no opcua installation on macos

fix possible crash fix deck & host_node set liquid with tube add test_resource_schema fix test resource schema registry update & workflow update add test mode support description & tags upload fix config load fix log add registry name & add always free correct config organic synthesis Adapt to new scheduler, sampels, and edge upload format (#230) * add sample_material * adapt to new samples sys * fix pump transfer. fix resource update when protocol & ros callback * Adapt to new scheduler. Feat/samples (#229) * add sample_material * adapt to new samples sys adapt to new samples sys adapt to new edge format workflow upload & prcxi transfer liquid lh liquid speed up registry load workflow upload & set liquid fix & add set liquid with plate fix upload workflow json
2026-03-24 09:17:39 +00:00 · 2026-02-02 17:18:45 +08:00
parent 5179a7e48e
commit b551e69f64
41 changed files with 2671 additions and 747 deletions
--- a/unilabos/workflow/common.py
+++ b/unilabos/workflow/common.py
@@ -19,7 +19,9 @@

 第一步: 按 slot 去重创建 create_resource 节点（创建板子）
 --------------------------------------------------------------------------------
+- 首先创建一个 Group 节点（type="Group", minimized=true），用于包含所有 create_resource 节点
 - 遍历所有 reagent，按 slot 去重，为每个唯一的 slot 创建一个板子
+- 所有 create_resource 节点的 parent_uuid 指向 Group 节点，minimized=true
 - 生成参数:
    res_id: plate_slot_{slot}
    device_id: /PRCXI
@@ -29,11 +31,13 @@
 - 输出端口: labware（用于连接 set_liquid_from_plate）
 - 控制流: create_resource 之间通过 ready 端口串联

-示例: slot=1, slot=4 -> 创建 2 个 create_resource 节点
+示例: slot=1, slot=4 -> 创建 1 个 Group + 2 个 create_resource 节点

 第二步: 为每个 reagent 创建 set_liquid_from_plate 节点（设置液体）
 --------------------------------------------------------------------------------
+- 首先创建一个 Group 节点（type="Group", minimized=true），用于包含所有 set_liquid_from_plate 节点
 - 遍历所有 reagent，为每个试剂创建 set_liquid_from_plate 节点
+- 所有 set_liquid_from_plate 节点的 parent_uuid 指向 Group 节点，minimized=true
 - 生成参数:
    plate: []（通过连接传递，来自 create_resource 的 labware）
    well_names: ["A1", "A3", "A5"]（来自 reagent 的 well 数组）
@@ -56,7 +60,11 @@
 ==================== 连接关系图 ====================

 控制流 (ready 端口串联):
-    create_resource_1 -> create_resource_2 -> ... -> set_liquid_1 -> set_liquid_2 -> ... -> transfer_liquid_1 -> transfer_liquid_2 -> ...
+    - create_resource 之间: 无 ready 连接
+    - set_liquid_from_plate 之间: 无 ready 连接
+    - create_resource 与 set_liquid_from_plate 之间: 无 ready 连接
+    - transfer_liquid 之间: 通过 ready 端口串联
+        transfer_liquid_1 -> transfer_liquid_2 -> transfer_liquid_3 -> ...

 物料流:
    [create_resource] --labware--> [set_liquid_from_plate] --output_wells--> [transfer_liquid] --sources_out/targets_out--> [下一个 transfer_liquid]
@@ -76,6 +84,13 @@ transfer_liquid:
    输入: sources -> sources_identifier, targets -> targets_identifier
    输出: sources -> sources_out, targets -> targets_out

+==================== 设备名配置 (device_name) ====================
+
+每个节点都有 device_name 字段，指定在哪个设备上执行:
+- create_resource: device_name = "host_node"（固定）
+- set_liquid_from_plate: device_name = "PRCXI"（可配置，见 DEVICE_NAME_DEFAULT）
+- transfer_liquid 等动作: device_name = "PRCXI"（可配置，见 DEVICE_NAME_DEFAULT）
+
 ==================== 校验规则 ====================

