修改工作流上传以及lh的物料初步判定

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -1159,11 +1159,19 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
             Number of mix cycles. If *None* (default) no mixing occurs regardless of
             mix_stage.
         """
-
+        num_sources = len(sources)
+        num_targets = len(targets)
+        len_asp_vols = len(asp_vols)
+        len_dis_vols = len(dis_vols)
         # 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]
+            use_channels = list(range(self.channel_num)) if self.channel_num == 8 else [0]
+        elif len(use_channels) == 8:
+            if self.channel_num != 8:
+                raise ValueError(f"if channel_num is 8, use_channels length must be 8, but got {len(use_channels)}")
+            if num_sources%8 != 0 or num_targets%8 != 0 or len_asp_vols%8 != 0 or len_dis_vols%8 != 0:
+                raise ValueError(f"if channel_num is 8, sources, targets, asp_vols, and dis_vols length must be divisible by 8, but got {num_sources}, {num_targets}, {len_asp_vols}, and {len_dis_vols}")
 
         if is_96_well:
             pass  # This mode is not verified.
@@ -1191,90 +1199,234 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         if mix_times is not None:
             mix_times = int(mix_times)
 
+        # 设置tip racks
+        self.set_tiprack(tip_racks)
+
         # 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)
+        len_asp_vols = len(asp_vols)
+        len_dis_vols = len(dis_vols)
 
-        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,
-            )
-        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,
-            )
-        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,
-            )
-        else:
-            raise ValueError(
-                f"Unsupported transfer mode: {num_sources} sources -> {num_targets} targets. "
-                "Supported modes: 1->N, N->1, or N->N."
-            )
+        # if num_targets != 1 and num_sources != 1:
+        #     if len_asp_vols != num_sources and len_asp_vols != num_targets:
+        #         raise ValueError(f"asp_vols length must be equal to sources or targets length, but got {len_asp_vols} and {num_sources} and {num_targets}")
+        #     if len_dis_vols != num_sources and len_dis_vols != num_targets:
+        #         raise ValueError(f"dis_vols length must be equal to sources or targets length, but got {len_dis_vols} and {num_sources} and {num_targets}")
+
+        if len(use_channels) == 1:
+            max_len = max(num_sources, num_targets)
+            for i in range(max_len):
+
+                # 辅助函数：安全地从列表中获取元素，如果列表为空则返回None
+                def safe_get(lst, idx, default=None):
+                    return [lst[idx]] if lst else default
+
+                # 动态构建参数字典，只传递实际提供的参数
+                kwargs = {
+                    'sources': [sources[i%num_sources]],
+                    'targets': [targets[i%num_targets]],
+                    'tip_racks': tip_racks,
+                    'use_channels': use_channels,
+                    'asp_vols': [asp_vols[i%len_asp_vols]],
+                    'dis_vols': [dis_vols[i%len_dis_vols]],
+                }
+
+                # 条件性添加可选参数
+                if asp_flow_rates is not None:
+                    kwargs['asp_flow_rates'] = [asp_flow_rates[i%len_asp_vols]]
+                if dis_flow_rates is not None:
+                    kwargs['dis_flow_rates'] = [dis_flow_rates[i%len_dis_vols]]
+                if offsets is not None:
+                    kwargs['offsets'] = safe_get(offsets, i)
+                if touch_tip is not None:
+                    kwargs['touch_tip'] = touch_tip if touch_tip else False
+                if liquid_height is not None:
+                    kwargs['liquid_height'] = safe_get(liquid_height, i)
+                if blow_out_air_volume is not None:
+                    kwargs['blow_out_air_volume'] = safe_get(blow_out_air_volume, i)
+                if spread is not None:
+                    kwargs['spread'] = spread
+                if mix_stage is not None:
+                    kwargs['mix_stage'] = safe_get(mix_stage, i)
+                if mix_times is not None:
+                    kwargs['mix_times'] = safe_get(mix_times, i)
+                if mix_vol is not None:
+                    kwargs['mix_vol'] = safe_get(mix_vol, i)
+                if mix_rate is not None:
+                    kwargs['mix_rate'] = safe_get(mix_rate, i)
+                if mix_liquid_height is not None:
+                    kwargs['mix_liquid_height'] = safe_get(mix_liquid_height, i)
+                if delays is not None:
+                    kwargs['delays'] = safe_get(delays, i)
+
+                await self._transfer_base_method(**kwargs)
+
+    
+
+        # 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,
+        #         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,
+        #     )
+        # 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,
+        #     )
+        # else:
+        #     raise ValueError(
+        #         f"Unsupported transfer mode: {num_sources} sources -> {num_targets} targets. "
+        #         "Supported modes: 1->N, N->1, or N->N."
+        #     )
 
