mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2026-02-04 13:25:13 +00:00
Compare commits
3 Commits
799813f85b
...
v0.10.13
| Author | SHA1 | Date | |
|---|---|---|---|
|
5dc81ec9be | ||
|
13a6795657 | ||
|
53219d8b04 |
@@ -2,6 +2,7 @@ import json
|
|||||||
import logging
|
import logging
|
||||||
import traceback
|
import traceback
|
||||||
import uuid
|
import uuid
|
||||||
|
import xml.etree.ElementTree as ET
|
||||||
from typing import Any, Dict, List
|
from typing import Any, Dict, List
|
||||||
|
|
||||||
import networkx as nx
|
import networkx as nx
|
||||||
@@ -24,15 +25,7 @@ class SimpleGraph:
|
|||||||
|
|
||||||
def add_edge(self, source, target, **attrs):
|
def add_edge(self, source, target, **attrs):
|
||||||
"""添加边"""
|
"""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)
|
self.edges.append(edge)
|
||||||
|
|
||||||
def to_dict(self):
|
def to_dict(self):
|
||||||
@@ -49,7 +42,6 @@ class SimpleGraph:
|
|||||||
"multigraph": False,
|
"multigraph": False,
|
||||||
"graph": {},
|
"graph": {},
|
||||||
"nodes": nodes_list,
|
"nodes": nodes_list,
|
||||||
"edges": self.edges,
|
|
||||||
"links": self.edges,
|
"links": self.edges,
|
||||||
}
|
}
|
||||||
|
|
||||||
@@ -66,8 +58,495 @@ def extract_json_from_markdown(text: str) -> str:
|
|||||||
return text
|
return text
|
||||||
|
|
||||||
|
|
||||||
|
def convert_to_type(val: str) -> Any:
|
||||||
|
"""将字符串值转换为适当的数据类型"""
|
||||||
|
if val == "True":
|
||||||
|
return True
|
||||||
|
if val == "False":
|
||||||
|
return False
|
||||||
|
if val == "?":
|
||||||
|
return None
|
||||||
|
if val.endswith(" g"):
|
||||||
|
return float(val.split(" ")[0])
|
||||||
|
if val.endswith("mg"):
|
||||||
|
return float(val.split("mg")[0])
|
||||||
|
elif val.endswith("mmol"):
|
||||||
|
return float(val.split("mmol")[0]) / 1000
|
||||||
|
elif val.endswith("mol"):
|
||||||
|
return float(val.split("mol")[0])
|
||||||
|
elif val.endswith("ml"):
|
||||||
|
return float(val.split("ml")[0])
|
||||||
|
elif val.endswith("RPM"):
|
||||||
|
return float(val.split("RPM")[0])
|
||||||
|
elif val.endswith(" °C"):
|
||||||
|
return float(val.split(" ")[0])
|
||||||
|
elif val.endswith(" %"):
|
||||||
|
return float(val.split(" ")[0])
|
||||||
|
return val
|
||||||
|
|
||||||
|
|
||||||
|
def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
|
||||||
|
"""统一的数据重构函数，根据操作类型自动选择模板"""
|
||||||
|
refactored_data = []
|
||||||
|
|
||||||
|
# 定义操作映射，包含生物实验和有机化学的所有操作
|
||||||
|
OPERATION_MAPPING = {
|
||||||
|
# 生物实验操作
|
||||||
|
"transfer_liquid": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
|
||||||
|
"transfer": "SynBioFactory-liquid_handler.biomek-transfer",
|
||||||
|
"incubation": "SynBioFactory-liquid_handler.biomek-incubation",
|
||||||
|
"move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
|
||||||
|
"oscillation": "SynBioFactory-liquid_handler.biomek-oscillation",
|
||||||
|
# 有机化学操作
|
||||||
|
"HeatChillToTemp": "SynBioFactory-workstation-HeatChillProtocol",
|
||||||
|
"StopHeatChill": "SynBioFactory-workstation-HeatChillStopProtocol",
|
||||||
|
"StartHeatChill": "SynBioFactory-workstation-HeatChillStartProtocol",
|
||||||
|
"HeatChill": "SynBioFactory-workstation-HeatChillProtocol",
|
||||||
|
"Dissolve": "SynBioFactory-workstation-DissolveProtocol",
|
||||||
|
"Transfer": "SynBioFactory-workstation-TransferProtocol",
|
||||||
|
"Evaporate": "SynBioFactory-workstation-EvaporateProtocol",
|
||||||
|
"Recrystallize": "SynBioFactory-workstation-RecrystallizeProtocol",
|
||||||
|
"Filter": "SynBioFactory-workstation-FilterProtocol",
|
||||||
|
"Dry": "SynBioFactory-workstation-DryProtocol",
|
||||||
|
"Add": "SynBioFactory-workstation-AddProtocol",
|
||||||
|
}
|
||||||
|
|
||||||
|
UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||||
|
|
||||||
|
for step in data:
|
||||||
|
operation = step.get("action")
|
||||||
|
if not operation or operation in UNSUPPORTED_OPERATIONS:
|
||||||
|
continue
|
||||||
|
|
||||||
|
# 处理重复操作
|
||||||
|
if operation == "Repeat":
|
||||||
|
times = step.get("times", step.get("parameters", {}).get("times", 1))
|
||||||
|
sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
|
||||||
|
for i in range(int(times)):
|
||||||
|
sub_data = refactor_data(sub_steps)
|
||||||
|
refactored_data.extend(sub_data)
|
||||||
|
continue
|
||||||
|
|
||||||
|
# 获取模板名称
|
||||||
|
template = OPERATION_MAPPING.get(operation)
|
||||||
|
if not template:
|
||||||
|
# 自动推断模板类型
|
||||||
|
if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
|
||||||
|
template = f"SynBioFactory-liquid_handler.biomek-{operation}"
|
||||||
|
else:
|
||||||
|
template = f"SynBioFactory-workstation-{operation}Protocol"
|
||||||
|
|
||||||
|
# 创建步骤数据
|
||||||
|
step_data = {
|
||||||
|
"template": template,
|
||||||
|
"description": step.get("description", step.get("purpose", f"{operation} operation")),
|
||||||
|
"lab_node_type": "Device",
|
||||||
|
"parameters": step.get("parameters", step.get("action_args", {})),
|
||||||
|
}
|
||||||
|
refactored_data.append(step_data)
|
||||||
|
|
||||||
|
return refactored_data
|
||||||
|
|
||||||
|
|
||||||
|
def build_protocol_graph(
|
||||||
|
labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
|
||||||
|
) -> SimpleGraph:
|
||||||
|
"""统一的协议图构建函数，根据设备类型自动选择构建逻辑"""
|
||||||
|
G = SimpleGraph()
|
||||||
|
resource_last_writer = {}
|
||||||
|
LAB_NAME = "SynBioFactory"
|
||||||
|
|
||||||
|
protocol_steps = refactor_data(protocol_steps)
|
||||||
|
|
||||||
|
# 检查协议步骤中的模板来判断协议类型
|
||||||
|
has_biomek_template = any(
|
||||||
|
("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
|
||||||
|
for step in protocol_steps
|
||||||
|
)
|
||||||
|
|
||||||
|
if has_biomek_template:
|
||||||
|
# 生物实验协议图构建
|
||||||
|
for labware_id, labware in labware_info.items():
|
||||||
|
node_id = str(uuid.uuid4())
|
||||||
|
|
||||||
|
labware_attrs = labware.copy()
|
||||||
|
labware_id = labware_attrs.pop("id", labware_attrs.get("name", f"labware_{uuid.uuid4()}"))
|
||||||
|
labware_attrs["description"] = labware_id
|
||||||
|
labware_attrs["lab_node_type"] = (
|
||||||
|
"Reagent" if "Plate" in str(labware_id) else "Labware" if "Rack" in str(labware_id) else "Sample"
|
||||||
|
)
|
||||||
|
labware_attrs["device_id"] = workstation_name
|
||||||
|
|
||||||
|
G.add_node(node_id, template=f"{LAB_NAME}-host_node-create_resource", **labware_attrs)
|
||||||
|
resource_last_writer[labware_id] = f"{node_id}:labware"
|
||||||
|
|
||||||
|
# 处理协议步骤
|
||||||
|
prev_node = None
|
||||||
|
for i, step in enumerate(protocol_steps):
|
||||||
|
node_id = str(uuid.uuid4())
|
||||||
|
G.add_node(node_id, **step)
|
||||||
|
|
||||||
|
# 添加控制流边
|
||||||
|
if prev_node is not None:
|
||||||
|
G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
|
||||||
|
prev_node = node_id
|
||||||
|
|
||||||
|
# 处理物料流
|
||||||
|
params = step.get("parameters", {})
|
||||||
|
if "sources" in params and params["sources"] in resource_last_writer:
|
||||||
|
source_node, source_port = resource_last_writer[params["sources"]].split(":")
|
||||||
|
G.add_edge(source_node, node_id, source_port=source_port, target_port="labware")
|
||||||
|
|
||||||
|
if "targets" in params:
|
||||||
|
resource_last_writer[params["targets"]] = f"{node_id}:labware"
|
||||||
|
|
||||||
|
# 添加协议结束节点
|
||||||
|
end_id = str(uuid.uuid4())
|
||||||
|
G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
|
||||||
|
if prev_node is not None:
|
||||||
|
G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
|
||||||
|
|
||||||
|
else:
|
||||||
|
# 有机化学协议图构建
|
||||||
|
WORKSTATION_ID = workstation_name
|
||||||
|
|
||||||
|
# 为所有labware创建资源节点
|
||||||
|
for item_id, item in labware_info.items():
|
||||||
|
# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
|
||||||
|
node_id = str(uuid.uuid4())
|
||||||
|
|
||||||
|
# 判断节点类型
|
||||||
|
if item.get("type") == "hardware" or "reactor" in str(item_id).lower():
|
||||||
|
if "reactor" not in str(item_id).lower():
|
||||||
|
continue
|
||||||
|
lab_node_type = "Sample"
|
||||||
|
description = f"Prepare Reactor: {item_id}"
|
||||||
|
liquid_type = []
|
||||||
|
liquid_volume = []
|
||||||
|
else:
|
||||||
|
lab_node_type = "Reagent"
|
||||||
|
description = f"Add Reagent to Flask: {item_id}"
|
||||||
|
liquid_type = [item_id]
|
||||||
|
liquid_volume = [1e5]
|
||||||
|
|
||||||
|
G.add_node(
|
||||||
|
node_id,
|
||||||
|
template=f"{LAB_NAME}-host_node-create_resource",
|
||||||
|
description=description,
|
||||||
|
lab_node_type=lab_node_type,
|
||||||
|
res_id=item_id,
|
||||||
|
device_id=WORKSTATION_ID,
|
||||||
|
class_name="container",
|
||||||
|
parent=WORKSTATION_ID,
|
||||||
|
bind_locations={"x": 0.0, "y": 0.0, "z": 0.0},
|
||||||
|
liquid_input_slot=[-1],
|
||||||
|
liquid_type=liquid_type,
|
||||||
|
liquid_volume=liquid_volume,
|
||||||
|
slot_on_deck="",
|
||||||
|
role=item.get("role", ""),
|
||||||
|
)
|
||||||
|
resource_last_writer[item_id] = f"{node_id}:labware"
|
||||||
|
|
||||||
|
last_control_node_id = None
|
||||||
|
|
||||||
|
# 处理协议步骤
|
||||||
|
for step in protocol_steps:
|
||||||
|
node_id = str(uuid.uuid4())
|
||||||
|
G.add_node(node_id, **step)
|
||||||
|
|
||||||
|
# 控制流
|
||||||
|
if last_control_node_id is not None:
|
||||||
|
G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
|
||||||
|
last_control_node_id = node_id
|
||||||
|
|
||||||
|
# 物料流
|
||||||
|
params = step.get("parameters", {})
|
||||||
|
input_resources = {
|
||||||
|
"Vessel": params.get("vessel"),
|
||||||
|
"ToVessel": params.get("to_vessel"),
|
||||||
|
"FromVessel": params.get("from_vessel"),
|
||||||
|
"reagent": params.get("reagent"),
|
||||||
|
"solvent": params.get("solvent"),
|
||||||
|
"compound": params.get("compound"),
|
||||||
|
"sources": params.get("sources"),
|
||||||
|
"targets": params.get("targets"),
|
||||||
|
}
|
||||||
|
|
||||||
|
for target_port, resource_name in input_resources.items():
|
||||||
|
if resource_name and resource_name in resource_last_writer:
|
||||||
|
source_node, source_port = resource_last_writer[resource_name].split(":")
|
||||||
|
G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
|
||||||
|
|
||||||
|
output_resources = {
|
||||||
|
"VesselOut": params.get("vessel"),
|
||||||
|
"FromVesselOut": params.get("from_vessel"),
|
||||||
|
"ToVesselOut": params.get("to_vessel"),
|
||||||
|
"FiltrateOut": params.get("filtrate_vessel"),
|
||||||
|
"reagent": params.get("reagent"),
|
||||||
|
"solvent": params.get("solvent"),
|
||||||
|
"compound": params.get("compound"),
|
||||||
|
"sources_out": params.get("sources"),
|
||||||
|
"targets_out": params.get("targets"),
|
||||||
|
}
|
||||||
|
|
||||||
|
for source_port, resource_name in output_resources.items():
|
||||||
|
if resource_name:
|
||||||
|
resource_last_writer[resource_name] = f"{node_id}:{source_port}"
|
||||||
|
|
||||||
|
return G
|
||||||
|
|
||||||
|
|
||||||
|
def draw_protocol_graph(protocol_graph: SimpleGraph, output_path: str):
|
||||||
|
"""
|
||||||
|
(辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图，用于可视化。
|
||||||
|
"""
|
||||||
|
if not protocol_graph:
|
||||||
|
print("Cannot draw graph: Graph object is empty.")
