Update docs

修改了mix，仿真流程报错问题

.conda/recipe.yaml

@@ -1,6 +1,6 @@
 package:
   name: unilabos
-  version: 0.10.11
+  version: 0.10.12
 
 source:
   path: ../unilabos

README.md

@@ -39,7 +39,9 @@ Uni-Lab-OS recommends using `mamba` for environment management. Choose the appro
 
 ```bash
 # Create new environment
-mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
+mamba create -n unilab python=3.11.11
+mamba activate unilab
+mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
 ```
 
 ## Install Dev Uni-Lab-OS

README_zh.md

@@ -41,7 +41,9 @@ Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适
 
 ```bash
 # 创建新环境
-mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
+mamba create -n unilab python=3.11.11
+mamba activate unilab
+mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
 ```
 
 2. 安装开发版 Uni-Lab-OS:

docs/user_guide/installation.md

@@ -317,45 +317,6 @@ unilab --help
 
 如果所有命令都正常输出，说明开发环境配置成功！
 
-### 开发工具推荐
-
-#### IDE
-
-- **PyCharm Professional**: 强大的 Python IDE，支持远程调试
-- **VS Code**: 轻量级，配合 Python 扩展使用
-- **Vim/Emacs**: 适合终端开发
-
-#### 推荐的 VS Code 扩展
-
-- Python
-- Pylance
-- ROS
-- URDF
-- YAML
-
-#### 调试工具
-
-```bash
-# 安装调试工具
-pip install ipdb pytest pytest-cov -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
-
-# 代码质量检查
-pip install black flake8 mypy -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
-```
-
-### 设置 pre-commit 钩子（可选）
-
-```bash
-# 安装 pre-commit
-pip install pre-commit -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
-
-# 设置钩子
-pre-commit install
-
-# 手动运行检查
-pre-commit run --all-files
-```
-
 ---
 
 ## 验证安装

recipes/msgs/recipe.yaml

@@ -1,6 +1,6 @@
 package:
   name: ros-humble-unilabos-msgs
-  version: 0.10.11
+  version: 0.10.12
 source:
   path: ../../unilabos_msgs
   target_directory: src

recipes/unilabos/recipe.yaml

@@ -1,6 +1,6 @@
 package:
   name: unilabos
-  version: "0.10.11"
+  version: "0.10.12"
 
 source:
   path: ../..

scripts/workflow.py

@@ -2,7 +2,6 @@ import json
 import logging
 import traceback
 import uuid
-import xml.etree.ElementTree as ET
 from typing import Any, Dict, List
 
 import networkx as nx
@@ -25,7 +24,15 @@ 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):
@@ -42,6 +49,7 @@ class SimpleGraph:
             "multigraph": False,
             "graph": {},
             "nodes": nodes_list,
+            "edges": self.edges,
             "links": self.edges,
         }
 
@@ -58,495 +66,8 @@ 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(

setup.py

@@ -4,7 +4,7 @@ package_name = 'unilabos'
 
 setup(
     name=package_name,
-    version='0.10.11',
+    version='0.10.12',
     packages=find_packages(),
     include_package_data=True,
     install_requires=['setuptools'],

test/workflow/merge_workflow.py

@@ -0,0 +1,35 @@
+import sys
+from datetime import datetime
+from pathlib import Path
+
+ROOT_DIR = Path(__file__).resolve().parents[2]
+if str(ROOT_DIR) not in sys.path:
+    sys.path.insert(0, str(ROOT_DIR))
+
+import pytest
+
+from unilabos.workflow.convert_from_json import (
+    convert_from_json,
+    normalize_steps as _normalize_steps,
+    normalize_labware as _normalize_labware,
+)
+from unilabos.workflow.common import draw_protocol_graph_with_ports
+
+
+@pytest.mark.parametrize(
+    "protocol_name",
+    [
+        "example_bio",
+        # "bioyond_materials_liquidhandling_1",
+        "example_prcxi",
+    ],
+)
+def test_build_protocol_graph(protocol_name):
+    data_path = Path(__file__).with_name(f"{protocol_name}.json")
+
+    graph = convert_from_json(data_path, workstation_name="PRCXi")
+
+    timestamp = datetime.now().strftime("%Y%m%d_%H%M")
+    output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
+    draw_protocol_graph_with_ports(graph, str(output_path))
+    print(graph)

unilabos/__init__.py

@@ -1 +1 @@
-__version__ = "0.10.11"
+__version__ = "0.10.12"

unilabos/app/communication.py

@@ -141,7 +141,7 @@ class CommunicationClientFactory:
         """
         if cls._client_cache is None:
             cls._client_cache = cls.create_client(protocol)
-            logger.info(f"[CommunicationFactory] Created {type(cls._client_cache).__name__} client")
+            logger.trace(f"[CommunicationFactory] Created {type(cls._client_cache).__name__} client")
 
         return cls._client_cache
 

unilabos/app/main.py

@@ -20,6 +20,7 @@ if unilabos_dir not in sys.path:
 from unilabos.utils.banner_print import print_status, print_unilab_banner
 from unilabos.config.config import load_config, BasicConfig, HTTPConfig
 
+
 def load_config_from_file(config_path):
     if config_path is None:
         config_path = os.environ.get("UNILABOS_BASICCONFIG_CONFIG_PATH", None)
@@ -41,7 +42,7 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
     for i, arg in enumerate(sys.argv):
         for option_string in option_strings:
             if arg.startswith(option_string):
-                new_arg = arg[:2] + arg[2:len(option_string)].replace("-", "_") + arg[len(option_string):]
+                new_arg = arg[:2] + arg[2 : len(option_string)].replace("-", "_") + arg[len(option_string) :]
                 sys.argv[i] = new_arg
                 break
 
@@ -49,6 +50,8 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
 def parse_args():
     """解析命令行参数"""
     parser = argparse.ArgumentParser(description="Start Uni-Lab Edge server.")
+    subparsers = parser.add_subparsers(title="Valid subcommands", dest="command")
+
     parser.add_argument("-g", "--graph", help="Physical setup graph file path.")
     parser.add_argument("-c", "--controllers", default=None, help="Controllers config file path.")
     parser.add_argument(
@@ -153,21 +156,54 @@ def parse_args():
         default=False,
         help="Complete registry information",
     )
+    # workflow upload subcommand
+    workflow_parser = subparsers.add_parser(
+        "workflow_upload",
+        aliases=["wf"],
+        help="Upload workflow from xdl/json/python files",
+    )
+    workflow_parser.add_argument(
+        "-f",
+        "--workflow_file",
+        type=str,
+        required=True,
+        help="Path to the workflow file (JSON format)",
+    )
+    workflow_parser.add_argument(
+        "-n",
+        "--workflow_name",
+        type=str,
+        default=None,
+        help="Workflow name, if not provided will use the name from file or filename",
+    )
+    workflow_parser.add_argument(
+        "--tags",
+        type=str,
+        nargs="*",
+        default=[],
+        help="Tags for the workflow (space-separated)",
+    )
+    workflow_parser.add_argument(
+        "--published",
+        action="store_true",
+        default=False,
+        help="Whether to publish the workflow (default: False)",
+    )
     return parser
 
 
 def main():
     """主函数"""
     # 解析命令行参数
-    args = parse_args()
-    convert_argv_dashes_to_underscores(args)
-    args_dict = vars(args.parse_args())
+    parser = parse_args()
+    convert_argv_dashes_to_underscores(parser)
+    args = parser.parse_args()
+    args_dict = vars(args)
 
     # 环境检查 - 检查并自动安装必需的包 (可选)
     if not args_dict.get("skip_env_check", False):
         from unilabos.utils.environment_check import check_environment
 
-        print_status("正在进行环境依赖检查...", "info")
         if not check_environment(auto_install=True):
             print_status("环境检查失败，程序退出", "error")
             os._exit(1)
@@ -218,19 +254,20 @@ def main():
 
     if hasattr(BasicConfig, "log_level"):
         logger.info(f"Log level set to '{BasicConfig.log_level}' from config file.")
-        configure_logger(loglevel=BasicConfig.log_level)
+    configure_logger(loglevel=BasicConfig.log_level, working_dir=working_dir)
 
-    if args_dict["addr"] == "test":
-        print_status("使用测试环境地址", "info")
-        HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
-    elif args_dict["addr"] == "uat":
-        print_status("使用uat环境地址", "info")
-        HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
-    elif args_dict["addr"] == "local":
-        print_status("使用本地环境地址", "info")
-        HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
-    else:
-        HTTPConfig.remote_addr = args_dict.get("addr", "")
+    if args.addr != parser.get_default("addr"):
+        if args.addr == "test":
+            print_status("使用测试环境地址", "info")
+            HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
+        elif args.addr == "uat":
+            print_status("使用uat环境地址", "info")
+            HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
+        elif args.addr == "local":
+            print_status("使用本地环境地址", "info")
+            HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
+        else:
+            HTTPConfig.remote_addr = args.addr
 
     # 设置BasicConfig参数
     if args_dict.get("ak", ""):
@@ -239,9 +276,12 @@ def main():
     if args_dict.get("sk", ""):
         BasicConfig.sk = args_dict.get("sk", "")
         print_status("传入了sk参数，优先采用传入参数！", "info")
+    BasicConfig.working_dir = working_dir
+
+    workflow_upload = args_dict.get("command") in ("workflow_upload", "wf")
 
     # 使用远程资源启动
-    if args_dict["use_remote_resource"]:
+    if not workflow_upload and args_dict["use_remote_resource"]:
         print_status("使用远程资源启动", "info")
         from unilabos.app.web import http_client
 
@@ -254,7 +294,6 @@ def main():
 
     BasicConfig.port = args_dict["port"] if args_dict["port"] else BasicConfig.port
     BasicConfig.disable_browser = args_dict["disable_browser"] or BasicConfig.disable_browser
-    BasicConfig.working_dir = working_dir
     BasicConfig.is_host_mode = not args_dict.get("is_slave", False)
     BasicConfig.slave_no_host = args_dict.get("slave_no_host", False)
     BasicConfig.upload_registry = args_dict.get("upload_registry", False)
@@ -283,9 +322,31 @@ def main():
 
