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https://github.com/deepmodeling/Uni-Lab-OS
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60073ff139 |
@@ -3,7 +3,7 @@
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package:
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name: unilabos
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version: 0.10.17
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version: 0.10.18
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source:
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path: ../../unilabos
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@@ -46,13 +46,15 @@ requirements:
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- jinja2
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- requests
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- uvicorn
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- opcua # [not osx]
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- if: not osx
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then:
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- opcua
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- pyserial
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- pandas
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- pymodbus
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- matplotlib
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- pylibftdi
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- uni-lab::unilabos-env ==0.10.17
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- uni-lab::unilabos-env ==0.10.18
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about:
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repository: https://github.com/deepmodeling/Uni-Lab-OS
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@@ -2,7 +2,7 @@
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package:
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name: unilabos-env
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version: 0.10.17
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version: 0.10.18
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build:
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noarch: generic
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@@ -3,7 +3,7 @@
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package:
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name: unilabos-full
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version: 0.10.17
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version: 0.10.18
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build:
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noarch: generic
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@@ -11,7 +11,7 @@ build:
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requirements:
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run:
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# Base unilabos package (includes unilabos-env)
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- uni-lab::unilabos ==0.10.17
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- uni-lab::unilabos ==0.10.18
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# Documentation tools
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- sphinx
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- sphinx_rtd_theme
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2
.github/workflows/conda-pack-build.yml
vendored
2
.github/workflows/conda-pack-build.yml
vendored
@@ -312,7 +312,7 @@ jobs:
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- name: Upload distribution package
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if: steps.should_build.outputs.should_build == 'true'
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uses: actions/upload-artifact@v6
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uses: actions/upload-artifact@v7
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with:
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name: unilab-pack-${{ matrix.platform }}-${{ github.event.inputs.branch }}
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path: dist-package/
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2
.github/workflows/multi-platform-build.yml
vendored
2
.github/workflows/multi-platform-build.yml
vendored
@@ -149,7 +149,7 @@ jobs:
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|
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- name: Upload conda package artifacts
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if: steps.should_build.outputs.should_build == 'true'
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uses: actions/upload-artifact@v6
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uses: actions/upload-artifact@v7
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with:
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name: conda-package-${{ matrix.platform }}
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path: conda-packages-temp
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2
.github/workflows/unilabos-conda-build.yml
vendored
2
.github/workflows/unilabos-conda-build.yml
vendored
@@ -195,7 +195,7 @@ jobs:
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|
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- name: Upload conda package artifacts
|
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if: steps.should_build.outputs.should_build == 'true'
