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https://github.com/deepmodeling/Uni-Lab-OS
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refactor: 14个协议编译器去重精简，删除死代码
- 统一debug_print为共享import，移除14个本地定义 - 移除重复工具函数（find_connected_stirrer, get_vessel_liquid_volume等） - 精简装饰性日志（emoji分隔线、进度提示），保留关键决策点 - 删除evacuateandrefill_protocol_old.py死代码 - 涉及文件：add, adjustph, clean_vessel, dissolve, dry, evacuateandrefill, evaporate, filter, pump, recrystallize, reset_handling, run_column, stir, wash_solid Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
This commit is contained in:
Junhan Chang
@@ -2,60 +2,54 @@ from typing import List, Dict, Any, Union
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import networkx as nx
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import logging
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import re
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from .utils.vessel_parser import get_vessel
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from .utils.vessel_parser import get_vessel, find_solvent_vessel
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from .utils.resource_helper import get_resource_id, get_resource_data, get_resource_liquid_volume, update_vessel_volume
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from .utils.logger_util import debug_print
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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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logger.info(f"[RUN_COLUMN] {message}")
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def parse_percentage(pct_str: str) -> float:
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"""
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解析百分比字符串为数值
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Args:
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pct_str: 百分比字符串（如 "40 %", "40%", "40"）
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Returns:
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float: 百分比数值（0-100）
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"""
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if not pct_str or not pct_str.strip():
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return 0.0
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pct_str = pct_str.strip().lower()
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debug_print(f"🔍 解析百分比: '{pct_str}'")
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# 移除百分号和空格
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pct_clean = re.sub(r'[%\s]', '', pct_str)
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# 提取数字
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match = re.search(r'([0-9]*\.?[0-9]+)', pct_clean)
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if match:
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value = float(match.group(1))
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debug_print(f"✅ 百分比解析结果: {value}%")
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return value
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debug_print(f"⚠️ 无法解析百分比: '{pct_str}'，返回0.0")
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debug_print(f"无法解析百分比: '{pct_str}'，返回0.0")
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return 0.0
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def parse_ratio(ratio_str: str) -> tuple:
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"""
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解析比例字符串为两个数值
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Args:
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ratio_str: 比例字符串（如 "5:95", "1:1", "40:60"）
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Returns:
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tuple: (ratio1, ratio2) 两个比例值
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tuple: (ratio1, ratio2) 两个比例值（百分比）
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"""
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if not ratio_str or not ratio_str.strip():
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return (50.0, 50.0) # 默认1:1
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return (50.0, 50.0)
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ratio_str = ratio_str.strip()
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debug_print(f"🔍 解析比例: '{ratio_str}'")
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# 支持多种分隔符：: / -
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if ':' in ratio_str:
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parts = ratio_str.split(':')
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@@ -66,101 +60,82 @@ def parse_ratio(ratio_str: str) -> tuple:
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elif 'to' in ratio_str.lower():
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parts = ratio_str.lower().split('to')
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else:
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debug_print(f"⚠️ 无法解析比例格式: '{ratio_str}'，使用默认1:1")
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debug_print(f"无法解析比例格式: '{ratio_str}'，使用默认1:1")
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return (50.0, 50.0)
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if len(parts) >= 2:
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try:
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ratio1 = float(parts[0].strip())
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ratio2 = float(parts[1].strip())
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total = ratio1 + ratio2
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# 转换为百分比
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pct1 = (ratio1 / total) * 100
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pct2 = (ratio2 / total) * 100
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debug_print(f"✅ 比例解析结果: {ratio1}:{ratio2} -> {pct1:.1f}%:{pct2:.1f}%")
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return (pct1, pct2)
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except ValueError as e:
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debug_print(f"⚠️ 比例数值转换失败: {str(e)}")
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debug_print(f"⚠️ 比例解析失败，使用默认1:1")
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debug_print(f"比例数值转换失败: {str(e)}")
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debug_print(f"比例解析失败，使用默认1:1")
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return (50.0, 50.0)
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def parse_rf_value(rf_str: str) -> float:
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"""
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解析Rf值字符串
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Args:
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rf_str: Rf值字符串（如 "0.3", "0.45", "?"）
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Returns:
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float: Rf值（0-1）
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"""
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if not rf_str or not rf_str.strip():
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return 0.3 # 默认Rf值
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return 0.3
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rf_str = rf_str.strip().lower()
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debug_print(f"🔍 解析Rf值: '{rf_str}'")
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# 处理未知Rf值
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if rf_str in ['?', 'unknown', 'tbd', 'to be determined']:
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default_rf = 0.3
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debug_print(f"❓ 检测到未知Rf值，使用默认值: {default_rf}")
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return default_rf
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# 提取数字
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return 0.3
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match = re.search(r'([0-9]*\.?[0-9]+)', rf_str)
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if match:
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value = float(match.group(1))
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# 确保Rf值在0-1范围内
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if value > 1.0:
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value = value / 100.0 # 可能是百分比形式
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value = max(0.0, min(1.0, value)) # 限制在0-1范围
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debug_print(f"✅ Rf值解析结果: {value}")
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value = value / 100.0
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value = max(0.0, min(1.0, value))
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return value
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debug_print(f"⚠️ 无法解析Rf值: '{rf_str}'，使用默认值0.3")
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return 0.3
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def find_column_device(G: nx.DiGraph) -> str:
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"""查找柱层析设备"""
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debug_print("🔍 查找柱层析设备...")
