
||||
]
|
||||
|
||||
for target_port in input_resources_possible_names:
|
||||
resource_name = params.get(target_port)
|
||||
if resource_name and resource_name in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[resource_name].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
|
||||
|
||||
output_resources = {
|
||||
"vessel_out": params.get("vessel"),
|
||||
"from_vessel_out": params.get("from_vessel"),
|
||||
"to_vessel_out": params.get("to_vessel"),
|
||||
"filtrate_out": params.get("filtrate_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources_out": params.get("sources"),
|
||||
"targets_out": params.get("targets"),
|
||||
}
|
||||
|
||||
for source_port, resource_name in output_resources.items():
|
||||
if resource_name:
|
||||
resource_last_writer[resource_name] = f"{node_id}:{source_port}"
|
||||
|
||||
return G
|
||||
|
||||
|
||||
def draw_protocol_graph(protocol_graph: WorkflowGraph, output_path: str):
|
||||
"""
|
||||
(辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图,用于可视化。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
G = nx.DiGraph()
|
||||
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template_name", node_id[:8]))
|
||||
G.add_node(node_id, label=label, **attrs)
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
G.add_edge(edge["source"], edge["target"])
|
||||
|
||||
plt.figure(figsize=(20, 15))
|
||||
try:
|
||||
pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
|
||||
except Exception:
|
||||
pos = nx.shell_layout(G) # Fallback layout
|
||||
|
||||
node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
|
||||
nx.draw(
|
||||
G,
|
||||
pos,
|
||||
with_labels=False,
|
||||
node_size=2500,
|
||||
node_color="skyblue",
|
||||
node_shape="o",
|
||||
edge_color="gray",
|
||||
width=1.5,
|
||||
arrowsize=15,
|
||||
)
|
||||
nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
|
||||
|
||||
plt.title("Chemical Protocol Workflow Graph", size=15)
|
||||
plt.savefig(output_path, dpi=300, bbox_inches="tight")
|
||||
plt.close()
|
||||
print(f" - Visualization saved to '{output_path}'")
|
||||
|
||||
|
||||
COMPASS = {"n", "e", "s", "w", "ne", "nw", "se", "sw", "c"}
|
||||
|
||||
|
||||
def _is_compass(port: str) -> bool:
|
||||
return isinstance(port, str) and port.lower() in COMPASS
|
||||
|
||||
|
||||
def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
|
||||
"""
|
||||
使用 Graphviz 端口语法绘制协议工作流图。
|
||||
- 若边上的 source_port/target_port 是 compass(n/e/s/w/...),直接用 compass。
|
||||
- 否则自动为节点创建 record 形状并定义命名端口 <portname>。
|
||||
最终由 PyGraphviz 渲染并输出到 output_path(后缀决定格式,如 .png/.svg/.pdf)。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
# 1) 先用 networkx 搭建有向图,保留端口属性
|
||||
G = nx.DiGraph()
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template_name", node_id[:8]))
|
||||
# 保留一个干净的“中心标签”,用于放在 record 的中间槽
|
||||
G.add_node(node_id, _core_label=str(label), **{k: v for k, v in attrs.items() if k not in ("label",)})
|
||||
|
||||
edges_data = []
|
||||
in_ports_by_node = {} # 收集命名输入端口
|
||||
out_ports_by_node = {} # 收集命名输出端口
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
u = edge["source"]
|
||||
v = edge["target"]
|
||||
sp = edge.get("source_handle_key") or edge.get("source_port")
|
||||
tp = edge.get("target_handle_key") or edge.get("target_port")
|
||||
|
||||
# 记录到图里(保留原始端口信息)
|
||||
G.add_edge(u, v, source_handle_key=sp, target_handle_key=tp)
|
||||
edges_data.append((u, v, sp, tp))
|
||||
|
||||
# 如果不是 compass,就按“命名端口”先归类,等会儿给节点造 record
|
||||
if sp and not _is_compass(sp):
|
||||
out_ports_by_node.setdefault(u, set()).add(str(sp))
|
||||
if tp and not _is_compass(tp):
|
||||
in_ports_by_node.setdefault(v, set()).add(str(tp))
|
||||
|
||||
# 2) 转为 AGraph,使用 Graphviz 渲染
|
||||
A = to_agraph(G)
|
||||
A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
|
||||
A.node_attr.update(
|
||||
shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica"
|
||||
)
|
||||
A.edge_attr.update(arrowsize="0.8", color="#666666")
|
||||
|
||||
# 3) 为需要命名端口的节点设置 record 形状与 label
|
||||
# 左列 = 输入端口;中间 = 核心标签;右列 = 输出端口
|
||||
for n in A.nodes():
|
||||
node = A.get_node(n)
|
||||
core = G.nodes[n].get("_core_label", n)
|
||||
|
||||
in_ports = sorted(in_ports_by_node.get(n, []))
|
||||
out_ports = sorted(out_ports_by_node.get(n, []))
|
||||
|
||||
# 如果该节点涉及命名端口,则用 record;否则保留原 box
|
||||
if in_ports or out_ports:
|
||||
|
||||
def port_fields(ports):
|
||||
if not ports:
|
||||
return " " # 必须留一个空槽占位
|
||||
# 每个端口一个小格子,<p> name
|
||||