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uses: actions/upload-artifact@v6
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uses: actions/upload-artifact@v7
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with:
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name: conda-package-unilabos-${{ matrix.platform }}
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path: conda-packages-temp
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@@ -1,6 +1,6 @@
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package:
|
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name: ros-humble-unilabos-msgs
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version: 0.10.17
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version: 0.10.18
|
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source:
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path: ../../unilabos_msgs
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target_directory: src
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@@ -1,6 +1,6 @@
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package:
|
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name: unilabos
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version: "0.10.17"
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version: "0.10.18"
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|
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source:
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path: ../..
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2
setup.py
2
setup.py
@@ -4,7 +4,7 @@ package_name = 'unilabos'
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setup(
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name=package_name,
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version='0.10.17',
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version='0.10.18',
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packages=find_packages(),
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include_package_data=True,
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install_requires=['setuptools'],
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@@ -1 +1 @@
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__version__ = "0.10.17"
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__version__ = "0.10.18"
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@@ -171,6 +171,12 @@ def parse_args():
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action="store_true",
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help="Disable sending update feedback to server",
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)
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parser.add_argument(
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"--test_mode",
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action="store_true",
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default=False,
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help="Test mode: all actions simulate execution and return mock results without running real hardware",
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)
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# workflow upload subcommand
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workflow_parser = subparsers.add_parser(
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"workflow_upload",
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@@ -204,6 +210,12 @@ def parse_args():
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default=False,
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help="Whether to publish the workflow (default: False)",
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)
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workflow_parser.add_argument(
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"--description",
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type=str,
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default="",
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help="Workflow description, used when publishing the workflow",
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)
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return parser
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@@ -231,52 +243,60 @@ def main():
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# 加载配置文件,优先加载config,然后从env读取
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config_path = args_dict.get("config")
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if check_mode:
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args_dict["working_dir"] = os.path.abspath(os.getcwd())
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# 当 skip_env_check 时,默认使用当前目录作为 working_dir
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if skip_env_check and not args_dict.get("working_dir") and not config_path:
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# === 解析 working_dir ===
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# 规则1: working_dir 传入 → 检测 unilabos_data 子目录,已是则不修改
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# 规则2: 仅 config_path 传入 → 用其父目录作为 working_dir
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# 规则4: 两者都传入 → 各用各的,但 working_dir 仍做 unilabos_data 子目录检测
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raw_working_dir = args_dict.get("working_dir")
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if raw_working_dir:
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working_dir = os.path.abspath(raw_working_dir)
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elif config_path and os.path.exists(config_path):
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working_dir = os.path.dirname(os.path.abspath(config_path))
|
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else:
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working_dir = os.path.abspath(os.getcwd())
|
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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")
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# 检查当前目录是否有 local_config.py
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local_config_in_cwd = os.path.join(working_dir, "local_config.py")
|
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if os.path.exists(local_config_in_cwd):
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config_path = local_config_in_cwd
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# unilabos_data 子目录自动检测
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if os.path.basename(working_dir) != "unilabos_data":
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unilabos_data_sub = os.path.join(working_dir, "unilabos_data")
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if os.path.isdir(unilabos_data_sub):
|
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working_dir = unilabos_data_sub
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elif not raw_working_dir and not (config_path and os.path.exists(config_path)):
|
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# 未显式指定路径,默认使用 cwd/unilabos_data
|
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working_dir = os.path.abspath(os.path.join(os.getcwd(), "unilabos_data"))
|
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|
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# === 解析 config_path ===
|
||||
if config_path and not os.path.exists(config_path):
|
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# config_path 传入但不存在,尝试在 working_dir 中查找
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candidate = os.path.join(working_dir, "local_config.py")
|
||||
if os.path.exists(candidate):
|
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config_path = candidate
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print_status(f"在工作目录中发现配置文件: {config_path}", "info")
|
||||
else:
|
||||
print_status(
|
||||
f"配置文件 {config_path} 不存在,工作目录 {working_dir} 中也未找到 local_config.py,"
|
||||
f"请通过 --config 传入 local_config.py 文件路径",
|
||||
"error",
|
||||
)
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os._exit(1)
|
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elif not config_path:
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# 规则3: 未传入 config_path,尝试 working_dir/local_config.py
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candidate = os.path.join(working_dir, "local_config.py")
|
||||
if os.path.exists(candidate):
|
||||
config_path = candidate
|
||||
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"))
|
||||
|
||||
if args_dict.get("working_dir"):
|
||||
working_dir = args_dict.get("working_dir", "")
|
||||
if config_path and not os.path.exists(config_path):
|
||||
config_path = os.path.join(working_dir, "local_config.py")
|
||||
if not os.path.exists(config_path):
|
||||
print_status(
|
||||
f"当前工作目录 {working_dir} 未找到local_config.py,请通过 --config 传入 local_config.py 文件路径",
|
||||
"error",
|
||||
print_status(f"您是否为第一次使用?并将当前路径 {working_dir} 作为工作目录? (Y/n)", "info")
|
||||
if check_mode or input() != "n":
|
||||
os.makedirs(working_dir, exist_ok=True)
|
||||
config_path = os.path.join(working_dir, "local_config.py")
|
||||
shutil.copy(
|
||||
os.path.join(os.path.dirname(os.path.dirname(__file__)), "config", "example_config.py"),
|
||||
config_path,
|
||||
)
|
||||
print_status(f"已创建 local_config.py 路径: {config_path}", "info")
|
||||
else:
|
||||
os._exit(1)
|
||||
elif config_path and os.path.exists(config_path):
|
||||
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 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")
|
||||
print_status(f"您是否为第一次使用?并将当前路径 {working_dir} 作为工作目录? (Y/n)", "info")
|
||||
if input() != "n":
|
||||
os.makedirs(working_dir, exist_ok=True)
|
||||
config_path = os.path.join(working_dir, "local_config.py")
|
||||
shutil.copy(
|
||||
os.path.join(os.path.dirname(os.path.dirname(__file__)), "config", "example_config.py"), config_path
|
||||
)
|
||||
print_status(f"已创建 local_config.py 路径: {config_path}", "info")
|
||||
else:
|
||||
os._exit(1)
|
||||
|
||||
# 加载配置文件 (check_mode 跳过)
|
||||
print_status(f"当前工作目录为 {working_dir}", "info")
|
||||
@@ -334,6 +354,9 @@ def main():
|
||||
BasicConfig.slave_no_host = args_dict.get("slave_no_host", False)
|
||||
BasicConfig.upload_registry = args_dict.get("upload_registry", False)
|
||||
BasicConfig.no_update_feedback = args_dict.get("no_update_feedback", False)
|
||||
BasicConfig.test_mode = args_dict.get("test_mode", False)
|
||||
if BasicConfig.test_mode:
|
||||
print_status("启用测试模式:所有动作将模拟执行,不调用真实硬件", "warning")
|
||||
BasicConfig.communication_protocol = "websocket"
|
||||
machine_name = os.popen("hostname").read().strip()
|
||||
machine_name = "".join([c if c.isalnum() or c == "_" else "_" for c in machine_name])
|
||||
|
||||
@@ -38,9 +38,9 @@ def register_devices_and_resources(lab_registry, gather_only=False) -> Optional[
|
||||
response = http_client.resource_registry({"resources": list(devices_to_register.values())})
|
||||
cost_time = time.time() - start_time
|
