diff --git a/unilabos/devices/liquid_handling/biomek.py b/unilabos/devices/liquid_handling/biomek.py index ea7a9e9c..2e9b7b13 100644 --- a/unilabos/devices/liquid_handling/biomek.py +++ b/unilabos/devices/liquid_handling/biomek.py @@ -16,20 +16,37 @@ from .liquid_handler_abstract import LiquidHandlerAbstract import json from typing import Sequence, Optional, List, Union, Literal -class LiquidHandlerBiomek(LiquidHandlerAbstract): - +#class LiquidHandlerBiomek(LiquidHandlerAbstract): +class LiquidHandlerBiomek: """ Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。 该类用于处理Biomek液体处理器的特定操作。 """ - def __init__(self, backend=None, deck=None, *args, **kwargs): - super().__init__(backend, deck, *args, **kwargs) + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) self._status = "Idle" # 初始状态为 Idle self._success = False # 初始成功状态为 False self._status_queue = kwargs.get("status_queue", None) # 状态队列 self.temp_protocol = {} self.py32_path = "/opt/py32" # Biomek的Python 3.2路径 + + # 预定义的仪器分类 + self.tip_racks = [ + "BC230", "BC1025F", "BC50", "TipRack200", "TipRack1000", + "tip", "tips", "Tip", "Tips" + ] + + self.reservoirs = [ + "AgilentReservoir", "nest_12_reservoir_15ml", "nest_1_reservoir_195ml", + "reservoir", "Reservoir", "waste", "Waste" + ] + + self.plates_96 = [ + "BCDeep96Round", "Matrix96_750uL", "NEST 2ml Deep Well Plate", "nest_96_wellplate_100ul_pcr_full_skirt", + "nest_96_wellplate_200ul_flat", "Matrix96", "96", "plate", "Plate" + ] + self.aspirate_techniques = { 'MC P300 high':{ 'Position': 'P1', @@ -88,6 +105,29 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract): 'UseExpression': False} } + def _get_instrument_type(self, class_name: str) -> str: + """ + 根据class_name判断仪器类型 + + Returns: + str: "tip_rack", "reservoir", "plate_96", 或 "unknown" + """ + # 检查是否是枪头架 + for tip_name in self.tip_racks: + if tip_name in class_name: + return "tip_rack" + + # 检查是否是储液槽 + for reservoir_name in self.reservoirs: + if reservoir_name in class_name: + return "reservoir" + + # 检查是否是96孔板 + for plate_name in self.plates_96: + if plate_name in class_name: + return "plate_96" + + return "unknown" @classmethod def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler: @@ -137,7 +177,7 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract): "date": protocol_date, "type": protocol_type, }, - "labwares": [], + "labwares": {}, "steps": [], } return self.temp_protocol @@ -303,6 +343,104 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract): return + def instrument_setup_biomek( + self, + id: str, + parent: str, + slot_on_deck: str, + class_name: str, + liquid_type: list[str], + liquid_volume: list[int], + liquid_input_wells: list[str], + ): + """ + 设置Biomek仪器的参数配置，按照DeckItems格式 + + 根据不同的仪器类型（容器、tip rack等）设置相应的参数结构 + 位置作为键，配置列表作为值 + """ + + # 判断仪器类型 + instrument_type = self._get_instrument_type(class_name) + + config = None # 初始化为None + + if instrument_type == "reservoir": + # 储液槽类型配置 + config = { + "Properties": { + "Name": id, # 使用id作为名称 + "Device": "", + "liquidtype": liquid_type[0] if liquid_type else "Water", + "BarCode": "", + "SenseEveryTime": False + }, + "Known": True, + "Class": f"LabwareClasses\\{class_name}", + "DataSets": {"Volume": {}}, + "RuntimeDataSets": {"Volume": {}}, + "EvalAmounts": (float(liquid_volume[0]),) if liquid_volume else (0,), + "Nominal": False, + "EvalLiquids": (liquid_type[0],) if liquid_type else ("Water",) + } + + elif instrument_type == "plate_96": + # 96孔板类型配置 + volume_per_well = float(liquid_volume[0]) if liquid_volume else 0 + liquid_per_well = liquid_type[0] if liquid_type else "Water" + + config = { + "Properties": { + "Name": id, # 使用id作为名称 + "Device": "", + "liquidtype": liquid_per_well, + "BarCode": "", + "SenseEveryTime": False + }, + "Known": True, + "Class": f"LabwareClasses\\{class_name}", + "DataSets": {"Volume": {}}, + "RuntimeDataSets": {"Volume": {}}, + "EvalAmounts": tuple([volume_per_well] * 