     # 注册表
     lab_registry = build_registry(
-        args_dict["registry_path"], args_dict.get("complete_registry", False), args_dict["upload_registry"]
+        args_dict["registry_path"], args_dict.get("complete_registry", False), BasicConfig.upload_registry
     )
 
+    if BasicConfig.upload_registry:
+        # 设备注册到服务端 - 需要 ak 和 sk
+        if BasicConfig.ak and BasicConfig.sk:
+            print_status("开始注册设备到服务端...", "info")
+            try:
+                register_devices_and_resources(lab_registry)
+                print_status("设备注册完成", "info")
+            except Exception as e:
+                print_status(f"设备注册失败: {e}", "error")
+        else:
+            print_status("未提供 ak 和 sk，跳过设备注册", "info")
+    else:
+        print_status("本次启动注册表不报送云端，如果您需要联网调试，请在启动命令增加--upload_registry", "warning")
+
+    # 处理 workflow_upload 子命令
+    if workflow_upload:
+        from unilabos.workflow.wf_utils import handle_workflow_upload_command
+
+        handle_workflow_upload_command(args_dict)
+        print_status("工作流上传完成，程序退出", "info")
+        os._exit(0)
+
     if not BasicConfig.ak or not BasicConfig.sk:
         print_status("后续运行必须拥有一个实验室，请前往 https://uni-lab.bohrium.com 注册实验室！", "warning")
         os._exit(1)
@@ -362,20 +423,6 @@ def main():
     args_dict["devices_config"] = resource_tree_set
     args_dict["graph"] = graph_res.physical_setup_graph
 
-    if BasicConfig.upload_registry:
-        # 设备注册到服务端 - 需要 ak 和 sk
-        if BasicConfig.ak and BasicConfig.sk:
-            print_status("开始注册设备到服务端...", "info")
-            try:
-                register_devices_and_resources(lab_registry)
-                print_status("设备注册完成", "info")
-            except Exception as e:
-                print_status(f"设备注册失败: {e}", "error")
-        else:
-            print_status("未提供 ak 和 sk，跳过设备注册", "info")
-    else:
-        print_status("本次启动注册表不报送云端，如果您需要联网调试，请在启动命令增加--upload_registry", "warning")
-
     if args_dict["controllers"] is not None:
         args_dict["controllers_config"] = yaml.safe_load(open(args_dict["controllers"], encoding="utf-8"))
     else:
@@ -390,6 +437,7 @@ def main():
         comm_client = get_communication_client()
         if "websocket" in args_dict["app_bridges"]:
             args_dict["bridges"].append(comm_client)
+
             def _exit(signum, frame):
                 comm_client.stop()
                 sys.exit(0)
@@ -431,16 +479,13 @@ def main():
                 resource_visualization.start()
             except OSError as e:
                 if "AMENT_PREFIX_PATH" in str(e):
-                    print_status(
-                        f"ROS 2环境未正确设置，跳过3D可视化启动。错误详情: {e}",
-                        "warning"
-                    )
+                    print_status(f"ROS 2环境未正确设置，跳过3D可视化启动。错误详情: {e}", "warning")
                     print_status(
                         "建议解决方案：\n"
                         "1. 激活Conda环境: conda activate unilab\n"
                         "2. 或使用 --backend simple 参数\n"
                         "3. 或使用 --visual disable 参数禁用可视化",
-                        "info"
+                        "info",
                     )
                 else:
                     raise

unilabos/app/oss_upload.py

@@ -34,14 +34,14 @@ def _get_oss_token(
         client = http_client
 
     # 构造scene参数: driver_name-exp_type
-    scene = f"{driver_name}-{exp_type}"
+    sub_path = f"{driver_name}-{exp_type}"
 
     # 构造请求URL，使用client的remote_addr（已包含/api/v1/）
     url = f"{client.remote_addr}/applications/token"
-    params = {"scene": scene, "filename": filename}
+    params = {"sub_path": sub_path, "filename": filename, "scene": "job"}
 
     try:
-        logger.info(f"[OSS] 请求预签名URL: scene={scene}, filename={filename}")
+        logger.info(f"[OSS] 请求预签名URL: sub_path={sub_path}, filename={filename}")
         response = requests.get(url, params=params, headers={"Authorization": f"Lab {client.auth}"}, timeout=10)
 
         if response.status_code == 200:

unilabos/app/web/client.py

@@ -76,7 +76,8 @@ class HTTPClient:
             Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
         """
         with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f:
-            f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
+            payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
+            f.write(json.dumps(payload, indent=4))
         # 从序列化数据中提取所有节点的UUID（保存旧UUID）
         old_uuids = {n.res_content.uuid: n for n in resources.all_nodes}
         if not self.initialized or first_add:
@@ -331,6 +332,67 @@ 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)
+        """
+        # target_lab_uuid 暂时使用默认值，后续由后端根据 ak/sk 获取
+        payload = {
+            "target_lab_uuid": "28c38bb0-63f6-4352-b0d8-b5b8eb1766d5",
+            "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

@@ -389,7 +389,7 @@ class MessageProcessor:
         self.is_running = True
         self.thread = threading.Thread(target=self._run, daemon=True, name="MessageProcessor")
         self.thread.start()
-        logger.info("[MessageProcessor] Started")
+        logger.trace("[MessageProcessor] Started")
 
     def stop(self) -> None:
         """停止消息处理线程"""
@@ -438,7 +438,7 @@ class MessageProcessor:
                     self.connected = True
                     self.reconnect_count = 0
 
-                    logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
+                    logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
 
                     # 启动发送协程
                     send_task = asyncio.create_task(self._send_handler())
@@ -503,7 +503,7 @@ class MessageProcessor:
 
     async def _send_handler(self):
         """处理发送队列中的消息"""
-        logger.debug("[MessageProcessor] Send handler started")
+        logger.trace("[MessageProcessor] Send handler started")
 
         try:
             while self.connected and self.websocket:
@@ -939,7 +939,7 @@ class QueueProcessor:
         # 事件通知机制
         self.queue_update_event = threading.Event()
 
-        logger.info("[QueueProcessor] Initialized")
+        logger.trace("[QueueProcessor] Initialized")
 
     def set_websocket_client(self, websocket_client: "WebSocketClient"):
         """设置WebSocket客户端引用"""
@@ -954,7 +954,7 @@ class QueueProcessor:
         self.is_running = True
         self.thread = threading.Thread(target=self._run, daemon=True, name="QueueProcessor")
         self.thread.start()
-        logger.info("[QueueProcessor] Started")
+        logger.trace("[QueueProcessor] Started")
 
     def stop(self) -> None:
         """停止队列处理线程"""
@@ -965,7 +965,7 @@ class QueueProcessor:
 
     def _run(self):
         """运行队列处理主循环"""
-        logger.debug("[QueueProcessor] Queue processor started")
+        logger.trace("[QueueProcessor] Queue processor started")
 
         while self.is_running:
             try:
@@ -1175,7 +1175,6 @@ 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:
@@ -1188,13 +1187,11 @@ 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.info("[WebSocketClient] All threads started")
+        logger.trace("[WebSocketClient] All threads started")
 
     def stop(self) -> None:
         """停止WebSocket客户端"""
@@ -1314,3 +1311,19 @@ class WebSocketClient(BaseCommunicationClient):
             logger.info(f"[WebSocketClient] Job {job_log} cancelled successfully")
         else:
             logger.warning(f"[WebSocketClient] Failed to cancel job {job_log}")
+
+    def publish_host_ready(self) -> None:
+        """发布host_node ready信号"""
+        if self.is_disabled or not self.is_connected():
+            logger.debug("[WebSocketClient] Not connected, cannot publish host ready signal")
+            return
+
+        message = {
+            "action": "host_node_ready",
+            "data": {
+                "status": "ready",
+                "timestamp": time.time(),
+            },
+        }
+        self.message_processor.send_message(message)
+        logger.info("[WebSocketClient] Host node ready signal published")

unilabos/config/config.py

@@ -21,7 +21,8 @@ class BasicConfig:
     startup_json_path = None  # 填写绝对路径
     disable_browser = False  # 禁止浏览器自动打开
     port = 8002  # 本地HTTP服务
-    log_level: Literal['TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] = "DEBUG"  # 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
+    # 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
+    log_level: Literal["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = "DEBUG"
 
     @classmethod
     def auth_secret(cls):
@@ -41,7 +42,7 @@ class WSConfig:
 
 # HTTP配置
 class HTTPConfig:
-    remote_addr = "http://127.0.0.1:48197/api/v1"
+    remote_addr = "https://uni-lab.bohrium.com/api/v1"
 
 
 # ROS配置
@@ -65,13 +66,14 @@ def _update_config_from_module(module):
                     if not attr.startswith("_"):
                         setattr(obj, attr, getattr(getattr(module, name), attr))
 
+
 def _update_config_from_env():
     prefix = "UNILABOS_"
     for env_key, env_value in os.environ.items():
         if not env_key.startswith(prefix):
             continue
         try:
-            key_path = env_key[len(prefix):]  # Remove UNILAB_ prefix
+            key_path = env_key[len(prefix) :]  # Remove UNILAB_ prefix
             class_field = key_path.upper().split("_", 1)
             if len(class_field) != 2:
                 logger.warning(f"[ENV] 环境变量格式不正确：{env_key}")

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -988,6 +988,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
                 dis_vols = [float(dis_vols)]
             else:
                 dis_vols = [float(v) for v in dis_vols]
+
+        # 统一混合次数为标量，防止数组/列表与 int 比较时报错
+        if mix_times is not None and not isinstance(mix_times, (int, float)):
+            try:
+                mix_times = mix_times[0] if len(mix_times) > 0 else None
+            except Exception:
+                try:
+                    mix_times = next(iter(mix_times))
+                except Exception:
+                    pass
+        if mix_times is not None:
+            mix_times = int(mix_times)
             