||||
if response.status_code in [200, 201]:
|
||||
logger.info(f"[UniLab Register] 成功注册 {len(devices_to_register)} 个设备 {cost_time}ms")
|
||||
logger.info(f"[UniLab Register] 成功注册 {len(devices_to_register)} 个设备 {cost_time}s")
|
||||
else:
|
||||
logger.error(f"[UniLab Register] 设备注册失败: {response.status_code}, {response.text} {cost_time}ms")
|
||||
logger.error(f"[UniLab Register] 设备注册失败: {response.status_code}, {response.text} {cost_time}s")
|
||||
except Exception as e:
|
||||
logger.error(f"[UniLab Register] 设备注册异常: {e}")
|
||||
|
||||
@@ -51,9 +51,9 @@ def register_devices_and_resources(lab_registry, gather_only=False) -> Optional[
|
||||
response = http_client.resource_registry({"resources": list(resources_to_register.values())})
|
||||
cost_time = time.time() - start_time
|
||||
if response.status_code in [200, 201]:
|
||||
logger.info(f"[UniLab Register] 成功注册 {len(resources_to_register)} 个资源 {cost_time}ms")
|
||||
logger.info(f"[UniLab Register] 成功注册 {len(resources_to_register)} 个资源 {cost_time}s")
|
||||
else:
|
||||
logger.error(f"[UniLab Register] 资源注册失败: {response.status_code}, {response.text} {cost_time}ms")
|
||||
logger.error(f"[UniLab Register] 资源注册失败: {response.status_code}, {response.text} {cost_time}s")
|
||||
except Exception as e:
|
||||
logger.error(f"[UniLab Register] 资源注册异常: {e}")
|
||||
|
||||
|
||||
@@ -343,9 +343,10 @@ class HTTPClient:
|
||||
edges: List[Dict[str, Any]],
|
||||
tags: Optional[List[str]] = None,
|
||||
published: bool = False,
|
||||
description: str = "",
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
导入工作流到服务器
|
||||
导入工作流到服务器,如果 published 为 True,则额外发起发布请求
|
||||
|
||||
Args:
|
||||
name: 工作流名称(顶层)
|
||||
@@ -355,6 +356,7 @@ class HTTPClient:
|
||||
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
|
||||
description: 工作流描述,发布时使用
|
||||
|
||||
Returns:
|
||||
Dict: API响应数据,包含 code 和 data (uuid, name)
|
||||
@@ -367,7 +369,6 @@ class HTTPClient:
|
||||
"nodes": nodes,
|
||||
"edges": edges,
|
||||
"tags": tags if tags is not None else [],
|
||||
"published": published,
|
||||
},
|
||||
}
|
||||
# 保存请求到文件
|
||||
@@ -388,11 +389,51 @@ class HTTPClient:
|
||||
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
|
||||
# 导入成功后,如果需要发布则额外发起发布请求
|
||||
if published:
|
||||
imported_uuid = res.get("data", {}).get("uuid", workflow_uuid)
|
||||
publish_res = self.workflow_publish(imported_uuid, description)
|
||||
res["publish_result"] = publish_res
|
||||
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}
|
||||
|
||||
def workflow_publish(self, workflow_uuid: str, description: str = "") -> Dict[str, Any]:
|
||||
"""
|
||||
发布工作流
|
||||
|
||||
Args:
|
||||
workflow_uuid: 工作流UUID
|
||||
description: 工作流描述
|
||||
|
||||
Returns:
|
||||
Dict: API响应数据
|
||||
"""
|
||||
payload = {
|
||||
"uuid": workflow_uuid,
|
||||
"description": description,
|
||||
"published": True,
|
||||
}
|
||||
logger.info(f"正在发布工作流: {workflow_uuid}")
|
||||
response = requests.patch(
|
||||
f"{self.remote_addr}/lab/workflow/owner",
|
||||
json=payload,
|
||||
headers={"Authorization": f"Lab {self.auth}"},
|
||||
timeout=60,
|
||||
)
|
||||
if response.status_code == 200:
|
||||
res = response.json()
|
||||
if "code" in res and res["code"] != 0:
|
||||
logger.error(f"发布工作流失败: {response.text}")
|
||||
else:
|
||||
logger.info(f"工作流发布成功: {workflow_uuid}")
|
||||
return res
|
||||
else:
|
||||
logger.error(f"发布工作流失败: {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()
|
||||
|
||||
@@ -1184,6 +1184,11 @@ class QueueProcessor:
|
||||
logger.debug(f"[QueueProcessor] Sending busy status for {len(queued_jobs)} queued jobs")
|
||||
|
||||
for job_info in queued_jobs:
|
||||
# 快照可能已过期:在遍历过程中 end_job() 可能已将此 job 移至 READY,
|
||||
# 此时不应再发送 busy/need_more,否则会覆盖已发出的 free=True 通知
|
||||
if job_info.status != JobStatus.QUEUE:
|
||||
continue
|
||||
|
||||
message = {
|
||||
"action": "report_action_state",
|
||||
"data": {
|
||||
|
||||
@@ -23,6 +23,7 @@ class BasicConfig:
|
||||
disable_browser = False # 禁止浏览器自动打开
|
||||
port = 8002 # 本地HTTP服务
|
||||
check_mode = False # CI 检查模式,用于验证 registry 导入和文件一致性
|
||||
test_mode = False # 测试模式,所有动作不实际执行,返回模拟结果
|
||||
# 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
||||
log_level: Literal["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = "DEBUG"
|
||||
|
||||
|
||||
@@ -21,7 +21,7 @@ from pylabrobot.resources import (
|
||||
ResourceHolder,
|
||||
Lid,
|
||||
Trash,
|
||||
Tip,
|
||||
Tip, TubeRack,
|
||||
)
|
||||
from typing_extensions import TypedDict
|
||||
|
||||
@@ -696,10 +696,13 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
|
||||
|
||||
如果 liquid_names 和 volumes 为空,但 plate 和 well_names 不为空,直接返回 plate 和 wells。
|
||||
"""
|
||||
assert issubclass(plate.__class__, Plate), "plate must be a Plate"
|
||||
plate: Plate = cast(Plate, cast(Resource, plate))
|
||||
assert issubclass(plate.__class__, Plate) or issubclass(plate.__class__, TubeRack) , f"plate must be a Plate, now: {type(plate)}"
|
||||
plate: Union[Plate, TubeRack]
|
||||
# 根据 well_names 获取对应的 Well 对象
|
||||
wells = [plate.get_well(name) for name in well_names]
|
||||
if issubclass(plate.__class__, Plate):
|
||||
wells = [plate.get_well(name) for name in well_names]
|
||||
elif issubclass(plate.__class__, TubeRack):
|
||||
wells = [plate.get_tube(name) for name in well_names]
|
||||
res_volumes = []
|
||||
|
||||
# 如果 liquid_names 和 volumes 都为空,直接返回
|
||||
|
||||
@@ -91,7 +91,7 @@ class PRCXI9300Deck(Deck):
|
||||
"""
|
||||
|
||||
def __init__(self, name: str, size_x: float, size_y: float, size_z: float, **kwargs):