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# 查找虚拟柱设备
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for node in G.nodes():
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node_data = G.nodes[node]
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node_class = node_data.get('class', '') or ''
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if 'virtual_column' in node_class.lower() or 'column' in node_class.lower():
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debug_print(f"🎉 找到柱层析设备: {node} ✨")
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debug_print(f"找到柱层析设备: {node}")
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return node
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# 如果没有找到，尝试创建虚拟设备名称
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possible_names = ['column_1', 'virtual_column_1', 'chromatography_column_1']
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for name in possible_names:
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if name in G.nodes():
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debug_print(f"🎉 找到柱设备: {name} ✨")
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debug_print(f"找到柱设备: {name}")
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return name
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debug_print("⚠️ 未找到柱层析设备，将使用pump protocol直接转移")
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debug_print("未找到柱层析设备，将使用pump protocol直接转移")
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return ""
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def find_column_vessel(G: nx.DiGraph, column: str) -> str:
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"""查找柱容器"""
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debug_print(f"🔍 查找柱容器: '{column}'")
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# 直接检查column参数是否是容器
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if column in G.nodes():
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node_type = G.nodes[column].get('type', '')
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if node_type == 'container':
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debug_print(f"🎉 找到柱容器: {column} ✨")
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return column
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# 尝试常见的命名规则
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possible_names = [
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f"column_{column}",
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f"{column}_column",
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f"{column}_column",
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f"vessel_{column}",
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f"{column}_vessel",
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"column_vessel",
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@@ -169,211 +144,25 @@ def find_column_vessel(G: nx.DiGraph, column: str) -> str:
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"preparative_column",
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"column"
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]
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for vessel_name in possible_names:
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if vessel_name in G.nodes():
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node_type = G.nodes[vessel_name].get('type', '')
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if node_type == 'container':
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debug_print(f"🎉 找到柱容器: {vessel_name} ✨")
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return vessel_name
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debug_print(f"⚠️ 未找到柱容器，将直接在源容器中进行分离")
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return ""
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def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
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"""查找溶剂容器 - 增强版"""
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if not solvent or not solvent.strip():
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return ""
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solvent = solvent.strip().replace(' ', '_').lower()
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debug_print(f"🔍 查找溶剂容器: '{solvent}'")
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# 🔧 方法1：直接搜索 data.reagent_name
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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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# 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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reagent_config = G.nodes[node].get('config', {}).get('reagent', '').lower()
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# 检查 data.reagent_name 和 config.reagent
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if reagent_name == solvent or reagent_config == solvent:
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debug_print(f"🎉 通过reagent_name找到溶剂容器: {node} (reagent: {reagent_name or reagent_config}) ✨")
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return node
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# 模糊匹配 reagent_name
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if solvent in reagent_name or reagent_name in solvent:
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debug_print(f"🎉 通过reagent_name模糊匹配到溶剂容器: {node} (reagent: {reagent_name}) ✨")
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return node
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if solvent in reagent_config or reagent_config in solvent:
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debug_print(f"🎉 通过config.reagent模糊匹配到溶剂容器: {node} (reagent: {reagent_config}) ✨")
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return node
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# 🔧 方法2：常见的溶剂容器命名规则
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possible_names = [
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f"flask_{solvent}",
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f"bottle_{solvent}",
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f"reagent_{solvent}",
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f"{solvent}_bottle",
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f"{solvent}_flask",
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f"solvent_{solvent}",
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f"reagent_bottle_{solvent}"
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]
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for vessel_name in possible_names:
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if vessel_name in G.nodes():
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node_type = G.nodes[vessel_name].get('type', '')
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if node_type == 'container':
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debug_print(f"🎉 通过命名规则找到溶剂容器: {vessel_name} ✨")