             # 识别传输模式
             num_sources = len(sources)

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -5,6 +5,7 @@ import json
 import os
 import socket
 import time
+import uuid
 from typing import Any, List, Dict, Optional, Tuple, TypedDict, Union, Sequence, Iterator, Literal
 
 from pylabrobot.liquid_handling import (
@@ -856,7 +857,30 @@ class PRCXI9300Api:
 
     def _raw_request(self, payload: str) -> str:
         if self.debug:
-            return " "
+            # 调试/仿真模式下直接返回可解析的模拟 JSON，避免后续 json.loads 报错
+            try:
+                req = json.loads(payload)
+                method = req.get("MethodName")
+            except Exception:
+                method = None
+
+            data: Any = True
+            if method in {"AddSolution"}:
+                data = str(uuid.uuid4())
+            elif method in {"AddWorkTabletMatrix", "AddWorkTabletMatrix2"}:
+                data = {"Success": True, "Message": "debug mock"}
+            elif method in {"GetErrorCode"}:
+                data = ""
+            elif method in {"RemoveErrorCodet", "Reset", "Start", "LoadSolution", "Pause", "Resume", "Stop"}:
+                data = True
+            elif method in {"GetStepStateList", "GetStepStatus", "GetStepState"}:
+                data = []
+            elif method in {"GetLocation"}:
+                data = {"X": 0, "Y": 0, "Z": 0}
+            elif method in {"GetResetStatus"}:
+                data = False
+
+            return json.dumps({"Success": True, "Msg": "debug mock", "Data": data})
         with contextlib.closing(socket.socket()) as sock:
             sock.settimeout(self.timeout)
             sock.connect((self.host, self.port))

unilabos/devices/virtual/virtual_multiway_valve.py

@@ -7,7 +7,7 @@ class VirtualMultiwayValve:
     """
     虚拟九通阀门 - 0号位连接transfer pump，1-8号位连接其他设备 🔄
     """
-    def __init__(self, port: str = "VIRTUAL", positions: int = 8):
+    def __init__(self, port: str = "VIRTUAL", positions: int = 8, **kwargs):
         self.port = port
         self.max_positions = positions  # 1-8号位
         self.total_positions = positions + 1  # 0-8号位，共9个位置

unilabos/devices/workstation/workstation_base.py

@@ -147,7 +147,7 @@ class WorkstationBase(ABC):
 
     def __init__(
         self,
-        deck: Deck,
+        deck: Optional[Deck],
         *args,
         **kwargs,  # 必须有kwargs
     ):
@@ -349,5 +349,5 @@ class WorkstationBase(ABC):
 
 
 class ProtocolNode(WorkstationBase):
-    def __init__(self, deck: Optional[PLRResource], *args, **kwargs):
+    def __init__(self, protocol_type: List[str], deck: Optional[PLRResource], *args, **kwargs):
         super().__init__(deck, *args, **kwargs)

unilabos/registry/devices/bioyond_dispensing_station.yaml

@@ -174,35 +174,6 @@ bioyond_dispensing_station:
           title: query_resource_by_name参数
           type: object
         type: UniLabJsonCommand
-      auto-transfer_materials_to_reaction_station:
-        feedback: {}
-        goal: {}
-        goal_default:
-          target_device_id: null
-          transfer_groups: null
-        handles: {}
-        placeholder_keys: {}
-        result: {}
-        schema:
-          description: ''
-          properties:
-            feedback: {}
-            goal:
-              properties:
-                target_device_id:
-                  type: string
-                transfer_groups:
-                  type: array
-              required:
-              - target_device_id
-              - transfer_groups
-              type: object
-            result: {}
-          required:
-          - goal
-          title: transfer_materials_to_reaction_station参数
-          type: object
-        type: UniLabJsonCommand
       auto-workflow_sample_locations:
         feedback: {}
         goal: {}

unilabos/registry/devices/liquid_handler.yaml

@@ -9333,7 +9333,34 @@ liquid_handler.prcxi:
           touch_tip: false
           use_channels:
           - 0
-        handles: {}
+        handles:
+          input:
+          - data_key: liquid
+            data_source: handle
+            data_type: resource
+            handler_key: sources
+            label: sources
+          - data_key: liquid
+            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: sources
+          - data_key: liquid
+            data_source: executor
+            data_type: resource
+            handler_key: targets_out
+            label: targets
         placeholder_keys:
           sources: unilabos_resources
           targets: unilabos_resources

unilabos/registry/devices/work_station.yaml

@@ -6036,7 +6036,12 @@ workstation:
       properties:
         deck:
           type: string
+        protocol_type:
+          items:
+            type: string
+          type: array
       required:
+      - protocol_type
       - deck
       type: object
     data:

unilabos/registry/registry.py

@@ -222,7 +222,7 @@ class Registry:
         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)}")
+        logger.trace(f"[UniLab Registry] load resources? {resource_path.exists()}, total: {len(files)}")
         current_resource_number = len(self.resource_type_registry) + 1
         for i, file in enumerate(files):
             with open(file, encoding="utf-8", mode="r") as f:

unilabos/registry/resources/organic/container.yaml

@@ -2,7 +2,7 @@ container:
   category:
   - container
   class:
-    module: unilabos.resources.container:RegularContainer
+    module: unilabos.resources.container:get_regular_container
     type: pylabrobot
   description: regular organic container
   handles:

unilabos/resources/container.py

@@ -22,6 +22,13 @@ class RegularContainer(Container):
 
     def load_state(self, state: Dict[str, Any]):
         self.state = state
+
+
+def get_regular_container(name="container"):
+    r = RegularContainer(name=name)
+    r.category = "container"
+    return RegularContainer(name=name)
+
 #
 # class RegularContainer(object):
 #     # 第一个参数必须是id传入

unilabos/resources/graphio.py

@@ -42,13 +42,16 @@ 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）
-    for node in nodes:
+    outer_host_node_id = None
+    for idx, node in enumerate(nodes):
         if node.get("label") is not None:
             node_id = node.pop("label")
             node["id"] = node["name"] = node_id
+        if node["id"] == "host_node":
+            outer_host_node_id = idx
         if not isinstance(node.get("config"), dict):
             node["config"] = {}
         if not node.get("type"):
@@ -58,25 +61,26 @@ def canonicalize_nodes_data(
             node["name"] = node.get("id")
             print_status(f"Warning: Node {node.get('id', 'unknown')} missing 'name', defaulting to {node['name']}", "warning")
         if not isinstance(node.get("position"), dict):
-            node["position"] = {"position": {}}
+            node["pose"] = {"position": {}}
             x = node.pop("x", None)
             if x is not None:
-                node["position"]["position"]["x"] = x
+                node["pose"]["position"]["x"] = x
             y = node.pop("y", None)
             if y is not None:
-                node["position"]["position"]["y"] = y
+                node["pose"]["position"]["y"] = y
             z = node.pop("z", None)
             if z is not None:
-                node["position"]["position"]["z"] = z
+                node["pose"]["position"]["z"] = z
         if "sample_id" in node:
             sample_id = node.pop("sample_id")
             if sample_id:
                 logger.error(f"{node}的sample_id参数已弃用，sample_id: {sample_id}")
         for k in list(node.keys()):
-            if k not in ["id", "uuid", "name", "description", "schema", "model", "icon", "parent_uuid", "parent", "type", "class", "position", "config", "data", "children"]:
+            if k not in ["id", "uuid", "name", "description", "schema", "model", "icon", "parent_uuid", "parent", "type", "class", "position", "config", "data", "children", "pose"]:
                 v = node.pop(k)
                 node["config"][k] = v
-
+    if outer_host_node_id is not None:
+        nodes.pop(outer_host_node_id)
     # 第二步：处理parent_relation
     id2idx = {node["id"]: idx for idx, node in enumerate(nodes)}
     for parent, children in parent_relation.items():
@@ -93,7 +97,7 @@ def canonicalize_nodes_data(
 
     for node in nodes:
         try:
-            print_status(f"DeviceId: {node['id']}, Class: {node['class']}", "info")
+            # print_status(f"DeviceId: {node['id']}, Class: {node['class']}", "info")
             # 使用标准化方法
             resource_instance = ResourceDictInstance.get_resource_instance_from_dict(node)
             known_nodes[node["id"]] = resource_instance
@@ -582,11 +586,15 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None, w
             "tip_rack": "tip_rack",
             "warehouse": "warehouse",
             "container": "container",
+            "tube": "tube",
+            "bottle_carrier": "bottle_carrier",
+            "plate_adapter": "plate_adapter",
         }
         if source in replace_info:
             return replace_info[source]
         else:
-            logger.warning(f"转换pylabrobot的时候，出现未知类型: {source}")
+            if source is not None:
+                logger.warning(f"转换pylabrobot的时候，出现未知类型: {source}")
             return source
 
     def resource_plr_to_ulab_inner(d: dict, all_states: dict, child=True) -> dict:

unilabos/ros/device_node_wrapper.py

@@ -5,6 +5,7 @@ from unilabos.ros.msgs.message_converter import (
     get_action_type,
 )
 from unilabos.ros.nodes.base_device_node import init_wrapper, ROS2DeviceNode
+from unilabos.ros.nodes.resource_tracker import ResourceDictInstance
 
 # 定义泛型类型变量
 T = TypeVar("T")
@@ -18,12 +19,11 @@ class ROS2DeviceNodeWrapper(ROS2DeviceNode):
 
 def ros2_device_node(
     cls: Type[T],
-    device_config: Optional[Dict[str, Any]] = None,
+    device_config: Optional[ResourceDictInstance] = None,
     status_types: Optional[Dict[str, Any]] = None,
     action_value_mappings: Optional[Dict[str, Any]] = None,
     hardware_interface: Optional[Dict[str, Any]] = None,
     print_publish: bool = False,
-    children: Optional[Dict[str, Any]] = None,
 ) -> Type[ROS2DeviceNodeWrapper]:
     """Create a ROS2 Node class for a device class with properties and actions.
 
