mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2025-12-17 21:11:12 +00:00
Merge branch '37-biomek-i5i7' of https://github.com/dptech-corp/Uni-Lab-OS into 37-biomek-i5i7
This commit is contained in:
Junhan Chang
@@ -692,8 +692,93 @@ if __name__ == "__main__":
|
||||
]
|
||||
}
|
||||
'''
|
||||
labware_with_liquid = '''
|
||||
[ {
|
||||
|
||||
|
||||
|
||||
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",
|
||||
@@ -707,232 +792,125 @@ if __name__ == "__main__":
|
||||
]
|
||||
},
|
||||
{
|
||||
"id": "Tip Rack BC230 TL2",
|
||||
"id": "stock plate on P2",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "TL2",
|
||||
"class_name": "BC230",
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"slot_on_deck": "P2",
|
||||
"class_name": "nest_12_reservoir_15ml",
|
||||
"liquid_type": [
|
||||
"bind beads"
|
||||
],
|
||||
"liquid_volume": [10000],
|
||||
"liquid_input_wells": [
|
||||
"A1"
|
||||
]
|
||||
},
|
||||
{
|
||||
"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 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 P7",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P7",
|
||||
"class_name": "BC230",
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
},
|
||||
{
|
||||
"id": "Tip Rack BC230 on P8",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P8",
|
||||
"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 4",
|
||||
"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 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": "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": [
|
||||
]
|
||||
}
|
||||
]
|
||||
|
||||
'''
|
||||
handler = LiquidHandlerBiomek()
|
||||
|
||||
handler.temp_protocol = {
|
||||
"meta": {},
|
||||
"labwares": [],
|
||||
"steps": []
|
||||
}
|
||||
|
||||
input_steps = json.loads(steps_info)
|
||||
labwares = json.loads(labware_with_liquid)
|
||||
|
||||
for step in input_steps['steps']:
|
||||
operation = step['operation']
|
||||
parameters = step['parameters']
|
||||
|
||||
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')
|
||||
elif operation == 'move_labware':
|
||||
handler.move_biomek(source=parameters['source'],
|
||||
target=parameters['target'])
|
||||
elif operation == 'oscillation':
|
||||
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))
|
||||
{
|
||||
"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": []
|
||||
}
|
||||
]
|
||||
'''
|
||||
|
||||
|
||||
|
||||
handler = LiquidHandlerBiomek()
|
||||
|
||||
handler.temp_protocol = {
|
||||
"meta": {},
|
||||
"labwares": [],
|
||||
"steps": []
|
||||
}
|
||||
|
||||
input_steps = json.loads(steps_info)
|
||||
labwares = json.loads(labware_with_liquid)
|
||||
|
||||
for step in input_steps['steps']:
|
||||
operation = step['operation']
|
||||
parameters = step['parameters']
|
||||
|
||||
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')
|
||||
elif operation == 'move_labware':
|
||||
handler.move_biomek(source=parameters['source'],
|
||||
target=parameters['target'])
|
||||
elif operation == 'oscillation':
|
||||
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))
|
||||
|
||||
|
||||
|
||||
@@ -13,6 +13,7 @@ from typing import List, Sequence, Optional, Union, Literal
|
||||
# from .liquid_handler_abstract import LiquidHandlerAbstract
|
||||
|
||||
import json
|
||||
import pathlib
|
||||
from typing import Sequence, Optional, List, Union, Literal
|
||||
|
||||
|
||||
@@ -33,6 +34,23 @@ class LiquidHandlerBiomek:
|
||||
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',
|
||||
@@ -49,7 +67,7 @@ class LiquidHandlerBiomek:
|
||||
'LocalPattern': True,
|
||||
'Operation': 'Aspirate',
|
||||
'OverrideHeight': False,
|
||||
'Pattern': (True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True),
|
||||
'Pattern': (True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True, True),
|
||||
'Prototype': 'MC P300 High',
|
||||
'ReferencedPattern': '',
