mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
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New parameter for biomek to run.
This commit is contained in:
Guangxin Zhang
@@ -285,20 +285,29 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
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处理Biomek的液体转移操作。
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"""
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items = []
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asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
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dis_params = self.dispense_techniques.get(dispense_techniques, {})
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asp_params['Position'] = source
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dis_params['Position'] = target
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asp_params['Volume'] = str(volume)
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dis_params['Volume'] = str(volume)
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items.append(asp_params)
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items.append(dis_params)
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transfer_params = {
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"Span8": False,
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"Pod": "Pod1",
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"items": {},
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"items": [],
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"Wash": False,
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"Dynamic?": True,
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"AutoSelectActiveWashTechnique": False,
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"ActiveWashTechnique": "",
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"ChangeTipsBetweenDests": False,
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"ChangeTipsBetweenSources": True,
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"ChangeTipsBetweenDests": True,
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"ChangeTipsBetweenSources": False,
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"DefaultCaption": "",
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"UseExpression": False,
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"LeaveTipsOn": False,
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@@ -315,31 +324,25 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
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"SplitVolume": False,
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"SplitVolumeCleaning": False,
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"Stop": "Destinations",
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"TipLocation": "BC1025F",
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"TipLocation": "BC230",
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"UseCurrentTips": False,
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"UseDisposableTips": True,
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"UseDisposableTips": False,
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"UseFixedTips": False,
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"UseJIT": True,
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"UseMandrelSelection": True,
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"UseProbes": [True, True, True, True, True, True, True, True],
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"WashCycles": "1",
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"WashCycles": "4",
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"WashVolume": "110%",
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"Wizard": False
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}
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items: dict = {}
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items["Source"] = source
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items["Destination"] = target
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items["Volume"] = volume
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transfer_params["items"] = items
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transfer_params["Solvent"] = asp_params['Solvent']
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transfer_params["Solvent"] = 'Water'
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transfer_params["TipLocation"] = tip_rack
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transfer_params.update(asp_params)
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transfer_params.update(dis_params)
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self.temp_protocol["steps"].append(transfer_params)
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return
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steps_info = '''
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{
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"steps": [
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@@ -604,6 +607,7 @@ steps_info = '''
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'''
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labware_with_liquid = '''
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[ {
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"id": "stock plate on P1",
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@@ -806,6 +810,7 @@ labware_with_liquid = '''
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'''
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handler = LiquidHandlerBiomek()
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handler.temp_protocol = {
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"meta": {},
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"labwares": [],
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@@ -819,16 +824,13 @@ for step in input_steps['steps']:
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if step['operation'] != 'transfer':
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continue
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parameters = step['parameters']
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tip_rack=parameters['tip_rack']
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# 找到labwares中与tip_rack匹配的项的id
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tip_rack_id = [lw['id'] for lw in labwares if lw['class_name'] == tip_rack][0]
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handler.transfer_biomek(source=parameters['source'],
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target=parameters['target'],
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volume=parameters['volume'],
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tip_rack=tip_rack_id,
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tip_rack=parameters['tip_rack'],
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aspirate_techniques='MC P300 high',
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dispense_techniques='MC P300 high'
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)
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print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))
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642
unilabos/devices/liquid_handling/biomek.txt
Normal file
642
unilabos/devices/liquid_handling/biomek.txt
Normal file
File diff suppressed because one or more lines are too long
2697
unilabos/devices/liquid_handling/biomek_temporary_protocol.json
Normal file
2697
unilabos/devices/liquid_handling/biomek_temporary_protocol.json
Normal file
File diff suppressed because it is too large
Load Diff
@@ -15,6 +15,262 @@ from pylabrobot.resources import (
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import json
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from typing import Sequence, Optional, List, Union, Literal
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#class LiquidHandlerBiomek(LiquidHandlerAbstract):
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class LiquidHandlerBiomek:
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"""
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Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
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该类用于处理Biomek液体处理器的特定操作。
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"""
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def __init__(self, *args, **kwargs):