@@ -45,7 +45,7 @@ def ros2_device_node(
     if status_types is None:
         status_types = {}
     if device_config is None:
-        device_config = {}
+        raise ValueError("device_config cannot be None")
     if action_value_mappings is None:
         action_value_mappings = {}
     if hardware_interface is None:
@@ -82,7 +82,6 @@ def ros2_device_node(
                 action_value_mappings=action_value_mappings,
                 hardware_interface=hardware_interface,
                 print_publish=print_publish,
-                children=children,
                 *args,
                 **kwargs,
             ),

unilabos/ros/initialize_device.py

@@ -4,13 +4,14 @@ from typing import Optional
 from unilabos.registry.registry import lab_registry
 from unilabos.ros.device_node_wrapper import ros2_device_node
 from unilabos.ros.nodes.base_device_node import ROS2DeviceNode, DeviceInitError
+from unilabos.ros.nodes.resource_tracker import ResourceDictInstance
 from unilabos.utils import logger
 from unilabos.utils.exception import DeviceClassInvalid
 from unilabos.utils.import_manager import default_manager
 
 
 
-def initialize_device_from_dict(device_id, device_config) -> Optional[ROS2DeviceNode]:
+def initialize_device_from_dict(device_id, device_config: ResourceDictInstance) -> Optional[ROS2DeviceNode]:
     """Initializes a device based on its configuration.
 
     This function dynamically imports the appropriate device class and creates an instance of it using the provided device configuration.
@@ -24,15 +25,14 @@ def initialize_device_from_dict(device_id, device_config) -> Optional[ROS2Device
         None
     """
     d = None
-    original_device_config = copy.deepcopy(device_config)
-    device_class_config = device_config["class"]
-    uid = device_config["uuid"]
+    device_class_config = device_config.res_content.klass
+    uid = device_config.res_content.uuid
     if isinstance(device_class_config, str):  # 如果是字符串，则直接去lab_registry中查找，获取class
         if len(device_class_config) == 0:
             raise DeviceClassInvalid(f"Device [{device_id}] class cannot be an empty string. {device_config}")
         if device_class_config not in lab_registry.device_type_registry:
             raise DeviceClassInvalid(f"Device [{device_id}] class {device_class_config} not found. {device_config}")
-        device_class_config = device_config["class"] = lab_registry.device_type_registry[device_class_config]["class"]
+        device_class_config = lab_registry.device_type_registry[device_class_config]["class"]
     elif isinstance(device_class_config, dict):
         raise DeviceClassInvalid(f"Device [{device_id}] class config should be type 'str' but 'dict' got. {device_config}")
     if isinstance(device_class_config, dict):
@@ -41,17 +41,16 @@ def initialize_device_from_dict(device_id, device_config) -> Optional[ROS2Device
         DEVICE = ros2_device_node(
             DEVICE,
             status_types=device_class_config.get("status_types", {}),
-            device_config=original_device_config,
+            device_config=device_config,
             action_value_mappings=device_class_config.get("action_value_mappings", {}),
             hardware_interface=device_class_config.get(
                 "hardware_interface",
                 {"name": "hardware_interface", "write": "send_command", "read": "read_data", "extra_info": []},
-            ),
-            children=device_config.get("children", {})
+            )
         )
         try:
             d = DEVICE(
-                device_id=device_id, device_uuid=uid, driver_is_ros=device_class_config["type"] == "ros2", driver_params=device_config.get("config", {})
+                device_id=device_id, device_uuid=uid, driver_is_ros=device_class_config["type"] == "ros2", driver_params=device_config.res_content.config
             )
         except DeviceInitError as ex:
             return d

unilabos/ros/main_slave_run.py

@@ -192,7 +192,7 @@ def slave(
     for device_config in devices_config.root_nodes:
         device_id = device_config.res_content.id
         if device_config.res_content.type == "device":
-            d = initialize_device_from_dict(device_id, device_config.get_nested_dict())
+            d = initialize_device_from_dict(device_id, device_config)
             if d is not None:
                 devices_instances[device_id] = d
                 logger.info(f"Device {device_id} initialized.")

unilabos/ros/nodes/base_device_node.py

@@ -48,7 +48,7 @@ from unilabos_msgs.msg import Resource  # type: ignore
 from unilabos.ros.nodes.resource_tracker import (
     DeviceNodeResourceTracker,
     ResourceTreeSet,
-    ResourceTreeInstance,
+    ResourceTreeInstance, ResourceDictInstance,
 )
 from unilabos.ros.x.rclpyx import get_event_loop
 from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator
@@ -133,12 +133,11 @@ def init_wrapper(
     device_id: str,
     device_uuid: str,
     driver_class: type[T],
-    device_config: Dict[str, Any],
+    device_config: ResourceTreeInstance,
     status_types: Dict[str, Any],
     action_value_mappings: Dict[str, Any],
     hardware_interface: Dict[str, Any],
     print_publish: bool,
-    children: Optional[list] = None,
     driver_params: Optional[Dict[str, Any]] = None,
     driver_is_ros: bool = False,
     *args,
@@ -147,8 +146,6 @@ def init_wrapper(
     """初始化设备节点的包装函数，和ROS2DeviceNode初始化保持一致"""
     if driver_params is None:
         driver_params = kwargs.copy()
-    if children is None:
-        children = []
     kwargs["device_id"] = device_id
     kwargs["device_uuid"] = device_uuid
     kwargs["driver_class"] = driver_class
@@ -157,7 +154,6 @@ def init_wrapper(
     kwargs["status_types"] = status_types
     kwargs["action_value_mappings"] = action_value_mappings
     kwargs["hardware_interface"] = hardware_interface
-    kwargs["children"] = children
     kwargs["print_publish"] = print_publish
     kwargs["driver_is_ros"] = driver_is_ros
     super(type(self), self).__init__(*args, **kwargs)
@@ -586,7 +582,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
         except Exception as e:
             self.lab_logger().error(f"更新资源uuid失败: {e}")
             self.lab_logger().error(traceback.format_exc())
-        self.lab_logger().debug(f"资源更新结果: {response}")
+        self.lab_logger().trace(f"资源更新结果: {response}")
 
     async def get_resource(self, resources_uuid: List[str], with_children: bool = True) -> ResourceTreeSet:
         """
@@ -1168,7 +1164,6 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                             execution_error = traceback.format_exc()
                             break
 
-            ##### self.lab_logger().info(f"准备执行: {action_kwargs}, 函数: {ACTION.__name__}")
             time_start = time.time()
             time_overall = 100
             future = None
@@ -1176,35 +1171,36 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                 # 将阻塞操作放入线程池执行
                 if asyncio.iscoroutinefunction(ACTION):
                     try:
-                        ##### self.lab_logger().info(f"异步执行动作 {ACTION}")
-                        future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs)
-
-                        def _handle_future_exception(fut):
+                        self.lab_logger().trace(f"异步执行动作 {ACTION}")
+                        def _handle_future_exception(fut: Future):
                             nonlocal execution_error, execution_success, action_return_value
                             try:
                                 action_return_value = fut.result()
+                                if isinstance(action_return_value, BaseException):
+                                    raise action_return_value
                                 execution_success = True
-                            except Exception as e:
+                            except Exception as _:
                                 execution_error = traceback.format_exc()
                                 error(
                                     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)
                     except Exception as e:
                         execution_error = traceback.format_exc()
                         execution_success = False
                         self.lab_logger().error(f"创建异步任务失败: {traceback.format_exc()}")
                 else:
-                    #####    self.lab_logger().info(f"同步执行动作 {ACTION}")
+                    self.lab_logger().trace(f"同步执行动作 {ACTION}")
                     future = self._executor.submit(ACTION, **action_kwargs)
 
-                    def _handle_future_exception(fut):
+                    def _handle_future_exception(fut: Future):
                         nonlocal execution_error, execution_success, action_return_value
                         try:
                             action_return_value = fut.result()
                             execution_success = True
-                        except Exception as e:
+                        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：{action_kwargs}"
@@ -1309,7 +1305,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         get_result_info_str(execution_error, execution_success, action_return_value),
                     )
 
-            ##### self.lab_logger().info(f"动作 {action_name} 完成并返回结果")
+            self.lab_logger().trace(f"动作 {action_name} 完成并返回结果")
             return result_msg
 
         return execute_callback
@@ -1544,17 +1540,29 @@ class ROS2DeviceNode:
     这个类封装了设备类实例和ROS2节点的功能，提供ROS2接口。
     它不继承设备类，而是通过代理模式访问设备类的属性和方法。
     """
+    @staticmethod
+    async def safe_task_wrapper(trace_callback, func, **kwargs):
+        try:
+            if callable(trace_callback):
+                trace_callback(await func(**kwargs))
+            return await func(**kwargs)
+        except Exception as e:
+            if callable(trace_callback):
+                trace_callback(e)
+            return e
 
     @classmethod
-    def run_async_func(cls, func, trace_error=True, **kwargs) -> Task:
-        def _handle_future_exception(fut):
+    def run_async_func(cls, func, trace_error=True, inner_trace_callback=None, **kwargs) -> Task:
+        def _handle_future_exception(fut: Future):
             try:
-                fut.result()
+                ret = fut.result()
+                if isinstance(ret, BaseException):
+                    raise ret
             except Exception as e:
-                error(f"异步任务 {func.__name__} 报错了")
+                error(f"异步任务 {func.__name__} 获取结果失败")
                 error(traceback.format_exc())
 
