Merge branch 'refs/heads/main' into dev

2025-12-17 21:11:12 +00:00 · 2025-04-29 10:04:56 +08:00
parent e971424220 74ae2a88ac
commit dbd1557095
13 changed files with 118 additions and 81 deletions
--- a/README.md
+++ b/README.md
@@ -25,21 +25,6 @@ Uni-Lab 操作系统是一个用于实验室自动化的综合平台，旨在连

 - [在线文档](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/)

-## 安装指南
-
-请先克隆此仓库:
-
-```bash
-git clone https://github.com/dptech-corp/Uni-Lab-OS.git
-cd Uni-Lab-OS
-```
-
-然后安装 Uni-Lab-OS:
-
-```bash
-pip install .
-```
-
 ## 快速开始

 1. 配置Conda环境
@@ -52,17 +37,30 @@ mamba env create -f unilabos-[YOUR_OS].yaml
 mamba activate unilab

 # 或更新现有环境
+# 其中 `[YOUR_OS]` 可以是 `win64`, `linux-64`, `osx-64`, 或 `osx-arm64`。
 conda env update --file unilabos-[YOUR_OS].yml -n 环境名

 # 现阶段，需要安装 `unilabos_msgs` 包
 # 可以前往 Release 页面下载系统对应的包进行安装
 conda install ros-humble-unilabos-msgs-0.8.0-xxxxx.tar.bz2
+
+# 安装PyLabRobot等前置
+git clone https://github.com/PyLabRobot/pylabrobot
+pip install .[opentrons]
 ```

-其中 `[YOUR_OS]` 可以是 `win64`, `linux-64`, `osx-64`, 或 `osx-arm64`。
+2. 安装 Uni-Lab-OS:

+```bash
+# 克隆仓库
+git clone https://github.com/dptech-corp/Uni-Lab-OS.git
+cd Uni-Lab-OS

-2. 启动 Uni-Lab 系统:
+# 安装 Uni-Lab-OS
+pip install .
+```
+
+3. 启动 Uni-Lab 系统:

 请见[文档-启动样例](https://readthedocs.dp.tech/Uni-Lab/v0.8.0/boot_examples/index.html)

--- a/unilabos/compile/clean_protocol.py
+++ b/unilabos/compile/clean_protocol.py
@@ -6,7 +6,7 @@ def generate_clean_protocol(
    G: nx.DiGraph, 
    vessel: str,  # Vessel to clean.
    solvent: str, # Solvent to clean vessel with.
-    volume: float = 25000.0, # Optional. Volume of solvent to clean vessel with.
+    volume: float = 25.0, # Optional. Volume of solvent to clean vessel with.
    temp: float = 25, # Optional. Temperature to heat vessel to while cleaning.
    repeats: int = 1, # Optional. Number of cleaning cycles to perform.
 ) -> list[dict]:
@@ -27,7 +27,7 @@ def generate_clean_protocol(
    from_vessel = f"flask_{solvent}"
    waste_vessel = f"waste_workup"
    
-    transfer_flowrate = flowrate = 2500.0
+    transfer_flowrate = flowrate = 2.5
    
    # 生成泵操作的动作序列
    for i in range(repeats):
--- a/unilabos/compile/evaporate_protocol.py
+++ b/unilabos/compile/evaporate_protocol.py
@@ -24,8 +24,8 @@ def generate_evaporate_protocol(
    
    # 生成泵操作的动作序列
    pump_action_sequence = []
-    reactor_volume = 500000.0
-    transfer_flowrate = flowrate = 2500.0
+    reactor_volume = 500.0
+    transfer_flowrate = flowrate = 2.5
    
    # 开启冷凝器
    pump_action_sequence.append({
--- a/unilabos/compile/pump_protocol.py
+++ b/unilabos/compile/pump_protocol.py
@@ -7,7 +7,7 @@ def generate_pump_protocol(
    from_vessel: str, 
    to_vessel: str, 
    volume: float, 
-    flowrate: float = 500.0,
+    flowrate: float = 0.5,
    transfer_flowrate: float = 0, 
 ) -> list[dict]:
    """
@@ -141,11 +141,11 @@ def generate_pump_protocol_with_rinsing(
    time: float = 0,
    viscous: bool = False,
    rinsing_solvent: str = "air",
-    rinsing_volume: float = 5000.0,
+    rinsing_volume: float = 5.0,
    rinsing_repeats: int = 2,
    solid: bool = False,
-    flowrate: float = 2500.0,
-    transfer_flowrate: float = 500.0, 
+    flowrate: float = 2.5,
+    transfer_flowrate: float = 0.5, 
 ) -> list[dict]:
    """
    Generates a pump protocol for transferring a specified volume between vessels, including rinsing steps with a chosen solvent. This function constructs a sequence of pump actions based on the provided parameters and the shortest path in a directed graph.
