From 3f4d247127d1a576094cd6ee1d57c95cb1139bf0 Mon Sep 17 00:00:00 2001 From: Guangxin Zhang Date: Sun, 8 Jun 2025 20:29:39 +0800 Subject: [PATCH] Refine biomek --- unilabos/devices/liquid_handling/biomek.py | 4 +- .../devices/liquid_handling/biomek_test.py | 9 +- .../complete_biomek_protocol.json | 3760 ----------------- .../complete_biomek_protocol_0608.json | 54 +- 4 files changed, 36 insertions(+), 3791 deletions(-) delete mode 100644 unilabos/devices/liquid_handling/complete_biomek_protocol.json diff --git a/unilabos/devices/liquid_handling/biomek.py b/unilabos/devices/liquid_handling/biomek.py index 2e9b7b1..d2ed340 100644 --- a/unilabos/devices/liquid_handling/biomek.py +++ b/unilabos/devices/liquid_handling/biomek.py @@ -9,7 +9,7 @@ from pylabrobot.resources import ( Container, Coordinate, ) - +import copy from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore from .liquid_handler_abstract import LiquidHandlerAbstract @@ -570,7 +570,7 @@ 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") diff --git a/unilabos/devices/liquid_handling/biomek_test.py b/unilabos/devices/liquid_handling/biomek_test.py index 1e56f18..4aa21dd 100644 --- a/unilabos/devices/liquid_handling/biomek_test.py +++ b/unilabos/devices/liquid_handling/biomek_test.py @@ -15,6 +15,7 @@ from typing import List, Sequence, Optional, Union, Literal import json import pathlib from typing import Sequence, Optional, List, Union, Literal +import copy @@ -351,8 +352,9 @@ class LiquidHandlerBiomek: """ items = [] - asp_params = self.aspirate_techniques.get(aspirate_techniques, {}) - dis_params = self.dispense_techniques.get(dispense_techniques, {}) + asp_params = copy.deepcopy(self.aspirate_techniques[aspirate_techniques]) + dis_params = copy.deepcopy(self.dispense_techniques[dispense_techniques]) + asp_params['Position'] = source dis_params['Position'] = target @@ -403,7 +405,9 @@ class LiquidHandlerBiomek: transfer_params["Solvent"] = 'Water' transfer_params["TipLocation"] = tip_rack tmp={'transfer': transfer_params} + self.temp_protocol["steps"].append(tmp) + return @@ -968,6 +972,7 @@ if __name__ == "__main__": print(f"步骤 {step['step_number']}: {description}") if operation == 'transfer': + handler.transfer_biomek( source=parameters['source'], target=parameters['target'], diff --git a/unilabos/devices/liquid_handling/complete_biomek_protocol.json b/unilabos/devices/liquid_handling/complete_biomek_protocol.json deleted file mode 100644 index 2c0e95f..0000000 --- a/unilabos/devices/liquid_handling/complete_biomek_protocol.json +++ /dev/null @@ -1,3760 +0,0 @@ -{ - "meta": { - "name": "DNA纯化完整流程", - "description": "使用磁珠进行DNA纯化的完整自动化流程", - "version": "1.0", - "author": "Biomek系统", - "date": "2024-01-01", - "type": "DNA_purification" - }, - "labwares": [ - { - "Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "RT_Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "Properties": {}, - "Known": false, - "Class": "LabwareClasses\\BC230", - "DataSets": { - "Volume": {} - }, - "RuntimeDataSets": { - "Volume": {} - }, - "Name": "Tip Rack BC230 on TL1", - "Position": "TL1" - }, - { - "Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "RT_Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "Properties": {}, - "Known": false, - "Class": "LabwareClasses\\BC230", - "DataSets": { - "Volume": {} - }, - "RuntimeDataSets": { - "Volume": {} - }, - "Name": "Tip Rack BC230 on TL2", - "Position": "TL2" - }, - { - "Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "RT_Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "Properties": {}, - "Known": false, - "Class": "LabwareClasses\\BC230", - "DataSets": { - "Volume": {} - }, - "RuntimeDataSets": { - "Volume": {} - }, - "Name": "Tip Rack BC230 on TL3", - "Position": "TL3" - }, - { - "Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "RT_Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "Properties": {}, - "Known": false, - "Class": "LabwareClasses\\BC230", - "DataSets": { - "Volume": {} - }, - "RuntimeDataSets": { - "Volume": {} - }, - "Name": "Tip Rack BC230 on TL4", - "Position": "TL4" - }, - { - "Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "RT_Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "Properties": {}, - "Known": false, - "Class": "LabwareClasses\\BC230", - "DataSets": { - "Volume": {} - }, - "RuntimeDataSets": { - "Volume": {} - }, - "Name": "Tip Rack BC230 on TL5", - "Position": "TL5" - }, - { - "Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "RT_Tips": { - "Class": "TipClasses\\T230", - "Contents": [], - "_RT_Contents": [], - "Used": false, - "RT_Used": false, - "Dirty": false, - "RT_Dirty": false, - "MaxVolumeUsed": 0.0, - "RT_MaxVolumeUsed": 0.0 - }, - "Properties": {}, - "Known": false, - "Class": "LabwareClasses\\BC230", - "DataSets": { - "Volume": {} - }, - "RuntimeDataSets": { - "Volume": {} - }, - 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true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - true, - 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 - } - } - ] -} \ No newline at end of file diff --git a/unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json b/unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json index 24b3d45..93d0d8a 100644 --- a/unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json +++ b/unilabos/devices/liquid_handling/complete_biomek_protocol_0608.json @@ -1326,9 +1326,9 @@ "Pod": "Pod1", "items": [ { - "Position": "P12", + "Position": "P1", "Height": -2.0, - "Volume": "40", + "Volume": "50", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -1451,9 +1451,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P11", "Height": -2.0, - "Volume": "40", + "Volume": "50", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -1626,9 +1626,9 @@ "Pod": "Pod1", "items": [ { - "Position": "P12", + "Position": "P2", "Height": -2.0, - "Volume": "40", + "Volume": "100", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -1751,9 +1751,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P11", "Height": -2.0, - "Volume": "40", + "Volume": "100", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -1957,7 +1957,7 @@ { "Position": "P12", "Height": -2.0, - "Volume": "40", + "Volume": "150", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -2080,9 +2080,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P22", "Height": -2.0, - "Volume": "40", + "Volume": "150", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -2255,9 +2255,9 @@ "Pod": "Pod1", "items": [ { - "Position": "P12", + "Position": "P3", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -2380,9 +2380,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P12", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -2595,7 +2595,7 @@ { "Position": "P12", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -2718,9 +2718,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P22", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -2893,9 +2893,9 @@ "Pod": "Pod1", "items": [ { - "Position": "P12", + "Position": "P3", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -3018,9 +3018,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P12", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -3233,7 +3233,7 @@ { "Position": "P12", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Well Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -3356,9 +3356,9 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P22", "Height": -2.0, - "Volume": "40", + "Volume": "400", "liquidtype": "Tip Contents", "WellsX": 12, "LabwareClass": "Matrix96_750uL", @@ -3548,7 +3548,7 @@ "Pod": "Pod1", "items": [ { - "Position": "P12", + "Position": "P4", "Height": -2.0, "Volume": "40", "liquidtype": "Well Contents", @@ -3673,7 +3673,7 @@ "UseExpression": false }, { - "Position": "P14", + "Position": "P13", "Height": -2.0, "Volume": "40", "liquidtype": "Tip Contents",