-        future = rclpy.get_global_executor().create_task(func(**kwargs))
+        future = rclpy.get_global_executor().create_task(ROS2DeviceNode.safe_task_wrapper(inner_trace_callback, func, **kwargs))
         if trace_error:
             future.add_done_callback(_handle_future_exception)
         return future
@@ -1582,12 +1590,11 @@ class ROS2DeviceNode:
         device_id: str,
         device_uuid: str,
         driver_class: Type[T],
-        device_config: Dict[str, Any],
+        device_config: ResourceDictInstance,
         driver_params: Dict[str, Any],
         status_types: Dict[str, Any],
         action_value_mappings: Dict[str, Any],
         hardware_interface: Dict[str, Any],
-        children: Dict[str, Any],
         print_publish: bool = True,
         driver_is_ros: bool = False,
     ):
@@ -1598,7 +1605,7 @@ class ROS2DeviceNode:
             device_id: 设备标识符
             device_uuid: 设备uuid
             driver_class: 设备类
-            device_config: 原始初始化的json
+            device_config: 原始初始化的ResourceDictInstance
             driver_params: driver初始化的参数
             status_types: 状态类型映射
             action_value_mappings: 动作值映射
@@ -1612,6 +1619,7 @@ class ROS2DeviceNode:
         self._has_async_context = hasattr(driver_class, "__aenter__") and hasattr(driver_class, "__aexit__")
         self._driver_class = driver_class
         self.device_config = device_config
+        children: List[ResourceDictInstance] = device_config.children
         self.driver_is_ros = driver_is_ros
         self.driver_is_workstation = False
         self.resource_tracker = DeviceNodeResourceTracker()

unilabos/ros/nodes/presets/host_node.py

@@ -289,6 +289,12 @@ class HostNode(BaseROS2DeviceNode):
         self.lab_logger().info("[Host Node] Host node initialized.")
         HostNode._ready_event.set()
 
+        # 发送host_node ready信号到所有桥接器
+        for bridge in self.bridges:
+            if hasattr(bridge, "publish_host_ready"):
+                bridge.publish_host_ready()
+                self.lab_logger().debug(f"Host ready signal sent via {bridge.__class__.__name__}")
+
     def _send_re_register(self, sclient):
         sclient.wait_for_service()
         request = SerialCommand.Request()
@@ -532,7 +538,7 @@ class HostNode(BaseROS2DeviceNode):
         self.lab_logger().info(f"[Host Node] Initializing device: {device_id}")
 
         try:
-            d = initialize_device_from_dict(device_id, device_config.get_nested_dict())
+            d = initialize_device_from_dict(device_id, device_config)
         except DeviceClassInvalid as e:
             self.lab_logger().error(f"[Host Node] Device class invalid: {e}")
             d = None
@@ -712,7 +718,7 @@ class HostNode(BaseROS2DeviceNode):
             feedback_callback=lambda feedback_msg: self.feedback_callback(item, action_id, feedback_msg),
             goal_uuid=goal_uuid_obj,
         )
-        future.add_done_callback(lambda future: self.goal_response_callback(item, action_id, future))
+        future.add_done_callback(lambda f: self.goal_response_callback(item, action_id, f))
 
     def goal_response_callback(self, item: "QueueItem", action_id: str, future) -> None:
         """目标响应回调"""
@@ -723,9 +729,11 @@ class HostNode(BaseROS2DeviceNode):
 
         self.lab_logger().info(f"[Host Node] Goal {action_id} ({item.job_id}) accepted")
         self._goals[item.job_id] = goal_handle
-        goal_handle.get_result_async().add_done_callback(
-            lambda future: self.get_result_callback(item, action_id, future)
+        goal_future = goal_handle.get_result_async()
+        goal_future.add_done_callback(
+            lambda f: self.get_result_callback(item, action_id, f)
         )
+        goal_future.result()
 
     def feedback_callback(self, item: "QueueItem", action_id: str, feedback_msg) -> None:
         """反馈回调"""
@@ -794,6 +802,7 @@ class HostNode(BaseROS2DeviceNode):
             # 存储结果供 HTTP API 查询
             try:
                 from unilabos.app.web.controller import store_job_result
+
                 if goal_status == GoalStatus.STATUS_CANCELED:
                     store_job_result(job_id, status, return_info, {})
                 else:

unilabos/ros/nodes/presets/workstation.py

@@ -24,7 +24,7 @@ from unilabos.ros.msgs.message_converter import (
     convert_from_ros_msg_with_mapping,
 )
 from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode, DeviceNodeResourceTracker, ROS2DeviceNode
-from unilabos.ros.nodes.resource_tracker import ResourceTreeSet
+from unilabos.ros.nodes.resource_tracker import ResourceTreeSet, ResourceDictInstance
 from unilabos.utils.type_check import get_result_info_str
 
 if TYPE_CHECKING:
@@ -47,7 +47,7 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
     def __init__(
         self,
         protocol_type: List[str],
-        children: Dict[str, Any],
+        children: List[ResourceDictInstance],
         *,
         driver_instance: "WorkstationBase",
         device_id: str,
@@ -81,10 +81,11 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
         # 初始化子设备
         self.communication_node_id_to_instance = {}
 
-        for device_id, device_config in self.children.items():
-            if device_config.get("type", "device") != "device":
+        for device_config in self.children:
+            device_id = device_config.res_content.id
+            if device_config.res_content.type != "device":
                 self.lab_logger().debug(
-                    f"[Protocol Node] Skipping type {device_config['type']} {device_id} already existed, skipping."
+                    f"[Protocol Node] Skipping type {device_config.res_content.type} {device_id} already existed, skipping."
                 )
                 continue
             try:
@@ -101,8 +102,9 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
                 self.communication_node_id_to_instance[device_id] = d
                 continue
 
-        for device_id, device_config in self.children.items():
-            if device_config.get("type", "device") != "device":
+        for device_config in self.children:
+            device_id = device_config.res_content.id
+            if device_config.res_content.type != "device":
                 continue
             # 设置硬件接口代理
             if device_id not in self.sub_devices:

unilabos/ros/nodes/resource_tracker.py

@@ -1,9 +1,11 @@
+import inspect
 import traceback
 import uuid
 from pydantic import BaseModel, field_serializer, field_validator
 from pydantic import Field
 from typing import List, Tuple, Any, Dict, Literal, Optional, cast, TYPE_CHECKING, Union
 
+from unilabos.resources.plr_additional_res_reg import register
 from unilabos.utils.log import logger
 
 if TYPE_CHECKING:
@@ -62,11 +64,10 @@ class ResourceDict(BaseModel):
     parent: Optional["ResourceDict"] = Field(description="Parent resource object", default=None, exclude=True)
     type: Union[Literal["device"], str] = Field(description="Resource type")
     klass: str = Field(alias="class", description="Resource class name")
-    position: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
     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")
-    extra: Dict[str, Any] = Field(description="Extra data")
+    data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
+    extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
 
     @field_serializer("parent_uuid")
     def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
@@ -146,15 +147,16 @@ class ResourceDictInstance(object):
         if not content.get("extra"):  # MagicCode
             content["extra"] = {}
         if "pose" not in content:
-            content["pose"] = content.get("position", {})
+            content["pose"] = content.pop("position", {})
         return ResourceDictInstance(ResourceDict.model_validate(content))
 
-    def get_nested_dict(self) -> Dict[str, Any]:
+    def get_plr_nested_dict(self) -> Dict[str, Any]:
         """获取资源实例的嵌套字典表示"""
         res_dict = self.res_content.model_dump(by_alias=True)
-        res_dict["children"] = {child.res_content.id: child.get_nested_dict() for child in self.children}
+        res_dict["children"] = {child.res_content.id: child.get_plr_nested_dict() for child in self.children}
         res_dict["parent"] = self.res_content.parent_instance_name
-        res_dict["position"] = self.res_content.position.position.model_dump()
+        res_dict["position"] = self.res_content.pose.position.model_dump()
+        del res_dict["pose"]
         return res_dict
 
 
@@ -429,9 +431,9 @@ class ResourceTreeSet(object):
         Returns:
             List[PLRResource]: PLR 资源实例列表
         """
+        register()
         from pylabrobot.resources import Resource as PLRResource
         from pylabrobot.utils.object_parsing import find_subclass
-        import inspect
 
         # 类型映射
         TYPE_MAP = {"plate": "Plate", "well": "Well", "deck": "Deck", "container": "RegularContainer"}
@@ -459,9 +461,9 @@ class ResourceTreeSet(object):
                 "size_y": res.config.get("size_y", 0),
                 "size_z": res.config.get("size_z", 0),
                 "location": {
-                    "x": res.position.position.x,
-                    "y": res.position.position.y,
-                    "z": res.position.position.z,
+                    "x": res.pose.position.x,
+                    "y": res.pose.position.y,
+                    "z": res.pose.position.z,
                     "type": "Coordinate",
                 },
                 "rotation": {"x": 0, "y": 0, "z": 0, "type": "Rotation"},

unilabos/ros/utils/driver_creator.py

@@ -9,10 +9,11 @@ import asyncio
 import inspect
 import traceback
 from abc import abstractmethod
-from typing import Type, Any, Dict, Optional, TypeVar, Generic
+from typing import Type, Any, Dict, Optional, TypeVar, Generic, List
 
 from unilabos.resources.graphio import nested_dict_to_list, resource_ulab_to_plr
-from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker
+from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker, ResourceTreeSet, ResourceDictInstance, \
+    ResourceTreeInstance
 from unilabos.utils import logger, import_manager
 from unilabos.utils.cls_creator import create_instance_from_config
 
@@ -33,7 +34,7 @@ class DeviceClassCreator(Generic[T]):
     这个类提供了从任意类创建实例的通用方法。
     """
 
-    def __init__(self, cls: Type[T], children: Dict[str, Any], resource_tracker: DeviceNodeResourceTracker):
+    def __init__(self, cls: Type[T], children: List[ResourceDictInstance], resource_tracker: DeviceNodeResourceTracker):
         """
         初始化设备类创建器
 
@@ -50,9 +51,9 @@ class DeviceClassCreator(Generic[T]):
         附加资源到设备类实例
         """
         if self.device_instance is not None:
-            for c in self.children.values():
-                if c["type"] != "device":
-                    self.resource_tracker.add_resource(c)
+            for c in self.children:
+                if c.res_content.type != "device":
+                    self.resource_tracker.add_resource(c.get_plr_nested_dict())
 
     def create_instance(self, data: Dict[str, Any]) -> T:
         """
@@ -94,7 +95,7 @@ class PyLabRobotCreator(DeviceClassCreator[T]):
     这个类提供了针对PyLabRobot设备类的实例创建方法，特别处理deserialize方法。
     """
 