@@ -159,11 +159,11 @@ def generate_pump_protocol_with_rinsing(
        time (float, optional): Time over which to perform the transfer (default is 0).
        viscous (bool, optional): Indicates if the fluid is viscous (default is False).
        rinsing_solvent (str, optional): The solvent to use for rinsing (default is "air").
-        rinsing_volume (float, optional): The volume of rinsing solvent to use (default is 5000.0).
+        rinsing_volume (float, optional): The volume of rinsing solvent to use (default is 5.0).
        rinsing_repeats (int, optional): The number of times to repeat rinsing (default is 2).
        solid (bool, optional): Indicates if the transfer involves a solid (default is False).
-        flowrate (float, optional): The flow rate for the transfer (default is 2500.0). 最终注入容器B时的流速
-        transfer_flowrate (float, optional): The flow rate for the transfer action (default is 500.0). 泵骨架中转移流速（若不指定，默认与注入流速相同）
+        flowrate (float, optional): The flow rate for the transfer (default is 2.5). 最终注入容器B时的流速
+        transfer_flowrate (float, optional): The flow rate for the transfer action (default is 0.5). 泵骨架中转移流速（若不指定，默认与注入流速相同）
    
    Returns:
        list[dict]: A sequence of pump actions to be executed for the transfer and rinsing process. 泵操作的动作序列.
@@ -172,7 +172,7 @@ def generate_pump_protocol_with_rinsing(
        AssertionError: If the number of rinsing solvents does not match the number of rinsing repeats.
    
    Examples:
-        pump_protocol = generate_pump_protocol_with_rinsing(G, "vessel_A", "vessel_B", 100.0, rinsing_solvent="water")
+        pump_protocol = generate_pump_protocol_with_rinsing(G, "vessel_A", "vessel_B", 0.1, rinsing_solvent="water")
    """
    air_vessel = "flask_air"
    waste_vessel = f"waste_workup"
--- a/unilabos/compile/separate_protocol.py
+++ b/unilabos/compile/separate_protocol.py
@@ -11,7 +11,7 @@ def generate_separate_protocol(
    to_vessel: str, # Vessel to send product phase to.
    waste_phase_to_vessel: str, # Optional. Vessel to send waste phase to.
    solvent: str, # Optional. Solvent to add to separation vessel after contents of from_vessel has been transferred to create two phases.
-    solvent_volume: float = 50000, # Optional. Volume of solvent to add.
+    solvent_volume: float = 50, # Optional. Volume of solvent to add (mL).
    through: str = "", # Optional. Solid chemical to send product phase through on way to to_vessel, e.g. 'celite'.
    repeats: int = 1, # Optional. Number of separations to perform.
    stir_time: float = 30, # Optional. Time stir for after adding solvent, before separation of phases.
