From 5179a7e48e922d65da7a6b782226d88c2bed4473 Mon Sep 17 00:00:00 2001 From: Xuwznln <18435084+Xuwznln@users.noreply.github.com> Date: Wed, 28 Jan 2026 13:23:25 +0800 Subject: [PATCH] workflow upload & set liquid fix & add set liquid with plate fix upload workflow json save class name when deserialize & protocol execute test Support root node change pos add unilabos_class gather query --- docs/user_guide/best_practice.md | 3 + docs/user_guide/image/add_protocol.png | Bin 0 -> 83318 bytes tests/workflow/test.json | 213 +++++ unilabos/app/web/client.py | 62 +- .../liquid_handler_abstract.py | 694 ++++++++++------ .../devices/liquid_handling/prcxi/prcxi.py | 399 +++++---- unilabos/registry/devices/liquid_handler.yaml | 165 +++- unilabos/registry/registry.py | 1 + unilabos/resources/graphio.py | 2 +- unilabos/resources/resource_tracker.py | 19 +- unilabos/ros/nodes/base_device_node.py | 30 +- unilabos/ros/nodes/presets/workstation.py | 63 +- unilabos/workflow/common.py | 770 ++++++++++++++++++ unilabos/workflow/convert_from_json.py | 315 +++++++ .../legacy/convert_from_json_legacy.py | 356 ++++++++ 15 files changed, 2619 insertions(+), 473 deletions(-) create mode 100644 docs/user_guide/image/add_protocol.png create mode 100644 tests/workflow/test.json create mode 100644 unilabos/workflow/common.py create mode 100644 unilabos/workflow/convert_from_json.py create mode 100644 unilabos/workflow/legacy/convert_from_json_legacy.py diff --git a/docs/user_guide/best_practice.md b/docs/user_guide/best_practice.md index 0fa4d1e..767dc4d 100644 --- a/docs/user_guide/best_practice.md +++ b/docs/user_guide/best_practice.md @@ -439,6 +439,9 @@ unilab --ak your_ak --sk your_sk -g test/experiments/mock_devices/mock_all.json 1. 访问 Web 界面，进入"仪器耗材"模块 2. 在"仪器设备"区域找到并添加上述设备 3. 在"物料耗材"区域找到并添加容器 +4. 在workstation中配置protocol_type包含PumpTransferProtocol + +![添加Protocol类型](image/add_protocol.png) ![物料列表](image/material.png) diff --git a/docs/user_guide/image/add_protocol.png 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--git a/tests/workflow/test.json b/tests/workflow/test.json new file mode 100644 index 0000000..8fc6449 --- /dev/null +++ b/tests/workflow/test.json @@ -0,0 +1,213 @@ +{ + "workflow": [ + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines", + "targets": "Liquid_1", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines", + "targets": "Liquid_2", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines", + "targets": "Liquid_3", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines_2", + "targets": "Liquid_4", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines_2", + "targets": "Liquid_5", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines_2", + "targets": "Liquid_6", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines_3", + "targets": "dest_set", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines_3", + "targets": "dest_set_2", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + }, + { + "action": "transfer_liquid", + "action_args": { + "sources": "cell_lines_3", + "targets": "dest_set_3", + "asp_vol": 100.0, + "dis_vol": 74.75, + "asp_flow_rate": 94.0, + "dis_flow_rate": 95.5 + } + } + ], + "reagent": { + "Liquid_1": { + "slot": 1, + "well": [ + "A4", + "A7", + "A10" + ], + "labware": "rep 1" + }, + "Liquid_4": { + "slot": 1, + "well": [ + "A4", + "A7", + "A10" + ], + "labware": "rep 1" + }, + "dest_set": { + "slot": 1, + "well": [ + "A4", + "A7", + "A10" + ], + "labware": "rep 1" + }, + "Liquid_2": { + "slot": 2, + "well": [ + "A3", + "A5", + "A8" + ], + "labware": "rep 2" + }, + "Liquid_5": { + "slot": 2, + "well": [ + "A3", + "A5", + "A8" + ], + "labware": "rep 2" + }, + "dest_set_2": { + "slot": 2, + "well": [ + "A3", + "A5", + "A8" + ], + "labware": "rep 2" + }, + "Liquid_3": { + "slot": 3, + "well": [ + "A4", + "A6", + "A10" + ], + "labware": "rep 3" + }, + "Liquid_6": { + "slot": 3, + "well": [ + "A4", + "A6", + "A10" + ], + "labware": "rep 3" + }, + "dest_set_3": { + "slot": 3, + "well": [ + "A4", + "A6", + "A10" + ], + "labware": "rep 3" + }, + "cell_lines": { + "slot": 4, + "well": [ + "A1", + "A3", + "A5" + ], + "labware": "DRUG + YOYO-MEDIA" + }, + "cell_lines_2": { + "slot": 4, + "well": [ + "A1", + "A3", + "A5" + ], + "labware": "DRUG + YOYO-MEDIA" + }, + "cell_lines_3": { + "slot": 4, + "well": [ + "A1", + "A3", + "A5" + ], + "labware": "DRUG + YOYO-MEDIA" + } + } +} \ No newline at end of file diff --git a/unilabos/app/web/client.py b/unilabos/app/web/client.py index 9660100..0ecf460 100644 --- a/unilabos/app/web/client.py +++ b/unilabos/app/web/client.py @@ -74,7 +74,8 @@ class HTTPClient: Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid} """ with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f: - f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4)) + payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid} + f.write(json.dumps(payload, indent=4)) # 从序列化数据中提取所有节点的UUID（保存旧UUID） old_uuids = {n.res_content.uuid: n for n in resources.all_nodes} if not self.initialized or first_add: @@ -333,6 +334,65 @@ class HTTPClient: logger.error(f"响应内容: {response.text}") return None + def workflow_import( + self, + name: str, + workflow_uuid: str, + workflow_name: str, + nodes: List[Dict[str, Any]], + edges: List[Dict[str, Any]], + tags: Optional[List[str]] = None, + published: bool = False, + ) -> Dict[str, Any]: + """ + 导入工作流到服务器 + + Args: + name: 工作流名称（顶层） + workflow_uuid: 工作流UUID + workflow_name: 工作流名称（data内部） + nodes: 工作流节点列表 + edges: 工作流边列表 + tags: 工作流标签列表，默认为空列表 + published: 是否发布工作流，默认为False + + Returns: + Dict: API响应数据，包含 code 和 data (uuid, name) + """ + payload = { + "name": name, + "data": { + "workflow_uuid": workflow_uuid, + "workflow_name": workflow_name, + "nodes": nodes, + "edges": edges, + "tags": tags if tags is not None else [], + "published": published, + }, + } + # 保存请求到文件 + with open(os.path.join(BasicConfig.working_dir, "req_workflow_upload.json"), "w", encoding="utf-8") as f: + f.write(json.dumps(payload, indent=4, ensure_ascii=False)) + + response = requests.post( + f"{self.remote_addr}/lab/workflow/owner/import", + json=payload, + headers={"Authorization": f"Lab {self.auth}"}, + timeout=60, + ) + # 保存响应到文件 + with open(os.path.join(BasicConfig.working_dir, "res_workflow_upload.json"), "w", encoding="utf-8") as f: + f.write(f"{response.status_code}" + "\n" + response.text) + + if response.status_code == 200: + res = response.json() + if "code" in res and res["code"] != 0: + logger.error(f"导入工作流失败: {response.text}") + return res + else: + logger.error(f"导入工作流失败: {response.status_code}, {response.text}") + return {"code": response.status_code, "message": response.text} + # 创建默认客户端实例 http_client = HTTPClient() diff --git a/unilabos/devices/liquid_handling/liquid_handler_abstract.py b/unilabos/devices/liquid_handling/liquid_handler_abstract.py index d02129c..aa695a0 100644 --- a/unilabos/devices/liquid_handling/liquid_handler_abstract.py +++ b/unilabos/devices/liquid_handling/liquid_handler_abstract.py @@ -28,21 +28,40 @@ from pylabrobot.resources import ( Tip, ) +from unilabos.registry.placeholder_type import ResourceSlot from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode +from unilabos.resources.resource_tracker import ResourceTreeSet + + class SimpleReturn(TypedDict): samples: list volumes: list + +class SetLiquidReturn(TypedDict): + wells: list + volumes: list + + +class SetLiquidFromPlateReturn(TypedDict): + plate: list + wells: list + volumes: list + + class LiquidHandlerMiddleware(LiquidHandler): - def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool = False, channel_num: int = 8, **kwargs): + def __init__( + self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool = False, channel_num: int = 8, **kwargs + ): self._simulator = simulator self.channel_num = channel_num self.pending_liquids_dict = {} joint_config = kwargs.get("joint_config", None) if simulator: if joint_config: - self._simulate_backend = UniLiquidHandlerRvizBackend(channel_num, kwargs["total_height"], - joint_config=joint_config, lh_device_id=deck.name) + self._simulate_backend = UniLiquidHandlerRvizBackend( + channel_num, kwargs["total_height"], joint_config=joint_config, lh_device_id=deck.name + ) else: self._simulate_backend = LiquidHandlerChatterboxBackend(channel_num) self._simulate_handler = LiquidHandlerAbstract(self._simulate_backend, deck, False) @@ -137,7 +156,7 @@ class LiquidHandlerMiddleware(LiquidHandler): ) await super().drop_tips(tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs) self.pending_liquids_dict = {} - return + return async def return_tips( self, use_channels: Optional[list[int]] = None, allow_nonzero_volume: bool = False, **backend_kwargs @@ -159,11 +178,13 @@ class LiquidHandlerMiddleware(LiquidHandler): if not offsets or (isinstance(offsets, list) and len(offsets) != len(use_channels)): offsets = [Coordinate.zero()] * len(use_channels) if self._simulator: - return await self._simulate_handler.discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs) + return await self._simulate_handler.discard_tips( + use_channels, allow_nonzero_volume, offsets, **backend_kwargs + ) await super().discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs) self.pending_liquids_dict = {} - return - + return + def _check_containers(self, resources: Sequence[Resource]): super()._check_containers(resources) @@ -180,7 +201,6 @@ class LiquidHandlerMiddleware(LiquidHandler): **backend_kwargs, ): - if self._simulator: return await self._simulate_handler.aspirate( resources, @@ -208,15 +228,16 @@ class LiquidHandlerMiddleware(LiquidHandler): res_samples = [] res_volumes = [] for resource, volume, channel in zip(resources, vols, use_channels): - res_samples.append({"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)}) + res_samples.append( + {"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)} + ) res_volumes.append(volume) self.pending_liquids_dict[channel] = { "sample_uuid": resource.unilabos_extra.get("sample_uuid", None), - "volume": volume + "volume": volume, } return SimpleReturn(samples=res_samples, volumes=res_volumes) - async def dispense( self, resources: Sequence[Container], @@ -261,7 +282,7 @@ class LiquidHandlerMiddleware(LiquidHandler): res_volumes.append(volume) return SimpleReturn(samples=res_samples, volumes=res_volumes) - + async def transfer( self, source: Well, @@ -578,10 +599,18 @@ class LiquidHandlerMiddleware(LiquidHandler): class LiquidHandlerAbstract(LiquidHandlerMiddleware): """Extended LiquidHandler with additional operations.""" + support_touch_tip = True _ros_node: BaseROS2DeviceNode - def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool=False, channel_num:int = 8, total_height:float = 310): + def __init__( + self, + backend: LiquidHandlerBackend, + deck: Deck, + simulator: bool = False, + channel_num: int = 8, + total_height: float = 310, + ): """Initialize a LiquidHandler. Args: @@ -605,6 +634,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): module_name = ".".join(components[:-1]) try: import importlib + mod = importlib.import_module(module_name) except ImportError: mod = None @@ -614,6 +644,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): # Try pylabrobot style import (if available) try: import pylabrobot + backend_cls = getattr(pylabrobot, type_str, None) except Exception: backend_cls = None @@ -631,16 +662,56 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): self._ros_node = ros_node @classmethod - def set_liquid(cls, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SimpleReturn: - """Set the liquid in a well.""" - res_samples = [] + def set_liquid(cls, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SetLiquidReturn: + """Set the liquid in a well. + + 如果 liquid_names 和 volumes 为空，但 wells 不为空，直接返回 wells。 + """ res_volumes = [] + # 如果 liquid_names 和 volumes 都为空，直接返回 wells + if not liquid_names and not volumes: + return SetLiquidReturn( + wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes # type: ignore + ) + for well, liquid_name, volume in zip(wells, liquid_names, volumes): well.set_liquids([(liquid_name, volume)]) # type: ignore - res_samples.append({"name": well.name, "sample_uuid": well.unilabos_extra.get("sample_uuid", None)}) res_volumes.append(volume) - - return SimpleReturn(samples=res_samples, volumes=res_volumes) + + return SetLiquidReturn( + wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes # type: ignore + ) + + @classmethod + def set_liquid_from_plate( + cls, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float] + ) -> SetLiquidFromPlateReturn: + """Set the liquid in wells of a plate by well names (e.g., A1, A2, B3). + + 如果 liquid_names 和 volumes 为空，但 plate 和 well_names 不为空，直接返回 plate 和 wells。 + """ + # 根据 well_names 获取对应的 Well 对象 + wells = [plate.get_well(name) for name in well_names] + res_volumes = [] + + # 如果 liquid_names 和 volumes 都为空，直接返回 + if not liquid_names and not volumes: + return SetLiquidFromPlateReturn( + plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(), # type: ignore + wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), # type: ignore + volumes=res_volumes, + ) + + for well, liquid_name, volume in zip(wells, liquid_names, volumes): + well.set_liquids([(liquid_name, volume)]) # type: ignore + res_volumes.append(volume) + + return SetLiquidFromPlateReturn( + plate=ResourceTreeSet.from_plr_resources([plate], known_newly_created=False).dump(), # type: ignore + wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), # type: ignore + volumes=res_volumes, + ) + # --------------------------------------------------------------- # REMOVE LIQUID -------------------------------------------------- # --------------------------------------------------------------- @@ -655,7 +726,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): source_wells = self.group_info.get(source_group_name, []) target_wells = self.group_info.get(target_group_name, []) - + rack_info = dict() for child in self.deck.children: if issubclass(child.