v0.10.18

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

scripts/workflow.py

@@ -2,6 +2,7 @@ import json
 import logging
 import traceback
 import uuid
+import xml.etree.ElementTree as ET
 from typing import Any, Dict, List
 
 import networkx as nx
@@ -24,15 +25,7 @@ class SimpleGraph:
 
     def add_edge(self, source, target, **attrs):
         """添加边"""
-        # edge = {"source": source, "target": target, **attrs}
+        edge = {"source": source, "target": target, **attrs}
-        edge = {
-            "source": source, "target": target,
-            "source_node_uuid": source,
-            "target_node_uuid": target,
-            "source_handle_io": "source",
-            "target_handle_io": "target",
-            **attrs
-        }
         self.edges.append(edge)
 
     def to_dict(self):
@@ -49,7 +42,6 @@ class SimpleGraph:
             "multigraph": False,
             "graph": {},
             "nodes": nodes_list,
-            "edges": self.edges,
             "links": self.edges,
         }
 
@@ -66,8 +58,495 @@ def extract_json_from_markdown(text: str) -> str:
     return text
 
 
+def convert_to_type(val: str) -> Any:
+    """将字符串值转换为适当的数据类型"""
+    if val == "True":
+        return True
+    if val == "False":
+        return False
+    if val == "?":
+        return None
+    if val.endswith(" g"):
+        return float(val.split(" ")[0])
+    if val.endswith("mg"):
+        return float(val.split("mg")[0])
+    elif val.endswith("mmol"):
+        return float(val.split("mmol")[0]) / 1000
+    elif val.endswith("mol"):
+        return float(val.split("mol")[0])
+    elif val.endswith("ml"):
+        return float(val.split("ml")[0])
+    elif val.endswith("RPM"):
+        return float(val.split("RPM")[0])
+    elif val.endswith(" °C"):
+        return float(val.split(" ")[0])
+    elif val.endswith(" %"):
+        return float(val.split(" ")[0])
+    return val
 