96), + "Nominal": False, + "EvalLiquids": tuple([liquid_per_well] * 96) + } + + elif instrument_type == "tip_rack": + # 枪头架类型配置 + tip_config = { + "Class": "TipClasses\\T230", + "Contents": [], + "_RT_Contents": [], + "Used": False, + "RT_Used": False, + "Dirty": False, + "RT_Dirty": False, + "MaxVolumeUsed": 0.0, + "RT_MaxVolumeUsed": 0.0 + } + + config = { + "Tips": tip_config, + "RT_Tips": tip_config.copy(), + "Properties": {}, + "Known": False, + "Class": f"LabwareClasses\\{class_name}", + "DataSets": {"Volume": {}}, + "RuntimeDataSets": {"Volume": {}} + } + + # 按照DeckItems格式存储：位置作为键，配置列表作为值 + if config is not None: + self.temp_protocol["labwares"][slot_on_deck] = [config] + else: + # 空位置 + self.temp_protocol["labwares"][slot_on_deck] = [] + + return + + + def transfer_biomek( self, source: str, @@ -369,9 +507,11 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract): transfer_params["items"] = items transfer_params["Solvent"] = 'Water' transfer_params["TipLocation"] = tip_rack - self.temp_protocol["steps"].append(transfer_params) + tmp={'transfer': transfer_params} + self.temp_protocol["steps"].append(tmp) + + return - return def move_biomek( self, @@ -430,483 +570,543 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract): if __name__ == "__main__": - steps_info = ''' + + print("=== Biomek完整流程测试 ===") + print("包含: 仪器设置 + 完整实验步骤") + + # 完整的步骤信息（从biomek.py复制） + steps_info = ''' { - "steps": [ - { - "step_number": 1, - "operation": "transfer", - "description": "转移PCR产物或酶促反应液至0.05ml 96孔板中", - "parameters": { - "source": "P1", - "target": "P11", - "tip_rack": "BC230", - "volume": 50 - } - }, - { - "step_number": 2, - "operation": "transfer", - "description": "加入2倍体积Bind Beads BC至产物中", - "parameters": { - "source": "P2", - "target": "P11", - "tip_rack": "BC230", - "volume": 100 - } - }, - { - "step_number": 3, - "operation": "move_labware", - "description": "移动P11至Orbital1用于振荡混匀", - "parameters": { - "source": "P11", - "target": "Orbital1" - } - }, - { - "step_number": 4, - "operation": "oscillation", - "description": "在Orbital1上振荡混匀Bind Beads BC与PCR产物（700-900rpm，300秒）", - "parameters": { - "rpm": 800, - "time": 300 - } - }, - { - "step_number": 5, - "operation": "move_labware", - "description": "移动混匀后的板回P11", - "parameters": { - "source": "Orbital1", - "target": "P11" - } - }, - { - "step_number": 6, - "operation": "move_labware", - "description": "将P11移动到磁力架（P12）吸附3分钟", - "parameters": { - "source": "P11", - "target": "P12" - } - }, - { - "step_number": 7, - "operation": "incubation", - "description": "磁力架上室温静置3分钟完成吸附", - "parameters": { - "time": 180 - } - }, - { - "step_number": 8, - "operation": "transfer", - "description": "去除上清液至废液槽", - "parameters": { - "source": "P12", - "target": "P22", - "tip_rack": "BC230", - "volume": 150 - } - }, - { - "step_number": 9, - "operation": "transfer", - "description": "加入300-500μl 75%乙醇清洗", - "parameters": { - "source": "P3", - "target": "P12", - "tip_rack": "BC230", - "volume": 400 - } - }, - { - "step_number": 10, - "operation": "move_labware", - "description": "移动清洗板到Orbital1进行振荡", - "parameters": { - "source": "P12", - "target": "Orbital1" - } - }, - { - "step_number": 11, - "operation": "oscillation", - "description": "乙醇清洗液振荡混匀（700-900rpm, 45秒）", - "parameters": { - "rpm": 800, - "time": 45 - } - }, - { - "step_number": 12, - "operation": "move_labware", - "description": "振荡后将板移回磁力架P12吸附", - "parameters": { - "source": "Orbital1", - "target": "P12" - } - }, - { - "step_number": 13, - "operation": "incubation", - "description": "吸附3分钟", - "parameters": { - "time": 180 - } - }, - { - "step_number": 14, - "operation": "transfer", - "description": "去除乙醇上清液至废液槽", - "parameters": { - "source": "P12", - "target": "P22", - "tip_rack": "BC230", - "volume": 400 - } - }, - { - "step_number": 