__class__, TipRack): @@ -666,17 +737,17 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): break else: rack_info[rack.name] = (rack, tip.maximal_volume - unit_volume) - + if len(rack_info) == 0: raise ValueError(f"No tip rack can support volume {unit_volume}.") - + rack_info = sorted(rack_info.items(), key=lambda x: x[1][1]) for child in self.deck.children: if child.name == rack_info[0][0]: target_rack = child target_rack = cast(TipRack, target_rack) available_tips = {} - for (idx, tipSpot) in enumerate(target_rack.get_all_items()): + for idx, tipSpot in enumerate(target_rack.get_all_items()): if tipSpot.has_tip(): available_tips[idx] = tipSpot continue @@ -684,10 +755,10 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): print("channel_num", self.channel_num) if self.channel_num == 8: - tip_prefix = list(available_tips.values())[0].name.split('_')[0] - colnum_list = [int(tip.name.split('_')[-1][1:]) for tip in available_tips.values()] + tip_prefix = list(available_tips.values())[0].name.split("_")[0] + colnum_list = [int(tip.name.split("_")[-1][1:]) for tip in available_tips.values()] available_cols = [colnum for colnum, count in dict(Counter(colnum_list)).items() if count == 8] - available_cols.sort() + available_cols.sort() available_tips_dict = {tip.name: tip for tip in available_tips.values()} tips_to_use = [available_tips_dict[f"{tip_prefix}_{chr(65 + i)}{available_cols[0]}"] for i in range(8)] print("tips_to_use", tips_to_use) @@ -698,16 +769,16 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): await self.dispense(target_wells, [unit_volume] * 8, use_channels=list(range(0, 8))) await self.discard_tips(use_channels=list(range(0, 8))) - elif self.channel_num == 1: - + elif self.channel_num == 1: + for num_well in range(len(target_wells)): - tip_to_use = available_tips[list(available_tips.keys())[num_well]] + tip_to_use = available_tips[list(available_tips.keys())[num_well]] print("tip_to_use", tip_to_use) await self.pick_up_tips([tip_to_use], use_channels=[0]) print("source_wells", source_wells) print("target_wells", target_wells) if len(source_wells) == 1: - await self.aspirate([source_wells[0]], [unit_volume], use_channels=[0]) + await self.aspirate([source_wells[0]], [unit_volume], use_channels=[0]) else: await self.aspirate([source_wells[num_well]], [unit_volume], use_channels=[0]) await self.dispense([target_wells[num_well]], [unit_volume], use_channels=[0]) @@ -729,7 +800,6 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): """Create a new protocol with the given metadata.""" pass - async def remove_liquid( self, vols: List[float], @@ -787,11 +857,12 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): await self.discard_tips() elif len(use_channels) == 8 and self.backend.num_channels == 8: - - + # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 if len(sources) % 8 != 0: - raise ValueError(f"Length of `sources` {len(sources)} must be a multiple of 8 for 8-channel mode.") + raise ValueError( + f"Length of `sources` {len(sources)} must be a multiple of 8 for 8-channel mode." + ) # 8个8个来取任务序列 @@ -800,18 +871,28 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) - current_targets = waste_liquid[i:i + 8] - current_reagent_sources = sources[i:i + 8] - current_asp_vols = vols[i:i + 8] - current_dis_vols = vols[i:i + 8] - current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8 - current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8 - current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8 - current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8 - current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 - current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8 + current_targets = waste_liquid[i : i + 8] + current_reagent_sources = sources[i : i + 8] + current_asp_vols = vols[i : i + 8] + current_dis_vols = vols[i : i + 8] + current_asp_flow_rates = flow_rates[i : i + 8] if flow_rates else [None] * 8 + current_dis_flow_rates = ( + flow_rates[-i * 8 - 8 : len(flow_rates) - i * 8] if flow_rates else [None] * 8 + ) + current_asp_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_dis_offset = offsets[-i * 8 - 8 : len(offsets) - i * 8] if offsets else [None] * 8 + current_asp_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_dis_liquid_height = ( + liquid_height[-i * 8 - 8 : len(liquid_height) - i * 8] if liquid_height else [None] * 8 + ) + current_asp_blow_out_air_volume = ( + blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + ) + current_dis_blow_out_air_volume = ( + blow_out_air_volume[-i * 8 - 8 : len(blow_out_air_volume) - i * 8] + if blow_out_air_volume + else [None] * 8 + ) await self.aspirate( resources=current_reagent_sources, @@ -838,7 +919,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): if delays is not None and len(delays) > 1: await self.custom_delay(seconds=delays[1]) await self.touch_tip(current_targets) - await self.discard_tips() + await self.discard_tips() except Exception as e: traceback.print_exc() @@ -872,127 +953,136 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): # """A complete *add* (aspirate reagent → dispense into targets) operation.""" # # try: - if is_96_well: - pass # This mode is not verified. - else: - if len(asp_vols) != len(targets): - raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.") - # 首先应该对任务分组，然后每次1个/8个进行操作处理 - if len(use_channels) == 1: - for _ in range(len(targets)): - tip = [] - for x in range(len(use_channels)): - tip.extend(next(self.current_tip)) - await self.pick_up_tips(tip) + if is_96_well: + pass # This mode is not verified. + else: + if len(asp_vols) != len(targets): + raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.") + # 首先应该对任务分组，然后每次1个/8个进行操作处理 + if len(use_channels) == 1: + for _ in range(len(targets)): + tip = [] + for x in range(len(use_channels)): + tip.extend(next(self.current_tip)) + await self.pick_up_tips(tip) - await self.aspirate( - resources=[reagent_sources[_]], - vols=[asp_vols[_]], - use_channels=use_channels, - flow_rates=[flow_rates[0]] if flow_rates else None, - offsets=[offsets[0]] if offsets else None, - liquid_height=[liquid_height[0]] if liquid_height else None, - blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None, - spread=spread, + await self.aspirate( + resources=[reagent_sources[_]], + vols=[asp_vols[_]], + use_channels=use_channels, + flow_rates=[flow_rates[0]] if flow_rates else None, + offsets=[offsets[0]] if offsets else None, + liquid_height=[liquid_height[0]] if liquid_height else None, + blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None, + spread=spread, + ) + + if delays is not None: + await self.custom_delay(seconds=delays[0]) + await self.dispense( + resources=[targets[_]], + vols=[dis_vols[_]], + use_channels=use_channels, + flow_rates=[flow_rates[1]] if flow_rates else None, + offsets=[offsets[1]] if offsets else None, + blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None, + liquid_height=[liquid_height[1]] if liquid_height else None, + spread=spread, + ) + + if delays is not None and len(delays) > 1: + await self.custom_delay(seconds=delays[1]) + # 只有在 mix_time 有效时才调用 mix + if mix_time is not None and mix_time > 0: + await self.mix( + targets=[targets[_]], + mix_time=mix_time, + mix_vol=mix_vol, + offsets=offsets if offsets else None, + height_to_bottom=mix_liquid_height if mix_liquid_height else None, + mix_rate=mix_rate if mix_rate else None, ) - - if delays is not None: - await self.custom_delay(seconds=delays[0]) - await self.dispense( - resources=[targets[_]], - vols=[dis_vols[_]], - use_channels=use_channels, - flow_rates=[flow_rates[1]] if flow_rates else None, - offsets=[offsets[1]] if offsets else None, - blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None, - liquid_height=[liquid_height[1]] if liquid_height else None, - spread=spread, + if delays is not None and len(delays) > 1: + await self.custom_delay(seconds=delays[1]) + await self.touch_tip(targets[_]) + await self.discard_tips() + + elif len(use_channels) == 8: + # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 + if len(targets) % 8 != 0: + raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.") + + for i in range(0, len(targets), 8): + tip = [] + for _ in range(len(use_channels)): + tip.extend(next(self.current_tip)) + await self.pick_up_tips(tip) + current_targets = targets[i : i + 8] + current_reagent_sources = reagent_sources[i : i + 8] + current_asp_vols = asp_vols[i : i + 8] + current_dis_vols = dis_vols[i : i + 8] + current_asp_flow_rates = flow_rates[i : i + 8] if flow_rates else [None] * 8 + current_dis_flow_rates = ( + flow_rates[-i * 8 - 8 : len(flow_rates) - i * 8] if flow_rates else [None] * 8 + ) + current_asp_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_dis_offset = offsets[-i * 8 - 8 : len(offsets) - i * 8] if offsets else [None] * 8 + current_asp_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_dis_liquid_height = ( + liquid_height[-i * 8 - 8 : len(liquid_height) - i * 8] if liquid_height else [None] * 8 + ) + current_asp_blow_out_air_volume = ( + blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + ) + current_dis_blow_out_air_volume = ( + blow_out_air_volume[-i * 8 - 8 : len(blow_out_air_volume) - i * 8] + if blow_out_air_volume + else [None] * 8 + ) + + await self.aspirate( + resources=current_reagent_sources, + vols=current_asp_vols, + use_channels=use_channels, + flow_rates=current_asp_flow_rates, + offsets=current_asp_offset, + liquid_height=current_asp_liquid_height, + blow_out_air_volume=current_asp_blow_out_air_volume, + spread=spread, + ) + if delays is not None: + await self.custom_delay(seconds=delays[0]) + await self.dispense( + resources=current_targets, + vols=current_dis_vols, + use_channels=use_channels, + flow_rates=current_dis_flow_rates, + offsets=current_dis_offset, + liquid_height=current_dis_liquid_height, + blow_out_air_volume=current_dis_blow_out_air_volume, + spread=spread, + ) + if delays is not None and len(delays) > 1: + await self.custom_delay(seconds=delays[1]) + + # 只有在 mix_time 有效时才调用 mix + if mix_time is not None and mix_time > 0: + await self.mix( + targets=current_targets, + mix_time=mix_time, + mix_vol=mix_vol, + offsets=offsets if offsets else None, + height_to_bottom=mix_liquid_height if mix_liquid_height else None, + mix_rate=mix_rate if mix_rate else None, ) + if delays is not None and len(delays) > 1: + await self.custom_delay(seconds=delays[1]) + await self.touch_tip(current_targets) + await self.discard_tips() - if delays is not None and len(delays) > 1: - await self.custom_delay(seconds=delays[1]) - # 只有在 mix_time 有效时才调用 mix - if mix_time is not None and mix_time > 0: - await self.mix( - targets=[targets[_]], - mix_time=mix_time, - mix_vol=mix_vol, - offsets=offsets if offsets else None, - height_to_bottom=mix_liquid_height if mix_liquid_height else None, - mix_rate=mix_rate if mix_rate else None, - ) - if delays is not None and len(delays) > 1: - await self.custom_delay(seconds=delays[1]) - await self.touch_tip(targets[_]) - await self.discard_tips() - - elif len(use_channels) == 8: - # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 - if len(targets) % 8 != 0: - raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.") - - for i in range(0, len(targets), 8): - tip = [] - for _ in range(len(use_channels)): - tip.extend(next(self.current_tip)) - await self.pick_up_tips(tip) - current_targets = targets[i:i + 8] - current_reagent_sources = reagent_sources[i:i + 8] - current_asp_vols = asp_vols[i:i + 8] - current_dis_vols = dis_vols[i:i + 8] - current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8 - current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8 - current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8 - current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8 - current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 - current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8 - - await self.aspirate( - resources=current_reagent_sources, - vols=current_asp_vols, - use_channels=use_channels, - flow_rates=current_asp_flow_rates, - offsets=current_asp_offset, - liquid_height=current_asp_liquid_height, - blow_out_air_volume=current_asp_blow_out_air_volume, - spread=spread, - ) - if delays is not None: - await self.custom_delay(seconds=delays[0]) - await self.dispense( - resources=current_targets, - vols=current_dis_vols, - use_channels=use_channels, - flow_rates=current_dis_flow_rates, - offsets=current_dis_offset, - liquid_height=current_dis_liquid_height, - blow_out_air_volume=current_dis_blow_out_air_volume, - spread=spread, - ) - if delays is not None and len(delays) > 1: - await self.custom_delay(seconds=delays[1]) - - # 只有在 mix_time 有效时才调用 mix - if mix_time is not None and mix_time > 0: - await self.mix( - targets=current_targets, - mix_time=mix_time, - mix_vol=mix_vol, - offsets=offsets if offsets else None, - height_to_bottom=mix_liquid_height if mix_liquid_height else None, - mix_rate=mix_rate if mix_rate else None, - ) - if delays is not None and len(delays) > 1: - await self.custom_delay(seconds=delays[1]) - await self.touch_tip(current_targets) - await self.discard_tips() - - - # except Exception as e: - # traceback.print_exc() - # raise RuntimeError(f"Liquid addition failed: {e}") from e + # except Exception as e: + # traceback.print_exc() + # raise RuntimeError(f"Liquid addition failed: {e}") from e # --------------------------------------------------------------- # TRANSFER LIQUID ------------------------------------------------ @@ -1050,12 +1140,12 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): Number of mix cycles. If *None* (default) no mixing occurs regardless of mix_stage. """ - + # 确保 use_channels 有默认值 if use_channels is None: # 默认使用设备所有通道（例如 8 通道移液站默认就是 0-7） use_channels = list(range(self.channel_num)) if self.channel_num > 0 else [0] - + if is_96_well: pass # This mode is not verified. else: @@ -1064,7 +1154,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): asp_vols = [float(asp_vols)] else: asp_vols = [float(v) for v in asp_vols] - + if isinstance(dis_vols, (int, float)): dis_vols = [float(dis_vols)] else: @@ -1081,37 +1171,79 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): pass if mix_times is not None: mix_times = int(mix_times) - + # 识别传输模式（mix_times 为 None 也应该能正常移液，只是不做 mix） num_sources = len(sources) num_targets = len(targets) - + if num_sources == 1 and num_targets > 1: # 模式1: 一对多 (1 source -> N targets) await self._transfer_one_to_many( - sources[0], targets, tip_racks, use_channels, - asp_vols, dis_vols, asp_flow_rates, dis_flow_rates, - offsets, touch_tip, liquid_height, blow_out_air_volume, - spread, mix_stage, mix_times, mix_vol, mix_rate, - mix_liquid_height, delays + sources[0], + targets, + tip_racks, + use_channels, + asp_vols, + dis_vols, + asp_flow_rates, + dis_flow_rates, + offsets, + touch_tip, + liquid_height, + blow_out_air_volume, + spread, + mix_stage, + mix_times, + mix_vol, + mix_rate, + mix_liquid_height, + delays, ) elif num_sources > 1 and num_targets == 1: # 模式2: 多对一 (N sources -> 1 target) await self._transfer_many_to_one( - sources, targets[0], tip_racks, use_channels, - asp_vols, dis_vols, asp_flow_rates, dis_flow_rates, - offsets, touch_tip, liquid_height, blow_out_air_volume, - spread, mix_stage, mix_times, mix_vol, mix_rate, - mix_liquid_height, delays + sources, + targets[0], + tip_racks, + use_channels, + asp_vols, + dis_vols, + asp_flow_rates, + dis_flow_rates, + offsets, + touch_tip, + liquid_height, + blow_out_air_volume, + spread, + mix_stage, + mix_times, + mix_vol, + mix_rate, + mix_liquid_height, + delays, ) elif num_sources == num_targets: # 模式3: 一对一 (N sources -> N targets) await self._transfer_one_to_one( - sources, targets, tip_racks, use_channels, - asp_vols, dis_vols, asp_flow_rates, dis_flow_rates, - offsets, touch_tip, liquid_height, blow_out_air_volume, - spread, mix_stage, mix_times, mix_vol, mix_rate, - mix_liquid_height, delays + sources, + targets, + tip_racks, + use_channels, + asp_vols, + dis_vols, + asp_flow_rates, + dis_flow_rates, + offsets, + touch_tip, + liquid_height, + blow_out_air_volume, + spread, + mix_stage, + mix_times, + mix_vol, + mix_rate, + mix_liquid_height, + delays, ) else: raise ValueError( @@ -1174,7 +1306,9 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): flow_rates=[asp_flow_rates[_]] if asp_flow_rates and len(asp_flow_rates) > _ else None, offsets=[offsets[_]] if offsets and len(offsets) > _ else None, liquid_height=[liquid_height[_]] if liquid_height and len(liquid_height) > _ else