|
||||||
|
return
|
||||||
|
|
||||||
|
G = nx.DiGraph()
|
||||||
|
|
||||||
|
for node_id, attrs in protocol_graph.nodes.items():
|
||||||
|
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
||||||
|
G.add_node(node_id, label=label, **attrs)
|
||||||
|
|
||||||
|
for edge in protocol_graph.edges:
|
||||||
|
G.add_edge(edge["source"], edge["target"])
|
||||||
|
|
||||||
|
plt.figure(figsize=(20, 15))
|
||||||
|
try:
|
||||||
|
pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
|
||||||
|
except Exception:
|
||||||
|
pos = nx.shell_layout(G) # Fallback layout
|
||||||
|
|
||||||
|
node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
|
||||||
|
nx.draw(
|
||||||
|
G,
|
||||||
|
pos,
|
||||||
|
with_labels=False,
|
||||||
|
node_size=2500,
|
||||||
|
node_color="skyblue",
|
||||||
|
node_shape="o",
|
||||||
|
edge_color="gray",
|
||||||
|
width=1.5,
|
||||||
|
arrowsize=15,
|
||||||
|
)
|
||||||
|
nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
|
||||||
|
|
||||||
|
plt.title("Chemical Protocol Workflow Graph", size=15)
|
||||||
|
plt.savefig(output_path, dpi=300, bbox_inches="tight")
|
||||||
|
plt.close()
|
||||||
|
print(f" - Visualization saved to '{output_path}'")
|
||||||
|
|
||||||
|
|
||||||
|
from networkx.drawing.nx_agraph import to_agraph
|
||||||
|
import re
|
||||||
|
|
||||||
|
COMPASS = {"n","e","s","w","ne","nw","se","sw","c"}
|
||||||
|
|
||||||
|
def _is_compass(port: str) -> bool:
|
||||||
|
return isinstance(port, str) and port.lower() in COMPASS
|
||||||
|
|
||||||
|
def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
|
||||||
|
"""
|
||||||
|
使用 Graphviz 端口语法绘制协议工作流图。
|
||||||
|
- 若边上的 source_port/target_port 是 compass（n/e/s/w/...），直接用 compass。
|
||||||
|
- 否则自动为节点创建 record 形状并定义命名端口 <portname>。
|
||||||
|
最终由 PyGraphviz 渲染并输出到 output_path（后缀决定格式，如 .png/.svg/.pdf）。
|
||||||
|
"""
|
||||||
|
if not protocol_graph:
|
||||||
|
print("Cannot draw graph: Graph object is empty.")
|
||||||
|
return
|
||||||
|
|
||||||
|
# 1) 先用 networkx 搭建有向图，保留端口属性
|
||||||
|
G = nx.DiGraph()
|
||||||
|
for node_id, attrs in protocol_graph.nodes.items():
|
||||||
|
label = attrs.get("description", attrs.get("template", node_id[:8]))
|
||||||
|
# 保留一个干净的“中心标签”，用于放在 record 的中间槽
|
||||||
|
G.add_node(node_id, _core_label=str(label), **{k:v for k,v in attrs.items() if k not in ("label",)})
|
||||||
|
|
||||||
|
edges_data = []
|
||||||
|
in_ports_by_node = {} # 收集命名输入端口
|
||||||
|
out_ports_by_node = {} # 收集命名输出端口
|
||||||
|
|
||||||
|
for edge in protocol_graph.edges:
|
||||||
|
u = edge["source"]
|
||||||
|
v = edge["target"]
|
||||||
|
sp = edge.get("source_port")
|
||||||
|
tp = edge.get("target_port")
|
||||||
|
|
||||||
|
# 记录到图里（保留原始端口信息）
|
||||||
|
G.add_edge(u, v, source_port=sp, target_port=tp)
|
||||||
|
edges_data.append((u, v, sp, tp))
|
||||||
|
|
||||||
|
# 如果不是 compass，就按“命名端口”先归类，等会儿给节点造 record
|
||||||
|
if sp and not _is_compass(sp):
|
||||||
|
out_ports_by_node.setdefault(u, set()).add(str(sp))
|
||||||
|
if tp and not _is_compass(tp):
|
||||||
|
in_ports_by_node.setdefault(v, set()).add(str(tp))
|
||||||
|
|
||||||
|
# 2) 转为 AGraph，使用 Graphviz 渲染
|
||||||
|
A = to_agraph(G)
|
||||||
|
A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
|
||||||
|
A.node_attr.update(shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica")
|
||||||
|
A.edge_attr.update(arrowsize="0.8", color="#666666")
|
||||||
|
|
||||||
|
# 3) 为需要命名端口的节点设置 record 形状与 label
|
||||||
|
# 左列 = 输入端口；中间 = 核心标签；右列 = 输出端口
|
||||||
|
for n in A.nodes():
|
||||||
|
node = A.get_node(n)
|
||||||
|
core = G.nodes[n].get("_core_label", n)
|
||||||
|
|
||||||
|
in_ports = sorted(in_ports_by_node.get(n, []))
|
||||||
|
out_ports = sorted(out_ports_by_node.get(n, []))
|
||||||
|
|
||||||
|
# 如果该节点涉及命名端口，则用 record；否则保留原 box
|
||||||
|
if in_ports or out_ports:
|
||||||
|
def port_fields(ports):
|
||||||
|
if not ports:
|
||||||
|
return " " # 必须留一个空槽占位
|
||||||
|
# 每个端口一个小格子，<p> name
|
||||||
|
return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
|
||||||
|
|
||||||
|
left = port_fields(in_ports)
|
||||||
|
right = port_fields(out_ports)
|
||||||
|
|
||||||
|
# 三栏：左(入) | 中(节点名) | 右(出)
|
||||||
|
record_label = f"{{ {left} | {core} | {right} }}"
|
||||||
|
node.attr.update(shape="record", label=record_label)
|
||||||
|
else:
|
||||||
|
# 没有命名端口：普通盒子，显示核心标签
|
||||||
|
node.attr.update(label=str(core))
|
||||||
|
|
||||||
|
# 4) 给边设置 headport / tailport
|
||||||
|
# - 若端口为 compass：直接用 compass（e.g., headport="e"）
|
||||||
|
# - 若端口为命名端口：使用在 record 中定义的 <port> 名（同名即可）
|
||||||
|
for (u, v, sp, tp) in edges_data:
|
||||||
|
e = A.get_edge(u, v)
|
||||||
|
|
||||||
|
# Graphviz 属性：tail 是源，head 是目标
|
||||||
|
if sp:
|
||||||
|
if _is_compass(sp):
|
||||||
|
e.attr["tailport"] = sp.lower()
|
||||||
|
else:
|
||||||
|
# 与 record label 中 <port> 名一致；特殊字符已在 label 中做了清洗
|
||||||
|
e.attr["tailport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(sp))
|
||||||
|
|
||||||
|
if tp:
|
||||||
|
if _is_compass(tp):
|
||||||
|
e.attr["headport"] = tp.lower()
|
||||||
|
else:
|
||||||
|
e.attr["headport"] = re.sub(r'[^A-Za-z0-9_:.|-]', '_', str(tp))
|
||||||
|
|
||||||
|
# 可选：若想让边更贴边缘，可设置 constraint/spline 等
|
||||||
|
# e.attr["arrowhead"] = "vee"
|
||||||
|
|
||||||
|
# 5) 输出
|
||||||
|
A.draw(output_path, prog="dot")
|
||||||
|
print(f" - Port-aware workflow rendered to '{output_path}'")
|
||||||
|
|
||||||
|
|
||||||
|
def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
|
||||||
|
"""展平嵌套的XDL程序结构"""
|
||||||
|
flattened_operations = []
|
||||||
|
TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
|
||||||
|
|
||||||
|
def extract_operations(element: ET.Element):
|
||||||
|
if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
|
||||||
|
if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
|
||||||
|
flattened_operations.append(element)
|
||||||
|
|
||||||
|
for child in element:
|
||||||
|
extract_operations(child)
|
||||||
|
|
||||||
|
for child in procedure_elem:
|
||||||
|
extract_operations(child)
|
||||||
|
|
||||||
|
return flattened_operations
|
||||||
|
|
||||||
|
|
||||||
|
def parse_xdl_content(xdl_content: str) -> tuple:
|
||||||
|
"""解析XDL内容"""
|
||||||
|
try:
|
||||||
|
xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
|
||||||
|
root = ET.fromstring(xdl_content_cleaned)
|
||||||
|
|
||||||
|
synthesis_elem = root.find("Synthesis")
|
||||||
|
if synthesis_elem is None:
|
||||||
|
return None, None, None
|
||||||
|
|
||||||
|
# 解析硬件组件
|
||||||
|
hardware_elem = synthesis_elem.find("Hardware")
|
||||||
|
hardware = []
|
||||||
|
if hardware_elem is not None:
|
||||||
|
hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
|
||||||
|
|
||||||
|
# 解析试剂
|
||||||
|
reagents_elem = synthesis_elem.find("Reagents")
|
||||||
|
reagents = []
|
||||||
|
if reagents_elem is not None:
|
||||||
|
reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
|
||||||
|
|
||||||
|
# 解析程序
|
||||||
|
procedure_elem = synthesis_elem.find("Procedure")
|
||||||
|
if procedure_elem is None:
|
||||||
|
return None, None, None
|
||||||
|
|
||||||
|
flattened_operations = flatten_xdl_procedure(procedure_elem)
|
||||||
|
return hardware, reagents, flattened_operations
|
||||||
|
|
||||||
|
except ET.ParseError as e:
|
||||||
|
raise ValueError(f"Invalid XDL format: {e}")
|
||||||
|
|
||||||
|
|
||||||
|
def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
|
||||||
|
"""
|
||||||
|
将XDL XML格式转换为标准的字典格式
|
||||||
|
|
||||||
|
Args:
|
||||||
|
xdl_content: XDL XML内容
|
||||||
|
|
||||||
|
Returns:
|
||||||
|
转换结果，包含步骤和器材信息
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
|
||||||
|
if hardware is None:
|
||||||
|
return {"error": "Failed to parse XDL content", "success": False}
|
||||||
|
|
||||||
|
# 将XDL元素转换为字典格式
|
||||||
|
steps_data = []
|
||||||
|
for elem in flattened_operations:
|
||||||
|
# 转换参数类型
|
||||||
|
parameters = {}
|
||||||
|
for key, val in elem.attrib.items():
|
||||||
|
converted_val = convert_to_type(val)
|
||||||
|
if converted_val is not None:
|
||||||
|
parameters[key] = converted_val
|
||||||
|
|
||||||
|
step_dict = {
|
||||||
|
"operation": elem.tag,
|
||||||
|
"parameters": parameters,
|
||||||
|
"description": elem.get("purpose", f"Operation: {elem.tag}"),
|
||||||
|
}
|
||||||
|
steps_data.append(step_dict)
|
||||||
|
|
||||||
|
# 合并硬件和试剂为统一的labware_info格式
|
||||||
|
labware_data = []
|
||||||
|
labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
|
||||||
|
labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
|
||||||
|
|
||||||
|
return {
|
||||||
|
"success": True,
|
||||||
|
"steps": steps_data,
|
||||||
|
"labware": labware_data,
|
||||||
|
"message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