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super().__init__(*args, **kwargs)
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self._status = "Idle" # 初始状态为 Idle
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self._success = False # 初始成功状态为 False
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self._status_queue = kwargs.get("status_queue", None) # 状态队列
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self.temp_protocol = {}
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self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
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self.aspirate_techniques = {
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'MC P300 high':{
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'Position': 'P1',
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'Height': -2.0,
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'Volume': '50',
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'liquidtype': 'Well Contents',
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'WellsX': 12,
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'LabwareClass': 'Matrix96_750uL',
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'AutoSelectPrototype': True,
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'ColsFirst': True,
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'CustomHeight': False,
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'DataSetPattern': False,
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'HeightFrom': 0,
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'LocalPattern': True,
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'Operation': 'Aspirate',
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'OverrideHeight': False,
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'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),
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'Prototype': 'MC P300 High',
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'ReferencedPattern': '',
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'RowsFirst': False,
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'SectionExpression': '',
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'SelectionInfo': (1,),
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'SetMark': True,
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'Source': True,
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'StartAtMark': False,
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'StartAtSelection': True,
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'UseExpression': False},
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}
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self.dispense_techniques = {
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'MC P300 high':{
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'Position': 'P11',
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'Height': -2.0,
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'Volume': '50',
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'liquidtype': 'Tip Contents',
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'WellsX': 12,
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'LabwareClass': 'Matrix96_750uL',
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'AutoSelectPrototype': True,
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'ColsFirst': True,
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'CustomHeight': False,
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'DataSetPattern': False,
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'HeightFrom': 0,
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'LocalPattern': True,
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'Operation': 'Dispense',
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'OverrideHeight': False,
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'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),
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'Prototype': 'MC P300 High',
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'ReferencedPattern': '',
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'RowsFirst': False,
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'SectionExpression': '',
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'SelectionInfo': (1,),
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'SetMark': True,
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'Source': False,
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'StartAtMark': False,
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'StartAtSelection': True,
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'UseExpression': False}
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}
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def create_protocol(
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self,
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protocol_name: str,
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protocol_description: str,
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protocol_version: str,
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protocol_author: str,
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protocol_date: str,
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protocol_type: str,
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none_keys: List[str] = [],
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):
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"""
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创建一个新的协议。
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Args:
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protocol_name (str): 协议名称
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protocol_description (str): 协议描述
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protocol_version (str): 协议版本
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protocol_author (str): 协议作者
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protocol_date (str): 协议日期
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protocol_type (str): 协议类型
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none_keys (List[str]): 需要设置为None的键列表
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Returns:
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dict: 创建的协议字典
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"""
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self.temp_protocol = {
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"meta": {
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"name": protocol_name,
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"description": protocol_description,
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"version": protocol_version,
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"author": protocol_author,
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"date": protocol_date,
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"type": protocol_type,
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},
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"labwares": [],
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"steps": [],
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}
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return self.temp_protocol
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# def run_protocol(self):
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# """
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# 执行创建的实验流程。
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# 工作站的完整执行流程是，
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# 从 create_protocol 开始，创建新的 method，
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# 随后执行 transfer_liquid 等操作向实验流程添加步骤，
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# 最后 run_protocol 执行整个方法。
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# Returns:
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# dict: 执行结果
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# """
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# #use popen or subprocess to create py32 process and communicate send the temp protocol to it
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# if not self.temp_protocol:
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# raise ValueError("No protocol created. Please create a protocol first.")