15, - "operation": "transfer", - "description": "第二次加入300-500μl 75%乙醇清洗", - "parameters": { - "source": "P3", - "target": "P12", - "tip_rack": "BC230", - "volume": 400 - } - }, - { - "step_number": 16, - "operation": "move_labware", - "description": "再次移动清洗板到Orbital1振荡", - "parameters": { - "source": "P12", - "target": "Orbital1" - } - }, - { - "step_number": 17, - "operation": "oscillation", - "description": "再次乙醇清洗液振荡混匀（700-900rpm, 45秒）", - "parameters": { - "rpm": 800, - "time": 45 - } - }, - { - "step_number": 18, - "operation": "move_labware", - "description": "振荡后板送回磁力架P12吸附", - "parameters": { - "source": "Orbital1", - "target": "P12" - } - }, - { - "step_number": 19, - "operation": "incubation", - "description": "再次吸附3分钟", - "parameters": { - "time": 180 - } - }, - { - "step_number": 20, - "operation": "transfer", - "description": "去除乙醇上清液至废液槽", - "parameters": { - "source": "P12", - "target": "P22", - "tip_rack": "BC230", - "volume": 400 - } - }, - { - "step_number": 21, - "operation": "incubation", - "description": "空气干燥15分钟", - "parameters": { - "time": 900 - } - }, - { - "step_number": 22, - "operation": "transfer", - "description": "加30-50μl Elution Buffer洗脱", - "parameters": { - "source": "P4", - "target": "P12", - "tip_rack": "BC230", - "volume": 40 - } - }, - { - "step_number": 23, - "operation": "move_labware", - "description": "移动到Orbital1振荡混匀（60秒）", - "parameters": { - "source": "P12", - "target": "Orbital1" - } - }, - { - "step_number": 24, - "operation": "oscillation", - "description": "Elution Buffer振荡混匀（700-900rpm, 60秒）", - "parameters": { - "rpm": 800, - "time": 60 - } - }, - { - "step_number": 25, - "operation": "move_labware", - "description": "振荡后送回磁力架P12", - "parameters": { - "source": "Orbital1", - "target": "P12" - } - }, - { - "step_number": 26, - "operation": "incubation", - "description": "室温静置3分钟（洗脱反应）", - "parameters": { - "time": 180 - } - }, - { - "step_number": 27, - "operation": "transfer", - "description": "将上清液（DNA）转移到新板（P13）", - "parameters": { - "source": "P12", - "target": "P13", - "tip_rack": "BC230", - "volume": 40 + "steps": [ + { + "step_number": 1, + "operation": "transfer", + "description": "转移PCR产物或酶促反应液至0.5ml 96孔板中", + "parameters": { + "source": "P1", + "target": "P11", + "tip_rack": "BC230", + "volume": 50 + } + }, + { + "step_number": 2, + "operation": "transfer", + "description": "加入2倍体积的Bind Beads BC至产物中", + "parameters": { + "source": "P2", + "target": "P11", + "tip_rack": "BC230", + "volume": 100 + } + }, + { + "step_number": 3, + "operation": "oscillation", + "description": "振荡混匀300秒", + "parameters": { + "rpm": 800, + "time": 300 + } + }, + { + "step_number": 4, + "operation": "move_labware", + "description": "转移至96孔磁力架上吸附3分钟", + "parameters": { + "source": "P11", + "target": "P12" + } + }, + { + "step_number": 5, + "operation": "incubation", + "description": "吸附3分钟", + "parameters": { + "time": 180 + } + }, + { + "step_number": 6, + "operation": "transfer", + "description": "吸弃或倒除上清液", + "parameters": { + "source": "P12", + "target": "P22", + "tip_rack": "BC230", + "volume": 150 + } + }, + { + "step_number": 7, + "operation": "transfer", + "description": "加入300-500μl 75%乙醇", + "parameters": { + "source": "P3", + "target": "P12", + "tip_rack": "BC230", + "volume": 400 + } + }, + { + "step_number": 8, + "operation": "move_labware", + "description": "移动至振荡器进行振荡混匀", + "parameters": { + "source": "P12", + "target": "Orbital1" + } + }, + { + "step_number": 9, + "operation": "oscillation", + "description": "振荡混匀60秒", + "parameters": { + "rpm": 800, + "time": 60 + } + }, + { + "step_number": 10, + "operation": "move_labware", + "description": "转移至96孔磁力架上吸附3分钟", + "parameters": { + "source": "Orbital1", + "target": "P12" + } + }, + { + "step_number": 11, + "operation": "incubation", + "description": "吸附3分钟", + "parameters": { + "time": 180 + } + }, + { + "step_number": 