workflow upload & set liquid fix & add set liquid with plate

fix upload workflow json

save class name when deserialize & protocol execute test

Support root node change pos

add unilabos_class

gather query

unilabos/workflow/convert_from_json.py

@@ -0,0 +1,315 @@
+"""
+JSON 工作流转换模块
+
+将 workflow/reagent 格式的 JSON 转换为统一工作流格式。
+
+输入格式:
+{
+    "workflow": [
+        {"action": "...", "action_args": {...}},
+        ...
+    ],
+    "reagent": {
+        "reagent_name": {"slot": int, "well": [...], "labware": "..."},
+        ...
+    }
+}
+"""
+
+import json
+from os import PathLike
+from pathlib import Path
+from typing import Any, Dict, List, Optional, Tuple, Union
+
+from unilabos.workflow.common import WorkflowGraph, build_protocol_graph
+from unilabos.registry.registry import lab_registry
+
+
+# ==================== 字段映射配置 ====================
+
+# action 到 resource_name 的映射
+ACTION_RESOURCE_MAPPING: Dict[str, str] = {
+    # 生物实验操作
+    "transfer_liquid": "liquid_handler.prcxi",
+    "transfer": "liquid_handler.prcxi",
+    "incubation": "incubator.prcxi",
+    "move_labware": "labware_mover.prcxi",
+    "oscillation": "shaker.prcxi",
+    # 有机化学操作
+    "HeatChillToTemp": "heatchill.chemputer",
+    "StopHeatChill": "heatchill.chemputer",
+    "StartHeatChill": "heatchill.chemputer",
+    "HeatChill": "heatchill.chemputer",
+    "Dissolve": "stirrer.chemputer",
+    "Transfer": "liquid_handler.chemputer",
+    "Evaporate": "rotavap.chemputer",
+    "Recrystallize": "reactor.chemputer",
+    "Filter": "filter.chemputer",
+    "Dry": "dryer.chemputer",
+    "Add": "liquid_handler.chemputer",
+}
+
+# action_args 字段到 parameters 字段的映射
+# 格式: {"old_key": "new_key"}, 仅映射需要重命名的字段
+ARGS_FIELD_MAPPING: Dict[str, str] = {
+    # 如果需要字段重命名，在这里配置
+    # "old_field_name": "new_field_name",
+}
+
+# 默认工作站名称
+DEFAULT_WORKSTATION = "PRCXI"
+
+
+# ==================== 核心转换函数 ====================
+
+
+def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]:
+    """
+    从 registry 获取指定设备和动作的 handles 配置
+
+    Args:
+        resource_name: 设备资源名称，如 "liquid_handler.prcxi"
+        template_name: 动作模板名称，如 "transfer_liquid"
+
+    Returns:
+        包含 source 和 target handler_keys 的字典:
+        {"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]}
+    """
+    result = {"source": [], "target": []}
+
+    device_info = lab_registry.device_type_registry.get(resource_name, {})
+    if not device_info:
+        return result
+
+    action_mappings = device_info.get("class", {}).get("action_value_mappings", {})
+    action_config = action_mappings.get(template_name, {})
+    handles = action_config.get("handles", {})
+
+    if isinstance(handles, dict):
+        for handle in handles.get("input", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["source"].append(handler_key)
+        for handle in handles.get("output", []):
+            handler_key = handle.get("handler_key", "")
+            if handler_key:
+                result["target"].append(handler_key)
+
+    return result
+
+
+def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]:
+    """
+    校验工作流图中所有边的句柄配置是否正确
+
+    Args:
+        graph: 工作流图对象
+
+    Returns:
+        (is_valid, errors): 是否有效，错误信息列表
+    """
+    errors = []
+    nodes = graph.nodes
+
+    for edge in graph.edges:
+        left_uuid = edge.get("source")
+        right_uuid = edge.get("target")
+        right_source_conn_key = edge.get("target_handle_key", "")
+        left_target_conn_key = edge.get("source_handle_key", "")
+
+        left_node = nodes.get(left_uuid, {})
+        right_node = nodes.get(right_uuid, {})
+
+        left_res_name = left_node.get("resource_name", "")
+        left_template_name = left_node.get("template_name", "")
+        right_res_name = right_node.get("resource_name", "")
+        right_template_name = right_node.get("template_name", "")
+
+        left_node_handles = get_action_handles(left_res_name, left_template_name)
+        target_valid_keys = left_node_handles.get("target", [])
+        target_valid_keys.append("ready")
+
+        right_node_handles = get_action_handles(right_res_name, right_template_name)
+        source_valid_keys = right_node_handles.get("source", [])
+        source_valid_keys.append("ready")
+
+        # 验证目标节点（right）的输入端口
+        if not right_source_conn_key:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(f"目标节点 '{node_name}' 的输入端口 (target_handle_key) 为空，应设置为: {source_valid_keys}")
+        elif right_source_conn_key not in source_valid_keys:
+            node_name = right_node.get("name", right_uuid[:8])
