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feature/ca
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154048107d |
@@ -1,6 +1,6 @@
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package:
|
||||
name: unilabos
|
||||
version: 0.10.11
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version: 0.10.12
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|
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source:
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path: ../unilabos
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@@ -39,7 +39,9 @@ Uni-Lab-OS recommends using `mamba` for environment management. Choose the appro
|
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|
||||
```bash
|
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# Create new environment
|
||||
mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
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mamba create -n unilab python=3.11.11
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mamba activate unilab
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mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
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```
|
||||
|
||||
## Install Dev Uni-Lab-OS
|
||||
|
||||
@@ -41,7 +41,9 @@ Uni-Lab-OS 建议使用 `mamba` 管理环境。根据您的操作系统选择适
|
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|
||||
```bash
|
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# 创建新环境
|
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mamba create -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
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||||
mamba create -n unilab python=3.11.11
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mamba activate unilab
|
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mamba install -n unilab uni-lab::unilabos -c robostack-staging -c conda-forge
|
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```
|
||||
|
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2. 安装开发版 Uni-Lab-OS:
|
||||
|
||||
@@ -317,45 +317,6 @@ unilab --help
|
||||
|
||||
如果所有命令都正常输出,说明开发环境配置成功!
|
||||
|
||||
### 开发工具推荐
|
||||
|
||||
#### IDE
|
||||
|
||||
- **PyCharm Professional**: 强大的 Python IDE,支持远程调试
|
||||
- **VS Code**: 轻量级,配合 Python 扩展使用
|
||||
- **Vim/Emacs**: 适合终端开发
|
||||
|
||||
#### 推荐的 VS Code 扩展
|
||||
|
||||
- Python
|
||||
- Pylance
|
||||
- ROS
|
||||
- URDF
|
||||
- YAML
|
||||
|
||||
#### 调试工具
|
||||
|
||||
```bash
|
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# 安装调试工具
|
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pip install ipdb pytest pytest-cov -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
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|
||||
# 代码质量检查
|
||||
pip install black flake8 mypy -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
```
|
||||
|
||||
### 设置 pre-commit 钩子(可选)
|
||||
|
||||
```bash
|
||||
# 安装 pre-commit
|
||||
pip install pre-commit -i https://mirrors.tuna.tsinghua.edu.cn/pypi/web/simple
|
||||
|
||||
# 设置钩子
|
||||
pre-commit install
|
||||
|
||||
# 手动运行检查
|
||||
pre-commit run --all-files
|
||||
```
|
||||
|
||||
---
|
||||
|
||||
## 验证安装
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
package:
|
||||
name: ros-humble-unilabos-msgs
|
||||
version: 0.10.11
|
||||
version: 0.10.12
|
||||
source:
|
||||
path: ../../unilabos_msgs
|
||||
target_directory: src
|
||||
|
||||
@@ -1,6 +1,6 @@
|
||||
package:
|
||||
name: unilabos
|
||||
version: "0.10.11"
|
||||
version: "0.10.12"
|
||||
|
||||
source:
|
||||
path: ../..
|
||||
|
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@@ -2,7 +2,6 @@ import json
|
||||
import logging
|
||||
import traceback
|
||||
import uuid
|
||||
import xml.etree.ElementTree as ET
|
||||
from typing import Any, Dict, List
|
||||
|
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import networkx as nx
|
||||
@@ -25,7 +24,15 @@ class SimpleGraph:
|
||||
|
||||
def add_edge(self, source, target, **attrs):
|
||||
"""添加边"""
|
||||
edge = {"source": source, "target": target, **attrs}
|
||||
# edge = {"source": source, "target": target, **attrs}
|
||||
edge = {
|
||||
"source": source, "target": target,
|
||||
"source_node_uuid": source,
|
||||
"target_node_uuid": target,
|
||||
"source_handle_io": "source",
|
||||
"target_handle_io": "target",
|
||||
**attrs
|
||||
}
|
||||
self.edges.append(edge)
|
||||
|
||||
def to_dict(self):
|
||||
@@ -42,6 +49,7 @@ class SimpleGraph:
|
||||
"multigraph": False,
|
||||
"graph": {},
|
||||
"nodes": nodes_list,
|
||||
"edges": self.edges,
|
||||
"links": self.edges,
|
||||
}
|
||||
|
||||
@@ -58,495 +66,8 @@ def extract_json_from_markdown(text: str) -> str:
|
||||
return text
|
||||
|
||||
|
||||
def convert_to_type(val: str) -> Any:
|
||||
"""将字符串值转换为适当的数据类型"""
|
||||
if val == "True":
|
||||
return True
|
||||
if val == "False":
|
||||
return False
|
||||
if val == "?":
|
||||
return None
|
||||
if val.endswith(" g"):
|
||||
return float(val.split(" ")[0])
|
||||
if val.endswith("mg"):
|
||||
return float(val.split("mg")[0])
|
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elif val.endswith("mmol"):
|
||||
return float(val.split("mmol")[0]) / 1000
|
||||
elif val.endswith("mol"):
|
||||
return float(val.split("mol")[0])
|
||||
elif val.endswith("ml"):
|
||||
return float(val.split("ml")[0])
|
||||
elif val.endswith("RPM"):
|
||||
return float(val.split("RPM")[0])
|
||||
elif val.endswith(" °C"):
|
||||
return float(val.split(" ")[0])
|
||||
elif val.endswith(" %"):
|
||||
return float(val.split(" ")[0])
|
||||
return val
|
||||
|
||||
|
||||
def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
||||
"""统一的数据重构函数,根据操作类型自动选择模板"""
|
||||
refactored_data = []
|
||||
|
||||
# 定义操作映射,包含生物实验和有机化学的所有操作
|
||||
OPERATION_MAPPING = {
|
||||
# 生物实验操作
|
||||
"transfer_liquid": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
|
||||
"transfer": "SynBioFactory-liquid_handler.biomek-transfer",
|
||||
"incubation": "SynBioFactory-liquid_handler.biomek-incubation",
|
||||
"move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
|
||||
"oscillation": "SynBioFactory-liquid_handler.biomek-oscillation",
|
||||
# 有机化学操作
|
||||
"HeatChillToTemp": "SynBioFactory-workstation-HeatChillProtocol",
|
||||
"StopHeatChill": "SynBioFactory-workstation-HeatChillStopProtocol",
|
||||
"StartHeatChill": "SynBioFactory-workstation-HeatChillStartProtocol",
|
||||
"HeatChill": "SynBioFactory-workstation-HeatChillProtocol",
|
||||
"Dissolve": "SynBioFactory-workstation-DissolveProtocol",
|
||||
"Transfer": "SynBioFactory-workstation-TransferProtocol",
|
||||
"Evaporate": "SynBioFactory-workstation-EvaporateProtocol",
|
||||
"Recrystallize": "SynBioFactory-workstation-RecrystallizeProtocol",
|
||||
"Filter": "SynBioFactory-workstation-FilterProtocol",
|
||||
"Dry": "SynBioFactory-workstation-DryProtocol",
|
||||
"Add": "SynBioFactory-workstation-AddProtocol",
|
||||
}
|
||||
|
||||
UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
for step in data:
|
||||
operation = step.get("action")
|
||||
if not operation or operation in UNSUPPORTED_OPERATIONS:
|
||||
continue
|
||||
|
||||
# 处理重复操作
|
||||
if operation == "Repeat":
|
||||
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
||||
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
||||
for i in range(int(times)):
|
||||
sub_data = refactor_data(sub_steps)
|
||||
refactored_data.extend(sub_data)
|
||||
continue
|
||||
|
||||
# 获取模板名称
|
||||
template = OPERATION_MAPPING.get(operation)
|
||||
if not template:
|
||||
# 自动推断模板类型
|
||||
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
||||
template = f"SynBioFactory-liquid_handler.biomek-{operation}"
|
||||
else:
|
||||
template = f"SynBioFactory-workstation-{operation}Protocol"
|
||||
|
||||
# 创建步骤数据
|
||||
step_data = {
|
||||
"template": template,
|
||||
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
||||
"lab_node_type": "Device",
|
||||
"parameters": step.get("parameters", step.get("action_args", {})),
|
||||
}
|
||||
refactored_data.append(step_data)
|
||||
|
||||
return refactored_data
|
||||
|
||||
|
||||
def build_protocol_graph(
|
||||
labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
|
||||
) -> SimpleGraph:
|
||||
"""统一的协议图构建函数,根据设备类型自动选择构建逻辑"""
|
||||
G = SimpleGraph()
|
||||
resource_last_writer = {}
|
||||
LAB_NAME = "SynBioFactory"
|
||||
|
||||
protocol_steps = refactor_data(protocol_steps)
|
||||
|
||||
# 检查协议步骤中的模板来判断协议类型
|
||||
has_biomek_template = any(
|
||||
("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
|
||||
for step in protocol_steps
|
||||
)
|
||||
|
||||
if has_biomek_template:
|
||||
# 生物实验协议图构建
|
||||
for labware_id, labware in labware_info.items():
|
||||
node_id = str(uuid.uuid4())
|
||||
|
||||
labware_attrs = labware.copy()
|
||||
labware_id = labware_attrs.pop("id", labware_attrs.get("name", f"labware_{uuid.uuid4()}"))
|
||||
labware_attrs["description"] = labware_id
|
||||
labware_attrs["lab_node_type"] = (
|
||||
"Reagent" if "Plate" in str(labware_id) else "Labware" if "Rack" in str(labware_id) else "Sample"
|
||||
)
|
||||
labware_attrs["device_id"] = workstation_name
|
||||
|
||||
G.add_node(node_id, template=f"{LAB_NAME}-host_node-create_resource", **labware_attrs)
|
||||
resource_last_writer[labware_id] = f"{node_id}:labware"
|
||||
|
||||
# 处理协议步骤
|
||||
prev_node = None
|
||||
for i, step in enumerate(protocol_steps):
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(node_id, **step)
|
||||
|
||||
# 添加控制流边
|
||||
if prev_node is not None:
|
||||
G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
|
||||
prev_node = node_id
|
||||
|
||||
# 处理物料流
|
||||
params = step.get("parameters", {})
|
||||
if "sources" in params and params["sources"] in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[params["sources"]].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port="labware")
|
||||
|
||||
if "targets" in params:
|
||||
resource_last_writer[params["targets"]] = f"{node_id}:labware"
|
||||
|
||||
# 添加协议结束节点
|
||||
end_id = str(uuid.uuid4())
|
||||
G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
|
||||
if prev_node is not None:
|
||||
G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
|
||||
|
||||
else:
|
||||
# 有机化学协议图构建
|
||||
WORKSTATION_ID = workstation_name
|
||||
|
||||
# 为所有labware创建资源节点
|
||||
for item_id, item in labware_info.items():
|
||||
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
||||
node_id = str(uuid.uuid4())
|
||||
|
||||
# 判断节点类型
|
||||
if item.get("type") == "hardware" or "reactor" in str(item_id).lower():
|
||||
if "reactor" not in str(item_id).lower():
|
||||
continue
|
||||
lab_node_type = "Sample"
|
||||
description = f"Prepare Reactor: {item_id}"
|
||||
liquid_type = []
|
||||
liquid_volume = []
|
||||
else:
|
||||
lab_node_type = "Reagent"
|
||||
description = f"Add Reagent to Flask: {item_id}"
|
||||
liquid_type = [item_id]
|
||||
liquid_volume = [1e5]
|
||||
|
||||
G.add_node(
|
||||
node_id,
|
||||
template=f"{LAB_NAME}-host_node-create_resource",
|
||||
description=description,
|
||||
lab_node_type=lab_node_type,
|
||||
res_id=item_id,
|
||||
device_id=WORKSTATION_ID,
|
||||
class_name="container",
|
||||
parent=WORKSTATION_ID,
|
||||
bind_locations={"x": 0.0, "y": 0.0, "z": 0.0},
|
||||
liquid_input_slot=[-1],
|
||||
liquid_type=liquid_type,
|
||||
liquid_volume=liquid_volume,
|
||||
slot_on_deck="",
|
||||
role=item.get("role", ""),
|
||||
)
|
||||
resource_last_writer[item_id] = f"{node_id}:labware"
|
||||
|
||||
last_control_node_id = None
|
||||
|
||||
# 处理协议步骤
|
||||
for step in protocol_steps:
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(node_id, **step)
|
||||
|
||||
# 控制流
|
||||
if last_control_node_id is not None:
|
||||
G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
|
||||
last_control_node_id = node_id
|
||||
|
||||
# 物料流
|
||||
params = step.get("parameters", {})
|
||||
input_resources = {
|
||||
"Vessel": params.get("vessel"),
|
||||
"ToVessel": params.get("to_vessel"),
|
||||
"FromVessel": params.get("from_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources": params.get("sources"),
|
||||
"targets": params.get("targets"),
|
||||
}
|
||||
|
||||
for target_port, resource_name in input_resources.items():
|
||||
if resource_name and resource_name in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[resource_name].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
|
||||
|
||||
output_resources = {
|
||||
"VesselOut": params.get("vessel"),
|
||||
"FromVesselOut": params.get("from_vessel"),
|
||||
"ToVesselOut": params.get("to_vessel"),
|
||||
"FiltrateOut": params.get("filtrate_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources_out": params.get("sources"),
|
||||
"targets_out": params.get("targets"),
|
||||
}
|
||||
|
||||
for source_port, resource_name in output_resources.items():
|
||||
if resource_name:
|
||||
resource_last_writer[resource_name] = f"{node_id}:{source_port}"
|
||||
|
||||
return G
|
||||
|
||||
|
||||
def draw_protocol_graph(protocol_graph: SimpleGraph, output_path: str):
|
||||
"""
|
||||
(辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图,用于可视化。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
G = nx.DiGraph()
|
||||
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
||||
G.add_node(node_id, label=label, **attrs)
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
G.add_edge(edge["source"], edge["target"])
|
||||
|
||||
plt.figure(figsize=(20, 15))
|
||||
try:
|
||||
pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
|
||||
except Exception:
|
||||
pos = nx.shell_layout(G) # Fallback layout
|
||||
|
||||
node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
|
||||
nx.draw(
|
||||
G,
|
||||
pos,
|
||||
with_labels=False,
|
||||
node_size=2500,
|
||||
node_color="skyblue",
|
||||
node_shape="o",
|
||||
edge_color="gray",
|
||||
width=1.5,
|
||||
arrowsize=15,
|
||||
)
|
||||
nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
|
||||
|
||||
plt.title("Chemical Protocol Workflow Graph", size=15)
|
||||
plt.savefig(output_path, dpi=300, bbox_inches="tight")
|
||||
plt.close()
|
||||
print(f" - Visualization saved to '{output_path}'")
|
||||
|
||||
|
||||
from networkx.drawing.nx_agraph import to_agraph
|
||||
import re
|
||||
|
||||
COMPASS = {"n","e","s","w","ne","nw","se","sw","c"}
|
||||
|
||||
def _is_compass(port: str) -> bool:
|
||||
return isinstance(port, str) and port.lower() in COMPASS
|
||||
|
||||
def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
|
||||
"""
|
||||
使用 Graphviz 端口语法绘制协议工作流图。
|
||||
- 若边上的 source_port/target_port 是 compass(n/e/s/w/...),直接用 compass。
|
||||
- 否则自动为节点创建 record 形状并定义命名端口 <portname>。
|
||||
最终由 PyGraphviz 渲染并输出到 output_path(后缀决定格式,如 .png/.svg/.pdf)。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
# 1) 先用 networkx 搭建有向图,保留端口属性
|
||||
G = nx.DiGraph()
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
||||
# 保留一个干净的“中心标签”,用于放在 record 的中间槽
|
||||
G.add_node(node_id, _core_label=str(label), **{k:v for k,v in attrs.items() if k not in ("label",)})
|
||||
|
||||
edges_data = []
|
||||
in_ports_by_node = {} # 收集命名输入端口
|
||||
out_ports_by_node = {} # 收集命名输出端口
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
u = edge["source"]
|
||||
v = edge["target"]
|
||||
sp = edge.get("source_port")
|
||||
tp = edge.get("target_port")
|
||||
|
||||
# 记录到图里(保留原始端口信息)
|
||||
G.add_edge(u, v, source_port=sp, target_port=tp)
|
||||
edges_data.append((u, v, sp, tp))
|
||||
|
||||
# 如果不是 compass,就按“命名端口”先归类,等会儿给节点造 record
|
||||
if sp and not _is_compass(sp):
|
||||
out_ports_by_node.setdefault(u, set()).add(str(sp))
|
||||
if tp and not _is_compass(tp):
|
||||
in_ports_by_node.setdefault(v, set()).add(str(tp))
|
||||
|
||||
# 2) 转为 AGraph,使用 Graphviz 渲染
|
||||
A = to_agraph(G)
|
||||
A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
|
||||
A.node_attr.update(shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica")
|
||||
A.edge_attr.update(arrowsize="0.8", color="#666666")
|
||||
|
||||
# 3) 为需要命名端口的节点设置 record 形状与 label
|
||||
# 左列 = 输入端口;中间 = 核心标签;右列 = 输出端口
|
||||
for n in A.nodes():
|
||||
node = A.get_node(n)
|
||||
core = G.nodes[n].get("_core_label", n)
|
||||
|
||||
in_ports = sorted(in_ports_by_node.get(n, []))
|
||||
out_ports = sorted(out_ports_by_node.get(n, []))
|
||||
|
||||
# 如果该节点涉及命名端口,则用 record;否则保留原 box
|
||||
if in_ports or out_ports:
|
||||
def port_fields(ports):
|
||||
if not ports:
|
||||
return " " # 必须留一个空槽占位
|
||||
# 每个端口一个小格子,<p> name
|
||||
return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
|
||||
|
||||
left = port_fields(in_ports)
|
||||
right = port_fields(out_ports)
|
||||
|
||||
# 三栏:左(入) | 中(节点名) | 右(出)
|
||||
record_label = f"{{ {left} | {core} | {right} }}"
|
||||
node.attr.update(shape="record", label=record_label)
|
||||
else:
|
||||
# 没有命名端口:普通盒子,显示核心标签
|
||||
node.attr.update(label=str(core))
|
||||
|
||||
# 4) 给边设置 headport / tailport
|
||||
# - 若端口为 compass:直接用 compass(e.g., headport="e")
|
||||
# - 若端口为命名端口:使用在 record 中定义的 <port> 名(同名即可)
|
||||
for (u, v, sp, tp) in edges_data:
|
||||
e = A.get_edge(u, v)
|
||||
|
||||
# Graphviz 属性:tail 是源,head 是目标
|
||||
if sp:
|
||||
if _is_compass(sp):
|
||||
e.attr["tailport"] = sp.lower()
|
||||
else:
|
||||
# 与 record label 中 <port> 名一致;特殊字符已在 label 中做了清洗
|
||||
e.attr["tailport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(sp))
|
||||
|
||||
if tp:
|
||||
if _is_compass(tp):
|
||||
e.attr["headport"] = tp.lower()
|
||||
else:
|
||||
e.attr["headport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(tp))
|
||||
|
||||
# 可选:若想让边更贴边缘,可设置 constraint/spline 等
|
||||
# e.attr["arrowhead"] = "vee"
|
||||
|
||||
# 5) 输出
|
||||
A.draw(output_path, prog="dot")
|
||||
print(f" - Port-aware workflow rendered to '{output_path}'")
|
||||
|
||||
|
||||
def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
|
||||
"""展平嵌套的XDL程序结构"""
|
||||
flattened_operations = []
|
||||
TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
def extract_operations(element: ET.Element):
|
||||
if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
|
||||
if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
|
||||
flattened_operations.append(element)
|
||||
|
||||
for child in element:
|
||||
extract_operations(child)
|
||||
|
||||
for child in procedure_elem:
|
||||
extract_operations(child)
|
||||
|
||||
return flattened_operations
|
||||
|
||||
|
||||
def parse_xdl_content(xdl_content: str) -> tuple:
|
||||
"""解析XDL内容"""
|
||||
try:
|
||||
xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
|
||||
root = ET.fromstring(xdl_content_cleaned)
|
||||
|
||||
synthesis_elem = root.find("Synthesis")
|
||||
if synthesis_elem is None:
|
||||
return None, None, None
|
||||
|
||||
# 解析硬件组件
|
||||
hardware_elem = synthesis_elem.find("Hardware")
|
||||
hardware = []
|
||||
if hardware_elem is not None:
|
||||
hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
|
||||
|
||||
# 解析试剂
|
||||
reagents_elem = synthesis_elem.find("Reagents")
|
||||
reagents = []
|
||||
if reagents_elem is not None:
|
||||
reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
|
||||
|
||||
# 解析程序
|
||||
procedure_elem = synthesis_elem.find("Procedure")
|
||||
if procedure_elem is None:
|
||||
return None, None, None
|
||||
|
||||
flattened_operations = flatten_xdl_procedure(procedure_elem)
|
||||
return hardware, reagents, flattened_operations
|
||||
|
||||
except ET.ParseError as e:
|
||||
raise ValueError(f"Invalid XDL format: {e}")
|
||||
|
||||
|
||||
def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
|
||||
"""
|
||||
将XDL XML格式转换为标准的字典格式
|
||||
|
||||
Args:
|
||||
xdl_content: XDL XML内容
|
||||
|
||||
Returns:
|
||||
转换结果,包含步骤和器材信息
|
||||
"""
|
||||
try:
|
||||
hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
|
||||
if hardware is None:
|
||||
return {"error": "Failed to parse XDL content", "success": False}
|
||||
|
||||
# 将XDL元素转换为字典格式
|
||||
steps_data = []
|
||||
for elem in flattened_operations:
|
||||
# 转换参数类型
|
||||
parameters = {}
|
||||
for key, val in elem.attrib.items():
|
||||
converted_val = convert_to_type(val)
|
||||
if converted_val is not None:
|
||||
parameters[key] = converted_val
|
||||
|
||||
step_dict = {
|
||||
"operation": elem.tag,
|
||||
"parameters": parameters,
|
||||
"description": elem.get("purpose", f"Operation: {elem.tag}"),
|
||||
}
|
||||
steps_data.append(step_dict)
|
||||
|
||||
# 合并硬件和试剂为统一的labware_info格式
|
||||
labware_data = []
|
||||
labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
|
||||
labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
|
||||
|
||||
return {
|
||||
"success": True,
|
||||
"steps": steps_data,
|
||||
"labware": labware_data,
|
||||
"message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
|
||||
}
|
||||
|
||||
except Exception as e:
|
||||
error_msg = f"XDL conversion failed: {str(e)}"
|
||||
logger.error(error_msg)
|
||||
return {"error": error_msg, "success": False}
|
||||
|
||||
|
||||
def create_workflow(
|
||||
|
||||
2
setup.py
2
setup.py
@@ -4,7 +4,7 @@ package_name = 'unilabos'
|
||||
|
||||
setup(
|
||||
name=package_name,
|
||||
version='0.10.11',
|
||||
version='0.10.12',
|
||||
packages=find_packages(),
|
||||
include_package_data=True,
|
||||
install_requires=['setuptools'],
|
||||
|
||||
|
Before Width: | Height: | Size: 148 KiB After Width: | Height: | Size: 148 KiB |
|
Before Width: | Height: | Size: 140 KiB After Width: | Height: | Size: 140 KiB |
|
Before Width: | Height: | Size: 117 KiB After Width: | Height: | Size: 117 KiB |
35
test/workflow/merge_workflow.py
Normal file
35
test/workflow/merge_workflow.py
Normal file
@@ -0,0 +1,35 @@
|
||||
import sys
|
||||
from datetime import datetime
|
||||
from pathlib import Path
|
||||
|
||||
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||||
if str(ROOT_DIR) not in sys.path:
|
||||
sys.path.insert(0, str(ROOT_DIR))
|
||||
|
||||
import pytest
|
||||
|
||||
from unilabos.workflow.convert_from_json import (
|
||||
convert_from_json,
|
||||
normalize_steps as _normalize_steps,
|
||||
normalize_labware as _normalize_labware,
|
||||
)
|
||||
from unilabos.workflow.common import draw_protocol_graph_with_ports
|
||||
|
||||
|
||||
@pytest.mark.parametrize(
|
||||
"protocol_name",
|
||||
[
|
||||
"example_bio",
|
||||
# "bioyond_materials_liquidhandling_1",
|
||||
"example_prcxi",
|
||||
],
|
||||
)
|
||||
def test_build_protocol_graph(protocol_name):
|
||||
data_path = Path(__file__).with_name(f"{protocol_name}.json")
|
||||
|
||||
graph = convert_from_json(data_path, workstation_name="PRCXi")
|
||||
|
||||
timestamp = datetime.now().strftime("%Y%m%d_%H%M")
|
||||
output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
|
||||
draw_protocol_graph_with_ports(graph, str(output_path))
|
||||
print(graph)
|
||||
@@ -1 +1 @@
|
||||
__version__ = "0.10.11"
|
||||
__version__ = "0.10.12"
|
||||
|
||||
@@ -141,7 +141,7 @@ class CommunicationClientFactory:
|
||||
"""
|
||||
if cls._client_cache is None:
|
||||
cls._client_cache = cls.create_client(protocol)
|
||||
logger.info(f"[CommunicationFactory] Created {type(cls._client_cache).__name__} client")
|
||||
logger.trace(f"[CommunicationFactory] Created {type(cls._client_cache).__name__} client")
|
||||
|
||||
return cls._client_cache
|
||||
|
||||
|
||||
@@ -20,6 +20,7 @@ if unilabos_dir not in sys.path:
|
||||
from unilabos.utils.banner_print import print_status, print_unilab_banner
|
||||
from unilabos.config.config import load_config, BasicConfig, HTTPConfig
|
||||
|
||||
|
||||
def load_config_from_file(config_path):
|
||||
if config_path is None:
|
||||
config_path = os.environ.get("UNILABOS_BASICCONFIG_CONFIG_PATH", None)
|
||||
@@ -41,7 +42,7 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
|
||||
for i, arg in enumerate(sys.argv):
|
||||
for option_string in option_strings:
|
||||
if arg.startswith(option_string):
|
||||
new_arg = arg[:2] + arg[2:len(option_string)].replace("-", "_") + arg[len(option_string):]
|
||||
new_arg = arg[:2] + arg[2 : len(option_string)].replace("-", "_") + arg[len(option_string) :]
|
||||
sys.argv[i] = new_arg
|
||||
break
|
||||
|
||||
@@ -49,6 +50,8 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
|
||||
def parse_args():
|
||||
"""解析命令行参数"""
|
||||
parser = argparse.ArgumentParser(description="Start Uni-Lab Edge server.")