12, + "operation": "transfer", + "description": "吸弃或倒弃废液", + "parameters": { + "source": "P12", + "target": "P22", + "tip_rack": "BC230", + "volume": 400 + } + }, + { + "step_number": 13, + "operation": "transfer", + "description": "重复加入75%乙醇", + "parameters": { + "source": "P3", + "target": "P12", + "tip_rack": "BC230", + "volume": 400 + } + }, + { + "step_number": 14, + "operation": "move_labware", + "description": "移动至振荡器进行振荡混匀", + "parameters": { + "source": "P12", + "target": "Orbital1" + } + }, + { + "step_number": 15, + "operation": "oscillation", + "description": "振荡混匀60秒", + "parameters": { + "rpm": 800, + "time": 60 + } + }, + { + "step_number": 16, + "operation": "move_labware", + "description": "转移至96孔磁力架上吸附3分钟", + "parameters": { + "source": "Orbital1", + "target": "P12" + } + }, + { + "step_number": 17, + "operation": "incubation", + "description": "吸附3分钟", + "parameters": { + "time": 180 + } + }, + { + "step_number": 18, + "operation": "transfer", + "description": "吸弃或倒弃废液", + "parameters": { + "source": "P12", + "target": "P22", + "tip_rack": "BC230", + "volume": 400 + } + }, + { + "step_number": 19, + "operation": "move_labware", + "description": "正放96孔板，空气干燥15分钟", + "parameters": { + "source": "P12", + "target": "P13" + } + }, + { + "step_number": 20, + "operation": "incubation", + "description": "空气干燥15分钟", + "parameters": { + "time": 900 + } + }, + { + "step_number": 21, + "operation": "transfer", + "description": "加入30-50μl Elution Buffer", + "parameters": { + "source": "P4", + "target": "P13", + "tip_rack": "BC230", + "volume": 40 + } + }, + { + "step_number": 22, + "operation": "move_labware", + "description": "移动至振荡器进行振荡混匀", + "parameters": { + "source": "P13", + "target": "Orbital1" + } + }, + { + "step_number": 23, + "operation": "oscillation", + "description": "振荡混匀60秒", + "parameters": { + "rpm": 800, + "time": 60 + } + }, + { + "step_number": 24, + "operation": "move_labware", + "description": "室温静置3分钟", + "parameters": { + "source": "Orbital1", + "target": "P13" + } + }, + { + "step_number": 25, + "operation": "incubation", + "description": "室温静置3分钟", + "parameters": { + "time": 180 + } + }, + { + "step_number": 26, + "operation": "move_labware", + "description": "转移至96孔磁力架上吸附2分钟", + "parameters": { + "source": "P13", + "target": "P12" + } + }, + { + "step_number": 27, + "operation": "incubation", + "description": "吸附2分钟", + "parameters": { + "time": 120 + } + }, + { + "step_number": 28, + "operation": "transfer", + "description": "将DNA转移至新的板中", + "parameters": { + "source": "P12", + "target": "P14", + "tip_rack": "BC230", + "volume": 40 } } ] } +''' + # 完整的labware配置信息 + labware_with_liquid = ''' + [ + { + "id": "Tip Rack BC230 TL1", + "parent": "deck", + "slot_on_deck": "TL1", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 TL2", + "parent": "deck", + "slot_on_deck": "TL2", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 TL3", + "parent": "deck", + "slot_on_deck": "TL3", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 TL4", + "parent": "deck", + "slot_on_deck": "TL4", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 TL5", + "parent": "deck", + "slot_on_deck": "TL5", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 P5", + "parent": "deck", + "slot_on_deck": "P5", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 P6", + "parent": "deck", + "slot_on_deck": "P6", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 P15", + "parent": "deck", + "slot_on_deck": "P15", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "Tip Rack BC230 P16", + "parent": "deck", + "slot_on_deck": "P16", + "class_name": "BC230", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "stock plate on P1", + "parent": "deck", + "slot_on_deck": "P1", + "class_name": "AgilentReservoir", + "liquid_type": ["PCR product"], + "liquid_volume": [5000], + "liquid_input_wells": ["A1"] + }, + { + "id": "stock