|
||||
super().__init__(name, size_x, size_y, size_z)
|
||||
super().__init__(size_x, size_y, size_z, name)
|
||||
self.slots = [None] * 16 # PRCXI 9300/9320 最大有 16 个槽位
|
||||
self.slot_locations = [Coordinate(0, 0, 0)] * 16
|
||||
|
||||
@@ -248,14 +248,15 @@ class PRCXI9300TipRack(TipRack):
|
||||
if ordered_items is not None:
|
||||
items = ordered_items
|
||||
elif ordering is not None:
|
||||
# 检查 ordering 中的值是否是字符串(从 JSON 反序列化时的情况)
|
||||
# 如果是字符串,说明这是位置名称,需要让 TipRack 自己创建 Tip 对象
|
||||
# 我们只传递位置信息(键),不传递值,使用 ordering 参数
|
||||
if ordering and isinstance(next(iter(ordering.values()), None), str):
|
||||
# ordering 的值是字符串,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 检查 ordering 中的值类型来决定如何处理:
|
||||
# - 字符串值(从 JSON 反序列化): 只用键创建 ordering_param
|
||||
# - None 值(从第二次往返序列化): 同样只用键创建 ordering_param
|
||||
# - 对象值(已经是实际的 Resource 对象): 直接作为 ordered_items 使用
|
||||
first_val = next(iter(ordering.values()), None) if ordering else None
|
||||
if not ordering or first_val is None or isinstance(first_val, str):
|
||||
# ordering 的值是字符串或 None,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 传递 ordering 参数而不是 ordered_items,让 TipRack 自己创建 Tip 对象
|
||||
items = None
|
||||
# 使用 ordering 参数,只包含位置信息(键)
|
||||
ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
|
||||
else:
|
||||
# ordering 的值已经是对象,可以直接使用
|
||||
@@ -397,14 +398,15 @@ class PRCXI9300TubeRack(TubeRack):
|
||||
items_to_pass = ordered_items
|
||||
ordering_param = None
|
||||
elif ordering is not None:
|
||||
# 检查 ordering 中的值是否是字符串(从 JSON 反序列化时的情况)
|
||||
# 如果是字符串,说明这是位置名称,需要让 TubeRack 自己创建 Tube 对象
|
||||
# 我们只传递位置信息(键),不传递值,使用 ordering 参数
|
||||
if ordering and isinstance(next(iter(ordering.values()), None), str):
|
||||
# ordering 的值是字符串,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 检查 ordering 中的值类型来决定如何处理:
|
||||
# - 字符串值(从 JSON 反序列化): 只用键创建 ordering_param
|
||||
# - None 值(从第二次往返序列化): 同样只用键创建 ordering_param
|
||||
# - 对象值(已经是实际的 Resource 对象): 直接作为 ordered_items 使用
|
||||
first_val = next(iter(ordering.values()), None) if ordering else None
|
||||
if not ordering or first_val is None or isinstance(first_val, str):
|
||||
# ordering 的值是字符串或 None,只使用键(位置信息)创建新的 OrderedDict
|
||||
# 传递 ordering 参数而不是 ordered_items,让 TubeRack 自己创建 Tube 对象
|
||||
items_to_pass = None
|
||||
# 使用 ordering 参数,只包含位置信息(键)
|
||||
ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
|
||||
else:
|
||||
# ordering 的值已经是对象,可以直接使用
|
||||
|
||||
@@ -96,10 +96,13 @@ serial:
|
||||
type: string
|
||||
port:
|
||||
type: string
|
||||
registry_name:
|
||||
type: string
|
||||
resource_tracker:
|
||||
type: object
|
||||
required:
|
||||
- device_id
|
||||
- registry_name
|
||||
- port
|
||||
type: object
|
||||
data:
|
||||
|
||||
@@ -67,6 +67,9 @@ camera:
|
||||
period:
|
||||
default: 0.1
|
||||
type: number
|
||||
registry_name:
|
||||
default: ''
|
||||
type: string
|
||||
resource_tracker:
|
||||
type: object
|
||||
required: []
|
||||
|
||||
@@ -5,6 +5,7 @@ import sys
|
||||
import inspect
|
||||
import importlib
|
||||
import threading
|
||||
import traceback
|
||||
from concurrent.futures import ThreadPoolExecutor, as_completed
|
||||
from pathlib import Path
|
||||
from typing import Any, Dict, List, Union, Tuple
|
||||
@@ -88,6 +89,14 @@ class Registry:
|
||||
)
|
||||
test_latency_schema["description"] = "用于测试延迟的动作,返回延迟时间和时间差。"
|
||||
|
||||
test_resource_method_info = host_node_enhanced_info.get("action_methods", {}).get("test_resource", {})
|
||||
test_resource_schema = self._generate_unilab_json_command_schema(
|
||||
test_resource_method_info.get("args", []),
|
||||
"test_resource",
|
||||
test_resource_method_info.get("return_annotation"),
|
||||
)
|
||||
test_resource_schema["description"] = "用于测试物料、设备和样本。"
|
||||
|
||||
self.device_type_registry.update(
|
||||
{
|
||||
"host_node": {
|
||||
@@ -189,32 +198,7 @@ class Registry:
|
||||
"goal": {},
|
||||
"feedback": {},
|
||||
"result": {},
|
||||
"schema": {
|
||||
"description": "",
|
||||
"properties": {
|
||||
"feedback": {},
|
||||
"goal": {
|
||||
"properties": {
|
||||
"resource": ros_message_to_json_schema(Resource, "resource"),
|
||||
"resources": {
|
||||
"items": {
|
||||
"properties": ros_message_to_json_schema(
|
||||
Resource, "resources"
|
||||
),
|
||||
"type": "object",
|
||||
},
|
||||
"type": "array",
|
||||
},
|
||||
"device": {"type": "string"},
|
||||
"devices": {"items": {"type": "string"}, "type": "array"},
|
||||
},
|
||||
"type": "object",
|
||||
},
|
||||
"result": {},
|
||||
},
|
||||
"title": "test_resource",
|
||||
"type": "object",
|
||||
},
|
||||
"schema": test_resource_schema,
|
||||
"placeholder_keys": {
|
||||
"device": "unilabos_devices",
|
||||
"devices": "unilabos_devices",
|
||||
@@ -944,6 +928,7 @@ class Registry:
|
||||
if is_valid:
|
||||
results.append((file, data, device_ids))
|
||||
except Exception as e:
|
||||
traceback.print_exc()
|
||||
logger.warning(f"[UniLab Registry] 处理设备文件异常: {file}, 错误: {e}")
|
||||
|
||||
# 线程安全地更新注册表
|
||||
|
||||
@@ -38,24 +38,52 @@ class LabSample(TypedDict):
|
||||
extra: Dict[str, Any]
|
||||
|
||||
|
||||
class ResourceDictPositionSizeType(TypedDict):
|
||||
depth: float
|
||||
width: float
|
||||
height: float
|
||||
|
||||
|
||||
class ResourceDictPositionSize(BaseModel):
|
||||
depth: float = Field(description="Depth", default=0.0) # z
|
||||
width: float = Field(description="Width", default=0.0) # x
|
||||
height: float = Field(description="Height", default=0.0) # y
|
||||
|
||||
|
||||
class ResourceDictPositionScaleType(TypedDict):
