import networkx as nx import re import logging from typing import List, Dict, Any, Union from .pump_protocol import generate_pump_protocol_with_rinsing logger = logging.getLogger(__name__) def debug_print(message): """调试输出""" print(f"[ADD] {message}", flush=True) logger.info(f"[ADD] {message}") def parse_volume_input(volume_input: Union[str, float]) -> float: """ 解析体积输入，支持带单位的字符串 Args: volume_input: 体积输入（如 "2.7 mL", "2.67 mL", "?", 10.0） Returns: float: 体积（毫升） """ if isinstance(volume_input, (int, float)): return float(volume_input) if not volume_input or not str(volume_input).strip(): return 0.0 volume_str = str(volume_input).lower().strip() debug_print(f"解析体积输入: '{volume_str}'") # 处理未知体积 if volume_str in ['?', 'unknown', 'tbd', 'to be determined']: default_volume = 10.0 # 默认10mL debug_print(f"检测到未知体积，使用默认值: {default_volume}mL") return default_volume # 移除空格并提取数字和单位 volume_clean = re.sub(r'\s+', '', volume_str) # 匹配数字和单位的正则表达式 match = re.match(r'([0-9]*\.?[0-9]+)\s*(ml|l|μl|ul|microliter|milliliter|liter)?', volume_clean) if not match: debug_print(f"⚠️ 无法解析体积: '{volume_str}'，使用默认值10mL") return 10.0 value = float(match.group(1)) unit = match.group(2) or 'ml' # 默认单位为毫升 # 转换为毫升 if unit in ['l', 'liter']: volume = value * 1000.0 # L -> mL elif unit in ['μl', 'ul', 'microliter']: volume = value / 1000.0 # μL -> mL else: # ml, milliliter 或默认 volume = value # 已经是mL debug_print(f"体积转换: {value}{unit} → {volume}mL") return volume def parse_mass_input(mass_input: Union[str, float]) -> float: """ 解析质量输入，支持带单位的字符串 Args: mass_input: 质量输入（如 "19.3 g", "4.5 g", 2.5） Returns: float: 质量（克） """ if isinstance(mass_input, (int, float)): return float(mass_input) if not mass_input or not str(mass_input).strip(): return 0.0 mass_str = str(mass_input).lower().strip() debug_print(f"解析质量输入: '{mass_str}'") # 移除空格并提取数字和单位 mass_clean = re.sub(r'\s+', '', mass_str) # 匹配数字和单位的正则表达式 match = re.match(r'([0-9]*\.?[0-9]+)\s*(g|mg|kg|gram|milligram|kilogram)?', mass_clean) if not match: debug_print(f"⚠️ 无法解析质量: '{mass_str}'，返回0.0g") return 0.0 value = float(match.group(1)) unit = match.group(2) or 'g' # 默认单位为克 # 转换为克 if unit in ['mg', 'milligram']: mass = value / 1000.0 # mg -> g elif unit in ['kg', 'kilogram']: mass = value * 1000.0 # kg -> g else: # g, gram 或默认 mass = value # 已经是g debug_print(f"质量转换: {value}{unit} → {mass}g") return mass def parse_time_input(time_input: Union[str, float]) -> float: """ 解析时间输入，支持带单位的字符串 Args: time_input: 时间输入（如 "1 h", "20 min", "30 s", 60.0） Returns: float: 时间（秒） """ if isinstance(time_input, (int, float)): return float(time_input) if not time_input or not str(time_input).strip(): return 0.0 time_str = str(time_input).lower().strip() debug_print(f"解析时间输入: '{time_str}'") # 处理未知时间 if time_str in ['?', 'unknown', 'tbd']: default_time = 60.0 # 默认1分钟 debug_print(f"检测到未知时间，使用默认值: {default_time}s") return default_time # 移除空格并提取数字和单位 time_clean = re.sub(r'\s+', '', time_str) # 匹配数字和单位的正则表达式 match = re.match(r'([0-9]*\.?