@@ -32,7 +32,7 @@ def generate_separate_protocol(
    
    # 生成泵操作的动作序列
    pump_action_sequence = []
-    reactor_volume = 500000.0
+    reactor_volume = 500.0
    waste_vessel = waste_phase_to_vessel
    
    # TODO：通过物料管理系统找到溶剂的容器
@@ -46,7 +46,7 @@ def generate_separate_protocol(
    separator_controller = f"{separation_vessel}_controller"
    separation_vessel_bottom = f"flask_{separation_vessel}"
    
-    transfer_flowrate = flowrate = 2500.0
+    transfer_flowrate = flowrate = 2.5
    
    if from_vessel != separation_vessel:
        pump_action_sequence.append(
@@ -140,8 +140,8 @@ def generate_separate_protocol(
                    "action_kwargs": {
                        "from_vessel": separation_vessel_bottom,
                        "to_vessel": to_vessel,
-                        "volume": 250000.0,
-                        "time": 250000.0 / flowrate,
+                        "volume": 250.0,
+                        "time": 250.0 / flowrate,
                        # "transfer_flowrate": transfer_flowrate,
                    }
                }
@@ -164,8 +164,8 @@ def generate_separate_protocol(
                    "action_kwargs": {
                        "from_vessel": separation_vessel_bottom,
                        "to_vessel": waste_vessel,
-                        "volume": 250000.0,
-                        "time": 250000.0 / flowrate,
+                        "volume": 250.0,
+                        "time": 250.0 / flowrate,
                        # "transfer_flowrate": transfer_flowrate,
                    }
                }
@@ -179,8 +179,8 @@ def generate_separate_protocol(
                    "action_kwargs": {
                        "from_vessel": separation_vessel_bottom,
                        "to_vessel": waste_vessel,
-                        "volume": 250000.0,
-                        "time": 250000.0 / flowrate,
+                        "volume": 250.0,
+                        "time": 250.0 / flowrate,
                        # "transfer_flowrate": transfer_flowrate,
                    }
                }
@@ -203,8 +203,8 @@ def generate_separate_protocol(
                    "action_kwargs": {
                        "from_vessel": separation_vessel_bottom,
                        "to_vessel": to_vessel,
-                        "volume": 250000.0,
-                        "time": 250000.0 / flowrate,
+                        "volume": 250.0,
+                        "time": 250.0 / flowrate,
                        # "transfer_flowrate": transfer_flowrate,
                    }
                }
@@ -221,8 +221,8 @@ def generate_separate_protocol(
                    "action_kwargs": {
                        "from_vessel": to_vessel,
                        "to_vessel": separation_vessel,
-                        "volume": 250000.0,
-                        "time": 250000.0 / flowrate,
+                        "volume": 250.0,
+                        "time": 250.0 / flowrate,
                        # "transfer_flowrate": transfer_flowrate,
                    }
                }
--- a/unilabos/config/config.py
+++ b/unilabos/config/config.py
@@ -75,20 +75,29 @@ def _update_config_from_module(module):
        # 需要先判断是否为相对路径
        if MQConfig.ca_file.startswith("."):
            MQConfig.ca_file = os.path.join(BasicConfig.config_path, MQConfig.ca_file)
-        with open(MQConfig.ca_file, "r", encoding="utf-8") as f:
-            MQConfig.ca_content = f.read()
+        if len(MQConfig.ca_file) != 0:
+            with open(MQConfig.ca_file, "r", encoding="utf-8") as f:
+                MQConfig.ca_content = f.read()
+        else:
+            logger.warning("Skipping CA file loading, ca_file is empty")
    if len(MQConfig.cert_content) == 0:
        # 需要先判断是否为相对路径
        if MQConfig.cert_file.startswith("."):
            MQConfig.cert_file = os.path.join(BasicConfig.config_path, MQConfig.cert_file)
-        with open(MQConfig.cert_file, "r", encoding="utf-8") as f:
-            MQConfig.cert_content = f.read()
+        if len(MQConfig.ca_file) != 0:
+            with open(MQConfig.cert_file, "r", encoding="utf-8") as f:
+                MQConfig.cert_content = f.read()
+        else:
+            logger.warning("Skipping cert file loading, cert_file is empty")
    if len(MQConfig.key_content) == 0:
        # 需要先判断是否为相对路径