 
+def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
+    """统一的数据重构函数，根据操作类型自动选择模板"""
+    refactored_data = []
+
+    # 定义操作映射，包含生物实验和有机化学的所有操作
+    OPERATION_MAPPING = {
+        # 生物实验操作
+        "transfer_liquid": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
+        "transfer": "SynBioFactory-liquid_handler.biomek-transfer",
+        "incubation": "SynBioFactory-liquid_handler.biomek-incubation",
+        "move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
+        "oscillation": "SynBioFactory-liquid_handler.biomek-oscillation",
+        # 有机化学操作
+        "HeatChillToTemp": "SynBioFactory-workstation-HeatChillProtocol",
+        "StopHeatChill": "SynBioFactory-workstation-HeatChillStopProtocol",
+        "StartHeatChill": "SynBioFactory-workstation-HeatChillStartProtocol",
+        "HeatChill": "SynBioFactory-workstation-HeatChillProtocol",
+        "Dissolve": "SynBioFactory-workstation-DissolveProtocol",
+        "Transfer": "SynBioFactory-workstation-TransferProtocol",
+        "Evaporate": "SynBioFactory-workstation-EvaporateProtocol",
+        "Recrystallize": "SynBioFactory-workstation-RecrystallizeProtocol",
+        "Filter": "SynBioFactory-workstation-FilterProtocol",
+        "Dry": "SynBioFactory-workstation-DryProtocol",
+        "Add": "SynBioFactory-workstation-AddProtocol",
+    }
+
+    UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
+
+    for step in data:
+        operation = step.get("action")
+        if not operation or operation in UNSUPPORTED_OPERATIONS:
+            continue
+
+        # 处理重复操作
+        if operation == "Repeat":
+            times = step.get("times", step.get("parameters", {}).get("times", 1))
+            sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
+            for i in range(int(times)):
+                sub_data = refactor_data(sub_steps)
+                refactored_data.extend(sub_data)
+            continue
+
+        # 获取模板名称
+        template = OPERATION_MAPPING.get(operation)
+        if not template:
+            # 自动推断模板类型
+            if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
+                template = f"SynBioFactory-liquid_handler.biomek-{operation}"
+            else:
+                template = f"SynBioFactory-workstation-{operation}Protocol"
+
+        # 创建步骤数据
+        step_data = {
+            "template": template,
+            "description": step.get("description", step.get("purpose", f"{operation} operation")),
+            "lab_node_type": "Device",
+            "parameters": step.get("parameters", step.get("action_args", {})),
+        }
+        refactored_data.append(step_data)
+
+    return refactored_data
+
+
+def build_protocol_graph(
+    labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
+) -> SimpleGraph:
+    """统一的协议图构建函数，根据设备类型自动选择构建逻辑"""
+    G = SimpleGraph()
+    resource_last_writer = {}
+    LAB_NAME = "SynBioFactory"
+
+    protocol_steps = refactor_data(protocol_steps)
+
+    # 检查协议步骤中的模板来判断协议类型
+    has_biomek_template = any(
+        ("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
+        for step in protocol_steps
+    )
+
+    if has_biomek_template:
+        # 生物实验协议图构建
+        for labware_id, labware in labware_info.items():
+            node_id = str(uuid.uuid4())
+
+            labware_attrs = labware.copy()
+            labware_id = labware_attrs.pop("id", labware_attrs.get("name", f"labware_{uuid.uuid4()}"))
+            labware_attrs["description"] = labware_id
+            labware_attrs["lab_node_type"] = (
+                "Reagent" if "Plate" in str(labware_id) else "Labware" if "Rack" in str(labware_id) else "Sample"
+            )
+            labware_attrs["device_id"] = workstation_name
+
+            G.add_node(node_id, template=f"{LAB_NAME}-host_node-create_resource", **labware_attrs)
+            resource_last_writer[labware_id] = f"{node_id}:labware"
+
+        # 处理协议步骤
+        prev_node = None
+        for i, step in enumerate(protocol_steps):
+            node_id = str(uuid.uuid4())
+            G.add_node(node_id, **step)
+
+            # 添加控制流边
+            if prev_node is not None:
+                G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
+            prev_node = node_id
+
+            # 处理物料流
+            params = step.get("parameters", {})
+            if "sources" in params and params["sources"] in resource_last_writer:
+                source_node, source_port = resource_last_writer[params["sources"]].split(":")
+                G.add_edge(source_node, node_id, source_port=source_port, target_port="labware")
+
+            if "targets" in params:
+                resource_last_writer[params["targets"]] = f"{node_id}:labware"
+
+        # 添加协议结束节点
+        end_id = str(uuid.uuid4())
+        G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
+        if prev_node is not None:
+            G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
+
+    else:
+        # 有机化学协议图构建
+        WORKSTATION_ID = workstation_name
+
+        # 为所有labware创建资源节点
+        for item_id, item in labware_info.items():
+            # item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
+            node_id = str(uuid.uuid4())
+
+            # 判断节点类型
+            if item.get("type") == "hardware" or "reactor" in str(item_id).lower():
+                if "reactor" not in str(item_id).lower():
+                    continue
+                lab_node_type = "Sample"
+                description = f"Prepare Reactor: {item_id}"
+                liquid_type = []
+                liquid_volume = []
+            else:
+                lab_node_type = "Reagent"
+                description = f"Add Reagent to Flask: {item_id}"
+                liquid_type = [item_id]
+                liquid_volume = [1e5]
+
+            G.add_node(
+                node_id,
+                template=f"{LAB_NAME}-host_node-create_resource",
+                description=description,
+                lab_node_type=lab_node_type,
+                res_id=item_id,
+                device_id=WORKSTATION_ID,
+                class_name="container",
+                parent=WORKSTATION_ID,
+                bind_locations={"x": 0.0, "y": 0.0, "z": 0.0},
+                liquid_input_slot=[-1],
+                liquid_type=liquid_type,
+                liquid_volume=liquid_volume,
+                slot_on_deck="",
+                role=item.get("role", ""),
+            )
+            resource_last_writer[item_id] = f"{node_id}:labware"
+
+        last_control_node_id = None
+
+        # 处理协议步骤
+        for step in protocol_steps:
+            node_id = str(uuid.uuid4())
+            G.add_node(node_id, **step)
+
+            # 控制流
+            if last_control_node_id is not None:
+                G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
+            last_control_node_id = node_id
+
+            # 物料流
+            params = step.get("parameters", {})
+            input_resources = {
+                "Vessel": params.get("vessel"),
+                "ToVessel": params.get("to_vessel"),
+                "FromVessel": params.get("from_vessel"),
+                "reagent": params.get("reagent"),
+                "solvent": params.get("solvent"),
+                "compound": params.get("compound"),
+                "sources": params.get("sources"),
+                "targets": params.get("targets"),
+            }
+
+            for target_port, resource_name in input_resources.items():
+                if resource_name and resource_name in resource_last_writer:
+                    source_node, source_port = resource_last_writer[resource_name].split(":")
+                    G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
+
+            output_resources = {
+                "VesselOut": params.get("vessel"),
+                "FromVesselOut": params.get("from_vessel"),
+                "ToVesselOut": params.get("to_vessel"),
+                "FiltrateOut": params.get("filtrate_vessel"),
+                "reagent": params.get("reagent"),
+                "solvent": params.get("solvent"),
+                "compound": params.get("compound"),
+                "sources_out": params.get("sources"),
+                "targets_out": params.get("targets"),
+            }
+
+            for source_port, resource_name in output_resources.items():
+                if resource_name:
+                    resource_last_writer[resource_name] = f"{node_id}:{source_port}"
+
+    return G
+
+
+def draw_protocol_graph(protocol_graph: SimpleGraph, output_path: str):
+    """
+    (辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图，用于可视化。
+    """
+    if not protocol_graph:
+        print("Cannot draw graph: Graph object is empty.")
+        return
+
+    G = nx.DiGraph()
+
+    for node_id, attrs in protocol_graph.nodes.items():
+        label = attrs.get("description", attrs.get("template", node_id[:8]))
+        G.add_node(node_id, label=label, **attrs)
+
+    for edge in protocol_graph.edges:
+        G.add_edge(edge["source"], edge["target"])
+
+    plt.figure(figsize=(20, 15))
+    try:
+        pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
+    except Exception:
+        pos = nx.shell_layout(G)  # Fallback layout
+
+    node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
+    nx.draw(
+        G,
+        pos,
+        with_labels=False,
+        node_size=2500,
+        node_color="skyblue",
+        node_shape="o",
+        edge_color="gray",
+        width=1.5,
+        arrowsize=15,
+    )
+    nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
+
+    plt.title("Chemical Protocol Workflow Graph", size=15)
+    plt.savefig(output_path, dpi=300, bbox_inches="tight")
+    plt.close()
+    print(f"  - Visualization saved to '{output_path}'")
+
+
+from networkx.drawing.nx_agraph import to_agraph
+import re
+
+COMPASS = {"n","e","s","w","ne","nw","se","sw","c"}
+
+def _is_compass(port: str) -> bool:
+    return isinstance(port, str) and port.lower() in COMPASS
+
+def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
+    """
+    使用 Graphviz 端口语法绘制协议工作流图。
+    - 若边上的 source_port/target_port 是 compass（n/e/s/w/...），直接用 compass。
+    - 否则自动为节点创建 record 形状并定义命名端口 <portname>。
+    最终由 PyGraphviz 渲染并输出到 output_path（后缀决定格式，如 .png/.svg/.pdf）。
+    """
+    if not protocol_graph:
+        print("Cannot draw graph: Graph object is empty.")
+        return
+
+    # 1) 先用 networkx 搭建有向图，保留端口属性
+    G = nx.DiGraph()
+    for node_id, attrs in protocol_graph.nodes.items():
+        label = attrs.get("description", attrs.get("template", node_id[:8]))
+        # 保留一个干净的“中心标签”，用于放在 record 的中间槽
+        G.add_node(node_id, _core_label=str(label), **{k:v for k,v in attrs.items() if k not in ("label",)})
+
+    edges_data = []
+    in_ports_by_node  = {}  # 收集命名输入端口
+    out_ports_by_node = {}  # 收集命名输出端口
+
+    for edge in protocol_graph.edges:
+        u = edge["source"]
+        v = edge["target"]
+        sp = edge.get("source_port")
+        tp = edge.get("target_port")
+
+        # 记录到图里（保留原始端口信息）
+        G.add_edge(u, v, source_port=sp, target_port=tp)
+        edges_data.append((u, v, sp, tp))
+
+        # 如果不是 compass，就按“命名端口”先归类，等会儿给节点造 record
+        if sp and not _is_compass(sp):
+            out_ports_by_node.setdefault(u, set()).add(str(sp))
+        if tp and not _is_compass(tp):
+            in_ports_by_node.setdefault(v, set()).add(str(tp))
+
+    # 2) 转为 AGraph，使用 Graphviz 渲染
+    A = to_agraph(G)
+    A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
+    A.node_attr.update(shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica")
+    A.edge_attr.update(arrowsize="0.8", color="#666666")
+
+    # 3) 为需要命名端口的节点设置 record 形状与 label
+    #    左列 = 输入端口；中间 = 核心标签；右列 = 输出端口
+    for n in A.nodes():
+        node = A.get_node(n)
+        core = G.nodes[n].get("_core_label", n)
+
+        in_ports  = sorted(in_ports_by_node.get(n, []))
+        out_ports = sorted(out_ports_by_node.get(n, []))
+
+        # 如果该节点涉及命名端口，则用 record；否则保留原 box
+        if in_ports or out_ports:
+            def port_fields(ports):
+                if not ports:
+                    return " "  # 必须留一个空槽占位
+                # 每个端口一个小格子，<p> name
+                return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
+
+            left  = port_fields(in_ports)
+            right = port_fields(out_ports)
+
+            # 三栏：左(入) | 中(节点名) | 右(出)
+            record_label = f"{{ {left} | {core} | {right} }}"
+            node.attr.update(shape="record", label=record_label)
+        else:
+            # 没有命名端口：普通盒子，显示核心标签
+            node.attr.update(label=str(core))
+
+    # 4) 给边设置 headport / tailport
+    #    - 若端口为 compass：直接用 compass（e.g., headport="e"）
+    #    - 若端口为命名端口：使用在 record 中定义的 <port> 名（同名即可）
+    for (u, v, sp, tp) in edges_data:
+        e = A.get_edge(u, v)
+
+        # Graphviz 属性：tail 是源，head 是目标
+        if sp:
+            if _is_compass(sp):
+                e.attr["tailport"] = sp.lower()
+            else:
+                # 与 record label 中 <port> 名一致；特殊字符已在 label 中做了清洗
+                e.attr["tailport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(sp))
+
+        if tp:
+            if _is_compass(tp):
+                e.attr["headport"] = tp.lower()
+            else:
+                e.attr["headport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(tp))
+
+        # 可选：若想让边更贴边缘，可设置 constraint/spline 等
+        # e.attr["arrowhead"] = "vee"
+
+    # 5) 输出
+    A.draw(output_path, prog="dot")
+    print(f"  - Port-aware workflow rendered to '{output_path}'")
+
+
+def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
+    """展平嵌套的XDL程序结构"""
+    flattened_operations = []
+    TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
+
+    def extract_operations(element: ET.Element):
+        if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
+            if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
+                flattened_operations.append(element)
+
+        for child in element:
+            extract_operations(child)
+
+    for child in procedure_elem:
+        extract_operations(child)
+
+    return flattened_operations
+
+
+def parse_xdl_content(xdl_content: str) -> tuple:
+    """解析XDL内容"""
+    try:
+        xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
+        root = ET.fromstring(xdl_content_cleaned)
+
+        synthesis_elem = root.find("Synthesis")
+        if synthesis_elem is None:
+            return None, None, None
+
+        # 解析硬件组件
+        hardware_elem = synthesis_elem.find("Hardware")
+        hardware = []
+        if hardware_elem is not None:
+            hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
+
+        # 解析试剂
+        reagents_elem = synthesis_elem.find("Reagents")
+        reagents = []
+        if reagents_elem is not None:
+            reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
+
+        # 解析程序
+        procedure_elem = synthesis_elem.find("Procedure")
+        if procedure_elem is None:
+            return None, None, None
+
+        flattened_operations = flatten_xdl_procedure(procedure_elem)
+        return hardware, reagents, flattened_operations
+
+    except ET.ParseError as e:
+        raise ValueError(f"Invalid XDL format: {e}")
+
+
+def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
+    """
+    将XDL XML格式转换为标准的字典格式
+
+    Args:
+        xdl_content: XDL XML内容
+
+    Returns:
+        转换结果，包含步骤和器材信息
+    """
+    try:
+        hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
+        if hardware is None:
+            return {"error": "Failed to parse XDL content", "success": False}
+
+        # 将XDL元素转换为字典格式
+        steps_data = []
+        for elem in flattened_operations:
+            # 转换参数类型
+            parameters = {}
+            for key, val in elem.attrib.items():
+                converted_val = convert_to_type(val)
+                if converted_val is not None:
+                    parameters[key] = converted_val
+
+            step_dict = {
+                "operation": elem.tag,
+                "parameters": parameters,
+                "description": elem.get("purpose", f"Operation: {elem.tag}"),
+            }
+            steps_data.append(step_dict)
+
+        # 合并硬件和试剂为统一的labware_info格式
+        labware_data = []
+        labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
+        labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
+
+        return {
+            "success": True,
+            "steps": steps_data,
+            "labware": labware_data,
+            "message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
+        }
+
+    except Exception as e:
+        error_msg = f"XDL conversion failed: {str(e)}"
+        logger.error(error_msg)
+        return {"error": error_msg, "success": False}
 
