v0.10.17

ci(deps): bump actions/checkout from 4 to 6 (#223)

Bumps [actions/checkout](https://github.com/actions/checkout) from 4 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](https://github.com/actions/checkout/compare/v4...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

ci(deps): bump actions/upload-pages-artifact from 3 to 4 (#225)

Bumps [actions/upload-pages-artifact](https://github.com/actions/upload-pages-artifact) from 3 to 4.
- [Release notes](https://github.com/actions/upload-pages-artifact/releases)
- [Commits](https://github.com/actions/upload-pages-artifact/compare/v3...v4)

---
updated-dependencies:
- dependency-name: actions/upload-pages-artifact
  dependency-version: '4'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

ci(deps): bump actions/upload-artifact from 4 to 6 (#224)

Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 6.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](https://github.com/actions/upload-artifact/compare/v4...v6)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

ci(deps): bump actions/configure-pages from 4 to 5 (#222)

Bumps [actions/configure-pages](https://github.com/actions/configure-pages) from 4 to 5.
- [Release notes](https://github.com/actions/configure-pages/releases)
- [Commits](https://github.com/actions/configure-pages/compare/v4...v5)

---
updated-dependencies:
- dependency-name: actions/configure-pages
  dependency-version: '5'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

.conda/base/recipe.yaml

@@ -41,12 +41,13 @@ requirements:
   - networkx
   - typing_extensions
   - websockets
+  - opentrons_shared_data
   - pint
   - fastapi
   - jinja2
   - requests
   - uvicorn
-  - opcua # [not osx]
+  - opcua
   - pyserial
   - pandas
   - pymodbus

.conda/environment/recipe.yaml

@@ -36,4 +36,4 @@ requirements:
 about:
   repository: https://github.com/deepmodeling/Uni-Lab-OS
   license: GPL-3.0-only
-  description: "UniLabOS Environment - ROS2 and conda dependencies"
+  description: "UniLabOS Environment - ROS2 and conda dependencies (for developers: pip install -e .)"

.github/workflows/ci-check.yml

@@ -47,7 +47,7 @@ jobs:
           uv pip install -r unilabos/utils/requirements.txt
           uv pip install pywinauto git+https://github.com/Xuwznln/pylabrobot.git
           uv pip uninstall enum34 || echo enum34 not installed, skipping
-          uv pip install .
+          uv pip install -e .
 
       - name: Run check mode (complete_registry)
         run: |

docs/user_guide/best_practice.md

@@ -439,9 +439,6 @@ 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)
 

scripts/workflow.py

@@ -2,6 +2,7 @@ import json
 import logging
 import traceback
 import uuid
+import xml.etree.ElementTree as ET
 from typing import Any, Dict, List
 
 import networkx as nx
@@ -24,15 +25,7 @@ class SimpleGraph:
 
     def add_edge(self, source, target, **attrs):
         """添加边"""
-        # edge = {"source": source, "target": target, **attrs}
+        edge = {"source": source, "target": target, **attrs}
-        edge = {
-            "source": source, "target": target,
-            "source_node_uuid": source,
-            "target_node_uuid": target,
-            "source_handle_io": "source",
-            "target_handle_io": "target",
-            **attrs
-        }
         self.edges.append(edge)
 
     def to_dict(self):
@@ -49,7 +42,6 @@ class SimpleGraph:
             "multigraph": False,
             "graph": {},
             "nodes": nodes_list,
-            "edges": self.edges,
             "links": self.edges,
         }
 
@@ -66,8 +58,495 @@ def extract_json_from_markdown(text: str) -> str:
     return text
 
 
+def convert_to_type(val: str) -> Any:
+    """将字符串值转换为适当的数据类型"""
+    if val == "True":
+        return True
+    if val == "False":
+        return False
+    if val == "?":
+        return None
+    if val.endswith(" g"):
+        return float(val.split(" ")[0])
+    if val.endswith("mg"):
+        return float(val.split("mg")[0])
+    elif val.endswith("mmol"):
+        return float(val.split("mmol")[0]) / 1000
+    elif val.endswith("mol"):
+        return float(val.split("mol")[0])
+    elif val.endswith("ml"):
+        return float(val.split("ml")[0])
+    elif val.endswith("RPM"):
+        return float(val.split("RPM")[0])
+    elif val.endswith(" °C"):
+        return float(val.split(" ")[0])
+    elif val.endswith(" %"):
+        return float(val.split(" ")[0])
+    return val
 
 
+def refactor_data(data: List[Dict[str, Any]]) -> 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"""
+    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": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
+        "transfer": "SynBioFactory-liquid_handler.biomek-transfer",
+        "incubation": "SynBioFactory-liquid_handler.biomek-incubation",
+        "move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
+        "oscillation": "SynBioFactory-liquid_handler.biomek-oscillation",
+        # 有机化学操作
+        "HeatChillToTemp": "SynBioFactory-workstation-HeatChillProtocol",
+        "StopHeatChill": "SynBioFactory-workstation-HeatChillStopProtocol",
+        "StartHeatChill": "SynBioFactory-workstation-HeatChillStartProtocol",
+        "HeatChill": "SynBioFactory-workstation-HeatChillProtocol",
+        "Dissolve": "SynBioFactory-workstation-DissolveProtocol",
+        "Transfer": "SynBioFactory-workstation-TransferProtocol",
+        "Evaporate": "SynBioFactory-workstation-EvaporateProtocol",
+        "Recrystallize": "SynBioFactory-workstation-RecrystallizeProtocol",
+        "Filter": "SynBioFactory-workstation-FilterProtocol",
+        "Dry": "SynBioFactory-workstation-DryProtocol",
+        "Add": "SynBioFactory-workstation-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)
+                refactored_data.extend(sub_data)
+            continue
+
+        # 获取模板名称
+        template = OPERATION_MAPPING.get(operation)
+        if not template:
+            # 自动推断模板类型
+            if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
+                template = f"SynBioFactory-liquid_handler.biomek-{operation}"
+            else:
+                template = f"SynBioFactory-workstation-{operation}Protocol"
+
+        # 创建步骤数据
+        step_data = {
+            "template": template,
+            "description": step.get("description", step.get("purpose", f"{operation} operation")),
+            "lab_node_type": "Device",
+            "parameters": step.get("parameters", step.get("action_args", {})),
+        }
+        refactored_data.append(step_data)
+
+    return refactored_data
+
+
+def build_protocol_graph(
+    labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
+) -> SimpleGraph:
+    """统一的协议图构建函数，根据设备类型自动选择构建逻辑"""
+    G = SimpleGraph()
+    resource_last_writer = {}
+    LAB_NAME = "SynBioFactory"
+
+    protocol_steps = refactor_data(protocol_steps)
+
+    # 检查协议步骤中的模板来判断协议类型
+    has_biomek_template = any(
+        ("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
+        for step in protocol_steps
+    )
+
+    if has_biomek_template:
+        # 生物实验协议图构建
+        for labware_id, labware in labware_info.items():
+            node_id = str(uuid.uuid4())
+
+            labware_attrs = labware.copy()
+            labware_id = labware_attrs.pop("id", labware_attrs.get("name", f"labware_{uuid.uuid4()}"))
+            labware_attrs["description"] = labware_id
+            labware_attrs["lab_node_type"] = (
+                "Reagent" if "Plate" in str(labware_id) else "Labware" if "Rack" in str(labware_id) else "Sample"
+            )
+            labware_attrs["device_id"] = workstation_name
+
+            G.add_node(node_id, template=f"{LAB_NAME}-host_node-create_resource", **labware_attrs)
+            resource_last_writer[labware_id] = f"{node_id}:labware"
+
+        # 处理协议步骤
+        prev_node = None
+        for i, step in enumerate(protocol_steps):
+            node_id = str(uuid.uuid4())
+            G.add_node(node_id, **step)
+
+            # 添加控制流边
+            if prev_node is not None:
+                G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
+            prev_node = node_id
+
+            # 处理物料流
+            params = step.get("parameters", {})
+            if "sources" in params and params["sources"] in resource_last_writer:
+                source_node, source_port = resource_last_writer[params["sources"]].split(":")
+                G.add_edge(source_node, node_id, source_port=source_port, target_port="labware")
+
+            if "targets" in params:
+                resource_last_writer[params["targets"]] = f"{node_id}:labware"
+
+        # 添加协议结束节点
+        end_id = str(uuid.uuid4())
+        G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
+        if prev_node is not None:
+            G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
+
+    else:
+        # 有机化学协议图构建
+        WORKSTATION_ID = workstation_name
+
+        # 为所有labware创建资源节点
+        for item_id, item in labware_info.items():
+            # item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
+            node_id = str(uuid.uuid4())
+
+            # 判断节点类型
+            if item.get("type") == "hardware" or "reactor" in str(item_id).lower():
+                if "reactor" not in str(item_id).lower():
+                    continue
+                lab_node_type = "Sample"
+                description = f"Prepare Reactor: {item_id}"
+                liquid_type = []
+                liquid_volume = []
+            else:
+                lab_node_type = "Reagent"
+                description = f"Add Reagent to Flask: {item_id}"
+                liquid_type = [item_id]
+                liquid_volume = [1e5]
+
+            G.add_node(
+                node_id,
+                template=f"{LAB_NAME}-host_node-create_resource",
+                description=description,
+                lab_node_type=lab_node_type,
+                res_id=item_id,
+                device_id=WORKSTATION_ID,
+                class_name="container",
+                parent=WORKSTATION_ID,
+                bind_locations={"x": 0.0, "y": 0.0, "z": 0.0},
+                liquid_input_slot=[-1],
+                liquid_type=liquid_type,
+                liquid_volume=liquid_volume,
+                slot_on_deck="",
+                role=item.get("role", ""),
+            )
+            resource_last_writer[item_id] = f"{node_id}:labware"
+
+        last_control_node_id = None
+
+        # 处理协议步骤
+        for step in protocol_steps:
+            node_id = str(uuid.uuid4())
+            G.add_node(node_id, **step)
+
+            # 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
+
+            # 物料流
+            params = step.get("parameters", {})
+            input_resources = {
+                "Vessel": params.get("vessel"),
+                "ToVessel": params.get("to_vessel"),
+                "FromVessel": params.get("from_vessel"),
+                "reagent": params.get("reagent"),
+                "solvent": params.get("solvent"),
+                "compound": params.get("compound"),
+                "sources": params.get("sources"),
+                "targets": params.get("targets"),
+            }
+
+            for target_port, resource_name in input_resources.items():
+                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)
+
+            output_resources = {
+                "VesselOut": params.get("vessel"),
+                "FromVesselOut": params.get("from_vessel"),
+                "ToVesselOut": params.get("to_vessel"),
+                "FiltrateOut": params.get("filtrate_vessel"),
+                "reagent": params.get("reagent"),
+                "solvent": params.get("solvent"),
+                "compound": params.get("compound"),
+                "sources_out": params.get("sources"),
+                "targets_out": params.get("targets"),
+            }
+
+            for source_port, resource_name in output_resources.items():
+                if resource_name:
+                    resource_last_writer[resource_name] = f"{node_id}:{source_port}"
+
+    return G
+
+
+def draw_protocol_graph(protocol_graph: SimpleGraph, 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", 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}'")
+
+
+from networkx.drawing.nx_agraph import to_agraph
+import re
+
+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 <portname>。
+    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", 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_port")
+        tp = edge.get("target_port")
+
+        # 记录到图里（保留原始端口信息）
+        G.add_edge(u, v, source_port=sp, target_port=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，<p> 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 <port> 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 <port> 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}'")
+
+
+def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
+    """展平嵌套的XDL程序结构"""
+    flattened_operations = []
+    TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
+
+    def extract_operations(element: ET.Element):
+        if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
+            if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
+                flattened_operations.append(element)
+
+        for child in element:
+            extract_operations(child)
+
+    for child in procedure_elem:
+        extract_operations(child)
+
+    return flattened_operations
+
+
+def parse_xdl_content(xdl_content: str) -> tuple:
+    """解析XDL内容"""
+    try:
+        xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
+        root = ET.fromstring(xdl_content_cleaned)
+
+        synthesis_elem = root.find("Synthesis")
+        if synthesis_elem is None:
+            return None, None, None
+
+        # 解析硬件组件
+        hardware_elem = synthesis_elem.find("Hardware")
+        hardware = []
+        if hardware_elem is not None:
+            hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
+
+        # 解析试剂
+        reagents_elem = synthesis_elem.find("Reagents")
+        reagents = []
+        if reagents_elem is not None:
+            reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
+
+        # 解析程序
+        procedure_elem = synthesis_elem.find("Procedure")
+        if procedure_elem is None:
+            return None, None, None
+
+        flattened_operations = flatten_xdl_procedure(procedure_elem)
+        return hardware, reagents, flattened_operations
+
+    except ET.ParseError as e:
+        raise ValueError(f"Invalid XDL format: {e}")
+
+
+def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
+    """
+    将XDL XML格式转换为标准的字典格式
+
+    Args:
+        xdl_content: XDL XML内容
+
+    Returns:
+        转换结果，包含步骤和器材信息
+    """
+    try:
+        hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
+        if hardware is None:
+            return {"error": "Failed to parse XDL content", "success": False}
+
+        # 将XDL元素转换为字典格式
+        steps_data = []
+        for elem in flattened_operations:
+            # 转换参数类型
+            parameters = {}
+            for key, val in elem.attrib.items():
+                converted_val = convert_to_type(val)
+                if converted_val is not None:
+                    parameters[key] = converted_val
+
+            step_dict = {
+                "operation": elem.tag,
+                "parameters": parameters,
+                "description": elem.get("purpose", f"Operation: {elem.tag}"),
+            }
+            steps_data.append(step_dict)
+
+        # 合并硬件和试剂为统一的labware_info格式
+        labware_data = []
+        labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
+        labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
+
+        return {
+            "success": True,
+            "steps": steps_data,
+            "labware": labware_data,
+            "message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
+        }
+
+    except Exception as e:
+        error_msg = f"XDL conversion failed: {str(e)}"
+        logger.error(error_msg)
+        return {"error": error_msg, "success": False}
 
 
 def create_workflow(

tests/workflow/test.json

@@ -1,213 +0,0 @@
-{
-  "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"
-    }
-  }
-}

unilabos/app/web/client.py

@@ -74,8 +74,7 @@ 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:
-            payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
+            f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
-            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:
@@ -334,65 +333,6 @@ 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()

unilabos/app/ws_client.py

@@ -439,7 +439,7 @@ class MessageProcessor:
                     self.connected = True
                     self.reconnect_count = 0
 