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return vessel_name
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# 🔧 方法3：节点名称模糊匹配
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for node in G.nodes():
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node_type = G.nodes[node].get('type', '')
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if node_type == 'container':
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if ('flask_' in node or 'bottle_' in node or 'reagent_' in node) and solvent in node.lower():
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debug_print(f"🎉 通过节点名称模糊匹配到溶剂容器: {node} ✨")
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return node
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# 🔧 方法4：特殊溶剂名称映射
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solvent_mapping = {
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'dmf': ['dmf', 'dimethylformamide', 'n,n-dimethylformamide'],
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'ethyl_acetate': ['ethyl_acetate', 'ethylacetate', 'etoac', 'ea'],
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'hexane': ['hexane', 'hexanes', 'n-hexane'],
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'methanol': ['methanol', 'meoh', 'ch3oh'],
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'water': ['water', 'h2o', 'distilled_water'],
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'acetone': ['acetone', 'ch3coch3', '2-propanone'],
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'dichloromethane': ['dichloromethane', 'dcm', 'ch2cl2', 'methylene_chloride'],
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'chloroform': ['chloroform', 'chcl3', 'trichloromethane']
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}
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# 查找映射的同义词
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for canonical_name, synonyms in solvent_mapping.items():
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if solvent in synonyms:
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debug_print(f"🔍 检测到溶剂同义词: '{solvent}' -> '{canonical_name}'")
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return find_solvent_vessel(G, canonical_name) # 递归搜索
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debug_print(f"⚠️ 未找到溶剂 '{solvent}' 的容器")
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return ""
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def get_vessel_liquid_volume(vessel: dict) -> float:
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"""
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获取容器中的液体体积 - 支持vessel字典
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Args:
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vessel: 容器字典
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Returns:
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float: 液体体积（mL）
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"""
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if not vessel or "data" not in vessel:
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debug_print(f"⚠️ 容器数据为空，返回 0.0mL")
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return 0.0
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vessel_data = vessel["data"]
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vessel_id = vessel.get("id", "unknown")
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debug_print(f"🔍 读取容器 '{vessel_id}' 体积数据: {vessel_data}")
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# 检查liquid_volume字段
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if "liquid_volume" in vessel_data:
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liquid_volume = vessel_data["liquid_volume"]
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# 处理列表格式
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if isinstance(liquid_volume, list):
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if len(liquid_volume) > 0:
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volume = liquid_volume[0]
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if isinstance(volume, (int, float)):
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debug_print(f"✅ 容器 '{vessel_id}' 体积: {volume}mL (列表格式)")
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return float(volume)
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# 处理直接数值格式
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elif isinstance(liquid_volume, (int, float)):
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debug_print(f"✅ 容器 '{vessel_id}' 体积: {liquid_volume}mL (数值格式)")
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return float(liquid_volume)
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# 检查其他可能的体积字段
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volume_keys = ['current_volume', 'total_volume', 'volume']
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for key in volume_keys:
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if key in vessel_data:
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try:
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volume = float(vessel_data[key])
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if volume > 0:
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debug_print(f"✅ 容器 '{vessel_id}' 体积: {volume}mL (字段: {key})")
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return volume
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except (ValueError, TypeError):
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continue
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debug_print(f"⚠️ 无法获取容器 '{vessel_id}' 的体积，返回默认值 50.0mL")
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return 50.0
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def update_vessel_volume(vessel: dict, G: nx.DiGraph, new_volume: float, description: str = "") -> None:
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"""
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更新容器体积（同时更新vessel字典和图节点）
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Args:
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vessel: 容器字典
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G: 网络图
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new_volume: 新体积
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description: 更新描述
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"""
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vessel_id = vessel.get("id", "unknown")
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if description:
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debug_print(f"🔧 更新容器体积 - {description}")
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# 更新vessel字典中的体积
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if "data" in vessel:
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if "liquid_volume" in vessel["data"]:
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current_volume = vessel["data"]["liquid_volume"]
