Merge remote-tracking branch 'origin/dev' into workstation_dev_YB3

This commit is contained in:
calvincao
2025-10-28 11:47:07 +08:00
22 changed files with 2315 additions and 665 deletions

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import json
import logging
import traceback
import uuid
import xml.etree.ElementTree as ET
from typing import Any, Dict, List
import networkx as nx
import matplotlib.pyplot as plt
import requests
logger = logging.getLogger(__name__)
class SimpleGraph:
"""简单的有向图实现,用于构建工作流图"""
def __init__(self):
self.nodes = {}
self.edges = []
def add_node(self, node_id, **attrs):
"""添加节点"""
self.nodes[node_id] = attrs
def add_edge(self, source, target, **attrs):
"""添加边"""
edge = {"source": source, "target": target, **attrs}
self.edges.append(edge)
def to_dict(self):
"""转换为工作流图格式"""
nodes_list = []
for node_id, attrs in self.nodes.items():
node_attrs = attrs.copy()
params = node_attrs.pop("parameters", {}) or {}
node_attrs.update(params)
nodes_list.append({"id": node_id, **node_attrs})
return {
"directed": True,
"multigraph": False,
"graph": {},
"nodes": nodes_list,
"links": self.edges,
}
def extract_json_from_markdown(text: str) -> str:
"""从markdown代码块中提取JSON"""
text = text.strip()
if text.startswith("```json\n"):
text = text[8:]
if text.startswith("```\n"):
text = text[4:]
if text.endswith("\n```"):
text = text[:-4]
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 compassn/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 compasse.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(
steps_info: str,
labware_info: str,
workflow_name: str = "Generated Workflow",
workstation_name: str = "workstation",
workflow_description: str = "Auto-generated workflow from protocol",
) -> Dict[str, Any]:
"""
创建工作流,输入数据已经是统一的字典格式
Args:
steps_info: 步骤信息 (JSON字符串已经是list of dict格式)
labware_info: 实验器材和试剂信息 (JSON字符串已经是list of dict格式)
workflow_name: 工作流名称
workflow_description: 工作流描述
Returns:
创建结果包含工作流UUID和详细信息
"""
try:
# 直接解析JSON数据
steps_info_clean = extract_json_from_markdown(steps_info)
labware_info_clean = extract_json_from_markdown(labware_info)
steps_data = json.loads(steps_info_clean)
labware_data = json.loads(labware_info_clean)
# 统一处理所有数据
protocol_graph = build_protocol_graph(labware_data, steps_data, workstation_name=workstation_name)
# 检测协议类型(用于标签)
protocol_type = "bio" if any("biomek" in step.get("template", "") for step in refactored_steps) else "organic"
# 转换为工作流格式
data = protocol_graph.to_dict()
# 转换节点格式
for i, node in enumerate(data["nodes"]):
description = node.get("description", "")
onode = {
"template": node.pop("template"),
"id": node["id"],
"lab_node_type": node.get("lab_node_type", "Device"),
"name": description or f"Node {i + 1}",
"params": {"default": node},
"handles": {},
}
# 处理边连接
for edge in data["links"]:
if edge["source"] == node["id"]:
source_port = edge.get("source_port", "output")
if source_port not in onode["handles"]:
onode["handles"][source_port] = {"type": "source"}
if edge["target"] == node["id"]:
target_port = edge.get("target_port", "input")
if target_port not in onode["handles"]:
onode["handles"][target_port] = {"type": "target"}
data["nodes"][i] = onode
# 发送到API创建工作流
api_secret = configs.Lab.Key
if not api_secret:
return {"error": "API SecretKey is not configured", "success": False}
# Step 1: 创建工作流
workflow_url = f"{configs.Lab.Api}/api/v1/workflow/"
headers = {
"Content-Type": "application/json",
}
params = {"secret_key": api_secret}
graph_data = {"name": workflow_name, **data}
logger.info(f"Creating workflow: {workflow_name}")
response = requests.post(
workflow_url, params=params, json=graph_data, headers=headers, timeout=configs.Lab.Timeout
)
response.raise_for_status()
workflow_info = response.json()
if workflow_info.get("code") != 0:
error_msg = f"API returned an error: {workflow_info.get('msg', 'Unknown Error')}"
logger.error(error_msg)
return {"error": error_msg, "success": False}
workflow_uuid = workflow_info.get("data", {}).get("uuid")
if not workflow_uuid:
return {"error": "Failed to get workflow UUID from response", "success": False}
# Step 2: 添加到模板库(可选)
try:
library_url = f"{configs.Lab.Api}/api/flociety/vs/workflows/library/"
lib_payload = {
"workflow_uuid": workflow_uuid,
"title": workflow_name,
"description": workflow_description,
"labels": [protocol_type.title(), "Auto-generated"],
}
library_response = requests.post(
library_url, params=params, json=lib_payload, headers=headers, timeout=configs.Lab.Timeout
)
library_response.raise_for_status()
library_info = library_response.json()
logger.info(f"Workflow added to library: {library_info}")
return {
"success": True,
"workflow_uuid": workflow_uuid,
"workflow_info": workflow_info.get("data"),
"library_info": library_info.get("data"),
"protocol_type": protocol_type,
"message": f"Workflow '{workflow_name}' created successfully",
}
except Exception as e:
# 即使添加到库失败,工作流创建仍然成功
logger.warning(f"Failed to add workflow to library: {str(e)}")
return {
"success": True,
"workflow_uuid": workflow_uuid,
"workflow_info": workflow_info.get("data"),
"protocol_type": protocol_type,
"message": f"Workflow '{workflow_name}' created successfully (library addition failed)",
}
except requests.exceptions.RequestException as e:
error_msg = f"Network error when calling API: {str(e)}"
logger.error(error_msg)
return {"error": error_msg, "success": False}
except json.JSONDecodeError as e:
error_msg = f"JSON parsing error: {str(e)}"
logger.error(error_msg)
return {"error": error_msg, "success": False}
except Exception as e:
error_msg = f"An unexpected error occurred: {str(e)}"
logger.error(error_msg)
logger.error(traceback.format_exc())
return {"error": error_msg, "success": False}

View File

@@ -8,7 +8,7 @@
],
"parent": null,
"type": "device",
"class": "workstation.bioyond_dispensing_station",
"class": "bioyond_dispensing_station",
"config": {
"config": {
"api_key": "DE9BDDA0",

View File

@@ -0,0 +1,186 @@
{
"workflow": [
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_1",
"targets": "Liquid_2",
"asp_vol": 66.0,
"dis_vol": 66.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_2",
"targets": "Liquid_3",
"asp_vol": 58.0,
"dis_vol": 96.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_4",
"targets": "Liquid_2",
"asp_vol": 85.0,
"dis_vol": 170.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_4",
"targets": "Liquid_2",
"asp_vol": 63.333333333333336,
"dis_vol": 170.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_2",
"targets": "Liquid_3",
"asp_vol": 72.0,
"dis_vol": 150.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_4",
"targets": "Liquid_2",
"asp_vol": 85.0,
"dis_vol": 170.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_4",
"targets": "Liquid_2",
"asp_vol": 63.333333333333336,
"dis_vol": 170.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_2",
"targets": "Liquid_3",
"asp_vol": 72.0,
"dis_vol": 150.0,
"asp_flow_rate": 94.0,
"dis_flow_rate": 94.0
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_2",
"targets": "Liquid_3",
"asp_vol": 20.0,
"dis_vol": 20.0,
"asp_flow_rate": 7.6,
"dis_flow_rate": 7.6
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_5",
"targets": "Liquid_2",
"asp_vol": 6.0,
"dis_vol": 12.0,
"asp_flow_rate": 7.6,
"dis_flow_rate": 7.6
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_5",
"targets": "Liquid_2",
"asp_vol": 10.666666666666666,
"dis_vol": 12.0,
"asp_flow_rate": 7.599999999999999,
"dis_flow_rate": 7.6
}
},
{
"action": "transfer_liquid",
"action_args": {
"sources": "Liquid_2",
"targets": "Liquid_6",
"asp_vol": 12.0,
"dis_vol": 10.0,
"asp_flow_rate": 7.6,
"dis_flow_rate": 7.6
}
}
],
"reagent": {
"Liquid_6": {
"slot": 1,
"well": [
"A2"
],
"labware": "elution plate"
},
"Liquid_1": {
"slot": 2,
"well": [
"A1",
"A2",
"A4"
],
"labware": "reagent reservoir"
},
"Liquid_4": {
"slot": 2,
"well": [
"A1",
"A2",
"A4"
],
"labware": "reagent reservoir"
},
"Liquid_5": {
"slot": 2,
"well": [
"A1",
"A2",
"A4"
],
"labware": "reagent reservoir"
},
"Liquid_2": {
"slot": 4,
"well": [
"A2"
],
"labware": "TAG1 plate on Magnetic Module GEN2"
},
"Liquid_3": {
"slot": 12,
"well": [
"A1"
],
"labware": "Opentrons Fixed Trash"
}
}
}

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@@ -0,0 +1,63 @@
{
"steps_info": [
{
"step_number": 1,
"action": "transfer_liquid",
"parameters": {
"source": "sample supernatant",
"target": "antibody-coated well",
"volume": 100
}
},
{
"step_number": 2,
"action": "transfer_liquid",
"parameters": {
"source": "washing buffer",
"target": "antibody-coated well",
"volume": 200
}
},
{
"step_number": 3,
"action": "transfer_liquid",
"parameters": {
"source": "washing buffer",
"target": "antibody-coated well",
"volume": 200
}
},
{
"step_number": 4,
"action": "transfer_liquid",
"parameters": {
"source": "washing buffer",
"target": "antibody-coated well",
"volume": 200
}
},
{
"step_number": 5,
"action": "transfer_liquid",
"parameters": {
"source": "TMB substrate",
"target": "antibody-coated well",
"volume": 100
}
}
],
"labware_info": [
{"reagent_name": "sample supernatant", "material_name": "96深孔板", "positions": 1},
{"reagent_name": "washing buffer", "material_name": "储液槽", "positions": 2},
{"reagent_name": "TMB substrate", "material_name": "储液槽", "positions": 3},
{"reagent_name": "antibody-coated well", "material_name": "96 细胞培养皿", "positions": 4},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 5},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 6},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 7},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 8},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 9},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 10},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 11},
{"reagent_name": "", "material_name": "300μL Tip头", "positions": 13}
]
}