-                    logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
+                    logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
 
                     # 启动发送协程
                     send_task = asyncio.create_task(self._send_handler())
@@ -517,7 +517,7 @@ class MessageProcessor:
 
     async def _send_handler(self):
         """处理发送队列中的消息"""
-        logger.trace("[MessageProcessor] Send handler started")
+        logger.debug("[MessageProcessor] Send handler started")
 
         try:
             while self.connected and self.websocket:
@@ -1026,7 +1026,7 @@ class QueueProcessor:
 
     def _run(self):
         """运行队列处理主循环"""
-        logger.trace("[QueueProcessor] Queue processor started")
+        logger.debug("[QueueProcessor] Queue processor started")
 
         while self.is_running:
             try:
@@ -1236,6 +1236,7 @@ class WebSocketClient(BaseCommunicationClient):
         else:
             url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
 
+        logger.debug(f"[WebSocketClient] URL: {url}")
         return url
 
     def start(self) -> None:
@@ -1248,11 +1249,13 @@ class WebSocketClient(BaseCommunicationClient):
             logger.error("[WebSocketClient] WebSocket URL not configured")
             return
 
+        logger.info(f"[WebSocketClient] Starting connection to {self.websocket_url}")
+
         # 启动两个核心线程
         self.message_processor.start()
         self.queue_processor.start()
 
-        logger.trace("[WebSocketClient] All threads started")
+        logger.info("[WebSocketClient] All threads started")
 
     def stop(self) -> None:
         """停止WebSocket客户端"""

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -1,11 +1,15 @@
 from __future__ import annotations
 
+import asyncio
 import time
 import traceback
 from collections import Counter
 from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set, cast
 
+from typing_extensions import TypedDict
 from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness
+from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
+from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend
 from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod
 from pylabrobot.liquid_handling.standard import GripDirection
 from pylabrobot.resources import (
@@ -23,53 +27,22 @@ from pylabrobot.resources import (
     Trash,
     Tip,
 )
-from typing_extensions import TypedDict
-
-from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend
-from unilabos.registry.placeholder_type import ResourceSlot
-from unilabos.resources.resource_tracker import (
-    ResourceTreeSet,
-    ResourceDict,
-    EXTRA_SAMPLE_UUID,
-    EXTRA_UNILABOS_SAMPLE_UUID,
-)
-from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, ROS2DeviceNode
-
 
+from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
 class SimpleReturn(TypedDict):
-    samples: List[List[ResourceDict]]
+    samples: list
-    volumes: List[float]
+    volumes: list
-
-
-class SetLiquidReturn(TypedDict):
-    wells: List[List[ResourceDict]]
-    volumes: List[float]
-
-
-class SetLiquidFromPlateReturn(TypedDict):
-    plate: List[List[ResourceDict]]
-    wells: List[List[ResourceDict]]
-    volumes: List[float]
-
-
-class TransferLiquidReturn(TypedDict):
-    sources: List[List[ResourceDict]]
-    targets: List[List[ResourceDict]]
-
 
 class LiquidHandlerMiddleware(LiquidHandler):
-    def __init__(
+    def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool = False, channel_num: int = 8, **kwargs):
-        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(
+                self._simulate_backend = UniLiquidHandlerRvizBackend(channel_num, kwargs["total_height"],
-                    channel_num, kwargs["total_height"], joint_config=joint_config, lh_device_id=deck.name
+                                                                     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)
@@ -186,9 +159,7 @@ 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(
+            return await self._simulate_handler.discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs)
-                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 
@@ -209,6 +180,7 @@ class LiquidHandlerMiddleware(LiquidHandler):
         **backend_kwargs,
     ):
 
+        
         if self._simulator:
             return await self._simulate_handler.aspirate(
                 resources,
@@ -236,15 +208,15 @@ class LiquidHandlerMiddleware(LiquidHandler):
         res_samples = []
         res_volumes = []
         for resource, volume, channel in zip(resources, vols, use_channels):
-            sample_uuid_value = resource.unilabos_extra.get(EXTRA_SAMPLE_UUID, None)
+            res_samples.append({"name": resource.name, "sample_uuid": resource.unilabos_extra.get("sample_uuid", None)})
-            res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: sample_uuid_value})
             res_volumes.append(volume)
             self.pending_liquids_dict[channel] = {
-                EXTRA_SAMPLE_UUID: sample_uuid_value,
+                "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],
@@ -282,10 +254,10 @@ class LiquidHandlerMiddleware(LiquidHandler):
         res_samples = []
         res_volumes = []
         for resource, volume, channel in zip(resources, vols, use_channels):
-            res_uuid = self.pending_liquids_dict[channel][EXTRA_SAMPLE_UUID]
+            res_uuid = self.pending_liquids_dict[channel]["sample_uuid"]
             self.pending_liquids_dict[channel]["volume"] -= volume
-            resource.unilabos_extra[EXTRA_SAMPLE_UUID] = res_uuid
+            resource.unilabos_extra["sample_uuid"] = res_uuid
-            res_samples.append({"name": resource.name, EXTRA_SAMPLE_UUID: res_uuid})
+            res_samples.append({"name": resource.name, "sample_uuid": res_uuid})
             res_volumes.append(volume)
 
         return SimpleReturn(samples=res_samples, volumes=res_volumes)
@@ -606,18 +578,10 @@ class LiquidHandlerMiddleware(LiquidHandler):
 
 class LiquidHandlerAbstract(LiquidHandlerMiddleware):
     """Extended LiquidHandler with additional operations."""
-
     support_touch_tip = True
     _ros_node: BaseROS2DeviceNode
 
-    def __init__(
+    def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool=False, channel_num:int = 8, total_height:float = 310):
-        self,
-        backend: LiquidHandlerBackend,
-        deck: Deck,
-        simulator: bool = False,
-        channel_num: int = 8,
-        total_height: float = 310,
-    ):
         """Initialize a LiquidHandler.
 
         Args:
@@ -641,7 +605,6 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         module_name = ".".join(components[:-1])
                         try:
                             import importlib
-
                             mod = importlib.import_module(module_name)
                         except ImportError:
                             mod = None
@@ -651,7 +614,6 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         # Try pylabrobot style import (if available)
                         try:
                             import pylabrobot
-
                             backend_cls = getattr(pylabrobot, type_str, None)
                         except Exception:
                             backend_cls = None
@@ -669,67 +631,16 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         self._ros_node = ros_node
 
     @classmethod
-    def set_liquid(cls, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SetLiquidReturn:
+    def set_liquid(cls, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SimpleReturn:
-        """Set the liquid in a well.
+        """Set the liquid in a well."""
-
+        res_samples = []
-        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 SetLiquidReturn(
+        return SimpleReturn(samples=res_samples, volumes=res_volumes)
-            wells=ResourceTreeSet.from_plr_resources(wells, known_newly_created=False).dump(), volumes=res_volumes  # type: ignore
-        )
-
-    def set_liquid_from_plate(
-        self, plate: List[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。
-        """
-        if isinstance(plate, list):  # 未来移除
-            plate = plate[0]
-        assert issubclass(plate.__class__, Plate), "plate must be a Plate"
-        plate: Plate = cast(Plate, plate)
-        # 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)
-
-        task = ROS2DeviceNode.run_async_func(self._ros_node.update_resource, True, **{"resources": wells})
-        submit_time = time.time()
-        while not task.done():
-            if time.time() - submit_time > 10:
-                self._ros_node.lab_logger().info(f"set_liquid_from_plate {plate} 超时")
-                break
-            time.sleep(0.01)
-
-        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 --------------------------------------------------
     # ---------------------------------------------------------------
@@ -765,7 +676,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                 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
@@ -773,8 +684,8 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         print("channel_num", self.channel_num)
         if self.channel_num == 8:
 
-            tip_prefix = list(available_tips.values())[0].name.split("_")[0]
+            tip_prefix = list(available_tips.values())[0].name.split('_')[0]
-            colnum_list = [int(tip.name.split("_")[-1][1:]) for tip in available_tips.values()]
+            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_tips_dict = {tip.name: tip for tip in available_tips.values()}
@@ -818,6 +729,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         """Create a new protocol with the given metadata."""
         pass
 
+
     async def remove_liquid(
         self,
         vols: List[float],
@@ -876,11 +788,10 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
 
                 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(
+                        raise ValueError(f"Length of `sources` {len(sources)} must be a multiple of 8 for 8-channel mode.")
-                            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
 
@@ -894,23 +805,13 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         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 = (
+                        current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8
-                            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 = (
+                        current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8
-                            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_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,
@@ -1040,23 +941,13 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         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 = (
+                        current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8
-                        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 = (
+                        current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8
-                        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_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,
@@ -1098,6 +989,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                         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
@@ -1129,7 +1021,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         mix_liquid_height: Optional[float] = None,
         delays: Optional[List[int]] = None,
         none_keys: List[str] = [],
-    ) -> TransferLiquidReturn:
+    ):
         """Transfer liquid with automatic mode detection.
 
         Supports three transfer modes:
@@ -1197,71 +1089,29 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
         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],
+                sources[0], targets, tip_racks, use_channels,
-                targets,
+                asp_vols, dis_vols, asp_flow_rates, dis_flow_rates,
-                tip_racks,
+                offsets, touch_tip, liquid_height, blow_out_air_volume,
-                use_channels,
+                spread, mix_stage, mix_times, mix_vol, mix_rate,
-                asp_vols,
+                mix_liquid_height, delays
-                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,
+                sources, targets[0], tip_racks, use_channels,
-                targets[0],
+                asp_vols, dis_vols, asp_flow_rates, dis_flow_rates,
-                tip_racks,
+                offsets, touch_tip, liquid_height, blow_out_air_volume,
-                use_channels,
+                spread, mix_stage, mix_times, mix_vol, mix_rate,
-                asp_vols,
+                mix_liquid_height, delays
-                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,
+                sources, targets, tip_racks, use_channels,
-                targets,
+                asp_vols, dis_vols, asp_flow_rates, dis_flow_rates,
-                tip_racks,
+                offsets, touch_tip, liquid_height, blow_out_air_volume,
-                use_channels,
+                spread, mix_stage, mix_times, mix_vol, mix_rate,
-                asp_vols,
+                mix_liquid_height, delays
-                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(
@@ -1269,11 +1119,6 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                 "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_one_to_one(
         self,
         sources: Sequence[Container],
@@ -1329,9 +1174,7 @@ 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=[blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None,
-                        [blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None
-                    ),
                     spread=spread,
                 )
                 if delays is not None:
@@ -1342,9 +1185,7 @@ 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=[blow_out_air_volume[_]] if blow_out_air_volume and len(blow_out_air_volume) > _ else None,
-                        [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,
                 )
@@ -1496,9 +1337,7 @@ 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=[blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None,
-                    [blow_out_air_volume[0]] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None
-                ),
                 spread=spread,
             )
             
@@ -1513,9 +1352,7 @@ 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=[blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None,
-                        [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,
                 )
@@ -1551,18 +1388,10 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                 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 = (
+                current_asp_flow_rates = asp_flow_rates[0:1] * 8 if asp_flow_rates and len(asp_flow_rates) > 0 else None
-                    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 = (
+                current_asp_liquid_height = liquid_height[0:1] * 8 if liquid_height and len(liquid_height) > 0 else [None] * 8
-                    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_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(
@@ -1695,9 +1524,7 @@ 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=[blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None,
-                        [blow_out_air_volume[idx]] if blow_out_air_volume and len(blow_out_air_volume) > idx else None
-                    ),
                     spread=spread,
                 )
                 
@@ -1711,18 +1538,14 @@ 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 = (
+                    dis_blow_out = blow_out_air_volume[idx] if blow_out_air_volume and len(blow_out_air_volume) > idx else None
-                        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 = (
+                    dis_blow_out = blow_out_air_volume[0] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None
-                        blow_out_air_volume[0] if blow_out_air_volume and len(blow_out_air_volume) > 0 else None
-                    )
                 
                 await self.dispense(
                     resources=[target],
@@ -1805,18 +1628,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                     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 = (
+                    current_dis_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
-                        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 = (
+                    current_dis_blow_out_air_volume = blow_out_air_volume[0:1] * 8 if blow_out_air_volume else [None] * 8
-                        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
@@ -1852,6 +1671,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
     #     traceback.print_exc()
     #     raise RuntimeError(f"Liquid addition failed: {e}") from e
 
+
     # ---------------------------------------------------------------
     # Helper utilities
     # ---------------------------------------------------------------
@@ -1872,6 +1692,7 @@ 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:

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -30,31 +30,9 @@ from pylabrobot.liquid_handling.standard import (
     ResourceMove,
     ResourceDrop,
 )
-from pylabrobot.resources import (
+from pylabrobot.resources import ResourceHolder, ResourceStack, Tip, Deck, Plate, Well, TipRack, Resource, Container, Coordinate, TipSpot, Trash, PlateAdapter, TubeRack
-    ResourceHolder,
-    ResourceStack,
-    Tip,
-    Deck,
-    Plate,
-    Well,
-    TipRack,
-    Resource,
-    Container,
-    Coordinate,
-    TipSpot,
-    Trash,
-    PlateAdapter,
-    TubeRack,
-)
 
-from unilabos.devices.liquid_handling.liquid_handler_abstract import (
+from unilabos.devices.liquid_handling.liquid_handler_abstract import LiquidHandlerAbstract, SimpleReturn
-    LiquidHandlerAbstract,
-    SimpleReturn,
-    SetLiquidReturn,
-    SetLiquidFromPlateReturn,
-    TransferLiquidReturn,
-)
-from unilabos.registry.placeholder_type import ResourceSlot
 from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
 