return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
|
||||
|
||||
left = port_fields(in_ports)
|
||||
right = port_fields(out_ports)
|
||||
|
||||
# 三栏:左(入) | 中(节点名) | 右(出)
|
||||
record_label = f"{{ {left} | {core} | {right} }}"
|
||||
node.attr.update(shape="record", label=record_label)
|
||||
else:
|
||||
# 没有命名端口:普通盒子,显示核心标签
|
||||
node.attr.update(label=str(core))
|
||||
|
||||
# 4) 给边设置 headport / tailport
|
||||
# - 若端口为 compass:直接用 compass(e.g., headport="e")
|
||||
# - 若端口为命名端口:使用在 record 中定义的 <port> 名(同名即可)
|
||||
for u, v, sp, tp in edges_data:
|
||||
e = A.get_edge(u, v)
|
||||
|
||||
# Graphviz 属性:tail 是源,head 是目标
|
||||
if sp:
|
||||
if _is_compass(sp):
|
||||
e.attr["tailport"] = sp.lower()
|
||||
else:
|
||||
# 与 record label 中 <port> 名一致;特殊字符已在 label 中做了清洗
|
||||
e.attr["tailport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(sp))
|
||||
|
||||
if tp:
|
||||
if _is_compass(tp):
|
||||
e.attr["headport"] = tp.lower()
|
||||
else:
|
||||
e.attr["headport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(tp))
|
||||
|
||||
# 可选:若想让边更贴边缘,可设置 constraint/spline 等
|
||||
# e.attr["arrowhead"] = "vee"
|
||||
|
||||
# 5) 输出
|
||||
A.draw(output_path, prog="dot")
|
||||
print(f" - Port-aware workflow rendered to '{output_path}'")
|
||||
|
||||
|
||||
# ---------------- Registry Adapter ----------------
|
||||
|
||||
|
||||
class RegistryAdapter:
|
||||
"""根据 module 的类名(冒号右侧)反查 registry 的 resource_name(原 device_class),并抽取参数顺序"""
|
||||
|
||||
def __init__(self, device_registry: Dict[str, Any]):
|
||||
self.device_registry = device_registry or {}
|
||||
self.module_class_to_resource = self._build_module_class_index()
|
||||
|
||||
def _build_module_class_index(self) -> Dict[str, str]:
|
||||
idx = {}
|
||||
for resource_name, info in self.device_registry.items():
|
||||
module = info.get("module")
|
||||
if isinstance(module, str) and ":" in module:
|
||||
cls = module.split(":")[-1]
|
||||
idx[cls] = resource_name
|
||||
idx[cls.lower()] = resource_name
|
||||
return idx
|
||||
|
||||
def resolve_resource_by_classname(self, class_name: str) -> Optional[str]:
|
||||
if not class_name:
|
||||
return None
|
||||
return self.module_class_to_resource.get(class_name) or self.module_class_to_resource.get(class_name.lower())
|
||||
|
||||
def get_device_module(self, resource_name: Optional[str]) -> Optional[str]:
|
||||
if not resource_name:
|
||||
return None
|
||||
return self.device_registry.get(resource_name, {}).get("module")
|
||||
|
||||
def get_actions(self, resource_name: Optional[str]) -> Dict[str, Any]:
|
||||
if not resource_name:
|
||||
return {}
|
||||
return (self.device_registry.get(resource_name, {}).get("class", {}).get("action_value_mappings", {})) or {}
|
||||
|
||||
def get_action_schema(self, resource_name: Optional[str], template_name: str) -> Optional[Json]:
|
||||
return (self.get_actions(resource_name).get(template_name) or {}).get("schema")
|
||||
|
||||
def get_action_goal_default(self, resource_name: Optional[str], template_name: str) -> Json:
|
||||
return (self.get_actions(resource_name).get(template_name) or {}).get("goal_default", {}) or {}
|
||||
|
||||
def get_action_input_keys(self, resource_name: Optional[str], template_name: str) -> List[str]:
|
||||
schema = self.get_action_schema(resource_name, template_name) or {}
|
||||
goal = (schema.get("properties") or {}).get("goal") or {}
|
||||
props = goal.get("properties") or {}
|
||||
required = goal.get("required") or []
|
||||
return list(dict.fromkeys(required + list(props.keys())))
|
||||
@@ -1,356 +0,0 @@
|
||||
"""
|
||||
JSON 工作流转换模块
|
||||
|
||||
提供从多种 JSON 格式转换为统一工作流格式的功能。
|
||||
支持的格式:
|
||||
1. workflow/reagent 格式
|
||||
2. steps_info/labware_info 格式
|
||||
"""
|
||||
|
||||
import json
|
||||
from os import PathLike
|
||||
from pathlib import Path
|
||||
from typing import Any, Dict, List, Optional, Set, Tuple, Union
|
||||
|
||||
from unilabos.workflow.common import WorkflowGraph, build_protocol_graph
|
||||
from unilabos.registry.registry import lab_registry
|
||||
|
||||
|
||||
def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]:
|
||||
"""
|
||||
从 registry 获取指定设备和动作的 handles 配置
|
||||
|
||||
Args:
|
||||
resource_name: 设备资源名称,如 "liquid_handler.prcxi"
|
||||
template_name: 动作模板名称,如 "transfer_liquid"
|
||||
|
||||
Returns:
|
||||
包含 source 和 target handler_keys 的字典:
|
||||
{"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]}
|
||||
"""
|
||||
result = {"source": [], "target": []}
|
||||
|
||||
