mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2025-12-18 21:41:16 +00:00
Compare commits
10 Commits
workflow_u
...
dev
| Author | SHA1 | Date | |
|---|---|---|---|
|
|
39cc280c91 | ||
|
|
152d3a7563 | ||
|
|
ef14737839 | ||
|
|
5d5569121c | ||
|
|
d23e85ade4 | ||
|
|
02afafd423 | ||
|
|
6ac510dcd2 | ||
|
|
ed56c1eba2 | ||
|
|
16ee3de086 | ||
|
|
ced961050d |
@@ -39,7 +39,9 @@ Uni-Lab-OS recommends using `mamba` for environment management. Choose the appro
|
|||||||
|
|
||||||
```bash
|
```bash
|
||||||
# Create new environment
|
# Create new environment
|
||||||
mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
mamba create -n unilab python=3.11.11
|
||||||
|
mamba activate unilab
|
||||||
|
mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||||
```
|
```
|
||||||
|
|
||||||
## Install Dev Uni-Lab-OS
|
## Install Dev Uni-Lab-OS
|
||||||
|
|||||||
@@ -41,7 +41,9 @@ Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适
|
|||||||
|
|
||||||
```bash
|
```bash
|
||||||
# 创建新环境
|
# 创建新环境
|
||||||
mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
mamba create -n unilab python=3.11.11
|
||||||
|
mamba activate unilab
|
||||||
|
mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
||||||
```
|
```
|
||||||
|
|
||||||
2. 安装开发版 Uni-Lab-OS:
|
2. 安装开发版 Uni-Lab-OS:
|
||||||
|
|||||||
@@ -317,45 +317,6 @@ unilab --help
|
|||||||
|
|
||||||
如果所有命令都正常输出,说明开发环境配置成功!
|
如果所有命令都正常输出,说明开发环境配置成功!
|
||||||
|
|
||||||
### 开发工具推荐
|
|
||||||
|
|
||||||
#### IDE
|
|
||||||
|
|
||||||
- **PyCharm Professional**: 强大的 Python IDE,支持远程调试
|
|
||||||
- **VS Code**: 轻量级,配合 Python 扩展使用
|
|
||||||
- **Vim/Emacs**: 适合终端开发
|
|
||||||
|
|
||||||
#### 推荐的 VS Code 扩展
|
|
||||||
|
|
||||||
- Python
|
|
||||||
- Pylance
|
|
||||||
- ROS
|
|
||||||
- URDF
|
|
||||||
- YAML
|
|
||||||
|
|
||||||
#### 调试工具
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# 安装调试工具
|
|
||||||
pip install ipdb pytest pytest-cov -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
|
||||||
|
|
||||||
# 代码质量检查
|
|
||||||
pip install black flake8 mypy -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
|
||||||
```
|
|
||||||
|
|
||||||
### 设置 pre-commit 钩子(可选)
|
|
||||||
|
|
||||||
```bash
|
|
||||||
# 安装 pre-commit
|
|
||||||
pip install pre-commit -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
|
||||||
|
|
||||||
# 设置钩子
|
|
||||||
pre-commit install
|
|
||||||
|
|
||||||
# 手动运行检查
|
|
||||||
pre-commit run --all-files
|
|
||||||
```
|
|
||||||
|
|
||||||
---
|
---
|
||||||
|
|
||||||
## 验证安装
|
## 验证安装
|
||||||
|
|||||||
|
Before Width: | Height: | Size: 148 KiB After Width: | Height: | Size: 148 KiB |
|
Before Width: | Height: | Size: 140 KiB After Width: | Height: | Size: 140 KiB |
|
Before Width: | Height: | Size: 117 KiB After Width: | Height: | Size: 117 KiB |
35
test/workflow/merge_workflow.py
Normal file
35
test/workflow/merge_workflow.py
Normal file
@@ -0,0 +1,35 @@
|
|||||||
|
import sys
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||||||
|
if str(ROOT_DIR) not in sys.path:
|
||||||
|
sys.path.insert(0, str(ROOT_DIR))
|
||||||
|
|
||||||
|
import pytest
|
||||||
|
|
||||||
|
from unilabos.workflow.convert_from_json import (
|
||||||
|
convert_from_json,
|
||||||
|
normalize_steps as _normalize_steps,
|
||||||
|
normalize_labware as _normalize_labware,
|
||||||
|
)
|
||||||
|
from unilabos.workflow.common import draw_protocol_graph_with_ports
|
||||||
|
|
||||||
|
|
||||||
|
@pytest.mark.parametrize(
|
||||||
|
"protocol_name",
|
||||||
|
[
|
||||||
|
"example_bio",
|
||||||
|
# "bioyond_materials_liquidhandling_1",
|
||||||
|
"example_prcxi",
|
||||||
|
],
|
||||||
|
)
|
||||||
|
def test_build_protocol_graph(protocol_name):
|
||||||
|
data_path = Path(__file__).with_name(f"{protocol_name}.json")
|
||||||
|
|
||||||
|
graph = convert_from_json(data_path, workstation_name="PRCXi")
|
||||||
|
|
||||||
|
timestamp = datetime.now().strftime("%Y%m%d_%H%M")
|
||||||
|
output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
|
||||||
|
draw_protocol_graph_with_ports(graph, str(output_path))
|
||||||
|
print(graph)
|
||||||
@@ -20,6 +20,7 @@ if unilabos_dir not in sys.path:
|
|||||||
from unilabos.utils.banner_print import print_status, print_unilab_banner
|
from unilabos.utils.banner_print import print_status, print_unilab_banner
|
||||||
from unilabos.config.config import load_config, BasicConfig, HTTPConfig
|
from unilabos.config.config import load_config, BasicConfig, HTTPConfig
|
||||||
|
|
||||||
|
|
||||||
def load_config_from_file(config_path):
|
def load_config_from_file(config_path):
|
||||||
if config_path is None:
|
if config_path is None:
|
||||||
config_path = os.environ.get("UNILABOS_BASICCONFIG_CONFIG_PATH", None)
|
config_path = os.environ.get("UNILABOS_BASICCONFIG_CONFIG_PATH", None)
|
||||||
@@ -41,7 +42,7 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
|
|||||||
for i, arg in enumerate(sys.argv):
|
for i, arg in enumerate(sys.argv):
|
||||||
for option_string in option_strings:
|
for option_string in option_strings:
|
||||||
if arg.startswith(option_string):
|
if arg.startswith(option_string):
|
||||||
new_arg = arg[:2] + arg[2:len(option_string)].replace("-", "_") + arg[len(option_string):]
|
new_arg = arg[:2] + arg[2 : len(option_string)].replace("-", "_") + arg[len(option_string) :]
|
||||||
sys.argv[i] = new_arg
|
sys.argv[i] = new_arg
|
||||||
break
|
break
|
||||||
|
|
||||||
@@ -155,32 +156,54 @@ def parse_args():
|
|||||||
default=False,
|
default=False,
|
||||||
help="Complete registry information",
|
help="Complete registry information",
|
||||||
)
|
)
|
||||||
|
# workflow upload subcommand
|
||||||
# label
|
|
||||||
workflow_parser = subparsers.add_parser(
|
workflow_parser = subparsers.add_parser(
|
||||||
"workflow_upload",
|
"workflow_upload",
|
||||||
|
aliases=["wf"],
|
||||||
help="Upload workflow from xdl/json/python files",
|
help="Upload workflow from xdl/json/python files",
|
||||||
)
|
)
|
||||||
workflow_parser.add_argument("-t", "--labeltype", default="singlepoint", type=str,
|
workflow_parser.add_argument(
|
||||||
help="QM calculation type, support 'singlepoint', 'optimize' and 'dimer' currently")
|
"-f",
|
||||||
|
"--workflow_file",
|
||||||
|
type=str,
|
||||||
|
required=True,
|
||||||
|
help="Path to the workflow file (JSON format)",
|
||||||
|
)
|
||||||
|
workflow_parser.add_argument(
|
||||||
|
"-n",
|
||||||
|
"--workflow_name",
|
||||||
|
type=str,
|
||||||
|
default=None,
|
||||||
|
help="Workflow name, if not provided will use the name from file or filename",
|
||||||
|
)
|
||||||
|
workflow_parser.add_argument(
|
||||||
|
"--tags",
|
||||||
|
type=str,
|
||||||
|
nargs="*",
|
||||||
|
default=[],
|
||||||
|
help="Tags for the workflow (space-separated)",
|
||||||
|
)
|
||||||
|
workflow_parser.add_argument(
|
||||||
|
"--published",
|
||||||
|
action="store_true",
|
||||||
|
default=False,
|
||||||
|
help="Whether to publish the workflow (default: False)",
|
||||||
|
)
|
||||||
return parser
|
return parser
|
||||||
|
|
||||||
|
|
||||||
def main():
|
def main():
|
||||||
"""主函数"""
|
"""主函数"""
|
||||||
# 解析命令行参数
|
# 解析命令行参数
|
||||||
args = parse_args()
|
parser = parse_args()
|
||||||
convert_argv_dashes_to_underscores(args)
|
convert_argv_dashes_to_underscores(parser)
|
||||||
args_dict = vars(args.parse_args())
|
args = parser.parse_args()
|
||||||
|
args_dict = vars(args)
|
||||||
# 显示启动横幅
|
|
||||||
print_unilab_banner(args_dict)
|
|
||||||
|
|
||||||
# 环境检查 - 检查并自动安装必需的包 (可选)
|
# 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):
|
if not args_dict.get("skip_env_check", False):
|
||||||
from unilabos.utils.environment_check import check_environment
|
from unilabos.utils.environment_check import check_environment
|
||||||
|
|
||||||
print_status("正在进行环境依赖检查...", "info")
|
|
||||||
if not check_environment(auto_install=True):
|
if not check_environment(auto_install=True):
|
||||||
print_status("环境检查失败,程序退出", "error")
|
print_status("环境检查失败,程序退出", "error")
|
||||||
os._exit(1)
|
os._exit(1)
|
||||||
@@ -233,17 +256,18 @@ def main():
|
|||||||
logger.info(f"Log level set to '{BasicConfig.log_level}' from config file.")
|
logger.info(f"Log level set to '{BasicConfig.log_level}' from config file.")
|
||||||
configure_logger(loglevel=BasicConfig.log_level, working_dir=working_dir)
|
configure_logger(loglevel=BasicConfig.log_level, working_dir=working_dir)
|
||||||
|
|
||||||
if args_dict["addr"] == "test":
|
if args.addr != parser.get_default("addr"):
|
||||||
print_status("使用测试环境地址", "info")
|
if args.addr == "test":
|
||||||
HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
|
print_status("使用测试环境地址", "info")
|
||||||
elif args_dict["addr"] == "uat":
|
HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
|
||||||
print_status("使用uat环境地址", "info")
|
elif args.addr == "uat":
|
||||||
HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
|
print_status("使用uat环境地址", "info")
|
||||||
elif args_dict["addr"] == "local":
|
HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
|
||||||
print_status("使用本地环境地址", "info")
|
elif args.addr == "local":
|
||||||
HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
|
print_status("使用本地环境地址", "info")
|
||||||
else:
|
HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
|
||||||
HTTPConfig.remote_addr = args_dict.get("addr", "")
|
else:
|
||||||
|
HTTPConfig.remote_addr = args.addr
|
||||||
|
|
||||||
# 设置BasicConfig参数
|
# 设置BasicConfig参数
|
||||||
if args_dict.get("ak", ""):
|
if args_dict.get("ak", ""):
|
||||||
@@ -254,18 +278,10 @@ def main():
|
|||||||
print_status("传入了sk参数,优先采用传入参数!", "info")
|
print_status("传入了sk参数,优先采用传入参数!", "info")
|
||||||
BasicConfig.working_dir = working_dir
|
BasicConfig.working_dir = working_dir
|
||||||
|
|
||||||
# 显示启动横幅
|
workflow_upload = args_dict.get("command") in ("workflow_upload", "wf")
|
||||||
print_unilab_banner(args_dict)
|
|
||||||
|
|
||||||
#####################################
|
|
||||||
######## 启动设备接入端(主入口) ########
|
|
||||||
#####################################
|
|
||||||
launch(args_dict)
|
|
||||||
|
|
||||||
|
|
||||||
def launch(args_dict: Dict[str, Any]):
|
|
||||||
# 使用远程资源启动
|
# 使用远程资源启动
|
||||||
if args_dict["use_remote_resource"]:
|
if not workflow_upload and args_dict["use_remote_resource"]:
|
||||||
print_status("使用远程资源启动", "info")
|
print_status("使用远程资源启动", "info")
|
||||||
from unilabos.app.web import http_client
|
from unilabos.app.web import http_client
|
||||||
|
|
||||||
@@ -301,11 +317,36 @@ def launch(args_dict: Dict[str, Any]):
|
|||||||
from unilabos.resources.graphio import modify_to_backend_format
|
from unilabos.resources.graphio import modify_to_backend_format
|
||||||
from unilabos.ros.nodes.resource_tracker import ResourceTreeSet, ResourceDict
|
from unilabos.ros.nodes.resource_tracker import ResourceTreeSet, ResourceDict
|
||||||
|
|
||||||
|
# 显示启动横幅
|
||||||
|
print_unilab_banner(args_dict)
|
||||||
|
|
||||||
# 注册表
|
# 注册表
|
||||||
lab_registry = build_registry(
|
lab_registry = build_registry(
|
||||||
args_dict["registry_path"], args_dict.get("complete_registry", False), args_dict["upload_registry"]
|
args_dict["registry_path"], args_dict.get("complete_registry", False), BasicConfig.upload_registry
|
||||||
)
|
)
|
||||||
|
|
||||||
|
if BasicConfig.upload_registry:
|
||||||
|
# 设备注册到服务端 - 需要 ak 和 sk
|
||||||
|
if BasicConfig.ak and BasicConfig.sk:
|
||||||
|
print_status("开始注册设备到服务端...", "info")
|
||||||
|
try:
|
||||||
|
register_devices_and_resources(lab_registry)
|
||||||
|
print_status("设备注册完成", "info")
|
||||||
|
except Exception as e:
|
||||||
|
print_status(f"设备注册失败: {e}", "error")
|
||||||
|
else:
|
||||||
|
print_status("未提供 ak 和 sk,跳过设备注册", "info")
|
||||||
|
else:
|
||||||
|
print_status("本次启动注册表不报送云端,如果您需要联网调试,请在启动命令增加--upload_registry", "warning")
|
||||||
|
|
||||||
|
# 处理 workflow_upload 子命令
|
||||||
|
if workflow_upload:
|
||||||
|
from unilabos.workflow.wf_utils import handle_workflow_upload_command
|
||||||
|
|
||||||
|
handle_workflow_upload_command(args_dict)
|
||||||
|
print_status("工作流上传完成,程序退出", "info")
|
||||||
|
os._exit(0)
|
||||||
|
|
||||||
if not BasicConfig.ak or not BasicConfig.sk:
|
if not BasicConfig.ak or not BasicConfig.sk:
|
||||||
print_status("后续运行必须拥有一个实验室,请前往 https://uni-lab.bohrium.com 注册实验室!", "warning")
|
print_status("后续运行必须拥有一个实验室,请前往 https://uni-lab.bohrium.com 注册实验室!", "warning")
|
||||||
os._exit(1)
|
os._exit(1)
|
||||||
@@ -382,20 +423,6 @@ def launch(args_dict: Dict[str, Any]):
|
|||||||
args_dict["devices_config"] = resource_tree_set
|
args_dict["devices_config"] = resource_tree_set
|
||||||
args_dict["graph"] = graph_res.physical_setup_graph
|
args_dict["graph"] = graph_res.physical_setup_graph
|
||||||
|
|
||||||
if BasicConfig.upload_registry:
|
|
||||||
# 设备注册到服务端 - 需要 ak 和 sk
|
|
||||||
if BasicConfig.ak and BasicConfig.sk:
|
|
||||||
print_status("开始注册设备到服务端...", "info")
|
|
||||||
try:
|
|
||||||
register_devices_and_resources(lab_registry)
|
|
||||||
print_status("设备注册完成", "info")
|
|
||||||
except Exception as e:
|
|
||||||
print_status(f"设备注册失败: {e}", "error")
|
|
||||||
else:
|
|
||||||
print_status("未提供 ak 和 sk,跳过设备注册", "info")
|
|
||||||
else:
|
|
||||||
print_status("本次启动注册表不报送云端,如果您需要联网调试,请在启动命令增加--upload_registry", "warning")
