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修补了一些单位处理，bump version to 0.9.11

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KCFeng425
2025-07-10 18:25:13 +08:00
parent 7b93332bf5
commit 23eb1139a9
21 changed files with 962 additions and 187 deletions
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121
unilabos/compile/recrystallize_protocol.py
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@@ -1,8 +1,80 @@
import networkx as nx
from typing import List, Dict, Any, Tuple
import re
from typing import List, Dict, Any, Tuple, Union
from .pump_protocol import generate_pump_protocol_with_rinsing
def parse_volume_with_units(volume_input: Union[str, float, int], default_unit: str = "mL") -> float:
"""
解析带单位的体积输入
Args:
volume_input: 体积输入（如 "100 mL", "2.5 L", "500", "?", 100.0）
default_unit: 默认单位（默认为毫升）
Returns:
float: 体积（毫升）
"""
if not volume_input:
return 0.0
# 处理数值输入
if isinstance(volume_input, (int, float)):
result = float(volume_input)
print(f"RECRYSTALLIZE: 数值体积输入: {volume_input} → {result}mL（默认单位）")
return result
# 处理字符串输入
volume_str = str(volume_input).lower().strip()
print(f"RECRYSTALLIZE: 解析体积字符串: '{volume_str}'")
# 处理特殊值
if volume_str in ['?', 'unknown', 'tbd', 'to be determined']:
default_volume = 50.0 # 50mL默认值
print(f"RECRYSTALLIZE: 检测到未知体积，使用默认值: {default_volume}mL")
return default_volume
# 如果是纯数字，使用默认单位
try:
value = float(volume_str)
if default_unit.lower() in ["ml", "milliliter"]:
result = value
elif default_unit.lower() in ["l", "liter"]:
result = value * 1000.0
elif default_unit.lower() in ["μl", "ul", "microliter"]:
result = value / 1000.0
else:
result = value # 默认mL
print(f"RECRYSTALLIZE: 纯数字输入: {volume_str} → {result}mL（单位: {default_unit}）")
return result
except ValueError:
pass
# 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:
print(f"RECRYSTALLIZE: ⚠️ 无法解析体积: '{volume_str}'，使用默认值: 50mL")
return 50.0
value = float(match.group(1))
unit = match.group(2) or default_unit.lower()
# 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
print(f"RECRYSTALLIZE: 体积解析: '{volume_str}' → {value} {unit} → {volume}mL")
return volume
def parse_ratio(ratio_str: str) -> Tuple[float, float]:
"""
解析比例字符串，支持多种格式
@@ -111,11 +183,11 @@ def generate_recrystallize_protocol(
solvent1: str,
solvent2: str,
vessel: str,
volume: float,
**kwargs # 接收其他可能的参数但不使用
volume: Union[str, float], # 🔧 修改：支持字符串和数值
**kwargs
) -> List[Dict[str, Any]]:
"""
生成重结晶协议序列
生成重结晶协议序列 - 支持单位
Args:
G: 有向图，节点为容器和设备
@@ -123,38 +195,42 @@ def generate_recrystallize_protocol(
solvent1: 第一种溶剂名称
solvent2: 第二种溶剂名称
vessel: 目标容器
volume: 总体积 (mL)
**kwargs: 其他可选参数，但不使用
volume: 总体积（支持 "100 mL", "50", "2.5 L" 等）
**kwargs: 其他可选参数
Returns:
List[Dict[str, Any]]: 动作序列
"""
action_sequence = []
print(f"RECRYSTALLIZE: 开始生成重结晶协议")
print(f"RECRYSTALLIZE: 开始生成重结晶协议（支持单位）")
print(f" - 比例: {ratio}")
print(f" - 溶剂1: {solvent1}")
print(f" - 溶剂2: {solvent2}")
