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fix biomek startup

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add action handles
This commit is contained in:
Xuwznln
2025-06-06 17:45:54 +08:00
parent 55be5e8188
commit 48c43d3303
2 changed files with 257 additions and 234 deletions
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459
unilabos/devices/liquid_handling/biomek.py
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@@ -23,8 +23,8 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
该类用于处理Biomek液体处理器的特定操作。 该类用于处理Biomek液体处理器的特定操作。
""" """
def __init__(self, *args, **kwargs): def __init__(self, backend=None, deck=None, *args, **kwargs):
super().__init__(*args, **kwargs) super().__init__(backend, deck, *args, **kwargs)
self._status = "Idle" # 初始状态为 Idle self._status = "Idle" # 初始状态为 Idle
self._success = False # 初始成功状态为 False self._success = False # 初始成功状态为 False
self._status_queue = kwargs.get("status_queue", None) # 状态队列 self._status_queue = kwargs.get("status_queue", None) # 状态队列
@@ -421,7 +421,6 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
if __name__ == "__main__": if __name__ == "__main__":
steps_info = ''' steps_info = '''
{ {
"steps": [ "steps": [
@@ -684,33 +683,20 @@ if __name__ == "__main__":
] ]
} }
''' '''
labware_with_liquid = '''
[ {
"id": "stock plate on P1",
labware_with_liquid = ''' "parent": "deck",
[ { "slot_on_deck": "P1",
"id": "stock plate on P1", "class_name": "nest_12_reservoir_15ml",
"parent": "deck", "liquid_type": [
"slot_on_deck": "P1", "master_mix"
"class_name": "nest_12_reservoir_15ml", ],
"liquid_type": [ "liquid_volume": [10000],
"master_mix" "liquid_input_wells": [
], "A1"
"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 TL2", "id": "Tip Rack BC230 TL2",
"parent": "deck", "parent": "deck",
@@ -722,215 +708,222 @@ labware_with_liquid = '''
] ]
}, },
{ {
"id": "Tip Rack BC230 on TL3", "id": "Tip Rack BC230 TL2",
"parent": "deck", "parent": "deck",
"slot_on_deck": "TL3", "slot_on_deck": "TL2",
"class_name": "BC230", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "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": [
]
},
{
"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", "id": "Tip Rack BC230 on TL3",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P5", "slot_on_deck": "TL3",
"class_name": "BC230", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "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": [
]
},
{
"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 P6", "id": "Tip Rack BC230 on P5",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P6", "slot_on_deck": "P5",
"class_name": "BC230", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "liquid_volume": [],
"liquid_input_wells": [ "liquid_input_wells": [
] ]
}, },
{ {
"id": "Tip Rack BC230 on P7", "id": "Tip Rack BC230 on P6",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P7", "slot_on_deck": "P6",
"class_name": "BC230", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "liquid_volume": [],
"liquid_input_wells": [ "liquid_input_wells": [
] ]
}, },
{ {
"id": "Tip Rack BC230 on P8", "id": "Tip Rack BC230 on P7",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P8", "slot_on_deck": "P7",
"class_name": "BC230", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "liquid_volume": [],
"liquid_input_wells": [ "liquid_input_wells": [
] ]
}, },
{ {
"id": "Tip Rack BC230 P16", "id": "Tip Rack BC230 on P8",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P16", "slot_on_deck": "P8",
"class_name": "BC230", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "liquid_volume": [],
"liquid_input_wells": [ "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", "id": "Tip Rack BC230 P16",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P12", "slot_on_deck": "P16",
"class_name": "magnetics module", "class_name": "BC230",
"liquid_type": [], "liquid_type": [],
"liquid_volume": [], "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_volume": [],
"liquid_input_wells": [
]
},
{ {
"id": "waste on P22", "id": "stock plate on 4",
"parent": "deck", "parent": "deck",
"slot_on_deck": "P22", "slot_on_deck": "P2",
"class_name": "nest_1_reservoir_195ml", "class_name": "nest_12_reservoir_15ml",
"liquid_type": [ "liquid_type": [
], "bind beads"
"liquid_volume": [], ],
"liquid_input_wells": [ "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",
handler = LiquidHandlerBiomek() "class_name": "Orbital",
"liquid_type": [],
handler.temp_protocol = { "liquid_volume": [],
"meta": {}, "liquid_input_wells": [
"labwares": [], ]
"steps": [] },
} {
"id": "working plate on P11",
input_steps = json.loads(steps_info) "parent": "deck",
labwares = json.loads(labware_with_liquid) "slot_on_deck": "P11",
"class_name": "NEST 2ml Deep Well Plate",
for step in input_steps['steps']: "liquid_type": [
operation = step['operation'] ],
parameters = step['parameters'] "liquid_volume": [],
"liquid_input_wells": [
if operation == 'transfer': ]
handler.transfer_biomek(source=parameters['source'], },
target=parameters['target'], {
volume=parameters['volume'], "id": "magnetics module on P12",
tip_rack=parameters['tip_rack'], "parent": "deck",
aspirate_techniques='MC P300 high', "slot_on_deck": "P12",
dispense_techniques='MC P300 high') "class_name": "magnetics module",
elif operation == 'move_labware': "liquid_type": [],
handler.move_biomek(source=parameters['source'], "liquid_volume": [],
target=parameters['target']) "liquid_input_wells": [
elif operation == 'oscillation': ]
handler.oscillation_biomek(rpm=parameters['rpm'], },
time=parameters['time']) {
elif operation == 'incubation': "id": "working plate on P13",
handler.incubation_biomek(time=parameters['time']) "parent": "deck",
"slot_on_deck": "P13",
print(json.dumps(handler.temp_protocol, indent=4)) "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))

30
unilabos/registry/devices/liquid_handler.yaml
View File

@@ -340,6 +340,21 @@ liquid_handler.biomek:
none_keys: none_keys none_keys: none_keys
feedback: {} feedback: {}
result: {} result: {}
handles:
input:
- handler_key: liquid-input
label: Liquid Input
data_type: resource
io_type: target
data_source: handle
data_key: liquid
output:
- handler_key: liquid-output
label: Liquid Output
data_type: resource
io_type: source
data_source: executor
data_key: liquid
transfer_biomek: transfer_biomek:
type: LiquidHandlerTransferBiomek type: LiquidHandlerTransferBiomek
goal: goal:
@@ -351,6 +366,21 @@ liquid_handler.biomek:
dispense_techniques: dispense_techniques dispense_techniques: dispense_techniques
feedback: {} feedback: {}
result: {} result: {}
handles:
input:
- handler_key: liquid-input
label: Liquid Input
data_type: resource
io_type: target
data_source: handle
data_key: liquid
output:
- handler_key: liquid-output
label: Liquid Output
data_type: resource
io_type: source
data_source: executor
data_key: liquid
schema: schema:
type: object type: object
properties: {} properties: {}