         return TransferLiquidReturn(
             sources=ResourceTreeSet.from_plr_resources(list(sources), known_newly_created=False).dump(),  # type: ignore
             targets=ResourceTreeSet.from_plr_resources(list(targets), known_newly_created=False).dump(),  # type: ignore
         )
+    async def _transfer_base_method(
+        self,
+        sources: Sequence[Container],
+        targets: Sequence[Container],
+        tip_racks: Sequence[TipRack],
+        use_channels: List[int],
+        asp_vols: List[float],
+        dis_vols: List[float],
+        **kwargs
+    ):
 
+        # 从kwargs中提取参数，提供默认值
+        asp_flow_rates = kwargs.get('asp_flow_rates')
+        dis_flow_rates = kwargs.get('dis_flow_rates')
+        offsets = kwargs.get('offsets')
+        touch_tip = kwargs.get('touch_tip', False)
+        liquid_height = kwargs.get('liquid_height')
+        blow_out_air_volume = kwargs.get('blow_out_air_volume')
+        spread = kwargs.get('spread', 'wide')
+        mix_stage = kwargs.get('mix_stage')
+        mix_times = kwargs.get('mix_times')
+        mix_vol = kwargs.get('mix_vol')
+        mix_rate = kwargs.get('mix_rate')
+        mix_liquid_height = kwargs.get('mix_liquid_height')
+        delays = kwargs.get('delays')
+
+        tip = []
+        tip.extend(next(self.current_tip))
+        await self.pick_up_tips(tip)
+
+        if mix_stage in ["before", "both"] and mix_times is not None and mix_times > 0:
+            await self.mix(
+                targets=[targets[0]],
+                mix_time=mix_times,
+                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,
+                use_channels=use_channels,
+            )
+
+        await self.aspirate(
+            resources=[sources[0]],
+            vols=[asp_vols[0]],
+            use_channels=use_channels,
+            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
+            ),
+            spread=spread,
+        )
+        if delays is not None:
+            await self.custom_delay(seconds=delays[0])
+        await self.dispense(
+            resources=[targets[0]],
+            vols=[dis_vols[0]],
+            use_channels=use_channels,
+            flow_rates=[dis_flow_rates[0]] if dis_flow_rates and len(dis_flow_rates) > 0 else None,
+            offsets=[offsets[0]] if offsets and len(offsets) > 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
+            ),
+            liquid_height=[liquid_height[0]] if liquid_height and len(liquid_height) > 0 else None,
+            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=[targets[0]],
+                mix_time=mix_times,
+                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,
+                use_channels=use_channels,
+            )
+        if delays is not None and len(delays) > 1:
+            await self.custom_delay(seconds=delays[0])
+        await self.touch_tip(targets[0])
+        await self.discard_tips(use_channels=use_channels)
+        
     async def _transfer_one_to_one(
         self,
         sources: Sequence[Container],

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -804,7 +804,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         delays: Optional[List[int]] = None,
         none_keys: List[str] = [],
     ) -> TransferLiquidReturn:
-        return await super().transfer_liquid(
+        if self.step_mode:
+            await self.create_protocol(f"transfer_liquid{time.time()}")
+        res =  await super().transfer_liquid(
             sources,
             targets,
             tip_racks,
@@ -827,6 +829,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
             delays=delays,
             none_keys=none_keys,
         )
+        if self.step_mode:
+            await self.run_protocol()
+        return res
 
     async def custom_delay(self, seconds=0, msg=None):
         return await super().custom_delay(seconds, msg)

unilabos/resources/resource_tracker.py

@@ -581,6 +581,71 @@ class ResourceTreeSet(object):
                 d["model"] = res.config.get("model", None)
             return d
 