|
|
||||||
|
|
||||||
if args_dict["controllers"] is not None:
|
if args_dict["controllers"] is not None:
|
||||||
args_dict["controllers_config"] = yaml.safe_load(open(args_dict["controllers"], encoding="utf-8"))
|
args_dict["controllers_config"] = yaml.safe_load(open(args_dict["controllers"], encoding="utf-8"))
|
||||||
else:
|
else:
|
||||||
@@ -410,6 +437,7 @@ def launch(args_dict: Dict[str, Any]):
|
|||||||
comm_client = get_communication_client()
|
comm_client = get_communication_client()
|
||||||
if "websocket" in args_dict["app_bridges"]:
|
if "websocket" in args_dict["app_bridges"]:
|
||||||
args_dict["bridges"].append(comm_client)
|
args_dict["bridges"].append(comm_client)
|
||||||
|
|
||||||
def _exit(signum, frame):
|
def _exit(signum, frame):
|
||||||
comm_client.stop()
|
comm_client.stop()
|
||||||
sys.exit(0)
|
sys.exit(0)
|
||||||
@@ -451,16 +479,13 @@ def launch(args_dict: Dict[str, Any]):
|
|||||||
resource_visualization.start()
|
resource_visualization.start()
|
||||||
except OSError as e:
|
except OSError as e:
|
||||||
if "AMENT_PREFIX_PATH" in str(e):
|
if "AMENT_PREFIX_PATH" in str(e):
|
||||||
print_status(
|
print_status(f"ROS 2环境未正确设置,跳过3D可视化启动。错误详情: {e}", "warning")
|
||||||
f"ROS 2环境未正确设置,跳过3D可视化启动。错误详情: {e}",
|
|
||||||
"warning"
|
|
||||||
)
|
|
||||||
print_status(
|
print_status(
|
||||||
"建议解决方案:\n"
|
"建议解决方案:\n"
|
||||||
"1. 激活Conda环境: conda activate unilab\n"
|
"1. 激活Conda环境: conda activate unilab\n"
|
||||||
"2. 或使用 --backend simple 参数\n"
|
"2. 或使用 --backend simple 参数\n"
|
||||||
"3. 或使用 --visual disable 参数禁用可视化",
|
"3. 或使用 --visual disable 参数禁用可视化",
|
||||||
"info"
|
"info",
|
||||||
)
|
)
|
||||||
else:
|
else:
|
||||||
raise
|
raise
|
||||||
|
|||||||
@@ -76,7 +76,8 @@ class HTTPClient:
|
|||||||
Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
|
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:
|
with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f:
|
||||||
f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
|
payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
|
||||||
|
f.write(json.dumps(payload, indent=4))
|
||||||
# 从序列化数据中提取所有节点的UUID(保存旧UUID)
|
# 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}
|
old_uuids = {n.res_content.uuid: n for n in resources.all_nodes}
|
||||||
if not self.initialized or first_add:
|
if not self.initialized or first_add:
|
||||||
@@ -331,6 +332,67 @@ class HTTPClient:
|
|||||||
logger.error(f"响应内容: {response.text}")
|
logger.error(f"响应内容: {response.text}")
|
||||||
return None
|
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
|
# 创建默认客户端实例
|
||||||
http_client = HTTPClient()
|
http_client = HTTPClient()
|
||||||
|
|||||||
@@ -438,7 +438,7 @@ class MessageProcessor:
|
|||||||
self.connected = True
|
self.connected = True
|
||||||
self.reconnect_count = 0
|
self.reconnect_count = 0
|
||||||
|
|
||||||
logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
|
logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
|
||||||
|
|
||||||
# 启动发送协程
|
# 启动发送协程
|
||||||
send_task = asyncio.create_task(self._send_handler())
|
send_task = asyncio.create_task(self._send_handler())
|
||||||
@@ -503,7 +503,7 @@ class MessageProcessor:
|
|||||||
|
|
||||||
async def _send_handler(self):
|
async def _send_handler(self):
|
||||||
"""处理发送队列中的消息"""
|
"""处理发送队列中的消息"""
|
||||||
logger.debug("[MessageProcessor] Send handler started")
|
logger.trace("[MessageProcessor] Send handler started")
|
||||||
|
|
||||||
try:
|
try:
|
||||||
while self.connected and self.websocket:
|
while self.connected and self.websocket:
|
||||||
@@ -965,7 +965,7 @@ class QueueProcessor:
|
|||||||
|
|
||||||
def _run(self):
|
def _run(self):
|
||||||
"""运行队列处理主循环"""
|
"""运行队列处理主循环"""
|
||||||
logger.debug("[QueueProcessor] Queue processor started")
|
logger.trace("[QueueProcessor] Queue processor started")
|
||||||
|
|
||||||
while self.is_running:
|
while self.is_running:
|
||||||
try:
|
try:
|
||||||
@@ -1175,7 +1175,6 @@ class WebSocketClient(BaseCommunicationClient):
|
|||||||
else:
|
else:
|
||||||
url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
|
url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
|
||||||
|
|
||||||
logger.debug(f"[WebSocketClient] URL: {url}")
|
|
||||||
return url
|
return url
|
||||||
|
|
||||||
def start(self) -> None:
|
def start(self) -> None:
|
||||||
@@ -1188,13 +1187,11 @@ class WebSocketClient(BaseCommunicationClient):
|
|||||||
logger.error("[WebSocketClient] WebSocket URL not configured")
|
logger.error("[WebSocketClient] WebSocket URL not configured")
|
||||||
return
|
return
|
||||||
|
|
||||||
logger.info(f"[WebSocketClient] Starting connection to {self.websocket_url}")
|
|
||||||
|
|
||||||
# 启动两个核心线程
|
# 启动两个核心线程
|
||||||
self.message_processor.start()
|
self.message_processor.start()
|
||||||
self.queue_processor.start()
|
self.queue_processor.start()
|
||||||
|
|
||||||
logger.info("[WebSocketClient] All threads started")
|
logger.trace("[WebSocketClient] All threads started")
|
||||||
|
|
||||||
def stop(self) -> None:
|
def stop(self) -> None:
|
||||||
"""停止WebSocket客户端"""
|
"""停止WebSocket客户端"""
|
||||||
|
|||||||
@@ -21,7 +21,8 @@ class BasicConfig:
|
|||||||
startup_json_path = None # 填写绝对路径
|
startup_json_path = None # 填写绝对路径
|
||||||
disable_browser = False # 禁止浏览器自动打开
|
disable_browser = False # 禁止浏览器自动打开
|
||||||
port = 8002 # 本地HTTP服务
|
port = 8002 # 本地HTTP服务
|
||||||
log_level: Literal['TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] = "DEBUG" # 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
# 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
||||||
|
log_level: Literal["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = "DEBUG"
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def auth_secret(cls):
|
def auth_secret(cls):
|
||||||
@@ -41,7 +42,7 @@ class WSConfig:
|
|||||||
|
|
||||||
# HTTP配置
|
# HTTP配置
|
||||||
class HTTPConfig:
|
class HTTPConfig:
|
||||||
remote_addr = "http://127.0.0.1:48197/api/v1"
|
remote_addr = "https://uni-lab.bohrium.com/api/v1"
|
||||||
|
|
||||||
|
|
||||||
# ROS配置
|
# ROS配置
|
||||||
@@ -65,13 +66,14 @@ def _update_config_from_module(module):
|
|||||||
if not attr.startswith("_"):
|
if not attr.startswith("_"):
|
||||||
setattr(obj, attr, getattr(getattr(module, name), attr))
|
setattr(obj, attr, getattr(getattr(module, name), attr))
|
||||||
|
|
||||||
|
|
||||||
def _update_config_from_env():
|
def _update_config_from_env():
|
||||||
prefix = "UNILABOS_"
|
prefix = "UNILABOS_"
|
||||||
for env_key, env_value in os.environ.items():
|
for env_key, env_value in os.environ.items():
|
||||||
if not env_key.startswith(prefix):
|
if not env_key.startswith(prefix):
|
||||||
continue
|
continue
|
||||||
try:
|
try:
|
||||||
key_path = env_key[len(prefix):] # Remove UNILAB_ prefix
|
key_path = env_key[len(prefix) :] # Remove UNILAB_ prefix
|
||||||
class_field = key_path.upper().split("_", 1)
|
class_field = key_path.upper().split("_", 1)
|
||||||
if len(class_field) != 2:
|
if len(class_field) != 2:
|
||||||
logger.warning(f"[ENV] 环境变量格式不正确:{env_key}")
|
logger.warning(f"[ENV] 环境变量格式不正确:{env_key}")
|
||||||
|
|||||||
0
unilabos/devices/laiyu_liquid_test/__init__.py
Normal file
0
unilabos/devices/laiyu_liquid_test/__init__.py
Normal file
0
unilabos/devices/liquid_handling/laiyu/__init__.py
Normal file
0
unilabos/devices/liquid_handling/laiyu/__init__.py
Normal file
@@ -988,6 +988,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
|
|||||||
dis_vols = [float(dis_vols)]
|
dis_vols = [float(dis_vols)]
|
||||||
else:
|
else:
|
||||||
dis_vols = [float(v) for v in dis_vols]
|
dis_vols = [float(v) for v in dis_vols]
|
||||||
|
|
||||||
|
# 统一混合次数为标量,防止数组/列表与 int 比较时报错
|
||||||
|
if mix_times is not None and not isinstance(mix_times, (int, float)):
|
||||||
|
try:
|
||||||
|
mix_times = mix_times[0] if len(mix_times) > 0 else None
|
||||||
|
except Exception:
|
||||||
|
try:
|
||||||
|
mix_times = next(iter(mix_times))
|
||||||
|
except Exception:
|
||||||
|
pass
|
||||||
|
if mix_times is not None:
|
||||||
|
mix_times = int(mix_times)
|
||||||
|
|
||||||
# 识别传输模式
|
# 识别传输模式
|
||||||
num_sources = len(sources)
|
num_sources = len(sources)
|
||||||
|
|||||||
@@ -5,6 +5,7 @@ import json
|
|||||||
import os
|
import os
|
||||||
import socket
|
import socket
|
||||||
import time
|
import time
|
||||||
|
import uuid
|
||||||
from typing import Any, List, Dict, Optional, Tuple, TypedDict, Union, Sequence, Iterator, Literal
|
from typing import Any, List, Dict, Optional, Tuple, TypedDict, Union, Sequence, Iterator, Literal
|
||||||
|
|
||||||
from pylabrobot.liquid_handling import (
|
from pylabrobot.liquid_handling import (
|
||||||
@@ -856,7 +857,30 @@ class PRCXI9300Api:
|
|||||||
|
|
||||||
def _raw_request(self, payload: str) -> str:
|
def _raw_request(self, payload: str) -> str:
|
||||||
if self.debug:
|
if self.debug:
|
||||||
return " "
|
# 调试/仿真模式下直接返回可解析的模拟 JSON,避免后续 json.loads 报错
|
||||||
|
try:
|
||||||
|
req = json.loads(payload)
|
||||||
|
method = req.get("MethodName")
|
||||||
|
except Exception:
|
||||||
|
method = None
|
||||||
|
|
||||||
|
data: Any = True
|
||||||
|
if method in {"AddSolution"}:
|
||||||
|
data = str(uuid.uuid4())
|
||||||
|
elif method in {"AddWorkTabletMatrix", "AddWorkTabletMatrix2"}:
|
||||||
|
data = {"Success": True, "Message": "debug mock"}
|
||||||
|
elif method in {"GetErrorCode"}:
|
||||||
|
data = ""
|
||||||
|
elif method in {"RemoveErrorCodet", "Reset", "Start", "LoadSolution", "Pause", "Resume", "Stop"}:
|
||||||
|
data = True
|
||||||
|
elif method in {"GetStepStateList", "GetStepStatus", "GetStepState"}:
|
||||||
|
data = []
|
||||||
|
elif method in {"GetLocation"}:
|
||||||
|
data = {"X": 0, "Y": 0, "Z": 0}
|
||||||
|
elif method in {"GetResetStatus"}:
|
||||||
|
data = False
|
||||||
|
|
||||||
|
return json.dumps({"Success": True, "Msg": "debug mock", "Data": data})
|
||||||
with contextlib.closing(socket.socket()) as sock:
|
with contextlib.closing(socket.socket()) as sock:
|
||||||
sock.settimeout(self.timeout)
|
sock.settimeout(self.timeout)
|
||||||
sock.connect((self.host, self.port))
|
sock.connect((self.host, self.port))
|
||||||
|
|||||||
@@ -1,282 +1,636 @@
|
|||||||
import sys
|
# -*- coding: utf-8 -*-
|
||||||
import threading
|
"""
|
||||||
import serial
|
Contains drivers for:
|
||||||
import serial.tools.list_ports
|
1. SyringePump: Runze Fluid SY-03B (ASCII)
|
||||||
import re
|
2. EmmMotor: Emm V5.0 Closed-loop Stepper (Modbus-RTU variant)
|
||||||
import time
|
3. XKCSensor: XKC Non-contact Level Sensor (Modbus-RTU)
|
||||||
from typing import Optional, List, Dict, Tuple
|
"""
|
||||||
|
|
||||||
class ChinweDevice:
|
import socket
|
||||||
|
import serial
|
||||||
|
import time
|
||||||
|
import threading
|
||||||
|
import struct
|
||||||
|
import re
|
||||||
|
import traceback
|
||||||
|
import queue
|
||||||
|
from typing import Optional, Dict, List, Any
|
||||||
|
|
||||||
|
try:
|
||||||
|
from unilabos.device_comms.universal_driver import UniversalDriver
|
||||||
|
except ImportError:
|
||||||
|
import logging
|
||||||
|
class UniversalDriver:
|
||||||
|
def __init__(self):
|
||||||
|
self.logger = logging.getLogger(self.__class__.__name__)
|
||||||
|
|
||||||
|
def execute_command_from_outer(self, command: str):
|
||||||
|
pass
|
||||||
|
|
||||||
|
# ==============================================================================
|
||||||
|
# 1. Transport Layer (通信层)
|
||||||
|
# ==============================================================================
|
||||||
|
|
||||||
|
class TransportManager:
|
||||||
"""
|
"""
|
||||||
ChinWe设备控制类
|
统一通信管理类。
|
||||||
提供串口通信、电机控制、传感器数据读取等功能
|
自动识别 串口 (Serial) 或 网络 (TCP) 连接。
|
||||||
"""
|
"""
|
||||||
|
def __init__(self, port: str, baudrate: int = 9600, timeout: float = 3.0, logger=None):
|
||||||
def __init__(self, port: str, baudrate: int = 115200, debug: bool = False):
|
|
||||||
"""
|
|
||||||
初始化ChinWe设备
|
|
||||||
|
|
||||||
Args:
|
|
||||||
port: 串口名称,如果为None则自动检测
|
|
||||||
baudrate: 波特率,默认115200
|
|
||||||
"""
|
|
||||||
self.debug = debug
|
|
||||||
self.port = port
|
self.port = port
|
||||||
self.baudrate = baudrate
|
self.baudrate = baudrate
|
||||||
self.serial_port: Optional[serial.Serial] = None
|
self.timeout = timeout
|
||||||
self._voltage: float = 0.0
|
self.logger = logger
|
||||||
self._ec_value: float = 0.0
|
self.lock = threading.RLock() # 线程锁,确保多设备共用一个连接时不冲突
|
||||||
self._ec_adc_value: int = 0
|
|
||||||
|
self.is_tcp = False
|
||||||
|
self.serial = None
|
||||||
|
self.socket = None
|
||||||
|
|
||||||
|
# 简单判断: 如果包含 ':' (如 192.168.1.1:8899) 或者看起来像 IP,则认为是 TCP
|
||||||
|
if ':' in self.port or (self.port.count('.') == 3 and not self.port.startswith('/')):
|
||||||
|
self.is_tcp = True
|
||||||
|
self._connect_tcp()
|
||||||
|
else:
|
||||||
|
self._connect_serial()
|
||||||
|
|
||||||
|
def _log(self, msg):
|
||||||
|
if self.logger:
|
||||||
|
pass
|
||||||
|
# self.logger.debug(f"[Transport] {msg}")
|
||||||
|
|
||||||
|
def _connect_tcp(self):
|
||||||
|
try:
|
||||||
|
if ':' in self.port:
|
||||||
|
host, p = self.port.split(':')
|
||||||
|
self.tcp_host = host
|
||||||
|
self.tcp_port = int(p)
|
||||||
|
else:
|
||||||
|
self.tcp_host = self.port
|
||||||
|
self.tcp_port = 8899 # 默认端口
|
||||||
|
|
||||||
|
# if self.logger: self.logger.info(f"Connecting TCP {self.tcp_host}:{self.tcp_port} ...")
|
||||||
|
self.socket = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
|
||||||
|
self.socket.settimeout(self.timeout)
|
||||||
|
self.socket.connect((self.tcp_host, self.tcp_port))
|
||||||
|
except Exception as e:
|
||||||
|
raise ConnectionError(f"TCP connection failed: {e}")
|
||||||
|
|
||||||
|
def _connect_serial(self):
|
||||||
|
try:
|
||||||
|
# if self.logger: self.logger.info(f"Opening Serial {self.port} (Baud: {self.baudrate}) ...")
|
||||||
|
self.serial = serial.Serial(
|
||||||
|
port=self.port,
|
||||||
|
baudrate=self.baudrate,
|
||||||
|
timeout=self.timeout
|
||||||
|
)
|
||||||
|
except Exception as e:
|
||||||
|
raise ConnectionError(f"Serial open failed: {e}")
|
||||||
|
|
||||||
|
def close(self):
|
||||||
|
"""关闭连接"""
|
||||||
|
if self.is_tcp and self.socket:
|
||||||
|
try: self.socket.close()
|
||||||
|
except: pass
|
||||||
|
elif not self.is_tcp and self.serial and self.serial.is_open:
|
||||||
|
self.serial.close()
|
||||||
|
|
||||||
|
def clear_buffer(self):
|
||||||
|
"""清空缓冲区 (Thread-safe)"""
|
||||||
|
with self.lock:
|
||||||
|
if self.is_tcp:
|
||||||
|
self.socket.setblocking(False)
|
||||||
|
try:
|
||||||
|
while True:
|
||||||
|
if not self.socket.recv(1024): break
|
||||||
|
except: pass
|
||||||
|
finally: self.socket.settimeout(self.timeout)
|
||||||
|
else:
|
||||||
|
self.serial.reset_input_buffer()
|
||||||
|
|
||||||
|
def write(self, data: bytes):
|
||||||
|
"""发送原始字节"""
|
||||||
|
with self.lock:
|
||||||
|
if self.is_tcp:
|
||||||
|
self.socket.sendall(data)
|
||||||
|
else:
|
||||||
|
self.serial.write(data)
|
||||||
|
|
||||||
|
def read(self, size: int) -> bytes:
|
||||||
|
"""读取指定长度字节"""
|
||||||
|
if self.is_tcp:
|
||||||
|
data = b''
|
||||||
|
start = time.time()
|
||||||
|
while len(data) < size:
|
||||||
|
if time.time() - start > self.timeout: break
|
||||||
|
try:
|
||||||
|
chunk = self.socket.recv(size - len(data))
|
||||||
|
if not chunk: break
|
||||||
|
data += chunk
|
||||||
|
except socket.timeout: break
|
||||||
|
return data
|
||||||
|
else:
|
||||||
|
return self.serial.read(size)
|
||||||
|
|
||||||
|
def send_ascii_command(self, command: str) -> str:
|
||||||
|
"""
|
||||||
|
发送 ASCII 字符串命令 (如注射泵指令),读取直到 '\r'。
|
||||||
|
"""
|
||||||
|
with self.lock:
|
||||||
|
data = command.encode('ascii') if isinstance(command, str) else command
|
||||||
|
self.clear_buffer()
|
||||||
|
self.write(data)
|
||||||
|
|
||||||
|
# Read until \r
|
||||||
|
if self.is_tcp:
|
||||||
|
resp = b''
|
||||||
|
start = time.time()
|
||||||
|
while True:
|
||||||
|
if time.time() - start > self.timeout: break
|
||||||
|
try:
|
||||||
|
char = self.socket.recv(1)
|
||||||
|
if not char: break
|
||||||
|
resp += char
|
||||||
|
if char == b'\r': break
|
||||||
|
except: break
|
||||||
|
return resp.decode('ascii', errors='ignore').strip()
|
||||||
|
else:
|
||||||
|
return self.serial.read_until(b'\r').decode('ascii', errors='ignore').strip()
|
||||||
|
|
||||||
|
# ==============================================================================
|
||||||
|
# 2. Syringe Pump Driver (注射泵)
|
||||||
|
# ==============================================================================
|
||||||
|
|
||||||
|
class SyringePump:
|
||||||
|
"""SY-03B 注射泵驱动 (ASCII协议)"""
|
||||||
|
|
||||||
|
CMD_INITIALIZE = "Z{speed},{drain_port},{output_port}R"
|
||||||
|
CMD_SWITCH_VALVE = "I{port}R"
|
||||||
|
CMD_ASPIRATE = "P{vol}R"
|
||||||
|
CMD_DISPENSE = "D{vol}R"
|
||||||
|
CMD_DISPENSE_ALL = "A0R"
|
||||||
|
CMD_STOP = "TR"
|
||||||
|
CMD_QUERY_STATUS = "Q"
|
||||||
|
CMD_QUERY_PLUNGER = "?0"
|
||||||
|
|
||||||
|
def __init__(self, device_id: int, transport: TransportManager):
|
||||||
|
if not 1 <= device_id <= 15:
|
||||||
|
pass # Allow all IDs for now
|
||||||
|
self.id = str(device_id)
|
||||||
|
self.transport = transport
|
||||||
|
|
||||||
|
def _send(self, template: str, **kwargs) -> str:
|
||||||
|
cmd = f"/{self.id}" + template.format(**kwargs) + "\r"
|
||||||
|
return self.transport.send_ascii_command(cmd)
|
||||||
|
|
||||||
|
def is_busy(self) -> bool:
|
||||||
|
"""查询繁忙状态"""
|
||||||
|
resp = self._send(self.CMD_QUERY_STATUS)
|
||||||
|
# 响应如 /0` (Ready, 0x60) 或 /0@ (Busy, 0x40)
|
||||||
|
if len(resp) >= 3:
|
||||||
|
status_byte = ord(resp[2])
|
||||||
|
# Bit 5: 1=Ready, 0=Busy
|
||||||
|
return (status_byte & 0x20) == 0
|
||||||
|
return False
|
||||||
|
|
||||||
|
def wait_until_idle(self, timeout=30):
|
||||||
|
"""阻塞等待直到空闲"""
|
||||||
|
start = time.time()
|
||||||
|
while time.time() - start < timeout:
|
||||||
|
if not self.is_busy(): return
|
||||||
|
time.sleep(0.5)
|
||||||
|
# raise TimeoutError(f"Pump {self.id} wait idle timeout")
|
||||||
|
pass
|
||||||
|
|
||||||
|
def initialize(self, drain_port=0, output_port=0, speed=10):
|
||||||
|
"""初始化"""
|
||||||
|
self._send(self.CMD_INITIALIZE, speed=speed, drain_port=drain_port, output_port=output_port)
|
||||||
|
|
||||||
|
def switch_valve(self, port: int):
|
||||||
|
"""切换阀门 (1-8)"""
|
||||||
|
self._send(self.CMD_SWITCH_VALVE, port=port)
|
||||||
|
|
||||||
|
def aspirate(self, steps: int):
|
||||||
|
"""吸液 (相对步数)"""
|
||||||
|
self._send(self.CMD_ASPIRATE, vol=steps)
|
||||||
|
|
||||||
|
def dispense(self, steps: int):
|
||||||
|
"""排液 (相对步数)"""
|
||||||
|
self._send(self.CMD_DISPENSE, vol=steps)
|
||||||
|
|
||||||
|
def stop(self):
|
||||||
|
"""停止"""
|
||||||
|
self._send(self.CMD_STOP)
|
||||||
|
|
||||||
|
def get_position(self) -> int:
|
||||||
|
"""获取柱塞位置 (步数)"""
|
||||||
|
resp = self._send(self.CMD_QUERY_PLUNGER)
|
||||||
|
m = re.search(r'\d+', resp)
|
||||||
|
return int(m.group()) if m else -1
|
||||||
|
|
||||||
|
# ==============================================================================
|
||||||
|
# 3. Stepper Motor Driver (步进电机)
|
||||||
|
# ==============================================================================
|
||||||
|
|
||||||
|
class EmmMotor:
|
||||||
|
"""Emm V5.0 闭环步进电机驱动"""
|
||||||
|
|
||||||
|
def __init__(self, device_id: int, transport: TransportManager):
|
||||||
|
self.id = device_id
|
||||||
|
self.transport = transport
|
||||||
|
|
||||||
|
def _send(self, func_code: int, payload: list) -> bytes:
|
||||||
|
with self.transport.lock:
|
||||||
|
self.transport.clear_buffer()
|
||||||
|
# 格式: [ID] [Func] [Data...] [Check=0x6B]
|
||||||
|
body = [self.id, func_code] + payload
|
||||||
|
body.append(0x6B) # Checksum
|
||||||
|
self.transport.write(bytes(body))
|
||||||
|
|
||||||
|
# 根据指令不同,读取不同长度响应
|
||||||
|
read_len = 10 if func_code in [0x31, 0x32, 0x35, 0x24, 0x27] else 4
|
||||||
|
return self.transport.read(read_len)
|
||||||
|
|
||||||
|
def enable(self, on=True):
|
||||||
|
"""使能 (True=锁轴, False=松轴)"""
|
||||||
|
state = 1 if on else 0
|
||||||
|
self._send(0xF3, [0xAB, state, 0])
|
||||||
|
|
||||||
|
def run_speed(self, speed_rpm: int, direction=0, acc=10):
|
||||||
|
"""速度模式运行"""
|
||||||
|
sp = struct.pack('>H', int(speed_rpm))
|
||||||
|
self._send(0xF6, [direction, sp[0], sp[1], acc, 0])
|
||||||
|
|
||||||
|
def run_position(self, pulses: int, speed_rpm: int, direction=0, acc=10, absolute=False):
|
||||||
|
"""位置模式运行"""
|
||||||
|
sp = struct.pack('>H', int(speed_rpm))
|
||||||
|
pl = struct.pack('>I', int(pulses))
|
||||||
|
is_abs = 1 if absolute else 0
|
||||||
|
self._send(0xFD, [direction, sp[0], sp[1], acc, pl[0], pl[1], pl[2], pl[3], is_abs, 0])
|
||||||
|
|
||||||
|
def stop(self):
|
||||||
|
"""停止"""
|
||||||
|
self._send(0xFE, [0x98, 0])
|
||||||
|
|
||||||
|
def set_zero(self):
|
||||||
|
"""清零位置"""
|
||||||
|
self._send(0x0A, [])
|
||||||
|
|
||||||
|
def get_position(self) -> int:
|
||||||
|
"""获取当前脉冲位置"""
|
||||||
|
resp = self._send(0x32, [])
|
||||||
|
if len(resp) >= 8:
|
||||||
|
sign = resp[2]
|
||||||
|
val = struct.unpack('>I', resp[3:7])[0]
|
||||||
|
return -val if sign == 1 else val
|
||||||
|
return 0
|
||||||
|
|
||||||
|
# ==============================================================================
|
||||||
|
# 4. Liquid Sensor Driver (液位传感器)
|
||||||
|
# ==============================================================================
|
||||||
|
|
||||||
|
class XKCSensor:
|
||||||
|
"""XKC RS485 液位传感器 (Modbus RTU)"""
|
||||||
|
|
||||||
|
def __init__(self, device_id: int, transport: TransportManager, threshold: int = 300):
|
||||||
|
self.id = device_id
|
||||||
|
self.transport = transport
|
||||||
|
self.threshold = threshold
|
||||||
|
|
||||||
|
def _crc(self, data: bytes) -> bytes:
|
||||||
|
crc = 0xFFFF
|
||||||
|
for byte in data:
|
||||||
|
crc ^= byte
|
||||||
|
for _ in range(8):
|
||||||
|
if crc & 0x0001: crc = (crc >> 1) ^ 0xA001
|
||||||
|
else: crc >>= 1
|
||||||
|
return struct.pack('<H', crc)
|
||||||
|
|
||||||
|
def read_level(self) -> Optional[Dict[str, Any]]:
|
||||||
|
"""
|
||||||
|
读取液位。
|
||||||
|
返回: {'level': bool, 'rssi': int}
|
||||||
|
"""
|
||||||
|
with self.transport.lock:
|
||||||
|
self.transport.clear_buffer()
|
||||||
|
# Modbus Read Registers: 01 03 00 01 00 02 CRC
|
||||||
|
payload = struct.pack('>HH', 0x0001, 0x0002)
|
||||||
|
msg = struct.pack('BB', self.id, 0x03) + payload
|
||||||
|
msg += self._crc(msg)
|
||||||
|
self.transport.write(msg)
|
||||||
|
|
||||||
|
# Read header
|
||||||
|
h = self.transport.read(3) # Addr, Func, Len
|
||||||
|
if len(h) < 3: return None
|
||||||
|
length = h[2]
|
||||||
|
|
||||||
|
# Read body + CRC
|
||||||
|
body = self.transport.read(length + 2)
|
||||||
|
if len(body) < length + 2:
|
||||||
|
# Firmware bug fix specific to some modules
|
||||||
|
if len(body) == 4 and length == 4:
|
||||||
|
pass
|
||||||
|
else:
|
||||||
|
return None
|
||||||
|
|
||||||
|
data = body[:-2]
|
||||||
|
if len(data) == 2:
|
||||||
|
rssi = data[1]
|
||||||
|
elif len(data) >= 4:
|
||||||
|
rssi = (data[2] << 8) | data[3]
|
||||||
|
else:
|
||||||
|
return None
|
||||||
|
|
||||||
|
return {
|
||||||
|
'level': rssi > self.threshold,
|
||||||
|
'rssi': rssi
|
||||||
|
}
|
||||||
|
|
||||||
|
# ==============================================================================
|
||||||
|
# 5. Main Device Class (ChinweDevice)
|
||||||
|