 - 检查 sources/targets 是否在 reagent 中定义
@@ -97,6 +112,13 @@ Json = Dict[str, Any]

 # ==================== 默认配置 ====================

+# 设备名配置
+DEVICE_NAME_HOST = "host_node"  # create_resource 固定在 host_node 上执行
+DEVICE_NAME_DEFAULT = "PRCXI"  # transfer_liquid, set_liquid_from_plate 等动作的默认设备名
+
+# 节点类型
+NODE_TYPE_DEFAULT = "ILab"  # 所有节点的默认类型
+
 # create_resource 节点默认参数
 CREATE_RESOURCE_DEFAULTS = {
    "device_id": "/PRCXI",
@@ -340,14 +362,16 @@ def build_protocol_graph(
    protocol_steps: List[Dict[str, Any]],
    workstation_name: str,
    action_resource_mapping: Optional[Dict[str, str]] = None,
+    labware_defs: Optional[List[Dict[str, Any]]] = None,
 ) -> WorkflowGraph:
    """统一的协议图构建函数，根据设备类型自动选择构建逻辑

    Args:
-        labware_info: labware 信息字典，格式为 {name: {slot, well, labware, ...}, ...}
+        labware_info: reagent 信息字典，格式为 {name: {slot, well}, ...}，用于 set_liquid 和 well 查找
        protocol_steps: 协议步骤列表
        workstation_name: 工作站名称
        action_resource_mapping: action 到 resource_name 的映射字典，可选
+        labware_defs: labware 定义列表，格式为 [{"name": "...", "slot": "1", "type": "lab_xxx"}, ...]
    """
    G = WorkflowGraph()
    resource_last_writer = {}  # reagent_name -> "node_id:port"
@@ -355,38 +379,51 @@ def build_protocol_graph(

    protocol_steps = refactor_data(protocol_steps, action_resource_mapping)

-    # ==================== 第一步：按 slot 去重创建 create_resource 节点 ====================
-    # 收集所有唯一的 slot
-    slots_info = {}  # slot -> {labware, res_id}
-    for labware_id, item in labware_info.items():
-        slot = str(item.get("slot", ""))
-        if slot and slot not in slots_info:
-            res_id = f"plate_slot_{slot}"
-            slots_info[slot] = {
-                "labware": item.get("labware", ""),
-                "res_id": res_id,
-            }
+    # ==================== 第一步：按 slot 创建 create_resource 节点 ====================
+    # 创建 Group 节点，包含所有 create_resource 节点
+    group_node_id = str(uuid.uuid4())
+    G.add_node(
+        group_node_id,
+        name="Resources Group",
+        type="Group",
+        parent_uuid="",
+        lab_node_type="Device",
+        template_name="",
+        resource_name="",
+        footer="",
+        minimized=True,
+        param=None,
+    )

-    # 为每个唯一的 slot 创建 create_resource 节点
+    # 直接使用 JSON 中的 labware 定义，每个 slot 一条记录，type 即 class_name
    res_index = 0
-    last_create_resource_id = None
-    for slot, info in slots_info.items():
-        node_id = str(uuid.uuid4())
-        res_id = info["res_id"]
+    for lw in (labware_defs or []):
+        slot = str(lw.get("slot", ""))
+        if not slot or slot in slot_to_create_resource:
+            continue  # 跳过空 slot 或已处理的 slot
+
+        lw_name = lw.get("name", f"slot {slot}")
+        lw_type = lw.get("type", CREATE_RESOURCE_DEFAULTS["class_name"])
+        res_id = f"plate_slot_{slot}"