 
 def create_workflow(

unilabos/app/main.py

@@ -1,7 +1,6 @@
 import argparse
 import asyncio
 import os
-import platform
 import shutil
 import signal
 import sys
@@ -359,7 +358,7 @@ def main():
     if BasicConfig.test_mode:
         print_status("启用测试模式：所有动作将模拟执行，不调用真实硬件", "warning")
     BasicConfig.communication_protocol = "websocket"
-    machine_name = platform.node()
+    machine_name = os.popen("hostname").read().strip()
     machine_name = "".join([c if c.isalnum() or c == "_" else "_" for c in machine_name])
     BasicConfig.machine_name = machine_name
     BasicConfig.vis_2d_enable = args_dict["2d_vis"]

unilabos/app/ws_client.py

@@ -478,7 +478,7 @@ class MessageProcessor:
                     self.connected = True
                     self.reconnect_count = 0
 
-                    logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
+                    logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
 
                     # 启动发送协程
                     send_task = asyncio.create_task(self._send_handler())
@@ -556,7 +556,7 @@ class MessageProcessor:
 
     async def _send_handler(self):
         """处理发送队列中的消息"""
-        logger.trace("[MessageProcessor] Send handler started")
+        logger.debug("[MessageProcessor] Send handler started")
 
         try:
             while self.connected and self.websocket:
@@ -1090,7 +1090,7 @@ class QueueProcessor:
 
     def _run(self):
         """运行队列处理主循环"""
-        logger.trace("[QueueProcessor] Queue processor started")
+        logger.debug("[QueueProcessor] Queue processor started")
 
         while self.is_running:
             try:
@@ -1305,6 +1305,7 @@ class WebSocketClient(BaseCommunicationClient):
         else:
             url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
 
+        logger.debug(f"[WebSocketClient] URL: {url}")
         return url
 
     def start(self) -> None:
@@ -1317,11 +1318,13 @@ class WebSocketClient(BaseCommunicationClient):
             logger.error("[WebSocketClient] WebSocket URL not configured")
             return
 
+        logger.info(f"[WebSocketClient] Starting connection to {self.websocket_url}")
+
         # 启动两个核心线程
         self.message_processor.start()
         self.queue_processor.start()
 
-        logger.trace("[WebSocketClient] All threads started")
+        logger.info("[WebSocketClient] All threads started")
 
     def stop(self) -> None:
         """停止WebSocket客户端"""

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -55,7 +55,6 @@ from unilabos.devices.liquid_handling.liquid_handler_abstract import (
     TransferLiquidReturn,
 )
 from unilabos.registry.placeholder_type import ResourceSlot
-from unilabos.resources.resource_tracker import ResourceTreeSet
 from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
 
 
@@ -91,107 +90,20 @@ class PRCXI9300Deck(Deck):
     该类定义了 PRCXI 9300 的工作台布局和槽位信息。
     """
 
-    # T1-T16 默认位置 (4列×4行)
+    def __init__(self, name: str, size_x: float, size_y: float, size_z: float, **kwargs):
-    _DEFAULT_SITE_POSITIONS = [
+        super().__init__(size_x, size_y, size_z, name)
-        (0, 0, 0), (138, 0, 0), (276, 0, 0), (414, 0, 0),         # T1-T4
+        self.slots = [None] * 16  # PRCXI 9300/9320 最大有 16 个槽位
-        (0, 96, 0), (138, 96, 0), (276, 96, 0), (414, 96, 0),     # T5-T8
+        self.slot_locations = [Coordinate(0, 0, 0)] * 16
-        (0, 192, 0), (138, 192, 0), (276, 192, 0), (414, 192, 0), # T9-T12
-        (0, 288, 0), (138, 288, 0), (276, 288, 0), (414, 288, 0), # T13-T16
-    ]
-    _DEFAULT_SITE_SIZE = {"width": 128.0, "height": 86, "depth": 0}
-    _DEFAULT_CONTENT_TYPE = ["plate", "tip_rack", "plates", "tip_racks", "tube_rack", "adaptor"]
-
-    def __init__(self, name: str, size_x: float, size_y: float, size_z: float,
-                 sites: Optional[List[Dict[str, Any]]] = None, **kwargs):
-        super().__init__(name, size_x, size_y, size_z)
-        if sites is not None:
-            self.sites: List[Dict[str, Any]] = [dict(s) for s in sites]
-        else:
-            self.sites = []
-            for i, (x, y, z) in enumerate(self._DEFAULT_SITE_POSITIONS):
-                self.sites.append({
-                    "label": f"T{i + 1}",
-                    "visible": True,
-                    "position": {"x": x, "y": y, "z": z},
-                    "size": dict(self._DEFAULT_SITE_SIZE),
-                    "content_type": list(self._DEFAULT_CONTENT_TYPE),
-                })
-        # _ordering: label -> None, 用于外部通过 list(keys()).index(site) 将 Tn 转换为 spot index
-        self._ordering = collections.OrderedDict(
-            (site["label"], None) for site in self.sites
-        )
-        self.root = self.get_root()
-
-    def _get_site_location(self, idx: int) -> Coordinate:
-        pos = self.sites[idx]["position"]
-        return Coordinate(pos["x"], pos["y"], pos["z"])
-
-    def _get_site_resource(self, idx: int) -> Optional[Resource]:
-        site_loc = self._get_site_location(idx)
-        for child in self.children:
-            if child.location == site_loc:
-                return child
-        return None
-
-    def assign_child_resource(
-        self,
-        resource: Resource,
-        location: Optional[Coordinate] = None,
-        reassign: bool = True,
-        spot: Optional[int] = None,
-    ):
-        idx = spot
-        if spot is not None:
-            idx = spot
-        else:
-            for i, site in enumerate(self.sites):
-                site_loc = self._get_site_location(i)
-                if site.get("label") == resource.name:
-                    idx = i
-                    break
-                if location is not None and site_loc == location:
-                    idx = i
-                    break
-
-        if idx is None:
-            for i in range(len(self.sites)):
-                if self._get_site_resource(i) is None:
-                    idx = i
-                    break
-
-        if idx is None:
-            raise ValueError(f"No available site on deck '{self.name}' for resource '{resource.name}'")
-
-        if not reassign and self._get_site_resource(idx) is not None:
-            existing = self.root.get_resource(resource.name)
-            if existing is not resource and existing.parent is not None:
-                existing.parent.unassign_child_resource(existing)
-
-
-        loc = self._get_site_location(idx)
-        super().assign_child_resource(resource, location=loc, reassign=reassign)
 
     def assign_child_at_slot(self, resource: Resource, slot: int, reassign: bool = False) -> None:
-        self.assign_child_resource(resource, spot=slot - 1, reassign=reassign)
+        if self.slots[slot - 1] is not None and not reassign:
+            raise ValueError(f"Spot {slot} is already occupied")
 
-    def serialize(self) -> dict:
+        self.slots[slot - 1] = resource
-        data = super().serialize()
+        super().assign_child_resource(resource, location=self.slot_locations[slot - 1])
-        sites_out = []
-        for i, site in enumerate(self.sites):
-            occupied = self._get_site_resource(i)
-            sites_out.append({
-                "label": site["label"],
-                "visible": site.get("visible", True),
-                "occupied_by": occupied.name if occupied is not None else None,
-                "position": site["position"],
-                "size": site["size"],
-                "content_type": site["content_type"],
-            })
-        data["sites"] = sites_out
-        return data
 
 
-class PRCXI9300Container(Container):
+class PRCXI9300Container(Plate):
     """PRCXI 9300 的专用 Container 类，继承自 Plate，用于槽位定位和未知模块。
 