None, - blow_out_air_volume=[blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None, + blow_out_air_volume=( + [blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None + ), spread=spread, ) if delays is not None: @@ -1185,7 +1319,9 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): use_channels=use_channels, flow_rates=[dis_flow_rates[_]] if dis_flow_rates and len(dis_flow_rates) > _ else None, offsets=[offsets[_]] if offsets and len(offsets) > _ else None, - blow_out_air_volume=[blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None, + blow_out_air_volume=( + [blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None + ), liquid_height=[liquid_height[_]] if liquid_height and len(liquid_height) > _ else None, spread=spread, ) @@ -1214,18 +1350,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) - current_targets = targets[i:i + 8] - current_reagent_sources = sources[i:i + 8] - current_asp_vols = asp_vols[i:i + 8] - current_dis_vols = dis_vols[i:i + 8] - current_asp_flow_rates = asp_flow_rates[i:i + 8] if asp_flow_rates else None - current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_dis_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_dis_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 - current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 - current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else None + current_targets = targets[i : i + 8] + current_reagent_sources = sources[i : i + 8] + current_asp_vols = asp_vols[i : i + 8] + current_dis_vols = dis_vols[i : i + 8] + current_asp_flow_rates = asp_flow_rates[i : i + 8] if asp_flow_rates else None + current_asp_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_dis_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_asp_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_dis_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_asp_blow_out_air_volume = blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + current_dis_blow_out_air_volume = blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + current_dis_flow_rates = dis_flow_rates[i : i + 8] if dis_flow_rates else None if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0: await self.mix( @@ -1275,7 +1411,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): if delays is not None and len(delays) > 1: await self.custom_delay(seconds=delays[1]) await self.touch_tip(current_targets) - await self.discard_tips([0,1,2,3,4,5,6,7]) + await self.discard_tips([0, 1, 2, 3, 4, 5, 6, 7]) async def _transfer_one_to_many( self, @@ -1307,7 +1443,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): asp_vol = asp_vols[0] if asp_vols[0] >= total_asp_vol else total_asp_vol else: raise ValueError("For one-to-many mode, `asp_vols` should be a single value or list with one element.") - + if len(dis_vols) != len(targets): raise ValueError(f"Length of `dis_vols` {len(dis_vols)} must match `targets` {len(targets)}.") @@ -1324,7 +1460,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): targets=[target], mix_time=mix_times, mix_vol=mix_vol, - offsets=offsets[idx:idx + 1] if offsets and len(offsets) > idx else None, + offsets=offsets[idx : idx + 1] if offsets and len(offsets) > idx else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) @@ -1337,13 +1473,15 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): flow_rates=[asp_flow_rates[0]] if asp_flow_rates and len(asp_flow_rates) > 0 else None, offsets=[offsets[0]] if offsets and len(offsets) > 0 else None, liquid_height=[liquid_height[0]] if liquid_height and len(liquid_height) > 0 else None, - blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None, + blow_out_air_volume=( + [blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None + ), spread=spread, ) - + if delays is not None: await self.custom_delay(seconds=delays[0]) - + # 分多次分液到不同的目标容器 for idx, target in enumerate(targets): await self.dispense( @@ -1352,7 +1490,9 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): use_channels=use_channels, flow_rates=[dis_flow_rates[idx]] if dis_flow_rates and len(dis_flow_rates) > idx else None, offsets=[offsets[idx]] if offsets and len(offsets) > idx else None, - blow_out_air_volume=[blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None, + blow_out_air_volume=( + [blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None + ), liquid_height=[liquid_height[idx]] if liquid_height and len(liquid_height) > idx else None, spread=spread, ) @@ -1363,46 +1503,54 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): targets=[target], mix_time=mix_times, mix_vol=mix_vol, - offsets=offsets[idx:idx+1] if offsets else None, + offsets=offsets[idx : idx + 1] if offsets else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) if touch_tip: await self.touch_tip([target]) - + await self.discard_tips(use_channels=use_channels) - + elif len(use_channels) == 8: # 8通道模式：需要确保目标数量是8的倍数 if len(targets) % 8 != 0: raise ValueError(f"For 8-channel mode, number of targets {len(targets)} must be a multiple of 8.") - + # 每次处理8个目标 for i in range(0, len(targets), 8): tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) - - current_targets = targets[i:i + 8] - current_dis_vols = dis_vols[i:i + 8] - + + current_targets = targets[i : i + 8] + current_dis_vols = dis_vols[i : i + 8] + # 8个通道都从同一个源容器吸液，每个通道的吸液体积等于对应的分液体积 - current_asp_flow_rates = asp_flow_rates[0:1] * 8 if asp_flow_rates and len(asp_flow_rates) > 0 else None + current_asp_flow_rates = ( + asp_flow_rates[0:1] * 8 if asp_flow_rates and len(asp_flow_rates) > 0 else None + ) current_asp_offset = offsets[0:1] * 8 if offsets and len(offsets) > 0 else [None] * 8 - current_asp_liquid_height = liquid_height[0:1] * 8 if liquid_height and len(liquid_height) > 0 else [None] * 8 - current_asp_blow_out_air_volume = blow_out_air_volume[0:1] * 8 if blow_out_air_volume and len(blow_out_air_volume) > 0 else [None] * 8 - + current_asp_liquid_height = ( + liquid_height[0:1] * 8 if liquid_height and len(liquid_height) > 0 else [None] * 8 + ) + current_asp_blow_out_air_volume = ( + blow_out_air_volume[0:1] * 8 + if blow_out_air_volume and len(blow_out_air_volume) > 0 + else [None] * 8 + ) + if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0: await self.mix( targets=current_targets, mix_time=mix_times, mix_vol=mix_vol, - offsets=offsets[i:i + 8] if offsets else None, + offsets=offsets[i : i + 8] if offsets else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) - + # 从源容器吸液（8个通道都从同一个源，但每个通道的吸液体积不同） await self.aspirate( resources=[source] * 8, # 8个通道都从同一个源 @@ -1414,16 +1562,16 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): blow_out_air_volume=current_asp_blow_out_air_volume, spread=spread, ) - + if delays is not None: await self.custom_delay(seconds=delays[0]) - + # 分液到8个目标 - current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else None - current_dis_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_dis_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 - + current_dis_flow_rates = dis_flow_rates[i : i + 8] if dis_flow_rates else None + current_dis_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_dis_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_dis_blow_out_air_volume = blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + await self.dispense( resources=current_targets, vols=current_dis_vols, @@ -1434,10 +1582,10 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): liquid_height=current_dis_liquid_height, spread=spread, ) - + if delays is not None and len(delays) > 1: await self.custom_delay(seconds=delays[1]) - + if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0: await self.mix( targets=current_targets, @@ -1447,11 +1595,11 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) - + if touch_tip: await self.touch_tip(current_targets) - - await self.discard_tips([0,1,2,3,4,5,6,7]) + + await self.discard_tips([0, 1, 2, 3, 4, 5, 6, 7]) async def _transfer_many_to_one( self, @@ -1479,7 +1627,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): # 验证和扩展体积参数 if len(asp_vols) != len(sources): raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `sources` {len(sources)}.") - + # 支持两种模式： # 1. dis_vols 为单个值：所有源汇总，使用总吸液体积或指定分液体积 # 2. dis_vols 长度等于 asp_vols：每个源按不同比例分液（按比例混合） @@ -1509,7 +1657,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) - + # 从每个源容器吸液并分液到目标容器 for idx, source in enumerate(sources): tip = [] @@ -1524,13 +1672,15 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): flow_rates=[asp_flow_rates[idx]] if asp_flow_rates and len(asp_flow_rates) > idx else None, offsets=[offsets[idx]] if offsets and len(offsets) > idx else None, liquid_height=[liquid_height[idx]] if liquid_height and len(liquid_height) > idx else None, - blow_out_air_volume=[blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None, + blow_out_air_volume=( + [blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None + ), spread=spread, ) - + if delays is not None: await self.custom_delay(seconds=delays[0]) - + # 分液到目标容器 if use_proportional_mixing: # 按不同比例混合：使用对应的 dis_vols @@ -1538,15 +1688,19 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): dis_flow_rate = dis_flow_rates[idx] if dis_flow_rates and len(dis_flow_rates) > idx else None dis_offset = offsets[idx] if offsets and len(offsets) > idx else None dis_liquid_height = liquid_height[idx] if liquid_height and len(liquid_height) > idx else None - dis_blow_out = blow_out_air_volume[idx] if blow_out_air_volume and len(blow_out_air_volume) > idx else None + dis_blow_out = ( + blow_out_air_volume[idx] if blow_out_air_volume and len(blow_out_air_volume) > idx else None + ) else: # 标准模式：分液体积等于吸液体积 dis_vol = asp_vols[idx] dis_flow_rate = dis_flow_rates[0] if dis_flow_rates and len(dis_flow_rates) > 0 else None dis_offset = offsets[0] if offsets and len(offsets) > 0 else None dis_liquid_height = liquid_height[0] if liquid_height and len(liquid_height) > 0 else None - dis_blow_out = blow_out_air_volume[0] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None - + dis_blow_out = ( + blow_out_air_volume[0] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None + ) + await self.dispense( resources=[target], vols=[dis_vol], @@ -1557,12 +1711,12 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): liquid_height=[dis_liquid_height] if dis_liquid_height is not None else None, spread=spread, ) - + if delays is not None and len(delays) > 1: await self.custom_delay(seconds=delays[1]) - + await self.discard_tips(use_channels=use_channels) - + # 最后在目标容器中混合（如果需要） if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0: await self.mix( @@ -1573,15 +1727,15 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) - + if touch_tip: await self.touch_tip([target]) - + elif len(use_channels) == 8: # 8通道模式：需要确保源数量是8的倍数 if len(sources) % 8 != 0: raise ValueError(f"For 8-channel mode, number of sources {len(sources)} must be a multiple of 8.") - + # 每次处理8个源 if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0: await self.mix( @@ -1598,14 +1752,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) - - current_sources = sources[i:i + 8] - current_asp_vols = asp_vols[i:i + 8] - current_asp_flow_rates = asp_flow_rates[i:i + 8] if asp_flow_rates else None - current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 - + + current_sources = sources[i : i + 8] + current_asp_vols = asp_vols[i : i + 8] + current_asp_flow_rates = asp_flow_rates[i : i + 8] if asp_flow_rates else None + current_asp_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_asp_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_asp_blow_out_air_volume = blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + # 从8个源容器吸液 await self.aspirate( resources=current_sources, @@ -1617,26 +1771,30 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): liquid_height=current_asp_liquid_height, spread=spread, ) - + if delays is not None: await self.custom_delay(seconds=delays[0]) - + # 分液到目标容器（每个通道分液到同一个目标） if use_proportional_mixing: # 按比例混合：使用对应的 dis_vols - current_dis_vols = dis_vols[i:i + 8] - current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else None - current_dis_offset = offsets[i:i + 8] if offsets else [None] * 8 - current_dis_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 - current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 + current_dis_vols = dis_vols[i : i + 8] + current_dis_flow_rates = dis_flow_rates[i : i + 8] if dis_flow_rates else None + current_dis_offset = offsets[i : i + 8] if offsets else [None] * 8 + current_dis_liquid_height = liquid_height[i : i + 8] if liquid_height else [None] * 8 + current_dis_blow_out_air_volume = ( + blow_out_air_volume[i : i + 8] if blow_out_air_volume else [None] * 8 + ) else: # 标准模式：每个通道分液体积等于其吸液体积 current_dis_vols = current_asp_vols current_dis_flow_rates = dis_flow_rates[0:1] * 8 if dis_flow_rates else None current_dis_offset = offsets[0:1] * 8 if offsets else [None] * 8 current_dis_liquid_height = liquid_height[0:1] * 8 if liquid_height else [None] * 8 - current_dis_blow_out_air_volume = blow_out_air_volume[0:1] * 8 if blow_out_air_volume else [None] * 8 - + current_dis_blow_out_air_volume = ( + blow_out_air_volume[0:1] * 8 if blow_out_air_volume else [None] * 8 + ) + await self.dispense( resources=[target] * 8, # 8个通道都分到同一个目标 vols=current_dis_vols, @@ -1647,12 +1805,12 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): liquid_height=current_dis_liquid_height, spread=spread, ) - + if delays is not None and len(delays) > 1: await self.custom_delay(seconds=delays[1]) - - await self.discard_tips([0,1,2,3,4,5,6,7]) - + + await self.discard_tips([0, 1, 2, 3, 4, 5, 6, 7]) + # 最后在目标容器中混合（如果需要） if mix_stage in ["after", "both"] and mix_times is not None and mix_times > 0: await self.mix( @@ -1663,7 +1821,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) - + if touch_tip: await self.touch_tip([target]) @@ -1671,7 +1829,6 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): # traceback.print_exc() # raise RuntimeError(f"Liquid addition failed: {e}") from e - # --------------------------------------------------------------- # Helper utilities # --------------------------------------------------------------- @@ -1692,7 +1849,6 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware): print(f"Current time: {time.strftime('%H:%M:%S')}") async def touch_tip(self, targets: Sequence[Container]): - """Touch the tip to the side of the well.""" if not self.support_touch_tip: diff --git a/unilabos/devices/liquid_handling/prcxi/prcxi.py b/unilabos/devices/liquid_handling/prcxi/prcxi.py index e0c7e80..4f96255 100644 --- a/unilabos/devices/liquid_handling/prcxi/prcxi.py +++ b/unilabos/devices/liquid_handling/prcxi/prcxi.py @@ -30,9 +30,30 @@ from pylabrobot.liquid_handling.standard import ( ResourceMove, ResourceDrop, ) -from pylabrobot.resources import ResourceHolder, ResourceStack, Tip, Deck, Plate, Well, TipRack, Resource, Container, Coordinate, TipSpot, Trash, PlateAdapter, TubeRack +from pylabrobot.resources import ( + ResourceHolder, + ResourceStack, + Tip, + Deck, + Plate, + Well, + TipRack, + Resource, + Container, + Coordinate, + TipSpot, + Trash, + PlateAdapter, + TubeRack, +) -from unilabos.devices.liquid_handling.liquid_handler_abstract import LiquidHandlerAbstract, SimpleReturn +from unilabos.devices.liquid_handling.liquid_handler_abstract import ( + LiquidHandlerAbstract, + SimpleReturn, + SetLiquidReturn, + SetLiquidFromPlateReturn, +) +from unilabos.registry.placeholder_type import ResourceSlot from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode @@ -80,6 +101,7 @@ class PRCXI9300Deck(Deck): self.slots[slot - 1] = resource super().assign_child_resource(resource, location=self.slot_locations[slot - 1]) + class PRCXI9300Container(Plate): """PRCXI 9300 的专用 Container 类，继承自 Plate，用于槽位定位和未知模块。 @@ -108,20 +130,29 @@ class PRCXI9300Container(Plate): def serialize_state(self) -> Dict[str, Dict[str, Any]]: data = super().serialize_state() data.update(self._unilabos_state) - return data + return data + + class PRCXI9300Plate(Plate): - """ + """ 专用孔板类： 1. 继承自 PLR 原生 Plate，保留所有物理特性。 2. 增加 material_info 参数，用于在初始化时直接绑定 Unilab UUID。 """ - def __init__(self, name: str, size_x: float, size_y: float, size_z: float, - category: str = "plate", - ordered_items: collections.OrderedDict = None, - ordering: Optional[collections.OrderedDict] = None, - model: Optional[str] = None, - material_info: Optional[Dict[str, Any]] = None, - **kwargs): + + def __init__( + self, + name: str, + size_x: float, + size_y: float, + size_z: float, + category: str = "plate", + ordered_items: collections.OrderedDict = None, + ordering: Optional[collections.OrderedDict] = None, + model: Optional[str] = None, + material_info: Optional[Dict[str, Any]] = None, + **kwargs, + ): # 如果 ordered_items 不为 None，直接使用 if ordered_items is not None: items = ordered_items @@ -142,40 +173,34 @@ class PRCXI9300Plate(Plate): else: items = None ordering_param = None - + # 根据情况传递不同的参数 if items is not None: - super().__init__(name, size_x, size_y, size_z, - ordered_items=items, - category=category, - model=model, **kwargs) + super().__init__( + name, size_x, size_y, size_z, ordered_items=items, category=category, model=model, **kwargs + ) elif ordering_param is not None: # 传递 ordering 参数，让 Plate 自己创建 Well 对象 - super().__init__(name, size_x, size_y, size_z, - ordering=ordering_param, - category=category, - model=model, **kwargs) + super().__init__( + name, size_x, size_y, size_z, ordering=ordering_param, category=category, model=model, **kwargs + ) else: - super().__init__(name, size_x, size_y, size_z, - category=category, - model=model, **kwargs) - + super().__init__(name, size_x, size_y, size_z, category=category, model=model, **kwargs) + self._unilabos_state = {} if material_info: self._unilabos_state["Material"] = material_info - def load_state(self, state: Dict[str, Any]) -> None: super().load_state(state) self._unilabos_state = state - def serialize_state(self) -> Dict[str, Dict[str, Any]]: try: data = super().serialize_state() except AttributeError: data = {} - if hasattr(self, '_unilabos_state') and self._unilabos_state: + if hasattr(self, "_unilabos_state") and self._unilabos_state: safe_state = {} for k, v in self._unilabos_state.items(): # 如果是 Material 字典，深入检查 @@ -188,23 +213,32 @@ class PRCXI9300Plate(Plate): else: # 打印日志提醒（可选） # print(f"Warning: Removing non-serializable key {mk} from {self.name}") - pass + pass safe_state[k] = safe_material # 其他顶层属性也进行类型检查 elif isinstance(v, (str, int, float, bool, list, dict, type(None))): safe_state[k] = v - + data.update(safe_state) - return data # 其他顶层属性也进行类型检查 + return data # 其他顶层属性也进行类型检查 + + class PRCXI9300TipRack(TipRack): - """ 专用吸头盒类 """ - def __init__(self, name: str, size_x: float, size_y: float, size_z: float, - category: str = "tip_rack", - ordered_items: collections.OrderedDict = None, - ordering: Optional[collections.OrderedDict] = None, - model: Optional[str] = None, - material_info: Optional[Dict[str, Any]] = None, - **kwargs): + """专用吸头盒类""" + + def __init__( + self, + name: str, + size_x: float, + size_y: float, + size_z: float, + category: str = "tip_rack", + ordered_items: collections.OrderedDict = None, + ordering: Optional[collections.OrderedDict] = None, + model: Optional[str] = None, + material_info: Optional[Dict[str, Any]] = None, + **kwargs, + ): # 如果 ordered_items 不为 None，直接使用 if ordered_items is not None: items = ordered_items @@ -225,27 +259,23 @@ class PRCXI9300TipRack(TipRack): else: items = None ordering_param = None - + # 根据情况传递不同的参数 if items is not None: - super().__init__(name, size_x, size_y, size_z, - ordered_items=items, - category=category, - model=model, **kwargs) + super().__init__( + name, size_x, size_y, size_z, ordered_items=items, category=category, model=model, **kwargs + ) elif ordering_param is not None: # 传递 ordering 参数，让 TipRack 自己创建 Tip 对象 - super().__init__(name, size_x, size_y, size_z, - ordering=ordering_param, - category=category, - model=model, **kwargs) + super().__init__( + name, size_x, size_y, size_z, ordering=ordering_param, category=category, model=model, **kwargs + ) else: - super().__init__(name, size_x, size_y, size_z, - category=category, - model=model, **kwargs) + super().__init__(name, size_x, size_y, size_z, category=category, model=model, **kwargs) self._unilabos_state = {} if material_info: self._unilabos_state["Material"] = material_info - + def load_state(self, state: Dict[str, Any]) -> None: super().load_state(state) self._unilabos_state = state @@ -255,7 +285,7 @@ class PRCXI9300TipRack(TipRack): data = super().serialize_state() except AttributeError: data = {} - if hasattr(self, '_unilabos_state') and self._unilabos_state: + if hasattr(self, "_unilabos_state") and self._unilabos_state: safe_state = {} for k, v in self._unilabos_state.items(): # 如果是 Material 字典，深入检查 @@ -268,26 +298,33 @@ class PRCXI9300TipRack(TipRack): else: # 打印日志提醒（可选） # print(f"Warning: Removing non-serializable key {mk} from {self.name}") - pass + pass safe_state[k] = safe_material # 其他顶层属性也进行类型检查 elif isinstance(v, (str, int, float, bool, list, dict, type(None))): safe_state[k] = v - + data.update(safe_state) return data - + + class PRCXI9300Trash(Trash): """PRCXI 9300 的专用 Trash 类，继承自 Trash。 该类定义了 PRCXI 9300 的工作台布局和槽位信息。 """ - def __init__(self, name: str, size_x: float, size_y: float, size_z: float, - category: str = "trash", - material_info: Optional[Dict[str, Any]] = None, - **kwargs): - + def __init__( + self, + name: str, + size_x: float, + size_y: float, + size_z: float, + category: str = "trash", + material_info: Optional[Dict[str, Any]] = None, + **kwargs, + ): + if name != "trash": print(f"Warning: PRCXI9300Trash usually expects name='trash' for backend logic, but got '{name}'.") super().__init__(name, size_x, size_y, size_z, **kwargs) @@ -306,7 +343,7 @@ class PRCXI9300Trash(Trash): data = super().serialize_state() except AttributeError: data = {} - if hasattr(self, '_unilabos_state') and self._unilabos_state: + if hasattr(self, "_unilabos_state") and self._unilabos_state: safe_state = {} for k, v in self._unilabos_state.items(): # 如果是 Material 字典，深入检查 @@ -319,29 +356,37 @@ class PRCXI9300Trash(Trash): else: # 打印日志提醒（可选） # print(f"Warning: Removing non-serializable key {mk} from {self.name}") - pass + pass safe_state[k] = safe_material # 其他顶层属性也进行类型检查 elif isinstance(v, (str, int, float, bool, list, dict, type(None))): safe_state[k] = v - + data.update(safe_state) return data + class PRCXI9300TubeRack(TubeRack): """ 专用管架类：用于 EP 管架、试管架等。 继承自 PLR 的 TubeRack，并支持注入 material_info (UUID)。 """ - def __init__(self, name: str, size_x: float, size_y: float, size_z: float, - category: str = "tube_rack", - items: Optional[Dict[str, Any]] = None, - ordered_items: Optional[OrderedDict] = None, - ordering: Optional[OrderedDict] = None, - model: Optional[str] = None, - material_info: Optional[Dict[str, Any]] = None, - **kwargs): - + + def __init__( + self, + name: str, + size_x: float, + size_y: float, + size_z: float, + category: str = "tube_rack", + items: Optional[Dict[str, Any]] = None, + ordered_items: Optional[OrderedDict] = None, + ordering: Optional[OrderedDict] = None, + model: Optional[str] = None, + material_info: Optional[Dict[str, Any]] = None, + **kwargs, + ): + # 如果 ordered_items 不为 None，直接使用 if ordered_items is not None: items_to_pass = ordered_items @@ -367,24 +412,16 @@ class PRCXI9300TubeRack(TubeRack): else: items_to_pass = None ordering_param = None - + # 根据情况传递不同的参数 if items_to_pass is not None: - super().__init__(name, size_x, size_y, size_z, - ordered_items=items_to_pass, - model=model, - **kwargs) + super().__init__(name, size_x, size_y, size_z, ordered_items=items_to_pass, model=model, **kwargs) elif ordering_param is not None: # 传递 ordering 参数，让 TubeRack 自己创建 Tube 对象 - super().__init__(name, size_x, size_y, size_z, - ordering=ordering_param, - model=model, - **kwargs) + super().__init__(name, size_x, size_y, size_z, ordering=ordering_param, model=model, **kwargs) else: - super().__init__(name, size_x, size_y, size_z, - model=model, - **kwargs) - + super().__init__(name, size_x, size_y, size_z, model=model, **kwargs) + self._unilabos_state = {} if material_info: self._unilabos_state["Material"] = material_info @@ -394,7 +431,7 @@ class PRCXI9300TubeRack(TubeRack): data = super().serialize_state() except AttributeError: data = {} - if hasattr(self, '_unilabos_state') and self._unilabos_state: + if hasattr(self, "_unilabos_state") and self._unilabos_state: safe_state = {} for k, v in self._unilabos_state.items(): # 如果是 Material 字典，深入检查 @@ -407,33 +444,41 @@ class PRCXI9300TubeRack(TubeRack): else: # 打印日志提醒（可选） # print(f"Warning: Removing non-serializable key {mk} from {self.name}") - pass + pass safe_state[k] = safe_material # 其他顶层属性也进行类型检查 elif isinstance(v, (str, int, float, bool, list, dict, type(None))): safe_state[k] = v - + data.update(safe_state) return data + class PRCXI9300PlateAdapter(PlateAdapter): """ 专用板式适配器类：用于承载 Plate 的底座（如 PCR 适配器、磁吸架等）。 支持注入 material_info (UUID)。 """ - def __init__(self, name: str, size_x: float, size_y: float, size_z: float, - category: str = "plate_adapter", - model: Optional[str] = None, - material_info: Optional[Dict[str, Any]] = None, - # 参数给予默认值 (标准96孔板尺寸) - adapter_hole_size_x: float = 127.76, - adapter_hole_size_y: float = 85.48, - adapter_hole_size_z: float = 10.0, # 假设凹槽深度或板子放置高度 - dx: Optional[float] = None, - dy: Optional[float] = None, - dz: float = 0.0, # 默认Z轴偏移 - **kwargs): - + + def __init__( + self, + name: str, + size_x: float, + size_y: float, + size_z: float, + category: str = "plate_adapter", + model: Optional[str] = None, + material_info: Optional[Dict[str, Any]] = None, + # 参数给予默认值 (标准96孔板尺寸) + adapter_hole_size_x: float = 127.76, + adapter_hole_size_y: float = 85.48, + adapter_hole_size_z: float = 10.0, # 假设凹槽深度或板子放置高度 + dx: Optional[float] = None, + dy: Optional[float] = None, + dz: float = 0.0, # 默认Z轴偏移 + **kwargs, + ): + # 自动居中计算：如果未指定 dx/dy，则根据适配器尺寸和孔尺寸计算居中位置 if dx is None: dx = (size_x - adapter_hole_size_x) / 2 @@ -441,20 +486,20 @@ class PRCXI9300PlateAdapter(PlateAdapter): dy = (size_y - adapter_hole_size_y) / 2 super().__init__( - name=name, - size_x=size_x, - size_y=size_y, - size_z=size_z, + name=name, + size_x=size_x, + size_y=size_y, + size_z=size_z, dx=dx, dy=dy, dz=dz, adapter_hole_size_x=adapter_hole_size_x, adapter_hole_size_y=adapter_hole_size_y, adapter_hole_size_z=adapter_hole_size_z, - model=model, - **kwargs + model=model, + **kwargs, ) - + self._unilabos_state = {} if material_info: self._unilabos_state["Material"] = material_info @@ -464,7 +509,7 @@ class PRCXI9300PlateAdapter(PlateAdapter): data = super().serialize_state() except AttributeError: data = {} - if hasattr(self, '_unilabos_state') and self._unilabos_state: + if hasattr(self, "_unilabos_state") and self._unilabos_state: safe_state = {} for k, v in self._unilabos_state.items(): # 如果是 Material 字典，深入检查 @@ -477,15 +522,16 @@ class PRCXI9300PlateAdapter(PlateAdapter): else: # 打印日志提醒（可选） # print(f"Warning: Removing non-serializable key {mk} from {self.name}") - pass + pass safe_state[k] = safe_material # 其他顶层属性也进行类型检查 elif isinstance(v, (str, int, float, bool, list, dict, type(None))): safe_state[k] = v - + data.update(safe_state) return data + class PRCXI9300Handler(LiquidHandlerAbstract): support_touch_tip = False @@ -518,7 +564,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract): if "Material" in child.children[0]._unilabos_state: number = int(child.name.replace("T", "")) tablets_info.append( - WorkTablets(Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"]) + WorkTablets( + Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"] + ) ) if is_9320: print("当前设备是9320") @@ -538,9 +586,14 @@ class PRCXI9300Handler(LiquidHandlerAbstract): super().post_init(ros_node) self._unilabos_backend.post_init(ros_node) - def set_liquid(self, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SimpleReturn: + def set_liquid(self, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SetLiquidReturn: return super().set_liquid(wells, liquid_names, volumes) + def set_liquid_from_plate( + self, plate: ResourceSlot, well_names: list[str], liquid_names: list[str], volumes: list[float] + ) -> SetLiquidFromPlateReturn: + return super().set_liquid_from_plate(plate, well_names, liquid_names, volumes) + def set_group(self, group_name: str, wells: List[Well], volumes: List[float]): return super().set_group(group_name, wells, volumes) @@ -799,7 +852,8 @@ class PRCXI9300Handler(LiquidHandlerAbstract): return await self._unilabos_backend.shaker_action(time, module_no, amplitude, is_wait) async def heater_action(self, temperature: float, time: int): - return await self._unilabos_backend.heater_action(temperature, time) + return await self._unilabos_backend.heater_action(temperature, time) + async def move_plate( self, plate: Plate, @@ -822,10 +876,11 @@ class PRCXI9300Handler(LiquidHandlerAbstract): drop_direction, pickup_direction, pickup_distance_from_top, - target_plate_number = to, + target_plate_number=to, **backend_kwargs, ) + class PRCXI9300Backend(LiquidHandlerBackend): """PRCXI 9300 的后端实现，继承自 LiquidHandlerBackend。 @@ -878,31 +933,28 @@ class PRCXI9300Backend(LiquidHandlerBackend): self.steps_todo_list.append(step) return step - async def pick_up_resource(self, pickup: ResourcePickup, **backend_kwargs): - - resource=pickup.resource - offset=pickup.offset - pickup_distance_from_top=pickup.pickup_distance_from_top - direction=pickup.direction + + resource = pickup.resource + offset = pickup.offset + pickup_distance_from_top = pickup.pickup_distance_from_top + direction = pickup.direction plate_number = int(resource.parent.name.replace("T", "")) is_whole_plate = True balance_height = 0 step = self.api_client.clamp_jaw_pick_up(plate_number, is_whole_plate, balance_height) - + self.steps_todo_list.append(step) return step async def drop_resource(self, drop: ResourceDrop, **backend_kwargs): - plate_number = None target_plate_number = backend_kwargs.get("target_plate_number", None) if target_plate_number is not None: plate_number = int(target_plate_number.name.replace("T", "")) - is_whole_plate = True balance_height = 0 if plate_number is None: @@ -911,7 +963,6 @@ class PRCXI9300Backend(LiquidHandlerBackend): self.steps_todo_list.append(step) return step - async def heater_action(self, temperature: float, time: int): print(f"\n\nHeater action: temperature={temperature}, time={time}\n\n") # return await self.api_client.heater_action(temperature, time) @@ -968,7 +1019,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): error_code = self.api_client.get_error_code() if error_code: print(f"PRCXI9300 error code detected: {error_code}") - + # 清除错误代码 self.api_client.clear_error_code() print("PRCXI9300 error code cleared.") @@ -976,11 +1027,11 @@ class PRCXI9300Backend(LiquidHandlerBackend): # 执行重置 print("Starting PRCXI9300 reset...") self.api_client.call("IAutomation", "Reset") - + # 检查重置状态并等待完成 while not self.is_reset_ok: print("Waiting for PRCXI9300 to reset...") - if hasattr(self, '_ros_node') and self._ros_node is not None: + if hasattr(self, "_ros_node") and self._ros_node is not None: await self._ros_node.sleep(1) else: await asyncio.sleep(1) @@ -998,7 +1049,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): """Pick up tips from the specified resource.""" # INSERT_YOUR_CODE # Ensure use_channels is converted to a list of ints if it's an array - if hasattr(use_channels, 'tolist'): + if hasattr(use_channels, "tolist"): _use_channels = use_channels.tolist() else: _use_channels = list(use_channels) if use_channels is not None else None @@ -1052,7 +1103,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): async def drop_tips(self, ops: List[Drop], use_channels: List[int] = None): """Pick up tips from the specified resource.""" - if hasattr(use_channels, 'tolist'): + if hasattr(use_channels, "tolist"): _use_channels = use_channels.tolist() else: _use_channels = list(use_channels) if use_channels is not None else None @@ -1135,7 +1186,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): none_keys: List[str] = [], ): """Mix liquid in the specified resources.""" - + plate_indexes = [] for op in targets: deck = op.parent.parent.parent @@ -1178,7 +1229,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): async def aspirate(self, ops: List[SingleChannelAspiration], use_channels: List[int] = None): """Aspirate liquid from the specified resources.""" - if hasattr(use_channels, 'tolist'): + if hasattr(use_channels, "tolist"): _use_channels = use_channels.tolist() else: _use_channels = list(use_channels) if use_channels is not None else None @@ -1235,7 +1286,7 @@ class PRCXI9300Backend(LiquidHandlerBackend): async def dispense(self, ops: List[SingleChannelDispense], use_channels: List[int] = None): """Dispense liquid into the specified resources.""" - if hasattr(use_channels, 'tolist'): + if hasattr(use_channels, "tolist"): _use_channels = use_channels.tolist() else: _use_channels = list(use_channels) if use_channels is not None else None @@ -1416,7 +1467,6 @@ class PRCXI9300Api: time.sleep(1) return success - def call(self, service: str, method: str, params: Optional[list] = None) -> Any: payload = json.dumps( {"ServiceName": service, "MethodName": method, "Paramters": params or []}, separators=(",", ":") @@ -1543,7 +1593,7 @@ class PRCXI9300Api: assist_fun5: str = "", liquid_method: str = "NormalDispense", axis: str = "Left", - ) -> Dict[str, Any]: + ) -> Dict[str, Any]: return { "StepAxis": axis, "Function": "Imbibing", @@ -1621,7 +1671,7 @@ class PRCXI9300Api: assist_fun5: str = "", liquid_method: str = "NormalDispense", axis: str = "Left", - ) -> Dict[str, Any]: + ) -> Dict[str, Any]: return { "StepAxis": axis, "Function": "Blending", @@ -1681,11 +1731,11 @@ class PRCXI9300Api: "LiquidDispensingMethod": liquid_method, } - def clamp_jaw_pick_up(self, + def clamp_jaw_pick_up( + self, plate_no: int, is_whole_plate: bool, balance_height: int, - ) -> Dict[str, Any]: return { "StepAxis": "ClampingJaw", @@ -1695,7 +1745,7 @@ class PRCXI9300Api: "HoleRow": 1, "HoleCol": 1, "BalanceHeight": balance_height, - "PlateOrHoleNum": f"T{plate_no}" + "PlateOrHoleNum": f"T{plate_no}", } def clamp_jaw_drop( @@ -1703,7 +1753,6 @@ class PRCXI9300Api: plate_no: int, is_whole_plate: bool, balance_height: int, - ) -> Dict[str, Any]: return { "StepAxis": "ClampingJaw", @@ -1713,7 +1762,7 @@ class PRCXI9300Api: "HoleRow": 1, "HoleCol": 1, "BalanceHeight": balance_height, - "PlateOrHoleNum": f"T{plate_no}" + "PlateOrHoleNum": f"T{plate_no}", } def shaker_action(self, time: int, module_no: int, amplitude: int, is_wait: bool): @@ -1726,6 +1775,7 @@ class PRCXI9300Api: "AssistFun4": is_wait, } + class DefaultLayout: def __init__(self, product_name: str = "PRCXI9300"): @@ -2104,7 +2154,9 @@ if __name__ == "__main__": size_y=50, size_z=10, category="tip_rack", - ordered_items=collections.OrderedDict({k: f"{child_prefix}_{k}" for k, v in tip_racks["ordering"].items()}), + ordered_items=collections.OrderedDict( + {k: f"{child_prefix}_{k}" for k, v in tip_racks["ordering"].items()} + ), ) tip_rack_serialized = tip_rack.serialize() tip_rack_serialized["parent_name"] = deck.name @@ -2299,43 +2351,37 @@ if __name__ == "__main__": A = tree_to_list([resource_plr_to_ulab(deck)]) with open("deck.json", "w", encoding="utf-8") as f: - A.insert(0, { - "id": "PRCXI", - "name": "PRCXI", - "parent": None, - "type": "device", - "class": "liquid_handler.prcxi", - "position": { - "x": 0, - "y": 0, - "z": 0 - }, - "config": { - "deck": { - "_resource_child_name": "PRCXI_Deck", - "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck" + A.insert( + 0, + { + "id": "PRCXI", + "name": "PRCXI", + "parent": None, + "type": "device", + "class": "liquid_handler.prcxi", + "position": {"x": 0, "y": 0, "z": 0}, + "config": { + "deck": { + "_resource_child_name": "PRCXI_Deck", + "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck", + }, + "host": "192.168.0.121", + "port": 9999, + "timeout": 10.0, + "axis": "Right", + "channel_num": 1, + "setup": False, + "debug": True, + "simulator": True, + "matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb", + "is_9320": True, }, - "host": "192.168.0.121", - "port": 9999, - "timeout": 10.0, - "axis": "Right", - "channel_num": 1, - "setup": False, - "debug": True, - "simulator": True, - "matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb", - "is_9320": True + "data": {}, + "children": ["PRCXI_Deck"], }, - "data": {}, - "children": [ - "PRCXI_Deck" - ] - }) + ) A[1]["parent"] = "PRCXI" - json.dump({ - "nodes": A, - "links": [] - }, f, indent=4, ensure_ascii=False) + json.dump({"nodes": A, "links": []}, f, indent=4, ensure_ascii=False) handler = PRCXI9300Handler( deck=deck, @@ -2377,7 +2423,6 @@ if __name__ == "__main__": time.sleep(5) os._exit(0) - prcxi_api = PRCXI9300Api(host="192.168.0.121", port=9999) prcxi_api.list_matrices() prcxi_api.get_all_materials() diff --git a/unilabos/registry/devices/liquid_handler.yaml b/unilabos/registry/devices/liquid_handler.yaml index 7e3aaeb..b2612e7 100644 --- a/unilabos/registry/devices/liquid_handler.yaml +++ b/unilabos/registry/devices/liquid_handler.yaml @@ -9284,7 +9284,13 @@ liquid_handler.prcxi: data_source: handle data_type: resource handler_key: input_wells - label: InputWells + label: 待设定液体孔 + output: + - data_key: wells.@flatten + data_source: executor + data_type: resource + handler_key: output_wells + label: 已设定液体孔 placeholder_keys: wells: unilabos_resources result: {} @@ -9400,6 +9406,163 @@ liquid_handler.prcxi: title: LiquidHandlerSetLiquid type: object type: LiquidHandlerSetLiquid + set_liquid_from_plate: + feedback: {} + goal: {} + goal_default: + liquid_names: null + plate: null + volumes: null + well_names: null + handles: + input: + - data_key: plate + data_source: handle + data_type: resource + handler_key: input_plate + label: 待设定液体板 + output: + - data_key: plate.@flatten + data_source: executor + data_type: resource + handler_key: output_plate + label: 已设定液体板 + - data_key: wells.@flatten + data_source: executor + data_type: resource + handler_key: output_wells + label: 已设定液体孔 + - data_key: volumes + data_source: executor + data_type: number_array + handler_key: output_volumes + label: 各孔设定体积 + placeholder_keys: + plate: unilabos_resources + result: {} + schema: + description: '' + properties: + feedback: {} + goal: + properties: + liquid_names: + items: + type: string + type: array + plate: + properties: + category: + type: string + children: + items: + type: string + type: array + config: + type: string + data: + type: string + id: + type: string + name: + type: string + parent: + type: string + pose: + properties: + orientation: + properties: + w: + type: number + x: + type: number + y: + type: number + z: + type: number + required: + - x + - y + - z + - w + title: orientation + type: object + position: + properties: + x: + type: number + y: + type: number + z: + type: number + required: + - x + - y + - z + title: position + type: object + required: + - position + - orientation + title: pose + type: object + sample_id: + type: string + type: + type: string + required: + - id + - name + - sample_id + - children + - parent + - type + - category + - pose + - config + - data + title: plate + type: object + volumes: + items: + type: number + type: array + well_names: + items: + type: string + type: array + required: + - plate + - well_names + - liquid_names + - volumes + type: object + result: + properties: + plate: + items: {} + title: Plate + type: array + volumes: + items: + type: number + title: Volumes + type: array + wells: + items: {} + title: Wells + type: array + required: + - plate + - wells + - volumes + title: SetLiquidFromPlateReturn + type: object + required: + - goal + title: set_liquid_from_plate参数 + type: object + type: UniLabJsonCommand set_tiprack: feedback: {} goal: diff --git a/unilabos/registry/registry.py b/unilabos/registry/registry.py index fa3efef..de2d812 100644 --- a/unilabos/registry/registry.py +++ b/unilabos/registry/registry.py @@ -163,6 +163,7 @@ class Registry: "res_id": "unilabos_resources", # 将当前实验室的全部物料id作为下拉框可选择 "device_id": "unilabos_devices", # 将当前实验室的全部设备id作为下拉框可选择 "parent": "unilabos_nodes", # 将当前实验室的设备/物料作为下拉框可选择 + "class_name": "unilabos_class", }, }, "test_latency": { diff --git a/unilabos/resources/graphio.py b/unilabos/resources/graphio.py index da36fb5..30764a1 100644 --- a/unilabos/resources/graphio.py +++ b/unilabos/resources/graphio.py @@ -260,7 +260,7 @@ def read_node_link_json( resource_tree_set = canonicalize_nodes_data(nodes) # 标准化边数据 - links = data.get("links", []) + links = data.get("links", data.get("edges", [])) standardized_links = canonicalize_links_ports(links, resource_tree_set) # 构建 NetworkX 图（需要转换回 dict 格式） diff --git a/unilabos/resources/resource_tracker.py b/unilabos/resources/resource_tracker.py index df48aff..906f4d1 100644 --- a/unilabos/resources/resource_tracker.py +++ b/unilabos/resources/resource_tracker.py @@ -13,6 +13,9 @@ if TYPE_CHECKING: from pylabrobot.resources import Resource as PLRResource +EXTRA_CLASS = "unilabos_resource_class" + + class ResourceDictPositionSize(BaseModel): depth: float = Field(description="Depth", default=0.0) # z width: float = Field(description="Width", default=0.0) # x @@ -393,7 +396,7 @@ class ResourceTreeSet(object): "parent": parent_resource, # 直接传入 ResourceDict 对象 "parent_uuid": parent_uuid, # 使用 parent_uuid 而不是 parent 对象 "type": replace_plr_type(d.get("category", "")), - "class": d.get("class", ""), + "class": extra.get(EXTRA_CLASS, ""), "position": pos, "pose": pos, "config": { @@ -443,7 +446,7 @@ class ResourceTreeSet(object): trees.append(tree_instance) return cls(trees) - def to_plr_resources(self) -> List["PLRResource"]: + def to_plr_resources(self, skip_devices=True) -> List["PLRResource"]: """ 将 ResourceTreeSet 转换为 PLR 资源列表 @@ -468,6 +471,7 @@ class ResourceTreeSet(object): name_to_uuid[node.res_content.name] = node.res_content.uuid all_states[node.res_content.name] = node.res_content.data name_to_extra[node.res_content.name] = node.res_content.extra + name_to_extra[node.res_content.name][EXTRA_CLASS] = node.res_content.klass for child in node.children: collect_node_data(child, name_to_uuid, all_states, name_to_extra) @@ -512,7 +516,10 @@ class ResourceTreeSet(object): plr_dict = node_to_plr_dict(tree.root_node, has_model) try: sub_cls = find_subclass(plr_dict["type"], PLRResource) - if sub_cls is None: + if skip_devices and plr_dict["type"] == "device": + logger.info(f"跳过更新 {plr_dict['name']} 设备是class") + continue + elif sub_cls is None: raise ValueError( f"无法找到类型 {plr_dict['type']} 对应的 PLR 资源类。原始信息：{tree.root_node.res_content}" ) @@ -520,6 +527,10 @@ class ResourceTreeSet(object): if "category" not in spec.parameters: plr_dict.pop("category", None) plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True) + from pylabrobot.resources import Coordinate + from pylabrobot.serializer import deserialize + location = cast(Coordinate, deserialize(plr_dict["location"])) + plr_resource.location = location plr_resource.load_all_state(all_states) # 使用 DeviceNodeResourceTracker 设置 UUID 和 Extra tracker.loop_set_uuid(plr_resource, name_to_uuid) @@ -986,7 +997,7 @@ class DeviceNodeResourceTracker(object): extra = name_to_extra_map[resource_name] self.set_resource_extra(res, extra) if len(extra): - logger.debug(f"设置资源Extra: {resource_name} -> {extra}") + logger.trace(f"设置资源Extra: {resource_name} -> {extra}") return 1 return 0 diff --git a/unilabos/ros/nodes/base_device_node.py b/unilabos/ros/nodes/base_device_node.py index 95fc075..3d1ffda 100644 --- a/unilabos/ros/nodes/base_device_node.py +++ b/unilabos/ros/nodes/base_device_node.py @@ -884,6 +884,9 @@ class BaseROS2DeviceNode(Node, Generic[T]): parent_appended = True # 加载状态 + original_instance.location = plr_resource.location + original_instance.rotation = plr_resource.rotation + original_instance.barcode = plr_resource.barcode original_instance.load_all_state(states) child_count = len(original_instance.get_all_children()) self.lab_logger().info( @@ -1319,19 +1322,32 @@ class BaseROS2DeviceNode(Node, Generic[T]): resource_inputs = action_kwargs[k] if is_sequence else [action_kwargs[k]] # 批量查询资源 - queried_resources = [] - for resource_data in resource_inputs: + queried_resources: list = [None] * len(resource_inputs) + uuid_indices: list[tuple[int, str, dict]] = [] # (index, uuid, resource_data) + + # 第一遍：处理没有uuid的资源，收集有uuid的资源信息 + for idx, resource_data in enumerate(resource_inputs): unilabos_uuid = resource_data.get("data", {}).get("unilabos_uuid") if unilabos_uuid is None: plr_resource = await self.get_resource_with_dir( resource_id=resource_data["id"], with_children=True ) + if "sample_id" in resource_data: + plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"] + queried_resources[idx] = plr_resource else: - resource_tree = await self.get_resource([unilabos_uuid]) - plr_resource = resource_tree.to_plr_resources()[0] - if "sample_id" in resource_data: - plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"] - queried_resources.append(plr_resource) + uuid_indices.append((idx, unilabos_uuid, resource_data)) + + # 第二遍：批量查询有uuid的资源 + if uuid_indices: + uuids = [item[1] for item in uuid_indices] + resource_tree = await self.get_resource(uuids) + plr_resources = resource_tree.to_plr_resources() + for i, (idx, _, resource_data) in enumerate(uuid_indices): + plr_resource = plr_resources[i] + if "sample_id" in resource_data: + plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"] + queried_resources[idx] = plr_resource self.lab_logger().debug(f"资源查询结果: 共 {len(queried_resources)} 个资源") diff --git a/unilabos/ros/nodes/presets/workstation.py b/unilabos/ros/nodes/presets/workstation.py index ed3fe14..f30e33b 100644 --- a/unilabos/ros/nodes/presets/workstation.py +++ b/unilabos/ros/nodes/presets/workstation.py @@ -6,8 +6,6 @@ from typing import List, Dict, Any, Optional, TYPE_CHECKING import rclpy