        res_index += 1
+        node_id = str(uuid.uuid4())
        G.add_node(
            node_id,
            template_name="create_resource",
            resource_name="host_node",
-            name=f"Plate {res_index}",
-            description=f"Create plate on slot {slot}",
+            name=lw_name,
+            description=f"Create {lw_name}",
            lab_node_type="Labware",
            footer="create_resource-host_node",
+            device_name=DEVICE_NAME_HOST,
+            type=NODE_TYPE_DEFAULT,
+            parent_uuid=group_node_id,
+            minimized=True,
            param={
                "res_id": res_id,
                "device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
-                "class_name": CREATE_RESOURCE_DEFAULTS["class_name"],
+                "class_name": lw_type,
                "parent": CREATE_RESOURCE_DEFAULTS["parent_template"].format(slot=slot),
                "bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
                "slot_on_deck": slot,
@@ -394,14 +431,23 @@ def build_protocol_graph(
        )
        slot_to_create_resource[slot] = node_id

-        # create_resource 之间通过 ready 串联
-        if last_create_resource_id is not None:
-            G.add_edge(last_create_resource_id, node_id, source_port="ready", target_port="ready")
-        last_create_resource_id = node_id
-
    # ==================== 第二步：为每个 reagent 创建 set_liquid_from_plate 节点 ====================
+    # 创建 Group 节点，包含所有 set_liquid_from_plate 节点
+    set_liquid_group_id = str(uuid.uuid4())
+    G.add_node(
+        set_liquid_group_id,
+        name="SetLiquid Group",
+        type="Group",
+        parent_uuid="",
+        lab_node_type="Device",
+        template_name="",
+        resource_name="",
+        footer="",
+        minimized=True,
+        param=None,
+    )
+
    set_liquid_index = 0
-    last_set_liquid_id = last_create_resource_id  # set_liquid_from_plate 连接在 create_resource 之后

    for labware_id, item in labware_info.items():
        # 跳过 Tip/Rack 类型
@@ -430,6 +476,10 @@ def build_protocol_graph(
            description=f"Set liquid: {labware_id}",
            lab_node_type="Reagent",
            footer="set_liquid_from_plate-liquid_handler.prcxi",
+            device_name=DEVICE_NAME_DEFAULT,
+            type=NODE_TYPE_DEFAULT,
+            parent_uuid=set_liquid_group_id,  # 指向 Group 节点
+            minimized=True,  # 折叠显示
            param={
                "plate": [],  # 通过连接传递
                "well_names": wells,  # 孔位名数组，如 ["A1", "A3", "A5"]
@@ -438,10 +488,7 @@ def build_protocol_graph(
            },
        )

-        # ready 连接：上一个节点 -> set_liquid_from_plate
-        if last_set_liquid_id is not None:
-            G.add_edge(last_set_liquid_id, node_id, source_port="ready", target_port="ready")
-        last_set_liquid_id = node_id
+        # set_liquid_from_plate 之间不需要 ready 连接

        # 物料流：create_resource 的 labware -> set_liquid_from_plate 的 input_plate
        create_res_node_id = slot_to_create_resource.get(slot)
@@ -451,7 +498,8 @@ def build_protocol_graph(
        # set_liquid_from_plate 的输出 output_wells 用于连接 transfer_liquid
        resource_last_writer[labware_id] = f"{node_id}:output_wells"

-    last_control_node_id = last_set_liquid_id
+    # transfer_liquid 之间通过 ready 串联，从 None 开始
+    last_control_node_id = None

    # 端口名称映射：JSON 字段名 -> 实际 handle key
    INPUT_PORT_MAPPING = {
@@ -544,9 +592,11 @@ def build_protocol_graph(
            if param_key in params:
                params[param_key] = []

-        # 更新 step 的 param 和 footer
+        # 更新 step 的 param、footer、device_name 和 type
        step_copy = step.copy()
        step_copy["param"] = params
+        step_copy["device_name"] = DEVICE_NAME_DEFAULT  # 动作节点使用默认设备名
+        step_copy["type"] = NODE_TYPE_DEFAULT  # 节点类型

        # 如果有警告，修改 footer 添加警告标记（警告放前面）
        if warnings:
--- a/unilabos/workflow/convert_from_json.py
+++ b/unilabos/workflow/convert_from_json.py
@@ -1,16 +1,20 @@
 """
 JSON 工作流转换模块