     该类定义了 PRCXI 9300 的工作台布局和槽位信息。
@@ -204,10 +116,11 @@ class PRCXI9300Container(Container):
         size_y: float,
         size_z: float,
         category: str,
+        ordering: collections.OrderedDict,
         model: Optional[str] = None,
         **kwargs,
     ):
-        super().__init__(name, size_x, size_y, size_z, category=category, model=model)
+        super().__init__(name, size_x, size_y, size_z, category=category, ordering=ordering, model=model)
         self._unilabos_state = {}
 
     def load_state(self, state: Dict[str, Any]) -> None:
@@ -654,14 +567,14 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         tablets_info = []
         count = 0
         for child in deck.children:
-            # 如果放其他类型的物料，是不可以的
+            if child.children:
-            if hasattr(child, "_unilabos_state") and "Material" in child._unilabos_state:
+                if "Material" in child.children[0]._unilabos_state:
-                number = int(child.name.replace("T", ""))
+                    number = int(child.name.replace("T", ""))
-                tablets_info.append(
+                    tablets_info.append(
-                    WorkTablets(
+                        WorkTablets(
-                        Number=number, Code=f"T{number}", Material=child._unilabos_state["Material"]
+                            Number=number, Code=f"T{number}", Material=child.children[0]._unilabos_state["Material"]
+                        )
                     )
-                )
         if is_9320:
             print("当前设备是9320")
         # 始终初始化 step_mode 属性
@@ -798,7 +711,6 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         touch_tip: bool = False,
         liquid_height: Optional[List[Optional[float]]] = None,
         blow_out_air_volume: Optional[List[Optional[float]]] = None,
-        blow_out_air_volume_before: Optional[List[Optional[float]]] = None,
         spread: Literal["wide", "tight", "custom"] = "wide",
         is_96_well: bool = False,
         mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
@@ -809,9 +721,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         delays: Optional[List[int]] = None,
         none_keys: List[str] = [],
     ) -> TransferLiquidReturn:
-        if self.step_mode:
+        return await super().transfer_liquid(
-            await self.create_protocol(f"transfer_liquid{time.time()}")
-        res =  await super().transfer_liquid(
             sources,
             targets,
             tip_racks,
@@ -824,7 +734,6 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
             touch_tip=touch_tip,
             liquid_height=liquid_height,
             blow_out_air_volume=blow_out_air_volume,
-            blow_out_air_volume_before=blow_out_air_volume_before,
             spread=spread,
             is_96_well=is_96_well,
             mix_stage=mix_stage,
@@ -835,9 +744,6 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
             delays=delays,
             none_keys=none_keys,
         )
-        if self.step_mode:
-            await self.run_protocol()
-        return res
 
     async def custom_delay(self, seconds=0, msg=None):
         return await super().custom_delay(seconds, msg)
@@ -854,10 +760,9 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
         offsets: Optional[Coordinate] = None,
         mix_rate: Optional[float] = None,
         none_keys: List[str] = [],
-        use_channels: Optional[List[int]] = [0],
     ):
         return await self._unilabos_backend.mix(
-            targets, mix_time, mix_vol, height_to_bottom, offsets, mix_rate, none_keys, use_channels
+            targets, mix_time, mix_vol, height_to_bottom, offsets, mix_rate, none_keys
         )
 
     def iter_tips(self, tip_racks: Sequence[TipRack]) -> Iterator[Resource]:
@@ -1286,15 +1191,9 @@ class PRCXI9300Backend(LiquidHandlerBackend):
         offsets: Optional[Coordinate] = None,
         mix_rate: Optional[float] = None,
         none_keys: List[str] = [],
-        use_channels: Optional[List[int]] = [0],
     ):
         """Mix liquid in the specified resources."""
-        if use_channels == [0]:
+
-            axis = "Left"
-        elif use_channels == [1]:
-            axis = "Right"
-        else:
-            raise ValueError("Invalid use channels: " + str(use_channels))
         plate_indexes = []
         for op in targets:
             deck = op.parent.parent.parent