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if isinstance(current_volume, list):
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if len(current_volume) > 0:
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vessel["data"]["liquid_volume"][0] = new_volume
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else:
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vessel["data"]["liquid_volume"] = [new_volume]
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else:
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vessel["data"]["liquid_volume"] = new_volume
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else:
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vessel["data"]["liquid_volume"] = new_volume
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else:
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vessel["data"] = {"liquid_volume": new_volume}
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# 同时更新图中的容器数据
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if vessel_id in G.nodes():
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if 'data' not in G.nodes[vessel_id]:
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G.nodes[vessel_id]['data'] = {}
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vessel_node_data = G.nodes[vessel_id]['data']
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current_node_volume = vessel_node_data.get('liquid_volume', 0.0)
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if isinstance(current_node_volume, list):
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if len(current_node_volume) > 0:
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G.nodes[vessel_id]['data']['liquid_volume'][0] = new_volume
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else:
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G.nodes[vessel_id]['data']['liquid_volume'] = [new_volume]
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else:
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G.nodes[vessel_id]['data']['liquid_volume'] = new_volume
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debug_print(f"📊 容器 '{vessel_id}' 体积已更新为: {new_volume:.2f}mL")
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def calculate_solvent_volumes(total_volume: float, pct1: float, pct2: float) -> tuple:
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"""根据百分比计算溶剂体积"""
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volume1 = (total_volume * pct1) / 100.0
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volume2 = (total_volume * pct2) / 100.0
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debug_print(f"🧮 溶剂体积计算: 总体积{total_volume}mL")
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debug_print(f" - 溶剂1: {pct1}% = {volume1}mL")
|
||||
debug_print(f" - 溶剂2: {pct2}% = {volume2}mL")
|
||||
|
||||
return (volume1, volume2)
|
||||
|
||||
def generate_run_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: dict, # 🔧 修改：从字符串改为字典类型
|
||||
to_vessel: dict, # 🔧 修改：从字符串改为字典类型
|
||||
from_vessel: dict,
|
||||
to_vessel: dict,
|
||||
column: str,
|
||||
rf: str = "",
|
||||
pct1: str = "",
|
||||
@@ -385,7 +174,7 @@ def generate_run_column_protocol(
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成柱层析分离的协议序列 - 支持vessel字典和体积运算
|
||||
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
from_vessel: 源容器字典（从XDL传入）
|
||||
@@ -398,173 +187,112 @@ def generate_run_column_protocol(
|
||||
solvent2: 第二种溶剂名称（可选）
|
||||
ratio: 溶剂比例（如 "5:95"，可选，优先级高于pct1/pct2）
|
||||
**kwargs: 其他可选参数
|
||||
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 柱层析分离操作的动作序列
|
||||
"""
|
||||
|
||||
# 🔧 核心修改：从字典中提取容器ID
|
||||
|
||||
from_vessel_id, _ = get_vessel(from_vessel)
|
||||
to_vessel_id, _ = get_vessel(to_vessel)
|
||||
|
||||
debug_print("🏛️" * 20)
|
||||
debug_print("🚀 开始生成柱层析协议（支持vessel字典和体积运算）✨")
|
||||
debug_print(f"📝 输入参数:")
|
||||
debug_print(f" 🥽 from_vessel: {from_vessel} (ID: {from_vessel_id})")
|
||||
debug_print(f" 🥽 to_vessel: {to_vessel} (ID: {to_vessel_id})")
|
||||
debug_print(f" 🏛️ column: '{column}'")
|
||||
debug_print(f" 📊 rf: '{rf}'")
|
||||
debug_print(f" 🧪 溶剂配比: pct1='{pct1}', pct2='{pct2}', ratio='{ratio}'")
|
||||
debug_print(f" 🧪 溶剂名称: solvent1='{solvent1}', solvent2='{solvent2}'")
|
||||
debug_print("🏛️" * 20)
|
||||
|
||||
debug_print(f"开始生成柱层析协议: {from_vessel_id} -> {to_vessel_id}, column={column}")
|
||||
|
||||
action_sequence = []
|
||||
|
||||
# 🔧 新增：记录柱层析前的容器状态
|
||||
debug_print("🔍 记录柱层析前容器状态...")
|
||||
original_from_volume = get_vessel_liquid_volume(from_vessel)
|
||||
original_to_volume = get_vessel_liquid_volume(to_vessel)
|
||||
|
||||
debug_print(f"📊 柱层析前状态:")
|
||||
debug_print(f" - 源容器 {from_vessel_id}: {original_from_volume:.2f}mL")
|
||||
debug_print(f" - 目标容器 {to_vessel_id}: {original_to_volume:.2f}mL")
|
||||
|
||||
|
||||
# 记录柱层析前的容器状态
|
||||
original_from_volume = get_resource_liquid_volume(from_vessel)
|
||||
original_to_volume = get_resource_liquid_volume(to_vessel)
|
||||
|
||||
# === 参数验证 ===
|
||||
debug_print("📍 步骤1: 参数验证...")
|
||||
|
||||
if not from_vessel_id: # 🔧 使用 from_vessel_id
|
||||
if not from_vessel_id:
|
||||
raise ValueError("from_vessel 参数不能为空")
|
||||
if not to_vessel_id: # 🔧 使用 to_vessel_id
|
||||
if not to_vessel_id:
|
||||
raise ValueError("to_vessel 参数不能为空")
|
||||
if not column:
|
||||
raise ValueError("column 参数不能为空")
|
||||
|
||||
if from_vessel_id not in G.nodes(): # 🔧 使用 from_vessel_id
|
||||
|
||||
if from_vessel_id not in G.nodes():
|
||||
raise ValueError(f"源容器 '{from_vessel_id}' 不存在于系统中")
|
||||
if to_vessel_id not in G.nodes(): # 🔧 使用 to_vessel_id
|
||||
if to_vessel_id not in G.nodes():
|
||||
raise ValueError(f"目标容器 '{to_vessel_id}' 不存在于系统中")
|
||||
|
||||
debug_print("✅ 基本参数验证通过")
|
||||
|
||||
|
||||
# === 参数解析 ===
|
||||
debug_print("📍 步骤2: 参数解析...")
|
||||
|
||||
# 解析Rf值
|
||||
final_rf = parse_rf_value(rf)
|
||||
debug_print(f"🎯 最终Rf值: {final_rf}")
|
||||
|
||||
# 解析溶剂比例（ratio优先级高于pct1/pct2）
|
||||
|
||||
if ratio and ratio.strip():
|
||||
final_pct1, final_pct2 = parse_ratio(ratio)
|
||||
debug_print(f"📊 使用ratio参数: {final_pct1:.1f}% : {final_pct2:.1f}%")
|
||||
else:
|
||||
final_pct1 = parse_percentage(pct1) if pct1 else 50.0
|
||||
final_pct2 = parse_percentage(pct2) if pct2 else 50.0
|
||||
|
||||
# 如果百分比和不是100%，进行归一化
|
||||
|
||||
total_pct = final_pct1 + final_pct2
|
||||
if total_pct == 0:
|
||||
final_pct1, final_pct2 = 50.0, 50.0
|
||||
elif total_pct != 100.0:
|
||||
final_pct1 = (final_pct1 / total_pct) * 100
|
||||
final_pct2 = (final_pct2 / total_pct) * 100
|
||||
|
||||
debug_print(f"📊 使用百分比参数: {final_pct1:.1f}% : {final_pct2:.1f}%")
|
||||
|
||||
# 设置默认溶剂（如果未指定）
|
||||
|
||||
final_solvent1 = solvent1.strip() if solvent1 else "ethyl_acetate"
|
||||
final_solvent2 = solvent2.strip() if solvent2 else "hexane"
|
||||
|
||||
debug_print(f"🧪 最终溶剂: {final_solvent1} : {final_solvent2}")
|
||||
|
||||
|
||||
debug_print(f"参数: rf={final_rf}, 溶剂={final_solvent1}:{final_solvent2} = {final_pct1:.1f}%:{final_pct2:.1f}%")
|
||||
|
||||
# === 查找设备和容器 ===
|
||||
debug_print("📍 步骤3: 查找设备和容器...")