-将 workflow/reagent 格式的 JSON 转换为统一工作流格式。
+将 workflow/reagent/labware 格式的 JSON 转换为统一工作流格式。

 输入格式:
 {
+    "labware": [
+        {"name": "...", "slot": "1", "type": "lab_xxx"},
+        ...
+    ],
    "workflow": [
        {"action": "...", "action_args": {...}},
        ...
    ],
    "reagent": {
-        "reagent_name": {"slot": int, "well": [...], "labware": "..."},
+        "reagent_name": {"slot": int, "well": [...]},
        ...
    }
 }
@@ -245,18 +249,18 @@ def convert_from_json(
    if "workflow" not in json_data or "reagent" not in json_data:
        raise ValueError(
            "不支持的 JSON 格式。请使用标准格式:\n"
-            '{"workflow": [{"action": "...", "action_args": {...}}, ...], '
-            '"reagent": {"name": {"slot": int, "well": [...], "labware": "..."}, ...}}'
+            '{"labware": [...], "workflow": [...], "reagent": {...}}'
        )

    # 提取数据
    workflow = json_data["workflow"]
    reagent = json_data["reagent"]
+    labware_defs = json_data.get("labware", [])  # 新的 labware 定义列表

    # 规范化步骤数据
    protocol_steps = normalize_workflow_steps(workflow)

-    # reagent 已经是字典格式，直接使用
+    # reagent 已经是字典格式，用于 set_liquid 和 well 数量查找
    labware_info = reagent

    # 构建工作流图
@@ -265,6 +269,7 @@ def convert_from_json(
        protocol_steps=protocol_steps,
        workstation_name=workstation_name,
        action_resource_mapping=ACTION_RESOURCE_MAPPING,
+        labware_defs=labware_defs,
    )

    # 校验句柄配置
--- a/unilabos/workflow/wf_utils.py
+++ b/unilabos/workflow/wf_utils.py
@@ -41,6 +41,7 @@ def upload_workflow(
    workflow_name: Optional[str] = None,
    tags: Optional[List[str]] = None,
    published: bool = False,
+    description: str = "",
 ) -> Dict[str, Any]:
    """
    上传工作流到服务器
@@ -56,6 +57,7 @@ def upload_workflow(
        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
+        description: 工作流描述，发布时使用

    Returns:
        Dict: API响应数据
@@ -75,6 +77,14 @@ def upload_workflow(
        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}"}

+    # 从 JSON 文件中提取 description 和 tags（作为 fallback）
+    if not description and "description" in workflow_data:
+        description = workflow_data["description"]
+        print_status(f"从文件中读取 description", "info")
+    if not tags and "tags" in workflow_data:
+        tags = workflow_data["tags"]
+        print_status(f"从文件中读取 tags: {tags}", "info")
+
    # 自动检测并转换格式
    if not _is_node_link_format(workflow_data):
        try:
@@ -96,6 +106,7 @@ def upload_workflow(
    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"  - 描述: {description[:50]}{'...' if len(description) > 50 else ''}", "info")
    print_status(f"  - 发布状态: {published}", "info")

    # 调用 http_client 上传
@@ -107,6 +118,7 @@ def upload_workflow(
        edges=edges,
        tags=tags,
        published=published,
+        description=description,
    )

    if result.get("code") == 0:
@@ -131,8 +143,9 @@ def handle_workflow_upload_command(args_dict: Dict[str, Any]) -> None:
    workflow_name = args_dict.get("workflow_name")
    tags = args_dict.get("tags", [])
    published = args_dict.get("published", False)
+    description = args_dict.get("description", "")

    if workflow_file:
-        upload_workflow(workflow_file, workflow_name, tags, published)
+        upload_workflow(workflow_file, workflow_name, tags, published, description)
    else:
        print_status("未指定工作流文件路径，请使用 -f/--workflow_file 参数", "error")