# ==============================================================================
|
||||||
|
|
||||||
|
class ChinweDevice(UniversalDriver):
|
||||||
|
"""
|
||||||
|
ChinWe 工作站主驱动
|
||||||
|
继承自 UniversalDriver,管理所有子设备(泵、电机、传感器)
|
||||||
|
"""
|
||||||
|
|
||||||
|
def __init__(self, port: str = "192.168.1.200:8899", baudrate: int = 9600,
|
||||||
|
pump_ids: List[int] = None, motor_ids: List[int] = None,
|
||||||
|
sensor_id: int = 6, sensor_threshold: int = 300):
|
||||||
|
"""
|
||||||
|
初始化 ChinWe 工作站
|
||||||
|
:param port: 串口号 或 IP:Port
|
||||||
|
:param baudrate: 串口波特率
|
||||||
|
:param pump_ids: 注射泵 ID列表 (默认 [1, 2, 3])
|
||||||
|
:param motor_ids: 步进电机 ID列表 (默认 [4, 5])
|
||||||
|
:param sensor_id: 液位传感器 ID (默认 6)
|
||||||
|
"""
|
||||||
|
super().__init__()
|
||||||
|
self.port = port
|
||||||
|
self.baudrate = baudrate
|
||||||
|
self.mgr = None
|
||||||
self._is_connected = False
|
self._is_connected = False
|
||||||
self.connect()
|
|
||||||
|
# 默认配置
|
||||||
|
if pump_ids is None: pump_ids = [1, 2, 3]
|
||||||
|
if motor_ids is None: motor_ids = [4, 5]
|
||||||
|
|
||||||
|
# 配置信息
|
||||||
|
self.pump_ids = pump_ids
|
||||||
|
self.motor_ids = motor_ids
|
||||||
|
self.sensor_id = sensor_id
|
||||||
|
self.sensor_threshold = sensor_threshold
|
||||||
|
|
||||||
|
# 子设备实例容器
|
||||||
|
self.pumps: Dict[int, SyringePump] = {}
|
||||||
|
self.motors: Dict[int, EmmMotor] = {}
|
||||||
|
self.sensor: Optional[XKCSensor] = None
|
||||||
|
|
||||||
|
# 轮询线程控制
|
||||||
|
self._stop_event = threading.Event()
|
||||||
|
self._poll_thread = None
|
||||||
|
|
||||||
|
# 实时状态缓存
|
||||||
|
self.status_cache = {
|
||||||
|
"sensor_rssi": 0,
|
||||||
|
"sensor_level": False,
|
||||||
|
"connected": False
|
||||||
|
}
|
||||||
|
|
||||||
|
# 自动连接
|
||||||
|
if self.port:
|
||||||
|
self.connect()
|
||||||
|
|
||||||
|
def connect(self) -> bool:
|
||||||
|
if self._is_connected: return True
|
||||||
|
try:
|
||||||
|
self.logger.info(f"Connecting to {self.port}...")
|
||||||
|
self.mgr = TransportManager(self.port, baudrate=self.baudrate, logger=self.logger)
|
||||||
|
|
||||||
|
# 初始化所有泵
|
||||||
|
for pid in self.pump_ids:
|
||||||
|
self.pumps[pid] = SyringePump(pid, self.mgr)
|
||||||
|
|
||||||
|
# 初始化所有电机
|
||||||
|
for mid in self.motor_ids:
|
||||||
|
self.motors[mid] = EmmMotor(mid, self.mgr)
|
||||||
|
|
||||||
|
# 初始化传感器
|
||||||
|
self.sensor = XKCSensor(self.sensor_id, self.mgr, self.sensor_threshold)
|
||||||
|
|
||||||
|
self._is_connected = True
|
||||||
|
self.status_cache["connected"] = True
|
||||||
|
|
||||||
|
# 启动轮询线程
|
||||||
|
self._start_polling()
|
||||||
|
return True
|
||||||
|
except Exception as e:
|
||||||
|
self.logger.error(f"Connection failed: {e}")
|
||||||
|
self._is_connected = False
|
||||||
|
self.status_cache["connected"] = False
|
||||||
|
return False
|
||||||
|
|
||||||
|
def disconnect(self):
|
||||||
|
self._stop_event.set()
|
||||||
|
if self._poll_thread:
|
||||||
|
self._poll_thread.join(timeout=2.0)
|
||||||
|
|
||||||
|
if self.mgr:
|
||||||
|
self.mgr.close()
|
||||||
|
|
||||||
|
self._is_connected = False
|
||||||
|
self.status_cache["connected"] = False
|
||||||
|
self.logger.info("Disconnected.")
|
||||||
|
|
||||||
|
def _start_polling(self):
|
||||||
|
"""启动传感器轮询线程"""
|
||||||
|
if self._poll_thread and self._poll_thread.is_alive():
|
||||||
|
return
|
||||||
|
|
||||||
|
self._stop_event.clear()
|
||||||
|
self._poll_thread = threading.Thread(target=self._polling_loop, daemon=True, name="ChinwePoll")
|
||||||
|
self._poll_thread.start()
|
||||||
|
|
||||||
|
def _polling_loop(self):
|
||||||
|
"""轮询主循环"""
|
||||||
|
self.logger.info("Sensor polling started.")
|
||||||
|
error_count = 0
|
||||||
|
while not self._stop_event.is_set():
|
||||||
|
if not self._is_connected or not self.sensor:
|
||||||
|
time.sleep(1)
|
||||||
|
continue
|
||||||
|
|
||||||
|
try:
|
||||||
|
# 获取传感器数据
|
||||||
|
data = self.sensor.read_level()
|
||||||
|
if data:
|
||||||
|
self.status_cache["sensor_rssi"] = data['rssi']
|
||||||
|
self.status_cache["sensor_level"] = data['level']
|
||||||
|
error_count = 0
|
||||||
|
else:
|
||||||
|
error_count += 1
|
||||||
|
|
||||||
|
# 降低轮询频率防止总线拥塞
|
||||||
|
time.sleep(0.2)
|
||||||
|
|
||||||
|
except Exception as e:
|
||||||
|
error_count += 1
|
||||||
|
if error_count > 10: # 连续错误记录日志
|
||||||
|
# self.logger.error(f"Polling error: {e}")
|
||||||
|
error_count = 0
|
||||||
|
time.sleep(1)
|
||||||
|
|
||||||
|
# --- 对外暴露属性 (Properties) ---
|
||||||
|
|
||||||
|
@property
|
||||||
|
def sensor_level(self) -> bool:
|
||||||
|
return self.status_cache["sensor_level"]
|
||||||
|
|
||||||
|
@property
|
||||||
|
def sensor_rssi(self) -> int:
|
||||||
|
return self.status_cache["sensor_rssi"]
|
||||||
|
|
||||||
@property
|
@property
|
||||||
def is_connected(self) -> bool:
|
def is_connected(self) -> bool:
|
||||||
"""获取连接状态"""
|
return self._is_connected
|
||||||
return self._is_connected and self.serial_port and self.serial_port.is_open
|
|
||||||
|
|
||||||
@property
|
|
||||||
def voltage(self) -> float:
|
|
||||||
"""获取电源电压值"""
|
|
||||||
return self._voltage
|
|
||||||
|
|
||||||
@property
|
|
||||||
def ec_value(self) -> float:
|
|
||||||
"""获取电导率值 (ms/cm)"""
|
|
||||||
return self._ec_value
|
|
||||||
|
|
||||||
@property
|
# --- 对外功能指令 (Actions) ---
|
||||||
def ec_adc_value(self) -> int:
|
|
||||||
"""获取EC ADC原始值"""
|
|
||||||
return self._ec_adc_value
|
|
||||||
|
|
||||||
|
|
||||||
@property
|
def pump_initialize(self, pump_id: int, drain_port=0, output_port=0, speed=10):
|
||||||
def device_status(self) -> Dict[str, any]:
|
"""指定泵初始化"""
|
||||||
"""
|
pump_id = int(pump_id)
|
||||||
获取设备状态信息
|
if pump_id in self.pumps:
|
||||||
|
self.pumps[pump_id].initialize(drain_port, output_port, speed)
|
||||||
Returns:
|
self.pumps[pump_id].wait_until_idle()
|
||||||
包含设备状态的字典
|
|
||||||
"""
|
|
||||||
return {
|
|
||||||
"connected": self.is_connected,
|
|
||||||
"port": self.port,
|
|
||||||
"baudrate": self.baudrate,
|
|
||||||
"voltage": self.voltage,
|
|
||||||
"ec_value": self.ec_value,
|
|
||||||
"ec_adc_value": self.ec_adc_value
|
|
||||||
}
|
|
||||||
|
|
||||||
def connect(self, port: Optional[str] = None, baudrate: Optional[int] = None) -> bool:
|
|
||||||
"""
|
|
||||||
连接到串口设备
|
|
||||||
|
|
||||||
Args:
|
|
||||||
port: 串口名称,如果为None则使用初始化时的port或自动检测
|
|
||||||
baudrate: 波特率,如果为None则使用初始化时的baudrate
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
连接是否成功
|
|
||||||
"""
|
|
||||||
if self.is_connected:
|
|
||||||
return True
|
return True
|
||||||
|
return False
|
||||||
target_port = port or self.port
|
|
||||||
target_baudrate = baudrate or self.baudrate
|
def pump_aspirate(self, pump_id: int, volume: int, valve_port: int):
|
||||||
|
"""
|
||||||
try:
|
泵吸液 (阻塞)
|
||||||
self.serial_port = serial.Serial(target_port, target_baudrate, timeout=0.5)
|
:param valve_port: 阀门端口 (1-8)
|
||||||
self._is_connected = True
|
"""
|
||||||
self.port = target_port
|
pump_id = int(pump_id)
|
||||||
self.baudrate = target_baudrate
|
valve_port = int(valve_port)
|
||||||
connect_allow_times = 5
|
if pump_id in self.pumps:
|
||||||
while not self.serial_port.is_open and connect_allow_times > 0:
|
pump = self.pumps[pump_id]
|
||||||
time.sleep(0.5)
|
# 1. 切换阀门
|
||||||
connect_allow_times -= 1
|
pump.switch_valve(valve_port)
|
||||||
print(f"尝试连接到 {target_port} @ {target_baudrate},剩余尝试次数: {connect_allow_times}", self.debug)
|
pump.wait_until_idle()
|
||||||
raise ValueError("串口未打开,请检查设备连接")
|
# 2. 吸液
|
||||||
print(f"已连接到 {target_port} @ {target_baudrate}", self.debug)
|
pump.aspirate(volume)
|
||||||
threading.Thread(target=self._read_data, daemon=True).start()
|
pump.wait_until_idle()
|
||||||
return True
|
return True
|
||||||
except Exception as e:
|
return False
|
||||||
print(f"ChinweDevice连接失败: {e}")
|
|
||||||
self._is_connected = False
|
def pump_dispense(self, pump_id: int, volume: int, valve_port: int):
|
||||||
return False
|
|
||||||
|
|
||||||
def disconnect(self) -> bool:
|
|
||||||
"""
|
"""
|
||||||
断开串口连接
|
泵排液 (阻塞)
|
||||||
|
:param valve_port: 阀门端口 (1-8)
|
||||||
Returns:
|
|
||||||
断开是否成功
|
|
||||||
"""
|
"""
|
||||||
if self.serial_port and self.serial_port.is_open:
|
pump_id = int(pump_id)
|
||||||
try:
|
valve_port = int(valve_port)
|
||||||
self.serial_port.close()
|
if pump_id in self.pumps:
|
||||||
self._is_connected = False
|
pump = self.pumps[pump_id]
|
||||||
print("已断开串口连接")
|
# 1. 切换阀门
|
||||||
return True
|
pump.switch_valve(valve_port)
|
||||||
except Exception as e:
|
pump.wait_until_idle()
|
||||||
print(f"断开连接失败: {e}")
|
# 2. 排液
|
||||||
return False
|
pump.dispense(volume)
|
||||||
|
pump.wait_until_idle()
|
||||||
|
return True
|
||||||
|
return False
|
||||||
|
|
||||||
|
def pump_valve(self, pump_id: int, port: int):
|
||||||
|
"""泵切换阀门 (阻塞)"""
|
||||||
|
pump_id = int(pump_id)
|
||||||
|
port = int(port)
|
||||||
|
if pump_id in self.pumps:
|
||||||
|
pump = self.pumps[pump_id]
|
||||||
|
pump.switch_valve(port)
|
||||||
|
pump.wait_until_idle()
|
||||||
|
return True
|
||||||
|
return False
|
||||||
|
|
||||||
|
def motor_run_continuous(self, motor_id: int, speed: int, direction: str = "顺时针"):
|
||||||
|
"""
|
||||||
|
电机一直旋转 (速度模式)
|
||||||
|
:param direction: "顺时针" or "逆时针"
|
||||||
|
"""
|
||||||
|
motor_id = int(motor_id)
|
||||||
|
if motor_id not in self.motors: return False
|
||||||
|
|
||||||
|
dir_val = 0 if direction == "顺时针" else 1
|
||||||
|
self.motors[motor_id].run_speed(speed, dir_val)
|
||||||
return True
|
return True
|
||||||
|
|
||||||
def _send_motor_command(self, command: str) -> bool:
|
def motor_rotate_quarter(self, motor_id: int, speed: int = 60, direction: str = "顺时针"):
|
||||||
"""
|
"""
|
||||||
发送电机控制命令
|
电机旋转1/4圈 (阻塞)
|
||||||
|
假设电机设置为 3200 脉冲/圈,1/4圈 = 800脉冲
|
||||||
Args:
|
|
||||||
command: 电机命令字符串,例如 "M 1 CW 1.5"
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
发送是否成功
|
|
||||||
"""
|
"""
|
||||||
if not self.is_connected:
|
motor_id = int(motor_id)
|
||||||
print("设备未连接")
|
if motor_id not in self.motors: return False
|
||||||
return False
|
|
||||||
|
pulses = 800
|
||||||
try:
|
dir_val = 0 if direction == "顺时针" else 1
|
||||||
self.serial_port.write((command + "\n").encode('utf-8'))
|
|
||||||
print(f"发送命令: {command}")
|
self.motors[motor_id].run_position(pulses, speed, dir_val, absolute=False)