device_info = lab_registry.device_type_registry.get(resource_name, {})
|
||||
if not device_info:
|
||||
return result
|
||||
|
||||
action_mappings = device_info.get("class", {}).get("action_value_mappings", {})
|
||||
action_config = action_mappings.get(template_name, {})
|
||||
handles = action_config.get("handles", {})
|
||||
|
||||
if isinstance(handles, dict):
|
||||
# 处理 input handles (作为 target)
|
||||
for handle in handles.get("input", []):
|
||||
handler_key = handle.get("handler_key", "")
|
||||
if handler_key:
|
||||
result["source"].append(handler_key)
|
||||
# 处理 output handles (作为 source)
|
||||
for handle in handles.get("output", []):
|
||||
handler_key = handle.get("handler_key", "")
|
||||
if handler_key:
|
||||
result["target"].append(handler_key)
|
||||
|
||||
return result
|
||||
|
||||
|
||||
def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]:
|
||||
"""
|
||||
校验工作流图中所有边的句柄配置是否正确
|
||||
|
||||
Args:
|
||||
graph: 工作流图对象
|
||||
|
||||
Returns:
|
||||
(is_valid, errors): 是否有效,错误信息列表
|
||||
"""
|
||||
errors = []
|
||||
nodes = graph.nodes
|
||||
|
||||
for edge in graph.edges:
|
||||
left_uuid = edge.get("source")
|
||||
right_uuid = edge.get("target")
|
||||
# target_handle_key是target, right的输入节点(入节点)
|
||||
# source_handle_key是source, left的输出节点(出节点)
|
||||
right_source_conn_key = edge.get("target_handle_key", "")
|
||||
left_target_conn_key = edge.get("source_handle_key", "")
|
||||
|
||||
# 获取源节点和目标节点信息
|
||||
left_node = nodes.get(left_uuid, {})
|
||||
right_node = nodes.get(right_uuid, {})
|
||||
|
||||
left_res_name = left_node.get("resource_name", "")
|
||||
left_template_name = left_node.get("template_name", "")
|
||||
right_res_name = right_node.get("resource_name", "")
|
||||
right_template_name = right_node.get("template_name", "")
|
||||
|
||||
# 获取源节点的 output handles
|
||||
left_node_handles = get_action_handles(left_res_name, left_template_name)
|
||||
target_valid_keys = left_node_handles.get("target", [])
|
||||
target_valid_keys.append("ready")
|
||||
|
||||
# 获取目标节点的 input handles
|
||||
right_node_handles = get_action_handles(right_res_name, right_template_name)
|
||||
source_valid_keys = right_node_handles.get("source", [])
|
||||
source_valid_keys.append("ready")
|
||||
|
||||
# 如果节点配置了 output handles,则 source_port 必须有效
|
||||
if not right_source_conn_key:
|
||||
node_name = left_node.get("name", left_uuid[:8])
|
||||
errors.append(f"源节点 '{node_name}' 的 source_handle_key 为空," f"应设置为: {source_valid_keys}")
|
||||
elif right_source_conn_key not in source_valid_keys:
|
||||
node_name = left_node.get("name", left_uuid[:8])
|
||||
errors.append(
|
||||
f"源节点 '{node_name}' 的 source 端点 '{right_source_conn_key}' 不存在," f"支持的端点: {source_valid_keys}"
|
||||
)
|
||||
|
||||
# 如果节点配置了 input handles,则 target_port 必须有效
|
||||
if not left_target_conn_key:
|
||||
node_name = right_node.get("name", right_uuid[:8])
|
||||
errors.append(f"目标节点 '{node_name}' 的 target_handle_key 为空," f"应设置为: {target_valid_keys}")
|
||||
elif left_target_conn_key not in target_valid_keys:
|
||||
node_name = right_node.get("name", right_uuid[:8])
|
||||
errors.append(
|
||||
f"目标节点 '{node_name}' 的 target 端点 '{left_target_conn_key}' 不存在,"
|
||||
f"支持的端点: {target_valid_keys}"
|
||||
)
|
||||
|
||||
return len(errors) == 0, errors
|
||||
|
||||
|
||||
# action 到 resource_name 的映射
|
||||
ACTION_RESOURCE_MAPPING: Dict[str, str] = {
|
||||
# 生物实验操作
|
||||
"transfer_liquid": "liquid_handler.prcxi",
|
||||
"transfer": "liquid_handler.prcxi",
|
||||
"incubation": "incubator.prcxi",
|
||||
"move_labware": "labware_mover.prcxi",
|
||||
"oscillation": "shaker.prcxi",
|
||||
# 有机化学操作
|
||||
"HeatChillToTemp": "heatchill.chemputer",
|
||||
"StopHeatChill": "heatchill.chemputer",
|
||||
"StartHeatChill": "heatchill.chemputer",
|
||||
"HeatChill": "heatchill.chemputer",
|
||||
"Dissolve": "stirrer.chemputer",
|
||||
"Transfer": "liquid_handler.chemputer",
|
||||
"Evaporate": "rotavap.chemputer",
|
||||
"Recrystallize": "reactor.chemputer",
|
||||
"Filter": "filter.chemputer",
|
||||
"Dry": "dryer.chemputer",
|
||||
"Add": "liquid_handler.chemputer",
|
||||
}
|
||||
|
||||
|
||||
def normalize_steps(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
将不同格式的步骤数据规范化为统一格式
|
||||
|
||||
支持的输入格式:
|
||||
- action + parameters
|
||||
- action + action_args
|
||||
- operation + parameters
|
||||
|
||||
Args:
|
||||
data: 原始步骤数据列表
|
||||
|
||||
Returns:
|
||||
规范化后的步骤列表,格式为 [{"action": str, "parameters": dict, "description": str?, "step_number": int?}, ...]