|
||||||
|
}
|
||||||
|
|
||||||
|
except Exception as e:
|
||||||
|
error_msg = f"XDL conversion failed: {str(e)}"
|
||||||
|
logger.error(error_msg)
|
||||||
|
return {"error": error_msg, "success": False}
|
||||||
|
|
||||||
|
|
||||||
def create_workflow(
|
def create_workflow(
|
||||||
|
|||||||
@@ -20,7 +20,6 @@ if unilabos_dir not in sys.path:
|
|||||||
from unilabos.utils.banner_print import print_status, print_unilab_banner
|
from unilabos.utils.banner_print import print_status, print_unilab_banner
|
||||||
from unilabos.config.config import load_config, BasicConfig, HTTPConfig
|
from unilabos.config.config import load_config, BasicConfig, HTTPConfig
|
||||||
|
|
||||||
|
|
||||||
def load_config_from_file(config_path):
|
def load_config_from_file(config_path):
|
||||||
if config_path is None:
|
if config_path is None:
|
||||||
config_path = os.environ.get("UNILABOS_BASICCONFIG_CONFIG_PATH", None)
|
config_path = os.environ.get("UNILABOS_BASICCONFIG_CONFIG_PATH", None)
|
||||||
@@ -42,7 +41,7 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
|
|||||||
for i, arg in enumerate(sys.argv):
|
for i, arg in enumerate(sys.argv):
|
||||||
for option_string in option_strings:
|
for option_string in option_strings:
|
||||||
if arg.startswith(option_string):
|
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
|
sys.argv[i] = new_arg
|
||||||
break
|
break
|
||||||
|
|
||||||
@@ -50,8 +49,6 @@ def convert_argv_dashes_to_underscores(args: argparse.ArgumentParser):
|
|||||||
def parse_args():
|
def parse_args():
|
||||||
"""解析命令行参数"""
|
"""解析命令行参数"""
|
||||||
parser = argparse.ArgumentParser(description="Start Uni-Lab Edge server.")
|
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("-g", "--graph", help="Physical setup graph file path.")
|
||||||
parser.add_argument("-c", "--controllers", default=None, help="Controllers config file path.")
|
parser.add_argument("-c", "--controllers", default=None, help="Controllers config file path.")
|
||||||
parser.add_argument(
|
parser.add_argument(
|
||||||
@@ -156,39 +153,6 @@ def parse_args():
|
|||||||
default=False,
|
default=False,
|
||||||
help="Complete registry information",
|
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
|
return parser
|
||||||
|
|
||||||
|
|
||||||
@@ -204,6 +168,7 @@ def main():
|
|||||||
if not args_dict.get("skip_env_check", False):
|
if not args_dict.get("skip_env_check", False):
|
||||||
from unilabos.utils.environment_check import check_environment
|
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):
|
if not check_environment(auto_install=True):
|
||||||
print_status("环境检查失败，程序退出", "error")
|
print_status("环境检查失败，程序退出", "error")
|
||||||
os._exit(1)
|
os._exit(1)
|
||||||
@@ -276,12 +241,9 @@ def main():
|
|||||||
if args_dict.get("sk", ""):
|
if args_dict.get("sk", ""):
|
||||||
BasicConfig.sk = 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")
|
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
|
# 使用远程资源启动
|
||||||
if not workflow_upload and args_dict["use_remote_resource"]:
|
if args_dict["use_remote_resource"]:
|
||||||
print_status("使用远程资源启动", "info")
|
print_status("使用远程资源启动", "info")
|
||||||
from unilabos.app.web import http_client
|
from unilabos.app.web import http_client
|
||||||
|
|
||||||
@@ -294,6 +256,7 @@ def main():
|
|||||||
|
|
||||||
BasicConfig.port = args_dict["port"] if args_dict["port"] else BasicConfig.port
|
BasicConfig.port = args_dict["port"] if args_dict["port"] else BasicConfig.port
|
||||||
BasicConfig.disable_browser = args_dict["disable_browser"] or BasicConfig.disable_browser
|
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.is_host_mode = not args_dict.get("is_slave", False)
|
||||||
BasicConfig.slave_no_host = args_dict.get("slave_no_host", False)
|
BasicConfig.slave_no_host = args_dict.get("slave_no_host", False)
|
||||||
BasicConfig.upload_registry = args_dict.get("upload_registry", False)
|
BasicConfig.upload_registry = args_dict.get("upload_registry", False)
|
||||||
@@ -322,31 +285,9 @@ def main():
|
|||||||
|
|
||||||
# 注册表
|
# 注册表
|
||||||
lab_registry = build_registry(
|
lab_registry = build_registry(
|
||||||
args_dict["registry_path"], args_dict.get("complete_registry", False), BasicConfig.upload_registry
|
args_dict["registry_path"], args_dict.get("complete_registry", False), args_dict["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:
|
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")
|
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)
|
os._exit(1)
|
||||||
@@ -427,6 +368,20 @@ def main():
|
|||||||
args_dict["devices_config"] = resource_tree_set
|
args_dict["devices_config"] = resource_tree_set
|
||||||
args_dict["graph"] = graph_res.physical_setup_graph
|
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:
|
if args_dict["controllers"] is not None:
|
||||||
args_dict["controllers_config"] = yaml.safe_load(open(args_dict["controllers"], encoding="utf-8"))
|
args_dict["controllers_config"] = yaml.safe_load(open(args_dict["controllers"], encoding="utf-8"))
|
||||||
else:
|
else:
|
||||||
@@ -441,7 +396,6 @@ def main():
|
|||||||
comm_client = get_communication_client()
|
comm_client = get_communication_client()
|
||||||
if "websocket" in args_dict["app_bridges"]:
|
if "websocket" in args_dict["app_bridges"]:
|
||||||
args_dict["bridges"].append(comm_client)
|
args_dict["bridges"].append(comm_client)
|
||||||
|
|
||||||
def _exit(signum, frame):
|
def _exit(signum, frame):
|
||||||
comm_client.stop()
|
comm_client.stop()
|
||||||
sys.exit(0)
|
sys.exit(0)
|
||||||
@@ -483,13 +437,16 @@ def main():
|
|||||||
resource_visualization.start()
|
resource_visualization.start()
|
||||||
except OSError as e:
|
except OSError as e:
|
||||||
if "AMENT_PREFIX_PATH" in str(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(
|
print_status(
|
||||||
"建议解决方案：\n"
|
"建议解决方案：\n"
|
||||||
"1. 激活Conda环境: conda activate unilab\n"
|
"1. 激活Conda环境: conda activate unilab\n"
|
||||||
"2. 或使用 --backend simple 参数\n"
|
"2. 或使用 --backend simple 参数\n"
|
||||||
"3. 或使用 --visual disable 参数禁用可视化",
|
"3. 或使用 --visual disable 参数禁用可视化",
|
||||||
"info",
|
"info"
|
||||||
)
|
)
|
||||||
else:
|
else:
|
||||||
raise
|
raise
|
||||||
|
|||||||
@@ -76,8 +76,7 @@ class HTTPClient:
|
|||||||
Dict[str, str]: 旧UUID到新UUID的映射关系 {old_uuid: new_uuid}
|
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:
|
with open(os.path.join(BasicConfig.working_dir, "req_resource_tree_add.json"), "w", encoding="utf-8") as f:
|
||||||
payload = {"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}
|
f.write(json.dumps({"nodes": [x for xs in resources.dump() for x in xs], "mount_uuid": mount_uuid}, indent=4))
|
||||||
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）
|
# 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}
|
old_uuids = {n.res_content.uuid: n for n in resources.all_nodes}
|
||||||
if not self.initialized or first_add:
|
if not self.initialized or first_add:
|
||||||
@@ -336,67 +335,6 @@ class HTTPClient:
|
|||||||
logger.error(f"响应内容: {response.text}")
|
logger.error(f"响应内容: {response.text}")
|
||||||
return None
|
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
|
# 创建默认客户端实例
|
||||||
http_client = HTTPClient()
|
http_client = HTTPClient()
|
||||||
|
|||||||
@@ -438,7 +438,7 @@ class MessageProcessor:
|
|||||||
self.connected = True
|
self.connected = True
|
||||||
self.reconnect_count = 0
|
self.reconnect_count = 0
|
||||||
|
|
||||||
logger.trace(f"[MessageProcessor] Connected to {self.websocket_url}")
|
logger.info(f"[MessageProcessor] Connected to {self.websocket_url}")
|
||||||
|
|
||||||
# 启动发送协程
|
# 启动发送协程
|
||||||
send_task = asyncio.create_task(self._send_handler())
|
send_task = asyncio.create_task(self._send_handler())
|
||||||
@@ -503,7 +503,7 @@ class MessageProcessor:
|
|||||||
|
|
||||||
async def _send_handler(self):
|
async def _send_handler(self):
|
||||||
"""处理发送队列中的消息"""
|
"""处理发送队列中的消息"""
|
||||||
logger.trace("[MessageProcessor] Send handler started")
|
logger.debug("[MessageProcessor] Send handler started")
|
||||||
|
|
||||||
try:
|
try:
|
||||||
while self.connected and self.websocket:
|
while self.connected and self.websocket:
|
||||||
@@ -965,7 +965,7 @@ class QueueProcessor:
|
|||||||
|
|
||||||
def _run(self):
|
def _run(self):
|
||||||
"""运行队列处理主循环"""
|
"""运行队列处理主循环"""
|
||||||
logger.trace("[QueueProcessor] Queue processor started")
|
logger.debug("[QueueProcessor] Queue processor started")
|
||||||
|
|
||||||
while self.is_running:
|
while self.is_running:
|
||||||
try:
|
try:
|
||||||
@@ -1175,6 +1175,7 @@ class WebSocketClient(BaseCommunicationClient):
|
|||||||
else:
|
else:
|
||||||
url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