|
||||||
|
|
||||||
|
# 预估时间阻塞 (单位: 分钟 -> 秒)
|
||||||
|
# Time(s) = revs / (RPM/60). revs = 0.25. time = 15 / RPM.
|
||||||
|
estimated_time = 15.0 / max(1, speed)
|
||||||
|
time.sleep(estimated_time + 0.5)
|
||||||
|
|
||||||
|
return True
|
||||||
|
|
||||||
|
def motor_stop(self, motor_id: int):
|
||||||
|
"""电机停止"""
|
||||||
|
motor_id = int(motor_id)
|
||||||
|
if motor_id in self.motors:
|
||||||
|
self.motors[motor_id].stop()
|
||||||
return True
|
return True
|
||||||
except Exception as e:
|
return False
|
||||||
print(f"发送命令失败: {e}")
|
|
||||||
return False
|
|
||||||
|
|
||||||
def rotate_motor(self, motor_id: int, turns: float, clockwise: bool = True) -> bool:
|
|
||||||
"""
|
|
||||||
使电机转动指定圈数
|
|
||||||
|
|
||||||
Args:
|
|
||||||
motor_id: 电机ID(1, 2, 3...)
|
|
||||||
turns: 转动圈数,支持小数
|
|
||||||
clockwise: True为顺时针,False为逆时针
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
命令发送是否成功
|
|
||||||
"""
|
|
||||||
if clockwise:
|
|
||||||
command = f"M {motor_id} CW {turns}"
|
|
||||||
else:
|
|
||||||
command = f"M {motor_id} CCW {turns}"
|
|
||||||
return self._send_motor_command(command)
|
|
||||||
|
|
||||||
def set_motor_speed(self, motor_id: int, speed: float) -> bool:
|
def wait_sensor_level(self, target_state: str = "有液", timeout: int = 30) -> bool:
|
||||||
"""
|
"""
|
||||||
设置电机转速(如果设备支持)
|
等待传感器达到指定电平
|
||||||
|
:param target_state: "有液" or "无液"
|
||||||
Args:
|
|
||||||
motor_id: 电机ID(1, 2, 3...)
|
|
||||||
speed: 转速值
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
命令发送是否成功
|
|
||||||
"""
|
"""
|
||||||
command = f"M {motor_id} SPEED {speed}"
|
target_bool = True if target_state == "有液" else False
|
||||||
return self._send_motor_command(command)
|
|
||||||
|
|
||||||
def _read_data(self) -> List[str]:
|
self.logger.info(f"Wait sensor: {target_state} ({target_bool}), timeout: {timeout}")
|
||||||
"""
|
start = time.time()
|
||||||
读取串口数据并解析
|
while time.time() - start < timeout:
|
||||||
|
if self.sensor_level == target_bool:
|
||||||
Returns:
|
return True
|
||||||
读取到的数据行列表
|
time.sleep(0.1)
|
||||||
"""
|
self.logger.warning("Wait sensor level timeout")
|
||||||
print("开始读取串口数据...")
|
return False
|
||||||
if not self.is_connected:
|
|
||||||
return []
|
|
||||||
|
|
||||||
data_lines = []
|
|
||||||
try:
|
|
||||||
while self.serial_port.in_waiting:
|
|
||||||
time.sleep(0.1) # 等待数据稳定
|
|
||||||
try:
|
|
||||||
line = self.serial_port.readline().decode('utf-8', errors='ignore').strip()
|
|
||||||
if line:
|
|
||||||
data_lines.append(line)
|
|
||||||
self._parse_sensor_data(line)
|
|
||||||
except Exception as ex:
|
|
||||||
print(f"解码数据错误: {ex}")
|
|
||||||
except Exception as e:
|
|
||||||
print(f"读取串口数据错误: {e}")
|
|
||||||
|
|
||||||
return data_lines
|
|
||||||
|
|
||||||
def _parse_sensor_data(self, line: str) -> None:
|
|
||||||
"""
|
|
||||||
解析传感器数据
|
|
||||||
|
|
||||||
Args:
|
|
||||||
line: 接收到的数据行
|
|
||||||
"""
|
|
||||||
# 解析电源电压
|
|
||||||
if "电源电压" in line:
|
|
||||||
try:
|
|
||||||
val = float(line.split(":")[1].replace("V", "").strip())
|
|
||||||
self._voltage = val
|
|
||||||
if self.debug:
|
|
||||||
print(f"电源电压更新: {val}V")
|
|
||||||
except Exception:
|
|
||||||
pass
|
|
||||||
|
|
||||||
# 解析电导率和ADC原始值(支持两种格式)
|
def execute_command_from_outer(self, command_dict: Dict[str, Any]) -> bool:
|
||||||
if "电导率" in line and "ADC原始值" in line:
|
"""支持标准 JSON 指令调用"""
|
||||||
try:
|
return super().execute_command_from_outer(command_dict)
|
||||||
# 支持格式如:电导率:2.50ms/cm, ADC原始值:2052
|
|
||||||
ec_match = re.search(r"电导率[::]\s*([\d\.]+)", line)
|
|
||||||
adc_match = re.search(r"ADC原始值[::]\s*(\d+)", line)
|
|
||||||
if ec_match:
|
|
||||||
ec_val = float(ec_match.group(1))
|
|
||||||
self._ec_value = ec_val
|
|
||||||
if self.debug:
|
|
||||||
print(f"电导率更新: {ec_val:.2f} ms/cm")
|
|
||||||
if adc_match:
|
|
||||||
adc_val = int(adc_match.group(1))
|
|
||||||
self._ec_adc_value = adc_val
|
|
||||||
if self.debug:
|
|
||||||
print(f"EC ADC原始值更新: {adc_val}")
|
|
||||||
except Exception:
|
|
||||||
pass
|
|
||||||
# 仅电导率,无ADC原始值
|
|
||||||
elif "电导率" in line:
|
|
||||||
try:
|
|
||||||
val = float(line.split(":")[1].replace("ms/cm", "").strip())
|
|
||||||
self._ec_value = val
|
|
||||||
if self.debug:
|
|
||||||
print(f"电导率更新: {val:.2f} ms/cm")
|
|
||||||
except Exception:
|
|
||||||
pass
|
|
||||||
# 仅ADC原始值(如有分开回传场景)
|
|
||||||
elif "ADC原始值" in line:
|
|
||||||
try:
|
|
||||||
adc_val = int(line.split(":")[1].strip())
|
|
||||||
self._ec_adc_value = adc_val
|
|
||||||
if self.debug:
|
|
||||||
print(f"EC ADC原始值更新: {adc_val}")
|
|
||||||
except Exception:
|
|
||||||
pass
|
|
||||||
|
|
||||||
def spin_when_ec_ge_0():
|
|
||||||
pass
|
|
||||||
|
|
||||||
|
|
||||||
def main():
|
|
||||||
"""测试函数"""
|
|
||||||
print("=== ChinWe设备测试 ===")
|
|
||||||
|
|
||||||
# 创建设备实例
|
|
||||||
device = ChinweDevice("/dev/tty.usbserial-A5069RR4", debug=True)
|
|
||||||
try:
|
|
||||||
# 测试5: 发送电机命令
|
|
||||||
print("\n5. 发送电机命令测试:")
|
|
||||||
print(" 5.3 使用通用函数控制电机20顺时针转2圈:")
|
|
||||||
device.rotate_motor(2, 20.0, clockwise=True)
|
|
||||||
time.sleep(0.5)
|
|
||||||
finally:
|
|
||||||
time.sleep(10)
|
|
||||||
# 测试7: 断开连接
|
|
||||||
print("\n7. 断开连接:")
|
|
||||||
device.disconnect()
|
|
||||||
if __name__ == "__main__":
|
if __name__ == "__main__":
|
||||||
main()
|
# Test
|
||||||
|
logging.basicConfig(level=logging.INFO)
|
||||||
|
dev = ChinweDevice(port="192.168.31.201:8899")
|
||||||
|
try:
|
||||||
|
if dev.is_connected:
|
||||||
|
print(f"Status: Level={dev.sensor_level}, RSSI={dev.sensor_rssi}")
|
||||||
|
|
||||||
|
# Test pump 1
|
||||||
|
# dev.pump_valve(1, 1)
|
||||||
|
# dev.pump_move(1, 1000, "aspirate")
|
||||||
|
|
||||||
|
# Test motor 4
|
||||||
|
# dev.motor_run(4, 60, 0, 2)
|
||||||
|
|
||||||
|
for _ in range(5):
|
||||||
|
print(f"Level={dev.sensor_level}, RSSI={dev.sensor_rssi}")
|
||||||
|
time.sleep(1)
|
||||||
|
finally:
|
||||||
|
dev.disconnect()
|
||||||
|
|||||||
@@ -174,35 +174,6 @@ bioyond_dispensing_station:
|
|||||||
title: query_resource_by_name参数
|
title: query_resource_by_name参数
|
||||||
type: object
|
type: object
|
||||||
type: UniLabJsonCommand
|
type: UniLabJsonCommand
|
||||||
auto-transfer_materials_to_reaction_station:
|
|
||||||
feedback: {}
|
|
||||||
goal: {}
|
|
||||||
goal_default:
|
|
||||||
target_device_id: null
|
|
||||||
transfer_groups: null
|
|
||||||
handles: {}
|
|
||||||
placeholder_keys: {}
|
|
||||||
result: {}
|
|
||||||
schema:
|
|
||||||
description: ''
|
|
||||||
properties:
|
|
||||||
feedback: {}
|
|
||||||
goal:
|
|
||||||
properties:
|
|
||||||
target_device_id:
|
|
||||||
type: string
|
|
||||||
transfer_groups:
|
|
||||||
type: array
|
|
||||||
required:
|
|
||||||
- target_device_id
|
|
||||||
- transfer_groups
|
|
||||||
type: object
|
|
||||||
result: {}
|
|
||||||
required:
|
|
||||||
- goal
|
|
||||||
title: transfer_materials_to_reaction_station参数
|
|
||||||
type: object
|
|
||||||
type: UniLabJsonCommand
|
|
||||||
auto-workflow_sample_locations:
|
auto-workflow_sample_locations:
|
||||||
feedback: {}
|
feedback: {}
|
||||||
goal: {}
|
goal: {}
|
||||||
|
|||||||
323
unilabos/registry/devices/chinwe.yaml
Normal file
323
unilabos/registry/devices/chinwe.yaml
Normal file
@@ -0,0 +1,323 @@
|
|||||||
|
separator.chinwe:
|
||||||
|
category:
|
||||||
|
- separator
|
||||||
|
- chinwe
|
||||||
|
class:
|
||||||
|
action_value_mappings:
|
||||||
|
motor_rotate_quarter:
|
||||||
|
goal:
|
||||||
|
direction: 顺时针
|
||||||
|
motor_id: 4
|
||||||
|
speed: 60
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 电机旋转 1/4 圈
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
direction:
|
||||||
|
default: 顺时针
|
||||||
|
description: 旋转方向
|
||||||
|
enum:
|
||||||
|
- 顺时针
|
||||||
|
- 逆时针
|
||||||
|
type: string
|
||||||
|
motor_id:
|
||||||
|
default: '4'
|
||||||
|
description: 选择电机 (4:搅拌, 5:旋钮)
|
||||||
|
enum:
|
||||||
|
- '4'
|
||||||
|
- '5'
|
||||||
|
type: string
|
||||||
|
speed:
|
||||||
|
default: 60
|
||||||
|
description: 速度 (RPM)
|
||||||
|
type: integer
|
||||||
|
required:
|
||||||
|
- motor_id
|
||||||
|
- speed
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
motor_run_continuous:
|
||||||
|
goal:
|
||||||
|
direction: 顺时针
|
||||||
|
motor_id: 4
|
||||||
|
speed: 60
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 电机一直旋转 (速度模式)
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
direction:
|
||||||
|
default: 顺时针
|
||||||
|
description: 旋转方向
|
||||||
|
enum:
|
||||||
|
- 顺时针
|
||||||
|
- 逆时针
|
||||||
|
type: string
|
||||||
|
motor_id:
|
||||||
|
default: '4'
|
||||||
|
description: 选择电机 (4:搅拌, 5:旋钮)
|
||||||
|
enum:
|
||||||
|
- '4'
|
||||||
|
- '5'
|
||||||
|
type: string
|
||||||
|
speed:
|
||||||
|
default: 60
|
||||||
|
description: 速度 (RPM)
|
||||||
|
type: integer
|
||||||
|
required:
|
||||||
|
- motor_id
|
||||||
|
- speed
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
motor_stop:
|
||||||
|
goal:
|
||||||
|
motor_id: 4
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 停止指定步进电机
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
motor_id:
|
||||||
|
default: '4'
|
||||||
|
description: 选择电机
|
||||||
|
enum:
|
||||||
|
- '4'
|
||||||
|
- '5'
|
||||||
|
title: '注: 4=搅拌, 5=旋钮'
|
||||||
|
type: string
|
||||||
|
required:
|
||||||
|
- motor_id
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
pump_aspirate:
|
||||||
|
goal:
|
||||||
|
pump_id: 1
|
||||||
|
valve_port: 1
|
||||||
|
volume: 1000
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 注射泵吸液
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
pump_id:
|
||||||
|
default: '1'
|
||||||
|
description: 选择泵
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
type: string
|
||||||
|
valve_port:
|
||||||
|
default: '1'
|
||||||
|
description: 阀门端口
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
- '4'
|
||||||
|
- '5'
|
||||||
|
- '6'
|
||||||
|
- '7'
|
||||||
|
- '8'
|
||||||
|
type: string
|
||||||
|
volume:
|
||||||
|
default: 1000
|
||||||
|
description: 吸液步数
|
||||||
|
type: integer
|
||||||
|
required:
|
||||||
|
- pump_id
|
||||||
|
- volume
|
||||||
|
- valve_port
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
pump_dispense:
|
||||||
|
goal:
|
||||||
|
pump_id: 1
|
||||||
|
valve_port: 1
|
||||||
|
volume: 1000
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 注射泵排液
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
pump_id:
|
||||||
|
default: '1'
|
||||||
|
description: 选择泵
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
type: string
|
||||||
|
valve_port:
|
||||||
|
default: '1'
|
||||||
|
description: 阀门端口
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
- '4'
|
||||||
|
- '5'
|
||||||
|
- '6'
|
||||||
|
- '7'
|
||||||
|
- '8'
|
||||||
|
type: string
|
||||||
|
volume:
|
||||||
|
default: 1000
|
||||||
|
description: 排液步数
|
||||||
|
type: integer
|
||||||
|
required:
|
||||||
|
- pump_id
|
||||||
|
- volume
|
||||||
|
- valve_port
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
pump_initialize:
|
||||||
|
goal:
|
||||||
|
drain_port: 0
|
||||||
|
output_port: 0
|
||||||
|
pump_id: 1
|
||||||
|
speed: 10
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 初始化指定注射泵
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
drain_port:
|
||||||
|
default: 0
|
||||||
|
description: 排液口索引
|
||||||
|
type: integer
|
||||||
|
output_port:
|
||||||
|
default: 0
|
||||||
|
description: 输出口索引
|
||||||
|
type: integer
|
||||||
|
pump_id:
|
||||||
|
default: '1'
|
||||||
|
description: 选择泵