|
||||
subparsers = parser.add_subparsers(title="Valid subcommands", dest="command")
|
||||
|
||||
parser.add_argument("-g", "--graph", help="Physical setup graph file path.")
|
||||
parser.add_argument("-c", "--controllers", default=None, help="Controllers config file path.")
|
||||
parser.add_argument(
|
||||
@@ -153,21 +156,54 @@ def parse_args():
|
||||
default=False,
|
||||
help="Complete registry information",
|
||||
)
|
||||
# workflow upload subcommand
|
||||
workflow_parser = subparsers.add_parser(
|
||||
"workflow_upload",
|
||||
aliases=["wf"],
|
||||
help="Upload workflow from xdl/json/python files",
|
||||
)
|
||||
workflow_parser.add_argument(
|
||||
"-f",
|
||||
"--workflow_file",
|
||||
type=str,
|
||||
required=True,
|
||||
help="Path to the workflow file (JSON format)",
|
||||
)
|
||||
workflow_parser.add_argument(
|
||||
"-n",
|
||||
"--workflow_name",
|
||||
type=str,
|
||||
default=None,
|
||||
help="Workflow name, if not provided will use the name from file or filename",
|
||||
)
|
||||
workflow_parser.add_argument(
|
||||
"--tags",
|
||||
type=str,
|
||||
nargs="*",
|
||||
default=[],
|
||||
help="Tags for the workflow (space-separated)",
|
||||
)
|
||||
workflow_parser.add_argument(
|
||||
"--published",
|
||||
action="store_true",
|
||||
default=False,
|
||||
help="Whether to publish the workflow (default: False)",
|
||||
)
|
||||
return parser
|
||||
|
||||
|
||||
def main():
|
||||
"""主函数"""
|
||||
# 解析命令行参数
|
||||
args = parse_args()
|
||||
convert_argv_dashes_to_underscores(args)
|
||||
args_dict = vars(args.parse_args())
|
||||
parser = parse_args()
|
||||
convert_argv_dashes_to_underscores(parser)
|
||||
args = parser.parse_args()
|
||||
args_dict = vars(args)
|
||||
|
||||
# 环境检查 - 检查并自动安装必需的包 (可选)
|
||||
if not args_dict.get("skip_env_check", False):
|
||||
from unilabos.utils.environment_check import check_environment
|
||||
|
||||
print_status("正在进行环境依赖检查...", "info")
|
||||
if not check_environment(auto_install=True):
|
||||
print_status("环境检查失败,程序退出", "error")
|
||||
os._exit(1)
|
||||
@@ -220,17 +256,18 @@ def main():
|
||||
logger.info(f"Log level set to '{BasicConfig.log_level}' from config file.")
|
||||
configure_logger(loglevel=BasicConfig.log_level, working_dir=working_dir)
|
||||
|
||||
if args_dict["addr"] == "test":
|
||||
print_status("使用测试环境地址", "info")
|
||||
HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
|
||||
elif args_dict["addr"] == "uat":
|
||||
print_status("使用uat环境地址", "info")
|
||||
HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
|
||||
elif args_dict["addr"] == "local":
|
||||
print_status("使用本地环境地址", "info")
|
||||
HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
|
||||
else:
|
||||
HTTPConfig.remote_addr = args_dict.get("addr", "")
|
||||
if args.addr != parser.get_default("addr"):
|
||||
if args.addr == "test":
|
||||
print_status("使用测试环境地址", "info")
|
||||
HTTPConfig.remote_addr = "https://uni-lab.test.bohrium.com/api/v1"
|
||||
elif args.addr == "uat":
|
||||
print_status("使用uat环境地址", "info")
|
||||
HTTPConfig.remote_addr = "https://uni-lab.uat.bohrium.com/api/v1"
|
||||
elif args.addr == "local":
|
||||
print_status("使用本地环境地址", "info")
|
||||
HTTPConfig.remote_addr = "http://127.0.0.1:48197/api/v1"
|
||||
else:
|
||||
HTTPConfig.remote_addr = args.addr
|
||||
|
||||
# 设置BasicConfig参数
|
||||
if args_dict.get("ak", ""):
|
||||
@@ -239,9 +276,12 @@ def main():
|
||||
if args_dict.get("sk", ""):
|
||||
BasicConfig.sk = args_dict.get("sk", "")
|
||||
print_status("传入了sk参数,优先采用传入参数!", "info")
|
||||
BasicConfig.working_dir = working_dir
|
||||
|
||||
workflow_upload = args_dict.get("command") in ("workflow_upload", "wf")
|
||||
|
||||
# 使用远程资源启动
|
||||
if args_dict["use_remote_resource"]:
|
||||
if not workflow_upload and args_dict["use_remote_resource"]:
|
||||
print_status("使用远程资源启动", "info")
|
||||
from unilabos.app.web import http_client
|
||||
|
||||
@@ -254,7 +294,6 @@ def main():
|
||||
|
||||
BasicConfig.port = args_dict["port"] if args_dict["port"] else BasicConfig.port
|
||||
BasicConfig.disable_browser = args_dict["disable_browser"] or BasicConfig.disable_browser
|
||||
BasicConfig.working_dir = working_dir
|
||||
BasicConfig.is_host_mode = not args_dict.get("is_slave", False)
|
||||
BasicConfig.slave_no_host = args_dict.get("slave_no_host", False)
|
||||
BasicConfig.upload_registry = args_dict.get("upload_registry", False)
|
||||
@@ -283,9 +322,31 @@ def main():
|
||||
|
||||
# 注册表
|
||||
lab_registry = build_registry(
|
||||
args_dict["registry_path"], args_dict.get("complete_registry", False), args_dict["upload_registry"]
|
||||
args_dict["registry_path"], args_dict.get("complete_registry", False), BasicConfig.upload_registry
|
||||
)
|
||||
|
||||
if BasicConfig.upload_registry:
|
||||
# 设备注册到服务端 - 需要 ak 和 sk
|
||||
if BasicConfig.ak and BasicConfig.sk:
|
||||
print_status("开始注册设备到服务端...", "info")
|
||||
try:
|
||||
register_devices_and_resources(lab_registry)
|
||||
print_status("设备注册完成", "info")
|
||||
except Exception as e:
|
||||
print_status(f"设备注册失败: {e}", "error")
|
||||
else:
|
||||
print_status("未提供 ak 和 sk,跳过设备注册", "info")
|
||||
else:
|
||||
print_status("本次启动注册表不报送云端,如果您需要联网调试,请在启动命令增加--upload_registry", "warning")
|
||||
|
||||
# 处理 workflow_upload 子命令
|
||||
if workflow_upload:
|
||||
from unilabos.workflow.wf_utils import handle_workflow_upload_command
|
||||
|
||||
handle_workflow_upload_command(args_dict)
|
||||
print_status("工作流上传完成,程序退出", "info")
|
||||
os._exit(0)
|
||||
|
||||
if not BasicConfig.ak or not BasicConfig.sk:
|
||||
print_status("后续运行必须拥有一个实验室,请前往 https://uni-lab.bohrium.com 注册实验室!", "warning")
|
||||
os._exit(1)
|
||||
@@ -362,20 +423,6 @@ def main():
|
||||
args_dict["devices_config"] = resource_tree_set
|
||||
args_dict["graph"] = graph_res.physical_setup_graph
|
||||
|
||||
if BasicConfig.upload_registry:
|
||||
# 设备注册到服务端 - 需要 ak 和 sk
|
||||
if BasicConfig.ak and BasicConfig.sk:
|
||||
print_status("开始注册设备到服务端...", "info")
|
||||
try:
|
||||
register_devices_and_resources(lab_registry)
|
||||
print_status("设备注册完成", "info")
|
||||
except Exception as e:
|
||||
print_status(f"设备注册失败: {e}", "error")
|
||||
else:
|
||||
print_status("未提供 ak 和 sk,跳过设备注册", "info")
|
||||
else:
|
||||
print_status("本次启动注册表不报送云端,如果您需要联网调试,请在启动命令增加--upload_registry", "warning")
|
||||
|
||||
if args_dict["controllers"] is not None:
|
||||
args_dict["controllers_config"] = yaml.safe_load(open(args_dict["controllers"], encoding="utf-8"))
|
||||
else:
|
||||
@@ -390,6 +437,7 @@ def main():
|
||||
comm_client = get_communication_client()
|
||||
if "websocket" in args_dict["app_bridges"]:
|
||||
args_dict["bridges"].append(comm_client)
|
||||
|
||||
def _exit(signum, frame):
|
||||
comm_client.stop()
|
||||
sys.exit(0)
|
||||
@@ -431,16 +479,13 @@ def main():
|
||||
resource_visualization.start()
|
||||
except OSError as e:
|
||||
if "AMENT_PREFIX_PATH" in str(e):
|
||||
print_status(
|
||||
f"ROS 2环境未正确设置,跳过3D可视化启动。错误详情: {e}",
|
||||
"warning"
|
||||
)
|
||||
print_status(f"ROS 2环境未正确设置,跳过3D可视化启动。错误详情: {e}", "warning")
|
||||
print_status(
|
||||
"建议解决方案:\n"
|
||||
"1. 激活Conda环境: conda activate unilab\n"
|
||||
"2. 或使用 --backend simple 参数\n"
|
||||
"3. 或使用 --visual disable 参数禁用可视化",
|
||||
"info"
|
||||
"info",
|
||||
)
|
||||
else:
|
||||
raise
|
||||
|
||||
@@ -76,7 +76,8 @@ class HTTPClient:
|
||||
Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
|
||||
"""
|
||||
with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f:
|
||||
f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
|
||||
payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
|
||||
f.write(json.dumps(payload, indent=4))
|
||||
# 从序列化数据中提取所有节点的UUID(保存旧UUID)
|
||||
old_uuids = {n.res_content.uuid: n for n in resources.all_nodes}
|
||||
if not self.initialized or first_add:
|
||||
@@ -331,6 +332,67 @@ class HTTPClient:
|
||||
logger.error(f"响应内容: {response.text}")
|
||||
return None
|
||||
|
||||
def workflow_import(
|
||||
self,
|
||||
name: str,
|
||||
workflow_uuid: str,
|
||||
workflow_name: str,
|
||||
nodes: List[Dict[str, Any]],
|
||||
edges: List[Dict[str, Any]],
|
||||
tags: Optional[List[str]] = None,
|
||||
published: bool = False,
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
导入工作流到服务器
|
||||
|
||||
Args:
|
||||
name: 工作流名称(顶层)
|
||||
workflow_uuid: 工作流UUID
|
||||
workflow_name: 工作流名称(data内部)
|
||||
nodes: 工作流节点列表
|
||||
edges: 工作流边列表
|
||||
tags: 工作流标签列表,默认为空列表
|
||||
published: 是否发布工作流,默认为False
|
||||
|
||||
Returns:
|
||||
Dict: API响应数据,包含 code 和 data (uuid, name)
|
||||
"""
|
||||
# target_lab_uuid 暂时使用默认值,后续由后端根据 ak/sk 获取
|
||||
payload = {
|
||||
"target_lab_uuid": "28c38bb0-63f6-4352-b0d8-b5b8eb1766d5",
|
||||
"name": name,
|
||||
"data": {
|
||||
"workflow_uuid": workflow_uuid,
|
||||
"workflow_name": workflow_name,
|
||||
"nodes": nodes,
|
||||
"edges": edges,
|
||||
"tags": tags if tags is not None else [],
|
||||
"published": published,
|
||||
},
|
||||
}
|
||||
# 保存请求到文件
|
||||
with open(os.path.join(BasicConfig.working_dir, "req_workflow_upload.json"), "w", encoding="utf-8") as f:
|
||||
f.write(json.dumps(payload, indent=4, ensure_ascii=False))
|
||||
|
||||
response = requests.post(
|
||||
f"{self.remote_addr}/lab/workflow/owner/import",
|
||||
json=payload,
|
||||
headers={"Authorization": f"Lab {self.auth}"},
|
||||
timeout=60,
|
||||
)
|
||||
# 保存响应到文件
|
||||
with open(os.path.join(BasicConfig.working_dir, "res_workflow_upload.json"), "w", encoding="utf-8") as f:
|
||||
f.write(f"{response.status_code}" + "\n" + response.text)
|
||||
|
||||
if response.status_code == 200:
|
||||
res = response.json()
|
||||
if "code" in res and res["code"] != 0:
|
||||
logger.error(f"导入工作流失败: {response.text}")
|
||||
return res
|
||||
else:
|
||||
logger.error(f"导入工作流失败: {response.status_code}, {response.text}")
|
||||
return {"code": response.status_code, "message": response.text}
|
||||
|
||||
|
||||
# 创建默认客户端实例
|
||||
http_client = HTTPClient()
|
||||
|
||||
@@ -389,7 +389,7 @@ class MessageProcessor:
|
||||
self.is_running = True
|
||||
self.thread = threading.Thread(target=self._run, daemon=True, name="MessageProcessor")
|
||||
self.thread.start()
|
||||
logger.info("[MessageProcessor] Started")
|
||||
logger.trace("[MessageProcessor] Started")
|
||||
|
||||
def stop(self) -> None:
|
||||
"""停止消息处理线程"""
|
||||
@@ -438,7 +438,7 @@ class MessageProcessor:
|
||||
self.connected = True
|
||||
self.reconnect_count = 0
|
||||
|
||||
logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
|
||||
logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
|
||||
|
||||
# 启动发送协程
|
||||
send_task = asyncio.create_task(self._send_handler())
|
||||
@@ -503,7 +503,7 @@ class MessageProcessor:
|
||||
|
||||
async def _send_handler(self):
|
||||
"""处理发送队列中的消息"""
|
||||
logger.debug("[MessageProcessor] Send handler started")
|
||||
logger.trace("[MessageProcessor] Send handler started")
|
||||
|
||||
try:
|
||||
while self.connected and self.websocket:
|
||||
@@ -939,7 +939,7 @@ class QueueProcessor:
|
||||
# 事件通知机制
|
||||
self.queue_update_event = threading.Event()
|
||||
|
||||
logger.info("[QueueProcessor] Initialized")
|
||||
logger.trace("[QueueProcessor] Initialized")
|
||||
|
||||
def set_websocket_client(self, websocket_client: "WebSocketClient"):
|
||||
"""设置WebSocket客户端引用"""
|
||||
@@ -954,7 +954,7 @@ class QueueProcessor:
|
||||
self.is_running = True
|
||||
self.thread = threading.Thread(target=self._run, daemon=True, name="QueueProcessor")
|
||||
self.thread.start()
|
||||
logger.info("[QueueProcessor] Started")
|
||||
logger.trace("[QueueProcessor] Started")
|
||||
|
||||
def stop(self) -> None:
|
||||
"""停止队列处理线程"""
|
||||
@@ -965,7 +965,7 @@ class QueueProcessor:
|
||||
|
||||
def _run(self):
|
||||
"""运行队列处理主循环"""
|
||||
logger.debug("[QueueProcessor] Queue processor started")
|
||||
logger.trace("[QueueProcessor] Queue processor started")
|
||||
|
||||
while self.is_running:
|
||||
try:
|
||||
@@ -1175,7 +1175,6 @@ class WebSocketClient(BaseCommunicationClient):
|
||||
else:
|
||||
url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
|
||||
|
||||
logger.debug(f"[WebSocketClient] URL: {url}")
|
||||
return url
|
||||
|
||||
def start(self) -> None:
|
||||
@@ -1188,13 +1187,11 @@ class WebSocketClient(BaseCommunicationClient):
|
||||
logger.error("[WebSocketClient] WebSocket URL not configured")
|
||||
return
|
||||
|
||||
logger.info(f"[WebSocketClient] Starting connection to {self.websocket_url}")
|
||||
|
||||
# 启动两个核心线程
|
||||
self.message_processor.start()
|
||||
self.queue_processor.start()
|
||||
|
||||
logger.info("[WebSocketClient] All threads started")
|
||||
logger.trace("[WebSocketClient] All threads started")
|
||||
|
||||
def stop(self) -> None:
|
||||
"""停止WebSocket客户端"""
|
||||
|
||||
@@ -21,7 +21,8 @@ class BasicConfig:
|
||||
startup_json_path = None # 填写绝对路径
|
||||
disable_browser = False # 禁止浏览器自动打开
|
||||
port = 8002 # 本地HTTP服务
|
||||
log_level: Literal['TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] = "DEBUG" # 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
||||
# 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
||||
log_level: Literal["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = "DEBUG"
|
||||
|
||||
@classmethod
|
||||
def auth_secret(cls):
|
||||
@@ -41,7 +42,7 @@ class WSConfig:
|
||||
|
||||
# HTTP配置
|
||||
class HTTPConfig:
|
||||
remote_addr = "http://127.0.0.1:48197/api/v1"
|
||||
remote_addr = "https://uni-lab.bohrium.com/api/v1"
|
||||
|
||||
|
||||
# ROS配置
|
||||
@@ -65,13 +66,14 @@ def _update_config_from_module(module):
|
||||
if not attr.startswith("_"):
|
||||
setattr(obj, attr, getattr(getattr(module, name), attr))
|
||||
|
||||
|
||||
def _update_config_from_env():
|
||||
prefix = "UNILABOS_"
|
||||
for env_key, env_value in os.environ.items():
|
||||
if not env_key.startswith(prefix):
|
||||
continue
|
||||
try:
|
||||
key_path = env_key[len(prefix):] # Remove UNILAB_ prefix
|
||||
key_path = env_key[len(prefix) :] # Remove UNILAB_ prefix
|
||||
class_field = key_path.upper().split("_", 1)
|
||||
if len(class_field) != 2:
|
||||
logger.warning(f"[ENV] 环境变量格式不正确:{env_key}")
|
||||
|
||||
0
unilabos/devices/cameraSII/__init__.py
Normal file
0
unilabos/devices/cameraSII/__init__.py
Normal file
712
unilabos/devices/cameraSII/cameraDriver.py
Normal file
712
unilabos/devices/cameraSII/cameraDriver.py
Normal file
@@ -0,0 +1,712 @@
|
||||
#!/usr/bin/env python3
|
||||
import asyncio
|
||||
import json
|
||||
import subprocess
|
||||
import sys
|
||||
import threading
|
||||
from typing import Optional, Dict, Any
|
||||
import logging
|
||||
|
||||
import requests
|
||||
import websockets
|
||||
|
||||
logging.getLogger("zeep").setLevel(logging.WARNING)
|
||||
logging.getLogger("zeep.xsd.schema").setLevel(logging.WARNING)
|
||||
logging.getLogger("zeep.xsd.schema.schema").setLevel(logging.WARNING)
|
||||
from onvif import ONVIFCamera # 新增:ONVIF PTZ 控制
|
||||
|
||||
|
||||
# ======================= 独立的 PTZController =======================
|
||||
class PTZController:
|
||||
def __init__(self, host: str, port: int, user: str, password: str):
|
||||
"""
|
||||
:param host: 摄像机 IP 或域名(和 RTSP 的一样即可)
|
||||
:param port: ONVIF 端口(多数为 80,看你的设备)
|
||||
:param user: 摄像机用户名
|
||||
:param password: 摄像机密码
|
||||
"""
|
||||
self.host = host
|
||||
self.port = port
|
||||
self.user = user
|
||||
self.password = password
|
||||
|
||||
self.cam: Optional[ONVIFCamera] = None
|
||||
self.media_service = None
|
||||
self.ptz_service = None
|
||||
self.profile = None
|
||||
|
||||
def connect(self) -> bool:
|
||||
"""
|
||||
建立 ONVIF 连接并初始化 PTZ 能力,失败返回 False(不抛异常)
|
||||
Note: 首先 pip install onvif-zeep
|
||||
"""
|
||||
try:
|
||||
self.cam = ONVIFCamera(self.host, self.port, self.user, self.password)
|
||||
self.media_service = self.cam.create_media_service()
|
||||
self.ptz_service = self.cam.create_ptz_service()
|
||||
profiles = self.media_service.GetProfiles()
|
||||
if not profiles:
|
||||
print("[PTZ] No media profiles found on camera.", file=sys.stderr)
|
||||
return False
|
||||
self.profile = profiles[0]
|
||||
return True
|
||||
except Exception as e:
|
||||
print(f"[PTZ] Failed to init ONVIF PTZ: {e}", file=sys.stderr)
|
||||
return False
|
||||
|
||||
def _continuous_move(self, pan: float, tilt: float, zoom: float, duration: float) -> bool:
|
||||
"""
|
||||
连续移动一段时间(秒),之后自动停止。
|
||||
此函数为阻塞模式:只有在 Stop 调用结束后,才返回 True/False。
|
||||
"""
|
||||
if not self.ptz_service or not self.profile:
|
||||
print("[PTZ] _continuous_move: ptz_service or profile not ready", file=sys.stderr)
|
||||
return False
|
||||
|
||||
# 进入前先强行停一下,避免前一次残留动作
|
||||
self._force_stop()
|
||||
|
||||
req = self.ptz_service.create_type("ContinuousMove")
|
||||
req.ProfileToken = self.profile.token
|
||||
|
||||
req.Velocity = {
|
||||
"PanTilt": {"x": pan, "y": tilt},
|
||||
"Zoom": {"x": zoom},
|
||||
}
|
||||
|
||||
try:
|
||||
print(f"[PTZ] ContinuousMove start: pan={pan}, tilt={tilt}, zoom={zoom}, duration={duration}", file=sys.stderr)
|
||||
self.ptz_service.ContinuousMove(req)
|
||||
except Exception as e:
|
||||
print(f"[PTZ] ContinuousMove failed: {e}", file=sys.stderr)
|
||||
return False
|
||||
|
||||
# 阻塞等待:这里决定“运动时间”
|
||||
import time
|
||||
wait_seconds = max(2 * duration, 0.0)
|
||||
time.sleep(wait_seconds)
|
||||
|
||||
# 运动完成后强制停止
|
||||
return self._force_stop()
|
||||
|
||||
def stop(self) -> bool:
|
||||
"""
|
||||