|
||||
x: float
|
||||
y: float
|
||||
z: float
|
||||
|
||||
|
||||
class ResourceDictPositionScale(BaseModel):
|
||||
x: float = Field(description="x scale", default=0.0)
|
||||
y: float = Field(description="y scale", default=0.0)
|
||||
z: float = Field(description="z scale", default=0.0)
|
||||
|
||||
|
||||
class ResourceDictPositionObjectType(TypedDict):
|
||||
x: float
|
||||
y: float
|
||||
z: float
|
||||
|
||||
|
||||
class ResourceDictPositionObject(BaseModel):
|
||||
x: float = Field(description="X coordinate", default=0.0)
|
||||
y: float = Field(description="Y coordinate", default=0.0)
|
||||
z: float = Field(description="Z coordinate", default=0.0)
|
||||
|
||||
|
||||
class ResourceDictPositionType(TypedDict):
|
||||
size: ResourceDictPositionSizeType
|
||||
scale: ResourceDictPositionScaleType
|
||||
layout: Literal["2d", "x-y", "z-y", "x-z"]
|
||||
position: ResourceDictPositionObjectType
|
||||
position3d: ResourceDictPositionObjectType
|
||||
rotation: ResourceDictPositionObjectType
|
||||
cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"]
|
||||
|
||||
|
||||
class ResourceDictPosition(BaseModel):
|
||||
size: ResourceDictPositionSize = Field(description="Resource size", default_factory=ResourceDictPositionSize)
|
||||
scale: ResourceDictPositionScale = Field(description="Resource scale", default_factory=ResourceDictPositionScale)
|
||||
@@ -74,6 +102,24 @@ class ResourceDictPosition(BaseModel):
|
||||
)
|
||||
|
||||
|
||||
class ResourceDictType(TypedDict):
|
||||
id: str
|
||||
uuid: str
|
||||
name: str
|
||||
description: str
|
||||
resource_schema: Dict[str, Any]
|
||||
model: Dict[str, Any]
|
||||
icon: str
|
||||
parent_uuid: Optional[str]
|
||||
parent: Optional["ResourceDictType"]
|
||||
type: Union[Literal["device"], str]
|
||||
klass: str
|
||||
pose: ResourceDictPositionType
|
||||
config: Dict[str, Any]
|
||||
data: Dict[str, Any]
|
||||
extra: Dict[str, Any]
|
||||
|
||||
|
||||
# 统一的资源字典模型,parent 自动序列化为 parent_uuid,children 不序列化
|
||||
class ResourceDict(BaseModel):
|
||||
id: str = Field(description="Resource ID")
|
||||
|
||||
@@ -460,7 +460,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
||||
}
|
||||
res.response = json.dumps(final_response)
|
||||
# 如果driver自己就有assign的方法,那就使用driver自己的assign方法
|
||||
if hasattr(self.driver_instance, "create_resource"):
|
||||
if hasattr(self.driver_instance, "create_resource") and self.node_name != "host_node":
|
||||
create_resource_func = getattr(self.driver_instance, "create_resource")
|
||||
try:
|
||||
ret = create_resource_func(
|
||||
|
||||
@@ -35,7 +35,7 @@ from unilabos.resources.resource_tracker import (
|
||||
ResourceTreeInstance,
|
||||
RETURN_UNILABOS_SAMPLES,
|
||||
JSON_UNILABOS_PARAM,
|
||||
PARAM_SAMPLE_UUIDS,
|
||||
PARAM_SAMPLE_UUIDS, SampleUUIDsType, LabSample,
|
||||
)
|
||||
from unilabos.ros.initialize_device import initialize_device_from_dict
|
||||
from unilabos.ros.msgs.message_converter import (
|
||||
@@ -51,6 +51,7 @@ from unilabos.utils import logger
|
||||
from unilabos.utils.exception import DeviceClassInvalid
|
||||
from unilabos.utils.log import warning
|
||||
from unilabos.utils.type_check import serialize_result_info
|
||||
from unilabos.config.config import BasicConfig
|
||||
|
||||
if TYPE_CHECKING:
|
||||
from unilabos.app.ws_client import QueueItem
|
||||
@@ -63,7 +64,8 @@ class DeviceActionStatus:
|
||||
|
||||
class TestResourceReturn(TypedDict):
|
||||
resources: List[List[ResourceDict]]
|
||||
devices: List[DeviceSlot]
|
||||
devices: List[Dict[str, Any]]
|
||||
unilabos_samples: List[LabSample]
|
||||
|
||||
|
||||
class TestLatencyReturn(TypedDict):
|
||||
@@ -776,6 +778,17 @@ class HostNode(BaseROS2DeviceNode):
|
||||
u = uuid.UUID(item.job_id)
|
||||
device_id = item.device_id
|
||||
action_name = item.action_name
|
||||
|
||||
if BasicConfig.test_mode:
|
||||
action_id = f"/devices/{device_id}/{action_name}"
|
||||
self.lab_logger().info(
|
||||
f"[TEST MODE] 模拟执行: {action_id} (job={item.job_id[:8]}), 参数: {str(action_kwargs)[:500]}"
|
||||
)
|
||||
# 根据注册表 handles 构建模拟返回值
|
||||
mock_return = self._build_test_mode_return(device_id, action_name, action_kwargs)
|
||||
self._handle_test_mode_result(item, action_id, mock_return)
|
||||
return
|
||||
|
||||
if action_type.startswith("UniLabJsonCommand"):
|
||||
if action_name.startswith("auto-"):
|
||||
action_name = action_name[5:]
|
||||
@@ -813,6 +826,51 @@ class HostNode(BaseROS2DeviceNode):
|
||||
)
|
||||
future.add_done_callback(lambda f: self.goal_response_callback(item, action_id, f))
|
||||
|
||||
def _build_test_mode_return(
|
||||
self, device_id: str, action_name: str, action_kwargs: Dict[str, Any]
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
根据注册表 handles 的 output 定义构建测试模式的模拟返回值
|
||||
|
||||
根据 data_key 中 @flatten 的层数决定嵌套数组层数,叶子值为空字典。
|
||||
例如: "vessel" → {}, "plate.@flatten" → [{}], "a.@flatten.@flatten" → [[{}]]
|
||||
"""
|
||||
mock_return: Dict[str, Any] = {"test_mode": True, "action_name": action_name}
|
||||
action_mappings = self._action_value_mappings.get(device_id, {})
|
||||
action_mapping = action_mappings.get(action_name, {})
|
||||
handles = action_mapping.get("handles", {})
|
||||
if isinstance(handles, dict):
|
||||
for output_handle in handles.get("output", []):
|
||||
data_key = output_handle.get("data_key", "")
|
||||
handler_key = output_handle.get("handler_key", "")
|
||||
# 根据 @flatten 层数构建嵌套数组,叶子为空字典
|
||||
flatten_count = data_key.count("@flatten")
|
||||
value: Any = {}
|