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# # 模拟执行协议
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# self._status = "Running"
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# self._success = True
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# # 在这里可以添加实际执行协议的逻辑
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# response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
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# def create_resource(
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# self,
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# resource_tracker: DeviceNodeResourceTracker,
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# resources: list[Resource],
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# bind_parent_id: str,
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# bind_location: dict[str, float],
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# liquid_input_slot: list[int],
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# liquid_type: list[str],
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# liquid_volume: list[int],
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# slot_on_deck: int,
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# res_id,
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# class_name,
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# bind_locations,
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# parent
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# ):
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# """
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# 创建一个新的资源。
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# Args:
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# device_id (str): 设备ID
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# res_id (str): 资源ID
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# class_name (str): 资源类名
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# parent (str): 父级ID
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# bind_locations (Point): 绑定位置
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# liquid_input_slot (list[int]): 液体输入槽列表
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# liquid_type (list[str]): 液体类型列表
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# liquid_volume (list[int]): 液体体积列表
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# slot_on_deck (int): 甲板上的槽位
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# Returns:
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# dict: 创建的资源字典
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# """
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# # TODO：需要对好接口，下面这个是临时的
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# resource = {
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# "id": res_id,
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# "class": class_name,
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# "parent": parent,
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# "bind_locations": bind_locations.to_dict(),
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# "liquid_input_slot": liquid_input_slot,
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# "liquid_type": liquid_type,
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# "liquid_volume": liquid_volume,
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# "slot_on_deck": slot_on_deck,
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# }
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# self.temp_protocol["labwares"].append(resource)
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# return resource
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def transfer_biomek(
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self,
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source: str,
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target: str,
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tip_rack: str,
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volume: float,
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aspirate_techniques: str,
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dispense_techniques: str,
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):
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"""
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处理Biomek的液体转移操作。
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"""
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items = []
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asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
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dis_params = self.dispense_techniques.get(dispense_techniques, {})
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asp_params['Position'] = source
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dis_params['Position'] = target
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asp_params['Volume'] = str(volume)
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dis_params['Volume'] = str(volume)
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items.append(asp_params)
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items.append(dis_params)
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transfer_params = {
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"Span8": False,
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"Pod": "Pod1",
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"items": [],
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"Wash": False,