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

View File

@@ -6,6 +6,8 @@ HTTP客户端模块
import json
import os
import time
from threading import Thread
from typing import List, Dict, Any, Optional
import requests
@@ -84,14 +86,14 @@ class HTTPClient:
f"{self.remote_addr}/edge/material",
json={"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid},
headers={"Authorization": f"Lab {self.auth}"},
timeout=100,
timeout=60,
)
else:
response = requests.put(
f"{self.remote_addr}/edge/material",
json={"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid},
headers={"Authorization": f"Lab {self.auth}"},
timeout=100,
timeout=10,
)
with open(os.path.join(BasicConfig.working_dir, "res_resource_tree_add.json"), "w", encoding="utf-8") as f:
@@ -126,12 +128,16 @@ class HTTPClient:
Returns:
Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
"""
with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_get.json"), "w", encoding="utf-8") as f:
f.write(json.dumps({"uuids": uuid_list, "with_children": with_children}, indent=4))
response = requests.post(
f"{self.remote_addr}/edge/material/query",
json={"uuids": uuid_list, "with_children": with_children},
headers={"Authorization": f"Lab {self.auth}"},
timeout=100,
)
with open(os.path.join(BasicConfig.working_dir, "res_resource_tree_get.json"), "w", encoding="utf-8") as f:
f.write(f"{response.status_code}" + "\n" + response.text)
if response.status_code == 200:
res = response.json()
if "code" in res and res["code"] != 0:
@@ -187,12 +193,16 @@ class HTTPClient:
Returns:
Dict: 返回的资源数据
"""
with open(os.path.join(BasicConfig.working_dir, "req_resource_get.json"), "w", encoding="utf-8") as f:
f.write(json.dumps({"id": id, "with_children": with_children}, indent=4))
response = requests.get(
f"{self.remote_addr}/lab/material",
params={"id": id, "with_children": with_children},
headers={"Authorization": f"Lab {self.auth}"},
timeout=20,
)
with open(os.path.join(BasicConfig.working_dir, "res_resource_get.json"), "w", encoding="utf-8") as f:
f.write(f"{response.status_code}" + "\n" + response.text)
return response.json()
def resource_del(self, id: str) -> requests.Response:

View File

@@ -7,7 +7,7 @@ from unilabos.devices.workstation.bioyond_studio.station import BioyondWorkstati
class BioyondDispensingStation(BioyondWorkstation):
def __init__(
self,
self,
config,
# 桌子
deck,
@@ -77,7 +77,7 @@ class BioyondDispensingStation(BioyondWorkstation):
- hold_m_name: 库位名称,如"C01"用于查找对应的holdMId
返回: 任务创建结果
异常:
- BioyondException: 各种错误情况下的统一异常
"""
@@ -85,7 +85,7 @@ class BioyondDispensingStation(BioyondWorkstation):
# 1. 参数验证
if not hold_m_name:
raise BioyondException("hold_m_name 是必填参数")
# 检查90%物料参数的完整性
# 90%_1物料如果有物料名称或目标重量就必须有全部参数
if percent_90_1_assign_material_name or percent_90_1_target_weigh:
@@ -93,21 +93,21 @@ class BioyondDispensingStation(BioyondWorkstation):
raise BioyondException("90%_1物料如果提供了目标重量必须同时提供物料名称")
if not percent_90_1_target_weigh:
raise BioyondException("90%_1物料如果提供了物料名称必须同时提供目标重量")
# 90%_2物料如果有物料名称或目标重量就必须有全部参数
if percent_90_2_assign_material_name or percent_90_2_target_weigh:
if not percent_90_2_assign_material_name:
raise BioyondException("90%_2物料如果提供了目标重量必须同时提供物料名称")
if not percent_90_2_target_weigh:
raise BioyondException("90%_2物料如果提供了物料名称必须同时提供目标重量")
# 90%_3物料如果有物料名称或目标重量就必须有全部参数
if percent_90_3_assign_material_name or percent_90_3_target_weigh:
if not percent_90_3_assign_material_name:
raise BioyondException("90%_3物料如果提供了目标重量必须同时提供物料名称")
if not percent_90_3_target_weigh:
raise BioyondException("90%_3物料如果提供了物料名称必须同时提供目标重量")
# 检查10%物料参数的完整性
# 10%_1物料如果有物料名称、目标重量、体积或液体物料名称中的任何一个就必须有全部参数
if any([percent_10_1_assign_material_name, percent_10_1_target_weigh, percent_10_1_volume, percent_10_1_liquid_material_name]):
@@ -119,7 +119,7 @@ class BioyondDispensingStation(BioyondWorkstation):
raise BioyondException("10%_1物料如果提供了其他参数必须同时提供液体体积")
if not percent_10_1_liquid_material_name:
raise BioyondException("10%_1物料如果提供了其他参数必须同时提供液体物料名称")
# 10%_2物料如果有物料名称、目标重量、体积或液体物料名称中的任何一个就必须有全部参数
if any([percent_10_2_assign_material_name, percent_10_2_target_weigh, percent_10_2_volume, percent_10_2_liquid_material_name]):
if not percent_10_2_assign_material_name:
@@ -130,7 +130,7 @@ class BioyondDispensingStation(BioyondWorkstation):
raise BioyondException("10%_2物料如果提供了其他参数必须同时提供液体体积")
if not percent_10_2_liquid_material_name:
raise BioyondException("10%_2物料如果提供了其他参数必须同时提供液体物料名称")
# 10%_3物料如果有物料名称、目标重量、体积或液体物料名称中的任何一个就必须有全部参数
if any([percent_10_3_assign_material_name, percent_10_3_target_weigh, percent_10_3_volume, percent_10_3_liquid_material_name]):
if not percent_10_3_assign_material_name:
@@ -141,7 +141,7 @@ class BioyondDispensingStation(BioyondWorkstation):
raise BioyondException("10%_3物料如果提供了其他参数必须同时提供液体体积")
if not percent_10_3_liquid_material_name:
raise BioyondException("10%_3物料如果提供了其他参数必须同时提供液体物料名称")
# 2. 生成任务编码和设置默认值
order_code = "task_vial_" + str(int(datetime.now().timestamp()))
if order_name is None:
@@ -152,7 +152,7 @@ class BioyondDispensingStation(BioyondWorkstation):
temperature = "40"
if delay_time is None:
delay_time = "600"
# 3. 工作流ID
workflow_id = "3a19310d-16b9-9d81-b109-0748e953694b"
@@ -160,22 +160,22 @@ class BioyondDispensingStation(BioyondWorkstation):
material_info = self.hardware_interface.material_id_query(workflow_id)
if not material_info:
raise BioyondException(f"无法查询工作流 {workflow_id} 的物料信息")
# 获取locations列表
locations = material_info.get("locations", []) if isinstance(material_info, dict) else []
if not locations:
raise BioyondException(f"工作流 {workflow_id} 没有找到库位信息")
# 查找指定名称的库位
hold_mid = None
for location in locations:
if location.get("holdMName") == hold_m_name:
hold_mid = location.get("holdMId")
break
if not hold_mid:
raise BioyondException(f"未找到库位名称为 {hold_m_name} 的库位,请检查名称是否正确")
extend_properties = f"{{\"{ hold_mid }\": {{}}}}"
self.hardware_interface._logger.info(f"找到库位 {hold_m_name} 对应的holdMId: {hold_mid}")
@@ -271,7 +271,7 @@ class BioyondDispensingStation(BioyondWorkstation):
result = self.hardware_interface.create_order(json_str)
self.hardware_interface._logger.info(f"创建90%10%小瓶投料任务结果: {result}")
return json.dumps({"suc": True})
except BioyondException:
# 重新抛出BioyondException
raise
@@ -307,7 +307,7 @@ class BioyondDispensingStation(BioyondWorkstation):
- hold_m_name: 库位名称,如"ODA-1"用于查找对应的holdMId
返回: 任务创建结果
异常:
- BioyondException: 各种错误情况下的统一异常
"""
@@ -321,8 +321,8 @@ class BioyondDispensingStation(BioyondWorkstation):
raise BioyondException("volume 是必填参数")
if not hold_m_name:
raise BioyondException("hold_m_name 是必填参数")
# 2. 生成任务编码和设置默认值
order_code = "task_oda_" + str(int(datetime.now().timestamp()))
if order_name is None:
@@ -333,30 +333,30 @@ class BioyondDispensingStation(BioyondWorkstation):
temperature = "20"
if delay_time is None:
delay_time = "600"
# 3. 工作流ID - 二胺溶液配置工作流
workflow_id = "3a15d4a1-3bbe-76f9-a458-292896a338f5"
# 4. 查询工作流对应的holdMID
material_info = self.material_id_query(workflow_id)
material_info = self.hardware_interface.material_id_query(workflow_id)
if not material_info:
raise BioyondException(f"无法查询工作流 {workflow_id} 的物料信息")
# 获取locations列表
locations = material_info.get("locations", []) if isinstance(material_info, dict) else []
if not locations:
raise BioyondException(f"工作流 {workflow_id} 没有找到库位信息")
# 查找指定名称的库位
hold_mid = None
for location in locations:
if location.get("holdMName") == hold_m_name:
hold_mid = location.get("holdMId")
break
if not hold_mid:
raise BioyondException(f"未找到库位名称为 {hold_m_name} 的库位,请检查名称是否正确")
extend_properties = f"{{\"{ hold_mid }\": {{}}}}"
self.hardware_interface._logger.info(f"找到库位 {hold_m_name} 对应的holdMId: {hold_mid}")
@@ -397,9 +397,9 @@ class BioyondDispensingStation(BioyondWorkstation):
# 7. 调用create_order方法创建任务
result = self.hardware_interface.create_order(json_str)
self.hardware_interface._logger.info(f"创建二胺溶液配置任务结果: {result}")
return json.dumps({"suc": True})
except BioyondException:
# 重新抛出BioyondException
raise
@@ -409,17 +409,278 @@ class BioyondDispensingStation(BioyondWorkstation):
self.hardware_interface._logger.error(error_msg)
raise BioyondException(error_msg)
# 批量创建二胺溶液配置任务
def batch_create_diamine_solution_tasks(self,
solutions,
liquid_material_name: str = "NMP",
speed: str = None,
temperature: str = None,
delay_time: str = None) -> str:
"""
批量创建二胺溶液配置任务
参数说明:
- solutions: 溶液列表数组或JSON字符串格式如下:
[
{
"name": "MDA",
"order": 0,
"solid_mass": 5.0,
"solvent_volume": 20,
...
},
...
]
- liquid_material_name: 液体物料名称,默认为"NMP"
- speed: 搅拌速度如果为None则使用默认值400
- temperature: 温度如果为None则使用默认值20
- delay_time: 延迟时间如果为None则使用默认值600
返回: JSON字符串格式的任务创建结果
异常:
- BioyondException: 各种错误情况下的统一异常
"""
try:
# 参数类型转换:如果是字符串则解析为列表
if isinstance(solutions, str):
try:
solutions = json.loads(solutions)
except json.JSONDecodeError as e:
raise BioyondException(f"solutions JSON解析失败: {str(e)}")
# 参数验证
if not isinstance(solutions, list):
raise BioyondException("solutions 必须是列表类型或有效的JSON数组字符串")
if not solutions:
raise BioyondException("solutions 列表不能为空")
# 批量创建任务
results = []
success_count = 0
failed_count = 0
for idx, solution in enumerate(solutions):
try:
# 提取参数
name = solution.get("name")
solid_mass = solution.get("solid_mass")
solvent_volume = solution.get("solvent_volume")
order = solution.get("order")
if not all([name, solid_mass is not None, solvent_volume is not None]):
self.hardware_interface._logger.warning(
f"跳过第 {idx + 1} 个溶液:缺少必要参数"
)
results.append({
"index": idx + 1,
"name": name,
"success": False,
"error": "缺少必要参数"
})
failed_count += 1
continue
# 生成库位名称(直接使用物料名称)
# 如果需要其他命名规则,可以在这里调整
hold_m_name = name
# 调用单个任务创建方法
result = self.create_diamine_solution_task(
order_name=f"二胺溶液配置-{name}",
material_name=name,
target_weigh=str(solid_mass),
volume=str(solvent_volume),
liquid_material_name=liquid_material_name,
speed=speed,
temperature=temperature,
delay_time=delay_time,
hold_m_name=hold_m_name
)
results.append({
"index": idx + 1,
"name": name,
"success": True,
"hold_m_name": hold_m_name
})
success_count += 1
self.hardware_interface._logger.info(
f"成功创建二胺溶液配置任务: {name}"
)
except BioyondException as e:
results.append({
"index": idx + 1,
"name": solution.get("name", "unknown"),
"success": False,
"error": str(e)
})
failed_count += 1
self.hardware_interface._logger.error(
f"创建第 {idx + 1} 个任务失败: {str(e)}"
)
except Exception as e:
results.append({
"index": idx + 1,
"name": solution.get("name", "unknown"),
"success": False,
"error": f"未知错误: {str(e)}"
})
failed_count += 1
self.hardware_interface._logger.error(
f"创建第 {idx + 1} 个任务时发生未知错误: {str(e)}"
)
# 返回汇总结果
summary = {
"total": len(solutions),
"success": success_count,
"failed": failed_count,
"details": results
}
self.hardware_interface._logger.info(
f"批量创建二胺溶液配置任务完成: 总数={len(solutions)}, "
f"成功={success_count}, 失败={failed_count}"
)
# 返回JSON字符串格式
return json.dumps(summary, ensure_ascii=False)
except BioyondException:
raise
except Exception as e:
error_msg = f"批量创建二胺溶液配置任务时发生未预期的错误: {str(e)}"
self.hardware_interface._logger.error(error_msg)
raise BioyondException(error_msg)
# 批量创建90%10%小瓶投料任务
def batch_create_90_10_vial_feeding_tasks(self,
titration,
hold_m_name: str = None,
speed: str = None,
temperature: str = None,
delay_time: str = None,
liquid_material_name: str = "NMP") -> str:
"""
批量创建90%10%小瓶投料任务仅创建1个任务但包含所有90%和10%物料)
参数说明:
- titration: 滴定信息的字典或JSON字符串格式如下:
{
"name": "BTDA",
"main_portion": 1.9152351915461294, # 主称固体质量(g) -> 90%物料
"titration_portion": 0.05923407808905555, # 滴定固体质量(g) -> 10%物料固体
"titration_solvent": 3.050555021586361 # 滴定溶液体积(mL) -> 10%物料液体
}
- hold_m_name: 库位名称,如"C01"。必填参数
- speed: 搅拌速度如果为None则使用默认值400
- temperature: 温度如果为None则使用默认值40
- delay_time: 延迟时间如果为None则使用默认值600
- liquid_material_name: 10%物料的液体物料名称,默认为"NMP"
返回: JSON字符串格式的任务创建结果
异常:
- BioyondException: 各种错误情况下的统一异常
"""
try:
# 参数类型转换:如果是字符串则解析为字典
if isinstance(titration, str):
try:
titration = json.loads(titration)
except json.JSONDecodeError as e:
raise BioyondException(f"titration参数JSON解析失败: {str(e)}")
# 参数验证
if not isinstance(titration, dict):
raise BioyondException("titration 必须是字典类型或有效的JSON字符串")
if not hold_m_name:
raise BioyondException("hold_m_name 是必填参数")
if not titration:
raise BioyondException("titration 参数不能为空")
# 提取滴定数据
name = titration.get("name")
main_portion = titration.get("main_portion") # 主称固体质量
titration_portion = titration.get("titration_portion") # 滴定固体质量
titration_solvent = titration.get("titration_solvent") # 滴定溶液体积
if not all([name, main_portion is not None, titration_portion is not None, titration_solvent is not None]):
raise BioyondException("titration 数据缺少必要参数")
# 将main_portion平均分成3份作为90%物料3个小瓶
portion_90 = main_portion / 3
# 调用单个任务创建方法
result = self.create_90_10_vial_feeding_task(
order_name=f"90%10%小瓶投料-{name}",
speed=speed,
temperature=temperature,
delay_time=delay_time,
# 90%物料 - 主称固体平均分成3份
percent_90_1_assign_material_name=name,
percent_90_1_target_weigh=str(round(portion_90, 6)),
percent_90_2_assign_material_name=name,
percent_90_2_target_weigh=str(round(portion_90, 6)),
percent_90_3_assign_material_name=name,
percent_90_3_target_weigh=str(round(portion_90, 6)),
# 10%物料 - 滴定固体 + 滴定溶剂只使用第1个10%小瓶)
percent_10_1_assign_material_name=name,
percent_10_1_target_weigh=str(round(titration_portion, 6)),
percent_10_1_volume=str(round(titration_solvent, 6)),
percent_10_1_liquid_material_name=liquid_material_name,
hold_m_name=hold_m_name
)
summary = {
"success": True,
"hold_m_name": hold_m_name,
"material_name": name,
"90_vials": {
"count": 3,
"weight_per_vial": round(portion_90, 6),
"total_weight": round(main_portion, 6)
},
"10_vials": {
"count": 1,
"solid_weight": round(titration_portion, 6),
"liquid_volume": round(titration_solvent, 6)
}
}
self.hardware_interface._logger.info(
f"成功创建90%10%小瓶投料任务: {hold_m_name}, "
f"90%物料={portion_90:.6f}g×3, 10%物料={titration_portion:.6f}g+{titration_solvent:.6f}mL"
)
# 返回JSON字符串格式
return json.dumps(summary, ensure_ascii=False)
except BioyondException:
raise
except Exception as e:
error_msg = f"批量创建90%10%小瓶投料任务时发生未预期的错误: {str(e)}"
self.hardware_interface._logger.error(error_msg)
raise BioyondException(error_msg)
if __name__ == "__main__":
bioyond = BioyondDispensingStation(config={
"api_key": "DE9BDDA0",
"api_host": "http://192.168.1.200:44388"
})
# ============ 原有示例代码 ============
# 示例1使用material_id_query查询工作流对应的holdMID
workflow_id_1 = "3a15d4a1-3bbe-76f9-a458-292896a338f5" # 二胺溶液配置工作流ID
workflow_id_2 = "3a19310d-16b9-9d81-b109-0748e953694b" # 90%10%小瓶投料工作流ID
#示例2创建二胺溶液配置任务 - ODA指定库位名称
# bioyond.create_diamine_solution_task(
# order_code="task_oda_" + str(int(datetime.now().timestamp())),
@@ -433,7 +694,7 @@ if __name__ == "__main__":
# delay_time="600",
# hold_m_name="烧杯ODA"
# )
# bioyond.create_diamine_solution_task(
# order_code="task_pda_" + str(int(datetime.now().timestamp())),
# order_name="二胺溶液配置-PDA",
@@ -446,7 +707,7 @@ if __name__ == "__main__":
# delay_time="600",
# hold_m_name="烧杯PDA-2"
# )
# bioyond.create_diamine_solution_task(
# order_code="task_mpda_" + str(int(datetime.now().timestamp())),
# order_name="二胺溶液配置-MPDA",
@@ -462,8 +723,8 @@ if __name__ == "__main__":
bioyond.material_id_query("3a19310d-16b9-9d81-b109-0748e953694b")
bioyond.material_id_query("3a15d4a1-3bbe-76f9-a458-292896a338f5")
#示例4创建90%10%小瓶投料任务
# vial_result = bioyond.create_90_10_vial_feeding_task(
# order_code="task_vial_" + str(int(datetime.now().timestamp())),
@@ -487,7 +748,7 @@ if __name__ == "__main__":
# delay_time="1200",
# hold_m_name="8.4分装板-1"
# )
# vial_result = bioyond.create_90_10_vial_feeding_task(
# order_code="task_vial_" + str(int(datetime.now().timestamp())),
# order_name="90%10%小瓶投料-2",
@@ -510,7 +771,7 @@ if __name__ == "__main__":
# delay_time="1200",
# hold_m_name="8.4分装板-2"
# )
#启动调度器
#bioyond.scheduler_start()
@@ -529,7 +790,7 @@ if __name__ == "__main__":
material_data_yp = {
"typeId": "3a14196e-b7a0-a5da-1931-35f3000281e9",
#"code": "物料编码001",
#"barCode": "物料条码001",
#"barCode": "物料条码001",
"name": "8.4样品板",
"unit": "",
"quantity": 1,
@@ -540,7 +801,7 @@ if __name__ == "__main__":
"name": "BTDA-1",
"quantity": 20,
"x": 1,
"y": 1,
"y": 1,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -585,7 +846,7 @@ if __name__ == "__main__":
material_data_yp = {
"typeId": "3a14196e-b7a0-a5da-1931-35f3000281e9",
#"code": "物料编码001",
#"barCode": "物料条码001",
#"barCode": "物料条码001",
"name": "8.7样品板",
"unit": "",
"quantity": 1,
@@ -596,7 +857,7 @@ if __name__ == "__main__":
"name": "mianfen",
"quantity": 13,
"x": 1,
"y": 1,
"y": 1,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -620,7 +881,7 @@ if __name__ == "__main__":
material_data_fzb_1 = {
"typeId": "3a14196e-5dfe-6e21-0c79-fe2036d052c4",
#"code": "物料编码001",
#"barCode": "物料条码001",
#"barCode": "物料条码001",
"name": "8.7分装板",
"unit": "",
"quantity": 1,
@@ -631,7 +892,7 @@ if __name__ == "__main__":
"name": "10%小瓶1",
"quantity": 1,
"x": 1,
"y": 1,
"y": 1,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -642,7 +903,7 @@ if __name__ == "__main__":
"name": "10%小瓶2",
"quantity": 1,
"x": 1,
"y": 2,
"y": 2,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -653,7 +914,7 @@ if __name__ == "__main__":
"name": "10%小瓶3",
"quantity": 1,
"x": 1,
"y": 3,
"y": 3,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -697,7 +958,7 @@ if __name__ == "__main__":
material_data_fzb_2 = {
"typeId": "3a14196e-5dfe-6e21-0c79-fe2036d052c4",
#"code": "物料编码001",
#"barCode": "物料条码001",
#"barCode": "物料条码001",
"name": "8.4分装板-2",
"unit": "",
"quantity": 1,
@@ -708,7 +969,7 @@ if __name__ == "__main__":
"name": "10%小瓶1",
"quantity": 1,
"x": 1,
"y": 1,
"y": 1,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -719,7 +980,7 @@ if __name__ == "__main__":
"name": "10%小瓶2",
"quantity": 1,
"x": 1,
"y": 2,
"y": 2,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -730,7 +991,7 @@ if __name__ == "__main__":
"name": "10%小瓶3",
"quantity": 1,
"x": 1,
"y": 3,
"y": 3,
#"unit": "单位"
"molecular": 1,
"Parameters":"{\"molecular\": 1}"
@@ -775,7 +1036,7 @@ if __name__ == "__main__":
material_data_sb_oda = {
"typeId": "3a14196b-24f2-ca49-9081-0cab8021bf1a",
#"code": "物料编码001",
#"barCode": "物料条码001",
#"barCode": "物料条码001",
"name": "mianfen1",
"unit": "",
"quantity": 1,
@@ -785,7 +1046,7 @@ if __name__ == "__main__":
material_data_sb_pda_2 = {
"typeId": "3a14196b-24f2-ca49-9081-0cab8021bf1a",
#"code": "物料编码001",
#"barCode": "物料条码001",
#"barCode": "物料条码001",
"name": "mianfen2",
"unit": "",
"quantity": 1,
@@ -795,7 +1056,7 @@ if __name__ == "__main__":
# material_data_sb_mpda = {
# "typeId": "3a14196b-24f2-ca49-9081-0cab8021bf1a",
# #"code": "物料编码001",
# #"barCode": "物料条码001",
# #"barCode": "物料条码001",
# "name": "烧杯MPDA",
# "unit": "个",
# "quantity": 1,

