potaserandClaude Opus 5
e641c8b9ab
【轻量拓展分析】 - 新增 gfa_core/extension_stage_lightweight/ 核心模块，支持用户上传代码/数据/原始命令 - 前端卡片式交互流程：候选核对 → 验证 → 结果审查 → 授权发布 → 运行 - Celery 不受限任务 + 轮询机制 + sessionStorage 操作恢复 - 启动脚本新增 BBAV5_LIGHTWEIGHT_* 环境变量 【WGS2GWAS 支持】 - 新增 13 个 WGS 阶段定义（QC → MAF/Missing Filter） - email_haplotype_region.py 新增 LTR-RT 分析功能 【结果区域重构】 - 单层折叠 → 三组双层折叠：RNA-seq / 基因家族 / WGS2GWAS - 结果按执行时间排序，保留最新尝试 【物种角色解析增强】 - 新增 _resolve_subfamily_request_species_roles() - 支持 reference 角色的识别 - 直接 stage 请求保留 intent 中的物种角色 【会话 Job 隔离】 - rebind_job() 跨 job 时创建新会话，返回新 conversation_id 【前端交互增强】 - RAG 文献问答模式 - NL 触发 config/samples 自动填写、亚家族确认表、基因家族成员确认表 - 执行状态从后端 resource_tasks 恢复 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
531 lines
20 KiB
Python
531 lines
20 KiB
Python
"""Durable conversation history and goal-ledger updates for the main Agent."""
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from __future__ import annotations
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import re
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from collections.abc import Mapping
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from dataclasses import dataclass
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from typing import Any
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from uuid import NAMESPACE_URL, UUID, uuid4, uuid5
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from gfa_core.mas.agent_state_repository import SQLiteAgentStateRepository
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from gfa_core.mas.workflow_models import GoalLedger
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_INTERACTION_KINDS = {
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"supplement",
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"correction",
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"switch",
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"cancel",
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"status",
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"independent",
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}
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def is_short_acknowledgement(text: str) -> bool:
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normalized = re.sub(r"[\s，,。.!！?？；;：:]+", "", str(text or "").lower())
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return normalized in {
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"同意",
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"确认",
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"可以",
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"好的",
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"好",
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"是",
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"是的",
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"继续",
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"开始吧",
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"执行吧",
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}
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@dataclass(frozen=True)
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class ConversationTurn:
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conversation_id: str
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job_id: str
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query: str
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history: tuple[dict[str, str], ...]
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goal_ledger: GoalLedger
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def _conversation_id(session_id: str) -> str:
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value = str(session_id or "").strip()
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if not value:
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return str(uuid4())
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try:
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parsed = UUID(value)
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except ValueError:
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return str(uuid5(NAMESPACE_URL, f"plantai-session:{value}"))
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return str(parsed) if str(parsed) == value else str(
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uuid5(NAMESPACE_URL, f"plantai-session:{value}")
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)
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def _history(items: Any) -> tuple[dict[str, str], ...]:
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normalized: list[dict[str, str]] = []
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for item in items or ():
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if not isinstance(item, dict) or item.get("role") not in {"user", "assistant"}:
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continue
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content = str(item.get("content") or "")
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if content:
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normalized.append({"role": item["role"], "content": content})
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return tuple(normalized[-10:])
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class PersistentConversationStore:
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def __init__(self, repository: SQLiteAgentStateRepository) -> None:
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self.repository = repository
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def resolve_job_binding(self, *, session_id: str, requested_job_id: str) -> str:
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"""Return the one job owned by a conversation, rejecting mixed jobs."""
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conversation_id = _conversation_id(session_id)
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conversation = self.repository.get_conversation(conversation_id)
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requested = str(requested_job_id or "").strip()
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if conversation is None:
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return requested
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ledger = self.repository.get_goal_ledger(conversation_id)
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conversation_job = str(conversation.job_id or "").strip()
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ledger_job = str(
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(ledger.user_terms if ledger is not None else {}).get("active_job_id")
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or ""
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).strip()
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persisted_jobs = {value for value in (conversation_job, ledger_job) if value}
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if len(persisted_jobs) > 1:
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raise ValueError("conversation job binding conflict")
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bound = next(iter(persisted_jobs), "")
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if requested and bound and requested != bound:
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raise ValueError("conversation job binding conflict")
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return bound or requested
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def rebind_job(self, *, session_id: str, job_id: str) -> str:
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"""Bind one conversation to one job without mixing histories."""