|
url = f"{scheme}://{parsed.netloc}/api/v1/ws/schedule"
|
||||||
|
|
||||||
|
logger.debug(f"[WebSocketClient] URL: {url}")
|
||||||
return url
|
return url
|
||||||
|
|
||||||
def start(self) -> None:
|
def start(self) -> None:
|
||||||
@@ -1187,11 +1188,13 @@ class WebSocketClient(BaseCommunicationClient):
|
|||||||
logger.error("[WebSocketClient] WebSocket URL not configured")
|
logger.error("[WebSocketClient] WebSocket URL not configured")
|
||||||
return
|
return
|
||||||
|
|
||||||
|
logger.info(f"[WebSocketClient] Starting connection to {self.websocket_url}")
|
||||||
|
|
||||||
# 启动两个核心线程
|
# 启动两个核心线程
|
||||||
self.message_processor.start()
|
self.message_processor.start()
|
||||||
self.queue_processor.start()
|
self.queue_processor.start()
|
||||||
|
|
||||||
logger.trace("[WebSocketClient] All threads started")
|
logger.info("[WebSocketClient] All threads started")
|
||||||
|
|
||||||
def stop(self) -> None:
|
def stop(self) -> None:
|
||||||
"""停止WebSocket客户端"""
|
"""停止WebSocket客户端"""
|
||||||
|
|||||||
@@ -21,8 +21,7 @@ class BasicConfig:
|
|||||||
startup_json_path = None # 填写绝对路径
|
startup_json_path = None # 填写绝对路径
|
||||||
disable_browser = False # 禁止浏览器自动打开
|
disable_browser = False # 禁止浏览器自动打开
|
||||||
port = 8002 # 本地HTTP服务
|
port = 8002 # 本地HTTP服务
|
||||||
# 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
log_level: Literal['TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] = "DEBUG" # 'TRACE', 'DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'
|
||||||
log_level: Literal["TRACE", "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"] = "DEBUG"
|
|
||||||
|
|
||||||
@classmethod
|
@classmethod
|
||||||
def auth_secret(cls):
|
def auth_secret(cls):
|
||||||
@@ -66,14 +65,13 @@ def _update_config_from_module(module):
|
|||||||
if not attr.startswith("_"):
|
if not attr.startswith("_"):
|
||||||
setattr(obj, attr, getattr(getattr(module, name), attr))
|
setattr(obj, attr, getattr(getattr(module, name), attr))
|
||||||
|
|
||||||
|
|
||||||
def _update_config_from_env():
|
def _update_config_from_env():
|
||||||
prefix = "UNILABOS_"
|
prefix = "UNILABOS_"
|
||||||
for env_key, env_value in os.environ.items():
|
for env_key, env_value in os.environ.items():
|
||||||
if not env_key.startswith(prefix):
|
if not env_key.startswith(prefix):
|
||||||
continue
|
continue
|
||||||
try:
|
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)
|
class_field = key_path.upper().split("_", 1)
|
||||||
if len(class_field) != 2:
|
if len(class_field) != 2:
|
||||||
logger.warning(f"[ENV] 环境变量格式不正确：{env_key}")
|
logger.warning(f"[ENV] 环境变量格式不正确：{env_key}")
|
||||||
|
|||||||
@@ -9737,34 +9737,7 @@ liquid_handler.prcxi:
|
|||||||
touch_tip: false
|
touch_tip: false
|
||||||
use_channels:
|
use_channels:
|
||||||
- 0
|
- 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:
|
placeholder_keys:
|
||||||
sources: unilabos_resources
|
sources: unilabos_resources
|
||||||
targets: unilabos_resources
|
targets: unilabos_resources
|
||||||
|
|||||||
@@ -222,7 +222,7 @@ class Registry:
|
|||||||
abs_path = Path(path).absolute()
|
abs_path = Path(path).absolute()
|
||||||
resource_path = abs_path / "resources"
|
resource_path = abs_path / "resources"
|
||||||
files = list(resource_path.glob("*/*.yaml"))
|
files = list(resource_path.glob("*/*.yaml"))
|
||||||
logger.trace(f"[UniLab Registry] load resources? {resource_path.exists()}, total: {len(files)}")
|
logger.debug(f"[UniLab Registry] resources: {resource_path.exists()}, total: {len(files)}")
|
||||||
current_resource_number = len(self.resource_type_registry) + 1
|
current_resource_number = len(self.resource_type_registry) + 1
|
||||||
for i, file in enumerate(files):
|
for i, file in enumerate(files):
|
||||||
with open(file, encoding="utf-8", mode="r") as f:
|
with open(file, encoding="utf-8", mode="r") as f:
|
||||||
|
|||||||
@@ -42,7 +42,7 @@ def canonicalize_nodes_data(
|
|||||||
Returns:
|
Returns:
|
||||||
ResourceTreeSet: 标准化后的资源树集合
|
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）
|
# 第一步：基本预处理（处理graphml的label字段）
|
||||||
outer_host_node_id = None
|
outer_host_node_id = None
|
||||||
|
|||||||
@@ -21,6 +21,7 @@ from rclpy.callback_groups import ReentrantCallbackGroup
|
|||||||
from rclpy.service import Service
|
from rclpy.service import Service
|
||||||
from unilabos_msgs.action import SendCmd
|
from unilabos_msgs.action import SendCmd
|
||||||
from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
|
from unilabos_msgs.srv._serial_command import SerialCommand_Request, SerialCommand_Response
|
||||||
|
from unilabos.utils.decorator import get_topic_config, get_all_subscriptions
|
||||||
|
|
||||||
from unilabos.resources.container import RegularContainer
|
from unilabos.resources.container import RegularContainer
|
||||||
from unilabos.resources.graphio import (
|
from unilabos.resources.graphio import (
|
||||||
@@ -48,7 +49,8 @@ from unilabos_msgs.msg import Resource # type: ignore
|
|||||||
from unilabos.ros.nodes.resource_tracker import (
|
from unilabos.ros.nodes.resource_tracker import (
|
||||||
DeviceNodeResourceTracker,
|
DeviceNodeResourceTracker,
|
||||||
ResourceTreeSet,
|
ResourceTreeSet,
|
||||||
ResourceTreeInstance, ResourceDictInstance,
|
ResourceTreeInstance,
|
||||||
|
ResourceDictInstance,
|
||||||
)
|
)
|
||||||
from unilabos.ros.x.rclpyx import get_event_loop
|
from unilabos.ros.x.rclpyx import get_event_loop
|
||||||
from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator
|
from unilabos.ros.utils.driver_creator import WorkstationNodeCreator, PyLabRobotCreator, DeviceClassCreator
|
||||||
@@ -168,6 +170,7 @@ class PropertyPublisher:
|
|||||||
msg_type,
|
msg_type,
|
||||||
initial_period: float = 5.0,
|
initial_period: float = 5.0,
|
||||||
print_publish=True,
|
print_publish=True,
|
||||||
|
qos: int = 10,
|
||||||
):
|
):
|
||||||
self.node = node
|
self.node = node
|
||||||
self.name = name
|
self.name = name
|
||||||
@@ -175,10 +178,11 @@ class PropertyPublisher:
|
|||||||
self.get_method = get_method
|
self.get_method = get_method
|
||||||
self.timer_period = initial_period
|
self.timer_period = initial_period
|
||||||
self.print_publish = print_publish
|
self.print_publish = print_publish
|
||||||
|
self.qos = qos
|
||||||
|
|
||||||
self._value = None
|
self._value = None
|
||||||
try:
|
try:
|
||||||
self.publisher_ = node.create_publisher(msg_type, f"{name}", 10)
|
self.publisher_ = node.create_publisher(msg_type, f"{name}", qos)
|
||||||
except AttributeError as ex:
|
except AttributeError as ex:
|
||||||
self.node.lab_logger().error(
|
self.node.lab_logger().error(
|
||||||
f"创建发布者 {name} 失败，可能由于注册表有误，类型: {msg_type}，错误: {ex}\n{traceback.format_exc()}"
|
f"创建发布者 {name} 失败，可能由于注册表有误，类型: {msg_type}，错误: {ex}\n{traceback.format_exc()}"
|
||||||
@@ -186,7 +190,7 @@ class PropertyPublisher:
|
|||||||
self.timer = node.create_timer(self.timer_period, self.publish_property)
|
self.timer = node.create_timer(self.timer_period, self.publish_property)
|
||||||
self.__loop = get_event_loop()
|
self.__loop = get_event_loop()
|
||||||
str_msg_type = str(msg_type)[8:-2]
|
str_msg_type = str(msg_type)[8:-2]
|
||||||
self.node.lab_logger().trace(f"发布属性: {name}, 类型: {str_msg_type}, 周期: {initial_period}秒")
|
self.node.lab_logger().trace(f"发布属性: {name}, 类型: {str_msg_type}, 周期: {initial_period}秒, QoS: {qos}")
|
||||||
|
|
||||||
def get_property(self):
|
def get_property(self):
|
||||||
if asyncio.iscoroutinefunction(self.get_method):
|
if asyncio.iscoroutinefunction(self.get_method):
|
||||||
@@ -326,6 +330,10 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
|||||||
continue
|
continue
|
||||||
self.create_ros_action_server(action_name, action_value_mapping)
|
self.create_ros_action_server(action_name, action_value_mapping)
|
||||||
|
|
||||||
|
# 创建订阅者（通过 @subscribe 装饰器）
|
||||||
|
self._topic_subscribers: Dict[str, Any] = {}
|
||||||
|
self._setup_decorated_subscribers()
|
||||||
|
|
||||||
# 创建线程池执行器
|
# 创建线程池执行器
|
||||||
self._executor = ThreadPoolExecutor(
|
self._executor = ThreadPoolExecutor(
|
||||||
max_workers=max(len(action_value_mappings), 1), thread_name_prefix=f"ROSDevice{self.device_id}"
|
max_workers=max(len(action_value_mappings), 1), thread_name_prefix=f"ROSDevice{self.device_id}"
|
||||||
@@ -1043,6 +1051,29 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
|||||||
|
|
||||||
def create_ros_publisher(self, attr_name, msg_type, initial_period=5.0):
|
def create_ros_publisher(self, attr_name, msg_type, initial_period=5.0):
|
||||||
"""创建ROS发布者"""
|
"""创建ROS发布者"""
|
||||||
|
# 检测装饰器配置（支持 get_{attr_name} 方法和 @property）
|
||||||
|
topic_config = {}
|
||||||
|
|
||||||
|
# 优先检测 get_{attr_name} 方法
|