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
title: '注: 1号泵, 2号泵, 3号泵'
|
||||||
|
type: string
|
||||||
|
speed:
|
||||||
|
default: 10
|
||||||
|
description: 运动速度
|
||||||
|
type: integer
|
||||||
|
required:
|
||||||
|
- pump_id
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
pump_valve:
|
||||||
|
goal:
|
||||||
|
port: 1
|
||||||
|
pump_id: 1
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 切换指定泵的阀门端口
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
port:
|
||||||
|
default: '1'
|
||||||
|
description: 阀门端口号 (1-8)
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
- '4'
|
||||||
|
- '5'
|
||||||
|
- '6'
|
||||||
|
- '7'
|
||||||
|
- '8'
|
||||||
|
type: string
|
||||||
|
pump_id:
|
||||||
|
default: '1'
|
||||||
|
description: 选择泵
|
||||||
|
enum:
|
||||||
|
- '1'
|
||||||
|
- '2'
|
||||||
|
- '3'
|
||||||
|
type: string
|
||||||
|
required:
|
||||||
|
- pump_id
|
||||||
|
- port
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
wait_sensor_level:
|
||||||
|
goal:
|
||||||
|
target_state: 有液
|
||||||
|
timeout: 30
|
||||||
|
handles: {}
|
||||||
|
schema:
|
||||||
|
description: 等待传感器液位条件
|
||||||
|
properties:
|
||||||
|
goal:
|
||||||
|
properties:
|
||||||
|
target_state:
|
||||||
|
default: 有液
|
||||||
|
description: 目标液位状态
|
||||||
|
enum:
|
||||||
|
- 有液
|
||||||
|
- 无液
|
||||||
|
type: string
|
||||||
|
timeout:
|
||||||
|
default: 30
|
||||||
|
description: 超时时间 (秒)
|
||||||
|
type: integer
|
||||||
|
required:
|
||||||
|
- target_state
|
||||||
|
type: object
|
||||||
|
type: UniLabJsonCommand
|
||||||
|
module: unilabos.devices.separator.chinwe:ChinweDevice
|
||||||
|
status_types:
|
||||||
|
is_connected: bool
|
||||||
|
sensor_level: bool
|
||||||
|
sensor_rssi: int
|
||||||
|
type: python
|
||||||
|
config_info: []
|
||||||
|
description: ChinWe 简易工作站控制器 (3泵, 2电机, 1传感器)
|
||||||
|
handles: []
|
||||||
|
icon: ''
|
||||||
|
init_param_schema:
|
||||||
|
goal:
|
||||||
|
baudrate:
|
||||||
|
default: 9600
|
||||||
|
description: 串口波特率
|
||||||
|
type: integer
|
||||||
|
motor_ids:
|
||||||
|
default:
|
||||||
|
- 4
|
||||||
|
- 5
|
||||||
|
description: 步进电机ID列表
|
||||||
|
items:
|
||||||
|
type: integer
|
||||||
|
type: array
|
||||||
|
port:
|
||||||
|
default: 192.168.1.200:8899
|
||||||
|
description: 串口号或 IP:Port
|
||||||
|
type: string
|
||||||
|
pump_ids:
|
||||||
|
default:
|
||||||
|
- 1
|
||||||
|
- 2
|
||||||
|
- 3
|
||||||
|
description: 注射泵ID列表
|
||||||
|
items:
|
||||||
|
type: integer
|
||||||
|
type: array
|
||||||
|
sensor_id:
|
||||||
|
default: 6
|
||||||
|
description: XKC传感器ID
|
||||||
|
type: integer
|
||||||
|
sensor_threshold:
|
||||||
|
default: 300
|
||||||
|
description: 传感器液位判定阈值
|
||||||
|
type: integer
|
||||||
|
version: 2.1.0
|
||||||
@@ -9333,7 +9333,34 @@ liquid_handler.prcxi:
|
|||||||
touch_tip: false
|
touch_tip: false
|
||||||
use_channels:
|
use_channels:
|
||||||
- 0
|
- 0
|
||||||
handles: {}
|
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
|
||||||
placeholder_keys:
|
placeholder_keys:
|
||||||
sources: unilabos_resources
|
sources: unilabos_resources
|
||||||
targets: unilabos_resources
|
targets: unilabos_resources
|
||||||
|
|||||||
@@ -222,7 +222,7 @@ class Registry:
|
|||||||
abs_path = Path(path).absolute()
|
abs_path = Path(path).absolute()
|
||||||
resource_path = abs_path / "resources"
|
resource_path = abs_path / "resources"
|
||||||
files = list(resource_path.glob("*/*.yaml"))
|
files = list(resource_path.glob("*/*.yaml"))
|
||||||
logger.debug(f"[UniLab Registry] resources: {resource_path.exists()}, total: {len(files)}")
|
logger.trace(f"[UniLab Registry] load resources? {resource_path.exists()}, total: {len(files)}")
|
||||||
current_resource_number = len(self.resource_type_registry) + 1
|
current_resource_number = len(self.resource_type_registry) + 1
|
||||||
for i, file in enumerate(files):
|
for i, file in enumerate(files):
|
||||||
with open(file, encoding="utf-8", mode="r") as f:
|
with open(file, encoding="utf-8", mode="r") as f:
|
||||||
|
|||||||
@@ -42,7 +42,7 @@ def canonicalize_nodes_data(
|
|||||||
Returns:
|
Returns:
|
||||||
ResourceTreeSet: 标准化后的资源树集合
|
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)
|
# 第一步:基本预处理(处理graphml的label字段)
|
||||||
outer_host_node_id = None
|
outer_host_node_id = None
|
||||||
|
|||||||
@@ -66,8 +66,8 @@ class ResourceDict(BaseModel):
|
|||||||
klass: str = Field(alias="class", description="Resource class name")
|
klass: str = Field(alias="class", description="Resource class name")
|
||||||
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
|
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
|
||||||
config: Dict[str, Any] = Field(description="Resource configuration")
|
config: Dict[str, Any] = Field(description="Resource configuration")
|
||||||
data: Dict[str, Any] = Field(description="Resource data")
|
data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
|
||||||
extra: Dict[str, Any] = Field(description="Extra data")
|
extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
|
||||||
|
|
||||||
@field_serializer("parent_uuid")
|
@field_serializer("parent_uuid")
|
||||||
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
|
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
|
||||||
|
|||||||
34
unilabos/test/experiments/chinwe.json
Normal file
34
unilabos/test/experiments/chinwe.json
Normal file
@@ -0,0 +1,34 @@
|
|||||||
|
{
|
||||||
|
"nodes": [
|
||||||
|
{
|
||||||
|
"id": "ChinWeStation",
|
||||||
|
"name": "分液工作站",
|
||||||
|
"children": [],
|
||||||
|
"parent": null,
|
||||||
|
"type": "device",
|
||||||
|
"class": "separator.chinwe",
|
||||||
|
"position": {
|
||||||
|
"x": 0,
|
||||||
|
"y": 0,
|
||||||
|
"z": 0
|
||||||
|
},
|
||||||
|
"config": {
|
||||||
|
"port": "192.168.31.13:8899",
|
||||||
|
"baudrate": 9600,
|
||||||
|
"pump_ids": [
|
||||||
|
1,
|
||||||
|
2,
|
||||||
|
3
|
||||||
|
],
|
||||||
|
"motor_ids": [
|
||||||
|
4,
|
||||||
|
5
|
||||||
|
],
|
||||||
|
"sensor_id": 6,
|
||||||
|
"sensor_threshold": 300
|
||||||
|
},
|
||||||
|
"data": {}
|
||||||
|
}
|
||||||
|
],
|
||||||
|
"links": []
|
||||||
|
}
|
||||||
@@ -1,94 +0,0 @@
|
|||||||
import json
|
|
||||||
import sys
|
|
||||||
from datetime import datetime
|
|
||||||
from pathlib import Path
|
|
||||||
|
|
||||||
ROOT_DIR = Path(__file__).resolve().parents[2]
|
|
||||||
if str(ROOT_DIR) not in sys.path:
|
|
||||||
sys.path.insert(0, str(ROOT_DIR))
|
|
||||||
|
|
||||||
import pytest
|
|
||||||
|
|
||||||
from unilabos.workflow.common import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
|
|
||||||
|
|
||||||
|
|
||||||
ROOT_DIR = Path(__file__).resolve().parents[2]
|
|
||||||
if str(ROOT_DIR) not in sys.path:
|
|
||||||
sys.path.insert(0, str(ROOT_DIR))
|
|
||||||
|
|
||||||
|
|
||||||
def _normalize_steps(data):
|
|
||||||
normalized = []
|
|
||||||
for step in data:
|
|
||||||
action = step.get("action") or step.get("operation")
|
|
||||||
if not action:
|
|
||||||
continue
|
|
||||||
raw_params = step.get("parameters") or step.get("action_args") or {}
|
|
||||||
params = dict(raw_params)
|
|
||||||
|
|
||||||
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"]
|
|
||||||
|
|
||||||
description = step.get("description") or step.get("purpose")
|
|
||||||
step_dict = {"action": action, "parameters": params}
|
|
||||||
if description:
|
|
||||||
step_dict["description"] = description
|
|
||||||
normalized.append(step_dict)
|
|
||||||
return normalized
|
|
||||||
|
|
||||||
|
|
||||||
def _normalize_labware(data):
|
|
||||||
labware = {}
|
|
||||||
for item in data:
|
|
||||||
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)
|
|
||||||
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
|
|
||||||
|
|
||||||
|
|
||||||
@pytest.mark.parametrize("protocol_name", [
|
|
||||||
"example_bio",
|
|
||||||
# "bioyond_materials_liquidhandling_1",
|
|
||||||
"example_prcxi",
|
|
||||||
])
|
|
||||||
def test_build_protocol_graph(protocol_name):
|
|
||||||
data_path = Path(__file__).with_name(f"{protocol_name}.json")
|
|
||||||
with data_path.open("r", encoding="utf-8") as fp:
|
|
||||||
d = json.load(fp)
|
|
||||||
|
|
||||||
if "workflow" in d and "reagent" in d:
|
|
||||||
protocol_steps = d["workflow"]
|
|
||||||
labware_info = d["reagent"]
|
|
||||||
elif "steps_info" in d and "labware_info" in d:
|
|
||||||
protocol_steps = _normalize_steps(d["steps_info"])
|
|
||||||
labware_info = _normalize_labware(d["labware_info"])
|
|
||||||
else:
|
|
||||||
raise ValueError("Unsupported protocol format")
|
|
||||||
|
|
||||||
graph = build_protocol_graph(
|
|
||||||
labware_info=labware_info,
|
|
||||||
protocol_steps=protocol_steps,
|
|
||||||
workstation_name="PRCXi",
|
|
||||||
)
|
|
||||||
timestamp = datetime.now().strftime("%Y%m%d_%H%M")
|
|
||||||
output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
|
|
||||||
draw_protocol_graph_with_ports(graph, str(output_path))
|
|
||||||
print(graph)
|
|
||||||
0
unilabos/workflow/__init__.py
Normal file
0
unilabos/workflow/__init__.py
Normal file
@@ -10,6 +10,7 @@ Json = Dict[str, Any]
|
|||||||
|
|
||||||
# ---------------- Graph ----------------
|
# ---------------- Graph ----------------
|
||||||
|
|
||||||
|
|
||||||
class WorkflowGraph:
|
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"""
|
"""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"""
|
||||||
|
|
||||||
@@ -21,20 +22,31 @@ class WorkflowGraph:
|
|||||||
self.nodes[node_id] = attrs
|
self.nodes[node_id] = attrs
|
||||||
|
|
||||||
def add_edge(self, source: str, target: str, **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 = {
|
edge = {
|
||||||
"source": source,
|
"source": source,
|
||||||
"target": target,
|
"target": target,
|
||||||
"source_node_uuid": source,
|
"source_node_uuid": source,
|
||||||
"target_node_uuid": target,
|
"target_node_uuid": target,
|
||||||
|
"source_handle_key": source_handle_key,
|
||||||
"source_handle_io": attrs.pop("source_handle_io", "source"),
|
"source_handle_io": attrs.pop("source_handle_io", "source"),
|
||||||
|
"target_handle_key": target_handle_key,
|
||||||
"target_handle_io": attrs.pop("target_handle_io", "target"),
|
"target_handle_io": attrs.pop("target_handle_io", "target"),
|
||||||
**attrs
|
**attrs,
|
||||||
}
|
}
|
||||||
self.edges.append(edge)
|
self.edges.append(edge)
|
||||||
|
|
||||||
def _materialize_wiring_into_inputs(self, obj: Any, inputs: Dict[str, Any],
|
def _materialize_wiring_into_inputs(
|
||||||
variable_sources: Dict[str, Dict[str, Any]],
|
self,
|
||||||
target_node_id: str, base_path: List[str]):
|
obj: Any,
|
||||||
|
inputs: Dict[str, Any],
|
||||||
|
variable_sources: Dict[str, Dict[str, Any]],
|
||||||
|
target_node_id: str,
|
||||||
|
base_path: List[str],
|
||||||
|
):
|
||||||
has_var = False
|
has_var = False
|
||||||
|
|
||||||
def walk(node: Any, path: List[str]):
|
def walk(node: Any, path: List[str]):
|
||||||
@@ -48,9 +60,12 @@ class WorkflowGraph:
|
|||||||
if src:
|
if src:
|
||||||
key = ".".join(path) # e.g. "params.foo.bar.0"
|
key = ".".join(path) # e.g. "params.foo.bar.0"
|
||||||
inputs[key] = {"node": src["node_id"], "output": src.get("output_name", "result")}
|
inputs[key] = {"node": src["node_id"], "output": src.get("output_name", "result")}
|
||||||
self.add_edge(str(src["node_id"]), target_node_id,
|
self.add_edge(
|
||||||
source_handle_io=src.get("output_name", "result"),
|
str(src["node_id"]),
|
||||||
target_handle_io=key)
|
target_node_id,
|
||||||
|
source_handle_io=src.get("output_name", "result"),