||||
for _ in range(flatten_count):
|
||||
value = [value]
|
||||
mock_return[handler_key] = value
|
||||
return mock_return
|
||||
|
||||
def _handle_test_mode_result(
|
||||
self, item: "QueueItem", action_id: str, mock_return: Dict[str, Any]
|
||||
) -> None:
|
||||
"""
|
||||
测试模式下直接构建结果并走正常的结果回调流程(跳过 ROS)
|
||||
"""
|
||||
job_id = item.job_id
|
||||
status = "success"
|
||||
return_info = serialize_result_info("", True, mock_return)
|
||||
|
||||
self.lab_logger().info(f"[TEST MODE] Result for {action_id} ({job_id[:8]}): {status}")
|
||||
|
||||
from unilabos.app.web.controller import store_job_result
|
||||
store_job_result(job_id, status, return_info, mock_return)
|
||||
|
||||
# 发布状态到桥接器
|
||||
for bridge in self.bridges:
|
||||
if hasattr(bridge, "publish_job_status"):
|
||||
bridge.publish_job_status(mock_return, item, status, return_info)
|
||||
|
||||
def goal_response_callback(self, item: "QueueItem", action_id: str, future) -> None:
|
||||
"""目标响应回调"""
|
||||
goal_handle = future.result()
|
||||
@@ -1525,6 +1583,7 @@ class HostNode(BaseROS2DeviceNode):
|
||||
|
||||
def test_resource(
|
||||
self,
|
||||
sample_uuids: SampleUUIDsType,
|
||||
resource: ResourceSlot = None,
|
||||
resources: List[ResourceSlot] = None,
|
||||
device: DeviceSlot = None,
|
||||
@@ -1539,6 +1598,7 @@ class HostNode(BaseROS2DeviceNode):
|
||||
return {
|
||||
"resources": ResourceTreeSet.from_plr_resources([resource, *resources], known_newly_created=True).dump(),
|
||||
"devices": [device, *devices],
|
||||
"unilabos_samples": [LabSample(sample_uuid=sample_uuid, oss_path="", extra={"material_uuid": content} if isinstance(content, str) else content.serialize()) for sample_uuid, content in sample_uuids.items()]
|
||||
}
|
||||
|
||||
def handle_pong_response(self, pong_data: dict):
|
||||
|
||||
@@ -362,14 +362,16 @@ def build_protocol_graph(
|
||||
protocol_steps: List[Dict[str, Any]],
|
||||
workstation_name: str,
|
||||
action_resource_mapping: Optional[Dict[str, str]] = None,
|
||||
labware_defs: Optional[List[Dict[str, Any]]] = 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,格式为 {name: {slot, well, labware, ...}, ...}
|
||||
labware_info: reagent 信息字典,格式为 {name: {slot, well}, ...},用于 set_liquid 和 well 查找
|
||||
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
|
||||
labware_defs: labware 定义列表,格式为 [{"name": "...", "slot": "1", "type": "lab_xxx"}, ...]
|
||||
"""
|
||||
G = WorkflowGraph()
|
||||
resource_last_writer = {} # reagent_name -> "node_id:port"
|
||||
@@ -377,18 +379,7 @@ def build_protocol_graph(
|
||||
|
||||
protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
|
||||
|
||||
# ==================== 第一步:按 slot 去重创建 create_resource 节点 ====================
|
||||
# 收集所有唯一的 slot
|
||||
slots_info = {} # slot -> {labware, res_id}
|
||||
for labware_id, item in labware_info.items():
|
||||
slot = str(item.get("slot", ""))
|
||||
if slot and slot not in slots_info:
|
||||
res_id = f"plate_slot_{slot}"
|
||||
slots_info[slot] = {
|
||||
"labware": item.get("labware", ""),
|
||||
"res_id": res_id,
|
||||
}
|
||||
|
||||
# ==================== 第一步:按 slot 创建 create_resource 节点 ====================
|
||||
# 创建 Group 节点,包含所有 create_resource 节点
|
||||
group_node_id = str(uuid.uuid4())
|
||||
G.add_node(
|
||||
@@ -404,29 +395,35 @@ def build_protocol_graph(
|
||||
param=None,
|
||||
)
|
||||
|
||||
# 为每个唯一的 slot 创建 create_resource 节点
|
||||
# 直接使用 JSON 中的 labware 定义,每个 slot 一条记录,type 即 class_name
|
||||
res_index = 0
|
||||
for slot, info in slots_info.items():
|
||||
node_id = str(uuid.uuid4())
|
||||
res_id = info["res_id"]
|
||||
for lw in (labware_defs or []):
|
||||
slot = str(lw.get("slot", ""))
|
||||
if not slot or slot in slot_to_create_resource:
|
||||
continue # 跳过空 slot 或已处理的 slot
|
||||
|
||||
lw_name = lw.get("name", f"slot {slot}")
|
||||
lw_type = lw.get("type", CREATE_RESOURCE_DEFAULTS["class_name"])
|
||||
res_id = f"plate_slot_{slot}"
|
||||
|
||||
res_index += 1
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(
|
||||
node_id,
|
||||
template_name="create_resource",
|
||||
resource_name="host_node",
|
||||
name=f"Plate {res_index}",
|
||||
description=f"Create plate on slot {slot}",
|
||||
name=lw_name,
|
||||
description=f"Create {lw_name}",
|
||||
lab_node_type="Labware",
|
||||
footer="create_resource-host_node",
|
||||
device_name=DEVICE_NAME_HOST,
|
||||
type=NODE_TYPE_DEFAULT,
|
||||
parent_uuid=group_node_id, # 指向 Group 节点
|
||||
minimized=True, # 折叠显示
|
||||
parent_uuid=group_node_id,
|
||||
minimized=True,
|
||||
param={
|
||||
"res_id": res_id,
|
||||
"device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
|
||||
"class_name": CREATE_RESOURCE_DEFAULTS["class_name"],
|
||||
"class_name": lw_type,
|
||||
"parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot),
|
||||
"bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
|
||||
"slot_on_deck": slot,
|
||||
@@ -434,8 +431,6 @@ def build_protocol_graph(
|
||||
)
|
||||
slot_to_create_resource[slot] = node_id
|
||||
|
||||
# create_resource 之间不需要 ready 连接
|
||||
|
||||
# ==================== 第二步:为每个 reagent 创建 set_liquid_from_plate 节点 ====================
|
||||
# 创建 Group 节点,包含所有 set_liquid_from_plate 节点
|
||||
set_liquid_group_id = str(uuid.uuid4())
|
||||
|
||||
@@ -1,16 +1,20 @@
|
||||
"""
|
||||
JSON 工作流转换模块
|
||||
|
||||
将 workflow/reagent 格式的 JSON 转换为统一工作流格式。
|
||||
将 workflow/reagent/labware 格式的 JSON 转换为统一工作流格式。
|
||||
|
||||
输入格式:
|
||||
{
|
||||
"labware": [
|
||||
{"name": "...", "slot": "1", "type": "lab_xxx"},
|
||||
...