 
@@ -102,7 +80,6 @@ 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。
 
@@ -132,80 +109,73 @@ class PRCXI9300Container(Plate):
         data = super().serialize_state()
         data.update(self._unilabos_state)
         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, 
-    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,
+                 **kwargs):
-    ):
         # 如果 ordered_items 不为 None，直接使用
-        items = None
-        ordering_param = None
         if ordered_items is not None:
             items = ordered_items
         elif ordering is not None:
             # 检查 ordering 中的值是否是字符串（从 JSON 反序列化时的情况）
             # 如果是字符串，说明这是位置名称，需要让 Plate 自己创建 Well 对象
             # 我们只传递位置信息（键），不传递值，使用 ordering 参数
-            if ordering:
+            if ordering and isinstance(next(iter(ordering.values()), None), str):
-                values = list(ordering.values())
-                value = values[0]
-                if isinstance(value, str):
                 # ordering 的值是字符串，只使用键（位置信息）创建新的 OrderedDict
                 # 传递 ordering 参数而不是 ordered_items，让 Plate 自己创建 Well 对象
                 items = None
                 # 使用 ordering 参数，只包含位置信息（键）
                 ordering_param = collections.OrderedDict((k, None) for k in ordering.keys())
-                elif value is None:
-                    ordering_param = ordering
             else:
                 # ordering 的值已经是对象，可以直接使用
                 items = ordering
                 ordering_param = None
+        else:
+            items = None
+            ordering_param = None
         
         # 根据情况传递不同的参数
         if items is not None:
-            super().__init__(
+            super().__init__(name, size_x, size_y, size_z, 
-                name, size_x, size_y, size_z, ordered_items=items, category=category, model=model, **kwargs
+                             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__(
+            super().__init__(name, size_x, size_y, size_z, 
-                name, size_x, size_y, size_z, ordering=ordering_param, category=category, model=model, **kwargs
+                             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
@@ -226,24 +196,15 @@ class PRCXI9300Plate(Plate):
             
             data.update(safe_state)
         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, 
-    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,
+                 **kwargs):
-    ):
         # 如果 ordered_items 不为 None，直接使用
         if ordered_items is not None:
             items = ordered_items
@@ -267,16 +228,20 @@ class PRCXI9300TipRack(TipRack):
         
         # 根据情况传递不同的参数
         if items is not None:
-            super().__init__(
+            super().__init__(name, size_x, size_y, size_z, 
-                name, size_x, size_y, size_z, ordered_items=items, category=category, model=model, **kwargs
+                             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__(
+            super().__init__(name, size_x, size_y, size_z, 
-                name, size_x, size_y, size_z, ordering=ordering_param, category=category, model=model, **kwargs
+                             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
@@ -290,7 +255,7 @@ 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
@@ -312,23 +277,16 @@ class PRCXI9300TipRack(TipRack):
             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__(
+    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, 
-        self,
-        name: str,
-        size_x: float,
-        size_y: float,
-        size_z: float,
                  category: str = "trash", 
                  material_info: Optional[Dict[str, Any]] = None,
-        **kwargs,
+                 **kwargs):
-    ):
         
         if name != "trash":
             print(f"Warning: PRCXI9300Trash usually expects name='trash' for backend logic, but got '{name}'.")
@@ -348,7 +306,7 @@ 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
@@ -370,27 +328,19 @@ class PRCXI9300Trash(Trash):
             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, 
-    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,
+                 **kwargs):
-    ):
         
         # 如果 ordered_items 不为 None，直接使用
         if ordered_items is not None:
@@ -420,12 +370,20 @@ class PRCXI9300TubeRack(TubeRack):
         
         # 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:
@@ -436,7 +394,7 @@ 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
@@ -458,19 +416,12 @@ class PRCXI9300TubeRack(TubeRack):
             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, 
-    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, 
@@ -481,8 +432,7 @@ class PRCXI9300PlateAdapter(PlateAdapter):
                  dx: Optional[float] = None,
                  dy: Optional[float] = None,
                  dz: float = 0.0, # 默认Z轴偏移
-        **kwargs,
+                 **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:
@@ -502,7 +452,7 @@ class PRCXI9300PlateAdapter(PlateAdapter):
             adapter_hole_size_y=adapter_hole_size_y,
             adapter_hole_size_z=adapter_hole_size_z,
             model=model, 
-            **kwargs,
+            **kwargs
         )
         
         self._unilabos_state = {}
@@ -514,7 +464,7 @@ 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
@@ -536,7 +486,6 @@ class PRCXI9300PlateAdapter(PlateAdapter):
             data.update(safe_state)
         return data
 
-
 class PRCXI9300Handler(LiquidHandlerAbstract):
     support_touch_tip = False
 
@@ -569,9 +518,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
                 if "Material" in child.children[0]._unilabos_state:
                     number = int(child.name.replace("T", ""))
                     tablets_info.append(
-                        WorkTablets(
+                        WorkTablets(Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"])
-                            Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"]
-                        )
                     )
         if is_9320:
             print("当前设备是9320")
@@ -591,14 +538,9 @@ 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]) -> SetLiquidReturn:
+    def set_liquid(self, wells: list[Well], liquid_names: list[str], volumes: list[float]) -> SimpleReturn:
         return super().set_liquid(wells, liquid_names, volumes)
 
-    def set_liquid_from_plate(
-        self, plate: List[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)
 
@@ -718,7 +660,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         mix_liquid_height: Optional[float] = None,
         delays: Optional[List[int]] = None,
         none_keys: List[str] = [],
-    ) -> TransferLiquidReturn:
+    ):
         return await super().transfer_liquid(
             sources,
             targets,
@@ -858,7 +800,6 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
 
     async def heater_action(self, temperature: float, time: int):
         return await self._unilabos_backend.heater_action(temperature, time)  
-
     async def move_plate(
         self,
         plate: Plate,
@@ -885,7 +826,6 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
             **backend_kwargs,
         )
 
-
 class PRCXI9300Backend(LiquidHandlerBackend):
     """PRCXI 9300 的后端实现，继承自 LiquidHandlerBackend。
 
@@ -938,6 +878,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
         self.steps_todo_list.append(step)
         return step
 
+
     async def pick_up_resource(self, pickup: ResourcePickup, **backend_kwargs):
         
         resource=pickup.resource
@@ -955,11 +896,13 @@ class PRCXI9300Backend(LiquidHandlerBackend):
 
     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:
@@ -968,6 +911,7 @@ 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)
@@ -1036,7 +980,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
                 # 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)
@@ -1054,7 +998,7 @@ 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
@@ -1108,7 +1052,7 @@ 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
@@ -1234,7 +1178,7 @@ 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
@@ -1291,7 +1235,7 @@ 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
@@ -1472,6 +1416,7 @@ 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=(",", ":")
@@ -1736,11 +1681,11 @@ class PRCXI9300Api:
             "LiquidDispensingMethod": liquid_method,
         }
 
-    def clamp_jaw_pick_up(
+    def clamp_jaw_pick_up(self,
-        self,
         plate_no: int,
         is_whole_plate: bool,
         balance_height: int,
+
     ) -> Dict[str, Any]:
         return {
             "StepAxis": "ClampingJaw",
@@ -1750,7 +1695,7 @@ class PRCXI9300Api:
             "HoleRow": 1,
             "HoleCol": 1,
             "BalanceHeight": balance_height,
-            "PlateOrHoleNum": f"T{plate_no}",
+            "PlateOrHoleNum": f"T{plate_no}"
         }
 
     def clamp_jaw_drop(
@@ -1758,6 +1703,7 @@ class PRCXI9300Api:
         plate_no: int,
         is_whole_plate: bool,
         balance_height: int,
+
     ) -> Dict[str, Any]:
         return {
             "StepAxis": "ClampingJaw",
@@ -1767,7 +1713,7 @@ 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):
@@ -1780,7 +1726,6 @@ class PRCXI9300Api:
             "AssistFun4": is_wait,
         }
 
-
 class DefaultLayout:
 
     def __init__(self, product_name: str = "PRCXI9300"):
@@ -2159,9 +2104,7 @@ if __name__ == "__main__":
             size_y=50,
             size_z=10,
             category="tip_rack",
-            ordered_items=collections.OrderedDict(
+            ordered_items=collections.OrderedDict({k: f"{child_prefix}_{k}" for k, v in tip_racks["ordering"].items()}),
-                {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
@@ -2356,19 +2299,21 @@ if __name__ == "__main__":
 
     A = tree_to_list([resource_plr_to_ulab(deck)])
     with open("deck.json", "w", encoding="utf-8") as f:
-        A.insert(
+        A.insert(0, {
-            0,
-            {
             "id": "PRCXI",
             "name": "PRCXI",
             "parent": None,
             "type": "device",
             "class": "liquid_handler.prcxi",
-                "position": {"x": 0, "y": 0, "z": 0},
+            "position": {
+                "x": 0,
+                "y": 0,
+                "z": 0
+            },
             "config": {
                 "deck": {
                     "_resource_child_name": "PRCXI_Deck",
-                        "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck",
+                    "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck"
                 },
                 "host": "192.168.0.121",
                 "port": 9999,
@@ -2379,14 +2324,18 @@ if __name__ == "__main__":
                 "debug": True,
                 "simulator": True,
                 "matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb",
-                    "is_9320": True,
+                "is_9320": True
             },
             "data": {},
-                "children": ["PRCXI_Deck"],
+            "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,
@@ -2428,6 +2377,7 @@ 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()

unilabos/registry/devices/liquid_handler.yaml

@@ -638,7 +638,7 @@ liquid_handler:
         placeholder_keys: {}
         result: {}
         schema:
-          description: 吸头迭代函数。用于自动管理和切换枪头盒中的吸头，实现批量实验中的吸头自动分配和追踪。该函数监控吸头使用状态，自动切换到下一个可用吸头位置，确保实验流程的连续性。适用于高通量实验、批量处理、自动化流水线等需要大量吸头管理的应用场景。
+          description: 吸头迭代函数。用于自动管理和切换吸头架中的吸头，实现批量实验中的吸头自动分配和追踪。该函数监控吸头使用状态，自动切换到下一个可用吸头位置，确保实验流程的连续性。适用于高通量实验、批量处理、自动化流水线等需要大量吸头管理的应用场景。
           properties:
             feedback: {}
             goal:
@@ -712,43 +712,6 @@ liquid_handler:
           title: set_group参数
           type: object
         type: UniLabJsonCommand
-      auto-set_liquid_from_plate:
-        feedback: {}
-        goal: {}
-        goal_default:
-          liquid_names: null
-          plate: null
-          volumes: null
-          well_names: null
-        handles: {}
-        placeholder_keys: {}
-        result: {}
-        schema:
-          description: ''
-          properties:
-            feedback: {}
-            goal:
-              properties:
-                liquid_names:
-                  type: string
-                plate:
-                  type: string
-                volumes:
-                  type: string
-                well_names:
-                  type: string
-              required:
-              - plate
-              - well_names
-              - liquid_names
-              - volumes
-              type: object
-            result: {}
-          required:
-          - goal
-          title: set_liquid_from_plate参数
-          type: object
-        type: UniLabJsonCommand
       auto-set_tiprack:
         feedback: {}
         goal: {}
@@ -758,7 +721,7 @@ liquid_handler:
         placeholder_keys: {}
         result: {}
         schema:
-          description: 枪头盒设置函数。用于配置和初始化液体处理系统的枪头盒信息，包括枪头盒位置、类型、容量等参数。该函数建立吸头资源管理系统，为后续的吸头选择和使用提供基础配置。适用于系统初始化、枪头盒更换、实验配置等需要吸头资源管理的操作场景。
+          description: 吸头架设置函数。用于配置和初始化液体处理系统的吸头架信息，包括吸头架位置、类型、容量等参数。该函数建立吸头资源管理系统，为后续的吸头选择和使用提供基础配置。适用于系统初始化、吸头架更换、实验配置等需要吸头资源管理的操作场景。
           properties:
             feedback: {}
             goal:
@@ -4130,32 +4093,32 @@ liquid_handler:
           - 0
         handles:
           input:
-          - data_key: sources
+          - data_key: liquid
             data_source: handle
             data_type: resource
             handler_key: sources
-            label: 待移动液体
+            label: sources
-          - data_key: targets
+          - data_key: liquid
-            data_source: handle
-            data_type: resource
-            handler_key: targets
-            label: 转移目标
-          - data_key: tip_racks
-            data_source: handle
-            data_type: resource
-            handler_key: tip_rack
-            label: 枪头盒
-          output:
-          - data_key: sources.@flatten
             data_source: executor
             data_type: resource
+            handler_key: targets
+            label: targets
+          - data_key: liquid
+            data_source: executor
+            data_type: resource
+            handler_key: tip_rack
+            label: tip_rack
+          output:
+          - data_key: liquid
+            data_source: handle
+            data_type: resource
             handler_key: sources_out
-            label: 移液后源孔
+            label: sources
-          - data_key: targets.@flatten
+          - data_key: liquid
             data_source: executor
             data_type: resource
             handler_key: targets_out
-            label: 移液后目标孔
+            label: targets
         placeholder_keys:
           sources: unilabos_resources
           targets: unilabos_resources
@@ -5151,34 +5114,19 @@ liquid_handler.biomek:
           - 0
         handles:
           input:
-          - data_key: sources
+          - data_key: liquid
             data_source: handle
             data_type: resource
-            handler_key: sources
+            handler_key: liquid-input
             io_type: target
-            label: 待移动液体
+            label: Liquid Input
-          - data_key: targets
-            data_source: handle
-            data_type: resource
-            handler_key: targets
-            label: 转移目标
-          - data_key: tip_racks
-            data_source: handle
-            data_type: resource
-            handler_key: tip_rack
-            label: 枪头盒
           output:
-          - data_key: sources.@flatten
+          - data_key: liquid
             data_source: executor
             data_type: resource
-            handler_key: sources_out
+            handler_key: liquid-output
             io_type: source
-            label: 移液后源孔
+            label: Liquid Output
-          - data_key: targets.@flatten
-            data_source: executor
-            data_type: resource
-            handler_key: targets_out
-            label: 移液后目标孔
         placeholder_keys:
           sources: unilabos_resources
           targets: unilabos_resources
@@ -9336,13 +9284,7 @@ liquid_handler.prcxi:
             data_source: handle
             data_type: resource
             handler_key: input_wells
-            label: 待设定液体孔
+            label: InputWells
-          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: {}
@@ -9458,165 +9400,6 @@ 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:
-                  items:
-                    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
-                  title: plate
-                  type: array
-                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: {}
-                  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:
@@ -9960,34 +9743,7 @@ liquid_handler.prcxi:
           touch_tip: false
           use_channels:
           - 0
-        handles:
+        handles: {}
-          input:
-          - data_key: sources
-            data_source: handle
-            data_type: resource
-            handler_key: sources_identifier
-            label: 待移动液体
-          - data_key: targets
-            data_source: handle
-            data_type: resource
-            handler_key: targets_identifier
-            label: 转移目标
-          - data_key: tip_rack
-            data_source: handle
-            data_type: resource
-            handler_key: tip_rack_identifier
-            label: 枪头盒
-          output:
-          - data_key: sources.@flatten
-            data_source: executor
-            data_type: resource
-            handler_key: sources_out
-            label: 移液后源孔
-          - data_key: targets.@flatten
-            data_source: executor
-            data_type: resource
-            handler_key: targets_out
-            label: 移液后目标孔
         placeholder_keys:
           sources: unilabos_resources
           targets: unilabos_resources

unilabos/registry/registry.py

@@ -4,8 +4,6 @@ import os
 import sys
 import inspect
 import importlib
-import threading
-from concurrent.futures import ThreadPoolExecutor, as_completed
 from pathlib import Path
 from typing import Any, Dict, List, Union, Tuple
 