阻塞调用 Stop(带重试),成功 True,失败 False。
|
||||
"""
|
||||
return self._force_stop()
|
||||
|
||||
# ------- 对外动作接口(给 CameraController 调用) -------
|
||||
# 所有接口都为“阻塞模式”:只有在运动 + Stop 完成后才返回 True/False
|
||||
|
||||
def move_up(self, speed: float = 0.5, duration: float = 1.0) -> bool:
|
||||
print(f"[PTZ] move_up called, speed={speed}, duration={duration}", file=sys.stderr)
|
||||
return self._continuous_move(pan=0.0, tilt=+speed, zoom=0.0, duration=duration)
|
||||
|
||||
def move_down(self, speed: float = 0.5, duration: float = 1.0) -> bool:
|
||||
print(f"[PTZ] move_down called, speed={speed}, duration={duration}", file=sys.stderr)
|
||||
return self._continuous_move(pan=0.0, tilt=-speed, zoom=0.0, duration=duration)
|
||||
|
||||
def move_left(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
print(f"[PTZ] move_left called, speed={speed}, duration={duration}", file=sys.stderr)
|
||||
return self._continuous_move(pan=-speed, tilt=0.0, zoom=0.0, duration=duration)
|
||||
|
||||
def move_right(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
print(f"[PTZ] move_right called, speed={speed}, duration={duration}", file=sys.stderr)
|
||||
return self._continuous_move(pan=+speed, tilt=0.0, zoom=0.0, duration=duration)
|
||||
|
||||
# ------- 占位的变倍接口(当前设备不支持) -------
|
||||
def zoom_in(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
"""
|
||||
当前设备不支持变倍;保留方法只是避免上层调用时报错。
|
||||
"""
|
||||
print("[PTZ] zoom_in is disabled for this device.", file=sys.stderr)
|
||||
return False
|
||||
|
||||
def zoom_out(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
"""
|
||||
当前设备不支持变倍;保留方法只是避免上层调用时报错。
|
||||
"""
|
||||
print("[PTZ] zoom_out is disabled for this device.", file=sys.stderr)
|
||||
return False
|
||||
|
||||
def _force_stop(self, retries: int = 3, delay: float = 0.1) -> bool:
|
||||
"""
|
||||
尝试多次调用 Stop,作为“强制停止”手段。
|
||||
:param retries: 重试次数
|
||||
:param delay: 每次重试间隔(秒)
|
||||
"""
|
||||
if not self.ptz_service or not self.profile:
|
||||
print("[PTZ] _force_stop: ptz_service or profile not ready", file=sys.stderr)
|
||||
return False
|
||||
|
||||
import time
|
||||
last_error = None
|
||||
for i in range(retries):
|
||||
try:
|
||||
print(f"[PTZ] _force_stop: calling Stop(), attempt={i+1}", file=sys.stderr)
|
||||
self.ptz_service.Stop({"ProfileToken": self.profile.token})
|
||||
print("[PTZ] _force_stop: Stop() returned OK", file=sys.stderr)
|
||||
return True
|
||||
except Exception as e:
|
||||
last_error = e
|
||||
print(f"[PTZ] _force_stop: Stop() failed at attempt {i+1}: {e}", file=sys.stderr)
|
||||
time.sleep(delay)
|
||||
|
||||
print(f"[PTZ] _force_stop: all {retries} attempts failed, last error: {last_error}", file=sys.stderr)
|
||||
return False
|
||||
|
||||
# ======================= CameraController(加入 PTZ) =======================
|
||||
|
||||
class CameraController:
|
||||
"""
|
||||
Uni-Lab-OS 摄像头驱动(driver 形式)
|
||||
启动 Uni-Lab-OS 后,立即开始推流
|
||||
|
||||
- WebSocket 信令:通过 signal_backend_url 连接到后端
|
||||
例如: wss://sciol.ac.cn/api/realtime/signal/host/<host_id>
|
||||
- 媒体服务器:通过 rtmp_url / webrtc_api / webrtc_stream_url
|
||||
当前配置为 SRS,与独立 HostSimulator 独立运行脚本保持一致。
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
host_id: str = "demo-host",
|
||||
|
||||
# (1)信令后端(WebSocket)
|
||||
signal_backend_url: str = "wss://sciol.ac.cn/api/realtime/signal/host",
|
||||
|
||||
# (2)媒体后端(RTMP + WebRTC API)
|
||||
rtmp_url: str = "rtmp://srs.sciol.ac.cn:4499/live/camera-01",
|
||||
webrtc_api: str = "https://srs.sciol.ac.cn/rtc/v1/play/",
|
||||
webrtc_stream_url: str = "webrtc://srs.sciol.ac.cn:4500/live/camera-01",
|
||||
camera_rtsp_url: str = "",
|
||||
|
||||
# (3)PTZ 控制相关(ONVIF)
|
||||
ptz_host: str = "", # 一般就是摄像头 IP,比如 "192.168.31.164"
|
||||
ptz_port: int = 80, # ONVIF 端口,不一定是 80,按实际情况改
|
||||
ptz_user: str = "", # admin
|
||||
ptz_password: str = "", # admin123
|
||||
):
|
||||
self.host_id = host_id
|
||||
self.camera_rtsp_url = camera_rtsp_url
|
||||
|
||||
# 拼接最终的 WebSocket URL:.../host/<host_id>
|
||||
signal_backend_url = signal_backend_url.rstrip("/")
|
||||
if not signal_backend_url.endswith("/host"):
|
||||
signal_backend_url = signal_backend_url + "/host"
|
||||
self.signal_backend_url = f"{signal_backend_url}/{host_id}"
|
||||
|
||||
# 媒体服务器配置
|
||||
self.rtmp_url = rtmp_url
|
||||
self.webrtc_api = webrtc_api
|
||||
self.webrtc_stream_url = webrtc_stream_url
|
||||
|
||||
# PTZ 控制
|
||||
self.ptz_host = ptz_host
|
||||
self.ptz_port = ptz_port
|
||||
self.ptz_user = ptz_user
|
||||
self.ptz_password = ptz_password
|
||||
self._ptz: Optional[PTZController] = None
|
||||
self._init_ptz_if_possible()
|
||||
|
||||
# 运行时状态
|
||||
self._ws: Optional[object] = None
|
||||
self._ffmpeg_process: Optional[subprocess.Popen] = None
|
||||
self._running = False
|
||||
self._loop_task: Optional[asyncio.Future] = None
|
||||
|
||||
# 事件循环 & 线程
|
||||
self._loop: Optional[asyncio.AbstractEventLoop] = None
|
||||
self._loop_thread: Optional[threading.Thread] = None
|
||||
|
||||
try:
|
||||
self.start()
|
||||
except Exception as e:
|
||||
print(f"[CameraController] __init__ auto start failed: {e}", file=sys.stderr)
|
||||
|
||||
# ------------------------ PTZ 初始化 ------------------------
|
||||
|
||||
# ------------------------ PTZ 公开动作方法(一个动作一个函数) ------------------------
|
||||
|
||||
def ptz_move_up(self, speed: float = 0.5, duration: float = 1.0) -> bool:
|
||||
print(f"[CameraController] ptz_move_up called, speed={speed}, duration={duration}")
|
||||
return self._ptz.move_up(speed=speed, duration=duration)
|
||||
|
||||
def ptz_move_down(self, speed: float = 0.5, duration: float = 1.0) -> bool:
|
||||
print(f"[CameraController] ptz_move_down called, speed={speed}, duration={duration}")
|
||||
return self._ptz.move_down(speed=speed, duration=duration)
|
||||
|
||||
def ptz_move_left(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
print(f"[CameraController] ptz_move_left called, speed={speed}, duration={duration}")
|
||||
return self._ptz.move_left(speed=speed, duration=duration)
|
||||
|
||||
def ptz_move_right(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
print(f"[CameraController] ptz_move_right called, speed={speed}, duration={duration}")
|
||||
return self._ptz.move_right(speed=speed, duration=duration)
|
||||
|
||||
def zoom_in(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
"""
|
||||
当前设备不支持变倍;保留方法只是避免上层调用时报错。
|
||||
"""
|
||||
print("[PTZ] zoom_in is disabled for this device.", file=sys.stderr)
|
||||
return False
|
||||
|
||||
def zoom_out(self, speed: float = 0.2, duration: float = 1.0) -> bool:
|
||||
"""
|
||||
当前设备不支持变倍;保留方法只是避免上层调用时报错。
|
||||
"""
|
||||
print("[PTZ] zoom_out is disabled for this device.", file=sys.stderr)
|
||||
return False
|
||||
|
||||
def ptz_stop(self):
|
||||
if self._ptz is None:
|
||||
print("[CameraController] PTZ not initialized.", file=sys.stderr)
|
||||
return
|
||||
self._ptz.stop()
|
||||
|
||||
def _init_ptz_if_possible(self):
|
||||
"""
|
||||
根据 ptz_host / user / password 初始化 PTZ;
|
||||
如果配置信息不全则不启用 PTZ(静默)。
|
||||
"""
|
||||
if not (self.ptz_host and self.ptz_user and self.ptz_password):
|
||||
return
|
||||
ctrl = PTZController(
|
||||
host=self.ptz_host,
|
||||
port=self.ptz_port,
|
||||
user=self.ptz_user,
|
||||
password=self.ptz_password,
|
||||
)
|
||||
if ctrl.connect():
|
||||
self._ptz = ctrl
|
||||
else:
|
||||
self._ptz = None
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# 对外暴露的方法:供 Uni-Lab-OS 调用
|
||||
# ---------------------------------------------------------------------
|
||||
|
||||
def start(self, config: Optional[Dict[str, Any]] = None):
|
||||
"""
|
||||
启动 Camera 连接 & 消息循环,并在启动时就开启 FFmpeg 推流,
|
||||
"""
|
||||
|
||||
if self._running:
|
||||
return {"status": "already_running", "host_id": self.host_id}
|
||||
|
||||
# 应用 config 覆盖(如果有)
|
||||
if config:
|
||||
self.camera_rtsp_url = config.get("camera_rtsp_url", self.camera_rtsp_url)
|
||||
cfg_host_id = config.get("host_id")
|
||||
if cfg_host_id:
|
||||
self.host_id = cfg_host_id
|
||||
|
||||
signal_backend_url = config.get("signal_backend_url")
|
||||
if signal_backend_url:
|
||||
signal_backend_url = signal_backend_url.rstrip("/")
|
||||
if not signal_backend_url.endswith("/host"):
|
||||
signal_backend_url = signal_backend_url + "/host"
|
||||
self.signal_backend_url = f"{signal_backend_url}/{self.host_id}"
|
||||
|
||||
self.rtmp_url = config.get("rtmp_url", self.rtmp_url)
|
||||
self.webrtc_api = config.get("webrtc_api", self.webrtc_api)
|
||||
self.webrtc_stream_url = config.get(
|
||||
"webrtc_stream_url", self.webrtc_stream_url
|
||||
)
|
||||
|
||||
# PTZ 相关配置也允许通过 config 注入
|
||||
self.ptz_host = config.get("ptz_host", self.ptz_host)
|
||||
self.ptz_port = int(config.get("ptz_port", self.ptz_port))
|
||||
self.ptz_user = config.get("ptz_user", self.ptz_user)
|
||||
self.ptz_password = config.get("ptz_password", self.ptz_password)
|
||||
self._init_ptz_if_possible()
|
||||
|
||||
self._running = True
|
||||
|
||||
# === start 时启动 FFmpeg 推流 ===
|
||||
self._start_ffmpeg()
|
||||
|
||||
# 创建新的事件循环和线程(用于 WebSocket 信令)
|
||||
self._loop = asyncio.new_event_loop()
|
||||
|
||||
def loop_runner(loop: asyncio.AbstractEventLoop):
|
||||
asyncio.set_event_loop(loop)
|
||||
try:
|
||||
loop.run_forever()
|
||||
except Exception as e:
|
||||
print(f"[CameraController] event loop error: {e}", file=sys.stderr)
|
||||
|
||||
self._loop_thread = threading.Thread(
|
||||
target=loop_runner, args=(self._loop,), daemon=True
|
||||
)
|
||||
self._loop_thread.start()
|
||||
|
||||
self._loop_task = asyncio.run_coroutine_threadsafe(
|
||||
self._run_main_loop(), self._loop
|
||||
)
|
||||
|
||||
return {
|
||||
"status": "started",
|
||||
"host_id": self.host_id,
|
||||
"signal_backend_url": self.signal_backend_url,
|
||||
"rtmp_url": self.rtmp_url,
|
||||
"webrtc_api": self.webrtc_api,
|
||||
"webrtc_stream_url": self.webrtc_stream_url,
|
||||
}
|
||||
|
||||
def stop(self) -> Dict[str, Any]:
|
||||
"""
|
||||
停止推流 & 断开 WebSocket,并关闭事件循环线程。
|
||||
"""
|
||||
self._running = False
|
||||
|
||||
self._stop_ffmpeg()
|
||||
|
||||
if self._ws and self._loop is not None:
|
||||
async def close_ws():
|
||||
try:
|
||||
await self._ws.close()
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when closing WebSocket: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
|
||||
asyncio.run_coroutine_threadsafe(close_ws(), self._loop)
|
||||
|
||||
if self._loop_task is not None:
|
||||
if not self._loop_task.done():
|
||||
self._loop_task.cancel()
|
||||
try:
|
||||
self._loop_task.result()
|
||||
except asyncio.CancelledError:
|
||||
pass
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] main loop task error in stop(): {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
finally:
|
||||
self._loop_task = None
|
||||
|
||||
if self._loop is not None:
|
||||
try:
|
||||
self._loop.call_soon_threadsafe(self._loop.stop)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when stopping event loop: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
|
||||
if self._loop_thread is not None:
|
||||
try:
|
||||
self._loop_thread.join(timeout=5)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when joining loop thread: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
finally:
|
||||
self._loop_thread = None
|
||||
|
||||
self._ws = None
|
||||
self._loop = None
|
||||
|
||||
return {"status": "stopped", "host_id": self.host_id}
|
||||
|
||||
def get_status(self) -> Dict[str, Any]:
|
||||
"""
|
||||
查询当前状态,方便在 Uni-Lab-OS 中做监控。
|
||||
"""
|
||||
ws_closed = None
|
||||
if self._ws is not None:
|
||||
ws_closed = getattr(self._ws, "closed", None)
|
||||
|
||||
if ws_closed is None:
|
||||
websocket_connected = self._ws is not None
|
||||
else:
|
||||
websocket_connected = (self._ws is not None) and (not ws_closed)
|
||||
|
||||
return {
|
||||
"host_id": self.host_id,
|
||||
"running": self._running,
|
||||
"websocket_connected": websocket_connected,
|
||||
"ffmpeg_running": bool(
|
||||
self._ffmpeg_process and self._ffmpeg_process.poll() is None
|
||||
),
|
||||
"signal_backend_url": self.signal_backend_url,
|
||||
"rtmp_url": self.rtmp_url,
|
||||
}
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# 内部实现逻辑:WebSocket 循环 / FFmpeg / WebRTC Offer 处理
|
||||
# ---------------------------------------------------------------------
|
||||
|
||||
async def _run_main_loop(self):
|
||||
try:
|
||||
while self._running:
|
||||
try:
|
||||
async with websockets.connect(self.signal_backend_url) as ws:
|
||||
self._ws = ws
|
||||
await self._recv_loop()
|
||||
except asyncio.CancelledError:
|
||||
raise
|
||||
except Exception as e:
|
||||
if self._running:
|
||||
print(
|
||||
f"[CameraController] WebSocket connection error: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
await asyncio.sleep(3)
|
||||
except asyncio.CancelledError:
|
||||
pass
|
||||
|
||||
async def _recv_loop(self):
|
||||
assert self._ws is not None
|
||||
ws = self._ws
|
||||
|
||||
async for message in ws:
|
||||
try:
|
||||
data = json.loads(message)
|
||||
except json.JSONDecodeError:
|
||||
print(
|
||||
f"[CameraController] received non-JSON message: {message}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
continue
|
||||
|
||||
try:
|
||||
await self._handle_message(data)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error while handling message {data}: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
|
||||
async def _handle_message(self, data: Dict[str, Any]):
|
||||
"""
|
||||
处理来自信令后端的消息:
|
||||
- command: start_stream / stop_stream / ptz_xxx
|
||||
- type: offer (WebRTC)
|
||||
"""
|
||||
cmd = data.get("command")
|
||||
|
||||
# ---------- 推流控制 ----------
|
||||
if cmd == "start_stream":
|
||||
try:
|
||||
self._start_ffmpeg()
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when starting FFmpeg on start_stream: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return
|
||||
|
||||
if cmd == "stop_stream":
|
||||
try:
|
||||
self._stop_ffmpeg()
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when stopping FFmpeg on stop_stream: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return
|
||||
|
||||
# # ---------- PTZ 控制 ----------
|
||||
# # 例如信令可以发:
|
||||
# # {"command": "ptz_move", "direction": "down", "speed": 0.5, "duration": 0.5}
|
||||
# if cmd == "ptz_move":
|
||||
# if self._ptz is None:
|
||||
# # 没有初始化 PTZ,静默忽略或打印一条
|
||||
# print("[CameraController] PTZ not initialized.", file=sys.stderr)
|
||||
# return
|
||||
|
||||
# direction = data.get("direction", "")
|
||||
# speed = float(data.get("speed", 0.5))
|
||||
# duration = float(data.get("duration", 0.5))
|
||||
|
||||
# try:
|
||||
# if direction == "up":
|
||||
# self._ptz.move_up(speed=speed, duration=duration)
|
||||
# elif direction == "down":
|
||||
# self._ptz.move_down(speed=speed, duration=duration)
|
||||
# elif direction == "left":
|
||||
# self._ptz.move_left(speed=speed, duration=duration)
|
||||
# elif direction == "right":
|
||||
# self._ptz.move_right(speed=speed, duration=duration)
|
||||
# elif direction == "zoom_in":
|
||||
# self._ptz.zoom_in(speed=speed, duration=duration)
|
||||
# elif direction == "zoom_out":
|
||||
# self._ptz.zoom_out(speed=speed, duration=duration)
|
||||
# elif direction == "stop":
|
||||
# self._ptz.stop()
|
||||
# else:
|
||||
# # 未知方向,忽略
|
||||
# pass
|
||||
# except Exception as e:
|
||||
# print(
|
||||
# f"[CameraController] error when handling PTZ move: {e}",
|
||||
# file=sys.stderr,
|
||||
# )
|
||||
# return
|
||||
|
||||
# ---------- WebRTC Offer ----------
|
||||
if data.get("type") == "offer":
|
||||
offer_sdp = data.get("sdp", "")
|
||||
camera_id = data.get("cameraId", "camera-01")
|
||||
try:
|
||||
answer_sdp = await self._handle_webrtc_offer(offer_sdp)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when handling WebRTC offer: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
return
|
||||
|
||||
if self._ws:
|
||||
answer_payload = {
|
||||
"type": "answer",
|
||||
"sdp": answer_sdp,
|
||||
"cameraId": camera_id,
|
||||
"hostId": self.host_id,
|
||||
}
|
||||
try:
|
||||
await self._ws.send(json.dumps(answer_payload))
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when sending WebRTC answer: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
|
||||
# ------------------------ FFmpeg 相关 ------------------------
|
||||
|
||||
def _start_ffmpeg(self):
|
||||
if self._ffmpeg_process and self._ffmpeg_process.poll() is None:
|
||||
return
|
||||
|
||||
cmd = [
|
||||
"ffmpeg",
|
||||
"-rtsp_transport", "tcp",
|
||||
"-i", self.camera_rtsp_url,
|
||||
|
||||
"-c:v", "libx264",
|
||||
"-preset", "ultrafast",
|
||||
"-tune", "zerolatency",
|
||||
"-profile:v", "baseline",
|
||||
"-b:v", "1M",
|
||||
"-maxrate", "1M",
|
||||
"-bufsize", "2M",
|
||||
"-g", "10",
|
||||
"-keyint_min", "10",
|
||||
"-sc_threshold", "0",
|
||||
"-pix_fmt", "yuv420p",
|
||||
"-x264-params", "bframes=0",
|
||||
|
||||
"-c:a", "aac",
|
||||
"-ar", "44100",
|
||||
"-ac", "1",
|
||||
"-b:a", "64k",
|
||||
|
||||
"-f", "flv",
|
||||
self.rtmp_url,
|
||||
]
|
||||
|
||||
try:
|
||||
self._ffmpeg_process = subprocess.Popen(
|
||||
cmd,
|
||||
stdout=subprocess.DEVNULL,
|
||||
stderr=subprocess.STDOUT,
|
||||
shell=False,
|
||||
)
|
||||
except Exception as e:
|
||||
print(f"[CameraController] failed to start FFmpeg: {e}", file=sys.stderr)
|
||||
self._ffmpeg_process = None
|
||||
raise
|
||||
|
||||
def _stop_ffmpeg(self):