|
||||
|
||||
# 查找柱层析设备
|
||||
column_device_id = find_column_device(G)
|
||||
|
||||
# 查找柱容器
|
||||
column_vessel = find_column_vessel(G, column)
|
||||
|
||||
# 查找溶剂容器
|
||||
solvent1_vessel = find_solvent_vessel(G, final_solvent1)
|
||||
solvent2_vessel = find_solvent_vessel(G, final_solvent2)
|
||||
|
||||
debug_print(f"🔧 设备映射:")
|
||||
debug_print(f" - 柱设备: '{column_device_id}'")
|
||||
debug_print(f" - 柱容器: '{column_vessel}'")
|
||||
debug_print(f" - 溶剂1容器: '{solvent1_vessel}'")
|
||||
debug_print(f" - 溶剂2容器: '{solvent2_vessel}'")
|
||||
|
||||
|
||||
# === 获取源容器体积 ===
|
||||
debug_print("📍 步骤4: 获取源容器体积...")
|
||||
|
||||
source_volume = original_from_volume
|
||||
if source_volume <= 0:
|
||||
source_volume = 50.0 # 默认体积
|
||||
debug_print(f"⚠️ 无法获取源容器体积，使用默认值: {source_volume}mL")
|
||||
else:
|
||||
debug_print(f"✅ 源容器体积: {source_volume}mL")
|
||||
|
||||
source_volume = 50.0
|
||||
|
||||
# === 计算溶剂体积 ===
|
||||
debug_print("📍 步骤5: 计算溶剂体积...")
|
||||
|
||||
# 洗脱溶剂通常是样品体积的2-5倍
|
||||
total_elution_volume = source_volume * 3.0
|
||||
solvent1_volume, solvent2_volume = calculate_solvent_volumes(
|
||||
total_elution_volume, final_pct1, final_pct2
|
||||
)
|
||||
|
||||
|
||||
# === 执行柱层析流程 ===
|
||||
debug_print("📍 步骤6: 执行柱层析流程...")
|
||||
|
||||
# 🔧 新增：体积变化跟踪变量
|
||||
current_from_volume = source_volume
|
||||
current_to_volume = original_to_volume
|
||||
current_column_volume = 0.0
|
||||
|
||||
|
||||
try:
|
||||
# 步骤6.1: 样品上柱（如果有独立的柱容器）
|
||||
if column_vessel and column_vessel != from_vessel_id: # 🔧 使用 from_vessel_id
|
||||
debug_print(f"📍 6.1: 样品上柱 - {source_volume}mL 从 {from_vessel_id} 到 {column_vessel}")
|
||||
|
||||
# 步骤1: 样品上柱
|
||||
if column_vessel and column_vessel != from_vessel_id:
|
||||
try:
|
||||
sample_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=from_vessel_id, # 🔧 使用 from_vessel_id
|
||||
from_vessel=from_vessel_id,
|
||||
to_vessel=column_vessel,
|
||||
volume=source_volume,
|
||||
flowrate=1.0, # 慢速上柱
|
||||
flowrate=1.0,
|
||||
transfer_flowrate=0.5,
|
||||
rinsing_solvent="", # 暂不冲洗
|
||||
rinsing_solvent="",
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0
|
||||
)
|
||||
action_sequence.extend(sample_transfer_actions)
|
||||
debug_print(f"✅ 样品上柱完成，添加了 {len(sample_transfer_actions)} 个动作")
|
||||
|
||||
# 🔧 新增：更新体积 - 样品转移到柱上
|
||||
current_from_volume = 0.0 # 源容器体积变为0
|
||||
current_column_volume = source_volume # 柱容器体积增加
|
||||
|
||||
|
||||
current_from_volume = 0.0
|
||||
current_column_volume = source_volume
|
||||
|
||||
update_vessel_volume(from_vessel, G, current_from_volume, "样品上柱后，源容器清空")
|
||||
|
||||
# 如果柱容器在图中，也更新其体积
|
||||
|
||||
if column_vessel in G.nodes():
|
||||
if 'data' not in G.nodes[column_vessel]:
|
||||
G.nodes[column_vessel]['data'] = {}
|
||||
G.nodes[column_vessel]['data']['liquid_volume'] = current_column_volume
|
||||
debug_print(f"📊 柱容器 '{column_vessel}' 体积更新为: {current_column_volume:.2f}mL")
|
||||
|
||||
|
||||
except Exception as e:
|
||||
debug_print(f"⚠️ 样品上柱失败: {str(e)}")
|
||||
|
||||
# 步骤6.2: 添加洗脱溶剂1（如果有溶剂容器）
|
||||
debug_print(f"样品上柱失败: {str(e)}")
|
||||
|
||||
# 步骤2: 添加洗脱溶剂1
|
||||
if solvent1_vessel and solvent1_volume > 0:
|
||||
debug_print(f"📍 6.2: 添加洗脱溶剂1 - {solvent1_volume:.1f}mL {final_solvent1}")
|
||||
|
||||
try:
|
||||
target_vessel = column_vessel if column_vessel else from_vessel_id # 🔧 使用 from_vessel_id
|
||||
target_vessel = column_vessel if column_vessel else from_vessel_id
|
||||
solvent1_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=solvent1_vessel,
|
||||
@@ -574,27 +302,22 @@ def generate_run_column_protocol(