|
||||
'RowsFirst': False,
|
||||
@@ -92,6 +110,30 @@ class LiquidHandlerBiomek:
|
||||
}
|
||||
|
||||
|
||||
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"
|
||||
|
||||
def create_protocol(
|
||||
self,
|
||||
protocol_name: str,
|
||||
@@ -126,7 +168,7 @@ class LiquidHandlerBiomek:
|
||||
"date": protocol_date,
|
||||
"type": protocol_type,
|
||||
},
|
||||
"labwares": [],
|
||||
"labwares": {}, # 改为字典格式以匹配DeckItems
|
||||
"steps": [],
|
||||
}
|
||||
return self.temp_protocol
|
||||
@@ -198,7 +240,101 @@ class LiquidHandlerBiomek:
|
||||
# }
|
||||
# self.temp_protocol["labwares"].append(resource)
|
||||
# return resource
|
||||
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 (0.0,),
|
||||
"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 500.0
|
||||
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,
|
||||
@@ -266,7 +402,8 @@ class LiquidHandlerBiomek:
|
||||
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
|
||||
|
||||
@@ -287,7 +424,8 @@ class LiquidHandlerBiomek:
|
||||
"Target": target,
|
||||
"LeaveBottomLabware": False,
|
||||
}
|
||||
self.temp_protocol["steps"].append(move_params)
|
||||
tmp={'move': move_params}
|
||||
self.temp_protocol["steps"].append(tmp)
|
||||
|
||||
return
|
||||
|
||||
@@ -304,7 +442,8 @@ class LiquidHandlerBiomek:
|
||||
"Time": time,
|
||||
"Mode": "TimedResource"
|
||||
}
|
||||
self.temp_protocol["steps"].append(incubation_params)
|
||||
tmp={'incubation': incubation_params}
|
||||
self.temp_protocol["steps"].append(tmp)
|
||||
|
||||
return
|
||||
|
||||
@@ -321,7 +460,8 @@ class LiquidHandlerBiomek:
|
||||
'Parameters': (str(rpm), '2', str(time), 'CounterClockwise'),
|
||||
'Command': 'Timed Shake'
|
||||
}
|
||||
self.temp_protocol["steps"].append(oscillation_params)
|
||||
tmp={'oscillation': oscillation_params}
|
||||
self.temp_protocol["steps"].append(tmp)
|
||||
|
||||
return
|
||||
|
||||
@@ -329,6 +469,10 @@ 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")
|
||||
|
||||
# 完整的步骤信息（从biomek.py复制）
|
||||
steps_info = '''
|
||||
{
|
||||
"steps": [
|
||||
@@ -592,136 +736,104 @@ if __name__ == "__main__":
|
||||
}
|
||||
'''
|
||||
|
||||
|
||||
|
||||
labware_with_liquid = '''
|
||||
[ {
|
||||
"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": "Tip Rack BC230 TL2",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "TL2",
|
||||
"class_name": "BC230",
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
},
|
||||
# 完整的labware配置信息（从biomek.py复制）
|
||||
labware_with_liquid = '''
|
||||
[
|
||||
{
|
||||
"id": "Tip Rack BC230 TL2",
|
||||
"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": [
|
||||
]
|
||||
"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": [
|
||||
]
|
||||
"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": [
|
||||
]
|
||||
"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": [
|
||||
]
|
||||
"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": [
|
||||
]
|
||||
"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 P7",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P7",
|
||||
"class_name": "BC230",
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
},
|
||||
{
|
||||
"id": "Tip Rack BC230 on P8",
|
||||
"id": "Tip Rack BC230 on P15",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P8",
|
||||
"slot_on_deck": "P15",
|
||||
"class_name": "BC230",
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
},
|
||||
{
|
||||
"id": "Tip Rack BC230 P16",
|
||||
{
|
||||
"id": "Tip Rack BC230 on P16",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P16",
|
||||
"class_name": "BC230",
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
},
|
||||
{
|
||||
"id": "stock plate on 4",
|
||||
"id": "stock plate on P1",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P2",
|
||||
"slot_on_deck": "P1",
|
||||
"class_name": "nest_12_reservoir_15ml",
|
||||
"liquid_type": [