|
||||
proc = self._ffmpeg_process
|
||||
|
||||
if proc and proc.poll() is None:
|
||||
try:
|
||||
proc.terminate()
|
||||
try:
|
||||
proc.wait(timeout=5)
|
||||
except subprocess.TimeoutExpired:
|
||||
try:
|
||||
proc.kill()
|
||||
try:
|
||||
proc.wait(timeout=2)
|
||||
except subprocess.TimeoutExpired:
|
||||
print(
|
||||
f"[CameraController] FFmpeg process did not exit even after kill (pid={proc.pid})",
|
||||
file=sys.stderr,
|
||||
)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] failed to kill FFmpeg process: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] error when stopping FFmpeg: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
|
||||
self._ffmpeg_process = None
|
||||
|
||||
# ------------------------ WebRTC Offer 相关 ------------------------
|
||||
|
||||
async def _handle_webrtc_offer(self, offer_sdp: str) -> str:
|
||||
payload = {
|
||||
"api": self.webrtc_api,
|
||||
"streamurl": self.webrtc_stream_url,
|
||||
"sdp": offer_sdp,
|
||||
}
|
||||
|
||||
headers = {"Content-Type": "application/json"}
|
||||
|
||||
def _do_request():
|
||||
return requests.post(
|
||||
self.webrtc_api,
|
||||
json=payload,
|
||||
headers=headers,
|
||||
timeout=10,
|
||||
)
|
||||
|
||||
try:
|
||||
loop = asyncio.get_running_loop()
|
||||
resp = await loop.run_in_executor(None, _do_request)
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] failed to send offer to media server: {e}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
raise
|
||||
|
||||
try:
|
||||
resp.raise_for_status()
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] media server HTTP error: {e}, "
|
||||
f"status={resp.status_code}, body={resp.text[:200]}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
raise
|
||||
|
||||
try:
|
||||
data = resp.json()
|
||||
except Exception as e:
|
||||
print(
|
||||
f"[CameraController] failed to parse media server JSON: {e}, "
|
||||
f"raw={resp.text[:200]}",
|
||||
file=sys.stderr,
|
||||
)
|
||||
raise
|
||||
|
||||
answer_sdp = data.get("sdp", "")
|
||||
if not answer_sdp:
|
||||
msg = f"empty SDP from media server: {data}"
|
||||
print(f"[CameraController] {msg}", file=sys.stderr)
|
||||
raise RuntimeError(msg)
|
||||
|
||||
return answer_sdp
|
||||
401
unilabos/devices/cameraSII/cameraUSB.py
Normal file
401
unilabos/devices/cameraSII/cameraUSB.py
Normal file
@@ -0,0 +1,401 @@
|
||||
#!/usr/bin/env python3
|
||||
import asyncio
|
||||
import json
|
||||
import subprocess
|
||||
import sys
|
||||
import threading
|
||||
from typing import Optional, Dict, Any
|
||||
|
||||
import requests
|
||||
import websockets
|
||||
|
||||
|
||||
class CameraController:
|
||||
"""
|
||||
Uni-Lab-OS 摄像头驱动(Linux USB 摄像头版,无 PTZ)
|
||||
|
||||
- WebSocket 信令:signal_backend_url 连接到后端
|
||||
例如: wss://sciol.ac.cn/api/realtime/signal/host/<host_id>
|
||||
- 媒体服务器:RTMP 推流到 rtmp_url;WebRTC offer 转发到 SRS 的 webrtc_api
|
||||
- 视频源:本地 USB 摄像头(V4L2,默认 /dev/video0)
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
host_id: str = "demo-host",
|
||||
signal_backend_url: str = "wss://sciol.ac.cn/api/realtime/signal/host",
|
||||
rtmp_url: str = "rtmp://srs.sciol.ac.cn:4499/live/camera-01",
|
||||
webrtc_api: str = "https://srs.sciol.ac.cn/rtc/v1/play/",
|
||||
webrtc_stream_url: str = "webrtc://srs.sciol.ac.cn:4500/live/camera-01",
|
||||
video_device: str = "/dev/video0",
|
||||
width: int = 1280,
|
||||
height: int = 720,
|
||||
fps: int = 30,
|
||||
video_bitrate: str = "1500k",
|
||||
audio_device: Optional[str] = None, # 比如 "hw:1,0",没有音频就保持 None
|
||||
audio_bitrate: str = "64k",
|
||||
):
|
||||
self.host_id = host_id
|
||||
|
||||
# 拼接最终 WebSocket URL:.../host/<host_id>
|
||||
signal_backend_url = signal_backend_url.rstrip("/")
|
||||
if not signal_backend_url.endswith("/host"):
|
||||
signal_backend_url = signal_backend_url + "/host"
|
||||
self.signal_backend_url = f"{signal_backend_url}/{host_id}"
|
||||
|
||||
# 媒体服务器配置
|
||||
self.rtmp_url = rtmp_url
|
||||
self.webrtc_api = webrtc_api
|
||||
self.webrtc_stream_url = webrtc_stream_url
|
||||
|
||||
# 本地采集配置
|
||||
self.video_device = video_device
|
||||
self.width = int(width)
|
||||
self.height = int(height)
|
||||
self.fps = int(fps)
|
||||
self.video_bitrate = video_bitrate
|
||||
self.audio_device = audio_device
|
||||
self.audio_bitrate = audio_bitrate
|
||||
|
||||
# 运行时状态
|
||||
self._ws: Optional[object] = None
|
||||
self._ffmpeg_process: Optional[subprocess.Popen] = None
|
||||
self._running = False
|
||||
self._loop_task: Optional[asyncio.Future] = None
|
||||
|
||||
# 事件循环 & 线程
|
||||
self._loop: Optional[asyncio.AbstractEventLoop] = None
|
||||
self._loop_thread: Optional[threading.Thread] = None
|
||||
|
||||
try:
|
||||
self.start()
|
||||
except Exception as e:
|
||||
print(f"[CameraController] __init__ auto start failed: {e}", file=sys.stderr)
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# 对外方法
|
||||
# ---------------------------------------------------------------------
|
||||
|
||||
def start(self, config: Optional[Dict[str, Any]] = None):
|
||||
if self._running:
|
||||
return {"status": "already_running", "host_id": self.host_id}
|
||||
|
||||
# 应用 config 覆盖(如果有)
|
||||
if config:
|
||||
cfg_host_id = config.get("host_id")
|
||||
if cfg_host_id:
|
||||
self.host_id = cfg_host_id
|
||||
|
||||
signal_backend_url = config.get("signal_backend_url")
|
||||
if signal_backend_url:
|
||||
signal_backend_url = signal_backend_url.rstrip("/")
|
||||
if not signal_backend_url.endswith("/host"):
|
||||
signal_backend_url = signal_backend_url + "/host"
|
||||
self.signal_backend_url = f"{signal_backend_url}/{self.host_id}"
|
||||
|
||||
self.rtmp_url = config.get("rtmp_url", self.rtmp_url)
|
||||
self.webrtc_api = config.get("webrtc_api", self.webrtc_api)
|
||||
self.webrtc_stream_url = config.get("webrtc_stream_url", self.webrtc_stream_url)
|
||||
|
||||
self.video_device = config.get("video_device", self.video_device)
|
||||
self.width = int(config.get("width", self.width))
|
||||
self.height = int(config.get("height", self.height))
|
||||
self.fps = int(config.get("fps", self.fps))
|
||||
self.video_bitrate = config.get("video_bitrate", self.video_bitrate)
|
||||
self.audio_device = config.get("audio_device", self.audio_device)
|
||||
self.audio_bitrate = config.get("audio_bitrate", self.audio_bitrate)
|
||||
|
||||
self._running = True
|
||||
|
||||
print("[CameraController] start(): starting FFmpeg streaming...", file=sys.stderr)
|
||||
self._start_ffmpeg()
|
||||
|
||||
self._loop = asyncio.new_event_loop()
|
||||
|
||||
def loop_runner(loop: asyncio.AbstractEventLoop):
|
||||
asyncio.set_event_loop(loop)
|
||||
try:
|
||||
loop.run_forever()
|
||||
except Exception as e:
|
||||
print(f"[CameraController] event loop error: {e}", file=sys.stderr)
|
||||
|
||||
self._loop_thread = threading.Thread(target=loop_runner, args=(self._loop,), daemon=True)
|
||||
self._loop_thread.start()
|
||||
|
||||
self._loop_task = asyncio.run_coroutine_threadsafe(self._run_main_loop(), self._loop)
|
||||
|
||||
return {
|
||||
"status": "started",
|
||||
"host_id": self.host_id,
|
||||
"signal_backend_url": self.signal_backend_url,
|
||||
"rtmp_url": self.rtmp_url,
|
||||
"webrtc_api": self.webrtc_api,
|
||||
"webrtc_stream_url": self.webrtc_stream_url,
|
||||
"video_device": self.video_device,
|
||||
"width": self.width,
|
||||
"height": self.height,
|
||||
"fps": self.fps,
|
||||
"video_bitrate": self.video_bitrate,
|
||||
"audio_device": self.audio_device,
|
||||
}
|
||||
|
||||
def stop(self) -> Dict[str, Any]:
|
||||
self._running = False
|
||||
|
||||
# 先取消主任务(让 ws connect/sleep 尽快退出)
|
||||
if self._loop_task is not None and not self._loop_task.done():
|
||||
self._loop_task.cancel()
|
||||
|
||||
# 停止推流
|
||||
self._stop_ffmpeg()
|
||||
|
||||
# 关闭 WebSocket(在 loop 中执行)
|
||||
if self._ws and self._loop is not None:
|
||||
|
||||
async def close_ws():
|
||||
try:
|
||||
await self._ws.close()
|
||||
except Exception as e:
|
||||
print(f"[CameraController] error closing WebSocket: {e}", file=sys.stderr)
|
||||
|
||||
try:
|
||||
asyncio.run_coroutine_threadsafe(close_ws(), self._loop)
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
# 停止事件循环
|
||||
if self._loop is not None:
|
||||
try:
|
||||
self._loop.call_soon_threadsafe(self._loop.stop)
|
||||
except Exception as e:
|
||||
print(f"[CameraController] error stopping loop: {e}", file=sys.stderr)
|
||||
|
||||
# 等待线程退出
|
||||
if self._loop_thread is not None:
|
||||
try:
|
||||
self._loop_thread.join(timeout=5)
|
||||
except Exception as e:
|
||||
print(f"[CameraController] error joining loop thread: {e}", file=sys.stderr)
|
||||
|
||||
self._ws = None
|
||||
self._loop_task = None
|
||||
self._loop = None
|
||||
self._loop_thread = None
|
||||
|
||||
return {"status": "stopped", "host_id": self.host_id}
|
||||
|
||||
def get_status(self) -> Dict[str, Any]:
|
||||
ws_closed = None
|
||||
if self._ws is not None:
|
||||
ws_closed = getattr(self._ws, "closed", None)
|
||||
|
||||
if ws_closed is None:
|
||||
websocket_connected = self._ws is not None
|
||||
else:
|
||||
websocket_connected = (self._ws is not None) and (not ws_closed)
|
||||
|
||||
return {
|
||||
"host_id": self.host_id,
|
||||
"running": self._running,
|
||||
"websocket_connected": websocket_connected,
|
||||
"ffmpeg_running": bool(self._ffmpeg_process and self._ffmpeg_process.poll() is None),
|
||||
"signal_backend_url": self.signal_backend_url,
|
||||
"rtmp_url": self.rtmp_url,
|
||||
"video_device": self.video_device,
|
||||
"width": self.width,
|
||||
"height": self.height,
|
||||
"fps": self.fps,
|
||||
"video_bitrate": self.video_bitrate,
|
||||
}
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# WebSocket / 信令
|
||||
# ---------------------------------------------------------------------
|
||||
|
||||
async def _run_main_loop(self):
|
||||
print("[CameraController] main loop started", file=sys.stderr)
|
||||
try:
|
||||
while self._running:
|
||||
try:
|
||||
async with websockets.connect(self.signal_backend_url) as ws:
|
||||
self._ws = ws
|
||||
print(f"[CameraController] WebSocket connected: {self.signal_backend_url}", file=sys.stderr)
|
||||
await self._recv_loop()
|
||||
except asyncio.CancelledError:
|
||||
raise
|
||||
except Exception as e:
|
||||
if self._running:
|
||||
print(f"[CameraController] WebSocket connection error: {e}", file=sys.stderr)
|
||||
await asyncio.sleep(3)
|
||||
except asyncio.CancelledError:
|
||||
pass
|
||||
finally:
|
||||
print("[CameraController] main loop exited", file=sys.stderr)
|
||||
|
||||
async def _recv_loop(self):
|
||||
assert self._ws is not None
|
||||
ws = self._ws
|
||||
|
||||
async for message in ws:
|
||||
try:
|
||||
data = json.loads(message)
|
||||
except json.JSONDecodeError:
|
||||
print(f"[CameraController] non-JSON message: {message}", file=sys.stderr)
|
||||
continue
|
||||
|
||||
try:
|
||||
await self._handle_message(data)
|
||||
except Exception as e:
|
||||
print(f"[CameraController] error handling message {data}: {e}", file=sys.stderr)
|
||||
|
||||
async def _handle_message(self, data: Dict[str, Any]):
|
||||
cmd = data.get("command")
|
||||
|
||||
if cmd == "start_stream":
|
||||
self._start_ffmpeg()
|
||||
return
|
||||
|
||||
if cmd == "stop_stream":
|
||||
self._stop_ffmpeg()
|
||||
return
|
||||
|
||||
if data.get("type") == "offer":
|
||||
offer_sdp = data.get("sdp", "")
|
||||
camera_id = data.get("cameraId", "camera-01")
|
||||
|
||||
answer_sdp = await self._handle_webrtc_offer(offer_sdp)
|
||||
|
||||
if self._ws:
|
||||
answer_payload = {
|
||||
"type": "answer",
|
||||
"sdp": answer_sdp,
|
||||
"cameraId": camera_id,
|
||||
"hostId": self.host_id,
|
||||
}
|
||||
await self._ws.send(json.dumps(answer_payload))
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# FFmpeg 推流(V4L2 USB 摄像头)
|
||||
# ---------------------------------------------------------------------
|
||||
|
||||
def _start_ffmpeg(self):
|
||||
if self._ffmpeg_process and self._ffmpeg_process.poll() is None:
|
||||
return
|
||||
|
||||
# 兼容性优先:不强制输入像素格式;失败再通过外部调整 width/height/fps
|
||||
video_size = f"{self.width}x{self.height}"
|
||||
|
||||
cmd = [
|
||||
"ffmpeg",
|
||||
"-hide_banner",
|
||||
"-loglevel",
|
||||
"warning",
|
||||
|
||||
# video input
|
||||
"-f", "v4l2",
|
||||
"-framerate", str(self.fps),
|
||||
"-video_size", video_size,
|
||||
"-i", self.video_device,
|
||||
]
|
||||
|
||||
# optional audio input
|
||||
if self.audio_device:
|
||||
cmd += [
|
||||
"-f", "alsa",
|
||||
"-i", self.audio_device,
|
||||
"-c:a", "aac",
|
||||
"-b:a", self.audio_bitrate,
|
||||
"-ar", "44100",
|
||||
"-ac", "1",
|
||||
]
|
||||
else:
|
||||
cmd += ["-an"]
|
||||
|
||||
# video encode + rtmp out
|
||||
cmd += [
|
||||
"-c:v", "libx264",
|
||||
"-preset", "ultrafast",
|
||||
"-tune", "zerolatency",
|
||||
"-profile:v", "baseline",
|
||||
"-pix_fmt", "yuv420p",
|
||||
"-b:v", self.video_bitrate,
|
||||
"-maxrate", self.video_bitrate,
|
||||
"-bufsize", "2M",
|
||||
"-g", str(max(self.fps, 10)),
|
||||
"-keyint_min", str(max(self.fps, 10)),
|
||||
"-sc_threshold", "0",
|
||||
"-x264-params", "bframes=0",
|
||||
|
||||
"-f", "flv",
|
||||
self.rtmp_url,
|
||||
]
|
||||
|
||||
print(f"[CameraController] starting FFmpeg: {' '.join(cmd)}", file=sys.stderr)
|
||||
|
||||
try:
|
||||
# 不再丢弃日志,至少能看到 ffmpeg 报错(调试很关键)
|
||||
self._ffmpeg_process = subprocess.Popen(
|
||||
cmd,
|
||||
stdout=subprocess.DEVNULL,
|
||||
stderr=sys.stderr,
|
||||
shell=False,
|
||||
)
|
||||
except Exception as e:
|
||||
self._ffmpeg_process = None
|
||||
print(f"[CameraController] failed to start FFmpeg: {e}", file=sys.stderr)
|
||||
|
||||
def _stop_ffmpeg(self):
|
||||
proc = self._ffmpeg_process
|
||||
if proc and proc.poll() is None:
|
||||
try:
|
||||
proc.terminate()
|
||||
try:
|
||||
proc.wait(timeout=5)
|
||||
except subprocess.TimeoutExpired:
|
||||
proc.kill()
|
||||
except Exception as e:
|
||||
print(f"[CameraController] error stopping FFmpeg: {e}", file=sys.stderr)
|
||||
self._ffmpeg_process = None
|
||||
|
||||
# ---------------------------------------------------------------------
|
||||
# WebRTC offer -> SRS
|
||||
# ---------------------------------------------------------------------
|
||||
|
||||
async def _handle_webrtc_offer(self, offer_sdp: str) -> str:
|
||||
payload = {
|
||||
"api": self.webrtc_api,
|
||||
"streamurl": self.webrtc_stream_url,
|
||||
"sdp": offer_sdp,
|
||||
}
|
||||
headers = {"Content-Type": "application/json"}
|
||||
|
||||
def _do_post():
|
||||
return requests.post(self.webrtc_api, json=payload, headers=headers, timeout=10)
|
||||
|
||||
loop = asyncio.get_running_loop()
|
||||
resp = await loop.run_in_executor(None, _do_post)
|
||||
|
||||
resp.raise_for_status()
|
||||
data = resp.json()
|
||||
answer_sdp = data.get("sdp", "")
|
||||
if not answer_sdp:
|
||||
raise RuntimeError(f"empty SDP from media server: {data}")
|
||||
return answer_sdp
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
# 直接运行用于手动测试
|
||||
c = CameraController(
|
||||
host_id="demo-host",
|
||||
video_device="/dev/video0",
|
||||
width=1280,
|
||||
height=720,
|
||||
fps=30,
|
||||
video_bitrate="1500k",
|
||||
audio_device=None,
|
||||
)
|
||||
try:
|
||||
while True:
|
||||
asyncio.sleep(1)
|
||||
except KeyboardInterrupt:
|
||||
c.stop()
|
||||
51
unilabos/devices/cameraSII/cameraUSB_test.py
Normal file
51
unilabos/devices/cameraSII/cameraUSB_test.py
Normal file
@@ -0,0 +1,51 @@
|
||||
#!/usr/bin/env python3
|
||||
import time
|
||||
import json
|
||||
|
||||
from cameraUSB import CameraController
|
||||
|
||||
|
||||
def main():
|
||||
# 按你的实际情况改
|
||||
cfg = dict(
|
||||
host_id="demo-host",
|
||||
signal_backend_url="wss://sciol.ac.cn/api/realtime/signal/host",
|
||||
rtmp_url="rtmp://srs.sciol.ac.cn:4499/live/camera-01",
|
||||
webrtc_api="https://srs.sciol.ac.cn/rtc/v1/play/",
|
||||
webrtc_stream_url="webrtc://srs.sciol.ac.cn:4500/live/camera-01",
|
||||
video_device="/dev/video7",
|
||||
width=1280,
|
||||
height=720,
|
||||
fps=30,
|
||||
video_bitrate="1500k",
|
||||
audio_device=None,
|
||||
)
|
||||
|
||||
c = CameraController(**cfg)
|
||||
|
||||
# 可选:如果你不想依赖 __init__ 自动 start,可以这样显式调用:
|
||||
# c = CameraController(host_id=cfg["host_id"])
|
||||
# c.start(cfg)
|
||||
|
||||
run_seconds = 30 # 测试运行时长
|
||||
t0 = time.time()
|
||||
|
||||
try:
|
||||
while True:
|
||||
st = c.get_status()
|
||||
print(json.dumps(st, ensure_ascii=False, indent=2))
|
||||
|
||||
if time.time() - t0 >= run_seconds:
|
||||
break
|
||||
|
||||
time.sleep(2)
|
||||
except KeyboardInterrupt:
|
||||
print("Interrupted, stopping...")
|
||||
finally:
|
||||
print("Stopping controller...")
|
||||
c.stop()
|
||||
print("Done.")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
36
unilabos/devices/cameraSII/demo_camera_pic.py
Normal file
36
unilabos/devices/cameraSII/demo_camera_pic.py
Normal file
@@ -0,0 +1,36 @@
|
||||
import cv2
|
||||
|
||||
# 推荐把 @ 进行 URL 编码:@ -> %40
|
||||
RTSP_URL = "rtsp://admin:admin123@192.168.31.164:554/stream1"
|
||||
OUTPUT_IMAGE = "rtsp_test_frame.jpg"
|
||||
|
||||
def main():
|
||||
print(f"尝试连接 RTSP 流: {RTSP_URL}")
|
||||
cap = cv2.VideoCapture(RTSP_URL)
|
||||
|
||||
if not cap.isOpened():
|
||||
print("错误:无法打开 RTSP 流,请检查:")
|
||||
print(" 1. IP/端口是否正确")
|
||||
print(" 2. 账号密码(尤其是 @ 是否已转成 %40)是否正确")
|
||||
print(" 3. 摄像头是否允许当前主机访问(同一网段、防火墙等)")
|
||||
return
|
||||
|
||||
print("连接成功,开始读取一帧...")