|
||||
],
|
||||
"workflow": [
|
||||
{"action": "...", "action_args": {...}},
|
||||
...
|
||||
],
|
||||
"reagent": {
|
||||
"reagent_name": {"slot": int, "well": [...], "labware": "..."},
|
||||
"reagent_name": {"slot": int, "well": [...]},
|
||||
...
|
||||
}
|
||||
}
|
||||
@@ -245,18 +249,18 @@ def convert_from_json(
|
||||
if "workflow" not in json_data or "reagent" not in json_data:
|
||||
raise ValueError(
|
||||
"不支持的 JSON 格式。请使用标准格式:\n"
|
||||
'{"workflow": [{"action": "...", "action_args": {...}}, ...], '
|
||||
'"reagent": {"name": {"slot": int, "well": [...], "labware": "..."}, ...}}'
|
||||
'{"labware": [...], "workflow": [...], "reagent": {...}}'
|
||||
)
|
||||
|
||||
# 提取数据
|
||||
workflow = json_data["workflow"]
|
||||
reagent = json_data["reagent"]
|
||||
labware_defs = json_data.get("labware", []) # 新的 labware 定义列表
|
||||
|
||||
# 规范化步骤数据
|
||||
protocol_steps = normalize_workflow_steps(workflow)
|
||||
|
||||
# reagent 已经是字典格式,直接使用
|
||||
# reagent 已经是字典格式,用于 set_liquid 和 well 数量查找
|
||||
labware_info = reagent
|
||||
|
||||
# 构建工作流图
|
||||
@@ -265,6 +269,7 @@ def convert_from_json(
|
||||
protocol_steps=protocol_steps,
|
||||
workstation_name=workstation_name,
|
||||
action_resource_mapping=ACTION_RESOURCE_MAPPING,
|
||||
labware_defs=labware_defs,
|
||||
)
|
||||
|
||||
# 校验句柄配置
|
||||
|
||||
@@ -41,6 +41,7 @@ def upload_workflow(
|
||||
workflow_name: Optional[str] = None,
|
||||
tags: Optional[List[str]] = None,
|
||||
published: bool = False,
|
||||
description: str = "",
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
上传工作流到服务器
|
||||
@@ -56,6 +57,7 @@ def upload_workflow(
|
||||
workflow_name: 工作流名称,如果不提供则从文件中读取或使用文件名
|
||||
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
|
||||
description: 工作流描述,发布时使用
|
||||
|
||||
Returns:
|
||||
Dict: API响应数据
|
||||
@@ -75,6 +77,14 @@ def upload_workflow(
|
||||
print_status(f"工作流文件JSON解析失败: {e}", "error")
|
||||
return {"code": -1, "message": f"JSON解析失败: {e}"}
|
||||
|
||||
# 从 JSON 文件中提取 description 和 tags(作为 fallback)
|
||||
if not description and "description" in workflow_data:
|
||||
description = workflow_data["description"]
|
||||
print_status(f"从文件中读取 description", "info")
|
||||
if not tags and "tags" in workflow_data:
|
||||
tags = workflow_data["tags"]
|
||||
print_status(f"从文件中读取 tags: {tags}", "info")
|
||||
|
||||
# 自动检测并转换格式
|
||||
if not _is_node_link_format(workflow_data):
|
||||
try:
|
||||
@@ -96,6 +106,7 @@ def upload_workflow(
|
||||
print_status(f" - 节点数量: {len(nodes)}", "info")
|
||||
print_status(f" - 边数量: {len(edges)}", "info")
|
||||
print_status(f" - 标签: {tags or []}", "info")
|
||||
print_status(f" - 描述: {description[:50]}{'...' if len(description) > 50 else ''}", "info")
|
||||
print_status(f" - 发布状态: {published}", "info")
|
||||
|
||||
# 调用 http_client 上传
|
||||
@@ -107,6 +118,7 @@ def upload_workflow(
|
||||
edges=edges,
|
||||
tags=tags,
|
||||
published=published,
|
||||
description=description,
|
||||
)
|
||||
|
||||
if result.get("code") == 0:
|
||||
@@ -131,8 +143,9 @@ def handle_workflow_upload_command(args_dict: Dict[str, Any]) -> None:
|
||||
workflow_name = args_dict.get("workflow_name")
|
||||
tags = args_dict.get("tags", [])
|
||||
published = args_dict.get("published", False)
|
||||
description = args_dict.get("description", "")
|
||||
|
||||
if workflow_file:
|
||||
upload_workflow(workflow_file, workflow_name, tags, published)
|
||||
upload_workflow(workflow_file, workflow_name, tags, published, description)
|
||||
else:
|
||||
print_status("未指定工作流文件路径,请使用 -f/--workflow_file 参数", "error")
|
||||
|
||||
@@ -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>0.10.17</version>
|
||||
<version>0.10.18</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