@@ -62,7 +60,6 @@ class Registry:
         self.device_module_to_registry = {}
         self.resource_type_registry = {}
         self._setup_called = False  # 跟踪setup是否已调用
-        self._registry_lock = threading.Lock()  # 多线程加载时的锁
         # 其他状态变量
         # self.is_host_mode = False  # 移至BasicConfig中
 
@@ -166,7 +163,6 @@ 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": {
@@ -180,7 +176,8 @@ class Registry:
                                 "result": {},
                                 "schema": test_latency_schema,
                                 "goal_default": {
-                                    arg["name"]: arg["default"] for arg in test_latency_method_info.get("args", [])
+                                    arg["name"]: arg["default"]
+                                    for arg in test_latency_method_info.get("args", [])
                                 },
                                 "handles": {},
                             },
@@ -264,26 +261,18 @@ class Registry:
         # 标记setup已被调用
         self._setup_called = True
 
-    def _load_single_resource_file(
+    def load_resource_types(self, path: os.PathLike, complete_registry: bool, upload_registry: bool):
-        self, file: Path, complete_registry: bool, upload_registry: bool
+        abs_path = Path(path).absolute()
-    ) -> Tuple[Dict[str, Any], Dict[str, Any], bool]:
+        resource_path = abs_path / "resources"
-        """
+        files = list(resource_path.glob("*/*.yaml"))
-        加载单个资源文件 (线程安全)
+        logger.debug(f"[UniLab Registry] resources: {resource_path.exists()}, total: {len(files)}")
-
+        current_resource_number = len(self.resource_type_registry) + 1
-        Returns:
+        for i, file in enumerate(files):
-            (data, complete_data, is_valid): 资源数据, 完整数据, 是否有效
-        """
-        try:
             with open(file, encoding="utf-8", mode="r") as f:
                 data = yaml.safe_load(io.StringIO(f.read()))
-        except Exception as e:
-            logger.warning(f"[UniLab Registry] 读取资源文件失败: {file}, 错误: {e}")
-            return {}, {}, False
-
-        if not data:
-            return {}, {}, False
-
             complete_data = {}
+            if data:
+                # 为每个资源添加文件路径信息
                 for resource_id, resource_info in data.items():
                     if "version" not in resource_info:
                         resource_info["version"] = "1.0.0"
@@ -311,68 +300,28 @@ class Registry:
                         if len(class_info) and "module" in class_info:
                             if class_info.get("type") == "pylabrobot":
                                 res_class = get_class(class_info["module"])
-                        if callable(res_class) and not isinstance(res_class, type):
+                                if callable(res_class) and not isinstance(
+                                    res_class, type
+                                ):  # 有的是类，有的是函数，这里暂时只登记函数类的
                                     res_instance = res_class(res_class.__name__)
                                     res_ulr = tree_to_list([resource_plr_to_ulab(res_instance)])
                                     resource_info["config_info"] = res_ulr
                     resource_info["registry_type"] = "resource"
                     resource_info["file_path"] = str(file.absolute()).replace("\\", "/")
-
                 complete_data = dict(sorted(complete_data.items()))
                 complete_data = copy.deepcopy(complete_data)
-
                 if complete_registry:
-            try:
                     with open(file, "w", encoding="utf-8") as f:
                         yaml.dump(complete_data, f, allow_unicode=True, default_flow_style=False, Dumper=NoAliasDumper)
-            except Exception as e:
-                logger.warning(f"[UniLab Registry] 写入资源文件失败: {file}, 错误: {e}")
 
-        return data, complete_data, True
-
-    def load_resource_types(self, path: os.PathLike, complete_registry: bool, upload_registry: bool):
-        abs_path = Path(path).absolute()
-        resource_path = abs_path / "resources"
-        files = list(resource_path.glob("*/*.yaml"))
-        logger.debug(f"[UniLab Registry] resources: {resource_path.exists()}, total: {len(files)}")
-
-        if not files:
-            return
-
-        # 使用线程池并行加载
-        max_workers = min(8, len(files))
-        results = []
-
-        with ThreadPoolExecutor(max_workers=max_workers) as executor:
-            future_to_file = {
-                executor.submit(self._load_single_resource_file, file, complete_registry, upload_registry): file
-                for file in files
-            }
-            for future in as_completed(future_to_file):
-                file = future_to_file[future]
-                try:
-                    data, complete_data, is_valid = future.result()
-                    if is_valid:
-                        results.append((file, data))
-                except Exception as e:
-                    logger.warning(f"[UniLab Registry] 处理资源文件异常: {file}, 错误: {e}")
-
-        # 线程安全地更新注册表
-        current_resource_number = len(self.resource_type_registry) + 1
-        with self._registry_lock:
-            for i, (file, data) in enumerate(results):
                 self.resource_type_registry.update(data)
-                logger.trace(
+                logger.trace(  # type: ignore
-                    f"[UniLab Registry] Resource-{current_resource_number} File-{i+1}/{len(results)} "
+                    f"[UniLab Registry] Resource-{current_resource_number} File-{i+1}/{len(files)} "
                     + f"Add {list(data.keys())}"
                 )
                 current_resource_number += 1
-
+            else:
-        # 记录无效文件
+                logger.debug(f"[UniLab Registry] Res File-{i+1}/{len(files)} Not Valid YAML File: {file.absolute()}")
-        valid_files = {r[0] for r in results}
-        for file in files:
-            if file not in valid_files:
-                logger.debug(f"[UniLab Registry] Res File Not Valid YAML File: {file.absolute()}")
 
     def _extract_class_docstrings(self, module_string: str) -> Dict[str, str]:
         """
@@ -724,34 +673,32 @@ class Registry:
                 "handles": {},
             }
 
-    def _load_single_device_file(
+    def load_device_types(self, path: os.PathLike, complete_registry: bool):
-        self, file: Path, complete_registry: bool, get_yaml_from_goal_type
+        # return
-    ) -> Tuple[Dict[str, Any], Dict[str, Any], bool, List[str]]:
+        abs_path = Path(path).absolute()
-        """
+        devices_path = abs_path / "devices"
-        加载单个设备文件 (线程安全)
+        device_comms_path = abs_path / "device_comms"
+        files = list(devices_path.glob("*.yaml")) + list(device_comms_path.glob("*.yaml"))
+        logger.trace(  # type: ignore
+            f"[UniLab Registry] devices: {devices_path.exists()}, device_comms: {device_comms_path.exists()}, "
+            + f"total: {len(files)}"
+        )
+        current_device_number = len(self.device_type_registry) + 1
+        from unilabos.app.web.utils.action_utils import get_yaml_from_goal_type
 
-        Returns:
+        for i, file in enumerate(files):
-            (data, complete_data, is_valid, device_ids): 设备数据, 完整数据, 是否有效, 设备ID列表
-        """
-        try:
             with open(file, encoding="utf-8", mode="r") as f:
                 data = yaml.safe_load(io.StringIO(f.read()))
-        except Exception as e:
-            logger.warning(f"[UniLab Registry] 读取设备文件失败: {file}, 错误: {e}")
-            return {}, {}, False, []
-
-        if not data:
-            return {}, {}, False, []
-
             complete_data = {}
             action_str_type_mapping = {
                 "UniLabJsonCommand": "UniLabJsonCommand",
                 "UniLabJsonCommandAsync": "UniLabJsonCommandAsync",
             }
             status_str_type_mapping = {}
-        device_ids = []
+            if data:
-
+                # 在添加到注册表前处理类型替换
                 for device_id, device_config in data.items():
+                    # 添加文件路径信息 - 使用规范化的完整文件路径
                     if "version" not in device_config:
                         device_config["version"] = "1.0.0"
                     if "category" not in device_config:
@@ -769,7 +716,10 @@ class Registry:
                     if "init_param_schema" not in device_config:
                         device_config["init_param_schema"] = {}
                     if "class" in device_config:
-                if "status_types" not in device_config["class"] or device_config["class"]["status_types"] is None:
+                        if (
+                            "status_types" not in device_config["class"]
+                            or device_config["class"]["status_types"] is None
+                        ):
                             device_config["class"]["status_types"] = {}
                         if (
                             "action_value_mappings" not in device_config["class"]
@@ -787,17 +737,25 @@ class Registry:
                             )
                         for status_name, status_type in device_config["class"]["status_types"].items():
                             if isinstance(status_type, tuple) or status_type in ["Any", "None", "Unknown"]:
-                        status_type = "String"
+                                status_type = "String"  # 替换成ROS的String，便于显示
                                 device_config["class"]["status_types"][status_name] = status_type
                             try:
-                        target_type = self._replace_type_with_class(status_type, device_id, f"状态 {status_name}")
+                                target_type = self._replace_type_with_class(
+                                    status_type, device_id, f"状态 {status_name}"
+                                )
                             except ROSMsgNotFound:
                                 continue
-                    if target_type in [dict, list]:
+                            if target_type in [
+                                dict,
+                                list,
+                            ]:  # 对于嵌套类型返回的对象，暂时处理成字符串，无法直接进行转换
                                 target_type = String
                             status_str_type_mapping[status_type] = target_type
-                device_config["class"]["status_types"] = dict(sorted(device_config["class"]["status_types"].items()))
+                        device_config["class"]["status_types"] = dict(
+                            sorted(device_config["class"]["status_types"].items())
+                        )
                         if complete_registry:
+                            # 保存原有的 action 配置（用于保留 schema 的 description 和 handles 等）
                             old_action_configs = {}
                             for action_name, action_config in device_config["class"]["action_value_mappings"].items():
                                 old_action_configs[action_name] = action_config
@@ -807,6 +765,7 @@ class Registry:
                                 for k, v in device_config["class"]["action_value_mappings"].items()
                                 if not k.startswith("auto-")
                             }
+                            # 处理动作值映射
                             device_config["class"]["action_value_mappings"].update(
                                 {
                                     f"auto-{k}": {
@@ -818,15 +777,18 @@ class Registry:
                                             v["args"],
                                             k,
                                             v.get("return_annotation"),
+                                            # 传入旧的 schema 以保留字段 description
                                             old_action_configs.get(f"auto-{k}", {}).get("schema"),
                                         ),
                                         "goal_default": {i["name"]: i["default"] for i in v["args"]},
+                                        # 保留原有的 handles 配置
                                         "handles": old_action_configs.get(f"auto-{k}", {}).get("handles", []),
                                         "placeholder_keys": {
                                             i["name"]: (
                                                 "unilabos_resources"
                                                 if i["type"] == "unilabos.registry.placeholder_type:ResourceSlot"
-                                        or i["type"] == ("list", "unilabos.registry.placeholder_type:ResourceSlot")
+                                                or i["type"]
+                                                == ("list", "unilabos.registry.placeholder_type:ResourceSlot")
                                                 else "unilabos_devices"
                                             )
                                             for i in v["args"]
@@ -839,12 +801,14 @@ class Registry:
                                             ]
                                         },
                                     }
+                                    # 不生成已配置action的动作
                                     for k, v in enhanced_info["action_methods"].items()
                                     if k not in device_config["class"]["action_value_mappings"]
                                 }
                             )
+                            # 恢复原有的 description 信息（非 auto- 开头的动作）
                             for action_name, old_config in old_action_configs.items():
-                        if action_name in device_config["class"]["action_value_mappings"]:
+                                if action_name in device_config["class"]["action_value_mappings"]:  # 有一些会被删除
                                     old_schema = old_config.get("schema", {})
                                     if "description" in old_schema and old_schema["description"]:
                                         device_config["class"]["action_value_mappings"][action_name]["schema"][
@@ -873,6 +837,7 @@ class Registry:
                                     action_config["handles"] = {}
                             if "type" in action_config:
                                 action_type_str: str = action_config["type"]
+                                # 通过Json发放指令，而不是通过特殊的ros action进行处理
                                 if not action_type_str.startswith("UniLabJsonCommand"):
                                     try:
                                         target_type = self._replace_type_with_class(
@@ -890,78 +855,31 @@ class Registry:
                                         logger.warning(
                                             f"[UniLab Registry] 设备 {device_id} 的动作 {action_name} 类型为空，跳过替换"
                                         )
-                complete_data[device_id] = copy.deepcopy(dict(sorted(device_config.items())))
+                        complete_data[device_id] = copy.deepcopy(dict(sorted(device_config.items())))  # 稍后dump到文件
                         for status_name, status_type in device_config["class"]["status_types"].items():
                             device_config["class"]["status_types"][status_name] = status_str_type_mapping[status_type]
                         for action_name, action_config in device_config["class"]["action_value_mappings"].items():
                             if action_config["type"] not in action_str_type_mapping:
                                 continue
                             action_config["type"] = action_str_type_mapping[action_config["type"]]
+                        # 添加内置的驱动命令动作
                         self._add_builtin_actions(device_config, device_id)
                     device_config["file_path"] = str(file.absolute()).replace("\\", "/")
                     device_config["registry_type"] = "device"
-            device_ids.append(device_id)
+                    logger.trace(  # type: ignore
-
+                        f"[UniLab Registry] Device-{current_device_number} File-{i+1}/{len(files)} Add {device_id} "
-        complete_data = dict(sorted(complete_data.items()))
-        complete_data = copy.deepcopy(complete_data)
-        try:
-            with open(file, "w", encoding="utf-8") as f:
-                yaml.dump(complete_data, f, allow_unicode=True, default_flow_style=False, Dumper=NoAliasDumper)
-        except Exception as e:
-            logger.warning(f"[UniLab Registry] 写入设备文件失败: {file}, 错误: {e}")
-
-        return data, complete_data, True, device_ids
-
-    def load_device_types(self, path: os.PathLike, complete_registry: bool):
-        abs_path = Path(path).absolute()
-        devices_path = abs_path / "devices"
-        device_comms_path = abs_path / "device_comms"
-        files = list(devices_path.glob("*.yaml")) + list(device_comms_path.glob("*.yaml"))
-        logger.trace(
-            f"[UniLab Registry] devices: {devices_path.exists()}, device_comms: {device_comms_path.exists()}, "
-            + f"total: {len(files)}"
-        )
-
-        if not files:
-            return
-
-        from unilabos.app.web.utils.action_utils import get_yaml_from_goal_type
-
-        # 使用线程池并行加载
-        max_workers = min(8, len(files))
-        results = []
-
-        with ThreadPoolExecutor(max_workers=max_workers) as executor:
-            future_to_file = {
-                executor.submit(self._load_single_device_file, file, complete_registry, get_yaml_from_goal_type): file
-                for file in files
-            }
-            for future in as_completed(future_to_file):
-                file = future_to_file[future]
-                try:
-                    data, complete_data, is_valid, device_ids = future.result()
-                    if is_valid:
-                        results.append((file, data, device_ids))
-                except Exception as e:
-                    logger.warning(f"[UniLab Registry] 处理设备文件异常: {file}, 错误: {e}")
-
-        # 线程安全地更新注册表
-        current_device_number = len(self.device_type_registry) + 1
-        with self._registry_lock:
-            for file, data, device_ids in results:
-                self.device_type_registry.update(data)
-                for device_id in device_ids:
-                    logger.trace(
-                        f"[UniLab Registry] Device-{current_device_number} Add {device_id} "
                         + f"[{data[device_id].get('name', '未命名设备')}]"
                     )
                     current_device_number += 1
-
+                complete_data = dict(sorted(complete_data.items()))
-        # 记录无效文件
+                complete_data = copy.deepcopy(complete_data)
-        valid_files = {r[0] for r in results}
+                with open(file, "w", encoding="utf-8") as f:
-        for file in files:
+                    yaml.dump(complete_data, f, allow_unicode=True, default_flow_style=False, Dumper=NoAliasDumper)
-            if file not in valid_files:
+                self.device_type_registry.update(data)
-                logger.debug(f"[UniLab Registry] Device File Not Valid YAML File: {file.absolute()}")
+            else:
+                logger.debug(
+                    f"[UniLab Registry] Device File-{i+1}/{len(files)} Not Valid YAML File: {file.absolute()}"
+                )
 