[0-9]+)\s*(s|sec|second|min|minute|h|hr|hour|d|day)?', time_clean) if not match: debug_print(f"⚠️ 无法解析时间: '{time_str}'，返回0s") return 0.0 value = float(match.group(1)) unit = match.group(2) or 's' # 默认单位为秒 # 转换为秒 if unit in ['min', 'minute']: time_sec = value * 60.0 # min -> s elif unit in ['h', 'hr', 'hour']: time_sec = value * 3600.0 # h -> s elif unit in ['d', 'day']: time_sec = value * 86400.0 # d -> s else: # s, sec, second 或默认 time_sec = value # 已经是s debug_print(f"时间转换: {value}{unit} → {time_sec}s") return time_sec def find_reagent_vessel(G: nx.DiGraph, reagent: str) -> str: """增强版试剂容器查找，支持固体和液体""" debug_print(f"查找试剂 '{reagent}' 的容器...") # 🔧 方法1：直接搜索 data.reagent_name 和 config.reagent for node in G.nodes(): node_data = G.nodes[node].get('data', {}) node_type = G.nodes[node].get('type', '') config_data = G.nodes[node].get('config', {}) # 只搜索容器类型的节点 if node_type == 'container': reagent_name = node_data.get('reagent_name', '').lower() config_reagent = config_data.get('reagent', '').lower() # 精确匹配 if reagent_name == reagent.lower() or config_reagent == reagent.lower(): debug_print(f"✅ 通过reagent字段找到容器: {node}") return node # 模糊匹配 if (reagent.lower() in reagent_name and reagent_name) or \ (reagent.lower() in config_reagent and config_reagent): debug_print(f"✅ 通过reagent字段模糊匹配到容器: {node}") return node # 🔧 方法2：常见的容器命名规则 reagent_clean = reagent.lower().replace(' ', '_').replace('-', '_') possible_names = [ reagent_clean, f"flask_{reagent_clean}", f"bottle_{reagent_clean}", f"vessel_{reagent_clean}", f"{reagent_clean}_flask", f"{reagent_clean}_bottle", f"reagent_{reagent_clean}", f"reagent_bottle_{reagent_clean}", f"solid_reagent_bottle_{reagent_clean}", f"reagent_bottle_1", # 通用试剂瓶 f"reagent_bottle_2", f"reagent_bottle_3" ] for name in possible_names: if name in G.nodes(): node_type = G.nodes[name].get('type', '') if node_type == 'container': debug_print(f"✅ 通过命名规则找到容器: {name}") return name # 🔧 方法3：节点名称模糊匹配 for node_id in G.nodes(): node_data = G.nodes[node_id] if node_data.get('type') == 'container': # 检查节点名称是否包含试剂名称 if reagent_clean in node_id.lower(): debug_print(f"✅ 通过节点名称模糊匹配到容器: {node_id}") return node_id # 检查液体类型匹配 vessel_data = node_data.get('data', {}) liquids = vessel_data.get('liquid', []) for liquid in liquids: if isinstance(liquid, dict): liquid_type = liquid.get('liquid_type') or liquid.get('name', '') if liquid_type.lower() == reagent.lower(): debug_print(f"✅ 通过液体类型匹配到容器: {node_id}") return node_id # 🔧 方法4：使用第一个试剂瓶作为备选 for node_id in G.nodes(): node_data = G.nodes[node_id] if (node_data.get('type') == 'container' and ('reagent' in node_id.lower() or 'bottle' in node_id.lower())): debug_print(f"⚠️ 未找到专用容器，使用备选试剂瓶: {node_id}") return node_id raise ValueError(f"找不到试剂 '{reagent}' 对应的容器") def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str: """查找连接到指定容器的搅拌器""" stirrer_nodes = [] for node in G.nodes(): node_class = G.nodes[node].get('class', '').lower() if 'stirrer' in node_class: stirrer_nodes.append(node) # 查找连接到容器的搅拌器 for stirrer in stirrer_nodes: if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer): debug_print(f"找到连接的搅拌器: {stirrer}") return stirrer # 返回第一个搅拌器 if stirrer_nodes: debug_print(f"使用第一个搅拌器: {stirrer_nodes[0]}") return stirrer_nodes[0] return "" def find_solid_dispenser(G: nx.DiGraph) -> str: """查找固体加样器""" for node in G.nodes(): node_class = G.nodes[node].get('class', '').lower() if 'solid_dispenser' in node_class or 'dispenser' in node_class: debug_print(f"找到固体加样器: {node}") return node debug_print("⚠️ 未找到固体加样器") return "" def generate_add_protocol( G: nx.DiGraph, vessel: str, reagent: str, # 🔧 修复：所有参数都用 Union 类型，支持字符串和数值 volume: Union[str, float] = 0.0, mass: Union[str, float] = 0.0, amount: str = "", time: Union[str, float] = 0.0, stir: bool = False, stir_speed: float = 300.0, viscous: bool = False, purpose: str = "添加试剂", # XDL扩展参数 mol: str = "", event: str = "", rate_spec: str = "", equiv: str = "", ratio: str = "", **kwargs ) -> List[Dict[str, Any]]: """ 生成添加试剂协议 - 修复版 支持所有XDL参数和单位： - volume: "2.7 mL", "2.67 mL", "?" 