plate on P2", + "parent": "deck", + "slot_on_deck": "P2", + "class_name": "AgilentReservoir", + "liquid_type": ["bind beads"], + "liquid_volume": [100000], + "liquid_input_wells": ["A1"] + }, + { + "id": "stock plate on P3", + "parent": "deck", + "slot_on_deck": "P3", + "class_name": "AgilentReservoir", + "liquid_type": ["75% ethanol"], + "liquid_volume": [100000], + "liquid_input_wells": ["A1"] + }, + { + "id": "stock plate on P4", + "parent": "deck", + "slot_on_deck": "P4", + "class_name": "AgilentReservoir", + "liquid_type": ["Elution Buffer"], + "liquid_volume": [5000], + "liquid_input_wells": ["A1"] + }, + { + "id": "working plate on P11", + "parent": "deck", + "slot_on_deck": "P11", + "class_name": "BCDeep96Round", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "working plate on P12", + "parent": "deck", + "slot_on_deck": "P12", + "class_name": "BCDeep96Round", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "working plate on P13", + "parent": "deck", + "slot_on_deck": "P13", + "class_name": "BCDeep96Round", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "working plate on P14", + "parent": "deck", + "slot_on_deck": "P14", + "class_name": "BCDeep96Round", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "waste on P22", + "parent": "deck", + "slot_on_deck": "P22", + "class_name": "AgilentReservoir", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + }, + { + "id": "oscillation", + "parent": "deck", + "slot_on_deck": "Orbital1", + "class_name": "Orbital", + "liquid_type": [], + "liquid_volume": [], + "liquid_input_wells": [] + } + ] ''' - labware_with_liquid = ''' - [ - { - "id": "Tip Rack BC230 on TL1", - "parent": "deck", - "slot_on_deck": "TL1", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on TL2", - "parent": "deck", - "slot_on_deck": "TL2", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on TL3", - "parent": "deck", - "slot_on_deck": "TL3", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on TL4", - "parent": "deck", - "slot_on_deck": "TL4", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on TL5", - "parent": "deck", - "slot_on_deck": "TL5", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on P5", - "parent": "deck", - "slot_on_deck": "P5", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on P6", - "parent": "deck", - "slot_on_deck": "P6", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on P15", - "parent": "deck", - "slot_on_deck": "P15", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "Tip Rack BC230 on P16", - "parent": "deck", - "slot_on_deck": "P16", - "class_name": "BC230", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "stock plate on P1", - "parent": "deck", - "slot_on_deck": "P1", - "class_name": "nest_12_reservoir_15ml", - "liquid_type": [ - "master_mix" - ], - "liquid_volume": [10000], - "liquid_input_wells": [ - "A1" - ] - }, - { - "id": "stock plate on P2", - "parent": "deck", - "slot_on_deck": "P2", - "class_name": "nest_12_reservoir_15ml", - "liquid_type": [ - "bind beads" - ], - "liquid_volume": [10000], - "liquid_input_wells": [ - "A1" - ] - }, - { - "id": "stock plate on P3", - "parent": "deck", - "slot_on_deck": "P3", - "class_name": "nest_12_reservoir_15ml", - "liquid_type": [ - "ethyl alcohol" - ], - "liquid_volume": [10000], - "liquid_input_wells": [ - "A1" - ] - }, - { - "id": "elution buffer on P4", - "parent": "deck", - "slot_on_deck": "P4", - "class_name": "nest_12_reservoir_15ml", - "liquid_type": [ - "elution buffer" - ], - "liquid_volume": [5000], - "liquid_input_wells": [ - "A1" - ] - }, - { - "id": "oscillation", - "parent": "deck", - "slot_on_deck": "Orbital1", - "class_name": "Orbital", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "working plate on P11", - "parent": "deck", - "slot_on_deck": "P11", - "class_name": "NEST 2ml Deep Well