print(f" - 容器: {vessel}")
print(f" - 总体积: {volume} mL")
print(f" - 总体积: {volume} (类型: {type(volume)})")
# 1. 验证目标容器存在
if vessel not in G.nodes():
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
# 2. 解析比例
# 2. 🔧 新增：解析体积（支持单位）
final_volume = parse_volume_with_units(volume, "mL")
print(f"RECRYSTALLIZE: 解析体积: {volume} → {final_volume}mL")
# 3. 解析比例
ratio1, ratio2 = parse_ratio(ratio)
total_ratio = ratio1 + ratio2
# 3. 计算各溶剂体积
volume1 = volume * (ratio1 / total_ratio)
volume2 = volume * (ratio2 / total_ratio)
# 4. 计算各溶剂体积
volume1 = final_volume * (ratio1 / total_ratio)
volume2 = final_volume * (ratio2 / total_ratio)
print(f"RECRYSTALLIZE: 解析比例: {ratio1}:{ratio2}")
print(f"RECRYSTALLIZE: {solvent1} 体积: {volume1:.2f} mL")
print(f"RECRYSTALLIZE: {solvent2} 体积: {volume2:.2f} mL")
# 4. 查找溶剂容器
# 5. 查找溶剂容器
try:
solvent1_vessel = find_solvent_vessel(G, solvent1)
print(f"RECRYSTALLIZE: 找到溶剂1容器: {solvent1_vessel}")
@@ -167,7 +243,7 @@ def generate_recrystallize_protocol(
except ValueError as e:
raise ValueError(f"无法找到溶剂2 '{solvent2}': {str(e)}")
# 5. 验证路径存在
# 6. 验证路径存在
try:
path1 = nx.shortest_path(G, source=solvent1_vessel, target=vessel)
print(f"RECRYSTALLIZE: 溶剂1路径: {' → '.join(path1)}")
@@ -180,7 +256,7 @@ def generate_recrystallize_protocol(
except nx.NetworkXNoPath:
raise ValueError(f"从溶剂2容器 '{solvent2_vessel}' 到目标容器 '{vessel}' 没有可用路径")
# 6. 添加第一种溶剂
# 7. 添加第一种溶剂
print(f"RECRYSTALLIZE: 开始添加溶剂1 {volume1:.2f} mL")
try:
@@ -188,7 +264,7 @@ def generate_recrystallize_protocol(
G=G,
from_vessel=solvent1_vessel,
to_vessel=vessel,
volume=volume1,
volume=volume1, # 使用解析后的体积
amount="",
time=0.0,
viscous=False,
@@ -205,7 +281,7 @@ def generate_recrystallize_protocol(
except Exception as e:
raise ValueError(f"生成溶剂1泵协议时出错: {str(e)}")
# 7. 等待溶剂1稳定
# 8. 等待溶剂1稳定
action_sequence.append({
"action_name": "wait",
"action_kwargs": {
@@ -214,7 +290,7 @@ def generate_recrystallize_protocol(
}
})
# 8. 添加第二种溶剂
# 9. 添加第二种溶剂
print(f"RECRYSTALLIZE: 开始添加溶剂2 {volume2:.2f} mL")
try:
@@ -222,7 +298,7 @@ def generate_recrystallize_protocol(
G=G,
from_vessel=solvent2_vessel,
to_vessel=vessel,
volume=volume2,
volume=volume2, # 使用解析后的体积
amount="",
time=0.0,
viscous=False,
@@ -239,7 +315,7 @@ def generate_recrystallize_protocol(
except Exception as e:
raise ValueError(f"生成溶剂2泵协议时出错: {str(e)}")
# 9. 等待溶剂2稳定
# 10. 等待溶剂2稳定
action_sequence.append({
"action_name": "wait",
"action_kwargs": {
@@ -248,17 +324,18 @@ def generate_recrystallize_protocol(
}
})
# 10. 等待重结晶完成
# 11. 等待重结晶完成
action_sequence.append({
"action_name": "wait",
"action_kwargs": {
"time": 600.0, # 等待10分钟进行重结晶
"description": f"等待重结晶完成（{solvent1}:{solvent2} = {ratio}）"
"description": f"等待重结晶完成（{solvent1}:{solvent2} = {ratio}，总体积 {final_volume}mL）"
}
})
print(f"RECRYSTALLIZE: 协议生成完成，共 {len(action_sequence)} 个动作")
print(f"RECRYSTALLIZE: 预计总时间: {620/60:.1f} 分钟")
print(f"RECRYSTALLIZE: 总体积: {final_volume}mL")
return action_sequence