        if MQConfig.key_file.startswith("."):
            MQConfig.key_file = os.path.join(BasicConfig.config_path, MQConfig.key_file)
-        with open(MQConfig.key_file, "r", encoding="utf-8") as f:
-            MQConfig.key_content = f.read()
+        if len(MQConfig.ca_file) != 0:
+            with open(MQConfig.key_file, "r", encoding="utf-8") as f:
+                MQConfig.key_content = f.read()
+        else:
+            logger.warning("Skipping key file loading, key_file is empty")


 def load_config(config_path=None):
--- a/unilabos/registry/device_comms/serial.yaml
+++ b/unilabos/registry/device_comms/serial.yaml
@@ -1,7 +1,7 @@
 serial:
  description: Serial communication interface, used when sharing same serial port for multiple devices
  class:
-    module: unilabos.ros.nodes.presets:ROS2SerialNode
+    module: unilabos.ros.nodes.presets.serial_node:ROS2SerialNode
    type: ros2
  schema:
    properties: {}
--- a/unilabos/registry/devices/organic_miscellaneous.yaml
+++ b/unilabos/registry/devices/organic_miscellaneous.yaml
@@ -1,7 +1,7 @@
 separator.homemade:
  description: Separator device with homemade grbl controller
  class:
-    module: unilabos.devices.separator.homemade_grbl_conductivity:Separator_Controller
+    module: unilabos.devices.separator.homemade_grbl_conductivity:SeparatorController
    type: python
    status_types:
      sensordata: Float64
--- a/unilabos/registry/devices/pump_and_valve.yaml
+++ b/unilabos/registry/devices/pump_and_valve.yaml
@@ -3,6 +3,10 @@ syringe_pump_with_valve.runze:
  class:
    module: unilabos.devices.pump_and_valve.runze_backbone:RunzeSyringePump
    type: python
+    hardware_interface:
+      name: hardware_interface
+      read: send_command
+      write: send_command
  schema:
    type: object
    properties:
--- a/unilabos/ros/nodes/base_device_node.py
+++ b/unilabos/ros/nodes/base_device_node.py
@@ -342,9 +342,15 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                else:
                    return getattr(self.driver_instance, attr_name)
            except AttributeError as ex:
-                self.lab_logger().error(
-                    f"publish error, {str(type(self.driver_instance))[8:-2]} has no attribute '{attr_name}'"
-                )
+                if ex.args[0].startswith(f"AttributeError: '{self.driver_instance.__class__.__name__}' object"):
+                    self.lab_logger().error(
+                        f"publish error, {str(type(self.driver_instance))[8:-2]} has no attribute '{attr_name}'"
+                    )
+                else:
+                    self.lab_logger().error(
+                        f"publish error, when {str(type(self.driver_instance))[8:-2]} getting attribute '{attr_name}'"
+                    )
+                    self.lab_logger().error(traceback.format_exc())

        self._property_publishers[attr_name] = PropertyPublisher(
            self, attr_name, get_device_attr, msg_type, initial_period, self._print_publish
@@ -430,6 +436,15 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                self.lab_logger().info(f"同步执行动作 {ACTION}")
                future = self._executor.submit(ACTION, **action_kwargs)

+                def _handle_future_exception(fut):
+                    try:
+                        fut.result()
+                    except Exception as e:
+                        error(f"同步任务 {ACTION.__name__} 报错了")
+                        error(traceback.format_exc())
+
+                future.add_done_callback(_handle_future_exception)
+
            action_type = action_value_mapping["type"]
            feedback_msg_types = action_type.Feedback.get_fields_and_field_types()
            result_msg_types = action_type.Result.get_fields_and_field_types()
--- a/unilabos/ros/nodes/presets/host_node.py
+++ b/unilabos/ros/nodes/presets/host_node.py
@@ -1,6 +1,7 @@
 import copy
 import threading
 import time
+import traceback
 import uuid
 from typing import Optional, Dict, Any, List, ClassVar, Set

@@ -132,10 +133,14 @@ class HostNode(BaseROS2DeviceNode):
                controller_config["update_rate"] = update_rate
                self.initialize_controller(controller_id, controller_config)

-        for bridge in self.bridges:
-            if hasattr(bridge, "resource_add"):
-                self.lab_logger().info("[Host Node-Resource] Adding resources to bridge.")