|
||||
ret, frame = cap.read()
|
||||
|
||||
if not ret or frame is None:
|
||||
print("错误:已连接但未能读取到帧数据(可能是码流未开启或网络抖动)")
|
||||
cap.release()
|
||||
return
|
||||
|
||||
# 保存当前帧
|
||||
success = cv2.imwrite(OUTPUT_IMAGE, frame)
|
||||
cap.release()
|
||||
|
||||
if success:
|
||||
print(f"成功截取一帧并保存为: {OUTPUT_IMAGE}")
|
||||
else:
|
||||
print("错误:写入图片失败,请检查磁盘权限/路径")
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
21
unilabos/devices/cameraSII/demo_camera_push.py
Normal file
21
unilabos/devices/cameraSII/demo_camera_push.py
Normal file
@@ -0,0 +1,21 @@
|
||||
# run_camera_push.py
|
||||
import time
|
||||
from cameraDriver import CameraController # 这里根据你的文件名调整
|
||||
|
||||
if __name__ == "__main__":
|
||||
controller = CameraController(
|
||||
host_id="demo-host",
|
||||
signal_backend_url="wss://sciol.ac.cn/api/realtime/signal/host",
|
||||
rtmp_url="rtmp://srs.sciol.ac.cn:4499/live/camera-01",
|
||||
webrtc_api="https://srs.sciol.ac.cn/rtc/v1/play/",
|
||||
webrtc_stream_url="webrtc://srs.sciol.ac.cn:4500/live/camera-01",
|
||||
camera_rtsp_url="rtsp://admin:admin123@192.168.31.164:554/stream1",
|
||||
)
|
||||
|
||||
try:
|
||||
while True:
|
||||
status = controller.get_status()
|
||||
print(status)
|
||||
time.sleep(5)
|
||||
except KeyboardInterrupt:
|
||||
controller.stop()
|
||||
78
unilabos/devices/cameraSII/ptz_cameracontroller_test.py
Normal file
78
unilabos/devices/cameraSII/ptz_cameracontroller_test.py
Normal file
@@ -0,0 +1,78 @@
|
||||
#!/usr/bin/env python3
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
"""
|
||||
使用 CameraController 来测试 PTZ:
|
||||
让摄像头按顺序向下、向上、向左、向右运动几次。
|
||||
"""
|
||||
|
||||
import time
|
||||
import sys
|
||||
|
||||
# 根据你的工程结构修改导入路径:
|
||||
# 假设 CameraController 定义在 cameraController.py 里
|
||||
from cameraDriver import CameraController
|
||||
|
||||
|
||||
def main():
|
||||
# === 根据你的实际情况填 IP、端口、账号密码 ===
|
||||
ptz_host = "192.168.31.164"
|
||||
ptz_port = 2020 # 注意要和你单独测试 PTZController 时保持一致
|
||||
ptz_user = "admin"
|
||||
ptz_password = "admin123"
|
||||
|
||||
# 1. 创建 CameraController 实例
|
||||
cam = CameraController(
|
||||
# 其他摄像机相关参数按你类的 __init__ 来补充
|
||||
ptz_host=ptz_host,
|
||||
ptz_port=ptz_port,
|
||||
ptz_user=ptz_user,
|
||||
ptz_password=ptz_password,
|
||||
)
|
||||
|
||||
# 2. 启动 / 初始化(如果你的 CameraController 有 start(config) 之类的接口)
|
||||
# 这里给一个最小的 config,重点是 PTZ 相关字段
|
||||
config = {
|
||||
"ptz_host": ptz_host,
|
||||
"ptz_port": ptz_port,
|
||||
"ptz_user": ptz_user,
|
||||
"ptz_password": ptz_password,
|
||||
}
|
||||
|
||||
try:
|
||||
cam.start(config)
|
||||
except Exception as e:
|
||||
print(f"[TEST] CameraController start() 失败: {e}", file=sys.stderr)
|
||||
return
|
||||
|
||||
# 这里可以判断一下内部 _ptz 是否初始化成功(如果你对 CameraController 做了封装)
|
||||
if getattr(cam, "_ptz", None) is None:
|
||||
print("[TEST] CameraController 内部 PTZ 未初始化成功,请检查 ptz_host/port/user/password 配置。", file=sys.stderr)
|
||||
return
|
||||
|
||||
# 3. 依次调用 CameraController 的 PTZ 方法
|
||||
# 这里假设你在 CameraController 中提供了这几个对外方法:
|
||||
# ptz_move_down / ptz_move_up / ptz_move_left / ptz_move_right
|
||||
# 如果你命名不一样,把下面调用名改成你的即可。
|
||||
|
||||
print("向下移动(通过 CameraController)...")
|
||||
cam.ptz_move_down(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("向上移动(通过 CameraController)...")
|
||||
cam.ptz_move_up(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("向左移动(通过 CameraController)...")
|
||||
cam.ptz_move_left(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("向右移动(通过 CameraController)...")
|
||||
cam.ptz_move_right(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("测试结束。")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
50
unilabos/devices/cameraSII/ptz_test.py
Normal file
50
unilabos/devices/cameraSII/ptz_test.py
Normal file
@@ -0,0 +1,50 @@
|
||||
#!/usr/bin/env python3
|
||||
# -*- coding: utf-8 -*-
|
||||
|
||||
"""
|
||||
测试 cameraDriver.py中的 PTZController 类,让摄像头按顺序运动几次
|
||||
"""
|
||||
|
||||
import time
|
||||
|
||||
from cameraDriver import PTZController
|
||||
|
||||
|
||||
def main():
|
||||
# 根据你的实际情况填 IP、端口、账号密码
|
||||
host = "192.168.31.164"
|
||||
port = 80
|
||||
user = "admin"
|
||||
password = "admin123"
|
||||
|
||||
ptz = PTZController(host=host, port=port, user=user, password=password)
|
||||
|
||||
# 1. 连接摄像头
|
||||
if not ptz.connect():
|
||||
print("连接 PTZ 失败,检查 IP/用户名/密码/端口。")
|
||||
return
|
||||
|
||||
# 2. 依次测试几个动作
|
||||
# 每个动作之间 sleep 一下方便观察
|
||||
|
||||
print("向下移动...")
|
||||
ptz.move_down(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("向上移动...")
|
||||
ptz.move_up(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("向左移动...")
|
||||
ptz.move_left(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("向右移动...")
|
||||
ptz.move_right(speed=0.5, duration=1.0)
|
||||
time.sleep(1)
|
||||
|
||||
print("测试结束。")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
0
unilabos/devices/laiyu_liquid_test/__init__.py
Normal file
0
unilabos/devices/laiyu_liquid_test/__init__.py
Normal file
0
unilabos/devices/liquid_handling/laiyu/__init__.py
Normal file
0
unilabos/devices/liquid_handling/laiyu/__init__.py
Normal file
@@ -988,6 +988,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
|
||||
dis_vols = [float(dis_vols)]
|
||||
else:
|
||||
dis_vols = [float(v) for v in dis_vols]
|
||||
|
||||
# 统一混合次数为标量,防止数组/列表与 int 比较时报错
|
||||
if mix_times is not None and not isinstance(mix_times, (int, float)):
|
||||
try:
|
||||
mix_times = mix_times[0] if len(mix_times) > 0 else None
|
||||
except Exception:
|
||||
try:
|
||||
mix_times = next(iter(mix_times))
|
||||
except Exception:
|
||||
pass
|
||||
if mix_times is not None:
|
||||
mix_times = int(mix_times)
|
||||
|
||||
# 识别传输模式
|
||||
num_sources = len(sources)
|
||||
|
||||
@@ -5,6 +5,7 @@ import json
|
||||
import os
|
||||
import socket
|
||||
import time
|
||||
import uuid
|
||||
from typing import Any, List, Dict, Optional, Tuple, TypedDict, Union, Sequence, Iterator, Literal
|
||||
|
||||
from pylabrobot.liquid_handling import (
|
||||
@@ -856,7 +857,30 @@ class PRCXI9300Api:
|
||||
|
||||
def _raw_request(self, payload: str) -> str:
|
||||
if self.debug:
|
||||
return " "
|
||||
# 调试/仿真模式下直接返回可解析的模拟 JSON,避免后续 json.loads 报错
|
||||
try:
|
||||
req = json.loads(payload)
|
||||
method = req.get("MethodName")
|
||||
except Exception:
|
||||
method = None
|
||||
|
||||
data: Any = True
|
||||
if method in {"AddSolution"}:
|
||||
data = str(uuid.uuid4())
|
||||
elif method in {"AddWorkTabletMatrix", "AddWorkTabletMatrix2"}:
|
||||
data = {"Success": True, "Message": "debug mock"}
|
||||
elif method in {"GetErrorCode"}:
|
||||
data = ""
|
||||
elif method in {"RemoveErrorCodet", "Reset", "Start", "LoadSolution", "Pause", "Resume", "Stop"}:
|
||||
data = True
|
||||
elif method in {"GetStepStateList", "GetStepStatus", "GetStepState"}:
|
||||
data = []
|
||||
elif method in {"GetLocation"}:
|
||||
data = {"X": 0, "Y": 0, "Z": 0}
|
||||
elif method in {"GetResetStatus"}:
|
||||
data = False
|
||||
|
||||
return json.dumps({"Success": True, "Msg": "debug mock", "Data": data})
|
||||
with contextlib.closing(socket.socket()) as sock:
|
||||
sock.settimeout(self.timeout)
|
||||
sock.connect((self.host, self.port))
|
||||
|
||||
@@ -174,35 +174,6 @@ bioyond_dispensing_station:
|
||||
title: query_resource_by_name参数
|
||||
type: object
|
||||
type: UniLabJsonCommand
|
||||
auto-transfer_materials_to_reaction_station:
|
||||
feedback: {}
|
||||
goal: {}
|
||||
goal_default:
|
||||
target_device_id: null
|
||||
transfer_groups: null
|
||||
handles: {}
|
||||
placeholder_keys: {}
|
||||
result: {}
|
||||
schema:
|
||||
description: ''
|
||||
properties:
|
||||
feedback: {}
|
||||
goal:
|
||||
properties:
|
||||
target_device_id:
|
||||
type: string
|
||||
transfer_groups:
|
||||
type: array
|
||||
required:
|
||||
- target_device_id
|
||||
- transfer_groups
|
||||
type: object
|
||||
result: {}
|
||||
required:
|
||||
- goal
|
||||
title: transfer_materials_to_reaction_station参数
|
||||
type: object
|
||||
type: UniLabJsonCommand
|
||||
auto-workflow_sample_locations:
|
||||
feedback: {}
|
||||
goal: {}
|
||||
|
||||
105
unilabos/registry/devices/cameraSII.yaml
Normal file
105
unilabos/registry/devices/cameraSII.yaml
Normal file
@@ -0,0 +1,105 @@
|
||||
cameracontroller_device:
|
||||
category:
|
||||
- cameraSII
|
||||
class:
|
||||
action_value_mappings:
|
||||
auto-start:
|
||||
feedback: {}
|
||||
goal: {}
|
||||
goal_default:
|
||||
config: null
|
||||
handles: {}
|
||||
result: {}
|
||||
schema:
|
||||
description: ''
|
||||
properties:
|
||||
feedback: {}
|
||||
goal:
|
||||
properties:
|
||||
config:
|
||||
type: string
|
||||
required: []
|
||||
type: object
|
||||
result: {}
|
||||
required:
|
||||
- goal
|
||||
title: start参数
|
||||
type: object
|
||||
type: UniLabJsonCommand
|
||||
auto-stop:
|
||||
feedback: {}
|
||||
goal: {}
|
||||
goal_default: {}
|
||||
handles: {}
|
||||
result: {}
|
||||
schema:
|
||||
description: ''
|
||||
properties:
|
||||
feedback: {}
|
||||
goal:
|
||||
properties: {}
|
||||
required: []
|
||||
type: object
|
||||
result: {}
|
||||
required:
|
||||
- goal
|
||||
title: stop参数
|
||||
type: object
|
||||
type: UniLabJsonCommand
|
||||
module: unilabos.devices.cameraSII.cameraUSB:CameraController
|
||||
status_types:
|
||||
status: dict
|
||||
type: python
|
||||
config_info: []
|
||||
description: Uni-Lab-OS 摄像头驱动(Linux USB 摄像头版,无 PTZ)
|
||||
handles: []
|
||||
icon: ''
|
||||
init_param_schema:
|
||||
config:
|
||||
properties:
|
||||
audio_bitrate:
|
||||
default: 64k
|
||||
type: string
|
||||
audio_device:
|
||||
type: string
|
||||
fps:
|
||||
default: 30
|
||||
type: integer
|
||||
height:
|
||||
default: 720
|
||||
type: integer
|
||||
host_id:
|
||||
default: demo-host
|
||||
type: string
|
||||
rtmp_url:
|
||||
default: rtmp://srs.sciol.ac.cn:4499/live/camera-01
|
||||
type: string
|
||||
signal_backend_url:
|
||||
default: wss://sciol.ac.cn/api/realtime/signal/host
|
||||
type: string
|
||||
video_bitrate:
|
||||
default: 1500k
|
||||
type: string
|
||||
video_device:
|
||||
default: /dev/video0
|
||||
type: string
|
||||
webrtc_api:
|
||||
default: https://srs.sciol.ac.cn/rtc/v1/play/
|
||||
type: string
|
||||
webrtc_stream_url:
|
||||
default: webrtc://srs.sciol.ac.cn:4500/live/camera-01
|
||||
type: string
|
||||
width:
|
||||
default: 1280
|
||||
type: integer
|
||||
required: []
|
||||
type: object
|
||||
data:
|
||||
properties:
|
||||
status:
|
||||
type: object
|
||||
required:
|
||||
- status
|
||||
type: object
|
||||
registry_type: device
|
||||
version: 1.0.0
|
||||
@@ -9333,7 +9333,34 @@ liquid_handler.prcxi:
|
||||
touch_tip: false
|
||||
use_channels:
|
||||
- 0
|
||||
handles: {}
|
||||
handles:
|
||||
input:
|
||||
- data_key: liquid
|
||||
data_source: handle
|
||||
data_type: resource
|
||||
handler_key: sources
|
||||
label: sources
|
||||
- data_key: liquid
|
||||
data_source: executor
|
||||
data_type: resource
|
||||
handler_key: targets
|
||||
label: targets
|
||||
- data_key: liquid
|
||||
data_source: executor
|
||||
data_type: resource
|
||||
handler_key: tip_rack
|
||||
label: tip_rack
|
||||
output:
|
||||
- data_key: liquid
|
||||
data_source: handle
|
||||
data_type: resource
|
||||
handler_key: sources_out
|
||||
label: sources
|
||||
- data_key: liquid
|
||||
data_source: executor
|
||||
data_type: resource
|
||||
handler_key: targets_out
|
||||
label: targets
|
||||
placeholder_keys:
|
||||
sources: unilabos_resources
|
||||
targets: unilabos_resources
|
||||
|
||||
@@ -222,7 +222,7 @@ class Registry:
|
||||
abs_path = Path(path).absolute()
|
||||
resource_path = abs_path / "resources"
|
||||
files = list(resource_path.glob("*/*.yaml"))
|
||||
logger.debug(f"[UniLab Registry] resources: {resource_path.exists()}, total: {len(files)}")
|
||||
logger.trace(f"[UniLab Registry] load resources? {resource_path.exists()}, total: {len(files)}")
|
||||
current_resource_number = len(self.resource_type_registry) + 1
|
||||
for i, file in enumerate(files):
|
||||
with open(file, encoding="utf-8", mode="r") as f:
|
||||
|
||||
@@ -42,7 +42,7 @@ def canonicalize_nodes_data(
|
||||
Returns:
|
||||
ResourceTreeSet: 标准化后的资源树集合
|
||||
"""
|
||||
print_status(f"{len(nodes)} Resources loaded:", "info")
|
||||
print_status(f"{len(nodes)} Resources loaded", "info")
|
||||
|
||||
# 第一步:基本预处理(处理graphml的label字段)
|
||||
outer_host_node_id = None
|
||||
@@ -97,7 +97,7 @@ def canonicalize_nodes_data(
|
||||
|
||||
for node in nodes:
|
||||
try:
|
||||
print_status(f"DeviceId: {node['id']}, Class: {node['class']}", "info")
|
||||
# print_status(f"DeviceId: {node['id']}, Class: {node['class']}", "info")
|
||||
# 使用标准化方法
|
||||
resource_instance = ResourceDictInstance.get_resource_instance_from_dict(node)
|
||||
known_nodes[node["id"]] = resource_instance
|
||||
|
||||
@@ -582,7 +582,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
||||
except Exception as e:
|
||||
self.lab_logger().error(f"更新资源uuid失败: {e}")
|
||||
self.lab_logger().error(traceback.format_exc())
|
||||
self.lab_logger().debug(f"资源更新结果: {response}")
|
||||
self.lab_logger().trace(f"资源更新结果: {response}")
|
||||
|
||||
async def get_resource(self, resources_uuid: List[str], with_children: bool = True) -> ResourceTreeSet:
|
||||
"""
|
||||
@@ -1164,7 +1164,6 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
||||
execution_error = traceback.format_exc()
|
||||
break
|
||||
|
||||
##### self.lab_logger().info(f"准备执行: {action_kwargs}, 函数: {ACTION.__name__}")
|
||||
time_start = time.time()
|
||||
time_overall = 100
|
||||
future = None
|
||||
@@ -1172,35 +1171,36 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
||||
# 将阻塞操作放入线程池执行
|
||||
if asyncio.iscoroutinefunction(ACTION):
|
||||
try:
|
||||
##### self.lab_logger().info(f"异步执行动作 {ACTION}")
|
||||
future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs)
|
||||
|
||||
def _handle_future_exception(fut):
|
||||
self.lab_logger().trace(f"异步执行动作 {ACTION}")
|
||||
def _handle_future_exception(fut: Future):
|
||||
nonlocal execution_error, execution_success, action_return_value
|
||||
try:
|
||||
action_return_value = fut.result()
|
||||
if isinstance(action_return_value, BaseException):
|
||||
raise action_return_value
|
||||
execution_success = True
|
||||
except Exception as e:
|
||||
except Exception as _:
|
||||
execution_error = traceback.format_exc()
|
||||
error(
|
||||
f"异步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{action_kwargs}"
|
||||
)
|
||||
|
||||
future = ROS2DeviceNode.run_async_func(ACTION, trace_error=False, **action_kwargs)
|
||||
future.add_done_callback(_handle_future_exception)
|
||||
except Exception as e:
|
||||
execution_error = traceback.format_exc()
|
||||
execution_success = False
|
||||
self.lab_logger().error(f"创建异步任务失败: {traceback.format_exc()}")
|
||||
else:
|
||||
##### self.lab_logger().info(f"同步执行动作 {ACTION}")
|
||||
self.lab_logger().trace(f"同步执行动作 {ACTION}")
|
||||
future = self._executor.submit(ACTION, **action_kwargs)
|
||||
|
||||
def _handle_future_exception(fut):
|
||||
def _handle_future_exception(fut: Future):
|
||||
nonlocal execution_error, execution_success, action_return_value
|
||||
try:
|
||||
action_return_value = fut.result()
|
||||
execution_success = True
|
||||
except Exception as e:
|
||||
except Exception as _:
|
||||
execution_error = traceback.format_exc()
|
||||
error(
|
||||
f"同步任务 {ACTION.__name__} 报错了\n{traceback.format_exc()}\n原始输入:{action_kwargs}"
|
||||
@@ -1305,7 +1305,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
||||
get_result_info_str(execution_error, execution_success, action_return_value),
|
||||
)
|
||||
|
||||
##### self.lab_logger().info(f"动作 {action_name} 完成并返回结果")
|
||||
self.lab_logger().trace(f"动作 {action_name} 完成并返回结果")
|
||||
return result_msg
|
||||
|
||||
return execute_callback
|
||||
@@ -1540,17 +1540,29 @@ class ROS2DeviceNode:
|
||||
这个类封装了设备类实例和ROS2节点的功能,提供ROS2接口。
|
||||
它不继承设备类,而是通过代理模式访问设备类的属性和方法。
|
||||
"""
|
||||
@staticmethod
|
||||
async def safe_task_wrapper(trace_callback, func, **kwargs):
|
||||
try:
|
||||
if callable(trace_callback):
|
||||
trace_callback(await func(**kwargs))
|
||||
return await func(**kwargs)
|
||||
except Exception as e:
|
||||
if callable(trace_callback):
|
||||
trace_callback(e)
|
||||
return e
|
||||
|
||||
@classmethod
|
||||
def run_async_func(cls, func, trace_error=True, **kwargs) -> Task:
|
||||
def _handle_future_exception(fut):
|
||||
def run_async_func(cls, func, trace_error=True, inner_trace_callback=None, **kwargs) -> Task:
|
||||
def _handle_future_exception(fut: Future):
|
||||
try:
|
||||
fut.result()
|
||||
ret = fut.result()
|
||||
if isinstance(ret, BaseException):
|
||||
raise ret
|
||||
except Exception as e:
|
||||
error(f"异步任务 {func.__name__} 报错了")
|
||||
error(f"异步任务 {func.__name__} 获取结果失败")
|
||||
error(traceback.format_exc())
|
||||
|
||||
future = rclpy.get_global_executor().create_task(func(**kwargs))
|
||||
future = rclpy.get_global_executor().create_task(ROS2DeviceNode.safe_task_wrapper(inner_trace_callback, func, **kwargs))
|
||||
if trace_error:
|
||||
future.add_done_callback(_handle_future_exception)
|
||||
return future
|
||||
|
||||
@@ -718,7 +718,7 @@ class HostNode(BaseROS2DeviceNode):
|
||||
feedback_callback=lambda feedback_msg: self.feedback_callback(item, action_id, feedback_msg),
|
||||
goal_uuid=goal_uuid_obj,
|
||||
)
|
||||
future.add_done_callback(lambda future: self.goal_response_callback(item, action_id, future))
|
||||
future.add_done_callback(lambda f: self.goal_response_callback(item, action_id, f))
|
||||
|
||||
def goal_response_callback(self, item: "QueueItem", action_id: str, future) -> None:
|
||||
"""目标响应回调"""
|
||||
@@ -729,9 +729,11 @@ class HostNode(BaseROS2DeviceNode):
|
||||
|
||||
self.lab_logger().info(f"[Host Node] Goal {action_id} ({item.job_id}) accepted")
|
||||
self._goals[item.job_id] = goal_handle
|
||||
goal_handle.get_result_async().add_done_callback(
|
||||
lambda future: self.get_result_callback(item, action_id, future)
|
||||
goal_future = goal_handle.get_result_async()
|
||||
goal_future.add_done_callback(
|
||||
lambda f: self.get_result_callback(item, action_id, f)
|
||||
)
|
||||
goal_future.result()
|
||||
|
||||
def feedback_callback(self, item: "QueueItem", action_id: str, feedback_msg) -> None:
|
||||
"""反馈回调"""
|
||||
|
||||
@@ -66,8 +66,8 @@ class ResourceDict(BaseModel):
|
||||
klass: str = Field(alias="class", description="Resource class name")
|
||||
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
|
||||
config: Dict[str, Any] = Field(description="Resource configuration")
|
||||
data: Dict[str, Any] = Field(description="Resource data")
|
||||
extra: Dict[str, Any] = Field(description="Extra data")
|
||||
data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
|
||||
extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
|
||||
|
||||
@field_serializer("parent_uuid")
|
||||
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
|
||||