+        # deserialize 会单独处理的元数据 key，不传给构造函数
+        _META_KEYS = {"type", "parent_name", "location", "children", "rotation", "barcode"}
+        # deserialize 自定义逻辑使用的 key（如 TipSpot 用 prototype_tip 构建 make_tip），需保留
+        _DESERIALIZE_PRESERVED_KEYS = {"prototype_tip"}
+
+        def remove_incompatible_params(plr_d: dict) -> None:
+            """递归移除 PLR 类不接受的参数，避免 deserialize 报错。
+            - 移除构造函数不接受的参数（如 compute_height_from_volume、ordering、category）
+            - 对 TubeRack：将 ordering 转为 ordered_items
+            - 保留 deserialize 自定义逻辑需要的 key（如 prototype_tip）
+            """
+            if "type" in plr_d:
+                sub_cls = find_subclass(plr_d["type"], PLRResource)
+                if sub_cls is not None:
+                    spec = inspect.signature(sub_cls)
+                    valid_params = set(spec.parameters.keys())
+                    # TubeRack 特殊处理：先转换 ordering，再参与后续过滤
+                    if "ordering" not in valid_params and "ordering" in plr_d:
+                        ordering = plr_d.pop("ordering", None)
+                        if sub_cls.__name__ == "TubeRack":
+                            plr_d["ordered_items"] = (
+                                _ordering_to_ordered_items(plr_d, ordering)
+                                if ordering
+                                else {}
+                            )
+                    # 移除构造函数不接受的参数（保留 META 和 deserialize 自定义逻辑需要的 key）
+                    for key in list(plr_d.keys()):
+                        if (
+                            key not in _META_KEYS
+                            and key not in _DESERIALIZE_PRESERVED_KEYS
+                            and key not in valid_params
+                        ):
+                            plr_d.pop(key, None)
+            for child in plr_d.get("children", []):
+                remove_incompatible_params(child)
+
+        def _ordering_to_ordered_items(plr_d: dict, ordering: dict) -> dict:
+            """将 ordering 转为 ordered_items，从 children 构建 Tube 对象"""
+            from pylabrobot.resources import Tube, Coordinate
+            from pylabrobot.serializer import deserialize as plr_deserialize
+
+            children = plr_d.get("children", [])
+            ordered_items = {}
+            for idx, (ident, child_name) in enumerate(ordering.items()):
+                child_data = children[idx] if idx < len(children) else None
+                if child_data is None:
+                    continue
+                loc_data = child_data.get("location")
+                loc = (
+                    plr_deserialize(loc_data)
+                    if loc_data
+                    else Coordinate(0, 0, 0)
+                )
+                tube = Tube(
+                    name=child_data.get("name", child_name or ident),
+                    size_x=child_data.get("size_x", 10),
+                    size_y=child_data.get("size_y", 10),
+                    size_z=child_data.get("size_z", 50),
+                    max_volume=child_data.get("max_volume", 1000),
+                )
+                tube.location = loc
+                ordered_items[ident] = tube
+            plr_d["children"] = []  # 已并入 ordered_items，避免重复反序列化
+            return ordered_items
+
         plr_resources = []
         tracker = DeviceNodeResourceTracker()
 
@@ -600,9 +665,7 @@ class ResourceTreeSet(object):
                     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}"
                     )
-                spec = inspect.signature(sub_cls)
-                if "category" not in spec.parameters:
-                    plr_dict.pop("category", None)
+                remove_incompatible_params(plr_dict)
                 plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True)
                 from pylabrobot.resources import Coordinate
                 from pylabrobot.serializer import deserialize

unilabos/workflow/common.py

@@ -119,11 +119,14 @@ DEVICE_NAME_DEFAULT = "PRCXI"  # transfer_liquid, set_liquid_from_plate 等动
 # 节点类型
 NODE_TYPE_DEFAULT = "ILab"  # 所有节点的默认类型
 