from rosidl_runtime_py import message_to_ordereddict -from unilabos_msgs.msg import Resource -from unilabos_msgs.srv import ResourceUpdate from unilabos.messages import * # type: ignore # protocol names from rclpy.action import ActionServer, ActionClient @@ -15,7 +13,6 @@ from rclpy.action.server import ServerGoalHandle from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response from unilabos.compile import action_protocol_generators -from unilabos.resources.graphio import nested_dict_to_list from unilabos.ros.initialize_device import initialize_device_from_dict from unilabos.ros.msgs.message_converter import ( get_action_type, @@ -231,15 +228,15 @@ class ROS2WorkstationNode(BaseROS2DeviceNode): try: # 统一处理单个或多个资源 resource_id = ( - protocol_kwargs[k]["id"] if v == "unilabos_msgs/Resource" else protocol_kwargs[k][0]["id"] + protocol_kwargs[k]["id"] + if v == "unilabos_msgs/Resource" + else protocol_kwargs[k][0]["id"] ) resource_uuid = protocol_kwargs[k].get("uuid", None) r = SerialCommand_Request() r.command = json.dumps({"id": resource_id, "uuid": resource_uuid, "with_children": True}) # 发送请求并等待响应 - response: SerialCommand_Response = await self._resource_clients[ - "resource_get" - ].call_async( + response: SerialCommand_Response = await self._resource_clients["resource_get"].call_async( r ) # type: ignore raw_data = json.loads(response.response) @@ -307,12 +304,52 @@ class ROS2WorkstationNode(BaseROS2DeviceNode): # 向Host更新物料当前状态 for k, v in goal.get_fields_and_field_types().items(): - if v in ["unilabos_msgs/Resource", "sequence"]: - r = ResourceUpdate.Request() - r.resources = [ - convert_to_ros_msg(Resource, rs) for rs in nested_dict_to_list(protocol_kwargs[k]) - ] - response = await self._resource_clients["resource_update"].call_async(r) + if v not in ["unilabos_msgs/Resource", "sequence"]: + continue + self.lab_logger().info(f"更新资源状态: {k}") + try: + # 去重：使用 seen 集合获取唯一的资源对象 + seen = set() + unique_resources = [] + + # 获取资源数据，统一转换为列表 + resource_data = protocol_kwargs[k] + is_sequence = v != "unilabos_msgs/Resource" + if not is_sequence: + resource_list = [resource_data] if isinstance(resource_data, dict) else resource_data + else: + # 处理序列类型，可能是嵌套列表 + resource_list = [] + if isinstance(resource_data, list): + for item in resource_data: + if isinstance(item, list): + resource_list.extend(item) + else: + resource_list.append(item) + else: + resource_list = [resource_data] + + for res_data in resource_list: + if not isinstance(res_data, dict): + continue + res_name = res_data.get("id") or res_data.get("name") + if not res_name: + continue + + # 使用 resource_tracker 获取本地 PLR 实例 + plr = self.resource_tracker.figure_resource({"name": res_name}, try_mode=False) + # 获取父资源 + res = self.resource_tracker.parent_resource(plr) + if id(res) not in seen: + seen.add(id(res)) + unique_resources.append(res) + + # 使用新的资源树接口更新 + if unique_resources: + await self.update_resource(unique_resources) + except Exception as e: + self.lab_logger().error(f"资源更新失败: {e}") + self.lab_logger().error(traceback.format_exc()) # 设置成功状态和返回值 execution_success = True diff --git a/unilabos/workflow/common.py b/unilabos/workflow/common.py new file mode 100644 index 0000000..ad073d9 --- /dev/null +++ b/unilabos/workflow/common.py @@ -0,0 +1,770 @@ +""" +工作流转换模块 - JSON 到 WorkflowGraph 的转换流程 + +==================== 输入格式 (JSON) ==================== + +{ + "workflow": [ + {"action": "transfer_liquid", "action_args": {"sources": "cell_lines", "targets": "Liquid_1", "asp_vol": 100.0, "dis_vol": 74.75, ...}}, + ... + ], + "reagent": { + "cell_lines": {"slot": 4, "well": ["A1", "A3", "A5"], "labware": "DRUG + YOYO-MEDIA"}, + "Liquid_1": {"slot": 1, "well": ["A4", "A7", "A10"], "labware": "rep 1"}, + ... + } +} + +==================== 转换步骤 ==================== + +第一步: 按 slot 去重创建 create_resource 节点（创建板子） +-------------------------------------------------------------------------------- +- 遍历所有 reagent，按 slot 去重，为每个唯一的 slot 创建一个板子 +- 生成参数: + res_id: plate_slot_{slot} + device_id: /PRCXI + class_name: PRCXI_BioER_96_wellplate + parent: /PRCXI/PRCXI_Deck/T{slot} + slot_on_deck: "{slot}" +- 输出端口: labware（用于连接 set_liquid_from_plate） +- 控制流: create_resource 之间通过 ready 端口串联 + +示例: slot=1, slot=4 -> 创建 2 个 create_resource 节点 + +第二步: 为每个 reagent 创建 set_liquid_from_plate 节点（设置液体） +-------------------------------------------------------------------------------- +- 遍历所有 reagent，为每个试剂创建 set_liquid_from_plate 节点 +- 生成参数: + plate: []（通过连接传递，来自 create_resource 的 labware） + well_names: ["A1", "A3", "A5"]（来自 reagent 的 well 数组） + liquid_names: ["cell_lines", "cell_lines", "cell_lines"]（与 well 数量一致） + volumes: [1e5, 1e5, 1e5]（与 well 数量一致，默认体积） +- 输入连接: create_resource (labware) -> set_liquid_from_plate (input_plate) +- 输出端口: output_wells（用于连接 transfer_liquid） +- 控制流: set_liquid_from_plate 连接在所有 create_resource 之后，通过 ready 端口串联 + +第三步: 解析 workflow，创建 transfer_liquid 等动作节点 +-------------------------------------------------------------------------------- +- 遍历 workflow 数组，为每个动作创建步骤节点 +- 参数重命名: asp_vol -> asp_vols, dis_vol -> dis_vols, asp_flow_rate -> asp_flow_rates, dis_flow_rate -> dis_flow_rates +- 参数扩展: 根据 targets 的 wells 数量，将单值扩展为数组 + 例: asp_vol=100.0, targets 有 3 个 wells -> asp_vols=[100.0, 100.0, 100.0] +- 连接处理: 如果 sources/targets 已通过 set_liquid_from_plate 连接，参数值改为 [] +- 输入连接: set_liquid_from_plate (output_wells) -> transfer_liquid (sources_identifier / targets_identifier) +- 输出端口: sources_out, targets_out（用于连接下一个 transfer_liquid） + +==================== 连接关系图 ==================== + +控制流 (ready 端口串联): + create_resource_1 -> create_resource_2 -> ... -> set_liquid_1 -> set_liquid_2 -> ... -> transfer_liquid_1 -> transfer_liquid_2 -> ... + +物料流: + [create_resource] --labware--> [set_liquid_from_plate] --output_wells--> [transfer_liquid] --sources_out/targets_out--> [下一个 transfer_liquid] + (slot=1) (cell_lines) (input_plate) (sources_identifier) (sources_identifier) + (slot=4) (Liquid_1) (targets_identifier) (targets_identifier) + +==================== 端口映射 ==================== + +create_resource: + 输出: labware + +set_liquid_from_plate: + 输入: input_plate + 输出: output_plate, output_wells + +transfer_liquid: + 输入: sources -> sources_identifier, targets -> targets_identifier + 输出: sources -> sources_out, targets -> targets_out + +==================== 校验规则 ==================== + +- 检查 sources/targets 是否在 reagent 中定义 +- 检查 sources 和 targets 的 wells 数量是否匹配 +- 检查参数数组长度是否与 wells 数量一致 +- 如有问题，在 footer 中添加 [WARN: ...] 标记 +""" + +import re +import uuid + +import networkx as nx +from networkx.drawing.nx_agraph import to_agraph +import matplotlib.pyplot as plt +from typing import Dict, List, Any, Tuple, Optional + +Json = Dict[str, Any] + + +# ==================== 默认配置 ==================== + +# create_resource 节点默认参数 +CREATE_RESOURCE_DEFAULTS = { + "device_id": "/PRCXI", + "parent_template": "/PRCXI/PRCXI_Deck/T{slot}", # {slot} 会被替换为实际的 slot 值 + "class_name": "PRCXI_BioER_96_wellplate", +} + +# 默认液体体积 (uL) +DEFAULT_LIQUID_VOLUME = 1e5 + +# 参数重命名映射：单数 -> 复数（用于 transfer_liquid 等动作） +PARAM_RENAME_MAPPING = { + "asp_vol": "asp_vols", + "dis_vol": "dis_vols", + "asp_flow_rate": "asp_flow_rates", + "dis_flow_rate": "dis_flow_rates", +} + + +# ---------------- Graph ---------------- + + +class WorkflowGraph: + """简单的有向图实现：使用 params 单层参数；inputs 内含连线；支持 node-link 导出""" + + def __init__(self): + self.nodes: Dict[str, Dict[str, Any]] = {} + self.edges: List[Dict[str, Any]] = [] + + def add_node(self, node_id: str, **attrs): + self.nodes[node_id] = attrs + + def add_edge(self, source: str, target: str, **attrs): + # 将 source_port/target_port 映射为服务端期望的 source_handle_key/target_handle_key + source_handle_key = attrs.pop("source_port", "") or attrs.pop("source_handle_key", "") + target_handle_key = attrs.pop("target_port", "") or attrs.pop("target_handle_key", "") + + edge = { + "source": source, + "target": target, + "source_node_uuid": source, + "target_node_uuid": target, + "source_handle_key": source_handle_key, + "source_handle_io": attrs.pop("source_handle_io", "source"), + "target_handle_key": target_handle_key, + "target_handle_io": attrs.pop("target_handle_io", "target"), + **attrs, + } + self.edges.append(edge) + + def _materialize_wiring_into_inputs( + self, + obj: Any, + inputs: Dict[str, Any], + variable_sources: Dict[str, Dict[str, Any]], + target_node_id: str, + base_path: List[str], + ): + has_var = False + + def walk(node: Any, path: List[str]): + nonlocal has_var + if isinstance(node, dict): + if "__var__" in node: + has_var = True + varname = node["__var__"] + placeholder = f"${{{varname}}}" + src = variable_sources.get(varname) + if src: + key = ".".join(path) # e.g. "params.foo.bar.0" + inputs[key] = {"node": src["node_id"], "output": src.get("output_name", "result")} + self.add_edge( + str(src["node_id"]), + target_node_id, + source_handle_io=src.get("output_name", "result"), + target_handle_io=key, + ) + return placeholder + return {k: walk(v, path + [k]) for k, v in node.items()} + if isinstance(node, list): + return [walk(v, path + [str(i)]) for i, v in enumerate(node)] + return node + + replaced = walk(obj, base_path[:]) + return replaced, has_var + + def add_workflow_node( + self, + node_id: int, + *, + device_key: Optional[str] = None, # 实例名，如 "ser" + resource_name: Optional[str] = None, # registry key（原 device_class） + module: Optional[str] = None, + template_name: Optional[str] = None, # 动作/模板名（原 action_key） + params: Dict[str, Any], + variable_sources: Dict[str, Dict[str, Any]], + add_ready_if_no_vars: bool = True, + prev_node_id: Optional[int] = None, + **extra_attrs, + ) -> None: + """添加工作流节点：params 单层；自动变量连线与 ready 串联；支持附加属性""" + node_id_str = str(node_id) + inputs: Dict[str, Any] = {} + + params, has_var = self._materialize_wiring_into_inputs( + params, inputs, variable_sources, node_id_str, base_path=["params"] + ) + + if add_ready_if_no_vars and not has_var: + last_id = str(prev_node_id) if prev_node_id is not None else "-1" + inputs["ready"] = {"node": int(last_id), "output": "ready"} + self.add_edge(last_id, node_id_str, source_handle_io="ready", target_handle_io="ready") + + node_obj = { + "device_key": device_key, + "resource_name": resource_name, # ✅ 新名字 + "module": module, + "template_name": template_name, # ✅ 新名字 + "params": params, + "inputs": inputs, + } + node_obj.update(extra_attrs or {}) + self.add_node(node_id_str, parameters=node_obj) + + # 顺序工作流导出（连线在 inputs，不返回 edges） + def to_dict(self) -> List[Dict[str, Any]]: + result = [] + for node_id, attrs in self.nodes.items(): + node = {"uuid": node_id} + params = dict(attrs.get("parameters", {}) or {}) + flat = {k: v for k, v in attrs.items() if k != "parameters"} + flat.update(params) + node.update(flat) + result.append(node) + return sorted(result, key=lambda n: int(n["uuid"]) if str(n["uuid"]).isdigit() else n["uuid"]) + + # node-link 导出（含 edges） + def to_node_link_dict(self) -> Dict[str, Any]: + nodes_list = [] + for node_id, attrs in self.nodes.items(): + node_attrs = attrs.copy() + params = node_attrs.pop("parameters", {}) or {} + node_attrs.update(params) + nodes_list.append({"uuid": node_id, **node_attrs}) + return { + "directed": True, + "multigraph": False, + "graph": {}, + "nodes": nodes_list, + "edges": self.edges, + "links": self.edges, + } + + +def refactor_data( + data: List[Dict[str, Any]], + action_resource_mapping: Optional[Dict[str, str]] = None, +) -> List[Dict[str, Any]]: + """统一的数据重构函数，根据操作类型自动选择模板 + + Args: + data: 原始步骤数据列表 + action_resource_mapping: action 到 resource_name 的映射字典，可选 + """ + refactored_data = [] + + # 定义操作映射，包含生物实验和有机化学的所有操作 + OPERATION_MAPPING = { + # 生物实验操作 + "transfer_liquid": "transfer_liquid", + "transfer": "transfer", + "incubation": "incubation", + "move_labware": "move_labware", + "oscillation": "oscillation", + # 有机化学操作 + "HeatChillToTemp": "HeatChillProtocol", + "StopHeatChill": "HeatChillStopProtocol", + "StartHeatChill": "HeatChillStartProtocol", + "HeatChill": "HeatChillProtocol", + "Dissolve": "DissolveProtocol", + "Transfer": "TransferProtocol", + "Evaporate": "EvaporateProtocol", + "Recrystallize": "RecrystallizeProtocol", + "Filter": "FilterProtocol", + "Dry": "DryProtocol", + "Add": "AddProtocol", + } + + UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"] + + for step in data: + operation = step.get("action") + if not operation or operation in UNSUPPORTED_OPERATIONS: + continue + + # 处理重复操作 + if operation == "Repeat": + times = step.get("times", step.get("parameters", {}).get("times", 1)) + sub_steps = step.get("steps", step.get("parameters", {}).get("steps", [])) + for i in range(int(times)): + sub_data = refactor_data(sub_steps, action_resource_mapping) + refactored_data.extend(sub_data) + continue + + # 获取模板名称 + template_name = OPERATION_MAPPING.get(operation) + if not template_name: + # 自动推断模板类型 + if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]: + template_name = f"biomek-{operation}" + else: + template_name = f"{operation}Protocol" + + # 获取 resource_name + resource_name = f"device.{operation.lower()}" + if action_resource_mapping: + resource_name = action_resource_mapping.get(operation, resource_name) + + # 获取步骤编号，生成 name 字段 + step_number = step.get("step_number") + name = f"Step {step_number}" if step_number is not None else None + + # 创建步骤数据 + step_data = { + "template_name": template_name, + "resource_name": resource_name, + "description": step.get("description", step.get("purpose", f"{operation} operation")), + "lab_node_type": "Device", + "param": step.get("parameters", step.get("action_args", {})), + "footer": f"{template_name}-{resource_name}", + } + if name: + step_data["name"] = name + refactored_data.append(step_data) + + return refactored_data + + +def build_protocol_graph( + labware_info: Dict[str, Dict[str, Any]], + protocol_steps: List[Dict[str, Any]], + workstation_name: str, + action_resource_mapping: Optional[Dict[str, str]] = None, +) -> WorkflowGraph: + """统一的协议图构建函数，根据设备类型自动选择构建逻辑 + + Args: + labware_info: labware 信息字典，格式为 {name: {slot, well, labware, ...}, ...