Plate", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "magnetics module on P12", - "parent": "deck", - "slot_on_deck": "P12", - "class_name": "magnetics module", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "working plate on P13", - "parent": "deck", - "slot_on_deck": "P13", - "class_name": "NEST 2ml Deep Well Plate", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - }, - { - "id": "waste on P22", - "parent": "deck", - "slot_on_deck": "P22", - "class_name": "nest_1_reservoir_195ml", - "liquid_type": [], - "liquid_volume": [], - "liquid_input_wells": [] - } - ] - ''' - # 创建Biomek液体处理器实例 + # 创建handler实例 handler = LiquidHandlerBiomek() + + # 创建协议 + protocol = handler.create_protocol( + protocol_name="DNA纯化完整流程", + protocol_description="使用磁珠进行DNA纯化的完整自动化流程", + protocol_version="1.0", + protocol_author="Biomek系统", + protocol_date="2024-01-01", + protocol_type="DNA_purification" + ) - handler.temp_protocol = { - "meta": {}, - "labwares": [], - "steps": [] - } - - input_steps = json.loads(steps_info) + print("\n=== 第一步：设置所有仪器 ===") + # 解析labware配置 labwares = json.loads(labware_with_liquid) + + # 设置所有仪器 + instrument_count = 0 + for labware in labwares: + print(f"设置仪器: {labware['id']} ({labware['class_name']}) 在位置 {labware['slot_on_deck']}") + handler.instrument_setup_biomek( + id=labware['id'], + parent=labware['parent'], + slot_on_deck=labware['slot_on_deck'], + class_name=labware['class_name'], + liquid_type=labware['liquid_type'], + liquid_volume=labware['liquid_volume'], + liquid_input_wells=labware['liquid_input_wells'] + ) + instrument_count += 1 + + print(f"总共设置了 {instrument_count} 个仪器位置") + print("\n=== 第二步：执行实验步骤 ===") + # 解析步骤信息 + input_steps = json.loads(steps_info) + + # 执行所有步骤 + step_count = 0 for step in input_steps['steps']: operation = step['operation'] parameters = step['parameters'] - + description = step['description'] + + print(f"步骤 {step['step_number']}: {description}") + if operation == 'transfer': - handler.transfer_biomek(source=parameters['source'], - target=parameters['target'], - volume=parameters['volume'], - tip_rack=parameters['tip_rack'], - aspirate_techniques='MC P300 high', - dispense_techniques='MC P300 high') + handler.transfer_biomek( + source=parameters['source'], + target=parameters['target'], + volume=parameters['volume'], + tip_rack=parameters['tip_rack'], + aspirate_techniques='MC P300 high', + dispense_techniques='MC P300 high' + ) elif operation == 'move_labware': - handler.move_biomek(source=parameters['source'], - target=parameters['target']) + handler.move_biomek( + source=parameters['source'], + target=parameters['target'] + ) elif operation == 'oscillation': - handler.oscillation_biomek(rpm=parameters['rpm'], - time=parameters['time']) + handler.oscillation_biomek( + rpm=parameters['rpm'], + time=parameters['time'] + ) elif operation == 'incubation': - handler.incubation_biomek(time=parameters['time']) - - print(json.dumps(handler.temp_protocol, indent=4)) - + handler.incubation_biomek( + time=parameters['time'] + ) + + step_count += 1 + + print(f"总共执行了 {step_count} 个步骤") + print("\n=== 第三步：保存完整协议 ===") + # 获取脚本目录 + script_dir = pathlib.Path(__file__).parent + + # 保存完整协议 + complete_output_path = script_dir / "complete_biomek_protocol_0608.json" + with open(complete_output_path, 'w', encoding='utf-8') as f: + json.dump(handler.temp_protocol, f, indent=4, ensure_ascii=False) + + print(f"完整协议已保存到: {complete_output_path}") + + print("\n=== 测试完成 ===") + print("完整的DNA纯化流程已成功转换为Biomek格式！") diff --git a/unilabos/devices/liquid_handling/biomek_test.py b/unilabos/devices/liquid_handling/biomek_test.py index e3865983..1e56f18e 100644 --- a/unilabos/devices/liquid_handling/biomek_test.py +++ b/unilabos/devices/liquid_handling/biomek_test.py @@ -468,7 +468,7 @@ class LiquidHandlerBiomek: if __name__ == "__main__": - + print("=== Biomek完整流程测试 ===") print("包含: 仪器设置 + 完整实验步骤")