View File

@@ -58,8 +58,8 @@ class BioyondReactionStation(BioyondWorkstation):
Args:
assign_material_name: 物料名称(不能为空)
cutoff: 截止值/通量配置(需为有效数字字符串,默认 "900000"
temperature: 温度上限°C范围-50.00 至 100.00
cutoff: 粘度上限(需为有效数字字符串,默认 "900000"
temperature: 温度设定°C范围-50.00 至 100.00
Returns:
str: JSON 字符串,格式为 {"suc": True}
@@ -113,11 +113,11 @@ class BioyondReactionStation(BioyondWorkstation):
"""固体进料小瓶
Args:
material_id: 粉末类型ID
material_id: 粉末类型ID1=盐21分钟2=面粉27分钟3=BTDA38分钟
time: 观察时间(分钟)
torque_variation: 是否观察扭矩变化(int类型, 1=否, 2=是)
torque_variation: 是否观察(int类型, 1=否, 2=是)
assign_material_name: 物料名称(用于获取试剂瓶位ID)
temperature: 温度上限(°C)
temperature: 温度设定(°C)
"""
self.append_to_workflow_sequence('{"web_workflow_name": "Solid_feeding_vials"}')
material_id_m = self.hardware_interface._get_material_id_by_name(assign_material_name) if assign_material_name else None
@@ -165,9 +165,9 @@ class BioyondReactionStation(BioyondWorkstation):
Args:
volume_formula: 分液公式(μL)
assign_material_name: 物料名称
titration_type: 是否滴定(1=滴定, 其他=非滴定)
titration_type: 是否滴定(1=否, 2=是)
time: 观察时间(分钟)
torque_variation: 是否观察扭矩变化(int类型, 1=否, 2=是)
torque_variation: 是否观察(int类型, 1=否, 2=是)
temperature: 温度(°C)
"""
self.append_to_workflow_sequence('{"web_workflow_name": "Liquid_feeding_vials(non-titration)"}')
@@ -208,7 +208,8 @@ class BioyondReactionStation(BioyondWorkstation):
def liquid_feeding_solvents(
self,
assign_material_name: str,
volume: str,
volume: str = None,
solvents = None,
titration_type: str = "1",
time: str = "360",
torque_variation: int = 2,
@@ -218,12 +219,41 @@ class BioyondReactionStation(BioyondWorkstation):
Args:
assign_material_name: 物料名称
volume: 分液量(μL)
titration_type: 是否滴定
volume: 分液量(μL),直接指定体积(可选,如果提供solvents则自动计算)
solvents: 溶剂信息的字典或JSON字符串(可选),格式如下:
{
"additional_solvent": 33.55092503597727, # 溶剂体积(mL)
"total_liquid_volume": 48.00916988195499
}
如果提供solvents,则从中提取additional_solvent并转换为μL
titration_type: 是否滴定(1=否, 2=是)
time: 观察时间(分钟)
torque_variation: 是否观察扭矩变化(int类型, 1=否, 2=是)
temperature: 温度上限(°C)
torque_variation: 是否观察(int类型, 1=否, 2=是)
temperature: 温度设定(°C)
"""
# 处理 volume 参数:优先使用直接传入的 volume,否则从 solvents 中提取
if volume is None and solvents is not None:
# 参数类型转换:如果是字符串则解析为字典
if isinstance(solvents, str):
try:
solvents = json.loads(solvents)
except json.JSONDecodeError as e:
raise ValueError(f"solvents参数JSON解析失败: {str(e)}")
# 参数验证
if not isinstance(solvents, dict):
raise ValueError("solvents 必须是字典类型或有效的JSON字符串")
# 提取 additional_solvent 值
additional_solvent = solvents.get("additional_solvent")
if additional_solvent is None:
raise ValueError("solvents 中没有找到 additional_solvent 字段")
# 转换为微升(μL) - 从毫升(mL)转换
volume = str(float(additional_solvent) * 1000)
elif volume is None:
raise ValueError("必须提供 volume 或 solvents 参数之一")
self.append_to_workflow_sequence('{"web_workflow_name": "Liquid_feeding_solvents"}')
material_id = self.hardware_interface._get_material_id_by_name(assign_material_name)
if material_id is None:
@@ -273,9 +303,9 @@ class BioyondReactionStation(BioyondWorkstation):
Args:
volume_formula: 分液公式(μL)
assign_material_name: 物料名称
titration_type: 是否滴定
titration_type: 是否滴定(1=否, 2=是)
time: 观察时间(分钟)
torque_variation: 是否观察扭矩变化(int类型, 1=否, 2=是)
torque_variation: 是否观察(int类型, 1=否, 2=是)
temperature: 温度(°C)
"""
self.append_to_workflow_sequence('{"web_workflow_name": "Liquid_feeding(titration)"}')
@@ -328,9 +358,9 @@ class BioyondReactionStation(BioyondWorkstation):
volume: 分液量(μL)
assign_material_name: 物料名称(试剂瓶位)
time: 观察时间(分钟)
torque_variation: 是否观察扭矩变化(int类型, 1=否, 2=是)
titration_type: 是否滴定
temperature: 温度上限(°C)
torque_variation: 是否观察(int类型, 1=否, 2=是)
titration_type: 是否滴定(1=否, 2=是)
temperature: 温度设定(°C)
"""
self.append_to_workflow_sequence('{"web_workflow_name": "liquid_feeding_beaker"}')
material_id = self.hardware_interface._get_material_id_by_name(assign_material_name)
@@ -381,9 +411,9 @@ class BioyondReactionStation(BioyondWorkstation):
Args:
assign_material_name: 物料名称(液体种类)
volume: 分液量(μL)
titration_type: 是否滴定
titration_type: 是否滴定(1=否, 2=是)
time: 观察时间(分钟)
torque_variation: 是否观察扭矩变化(int类型, 1=否, 2=是)
torque_variation: 是否观察(int类型, 1=否, 2=是)
temperature: 温度(°C)
"""
self.append_to_workflow_sequence('{"web_workflow_name": "drip_back"}')
@@ -605,7 +635,8 @@ class BioyondReactionStation(BioyondWorkstation):
total_params += 1
step_parameters[step_id][action_name].append({
"Key": param_key,
"DisplayValue": param_value
"DisplayValue": param_value,
"Value": param_value
})
successful_params += 1
# print(f" ✓ {param_key} = {param_value}")

View File

@@ -4,6 +4,7 @@ Bioyond Workstation Implementation
集成Bioyond物料管理的工作站示例
"""
import time
import traceback
from datetime import datetime
from typing import Dict, Any, List, Optional, Union