     def obtain_registry_device_info(self):
         devices = []

unilabos/resources/graphio.py

@@ -42,7 +42,7 @@ def canonicalize_nodes_data(
     Returns:
         ResourceTreeSet: 标准化后的资源树集合
     """
-    print_status(f"{len(nodes)} Resources loaded", "info")
+    print_status(f"{len(nodes)} Resources loaded:", "info")
 
     # 第一步：基本预处理（处理graphml的label字段）
     outer_host_node_id = None
@@ -151,40 +151,12 @@ def canonicalize_links_ports(links: List[Dict[str, Any]], resource_tree_set: Res
     """
     # 构建 id 到 uuid 的映射
     id_to_uuid: Dict[str, str] = {}
-    uuid_to_id: Dict[str, str] = {}
     for node in resource_tree_set.all_nodes:
         id_to_uuid[node.res_content.id] = node.res_content.uuid
-        uuid_to_id[node.res_content.uuid] = node.res_content.id
-
-    # 第三遍处理：为每个 link 添加 source_uuid 和 target_uuid
-    for link in links:
-        source_id = link.get("source")
-        target_id = link.get("target")
-
-        # 添加 source_uuid
-        if source_id and source_id in id_to_uuid:
-            link["source_uuid"] = id_to_uuid[source_id]
-
-        # 添加 target_uuid
-        if target_id and target_id in id_to_uuid:
-            link["target_uuid"] = id_to_uuid[target_id]
-
-        source_uuid = link.get("source_uuid")
-        target_uuid = link.get("target_uuid")
-
-        # 添加 source_uuid
-        if source_uuid and source_uuid in uuid_to_id:
-            link["source"] = uuid_to_id[source_uuid]
-
-        # 添加 target_uuid
-        if target_uuid and target_uuid in uuid_to_id:
-            link["target"] = uuid_to_id[target_uuid]
 
     # 第一遍处理：将字符串类型的port转换为字典格式
     for link in links:
         port = link.get("port")
-        if port is None:
-            continue
         if link.get("type", "physical") == "physical":
             link["type"] = "fluid"
         if isinstance(port, int):
@@ -207,15 +179,13 @@ def canonicalize_links_ports(links: List[Dict[str, Any]], resource_tree_set: Res
             link["port"] = {link["source"]: None, link["target"]: None}
 
     # 构建边字典，键为(source节点, target节点)，值为对应的port信息
-    edges = {(link["source"], link["target"]): link["port"] for link in links if link.get("port")}
+    edges = {(link["source"], link["target"]): link["port"] for link in links}
 
     # 第二遍处理：填充反向边的dest信息
     delete_reverses = []
     for i, link in enumerate(links):
         s, t = link["source"], link["target"]
-        current_port = link.get("port")
+        current_port = link["port"]
-        if current_port is None:
-            continue
         if current_port.get(t) is None:
             reverse_key = (t, s)
             reverse_port = edges.get(reverse_key)
@@ -230,6 +200,20 @@ def canonicalize_links_ports(links: List[Dict[str, Any]], resource_tree_set: Res
                 current_port[t] = current_port[s]
     # 删除已被使用反向端口信息的反向边
     standardized_links = [link for i, link in enumerate(links) if i not in delete_reverses]
+
+    # 第三遍处理：为每个 link 添加 source_uuid 和 target_uuid
+    for link in standardized_links:
+        source_id = link.get("source")
+        target_id = link.get("target")
+
+        # 添加 source_uuid
+        if source_id and source_id in id_to_uuid:
+            link["source_uuid"] = id_to_uuid[source_id]
+
+        # 添加 target_uuid
+        if target_id and target_id in id_to_uuid:
+            link["target_uuid"] = id_to_uuid[target_id]
+
     return standardized_links
 
 
@@ -276,7 +260,7 @@ def read_node_link_json(
     resource_tree_set = canonicalize_nodes_data(nodes)
 
     # 标准化边数据
-    links = data.get("links", data.get("edges", []))
+    links = data.get("links", [])
     standardized_links = canonicalize_links_ports(links, resource_tree_set)
 
     # 构建 NetworkX 图（需要转换回 dict 格式）
@@ -300,8 +284,6 @@ def modify_to_backend_format(data: list[dict[str, Any]]) -> list[dict[str, Any]]
             edge["sourceHandle"] = port[source]
         elif "source_port" in edge:
             edge["sourceHandle"] = edge.pop("source_port")
-        elif "source_handle" in edge:
-            edge["sourceHandle"] = edge.pop("source_handle")
         else:
             typ = edge.get("type")
             if typ == "communication":
@@ -310,8 +292,6 @@ def modify_to_backend_format(data: list[dict[str, Any]]) -> list[dict[str, Any]]
             edge["targetHandle"] = port[target]
         elif "target_port" in edge:
             edge["targetHandle"] = edge.pop("target_port")
-        elif "target_handle" in edge:
-            edge["targetHandle"] = edge.pop("target_handle")
         else:
             typ = edge.get("type")
             if typ == "communication":
@@ -617,8 +597,6 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None, w
             "tube": "tube",
             "bottle_carrier": "bottle_carrier",
             "plate_adapter": "plate_adapter",
-            "electrode_sheet": "electrode_sheet",
-            "material_hole": "material_hole",
         }
         if source in replace_info:
             return replace_info[source]

unilabos/resources/resource_tracker.py

@@ -13,23 +13,6 @@ if TYPE_CHECKING:
     from pylabrobot.resources import Resource as PLRResource
 
 
-EXTRA_CLASS = "unilabos_resource_class"
-EXTRA_SAMPLE_UUID = "sample_uuid"
-EXTRA_UNILABOS_SAMPLE_UUID = "unilabos_sample_uuid"
-
-# 函数参数名常量 - 用于自动注入 sample_uuids 列表
-PARAM_SAMPLE_UUIDS = "sample_uuids"
-
-# JSON Command 中的系统参数字段名
-JSON_UNILABOS_PARAM = "unilabos_param"
-
-# 返回值中的 samples 字段名
-RETURN_UNILABOS_SAMPLES = "unilabos_samples"
-
-# sample_uuids 参数类型 (用于 virtual bench 等设备添加 sample_uuids 参数)
-SampleUUIDsType = Dict[str, Optional["PLRResource"]]
-
-
 class ResourceDictPositionSize(BaseModel):
     depth: float = Field(description="Depth", default=0.0)  # z
     width: float = Field(description="Width", default=0.0)  # x
@@ -83,8 +66,8 @@ class ResourceDict(BaseModel):
     klass: str = Field(alias="class", description="Resource class name")
     pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
     config: Dict[str, Any] = Field(description="Resource configuration")
-    data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
+    data: Dict[str, Any] = Field(description="Resource data")
-    extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
+    extra: Dict[str, Any] = Field(description="Extra data")
 
     @field_serializer("parent_uuid")
     def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
@@ -410,7 +393,7 @@ 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": extra.get(EXTRA_CLASS, ""),
+                "class": d.get("class", ""),
                 "position": pos,
                 "pose": pos,
                 "config": {
@@ -460,7 +443,7 @@ class ResourceTreeSet(object):
             trees.append(tree_instance)
         return cls(trees)
 
-    def to_plr_resources(self, skip_devices=True) -> List["PLRResource"]:
+    def to_plr_resources(self) -> List["PLRResource"]:
         """
         将 ResourceTreeSet 转换为 PLR 资源列表
 
@@ -485,7 +468,6 @@ 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)
 
@@ -530,10 +512,7 @@ class ResourceTreeSet(object):
             plr_dict = node_to_plr_dict(tree.root_node, has_model)
             try:
                 sub_cls = find_subclass(plr_dict["type"], PLRResource)
-                if skip_devices and plr_dict["type"] == "device":
+                if sub_cls is None:
-                    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}"
                     )
@@ -541,11 +520,6 @@ 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)
@@ -1012,7 +986,7 @@ class DeviceNodeResourceTracker(object):
                 extra = name_to_extra_map[resource_name]
                 self.set_resource_extra(res, extra)
                 if len(extra):
-                    logger.trace(f"设置资源Extra: {resource_name} -> {extra}")
+                    logger.debug(f"设置资源Extra: {resource_name} -> {extra}")
                 return 1
             return 0
 

unilabos/ros/nodes/base_device_node.py

@@ -4,20 +4,8 @@ import json
 import threading
 import time
 import traceback
-from typing import (
+from typing import get_type_hints, TypeVar, Generic, Dict, Any, Type, TypedDict, Optional, List, TYPE_CHECKING, Union, \
-    get_type_hints,
+    Tuple
-    TypeVar,
-    Generic,
-    Dict,
-    Any,
-    Type,
-    TypedDict,
-    Optional,
-    List,
-    TYPE_CHECKING,
-    Union,
-    Tuple,
-)
 
 from concurrent.futures import ThreadPoolExecutor
 import asyncio
@@ -60,9 +48,6 @@ from unilabos.resources.resource_tracker import (
     ResourceTreeSet,
     ResourceTreeInstance,
     ResourceDictInstance,
-    EXTRA_SAMPLE_UUID,
-    PARAM_SAMPLE_UUIDS,
-    JSON_UNILABOS_PARAM,
 )
 from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator
 from rclpy.task import Task, Future
@@ -376,7 +361,6 @@ class BaseROS2DeviceNode(Node, Generic[T]):
             from pylabrobot.resources.deck import Deck
             from pylabrobot.resources import Coordinate
             from pylabrobot.resources import Plate
-
             # 物料传输到对应的node节点
             client = self._resource_clients["c2s_update_resource_tree"]
             request = SerialCommand.Request()
@@ -404,7 +388,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
             rts: ResourceTreeSet = ResourceTreeSet.from_raw_dict_list(input_resources)
             parent_resource = None
             if bind_parent_id != self.node_name:
-                parent_resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
+                parent_resource = self.resource_tracker.figure_resource(
+                    {"name": bind_parent_id}
+                )
                 for r in rts.root_nodes:
                     # noinspection PyUnresolvedReferences
                     r.res_content.parent_uuid = parent_resource.unilabos_uuid
@@ -412,20 +398,19 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 for r in rts.root_nodes:
                     r.res_content.parent_uuid = self.uuid
 