unilabos/registry/devices/liquid_handler.yaml

@@ -4976,13 +4976,13 @@ liquid_handler.biomek:
             handler_key: tip_rack
             label: tip_rack
           output:
-          - data_key: sources
+          - data_key: liquid
             data_source: handle
             data_type: resource
             handler_key: sources_out
             label: sources
-          - data_key: targets
+          - data_key: liquid
-            data_source: handle
+            data_source: executor
             data_type: resource
             handler_key: targets_out
             label: targets
@@ -7656,43 +7656,6 @@ liquid_handler.prcxi:
           title: iter_tips参数
           type: object
         type: UniLabJsonCommand
-      auto-magnetic_action:
-        feedback: {}
-        goal: {}
-        goal_default:
-          height: null
-          is_wait: null
-          module_no: null
-          time: null
-        handles: {}
-        placeholder_keys: {}
-        result: {}
-        schema:
-          description: ''
-          properties:
-            feedback: {}
-            goal:
-              properties:
-                height:
-                  type: integer
-                is_wait:
-                  type: boolean
-                module_no:
-                  type: integer
-                time:
-                  type: integer
-              required:
-              - time
-              - module_no
-              - height
-              - is_wait
-              type: object
-            result: {}
-          required:
-          - goal
-          title: magnetic_action参数
-          type: object
-        type: UniLabJsonCommandAsync
       auto-move_to:
         feedback: {}
         goal: {}
@@ -7726,31 +7689,6 @@ liquid_handler.prcxi:
           title: move_to参数
           type: object
         type: UniLabJsonCommandAsync
-      auto-plr_pos_to_prcxi:
-        feedback: {}
-        goal: {}
-        goal_default:
-          resource: null
-        handles: {}
-        placeholder_keys: {}
-        result: {}
-        schema:
-          description: ''
-          properties:
-            feedback: {}
-            goal:
-              properties:
-                resource:
-                  type: object
-              required:
-              - resource
-              type: object
-            result: {}
-          required:
-          - goal
-          title: plr_pos_to_prcxi参数
-          type: object
-        type: UniLabJsonCommand
       auto-post_init:
         feedback: {}
         goal: {}
@@ -7871,47 +7809,6 @@ liquid_handler.prcxi:
           title: shaker_action参数
           type: object
         type: UniLabJsonCommandAsync
-      auto-shaking_incubation_action:
-        feedback: {}
-        goal: {}
-        goal_default:
-          amplitude: null
-          is_wait: null
-          module_no: null
-          temperature: null
-          time: null
-        handles: {}
-        placeholder_keys: {}
-        result: {}
-        schema:
-          description: ''
-          properties:
-            feedback: {}
-            goal:
-              properties:
-                amplitude:
-                  type: integer
-                is_wait:
-                  type: boolean
-                module_no:
-                  type: integer
-                temperature:
-                  type: integer
-                time:
-                  type: integer
-              required:
-              - time
-              - module_no
-              - amplitude
-              - is_wait
-              - temperature
-              type: object
-            result: {}
-          required:
-          - goal
-          title: shaking_incubation_action参数
-          type: object
-        type: UniLabJsonCommandAsync
       auto-touch_tip:
         feedback: {}
         goal: {}
@@ -10137,28 +10034,116 @@ liquid_handler.prcxi:
         type: Transfer
       transfer_liquid:
         feedback: {}
-        goal: {}
+        goal:
+          asp_flow_rates: asp_flow_rates
+          asp_vols: asp_vols
+          blow_out_air_volume: blow_out_air_volume
+          delays: delays
+          dis_flow_rates: dis_flow_rates
+          dis_vols: dis_vols
+          is_96_well: is_96_well
+          liquid_height: liquid_height
+          mix_liquid_height: mix_liquid_height
+          mix_rate: mix_rate
+          mix_stage: mix_stage
+          mix_times: mix_times
+          mix_vol: mix_vol
+          none_keys: none_keys
+          offsets: offsets
+          sources: sources
+          spread: spread
+          targets: targets
+          tip_racks: tip_racks
+          touch_tip: touch_tip
+          use_channels: use_channels
         goal_default:
-          asp_flow_rates: null
+          asp_flow_rates:
-          asp_vols: null
+          - 0.0
-          blow_out_air_volume: null
+          asp_vols:
-          blow_out_air_volume_before: null
+          - 0.0
-          delays: null
+          blow_out_air_volume:
-          dis_flow_rates: null
+          - 0.0
-          dis_vols: null
+          delays:
+          - 0
+          dis_flow_rates:
+          - 0.0
+          dis_vols:
+          - 0.0
           is_96_well: false
-          liquid_height: null
+          liquid_height:
-          mix_liquid_height: null
+          - 0.0
-          mix_rate: null
+          mix_liquid_height: 0.0
-          mix_stage: none
+          mix_rate: 0
-          mix_times: null
+          mix_stage: ''
-          mix_vol: null
+          mix_times: 0
-          none_keys: []
+          mix_vol: 0
-          offsets: null
+          none_keys:
-          sources: null
+          - ''
-          spread: wide
+          offsets:
-          targets: null
+          - x: 0.0
-          tip_racks: null
+            y: 0.0
+            z: 0.0
+          sources:
+          - category: ''
+            children: []
+            config: ''
+            data: ''
+            id: ''
+            name: ''
+            parent: ''
+            pose:
+              orientation:
+                w: 1.0
+                x: 0.0
+                y: 0.0
+                z: 0.0
+              position:
+                x: 0.0
+                y: 0.0
+                z: 0.0
+            sample_id: ''
+            type: ''
+          spread: ''
+          targets:
+          - category: ''
+            children: []
+            config: ''
+            data: ''
+            id: ''
+            name: ''
+            parent: ''
+            pose:
+              orientation:
+                w: 1.0
+                x: 0.0
+                y: 0.0
+                z: 0.0
+              position:
+                x: 0.0
+                y: 0.0
+                z: 0.0
+            sample_id: ''
+            type: ''
+          tip_racks:
+          - category: ''
+            children: []
+            config: ''
+            data: ''
+            id: ''
+            name: ''
+            parent: ''
+            pose:
+              orientation:
+                w: 1.0
+                x: 0.0
+                y: 0.0
+                z: 0.0
+              position:
+                x: 0.0
+                y: 0.0
+                z: 0.0
+            sample_id: ''
+            type: ''
           touch_tip: false
           use_channels:
           - 0
@@ -10174,7 +10159,7 @@ liquid_handler.prcxi:
             data_type: resource
             handler_key: targets_identifier
             label: 转移目标
-          - data_key: tip_racks
+          - data_key: tip_rack
             data_source: handle
             data_type: resource
             handler_key: tip_rack_identifier
@@ -10198,7 +10183,11 @@ liquid_handler.prcxi:
         schema:
           description: ''
           properties:
-            feedback: {}
+            feedback:
+              properties: {}
+              required: []
+              title: LiquidHandlerTransfer_Feedback
+              type: object
             goal:
               properties:
                 asp_flow_rates:
@@ -10213,10 +10202,6 @@ liquid_handler.prcxi:
                   items:
                     type: number
                   type: array
-                blow_out_air_volume_before:
-                  items:
-                    type: number
-                  type: array
                 delays:
                   items:
                     maximum: 2147483647
@@ -10232,7 +10217,6 @@ liquid_handler.prcxi:
                     type: number
                   type: array
                 is_96_well:
-                  default: false
                   type: boolean
                 liquid_height:
                   items:
@@ -10245,7 +10229,6 @@ liquid_handler.prcxi:
                   minimum: -2147483648
                   type: integer
                 mix_stage:
-                  default: none
                   type: string
                 mix_times:
                   maximum: 2147483647
@@ -10256,7 +10239,6 @@ liquid_handler.prcxi:
                   minimum: -2147483648
                   type: integer
                 none_keys:
-                  default: []
                   items:
                     type: string
                   type: array
@@ -10352,7 +10334,6 @@ liquid_handler.prcxi:
                     type: object
                   type: array
                 spread:
-                  default: wide
                   type: string
                 targets:
                   items:
@@ -10505,7 +10486,6 @@ liquid_handler.prcxi:
                     type: object
                   type: array
                 touch_tip:
-                  default: false
                   type: boolean
                 use_channels:
                   items:
@@ -10514,221 +10494,45 @@ liquid_handler.prcxi:
                     type: integer
                   type: array
               required:
+              - asp_vols
+              - dis_vols
               - sources
               - targets
               - tip_racks
-              - asp_vols
+              - use_channels
-              - dis_vols
+              - asp_flow_rates
+              - dis_flow_rates
+              - offsets
+              - touch_tip
+              - liquid_height
+              - blow_out_air_volume
+              - spread
+              - is_96_well
+              - mix_stage
+              - mix_times
+              - mix_vol
+              - mix_rate
+              - mix_liquid_height
+              - delays
+              - none_keys
+              title: LiquidHandlerTransfer_Goal
               type: object
             result:
-              $defs:
-                ResourceDict:
-                  properties:
-                    class:
-                      description: Resource class name
-                      title: Class
-                      type: string
-                    config:
-                      additionalProperties: true
-                      description: Resource configuration
-                      title: Config
-                      type: object
-                    data:
-                      additionalProperties: true
-                      description: 'Resource data, eg: container liquid data'
-                      title: Data
-                      type: object
-                    description:
-                      default: ''
-                      description: Resource description
-                      title: Description
-                      type: string
-                    extra:
-                      additionalProperties: true
-                      description: 'Extra data, eg: slot index'
-                      title: Extra
-                      type: object
-                    icon:
-                      default: ''
-                      description: Resource icon
-                      title: Icon
-                      type: string
-                    id:
-                      description: Resource ID
-                      title: Id
-                      type: string
-                    model:
-                      additionalProperties: true
-                      description: Resource model
-                      title: Model
-                      type: object
-                    name:
-                      description: Resource name
-                      title: Name
-                      type: string
-                    parent:
-                      anyOf:
-                      - $ref: '#/$defs/ResourceDict'
-                      - type: 'null'
-                      default: null
-                      description: Parent resource object
-                    parent_uuid:
-                      anyOf:
-                      - type: string
-                      - type: 'null'
-                      default: null
-                      description: Parent resource uuid
-                      title: Parent Uuid
-                    pose:
-                      $ref: '#/$defs/ResourceDictPosition'
-                      description: Resource position
-                    schema:
-                      additionalProperties: true
-                      description: Resource schema
-                      title: Schema
-                      type: object
-                    type:
-                      anyOf:
-                      - const: device
-                        type: string
-                      - type: string
-                      description: Resource type
-                      title: Type
-                    uuid:
-                      description: Resource UUID
-                      title: Uuid
-                      type: string
-                  required:
-                  - id
-                  - uuid
-                  - name
-                  - type
-                  - class
-                  - config
-                  - data
-                  - extra
-                  title: ResourceDict
-                  type: object
-                ResourceDictPosition:
-                  properties:
-                    cross_section_type:
-                      default: rectangle
-                      description: Cross section type
-                      enum:
-                      - rectangle
-                      - circle
-                      - rounded_rectangle
-                      title: Cross Section Type
-                      type: string
-                    layout:
-                      default: x-y
-                      description: Resource layout
-                      enum:
-                      - 2d
-                      - x-y
-                      - z-y
-                      - x-z
-                      title: Layout
-                      type: string
-                    position:
-                      $ref: '#/$defs/ResourceDictPositionObject'
-                      description: Resource position
-                    position3d:
-                      $ref: '#/$defs/ResourceDictPositionObject'
-                      description: Resource position in 3D space
-                    rotation:
-                      $ref: '#/$defs/ResourceDictPositionObject'
-                      description: Resource rotation
-                    scale:
-                      $ref: '#/$defs/ResourceDictPositionScale'
-                      description: Resource scale
-                    size:
-                      $ref: '#/$defs/ResourceDictPositionSize'
-                      description: Resource size
-                  title: ResourceDictPosition
-                  type: object
-                ResourceDictPositionObject:
-                  properties:
-                    x:
-                      default: 0.0
-                      description: X coordinate
-                      title: X
-                      type: number
-                    y:
-                      default: 0.0
-                      description: Y coordinate
-                      title: Y
-                      type: number
-                    z:
-                      default: 0.0
-                      description: Z coordinate
-                      title: Z
-                      type: number
-                  title: ResourceDictPositionObject
-                  type: object
-                ResourceDictPositionScale:
-                  properties:
-                    x:
-                      default: 0.0
-                      description: x scale
-                      title: X
-                      type: number
-                    y:
-                      default: 0.0
-                      description: y scale
-                      title: Y
-                      type: number
-                    z:
-                      default: 0.0
-                      description: z scale
-                      title: Z
-                      type: number
-                  title: ResourceDictPositionScale
-                  type: object
-                ResourceDictPositionSize:
-                  properties:
-                    depth:
-                      default: 0.0
-                      description: Depth
-                      title: Depth
-                      type: number
-                    height:
-                      default: 0.0
-                      description: Height
-                      title: Height
-                      type: number
-                    width:
-                      default: 0.0
-                      description: Width
-                      title: Width
-                      type: number
-                  title: ResourceDictPositionSize
-                  type: object
               properties:
-                sources:
+                return_info:
-                  items:
+                  type: string
-                    items:
+                success:
-                      $ref: '#/$defs/ResourceDict'
+                  type: boolean
-                    type: array
-                  title: Sources
-                  type: array
-                targets:
-                  items:
-                    items:
-                      $ref: '#/$defs/ResourceDict'
-                    type: array
-                  title: Targets
-                  type: array
               required:
-              - sources
+              - return_info
-              - targets
+              - success
-              title: TransferLiquidReturn
+              title: LiquidHandlerTransfer_Result
               type: object
           required:
           - goal
-          title: transfer_liquid参数
+          title: LiquidHandlerTransfer
           type: object
-        type: UniLabJsonCommandAsync
+        type: LiquidHandlerTransfer
     module: unilabos.devices.liquid_handling.prcxi.prcxi:PRCXI9300Handler
     status_types:
       reset_ok: bool
@@ -10751,12 +10555,6 @@ liquid_handler.prcxi:
           type: string
         deck:
           type: object
-        deck_y:
-          default: 400
-          type: string
-        deck_z:
-          default: 300
-          type: string
         host:
           type: string
         is_9320:
@@ -10767,44 +10565,17 @@ liquid_handler.prcxi:
           type: string
         port:
           type: integer
-        rail_interval:
-          default: 0
-          type: string
-        rail_nums:
-          default: 4
-          type: string
-        rail_width:
-          default: 27.5
-          type: string
         setup:
           default: true
           type: string
         simulator:
           default: false
           type: string
-        start_rail:
-          default: 2
-          type: string
         step_mode:
           default: false
           type: string
         timeout:
           type: number
-        x_increase:
-          default: -0.003636
-          type: string
-        x_offset:
-          default: -0.8
-          type: string
-        xy_coupling:
-          default: -0.0045
-          type: string
-        y_increase:
-          default: -0.003636
-          type: string
-        y_offset:
-          default: -37.98
-          type: string
       required:
       - deck
       - host