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(solvent1_transfer_actions)
|
||||
debug_print(f"✅ 溶剂1添加完成，添加了 {len(solvent1_transfer_actions)} 个动作")
|
||||
|
||||
# 🔧 新增：更新体积 - 添加溶剂1
|
||||
|
||||
if target_vessel == column_vessel:
|
||||
current_column_volume += solvent1_volume
|
||||
if column_vessel in G.nodes():
|
||||
G.nodes[column_vessel]['data']['liquid_volume'] = current_column_volume
|
||||
debug_print(f"📊 柱容器体积增加: +{solvent1_volume:.2f}mL = {current_column_volume:.2f}mL")
|
||||
elif target_vessel == from_vessel_id:
|
||||
current_from_volume += solvent1_volume
|
||||
update_vessel_volume(from_vessel, G, current_from_volume, "添加溶剂1后")
|
||||
|
||||
|
||||
except Exception as e:
|
||||
debug_print(f"⚠️ 溶剂1添加失败: {str(e)}")
|
||||
|
||||
# 步骤6.3: 添加洗脱溶剂2（如果有溶剂容器）
|
||||
debug_print(f"溶剂1添加失败: {str(e)}")
|
||||
|
||||
# 步骤3: 添加洗脱溶剂2
|
||||
if solvent2_vessel and solvent2_volume > 0:
|
||||
debug_print(f"📍 6.3: 添加洗脱溶剂2 - {solvent2_volume:.1f}mL {final_solvent2}")
|
||||
|
||||
try:
|
||||
target_vessel = column_vessel if column_vessel else from_vessel_id # 🔧 使用 from_vessel_id
|
||||
target_vessel = column_vessel if column_vessel else from_vessel_id
|
||||
solvent2_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=solvent2_vessel,
|
||||
@@ -604,31 +327,26 @@ def generate_run_column_protocol(
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(solvent2_transfer_actions)
|
||||
debug_print(f"✅ 溶剂2添加完成，添加了 {len(solvent2_transfer_actions)} 个动作")
|
||||
|
||||
# 🔧 新增：更新体积 - 添加溶剂2
|
||||
|
||||
if target_vessel == column_vessel:
|
||||
current_column_volume += solvent2_volume
|
||||
if column_vessel in G.nodes():
|
||||
G.nodes[column_vessel]['data']['liquid_volume'] = current_column_volume
|
||||
debug_print(f"📊 柱容器体积增加: +{solvent2_volume:.2f}mL = {current_column_volume:.2f}mL")
|
||||
elif target_vessel == from_vessel_id:
|
||||
current_from_volume += solvent2_volume
|
||||
update_vessel_volume(from_vessel, G, current_from_volume, "添加溶剂2后")
|
||||
|
||||
|
||||
except Exception as e:
|
||||
debug_print(f"⚠️ 溶剂2添加失败: {str(e)}")
|
||||
|
||||
# 步骤6.4: 使用柱层析设备执行分离（如果有设备）
|
||||
debug_print(f"溶剂2添加失败: {str(e)}")
|
||||
|
||||
# 步骤4: 使用柱层析设备执行分离
|
||||
if column_device_id:
|
||||
debug_print(f"📍 6.4: 使用柱层析设备执行分离")
|
||||
|
||||
column_separation_action = {
|
||||
"device_id": column_device_id,
|
||||
"action_name": "run_column",
|
||||
"action_kwargs": {
|
||||
"from_vessel": from_vessel_id, # 🔧 使用 from_vessel_id
|
||||
"to_vessel": to_vessel_id, # 🔧 使用 to_vessel_id
|
||||
"from_vessel": from_vessel_id,
|
||||
"to_vessel": to_vessel_id,
|
||||
"column": column,
|
||||
"rf": rf,
|
||||
"pct1": pct1,
|
||||
@@ -639,85 +357,65 @@ def generate_run_column_protocol(
|
||||
}
|
||||
}
|
||||
action_sequence.append(column_separation_action)
|
||||
debug_print(f"✅ 柱层析设备动作已添加")
|
||||
|
||||
# 等待分离完成
|
||||
separation_time = max(30, min(120, int(total_elution_volume / 2))) # 30-120秒，基于体积
|
||||
|
||||
separation_time = max(30, min(120, int(total_elution_volume / 2)))
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": separation_time}
|
||||
})
|
||||
debug_print(f"✅ 等待分离完成: {separation_time}秒")
|
||||
|
||||
# 步骤6.5: 产物收集（从柱容器到目标容器）
|
||||
if column_vessel and column_vessel != to_vessel_id: # 🔧 使用 to_vessel_id
|
||||
debug_print(f"📍 6.5: 产物收集 - 从 {column_vessel} 到 {to_vessel_id}")
|
||||
|
||||
|
||||
# 步骤5: 产物收集
|
||||
if column_vessel and column_vessel != to_vessel_id:
|
||||
try:
|
||||
# 估算产物体积（原始样品体积的70-90%，收率考虑）
|
||||
product_volume = source_volume * 0.8
|
||||
|
||||
|
||||
product_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=column_vessel,
|
||||