|
||||
"""
|
||||
normalized = []
|
||||
for idx, step in enumerate(data):
|
||||
# 获取动作名称(支持 action 或 operation 字段)
|
||||
action = step.get("action") or step.get("operation")
|
||||
if not action:
|
||||
continue
|
||||
|
||||
# 获取参数(支持 parameters 或 action_args 字段)
|
||||
raw_params = step.get("parameters") or step.get("action_args") or {}
|
||||
params = dict(raw_params)
|
||||
|
||||
# 规范化 source/target -> sources/targets
|
||||
if "source" in raw_params and "sources" not in raw_params:
|
||||
params["sources"] = raw_params["source"]
|
||||
if "target" in raw_params and "targets" not in raw_params:
|
||||
params["targets"] = raw_params["target"]
|
||||
|
||||
# 获取描述(支持 description 或 purpose 字段)
|
||||
description = step.get("description") or step.get("purpose")
|
||||
|
||||
# 获取步骤编号(优先使用原始数据中的 step_number,否则使用索引+1)
|
||||
step_number = step.get("step_number", idx + 1)
|
||||
|
||||
step_dict = {"action": action, "parameters": params, "step_number": step_number}
|
||||
if description:
|
||||
step_dict["description"] = description
|
||||
|
||||
normalized.append(step_dict)
|
||||
|
||||
return normalized
|
||||
|
||||
|
||||
def normalize_labware(data: List[Dict[str, Any]]) -> Dict[str, Dict[str, Any]]:
|
||||
"""
|
||||
将不同格式的 labware 数据规范化为统一的字典格式
|
||||
|
||||
支持的输入格式:
|
||||
- reagent_name + material_name + positions
|
||||
- name + labware + slot
|
||||
|
||||
Args:
|
||||
data: 原始 labware 数据列表
|
||||
|
||||
Returns:
|
||||
规范化后的 labware 字典,格式为 {name: {"slot": int, "labware": str, "well": list, "type": str, "role": str, "name": str}, ...}
|
||||
"""
|
||||
labware = {}
|
||||
for item in data:
|
||||
# 获取 key 名称(优先使用 reagent_name,其次是 material_name 或 name)
|
||||
reagent_name = item.get("reagent_name")
|
||||
key = reagent_name or item.get("material_name") or item.get("name")
|
||||
if not key:
|
||||
continue
|
||||
|
||||
key = str(key)
|
||||
|
||||
# 处理重复 key,自动添加后缀
|
||||
idx = 1
|
||||
original_key = key
|
||||
while key in labware:
|
||||
idx += 1
|
||||
key = f"{original_key}_{idx}"
|
||||
|
||||
labware[key] = {
|
||||
"slot": item.get("positions") or item.get("slot"),
|
||||
"labware": item.get("material_name") or item.get("labware"),
|
||||
"well": item.get("well", []),
|
||||
"type": item.get("type", "reagent"),
|
||||
"role": item.get("role", ""),
|
||||
"name": key,
|
||||
}
|
||||
|
||||
return labware
|
||||
|
||||
|
||||
def convert_from_json(
|
||||
data: Union[str, PathLike, Dict[str, Any]],
|
||||
workstation_name: str = "PRCXi",
|
||||
validate: bool = True,
|
||||
) -> WorkflowGraph:
|
||||
"""
|
||||
从 JSON 数据或文件转换为 WorkflowGraph
|
||||
|
||||
支持的 JSON 格式:
|
||||
1. {"workflow": [...], "reagent": {...}} - 直接格式
|
||||
2. {"steps_info": [...], "labware_info": [...]} - 需要规范化的格式
|
||||
|
||||
Args:
|
||||
data: JSON 文件路径、字典数据、或 JSON 字符串
|
||||
workstation_name: 工作站名称,默认 "PRCXi"
|
||||
validate: 是否校验句柄配置,默认 True
|
||||
|
||||
Returns:
|
||||
WorkflowGraph: 构建好的工作流图
|
||||
|
||||
Raises:
|
||||
ValueError: 不支持的 JSON 格式 或 句柄校验失败
|
||||
FileNotFoundError: 文件不存在
|
||||
json.JSONDecodeError: JSON 解析失败
|
||||
"""
|
||||
# 处理输入数据
|
||||
if isinstance(data, (str, PathLike)):
|
||||
path = Path(data)
|
||||
if path.exists():
|
||||
with path.open("r", encoding="utf-8") as fp:
|
||||
json_data = json.load(fp)
|
||||
elif isinstance(data, str):
|
||||
# 尝试作为 JSON 字符串解析
|
||||
json_data = json.loads(data)
|
||||
else:
|
||||
raise FileNotFoundError(f"文件不存在: {data}")
|
||||
elif isinstance(data, dict):
|
||||
json_data = data
|
||||
else:
|
||||
raise TypeError(f"不支持的数据类型: {type(data)}")
|
||||
|
||||
# 根据格式解析数据
|
||||
if "workflow" in json_data and "reagent" in json_data:
|
||||
# 格式1: workflow/reagent(已经是规范格式)
|
||||
protocol_steps = json_data["workflow"]
|
||||
labware_info = json_data["reagent"]
|
||||
elif "steps_info" in json_data and "labware_info" in json_data:
|
||||
# 格式2: steps_info/labware_info(需要规范化)
|
