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