to_vessel=to_vessel_id, # 🔧 使用 to_vessel_id
|
||||
to_vessel=to_vessel_id,
|
||||
volume=product_volume,
|
||||
flowrate=1.5,
|
||||
transfer_flowrate=0.8
|
||||
)
|
||||
action_sequence.extend(product_transfer_actions)
|
||||
debug_print(f"✅ 产物收集完成，添加了 {len(product_transfer_actions)} 个动作")
|
||||
|
||||
# 🔧 新增：更新体积 - 产物收集到目标容器
|
||||
|
||||
current_to_volume += product_volume
|
||||
current_column_volume -= product_volume # 柱容器体积减少
|
||||
|
||||
current_column_volume -= product_volume
|
||||
|
||||
update_vessel_volume(to_vessel, G, current_to_volume, "产物收集后")
|
||||
|
||||
# 更新柱容器体积
|
||||
|
||||
if column_vessel in G.nodes():
|
||||
G.nodes[column_vessel]['data']['liquid_volume'] = max(0.0, current_column_volume)
|
||||
debug_print(f"📊 柱容器体积减少: -{product_volume:.2f}mL = {current_column_volume:.2f}mL")
|
||||
|
||||
|
||||
except Exception as e:
|
||||
debug_print(f"⚠️ 产物收集失败: {str(e)}")
|
||||
|
||||
# 步骤6.6: 如果没有独立的柱设备和容器，执行简化的直接转移
|
||||
debug_print(f"产物收集失败: {str(e)}")
|
||||
|
||||
# 步骤6: 简化模式 - 直接转移
|
||||
if not column_device_id and not column_vessel:
|
||||
debug_print(f"📍 6.6: 简化模式 - 直接转移 {source_volume}mL 从 {from_vessel_id} 到 {to_vessel_id}")
|
||||
|
||||
try:
|
||||
direct_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=from_vessel_id, # 🔧 使用 from_vessel_id
|
||||
to_vessel=to_vessel_id, # 🔧 使用 to_vessel_id
|
||||
from_vessel=from_vessel_id,
|
||||
to_vessel=to_vessel_id,
|
||||
volume=source_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(direct_transfer_actions)
|
||||
debug_print(f"✅ 直接转移完成，添加了 {len(direct_transfer_actions)} 个动作")
|
||||
|
||||
# 🔧 新增：更新体积 - 直接转移
|
||||
current_from_volume = 0.0 # 源容器清空
|
||||
current_to_volume += source_volume # 目标容器增加
|
||||
|
||||
|
||||
current_from_volume = 0.0
|
||||
current_to_volume += source_volume
|
||||
|
||||
update_vessel_volume(from_vessel, G, current_from_volume, "直接转移后，源容器清空")
|
||||
update_vessel_volume(to_vessel, G, current_to_volume, "直接转移后，目标容器增加")
|
||||
|
||||
|
||||
except Exception as e:
|
||||
debug_print(f"⚠️ 直接转移失败: {str(e)}")
|
||||
|
||||
debug_print(f"直接转移失败: {str(e)}")
|
||||
|
||||
except Exception as e:
|
||||
debug_print(f"❌ 协议生成失败: {str(e)} 😭")
|
||||
|
||||
# 不添加不确定的动作，直接让action_sequence保持为空列表
|
||||
# action_sequence 已经在函数开始时初始化为 []
|
||||
|
||||
# 确保至少有一个有效的动作，如果完全失败就返回空列表
|
||||
debug_print(f"协议生成失败: {str(e)}")
|
||||
|
||||
if not action_sequence:
|
||||
debug_print("⚠️ 没有生成任何有效动作")
|
||||
# 可以选择返回空列表或添加一个基本的等待动作
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
@@ -725,83 +423,50 @@ def generate_run_column_protocol(
|
||||
"description": "柱层析协议执行完成"
|
||||
}
|
||||
})
|
||||
|
||||
# 🔧 新增：柱层析完成后的最终状态报告
|
||||
final_from_volume = get_vessel_liquid_volume(from_vessel)
|
||||
final_to_volume = get_vessel_liquid_volume(to_vessel)
|
||||
|
||||
# 🎊 总结
|
||||
debug_print("🏛️" * 20)
|
||||
debug_print(f"🎉 柱层析协议生成完成! ✨")
|
||||
debug_print(f"📊 总动作数: {len(action_sequence)} 个")
|
||||
debug_print(f"🥽 路径: {from_vessel_id} → {to_vessel_id}")
|
||||
debug_print(f"🏛️ 柱子: {column}")
|
||||
debug_print(f"🧪 溶剂: {final_solvent1}:{final_solvent2} = {final_pct1:.1f}%:{final_pct2:.1f}%")
|
||||
debug_print(f"📊 体积变化统计:")
|
||||
debug_print(f" 源容器 {from_vessel_id}:")
|
||||
debug_print(f" - 柱层析前: {original_from_volume:.2f}mL")
|
||||
debug_print(f" - 柱层析后: {final_from_volume:.2f}mL")
|
||||
debug_print(f" 目标容器 {to_vessel_id}:")
|
||||
debug_print(f" - 柱层析前: {original_to_volume:.2f}mL")
|
||||
debug_print(f" - 柱层析后: {final_to_volume:.2f}mL")
|
||||
debug_print(f" - 收集体积: {final_to_volume - original_to_volume:.2f}mL")
|
||||
debug_print(f"⏱️ 预计总时间: {len(action_sequence) * 5:.0f} 秒 ⌛")