||||||
|
if hasattr(self.driver_instance, f"get_{attr_name}"):
|
||||||
|
getter_method = getattr(self.driver_instance, f"get_{attr_name}")
|
||||||
|
topic_config = get_topic_config(getter_method)
|
||||||
|
|
||||||
|
# 如果没有配置，检测 @property 装饰的属性
|
||||||
|
if not topic_config:
|
||||||
|
driver_class = type(self.driver_instance)
|
||||||
|
if hasattr(driver_class, attr_name):
|
||||||
|
class_attr = getattr(driver_class, attr_name)
|
||||||
|
if isinstance(class_attr, property) and class_attr.fget is not None:
|
||||||
|
topic_config = get_topic_config(class_attr.fget)
|
||||||
|
|
||||||
|
# 使用装饰器配置或默认值
|
||||||
|
cfg_period = topic_config.get("period")
|
||||||
|
cfg_print = topic_config.get("print_publish")
|
||||||
|
cfg_qos = topic_config.get("qos")
|
||||||
|
period: float = cfg_period if cfg_period is not None else initial_period
|
||||||
|
print_publish: bool = cfg_print if cfg_print is not None else self._print_publish
|
||||||
|
qos: int = cfg_qos if cfg_qos is not None else 10
|
||||||
|
|
||||||
# 获取属性值的方法
|
# 获取属性值的方法
|
||||||
def get_device_attr():
|
def get_device_attr():
|
||||||
@@ -1063,7 +1094,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
|||||||
self.lab_logger().error(traceback.format_exc())
|
self.lab_logger().error(traceback.format_exc())
|
||||||
|
|
||||||
self._property_publishers[attr_name] = PropertyPublisher(
|
self._property_publishers[attr_name] = PropertyPublisher(
|
||||||
self, attr_name, get_device_attr, msg_type, initial_period, self._print_publish
|
self, attr_name, get_device_attr, msg_type, period, print_publish, qos
|
||||||
)
|
)
|
||||||
|
|
||||||
def create_ros_action_server(self, action_name, action_value_mapping):
|
def create_ros_action_server(self, action_name, action_value_mapping):
|
||||||
@@ -1081,6 +1112,76 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
|||||||
|
|
||||||
self.lab_logger().trace(f"发布动作: {action_name}, 类型: {str_action_type}")
|
self.lab_logger().trace(f"发布动作: {action_name}, 类型: {str_action_type}")
|
||||||
|
|
||||||
|
def _setup_decorated_subscribers(self):
|
||||||
|
"""扫描 driver_instance 中带有 @subscribe 装饰器的方法并创建订阅者"""
|
||||||
|
subscriptions = get_all_subscriptions(self.driver_instance)
|
||||||
|
|
||||||
|
for method_name, method, config in subscriptions:
|
||||||
|
topic_template = config.get("topic")
|
||||||
|
msg_type = config.get("msg_type")
|
||||||
|
qos = config.get("qos", 10)
|
||||||
|
|
||||||
|
if not topic_template:
|
||||||
|
self.lab_logger().warning(f"订阅方法 {method_name} 缺少 topic 配置，跳过")
|
||||||
|
continue
|
||||||
|
|
||||||
|
# 如果没有指定 msg_type，尝试从类型注解推断
|
||||||
|
if msg_type is None:
|
||||||
|
try:
|
||||||
|
hints = get_type_hints(method)
|
||||||
|
# 第一个参数是 self，第二个是 msg
|
||||||
|
param_names = list(hints.keys())
|
||||||
|
if param_names:
|
||||||
|
msg_type = hints[param_names[0]]
|
||||||
|
except Exception:
|
||||||
|
pass
|
||||||
|
|
||||||
|
if msg_type is None:
|
||||||
|
self.lab_logger().warning(f"订阅方法 {method_name} 缺少 msg_type 配置且无法从类型注解推断，跳过")
|
||||||
|
continue
|
||||||
|
|
||||||
|
# 替换 topic 模板中的占位符
|
||||||
|
topic = self._resolve_topic_template(topic_template)
|
||||||
|
|
||||||
|
self.create_ros_subscriber(topic, msg_type, method, qos)
|
||||||
|
|
||||||
|
def _resolve_topic_template(self, topic_template: str) -> str:
|
||||||
|
"""
|
||||||
|
解析 topic 模板，替换占位符
|
||||||
|
|
||||||
|
支持的占位符:
|
||||||
|
- {device_id}: 设备ID
|
||||||
|
- {namespace}: 完整命名空间
|
||||||
|
"""
|
||||||
|
return topic_template.format(
|
||||||
|
device_id=self.device_id,
|
||||||
|
namespace=self.namespace,
|
||||||
|
)
|
||||||
|
|
||||||
|
def create_ros_subscriber(self, topic: str, msg_type, callback, qos: int = 10):
|
||||||
|
"""
|
||||||
|
创建ROS订阅者
|
||||||
|
|
||||||
|
Args:
|
||||||
|
topic: Topic 名称
|
||||||
|
msg_type: ROS 消息类型
|
||||||
|
callback: 回调方法（会自动绑定到 driver_instance）
|
||||||
|
qos: QoS 深度配置
|
||||||
|
"""
|
||||||
|
try:
|
||||||
|
subscription = self.create_subscription(
|
||||||
|
msg_type,
|
||||||
|
topic,
|
||||||
|
callback,
|
||||||
|
qos,
|
||||||
|
callback_group=self.callback_group,
|
||||||
|
)
|
||||||
|
self._topic_subscribers[topic] = subscription
|
||||||
|
str_msg_type = str(msg_type)[8:-2] if str(msg_type).startswith("<class") else str(msg_type)
|
||||||
|
self.lab_logger().trace(f"订阅Topic: {topic}, 类型: {str_msg_type}, QoS: {qos}")
|
||||||
|
except Exception as ex:
|
||||||
|
self.lab_logger().error(f"创建订阅者 {topic} 失败，类型: {msg_type}，错误: {ex}\n{traceback.format_exc()}")
|
||||||
|
|
||||||
def get_real_function(self, instance, attr_name):
|
def get_real_function(self, instance, attr_name):
|
||||||
if hasattr(instance.__class__, attr_name):
|
if hasattr(instance.__class__, attr_name):
|
||||||
obj = getattr(instance.__class__, attr_name)
|
obj = getattr(instance.__class__, attr_name)
|
||||||
@@ -1180,6 +1281,7 @@ class BaseROS2DeviceNode(Node, Generic[T]):
|
|||||||
if asyncio.iscoroutinefunction(ACTION):
|
if asyncio.iscoroutinefunction(ACTION):
|
||||||
try:
|
try:
|
||||||
self.lab_logger().trace(f"异步执行动作 {ACTION}")
|
self.lab_logger().trace(f"异步执行动作 {ACTION}")
|
||||||
|
|
||||||
def _handle_future_exception(fut: Future):
|
def _handle_future_exception(fut: Future):
|
||||||
nonlocal execution_error, execution_success, action_return_value
|
nonlocal execution_error, execution_success, action_return_value
|
||||||
try:
|
try:
|
||||||
@@ -1552,6 +1654,7 @@ 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。
|
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。
|
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
|
@staticmethod
|
||||||
async def safe_task_wrapper(trace_callback, func, **kwargs):
|
async def safe_task_wrapper(trace_callback, func, **kwargs):
|
||||||
try:
|
try:
|
||||||
@@ -1574,7 +1677,9 @@ class ROS2DeviceNode:
|
|||||||
error(f"异步任务 {func.__name__} 获取结果失败")
|
error(f"异步任务 {func.__name__} 获取结果失败")
|
||||||
error(traceback.format_exc())
|
error(traceback.format_exc())
|
||||||
|
|
||||||
future = rclpy.get_global_executor().create_task(ROS2DeviceNode.safe_task_wrapper(inner_trace_callback, func, **kwargs))
|
future = rclpy.get_global_executor().create_task(
|
||||||
|
ROS2DeviceNode.safe_task_wrapper(inner_trace_callback, func, **kwargs)
|
||||||
|
)
|
||||||
if trace_error:
|
if trace_error:
|
||||||
future.add_done_callback(_handle_future_exception)
|
future.add_done_callback(_handle_future_exception)
|
||||||
return future
|
return future
|
||||||
|
|||||||
@@ -1167,12 +1167,11 @@ class HostNode(BaseROS2DeviceNode):
|
|||||||
响应对象，包含查询到的资源
|
响应对象，包含查询到的资源
|
||||||
"""
|
"""
|
||||||
try:
|
try:
|
||||||
from unilabos.app.web import http_client
|
|
||||||
data = json.loads(request.command)
|
data = json.loads(request.command)
|
||||||
if "uuid" in data and data["uuid"] is not None:
|
if "uuid" in data and data["uuid"] is not None:
|
||||||
http_req = http_client.resource_tree_get([data["uuid"]], data["with_children"])
|
http_req = self.bridges[-1].resource_tree_get([data["uuid"]], data["with_children"])
|
||||||
elif "id" in data and data["id"].startswith("/"):
|
elif "id" in data and data["id"].startswith("/"):
|
||||||
http_req = http_client.resource_get(data["id"], data["with_children"])
|
http_req = self.bridges[-1].resource_get(data["id"], data["with_children"])
|
||||||
else:
|
else:
|
||||||
raise ValueError("没有使用正确的物料 id 或 uuid")
|
raise ValueError("没有使用正确的物料 id 或 uuid")
|
||||||
response.response = json.dumps(http_req["data"])
|
response.response = json.dumps(http_req["data"])
|
||||||
|
|||||||
@@ -66,8 +66,8 @@ class ResourceDict(BaseModel):
|
|||||||
klass: str = Field(alias="class", description="Resource class name")
|
klass: str = Field(alias="class", description="Resource class name")
|
||||||
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
|
pose: ResourceDictPosition = Field(description="Resource position", default_factory=ResourceDictPosition)
|
||||||
config: Dict[str, Any] = Field(description="Resource configuration")
|
config: Dict[str, Any] = Field(description="Resource configuration")
|
||||||
data: Dict[str, Any] = Field(description="Resource data, eg: container liquid data")
|
data: Dict[str, Any] = Field(description="Resource data")
|
||||||
extra: Dict[str, Any] = Field(description="Extra data, eg: slot index")
|
extra: Dict[str, Any] = Field(description="Extra data")
|
||||||
|
|
||||||
@field_serializer("parent_uuid")
|
@field_serializer("parent_uuid")
|
||||||
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
|
def _serialize_parent(self, parent_uuid: Optional["ResourceDict"]):
|
||||||
|
|||||||
@@ -7,49 +7,18 @@ from typing import Dict, Any, List
|
|||||||
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
