diff --git a/README.md b/README.md index 4658432a..b3256575 100644 --- 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) diff --git a/unilabos/compile/clean_protocol.py b/unilabos/compile/clean_protocol.py index b2ab1414..655ce217 100644 --- 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): diff --git a/unilabos/compile/evaporate_protocol.py b/unilabos/compile/evaporate_protocol.py index 8c729666..15af5e11 100644 --- 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({ diff --git a/unilabos/compile/pump_protocol.py b/unilabos/compile/pump_protocol.py index 9b4c2884..60670286 100644 --- 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" diff --git a/unilabos/compile/separate_protocol.py b/unilabos/compile/separate_protocol.py index 0ba0d1c8..cbb028cb 100644 --- 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, } } diff --git a/unilabos/config/config.py b/unilabos/config/config.py index 5f117a74..5c1f7b9c 100644 --- 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): diff --git a/unilabos/registry/device_comms/serial.yaml b/unilabos/registry/device_comms/serial.yaml index 3a0d72a5..86cf7e50 100644 --- 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: {} \ No newline at end of file diff --git a/unilabos/registry/devices/organic_miscellaneous.yaml b/unilabos/registry/devices/organic_miscellaneous.yaml index 3085efac..a3f6f0e3 100644 --- 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 diff --git a/unilabos/registry/devices/pump_and_valve.yaml b/unilabos/registry/devices/pump_and_valve.yaml index ba35700d..5fdd8606 100644 --- 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: diff --git a/unilabos/ros/nodes/base_device_node.py b/unilabos/ros/nodes/base_device_node.py index 1424b0c6..0ff03a68 100644 --- 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() diff --git a/unilabos/ros/nodes/presets/host_node.py b/unilabos/ros/nodes/presets/host_node.py index d5280a42..34132b35 100644 --- 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( diff --git a/unilabos/ros/nodes/presets/protocol_node.py b/unilabos/ros/nodes/presets/protocol_node.py index 323f6880..c4dfd083 100644 --- 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): diff --git a/unilabos/ros/nodes/presets/serial_node.py b/unilabos/ros/nodes/presets/serial_node.py index 6f01a07a..545682bd 100644 --- 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):