diff --git a/unilabos/devices/liquid_handling/biomek_test.py b/unilabos/devices/liquid_handling/biomek_test.py index 25e669d0..e3865983 100644 --- a/unilabos/devices/liquid_handling/biomek_test.py +++ b/unilabos/devices/liquid_handling/biomek_test.py @@ -473,7 +473,8 @@ if __name__ == "__main__": 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_info = ''' + { "steps": [ { "step_number": 1, @@ -737,12 +738,14 @@ if __name__ == "__main__": "target": "P14", "tip_rack": "BC230", "volume": 40 - } + } + } + ] } - ] -} +''' # 完整的labware配置信息 - labware_with_liquid = [ + labware_with_liquid = ''' + [ { "id": "Tip Rack BC230 TL1", "parent": "deck", @@ -914,7 +917,8 @@ if __name__ == "__main__": "liquid_volume": [], "liquid_input_wells": [] } -] + ] + ''' # 创建handler实例 handler = LiquidHandlerBiomek() @@ -996,7 +1000,7 @@ if __name__ == "__main__": script_dir = pathlib.Path(__file__).parent # 保存完整协议 - complete_output_path = script_dir / "complete_biomek_protocol_0607.json" + 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) diff --git a/unilabos/devices/liquid_handling/complete_biomek_protocol_0607.json b/unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json similarity index 87% rename from unilabos/devices/liquid_handling/complete_biomek_protocol_0607.json rename to unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json index be73033c..24b3d455 100644 --- a/unilabos/devices/liquid_handling/complete_biomek_protocol_0607.json +++ b/unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json @@ -328,12 +328,12 @@ "Properties": { "Name": "stock plate on P1", "Device": "", - "liquidtype": "master_mix", + "liquidtype": "PCR product", "BarCode": "", "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\nest_12_reservoir_15ml", + "Class": "LabwareClasses\\AgilentReservoir", "DataSets": { "Volume": {} }, @@ -341,11 +341,11 @@ "Volume": {} }, "EvalAmounts": [ - 10000.0 + 5000.0 ], "Nominal": false, "EvalLiquids": [ - "master_mix" + "PCR product" ] } ], @@ -359,7 +359,7 @@ "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\nest_12_reservoir_15ml", + "Class": "LabwareClasses\\AgilentReservoir", "DataSets": { "Volume": {} }, @@ -367,7 +367,7 @@ "Volume": {} }, "EvalAmounts": [ - 10000.0 + 100000.0 ], "Nominal": false, "EvalLiquids": [ @@ -380,12 +380,12 @@ "Properties": { "Name": "stock plate on P3", "Device": "", - "liquidtype": "ethyl alcohol", + "liquidtype": "75% ethanol", "BarCode": "", "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\nest_12_reservoir_15ml", + "Class": "LabwareClasses\\AgilentReservoir", "DataSets": { "Volume": {} }, @@ -393,25 +393,25 @@ "Volume": {} }, "EvalAmounts": [ - 10000.0 + 100000.0 ], "Nominal": false, "EvalLiquids": [ - "ethyl alcohol" + "75% ethanol" ] } ], "P4": [ { "Properties": { - "Name": "elution buffer on P4", + "Name": "stock plate on P4", "Device": "", - "liquidtype": "elution buffer", + "liquidtype": "Elution Buffer", "BarCode": "", "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\nest_12_reservoir_15ml", + "Class": "LabwareClasses\\AgilentReservoir", "DataSets": { "Volume": {} }, @@ -423,11 +423,10 @@ ], "Nominal": false, "EvalLiquids": [ - "elution buffer" + "Elution Buffer" ] } ], - "Orbital1": [], "P11": [ { "Properties": { @@ -438,7 +437,7 @@ "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\NEST 2ml Deep Well