|
||||||
|
target_handle_io=key,
|
||||||
|
)
|
||||||
return placeholder
|
return placeholder
|
||||||
return {k: walk(v, path + [k]) for k, v in node.items()}
|
return {k: walk(v, path + [k]) for k, v in node.items()}
|
||||||
if isinstance(node, list):
|
if isinstance(node, list):
|
||||||
@@ -60,18 +75,20 @@ class WorkflowGraph:
|
|||||||
replaced = walk(obj, base_path[:])
|
replaced = walk(obj, base_path[:])
|
||||||
return replaced, has_var
|
return replaced, has_var
|
||||||
|
|
||||||
def add_workflow_node(self,
|
def add_workflow_node(
|
||||||
node_id: int,
|
self,
|
||||||
*,
|
node_id: int,
|
||||||
device_key: Optional[str] = None, # 实例名,如 "ser"
|
*,
|
||||||
resource_name: Optional[str] = None, # registry key(原 device_class)
|
device_key: Optional[str] = None, # 实例名,如 "ser"
|
||||||
module: Optional[str] = None,
|
resource_name: Optional[str] = None, # registry key(原 device_class)
|
||||||
template_name: Optional[str] = None, # 动作/模板名(原 action_key)
|
module: Optional[str] = None,
|
||||||
params: Dict[str, Any],
|
template_name: Optional[str] = None, # 动作/模板名(原 action_key)
|
||||||
variable_sources: Dict[str, Dict[str, Any]],
|
params: Dict[str, Any],
|
||||||
add_ready_if_no_vars: bool = True,
|
variable_sources: Dict[str, Dict[str, Any]],
|
||||||
prev_node_id: Optional[int] = None,
|
add_ready_if_no_vars: bool = True,
|
||||||
**extra_attrs) -> None:
|
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"""
|
"""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)
|
node_id_str = str(node_id)
|
||||||
inputs: Dict[str, Any] = {}
|
inputs: Dict[str, Any] = {}
|
||||||
@@ -87,9 +104,9 @@ class WorkflowGraph:
|
|||||||
|
|
||||||
node_obj = {
|
node_obj = {
|
||||||
"device_key": device_key,
|
"device_key": device_key,
|
||||||
"resource_name": resource_name, # ✅ 新名字
|
"resource_name": resource_name, # ✅ 新名字
|
||||||
"module": module,
|
"module": module,
|
||||||
"template_name": template_name, # ✅ 新名字
|
"template_name": template_name, # ✅ 新名字
|
||||||
"params": params,
|
"params": params,
|
||||||
"inputs": inputs,
|
"inputs": inputs,
|
||||||
}
|
}
|
||||||
@@ -100,13 +117,13 @@ class WorkflowGraph:
|
|||||||
def to_dict(self) -> List[Dict[str, Any]]:
|
def to_dict(self) -> List[Dict[str, Any]]:
|
||||||
result = []
|
result = []
|
||||||
for node_id, attrs in self.nodes.items():
|
for node_id, attrs in self.nodes.items():
|
||||||
node = {"id": node_id}
|
node = {"uuid": node_id}
|
||||||
params = dict(attrs.get("parameters", {}) or {})
|
params = dict(attrs.get("parameters", {}) or {})
|
||||||
flat = {k: v for k, v in attrs.items() if k != "parameters"}
|
flat = {k: v for k, v in attrs.items() if k != "parameters"}
|
||||||
flat.update(params)
|
flat.update(params)
|
||||||
node.update(flat)
|
node.update(flat)
|
||||||
result.append(node)
|
result.append(node)
|
||||||
return sorted(result, key=lambda n: int(n["id"]) if str(n["id"]).isdigit() else n["id"])
|
return sorted(result, key=lambda n: int(n["uuid"]) if str(n["uuid"]).isdigit() else n["uuid"])
|
||||||
|
|
||||||
# node-link 导出(含 edges)
|
# node-link 导出(含 edges)
|
||||||
def to_node_link_dict(self) -> Dict[str, Any]:
|
def to_node_link_dict(self) -> Dict[str, Any]:
|
||||||
@@ -115,12 +132,27 @@ class WorkflowGraph:
|
|||||||
node_attrs = attrs.copy()
|
node_attrs = attrs.copy()
|
||||||
params = node_attrs.pop("parameters", {}) or {}
|
params = node_attrs.pop("parameters", {}) or {}
|
||||||
node_attrs.update(params)
|
node_attrs.update(params)
|
||||||
nodes_list.append({"id": node_id, **node_attrs})
|
nodes_list.append({"uuid": node_id, **node_attrs})
|
||||||
return {"directed": True, "multigraph": False, "graph": {}, "nodes": nodes_list, "edges": self.edges, "links": self.edges}
|
return {
|
||||||
|
"directed": True,
|
||||||
|
"multigraph": False,
|
||||||
|
"graph": {},
|
||||||
|
"nodes": nodes_list,
|
||||||
|
"edges": self.edges,
|
||||||
|
"links": self.edges,
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
def refactor_data(
|
||||||
"""统一的数据重构函数,根据操作类型自动选择模板"""
|
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 = []
|
refactored_data = []
|
||||||
|
|
||||||
# 定义操作映射,包含生物实验和有机化学的所有操作
|
# 定义操作映射,包含生物实验和有机化学的所有操作
|
||||||
@@ -157,43 +189,67 @@ def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
|||||||
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
||||||
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
||||||
for i in range(int(times)):
|
for i in range(int(times)):
|
||||||
sub_data = refactor_data(sub_steps)
|
sub_data = refactor_data(sub_steps, action_resource_mapping)
|
||||||
refactored_data.extend(sub_data)
|
refactored_data.extend(sub_data)
|
||||||
continue
|
continue
|
||||||
|
|
||||||
# 获取模板名称
|
# 获取模板名称
|
||||||
template = OPERATION_MAPPING.get(operation)
|
template_name = OPERATION_MAPPING.get(operation)
|
||||||
if not template:
|
if not template_name:
|
||||||
# 自动推断模板类型
|
# 自动推断模板类型
|
||||||
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
||||||
template = f"biomek-{operation}"
|
template_name = f"biomek-{operation}"
|
||||||
else:
|
else:
|
||||||
template = f"{operation}Protocol"
|
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
|
# 创建步骤数据
|
||||||
step_data = {
|
step_data = {
|
||||||
"template": template,
|
"template_name": template_name,
|
||||||
|
"resource_name": resource_name,
|
||||||
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
||||||
"lab_node_type": "Device",
|
"lab_node_type": "Device",
|
||||||
"parameters": step.get("parameters", step.get("action_args", {})),
|
"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)
|
refactored_data.append(step_data)
|
||||||
|
|
||||||
return refactored_data
|
return refactored_data
|
||||||
|
|
||||||
|
|
||||||
def build_protocol_graph(
|
def build_protocol_graph(
|
||||||
labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
|
labware_info: List[Dict[str, Any]],
|
||||||
|
protocol_steps: List[Dict[str, Any]],
|
||||||
|
workstation_name: str,
|
||||||
|
action_resource_mapping: Optional[Dict[str, str]] = None,
|
||||||
) -> WorkflowGraph:
|
) -> 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"""
|
"""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()
|
G = WorkflowGraph()
|
||||||
resource_last_writer = {}
|
resource_last_writer = {}
|
||||||
|
|
||||||
protocol_steps = refactor_data(protocol_steps)
|
protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
|
||||||
# 有机化学&移液站协议图构建
|
# 有机化学&移液站协议图构建
|
||||||
WORKSTATION_ID = workstation_name
|
WORKSTATION_ID = workstation_name
|
||||||
|
|
||||||
# 为所有labware创建资源节点
|
# 为所有labware创建资源节点
|
||||||
|
res_index = 0
|
||||||
for labware_id, item in labware_info.items():
|
for labware_id, item in labware_info.items():
|
||||||
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
||||||
node_id = str(uuid.uuid4())
|
node_id = str(uuid.uuid4())
|
||||||
@@ -217,13 +273,16 @@ def build_protocol_graph(
|
|||||||
liquid_type = [labware_id]
|
liquid_type = [labware_id]
|
||||||
liquid_volume = [1e5]
|
liquid_volume = [1e5]
|
||||||
|
|
||||||
|
res_index += 1
|
||||||
G.add_node(
|
G.add_node(
|
||||||
node_id,
|
node_id,
|
||||||
template_name=f"create_resource",
|
template_name="create_resource",
|
||||||
resource_name="host_node",
|
resource_name="host_node",
|
||||||
|
name=f"Res {res_index}",
|
||||||
description=description,
|
description=description,
|
||||||
lab_node_type=lab_node_type,
|
lab_node_type=lab_node_type,
|
||||||
params={
|
footer="create_resource-host_node",
|
||||||
|
param={
|
||||||
"res_id": labware_id,
|
"res_id": labware_id,
|
||||||
"device_id": WORKSTATION_ID,
|
"device_id": WORKSTATION_ID,
|
||||||
"class_name": "container",
|
"class_name": "container",
|
||||||
@@ -234,7 +293,6 @@ def build_protocol_graph(
|
|||||||
"liquid_volume": liquid_volume,
|
"liquid_volume": liquid_volume,
|
||||||
"slot_on_deck": "",
|
"slot_on_deck": "",
|
||||||
},
|
},
|
||||||
role=item.get("role", ""),
|
|
||||||
)
|
)
|
||||||
resource_last_writer[labware_id] = f"{node_id}:labware"
|
resource_last_writer[labware_id] = f"{node_id}:labware"
|
||||||
|
|
||||||
@@ -251,7 +309,7 @@ def build_protocol_graph(
|
|||||||
last_control_node_id = node_id
|
last_control_node_id = node_id
|
||||||
|
|
||||||
# 物料流
|
# 物料流
|
||||||
params = step.get("parameters", {})
|
params = step.get("param", {})
|
||||||
input_resources_possible_names = [
|
input_resources_possible_names = [
|
||||||
"vessel",
|
"vessel",
|
||||||
"to_vessel",
|
"to_vessel",
|
||||||
@@ -299,7 +357,7 @@ def draw_protocol_graph(protocol_graph: WorkflowGraph, output_path: str):
|
|||||||
G = nx.DiGraph()
|
G = nx.DiGraph()
|
||||||
|
|
||||||
for node_id, attrs in protocol_graph.nodes.items():
|
for node_id, attrs in protocol_graph.nodes.items():
|
||||||
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
label = attrs.get("description", attrs.get("template_name", node_id[:8]))
|
||||||
G.add_node(node_id, label=label, **attrs)
|
G.add_node(node_id, label=label, **attrs)
|
||||||
|
|
||||||
for edge in protocol_graph.edges:
|
for edge in protocol_graph.edges:
|
||||||
@@ -331,11 +389,13 @@ def draw_protocol_graph(protocol_graph: WorkflowGraph, output_path: str):
|
|||||||
print(f" - Visualization saved to '{output_path}'")
|
print(f" - Visualization saved to '{output_path}'")
|
||||||
|
|
||||||
|
|
||||||
COMPASS = {"n","e","s","w","ne","nw","se","sw","c"}
|
COMPASS = {"n", "e", "s", "w", "ne", "nw", "se", "sw", "c"}
|
||||||
|
|
||||||
|
|
||||||
def _is_compass(port: str) -> bool:
|
def _is_compass(port: str) -> bool:
|
||||||
return isinstance(port, str) and port.lower() in COMPASS
|
return isinstance(port, str) and port.lower() in COMPASS
|
||||||
|
|
||||||
|
|
||||||
def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
|
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。
|
使用 Graphviz 端口语法绘制协议工作流图。
|
||||||
@@ -350,22 +410,22 @@ def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: st
|
|||||||
# 1) 先用 networkx 搭建有向图,保留端口属性
|
# 1) 先用 networkx 搭建有向图,保留端口属性
|
||||||
G = nx.DiGraph()
|
G = nx.DiGraph()
|
||||||
for node_id, attrs in protocol_graph.nodes.items():
|
for node_id, attrs in protocol_graph.nodes.items():
|
||||||
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
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
|
# 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",)})
|
G.add_node(node_id, _core_label=str(label), **{k: v for k, v in attrs.items() if k not in ("label",)})
|
||||||
|
|
||||||
edges_data = []
|
edges_data = []
|
||||||
in_ports_by_node = {} # 收集命名输入端口
|
in_ports_by_node = {} # 收集命名输入端口
|
||||||
out_ports_by_node = {} # 收集命名输出端口
|
out_ports_by_node = {} # 收集命名输出端口
|
||||||
|
|
||||||
for edge in protocol_graph.edges:
|
for edge in protocol_graph.edges:
|
||||||
u = edge["source"]
|
u = edge["source"]
|
||||||
v = edge["target"]
|
v = edge["target"]
|
||||||
sp = edge.get("source_port")
|
sp = edge.get("source_handle_key") or edge.get("source_port")
|
||||||
tp = edge.get("target_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)
|
# 记录到图里(保留原始端口信息)
|
||||||
G.add_edge(u, v, source_port=sp, target_port=tp)
|
G.add_edge(u, v, source_handle_key=sp, target_handle_key=tp)
|
||||||
edges_data.append((u, v, sp, 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
|
# 如果不是 compass,就按“命名端口”先归类,等会儿给节点造 record
|
||||||
@@ -377,7 +437,9 @@ def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: st
|
|||||||
# 2) 转为 AGraph,使用 Graphviz 渲染
|