|
||||
"bind beads"
|
||||
"master_mix"
|
||||
],
|
||||
"liquid_volume": [10000],
|
||||
"liquid_input_wells": [
|
||||
"A1"
|
||||
]
|
||||
},
|
||||
{
|
||||
{
|
||||
"id": "stock plate on P2",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P2",
|
||||
@@ -734,7 +846,7 @@ labware_with_liquid = '''
|
||||
"A1"
|
||||
]
|
||||
},
|
||||
{
|
||||
{
|
||||
"id": "stock plate on P3",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P3",
|
||||
@@ -747,95 +859,152 @@ labware_with_liquid = '''
|
||||
"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": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
},
|
||||
{
|
||||
{
|
||||
"id": "working plate on P11",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P11",
|
||||
"class_name": "NEST 2ml Deep Well Plate",
|
||||
"liquid_type": [
|
||||
],
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
"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": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
},
|
||||
{
|
||||
{
|
||||
"id": "working plate on P13",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P13",
|
||||
"class_name": "NEST 2ml Deep Well Plate",
|
||||
"liquid_type": [
|
||||
],
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
},
|
||||
{
|
||||
{
|
||||
"id": "waste on P22",
|
||||
"parent": "deck",
|
||||
"slot_on_deck": "P22",
|
||||
"class_name": "nest_1_reservoir_195ml",
|
||||
"liquid_type": [
|
||||
],
|
||||
"liquid_type": [],
|
||||
"liquid_volume": [],
|
||||
"liquid_input_wells": [
|
||||
]
|
||||
"liquid_input_wells": []
|
||||
}
|
||||
]
|
||||
|
||||
'''
|
||||
|
||||
# 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 = LiquidHandlerBiomek()
|
||||
print("\n=== 第一步：设置所有仪器 ===")
|
||||
# 解析labware配置
|
||||
labwares = json.loads(labware_with_liquid)
|
||||
|
||||
handler.temp_protocol = {
|
||||
"meta": {},
|
||||
"labwares": [],
|
||||
"steps": []
|
||||
}
|
||||
# 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
|
||||
|
||||
input_steps = json.loads(steps_info)
|
||||
labwares = json.loads(labware_with_liquid)
|
||||
print(f"总共设置了 {instrument_count} 个仪器位置")
|
||||
|
||||
for step in input_steps['steps']:
|
||||
operation = step['operation']
|
||||
parameters = step['parameters']
|
||||
print("\n=== 第二步：执行实验步骤 ===")
|
||||
# 解析步骤信息
|
||||
input_steps = json.loads(steps_info)
|
||||
|
||||
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')
|
||||
elif operation == 'move_labware':
|
||||
handler.move_biomek(source=parameters['source'],
|
||||
target=parameters['target'])
|
||||
elif operation == 'oscillation':
|
||||
handler.oscillation_biomek(rpm=parameters['rpm'],
|
||||
time=parameters['time'])
|
||||
elif operation == 'incubation':
|
||||
handler.incubation_biomek(time=parameters['time'])
|
||||
# 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(json.dumps(handler.temp_protocol, indent=4))
|
||||
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'
|
||||
)
|
||||
elif operation == 'move_labware':
|
||||
handler.move_biomek(
|
||||
source=parameters['source'],
|
||||
target=parameters['target']
|
||||
)
|
||||
elif operation == 'oscillation':
|
||||
handler.oscillation_biomek(
|
||||
rpm=parameters['rpm'],
|
||||
time=parameters['time']
|
||||
)
|
||||
elif operation == 'incubation':
|
||||
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_0607.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！")
|
||||
|
||||
3760
unilabos/devices/liquid_handling/complete_biomek_protocol.json
Normal file
3760
unilabos/devices/liquid_handling/complete_biomek_protocol.json
Normal file
File diff suppressed because it is too large
Load Diff
3762
unilabos/devices/liquid_handling/complete_biomek_protocol_0607.json
Normal file
3762
unilabos/devices/liquid_handling/complete_biomek_protocol_0607.json
Normal file
File diff suppressed because it is too large
Load Diff
Reference in New Issue
Block a user