Plate", + "Class": "LabwareClasses\\BCDeep96Round", "DataSets": { "Volume": {} }, @@ -446,102 +445,318 @@ "Volume": {} }, "EvalAmounts": [ - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0 + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ], + "Nominal": false, + "EvalLiquids": [ + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water" + ] + } + ], + "P12": [ + { + "Properties": { + "Name": "working plate on P12", + "Device": "", + "liquidtype": "Water", + "BarCode": "", + "SenseEveryTime": false + }, + "Known": true, + "Class": "LabwareClasses\\BCDeep96Round", + "DataSets": { + "Volume": {} + }, + "RuntimeDataSets": { + "Volume": {} + }, + "EvalAmounts": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 ], "Nominal": false, "EvalLiquids": [ @@ -644,7 +859,6 @@ ] } ], - "P12": [], "P13": [ { "Properties": { @@ -655,7 +869,7 @@ "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\NEST 2ml Deep Well Plate", + "Class": "LabwareClasses\\BCDeep96Round", "DataSets": { "Volume": {} }, @@ -663,102 +877,318 @@ "Volume": {} }, "EvalAmounts": [ - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0, - 500.0 + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 + ], + "Nominal": false, + "EvalLiquids": [ + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water", + "Water" + ] + } + ], + "P14": [ + { + "Properties": { + "Name": "working plate on P14", + "Device": "", + "liquidtype": "Water", + "BarCode": "", + "SenseEveryTime": false + }, + "Known": true, + "Class": "LabwareClasses\\BCDeep96Round", + "DataSets": { + "Volume": {} + }, + "RuntimeDataSets": { + "Volume": {} + }, + "EvalAmounts": [ + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0, + 0 ], "Nominal": false, "EvalLiquids": [ @@ -871,7 +1301,7 @@ "SenseEveryTime": false }, "Known": true, - "Class": "LabwareClasses\\nest_1_reservoir_195ml", + "Class": "LabwareClasses\\AgilentReservoir", "DataSets": { "Volume": {} }, @@ -879,14 +1309,15 @@ "Volume": {} }, "EvalAmounts": [ - 0.0 + 0 ], "Nominal": false, "EvalLiquids": [ "Water" ] } - ] + ], + "Orbital1": [] }, "steps": [ { @@ -1020,7 +1451,7 @@ "UseExpression": false }, { - "Position": "P13", + "Position": "P14", "Height": -2.0, "Volume": "40", "liquidtype": "Tip Contents", @@ -1320,7 +1751,7 @@ "UseExpression": false }, { - "Position": "P13", + "Position": "P14", "Height": -2.0, "Volume": "40", "liquidtype": "Tip Contents", @@ -1489,15 +1920,6 @@ "Wizard": false } }, - { - "move": { - "Pod": "Pod1", - "GripSide": "A1 near", - "Source": "P11", - "Target": "Orbital1", - "LeaveBottomLabware": false - } - }, { "oscillation": { "Device": "OrbitalShaker0", @@ -1510,15 +1932,6 @@ "Command": "Timed Shake" } }, - { - "move": { - "Pod": "Pod1", - "GripSide": "A1 near", - "Source": "Orbital1", - "Target": "P11", - "LeaveBottomLabware": false - } - }, { "move": { "Pod": "Pod1", @@ -1667,7 +2080,7 @@ "UseExpression": false }, { - "Position": "P13", + "Position": "P14", "Height": -2.0, "Volume": "40", "liquidtype": "Tip Contents", @@ -1967,1291 +2380,7 @@ "UseExpression": false }, { - "Position": "P13", - "Height": -2.0, - "Volume": "40", - "liquidtype": "Tip Contents", - "WellsX": 12, - "LabwareClass": "Matrix96_750uL", - "AutoSelectPrototype": true, - "ColsFirst": true, - "CustomHeight": false, - "DataSetPattern": false, - "HeightFrom": 0, - "LocalPattern": true, - "Operation": "Dispense", - "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 - ], - "Prototype": "MC P300 High", - "ReferencedPattern": "", - "RowsFirst": false, - "SectionExpression": "", - "SelectionInfo": [ - 1 - ], - "SetMark": true, - "Source": false, - "StartAtMark": false, - "StartAtSelection": true, - "UseExpression": false - } - ], - "Wash": false, - "Dynamic?": true, - "AutoSelectActiveWashTechnique": false, - "ActiveWashTechnique": "", - "ChangeTipsBetweenDests": true, - "ChangeTipsBetweenSources": false, - "DefaultCaption": "", - "UseExpression": false, - "LeaveTipsOn": false, - "MandrelExpression": "", - "Repeats": "1", - "RepeatsByVolume": false, - "Replicates": "1", - "ShowTipHandlingDetails": false, - "ShowTransferDetails": true, - "Solvent": "Water", - "Span8Wash": false, - "Span8WashVolume": "2", - "Span8WasteVolume": "1", - "SplitVolume": false, - "SplitVolumeCleaning": false, - "Stop": "Destinations", - "TipLocation": "BC230", - "UseCurrentTips": false, - "UseDisposableTips": false, - "UseFixedTips": false, - "UseJIT": true, - "UseMandrelSelection": true, - "UseProbes": [ - true, - true, - true, - true, - true, - true, - true, - true - ], - "WashCycles": "4", - "WashVolume": "110%", - "Wizard": false - } - }, - { - "move": { - "Pod": "Pod1", - "GripSide": "A1 near", - "Source": "P12", - "Target": "Orbital1", - "LeaveBottomLabware": false - } - }, - { - "oscillation": { - "Device": "OrbitalShaker0", - "Parameters": [ - "800", - "2", - "45", - "CounterClockwise" - ], - "Command": "Timed Shake" - } - }, - { - "move": { - "Pod": "Pod1", - "GripSide": "A1 near", - "Source": "Orbital1", - "Target": "P12", - "LeaveBottomLabware": false - } - }, - { - "incubation": { - "Message": "Paused", - "Location": "the whole system", - "Time": 180, - "Mode": "TimedResource" - } - }, - { - "transfer": { - "Span8": false, - "Pod": "Pod1", - "items": [ - { - "Position": "P12", - "Height": -2.0, - "Volume": "40", - "liquidtype": "Well Contents", - "WellsX": 12, - "LabwareClass": "Matrix96_750uL", - "AutoSelectPrototype": true, - "ColsFirst": true, - "CustomHeight": false, - "DataSetPattern": false, - "HeightFrom": 0, - "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 - ], - "Prototype": "MC P300 High", - "ReferencedPattern": "", - "RowsFirst": false, - "SectionExpression": "", - "SelectionInfo": [ - 1 - ], - "SetMark": true, - "Source": true, - "StartAtMark": false, - "StartAtSelection": true, - "UseExpression": false - }, - { - "Position": "P13", - "Height": -2.0, - "Volume": "40", - "liquidtype": "Tip Contents", - "WellsX": 12, - "LabwareClass": "Matrix96_750uL", - "AutoSelectPrototype": true, - "ColsFirst": true, - "CustomHeight": false, - "DataSetPattern": false, - "HeightFrom": 0, - "LocalPattern": true, - "Operation": "Dispense", - "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 - ], - "Prototype": "MC P300 High", - "ReferencedPattern": "", - "RowsFirst": false, - "SectionExpression": "", - "SelectionInfo": [ - 1 - ], - "SetMark": true, - "Source": false, - "StartAtMark": false, - "StartAtSelection": true, - "UseExpression": false - } - ], - "Wash": false, - "Dynamic?": true, - "AutoSelectActiveWashTechnique": false, - "ActiveWashTechnique": "", - "ChangeTipsBetweenDests": true, - "ChangeTipsBetweenSources": false, - "DefaultCaption": "", - "UseExpression": false, - "LeaveTipsOn": false, - "MandrelExpression": "", - 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