-            if (
+            if len(LIQUID_INPUT_SLOT) and LIQUID_INPUT_SLOT[0] == -1 and len(rts.root_nodes) == 1 and isinstance(rts.root_nodes[0], RegularContainer):
-                len(LIQUID_INPUT_SLOT)
-                and LIQUID_INPUT_SLOT[0] == -1
-                and len(rts.root_nodes) == 1
-                and isinstance(rts.root_nodes[0], RegularContainer)
-            ):
                 # noinspection PyTypeChecker
                 container_instance: RegularContainer = rts.root_nodes[0]
-                found_resources = self.resource_tracker.figure_resource({"id": container_instance.name}, try_mode=True)
+                found_resources = self.resource_tracker.figure_resource(
+                    {"id": container_instance.name}, try_mode=True
+                )
                 if not len(found_resources):
                     self.resource_tracker.add_resource(container_instance)
                     logger.info(f"添加物料{container_instance.name}到资源跟踪器")
                 else:
-                    assert len(found_resources) == 1, f"找到多个同名物料: {container_instance.name}, 请检查物料系统"
+                    assert (
+                        len(found_resources) == 1
+                    ), f"找到多个同名物料: {container_instance.name}, 请检查物料系统"
                     found_resource = found_resources[0]
                     if isinstance(found_resource, RegularContainer):
                         logger.info(f"更新物料{container_instance.name}的数据{found_resource.state}")
@@ -437,16 +422,14 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                             f"更新物料{container_instance.name}出现不支持的数据类型{type(found_resource)} {found_resource}"
                         )
             # noinspection PyUnresolvedReferences
-            request.command = json.dumps(
+            request.command = json.dumps({
-                {
                 "action": "add",
                 "data": {
                     "data": rts.dump(),
                     "mount_uuid": parent_resource.unilabos_uuid if parent_resource is not None else "",
                     "first_add": False,
                 },
-                }
+            })
-            )
             tree_response: SerialCommand.Response = await client.call_async(request)
             uuid_maps = json.loads(tree_response.response)
             plr_instances = rts.to_plr_resources()
@@ -488,9 +471,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         if len(ADD_LIQUID_TYPE) == 1 and len(LIQUID_VOLUME) == 1 and len(LIQUID_INPUT_SLOT) > 1:
                             ADD_LIQUID_TYPE = ADD_LIQUID_TYPE * len(LIQUID_INPUT_SLOT)
                             LIQUID_VOLUME = LIQUID_VOLUME * len(LIQUID_INPUT_SLOT)
-                            self.lab_logger().warning(
+                            self.lab_logger().warning(f"增加液体资源时，数量为1，自动补全为 {len(LIQUID_INPUT_SLOT)} 个")
-                                f"增加液体资源时，数量为1，自动补全为 {len(LIQUID_INPUT_SLOT)} 个"
-                            )
                         for liquid_type, liquid_volume, liquid_input_slot in zip(
                             ADD_LIQUID_TYPE, LIQUID_VOLUME, LIQUID_INPUT_SLOT
                         ):
@@ -509,15 +490,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                             input_wells = []
                             for r in LIQUID_INPUT_SLOT:
                                 input_wells.append(plr_instance.children[r])
-                        final_response["liquid_input_resource_tree"] = ResourceTreeSet.from_plr_resources(
+                        final_response["liquid_input_resource_tree"] = ResourceTreeSet.from_plr_resources(input_wells).dump()
-                            input_wells
-                        ).dump()
                         res.response = json.dumps(final_response)
-                    if (
+                    if issubclass(parent_resource.__class__, Deck) and hasattr(parent_resource, "assign_child_at_slot") and "slot" in other_calling_param:
-                        issubclass(parent_resource.__class__, Deck)
-                        and hasattr(parent_resource, "assign_child_at_slot")
-                        and "slot" in other_calling_param
-                    ):
                         other_calling_param["slot"] = int(other_calling_param["slot"])
                         parent_resource.assign_child_at_slot(plr_instance, **other_calling_param)
                     else:
@@ -532,16 +507,14 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                     rts_with_parent = ResourceTreeSet.from_plr_resources([parent_resource])
                     if rts_with_parent.root_nodes[0].res_content.uuid_parent is None:
                         rts_with_parent.root_nodes[0].res_content.parent_uuid = self.uuid
-                    request.command = json.dumps(
+                    request.command = json.dumps({
-                        {
                         "action": "add",
                         "data": {
                             "data": rts_with_parent.dump(),
                             "mount_uuid": rts_with_parent.root_nodes[0].res_content.uuid_parent,
                             "first_add": False,
                         },
-                        }
+                    })
-                    )
                     tree_response: SerialCommand.Response = await client.call_async(request)
                     uuid_maps = json.loads(tree_response.response)
                     self.resource_tracker.loop_update_uuid(input_resources, uuid_maps)
@@ -838,9 +811,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
             }
 
         def _handle_update(
-            plr_resources: List[Union[ResourcePLR, ResourceDictInstance]],
+            plr_resources: List[Union[ResourcePLR, ResourceDictInstance]], tree_set: ResourceTreeSet, additional_add_params: Dict[str, Any]
-            tree_set: ResourceTreeSet,
-            additional_add_params: Dict[str, Any],
         ) -> Tuple[Dict[str, Any], List[ResourcePLR]]:
             """
             处理资源更新操作的内部函数
@@ -865,10 +836,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 original_parent_resource = original_instance.parent
                 original_parent_resource_uuid = getattr(original_parent_resource, "unilabos_uuid", None)
                 target_parent_resource_uuid = tree.root_node.res_content.uuid_parent
-                not_same_parent = (
+                not_same_parent = original_parent_resource_uuid != target_parent_resource_uuid and original_parent_resource is not None
-                    original_parent_resource_uuid != target_parent_resource_uuid
-                    and original_parent_resource is not None
-                )
                 old_name = original_instance.name
                 new_name = plr_resource.name
                 parent_appended = False
@@ -904,16 +872,8 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 else:
                     # 判断是否变更了resource_site，重新登记
                     target_site = original_instance.unilabos_extra.get("update_resource_site")
-                    sites = (
+                    sites = original_instance.parent.sites if original_instance.parent is not None and hasattr(original_instance.parent, "sites") else None
-                        original_instance.parent.sites
+                    site_names = list(original_instance.parent._ordering.keys()) if original_instance.parent is not None and hasattr(original_instance.parent, "sites") else []
-                        if original_instance.parent is not None and hasattr(original_instance.parent, "sites")
-                        else None
-                    )
-                    site_names = (
-                        list(original_instance.parent._ordering.keys())
-                        if original_instance.parent is not None and hasattr(original_instance.parent, "sites")
-                        else []
-                    )
                     if target_site is not None and sites is not None and site_names is not None:
                         site_index = sites.index(original_instance)
                         site_name = site_names[site_index]
@@ -924,9 +884,6 @@ 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(
@@ -950,7 +907,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 action = i.get("action")  # remove, add, update
                 resources_uuid: List[str] = i.get("data")  # 资源数据
                 additional_add_params = i.get("additional_add_params", {})  # 额外参数
-                self.lab_logger().trace(f"[资源同步] 处理 {action}, " f"resources count: {len(resources_uuid)}")
+                self.lab_logger().trace(
+                    f"[资源同步] 处理 {action}, " f"resources count: {len(resources_uuid)}"
+                )
                 tree_set = None
                 if action in ["add", "update"]:
                     tree_set = await self.get_resource(
@@ -977,13 +936,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                 tree.root_node.res_content.parent_uuid = self.uuid
                         r = SerialCommand.Request()
                         r.command = json.dumps(
-                            {"data": {"data": new_tree_set.dump()}, "action": "update"}
+                            {"data": {"data": new_tree_set.dump()}, "action": "update"})  # 和Update Resource一致
-                        )  # 和Update Resource一致
                         response: SerialCommand_Response = await self._resource_clients[
-                            "c2s_update_resource_tree"
+                            "c2s_update_resource_tree"].call_async(r)  # type: ignore
-                        ].call_async(
-                            r
-                        )  # type: ignore
                         self.lab_logger().info(f"确认资源云端 Add 结果: {response.response}")
                         results.append(result)
                     elif action == "update":
@@ -1003,13 +958,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                     tree.root_node.res_content.parent_uuid = self.uuid
                             r = SerialCommand.Request()
                             r.command = json.dumps(
-                                {"data": {"data": new_tree_set.dump()}, "action": "update"}
+                                {"data": {"data": new_tree_set.dump()}, "action": "update"})  # 和Update Resource一致
-                            )  # 和Update Resource一致
                             response: SerialCommand_Response = await self._resource_clients[
-                                "c2s_update_resource_tree"
+                                "c2s_update_resource_tree"].call_async(r)  # type: ignore
-                            ].call_async(
-                                r
-                            )  # type: ignore
                             self.lab_logger().info(f"确认资源云端 Update 结果: {response.response}")
                         results.append(result)
                     elif action == "remove":
@@ -1368,41 +1319,26 @@ 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: list = [None] * len(resource_inputs)
+                            queried_resources = []
-                            uuid_indices: list[tuple[int, str, dict]] = []  # (index, uuid, resource_data)
+                            for resource_data in resource_inputs:
-
-                            # 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[EXTRA_SAMPLE_UUID] = resource_data["sample_id"]
-                                    queried_resources[idx] = plr_resource
                                 else:
-                                    uuid_indices.append((idx, unilabos_uuid, resource_data))
+                                    resource_tree = await self.get_resource([unilabos_uuid])
-
+                                    plr_resource = resource_tree.to_plr_resources()[0]
-                            # 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[EXTRA_SAMPLE_UUID] = resource_data["sample_id"]
+                                    plr_resource.unilabos_extra["sample_uuid"] = resource_data["sample_id"]
-                                    queried_resources[idx] = plr_resource
+                                queried_resources.append(plr_resource)
 
                             self.lab_logger().debug(f"资源查询结果: 共 {len(queried_resources)} 个资源")
 
                             # 通过资源跟踪器获取本地实例
                             final_resources = queried_resources if is_sequence else queried_resources[0]
                             if not is_sequence:
-                                plr = self.resource_tracker.figure_resource(
+                                plr = self.resource_tracker.figure_resource({"name": final_resources.name}, try_mode=False)
-                                    {"name": final_resources.name}, try_mode=False
-                                )
                                 # 保留unilabos_extra
                                 if hasattr(final_resources, "unilabos_extra") and hasattr(plr, "unilabos_extra"):
                                     plr.unilabos_extra = getattr(final_resources, "unilabos_extra", {}).copy()
@@ -1441,12 +1377,8 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                 execution_success = True
                             except Exception as _:
                                 execution_error = traceback.format_exc()
-                                error(
+                                error(f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{str(action_kwargs)[:1000]}")
-                                    f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{str(action_kwargs)[:1000]}"
+                                trace(f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{action_kwargs}")
-                                )
-                                trace(
-                                    f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{action_kwargs}"
-                                )
 
                         future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs)
                         future.add_done_callback(_handle_future_exception)
@@ -1466,11 +1398,9 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         except Exception as _:
                             execution_error = traceback.format_exc()
                             error(
-                                f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{str(action_kwargs)[:1000]}"
+                                f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{str(action_kwargs)[:1000]}")
-                            )
                             trace(
-                                f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{action_kwargs}"
+                                f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入：{action_kwargs}")
-                            )
 
                     future.add_done_callback(_handle_future_exception)
 
@@ -1593,29 +1523,20 @@ class BaseROS2DeviceNode(Node, Generic[T]):
         try:
             function_name = target["function_name"]
             function_args = target["function_args"]
-            # 获取 unilabos 系统参数
-            unilabos_param: Dict[str, Any] = target.get(JSON_UNILABOS_PARAM, {})
-
             assert isinstance(function_args, dict), "执行动作时JSON必须为dict类型\n原JSON: {string}"
             function = getattr(self.driver_instance, function_name)
             assert callable(
                 function
             ), f"执行动作时JSON中的function_name对应的函数不可调用: {function_name}\n原JSON: {string}"
 
-            # 处理参数（包含 unilabos 系统参数如 sample_uuids）
+            # 处理 ResourceSlot 类型参数
-            args_list = default_manager._analyze_method_signature(function, skip_unilabos_params=False)["args"]
+            args_list = default_manager._analyze_method_signature(function)["args"]
             for arg in args_list:
                 arg_name = arg["name"]
                 arg_type = arg["type"]
 
                 # 跳过不在 function_args 中的参数
                 if arg_name not in function_args:
-                    # 处理 sample_uuids 参数注入
-                    if arg_name == PARAM_SAMPLE_UUIDS:
-                        function_args[PARAM_SAMPLE_UUIDS] = unilabos_param.get(PARAM_SAMPLE_UUIDS, [])
-                        self.lab_logger().debug(
-                            f"[JsonCommand] 注入 {PARAM_SAMPLE_UUIDS}: {function_args[PARAM_SAMPLE_UUIDS]}"
-                        )
                     continue
 
                 # 处理单个 ResourceSlot
@@ -1645,7 +1566,6 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                 )
                                 raise JsonCommandInitError(f"ResourceSlot列表参数转换失败: {arg_name}")
 
-            # todo: 默认反报送
             return function(**function_args)
         except KeyError as ex:
             raise JsonCommandInitError(
@@ -1665,23 +1585,21 @@ class BaseROS2DeviceNode(Node, Generic[T]):
             raise ValueError("至少需要提供一个 UUID")
 
         uuids_list = list(uuids)
-        future = self._resource_clients["c2s_update_resource_tree"].call_async(
+        future = self._resource_clients["c2s_update_resource_tree"].call_async(SerialCommand.Request(
-            SerialCommand.Request(
             command=json.dumps(
                 {
                     "data": {"data": uuids_list, "with_children": True},
                     "action": "get",
                 }
             )
-            )
+        ))
-        )
 
         # 等待结果（使用while循环，每次sleep 0.05秒，最多等待30秒）
         timeout = 30.0
         elapsed = 0.0
         while not future.done() and elapsed < timeout:
-            time.sleep(0.02)
+            time.sleep(0.05)
-            elapsed += 0.02
+            elapsed += 0.05
 
         if not future.done():
             raise Exception(f"资源查询超时: {uuids_list}")
@@ -1732,9 +1650,6 @@ class BaseROS2DeviceNode(Node, Generic[T]):
         try:
             function_name = target["function_name"]
             function_args = target["function_args"]
-            # 获取 unilabos 系统参数
-            unilabos_param: Dict[str, Any] = target.get(JSON_UNILABOS_PARAM, {})
-
             assert isinstance(function_args, dict), "执行动作时JSON必须为dict类型\n原JSON: {string}"
             function = getattr(self.driver_instance, function_name)
             assert callable(
@@ -1744,20 +1659,14 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 function
             ), f"执行动作时JSON中的function并非异步: {function_name}\n原JSON: {string}"
 
-            # 处理参数（包含 unilabos 系统参数如 sample_uuids）
+            # 处理 ResourceSlot 类型参数
-            args_list = default_manager._analyze_method_signature(function, skip_unilabos_params=False)["args"]
+            args_list = default_manager._analyze_method_signature(function)["args"]
             for arg in args_list:
                 arg_name = arg["name"]
                 arg_type = arg["type"]
 