# 2) 转为 AGraph,使用 Graphviz 渲染
|
||||||
A = to_agraph(G)
|
A = to_agraph(G)
|
||||||
A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
|
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.node_attr.update(
|
||||||
|
shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica"
|
||||||
|
)
|
||||||
A.edge_attr.update(arrowsize="0.8", color="#666666")
|
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
|
# 3) 为需要命名端口的节点设置 record 形状与 label
|
||||||
@@ -386,18 +448,19 @@ def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: st
|
|||||||
node = A.get_node(n)
|
node = A.get_node(n)
|
||||||
core = G.nodes[n].get("_core_label", n)
|
core = G.nodes[n].get("_core_label", n)
|
||||||
|
|
||||||
in_ports = sorted(in_ports_by_node.get(n, []))
|
in_ports = sorted(in_ports_by_node.get(n, []))
|
||||||
out_ports = sorted(out_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
|
# 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:
|
if in_ports or out_ports:
|
||||||
|
|
||||||
def port_fields(ports):
|
def port_fields(ports):
|
||||||
if not ports:
|
if not ports:
|
||||||
return " " # 必须留一个空槽占位
|
return " " # 必须留一个空槽占位
|
||||||
# 每个端口一个小格子,<p> name
|
# 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)
|
return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
|
||||||
|
|
||||||
left = port_fields(in_ports)
|
left = port_fields(in_ports)
|
||||||
right = port_fields(out_ports)
|
right = port_fields(out_ports)
|
||||||
|
|
||||||
# 三栏:左(入) | 中(节点名) | 右(出)
|
# 三栏:左(入) | 中(节点名) | 右(出)
|
||||||
@@ -410,7 +473,7 @@ def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: st
|
|||||||
# 4) 给边设置 headport / tailport
|
# 4) 给边设置 headport / tailport
|
||||||
# - 若端口为 compass:直接用 compass(e.g., headport="e")
|
# - 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)
|
# - 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:
|
for u, v, sp, tp in edges_data:
|
||||||
e = A.get_edge(u, v)
|
e = A.get_edge(u, v)
|
||||||
|
|
||||||
# Graphviz 属性:tail 是源,head 是目标
|
# Graphviz 属性:tail 是源,head 是目标
|
||||||
@@ -419,13 +482,13 @@ def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: st
|
|||||||
e.attr["tailport"] = sp.lower()
|
e.attr["tailport"] = sp.lower()
|
||||||
else:
|
else:
|
||||||
# 与 record label 中 <port> 名一致;特殊字符已在 label 中做了清洗
|
# 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))
|
e.attr["tailport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(sp))
|
||||||
|
|
||||||
if tp:
|
if tp:
|
||||||
if _is_compass(tp):
|
if _is_compass(tp):
|
||||||
e.attr["headport"] = tp.lower()
|
e.attr["headport"] = tp.lower()
|
||||||
else:
|
else:
|
||||||
e.attr["headport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(tp))
|
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
|
# 可选:若想让边更贴边缘,可设置 constraint/spline 等
|
||||||
# e.attr["arrowhead"] = "vee"
|
# e.attr["arrowhead"] = "vee"
|
||||||
@@ -433,11 +496,14 @@ def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: st
|
|||||||
# 5) 输出
|
# 5) 输出
|
||||||
A.draw(output_path, prog="dot")
|
A.draw(output_path, prog="dot")
|
||||||
print(f" - Port-aware workflow rendered to '{output_path}'")
|
print(f" - Port-aware workflow rendered to '{output_path}'")
|
||||||
|
|
||||||
|
|
||||||
# ---------------- Registry Adapter ----------------
|
# ---------------- Registry Adapter ----------------
|
||||||
|
|
||||||
|
|
||||||
class RegistryAdapter:
|
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"""
|
"""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]):
|
def __init__(self, device_registry: Dict[str, Any]):
|
||||||
self.device_registry = device_registry or {}
|
self.device_registry = device_registry or {}
|
||||||
self.module_class_to_resource = self._build_module_class_index()
|
self.module_class_to_resource = self._build_module_class_index()
|
||||||
@@ -455,8 +521,7 @@ class RegistryAdapter:
|
|||||||
def resolve_resource_by_classname(self, class_name: str) -> Optional[str]:
|
def resolve_resource_by_classname(self, class_name: str) -> Optional[str]:
|
||||||
if not class_name:
|
if not class_name:
|
||||||
return None
|
return None
|
||||||
return (self.module_class_to_resource.get(class_name)
|
return self.module_class_to_resource.get(class_name) or self.module_class_to_resource.get(class_name.lower())
|
||||||
or self.module_class_to_resource.get(class_name.lower()))
|
|
||||||
|
|
||||||
def get_device_module(self, resource_name: Optional[str]) -> Optional[str]:
|
def get_device_module(self, resource_name: Optional[str]) -> Optional[str]:
|
||||||
if not resource_name:
|
if not resource_name:
|
||||||
@@ -466,9 +531,7 @@ class RegistryAdapter:
|
|||||||
def get_actions(self, resource_name: Optional[str]) -> Dict[str, Any]:
|
def get_actions(self, resource_name: Optional[str]) -> Dict[str, Any]:
|
||||||
if not resource_name:
|
if not resource_name:
|
||||||
return {}
|
return {}
|
||||||
return (self.device_registry.get(resource_name, {})
|
return (self.device_registry.get(resource_name, {}).get("class", {}).get("action_value_mappings", {})) or {}
|
||||||
.get("class", {})
|
|
||||||
.get("action_value_mappings", {})) or {}
|
|
||||||
|
|
||||||
def get_action_schema(self, resource_name: Optional[str], template_name: str) -> Optional[Json]:
|
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")
|
return (self.get_actions(resource_name).get(template_name) or {}).get("schema")
|
||||||
|
|||||||
356
unilabos/workflow/convert_from_json.py
Normal file
356
unilabos/workflow/convert_from_json.py
Normal file
@@ -0,0 +1,356 @@
|
|||||||
|
"""
|
||||||
|
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
|
||||||
@@ -1,24 +0,0 @@
|
|||||||
import json
|
|
||||||
from os import PathLike
|
|
||||||
|
|
||||||
from unilabos.workflow.common import build_protocol_graph
|
|
||||||
|
|
||||||
|
|
||||||
def from_labwares_and_steps(data_path: PathLike):
|
|
||||||
with data_path.open("r", encoding="utf-8") as fp:
|
|
||||||
d = json.load(fp)
|
|
||||||
|
|
||||||
if "workflow" in d and "reagent" in d:
|
|
||||||
protocol_steps = d["workflow"]
|
|
||||||
labware_info = d["reagent"]
|
|
||||||
elif "steps_info" in d and "labware_info" in d:
|
|
||||||
protocol_steps = _normalize_steps(d["steps_info"])
|
|
||||||
labware_info = _normalize_labware(d["labware_info"])
|
|
||||||
else:
|
|
||||||
raise ValueError("Unsupported protocol format")
|
|
||||||
|
|
||||||
graph = build_protocol_graph(
|
|
||||||
labware_info=labware_info,
|
|
||||||
protocol_steps=protocol_steps,
|
|
||||||
workstation_name="PRCXi",
|
|
||||||
)
|
|
||||||
138
unilabos/workflow/wf_utils.py
Normal file
138
unilabos/workflow/wf_utils.py
Normal file
@@ -0,0 +1,138 @@
|
|||||||
|
"""
|
||||||
|
工作流工具模块
|
||||||
|
|
||||||
|
提供工作流上传等功能
|
||||||
|
"""
|
||||||
|
|
||||||
|
import json
|
||||||
|
import os
|
||||||
|
import uuid
|
||||||
|
from typing import Any, Dict, List, Optional
|
||||||
|
|
||||||
|
from unilabos.utils.banner_print import print_status
|
||||||
|
|
||||||
|
|
||||||
|
def _is_node_link_format(data: Dict[str, Any]) -> bool:
|
||||||
|
"""检查数据是否为 node-link 格式"""
|
||||||
|
return "nodes" in data and "edges" in data
|
||||||
|
|
||||||
|
|
||||||
|
def _convert_to_node_link(workflow_file: str, workflow_data: Dict[str, Any]) -> Dict[str, Any]:
|
||||||
|
"""
|
||||||
|
将非 node-link 格式的工作流数据转换为 node-link 格式
|
||||||
|
|
||||||
|
Args:
|
||||||
|
workflow_file: 工作流文件路径(用于日志)
|
||||||
|
workflow_data: 原始工作流数据
|
||||||
|
|
||||||
|
Returns:
|
||||||
|
node-link 格式的工作流数据
|
||||||
|
"""
|
||||||
|
from unilabos.workflow.convert_from_json import convert_json_to_node_link
|
||||||
|
|
||||||
|
print_status(f"检测到非 node-link 格式,正在转换...", "info")
|
||||||
|
node_link_data = convert_json_to_node_link(workflow_data)
|
||||||
|
print_status(f"转换完成", "success")
|
||||||
|
return node_link_data
|
||||||
|
|
||||||
|
|
||||||
|
def upload_workflow(
|
||||||
|
workflow_file: str,
|
||||||
|
workflow_name: Optional[str] = None,
|
||||||
|
tags: Optional[List[str]] = None,
|
||||||
|
published: bool = False,
|
||||||
|
) -> Dict[str, Any]:
|
||||||
|
"""
|
||||||
|
上传工作流到服务器
|
||||||
|
|
||||||
|
支持的输入格式:
|
||||||
|
1. node-link 格式: {"nodes": [...], "edges": [...]}
|
||||||
|
2. workflow/reagent 格式: {"workflow": [...], "reagent": {...}}
|
||||||
|
3. steps_info/labware_info 格式: {"steps_info": [...], "labware_info": [...]}
|
||||||
|
4. steps/labware 格式: {"steps": [...], "labware": [...]}
|
||||||
|
|
||||||
|
Args:
|
||||||
|
workflow_file: 工作流文件路径(JSON格式)
|
||||||
|
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
|
||||||
|
|
||||||
|
Returns:
|
||||||
|
Dict: API响应数据
|
||||||
|
"""
|
||||||
|
# 延迟导入,避免在配置文件加载之前初始化 http_client
|
||||||
|
from unilabos.app.web import http_client
|
||||||
|
|
||||||
|
if not os.path.exists(workflow_file):
|
||||||
|
print_status(f"工作流文件不存在: {workflow_file}", "error")
|
||||||
|
return {"code": -1, "message": f"文件不存在: {workflow_file}"}
|
||||||
|
|
||||||
|
# 读取工作流文件
|
||||||
|
try:
|
||||||
|
with open(workflow_file, "r", encoding="utf-8") as f:
|
||||||
|
workflow_data = json.load(f)
|
||||||
|
except json.JSONDecodeError as e:
|
||||||
|
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}"}
|
||||||
|
|
||||||
|
# 自动检测并转换格式
|
||||||
|
if not _is_node_link_format(workflow_data):
|
||||||
|
try:
|
||||||
|
workflow_data = _convert_to_node_link(workflow_file, workflow_data)
|
||||||
|
except Exception as e:
|
||||||
|
print_status(f"工作流格式转换失败: {e}", "error")
|
||||||
|
return {"code": -1, "message": f"格式转换失败: {e}"}
|
||||||
|
|
||||||
|
# 提取工作流数据
|
||||||
|
nodes = workflow_data.get("nodes", [])
|
||||||
|
edges = workflow_data.get("edges", [])
|
||||||
|
workflow_uuid_val = workflow_data.get("workflow_uuid", str(uuid.uuid4()))
|
||||||
|
wf_name_from_file = workflow_data.get("workflow_name", os.path.basename(workflow_file).replace(".json", ""))
|
||||||
|
|
||||||
|
# 确定工作流名称
|
||||||
|
final_name = workflow_name or wf_name_from_file
|
||||||
|
|
||||||
|
print_status(f"正在上传工作流: {final_name}", "info")
|
||||||
|
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" - 发布状态: {published}", "info")
|
||||||
|
|
||||||
|
# 调用 http_client 上传
|
||||||
|
result = http_client.workflow_import(
|
||||||
|
name=final_name,
|
||||||
|
workflow_uuid=workflow_uuid_val,
|
||||||
|
workflow_name=final_name,
|
||||||
|
nodes=nodes,
|
||||||
|
edges=edges,
|
||||||
|
tags=tags,
|
||||||
|
published=published,
|
||||||
|
)
|
||||||
|
|
||||||
|
if result.get("code") == 0:
|
||||||
|
data = result.get("data", {})
|
||||||
|
print_status("工作流上传成功!", "success")
|
||||||
|
print_status(f" - UUID: {data.get('uuid', 'N/A')}", "info")
|
||||||
|
print_status(f" - 名称: {data.get('name', 'N/A')}", "info")
|
||||||
|
else:
|
||||||
|
print_status(f"工作流上传失败: {result.get('message', '未知错误')}", "error")
|
||||||
|
|
||||||
|
return result
|
||||||
|
|
||||||
|
|
||||||
|
def handle_workflow_upload_command(args_dict: Dict[str, Any]) -> None:
|
||||||
|
"""
|
||||||
|
处理 workflow_upload 子命令
|
||||||
|
|
||||||
|
Args:
|
||||||
|
args_dict: 命令行参数字典
|
||||||
|
"""
|
||||||
|
workflow_file = args_dict.get("workflow_file")
|
||||||
|
workflow_name = args_dict.get("workflow_name")
|
||||||
|
tags = args_dict.get("tags", [])
|
||||||
|
published = args_dict.get("published", False)
|
||||||
|
|
||||||
|
if workflow_file:
|
||||||
|
upload_workflow(workflow_file, workflow_name, tags, published)
|
||||||
|
else:
|
||||||
|
print_status("未指定工作流文件路径,请使用 -f/--workflow_file 参数", "error")
|
||||||
Reference in New Issue
Block a user