|
from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode
|
||||||
|
|
||||||
|
|
||||||
class SmartPumpController:
|
class AnyDevice:
|
||||||
"""
|
@property
|
||||||
智能泵控制器
|
def status(self) -> str:
|
||||||
|
return "Idle"
|
||||||
|
|
||||||
支持多种泵送模式，具有高精度流量控制和自动校准功能。
|
async def action(self, addr: str) -> bool:
|
||||||
适用于实验室自动化系统中的液体处理任务。
|
|
||||||
"""
|
|
||||||
|
|
||||||
_ros_node: BaseROS2DeviceNode
|
|
||||||
|
|
||||||
def __init__(self, device_id: str = "smart_pump_01", port: str = "/dev/ttyUSB0"):
|
|
||||||
"""
|
|
||||||
初始化智能泵控制器
|
|
||||||
|
|
||||||
Args:
|
|
||||||
device_id: 设备唯一标识符
|
|
||||||
port: 通信端口
|
|
||||||
"""
|
|
||||||
self.device_id = device_id
|
|
||||||
self.port = port
|
|
||||||
self.is_connected = False
|
|
||||||
self.current_flow_rate = 0.0
|
|
||||||
self.total_volume_pumped = 0.0
|
|
||||||
self.calibration_factor = 1.0
|
|
||||||
self.pump_mode = "continuous" # continuous, volume, rate
|
|
||||||
|
|
||||||
def post_init(self, ros_node: BaseROS2DeviceNode):
|
|
||||||
self._ros_node = ros_node
|
|
||||||
|
|
||||||
def connect_device(self, timeout: int = 10) -> bool:
|
|
||||||
"""
|
|
||||||
连接到泵设备
|
|
||||||
|
|
||||||
Args:
|
|
||||||
timeout: 连接超时时间（秒）
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
bool: 连接是否成功
|
|
||||||
"""
|
|
||||||
# 模拟连接过程
|
|
||||||
self.is_connected = True
|
|
||||||
return True
|
return True
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def disconnect_device(self) -> bool:
|
def disconnect_device(self) -> bool:
|
||||||
"""
|
"""
|
||||||
断开设备连接
|
断开设备连接
|
||||||
|
|||||||
0
unilabos/test/ros/__init__.py
Normal file
0
unilabos/test/ros/__init__.py
Normal file
0
unilabos/test/workflow/__init__.py
Normal file
0
unilabos/test/workflow/__init__.py
Normal file
94
unilabos/test/workflow/merge_workflow.py
Normal file
94
unilabos/test/workflow/merge_workflow.py
Normal file
@@ -0,0 +1,94 @@
|
|||||||
|
import json
|
||||||
|
import sys
|
||||||
|
from datetime import datetime
|
||||||
|
from pathlib import Path
|
||||||
|
|
||||||
|
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||||||
|
if str(ROOT_DIR) not in sys.path:
|
||||||
|
sys.path.insert(0, str(ROOT_DIR))
|
||||||
|
|
||||||
|
import pytest
|
||||||
|
|
||||||
|
from scripts.workflow import build_protocol_graph, draw_protocol_graph, draw_protocol_graph_with_ports
|
||||||
|
|
||||||
|
|
||||||
|
ROOT_DIR = Path(__file__).resolve().parents[2]
|
||||||
|
if str(ROOT_DIR) not in sys.path:
|
||||||
|
sys.path.insert(0, str(ROOT_DIR))
|
||||||
|
|
||||||
|
|
||||||
|
def _normalize_steps(data):
|
||||||
|
normalized = []
|
||||||
|
for step in data:
|
||||||
|
action = step.get("action") or step.get("operation")
|
||||||
|
if not action:
|
||||||
|
continue
|
||||||
|
raw_params = step.get("parameters") or step.get("action_args") or {}
|
||||||
|
params = dict(raw_params)
|
||||||
|
|
||||||
|
if "source" in raw_params and "sources" not in raw_params:
|
||||||
|
params["sources"] = raw_params["source"]
|
||||||
|
if "target" in raw_params and "targets" not in raw_params:
|
||||||
|
params["targets"] = raw_params["target"]
|
||||||
|
|
||||||
|
description = step.get("description") or step.get("purpose")
|
||||||
|
step_dict = {"action": action, "parameters": params}
|
||||||
|
if description:
|
||||||
|
step_dict["description"] = description
|
||||||
|
normalized.append(step_dict)
|
||||||
|
return normalized
|
||||||
|
|
||||||
|
|
||||||
|
def _normalize_labware(data):
|
||||||
|
labware = {}
|
||||||
|
for item in data:
|
||||||
|
reagent_name = item.get("reagent_name")
|
||||||
|
key = reagent_name or item.get("material_name") or item.get("name")
|
||||||
|
if not key:
|
||||||
|
continue
|
||||||
|
key = str(key)
|
||||||
|
idx = 1
|
||||||
|
original_key = key
|
||||||
|
while key in labware:
|
||||||
|
idx += 1
|
||||||
|
key = f"{original_key}_{idx}"
|
||||||
|
|
||||||
|
labware[key] = {
|
||||||
|
"slot": item.get("positions") or item.get("slot"),
|
||||||
|
"labware": item.get("material_name") or item.get("labware"),
|
||||||
|
"well": item.get("well", []),
|
||||||
|
"type": item.get("type", "reagent"),
|
||||||
|
"role": item.get("role", ""),
|
||||||
|
"name": key,
|
||||||
|
}
|
||||||
|
return labware
|
||||||
|
|
||||||
|
|
||||||
|
@pytest.mark.parametrize("protocol_name", [
|
||||||
|
"example_bio",
|
||||||
|
# "bioyond_materials_liquidhandling_1",
|
||||||
|
"example_prcxi",
|
||||||
|
])
|
||||||
|
def test_build_protocol_graph(protocol_name):
|
||||||
|
data_path = Path(__file__).with_name(f"{protocol_name}.json")
|
||||||
|
with data_path.open("r", encoding="utf-8") as fp:
|
||||||
|
d = json.load(fp)
|
||||||
|
|
||||||
|
if "workflow" in d and "reagent" in d:
|
||||||
|
protocol_steps = d["workflow"]
|
||||||
|
labware_info = d["reagent"]
|
||||||
|
elif "steps_info" in d and "labware_info" in d:
|
||||||
|
protocol_steps = _normalize_steps(d["steps_info"])
|
||||||
|
labware_info = _normalize_labware(d["labware_info"])
|
||||||
|
else:
|
||||||
|
raise ValueError("Unsupported protocol format")
|
||||||
|
|
||||||
|
graph = build_protocol_graph(
|
||||||
|
labware_info=labware_info,
|
||||||
|
protocol_steps=protocol_steps,
|
||||||
|
workstation_name="PRCXi",
|
||||||
|
)
|
||||||
|
timestamp = datetime.now().strftime("%Y%m%d_%H%M")
|
||||||
|
output_path = data_path.with_name(f"{protocol_name}_graph_{timestamp}.png")
|
||||||
|
draw_protocol_graph_with_ports(graph, str(output_path))
|
||||||
|
print(graph)
|
||||||
@@ -1,3 +1,9 @@
|
|||||||
|
from functools import wraps
|
||||||
|
from typing import Any, Callable, Optional, TypeVar
|
||||||
|
|
||||||
|
F = TypeVar("F", bound=Callable[..., Any])
|
||||||
|
|
||||||
|
|
||||||
def singleton(cls):
|
def singleton(cls):
|
||||||
"""
|
"""
|
||||||
单例装饰器
|
单例装饰器
|
||||||
@@ -12,3 +18,167 @@ def singleton(cls):
|
|||||||
|
|
||||||
return get_instance
|
return get_instance
|
||||||
|
|
||||||
|
|
||||||
|
def topic_config(
|
||||||
|
period: Optional[float] = None,
|
||||||
|
print_publish: Optional[bool] = None,
|
||||||
|
qos: Optional[int] = None,
|
||||||
|
) -> Callable[[F], F]:
|
||||||
|
"""
|
||||||
|
Topic发布配置装饰器
|
||||||
|
|
||||||
|
用于装饰 get_{attr_name} 方法或 @property，控制对应属性的ROS topic发布行为。
|
||||||
|
|
||||||
|
Args:
|
||||||
|
period: 发布周期（秒）。None 表示使用默认值 5.0
|
||||||
|
print_publish: 是否打印发布日志。None 表示使用节点默认配置
|
||||||
|
qos: QoS深度配置。None 表示使用默认值 10
|
||||||
|
|
||||||
|
Example:
|
||||||
|
class MyDriver:
|
||||||
|
# 方式1: 装饰 get_{attr_name} 方法
|
||||||
|
@topic_config(period=1.0, print_publish=False, qos=5)
|
||||||
|
def get_temperature(self):
|
||||||
|
return self._temperature
|
||||||
|
|
||||||
|
# 方式2: 与 @property 连用（topic_config 放在下面）
|
||||||
|
@property
|
||||||
|
@topic_config(period=0.1)
|
||||||
|
def position(self):
|
||||||
|
return self._position
|
||||||
|
|
||||||
|
Note:
|
||||||
|
与 @property 连用时，@topic_config 必须放在 @property 下面，
|
||||||
|
这样装饰器执行顺序为：先 topic_config 添加配置，再 property 包装。
|
||||||
|
"""
|
||||||
|
|
||||||
|
def decorator(func: F) -> F:
|
||||||
|
@wraps(func)
|
||||||
|
def wrapper(*args, **kwargs):
|
||||||
|
return func(*args, **kwargs)
|
||||||
|
|
||||||
|
# 在函数上附加配置属性 (type: ignore 用于动态属性)
|
||||||
|
wrapper._topic_period = period # type: ignore[attr-defined]
|
||||||
|
wrapper._topic_print_publish = print_publish # type: ignore[attr-defined]
|
||||||
|
wrapper._topic_qos = qos # type: ignore[attr-defined]
|
||||||
|
wrapper._has_topic_config = True # type: ignore[attr-defined]
|
||||||
|
|
||||||
|
return wrapper # type: ignore[return-value]
|
||||||
|
|
||||||
|
return decorator
|
||||||
|
|
||||||
|
|
||||||
|
def get_topic_config(func) -> dict:
|
||||||
|
"""
|
||||||
|
获取函数上的topic配置
|
||||||
|
|
||||||
|
Args:
|
||||||
|
func: 被装饰的函数
|
||||||
|
|
||||||
|
Returns:
|
||||||
|
包含 period, print_publish, qos 的配置字典
|
||||||
|
"""
|
||||||
|
if hasattr(func, "_has_topic_config") and getattr(func, "_has_topic_config", False):
|
||||||
|
return {
|
||||||
|
"period": getattr(func, "_topic_period", None),
|
||||||
|
"print_publish": getattr(func, "_topic_print_publish", None),
|
||||||
|
"qos": getattr(func, "_topic_qos", None),
|
||||||
|
}
|
||||||
|
return {}
|
||||||
|
|
||||||
|
|
||||||
|
def subscribe(
|
||||||
|
topic: str,
|
||||||
|
msg_type: Optional[type] = None,
|
||||||
|
qos: int = 10,
|
||||||
|
) -> Callable[[F], F]:
|
||||||
|
"""
|
||||||
|
Topic订阅装饰器
|
||||||
|
|
||||||
|
用于装饰 driver 类中的方法，使其成为 ROS topic 的订阅回调。
|
||||||
|
当 ROS2DeviceNode 初始化时，会自动扫描并创建对应的订阅者。
|
||||||
|
|
||||||
|
Args:
|
||||||
|
topic: Topic 名称模板，支持以下占位符：
|
||||||
|
- {device_id}: 设备ID (如 "pump_1")
|
||||||
|
- {namespace}: 完整命名空间 (如 "/devices/pump_1")
|
||||||
|