|
||||
debug_print("🏛️" * 20)
|
||||
|
||||
|
||||
final_from_volume = get_resource_liquid_volume(from_vessel)
|
||||
final_to_volume = get_resource_liquid_volume(to_vessel)
|
||||
|
||||
debug_print(f"柱层析协议生成完成: {len(action_sequence)} 个动作, {from_vessel_id} -> {to_vessel_id}, 收集={final_to_volume - original_to_volume:.2f}mL")
|
||||
|
||||
return action_sequence
|
||||
|
||||
# 🔧 新增：便捷函数
|
||||
def generate_ethyl_acetate_hexane_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
# 便捷函数
|
||||
def generate_ethyl_acetate_hexane_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
column: str, ratio: str = "30:70") -> List[Dict[str, Any]]:
|
||||
"""乙酸乙酯-己烷柱层析（常用组合）"""
|
||||
from_vessel_id = from_vessel["id"]
|
||||
to_vessel_id = to_vessel["id"]
|
||||
debug_print(f"🧪⛽ 乙酸乙酯-己烷柱层析: {from_vessel_id} → {to_vessel_id} @ {ratio}")
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
solvent1="ethyl_acetate", solvent2="hexane", ratio=ratio)
|
||||
|
||||
def generate_methanol_dcm_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
def generate_methanol_dcm_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
column: str, ratio: str = "5:95") -> List[Dict[str, Any]]:
|
||||
"""甲醇-二氯甲烷柱层析"""
|
||||
from_vessel_id = from_vessel["id"]
|
||||
to_vessel_id = to_vessel["id"]
|
||||
debug_print(f"🧪🧪 甲醇-DCM柱层析: {from_vessel_id} → {to_vessel_id} @ {ratio}")
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
solvent1="methanol", solvent2="dichloromethane", ratio=ratio)
|
||||
|
||||
def generate_gradient_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
column: str, start_ratio: str = "10:90",
|
||||
def generate_gradient_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
column: str, start_ratio: str = "10:90",
|
||||
end_ratio: str = "50:50") -> List[Dict[str, Any]]:
|
||||
"""梯度洗脱柱层析（中等比例）"""
|
||||
from_vessel_id, _ = get_vessel(from_vessel)
|
||||
to_vessel_id, _ = get_vessel(to_vessel)
|
||||
debug_print(f"📈 梯度柱层析: {from_vessel_id} → {to_vessel_id} ({start_ratio} → {end_ratio})")
|
||||
# 使用中间比例作为近似
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column, ratio="30:70")
|
||||
|
||||
def generate_polar_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
def generate_polar_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
column: str) -> List[Dict[str, Any]]:
|
||||
"""极性化合物柱层析（高极性溶剂比例）"""
|
||||
from_vessel_id, _ = get_vessel(from_vessel)
|
||||
to_vessel_id, _ = get_vessel(to_vessel)
|
||||
debug_print(f"⚡ 极性化合物柱层析: {from_vessel_id} → {to_vessel_id}")
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
solvent1="ethyl_acetate", solvent2="hexane", ratio="70:30")
|
||||
|
||||
def generate_nonpolar_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
def generate_nonpolar_column_protocol(G: nx.DiGraph, from_vessel: dict, to_vessel: dict,
|
||||
column: str) -> List[Dict[str, Any]]:
|
||||
"""非极性化合物柱层析（低极性溶剂比例）"""
|
||||
from_vessel_id, _ = get_vessel(from_vessel)
|
||||
to_vessel_id, _ = get_vessel(to_vessel)
|
||||
debug_print(f"🛢️ 非极性化合物柱层析: {from_vessel_id} → {to_vessel_id}")
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
return generate_run_column_protocol(G, from_vessel, to_vessel, column,
|
||||
solvent1="ethyl_acetate", solvent2="hexane", ratio="5:95")
|
||||
|
||||
# 测试函数
|
||||
def test_run_column_protocol():
|
||||
"""测试柱层析协议"""
|
||||
debug_print("🧪 === RUN COLUMN PROTOCOL 测试 === ✨")
|
||||
debug_print("✅ 测试完成 🎉")
|
||||
debug_print("=== RUN COLUMN PROTOCOL 测试 ===")
|
||||
debug_print("测试完成")
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_run_column_protocol()
|
||||
|
||||
Reference in New Issue
Block a user