-                bridge.resource_add(add_schema(resources_config))
+        try:
+            for bridge in self.bridges:
+                if hasattr(bridge, "resource_add"):
+                    self.lab_logger().info("[Host Node-Resource] Adding resources to bridge.")
+                    bridge.resource_add(add_schema(resources_config))
+        except Exception as ex:
+            self.lab_logger().error("[Host Node-Resource] 添加物料出错！")
+            self.lab_logger().error(traceback.format_exc())

        # 创建定时器，定期发现设备
        self._discovery_timer = self.create_timer(
--- a/unilabos/ros/nodes/presets/protocol_node.py
+++ b/unilabos/ros/nodes/presets/protocol_node.py
@@ -20,7 +20,7 @@ from unilabos.ros.msgs.message_converter import (
    convert_from_ros_msg,
    convert_from_ros_msg_with_mapping,
 )
-from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, DeviceNodeResourceTracker
+from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, DeviceNodeResourceTracker, ROS2DeviceNode


 class ROS2ProtocolNode(BaseROS2DeviceNode):
@@ -55,34 +55,39 @@ class ROS2ProtocolNode(BaseROS2DeviceNode):
        )

        # 初始化子设备
-        communication_node_id = None
+        self.communication_node_id_to_instance = {}
+
        for device_id, device_config in self.children.items():
            if device_config.get("type", "device") != "device":
                self.lab_logger().debug(f"[Protocol Node] Skipping type {device_config['type']} {device_id} already existed, skipping.")
                continue
-            d = self.initialize_device(device_id, device_config)
+            try:
+                d = self.initialize_device(device_id, device_config)
+            except Exception as ex:
+                self.lab_logger().error(f"[Protocol Node] Failed to initialize device {device_id}: {ex}")
+                d = None
            if d is None:
                continue

            if "serial_" in device_id or "io_" in device_id:
-                communication_node_id = device_id
+                self.communication_node_id_to_instance[device_id] = d
                continue

            # 设置硬件接口代理
-            if d and hasattr(d, "_hardware_interface"):
+            if d:
                if (
-                    hasattr(d, d._hardware_interface["name"])
-                    and hasattr(d, d._hardware_interface["write"])
-                    and (d._hardware_interface["read"] is None or hasattr(d, d._hardware_interface["read"]))
+                    hasattr(d.driver_instance, d.ros_node_instance._hardware_interface["name"])
+                    and hasattr(d.driver_instance, d.ros_node_instance._hardware_interface["write"])
+                    and (d.ros_node_instance._hardware_interface["read"] is None or hasattr(d.driver_instance, d.ros_node_instance._hardware_interface["read"]))
                ):

-                    name = getattr(d, d._hardware_interface["name"])
-                    read = d._hardware_interface.get("read", None)
-                    write = d._hardware_interface.get("write", None)
+                    name = getattr(d.driver_instance, d.ros_node_instance._hardware_interface["name"])
+                    read = d.ros_node_instance._hardware_interface.get("read", None)
+                    write = d.ros_node_instance._hardware_interface.get("write", None)

                    # 如果硬件接口是字符串，通过通信设备提供
-                    if isinstance(name, str) and communication_node_id in self.sub_devices:
-                        self._setup_hardware_proxy(d, self.sub_devices[communication_node_id], read, write)
+                    if isinstance(name, str) and name in self.sub_devices:
+                        self._setup_hardware_proxy(d, self.sub_devices[name], read, write)

    def _setup_protocol_names(self, protocol_type):
        # 处理协议类型
@@ -234,11 +239,11 @@ class ROS2ProtocolNode(BaseROS2DeviceNode):

    """还没有改过的部分"""

-    def _setup_hardware_proxy(self, device, communication_device, read_method, write_method):