||||
protocol_steps = normalize_steps(json_data["steps_info"])
|
||||
labware_info = normalize_labware(json_data["labware_info"])
|
||||
elif "steps" in json_data and "labware" in json_data:
|
||||
# 格式3: steps/labware(另一种常见格式)
|
||||
protocol_steps = normalize_steps(json_data["steps"])
|
||||
if isinstance(json_data["labware"], list):
|
||||
labware_info = normalize_labware(json_data["labware"])
|
||||
else:
|
||||
labware_info = json_data["labware"]
|
||||
else:
|
||||
raise ValueError(
|
||||
"不支持的 JSON 格式。支持的格式:\n"
|
||||
"1. {'workflow': [...], 'reagent': {...}}\n"
|
||||
"2. {'steps_info': [...], 'labware_info': [...]}\n"
|
||||
"3. {'steps': [...], 'labware': [...]}"
|
||||
)
|
||||
|
||||
# 构建工作流图
|
||||
graph = build_protocol_graph(
|
||||
labware_info=labware_info,
|
||||
protocol_steps=protocol_steps,
|
||||
workstation_name=workstation_name,
|
||||
action_resource_mapping=ACTION_RESOURCE_MAPPING,
|
||||
)
|
||||
|
||||
# 校验句柄配置
|
||||
if validate:
|
||||
is_valid, errors = validate_workflow_handles(graph)
|
||||
if not is_valid:
|
||||
import warnings
|
||||
|
||||
for error in errors:
|
||||
warnings.warn(f"句柄校验警告: {error}")
|
||||
|
||||
return graph
|
||||
|
||||
|
||||
def convert_json_to_node_link(
|
||||
data: Union[str, PathLike, Dict[str, Any]],
|
||||
workstation_name: str = "PRCXi",
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
将 JSON 数据转换为 node-link 格式的字典
|
||||
|
||||
Args:
|
||||
data: JSON 文件路径、字典数据、或 JSON 字符串
|
||||
workstation_name: 工作站名称,默认 "PRCXi"
|
||||
|
||||
Returns:
|
||||
Dict: node-link 格式的工作流数据
|
||||
"""
|
||||
graph = convert_from_json(data, workstation_name)
|
||||
return graph.to_node_link_dict()
|
||||
|
||||
|
||||
def convert_json_to_workflow_list(
|
||||
data: Union[str, PathLike, Dict[str, Any]],
|
||||
workstation_name: str = "PRCXi",
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
将 JSON 数据转换为工作流列表格式
|
||||
|
||||
Args:
|
||||
data: JSON 文件路径、字典数据、或 JSON 字符串
|
||||
workstation_name: 工作站名称,默认 "PRCXi"
|
||||
|
||||
Returns:
|
||||
List: 工作流节点列表
|
||||
"""
|
||||
graph = convert_from_json(data, workstation_name)
|
||||
return graph.to_dict()
|
||||
|
||||
|
||||
# 为了向后兼容,保留下划线前缀的别名
|
||||
_normalize_steps = normalize_steps
|
||||
_normalize_labware = normalize_labware
|
||||
@@ -1,241 +0,0 @@
|
||||
import ast
|
||||
import json
|
||||
from typing import Dict, List, Any, Tuple, Optional
|
||||
|
||||
from .common import WorkflowGraph, RegistryAdapter
|
||||
|
||||
Json = Dict[str, Any]
|
||||
|
||||
# ---------------- Converter ----------------
|
||||
|
||||
class DeviceMethodConverter:
|
||||
"""
|
||||
- 字段统一:resource_name(原 device_class)、template_name(原 action_key)
|
||||
- params 单层;inputs 使用 'params.' 前缀
|
||||
- SimpleGraph.add_workflow_node 负责变量连线与边
|
||||
"""
|
||||
def __init__(self, device_registry: Optional[Dict[str, Any]] = None):
|
||||
self.graph = WorkflowGraph()
|
||||
self.variable_sources: Dict[str, Dict[str, Any]] = {} # var -> {node_id, output_name}
|
||||
self.instance_to_resource: Dict[str, Optional[str]] = {} # 实例名 -> resource_name
|
||||
self.node_id_counter: int = 0
|
||||
self.registry = RegistryAdapter(device_registry or {})
|
||||
|
||||
# ---- helpers ----
|
||||
def _new_node_id(self) -> int:
|
||||
nid = self.node_id_counter
|
||||
self.node_id_counter += 1
|
||||
return nid
|
||||
|
||||
def _assign_targets(self, targets) -> List[str]:
|
||||
names: List[str] = []
|
||||
import ast
|
||||
if isinstance(targets, ast.Tuple):
|
||||
for elt in targets.elts:
|
||||
if isinstance(elt, ast.Name):
|
||||
names.append(elt.id)
|
||||
elif isinstance(targets, ast.Name):
|
||||
names.append(targets.id)
|
||||
return names
|
||||
|
||||
def _extract_device_instantiation(self, node) -> Optional[Tuple[str, str]]:
|
||||
import ast
|
||||
if not isinstance(node.value, ast.Call):
|
||||
return None
|
||||
callee = node.value.func