-    def __init__(self, cls: Type[T], children: Dict[str, Any], resource_tracker: DeviceNodeResourceTracker):
+    def __init__(self, cls: Type[T], children: List[ResourceDictInstance], resource_tracker: DeviceNodeResourceTracker):
         """
         初始化PyLabRobot设备类创建器
 
@@ -111,12 +112,12 @@ class PyLabRobotCreator(DeviceClassCreator[T]):
     def attach_resource(self):
         pass  # 只能增加实例化物料，原来默认物料仅为字典查询
 
-    def _process_resource_mapping(self, resource, source_type):
-        if source_type == dict:
-            from pylabrobot.resources.resource import Resource
-
-            return nested_dict_to_list(resource), Resource
-        return resource, source_type
+    # def _process_resource_mapping(self, resource, source_type):
+    #     if source_type == dict:
+    #         from pylabrobot.resources.resource import Resource
+    #
+    #         return nested_dict_to_list(resource), Resource
+    #     return resource, source_type
 
     def _process_resource_references(
         self, data: Any, to_dict=False, states=None, prefix_path="", name_to_uuid=None
@@ -142,15 +143,21 @@ class PyLabRobotCreator(DeviceClassCreator[T]):
         if isinstance(data, dict):
             if "_resource_child_name" in data:
                 child_name = data["_resource_child_name"]
-                if child_name in self.children:
-                    resource = self.children[child_name]
+                resource: Optional[ResourceDictInstance] = None
+                for child in self.children:
+                    if child.res_content.name == child_name:
+                        resource = child
+                if resource is not None:
                     if "_resource_type" in data:
                         type_path = data["_resource_type"]
                         try:
-                            target_type = import_manager.get_class(type_path)
-                            contain_model = not issubclass(target_type, Deck)
-                            resource, target_type = self._process_resource_mapping(resource, target_type)
-                            resource_instance: Resource = resource_ulab_to_plr(resource, contain_model)  # 带state
+                            # target_type = import_manager.get_class(type_path)
+                            # contain_model = not issubclass(target_type, Deck)
+                            # resource, target_type = self._process_resource_mapping(resource, target_type)
+                            res_tree = ResourceTreeInstance(resource)
+                            res_tree_set = ResourceTreeSet([res_tree])
+                            resource_instance: Resource = res_tree_set.to_plr_resources()[0]
+                            # resource_instance: Resource = resource_ulab_to_plr(resource, contain_model)  # 带state
                             states[prefix_path] = resource_instance.serialize_all_state()
                             # 使用 prefix_path 作为 key 存储资源状态
                             if to_dict:
@@ -202,12 +209,12 @@ class PyLabRobotCreator(DeviceClassCreator[T]):
         stack = None
 
         # 递归遍历 children 构建 name_to_uuid 映射
-        def collect_name_to_uuid(children_dict: Dict[str, Any], result: Dict[str, str]):
+        def collect_name_to_uuid(children_list: List[ResourceDictInstance], result: Dict[str, str]):
             """递归遍历嵌套的 children 字典，收集 name 到 uuid 的映射"""
-            for child in children_dict.values():
-                if isinstance(child, dict):
-                    result[child["name"]] = child["uuid"]
-                    collect_name_to_uuid(child["children"], result)
+            for child in children_list:
+                if isinstance(child, ResourceDictInstance):
+                    result[child.res_content.name] = child.res_content.uuid
+                    collect_name_to_uuid(child.children, result)
 
         name_to_uuid = {}
         collect_name_to_uuid(self.children, name_to_uuid)
@@ -313,7 +320,7 @@ class WorkstationNodeCreator(DeviceClassCreator[T]):
     这个类提供了针对WorkstationNode设备类的实例创建方法，处理children参数。
     """
 
-    def __init__(self, cls: Type[T], children: Dict[str, Any], resource_tracker: DeviceNodeResourceTracker):
+    def __init__(self, cls: Type[T], children: List[ResourceDictInstance], resource_tracker: DeviceNodeResourceTracker):
         """
         初始化WorkstationNode设备类创建器
 
@@ -336,9 +343,9 @@ class WorkstationNodeCreator(DeviceClassCreator[T]):
         try:
             # 创建实例，额外补充一个给protocol node的字段，后面考虑取消
             data["children"] = self.children
-            for material_id, child in self.children.items():
-                if child["type"] != "device":
-                    self.resource_tracker.add_resource(self.children[material_id])
+            for child in self.children:
+                if child.res_content.type != "device":
+                    self.resource_tracker.add_resource(child.get_plr_nested_dict())
             deck_dict = data.get("deck")
             if deck_dict:
                 from pylabrobot.resources import Deck, Resource

unilabos/test/workflow/merge_workflow.py

@@ -1,94 +0,0 @@
-import json
-import sys
-from datetime import datetime
-from pathlib import Path
-
-ROOT_DIR = Path(__file__).resolve().parents[2]
-if str(ROOT_DIR) not in sys.path:
-    sys.path.insert(0, str(ROOT_DIR))
-
-import pytest
-
-from scripts.workflow import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
-
-
-ROOT_DIR = Path(__file__).resolve().parents[2]
-if str(ROOT_DIR) not in sys.path:
-    sys.path.insert(0, str(ROOT_DIR))
-
-
-def _normalize_steps(data):
-    normalized = []
-    for step in data:
-        action = step.get("action") or step.get("operation")
-        if not action:
-            continue
-        raw_params = step.get("parameters") or step.get("action_args") or {}
-        params = dict(raw_params)
-
-        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"]
-
-        description = step.get("description") or step.get("purpose")
-        step_dict = {"action": action, "parameters": params}
-        if description:
-            step_dict["description"] = description
-        normalized.append(step_dict)
-    return normalized
-
-
-def _normalize_labware(data):
-    labware = {}
-    for item in data:
-        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)
-        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
-
-
-@pytest.mark.parametrize("protocol_name", [
-    "example_bio",
-    # "bioyond_materials_liquidhandling_1",
-    "example_prcxi",
-])
-def test_build_protocol_graph(protocol_name):
-    data_path = Path(__file__).with_name(f"{protocol_name}.json")
-    with data_path.open("r", encoding="utf-8") as fp:
-        d = json.load(fp)
-
-    if "workflow" in d and "reagent" in d:
-        protocol_steps = d["workflow"]
-        labware_info = d["reagent"]
-    elif "steps_info" in d and "labware_info" in d:
-        protocol_steps = _normalize_steps(d["steps_info"])
-        labware_info = _normalize_labware(d["labware_info"])
-    else:
-        raise ValueError("Unsupported protocol format")
-
-    graph = build_protocol_graph(
-        labware_info=labware_info,
-        protocol_steps=protocol_steps,
-        workstation_name="PRCXi",
-    )
-    timestamp = datetime.now().strftime("%Y%m%d_%H%M")
-    output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
-    draw_protocol_graph_with_ports(graph, str(output_path))
-    print(graph)

unilabos/utils/log.py

@@ -124,11 +124,14 @@ class ColoredFormatter(logging.Formatter):
     def _format_basic(self, record):
         """基本格式化，不包含颜色"""
         datetime_str = datetime.fromtimestamp(record.created).strftime("%y-%m-%d [%H:%M:%S,%f")[:-3] + "]"
-        filename = os.path.basename(record.filename).rsplit(".", 1)[0]  # 提取文件名（不含路径和扩展名）
+        filename = record.filename.replace(".py", "").split("\\")[-1]  # 提取文件名（不含路径和扩展名）
+        if "/" in filename:
+            filename = filename.split("/")[-1]
         module_path = f"{record.name}.{filename}"
         func_line = f"{record.funcName}:{record.lineno}"
+        right_info = f" [{func_line}] [{module_path}]"
 
-        formatted_message = f"{datetime_str} [{record.levelname}] [{module_path}] [{func_line}]: {record.getMessage()}"
+        formatted_message = f"{datetime_str} [{record.levelname}] {record.getMessage()}{right_info}"
 
         if record.exc_info:
             exc_text = self.formatException(record.exc_info)
@@ -150,7 +153,7 @@ class ColoredFormatter(logging.Formatter):
 
 
 # 配置日志处理器
-def configure_logger(loglevel=None):
+def configure_logger(loglevel=None, working_dir=None):
     """配置日志记录器
 
     Args:
@@ -159,8 +162,9 @@ def configure_logger(loglevel=None):
     """
     # 获取根日志记录器
     root_logger = logging.getLogger()
-
+    root_logger.setLevel(TRACE_LEVEL)
     # 设置日志级别
+    numeric_level = logging.DEBUG
     if loglevel is not None:
         if isinstance(loglevel, str):
             # 将字符串转换为logging级别
@@ -170,12 +174,8 @@ def configure_logger(loglevel=None):
                 numeric_level = getattr(logging, loglevel.upper(), None)
                 if not isinstance(numeric_level, int):
                     print(f"警告: 无效的日志级别 '{loglevel}'，使用默认级别 DEBUG")
-                    numeric_level = logging.DEBUG
         else:
             numeric_level = loglevel
-        root_logger.setLevel(numeric_level)
-    else:
-        root_logger.setLevel(logging.DEBUG)  # 默认级别
 
     # 移除已存在的处理器
     for handler in root_logger.handlers[:]:
@@ -183,7 +183,7 @@ def configure_logger(loglevel=None):
 
     # 创建控制台处理器
     console_handler = logging.StreamHandler()
-    console_handler.setLevel(root_logger.level)  # 使用与根记录器相同的级别
+    console_handler.setLevel(numeric_level)  # 使用与根记录器相同的级别
 