                 # 跳过不在 function_args 中的参数
                 if arg_name not in function_args:
-                    # 处理 sample_uuids 参数注入
-                    if arg_name == PARAM_SAMPLE_UUIDS:
-                        function_args[PARAM_SAMPLE_UUIDS] = unilabos_param.get(PARAM_SAMPLE_UUIDS, [])
-                        self.lab_logger().debug(
-                            f"[JsonCommandAsync] 注入 {PARAM_SAMPLE_UUIDS}: {function_args[PARAM_SAMPLE_UUIDS]}"
-                        )
                     continue
 
                 # 处理单个 ResourceSlot
@@ -2035,9 +1944,7 @@ class ROS2DeviceNode:
             asyncio.set_event_loop(loop)
             loop.run_forever()
 
-        ROS2DeviceNode._asyncio_loop_thread = threading.Thread(
+        ROS2DeviceNode._asyncio_loop_thread = threading.Thread(target=run_event_loop, daemon=True, name="ROS2DeviceNode")
-            target=run_event_loop, daemon=True, name="ROS2DeviceNode"
-        )
         ROS2DeviceNode._asyncio_loop_thread.start()
         logger.info(f"循环线程已启动")
 

unilabos/ros/nodes/presets/host_node.py

@@ -42,9 +42,6 @@ from unilabos.resources.resource_tracker import (
     ResourceDictInstance,
     ResourceTreeSet,
     ResourceTreeInstance,
-    EXTRA_SAMPLE_UUID,
-    EXTRA_UNILABOS_SAMPLE_UUID,
-    RETURN_UNILABOS_SAMPLES,
 )
 from unilabos.utils import logger
 from unilabos.utils.exception import DeviceClassInvalid
@@ -794,17 +791,12 @@ class HostNode(BaseROS2DeviceNode):
 
         action_client: ActionClient = self._action_clients[action_id]
 
-        # 遍历action_kwargs下的所有子dict，将sample_uuid的值赋给sample_id
+        # 遍历action_kwargs下的所有子dict，将"sample_uuid"的值赋给"sample_id"
         def assign_sample_id(obj):
             if isinstance(obj, dict):
-                # 处理 EXTRA_SAMPLE_UUID ("sample_uuid")
+                if "sample_uuid" in obj:
-                if EXTRA_SAMPLE_UUID in obj:
+                    obj["sample_id"] = obj["sample_uuid"]
-                    obj["sample_id"] = obj[EXTRA_SAMPLE_UUID]
+                    obj.pop("sample_uuid")
-                    obj.pop(EXTRA_SAMPLE_UUID)
-                # 处理 EXTRA_UNILABOS_SAMPLE_UUID ("unilabos_sample_uuid")
-                if EXTRA_UNILABOS_SAMPLE_UUID in obj:
-                    obj["sample_id"] = obj[EXTRA_UNILABOS_SAMPLE_UUID]
-                    obj.pop(EXTRA_UNILABOS_SAMPLE_UUID)
                 for k, v in obj.items():
                     if k != "unilabos_extra":
                         assign_sample_id(v)
@@ -815,8 +807,7 @@ class HostNode(BaseROS2DeviceNode):
         assign_sample_id(action_kwargs)
         goal_msg = convert_to_ros_msg(action_client._action_type.Goal(), action_kwargs)
 
-        # self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {str(goal_msg)[:1000]}")
+        self.lab_logger().info(f"[Host Node] Sending goal for {action_id}: {str(goal_msg)[:1000]}")
-        self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {action_kwargs}")
         self.lab_logger().trace(f"[Host Node] Sending goal for {action_id}: {goal_msg}")
         action_client.wait_for_server()
         goal_uuid_obj = UUID(uuid=list(u.bytes))
@@ -875,14 +866,14 @@ class HostNode(BaseROS2DeviceNode):
                         # 适配后端的一些额外处理
                         return_value = return_info.get("return_value")
                         if isinstance(return_value, dict):
-                            unilabos_samples = return_value.pop(RETURN_UNILABOS_SAMPLES, None)
+                            unilabos_samples = return_value.pop("unilabos_samples", None)
                             if isinstance(unilabos_samples, list) and unilabos_samples:
                                 self.lab_logger().info(
                                     f"[Host Node] Job {job_id[:8]} returned {len(unilabos_samples)} sample(s): "
                                     f"{[s.get('name', s.get('id', 'unknown')) if isinstance(s, dict) else str(s)[:20] for s in unilabos_samples[:5]]}"
                                     f"{'...' if len(unilabos_samples) > 5 else ''}"
                                 )
-                                return_info[RETURN_UNILABOS_SAMPLES] = unilabos_samples
+                                return_info["unilabos_samples"] = unilabos_samples
                         suc = return_info.get("suc", False)
                         if not suc:
                             status = "failed"
@@ -1188,7 +1179,7 @@ class HostNode(BaseROS2DeviceNode):
         """
         更新节点信息回调
         """
-        self.lab_logger().trace(f"[Host Node] Node info update request received: {request}")
+        # self.lab_logger().info(f"[Host Node] Node info update request received: {request}")
         try:
             from unilabos.app.communication import get_communication_client
             from unilabos.app.web.client import HTTPClient, http_client

unilabos/ros/nodes/presets/workstation.py

@@ -6,6 +6,8 @@ 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
@@ -13,6 +15,7 @@ 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,
@@ -228,15 +231,15 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
                         try:
                             # 统一处理单个或多个资源
                             resource_id = (
-                                protocol_kwargs[k]["id"]
+                                protocol_kwargs[k]["id"] if v == "unilabos_msgs/Resource" else protocol_kwargs[k][0]["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)
@@ -304,52 +307,12 @@ 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 not in ["unilabos_msgs/Resource", "sequence<unilabos_msgs/Resource>"]:
+                    if v in ["unilabos_msgs/Resource", "sequence<unilabos_msgs/Resource>"]:
-                        continue
+                        r = ResourceUpdate.Request()
-                    self.lab_logger().info(f"更新资源状态: {k}")
+                        r.resources = [
-                    try:
+                            convert_to_ros_msg(Resource, rs) for rs in nested_dict_to_list(protocol_kwargs[k])
-                        # 去重：使用 seen 集合获取唯一的资源对象
+                        ]
-                        seen = set()
+                        response = await self._resource_clients["resource_update"].call_async(r)
-                        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

unilabos/test/experiments/prcxi_9320_slim.json

@@ -1,795 +0,0 @@
-{
-  "nodes": [
-    {
-      "id": "PRCXI",
-      "name": "PRCXI",
-      "type": "device",
-      "class": "liquid_handler.prcxi",
-      "parent": "",
-      "pose": {
-        "size": {
-          "width": 562,
-          "height": 394,
-          "depth": 0
-        }
-      },
-      "config": {
-        "axis": "Left",
-        "deck": {
-          "_resource_type": "unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Deck",
-          "_resource_child_name": "PRCXI_Deck"
-        },
-        "host": "10.20.30.184",
-        "port": 9999,
-        "debug": true,
-        "setup": true,
-        "is_9320": true,
-        "timeout": 10,
-        "matrix_id": "5de524d0-3f95-406c-86dd-f83626ebc7cb",
-        "simulator": true,
-        "channel_num": 2
-      },
-      "data": {
-        "reset_ok": true
-      },
-      "schema": {},
-      "description": "",
-      "model": null,
-      "position": {
-        "x": 0,
-        "y": 240,
-        "z": 0
-      }
-    },
-    {
-      "id": "PRCXI_Deck",
-      "name": "PRCXI_Deck",
-
-      "children": [],
-      "parent": "PRCXI",
-      "type": "deck",
-      "class": "",
-      "position": {
-        "x": 10,
-        "y": 10,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Deck",
-        "size_x": 542,
-        "size_y": 374,
-        "size_z": 0,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "deck",
-        "barcode": null
-      },
-      "data": {}
-    },
-    {
-      "id": "T1",
-      "name": "T1",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 0,
-        "y": 288,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T1",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T2",
-      "name": "T2",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 138,
-        "y": 288,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T2",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T3",
-      "name": "T3",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 276,
-        "y": 288,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T3",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T4",
-      "name": "T4",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 414,
-        "y": 288,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T4",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T5",
-      "name": "T5",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 0,
-        "y": 192,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T5",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T6",
-      "name": "T6",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 138,
-        "y": 192,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T6",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T7",
-      "name": "T7",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 276,
-        "y": 192,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T7",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T8",
-      "name": "T8",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 414,
-        "y": 192,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T8",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T9",
-      "name": "T9",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 0,
-        "y": 96,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T9",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T10",
-      "name": "T10",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 138,
-        "y": 96,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T10",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T11",
-      "name": "T11",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 276,
-        "y": 96,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T11",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T12",
-      "name": "T12",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 414,
-        "y": 96,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T12",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T13",
-      "name": "T13",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 0,
-        "y": 0,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T13",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T14",
-      "name": "T14",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 138,
-        "y": 0,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T14",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T15",
-      "name": "T15",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 276,
-        "y": 0,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T15",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    },
-    {
-      "id": "T16",
-      "name": "T16",
-      "children": [],
-      "parent": "PRCXI_Deck",
-      "type": "plate",
-      "class": "",
-      "position": {
-        "x": 414,
-        "y": 0,
-        "z": 0
-      },
-      "config": {
-        "type": "PRCXI9300Container",
-        "size_x": 127,
-        "size_y": 85.5,
-        "size_z": 10,
-        "rotation": {
-          "x": 0,
-          "y": 0,
-          "z": 0,
-          "type": "Rotation"
-        },
-        "category": "plate",
-        "model": null,
-        "barcode": null,
-        "ordering": {},
-        "sites": [
-          {
-            "label": "T16",
-            "visible": true,
-            "position": { "x": 0, "y": 0, "z": 0 },
-            "size": { "width": 128.0, "height": 86, "depth": 0 },
-            "content_type": [
-              "plate",
-              "tip_rack",
-              "plates",
-              "tip_racks",
-              "tube_rack"
-            ]
-          }
-        ]
-      },
-      "data": {}
-    }
-  ],
-  "edges": []
-}

unilabos/utils/import_manager.py

@@ -27,7 +27,6 @@ __all__ = [
 
 from ast import Constant
 
-from unilabos.resources.resource_tracker import PARAM_SAMPLE_UUIDS
 from unilabos.utils import logger
 from unilabos.utils.decorator import is_not_action
 
@@ -342,18 +341,13 @@ class ImportManager:
                     result["action_methods"][method_name] = method_info
         return result
 
-    def _analyze_method_signature(self, method, skip_unilabos_params: bool = True) -> Dict[str, Any]:
+    def _analyze_method_signature(self, method) -> Dict[str, Any]:
         """
         分析方法签名，提取具体的命名参数信息
 
         注意：此方法会跳过*args和**kwargs，只提取具体的命名参数
         这样可以确保通过**dict方式传参时的准确性
 
-        Args:
-            method: 要分析的方法
-            skip_unilabos_params: 是否跳过 unilabos 系统参数（如 sample_uuids），
-                                  registry 补全时为 True，JsonCommand 执行时为 False
-
         示例用法：
             method_info = self._analyze_method_signature(some_method)
             params = {"param1": "value1", "param2": "value2"}
@@ -374,10 +368,6 @@ class ImportManager:
             if param.kind == param.VAR_KEYWORD:  # **kwargs
                 continue
 
-            # 跳过 sample_uuids 参数（由系统自动注入，registry 补全时跳过）
-            if skip_unilabos_params and param_name == PARAM_SAMPLE_UUIDS:
-                continue
-
             is_required = param.default == inspect.Parameter.empty
             if is_required:
                 num_required += 1
@@ -573,9 +563,6 @@ class ImportManager:
         for i, arg in enumerate(node.args.args):
             if arg.arg == "self":
                 continue
-            # 跳过 sample_uuids 参数（由系统自动注入）
-            if arg.arg == PARAM_SAMPLE_UUIDS:
-                continue
             arg_info = {
                 "name": arg.arg,
                 "type": None,

unilabos/workflow/common.py

@@ -1,825 +0,0 @@
-"""
-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）
---------------------------------------------------------------------------------
-- 首先创建一个 Group 节点（type="Group", minimized=true），用于包含所有 create_resource 节点
-- 遍历所有 reagent，按 slot 去重，为每个唯一的 slot 创建一个板子
-- 所有 create_resource 节点的 parent_uuid 指向 Group 节点，minimized=true
-- 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 1 个 Group + 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）
---------------------------------------------------------------------------------
-- 首先创建一个 Group 节点（type="Group", minimized=true），用于包含所有 set_liquid_from_plate 节点
-- 遍历所有 reagent，为每个试剂创建 set_liquid_from_plate 节点
-- 所有 set_liquid_from_plate 节点的 parent_uuid 指向 Group 节点，minimized=true
-- 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 之间: 无 ready 连接
-    - set_liquid_from_plate 之间: 无 ready 连接
-    - create_resource 与 set_liquid_from_plate 之间: 无 ready 连接
-    - transfer_liquid 之间: 通过 ready 端口串联
-        transfer_liquid_1 -> transfer_liquid_2 -> transfer_liquid_3 -> ...
-
-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
-
-==================== 设备名配置 (device_name) ====================
-
-每个节点都有 device_name 字段，指定在哪个设备上执行:
-- create_resource: device_name = "host_node"（固定）
-- set_liquid_from_plate: device_name = "PRCXI"（可配置，见 DEVICE_NAME_DEFAULT）
-- transfer_liquid 等动作: device_name = "PRCXI"（可配置，见 DEVICE_NAME_DEFAULT）
-
-==================== 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 ====================
-
-# 设备名配置
-DEVICE_NAME_HOST = "host_node"  # create_resource 固定在 host_node 上执行
-DEVICE_NAME_DEFAULT = "PRCXI"  # transfer_liquid, set_liquid_from_plate 等动作的默认设备名
-
-# 节点类型
-NODE_TYPE_DEFAULT = "ILab"  # 所有节点的默认类型
-
-# 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,
-            }
-
-    # 创建 Group 节点，包含所有 create_resource 节点
-    group_node_id = str(uuid.uuid4())
-    G.add_node(
-        group_node_id,
-        name="Resources Group",
-        type="Group",
-        parent_uuid="",
-        lab_node_type="Device",
-        template_name="",
-        resource_name="",
-        footer="",
-        minimized=True,
-        param=None,
-    )
-
-    # 为每个唯一的 slot 创建 create_resource 节点
-    res_index = 0
-    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",
-            device_name=DEVICE_NAME_HOST,
-            type=NODE_TYPE_DEFAULT,
-            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": 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
-    set_liquid_group_id = str(uuid.uuid4())
-    G.add_node(
-        set_liquid_group_id,
-        name="SetLiquid Group",
-        type="Group",
-        parent_uuid="",
-        lab_node_type="Device",
-        template_name="",
-        resource_name="",
-        footer="",
-        minimized=True,
-        param=None,
-    )
-
-    set_liquid_index = 0
-
-    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",
-            device_name=DEVICE_NAME_DEFAULT,
-            type=NODE_TYPE_DEFAULT,
-            parent_uuid=set_liquid_group_id,  # 指向 Group 节点
-            minimized=True,  # 折叠显示
-            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,
-            },
-        )
-
-        # set_liquid_from_plate 之间不需要 ready 连接
-
-        # 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"
-
-    # transfer_liquid 之间通过 ready 串联，从 None 开始
-    last_control_node_id = None
-
-    # 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、footer、device_name 和 type
-        step_copy = step.copy()
-        step_copy["param"] = params
-        step_copy["device_name"] = DEVICE_NAME_DEFAULT  # 动作节点使用默认设备名
-        step_copy["type"] = NODE_TYPE_DEFAULT  # 节点类型
-
-        # 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 <portname>。
-    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，<p> 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 <port> 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 <port> 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())))