+            errors.append(
+                f"目标节点 '{node_name}' 的输入端口 '{right_source_conn_key}' 不存在，支持的输入端口: {source_valid_keys}"
+            )
+
+        # 验证源节点（left）的输出端口
+        if not left_target_conn_key:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(f"源节点 '{node_name}' 的输出端口 (source_handle_key) 为空，应设置为: {target_valid_keys}")
+        elif left_target_conn_key not in target_valid_keys:
+            node_name = left_node.get("name", left_uuid[:8])
+            errors.append(
+                f"源节点 '{node_name}' 的输出端口 '{left_target_conn_key}' 不存在，支持的输出端口: {target_valid_keys}"
+            )
+
+    return len(errors) == 0, errors
+
+
+def normalize_workflow_steps(workflow: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    """
+    将 workflow 格式的步骤数据规范化
+
+    输入格式:
+        [{"action": "...", "action_args": {...}}, ...]
+
+    输出格式:
+        [{"action": "...", "parameters": {...}, "step_number": int}, ...]
+
+    Args:
+        workflow: workflow 数组
+
+    Returns:
+        规范化后的步骤列表
+    """
+    normalized = []
+    for idx, step in enumerate(workflow):
+        action = step.get("action")
+        if not action:
+            continue
+
+        # 获取参数: action_args
+        raw_params = step.get("action_args", {})
+        params = {}
+
+        # 应用字段映射
+        for key, value in raw_params.items():
+            mapped_key = ARGS_FIELD_MAPPING.get(key, key)
+            params[mapped_key] = value
+
+        step_dict = {
+            "action": action,
+            "parameters": params,
+            "step_number": idx + 1,
+        }
+
+        # 保留描述字段
+        if "description" in step:
+            step_dict["description"] = step["description"]
+
+        normalized.append(step_dict)
+
+    return normalized
+
+
+def convert_from_json(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = DEFAULT_WORKSTATION,
+    validate: bool = True,
+) -> WorkflowGraph:
+    """
+    从 JSON 数据或文件转换为 WorkflowGraph
+
+    JSON 格式:
+        {"workflow": [...], "reagent": {...}}
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+        validate: 是否校验句柄配置，默认 True
+
+    Returns:
+        WorkflowGraph: 构建好的工作流图
+
+    Raises:
+        ValueError: 不支持的 JSON 格式
+        FileNotFoundError: 文件不存在
+        json.JSONDecodeError: JSON 解析失败
+    """
+    # 处理输入数据
+    if isinstance(data, (str, PathLike)):
+        path = Path(data)
+        if path.exists():
+            with path.open("r", encoding="utf-8") as fp:
+                json_data = json.load(fp)
+        elif isinstance(data, str):
+            json_data = json.loads(data)
+        else:
+            raise FileNotFoundError(f"文件不存在: {data}")
+    elif isinstance(data, dict):
+        json_data = data
+    else:
+        raise TypeError(f"不支持的数据类型: {type(data)}")
+
+    # 校验格式
+    if "workflow" not in json_data or "reagent" not in json_data:
+        raise ValueError(
+            "不支持的 JSON 格式。请使用标准格式:\n"
+            '{"workflow": [{"action": "...", "action_args": {...}}, ...], '
+            '"reagent": {"name": {"slot": int, "well": [...], "labware": "..."}, ...}}'
+        )
+
+    # 提取数据
+    workflow = json_data["workflow"]
+    reagent = json_data["reagent"]
+
+    # 规范化步骤数据
+    protocol_steps = normalize_workflow_steps(workflow)
+
+    # reagent 已经是字典格式，直接使用
+    labware_info = reagent
+
+    # 构建工作流图
+    graph = build_protocol_graph(
+        labware_info=labware_info,
+        protocol_steps=protocol_steps,
+        workstation_name=workstation_name,
+        action_resource_mapping=ACTION_RESOURCE_MAPPING,
+    )
+
+    # 校验句柄配置
+    if validate:
+        is_valid, errors = validate_workflow_handles(graph)
+        if not is_valid:
+            import warnings
+
+            for error in errors:
+                warnings.warn(f"句柄校验警告: {error}")
+
+    return graph
+
+
+def convert_json_to_node_link(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = DEFAULT_WORKSTATION,
+) -> Dict[str, Any]:
+    """
+    将 JSON 数据转换为 node-link 格式的字典
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        Dict: node-link 格式的工作流数据
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_node_link_dict()
+
+
+def convert_json_to_workflow_list(
+    data: Union[str, PathLike, Dict[str, Any]],
+    workstation_name: str = DEFAULT_WORKSTATION,
+) -> List[Dict[str, Any]]:
+    """
+    将 JSON 数据转换为工作流列表格式
+
+    Args:
+        data: JSON 文件路径、字典数据、或 JSON 字符串
+        workstation_name: 工作站名称，默认 "PRCXi"
+
+    Returns:
+        List: 工作流节点列表
+    """
+    graph = convert_from_json(data, workstation_name)
+    return graph.to_dict()