View File

@@ -0,0 +1,404 @@
bioyond_dispensing_station:
category:
- workstation
- bioyond
- bioyond_dispensing_station
class:
action_value_mappings:
batch_create_90_10_vial_feeding_tasks:
feedback: {}
goal:
delay_time: delay_time
hold_m_name: hold_m_name
liquid_material_name: liquid_material_name
speed: speed
temperature: temperature
titration: titration
goal_default:
delay_time: '600'
hold_m_name: ''
liquid_material_name: NMP
speed: '400'
temperature: '40'
titration: ''
handles:
input:
- data_key: titration
data_source: handle
data_type: object
handler_key: titration
io_type: source
label: Titration Data From Calculation Node
result:
return_info: return_info
schema:
description: 批量创建90%10%小瓶投料任务。从计算节点接收titration数据,包含物料名称、主称固体质量、滴定固体质量和滴定溶剂体积。
properties:
feedback:
properties: {}
required: []
title: BatchCreate9010VialFeedingTasks_Feedback
type: object
goal:
properties:
delay_time:
default: '600'
description: 延迟时间(秒),默认600
type: string
hold_m_name:
description: 库位名称,如"C01",必填参数
type: string
liquid_material_name:
default: NMP
description: 10%物料的液体物料名称,默认为"NMP"
type: string
speed:
default: '400'
description: 搅拌速度,默认400
type: string
temperature:
default: '40'
description: 温度(℃),默认40
type: string
titration:
description: '滴定信息对象,包含: name(物料名称), main_portion(主称固体质量g), titration_portion(滴定固体质量g),
titration_solvent(滴定溶液体积mL)'
type: string
required:
- titration
- hold_m_name
title: BatchCreate9010VialFeedingTasks_Goal
type: object
result:
properties:
return_info:
type: string
required:
- return_info
title: BatchCreate9010VialFeedingTasks_Result
type: object
required:
- goal
title: BatchCreate9010VialFeedingTasks
type: object
type: UniLabJsonCommand
batch_create_diamine_solution_tasks:
feedback: {}
goal:
delay_time: delay_time
liquid_material_name: liquid_material_name
solutions: solutions
speed: speed
temperature: temperature
goal_default:
delay_time: '600'
liquid_material_name: NMP
solutions: ''
speed: '400'
temperature: '20'
handles:
input:
- data_key: solutions
data_source: handle
data_type: array
handler_key: solutions
io_type: source
label: Solution Data From Python
result:
return_info: return_info
schema:
description: 批量创建二胺溶液配置任务。自动为多个二胺样品创建溶液配置任务,每个任务包含固体物料称量、溶剂添加、搅拌混合等步骤。
properties:
feedback:
properties: {}
required: []
title: BatchCreateDiamineSolutionTasks_Feedback
type: object
goal:
properties:
delay_time:
default: '600'
description: 溶液配置完成后的延迟时间用于充分混合和溶解默认600秒
type: string
liquid_material_name:
default: NMP
description: 液体溶剂名称用于溶解固体物料默认为NMPN-甲基吡咯烷酮)
type: string
solutions:
description: '溶液列表JSON数组格式每个元素包含: name(物料名称), order(序号), solid_mass(固体质量g),
solvent_volume(溶剂体积mL)。示例: [{"name": "MDA", "order": 0, "solid_mass":
5.0, "solvent_volume": 20}, {"name": "MPDA", "order": 1, "solid_mass":
4.5, "solvent_volume": 18}]'
type: string
speed:
default: '400'
description: 搅拌速度rpm用于混合溶液默认400转/分钟
type: string
temperature:
default: '20'
description: 配置温度溶液配置过程的目标温度默认20℃室温
type: string
required:
- solutions
title: BatchCreateDiamineSolutionTasks_Goal
type: object
result:
properties:
return_info:
description: 批量任务创建结果汇总JSON格式包含总数、成功数、失败数及每个任务的详细信息
type: string
required:
- return_info
title: BatchCreateDiamineSolutionTasks_Result
type: object
required:
- goal
title: BatchCreateDiamineSolutionTasks
type: object
type: UniLabJsonCommand
create_90_10_vial_feeding_task:
feedback: {}
goal:
delay_time: delay_time
hold_m_name: hold_m_name
order_name: order_name
percent_10_1_assign_material_name: percent_10_1_assign_material_name
percent_10_1_liquid_material_name: percent_10_1_liquid_material_name
percent_10_1_target_weigh: percent_10_1_target_weigh
percent_10_1_volume: percent_10_1_volume
percent_10_2_assign_material_name: percent_10_2_assign_material_name
percent_10_2_liquid_material_name: percent_10_2_liquid_material_name
percent_10_2_target_weigh: percent_10_2_target_weigh
percent_10_2_volume: percent_10_2_volume
percent_10_3_assign_material_name: percent_10_3_assign_material_name
percent_10_3_liquid_material_name: percent_10_3_liquid_material_name
percent_10_3_target_weigh: percent_10_3_target_weigh
percent_10_3_volume: percent_10_3_volume
percent_90_1_assign_material_name: percent_90_1_assign_material_name
percent_90_1_target_weigh: percent_90_1_target_weigh
percent_90_2_assign_material_name: percent_90_2_assign_material_name
percent_90_2_target_weigh: percent_90_2_target_weigh
percent_90_3_assign_material_name: percent_90_3_assign_material_name
percent_90_3_target_weigh: percent_90_3_target_weigh
speed: speed
temperature: temperature
goal_default:
delay_time: ''
hold_m_name: ''
order_name: ''
percent_10_1_assign_material_name: ''
percent_10_1_liquid_material_name: ''
percent_10_1_target_weigh: ''
percent_10_1_volume: ''
percent_10_2_assign_material_name: ''
percent_10_2_liquid_material_name: ''
percent_10_2_target_weigh: ''
percent_10_2_volume: ''
percent_10_3_assign_material_name: ''
percent_10_3_liquid_material_name: ''
percent_10_3_target_weigh: ''
percent_10_3_volume: ''
percent_90_1_assign_material_name: ''
percent_90_1_target_weigh: ''
percent_90_2_assign_material_name: ''
percent_90_2_target_weigh: ''
percent_90_3_assign_material_name: ''
percent_90_3_target_weigh: ''
speed: ''
temperature: ''
handles: {}
result:
return_info: return_info
schema:
description: ''
properties:
feedback:
properties: {}
required: []
title: DispenStationVialFeed_Feedback
type: object
goal:
properties:
delay_time:
type: string
hold_m_name:
type: string
order_name:
type: string
percent_10_1_assign_material_name:
type: string
percent_10_1_liquid_material_name:
type: string
percent_10_1_target_weigh:
type: string
percent_10_1_volume:
type: string
percent_10_2_assign_material_name:
type: string
percent_10_2_liquid_material_name:
type: string
percent_10_2_target_weigh:
type: string
percent_10_2_volume:
type: string
percent_10_3_assign_material_name:
type: string
percent_10_3_liquid_material_name:
type: string
percent_10_3_target_weigh:
type: string
percent_10_3_volume:
type: string
percent_90_1_assign_material_name:
type: string
percent_90_1_target_weigh:
type: string
percent_90_2_assign_material_name:
type: string
percent_90_2_target_weigh:
type: string
percent_90_3_assign_material_name:
type: string
percent_90_3_target_weigh:
type: string
speed:
type: string
temperature:
type: string
required:
- order_name
- percent_90_1_assign_material_name
- percent_90_1_target_weigh
- percent_90_2_assign_material_name
- percent_90_2_target_weigh
- percent_90_3_assign_material_name
- percent_90_3_target_weigh
- percent_10_1_assign_material_name
- percent_10_1_target_weigh
- percent_10_1_volume
- percent_10_1_liquid_material_name
- percent_10_2_assign_material_name
- percent_10_2_target_weigh
- percent_10_2_volume
- percent_10_2_liquid_material_name
- percent_10_3_assign_material_name
- percent_10_3_target_weigh
- percent_10_3_volume
- percent_10_3_liquid_material_name
- speed
- temperature
- delay_time
- hold_m_name
title: DispenStationVialFeed_Goal
type: object
result:
properties:
return_info:
type: string
required:
- return_info
title: DispenStationVialFeed_Result
type: object
required:
- goal
title: DispenStationVialFeed
type: object
type: DispenStationVialFeed
create_diamine_solution_task:
feedback: {}
goal:
delay_time: delay_time
hold_m_name: hold_m_name
liquid_material_name: liquid_material_name
material_name: material_name
order_name: order_name
speed: speed
target_weigh: target_weigh
temperature: temperature
volume: volume
goal_default:
delay_time: ''
hold_m_name: ''
liquid_material_name: ''
material_name: ''
order_name: ''
speed: ''
target_weigh: ''
temperature: ''
volume: ''
handles: {}
result:
return_info: return_info
schema:
description: ''
properties:
feedback:
properties: {}
required: []
title: DispenStationSolnPrep_Feedback
type: object
goal:
properties:
delay_time:
type: string
hold_m_name:
type: string
liquid_material_name:
type: string
material_name:
type: string
order_name:
type: string
speed:
type: string
target_weigh:
type: string
temperature:
type: string
volume:
type: string
required:
- order_name
- material_name
- target_weigh
- volume
- liquid_material_name
- speed
- temperature
- delay_time
- hold_m_name
title: DispenStationSolnPrep_Goal
type: object
result:
properties:
return_info:
type: string
required:
- return_info
title: DispenStationSolnPrep_Result
type: object
required:
- goal
title: DispenStationSolnPrep
type: object
type: DispenStationSolnPrep
module: unilabos.devices.workstation.bioyond_studio.dispensing_station:BioyondDispensingStation
status_types: {}
type: python
config_info: []
description: ''
handles: []
icon: preparation_station.webp
init_param_schema:
config:
properties:
config:
type: string
required:
- config
type: object
data:
properties: {}
required: []
type: object
version: 1.0.0