或数值 - mass: "19.3 g", "4.5 g" 或数值 - time: "1 h", "20 min" 或数值（秒） - mol: "0.28 mol", "16.2 mmol", "25.2 mmol" - rate_spec: "portionwise", "dropwise" - event: "A", "B" - equiv: "1.1" - ratio: "?", "1:1" """ debug_print("=" * 60) debug_print("开始生成添加试剂协议") debug_print(f"原始参数:") debug_print(f" - vessel: '{vessel}'") debug_print(f" - reagent: '{reagent}'") debug_print(f" - volume: {volume} (类型: {type(volume)})") debug_print(f" - mass: {mass} (类型: {type(mass)})") debug_print(f" - time: {time} (类型: {type(time)})") debug_print(f" - mol: '{mol}'") debug_print(f" - event: '{event}'") debug_print(f" - rate_spec: '{rate_spec}'") debug_print("=" * 60) action_sequence = [] # === 参数验证 === debug_print("步骤1: 参数验证...") if not vessel: raise ValueError("vessel 参数不能为空") if not reagent: raise ValueError("reagent 参数不能为空") if vessel not in G.nodes(): raise ValueError(f"容器 '{vessel}' 不存在于系统中") debug_print("✅ 基本参数验证通过") # === 🔧 关键修复：参数解析 === debug_print("步骤2: 参数解析...") # 解析各种参数为数值 final_volume = parse_volume_input(volume) final_mass = parse_mass_input(mass) final_time = parse_time_input(time) debug_print(f"解析结果:") debug_print(f" - 体积: {final_volume}mL") debug_print(f" - 质量: {final_mass}g") debug_print(f" - 时间: {final_time}s") debug_print(f" - 摩尔: '{mol}'") debug_print(f" - 事件: '{event}'") debug_print(f" - 速率: '{rate_spec}'") # === 判断添加类型 === debug_print("步骤3: 判断添加类型...") # 🔧 修复：现在使用解析后的数值进行比较 is_solid = (final_mass > 0 or (mol and mol.strip() != "")) is_liquid = (final_volume > 0) if not is_solid and not is_liquid: # 默认为液体，10mL is_liquid = True final_volume = 10.0 debug_print("⚠️ 未指定体积或质量，默认为10mL液体") debug_print(f"添加类型: {'固体' if is_solid else '液体'}") # === 执行添加流程 === debug_print("步骤4: 执行添加流程...") try: if is_solid: # === 固体添加路径 === debug_print(f"使用固体添加路径") solid_dispenser = find_solid_dispenser(G) if solid_dispenser: # 启动搅拌 if stir: stirrer_id = find_connected_stirrer(G, vessel) if stirrer_id: action_sequence.append({ "device_id": stirrer_id, "action_name": "start_stir", "action_kwargs": { "vessel": vessel, "stir_speed": stir_speed, "purpose": f"准备添加固体 {reagent}" } }) # 等待搅拌稳定 action_sequence.append({ "action_name": "wait", "action_kwargs": {"time": 3} }) # 固体加样 add_kwargs = { "vessel": vessel, "reagent": reagent, "purpose": purpose, "event": event, "rate_spec": rate_spec } if final_mass > 0: add_kwargs["mass"] = str(final_mass) if mol and mol.strip(): add_kwargs["mol"] = mol if equiv and equiv.strip(): add_kwargs["equiv"] = equiv action_sequence.append({ "device_id": solid_dispenser, "action_name": "add_solid", "action_kwargs": add_kwargs }) # 添加后等待 if final_time > 0: action_sequence.append({ "action_name": "wait", "action_kwargs": {"time": final_time} }) debug_print(f"✅ 固体添加完成") else: debug_print("⚠️ 未找到固体加样器，跳过固体添加") else: # === 液体添加路径 === debug_print(f"使用液体添加路径") # 查找试剂容器 reagent_vessel = find_reagent_vessel(G, reagent) # 启动搅拌 if stir: stirrer_id = find_connected_stirrer(G, vessel) if stirrer_id: action_sequence.append({ "device_id": stirrer_id, "action_name": "start_stir", "action_kwargs": { "vessel": vessel, "stir_speed": stir_speed, "purpose": f"准备添加液体 {reagent}" } }) # 等待搅拌稳定 action_sequence.append({ "action_name": "wait", "action_kwargs": {"time": 