msg_type: ROS 消息类型。如果为 None，需要在回调函数的类型注解中指定
|
||||||
|
qos: QoS 深度配置，默认为 10
|
||||||
|
|
||||||
|
Example:
|
||||||
|
from std_msgs.msg import String, Float64
|
||||||
|
|
||||||
|
class MyDriver:
|
||||||
|
@subscribe(topic="/devices/{device_id}/set_speed", msg_type=Float64)
|
||||||
|
def on_speed_update(self, msg: Float64):
|
||||||
|
self._speed = msg.data
|
||||||
|
print(f"Speed updated to: {self._speed}")
|
||||||
|
|
||||||
|
@subscribe(topic="{namespace}/command")
|
||||||
|
def on_command(self, msg: String):
|
||||||
|
# msg_type 可从类型注解推断
|
||||||
|
self.execute_command(msg.data)
|
||||||
|
|
||||||
|
Note:
|
||||||
|
- 回调方法的第一个参数是 self，第二个参数是收到的 ROS 消息
|
||||||
|
- topic 中的占位符会在创建订阅时被实际值替换
|
||||||
|
"""
|
||||||
|
|
||||||
|
def decorator(func: F) -> F:
|
||||||
|
@wraps(func)
|
||||||
|
def wrapper(*args, **kwargs):
|
||||||
|
return func(*args, **kwargs)
|
||||||
|
|
||||||
|
# 在函数上附加订阅配置
|
||||||
|
wrapper._subscribe_topic = topic # type: ignore[attr-defined]
|
||||||
|
wrapper._subscribe_msg_type = msg_type # type: ignore[attr-defined]
|
||||||
|
wrapper._subscribe_qos = qos # type: ignore[attr-defined]
|
||||||
|
wrapper._has_subscribe = True # type: ignore[attr-defined]
|
||||||
|
|
||||||
|
return wrapper # type: ignore[return-value]
|
||||||
|
|
||||||
|
return decorator
|
||||||
|
|
||||||
|
|
||||||
|
def get_subscribe_config(func) -> dict:
|
||||||
|
"""
|
||||||
|
获取函数上的订阅配置
|
||||||
|
|
||||||
|
Args:
|
||||||
|
func: 被装饰的函数
|
||||||
|
|
||||||
|
Returns:
|
||||||
|
包含 topic, msg_type, qos 的配置字典
|
||||||
|
"""
|
||||||
|
if hasattr(func, "_has_subscribe") and getattr(func, "_has_subscribe", False):
|
||||||
|
return {
|
||||||
|
"topic": getattr(func, "_subscribe_topic", None),
|
||||||
|
"msg_type": getattr(func, "_subscribe_msg_type", None),
|
||||||
|
"qos": getattr(func, "_subscribe_qos", 10),
|
||||||
|
}
|
||||||
|
return {}
|
||||||
|
|
||||||
|
|
||||||
|
def get_all_subscriptions(instance) -> list:
|
||||||
|
"""
|
||||||
|
扫描实例的所有方法，获取带有 @subscribe 装饰器的方法及其配置
|
||||||
|
|
||||||
|
Args:
|
||||||
|
instance: 要扫描的实例
|
||||||
|
|
||||||
|
Returns:
|
||||||
|
包含 (method_name, method, config) 元组的列表
|
||||||
|
"""
|
||||||
|
subscriptions = []
|
||||||
|
for attr_name in dir(instance):
|
||||||
|
if attr_name.startswith("_"):
|
||||||
|
continue
|
||||||
|
try:
|
||||||
|
attr = getattr(instance, attr_name)
|
||||||
|
if callable(attr):
|
||||||
|
config = get_subscribe_config(attr)
|
||||||
|
if config:
|
||||||
|
subscriptions.append((attr_name, attr, config))
|
||||||
|
except Exception:
|
||||||
|
pass
|
||||||
|
return subscriptions
|
||||||
|
|||||||
@@ -1,547 +0,0 @@
|
|||||||
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())))
|
|
||||||
@@ -1,356 +0,0 @@
|
|||||||
"""
|
|
||||||
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
|
|
||||||
@@ -1,241 +0,0 @@
|
|||||||
import ast
|
|
||||||
import json
|
|
||||||
from typing import Dict, List, Any, Tuple, Optional
|
|
||||||
|
|
||||||
from .common import WorkflowGraph, RegistryAdapter
|
|
||||||
|
|
||||||
Json = Dict[str, Any]
|
|
||||||
|
|
||||||
# ---------------- Converter ----------------
|
|
||||||
|
|
||||||
class DeviceMethodConverter:
|
|
||||||
"""
|
|
||||||
- 字段统一：resource_name（原 device_class）、template_name（原 action_key）
|
|
||||||
- params 单层；inputs 使用 'params.' 前缀
|
|
||||||
- SimpleGraph.add_workflow_node 负责变量连线与边
|
|
||||||
"""
|
|
||||||
def __init__(self, device_registry: Optional[Dict[str, Any]] = None):
|
|
||||||
self.graph = WorkflowGraph()
|
|
||||||
self.variable_sources: Dict[str, Dict[str, Any]] = {} # var -> {node_id, output_name}
|
|
||||||
self.instance_to_resource: Dict[str, Optional[str]] = {} # 实例名 -> resource_name
|
|
||||||
self.node_id_counter: int = 0
|
|
||||||
self.registry = RegistryAdapter(device_registry or {})
|
|
||||||
|
|
||||||
# ---- helpers ----
|
|
||||||
def _new_node_id(self) -> int:
|
|
||||||
nid = self.node_id_counter
|
|
||||||
self.node_id_counter += 1
|
|
||||||
return nid
|
|
||||||
|
|
||||||
def _assign_targets(self, targets) -> List[str]:
|
|
||||||
names: List[str] = []
|
|
||||||
import ast
|
|
||||||
if isinstance(targets, ast.Tuple):
|
|
||||||
for elt in targets.elts:
|
|
||||||
if isinstance(elt, ast.Name):
|
|
||||||
names.append(elt.id)
|
|
||||||
elif isinstance(targets, ast.Name):
|
|
||||||
names.append(targets.id)
|
|
||||||
return names
|
|
||||||
|
|
||||||
def _extract_device_instantiation(self, node) -> Optional[Tuple[str, str]]:
|
|
||||||
import ast
|
|
||||||
if not isinstance(node.value, ast.Call):
|
|
||||||
return None
|
|
||||||
callee = node.value.func
|
|
||||||
if isinstance(callee, ast.Name):
|
|
||||||
class_name = callee.id
|
|
||||||
elif isinstance(callee, ast.Attribute) and isinstance(callee.value, ast.Name):
|
|
||||||
class_name = callee.attr
|
|
||||||
else:
|
|
||||||
return None
|
|
||||||
if isinstance(node.targets[0], ast.Name):
|
|
||||||
instance = node.targets[0].id
|
|
||||||
return instance, class_name
|
|
||||||
return None
|
|
||||||
|
|
||||||
def _extract_call(self, call) -> Tuple[str, str, Dict[str, Any], str]:
|
|
||||||
import ast
|
|
||||||
owner_name, method_name, call_kind = "", "", "func"
|
|
||||||
if isinstance(call.func, ast.Attribute):
|
|
||||||
method_name = call.func.attr
|
|
||||||
if isinstance(call.func.value, ast.Name):
|
|
||||||
owner_name = call.func.value.id
|
|
||||||
call_kind = "instance" if owner_name in self.instance_to_resource else "class_or_module"
|
|
||||||
elif isinstance(call.func.value, ast.Attribute) and isinstance(call.func.value.value, ast.Name):
|
|
||||||
owner_name = call.func.value.attr
|
|
||||||
call_kind = "class_or_module"
|
|
||||||
elif isinstance(call.func, ast.Name):
|
|
||||||
method_name = call.func.id
|
|
||||||
call_kind = "func"
|
|
||||||
|
|
||||||
def pack(node):
|
|
||||||
if isinstance(node, ast.Name):
|
|
||||||
return {"type": "variable", "value": node.id}
|
|
||||||
if isinstance(node, ast.Constant):
|
|
||||||
return {"type": "constant", "value": node.value}
|
|
||||||
if isinstance(node, ast.Dict):
|
|
||||||
return {"type": "dict", "value": self._parse_dict(node)}
|
|
||||||
if isinstance(node, ast.List):
|
|
||||||
return {"type": "list", "value": self._parse_list(node)}
|
|
||||||
return {"type": "raw", "value": ast.unparse(node) if hasattr(ast, "unparse") else str(node)}
|
|
||||||
|
|
||||||
args: Dict[str, Any] = {}
|
|
||||||
pos: List[Any] = []
|
|
||||||
for a in call.args:
|
|
||||||
pos.append(pack(a))
|
|
||||||
for kw in call.keywords:
|
|
||||||
args[kw.arg] = pack(kw.value)
|
|
||||||
if pos:
|
|
||||||
args["_positional"] = pos
|
|
||||||
return owner_name, method_name, args, call_kind
|
|
||||||
|
|
||||||
def _parse_dict(self, node) -> Dict[str, Any]:
|
|
||||||
import ast
|
|
||||||
out: Dict[str, Any] = {}
|
|
||||||
for k, v in zip(node.keys, node.values):
|
|
||||||
if isinstance(k, ast.Constant):
|
|
||||||
key = str(k.value)
|
|
||||||
if isinstance(v, ast.Name):
|
|
||||||
out[key] = f"var:{v.id}"
|
|
||||||
elif isinstance(v, ast.Constant):
|
|
||||||
out[key] = v.value
|
|
||||||
elif isinstance(v, ast.Dict):
|
|
||||||
out[key] = self._parse_dict(v)
|
|
||||||
elif isinstance(v, ast.List):
|
|
||||||
out[key] = self._parse_list(v)
|
|
||||||
return out
|
|
||||||
|
|
||||||
def _parse_list(self, node) -> List[Any]:
|
|
||||||
import ast
|
|
||||||
out: List[Any] = []
|
|
||||||
for elt in node.elts:
|
|
||||||
if isinstance(elt, ast.Name):
|
|
||||||
out.append(f"var:{elt.id}")
|
|
||||||
elif isinstance(elt, ast.Constant):
|
|
||||||
out.append(elt.value)
|
|
||||||
elif isinstance(elt, ast.Dict):
|
|
||||||
out.append(self._parse_dict(elt))
|
|
||||||
elif isinstance(elt, ast.List):
|
|
||||||
out.append(self._parse_list(elt))
|
|
||||||
return out
|
|
||||||
|
|
||||||
def _normalize_var_tokens(self, x: Any) -> Any:
|
|
||||||
if isinstance(x, str) and x.startswith("var:"):
|
|
||||||
return {"__var__": x[4:]}
|
|
||||||
if isinstance(x, list):
|
|
||||||
return [self._normalize_var_tokens(i) for i in x]
|
|
||||||
if isinstance(x, dict):
|
|
||||||
return {k: self._normalize_var_tokens(v) for k, v in x.items()}
|
|
||||||
return x
|
|
||||||
|
|
||||||
def _make_params_payload(self, resource_name: Optional[str], template_name: str, call_args: Dict[str, Any]) -> Dict[str, Any]:
|
|
||||||
input_keys = self.registry.get_action_input_keys(resource_name, template_name) if resource_name else []
|
|
||||||
defaults = self.registry.get_action_goal_default(resource_name, template_name) if resource_name else {}
|
|
||||||
params: Dict[str, Any] = dict(defaults)
|
|
||||||
|
|
||||||
def unpack(p):
|
|
||||||
t, v = p.get("type"), p.get("value")