@@ -155,7 +155,7 @@ class ResourceDictInstance(object):
|
||||
res_dict = self.res_content.model_dump(by_alias=True)
|
||||
res_dict["children"] = {child.res_content.id: child.get_plr_nested_dict() for child in self.children}
|
||||
res_dict["parent"] = self.res_content.parent_instance_name
|
||||
res_dict["position"] = self.res_content.position.position.model_dump()
|
||||
res_dict["position"] = self.res_content.pose.position.model_dump()
|
||||
del res_dict["pose"]
|
||||
return res_dict
|
||||
|
||||
|
||||
@@ -1,94 +0,0 @@
|
||||
import json
|
||||
import sys
|
||||
from datetime import datetime
|
||||
from pathlib import Path
|
||||
|
||||
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||||
if str(ROOT_DIR) not in sys.path:
|
||||
sys.path.insert(0, str(ROOT_DIR))
|
||||
|
||||
import pytest
|
||||
|
||||
from scripts.workflow import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
|
||||
|
||||
|
||||
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||||
if str(ROOT_DIR) not in sys.path:
|
||||
sys.path.insert(0, str(ROOT_DIR))
|
||||
|
||||
|
||||
def _normalize_steps(data):
|
||||
normalized = []
|
||||
for step in data:
|
||||
action = step.get("action") or step.get("operation")
|
||||
if not action:
|
||||
continue
|
||||
raw_params = step.get("parameters") or step.get("action_args") or {}
|
||||
params = dict(raw_params)
|
||||
|
||||
if "source" in raw_params and "sources" not in raw_params:
|
||||
params["sources"] = raw_params["source"]
|
||||
if "target" in raw_params and "targets" not in raw_params:
|
||||
params["targets"] = raw_params["target"]
|
||||
|
||||
description = step.get("description") or step.get("purpose")
|
||||
step_dict = {"action": action, "parameters": params}
|
||||
if description:
|
||||
step_dict["description"] = description
|
||||
normalized.append(step_dict)
|
||||
return normalized
|
||||
|
||||
|
||||
def _normalize_labware(data):
|
||||
labware = {}
|
||||
for item in data:
|
||||
reagent_name = item.get("reagent_name")
|
||||
key = reagent_name or item.get("material_name") or item.get("name")
|
||||
if not key:
|
||||
continue
|
||||
key = str(key)
|
||||
idx = 1
|
||||
original_key = key
|
||||
while key in labware:
|
||||
idx += 1
|
||||
key = f"{original_key}_{idx}"
|
||||
|
||||
labware[key] = {
|
||||
"slot": item.get("positions") or item.get("slot"),
|
||||
"labware": item.get("material_name") or item.get("labware"),
|
||||
"well": item.get("well", []),
|
||||
"type": item.get("type", "reagent"),
|
||||
"role": item.get("role", ""),
|
||||
"name": key,
|
||||
}
|
||||
return labware
|
||||
|
||||
|
||||
@pytest.mark.parametrize("protocol_name", [
|
||||
"example_bio",
|
||||
# "bioyond_materials_liquidhandling_1",
|
||||
"example_prcxi",
|
||||
])
|
||||
def test_build_protocol_graph(protocol_name):
|
||||
data_path = Path(__file__).with_name(f"{protocol_name}.json")
|
||||
with data_path.open("r", encoding="utf-8") as fp:
|
||||
d = json.load(fp)
|
||||
|
||||
if "workflow" in d and "reagent" in d:
|
||||
protocol_steps = d["workflow"]
|
||||
labware_info = d["reagent"]
|
||||
elif "steps_info" in d and "labware_info" in d:
|
||||
protocol_steps = _normalize_steps(d["steps_info"])
|
||||
labware_info = _normalize_labware(d["labware_info"])
|
||||
else:
|
||||
raise ValueError("Unsupported protocol format")
|
||||
|
||||
graph = build_protocol_graph(
|
||||
labware_info=labware_info,
|
||||
protocol_steps=protocol_steps,
|
||||
workstation_name="PRCXi",
|
||||
)
|
||||
timestamp = datetime.now().strftime("%Y%m%d_%H%M")
|
||||
output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
|
||||
draw_protocol_graph_with_ports(graph, str(output_path))
|
||||
print(graph)
|
||||
@@ -162,8 +162,9 @@ def configure_logger(loglevel=None, working_dir=None):
|
||||
"""
|
||||
# 获取根日志记录器
|
||||
root_logger = logging.getLogger()
|
||||
|
||||
root_logger.setLevel(TRACE_LEVEL)
|
||||
# 设置日志级别
|
||||
numeric_level = logging.DEBUG
|
||||
if loglevel is not None:
|
||||
if isinstance(loglevel, str):
|
||||
# 将字符串转换为logging级别
|
||||
@@ -173,12 +174,8 @@ def configure_logger(loglevel=None, working_dir=None):
|
||||
numeric_level = getattr(logging, loglevel.upper(), None)
|
||||
if not isinstance(numeric_level, int):
|
||||
print(f"警告: 无效的日志级别 '{loglevel}',使用默认级别 DEBUG")
|
||||
numeric_level = logging.DEBUG
|
||||
else:
|
||||
numeric_level = loglevel
|
||||
root_logger.setLevel(numeric_level)
|
||||
else:
|
||||
root_logger.setLevel(logging.DEBUG) # 默认级别
|
||||
|
||||
# 移除已存在的处理器
|
||||
for handler in root_logger.handlers[:]:
|
||||
@@ -186,7 +183,7 @@ def configure_logger(loglevel=None, working_dir=None):
|
||||
|
||||
# 创建控制台处理器
|
||||
console_handler = logging.StreamHandler()
|
||||
console_handler.setLevel(root_logger.level) # 使用与根记录器相同的级别
|
||||
console_handler.setLevel(numeric_level) # 使用与根记录器相同的级别
|
||||
|
||||
# 使用自定义的颜色格式化器
|
||||
color_formatter = ColoredFormatter()
|
||||
@@ -206,7 +203,7 @@ def configure_logger(loglevel=None, working_dir=None):
|
||||
|
||||
# 创建文件处理器
|
||||
file_handler = logging.FileHandler(log_filepath, encoding="utf-8")
|
||||
file_handler.setLevel(root_logger.level)
|
||||
file_handler.setLevel(TRACE_LEVEL)
|
||||
|
||||
# 使用不带颜色的格式化器
|
||||
file_formatter = ColoredFormatter(use_colors=False)
|
||||
|
||||
0
unilabos/workflow/__init__.py
Normal file
0
unilabos/workflow/__init__.py
Normal file
547
unilabos/workflow/common.py
Normal file
547
unilabos/workflow/common.py
Normal file
@@ -0,0 +1,547 @@
|
||||
import re
|
||||
import uuid
|
||||
|
||||
import networkx as nx
|
||||
from networkx.drawing.nx_agraph import to_agraph
|
||||
import matplotlib.pyplot as plt
|
||||
from typing import Dict, List, Any, Tuple, Optional
|
||||
|
||||
Json = Dict[str, Any]
|
||||
|
||||
# ---------------- Graph ----------------
|
||||
|
||||
|
||||
class WorkflowGraph:
|
||||
"""简单的有向图实现:使用 params 单层参数;inputs 内含连线;支持 node-link 导出"""
|
||||
|
||||
def __init__(self):
|
||||
self.nodes: Dict[str, Dict[str, Any]] = {}
|
||||
self.edges: List[Dict[str, Any]] = []
|
||||
|
||||
def add_node(self, node_id: str, **attrs):
|
||||
self.nodes[node_id] = attrs
|
||||
|
||||
def add_edge(self, source: str, target: str, **attrs):
|
||||
# 将 source_port/target_port 映射为服务端期望的 source_handle_key/target_handle_key
|
||||
source_handle_key = attrs.pop("source_port", "") or attrs.pop("source_handle_key", "")
|
||||
target_handle_key = attrs.pop("target_port", "") or attrs.pop("target_handle_key", "")
|
||||
|
||||
edge = {
|
||||
"source": source,
|
||||
"target": target,
|
||||
"source_node_uuid": source,
|
||||
"target_node_uuid": target,
|
||||
"source_handle_key": source_handle_key,
|
||||
"source_handle_io": attrs.pop("source_handle_io", "source"),
|
||||
"target_handle_key": target_handle_key,
|
||||
"target_handle_io": attrs.pop("target_handle_io", "target"),
|
||||
**attrs,
|
||||
}
|
||||
self.edges.append(edge)
|
||||
|
||||
def _materialize_wiring_into_inputs(
|
||||
self,
|
||||
obj: Any,
|
||||
inputs: Dict[str, Any],
|
||||
variable_sources: Dict[str, Dict[str, Any]],
|
||||
target_node_id: str,
|
||||
base_path: List[str],
|
||||
):
|
||||
has_var = False
|
||||
|
||||
def walk(node: Any, path: List[str]):
|
||||
nonlocal has_var
|
||||
if isinstance(node, dict):
|
||||
if "__var__" in node:
|
||||
has_var = True
|
||||
varname = node["__var__"]
|
||||
placeholder = f"${{{varname}}}"
|
||||
src = variable_sources.get(varname)
|
||||
if src:
|
||||
key = ".".join(path) # e.g. "params.foo.bar.0"
|
||||
inputs[key] = {"node": src["node_id"], "output": src.get("output_name", "result")}
|
||||
self.add_edge(
|
||||
str(src["node_id"]),
|
||||
target_node_id,
|
||||
source_handle_io=src.get("output_name", "result"),
|
||||
target_handle_io=key,
|
||||
)
|
||||
return placeholder
|
||||
return {k: walk(v, path + [k]) for k, v in node.items()}
|
||||
if isinstance(node, list):
|
||||
return [walk(v, path + [str(i)]) for i, v in enumerate(node)]
|
||||
return node
|
||||
|
||||
replaced = walk(obj, base_path[:])
|
||||
return replaced, has_var
|
||||
|
||||
def add_workflow_node(
|
||||
self,
|
||||
node_id: int,
|
||||
*,
|
||||
device_key: Optional[str] = None, # 实例名,如 "ser"
|
||||
resource_name: Optional[str] = None, # registry key(原 device_class)
|
||||
module: Optional[str] = None,
|
||||
template_name: Optional[str] = None, # 动作/模板名(原 action_key)
|
||||
params: Dict[str, Any],
|
||||
variable_sources: Dict[str, Dict[str, Any]],
|
||||
add_ready_if_no_vars: bool = True,
|
||||
prev_node_id: Optional[int] = None,
|
||||
**extra_attrs,
|
||||
) -> None:
|
||||
"""添加工作流节点:params 单层;自动变量连线与 ready 串联;支持附加属性"""
|
||||
node_id_str = str(node_id)
|
||||
inputs: Dict[str, Any] = {}
|
||||
|
||||
params, has_var = self._materialize_wiring_into_inputs(
|
||||
params, inputs, variable_sources, node_id_str, base_path=["params"]
|
||||
)
|
||||
|
||||
if add_ready_if_no_vars and not has_var:
|
||||
last_id = str(prev_node_id) if prev_node_id is not None else "-1"
|
||||
inputs["ready"] = {"node": int(last_id), "output": "ready"}
|
||||
self.add_edge(last_id, node_id_str, source_handle_io="ready", target_handle_io="ready")
|
||||
|
||||
node_obj = {
|
||||
"device_key": device_key,
|
||||
"resource_name": resource_name, # ✅ 新名字
|
||||
"module": module,
|
||||
"template_name": template_name, # ✅ 新名字
|
||||
"params": params,
|
||||
"inputs": inputs,
|
||||
}
|
||||
node_obj.update(extra_attrs or {})
|
||||
self.add_node(node_id_str, parameters=node_obj)
|
||||
|
||||
# 顺序工作流导出(连线在 inputs,不返回 edges)
|
||||
def to_dict(self) -> List[Dict[str, Any]]:
|
||||
result = []
|
||||
for node_id, attrs in self.nodes.items():
|
||||
node = {"uuid": node_id}
|
||||
params = dict(attrs.get("parameters", {}) or {})
|
||||
flat = {k: v for k, v in attrs.items() if k != "parameters"}
|
||||
flat.update(params)
|
||||
node.update(flat)
|
||||
result.append(node)
|
||||
return sorted(result, key=lambda n: int(n["uuid"]) if str(n["uuid"]).isdigit() else n["uuid"])
|
||||
|
||||
# node-link 导出(含 edges)
|
||||
def to_node_link_dict(self) -> Dict[str, Any]:
|
||||
nodes_list = []
|
||||
for node_id, attrs in self.nodes.items():
|
||||
node_attrs = attrs.copy()
|
||||
params = node_attrs.pop("parameters", {}) or {}
|
||||
node_attrs.update(params)
|
||||
nodes_list.append({"uuid": node_id, **node_attrs})
|
||||
return {
|
||||
"directed": True,
|
||||
"multigraph": False,
|
||||
"graph": {},
|
||||
"nodes": nodes_list,
|
||||
"edges": self.edges,
|
||||
"links": self.edges,
|
||||
}
|
||||
|
||||
|
||||
def refactor_data(
|
||||
data: List[Dict[str, Any]],
|
||||
action_resource_mapping: Optional[Dict[str, str]] = None,
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""统一的数据重构函数,根据操作类型自动选择模板
|
||||
|
||||
Args:
|
||||
data: 原始步骤数据列表
|
||||
action_resource_mapping: action 到 resource_name 的映射字典,可选
|
||||
"""
|
||||
refactored_data = []
|
||||
|
||||
# 定义操作映射,包含生物实验和有机化学的所有操作
|
||||
OPERATION_MAPPING = {
|
||||
# 生物实验操作
|
||||
"transfer_liquid": "transfer_liquid",
|
||||
"transfer": "transfer",
|
||||
"incubation": "incubation",
|
||||
"move_labware": "move_labware",
|
||||
"oscillation": "oscillation",
|
||||
# 有机化学操作
|
||||
"HeatChillToTemp": "HeatChillProtocol",
|
||||
"StopHeatChill": "HeatChillStopProtocol",
|
||||
"StartHeatChill": "HeatChillStartProtocol",
|
||||
"HeatChill": "HeatChillProtocol",
|
||||
"Dissolve": "DissolveProtocol",
|
||||
"Transfer": "TransferProtocol",
|
||||
"Evaporate": "EvaporateProtocol",
|
||||
"Recrystallize": "RecrystallizeProtocol",
|
||||
"Filter": "FilterProtocol",
|
||||
"Dry": "DryProtocol",
|
||||
"Add": "AddProtocol",
|
||||
}
|
||||
|
||||
UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
for step in data:
|
||||
operation = step.get("action")
|
||||
if not operation or operation in UNSUPPORTED_OPERATIONS:
|
||||
continue
|
||||
|
||||
# 处理重复操作
|
||||
if operation == "Repeat":
|
||||
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
||||
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
||||
for i in range(int(times)):
|
||||
sub_data = refactor_data(sub_steps, action_resource_mapping)
|
||||
refactored_data.extend(sub_data)
|
||||
continue
|
||||
|
||||
# 获取模板名称
|
||||
template_name = OPERATION_MAPPING.get(operation)
|
||||
if not template_name:
|
||||
# 自动推断模板类型
|
||||
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
||||
template_name = f"biomek-{operation}"
|
||||
else:
|
||||
template_name = f"{operation}Protocol"
|
||||
|
||||
# 获取 resource_name
|
||||
resource_name = f"device.{operation.lower()}"
|
||||
if action_resource_mapping:
|
||||
resource_name = action_resource_mapping.get(operation, resource_name)
|
||||
|
||||
# 获取步骤编号,生成 name 字段
|
||||
step_number = step.get("step_number")
|
||||
name = f"Step {step_number}" if step_number is not None else None
|
||||
|
||||
# 创建步骤数据
|
||||
step_data = {
|
||||
"template_name": template_name,
|
||||
"resource_name": resource_name,
|
||||
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
||||
"lab_node_type": "Device",
|
||||
"param": step.get("parameters", step.get("action_args", {})),
|
||||
"footer": f"{template_name}-{resource_name}",
|
||||
}
|
||||
if name:
|
||||
step_data["name"] = name
|
||||
refactored_data.append(step_data)
|
||||
|
||||
return refactored_data
|
||||
|
||||
|
||||
def build_protocol_graph(
|
||||
labware_info: List[Dict[str, Any]],
|
||||
protocol_steps: List[Dict[str, Any]],
|
||||
workstation_name: str,
|
||||
action_resource_mapping: Optional[Dict[str, str]] = None,
|
||||
) -> WorkflowGraph:
|
||||
"""统一的协议图构建函数,根据设备类型自动选择构建逻辑
|
||||
|
||||
Args:
|
||||
labware_info: labware 信息字典
|
||||
protocol_steps: 协议步骤列表
|
||||
workstation_name: 工作站名称
|
||||
action_resource_mapping: action 到 resource_name 的映射字典,可选
|
||||
"""
|
||||
G = WorkflowGraph()
|
||||
resource_last_writer = {}
|
||||
|
||||
protocol_steps = refactor_data(protocol_steps, action_resource_mapping)
|
||||
# 有机化学&移液站协议图构建
|
||||
WORKSTATION_ID = workstation_name
|
||||
|
||||
# 为所有labware创建资源节点
|
||||
res_index = 0
|
||||
for labware_id, item in labware_info.items():
|
||||
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
||||
node_id = str(uuid.uuid4())
|
||||
|
||||
# 判断节点类型
|
||||
if "Rack" in str(labware_id) or "Tip" in str(labware_id):
|
||||
lab_node_type = "Labware"
|
||||
description = f"Prepare Labware: {labware_id}"
|
||||
liquid_type = []
|
||||
liquid_volume = []
|
||||
elif item.get("type") == "hardware" or "reactor" in str(labware_id).lower():
|
||||
if "reactor" not in str(labware_id).lower():
|
||||
continue
|
||||
lab_node_type = "Sample"
|
||||
description = f"Prepare Reactor: {labware_id}"
|
||||
liquid_type = []
|
||||
liquid_volume = []
|
||||
else:
|
||||
lab_node_type = "Reagent"
|
||||
description = f"Add Reagent to Flask: {labware_id}"
|
||||
liquid_type = [labware_id]
|
||||
liquid_volume = [1e5]
|
||||
|
||||
res_index += 1
|
||||
G.add_node(
|
||||
node_id,
|
||||
template_name="create_resource",
|
||||
resource_name="host_node",
|
||||
name=f"Res {res_index}",
|
||||
description=description,
|
||||
lab_node_type=lab_node_type,
|
||||
footer="create_resource-host_node",
|
||||
param={
|
||||
"res_id": labware_id,
|
||||
"device_id": WORKSTATION_ID,
|
||||
"class_name": "container",
|
||||
"parent": WORKSTATION_ID,
|
||||
"bind_locations": {"x": 0.0, "y": 0.0, "z": 0.0},
|
||||
"liquid_input_slot": [-1],
|
||||
"liquid_type": liquid_type,
|
||||
"liquid_volume": liquid_volume,
|
||||
"slot_on_deck": "",
|
||||
},
|
||||
)
|
||||
resource_last_writer[labware_id] = f"{node_id}:labware"
|
||||
|
||||
last_control_node_id = None
|
||||
|
||||
# 处理协议步骤
|
||||
for step in protocol_steps:
|
||||
node_id = str(uuid.uuid4())
|
||||
G.add_node(node_id, **step)
|
||||
|
||||
# 控制流
|
||||
if last_control_node_id is not None:
|
||||
G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
|
||||
last_control_node_id = node_id
|
||||
|
||||
# 物料流
|
||||
params = step.get("param", {})
|
||||
input_resources_possible_names = [
|
||||
"vessel",
|
||||
"to_vessel",
|
||||
"from_vessel",
|
||||
"reagent",
|
||||
"solvent",
|
||||
"compound",
|
||||
"sources",
|
||||
"targets",
|
||||
]
|
||||
|
||||
for target_port in input_resources_possible_names:
|
||||
resource_name = params.get(target_port)
|
||||
if resource_name and resource_name in resource_last_writer:
|
||||
source_node, source_port = resource_last_writer[resource_name].split(":")
|
||||
G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
|
||||
|
||||
output_resources = {
|
||||
"vessel_out": params.get("vessel"),
|
||||
"from_vessel_out": params.get("from_vessel"),
|
||||
"to_vessel_out": params.get("to_vessel"),
|
||||
"filtrate_out": params.get("filtrate_vessel"),
|
||||
"reagent": params.get("reagent"),
|
||||
"solvent": params.get("solvent"),
|
||||
"compound": params.get("compound"),
|
||||
"sources_out": params.get("sources"),
|
||||
"targets_out": params.get("targets"),
|
||||
}
|
||||
|
||||
for source_port, resource_name in output_resources.items():
|
||||
if resource_name:
|
||||
resource_last_writer[resource_name] = f"{node_id}:{source_port}"
|
||||
|
||||
return G
|
||||
|
||||
|
||||
def draw_protocol_graph(protocol_graph: WorkflowGraph, output_path: str):
|
||||
"""
|
||||
(辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图,用于可视化。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
G = nx.DiGraph()
|
||||
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template_name", node_id[:8]))
|
||||
G.add_node(node_id, label=label, **attrs)
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
G.add_edge(edge["source"], edge["target"])
|
||||
|
||||
plt.figure(figsize=(20, 15))
|
||||
try:
|
||||
pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
|
||||
except Exception:
|
||||
pos = nx.shell_layout(G) # Fallback layout
|
||||
|
||||
node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
|
||||
nx.draw(
|
||||
G,
|
||||
pos,
|
||||
with_labels=False,
|
||||
node_size=2500,
|
||||
node_color="skyblue",
|
||||
node_shape="o",
|
||||
edge_color="gray",
|
||||
width=1.5,
|
||||
arrowsize=15,
|
||||
)
|
||||
nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
|
||||
|
||||
plt.title("Chemical Protocol Workflow Graph", size=15)
|
||||
plt.savefig(output_path, dpi=300, bbox_inches="tight")
|
||||
plt.close()
|
||||
print(f" - Visualization saved to '{output_path}'")
|
||||
|
||||
|
||||
COMPASS = {"n", "e", "s", "w", "ne", "nw", "se", "sw", "c"}
|
||||
|
||||
|
||||
def _is_compass(port: str) -> bool:
|
||||
return isinstance(port, str) and port.lower() in COMPASS
|
||||
|
||||
|
||||
def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
|
||||
"""
|
||||
使用 Graphviz 端口语法绘制协议工作流图。
|
||||
- 若边上的 source_port/target_port 是 compass(n/e/s/w/...),直接用 compass。
|
||||
- 否则自动为节点创建 record 形状并定义命名端口 <portname>。
|
||||
最终由 PyGraphviz 渲染并输出到 output_path(后缀决定格式,如 .png/.svg/.pdf)。
|
||||
"""
|
||||
if not protocol_graph:
|
||||
print("Cannot draw graph: Graph object is empty.")