|
||||
if isinstance(callee, ast.Name):
|
||||
class_name = callee.id
|
||||
elif isinstance(callee, ast.Attribute) and isinstance(callee.value, ast.Name):
|
||||
class_name = callee.attr
|
||||
else:
|
||||
return None
|
||||
if isinstance(node.targets[0], ast.Name):
|
||||
instance = node.targets[0].id
|
||||
return instance, class_name
|
||||
return None
|
||||
|
||||
def _extract_call(self, call) -> Tuple[str, str, Dict[str, Any], str]:
|
||||
import ast
|
||||
owner_name, method_name, call_kind = "", "", "func"
|
||||
if isinstance(call.func, ast.Attribute):
|
||||
method_name = call.func.attr
|
||||
if isinstance(call.func.value, ast.Name):
|
||||
owner_name = call.func.value.id
|
||||
call_kind = "instance" if owner_name in self.instance_to_resource else "class_or_module"
|
||||
elif isinstance(call.func.value, ast.Attribute) and isinstance(call.func.value.value, ast.Name):
|
||||
owner_name = call.func.value.attr
|
||||
call_kind = "class_or_module"
|
||||
elif isinstance(call.func, ast.Name):
|
||||
method_name = call.func.id
|
||||
call_kind = "func"
|
||||
|
||||
def pack(node):
|
||||
if isinstance(node, ast.Name):
|
||||
return {"type": "variable", "value": node.id}
|
||||
if isinstance(node, ast.Constant):
|
||||
return {"type": "constant", "value": node.value}
|
||||
if isinstance(node, ast.Dict):
|
||||
return {"type": "dict", "value": self._parse_dict(node)}
|
||||
if isinstance(node, ast.List):
|
||||
return {"type": "list", "value": self._parse_list(node)}
|
||||
return {"type": "raw", "value": ast.unparse(node) if hasattr(ast, "unparse") else str(node)}
|
||||
|
||||
args: Dict[str, Any] = {}
|
||||
pos: List[Any] = []
|
||||
for a in call.args:
|
||||
pos.append(pack(a))
|
||||
for kw in call.keywords:
|
||||
args[kw.arg] = pack(kw.value)
|
||||
if pos:
|
||||
args["_positional"] = pos
|
||||
return owner_name, method_name, args, call_kind
|
||||
|
||||
def _parse_dict(self, node) -> Dict[str, Any]:
|
||||
import ast
|
||||
out: Dict[str, Any] = {}
|
||||
for k, v in zip(node.keys, node.values):
|
||||
if isinstance(k, ast.Constant):
|
||||
key = str(k.value)
|
||||
if isinstance(v, ast.Name):
|
||||
out[key] = f"var:{v.id}"
|
||||
elif isinstance(v, ast.Constant):
|
||||
out[key] = v.value
|
||||
elif isinstance(v, ast.Dict):
|
||||
out[key] = self._parse_dict(v)
|
||||
elif isinstance(v, ast.List):
|
||||
out[key] = self._parse_list(v)
|
||||
return out
|
||||
|
||||
def _parse_list(self, node) -> List[Any]:
|
||||
import ast
|
||||
out: List[Any] = []
|
||||
for elt in node.elts:
|
||||
if isinstance(elt, ast.Name):
|
||||
out.append(f"var:{elt.id}")
|
||||
elif isinstance(elt, ast.Constant):
|
||||
out.append(elt.value)
|
||||
elif isinstance(elt, ast.Dict):
|
||||
out.append(self._parse_dict(elt))
|
||||
elif isinstance(elt, ast.List):
|
||||
out.append(self._parse_list(elt))
|
||||
return out
|
||||
|
||||
def _normalize_var_tokens(self, x: Any) -> Any:
|
||||
if isinstance(x, str) and x.startswith("var:"):
|
||||
return {"__var__": x[4:]}
|
||||
if isinstance(x, list):
|
||||
return [self._normalize_var_tokens(i) for i in x]
|
||||
if isinstance(x, dict):
|
||||
return {k: self._normalize_var_tokens(v) for k, v in x.items()}
|
||||
return x
|
||||
|
||||
def _make_params_payload(self, resource_name: Optional[str], template_name: str, call_args: Dict[str, Any]) -> Dict[str, Any]:
|
||||
input_keys = self.registry.get_action_input_keys(resource_name, template_name) if resource_name else []
|
||||
defaults = self.registry.get_action_goal_default(resource_name, template_name) if resource_name else {}
|
||||
params: Dict[str, Any] = dict(defaults)
|
||||
|
||||
def unpack(p):
|
||||
t, v = p.get("type"), p.get("value")
|
||||
if t == "variable":
|
||||
return {"__var__": v}
|
||||
if t == "dict":
|
||||
return self._normalize_var_tokens(v)
|
||||
if t == "list":
|
||||
