mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2025-12-17 04:51:10 +00:00
add unilabos/workflow and entrypoint
This commit is contained in:
Junhan Chang
Xuwznln
@@ -2,7 +2,6 @@ import json
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import logging
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import traceback
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import uuid
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import xml.etree.ElementTree as ET
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from typing import Any, Dict, List
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import networkx as nx
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@@ -25,7 +24,15 @@ class SimpleGraph:
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def add_edge(self, source, target, **attrs):
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"""添加边"""
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edge = {"source": source, "target": target, **attrs}
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# edge = {"source": source, "target": target, **attrs}
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edge = {
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"source": source, "target": target,
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"source_node_uuid": source,
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"target_node_uuid": target,
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"source_handle_io": "source",
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"target_handle_io": "target",
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**attrs
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}
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self.edges.append(edge)
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def to_dict(self):
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@@ -42,6 +49,7 @@ class SimpleGraph:
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"multigraph": False,
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"graph": {},
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"nodes": nodes_list,
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"edges": self.edges,
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"links": self.edges,
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}
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@@ -58,495 +66,8 @@ def extract_json_from_markdown(text: str) -> str:
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return text
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def convert_to_type(val: str) -> Any:
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"""将字符串值转换为适当的数据类型"""
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if val == "True":
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return True
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if val == "False":
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return False
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if val == "?":
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return None
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if val.endswith(" g"):
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return float(val.split(" ")[0])
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if val.endswith("mg"):
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return float(val.split("mg")[0])
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elif val.endswith("mmol"):
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return float(val.split("mmol")[0]) / 1000
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elif val.endswith("mol"):
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return float(val.split("mol")[0])
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elif val.endswith("ml"):
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return float(val.split("ml")[0])
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elif val.endswith("RPM"):
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return float(val.split("RPM")[0])
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elif val.endswith(" °C"):
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return float(val.split(" ")[0])
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elif val.endswith(" %"):
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return float(val.split(" ")[0])
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return val
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def refactor_data(data: List[Dict[str, Any]]) -> List[Dict[str, Any]]:
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"""统一的数据重构函数，根据操作类型自动选择模板"""
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refactored_data = []
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# 定义操作映射，包含生物实验和有机化学的所有操作
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OPERATION_MAPPING = {
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# 生物实验操作
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"transfer_liquid": "SynBioFactory-liquid_handler.prcxi-transfer_liquid",
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"transfer": "SynBioFactory-liquid_handler.biomek-transfer",
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"incubation": "SynBioFactory-liquid_handler.biomek-incubation",
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"move_labware": "SynBioFactory-liquid_handler.biomek-move_labware",
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"oscillation": "SynBioFactory-liquid_handler.biomek-oscillation",
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# 有机化学操作
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"HeatChillToTemp": "SynBioFactory-workstation-HeatChillProtocol",
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"StopHeatChill": "SynBioFactory-workstation-HeatChillStopProtocol",
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"StartHeatChill": "SynBioFactory-workstation-HeatChillStartProtocol",
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"HeatChill": "SynBioFactory-workstation-HeatChillProtocol",
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"Dissolve": "SynBioFactory-workstation-DissolveProtocol",
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"Transfer": "SynBioFactory-workstation-TransferProtocol",
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"Evaporate": "SynBioFactory-workstation-EvaporateProtocol",
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"Recrystallize": "SynBioFactory-workstation-RecrystallizeProtocol",
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"Filter": "SynBioFactory-workstation-FilterProtocol",
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"Dry": "SynBioFactory-workstation-DryProtocol",
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"Add": "SynBioFactory-workstation-AddProtocol",
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}
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UNSUPPORTED_OPERATIONS = ["Purge", "Wait", "Stir", "ResetHandling"]
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for step in data:
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operation = step.get("action")
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if not operation or operation in UNSUPPORTED_OPERATIONS:
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continue
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# 处理重复操作
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if operation == "Repeat":
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times = step.get("times", step.get("parameters", {}).get("times", 1))
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sub_steps = step.get("steps", step.get("parameters", {}).get("steps", []))
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for i in range(int(times)):
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sub_data = refactor_data(sub_steps)
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refactored_data.extend(sub_data)
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continue
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# 获取模板名称
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template = OPERATION_MAPPING.get(operation)