|
||||
return
|
||||
|
||||
# 1) 先用 networkx 搭建有向图,保留端口属性
|
||||
G = nx.DiGraph()
|
||||
for node_id, attrs in protocol_graph.nodes.items():
|
||||
label = attrs.get("description", attrs.get("template_name", node_id[:8]))
|
||||
# 保留一个干净的“中心标签”,用于放在 record 的中间槽
|
||||
G.add_node(node_id, _core_label=str(label), **{k: v for k, v in attrs.items() if k not in ("label",)})
|
||||
|
||||
edges_data = []
|
||||
in_ports_by_node = {} # 收集命名输入端口
|
||||
out_ports_by_node = {} # 收集命名输出端口
|
||||
|
||||
for edge in protocol_graph.edges:
|
||||
u = edge["source"]
|
||||
v = edge["target"]
|
||||
sp = edge.get("source_handle_key") or edge.get("source_port")
|
||||
tp = edge.get("target_handle_key") or edge.get("target_port")
|
||||
|
||||
# 记录到图里(保留原始端口信息)
|
||||
G.add_edge(u, v, source_handle_key=sp, target_handle_key=tp)
|
||||
edges_data.append((u, v, sp, tp))
|
||||
|
||||
# 如果不是 compass,就按“命名端口”先归类,等会儿给节点造 record
|
||||
if sp and not _is_compass(sp):
|
||||
out_ports_by_node.setdefault(u, set()).add(str(sp))
|
||||
if tp and not _is_compass(tp):
|
||||
in_ports_by_node.setdefault(v, set()).add(str(tp))
|
||||
|
||||
# 2) 转为 AGraph,使用 Graphviz 渲染
|
||||
A = to_agraph(G)
|
||||
A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
|
||||
A.node_attr.update(
|
||||
shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica"
|
||||
)
|
||||
A.edge_attr.update(arrowsize="0.8", color="#666666")
|
||||
|
||||
# 3) 为需要命名端口的节点设置 record 形状与 label
|
||||
# 左列 = 输入端口;中间 = 核心标签;右列 = 输出端口
|
||||
for n in A.nodes():
|
||||
node = A.get_node(n)
|
||||
core = G.nodes[n].get("_core_label", n)
|
||||
|
||||
in_ports = sorted(in_ports_by_node.get(n, []))
|
||||
out_ports = sorted(out_ports_by_node.get(n, []))
|
||||
|
||||
# 如果该节点涉及命名端口,则用 record;否则保留原 box
|
||||
if in_ports or out_ports:
|
||||
|
||||
def port_fields(ports):
|
||||
if not ports:
|
||||
return " " # 必须留一个空槽占位
|
||||
# 每个端口一个小格子,<p> name
|
||||
return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
|
||||
|
||||
left = port_fields(in_ports)
|
||||
right = port_fields(out_ports)
|
||||
|
||||
# 三栏:左(入) | 中(节点名) | 右(出)
|
||||
record_label = f"{{ {left} | {core} | {right} }}"
|
||||
node.attr.update(shape="record", label=record_label)
|
||||
else:
|
||||
# 没有命名端口:普通盒子,显示核心标签
|
||||
node.attr.update(label=str(core))
|
||||
|
||||
# 4) 给边设置 headport / tailport
|
||||
# - 若端口为 compass:直接用 compass(e.g., headport="e")
|
||||
# - 若端口为命名端口:使用在 record 中定义的 <port> 名(同名即可)
|
||||
for u, v, sp, tp in edges_data:
|
||||
e = A.get_edge(u, v)
|
||||
|
||||
# Graphviz 属性:tail 是源,head 是目标
|
||||
if sp:
|
||||
if _is_compass(sp):
|
||||
e.attr["tailport"] = sp.lower()
|
||||
else:
|
||||
# 与 record label 中 <port> 名一致;特殊字符已在 label 中做了清洗
|
||||
e.attr["tailport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(sp))
|
||||
|
||||
if tp:
|
||||
if _is_compass(tp):
|
||||
e.attr["headport"] = tp.lower()
|
||||
else:
|
||||
e.attr["headport"] = re.sub(r"[^A-Za-z0-9_:.|-]", "_", str(tp))
|
||||
|
||||
# 可选:若想让边更贴边缘,可设置 constraint/spline 等
|
||||
# e.attr["arrowhead"] = "vee"
|
||||
|
||||
# 5) 输出
|
||||
A.draw(output_path, prog="dot")
|
||||
print(f" - Port-aware workflow rendered to '{output_path}'")
|
||||
|
||||
|
||||
# ---------------- Registry Adapter ----------------
|
||||
|
||||
|
||||
class RegistryAdapter:
|
||||
"""根据 module 的类名(冒号右侧)反查 registry 的 resource_name(原 device_class),并抽取参数顺序"""
|
||||
|
||||
def __init__(self, device_registry: Dict[str, Any]):
|
||||
self.device_registry = device_registry or {}
|
||||
self.module_class_to_resource = self._build_module_class_index()
|
||||
|
||||
def _build_module_class_index(self) -> Dict[str, str]:
|
||||
idx = {}
|
||||
for resource_name, info in self.device_registry.items():
|
||||
module = info.get("module")
|
||||
if isinstance(module, str) and ":" in module:
|
||||
cls = module.split(":")[-1]
|
||||
idx[cls] = resource_name
|
||||
idx[cls.lower()] = resource_name
|
||||
return idx
|
||||
|
||||
def resolve_resource_by_classname(self, class_name: str) -> Optional[str]:
|
||||
if not class_name:
|
||||
return None
|
||||
return self.module_class_to_resource.get(class_name) or self.module_class_to_resource.get(class_name.lower())
|
||||
|
||||
def get_device_module(self, resource_name: Optional[str]) -> Optional[str]:
|
||||
if not resource_name:
|
||||
return None
|
||||
return self.device_registry.get(resource_name, {}).get("module")
|
||||
|
||||
def get_actions(self, resource_name: Optional[str]) -> Dict[str, Any]:
|
||||
if not resource_name:
|
||||
return {}
|
||||
return (self.device_registry.get(resource_name, {}).get("class", {}).get("action_value_mappings", {})) or {}
|
||||
|
||||
def get_action_schema(self, resource_name: Optional[str], template_name: str) -> Optional[Json]:
|
||||
return (self.get_actions(resource_name).get(template_name) or {}).get("schema")
|
||||
|
||||
def get_action_goal_default(self, resource_name: Optional[str], template_name: str) -> Json:
|
||||
return (self.get_actions(resource_name).get(template_name) or {}).get("goal_default", {}) or {}
|
||||
|
||||
def get_action_input_keys(self, resource_name: Optional[str], template_name: str) -> List[str]:
|
||||
schema = self.get_action_schema(resource_name, template_name) or {}
|
||||
goal = (schema.get("properties") or {}).get("goal") or {}
|
||||
props = goal.get("properties") or {}
|
||||
required = goal.get("required") or []
|
||||
return list(dict.fromkeys(required + list(props.keys())))
|
||||
356
unilabos/workflow/convert_from_json.py
Normal file
356
unilabos/workflow/convert_from_json.py
Normal file
@@ -0,0 +1,356 @@
|
||||
"""
|
||||
JSON 工作流转换模块
|
||||
|
||||
提供从多种 JSON 格式转换为统一工作流格式的功能。
|
||||
支持的格式:
|
||||
1. workflow/reagent 格式
|
||||
2. steps_info/labware_info 格式
|
||||
"""
|
||||
|
||||
import json
|
||||
from os import PathLike
|
||||
from pathlib import Path
|
||||
from typing import Any, Dict, List, Optional, Set, Tuple, Union
|
||||
|
||||
from unilabos.workflow.common import WorkflowGraph, build_protocol_graph
|
||||
from unilabos.registry.registry import lab_registry
|
||||
|
||||
|
||||
def get_action_handles(resource_name: str, template_name: str) -> Dict[str, List[str]]:
|
||||
"""
|
||||
从 registry 获取指定设备和动作的 handles 配置
|
||||
|
||||
Args:
|
||||
resource_name: 设备资源名称,如 "liquid_handler.prcxi"
|
||||
template_name: 动作模板名称,如 "transfer_liquid"
|
||||
|
||||
Returns:
|
||||
包含 source 和 target handler_keys 的字典:
|
||||
{"source": ["sources_out", "targets_out", ...], "target": ["sources", "targets", ...]}
|
||||
"""
|
||||
result = {"source": [], "target": []}
|
||||
|
||||
device_info = lab_registry.device_type_registry.get(resource_name, {})
|
||||
if not device_info:
|
||||
return result
|
||||
|
||||
action_mappings = device_info.get("class", {}).get("action_value_mappings", {})
|
||||
action_config = action_mappings.get(template_name, {})
|
||||
handles = action_config.get("handles", {})
|
||||
|
||||
if isinstance(handles, dict):
|
||||
# 处理 input handles (作为 target)
|
||||
for handle in handles.get("input", []):
|
||||
handler_key = handle.get("handler_key", "")
|
||||
if handler_key:
|
||||
result["source"].append(handler_key)
|
||||
# 处理 output handles (作为 source)
|
||||
for handle in handles.get("output", []):
|
||||
handler_key = handle.get("handler_key", "")
|
||||
if handler_key:
|
||||
result["target"].append(handler_key)
|
||||
|
||||
return result
|
||||
|
||||
|
||||
def validate_workflow_handles(graph: WorkflowGraph) -> Tuple[bool, List[str]]:
|
||||
"""
|
||||
校验工作流图中所有边的句柄配置是否正确
|
||||
|
||||
Args:
|
||||
graph: 工作流图对象
|
||||
|
||||
Returns:
|
||||
(is_valid, errors): 是否有效,错误信息列表
|
||||
"""
|
||||
errors = []
|
||||
nodes = graph.nodes
|
||||
|
||||
for edge in graph.edges:
|
||||
left_uuid = edge.get("source")
|
||||
right_uuid = edge.get("target")
|
||||
# target_handle_key是target, right的输入节点(入节点)
|
||||
# source_handle_key是source, left的输出节点(出节点)
|
||||
right_source_conn_key = edge.get("target_handle_key", "")
|
||||
left_target_conn_key = edge.get("source_handle_key", "")
|
||||
|
||||
# 获取源节点和目标节点信息
|
||||
left_node = nodes.get(left_uuid, {})
|
||||
right_node = nodes.get(right_uuid, {})
|
||||
|
||||
left_res_name = left_node.get("resource_name", "")
|
||||
left_template_name = left_node.get("template_name", "")
|
||||
right_res_name = right_node.get("resource_name", "")
|
||||
right_template_name = right_node.get("template_name", "")
|
||||
|
||||
# 获取源节点的 output handles
|
||||
left_node_handles = get_action_handles(left_res_name, left_template_name)
|
||||
target_valid_keys = left_node_handles.get("target", [])
|
||||
target_valid_keys.append("ready")
|
||||
|
||||
# 获取目标节点的 input handles
|
||||
right_node_handles = get_action_handles(right_res_name, right_template_name)
|
||||
source_valid_keys = right_node_handles.get("source", [])
|
||||
source_valid_keys.append("ready")
|
||||
|
||||
# 如果节点配置了 output handles,则 source_port 必须有效
|
||||
if not right_source_conn_key:
|
||||
node_name = left_node.get("name", left_uuid[:8])
|
||||
errors.append(f"源节点 '{node_name}' 的 source_handle_key 为空," f"应设置为: {source_valid_keys}")
|
||||
elif right_source_conn_key not in source_valid_keys:
|
||||
node_name = left_node.get("name", left_uuid[:8])
|
||||
errors.append(
|
||||
f"源节点 '{node_name}' 的 source 端点 '{right_source_conn_key}' 不存在," f"支持的端点: {source_valid_keys}"
|
||||
)
|
||||
|
||||
# 如果节点配置了 input handles,则 target_port 必须有效
|
||||
if not left_target_conn_key:
|
||||
node_name = right_node.get("name", right_uuid[:8])
|
||||
errors.append(f"目标节点 '{node_name}' 的 target_handle_key 为空," f"应设置为: {target_valid_keys}")
|
||||
elif left_target_conn_key not in target_valid_keys:
|
||||
node_name = right_node.get("name", right_uuid[:8])
|
||||
errors.append(
|
||||
f"目标节点 '{node_name}' 的 target 端点 '{left_target_conn_key}' 不存在,"
|
||||
f"支持的端点: {target_valid_keys}"
|
||||
)
|
||||
|
||||
return len(errors) == 0, errors
|
||||
|
||||
|
||||
# action 到 resource_name 的映射
|
||||
ACTION_RESOURCE_MAPPING: Dict[str, str] = {
|
||||
# 生物实验操作
|
||||
"transfer_liquid": "liquid_handler.prcxi",
|
||||
"transfer": "liquid_handler.prcxi",
|
||||
"incubation": "incubator.prcxi",
|
||||
"move_labware": "labware_mover.prcxi",
|
||||
"oscillation": "shaker.prcxi",
|
||||
# 有机化学操作
|
||||
"HeatChillToTemp": "heatchill.chemputer",
|
||||
"StopHeatChill": "heatchill.chemputer",
|
||||
"StartHeatChill": "heatchill.chemputer",
|
||||
"HeatChill": "heatchill.chemputer",
|
||||
"Dissolve": "stirrer.chemputer",
|
||||
"Transfer": "liquid_handler.chemputer",
|
||||
"Evaporate": "rotavap.chemputer",
|
||||
"Recrystallize": "reactor.chemputer",
|
||||
"Filter": "filter.chemputer",
|
||||
"Dry": "dryer.chemputer",
|
||||
"Add": "liquid_handler.chemputer",
|
||||
}
|
||||
|
||||
|
||||
def normalize_steps(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
将不同格式的步骤数据规范化为统一格式
|
||||
|
||||
支持的输入格式:
|
||||
- action + parameters
|
||||
- action + action_args
|
||||
- operation + parameters
|
||||
|
||||
Args:
|
||||
data: 原始步骤数据列表
|
||||
|
||||
Returns:
|
||||
规范化后的步骤列表,格式为 [{"action": str, "parameters": dict, "description": str?, "step_number": int?}, ...]
|
||||
"""
|
||||
normalized = []
|
||||
for idx, step in enumerate(data):
|
||||
# 获取动作名称(支持 action 或 operation 字段)
|
||||
action = step.get("action") or step.get("operation")
|
||||
if not action:
|
||||
continue
|
||||
|
||||
# 获取参数(支持 parameters 或 action_args 字段)
|
||||
raw_params = step.get("parameters") or step.get("action_args") or {}
|
||||
params = dict(raw_params)
|
||||
|
||||
# 规范化 source/target -> sources/targets
|
||||
if "source" in raw_params and "sources" not in raw_params:
|
||||
params["sources"] = raw_params["source"]
|
||||
if "target" in raw_params and "targets" not in raw_params:
|
||||
params["targets"] = raw_params["target"]
|
||||
|
||||
# 获取描述(支持 description 或 purpose 字段)
|
||||
description = step.get("description") or step.get("purpose")
|
||||
|
||||
# 获取步骤编号(优先使用原始数据中的 step_number,否则使用索引+1)
|
||||
step_number = step.get("step_number", idx + 1)
|
||||
|
||||
step_dict = {"action": action, "parameters": params, "step_number": step_number}
|
||||
if description:
|
||||
step_dict["description"] = description
|
||||
|
||||
normalized.append(step_dict)
|
||||
|
||||
return normalized
|
||||
|
||||
|
||||
def normalize_labware(data: List[Dict[str, Any]]) -> Dict[str, Dict[str, Any]]:
|
||||
"""
|
||||
将不同格式的 labware 数据规范化为统一的字典格式
|
||||
|
||||
支持的输入格式:
|
||||
- reagent_name + material_name + positions
|
||||
- name + labware + slot
|
||||
|
||||
Args:
|
||||
data: 原始 labware 数据列表
|
||||
|
||||
Returns:
|
||||
规范化后的 labware 字典,格式为 {name: {"slot": int, "labware": str, "well": list, "type": str, "role": str, "name": str}, ...}
|
||||
"""
|
||||
labware = {}
|
||||
for item in data:
|
||||
# 获取 key 名称(优先使用 reagent_name,其次是 material_name 或 name)
|
||||
reagent_name = item.get("reagent_name")
|
||||
key = reagent_name or item.get("material_name") or item.get("name")
|
||||
if not key:
|
||||
continue
|
||||
|
||||
key = str(key)
|
||||
|
||||
# 处理重复 key,自动添加后缀
|
||||
idx = 1
|
||||
original_key = key
|
||||
while key in labware:
|
||||
idx += 1
|
||||
key = f"{original_key}_{idx}"
|
||||
|
||||
labware[key] = {
|
||||
"slot": item.get("positions") or item.get("slot"),
|
||||
"labware": item.get("material_name") or item.get("labware"),
|
||||
"well": item.get("well", []),
|
||||
"type": item.get("type", "reagent"),
|
||||
"role": item.get("role", ""),
|
||||
"name": key,
|
||||
}
|
||||
|
||||
return labware
|
||||
|
||||
|
||||
def convert_from_json(
|
||||
data: Union[str, PathLike, Dict[str, Any]],
|
||||
workstation_name: str = "PRCXi",
|
||||
validate: bool = True,
|
||||
) -> WorkflowGraph:
|
||||
"""
|
||||
从 JSON 数据或文件转换为 WorkflowGraph
|
||||
|
||||
支持的 JSON 格式:
|
||||
1. {"workflow": [...], "reagent": {...}} - 直接格式
|
||||
2. {"steps_info": [...], "labware_info": [...]} - 需要规范化的格式
|
||||
|
||||
Args:
|
||||
data: JSON 文件路径、字典数据、或 JSON 字符串
|
||||
workstation_name: 工作站名称,默认 "PRCXi"
|
||||
validate: 是否校验句柄配置,默认 True
|
||||
|
||||
Returns:
|
||||
WorkflowGraph: 构建好的工作流图
|
||||
|
||||
Raises:
|
||||
ValueError: 不支持的 JSON 格式 或 句柄校验失败
|
||||
FileNotFoundError: 文件不存在
|
||||
json.JSONDecodeError: JSON 解析失败
|
||||
"""
|
||||
# 处理输入数据
|
||||
if isinstance(data, (str, PathLike)):
|
||||
path = Path(data)
|
||||
if path.exists():
|
||||
with path.open("r", encoding="utf-8") as fp:
|
||||
json_data = json.load(fp)
|
||||
elif isinstance(data, str):
|
||||
# 尝试作为 JSON 字符串解析
|
||||
json_data = json.loads(data)
|
||||
else:
|
||||
raise FileNotFoundError(f"文件不存在: {data}")
|
||||
elif isinstance(data, dict):
|
||||
json_data = data
|
||||
else:
|
||||
raise TypeError(f"不支持的数据类型: {type(data)}")
|
||||
|
||||
# 根据格式解析数据
|
||||
if "workflow" in json_data and "reagent" in json_data:
|
||||
# 格式1: workflow/reagent(已经是规范格式)
|
||||
protocol_steps = json_data["workflow"]
|
||||
labware_info = json_data["reagent"]
|
||||
elif "steps_info" in json_data and "labware_info" in json_data:
|
||||
# 格式2: steps_info/labware_info(需要规范化)
|
||||
protocol_steps = normalize_steps(json_data["steps_info"])
|
||||
labware_info = normalize_labware(json_data["labware_info"])
|
||||
elif "steps" in json_data and "labware" in json_data:
|
||||
# 格式3: steps/labware(另一种常见格式)
|
||||
protocol_steps = normalize_steps(json_data["steps"])
|
||||
if isinstance(json_data["labware"], list):
|
||||
labware_info = normalize_labware(json_data["labware"])
|
||||
else:
|
||||
labware_info = json_data["labware"]
|
||||
else:
|
||||
raise ValueError(
|
||||
"不支持的 JSON 格式。支持的格式:\n"
|
||||
"1. {'workflow': [...], 'reagent': {...}}\n"
|
||||
"2. {'steps_info': [...], 'labware_info': [...]}\n"
|
||||
"3. {'steps': [...], 'labware': [...]}"
|
||||
)
|
||||
|
||||
# 构建工作流图
|
||||
graph = build_protocol_graph(
|
||||
labware_info=labware_info,
|
||||
protocol_steps=protocol_steps,
|
||||
workstation_name=workstation_name,
|
||||
action_resource_mapping=ACTION_RESOURCE_MAPPING,
|
||||
)
|
||||
|
||||
# 校验句柄配置
|
||||
if validate:
|
||||
is_valid, errors = validate_workflow_handles(graph)
|
||||
if not is_valid:
|
||||
import warnings
|
||||
|
||||
for error in errors:
|
||||
warnings.warn(f"句柄校验警告: {error}")
|
||||
|
||||
return graph
|
||||
|
||||
|
||||
def convert_json_to_node_link(
|
||||
data: Union[str, PathLike, Dict[str, Any]],
|
||||
workstation_name: str = "PRCXi",
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
将 JSON 数据转换为 node-link 格式的字典
|
||||
|
||||
Args:
|
||||
data: JSON 文件路径、字典数据、或 JSON 字符串
|
||||
workstation_name: 工作站名称,默认 "PRCXi"
|
||||
|
||||
Returns:
|
||||
Dict: node-link 格式的工作流数据
|
||||
"""
|
||||
graph = convert_from_json(data, workstation_name)
|
||||
return graph.to_node_link_dict()
|
||||
|
||||
|
||||
def convert_json_to_workflow_list(
|
||||
data: Union[str, PathLike, Dict[str, Any]],
|
||||
workstation_name: str = "PRCXi",
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
将 JSON 数据转换为工作流列表格式
|
||||
|
||||
Args:
|
||||
data: JSON 文件路径、字典数据、或 JSON 字符串
|
||||
workstation_name: 工作站名称,默认 "PRCXi"
|
||||
|
||||
Returns:
|
||||
List: 工作流节点列表
|
||||
"""
|
||||
graph = convert_from_json(data, workstation_name)
|
||||
return graph.to_dict()
|
||||
|
||||
|
||||
# 为了向后兼容,保留下划线前缀的别名
|
||||
_normalize_steps = normalize_steps
|
||||
_normalize_labware = normalize_labware
|
||||
241
unilabos/workflow/from_python_script.py
Normal file
241
unilabos/workflow/from_python_script.py
Normal file
@@ -0,0 +1,241 @@
|
||||
import ast
|
||||
import json
|
||||
from typing import Dict, List, Any, Tuple, Optional
|
||||
|
||||
from .common import WorkflowGraph, RegistryAdapter
|
||||
|
||||
Json = Dict[str, Any]
|
||||
|
||||
# ---------------- Converter ----------------
|