unilabos/registry/registry.py

@@ -175,8 +175,7 @@ class Registry:
                                     "res_id": "unilabos_resources",  # 将当前实验室的全部物料id作为下拉框可选择
                                     "device_id": "unilabos_devices",  # 将当前实验室的全部设备id作为下拉框可选择
                                     "parent": "unilabos_nodes",  # 将当前实验室的设备/物料作为下拉框可选择
-                                    "class_name": "unilabos_class",  # 当前实验室物料的class name
+                                    "class_name": "unilabos_class",
-                                    "slot_on_deck": "unilabos_resource_slot:parent",  # 勾选的parent的config中的sites的name，展示name，参数对应slot（index）
                                 },
                             },
                             "test_latency": {

unilabos/resources/container.py

@@ -1,6 +1,10 @@
+import json
 from typing import Dict, Any
 
 from pylabrobot.resources import Container
+from unilabos_msgs.msg import Resource
+
+from unilabos.ros.msgs.message_converter import convert_from_ros_msg
 
 
 class RegularContainer(Container):
@@ -12,12 +16,12 @@ class RegularContainer(Container):
             kwargs["size_y"] = 0
         if "size_z" not in kwargs:
             kwargs["size_z"] = 0
-
         self.kwargs = kwargs
+        self.state = {}
         super().__init__(*args, category="container", **kwargs)
 
     def load_state(self, state: Dict[str, Any]):
-        super().load_state(state)
+        self.state = state
 
 
 def get_regular_container(name="container"):
@@ -25,6 +29,7 @@ def get_regular_container(name="container"):
     r.category = "container"
     return r
 
+#
 # class RegularContainer(object):
 #     # 第一个参数必须是id传入
 #     # noinspection PyShadowingBuiltins
@@ -84,4 +89,4 @@ def get_regular_container(name="container"):
 #         return to_dict
 #
 #     def __str__(self):
-#         return f"{self.id}"
+#         return f"{self.id}"

unilabos/resources/graphio.py

@@ -42,7 +42,7 @@ def canonicalize_nodes_data(
     Returns:
         ResourceTreeSet: 标准化后的资源树集合
     """
-    print_status(f"{len(nodes)} Resources loaded", "info")
+    print_status(f"{len(nodes)} Resources loaded:", "info")
 
     # 第一步：基本预处理（处理graphml的label字段）
     outer_host_node_id = None
@@ -76,7 +76,7 @@ def canonicalize_nodes_data(
             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", "pose", "extra"]:
+            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:

unilabos/resources/resource_tracker.py

@@ -16,7 +16,6 @@ if TYPE_CHECKING:
 
 
 EXTRA_CLASS = "unilabos_resource_class"
-FRONTEND_POSE_EXTRA = "unilabos_frontend_pose_extra"
 EXTRA_SAMPLE_UUID = "sample_uuid"
 EXTRA_UNILABOS_SAMPLE_UUID = "unilabos_sample_uuid"
 
@@ -75,14 +74,6 @@ class ResourceDictPositionObject(BaseModel):
     z: float = Field(description="Z coordinate", default=0.0)
 
 
-class ResourceDictPoseExtraObjectType(BaseModel):
-    z_index: int
-
-
-class ResourceDictPoseExtraObject(BaseModel):
-    z_index: Optional[int] = Field(alias="zIndex", default=None)
-
-
 class ResourceDictPositionType(TypedDict):
     size: ResourceDictPositionSizeType
     scale: ResourceDictPositionScaleType
@@ -109,7 +100,6 @@ class ResourceDictPosition(BaseModel):
     cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"] = Field(
         description="Cross section type", default="rectangle"
     )
-    extra: Optional[ResourceDictPoseExtraObject] = Field(description="Extra data", default=None)
 
 
 class ResourceDictType(TypedDict):
@@ -147,8 +137,8 @@ class ResourceDict(BaseModel):
     klass: str = Field(alias="class", description="Resource class name")
     pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
     config: Dict[str, Any] = Field(description="Resource configuration")
-    data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
+    data: Dict[str, Any] = Field(description="Resource data")
-    extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
+    extra: Dict[str, Any] = Field(description="Extra data")
 
     @field_serializer("parent_uuid")
     def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
@@ -421,15 +411,6 @@ class ResourceTreeSet(object):
                 "tip_spot": "tip_spot",
                 "tube": "tube",
                 "bottle_carrier": "bottle_carrier",
-                "material_hole": "material_hole",
-                "container": "container",
-                "material_plate": "material_plate",
-                "electrode_sheet": "electrode_sheet",
-                "warehouse": "warehouse",
-                "magazine_holder": "magazine_holder",
-                "resource_group": "resource_group",
-                "trash": "trash",
-                "plate_adapter": "plate_adapter",
             }
             if source in replace_info:
                 return replace_info[source]
@@ -473,7 +454,6 @@ class ResourceTreeSet(object):
                 "position3d": raw_pos,
                 "rotation": d["rotation"],
                 "cross_section_type": d.get("cross_section_type", "rectangle"),
-                "extra": extra.get(FRONTEND_POSE_EXTRA)
             }
 
             # 先构建当前节点的字典（不包含children）
@@ -534,17 +514,10 @@ class ResourceTreeSet(object):
             trees.append(tree_instance)
         return cls(trees)
 
-    def to_plr_resources(
+    def to_plr_resources(self, skip_devices=True) -> List["PLRResource"]:
-        self, skip_devices: bool = True, requested_uuids: Optional[List[str]] = None
-    ) -> List["PLRResource"]:
         """
         将 ResourceTreeSet 转换为 PLR 资源列表
 
-        Args:
-            skip_devices: 是否跳过 device 类型节点
-            requested_uuids: 若指定，则按此 UUID 顺序返回对应资源（用于批量查询时一一对应），
-                否则返回各树的根节点列表
-
         Returns:
             List[PLRResource]: PLR 资源实例列表
         """
@@ -566,7 +539,6 @@ class ResourceTreeSet(object):
             name_to_uuid[node.res_content.name] = node.res_content.uuid
             all_states[node.res_content.name] = node.res_content.data
             name_to_extra[node.res_content.name] = node.res_content.extra
-            name_to_extra[node.res_content.name][FRONTEND_POSE_EXTRA] = node.res_content.pose.extra
             name_to_extra[node.res_content.name][EXTRA_CLASS] = node.res_content.klass
             for child in node.children:
                 collect_node_data(child, name_to_uuid, all_states, name_to_extra)
@@ -600,71 +572,6 @@ class ResourceTreeSet(object):
                 d["model"] = res.config.get("model", None)
             return d
 