     # 使用自定义的颜色格式化器
     color_formatter = ColoredFormatter()
@@ -191,9 +191,30 @@ def configure_logger(loglevel=None):
 
     # 添加处理器到根日志记录器
     root_logger.addHandler(console_handler)
+
+    # 如果指定了工作目录，添加文件处理器
+    if working_dir is not None:
+        logs_dir = os.path.join(working_dir, "logs")
+        os.makedirs(logs_dir, exist_ok=True)
+
+        # 生成日志文件名：日期 时间.log
+        log_filename = datetime.now().strftime("%Y-%m-%d %H-%M-%S") + ".log"
+        log_filepath = os.path.join(logs_dir, log_filename)
+
+        # 创建文件处理器
+        file_handler = logging.FileHandler(log_filepath, encoding="utf-8")
+        file_handler.setLevel(TRACE_LEVEL)
+
+        # 使用不带颜色的格式化器
+        file_formatter = ColoredFormatter(use_colors=False)
+        file_handler.setFormatter(file_formatter)
+
+        root_logger.addHandler(file_handler)
+
     logging.getLogger("asyncio").setLevel(logging.INFO)
     logging.getLogger("urllib3").setLevel(logging.INFO)
 
+
 # 配置日志系统
 configure_logger()
 

unilabos/workflow/common.py

@@ -0,0 +1,547 @@
+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]
+
+# ---------------- 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: List[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
+        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 = {}
+
+    protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
+    # 有机化学&移液站协议图构建
+    WORKSTATION_ID = workstation_name
+
+    # 为所有labware创建资源节点
+    res_index = 0
+    for labware_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 "Rack" in str(labware_id) or "Tip" in str(labware_id):
+            lab_node_type = "Labware"
+            description = f"Prepare Labware: {labware_id}"
+            liquid_type = []
+            liquid_volume = []
+        elif item.get("type") == "hardware" or "reactor" in str(labware_id).lower():
+            if "reactor" not in str(labware_id).lower():
+                continue
+            lab_node_type = "Sample"
+            description = f"Prepare Reactor: {labware_id}"
+            liquid_type = []
+            liquid_volume = []
+        else:
+            lab_node_type = "Reagent"
+            description = f"Add Reagent to Flask: {labware_id}"
+            liquid_type = [labware_id]
+            liquid_volume = [1e5]
+
+        res_index += 1
+        G.add_node(
+            node_id,
+            template_name="create_resource",
+            resource_name="host_node",
+            name=f"Res {res_index}",
+            description=description,
+            lab_node_type=lab_node_type,
+            footer="create_resource-host_node",
+            param={
+                "res_id": labware_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": "",
+            },
+        )
+        resource_last_writer[labware_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("param", {})
+        input_resources_possible_names = [
+            "vessel",
+            "to_vessel",
+            "from_vessel",
+            "reagent",
+            "solvent",
+            "compound",
+            "sources",
+            "targets",
+        ]
+
+        for target_port in input_resources_possible_names:
+            resource_name = params.get(target_port)
+            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 = {
+            "vessel_out": params.get("vessel"),
+            "from_vessel_out": params.get("from_vessel"),
+            "to_vessel_out": params.get("to_vessel"),
+            "filtrate_out": 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: 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

@@ -0,0 +1,356 @@
+"""
+JSON 工作流转换模块
+
+提供从多种 JSON 格式转换为统一工作流格式的功能。
+支持的格式：
+1. workflow/reagent 格式
+2. steps_info/labware_info 格式
+"""
+
+import json
+from os import PathLike
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Set, Tuple, Union
+
+from unilabos.workflow.common import WorkflowGraph, build_protocol_graph
+from unilabos.registry.registry import lab_registry
+
+
+def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]:
+    """
+    从 registry 获取指定设备和动作的 handles 配置
+
+    Args:
+        resource_name: 设备资源名称，如 "liquid_handler.prcxi"
+        template_name: 动作模板名称，如 "transfer_liquid"
+
+    Returns:
+        包含 source 和 target handler_keys 的字典:
+        {"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]}
+    """
+    result = {"source": [], "target": []}
+
+    device_info = lab_registry.device_type_registry.get(resource_name, {})
+    if not device_info:
+        return result
+
+    action_mappings = device_info.get("class", {}).get("action_value_mappings", {})
+    action_config = action_mappings.get(template_name, {})
+    handles = action_config.get("handles", {})
+
+    if isinstance(handles, dict):
+        # 处理 input handles (作为 target)
+        for handle in handles.get("input", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["source"].append(handler_key)
+        # 处理 output handles (作为 source)
+        for handle in handles.get("output", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["target"].append(handler_key)
+
+    return result
+
+
+def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]:
+    """
+    校验工作流图中所有边的句柄配置是否正确
+
+    Args:
+        graph: 工作流图对象
+
+    Returns:
+        (is_valid, errors): 是否有效，错误信息列表
+    """
+    errors = []
+    nodes = graph.nodes
+
+    for edge in graph.edges:
+        left_uuid = edge.get("source")
+        right_uuid = edge.get("target")
+        # target_handle_key是target, right的输入节点（入节点）
+        # source_handle_key是source, left的输出节点（出节点）
+        right_source_conn_key = edge.get("target_handle_key", "")
+        left_target_conn_key = edge.get("source_handle_key", "")
+
+        # 获取源节点和目标节点信息
+        left_node = nodes.get(left_uuid, {})
+        right_node = nodes.get(right_uuid, {})
+
+        left_res_name = left_node.get("resource_name", "")
+        left_template_name = left_node.get("template_name", "")
+        right_res_name = right_node.get("resource_name", "")
+        right_template_name = right_node.get("template_name", "")
+
+        # 获取源节点的 output handles
+        left_node_handles = get_action_handles(left_res_name, left_template_name)
+        target_valid_keys = left_node_handles.get("target", [])
+        target_valid_keys.append("ready")
+
+        # 获取目标节点的 input handles
+        right_node_handles = get_action_handles(right_res_name, right_template_name)
+        source_valid_keys = right_node_handles.get("source", [])
+        source_valid_keys.append("ready")
+
+        # 如果节点配置了 output handles，则 source_port 必须有效
+        if not right_source_conn_key:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(f"源节点 '{node_name}' 的 source_handle_key 为空，" f"应设置为: {source_valid_keys}")
+        elif right_source_conn_key not in source_valid_keys:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(
+                f"源节点 '{node_name}' 的 source 端点 '{right_source_conn_key}' 不存在，" f"支持的端点: {source_valid_keys}"
+            )
+
+        # 如果节点配置了 input handles，则 target_port 必须有效
+        if not left_target_conn_key:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(f"目标节点 '{node_name}' 的 target_handle_key 为空，" f"应设置为: {target_valid_keys}")
+        elif left_target_conn_key not in target_valid_keys:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(
+                f"目标节点 '{node_name}' 的 target 端点 '{left_target_conn_key}' 不存在，"
+                f"支持的端点: {target_valid_keys}"
+            )
+
+    return len(errors) == 0, errors
+
+
+# action 到 resource_name 的映射
+ACTION_RESOURCE_MAPPING: Dict[str, str] = {
+    # 生物实验操作
+    "transfer_liquid": "liquid_handler.prcxi",
+    "transfer": "liquid_handler.prcxi",
+    "incubation": "incubator.prcxi",
+    "move_labware": "labware_mover.prcxi",
+    "oscillation": "shaker.prcxi",
+    # 有机化学操作
+    "HeatChillToTemp": "heatchill.chemputer",
+    "StopHeatChill": "heatchill.chemputer",
+    "StartHeatChill": "heatchill.chemputer",
+    "HeatChill": "heatchill.chemputer",
+    "Dissolve": "stirrer.chemputer",
+    "Transfer": "liquid_handler.chemputer",
+    "Evaporate": "rotavap.chemputer",
+    "Recrystallize": "reactor.chemputer",
+    "Filter": "filter.chemputer",
+    "Dry": "dryer.chemputer",
+    "Add": "liquid_handler.chemputer",
+}
+
+
+def normalize_steps(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    """
+    将不同格式的步骤数据规范化为统一格式
+
+    支持的输入格式：
+    - action + parameters
+    - action + action_args
+    - operation + parameters
+
+    Args:
+        data: 原始步骤数据列表
+
+    Returns:
+        规范化后的步骤列表，格式为 [{"action": str, "parameters": dict, "description": str?, "step_number": int?}, ...]
+    """
+    normalized = []
+    for idx, step in enumerate(data):
+        # 获取动作名称（支持 action 或 operation 字段）
+        action = step.get("action") or step.get("operation")
+        if not action:
+            continue
+
+        # 获取参数（支持 parameters 或 action_args 字段）
+        raw_params = step.get("parameters") or step.get("action_args") or {}
+        params = dict(raw_params)
+
+        # 规范化 source/target -> sources/targets
+        if "source" in raw_params and "sources" not in raw_params:
+            params["sources"] = raw_params["source"]
+        if "target" in raw_params and "targets" not in raw_params:
+            params["targets"] = raw_params["target"]
+
+        # 获取描述（支持 description 或 purpose 字段）
+        description = step.get("description") or step.get("purpose")
+
+        # 获取步骤编号（优先使用原始数据中的 step_number，否则使用索引+1）
+        step_number = step.get("step_number", idx + 1)
+
+        step_dict = {"action": action, "parameters": params, "step_number": step_number}
+        if description:
+            step_dict["description"] = description
+
+        normalized.append(step_dict)
+
+    return normalized
+
+
+def normalize_labware(data: List[Dict[str, Any]]) -> Dict[str, Dict[str, Any]]:
+    """
+    将不同格式的 labware 数据规范化为统一的字典格式
+
+    支持的输入格式：
+    - reagent_name + material_name + positions
+    - name + labware + slot
+
+    Args:
+        data: 原始 labware 数据列表
+
+    Returns:
+        规范化后的 labware 字典，格式为 {name: {"slot": int, "labware": str, "well": list, "type": str, "role": str, "name": str}, ...}
+    """
+    labware = {}
+    for item in data:
+        # 获取 key 名称（优先使用 reagent_name，其次是 material_name 或 name）
+        reagent_name = item.get("reagent_name")
+        key = reagent_name or item.get("material_name") or item.get("name")
+        if not key:
+            continue
+
+        key = str(key)
+
+        # 处理重复 key，自动添加后缀
+        idx = 1
+        original_key = key
+        while key in labware:
+            idx += 1
+            key = f"{original_key}_{idx}"
+
+        labware[key] = {
+            "slot": item.get("positions") or item.get("slot"),
+            "labware": item.get("material_name") or item.get("labware"),
+            "well": item.get("well", []),
+            "type": item.get("type", "reagent"),
+            "role": item.get("role", ""),
+            "name": key,
+        }
+
+    return labware
+
+
+def convert_from_json(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = "PRCXi",
+    validate: bool = True,
+) -> WorkflowGraph:
+    """
+    从 JSON 数据或文件转换为 WorkflowGraph
+
+    支持的 JSON 格式：
+    1. {"workflow": [...], "reagent": {...}} - 直接格式
+    2. {"steps_info": [...], "labware_info": [...]} - 需要规范化的格式
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+        validate: 是否校验句柄配置，默认 True
+
+    Returns:
+        WorkflowGraph: 构建好的工作流图
+
+    Raises:
+        ValueError: 不支持的 JSON 格式 或 句柄校验失败
+        FileNotFoundError: 文件不存在
+        json.JSONDecodeError: JSON 解析失败
+    """
+    # 处理输入数据
+    if isinstance(data, (str, PathLike)):
+        path = Path(data)
+        if path.exists():
+            with path.open("r", encoding="utf-8") as fp:
+                json_data = json.load(fp)
+        elif isinstance(data, str):
+            # 尝试作为 JSON 字符串解析
+            json_data = json.loads(data)
+        else:
+            raise FileNotFoundError(f"文件不存在: {data}")
+    elif isinstance(data, dict):
+        json_data = data
+    else:
+        raise TypeError(f"不支持的数据类型: {type(data)}")
+
+    # 根据格式解析数据
+    if "workflow" in json_data and "reagent" in json_data:
+        # 格式1: workflow/reagent（已经是规范格式）
+        protocol_steps = json_data["workflow"]
+        labware_info = json_data["reagent"]
+    elif "steps_info" in json_data and "labware_info" in json_data:
+        # 格式2: steps_info/labware_info（需要规范化）
+        protocol_steps = normalize_steps(json_data["steps_info"])
+        labware_info = normalize_labware(json_data["labware_info"])
+    elif "steps" in json_data and "labware" in json_data:
+        # 格式3: steps/labware（另一种常见格式）
+        protocol_steps = normalize_steps(json_data["steps"])
+        if isinstance(json_data["labware"], list):
+            labware_info = normalize_labware(json_data["labware"])
+        else:
+            labware_info = json_data["labware"]
+    else:
+        raise ValueError(
+            "不支持的 JSON 格式。支持的格式：\n"
+            "1. {'workflow': [...], 'reagent': {...}}\n"
+            "2. {'steps_info': [...], 'labware_info': [...]}\n"
+            "3. {'steps': [...], 'labware': [...]}"
+        )
+
+    # 构建工作流图
+    graph = build_protocol_graph(
+        labware_info=labware_info,
+        protocol_steps=protocol_steps,
+        workstation_name=workstation_name,
+        action_resource_mapping=ACTION_RESOURCE_MAPPING,
+    )
+
+    # 校验句柄配置
+    if validate:
+        is_valid, errors = validate_workflow_handles(graph)
+        if not is_valid:
+            import warnings
+
+            for error in errors:
+                warnings.warn(f"句柄校验警告: {error}")
+
+    return graph
+
+
+def convert_json_to_node_link(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = "PRCXi",
+) -> Dict[str, Any]:
+    """
+    将 JSON 数据转换为 node-link 格式的字典
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        Dict: node-link 格式的工作流数据
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_node_link_dict()
+
+
+def convert_json_to_workflow_list(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = "PRCXi",
+) -> List[Dict[str, Any]]:
+    """
+    将 JSON 数据转换为工作流列表格式
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        List: 工作流节点列表
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_dict()
+
+
+# 为了向后兼容，保留下划线前缀的别名
+_normalize_steps = normalize_steps
+_normalize_labware = normalize_labware