||||
|
||||
class DeviceMethodConverter:
|
||||
"""
|
||||
- 字段统一:resource_name(原 device_class)、template_name(原 action_key)
|
||||
- params 单层;inputs 使用 'params.' 前缀
|
||||
- SimpleGraph.add_workflow_node 负责变量连线与边
|
||||
"""
|
||||
def __init__(self, device_registry: Optional[Dict[str, Any]] = None):
|
||||
self.graph = WorkflowGraph()
|
||||
self.variable_sources: Dict[str, Dict[str, Any]] = {} # var -> {node_id, output_name}
|
||||
self.instance_to_resource: Dict[str, Optional[str]] = {} # 实例名 -> resource_name
|
||||
self.node_id_counter: int = 0
|
||||
self.registry = RegistryAdapter(device_registry or {})
|
||||
|
||||
# ---- helpers ----
|
||||
def _new_node_id(self) -> int:
|
||||
nid = self.node_id_counter
|
||||
self.node_id_counter += 1
|
||||
return nid
|
||||
|
||||
def _assign_targets(self, targets) -> List[str]:
|
||||
names: List[str] = []
|
||||
import ast
|
||||
if isinstance(targets, ast.Tuple):
|
||||
for elt in targets.elts:
|
||||
if isinstance(elt, ast.Name):
|
||||
names.append(elt.id)
|
||||
elif isinstance(targets, ast.Name):
|
||||
names.append(targets.id)
|
||||
return names
|
||||
|
||||
def _extract_device_instantiation(self, node) -> Optional[Tuple[str, str]]:
|
||||
import ast
|
||||
if not isinstance(node.value, ast.Call):
|
||||
return None
|
||||
callee = node.value.func
|
||||
if isinstance(callee, ast.Name):
|
||||
class_name = callee.id
|
||||
elif isinstance(callee, ast.Attribute) and isinstance(callee.value, ast.Name):
|
||||
class_name = callee.attr
|
||||
else:
|
||||
return None
|
||||
if isinstance(node.targets[0], ast.Name):
|
||||
instance = node.targets[0].id
|
||||
return instance, class_name
|
||||
return None
|
||||
|
||||
def _extract_call(self, call) -> Tuple[str, str, Dict[str, Any], str]:
|
||||
import ast
|
||||
owner_name, method_name, call_kind = "", "", "func"
|
||||
if isinstance(call.func, ast.Attribute):
|
||||
method_name = call.func.attr
|
||||
if isinstance(call.func.value, ast.Name):
|
||||
owner_name = call.func.value.id
|
||||
call_kind = "instance" if owner_name in self.instance_to_resource else "class_or_module"
|
||||
elif isinstance(call.func.value, ast.Attribute) and isinstance(call.func.value.value, ast.Name):
|
||||
owner_name = call.func.value.attr
|
||||
call_kind = "class_or_module"
|
||||
elif isinstance(call.func, ast.Name):
|
||||
method_name = call.func.id
|
||||
call_kind = "func"
|
||||
|
||||
def pack(node):
|
||||
if isinstance(node, ast.Name):
|
||||
return {"type": "variable", "value": node.id}
|
||||
if isinstance(node, ast.Constant):
|
||||
return {"type": "constant", "value": node.value}
|
||||
if isinstance(node, ast.Dict):
|
||||
return {"type": "dict", "value": self._parse_dict(node)}
|
||||
if isinstance(node, ast.List):
|
||||
return {"type": "list", "value": self._parse_list(node)}
|
||||
return {"type": "raw", "value": ast.unparse(node) if hasattr(ast, "unparse") else str(node)}
|
||||
|
||||
args: Dict[str, Any] = {}
|
||||
pos: List[Any] = []
|
||||
for a in call.args:
|
||||
pos.append(pack(a))
|
||||
for kw in call.keywords:
|
||||
args[kw.arg] = pack(kw.value)
|
||||
if pos:
|
||||
args["_positional"] = pos
|
||||
return owner_name, method_name, args, call_kind
|
||||
|
||||
def _parse_dict(self, node) -> Dict[str, Any]:
|
||||
import ast
|
||||
out: Dict[str, Any] = {}
|
||||
for k, v in zip(node.keys, node.values):
|
||||
if isinstance(k, ast.Constant):
|
||||
key = str(k.value)
|
||||
if isinstance(v, ast.Name):
|
||||
out[key] = f"var:{v.id}"
|
||||
elif isinstance(v, ast.Constant):
|
||||
out[key] = v.value
|
||||
elif isinstance(v, ast.Dict):
|
||||
out[key] = self._parse_dict(v)
|
||||
elif isinstance(v, ast.List):
|
||||
out[key] = self._parse_list(v)
|
||||
return out
|
||||
|
||||
def _parse_list(self, node) -> List[Any]:
|
||||
import ast
|
||||
out: List[Any] = []
|
||||
for elt in node.elts:
|
||||
if isinstance(elt, ast.Name):
|
||||
out.append(f"var:{elt.id}")
|
||||
elif isinstance(elt, ast.Constant):
|
||||
out.append(elt.value)
|
||||
elif isinstance(elt, ast.Dict):
|
||||
out.append(self._parse_dict(elt))
|
||||
elif isinstance(elt, ast.List):
|
||||
out.append(self._parse_list(elt))
|
||||
return out
|
||||
|
||||
def _normalize_var_tokens(self, x: Any) -> Any:
|
||||
if isinstance(x, str) and x.startswith("var:"):
|
||||
return {"__var__": x[4:]}
|
||||
if isinstance(x, list):
|
||||
return [self._normalize_var_tokens(i) for i in x]
|
||||
if isinstance(x, dict):
|
||||
return {k: self._normalize_var_tokens(v) for k, v in x.items()}
|
||||
return x
|
||||
|
||||
def _make_params_payload(self, resource_name: Optional[str], template_name: str, call_args: Dict[str, Any]) -> Dict[str, Any]:
|
||||
input_keys = self.registry.get_action_input_keys(resource_name, template_name) if resource_name else []
|
||||
defaults = self.registry.get_action_goal_default(resource_name, template_name) if resource_name else {}
|
||||
params: Dict[str, Any] = dict(defaults)
|
||||
|
||||
def unpack(p):
|
||||
t, v = p.get("type"), p.get("value")
|
||||
if t == "variable":
|
||||
return {"__var__": v}
|
||||
if t == "dict":
|
||||
return self._normalize_var_tokens(v)
|
||||
if t == "list":
|
||||
return self._normalize_var_tokens(v)
|
||||
return v
|
||||
|
||||
for k, p in call_args.items():
|
||||
if k == "_positional":
|
||||
continue
|
||||
params[k] = unpack(p)
|
||||
|
||||
pos = call_args.get("_positional", [])
|
||||
if pos:
|
||||
if input_keys:
|
||||
for i, p in enumerate(pos):
|
||||
if i >= len(input_keys):
|
||||
break
|
||||
name = input_keys[i]
|
||||
if name in params:
|
||||
continue
|
||||
params[name] = unpack(p)
|
||||
else:
|
||||
for i, p in enumerate(pos):
|
||||
params[f"arg_{i}"] = unpack(p)
|
||||
return params
|
||||
|
||||
# ---- handlers ----
|
||||
def _on_assign(self, stmt):
|
||||
import ast
|
||||
inst = self._extract_device_instantiation(stmt)
|
||||
if inst:
|
||||
instance, code_class = inst
|
||||
resource_name = self.registry.resolve_resource_by_classname(code_class)
|
||||
self.instance_to_resource[instance] = resource_name
|
||||
return
|
||||
|
||||
if isinstance(stmt.value, ast.Call):
|
||||
owner, method, call_args, kind = self._extract_call(stmt.value)
|
||||
if kind == "instance":
|
||||
device_key = owner
|
||||
resource_name = self.instance_to_resource.get(owner)
|
||||
else:
|
||||
device_key = owner
|
||||
resource_name = self.registry.resolve_resource_by_classname(owner)
|
||||
|
||||
module = self.registry.get_device_module(resource_name)
|
||||
params = self._make_params_payload(resource_name, method, call_args)
|
||||
|
||||
nid = self._new_node_id()
|
||||
self.graph.add_workflow_node(
|
||||
nid,
|
||||
device_key=device_key,
|
||||
resource_name=resource_name, # ✅
|
||||
module=module,
|
||||
template_name=method, # ✅
|
||||
params=params,
|
||||
variable_sources=self.variable_sources,
|
||||
add_ready_if_no_vars=True,
|
||||
prev_node_id=(nid - 1) if nid > 0 else None,
|
||||
)
|
||||
|
||||
out_vars = self._assign_targets(stmt.targets[0])
|
||||
for var in out_vars:
|
||||
self.variable_sources[var] = {"node_id": nid, "output_name": "result"}
|
||||
|
||||
def _on_expr(self, stmt):
|
||||
import ast
|
||||
if not isinstance(stmt.value, ast.Call):
|
||||
return
|
||||
owner, method, call_args, kind = self._extract_call(stmt.value)
|
||||
if kind == "instance":
|
||||
device_key = owner
|
||||
resource_name = self.instance_to_resource.get(owner)
|
||||
else:
|
||||
device_key = owner
|
||||
resource_name = self.registry.resolve_resource_by_classname(owner)
|
||||
|
||||
module = self.registry.get_device_module(resource_name)
|
||||
params = self._make_params_payload(resource_name, method, call_args)
|
||||
|
||||
nid = self._new_node_id()
|
||||
self.graph.add_workflow_node(
|
||||
nid,
|
||||
device_key=device_key,
|
||||
resource_name=resource_name, # ✅
|
||||
module=module,
|
||||
template_name=method, # ✅
|
||||
params=params,
|
||||
variable_sources=self.variable_sources,
|
||||
add_ready_if_no_vars=True,
|
||||
prev_node_id=(nid - 1) if nid > 0 else None,
|
||||
)
|
||||
|
||||
def convert(self, python_code: str):
|
||||
tree = ast.parse(python_code)
|
||||
for stmt in tree.body:
|
||||
if isinstance(stmt, ast.Assign):
|
||||
self._on_assign(stmt)
|
||||
elif isinstance(stmt, ast.Expr):
|
||||
self._on_expr(stmt)
|
||||
return self
|
||||
131
unilabos/workflow/from_xdl.py
Normal file
131
unilabos/workflow/from_xdl.py
Normal file
@@ -0,0 +1,131 @@
|
||||
from typing import List, Any, Dict
|
||||
import xml.etree.ElementTree as ET
|
||||
|
||||
|
||||
def convert_to_type(val: str) -> Any:
|
||||
"""将字符串值转换为适当的数据类型"""
|
||||
if val == "True":
|
||||
return True
|
||||
if val == "False":
|
||||
return False
|
||||
if val == "?":
|
||||
return None
|
||||
if val.endswith(" g"):
|
||||
return float(val.split(" ")[0])
|
||||
if val.endswith("mg"):
|
||||
return float(val.split("mg")[0])
|
||||
elif val.endswith("mmol"):
|
||||
return float(val.split("mmol")[0]) / 1000
|
||||
elif val.endswith("mol"):
|
||||
return float(val.split("mol")[0])
|
||||
elif val.endswith("ml"):
|
||||
return float(val.split("ml")[0])
|
||||
elif val.endswith("RPM"):
|
||||
return float(val.split("RPM")[0])
|
||||
elif val.endswith(" °C"):
|
||||
return float(val.split(" ")[0])
|
||||
elif val.endswith(" %"):
|
||||
return float(val.split(" ")[0])
|
||||
return val
|
||||
|
||||
|
||||
def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
|
||||
"""展平嵌套的XDL程序结构"""
|
||||
flattened_operations = []
|
||||
TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||
|
||||
def extract_operations(element: ET.Element):
|
||||
if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
|
||||
if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
|
||||
flattened_operations.append(element)
|
||||
|
||||
for child in element:
|
||||
extract_operations(child)
|
||||
|
||||
for child in procedure_elem:
|
||||
extract_operations(child)
|
||||
|
||||
return flattened_operations
|
||||
|
||||
|
||||
def parse_xdl_content(xdl_content: str) -> tuple:
|
||||
"""解析XDL内容"""
|
||||
try:
|
||||
xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
|
||||
root = ET.fromstring(xdl_content_cleaned)
|
||||
|
||||
synthesis_elem = root.find("Synthesis")
|
||||
if synthesis_elem is None:
|
||||
return None, None, None
|
||||
|
||||
# 解析硬件组件
|
||||
hardware_elem = synthesis_elem.find("Hardware")
|
||||
hardware = []
|
||||
if hardware_elem is not None:
|
||||
hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
|
||||
|
||||
# 解析试剂
|
||||
reagents_elem = synthesis_elem.find("Reagents")
|
||||
reagents = []
|
||||
if reagents_elem is not None:
|
||||
reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
|
||||
|
||||
# 解析程序
|
||||
procedure_elem = synthesis_elem.find("Procedure")
|
||||
if procedure_elem is None:
|
||||
return None, None, None
|
||||
|
||||
flattened_operations = flatten_xdl_procedure(procedure_elem)
|
||||
return hardware, reagents, flattened_operations
|
||||
|
||||
except ET.ParseError as e:
|
||||
raise ValueError(f"Invalid XDL format: {e}")
|
||||
|
||||
|
||||
def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
|
||||
"""
|
||||
将XDL XML格式转换为标准的字典格式
|
||||
|
||||
Args:
|
||||
xdl_content: XDL XML内容
|
||||
|
||||
Returns:
|
||||
转换结果,包含步骤和器材信息
|
||||
"""
|
||||
try:
|
||||
hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
|
||||
if hardware is None:
|
||||
return {"error": "Failed to parse XDL content", "success": False}
|
||||
|
||||
# 将XDL元素转换为字典格式
|
||||
steps_data = []
|
||||
for elem in flattened_operations:
|
||||
# 转换参数类型
|
||||
parameters = {}
|
||||
for key, val in elem.attrib.items():
|
||||
converted_val = convert_to_type(val)
|
||||
if converted_val is not None:
|
||||
parameters[key] = converted_val
|
||||
|
||||
step_dict = {
|
||||
"operation": elem.tag,
|
||||
"parameters": parameters,
|
||||
"description": elem.get("purpose", f"Operation: {elem.tag}"),
|
||||
}
|
||||
steps_data.append(step_dict)
|
||||
|
||||
# 合并硬件和试剂为统一的labware_info格式
|
||||
labware_data = []
|
||||
labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
|
||||
labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
|
||||
|
||||
return {
|
||||
"success": True,
|
||||
"steps": steps_data,
|
||||
"labware": labware_data,
|
||||
"message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
|
||||
}
|
||||
|
||||
except Exception as e:
|
||||
error_msg = f"XDL conversion failed: {str(e)}"
|
||||
return {"error": error_msg, "success": False}
|
||||
138
unilabos/workflow/wf_utils.py
Normal file
138
unilabos/workflow/wf_utils.py
Normal file
@@ -0,0 +1,138 @@
|
||||
"""
|
||||
工作流工具模块
|
||||
|
||||
提供工作流上传等功能
|
||||
"""
|
||||
|
||||
import json
|
||||
import os
|
||||
import uuid
|
||||
from typing import Any, Dict, List, Optional
|
||||
|
||||
from unilabos.utils.banner_print import print_status
|
||||
|
||||
|
||||
def _is_node_link_format(data: Dict[str, Any]) -> bool:
|
||||
"""检查数据是否为 node-link 格式"""
|
||||
return "nodes" in data and "edges" in data
|
||||
|
||||
|
||||
def _convert_to_node_link(workflow_file: str, workflow_data: Dict[str, Any]) -> Dict[str, Any]:
|
||||
"""
|
||||
将非 node-link 格式的工作流数据转换为 node-link 格式
|
||||
|
||||
Args:
|
||||
workflow_file: 工作流文件路径(用于日志)
|
||||
workflow_data: 原始工作流数据
|
||||
|
||||
Returns:
|
||||
node-link 格式的工作流数据
|
||||
"""
|
||||
from unilabos.workflow.convert_from_json import convert_json_to_node_link
|
||||
|
||||
print_status(f"检测到非 node-link 格式,正在转换...", "info")
|
||||
node_link_data = convert_json_to_node_link(workflow_data)
|
||||
print_status(f"转换完成", "success")
|
||||
return node_link_data
|
||||
|
||||
|
||||
def upload_workflow(
|
||||
workflow_file: str,
|
||||
workflow_name: Optional[str] = None,
|
||||
tags: Optional[List[str]] = None,
|
||||
published: bool = False,
|
||||
) -> Dict[str, Any]:
|
||||
"""
|
||||
上传工作流到服务器
|
||||
|
||||
支持的输入格式:
|
||||
1. node-link 格式: {"nodes": [...], "edges": [...]}
|
||||
2. workflow/reagent 格式: {"workflow": [...], "reagent": {...}}
|
||||
3. steps_info/labware_info 格式: {"steps_info": [...], "labware_info": [...]}
|
||||
4. steps/labware 格式: {"steps": [...], "labware": [...]}
|
||||
|
||||
Args:
|
||||
workflow_file: 工作流文件路径(JSON格式)
|
||||
workflow_name: 工作流名称,如果不提供则从文件中读取或使用文件名
|
||||
tags: 工作流标签列表,默认为空列表
|
||||
published: 是否发布工作流,默认为False
|
||||
|
||||
Returns:
|
||||
Dict: API响应数据
|
||||
"""
|
||||
# 延迟导入,避免在配置文件加载之前初始化 http_client
|
||||
from unilabos.app.web import http_client
|
||||
|
||||
if not os.path.exists(workflow_file):
|
||||
print_status(f"工作流文件不存在: {workflow_file}", "error")
|
||||
return {"code": -1, "message": f"文件不存在: {workflow_file}"}
|
||||
|
||||
# 读取工作流文件
|
||||
try:
|
||||
with open(workflow_file, "r", encoding="utf-8") as f:
|
||||
workflow_data = json.load(f)
|
||||
except json.JSONDecodeError as e:
|
||||
print_status(f"工作流文件JSON解析失败: {e}", "error")
|
||||
return {"code": -1, "message": f"JSON解析失败: {e}"}
|
||||
|
||||
# 自动检测并转换格式
|
||||
if not _is_node_link_format(workflow_data):
|
||||
try:
|
||||
workflow_data = _convert_to_node_link(workflow_file, workflow_data)
|
||||
except Exception as e:
|
||||
print_status(f"工作流格式转换失败: {e}", "error")
|
||||
return {"code": -1, "message": f"格式转换失败: {e}"}
|
||||
|
||||
# 提取工作流数据
|
||||
nodes = workflow_data.get("nodes", [])
|
||||
edges = workflow_data.get("edges", [])
|
||||
workflow_uuid_val = workflow_data.get("workflow_uuid", str(uuid.uuid4()))
|
||||
wf_name_from_file = workflow_data.get("workflow_name", os.path.basename(workflow_file).replace(".json", ""))
|
||||
|
||||
# 确定工作流名称
|
||||
final_name = workflow_name or wf_name_from_file
|
||||
|
||||
print_status(f"正在上传工作流: {final_name}", "info")
|
||||
print_status(f" - 节点数量: {len(nodes)}", "info")
|
||||
print_status(f" - 边数量: {len(edges)}", "info")
|
||||
print_status(f" - 标签: {tags or []}", "info")
|
||||
print_status(f" - 发布状态: {published}", "info")
|
||||
|
||||
# 调用 http_client 上传
|
||||
result = http_client.workflow_import(
|
||||
name=final_name,
|
||||
workflow_uuid=workflow_uuid_val,
|
||||
workflow_name=final_name,
|
||||
nodes=nodes,
|
||||
edges=edges,
|
||||
tags=tags,
|
||||
published=published,
|
||||
)
|
||||
|
||||
if result.get("code") == 0:
|
||||
data = result.get("data", {})
|
||||
print_status("工作流上传成功!", "success")
|
||||
print_status(f" - UUID: {data.get('uuid', 'N/A')}", "info")
|
||||
print_status(f" - 名称: {data.get('name', 'N/A')}", "info")
|
||||
else:
|
||||
print_status(f"工作流上传失败: {result.get('message', '未知错误')}", "error")
|
||||
|
||||
return result
|
||||
|
||||
|
||||
def handle_workflow_upload_command(args_dict: Dict[str, Any]) -> None:
|
||||
"""
|
||||
处理 workflow_upload 子命令
|
||||
|
||||
Args:
|
||||
args_dict: 命令行参数字典
|
||||
"""
|
||||
workflow_file = args_dict.get("workflow_file")
|
||||
workflow_name = args_dict.get("workflow_name")
|
||||
tags = args_dict.get("tags", [])
|
||||
published = args_dict.get("published", False)
|
||||
|
||||
if workflow_file:
|
||||
upload_workflow(workflow_file, workflow_name, tags, published)
|
||||
else:
|
||||
print_status("未指定工作流文件路径,请使用 -f/--workflow_file 参数", "error")
|
||||
@@ -2,7 +2,7 @@
|
||||
<?xml-model href="http://download.ros.org/schema/package_format3.xsd" schematypens="http://www.w3.org/2001/XMLSchema"?>
|
||||
<package format="3">
|
||||
<name>unilabos_msgs</name>
|
||||
<version>0.10.11</version>
|
||||
<version>0.10.12</version>
|
||||
<description>ROS2 Messages package for unilabos devices</description>
|
||||
<maintainer email="changjh@pku.edu.cn">Junhan Chang</maintainer>
|
||||
<maintainer email="18435084+Xuwznln@users.noreply.github.com">Xuwznln</maintainer>
|
||||
|
||||
Reference in New Issue
Block a user