+    def _setup_hardware_proxy(self, device: ROS2DeviceNode, communication_device: ROS2DeviceNode, read_method, write_method):
        """为设备设置硬件接口代理"""
-        extra_info = [getattr(device, info) for info in communication_device._hardware_interface.get("extra_info", [])]
-        write_func = getattr(communication_device, communication_device._hardware_interface["write"])
-        read_func = getattr(communication_device, communication_device._hardware_interface["read"])
+        extra_info = [getattr(device.driver_instance, info) for info in communication_device.ros_node_instance._hardware_interface.get("extra_info", [])]
+        write_func = getattr(communication_device.ros_node_instance, communication_device.ros_node_instance._hardware_interface["write"])
+        read_func = getattr(communication_device.ros_node_instance, communication_device.ros_node_instance._hardware_interface["read"])

        def _read():
            return read_func(*extra_info)
@@ -247,9 +252,9 @@ class ROS2ProtocolNode(BaseROS2DeviceNode):
            return write_func(*extra_info, command)

        if read_method:
-            setattr(device, read_method, _read)
+            setattr(device.driver_instance, read_method, _read)
        if write_method:
-            setattr(device, write_method, _write)
+            setattr(device.driver_instance, write_method, _write)


    async def _update_resources(self, goal, protocol_kwargs):
--- a/unilabos/ros/nodes/presets/serial_node.py
+++ b/unilabos/ros/nodes/presets/serial_node.py
@@ -21,6 +21,7 @@ class ROS2SerialNode(BaseROS2DeviceNode):
            self.hardware_interface = Serial(baudrate=baudrate, port=port)
        except (OSError, SerialException) as e:
            # 因为还没调用父类初始化，无法使用日志，直接抛出异常
+            # print(f"Failed to connect to serial port {port} at {baudrate} baudrate.")
            raise RuntimeError(f"Failed to connect to serial port {port} at {baudrate} baudrate.") from e

        # 初始化BaseROS2DeviceNode，使用自身作为driver_instance
@@ -46,7 +47,7 @@ class ROS2SerialNode(BaseROS2DeviceNode):
        self.lab_logger().info(f"【ROS2SerialNode.__init__】创建串口写入服务: serialwrite")

    def send_command(self, command: str):
-        self.lab_logger().info(f"【ROS2SerialNode.send_command】发送命令: {command}")
+        # self.lab_logger().debug(f"【ROS2SerialNode.send_command】发送命令: {command}")
        with self._query_lock:
            if self._closing:
                self.lab_logger().error(f"【ROS2SerialNode.send_command】设备正在关闭，无法发送命令")
@@ -58,23 +59,23 @@ class ROS2SerialNode(BaseROS2DeviceNode):
            response = self.hardware_interface.write(full_command_data)
            # time.sleep(0.05)
            output = self._receive(self.hardware_interface.read_until(b"\n"))
-            self.lab_logger().info(f"【ROS2SerialNode.send_command】接收响应: {output}")
+            # self.lab_logger().debug(f"【ROS2SerialNode.send_command】接收响应: {output}")
        return output

    def read_data(self):
-        self.lab_logger().debug(f"【ROS2SerialNode.read_data】读取数据")
+        # self.lab_logger().debug(f"【ROS2SerialNode.read_data】读取数据")
        with self._query_lock:
            if self._closing:
                self.lab_logger().error(f"【ROS2SerialNode.read_data】设备正在关闭，无法读取数据")
                raise RuntimeError
            data = self.hardware_interface.read_until(b"\n")
            result = self._receive(data)
-            self.lab_logger().debug(f"【ROS2SerialNode.read_data】读取到数据: {result}")
+            # self.lab_logger().debug(f"【ROS2SerialNode.read_data】读取到数据: {result}")
            return result

    def _receive(self, data: bytes):
        ascii_string = "".join(chr(byte) for byte in data)
-        self.lab_logger().debug(f"【ROS2SerialNode._receive】接收数据: {ascii_string}")
+        # self.lab_logger().debug(f"【ROS2SerialNode._receive】接收数据: {ascii_string}")
        return ascii_string

    def handle_serial_request(self, request, response):