View File

@@ -4,67 +4,38 @@ reaction_station.bioyond:
- reaction_station_bioyond
class:
action_value_mappings:
auto-append_to_workflow_sequence:
drip_back:
feedback: {}
goal: {}
goal:
assign_material_name: assign_material_name
temperature: temperature
time: time
titration_type: titration_type
torque_variation: torque_variation
volume: volume
goal_default:
web_workflow_name: null
assign_material_name: ''
temperature: ''
time: ''
titration_type: ''
torque_variation: ''
volume: ''
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
description: 滴回去
properties:
feedback: {}
goal:
properties:
web_workflow_name:
assign_material_name:
description: 物料名称(不能为空)
type: string
required:
- web_workflow_name
type: object
result: {}
required:
- goal
title: append_to_workflow_sequence参数
type: object
type: UniLabJsonCommand
auto-clear_workflows:
feedback: {}
goal: {}
goal_default: {}
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties: {}
required: []
type: object
result: {}
required:
- goal
title: clear_workflows参数
type: object
type: UniLabJsonCommand
auto-load_bioyond_data_from_file:
feedback: {}
goal: {}
goal_default:
file_path: null
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties:
file_path:
temperature:
description: 温度设定(°C)
type: string
time:
description: 观察时间(分钟)
type: string
required:
- file_path
@@ -116,397 +87,35 @@ reaction_station.bioyond:
properties:
json_str:
type: string
required:
- json_str
type: object
result: {}
required:
- goal
title: process_web_workflows参数
type: object
type: UniLabJsonCommand
auto-reset_workstation:
feedback: {}
goal: {}
goal_default: {}
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties: {}
required: []
type: object
result: {}
required:
- goal
title: reset_workstation参数
type: object
type: UniLabJsonCommand
auto-resource_tree_add:
feedback: {}
goal: {}
goal_default:
resources: null
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties:
resources:
items:
type: object
type: array
required:
- resources
type: object
result: {}
required:
- goal
title: resource_tree_add参数
type: object
type: UniLabJsonCommand
auto-set_workflow_sequence:
feedback: {}
goal: {}
goal_default:
json_str: null
handles: {}
placeholder_keys: {}
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties:
json_str:
type: string
required:
- json_str
type: object
result: {}
required:
- goal
title: set_workflow_sequence参数
type: object
type: UniLabJsonCommand
auto-transfer_resource_to_another:
feedback: {}
goal: {}
goal_default:
mount_device_id: null
mount_resource: null
resource: null
sites: null
handles: {}
placeholder_keys:
mount_device_id: unilabos_devices
mount_resource: unilabos_resources
resource: unilabos_resources
result: {}
schema:
description: ''
properties:
feedback: {}
goal:
properties:
mount_device_id:
type: object
mount_resource:
items:
properties:
category:
type: string
children:
items:
type: string
type: array
config:
type: string
data:
type: string
id:
type: string
name:
type: string
parent:
type: string
pose:
properties:
orientation:
properties:
w:
type: number
x:
type: number
y:
type: number
z:
type: number
required:
- x
- y
- z
- w
title: orientation
type: object
position:
properties:
x:
type: number
y:
type: number
z:
type: number
required:
- x
- y
- z
title: position
type: object
required:
- position
- orientation
title: pose
type: object
sample_id:
type: string
type:
type: string
required:
- id
- name
- sample_id
- children
- parent
- type
- category
- pose
- config
- data
title: mount_resource
type: object
type: array
resource:
items:
properties:
category:
type: string
children:
items:
type: string
type: array
config:
type: string
data:
type: string
id:
type: string
name:
type: string
parent:
type: string
pose:
properties:
orientation:
properties:
w:
type: number
x:
type: number
y:
type: number
z:
type: number
required:
- x
- y
- z
- w
title: orientation
type: object
position:
properties:
x:
type: number
y:
type: number
z:
type: number
required:
- x
- y
- z
title: position
type: object
required:
- position
- orientation
title: pose
type: object
sample_id:
type: string
type:
type: string
required:
- id
- name
- sample_id
- children
- parent
- type
- category
- pose
- config
- data
title: resource
type: object
type: array
sites:
items:
type: string
type: array
required:
- resource
- mount_resource
- sites
- mount_device_id
type: object
result: {}
required:
- goal
title: transfer_resource_to_another参数
type: object
type: UniLabJsonCommand
bioyond_sync:
feedback: {}
goal:
force_sync: force_sync
sync_type: sync_type
goal_default:
force_sync: false
sync_type: full
handles: {}
result: {}
schema:
description: 从Bioyond系统同步物料
properties:
feedback: {}
goal:
properties:
force_sync:
description: 是否强制同步
type: boolean
sync_type:
description: 同步类型
enum:
- full
- incremental
type: string
required:
- sync_type
type: object
result: {}
required:
- goal
title: bioyond_sync参数
type: object
type: UniLabJsonCommand
bioyond_update:
feedback: {}
goal:
material_ids: material_ids
sync_all: sync_all
goal_default:
material_ids: []
sync_all: true
handles: {}
result: {}
schema:
description: 将本地物料变更同步到Bioyond
properties:
feedback: {}
goal:
properties:
material_ids:
description: 要同步的物料ID列表
items:
type: string
type: array
sync_all:
description: 是否同步所有物料
type: boolean
required:
- sync_all
type: object
result: {}
required:
- goal
title: bioyond_update参数
type: object
type: UniLabJsonCommand
reaction_station_drip_back:
feedback: {}
goal:
assign_material_name: assign_material_name
time: time
torque_variation: torque_variation
volume: volume
goal_default:
assign_material_name: ''
time: ''
torque_variation: ''
volume: ''
handles: {}
result: {}
schema:
description: 反应站滴回操作
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 溶剂名称
type: string
time:
description: 观察时间单位min
type: string
torque_variation:
description: 是否观察1否2是
type: string
volume:
description: 投料体积
description: 分液公式(μL)
type: string
required:
- volume
- assign_material_name
- time
- torque_variation
- titration_type
- temperature
type: object
result: {}
required:
- goal
title: reaction_station_drip_back参数
title: drip_back参数
type: object
type: UniLabJsonCommand
reaction_station_liquid_feed:
liquid_feeding_beaker:
feedback: {}
goal:
assign_material_name: assign_material_name
temperature: temperature
time: time
titration_type: titration_type
torque_variation: torque_variation
volume: volume
goal_default:
assign_material_name: ''
temperature: ''
time: ''
titration_type: ''
torque_variation: ''
@@ -514,40 +123,223 @@ reaction_station.bioyond:
handles: {}
result: {}
schema:
description: 反应站液体进料操作
description: 液体进料烧杯
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 溶剂名称
description: 物料名称
type: string
temperature:
description: 温度设定(°C)
type: string
time:
description: 观察时间单位min
description: 观察时间(分钟)
type: string
titration_type:
description: 滴定类型1否2是
description: 是否滴定(1=否, 2=是)
type: string
torque_variation:
description: 是否观察1否2是
description: 是否观察 (1=否, 2=是)
type: string
volume:
description: 投料体积
description: 分液公式(μL)
type: string
required:
- titration_type
- volume
- assign_material_name
- time
- torque_variation
- titration_type
- temperature
type: object
result: {}
required:
- goal
title: reaction_station_liquid_feed参数
title: liquid_feeding_beaker参数
type: object
type: UniLabJsonCommand
reaction_station_process_execute:
liquid_feeding_solvents:
feedback: {}
goal:
assign_material_name: assign_material_name
solvents: solvents
temperature: temperature
time: time
titration_type: titration_type
torque_variation: torque_variation
volume: volume
goal_default:
assign_material_name: ''
solvents: ''
temperature: '25.00'
time: '360'
titration_type: '1'
torque_variation: '2'
volume: ''
handles:
input:
- data_key: solvents
data_source: handle
data_type: object
handler_key: solvents
io_type: source
label: Solvents Data From Calculation Node
result: {}
schema:
description: 液体投料-溶剂。可以直接提供volume(μL),或通过solvents对象自动从additional_solvent(mL)计算volume。
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 物料名称
type: string
solvents:
description: '溶剂信息对象(可选),包含: additional_solvent(溶剂体积mL), total_liquid_volume(总液体体积mL)。如果提供,将自动计算volume'
type: string
temperature:
default: '25.00'
description: 温度设定(°C),默认25.00
type: string
time:
default: '360'
description: 观察时间(分钟),默认360
type: string
titration_type:
default: '1'
description: 是否滴定(1=否, 2=是),默认1
type: string
torque_variation:
default: '2'
description: 是否观察 (1=否, 2=是),默认2
type: string
volume:
description: 分液量(μL)。可直接提供,或通过solvents参数自动计算
type: string
required:
- assign_material_name
type: object
result: {}
required:
- goal
title: liquid_feeding_solvents参数
type: object
type: UniLabJsonCommand
liquid_feeding_titration:
feedback: {}
goal:
assign_material_name: assign_material_name
temperature: temperature
time: time
titration_type: titration_type
torque_variation: torque_variation
volume_formula: volume_formula
goal_default:
assign_material_name: ''
temperature: ''
time: ''
titration_type: ''
torque_variation: ''
volume_formula: ''
handles: {}
result: {}
schema:
description: 液体进料(滴定)
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 物料名称
type: string
temperature:
description: 温度设定(°C)
type: string
time:
description: 观察时间(分钟)
type: string
titration_type:
description: 是否滴定(1=否, 2=是)
type: string
torque_variation:
description: 是否观察 (1=否, 2=是)
type: string
volume_formula:
description: 分液公式(μL)
type: string
required:
- volume_formula
- assign_material_name
- time
- torque_variation
- titration_type
- temperature
type: object
result: {}
required:
- goal
title: liquid_feeding_titration参数
type: object
type: UniLabJsonCommand
liquid_feeding_vials_non_titration:
feedback: {}
goal:
assign_material_name: assign_material_name
temperature: temperature
time: time
titration_type: titration_type
torque_variation: torque_variation
volume_formula: volume_formula
goal_default:
assign_material_name: ''
temperature: ''
time: ''
titration_type: ''
torque_variation: ''
volume_formula: ''
handles: {}
result: {}
schema:
description: 液体进料小瓶(非滴定)
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 物料名称
type: string
temperature:
description: 温度设定(°C)
type: string
time:
description: 观察时间(分钟)
type: string
titration_type:
description: 是否滴定(1=否, 2=是)
type: string
torque_variation:
description: 是否观察 (1=否, 2=是)
type: string
volume_formula:
description: 分液公式(μL)
type: string
required:
- volume_formula
- assign_material_name
- time
- torque_variation
- titration_type
- temperature
type: object
result: {}
required:
- goal
title: liquid_feeding_vials_non_titration参数
type: object
type: UniLabJsonCommand
process_and_execute_workflow:
feedback: {}
goal:
task_name: task_name
@@ -558,7 +350,7 @@ reaction_station.bioyond:
handles: {}
result: {}
schema:
description: 反应站流程执行
description: 处理并执行工作流
properties:
feedback: {}
goal:
@@ -576,92 +368,10 @@ reaction_station.bioyond:
result: {}
required:
- goal
title: reaction_station_process_execute参数
title: process_and_execute_workflow参数
type: object
type: UniLabJsonCommand
reaction_station_reactor_taken_out:
feedback: {}
goal:
order_id: order_id
preintake_id: preintake_id
goal_default:
order_id: ''
preintake_id: ''
handles: {}
result: {}
schema:
description: 反应站反应器取出操作 - 通过订单ID和预取样ID进行精确控制
properties:
feedback: {}
goal:
properties:
order_id:
description: 订单ID用于标识要取出的订单
type: string
preintake_id:
description: 预取样ID用于标识具体的取样任务
type: string
required: []
type: object
result:
properties:
code:
description: 操作结果代码1表示成功0表示失败
type: integer
return_info:
description: 操作结果详细信息
type: string
type: object
required:
- goal
title: reaction_station_reactor_taken_out参数
type: object
type: UniLabJsonCommand
reaction_station_solid_feed_vial:
feedback: {}
goal:
assign_material_name: assign_material_name
material_id: material_id
time: time
torque_variation: torque_variation
goal_default:
assign_material_name: ''
material_id: ''
time: ''
torque_variation: ''
handles: {}
result: {}
schema:
description: 反应站固体进料操作
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 固体名称_粉末加样模块-投料
type: string
material_id:
description: 固体投料类型_粉末加样模块-投料
type: string
time:
description: 观察时间_反应模块-观察搅拌结果
type: string
torque_variation:
description: 是否观察1否2是_反应模块-观察搅拌结果
type: string
required:
- assign_material_name
- material_id
- time
- torque_variation
type: object
result: {}
required:
- goal
title: reaction_station_solid_feed_vial参数
type: object
type: UniLabJsonCommand
reaction_station_take_in:
reactor_taken_in:
feedback: {}
goal:
assign_material_name: assign_material_name
@@ -674,7 +384,7 @@ reaction_station.bioyond:
handles: {}
result: {}
schema:
description: 反应站取入操作
description: 反应器放入 - 将反应器放入工作站,配置物料名称、粘度上限和温度参数
properties:
feedback: {}
goal:
@@ -683,10 +393,10 @@ reaction_station.bioyond:
description: 物料名称
type: string
cutoff:
description: 截止参数
description: 粘度上限
type: string
temperature:
description: 温度
description: 温度设定(°C)
type: string
required:
- cutoff
@@ -696,10 +406,88 @@ reaction_station.bioyond:
result: {}
required:
- goal
title: reaction_station_take_in参数
title: reactor_taken_in参数
type: object
type: UniLabJsonCommand
module: unilabos.devices.workstation.bioyond_studio.station:BioyondWorkstation
reactor_taken_out:
feedback: {}
goal: {}
goal_default: {}
handles: {}
result: {}
schema:
description: 反应器取出 - 从工作站中取出反应器,无需参数的简单操作
properties:
feedback: {}
goal:
properties: {}
required: []
type: object
result:
properties:
code:
description: 操作结果代码(1表示成功,0表示失败)
type: integer
return_info:
description: 操作结果详细信息
type: string
type: object
required:
- goal
title: reactor_taken_out参数
type: object
type: UniLabJsonCommand
solid_feeding_vials:
feedback: {}
goal:
assign_material_name: assign_material_name
material_id: material_id
temperature: temperature
time: time
torque_variation: torque_variation
goal_default:
assign_material_name: ''
material_id: ''
temperature: ''
time: ''
torque_variation: ''
handles: {}
result: {}
schema:
description: 固体进料小瓶 - 通过小瓶向反应器中添加固体物料,支持多种粉末类型(盐、面粉、BTDA)
properties:
feedback: {}
goal:
properties:
assign_material_name:
description: 物料名称(用于获取试剂瓶位ID)
type: string
material_id:
description: 粉末类型ID1=盐21分钟2=面粉27分钟3=BTDA38分钟
type: string
temperature:
description: 温度设定(°C)
type: string
time:
description: 观察时间(分钟)
type: string
torque_variation:
description: 是否观察 (1=否, 2=是)
type: string
required:
- assign_material_name
- material_id
- time
- torque_variation
- temperature
type: object
result: {}
required:
- goal
title: solid_feeding_vials参数
type: object
type: UniLabJsonCommand
module: unilabos.devices.workstation.bioyond_studio.reaction_station:BioyondReactionStation
protocol_type: []
status_types:
all_workflows: dict
@@ -708,14 +496,14 @@ reaction_station.bioyond:
workstation_status: dict
type: python
config_info: []
description: Bioyond反应站 - 专门用于化学反应操作的工作站
description: Bioyond反应站
handles: []
icon: 反应站.webp
icon: reaction_station.webp
init_param_schema:
config:
properties:
bioyond_config:
type: string
config:
type: object
deck:
type: string
required: []

View File

@@ -18,6 +18,7 @@ def bioyond_warehouse_1x4x4(name: str) -> WareHouse:
)
def bioyond_warehouse_1x4x2(name: str) -> WareHouse:
"""创建BioYond 4x1x2仓库"""
return warehouse_factory(

View File

@@ -535,6 +535,7 @@ def resource_ulab_to_plr(resource: dict, plr_model=False) -> "ResourcePLR":
def resource_ulab_to_plr_inner(resource: dict):
all_states[resource["name"]] = resource["data"]
extra = resource.pop("extra", {})
d = {
"name": resource["name"],
"type": resource["type"],
@@ -575,16 +576,16 @@ def resource_plr_to_ulab(resource_plr: "ResourcePLR", parent_name: str = None, w
replace_info = {
"plate": "plate",
"well": "well",
"tip_spot": "container",
"trash": "container",
"tip_spot": "tip_spot",
"trash": "trash",
"deck": "deck",
"tip_rack": "container",
"tip_rack": "tip_rack",
}
if source in replace_info:
return replace_info[source]
else:
print("转换pylabrobot的时候出现未知类型", source)
return "container"
return source
def resource_plr_to_ulab_inner(d: dict, all_states: dict, child=True) -> dict:
r = {