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if not template:
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# 自动推断模板类型
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if operation.lower() in ["transfer", "incubation", "move_labware", "oscillation"]:
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template = f"SynBioFactory-liquid_handler.biomek-{operation}"
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else:
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template = f"SynBioFactory-workstation-{operation}Protocol"
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# 创建步骤数据
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step_data = {
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"template": template,
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"description": step.get("description", step.get("purpose", f"{operation} operation")),
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"lab_node_type": "Device",
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"parameters": step.get("parameters", step.get("action_args", {})),
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}
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refactored_data.append(step_data)
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return refactored_data
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def build_protocol_graph(
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labware_info: List[Dict[str, Any]], protocol_steps: List[Dict[str, Any]], workstation_name: str
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) -> SimpleGraph:
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"""统一的协议图构建函数，根据设备类型自动选择构建逻辑"""
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G = SimpleGraph()
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resource_last_writer = {}
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LAB_NAME = "SynBioFactory"
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protocol_steps = refactor_data(protocol_steps)
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# 检查协议步骤中的模板来判断协议类型
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has_biomek_template = any(
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("biomek" in step.get("template", "")) or ("prcxi" in step.get("template", ""))
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for step in protocol_steps
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)
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if has_biomek_template:
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# 生物实验协议图构建
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for labware_id, labware in labware_info.items():
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node_id = str(uuid.uuid4())
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labware_attrs = labware.copy()
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labware_id = labware_attrs.pop("id", labware_attrs.get("name", f"labware_{uuid.uuid4()}"))
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labware_attrs["description"] = labware_id
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labware_attrs["lab_node_type"] = (
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"Reagent" if "Plate" in str(labware_id) else "Labware" if "Rack" in str(labware_id) else "Sample"
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)
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labware_attrs["device_id"] = workstation_name
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G.add_node(node_id, template=f"{LAB_NAME}-host_node-create_resource", **labware_attrs)
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resource_last_writer[labware_id] = f"{node_id}:labware"
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# 处理协议步骤
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prev_node = None
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for i, step in enumerate(protocol_steps):
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node_id = str(uuid.uuid4())
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G.add_node(node_id, **step)
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# 添加控制流边
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if prev_node is not None:
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G.add_edge(prev_node, node_id, source_port="ready", target_port="ready")
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prev_node = node_id
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# 处理物料流
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params = step.get("parameters", {})
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if "sources" in params and params["sources"] in resource_last_writer:
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source_node, source_port = resource_last_writer[params["sources"]].split(":")
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G.add_edge(source_node, node_id, source_port=source_port, target_port="labware")
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if "targets" in params:
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resource_last_writer[params["targets"]] = f"{node_id}:labware"
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# 添加协议结束节点
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end_id = str(uuid.uuid4())
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G.add_node(end_id, template=f"{LAB_NAME}-liquid_handler.biomek-run_protocol")
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if prev_node is not None:
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G.add_edge(prev_node, end_id, source_port="ready", target_port="ready")
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else:
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# 有机化学协议图构建
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WORKSTATION_ID = workstation_name
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# 为所有labware创建资源节点
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for item_id, item in labware_info.items():
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# item_id = item.get("id") or item.get("name", f"item_{uuid.uuid4()}")
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node_id = str(uuid.uuid4())
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# 判断节点类型
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if item.get("type") == "hardware" or "reactor" in str(item_id).lower():
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if "reactor" not in str(item_id).lower():
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continue
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lab_node_type = "Sample"
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description = f"Prepare Reactor: {item_id}"
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liquid_type = []
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liquid_volume = []
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else:
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lab_node_type = "Reagent"
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description = f"Add Reagent to Flask: {item_id}"
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liquid_type = [item_id]
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liquid_volume = [1e5]
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G.add_node(
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node_id,
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template=f"{LAB_NAME}-host_node-create_resource",
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description=description,
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lab_node_type=lab_node_type,
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res_id=item_id,
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device_id=WORKSTATION_ID,
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class_name="container",
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parent=WORKSTATION_ID,
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bind_locations={"x": 0.0, "y": 0.0, "z": 0.0},
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liquid_input_slot=[-1],