5} }) # 计算流速 if final_time > 0: flowrate = final_volume / final_time * 60 # mL/min transfer_flowrate = flowrate else: if rate_spec == "dropwise": flowrate = 0.5 # 滴加，很慢 transfer_flowrate = 0.2 elif viscous: flowrate = 1.0 # 粘性液体 transfer_flowrate = 0.3 else: flowrate = 2.5 # 正常流速 transfer_flowrate = 0.5 debug_print(f"流速设置: {flowrate} mL/min") # 调用pump protocol pump_actions = generate_pump_protocol_with_rinsing( G=G, from_vessel=reagent_vessel, to_vessel=vessel, volume=final_volume, amount=amount, time=final_time, viscous=viscous, rinsing_solvent="", rinsing_volume=0.0, rinsing_repeats=0, solid=False, flowrate=flowrate, transfer_flowrate=transfer_flowrate, rate_spec=rate_spec, event=event, through="", **kwargs ) action_sequence.extend(pump_actions) debug_print(f"✅ 液体转移完成，添加了 {len(pump_actions)} 个动作") except Exception as e: debug_print(f"⚠️ 试剂添加失败: {str(e)}") # 添加错误日志 action_sequence.append({ "device_id": "system", "action_name": "log_message", "action_kwargs": { "message": f"试剂 '{reagent}' 添加失败: {str(e)}" } }) # === 最终结果 === debug_print("=" * 60) debug_print(f"✅ 添加试剂协议生成完成") debug_print(f"📊 总动作数: {len(action_sequence)}") debug_print(f"📋 处理总结:") debug_print(f" - 试剂: {reagent}") debug_print(f" - 添加类型: {'固体' if is_solid else '液体'}") debug_print(f" - 目标容器: {vessel}") if is_liquid: debug_print(f" - 体积: {final_volume}mL") if is_solid: debug_print(f" - 质量: {final_mass}g") debug_print(f" - 摩尔: {mol}") debug_print("=" * 60) return action_sequence # === 便捷函数 === def add_liquid_volume(G: nx.DiGraph, vessel: str, reagent: str, volume: Union[str, float], time: Union[str, float] = 0.0, rate_spec: str = "") -> List[Dict[str, Any]]: """添加指定体积的液体试剂""" return generate_add_protocol( G, vessel, reagent, volume=volume, time=time, rate_spec=rate_spec ) def add_solid_mass(G: nx.DiGraph, vessel: str, reagent: str, mass: Union[str, float], event: str = "") -> List[Dict[str, Any]]: """添加指定质量的固体试剂""" return generate_add_protocol( G, vessel, reagent, mass=mass, event=event ) def add_solid_moles(G: nx.DiGraph, vessel: str, reagent: str, mol: str, event: str = "") -> List[Dict[str, Any]]: """按摩尔数添加固体试剂""" return generate_add_protocol( G, vessel, reagent, mol=mol, event=event ) def add_dropwise_liquid(G: nx.DiGraph, vessel: str, reagent: str, volume: Union[str, float], time: Union[str, float] = "20 min", event: str = "") -> List[Dict[str, Any]]: """滴加液体试剂""" return generate_add_protocol( G, vessel, reagent, volume=volume, time=time, rate_spec="dropwise", event=event ) def add_portionwise_solid(G: nx.DiGraph, vessel: str, reagent: str, mass: Union[str, float], time: Union[str, float] = "1 h", event: str = "") -> List[Dict[str, Any]]: """分批添加固体试剂""" return generate_add_protocol( G, vessel, reagent, mass=mass, time=time, rate_spec="portionwise", event=event ) # 测试函数 def test_add_protocol(): """测试添加协议的各种参数解析""" print("=== ADD PROTOCOL 增强版测试 ===") # 测试体积解析 volumes = ["2.7 mL", "2.67 mL", "?", 10.0, "1 L", "500 μL"] for vol in volumes: result = parse_volume_input(vol) print(f"体积解析: {vol} → {result}mL") # 测试质量解析 masses = ["19.3 g", "4.5 g", 2.5, "500 mg", "1 kg"] for mass in masses: result = parse_mass_input(mass) print(f"质量解析: {mass} → {result}g") # 测试时间解析 times = ["1 h", "20 min", "30 s", 60.0, "?"] for time in times: result = parse_time_input(time) print(f"时间解析: {time} → {result}s") print("✅ 测试完成") if __name__ == "__main__": test_add_protocol()