unilabos/workflow/convert_from_json.py

@@ -1,315 +0,0 @@
-"""
-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()

unilabos/workflow/from_python_script.py

@@ -1,241 +0,0 @@
-import ast
-import json
-from typing import Dict, List, Any, Tuple, Optional
-
-from .common import WorkflowGraph, RegistryAdapter
-
-Json = Dict[str, Any]
-
-# ---------------- Converter ----------------
-
-class DeviceMethodConverter:
-    """
-    - 字段统一：resource_name（原 device_class）、template_name（原 action_key）
-    - params 单层；inputs 使用 'params.' 前缀
-    - SimpleGraph.add_workflow_node 负责变量连线与边
-    """
-    def __init__(self, device_registry: Optional[Dict[str, Any]] = None):
-        self.graph = WorkflowGraph()
-        self.variable_sources: Dict[str, Dict[str, Any]] = {}        # var -> {node_id, output_name}
-        self.instance_to_resource: Dict[str, Optional[str]] = {}     # 实例名 -> resource_name
-        self.node_id_counter: int = 0
-        self.registry = RegistryAdapter(device_registry or {})
-
-    # ---- helpers ----
-    def _new_node_id(self) -> int:
-        nid = self.node_id_counter
-        self.node_id_counter += 1
-        return nid
-
-    def _assign_targets(self, targets) -> List[str]:
-        names: List[str] = []
-        import ast
-        if isinstance(targets, ast.Tuple):
-            for elt in targets.elts:
-                if isinstance(elt, ast.Name):
-                    names.append(elt.id)
-        elif isinstance(targets, ast.Name):
-            names.append(targets.id)
-        return names
-
-    def _extract_device_instantiation(self, node) -> Optional[Tuple[str, str]]:
-        import ast
-        if not isinstance(node.value, ast.Call):
-            return None
-        callee = node.value.func
-        if isinstance(callee, ast.Name):
-            class_name = callee.id
-        elif isinstance(callee, ast.Attribute) and isinstance(callee.value, ast.Name):
-            class_name = callee.attr
-        else:
-            return None
-        if isinstance(node.targets[0], ast.Name):
-            instance = node.targets[0].id
-            return instance, class_name
-        return None
-
-    def _extract_call(self, call) -> Tuple[str, str, Dict[str, Any], str]:
-        import ast
-        owner_name, method_name, call_kind = "", "", "func"
-        if isinstance(call.func, ast.Attribute):
-            method_name = call.func.attr
-            if isinstance(call.func.value, ast.Name):
-                owner_name = call.func.value.id
-                call_kind = "instance" if owner_name in self.instance_to_resource else "class_or_module"
-            elif isinstance(call.func.value, ast.Attribute) and isinstance(call.func.value.value, ast.Name):
-                owner_name = call.func.value.attr
-                call_kind = "class_or_module"
-        elif isinstance(call.func, ast.Name):
-            method_name = call.func.id
-            call_kind = "func"
-
-        def pack(node):
-            if isinstance(node, ast.Name):
-                return {"type": "variable", "value": node.id}
-            if isinstance(node, ast.Constant):
-                return {"type": "constant", "value": node.value}
-            if isinstance(node, ast.Dict):
-                return {"type": "dict", "value": self._parse_dict(node)}
-            if isinstance(node, ast.List):
-                return {"type": "list", "value": self._parse_list(node)}
-            return {"type": "raw", "value": ast.unparse(node) if hasattr(ast, "unparse") else str(node)}
-
-        args: Dict[str, Any] = {}
-        pos: List[Any] = []
-        for a in call.args:
-            pos.append(pack(a))
-        for kw in call.keywords:
-            args[kw.arg] = pack(kw.value)
-        if pos:
-            args["_positional"] = pos
-        return owner_name, method_name, args, call_kind
-
-    def _parse_dict(self, node) -> Dict[str, Any]:
-        import ast
-        out: Dict[str, Any] = {}
-        for k, v in zip(node.keys, node.values):
-            if isinstance(k, ast.Constant):
-                key = str(k.value)
-                if isinstance(v, ast.Name):
-                    out[key] = f"var:{v.id}"
-                elif isinstance(v, ast.Constant):
-                    out[key] = v.value
-                elif isinstance(v, ast.Dict):
-                    out[key] = self._parse_dict(v)
-                elif isinstance(v, ast.List):
-                    out[key] = self._parse_list(v)
-        return out
-
-    def _parse_list(self, node) -> List[Any]:
-        import ast
-        out: List[Any] = []
-        for elt in node.elts:
-            if isinstance(elt, ast.Name):
-                out.append(f"var:{elt.id}")
-            elif isinstance(elt, ast.Constant):
-                out.append(elt.value)
-            elif isinstance(elt, ast.Dict):
-                out.append(self._parse_dict(elt))
-            elif isinstance(elt, ast.List):
-                out.append(self._parse_list(elt))
-        return out
-
-    def _normalize_var_tokens(self, x: Any) -> Any:
-        if isinstance(x, str) and x.startswith("var:"):
-            return {"__var__": x[4:]}
-        if isinstance(x, list):
-            return [self._normalize_var_tokens(i) for i in x]
-        if isinstance(x, dict):
-            return {k: self._normalize_var_tokens(v) for k, v in x.items()}
-        return x
-
-    def _make_params_payload(self, resource_name: Optional[str], template_name: str, call_args: Dict[str, Any]) -> Dict[str, Any]:
-        input_keys = self.registry.get_action_input_keys(resource_name, template_name) if resource_name else []
-        defaults = self.registry.get_action_goal_default(resource_name, template_name) if resource_name else {}
-        params: Dict[str, Any] = dict(defaults)
-
-        def unpack(p):
-            t, v = p.get("type"), p.get("value")
-            if t == "variable":
-                return {"__var__": v}
-            if t == "dict":
-                return self._normalize_var_tokens(v)
-            if t == "list":
-                return self._normalize_var_tokens(v)
-            return v
-
-        for k, p in call_args.items():
-            if k == "_positional":
-                continue
-            params[k] = unpack(p)
-
-        pos = call_args.get("_positional", [])
-        if pos:
-            if input_keys:
-                for i, p in enumerate(pos):
-                    if i >= len(input_keys):
-                        break
-                    name = input_keys[i]
-                    if name in params:
-                        continue
-                    params[name] = unpack(p)
-            else:
-                for i, p in enumerate(pos):
-                    params[f"arg_{i}"] = unpack(p)
-        return params
-
-    # ---- handlers ----
-    def _on_assign(self, stmt):
-        import ast
-        inst = self._extract_device_instantiation(stmt)
-        if inst:
-            instance, code_class = inst
-            resource_name = self.registry.resolve_resource_by_classname(code_class)
-            self.instance_to_resource[instance] = resource_name
-            return
-
-        if isinstance(stmt.value, ast.Call):
-            owner, method, call_args, kind = self._extract_call(stmt.value)
-            if kind == "instance":
-                device_key = owner
-                resource_name = self.instance_to_resource.get(owner)
-            else:
-                device_key = owner
-                resource_name = self.registry.resolve_resource_by_classname(owner)
-
-            module = self.registry.get_device_module(resource_name)
-            params = self._make_params_payload(resource_name, method, call_args)
-
-            nid = self._new_node_id()
-            self.graph.add_workflow_node(
-                nid,
-                device_key=device_key,
-                resource_name=resource_name,      # ✅
-                module=module,
-                template_name=method,             # ✅
-                params=params,
-                variable_sources=self.variable_sources,
-                add_ready_if_no_vars=True,
-                prev_node_id=(nid - 1) if nid > 0 else None,
-            )
-
-            out_vars = self._assign_targets(stmt.targets[0])
-            for var in out_vars:
-                self.variable_sources[var] = {"node_id": nid, "output_name": "result"}
-
-    def _on_expr(self, stmt):
-        import ast
-        if not isinstance(stmt.value, ast.Call):
-            return
-        owner, method, call_args, kind = self._extract_call(stmt.value)
-        if kind == "instance":
-            device_key = owner
-            resource_name = self.instance_to_resource.get(owner)
-        else:
-            device_key = owner
-            resource_name = self.registry.resolve_resource_by_classname(owner)
-
-        module = self.registry.get_device_module(resource_name)
-        params = self._make_params_payload(resource_name, method, call_args)
-
-        nid = self._new_node_id()
-        self.graph.add_workflow_node(
-            nid,
-            device_key=device_key,
-            resource_name=resource_name,      # ✅
-            module=module,
-            template_name=method,             # ✅
-            params=params,
-            variable_sources=self.variable_sources,
-            add_ready_if_no_vars=True,
-            prev_node_id=(nid - 1) if nid > 0 else None,
-        )
-
-    def convert(self, python_code: str):
-        tree = ast.parse(python_code)
-        for stmt in tree.body:
-            if isinstance(stmt, ast.Assign):
-                self._on_assign(stmt)
-            elif isinstance(stmt, ast.Expr):
-                self._on_expr(stmt)
-        return self

unilabos/workflow/from_xdl.py

@@ -1,131 +0,0 @@
-from typing import List, Any, Dict
-import xml.etree.ElementTree as ET
-
-
-def convert_to_type(val: str) -> Any:
-    """将字符串值转换为适当的数据类型"""
-    if val == "True":
-        return True
-    if val == "False":
-        return False
-    if val == "?":
-        return None
-    if val.endswith(" g"):
-        return float(val.split(" ")[0])
-    if val.endswith("mg"):
-        return float(val.split("mg")[0])
-    elif val.endswith("mmol"):
-        return float(val.split("mmol")[0]) / 1000
-    elif val.endswith("mol"):
-        return float(val.split("mol")[0])
-    elif val.endswith("ml"):
-        return float(val.split("ml")[0])
-    elif val.endswith("RPM"):
-        return float(val.split("RPM")[0])
-    elif val.endswith(" °C"):
-        return float(val.split(" ")[0])
-    elif val.endswith(" %"):
-        return float(val.split(" ")[0])
-    return val
-
-
-def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
-    """展平嵌套的XDL程序结构"""
-    flattened_operations = []
-    TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
-
-    def extract_operations(element: ET.Element):
-        if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
-            if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
-                flattened_operations.append(element)
-
-        for child in element:
-            extract_operations(child)
-
-    for child in procedure_elem:
-        extract_operations(child)
-
-    return flattened_operations
-
-
-def parse_xdl_content(xdl_content: str) -> tuple:
-    """解析XDL内容"""
-    try:
-        xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
-        root = ET.fromstring(xdl_content_cleaned)
-
-        synthesis_elem = root.find("Synthesis")
-        if synthesis_elem is None:
-            return None, None, None
-
-        # 解析硬件组件
-        hardware_elem = synthesis_elem.find("Hardware")
-        hardware = []
-        if hardware_elem is not None:
-            hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
-
-        # 解析试剂
-        reagents_elem = synthesis_elem.find("Reagents")
-        reagents = []
-        if reagents_elem is not None:
-            reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
-
-        # 解析程序
-        procedure_elem = synthesis_elem.find("Procedure")
-        if procedure_elem is None:
-            return None, None, None
-
-        flattened_operations = flatten_xdl_procedure(procedure_elem)
-        return hardware, reagents, flattened_operations
-
-    except ET.ParseError as e:
-        raise ValueError(f"Invalid XDL format: {e}")
-
-
-def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
-    """
-    将XDL XML格式转换为标准的字典格式
-
-    Args:
-        xdl_content: XDL XML内容
-
-    Returns:
-        转换结果，包含步骤和器材信息
-    """
-    try:
-        hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
-        if hardware is None:
-            return {"error": "Failed to parse XDL content", "success": False}
-
-        # 将XDL元素转换为字典格式
-        steps_data = []
-        for elem in flattened_operations:
-            # 转换参数类型
-            parameters = {}
-            for key, val in elem.attrib.items():
-                converted_val = convert_to_type(val)
-                if converted_val is not None:
-                    parameters[key] = converted_val
-
-            step_dict = {
-                "operation": elem.tag,
-                "parameters": parameters,
-                "description": elem.get("purpose", f"Operation: {elem.tag}"),
-            }
-            steps_data.append(step_dict)
-
-        # 合并硬件和试剂为统一的labware_info格式
-        labware_data = []
-        labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
-        labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
-
-        return {
-            "success": True,
-            "steps": steps_data,
-            "labware": labware_data,
-            "message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
-        }
-
-    except Exception as e:
-        error_msg = f"XDL conversion failed: {str(e)}"
-        return {"error": error_msg, "success": False}

unilabos/workflow/legacy/convert_from_json_legacy.py

@@ -1,356 +0,0 @@
-"""
-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