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liquid_type=liquid_type,
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liquid_volume=liquid_volume,
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slot_on_deck="",
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role=item.get("role", ""),
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)
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resource_last_writer[item_id] = f"{node_id}:labware"
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last_control_node_id = None
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# 处理协议步骤
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for step in protocol_steps:
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node_id = str(uuid.uuid4())
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G.add_node(node_id, **step)
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# 控制流
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if last_control_node_id is not None:
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G.add_edge(last_control_node_id, node_id, source_port="ready", target_port="ready")
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last_control_node_id = node_id
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# 物料流
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params = step.get("parameters", {})
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input_resources = {
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"Vessel": params.get("vessel"),
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"ToVessel": params.get("to_vessel"),
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"FromVessel": params.get("from_vessel"),
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"reagent": params.get("reagent"),
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"solvent": params.get("solvent"),
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"compound": params.get("compound"),
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"sources": params.get("sources"),
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"targets": params.get("targets"),
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}
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for target_port, resource_name in input_resources.items():
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if resource_name and resource_name in resource_last_writer:
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source_node, source_port = resource_last_writer[resource_name].split(":")
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G.add_edge(source_node, node_id, source_port=source_port, target_port=target_port)
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output_resources = {
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"VesselOut": params.get("vessel"),
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"FromVesselOut": params.get("from_vessel"),
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"ToVesselOut": params.get("to_vessel"),
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"FiltrateOut": params.get("filtrate_vessel"),
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"reagent": params.get("reagent"),
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"solvent": params.get("solvent"),
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"compound": params.get("compound"),
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"sources_out": params.get("sources"),
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"targets_out": params.get("targets"),
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}
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for source_port, resource_name in output_resources.items():
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if resource_name:
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resource_last_writer[resource_name] = f"{node_id}:{source_port}"
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return G
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def draw_protocol_graph(protocol_graph: SimpleGraph, output_path: str):
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"""
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(辅助功能) 使用 networkx 和 matplotlib 绘制协议工作流图，用于可视化。
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"""
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if not protocol_graph:
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print("Cannot draw graph: Graph object is empty.")
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return
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G = nx.DiGraph()
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for node_id, attrs in protocol_graph.nodes.items():
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label = attrs.get("description", attrs.get("template", node_id[:8]))
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G.add_node(node_id, label=label, **attrs)
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for edge in protocol_graph.edges:
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G.add_edge(edge["source"], edge["target"])
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plt.figure(figsize=(20, 15))
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try:
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pos = nx.nx_agraph.graphviz_layout(G, prog="dot")
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except Exception:
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pos = nx.shell_layout(G) # Fallback layout
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node_labels = {node: data["label"] for node, data in G.nodes(data=True)}
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nx.draw(
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G,
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pos,
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with_labels=False,
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node_size=2500,
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node_color="skyblue",
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node_shape="o",
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edge_color="gray",
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width=1.5,
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arrowsize=15,
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)
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nx.draw_networkx_labels(G, pos, labels=node_labels, font_size=8, font_weight="bold")
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plt.title("Chemical Protocol Workflow Graph", size=15)
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plt.savefig(output_path, dpi=300, bbox_inches="tight")
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plt.close()
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print(f" - Visualization saved to '{output_path}'")
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from networkx.drawing.nx_agraph import to_agraph
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import re
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COMPASS = {"n","e","s","w","ne","nw","se","sw","c"}
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def _is_compass(port: str) -> bool:
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return isinstance(port, str) and port.lower() in COMPASS
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def draw_protocol_graph_with_ports(protocol_graph, output_path: str, rankdir: str = "LR"):
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"""
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使用 Graphviz 端口语法绘制协议工作流图。
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- 若边上的 source_port/target_port 是 compass（n/e/s/w/...），直接用 compass。
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- 否则自动为节点创建 record 形状并定义命名端口 <portname>。
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最终由 PyGraphviz 渲染并输出到 output_path（后缀决定格式，如 .png/.svg/.pdf）。
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"""
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if not protocol_graph:
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print("Cannot draw graph: Graph object is empty.")