View File

@@ -78,6 +78,7 @@ class ItemizedCarrier(ResourcePLR):
sites: Optional[Dict[Union[int, str], Optional[ResourcePLR]]] = None,
category: Optional[str] = "carrier",
model: Optional[str] = None,
invisible_slots: Optional[str] = None,
):
super().__init__(
name=name,
@@ -89,6 +90,7 @@ class ItemizedCarrier(ResourcePLR):
)
self.num_items = len(sites)
self.num_items_x, self.num_items_y, self.num_items_z = num_items_x, num_items_y, num_items_z
self.invisible_slots = [] if invisible_slots is None else invisible_slots
self.layout = "z-y" if self.num_items_z > 1 and self.num_items_x == 1 else "x-z" if self.num_items_z > 1 and self.num_items_y == 1 else "x-y"
if isinstance(sites, dict):
@@ -410,7 +412,7 @@ class ItemizedCarrier(ResourcePLR):
"layout": self.layout,
"sites": [{
"label": str(identifier),
"visible": True if self[identifier] is not None else False,
"visible": False if identifier in self.invisible_slots else True,
"occupied_by": self[identifier].name
if isinstance(self[identifier], ResourcePLR) and not isinstance(self[identifier], ResourceHolder) else
self[identifier] if isinstance(self[identifier], str) else None,
@@ -433,6 +435,7 @@ class BottleCarrier(ItemizedCarrier):
sites: Optional[Dict[Union[int, str], ResourceHolder]] = None,
category: str = "bottle_carrier",
model: Optional[str] = None,
invisible_slots: List[str] = None,
**kwargs,
):
super().__init__(
@@ -443,4 +446,5 @@ class BottleCarrier(ItemizedCarrier):
sites=sites,
category=category,
model=model,
invisible_slots=invisible_slots,
)

View File

@@ -10,7 +10,7 @@ from unilabos.ros.nodes.presets.resource_mesh_manager import ResourceMeshManager
from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker, ResourceTreeSet
from unilabos.devices.ros_dev.liquid_handler_joint_publisher import LiquidHandlerJointPublisher
from unilabos_msgs.srv import SerialCommand # type: ignore
from rclpy.executors import MultiThreadedExecutor
from rclpy.executors import MultiThreadedExecutor, SingleThreadedExecutor
from rclpy.node import Node
from rclpy.timer import Timer

View File

@@ -49,7 +49,7 @@ from unilabos_msgs.msg import Resource # type: ignore
from unilabos.ros.nodes.resource_tracker import (
DeviceNodeResourceTracker,
ResourceTreeSet,
ResourceTreeSet, ResourceTreeInstance,
)
from unilabos.ros.x.rclpyx import get_event_loop
from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator
@@ -338,12 +338,12 @@ class BaseROS2DeviceNode(Node, Generic[T]):
# 创建资源管理客户端
self._resource_clients: Dict[str, Client] = {
"resource_add": self.create_client(ResourceAdd, "/resources/add"),
"resource_get": self.create_client(SerialCommand, "/resources/get"),
"resource_delete": self.create_client(ResourceDelete, "/resources/delete"),
"resource_update": self.create_client(ResourceUpdate, "/resources/update"),
"resource_list": self.create_client(ResourceList, "/resources/list"),
"c2s_update_resource_tree": self.create_client(SerialCommand, "/c2s_update_resource_tree"),
"resource_add": self.create_client(ResourceAdd, "/resources/add", callback_group=self.callback_group),
"resource_get": self.create_client(SerialCommand, "/resources/get", callback_group=self.callback_group),
"resource_delete": self.create_client(ResourceDelete, "/resources/delete", callback_group=self.callback_group),
"resource_update": self.create_client(ResourceUpdate, "/resources/update", callback_group=self.callback_group),
"resource_list": self.create_client(ResourceList, "/resources/list", callback_group=self.callback_group),
"c2s_update_resource_tree": self.create_client(SerialCommand, "/c2s_update_resource_tree", callback_group=self.callback_group),
}
def re_register_device(req, res):
@@ -573,6 +573,52 @@ class BaseROS2DeviceNode(Node, Generic[T]):
self.lab_logger().error(traceback.format_exc())
self.lab_logger().debug(f"资源更新结果: {response}")
def transfer_to_new_resource(self, plr_resource: "ResourcePLR", tree: ResourceTreeInstance, additional_add_params: Dict[str, Any]):
parent_uuid = tree.root_node.res_content.parent_uuid
if parent_uuid:
parent_resource: ResourcePLR = self.resource_tracker.uuid_to_resources.get(parent_uuid)
if parent_resource is None:
self.lab_logger().warning(
f"物料{plr_resource}请求挂载{tree.root_node.res_content.name}的父节点{parent_uuid}不存在"
)
else:
try:
# 特殊兼容所有plr的物料的assign方法和create_resource append_resource后期同步
additional_params = {}
extra = getattr(plr_resource, "unilabos_extra", {})
if len(extra):
self.lab_logger().info(f"发现物料{plr_resource}额外参数: " + str(extra))
if "update_resource_site" in extra:
additional_add_params["site"] = extra["update_resource_site"]
site = additional_add_params.get("site", None)
spec = inspect.signature(parent_resource.assign_child_resource)
if "spot" in spec.parameters:
ordering_dict: Dict[str, Any] = getattr(parent_resource, "_ordering")
if ordering_dict:
site = list(ordering_dict.keys()).index(site)
additional_params["spot"] = site
old_parent = plr_resource.parent
if old_parent is not None:
# plr并不支持同一个deck的加载和卸载
self.lab_logger().warning(
f"物料{plr_resource}请求从{old_parent}卸载"
)
old_parent.unassign_child_resource(plr_resource)
self.lab_logger().warning(
f"物料{plr_resource}请求挂载到{parent_resource},额外参数:{additional_params}"
)
parent_resource.assign_child_resource(
plr_resource, location=None, **additional_params
)
func = getattr(self.driver_instance, "resource_tree_transfer", None)
if callable(func):
# 分别是 物料的原来父节点当前物料的状态物料的新父节点此时物料已经重新assign了
func(old_parent, plr_resource, parent_resource)
except Exception as e:
self.lab_logger().warning(
f"物料{plr_resource}请求挂载{tree.root_node.res_content.name}的父节点{parent_resource}[{parent_uuid}]失败!\n{traceback.format_exc()}"
)
async def s2c_resource_tree(self, req: SerialCommand_Request, res: SerialCommand_Response):
"""
处理资源树更新请求
@@ -613,28 +659,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
plr_resources = tree_set.to_plr_resources()
for plr_resource, tree in zip(plr_resources, tree_set.trees):
self.resource_tracker.add_resource(plr_resource)
parent_uuid = tree.root_node.res_content.parent_uuid
if parent_uuid:
parent_resource: ResourcePLR = self.resource_tracker.uuid_to_resources.get(parent_uuid)
if parent_resource is None:
self.lab_logger().warning(
f"物料{plr_resource}请求挂载{tree.root_node.res_content.name}的父节点{parent_uuid}不存在"
)
else:
try:
# 特殊兼容所有plr的物料的assign方法和create_resource append_resource后期同步
additional_params = {}
site = additional_add_params.get("site", None)
spec = inspect.signature(parent_resource.assign_child_resource)
if "spot" in spec.parameters:
additional_params["spot"] = site
parent_resource.assign_child_resource(
plr_resource, location=None, **additional_params
)
except Exception as e:
self.lab_logger().warning(
f"物料{plr_resource}请求挂载{tree.root_node.res_content.name}的父节点{parent_resource}[{parent_uuid}]失败!\n{traceback.format_exc()}"
)
self.transfer_to_new_resource(plr_resource, tree, additional_add_params)
func = getattr(self.driver_instance, "resource_tree_add", None)
if callable(func):
func(plr_resources)
@@ -647,6 +672,17 @@ class BaseROS2DeviceNode(Node, Generic[T]):
original_instance: ResourcePLR = self.resource_tracker.figure_resource(
{"uuid": tree.root_node.res_content.uuid}, try_mode=False
)
original_parent_resource = original_instance.parent
original_parent_resource_uuid = getattr(original_parent_resource, "unilabos_uuid", None)
target_parent_resource_uuid = tree.root_node.res_content.uuid_parent
self.lab_logger().info(
f"物料{original_instance} 原始父节点{original_parent_resource_uuid} 目标父节点{target_parent_resource_uuid} 更新"
)
# todo: 对extra进行update
if getattr(plr_resource, "unilabos_extra", None) is not None:
original_instance.unilabos_extra = getattr(plr_resource, "unilabos_extra")
if original_parent_resource_uuid != target_parent_resource_uuid and original_parent_resource is not None:
self.transfer_to_new_resource(original_instance, tree, additional_add_params)
original_instance.load_all_state(states)
self.lab_logger().info(
f"更新了资源属性 {plr_resource}[{tree.root_node.res_content.uuid}] 及其子节点 {len(original_instance.get_all_children())}"
@@ -879,7 +915,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
action_type,
action_name,
execute_callback=self._create_execute_callback(action_name, action_value_mapping),
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
)
self.lab_logger().trace(f"发布动作: {action_name}, 类型: {str_action_type}")
@@ -1500,7 +1536,7 @@ class ROS2DeviceNode:
asyncio.set_event_loop(loop)
loop.run_forever()
ROS2DeviceNode._loop_thread = threading.Thread(target=run_event_loop, daemon=True, name="ROS2DeviceNode")
ROS2DeviceNode._loop_thread = threading.Thread(target=run_event_loop, daemon=True, name="ROS2DeviceNodeLoop")
ROS2DeviceNode._loop_thread.start()
logger.info(f"循环线程已启动")