unilabos/workflow/from_python_script.py

@@ -0,0 +1,241 @@
+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

@@ -0,0 +1,131 @@
+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/wf_utils.py

@@ -0,0 +1,138 @@
+"""
+工作流工具模块
+
+提供工作流上传等功能
+"""
+
+import json
+import os
+import uuid
+from typing import Any, Dict, List, Optional
+
+from unilabos.utils.banner_print import print_status
+
+
+def _is_node_link_format(data: Dict[str, Any]) -> bool:
+    """检查数据是否为 node-link 格式"""
+    return "nodes" in data and "edges" in data
+
+
+def _convert_to_node_link(workflow_file: str, workflow_data: Dict[str, Any]) -> Dict[str, Any]:
+    """
+    将非 node-link 格式的工作流数据转换为 node-link 格式
+
+    Args:
+        workflow_file: 工作流文件路径（用于日志）
+        workflow_data: 原始工作流数据
+
+    Returns:
+        node-link 格式的工作流数据
+    """
+    from unilabos.workflow.convert_from_json import convert_json_to_node_link
+
+    print_status(f"检测到非 node-link 格式，正在转换...", "info")
+    node_link_data = convert_json_to_node_link(workflow_data)
+    print_status(f"转换完成", "success")
+    return node_link_data
+
+
+def upload_workflow(
+    workflow_file: str,
+    workflow_name: Optional[str] = None,
+    tags: Optional[List[str]] = None,
+    published: bool = False,
+) -> Dict[str, Any]:
+    """
+    上传工作流到服务器
+
+    支持的输入格式：
+    1. node-link 格式: {"nodes": [...], "edges": [...]}
+    2. workflow/reagent 格式: {"workflow": [...], "reagent": {...}}
+    3. steps_info/labware_info 格式: {"steps_info": [...], "labware_info": [...]}
+    4. steps/labware 格式: {"steps": [...], "labware": [...]}
+
+    Args:
+        workflow_file: 工作流文件路径（JSON格式）
+        workflow_name: 工作流名称，如果不提供则从文件中读取或使用文件名
+        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
+    """
+    # 延迟导入，避免在配置文件加载之前初始化 http_client
+    from unilabos.app.web import http_client
+
+    if not os.path.exists(workflow_file):
+        print_status(f"工作流文件不存在: {workflow_file}", "error")
+        return {"code": -1, "message": f"文件不存在: {workflow_file}"}
+
+    # 读取工作流文件
+    try:
+        with open(workflow_file, "r", encoding="utf-8") as f:
+            workflow_data = json.load(f)
+    except json.JSONDecodeError as e:
+        print_status(f"工作流文件JSON解析失败: {e}", "error")
+        return {"code": -1, "message": f"JSON解析失败: {e}"}
+
+    # 自动检测并转换格式
+    if not _is_node_link_format(workflow_data):
+        try:
+            workflow_data = _convert_to_node_link(workflow_file, workflow_data)
+        except Exception as e:
+            print_status(f"工作流格式转换失败: {e}", "error")
+            return {"code": -1, "message": f"格式转换失败: {e}"}
+
+    # 提取工作流数据
+    nodes = workflow_data.get("nodes", [])
+    edges = workflow_data.get("edges", [])
+    workflow_uuid_val = workflow_data.get("workflow_uuid", str(uuid.uuid4()))
+    wf_name_from_file = workflow_data.get("workflow_name", os.path.basename(workflow_file).replace(".json", ""))
+
+    # 确定工作流名称
+    final_name = workflow_name or wf_name_from_file
+
+    print_status(f"正在上传工作流: {final_name}", "info")
+    print_status(f"  - 节点数量: {len(nodes)}", "info")
+    print_status(f"  - 边数量: {len(edges)}", "info")
+    print_status(f"  - 标签: {tags or []}", "info")
+    print_status(f"  - 发布状态: {published}", "info")
+
+    # 调用 http_client 上传
+    result = http_client.workflow_import(
+        name=final_name,
+        workflow_uuid=workflow_uuid_val,
+        workflow_name=final_name,
+        nodes=nodes,
+        edges=edges,
+        tags=tags,
+        published=published,
+    )
+
+    if result.get("code") == 0:
+        data = result.get("data", {})
+        print_status("工作流上传成功！", "success")
+        print_status(f"  - UUID: {data.get('uuid', 'N/A')}", "info")
+        print_status(f"  - 名称: {data.get('name', 'N/A')}", "info")
+    else:
+        print_status(f"工作流上传失败: {result.get('message', '未知错误')}", "error")
+
+    return result
+
+
+def handle_workflow_upload_command(args_dict: Dict[str, Any]) -> None:
+    """
+    处理 workflow_upload 子命令
+
+    Args:
+        args_dict: 命令行参数字典
+    """
+    workflow_file = args_dict.get("workflow_file")
+    workflow_name = args_dict.get("workflow_name")
+    tags = args_dict.get("tags", [])
+    published = args_dict.get("published", False)
+
+    if workflow_file:
+        upload_workflow(workflow_file, workflow_name, tags, published)
+    else:
+        print_status("未指定工作流文件路径，请使用 -f/--workflow_file 参数", "error")

unilabos_msgs/package.xml

@@ -2,7 +2,7 @@
 <?xml-model href="http://download.ros.org/schema/package_format3.xsd" schematypens="http://www.w3.org/2001/XMLSchema"?>
 <package format="3">
   <name>unilabos_msgs</name>
-  <version>0.10.11</version>
+  <version>0.10.12</version>
   <description>ROS2 Messages package for unilabos devices</description>
   <maintainer email="changjh@pku.edu.cn">Junhan Chang</maintainer>
   <maintainer email="18435084+Xuwznln@users.noreply.github.com">Xuwznln</maintainer>