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"Dynamic?": True,
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"AutoSelectActiveWashTechnique": False,
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"ActiveWashTechnique": "",
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"ChangeTipsBetweenDests": True,
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"ChangeTipsBetweenSources": False,
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"DefaultCaption": "",
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"UseExpression": False,
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"LeaveTipsOn": False,
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"MandrelExpression": "",
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"Repeats": "1",
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"RepeatsByVolume": False,
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"Replicates": "1",
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"ShowTipHandlingDetails": False,
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"ShowTransferDetails": True,
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"Solvent": "Water",
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"Span8Wash": False,
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"Span8WashVolume": "2",
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"Span8WasteVolume": "1",
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"SplitVolume": False,
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"SplitVolumeCleaning": False,
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"Stop": "Destinations",
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"TipLocation": "BC230",
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"UseCurrentTips": False,
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"UseDisposableTips": False,
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"UseFixedTips": False,
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"UseJIT": True,
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"UseMandrelSelection": True,
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"UseProbes": [True, True, True, True, True, True, True, True],
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"WashCycles": "4",
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"WashVolume": "110%",
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"Wizard": False
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}
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transfer_params["items"] = items
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transfer_params["Solvent"] = 'Water'
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transfer_params["TipLocation"] = tip_rack
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self.temp_protocol["steps"].append(transfer_params)
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return
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steps_info = '''
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{
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"steps": [
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@@ -280,241 +536,6 @@ steps_info = '''
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#class LiquidHandlerBiomek(LiquidHandlerAbstract):
|
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|
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|
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class LiquidHandlerBiomek:
|
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"""
|
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Biomek液体处理器的实现类，继承自LiquidHandlerAbstract。
|
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该类用于处理Biomek液体处理器的特定操作。
|
||||
"""
|
||||
|
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def __init__(self, *args, **kwargs):
|
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super().__init__(*args, **kwargs)
|
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self._status = "Idle" # 初始状态为 Idle
|
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self._success = False # 初始成功状态为 False
|
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self._status_queue = kwargs.get("status_queue", None) # 状态队列
|
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self.temp_protocol = {}
|
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self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
|
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self.aspirate_techniques = {
|
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'MC P300 high':{
|
||||
"Solvent": "Water",
|
||||
}
|
||||
}
|
||||
self.dispense_techniques = {
|
||||
'MC P300 high':{
|
||||
"Span8": False,
|
||||
"Pod": "Pod1",
|
||||
"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,
|
||||
"Span8Wash": False,
|
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"Span8WashVolume": "2",
|
||||
"Span8WasteVolume": "1",
|
||||
"SplitVolume": False,
|
||||
"SplitVolumeCleaning": False,
|
||||
"Stop": "Destinations",
|
||||
"UseCurrentTips": False,
|
||||
"UseDisposableTips": False,
|
||||
"UseFixedTips": False,
|
||||
"UseJIT": True,
|
||||
"UseMandrelSelection": True,
|
||||
"UseProbes": [True, True, True, True, True, True, True, True],
|
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"WashCycles": "3",
|
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"WashVolume": "110%",
|
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"Wizard": False
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}
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}
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|