return self._normalize_var_tokens(v)
|
||||
return v
|
||||
|
||||
for k, p in call_args.items():
|
||||
if k == "_positional":
|
||||
continue
|
||||
params[k] = unpack(p)
|
||||
|
||||
pos = call_args.get("_positional", [])
|
||||
if pos:
|
||||
if input_keys:
|
||||
for i, p in enumerate(pos):
|
||||
if i >= len(input_keys):
|
||||
break
|
||||
name = input_keys[i]
|
||||
if name in params:
|
||||
continue
|
||||
params[name] = unpack(p)
|
||||
else:
|
||||
for i, p in enumerate(pos):
|
||||
params[f"arg_{i}"] = unpack(p)
|
||||
return params
|
||||
|
||||
# ---- handlers ----
|
||||
def _on_assign(self, stmt):
|
||||
import ast
|
||||
inst = self._extract_device_instantiation(stmt)
|
||||
if inst:
|
||||
instance, code_class = inst
|
||||
resource_name = self.registry.resolve_resource_by_classname(code_class)
|
||||
self.instance_to_resource[instance] = resource_name
|
||||
return
|
||||
|
||||
if isinstance(stmt.value, ast.Call):
|
||||
owner, method, call_args, kind = self._extract_call(stmt.value)
|
||||
if kind == "instance":
|
||||
device_key = owner
|
||||
resource_name = self.instance_to_resource.get(owner)
|
||||
else:
|
||||
device_key = owner
|
||||
resource_name = self.registry.resolve_resource_by_classname(owner)
|
||||
|
||||
module = self.registry.get_device_module(resource_name)
|
||||
params = self._make_params_payload(resource_name, method, call_args)
|
||||
|
||||
nid = self._new_node_id()
|
||||
self.graph.add_workflow_node(
|
||||
nid,
|
||||
device_key=device_key,
|
||||
resource_name=resource_name, # ✅
|
||||
module=module,
|
||||
template_name=method, # ✅
|
||||
params=params,
|
||||
variable_sources=self.variable_sources,
|
||||
add_ready_if_no_vars=True,
|
||||
prev_node_id=(nid - 1) if nid > 0 else None,
|
||||
)
|
||||
|
||||
out_vars = self._assign_targets(stmt.targets[0])
|
||||
for var in out_vars:
|
||||
self.variable_sources[var] = {"node_id": nid, "output_name": "result"}
|
||||
|
||||
def _on_expr(self, stmt):
|
||||
import ast
|
||||
if not isinstance(stmt.value, ast.Call):
|
||||
return
|
||||
owner, method, call_args, kind = self._extract_call(stmt.value)
|
||||
if kind == "instance":
|
||||
device_key = owner
|
||||
resource_name = self.instance_to_resource.get(owner)
|
||||
else:
|
||||
device_key = owner
|
||||
resource_name = self.registry.resolve_resource_by_classname(owner)
|
||||
|
||||
module = self.registry.get_device_module(resource_name)
|
||||
params = self._make_params_payload(resource_name, method, call_args)
|
||||
|
||||
nid = self._new_node_id()
|
||||
self.graph.add_workflow_node(
|
||||
nid,
|
||||
device_key=device_key,
|
||||
resource_name=resource_name, # ✅
|
||||
module=module,
|
||||
template_name=method, # ✅
|
||||
params=params,
|
||||
variable_sources=self.variable_sources,
|
||||
add_ready_if_no_vars=True,
|
||||
prev_node_id=(nid - 1) if nid > 0 else None,
|
||||
)
|
||||
|
||||
def convert(self, python_code: str):
|
||||
tree = ast.parse(python_code)
|
||||
for stmt in tree.body:
|
||||
if isinstance(stmt, ast.Assign):
|
||||
self._on_assign(stmt)
|
||||
elif isinstance(stmt, ast.Expr):
|
||||
self._on_expr(stmt)
|
||||
return self
|
||||
@@ -1,131 +0,0 @@
|
||||
from typing import List, Any, Dict
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
|
||||
def convert_to_type(val: str) -> Any:
|
||||
"""将字符串值转换为适当的数据类型"""
|
||||
if val == "True":
|
||||
return True
|
||||
if val == "False":
|
||||
return False
|
||||
if val == "?":
|
||||
return None
|
||||
if val.endswith(" g"):
|
||||
return float(val.split(" ")[0])
|
||||
if val.endswith("mg"):
|
||||
return float(val.split("mg")[0])
|
||||
elif val.endswith("mmol"):
|
||||
return float(val.split("mmol")[0]) / 1000
|
||||
elif val.endswith("mol"):
|
||||
return float(val.split("mol")[0])
|
||||
elif val.endswith("ml"):
|
||||
return float(val.split("ml")[0])
|
||||
elif val.endswith("RPM"):
|
||||