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return
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# 1) 先用 networkx 搭建有向图，保留端口属性
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G = nx.DiGraph()
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for node_id, attrs in protocol_graph.nodes.items():
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label = attrs.get("description", attrs.get("template", node_id[:8]))
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# 保留一个干净的“中心标签”，用于放在 record 的中间槽
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G.add_node(node_id, _core_label=str(label), **{k:v for k,v in attrs.items() if k not in ("label",)})
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edges_data = []
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in_ports_by_node = {} # 收集命名输入端口
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out_ports_by_node = {} # 收集命名输出端口
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for edge in protocol_graph.edges:
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u = edge["source"]
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v = edge["target"]
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sp = edge.get("source_port")
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tp = edge.get("target_port")
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# 记录到图里（保留原始端口信息）
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G.add_edge(u, v, source_port=sp, target_port=tp)
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edges_data.append((u, v, sp, tp))
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# 如果不是 compass，就按“命名端口”先归类，等会儿给节点造 record
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if sp and not _is_compass(sp):
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out_ports_by_node.setdefault(u, set()).add(str(sp))
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if tp and not _is_compass(tp):
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in_ports_by_node.setdefault(v, set()).add(str(tp))
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# 2) 转为 AGraph，使用 Graphviz 渲染
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A = to_agraph(G)
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A.graph_attr.update(rankdir=rankdir, splines="true", concentrate="false", fontsize="10")
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A.node_attr.update(shape="box", style="rounded,filled", fillcolor="lightyellow", color="#999999", fontname="Helvetica")
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A.edge_attr.update(arrowsize="0.8", color="#666666")
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# 3) 为需要命名端口的节点设置 record 形状与 label
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# 左列 = 输入端口；中间 = 核心标签；右列 = 输出端口
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for n in A.nodes():
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node = A.get_node(n)
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core = G.nodes[n].get("_core_label", n)
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in_ports = sorted(in_ports_by_node.get(n, []))
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out_ports = sorted(out_ports_by_node.get(n, []))
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# 如果该节点涉及命名端口，则用 record；否则保留原 box
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if in_ports or out_ports:
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def port_fields(ports):
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if not ports:
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return " " # 必须留一个空槽占位
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# 每个端口一个小格子，<p> name
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return "|".join(f"<{re.sub(r'[^A-Za-z0-9_:.|-]', '_', p)}> {p}" for p in ports)
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left = port_fields(in_ports)
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right = port_fields(out_ports)
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# 三栏：左(入) | 中(节点名) | 右(出)
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record_label = f"{{ {left} | {core} | {right} }}"
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node.attr.update(shape="record", label=record_label)
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else:
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# 没有命名端口：普通盒子，显示核心标签
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node.attr.update(label=str(core))
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# 4) 给边设置 headport / tailport
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# - 若端口为 compass：直接用 compass（e.g., headport="e"）
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# - 若端口为命名端口：使用在 record 中定义的 <port> 名（同名即可）
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for (u, v, sp, tp) in edges_data:
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e = A.get_edge(u, v)
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# Graphviz 属性：tail 是源，head 是目标
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if sp:
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if _is_compass(sp):
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e.attr["tailport"] = sp.lower()
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else:
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# 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(
|
||||
|
||||
Reference in New Issue
Block a user