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def create_protocol(
|
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self,
|
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protocol_name: str,
|
||||
protocol_description: str,
|
||||
protocol_version: str,
|
||||
protocol_author: str,
|
||||
protocol_date: str,
|
||||
protocol_type: str,
|
||||
none_keys: List[str] = [],
|
||||
):
|
||||
"""
|
||||
创建一个新的协议。
|
||||
|
||||
Args:
|
||||
protocol_name (str): 协议名称
|
||||
protocol_description (str): 协议描述
|
||||
protocol_version (str): 协议版本
|
||||
protocol_author (str): 协议作者
|
||||
protocol_date (str): 协议日期
|
||||
protocol_type (str): 协议类型
|
||||
none_keys (List[str]): 需要设置为None的键列表
|
||||
|
||||
Returns:
|
||||
dict: 创建的协议字典
|
||||
"""
|
||||
self.temp_protocol = {
|
||||
"meta": {
|
||||
"name": protocol_name,
|
||||
"description": protocol_description,
|
||||
"version": protocol_version,
|
||||
"author": protocol_author,
|
||||
"date": protocol_date,
|
||||
"type": protocol_type,
|
||||
},
|
||||
"labwares": [],
|
||||
"steps": [],
|
||||
}
|
||||
return self.temp_protocol
|
||||
|
||||
# def run_protocol(self):
|
||||
# """
|
||||
# 执行创建的实验流程。
|
||||
# 工作站的完整执行流程是，
|
||||
# 从 create_protocol 开始，创建新的 method，
|
||||
# 随后执行 transfer_liquid 等操作向实验流程添加步骤，
|
||||
# 最后 run_protocol 执行整个方法。
|
||||
|
||||
# Returns:
|
||||
# dict: 执行结果
|
||||
# """
|
||||
# #use popen or subprocess to create py32 process and communicate send the temp protocol to it
|
||||
# if not self.temp_protocol:
|
||||
# raise ValueError("No protocol created. Please create a protocol first.")
|
||||
|
||||
# # 模拟执行协议
|
||||
# self._status = "Running"
|
||||
# self._success = True
|
||||
# # 在这里可以添加实际执行协议的逻辑
|
||||
|
||||
# response = requests.post("localhost:5000/api/protocols", json=self.temp_protocol)
|
||||
|
||||
# def create_resource(
|
||||
# self,
|
||||
# resource_tracker: DeviceNodeResourceTracker,
|
||||
# resources: list[Resource],
|
||||
# bind_parent_id: str,
|
||||
# bind_location: dict[str, float],
|
||||
# liquid_input_slot: list[int],
|
||||
# liquid_type: list[str],
|
||||
# liquid_volume: list[int],
|
||||
# slot_on_deck: int,
|
||||
# res_id,
|
||||
# class_name,
|
||||
# bind_locations,
|
||||
# parent
|
||||
# ):
|
||||
# """
|
||||
# 创建一个新的资源。
|
||||
|
||||
# Args:
|
||||
# device_id (str): 设备ID
|
||||
# res_id (str): 资源ID
|
||||
# class_name (str): 资源类名
|
||||
# parent (str): 父级ID
|
||||
# bind_locations (Point): 绑定位置
|
||||
# liquid_input_slot (list[int]): 液体输入槽列表
|
||||
# liquid_type (list[str]): 液体类型列表
|
||||
# liquid_volume (list[int]): 液体体积列表
|
||||
# slot_on_deck (int): 甲板上的槽位
|
||||
|
||||
# Returns:
|
||||
# dict: 创建的资源字典
|
||||
# """
|
||||
# # TODO：需要对好接口，下面这个是临时的
|
||||
# resource = {
|
||||
# "id": res_id,
|
||||
# "class": class_name,
|
||||
# "parent": parent,
|
||||
# "bind_locations": bind_locations.to_dict(),
|
||||
# "liquid_input_slot": liquid_input_slot,
|
||||
# "liquid_type": liquid_type,
|
||||
# "liquid_volume": liquid_volume,
|
||||
# "slot_on_deck": slot_on_deck,
|
||||
# }
|
||||
# self.temp_protocol["labwares"].append(resource)
|
||||
# return resource
|
||||
|
||||
|
||||
def transfer_biomek(
|
||||
self,
|
||||
source: str,
|
||||
target: str,
|
||||
tip_rack: str,
|
||||
volume: float,
|
||||
aspirate_techniques: str,
|
||||
dispense_techniques: str,
|
||||
):
|
||||
"""
|
||||
处理Biomek的液体转移操作。
|
||||
|
||||
"""
|
||||
|
||||
asp_params = self.aspirate_techniques.get(aspirate_techniques, {})
|
||||
dis_params = self.dispense_techniques.get(dispense_techniques, {})
|
||||
|
||||
transfer_params = {
|
||||
"Span8": False,
|
||||
"Pod": "Pod1",
|
||||
"items": {},
|
||||
"Wash": False,
|
||||
"Dynamic?": True,
|
||||
"AutoSelectActiveWashTechnique": False,
|
||||
"ActiveWashTechnique": "",
|
||||
"ChangeTipsBetweenDests": False,
|
||||
"ChangeTipsBetweenSources": True,
|
||||
"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": "BC1025F",
|
||||
"UseCurrentTips": False,
|
||||
"UseDisposableTips": True,
|
||||
"UseFixedTips": False,
|
||||
"UseJIT": True,
|
||||
"UseMandrelSelection": True,
|
||||
"UseProbes": [True, True, True, True, True, True, True, True],
|
||||
"WashCycles": "1",
|
||||
"WashVolume": "110%",
|
||||
"Wizard": False
|
||||
}
|
||||
|
||||
items: dict = {}
|
||||
items["Source"] = source
|
||||
items["Destination"] = target
|
||||
items["Volume"] = volume
|
||||
transfer_params["items"] = items
|
||||
transfer_params["Solvent"] = asp_params['Solvent']
|
||||
transfer_params["TipLocation"] = tip_rack
|
||||
transfer_params.update(asp_params)
|
||||
transfer_params.update(dis_params)
|
||||
self.temp_protocol["steps"].append(transfer_params)
|
||||
|
||||
return
|
||||
|
||||
labware_with_liquid = '''
|
||||
[ {
|
||||
"id": "stock plate on P1",
|
||||
@@ -716,8 +737,6 @@ labware_with_liquid = '''
|
||||
|
||||
'''
|
||||
|
||||
|
||||
|
||||
handler = LiquidHandlerBiomek()
|
||||
|
||||
handler.temp_protocol = {
|
||||
@@ -734,7 +753,6 @@ for step in input_steps['steps']:
|
||||
continue
|
||||
parameters = step['parameters']
|
||||
|
||||
|
||||
handler.transfer_biomek(source=parameters['source'],
|
||||
target=parameters['target'],
|
||||
volume=parameters['volume'],
|
||||
@@ -742,6 +760,6 @@ for step in input_steps['steps']:
|
||||
aspirate_techniques='MC P300 high',
|
||||
dispense_techniques='MC P300 high'
|
||||
)
|
||||
|
||||
print(json.dumps(handler.temp_protocol['steps'],indent=4, ensure_ascii=False))
|
||||
with open('biomek_temporary_protocol.json', 'w') as f:
|
||||
json.dump(handler.temp_protocol, f, indent=4, ensure_ascii=False)
|
||||
|
||||
|
||||
Reference in New Issue
Block a user