return float(val.split("RPM")[0])
|
||||
elif val.endswith(" °C"):
|
||||
return float(val.split(" ")[0])
|
||||
elif val.endswith(" %"):
|
||||
return float(val.split(" ")[0])
|
||||
return val
|
||||
|
||||
|
||||
def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
|
||||
"""展平嵌套的XDL程序结构"""
|
||||
flattened_operations = []
|
||||
TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
def extract_operations(element: ET.Element):
|
||||
if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
|
||||
if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
|
||||
flattened_operations.append(element)
|
||||
|
||||
for child in element:
|
||||
extract_operations(child)
|
||||
|
||||
for child in procedure_elem:
|
||||
extract_operations(child)
|
||||
|
||||
return flattened_operations
|
||||
|
||||
|
||||
def parse_xdl_content(xdl_content: str) -> tuple:
|
||||
"""解析XDL内容"""
|
||||
try:
|
||||
xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
|
||||
root = ET.fromstring(xdl_content_cleaned)
|
||||
|
||||
synthesis_elem = root.find("Synthesis")
|
||||
if synthesis_elem is None:
|
||||
return None, None, None
|
||||
|
||||
# 解析硬件组件
|
||||
hardware_elem = synthesis_elem.find("Hardware")
|
||||
hardware = []
|
||||
if hardware_elem is not None:
|
||||
hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
|
||||
|
||||
# 解析试剂
|
||||
reagents_elem = synthesis_elem.find("Reagents")
|
||||
reagents = []
|
||||
if reagents_elem is not None:
|
||||
reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
|
||||
|
||||
# 解析程序
|
||||
procedure_elem = synthesis_elem.find("Procedure")
|
||||
if procedure_elem is None:
|
||||
return None, None, None
|
||||
|
||||
flattened_operations = flatten_xdl_procedure(procedure_elem)
|
||||
return hardware, reagents, flattened_operations
|
||||
|
||||
except ET.ParseError as e:
|
||||
raise ValueError(f"Invalid XDL format: {e}")
|
||||
|
||||
|
||||
def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
|
||||
"""
|
||||
将XDL XML格式转换为标准的字典格式
|
||||
|
||||
Args:
|
||||
xdl_content: XDL XML内容
|
||||
|
||||
Returns:
|
||||
转换结果,包含步骤和器材信息
|
||||
"""
|
||||
try:
|
||||
hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
|
||||
if hardware is None:
|
||||
return {"error": "Failed to parse XDL content", "success": False}
|
||||
|
||||
# 将XDL元素转换为字典格式
|
||||
steps_data = []
|
||||
for elem in flattened_operations:
|
||||
# 转换参数类型
|
||||
parameters = {}
|
||||
for key, val in elem.attrib.items():
|
||||
converted_val = convert_to_type(val)
|
||||
if converted_val is not None:
|
||||
parameters[key] = converted_val
|
||||
|
||||
step_dict = {
|
||||
"operation": elem.tag,
|
||||
"parameters": parameters,
|
||||
"description": elem.get("purpose", f"Operation: {elem.tag}"),
|
||||
}
|
||||
steps_data.append(step_dict)
|
||||
|
||||
# 合并硬件和试剂为统一的labware_info格式
|
||||
labware_data = []
|
||||
labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
|
||||
labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
|
||||
|
||||
return {
|
||||
"success": True,
|
||||
"steps": steps_data,
|
||||
"labware": labware_data,
|
||||
"message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
|
||||
}
|
||||
|
||||
except Exception as e:
|
||||
error_msg = f"XDL conversion failed: {str(e)}"
|
||||
return {"error": error_msg, "success": False}
|
||||
@@ -2,7 +2,7 @@
|
||||
<?xml-model href="http://download.ros.org/schema/package_format3.xsd" schematypens="http://www.w3.org/2001/XMLSchema"?>
|
||||
<package format="3">
|
||||
<name>unilabos_msgs</name>
|
||||
<version>0.10.16</version>
|
||||
<version>0.10.17</version>
|
||||
<description>ROS2 Messages package for unilabos devices</description>
|
||||
<maintainer email="changjh@pku.edu.cn">Junhan Chang</maintainer>
|
||||
<maintainer email="18435084+Xuwznln@users.noreply.github.com">Xuwznln</maintainer>
|
||||
|
||||
Reference in New Issue
Block a user