View File

@@ -285,7 +285,7 @@ class HostNode(BaseROS2DeviceNode):
# 创建定时器,定期发现设备
self._discovery_timer = self.create_timer(
discovery_interval, self._discovery_devices_callback, callback_group=ReentrantCallbackGroup()
discovery_interval, self._discovery_devices_callback, callback_group=self.callback_group
)
# 添加ping-pong相关属性
@@ -494,7 +494,7 @@ class HostNode(BaseROS2DeviceNode):
if len(init_new_res) > 1: # 一个物料,多个子节点
init_new_res = [init_new_res]
resources: List[Resource] | List[List[Resource]] = init_new_res # initialize_resource已经返回list[dict]
device_ids = [device_id]
device_ids = [device_id.split("/")[-1]]
bind_parent_id = [res_creation_input["parent"]]
bind_location = [bind_locations]
other_calling_param = [
@@ -618,7 +618,7 @@ class HostNode(BaseROS2DeviceNode):
topic,
lambda msg, d=device_id, p=property_name: self.property_callback(msg, d, p),
1,
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
)
# 标记为已订阅
self._subscribed_topics.add(topic)
@@ -829,37 +829,37 @@ class HostNode(BaseROS2DeviceNode):
def _init_host_service(self):
self._resource_services: Dict[str, Service] = {
"resource_add": self.create_service(
ResourceAdd, "/resources/add", self._resource_add_callback, callback_group=ReentrantCallbackGroup()
ResourceAdd, "/resources/add", self._resource_add_callback, callback_group=self.callback_group
),
"resource_get": self.create_service(
SerialCommand, "/resources/get", self._resource_get_callback, callback_group=ReentrantCallbackGroup()
SerialCommand, "/resources/get", self._resource_get_callback, callback_group=self.callback_group
),
"resource_delete": self.create_service(
ResourceDelete,
"/resources/delete",
self._resource_delete_callback,
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
),
"resource_update": self.create_service(
ResourceUpdate,
"/resources/update",
self._resource_update_callback,
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
),
"resource_list": self.create_service(
ResourceList, "/resources/list", self._resource_list_callback, callback_group=ReentrantCallbackGroup()
ResourceList, "/resources/list", self._resource_list_callback, callback_group=self.callback_group
),
"node_info_update": self.create_service(
SerialCommand,
"/node_info_update",
self._node_info_update_callback,
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
),
"c2s_update_resource_tree": self.create_service(
SerialCommand,
"/c2s_update_resource_tree",
self._resource_tree_update_callback,
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
),
}

View File

@@ -194,7 +194,7 @@ class ROS2WorkstationNode(BaseROS2DeviceNode):
action_type,
action_name,
execute_callback=self._create_protocol_execute_callback(action_name, protocol_steps_generator),
callback_group=ReentrantCallbackGroup(),
callback_group=self.callback_group,
)
self.lab_logger().trace(f"发布动作: {action_name}, 类型: {str_action_type}")
return

View File

@@ -42,7 +42,9 @@ class ResourceDictPosition(BaseModel):
rotation: ResourceDictPositionObject = Field(
description="Resource rotation", default_factory=ResourceDictPositionObject
)
cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"] = Field(description="Cross section type", default="rectangle")
cross_section_type: Literal["rectangle", "circle", "rounded_rectangle"] = Field(
description="Cross section type", default="rectangle"
)
# 统一的资源字典模型parent 自动序列化为 parent_uuidchildren 不序列化
@@ -51,7 +53,9 @@ class ResourceDict(BaseModel):
uuid: str = Field(description="Resource UUID")
name: str = Field(description="Resource name")
description: str = Field(description="Resource description", default="")
resource_schema: Dict[str, Any] = Field(description="Resource schema", default_factory=dict, serialization_alias="schema", validation_alias="schema")
resource_schema: Dict[str, Any] = Field(
description="Resource schema", default_factory=dict, serialization_alias="schema", validation_alias="schema"
)
model: Dict[str, Any] = Field(description="Resource model", default_factory=dict)
icon: str = Field(description="Resource icon", default="")
parent_uuid: Optional["str"] = Field(description="Parent resource uuid", default=None) # 先设定parent_uuid
@@ -62,6 +66,7 @@ class ResourceDict(BaseModel):
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
config: Dict[str, Any] = Field(description="Resource configuration")
data: Dict[str, Any] = Field(description="Resource data")
extra: Dict[str, Any] = Field(description="Extra data")
@field_serializer("parent_uuid")
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
@@ -138,6 +143,8 @@ class ResourceDictInstance(object):
content["config"] = {}
if not content.get("data"):
content["data"] = {}
if not content.get("extra"): # MagicCode
content["extra"] = {}
if "pose" not in content:
content["pose"] = content.get("position", {})
return ResourceDictInstance(ResourceDict.model_validate(content))
@@ -311,28 +318,36 @@ class ResourceTreeSet(object):
"plate": "plate",
"well": "well",
"deck": "deck",
"tip_rack": "tip_rack",
"tip_spot": "tip_spot",
"tube": "tube",
"bottle_carrier": "bottle_carrier",
}
if source in replace_info:
return replace_info[source]
else:
print("转换pylabrobot的时候出现未知类型", source)
return "container"
return source
def build_uuid_mapping(res: "PLRResource", uuid_list: list):
"""递归构建uuid映射字典"""
def build_uuid_mapping(res: "PLRResource", uuid_list: list, parent_uuid: Optional[str] = None):
"""递归构建uuid和extra映射字典返回(current_uuid, parent_uuid, extra)元组列表"""
uid = getattr(res, "unilabos_uuid", "")
if not uid:
uid = str(uuid.uuid4())
res.unilabos_uuid = uid
logger.warning(f"{res}没有uuid请设置后再传入默认填充{uid}\n{traceback.format_exc()}")
uuid_list.append(uid)
# 获取unilabos_extra默认为空字典
extra = getattr(res, "unilabos_extra", {})
uuid_list.append((uid, parent_uuid, extra))
for child in res.children:
build_uuid_mapping(child, uuid_list)
build_uuid_mapping(child, uuid_list, uid)
def resource_plr_inner(
d: dict, parent_resource: Optional[ResourceDict], states: dict, uuids: list
) -> ResourceDictInstance:
current_uuid = uuids.pop(0)
current_uuid, parent_uuid, extra = uuids.pop(0)
raw_pos = (
{"x": d["location"]["x"], "y": d["location"]["y"], "z": d["location"]["z"]}
@@ -355,13 +370,30 @@ class ResourceTreeSet(object):
"uuid": current_uuid,
"name": d["name"],
"parent": parent_resource, # 直接传入 ResourceDict 对象
"parent_uuid": parent_uuid, # 使用 parent_uuid 而不是 parent 对象
"type": replace_plr_type(d.get("category", "")),
"class": d.get("class", ""),
"position": pos,
"pose": pos,
"config": {k: v for k, v in d.items() if k not in
["name", "children", "parent_name", "location", "rotation", "size_x", "size_y", "size_z", "cross_section_type", "bottom_type"]},
"config": {
k: v
for k, v in d.items()
if k
not in [
"name",
"children",
"parent_name",
"location",
"rotation",
"size_x",
"size_y",
"size_z",
"cross_section_type",
"bottom_type",
]
},
"data": states[d["name"]],
"extra": extra,
}
# 先转换为 ResourceDictInstance获取其中的 ResourceDict
@@ -379,7 +411,7 @@ class ResourceTreeSet(object):
for resource in resources:
# 构建uuid列表
uuid_list = []
build_uuid_mapping(resource, uuid_list)
build_uuid_mapping(resource, uuid_list, getattr(resource.parent, "unilabos_uuid", None))
serialized_data = resource.serialize()
all_states = resource.serialize_all_state()
@@ -402,14 +434,15 @@ class ResourceTreeSet(object):
import inspect
# 类型映射
TYPE_MAP = {"plate": "Plate", "well": "Well", "deck": "Deck"}
TYPE_MAP = {"plate": "Plate", "well": "Well", "deck": "Deck", "container": "RegularContainer"}
def collect_node_data(node: ResourceDictInstance, name_to_uuid: dict, all_states: dict):
"""一次遍历收集 name_to_uuid all_states"""
def collect_node_data(node: ResourceDictInstance, name_to_uuid: dict, all_states: dict, name_to_extra: dict):
"""一次遍历收集 name_to_uuid, all_states 和 name_to_extra"""
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
for child in node.children:
collect_node_data(child, name_to_uuid, all_states)
collect_node_data(child, name_to_uuid, all_states, name_to_extra)
def node_to_plr_dict(node: ResourceDictInstance, has_model: bool):
"""转换节点为 PLR 字典格式"""
@@ -419,6 +452,7 @@ class ResourceTreeSet(object):
logger.warning(f"未知类型 {res.type}")
d = {
**res.config,
"name": res.name,
"type": res.config.get("type", plr_type),
"size_x": res.config.get("size_x", 0),
@@ -434,33 +468,35 @@ class ResourceTreeSet(object):
"category": res.config.get("category", plr_type),
"children": [node_to_plr_dict(child, has_model) for child in node.children],
"parent_name": res.parent_instance_name,
**res.config,
}
if has_model:
d["model"] = res.config.get("model", None)
return d
plr_resources = []
trees = []
tracker = DeviceNodeResourceTracker()
for tree in self.trees:
name_to_uuid: Dict[str, str] = {}
all_states: Dict[str, Any] = {}
collect_node_data(tree.root_node, name_to_uuid, all_states)
name_to_extra: Dict[str, dict] = {}
collect_node_data(tree.root_node, name_to_uuid, all_states, name_to_extra)
has_model = tree.root_node.res_content.type != "deck"
plr_dict = node_to_plr_dict(tree.root_node, has_model)
try:
sub_cls = find_subclass(plr_dict["type"], PLRResource)
if sub_cls is None:
raise ValueError(f"无法找到类型 {plr_dict['type']} 对应的 PLR 资源类。原始信息:{tree.root_node.res_content}")
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}"
)
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)
plr_resource.load_all_state(all_states)
# 使用 DeviceNodeResourceTracker 设置 UUID
# 使用 DeviceNodeResourceTracker 设置 UUID 和 Extra
tracker.loop_set_uuid(plr_resource, name_to_uuid)
tracker.loop_set_extra(plr_resource, name_to_extra)
plr_resources.append(plr_resource)
except Exception as e:
@@ -802,6 +838,20 @@ class DeviceNodeResourceTracker(object):
else:
setattr(resource, "unilabos_uuid", new_uuid)
@staticmethod
def set_resource_extra(resource, extra: dict):
"""
设置资源的 extra统一处理 dict 和 instance 两种类型
Args:
resource: 资源对象dict或实例
extra: extra字典值
"""
if isinstance(resource, dict):
resource["extra"] = extra
else:
setattr(resource, "unilabos_extra", extra)
def _traverse_and_process(self, resource, process_func) -> int:
"""
递归遍历资源树,对每个节点执行处理函数
@@ -850,6 +900,29 @@ class DeviceNodeResourceTracker(object):
return self._traverse_and_process(resource, process)
def loop_set_extra(self, resource, name_to_extra_map: Dict[str, dict]) -> int:
"""
递归遍历资源树,根据 name 设置所有节点的 extra
Args:
resource: 资源对象可以是dict或实例
name_to_extra_map: name到extra的映射字典{name: extra}
Returns:
更新的资源数量
"""
def process(res):
resource_name = self._get_resource_attr(res, "name")
if resource_name and resource_name in name_to_extra_map:
extra = name_to_extra_map[resource_name]
self.set_resource_extra(res, extra)
logger.debug(f"设置资源Extra: {resource_name} -> {extra}")
return 1
return 0
return self._traverse_and_process(resource, process)
def loop_update_uuid(self, resource, uuid_map: Dict[str, str]) -> int:
"""
递归遍历资源树更新所有节点的uuid
@@ -892,7 +965,9 @@ class DeviceNodeResourceTracker(object):
if current_uuid:
old = self.uuid_to_resources.get(current_uuid)
self.uuid_to_resources[current_uuid] = res
logger.debug(f"收集资源UUID映射: {current_uuid} -> {res} {'' if old is None else f'(覆盖旧值: {old})'}")
logger.debug(
f"收集资源UUID映射: {current_uuid} -> {res} {'' if old is None else f'(覆盖旧值: {old})'}"
)
return 0
self._traverse_and_process(resource, process)