} + protocol_steps: 协议步骤列表 + workstation_name: 工作站名称 + action_resource_mapping: action 到 resource_name 的映射字典，可选 + """ + G = WorkflowGraph() + resource_last_writer = {} # reagent_name -> "node_id:port" + slot_to_create_resource = {} # slot -> create_resource node_id + + protocol_steps = refactor_data(protocol_steps, action_resource_mapping) + + # ==================== 第一步：按 slot 去重创建 create_resource 节点 ==================== + # 收集所有唯一的 slot + slots_info = {} # slot -> {labware, res_id} + for labware_id, item in labware_info.items(): + slot = str(item.get("slot", "")) + if slot and slot not in slots_info: + res_id = f"plate_slot_{slot}" + slots_info[slot] = { + "labware": item.get("labware", ""), + "res_id": res_id, + } + + # 为每个唯一的 slot 创建 create_resource 节点 + res_index = 0 + last_create_resource_id = None + for slot, info in slots_info.items(): + node_id = str(uuid.uuid4()) + res_id = info["res_id"] + + res_index += 1 + G.add_node( + node_id, + template_name="create_resource", + resource_name="host_node", + name=f"Plate {res_index}", + description=f"Create plate on slot {slot}", + lab_node_type="Labware", + footer="create_resource-host_node", + param={ + "res_id": res_id, + "device_id": CREATE_RESOURCE_DEFAULTS["device_id"], + "class_name": CREATE_RESOURCE_DEFAULTS["class_name"], + "parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot), + "bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0}, + "slot_on_deck": slot, + }, + ) + slot_to_create_resource[slot] = node_id + + # create_resource 之间通过 ready 串联 + if last_create_resource_id is not None: + G.add_edge(last_create_resource_id, node_id, source_port="ready", target_port="ready") + last_create_resource_id = node_id + + # ==================== 第二步：为每个 reagent 创建 set_liquid_from_plate 节点 ==================== + set_liquid_index = 0 + last_set_liquid_id = last_create_resource_id # set_liquid_from_plate 连接在 create_resource 之后 + + for labware_id, item in labware_info.items(): + # 跳过 Tip/Rack 类型 + if "Rack" in str(labware_id) or "Tip" in str(labware_id): + continue + if item.get("type") == "hardware": + continue + + slot = str(item.get("slot", "")) + wells = item.get("well", []) + if not wells or not slot: + continue + + # res_id 不能有空格 + res_id = str(labware_id).replace(" ", "_") + well_count = len(wells) + + node_id = str(uuid.uuid4()) + set_liquid_index += 1 + + G.add_node( + node_id, + template_name="set_liquid_from_plate", + resource_name="liquid_handler.prcxi", + name=f"SetLiquid {set_liquid_index}", + description=f"Set liquid: {labware_id}", + lab_node_type="Reagent", + footer="set_liquid_from_plate-liquid_handler.prcxi", + param={ + "plate": [], # 通过连接传递 + "well_names": wells, # 孔位名数组，如 ["A1", "A3", "A5"] + "liquid_names": [res_id] * well_count, + "volumes": [DEFAULT_LIQUID_VOLUME] * well_count, + }, + ) + + # ready 连接：上一个节点 -> set_liquid_from_plate + if last_set_liquid_id is not None: + G.add_edge(last_set_liquid_id, node_id, source_port="ready", target_port="ready") + last_set_liquid_id = node_id + + # 物料流：create_resource 的 labware -> set_liquid_from_plate 的 input_plate + create_res_node_id = slot_to_create_resource.get(slot) + if create_res_node_id: + G.add_edge(create_res_node_id, node_id, source_port="labware", target_port="input_plate") + + # set_liquid_from_plate 的输出 output_wells 用于连接 transfer_liquid + resource_last_writer[labware_id] = f"{node_id}:output_wells" + + last_control_node_id = last_set_liquid_id + + # 端口名称映射：JSON 字段名 -> 实际 handle key + INPUT_PORT_MAPPING = { + "sources": "sources_identifier", + "targets": "targets_identifier", + "vessel": "vessel", + "to_vessel": "to_vessel", + "from_vessel": "from_vessel", + "reagent": "reagent", + "solvent": "solvent", + "compound": "compound", + } + + OUTPUT_PORT_MAPPING = { + "sources": "sources_out", # 输出端口是 xxx_out + "targets": "targets_out", # 输出端口是 xxx_out + "vessel": "vessel_out", + "to_vessel": "to_vessel_out", + "from_vessel": "from_vessel_out", + "filtrate_vessel": "filtrate_out", + "reagent": "reagent", + "solvent": "solvent", + "compound": "compound", + } + + # 需要根据 wells 数量扩展的参数列表（复数形式） + EXPAND_BY_WELLS_PARAMS = ["asp_vols", "dis_vols", "asp_flow_rates", "dis_flow_rates"] + + # 处理协议步骤 + for step in protocol_steps: + node_id = str(uuid.uuid4()) + params = step.get("param", {}).copy() # 复制一份，避免修改原数据 + connected_params = set() # 记录被连接的参数 + warnings = [] # 收集警告信息 + + # 参数重命名：单数 -> 复数 + for old_name, new_name in PARAM_RENAME_MAPPING.items(): + if old_name in params: + params[new_name] = params.pop(old_name) + + # 处理输入连接 + for param_key, target_port in INPUT_PORT_MAPPING.items(): + resource_name = params.get(param_key) + if resource_name and resource_name in resource_last_writer: + source_node, source_port = resource_last_writer[resource_name].split(":") + G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port) + connected_params.add(param_key) + elif resource_name and resource_name not in resource_last_writer: + # 资源名在 labware_info 中不存在 + warnings.append(f"{param_key}={resource_name} 未找到") + + # 获取 targets 对应的 wells 数量，用于扩展参数 + targets_name = params.get("targets") + sources_name = params.get("sources") + targets_wells_count = 1 + sources_wells_count = 1 + + if targets_name and targets_name in labware_info: + target_wells = labware_info[targets_name].get("well", []) + targets_wells_count = len(target_wells) if target_wells else 1 + elif targets_name: + warnings.append(f"targets={targets_name} 未在 reagent 中定义") + + if sources_name and sources_name in labware_info: + source_wells = labware_info[sources_name].get("well", []) + sources_wells_count = len(source_wells) if source_wells else 1 + elif sources_name: + warnings.append(f"sources={sources_name} 未在 reagent 中定义") + + # 检查 sources 和 targets 的 wells 数量是否匹配 + if targets_wells_count != sources_wells_count and targets_name and sources_name: + warnings.append(f"wells 数量不匹配: sources={sources_wells_count}, targets={targets_wells_count}") + + # 使用 targets 的 wells 数量来扩展参数 + wells_count = targets_wells_count + + # 扩展单值参数为数组（根据 targets 的 wells 数量） + for expand_param in EXPAND_BY_WELLS_PARAMS: + if expand_param in params: + value = params[expand_param] + # 如果是单个值，扩展为数组 + if not isinstance(value, list): + params[expand_param] = [value] * wells_count + # 如果已经是数组但长度不对，记录警告 + elif len(value) != wells_count: + warnings.append(f"{expand_param} 数量({len(value)})与 wells({wells_count})不匹配") + + # 如果 sources/targets 已通过连接传递，将参数值改为空数组 + for param_key in connected_params: + if param_key in params: + params[param_key] = [] + + # 更新 step 的 param 和 footer + step_copy = step.copy() + step_copy["param"] = params + + # 如果有警告，修改 footer 添加警告标记（警告放前面） + if warnings: + original_footer = step.get("footer", "") + step_copy["footer"] = f"[WARN: {'; '.join(warnings)}] {original_footer}" + + G.add_node(node_id, **step_copy) + + # 控制流 + if last_control_node_id is not None: + G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready") + last_control_node_id = node_id + + # 处理输出：更新 resource_last_writer + for param_key, output_port in OUTPUT_PORT_MAPPING.items(): + resource_name = step.get("param", {}).get(param_key) # 使用原始参数值 + if resource_name: + resource_last_writer[resource_name] = f"{node_id}:{output_port}" + + return G + + +def draw_protocol_graph(protocol_graph: WorkflowGraph, output_path: str): + """ + (辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图，用于可视化。 + """ + if not protocol_graph: + print("Cannot draw graph: Graph object is empty.") + return + + G = nx.DiGraph() + + for node_id, attrs in protocol_graph.nodes.items(): + label = attrs.get("description", attrs.get("template_name", node_id[:8])) + G.add_node(node_id, label=label, **attrs) + + for edge in protocol_graph.edges: + G.add_edge(edge["source"], edge["target"]) + + plt.figure(figsize=(20, 15)) + try: + pos = nx.nx_agraph.graphviz_layout(G, prog="dot") + except Exception: + pos = nx.shell_layout(G) # Fallback layout + + node_labels = {node: data["label"] for node, data in G.nodes(data=True)} + nx.draw( + G, + pos, + with_labels=False, + node_size=2500, + node_color="skyblue", + node_shape="o", + edge_color="gray", + width=1.5, + arrowsize=15, + ) + nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold") + + plt.title("Chemical Protocol Workflow Graph", size=15) + plt.savefig(output_path, dpi=300, bbox_inches="tight") + plt.close() + print(f" - Visualization saved to '{output_path}'") + + +COMPASS = {"n", "e", "s", "w", "ne", "nw", "se", "sw", "c"} + + +def _is_compass(port: str) -> bool: + return isinstance(port, str) and port.lower() in COMPASS + + +def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"): + """ + 使用 Graphviz 端口语法绘制协议工作流图。 + - 若边上的 source_port/target_port 是 compass（n/e/s/w/...），直接用 compass。 + - 否则自动为节点创建 record 形状并定义命名端口 。 + 最终由 PyGraphviz 渲染并输出到 output_path（后缀决定格式，如 .png/.svg/.pdf）。 + """ + if not protocol_graph: + print("Cannot draw graph: Graph object is empty.") + return + + # 1) 先用 networkx 搭建有向图，保留端口属性 + G = nx.DiGraph() + for node_id, attrs in protocol_graph.nodes.items(): + label = attrs.get("description", attrs.get("template_name", node_id[:8])) + # 保留一个干净的“中心标签”，用于放在 record 的中间槽 + G.add_node(node_id, _core_label=str(label), **{k: v for k, v in attrs.items() if k not in ("label",)}) + + edges_data = [] + in_ports_by_node = {} # 收集命名输入端口 + out_ports_by_node = {} # 收集命名输出端口 + + for edge in protocol_graph.edges: + u = edge["source"] + v = edge["target"] + sp = edge.get("source_handle_key") or edge.get("source_port") + tp = edge.get("target_handle_key") or edge.get("target_port") + + # 记录到图里（保留原始端口信息） + G.add_edge(u, v, source_handle_key=sp, target_handle_key=tp) + edges_data.append((u, v, sp, tp)) + + # 如果不是 compass，就按“命名端口”先归类，等会儿给节点造 record + if sp and not _is_compass(sp): + out_ports_by_node.setdefault(u, set()).add(str(sp)) + if tp and not _is_compass(tp): + in_ports_by_node.setdefault(v, set()).add(str(tp)) + + # 2) 转为 AGraph，使用 Graphviz 渲染 + A = to_agraph(G) + A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10") + A.node_attr.update( + shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica" + ) + A.edge_attr.update(arrowsize="0.8", color="#666666") + + # 3) 为需要命名端口的节点设置 record 形状与 label + # 左列 = 输入端口；中间 = 核心标签；右列 = 输出端口 + for n in A.nodes(): + node = A.get_node(n) + core = G.nodes[n].get("_core_label", n) + + in_ports = sorted(in_ports_by_node.get(n, [])) + out_ports = sorted(out_ports_by_node.get(n, [])) + + # 如果该节点涉及命名端口，则用 record；否则保留原 box + if in_ports or out_ports: + + def port_fields(ports): + if not ports: + return " " # 必须留一个空槽占位 + # 每个端口一个小格子，

name + return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports) + + left = port_fields(in_ports) + right = port_fields(out_ports) + + # 三栏：左(入) | 中(节点名) | 右(出) + record_label = f"{{ {left} | {core} | {right} }}" + node.attr.update(shape="record", label=record_label) + else: + # 没有命名端口：普通盒子，显示核心标签 + node.attr.update(label=str(core)) + + # 4) 给边设置 headport / tailport + # - 若端口为 compass：直接用 compass（e.g., headport="e"） + # - 若端口为命名端口：使用在 record 中定义的 名（同名即可） + for u, v, sp, tp in edges_data: + e = A.get_edge(u, v) + + # Graphviz 属性：tail 是源，head 是目标 + if sp: + if _is_compass(sp): + e.attr["tailport"] = sp.lower() + else: + # 与 record label 中 名一致；特殊字符已在 label 中做了清洗 + e.attr["tailport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(sp)) + + if tp: + if _is_compass(tp): + e.attr["headport"] = tp.lower() + else: + e.attr["headport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(tp)) + + # 可选：若想让边更贴边缘，可设置 constraint/spline 等 + # e.attr["arrowhead"] = "vee" + + # 5) 输出 + A.draw(output_path, prog="dot") + print(f" - Port-aware workflow rendered to '{output_path}'") + + +# ---------------- Registry Adapter ---------------- + + +class RegistryAdapter: + """根据 module 的类名（冒号右侧）反查 registry 的 resource_name（原 device_class），并抽取参数顺序""" + + def __init__(self, device_registry: Dict[str, Any]): + self.device_registry = device_registry or {} + self.module_class_to_resource = self._build_module_class_index() + + def _build_module_class_index(self) -> Dict[str, str]: + idx = {} + for resource_name, info in self.device_registry.items(): + module = info.get("module") + if isinstance(module, str) and ":" in module: + cls = module.split(":")[-1] + idx[cls] = resource_name + idx[cls.lower()] = resource_name + return idx + + def resolve_resource_by_classname(self, class_name: str) -> Optional[str]: + if not class_name: + return None + return self.module_class_to_resource.get(class_name) or self.module_class_to_resource.get(class_name.lower()) + + def get_device_module(self, resource_name: Optional[str]) -> Optional[str]: + if not resource_name: + return None + return self.device_registry.get(resource_name, {}).get("module") + + def get_actions(self, resource_name: Optional[str]) -> Dict[str, Any]: + if not resource_name: + return {} + return (self.device_registry.get(resource_name, {}).get("class", {}).get("action_value_mappings", {})) or {} + + def get_action_schema(self, resource_name: Optional[str], template_name: str) -> Optional[Json]: + return (self.get_actions(resource_name).get(template_name) or {}).get("schema") + + def get_action_goal_default(self, resource_name: Optional[str], template_name: str) -> Json: + return (self.get_actions(resource_name).get(template_name) or {}).get("goal_default", {}) or {} + + def get_action_input_keys(self, resource_name: Optional[str], template_name: str) -> List[str]: + schema = self.get_action_schema(resource_name, template_name) or {} + goal = (schema.get("properties") or {}).get("goal") or {} + props = goal.get("properties") or {} + required = goal.get("required") or [] + return list(dict.fromkeys(required + list(props.keys()))) diff --git a/unilabos/workflow/convert_from_json.py b/unilabos/workflow/convert_from_json.py new file mode 100644 index 0000000..ff749d7 --- /dev/null +++ b/unilabos/workflow/convert_from_json.py @@ -0,0 +1,315 @@ +""" +JSON 工作流转换模块 + +将 workflow/reagent 格式的 JSON 转换为统一工作流格式。 + +输入格式: +{ + "workflow": [ + {"action": "...", "action_args": {...}}, + ... + ], + "reagent": { + "reagent_name": {"slot": int, "well": [...], "labware": "..."}, + ... + } +} +""" + +import json +from os import PathLike +from pathlib import Path +from typing import Any, Dict, List, Optional, Tuple, Union + +from unilabos.workflow.common import WorkflowGraph, build_protocol_graph +from unilabos.registry.registry import lab_registry + + +# ==================== 字段映射配置 ==================== + +# action 到 resource_name 的映射 +ACTION_RESOURCE_MAPPING: Dict[str, str] = { + # 生物实验操作 + "transfer_liquid": "liquid_handler.prcxi", + "transfer": "liquid_handler.prcxi", + "incubation": "incubator.prcxi", + "move_labware": "labware_mover.prcxi", + "oscillation": "shaker.prcxi", + # 有机化学操作 + "HeatChillToTemp": "heatchill.chemputer", + "StopHeatChill": "heatchill.chemputer", + "StartHeatChill": "heatchill.chemputer", + "HeatChill": "heatchill.chemputer", + "Dissolve": "stirrer.chemputer", + "Transfer": "liquid_handler.chemputer", + "Evaporate": "rotavap.chemputer", + "Recrystallize": "reactor.chemputer", + "Filter": "filter.chemputer", + "Dry": "dryer.chemputer", + "Add": "liquid_handler.chemputer", +} + +# action_args 字段到 parameters 字段的映射 +# 格式: {"old_key": "new_key"}, 仅映射需要重命名的字段 +ARGS_FIELD_MAPPING: Dict[str, str] = { + # 如果需要字段重命名，在这里配置 + # "old_field_name": "new_field_name", +} + +# 默认工作站名称 +DEFAULT_WORKSTATION = "PRCXI" + + +# ==================== 核心转换函数 ==================== + + +def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]: + """ + 从 registry 获取指定设备和动作的 handles 配置 + + Args: + resource_name: 设备资源名称，如 "liquid_handler.prcxi" + template_name: 动作模板名称，如 "transfer_liquid" + + Returns: + 包含 source 和 target handler_keys 的字典: + {"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]} + """ + result = {"source": [], "target": []} + + device_info = lab_registry.device_type_registry.get(resource_name, {}) + if not device_info: + return result + + action_mappings = device_info.get("class", {}).get("action_value_mappings", {}) + action_config = action_mappings.get(template_name, {}) + handles = action_config.get("handles", {}) + + if isinstance(handles, dict): + for handle in handles.get("input", []): + handler_key = handle.get("handler_key", "") + if handler_key: + result["source"].append(handler_key) + for handle in handles.get("output", []): + handler_key = handle.get("handler_key", "") + if handler_key: + result["target"].append(handler_key) + + return result + + +def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]: + """ + 校验工作流图中所有边的句柄配置是否正确 + + Args: + graph: 工作流图对象 + + Returns: + (is_valid, errors): 是否有效，错误信息列表 + """ + errors = [] + nodes = graph.nodes + + for edge in graph.edges: + left_uuid = edge.get("source") + right_uuid = edge.get("target") + right_source_conn_key = edge.get("target_handle_key", "") + left_target_conn_key = edge.get("source_handle_key", "") + + left_node = nodes.get(left_uuid, {}) + right_node = nodes.get(right_uuid, {}) + + left_res_name = left_node.get("resource_name", "") + left_template_name = left_node.get("template_name", "") + right_res_name = right_node.get("resource_name", "") + right_template_name = right_node.get("template_name", "") + + left_node_handles = get_action_handles(left_res_name, left_template_name) + target_valid_keys = left_node_handles.get("target", []) + target_valid_keys.append("ready") + + right_node_handles = get_action_handles(right_res_name, right_template_name) + source_valid_keys = right_node_handles.get("source", []) + source_valid_keys.append("ready") + + # 验证目标节点（right）的输入端口 + if not right_source_conn_key: + node_name = right_node.get("name", right_uuid[:8]) + errors.append(f"目标节点 '{node_name}' 的输入端口 (target_handle_key) 为空，应设置为: {source_valid_keys}") + elif right_source_conn_key not in source_valid_keys: + node_name = right_node.get("name", right_uuid[:8]) + errors.append( + f"目标节点 '{node_name}' 的输入端口 '{right_source_conn_key}' 不存在，支持的输入端口: {source_valid_keys}" + ) + + # 验证源节点（left）的输出端口 + if not left_target_conn_key: + node_name = left_node.get("name", left_uuid[:8]) + errors.append(f"源节点 '{node_name}' 的输出端口 (source_handle_key) 为空，应设置为: {target_valid_keys}") + elif left_target_conn_key not in target_valid_keys: + node_name = left_node.get("name", left_uuid[:8]) + errors.append( + f"源节点 '{node_name}' 的输出端口 '{left_target_conn_key}' 不存在，支持的输出端口: {target_valid_keys}" + ) + + return len(errors) == 0, errors + + +def normalize_workflow_steps(workflow: List[Dict[str, Any]]) -> List[Dict[str, Any]]: + """ + 将 workflow 格式的步骤数据规范化 + + 输入格式: + [{"action": "...", "action_args": {...