|
|
||||||
if t == "variable":
|
|
||||||
return {"__var__": v}
|
|
||||||
if t == "dict":
|
|
||||||
return self._normalize_var_tokens(v)
|
|
||||||
if t == "list":
|
|
||||||
return self._normalize_var_tokens(v)
|
|
||||||
return v
|
|
||||||
|
|
||||||
for k, p in call_args.items():
|
|
||||||
if k == "_positional":
|
|
||||||
continue
|
|
||||||
params[k] = unpack(p)
|
|
||||||
|
|
||||||
pos = call_args.get("_positional", [])
|
|
||||||
if pos:
|
|
||||||
if input_keys:
|
|
||||||
for i, p in enumerate(pos):
|
|
||||||
if i >= len(input_keys):
|
|
||||||
break
|
|
||||||
name = input_keys[i]
|
|
||||||
if name in params:
|
|
||||||
continue
|
|
||||||
params[name] = unpack(p)
|
|
||||||
else:
|
|
||||||
for i, p in enumerate(pos):
|
|
||||||
params[f"arg_{i}"] = unpack(p)
|
|
||||||
return params
|
|
||||||
|
|
||||||
# ---- handlers ----
|
|
||||||
def _on_assign(self, stmt):
|
|
||||||
import ast
|
|
||||||
inst = self._extract_device_instantiation(stmt)
|
|
||||||
if inst:
|
|
||||||
instance, code_class = inst
|
|
||||||
resource_name = self.registry.resolve_resource_by_classname(code_class)
|
|
||||||
self.instance_to_resource[instance] = resource_name
|
|
||||||
return
|
|
||||||
|
|
||||||
if isinstance(stmt.value, ast.Call):
|
|
||||||
owner, method, call_args, kind = self._extract_call(stmt.value)
|
|
||||||
if kind == "instance":
|
|
||||||
device_key = owner
|
|
||||||
resource_name = self.instance_to_resource.get(owner)
|
|
||||||
else:
|
|
||||||
device_key = owner
|
|
||||||
resource_name = self.registry.resolve_resource_by_classname(owner)
|
|
||||||
|
|
||||||
module = self.registry.get_device_module(resource_name)
|
|
||||||
params = self._make_params_payload(resource_name, method, call_args)
|
|
||||||
|
|
||||||
nid = self._new_node_id()
|
|
||||||
self.graph.add_workflow_node(
|
|
||||||
nid,
|
|
||||||
device_key=device_key,
|
|
||||||
resource_name=resource_name, # ✅
|
|
||||||
module=module,
|
|
||||||
template_name=method, # ✅
|
|
||||||
params=params,
|
|
||||||
variable_sources=self.variable_sources,
|
|
||||||
add_ready_if_no_vars=True,
|
|
||||||
prev_node_id=(nid - 1) if nid > 0 else None,
|
|
||||||
)
|
|
||||||
|
|
||||||
out_vars = self._assign_targets(stmt.targets[0])
|
|
||||||
for var in out_vars:
|
|
||||||
self.variable_sources[var] = {"node_id": nid, "output_name": "result"}
|
|
||||||
|
|
||||||
def _on_expr(self, stmt):
|
|
||||||
import ast
|
|
||||||
if not isinstance(stmt.value, ast.Call):
|
|
||||||
return
|
|
||||||
owner, method, call_args, kind = self._extract_call(stmt.value)
|
|
||||||
if kind == "instance":
|
|
||||||
device_key = owner
|
|
||||||
resource_name = self.instance_to_resource.get(owner)
|
|
||||||
else:
|
|
||||||
device_key = owner
|
|
||||||
resource_name = self.registry.resolve_resource_by_classname(owner)
|
|
||||||
|
|
||||||
module = self.registry.get_device_module(resource_name)
|
|
||||||
params = self._make_params_payload(resource_name, method, call_args)
|
|
||||||
|
|
||||||
nid = self._new_node_id()
|
|
||||||
self.graph.add_workflow_node(
|
|
||||||
nid,
|
|
||||||
device_key=device_key,
|
|
||||||
resource_name=resource_name, # ✅
|
|
||||||
module=module,
|
|
||||||
template_name=method, # ✅
|
|
||||||
params=params,
|
|
||||||
variable_sources=self.variable_sources,
|
|
||||||
add_ready_if_no_vars=True,
|
|
||||||
prev_node_id=(nid - 1) if nid > 0 else None,
|
|
||||||
)
|
|
||||||
|
|
||||||
def convert(self, python_code: str):
|
|
||||||
tree = ast.parse(python_code)
|
|
||||||
for stmt in tree.body:
|
|
||||||
if isinstance(stmt, ast.Assign):
|
|
||||||
self._on_assign(stmt)
|
|
||||||
elif isinstance(stmt, ast.Expr):
|
|
||||||
self._on_expr(stmt)
|
|
||||||
return self
|
|
||||||
@@ -1,131 +0,0 @@
|
|||||||
from typing import List, Any, Dict
|
|
||||||
import xml.etree.ElementTree as ET
|
|
||||||
|
|
||||||
|
|
||||||
def convert_to_type(val: str) -> Any:
|
|
||||||
"""将字符串值转换为适当的数据类型"""
|
|
||||||
if val == "True":
|
|
||||||
return True
|
|
||||||
if val == "False":
|
|
||||||
return False
|
|
||||||
if val == "?":
|
|
||||||
return None
|
|
||||||
if val.endswith(" g"):
|
|
||||||
return float(val.split(" ")[0])
|
|
||||||
if val.endswith("mg"):
|
|
||||||
return float(val.split("mg")[0])
|
|
||||||
elif val.endswith("mmol"):
|
|
||||||
return float(val.split("mmol")[0]) / 1000
|
|
||||||
elif val.endswith("mol"):
|
|
||||||
return float(val.split("mol")[0])
|
|
||||||
elif val.endswith("ml"):
|
|
||||||
return float(val.split("ml")[0])
|
|
||||||
elif val.endswith("RPM"):
|
|
||||||
return float(val.split("RPM")[0])
|
|
||||||
elif val.endswith(" °C"):
|
|
||||||
return float(val.split(" ")[0])
|
|
||||||
elif val.endswith(" %"):
|
|
||||||
return float(val.split(" ")[0])
|
|
||||||
return val
|
|
||||||
|
|
||||||
|
|
||||||
def flatten_xdl_procedure(procedure_elem: ET.Element) -> List[ET.Element]:
|
|
||||||
"""展平嵌套的XDL程序结构"""
|
|
||||||
flattened_operations = []
|
|
||||||
TEMP_UNSUPPORTED_PROTOCOL = ["Purge", "Wait", "Stir", "ResetHandling"]
|
|
||||||
|
|
||||||
def extract_operations(element: ET.Element):
|
|
||||||
if element.tag not in ["Prep", "Reaction", "Workup", "Purification", "Procedure"]:
|
|
||||||
if element.tag not in TEMP_UNSUPPORTED_PROTOCOL:
|
|
||||||
flattened_operations.append(element)
|
|
||||||
|
|
||||||
for child in element:
|
|
||||||
extract_operations(child)
|
|
||||||
|
|
||||||
for child in procedure_elem:
|
|
||||||
extract_operations(child)
|
|
||||||
|
|
||||||
return flattened_operations
|
|
||||||
|
|
||||||
|
|
||||||
def parse_xdl_content(xdl_content: str) -> tuple:
|
|
||||||
"""解析XDL内容"""
|
|
||||||
try:
|
|
||||||
xdl_content_cleaned = "".join(c for c in xdl_content if c.isprintable())
|
|
||||||
root = ET.fromstring(xdl_content_cleaned)
|
|
||||||
|
|
||||||
synthesis_elem = root.find("Synthesis")
|
|
||||||
if synthesis_elem is None:
|
|
||||||
return None, None, None
|
|
||||||
|
|
||||||
# 解析硬件组件
|
|
||||||
hardware_elem = synthesis_elem.find("Hardware")
|
|
||||||
hardware = []
|
|
||||||
if hardware_elem is not None:
|
|
||||||
hardware = [{"id": c.get("id"), "type": c.get("type")} for c in hardware_elem.findall("Component")]
|
|
||||||
|
|
||||||
# 解析试剂
|
|
||||||
reagents_elem = synthesis_elem.find("Reagents")
|
|
||||||
reagents = []
|
|
||||||
if reagents_elem is not None:
|
|
||||||
reagents = [{"name": r.get("name"), "role": r.get("role", "")} for r in reagents_elem.findall("Reagent")]
|
|
||||||
|
|
||||||
# 解析程序
|
|
||||||
procedure_elem = synthesis_elem.find("Procedure")
|
|
||||||
if procedure_elem is None:
|
|
||||||
return None, None, None
|
|
||||||
|
|
||||||
flattened_operations = flatten_xdl_procedure(procedure_elem)
|
|
||||||
return hardware, reagents, flattened_operations
|
|
||||||
|
|
||||||
except ET.ParseError as e:
|
|
||||||
raise ValueError(f"Invalid XDL format: {e}")
|
|
||||||
|
|
||||||
|
|
||||||
def convert_xdl_to_dict(xdl_content: str) -> Dict[str, Any]:
|
|
||||||
"""
|
|
||||||
将XDL XML格式转换为标准的字典格式
|
|
||||||
|
|
||||||
Args:
|
|
||||||
xdl_content: XDL XML内容
|
|
||||||
|
|
||||||
Returns:
|
|
||||||
转换结果，包含步骤和器材信息
|
|
||||||
"""
|
|
||||||
try:
|
|
||||||
hardware, reagents, flattened_operations = parse_xdl_content(xdl_content)
|
|
||||||
if hardware is None:
|
|
||||||
return {"error": "Failed to parse XDL content", "success": False}
|
|
||||||
|
|
||||||
# 将XDL元素转换为字典格式
|
|
||||||
steps_data = []
|
|
||||||
for elem in flattened_operations:
|
|
||||||
# 转换参数类型
|
|
||||||
parameters = {}
|
|
||||||
for key, val in elem.attrib.items():
|
|
||||||
converted_val = convert_to_type(val)
|
|
||||||
if converted_val is not None:
|
|
||||||
parameters[key] = converted_val
|
|
||||||
|
|
||||||
step_dict = {
|
|
||||||
"operation": elem.tag,
|
|
||||||
"parameters": parameters,
|
|
||||||
"description": elem.get("purpose", f"Operation: {elem.tag}"),
|
|
||||||
}
|
|
||||||
steps_data.append(step_dict)
|
|
||||||
|
|
||||||
# 合并硬件和试剂为统一的labware_info格式
|
|
||||||
labware_data = []
|
|
||||||
labware_data.extend({"id": hw["id"], "type": "hardware", **hw} for hw in hardware)
|
|
||||||
labware_data.extend({"name": reagent["name"], "type": "reagent", **reagent} for reagent in reagents)
|
|
||||||
|
|
||||||
return {
|
|
||||||
"success": True,
|
|
||||||
"steps": steps_data,
|
|
||||||
"labware": labware_data,
|
|
||||||
"message": f"Successfully converted XDL to dict format. Found {len(steps_data)} steps and {len(labware_data)} labware items.",
|
|
||||||
}
|
|
||||||
|
|
||||||
except Exception as e:
|
|
||||||
error_msg = f"XDL conversion failed: {str(e)}"
|
|
||||||
return {"error": error_msg, "success": False}
|
|
||||||
Reference in New Issue
Block a user