-        # deserialize 会单独处理的元数据 key，不传给构造函数
-        _META_KEYS = {"type", "parent_name", "location", "children", "rotation", "barcode"}
-        # deserialize 自定义逻辑使用的 key（如 TipSpot 用 prototype_tip 构建 make_tip），需保留
-        _DESERIALIZE_PRESERVED_KEYS = {"prototype_tip"}
-
-        def remove_incompatible_params(plr_d: dict) -> None:
-            """递归移除 PLR 类不接受的参数，避免 deserialize 报错。
-            - 移除构造函数不接受的参数（如 compute_height_from_volume、ordering、category）
-            - 对 TubeRack：将 ordering 转为 ordered_items
-            - 保留 deserialize 自定义逻辑需要的 key（如 prototype_tip）
-            """
-            if "type" in plr_d:
-                sub_cls = find_subclass(plr_d["type"], PLRResource)
-                if sub_cls is not None:
-                    spec = inspect.signature(sub_cls)
-                    valid_params = set(spec.parameters.keys())
-                    # TubeRack 特殊处理：先转换 ordering，再参与后续过滤
-                    if "ordering" not in valid_params and "ordering" in plr_d:
-                        ordering = plr_d.pop("ordering", None)
-                        if sub_cls.__name__ == "TubeRack":
-                            plr_d["ordered_items"] = (
-                                _ordering_to_ordered_items(plr_d, ordering)
-                                if ordering
-                                else {}
-                            )
-                    # 移除构造函数不接受的参数（保留 META 和 deserialize 自定义逻辑需要的 key）
-                    for key in list(plr_d.keys()):
-                        if (
-                            key not in _META_KEYS
-                            and key not in _DESERIALIZE_PRESERVED_KEYS
-                            and key not in valid_params
-                        ):
-                            plr_d.pop(key, None)
-            for child in plr_d.get("children", []):
-                remove_incompatible_params(child)
-
-        def _ordering_to_ordered_items(plr_d: dict, ordering: dict) -> dict:
-            """将 ordering 转为 ordered_items，从 children 构建 Tube 对象"""
-            from pylabrobot.resources import Tube, Coordinate
-            from pylabrobot.serializer import deserialize as plr_deserialize
-
-            children = plr_d.get("children", [])
-            ordered_items = {}
-            for idx, (ident, child_name) in enumerate(ordering.items()):
-                child_data = children[idx] if idx < len(children) else None
-                if child_data is None:
-                    continue
-                loc_data = child_data.get("location")
-                loc = (
-                    plr_deserialize(loc_data)
-                    if loc_data
-                    else Coordinate(0, 0, 0)
-                )
-                tube = Tube(
-                    name=child_data.get("name", child_name or ident),
-                    size_x=child_data.get("size_x", 10),
-                    size_y=child_data.get("size_y", 10),
-                    size_z=child_data.get("size_z", 50),
-                    max_volume=child_data.get("max_volume", 1000),
-                )
-                tube.location = loc
-                ordered_items[ident] = tube
-            plr_d["children"] = []  # 已并入 ordered_items，避免重复反序列化
-            return ordered_items
-
         plr_resources = []
         tracker = DeviceNodeResourceTracker()
 
@@ -684,7 +591,9 @@ class ResourceTreeSet(object):
                     raise ValueError(
                         f"无法找到类型 {plr_dict['type']} 对应的 PLR 资源类。原始信息：{tree.root_node.res_content}"
                     )
-                remove_incompatible_params(plr_dict)
+                spec = inspect.signature(sub_cls)
+                if "category" not in spec.parameters:
+                    plr_dict.pop("category", None)
                 plr_resource = sub_cls.deserialize(plr_dict, allow_marshal=True)
                 from pylabrobot.resources import Coordinate
                 from pylabrobot.serializer import deserialize
@@ -704,41 +613,6 @@ class ResourceTreeSet(object):
                 logger.error(f"堆栈: {traceback.format_exc()}")
                 raise
 
-        if requested_uuids:
-            # 按请求的 UUID 顺序返回对应资源（从整棵树中按 uuid 提取）
-            # 优先使用 tracker.uuid_to_resources；若映射缺失，再递归遍历 PLR 树兜底搜索。
-            def _find_plr_by_uuid(roots: List["PLRResource"], uid: str) -> Optional["PLRResource"]:
-                stack = list(roots)
-                while stack:
-                    node = stack.pop()
-                    node_uid = getattr(node, "unilabos_uuid", None)
-                    if node_uid == uid:
-                        return node
-                    children = getattr(node, "children", None) or []
-                    stack.extend(children)
-                return None
-
-            result = []
-            missing_uuids = []
-            for uid in requested_uuids:
-                found = tracker.uuid_to_resources.get(uid)
-                if found is None:
-                    found = _find_plr_by_uuid(plr_resources, uid)
-                    if found is not None:
-                        # 回填缓存，后续相同 uuid 可直接命中
-                        tracker.uuid_to_resources[uid] = found
-                if found is None:
-                    missing_uuids.append(uid)
-                else:
-                    result.append(found)
-
-            if missing_uuids:
-                raise ValueError(
-                    f"请求的 UUID 未在资源树中找到: {missing_uuids}。"
-                    f"可用 UUID 数量: {len(tracker.uuid_to_resources)}，"
-                    f"资源树数量: {len(self.trees)}"
-                )
-            return result
         return plr_resources
 
     @classmethod

unilabos/ros/nodes/base_device_node.py

@@ -915,24 +915,8 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         else []
                     )
                     if target_site is not None and sites is not None and site_names is not None:
-                        site_index = None
+                        site_index = sites.index(original_instance)
-                        try:
+                        site_name = site_names[site_index]
-                            # sites 可能是 Resource 列表或 dict 列表 (如 PRCXI9300Deck)
-                            # 只有itemized_carrier在使用，准备弃用
-                            site_index = sites.index(original_instance)
-                        except ValueError:
-                            # dict 类型的 sites: 通过name匹配
-                            for idx, site in enumerate(sites):
-                                if original_instance.name == site["occupied_by"]:
-                                    site_index = idx
-                                    break
-                                elif (original_instance.location.x == site["position"]["x"] and original_instance.location.y == site["position"]["y"] and original_instance.location.z == site["position"]["z"]):
-                                    site_index = idx
-                                    break
-                        if site_index is None:
-                            site_name = None
-                        else:
-                            site_name = site_names[site_index]
                         if site_name != target_site:
                             parent = self.transfer_to_new_resource(original_instance, tree, additional_add_params)
                             if parent is not None:
@@ -940,14 +924,6 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                                 parent_appended = True
 
                 # 加载状态
-                # noinspection PyProtectedMember
-                original_instance._size_x = plr_resource._size_x
-                # noinspection PyProtectedMember
-                original_instance._size_y = plr_resource._size_y
-                # noinspection PyProtectedMember
-                original_instance._size_z = plr_resource._size_z
-                # noinspection PyProtectedMember
-                original_instance._local_size_z = plr_resource._local_size_z
                 original_instance.location = plr_resource.location
                 original_instance.rotation = plr_resource.rotation
                 original_instance.barcode = plr_resource.barcode
@@ -1008,7 +984,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                         ].call_async(
                             r
                         )  # type: ignore
-                        self.lab_logger().trace(f"确认资源云端 Add 结果: {response.response}")
+                        self.lab_logger().info(f"确认资源云端 Add 结果: {response.response}")
                         results.append(result)
                     elif action == "update":
                         if tree_set is None:
@@ -1034,7 +1010,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
                             ].call_async(
                                 r
                             )  # type: ignore
-                            self.lab_logger().trace(f"确认资源云端 Update 结果: {response.response}")
+                            self.lab_logger().info(f"确认资源云端 Update 结果: {response.response}")
                         results.append(result)
                     elif action == "remove":
                         result = _handle_remove(resources_uuid)

unilabos/ros/nodes/presets/host_node.py

@@ -1195,7 +1195,7 @@ class HostNode(BaseROS2DeviceNode):
                 self.lab_logger().info(f"[Host Node-Resource] UUID映射: {len(uuid_mapping)} 个节点")
             # 还需要加入到资源图中，暂不实现，考虑资源图新的获取方式
             response.response = json.dumps(uuid_mapping)
-            self.lab_logger().info(f"[Host Node-Resource] Resource tree update completed, success: {success}")
+            self.lab_logger().info(f"[Host Node-Resource] Resource tree add completed, success: {success}")
 
     async def _resource_tree_update_callback(self, request: SerialCommand_Request, response: SerialCommand_Response):
         """

unilabos/workflow/common.py

@@ -26,7 +26,7 @@
     res_id: plate_slot_{slot}
     device_id: /PRCXI
     class_name: PRCXI_BioER_96_wellplate
-    parent: /PRCXI/PRCXI_Deck
+    parent: /PRCXI/PRCXI_Deck/T{slot}
     slot_on_deck: "{slot}"
 - 输出端口: labware（用于连接 set_liquid_from_plate）
 - 控制流: create_resource 之间通过 ready 端口串联
@@ -51,7 +51,6 @@
 --------------------------------------------------------------------------------
 - 遍历 workflow 数组，为每个动作创建步骤节点
 - 参数重命名: asp_vol -> asp_vols, dis_vol -> dis_vols, asp_flow_rate -> asp_flow_rates, dis_flow_rate -> dis_flow_rates
-- 参数输入转换: liquid_height（按 wells 扩展）；mix_stage/mix_times/mix_vol/mix_rate/mix_liquid_height 保持标量
 - 参数扩展: 根据 targets 的 wells 数量，将单值扩展为数组
     例: asp_vol=100.0, targets 有 3 个 wells -> asp_vols=[100.0, 100.0, 100.0]
 - 连接处理: 如果 sources/targets 已通过 set_liquid_from_plate 连接，参数值改为 []
@@ -120,14 +119,11 @@ DEVICE_NAME_DEFAULT = "PRCXI"  # transfer_liquid, set_liquid_from_plate 等动
 # 节点类型
 NODE_TYPE_DEFAULT = "ILab"  # 所有节点的默认类型
 