+CLASS_NAMES_MAPPING = {
+    "plate": "PRCXI_BioER_96_wellplate",
+    "tip_rack": "PRCXI_300ul_Tips",
+}
 # create_resource 节点默认参数
 CREATE_RESOURCE_DEFAULTS = {
     "device_id": "/PRCXI",
     "parent_template": "/PRCXI/PRCXI_Deck",
-    "class_name": "PRCXI_BioER_96_wellplate",
 }
 
 # 默认液体体积 (uL)
@@ -367,11 +370,10 @@ def build_protocol_graph(
     """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: reagent 信息字典，格式为 {name: {slot, well}, ...}，用于 set_liquid 和 well 查找
+        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
-        labware_defs: labware 定义列表，格式为 [{"name": "...", "slot": "1", "type": "lab_xxx"}, ...]
     """
     G = WorkflowGraph()
     resource_last_writer = {}  # reagent_name -> "node_id:port"
@@ -379,7 +381,19 @@ def build_protocol_graph(
 
     protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
 
-    # ==================== 第一步：按 slot 创建 create_resource 节点 ====================
+    # ==================== 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,
+                "labware_id": labware_id,
+            }
+
     # 创建 Group 节点，包含所有 create_resource 节点
     group_node_id = str(uuid.uuid4())
     G.add_node(
@@ -395,41 +409,38 @@ def build_protocol_graph(
         param=None,
     )
 
-    # 直接使用 JSON 中的 labware 定义，每个 slot 一条记录，type 即 class_name
-    res_index = 0
-    for lw in (labware_defs or []):
-        slot = str(lw.get("slot", ""))
-        if not slot or slot in slot_to_create_resource:
-            continue  # 跳过空 slot 或已处理的 slot
-
-        lw_name = lw.get("name", f"slot {slot}")
-        lw_type = lw.get("type", CREATE_RESOURCE_DEFAULTS["class_name"])
-        res_id = f"plate_slot_{slot}"
-
-        res_index += 1
+    # 为每个唯一的 slot 创建 create_resource 节点
+    for slot, info in slots_info.items():
         node_id = str(uuid.uuid4())
+        res_id = info["res_id"]
+        res_type_name = info["labware"].lower().replace(".", "point")
+        res_type_name = f"lab_{res_type_name}"
+        
         G.add_node(
             node_id,
             template_name="create_resource",
             resource_name="host_node",
-            name=lw_name,
-            description=f"Create {lw_name}",
+            name=f"{res_type_name}_slot{slot}",
+            description=f"Create plate on slot {slot}",
             lab_node_type="Labware",
             footer="create_resource-host_node",
             device_name=DEVICE_NAME_HOST,
             type=NODE_TYPE_DEFAULT,
-            parent_uuid=group_node_id,
-            minimized=True,
+            parent_uuid=group_node_id,  # 指向 Group 节点
+            minimized=True,  # 折叠显示
             param={
                 "res_id": res_id,
                 "device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
-                "class_name": lw_type,
-                "parent": CREATE_RESOURCE_DEFAULTS["parent_template"],
+                "class_name": res_type_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
+        if "tip" in res_type_name and "rack" in res_type_name:
+            resource_last_writer[info["labware_id"]] = f"{node_id}:labware"
+        # create_resource 之间不需要 ready 连接
 
     # ==================== 第二步：为每个 reagent 创建 set_liquid_from_plate 节点 ====================
     # 创建 Group 节点，包含所有 set_liquid_from_plate 节点
@@ -511,6 +522,7 @@ def build_protocol_graph(
         "reagent": "reagent",
         "solvent": "solvent",
         "compound": "compound",
+        "tip_racks": "tip_rack_identifier",
     }
 
     OUTPUT_PORT_MAPPING = {