}}, ...] + + 输出格式: + [{"action": "...", "parameters": {...}, "step_number": int}, ...] + + Args: + workflow: workflow 数组 + + Returns: + 规范化后的步骤列表 + """ + normalized = [] + for idx, step in enumerate(workflow): + action = step.get("action") + if not action: + continue + + # 获取参数: action_args + raw_params = step.get("action_args", {}) + params = {} + + # 应用字段映射 + for key, value in raw_params.items(): + mapped_key = ARGS_FIELD_MAPPING.get(key, key) + params[mapped_key] = value + + step_dict = { + "action": action, + "parameters": params, + "step_number": idx + 1, + } + + # 保留描述字段 + if "description" in step: + step_dict["description"] = step["description"] + + normalized.append(step_dict) + + return normalized + + +def convert_from_json( + data: Union[str, PathLike, Dict[str, Any]], + workstation_name: str = DEFAULT_WORKSTATION, + validate: bool = True, +) -> WorkflowGraph: + """ + 从 JSON 数据或文件转换为 WorkflowGraph + + JSON 格式: + {"workflow": [...], "reagent": {...}} + + Args: + data: JSON 文件路径、字典数据、或 JSON 字符串 + workstation_name: 工作站名称，默认 "PRCXi" + validate: 是否校验句柄配置，默认 True + + Returns: + WorkflowGraph: 构建好的工作流图 + + Raises: + ValueError: 不支持的 JSON 格式 + FileNotFoundError: 文件不存在 + json.JSONDecodeError: JSON 解析失败 + """ + # 处理输入数据 + if isinstance(data, (str, PathLike)): + path = Path(data) + if path.exists(): + with path.open("r", encoding="utf-8") as fp: + json_data = json.load(fp) + elif isinstance(data, str): + json_data = json.loads(data) + else: + raise FileNotFoundError(f"文件不存在: {data}") + elif isinstance(data, dict): + json_data = data + else: + raise TypeError(f"不支持的数据类型: {type(data)}") + + # 校验格式 + if "workflow" not in json_data or "reagent" not in json_data: + raise ValueError( + "不支持的 JSON 格式。请使用标准格式:\n" + '{"workflow": [{"action": "...", "action_args": {...}}, ...], ' + '"reagent": {"name": {"slot": int, "well": [...], "labware": "..."}, ...}}' + ) + + # 提取数据 + workflow = json_data["workflow"] + reagent = json_data["reagent"] + + # 规范化步骤数据 + protocol_steps = normalize_workflow_steps(workflow) + + # reagent 已经是字典格式，直接使用 + labware_info = reagent + + # 构建工作流图 + graph = build_protocol_graph( + labware_info=labware_info, + protocol_steps=protocol_steps, + workstation_name=workstation_name, + action_resource_mapping=ACTION_RESOURCE_MAPPING, + ) + + # 校验句柄配置 + if validate: + is_valid, errors = validate_workflow_handles(graph) + if not is_valid: + import warnings + + for error in errors: + warnings.warn(f"句柄校验警告: {error}") + + return graph + + +def convert_json_to_node_link( + data: Union[str, PathLike, Dict[str, Any]], + workstation_name: str = DEFAULT_WORKSTATION, +) -> Dict[str, Any]: + """ + 将 JSON 数据转换为 node-link 格式的字典 + + Args: + data: JSON 文件路径、字典数据、或 JSON 字符串 + workstation_name: 工作站名称，默认 "PRCXi" + + Returns: + Dict: node-link 格式的工作流数据 + """ + graph = convert_from_json(data, workstation_name) + return graph.to_node_link_dict() + + +def convert_json_to_workflow_list( + data: Union[str, PathLike, Dict[str, Any]], + workstation_name: str = DEFAULT_WORKSTATION, +) -> List[Dict[str, Any]]: + """ + 将 JSON 数据转换为工作流列表格式 + + Args: + data: JSON 文件路径、字典数据、或 JSON 字符串 + workstation_name: 工作站名称，默认 "PRCXi" + + Returns: + List: 工作流节点列表 + """ + graph = convert_from_json(data, workstation_name) + return graph.to_dict() diff --git a/unilabos/workflow/legacy/convert_from_json_legacy.py b/unilabos/workflow/legacy/convert_from_json_legacy.py new file mode 100644 index 0000000..7a6d2b4 --- /dev/null +++ b/unilabos/workflow/legacy/convert_from_json_legacy.py @@ -0,0 +1,356 @@ +""" +JSON 工作流转换模块 + +提供从多种 JSON 格式转换为统一工作流格式的功能。 +支持的格式： +1. workflow/reagent 格式 +2. steps_info/labware_info 格式 +""" + +import json +from os import PathLike +from pathlib import Path +from typing import Any, Dict, List, Optional, Set, Tuple, Union + +from unilabos.workflow.common import WorkflowGraph, build_protocol_graph +from unilabos.registry.registry import lab_registry + + +def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]: + """ + 从 registry 获取指定设备和动作的 handles 配置 + + Args: + resource_name: 设备资源名称，如 "liquid_handler.prcxi" + template_name: 动作模板名称，如 "transfer_liquid" + + Returns: + 包含 source 和 target handler_keys 的字典: + {"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]} + """ + result = {"source": [], "target": []} + + device_info = lab_registry.device_type_registry.get(resource_name, {}) + if not device_info: + return result + + action_mappings = device_info.get("class", {}).get("action_value_mappings", {}) + action_config = action_mappings.get(template_name, {}) + handles = action_config.get("handles", {}) + + if isinstance(handles, dict): + # 处理 input handles (作为 target) + for handle in handles.get("input", []): + handler_key = handle.get("handler_key", "") + if handler_key: + result["source"].append(handler_key) + # 处理 output handles (作为 source) + for handle in handles.get("output", []): + handler_key = handle.get("handler_key", "") + if handler_key: + result["target"].append(handler_key) + + return result + + +def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]: + """ + 校验工作流图中所有边的句柄配置是否正确 + + Args: + graph: 工作流图对象 + + Returns: + (is_valid, errors): 是否有效，错误信息列表 + """ + errors = [] + nodes = graph.nodes + + for edge in graph.edges: + left_uuid = edge.get("source") + right_uuid = edge.get("target") + # target_handle_key是target, right的输入节点（入节点） + # source_handle_key是source, left的输出节点（出节点） + right_source_conn_key = edge.get("target_handle_key", "") + left_target_conn_key = edge.get("source_handle_key", "") + + # 获取源节点和目标节点信息 + left_node = nodes.get(left_uuid, {}) + right_node = nodes.get(right_uuid, {}) + + left_res_name = left_node.get("resource_name", "") + left_template_name = left_node.get("template_name", "") + right_res_name = right_node.get("resource_name", "") + right_template_name = right_node.get("template_name", "") + + # 获取源节点的 output handles + left_node_handles = get_action_handles(left_res_name, left_template_name) + target_valid_keys = left_node_handles.get("target", []) + target_valid_keys.append("ready") + + # 获取目标节点的 input handles + right_node_handles = get_action_handles(right_res_name, right_template_name) + source_valid_keys = right_node_handles.get("source", []) + source_valid_keys.append("ready") + + # 如果节点配置了 output handles，则 source_port 必须有效 + if not right_source_conn_key: + node_name = left_node.get("name", left_uuid[:8]) + errors.append(f"源节点 '{node_name}' 的 source_handle_key 为空，" f"应设置为: {source_valid_keys}") + elif right_source_conn_key not in source_valid_keys: + node_name = left_node.get("name", left_uuid[:8]) + errors.append( + f"源节点 '{node_name}' 的 source 端点 '{right_source_conn_key}' 不存在，" f"支持的端点: {source_valid_keys}" + ) + + # 如果节点配置了 input handles，则 target_port 必须有效 + if not left_target_conn_key: + node_name = right_node.get("name", right_uuid[:8]) + errors.append(f"目标节点 '{node_name}' 的 target_handle_key 为空，" f"应设置为: {target_valid_keys}") + elif left_target_conn_key not in target_valid_keys: + node_name = right_node.get("name", right_uuid[:8]) + errors.append( + f"目标节点 '{node_name}' 的 target 端点 '{left_target_conn_key}' 不存在，" + f"支持的端点: {target_valid_keys}" + ) + + return len(errors) == 0, errors + + +# action 到 resource_name 的映射 +ACTION_RESOURCE_MAPPING: Dict[str, str] = { + # 生物实验操作 + "transfer_liquid": "liquid_handler.prcxi", + "transfer": "liquid_handler.prcxi", + "incubation": "incubator.prcxi", + "move_labware": "labware_mover.prcxi", + "oscillation": "shaker.prcxi", + # 有机化学操作 + "HeatChillToTemp": "heatchill.chemputer", + "StopHeatChill": "heatchill.chemputer", + "StartHeatChill": "heatchill.chemputer", + "HeatChill": "heatchill.chemputer", + "Dissolve": "stirrer.chemputer", + "Transfer": "liquid_handler.chemputer", + "Evaporate": "rotavap.chemputer", + "Recrystallize": "reactor.chemputer", + "Filter": "filter.chemputer", + "Dry": "dryer.chemputer", + "Add": "liquid_handler.chemputer", +} + + +def normalize_steps(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]: + """ + 将不同格式的步骤数据规范化为统一格式 + + 支持的输入格式： + - action + parameters + - action + action_args + - operation + parameters + + Args: + data: 原始步骤数据列表 + + Returns: + 规范化后的步骤列表，格式为 [{"action": str, "parameters": dict, "description": str?, "step_number": int?}, ...] + """ + normalized = [] + for idx, step in enumerate(data): + # 获取动作名称（支持 action 或 operation 字段） + action = step.get("action") or step.get("operation") + if not action: + continue + + # 获取参数（支持 parameters 或 action_args 字段） + raw_params = step.get("parameters") or step.get("action_args") or {} + params = dict(raw_params) + + # 规范化 source/target -> sources/targets + if "source" in raw_params and "sources" not in raw_params: + params["sources"] = raw_params["source"] + if "target" in raw_params and "targets" not in raw_params: + params["targets"] = raw_params["target"] + + # 获取描述（支持 description 或 purpose 字段） + description = step.get("description") or step.get("purpose") + + # 获取步骤编号（优先使用原始数据中的 step_number，否则使用索引+1） + step_number = step.get("step_number", idx + 1) + + step_dict = {"action": action, "parameters": params, "step_number": step_number} + if description: + step_dict["description"] = description + + normalized.append(step_dict) + + return normalized + + +def normalize_labware(data: List[Dict[str, Any]]) -> Dict[str, Dict[str, Any]]: + """ + 将不同格式的 labware 数据规范化为统一的字典格式 + + 支持的输入格式： + - reagent_name + material_name + positions + - name + labware + slot + + Args: + data: 原始 labware 数据列表 + + Returns: + 规范化后的 labware 字典，格式为 {name: {"slot": int, "labware": str, "well": list, "type": str, "role": str, "name": str}, ...} + """ + labware = {} + for item in data: + # 获取 key 名称（优先使用 reagent_name，其次是 material_name 或 name） + reagent_name = item.get("reagent_name") + key = reagent_name or item.get("material_name") or item.get("name") + if not key: + continue + + key = str(key) + + # 处理重复 key，自动添加后缀 + idx = 1 + original_key = key + while key in labware: + idx += 1 + key = f"{original_key}_{idx}" + + labware[key] = { + "slot": item.get("positions") or item.get("slot"), + "labware": item.get("material_name") or item.get("labware"), + "well": item.get("well", []), + "type": item.get("type", "reagent"), + "role": item.get("role", ""), + "name": key, + } + + return labware + + +def convert_from_json( + data: Union[str, PathLike, Dict[str, Any]], + workstation_name: str = "PRCXi", + validate: bool = True, +) -> WorkflowGraph: + """ + 从 JSON 数据或文件转换为 WorkflowGraph + + 支持的 JSON 格式： + 1. {"workflow": [...], "reagent": {...}} - 直接格式 + 2. {"steps_info": [...], "labware_info": [...]} - 需要规范化的格式 + + Args: + data: JSON 文件路径、字典数据、或 JSON 字符串 + workstation_name: 工作站名称，默认 "PRCXi" + validate: 是否校验句柄配置，默认 True + + Returns: + WorkflowGraph: 构建好的工作流图 + + Raises: + ValueError: 不支持的 JSON 格式 或 句柄校验失败 + FileNotFoundError: 文件不存在 + json.JSONDecodeError: JSON 解析失败 + """ + # 处理输入数据 + if isinstance(data, (str, PathLike)): + path = Path(data) + if path.exists(): + with path.open("r", encoding="utf-8") as fp: + json_data = json.load(fp) + elif isinstance(data, str): + # 尝试作为 JSON 字符串解析 + json_data = json.loads(data) + else: + raise FileNotFoundError(f"文件不存在: {data}") + elif isinstance(data, dict): + json_data = data + else: + raise TypeError(f"不支持的数据类型: {type(data)}") + + # 根据格式解析数据 + if "workflow" in json_data and "reagent" in json_data: + # 格式1: workflow/reagent（已经是规范格式） + protocol_steps = json_data["workflow"] + labware_info = json_data["reagent"] + elif "steps_info" in json_data and "labware_info" in json_data: + # 格式2: steps_info/labware_info（需要规范化） + protocol_steps = normalize_steps(json_data["steps_info"]) + labware_info = normalize_labware(json_data["labware_info"]) + elif "steps" in json_data and "labware" in json_data: + # 格式3: steps/labware（另一种常见格式） + protocol_steps = normalize_steps(json_data["steps"]) + if isinstance(json_data["labware"], list): + labware_info = normalize_labware(json_data["labware"]) + else: + labware_info = json_data["labware"] + else: + raise ValueError( + "不支持的 JSON 格式。支持的格式：\n" + "1. {'workflow': [...], 'reagent': {...}}\n" + "2. {'steps_info': [...], 'labware_info': [...]}\n" + "3. {'steps': [...], 'labware': [...]}" + ) + + # 构建工作流图 + graph = build_protocol_graph( + labware_info=labware_info, + protocol_steps=protocol_steps, + workstation_name=workstation_name, + action_resource_mapping=ACTION_RESOURCE_MAPPING, + ) + + # 校验句柄配置 + if validate: + is_valid, errors = validate_workflow_handles(graph) + if not is_valid: + import warnings + + for error in errors: + warnings.warn(f"句柄校验警告: {error}") + + return graph + + +def convert_json_to_node_link( + data: Union[str, PathLike, Dict[str, Any]], + workstation_name: str = "PRCXi", +) -> Dict[str, Any]: + """ + 将 JSON 数据转换为 node-link 格式的字典 + + Args: + data: JSON 文件路径、字典数据、或 JSON 字符串 + workstation_name: 工作站名称，默认 "PRCXi" + + Returns: + Dict: node-link 格式的工作流数据 + """ + graph = convert_from_json(data, workstation_name) + return graph.to_node_link_dict() + + +def convert_json_to_workflow_list( + data: Union[str, PathLike, Dict[str, Any]], + workstation_name: str = "PRCXi", +) -> List[Dict[str, Any]]: + """ + 将 JSON 数据转换为工作流列表格式 + + Args: + data: JSON 文件路径、字典数据、或 JSON 字符串 + workstation_name: 工作站名称，默认 "PRCXi" + + Returns: + List: 工作流节点列表 + """ + graph = convert_from_json(data, workstation_name) + return graph.to_dict() + + +# 为了向后兼容，保留下划线前缀的别名 +_normalize_steps = normalize_steps +_normalize_labware = normalize_labware