-CLASS_NAMES_MAPPING = {
-    "plate": "PRCXI_BioER_96_wellplate",
-    "tip_rack": "PRCXI_300ul_Tips",
-}
 # create_resource 节点默认参数
 CREATE_RESOURCE_DEFAULTS = {
     "device_id": "/PRCXI",
-    "parent_template": "/PRCXI/PRCXI_Deck",
+    "parent_template": "/PRCXI/PRCXI_Deck/T{slot}",  # {slot} 会被替换为实际的 slot 值
+    "class_name": "PRCXI_BioER_96_wellplate",
 }
 
 # 默认液体体积 (uL)
@@ -371,10 +367,11 @@ def build_protocol_graph(
     """统一的协议图构建函数，根据设备类型自动选择构建逻辑
 
     Args:
-        labware_info: 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"
@@ -382,21 +379,7 @@ 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 ====================
+    # ==================== 第一步：按 slot 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", ""))
-        labware = item.get("labware", "")
-        if slot and slot not in slots_info:
-            res_id = f"{labware}_slot_{slot}"
-            slots_info[slot] = {
-                "labware": labware,
-                "res_id": res_id,
-                "labware_id": labware_id,
-                "object": item.get("object", ""),
-            }
-
     # 创建 Group 节点，包含所有 create_resource 节点
     group_node_id = str(uuid.uuid4())
     G.add_node(
@@ -412,40 +395,41 @@ def build_protocol_graph(
         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
-    for slot, info in slots_info.items():
+    res_index = 0
+    for lw in (labware_defs or []):
+        slot = str(lw.get("slot", ""))
+        if not slot or slot in slot_to_create_resource:
+            continue  # 跳过空 slot 或已处理的 slot
+
+        lw_name = lw.get("name", f"slot {slot}")
+        lw_type = lw.get("type", CREATE_RESOURCE_DEFAULTS["class_name"])
+        res_id = f"plate_slot_{slot}"
+
+        res_index += 1
         node_id = str(uuid.uuid4())
-        res_id = info["res_id"]
-        res_type_name = info["labware"].lower().replace(".", "point")
-        object_type = info.get("object", "")
-        res_type_name = f"lab_{res_type_name}"
-        if object_type == "trash":
-            res_type_name = "PRCXI_trash"
         G.add_node(
             node_id,
             template_name="create_resource",
             resource_name="host_node",
-            name=f"{res_type_name}_slot{slot}",
+            name=lw_name,
-            description=f"Create plate on slot {slot}",
+            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,  # 指向 Group 节点
+            parent_uuid=group_node_id,
-            minimized=True,  # 折叠显示
+            minimized=True,
             param={
                 "res_id": res_id,
                 "device_id": CREATE_RESOURCE_DEFAULTS["device_id"],
-                "class_name": res_type_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,
             },
         )
         slot_to_create_resource[slot] = node_id
-        if object_type == "tiprack":
-            resource_last_writer[info["labware_id"]] = f"{node_id}:labware"
-        # create_resource 之间不需要 ready 连接
 
     # ==================== 第二步：为每个 reagent 创建 set_liquid_from_plate 节点 ====================
     # 创建 Group 节点，包含所有 set_liquid_from_plate 节点
@@ -480,8 +464,6 @@ def build_protocol_graph(
         # res_id 不能有空格
         res_id = str(labware_id).replace(" ", "_")
         well_count = len(wells)
-        object_type = item.get("object", "")
-        liquid_volume = DEFAULT_LIQUID_VOLUME if object_type == "source" else 0
 
         node_id = str(uuid.uuid4())
         set_liquid_index += 1
@@ -502,7 +484,7 @@ def build_protocol_graph(
                 "plate": [],  # 通过连接传递
                 "well_names": wells,  # 孔位名数组，如 ["A1", "A3", "A5"]
                 "liquid_names": [res_id] * well_count,
-                "volumes": [liquid_volume] * well_count,
+                "volumes": [DEFAULT_LIQUID_VOLUME] * well_count,
             },
         )
 
@@ -529,7 +511,6 @@ def build_protocol_graph(
         "reagent": "reagent",
         "solvent": "solvent",
         "compound": "compound",
-        "tip_racks": "tip_rack_identifier",
     }
 
     OUTPUT_PORT_MAPPING = {
@@ -544,17 +525,8 @@ def build_protocol_graph(
         "compound": "compound",
     }
 
-    # 需要根据 wells 数量扩展的参数列表：
+    # 需要根据 wells 数量扩展的参数列表（复数形式）
-    # - 复数参数（asp_vols 等）支持单值自动扩展
+    EXPAND_BY_WELLS_PARAMS = ["asp_vols", "dis_vols", "asp_flow_rates", "dis_flow_rates"]
-    # - liquid_height 按 wells 扩展为数组
-    # - mix_* 参数保持标量，避免被转换为 list
-    EXPAND_BY_WELLS_PARAMS = [
-        "asp_vols",
-        "dis_vols",
-        "asp_flow_rates",
-        "dis_flow_rates",
-        "liquid_height",
-    ]
 
     # 处理协议步骤
     for step in protocol_steps:
@@ -568,57 +540,6 @@ def build_protocol_graph(
             if old_name in params:
                 params[new_name] = params.pop(old_name)
 
-        # touch_tip 输入归一化：
-        # - 支持 bool / 0/1 / "true"/"false" / 单元素 list
-        # - 最终统一为 bool 标量，避免被下游误当作序列处理
-        if "touch_tip" in params:
-            touch_tip_value = params.get("touch_tip")
-            if isinstance(touch_tip_value, list):
-                if len(touch_tip_value) == 1:
-                    touch_tip_value = touch_tip_value[0]
-                elif len(touch_tip_value) == 0:
-                    touch_tip_value = False
-                else:
-                    warnings.append(f"touch_tip 期望标量，但收到长度为 {len(touch_tip_value)} 的列表，使用首个值")
-                    touch_tip_value = touch_tip_value[0]
-            if isinstance(touch_tip_value, str):
-                norm = touch_tip_value.strip().lower()
-                if norm in {"true", "1", "yes", "y", "on"}:
-                    touch_tip_value = True
-                elif norm in {"false", "0", "no", "n", "off", ""}:
-                    touch_tip_value = False
-                else:
-                    warnings.append(f"touch_tip 字符串值无法识别: {touch_tip_value}，按 True 处理")
-                    touch_tip_value = True
-            elif isinstance(touch_tip_value, (int, float)):
-                touch_tip_value = bool(touch_tip_value)
-            elif touch_tip_value is None:
-                touch_tip_value = False
-            else:
-                touch_tip_value = bool(touch_tip_value)
-            params["touch_tip"] = touch_tip_value
-
-        # delays 输入归一化：
-        # - 支持标量（int/float/字符串数字）与 list
-        # - 最终统一为数字列表，供下游按 delays[0]/delays[1] 使用
-        if "delays" in params:
-            delays_value = params.get("delays")
-            if delays_value is None or delays_value == "":
-                params["delays"] = []
-            else:
-                raw_list = delays_value if isinstance(delays_value, list) else [delays_value]
-                normalized_delays = []
-                for delay_item in raw_list:
-                    if isinstance(delay_item, str):
-                        delay_item = delay_item.strip()
-                        if delay_item == "":
-                            continue
-                    try:
-                        normalized_delays.append(float(delay_item))
-                    except (TypeError, ValueError):
-                        warnings.append(f"delays 包含无法转换为数字的值: {delay_item}，已忽略")
-                params["delays"] = normalized_delays
-
         # 处理输入连接
         for param_key, target_port in INPUT_PORT_MAPPING.items():
             resource_name = params.get(param_key)

unilabos/workflow/from_python_script.py

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

unilabos/workflow/from_xdl.py

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