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conversation_id = _conversation_id(session_id)
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requested = str(job_id or "").strip()
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if not requested:
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raise ValueError("job_id is required")
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conversation = self.repository.get_conversation(conversation_id)
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if conversation is None:
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raise ValueError("conversation is missing")
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previous_job = str(conversation.job_id or "")
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current = self.repository.get_goal_ledger(conversation_id)
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ledger_job = str(
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(current.user_terms if current is not None else {}).get("active_job_id")
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or ""
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).strip()
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bound_job = previous_job or ledger_job
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if bound_job == requested:
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return conversation_id
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if bound_job:
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replacement_id = str(uuid4())
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self.repository.create_conversation(
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conversation_id=replacement_id,
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principal_id=conversation.principal_id,
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job_id=requested,
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)
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self.repository.put_goal_ledger(
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GoalLedger(
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conversation_id=replacement_id,
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revision=0,
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user_terms={"active_job_id": requested},
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),
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expected_revision=None,
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)
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return replacement_id
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self.repository.update_conversation(
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conversation_id=conversation_id,
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principal_id=conversation.principal_id,
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job_id=requested,
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)
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if current is None:
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return conversation_id
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replacement = GoalLedger(
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conversation_id=conversation_id,
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revision=current.revision + 1,
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user_terms={"active_job_id": requested},
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)
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try:
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self.repository.put_goal_ledger(
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replacement,
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expected_revision=current.revision,
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)
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except Exception:
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self.repository.update_conversation(
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conversation_id=conversation_id,
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principal_id=conversation.principal_id,
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job_id=previous_job,
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)
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raise
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return conversation_id
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def begin_turn(
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self,
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*,
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session_id: str,
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job_id: str,
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query: str,
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client_history: Any,
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) -> ConversationTurn:
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conversation_id = _conversation_id(session_id)
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conversation = self.repository.get_conversation(conversation_id)
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if conversation is None:
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conversation = self.repository.create_conversation(
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conversation_id=conversation_id,
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principal_id="web-session",
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job_id=str(job_id or ""),
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)
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ledger = self.repository.get_goal_ledger(conversation_id)
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if ledger is None:
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initial_terms = {"active_job_id": job_id} if job_id else {}
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ledger = self.repository.put_goal_ledger(
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GoalLedger(
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conversation_id=conversation_id,
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revision=0,
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user_terms=initial_terms,
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),
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expected_revision=None,
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)
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effective_job_id = self.resolve_job_binding(
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session_id=conversation_id,
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requested_job_id=job_id,
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)
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if effective_job_id and not conversation.job_id:
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conversation = self.repository.update_conversation(
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conversation_id=conversation_id,
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principal_id=conversation.principal_id,
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job_id=effective_job_id,
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)
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if effective_job_id and not ledger.user_terms.get("active_job_id"):
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serialized = ledger.model_dump(mode="json")
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user_terms = dict(serialized["user_terms"])
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user_terms["active_job_id"] = effective_job_id
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ledger = self.repository.put_goal_ledger(
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GoalLedger(
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**{
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**serialized,
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"revision": ledger.revision + 1,
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"user_terms": user_terms,
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}
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),
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expected_revision=ledger.revision,
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)
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stored_messages = self.repository.list_recent_messages(conversation_id, limit=10)
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if not stored_messages:
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for item in _history(client_history):
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persisted = self.repository.append_message(
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conversation_id=conversation_id,
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message_id=str(uuid4()),
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role=item["role"],
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content=item["content"],
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expected_revision=conversation.revision,
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)
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conversation = self.repository.get_conversation(conversation_id)
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assert conversation is not None
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assert conversation.revision == persisted.revision
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stored_messages = self.repository.list_recent_messages(
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conversation_id,
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limit=10,
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)
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current_user_already_saved = bool(
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stored_messages
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and stored_messages[-1].role == "user"
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and stored_messages[-1].content == query
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)
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history_messages = (
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stored_messages[:-1]
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if current_user_already_saved
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else stored_messages
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)
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prior_history = tuple(
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{"role": item.role, "content": item.content}
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for item in history_messages
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if item.role in {"user", "assistant"}
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)
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if not current_user_already_saved:
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self.repository.append_message(
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conversation_id=conversation_id,
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message_id=str(uuid4()),
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role="user",
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content=query,
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expected_revision=conversation.revision,
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)
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return ConversationTurn(
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conversation_id=conversation_id,
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job_id=effective_job_id,
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query=query,
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history=prior_history,
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goal_ledger=ledger,
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)
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def finish_turn(
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self,
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turn: ConversationTurn,
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*,
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assistant_message: str,
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interaction_kind: str,
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action: str | None,
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intent: dict[str, Any] | None = None,
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proposal: dict[str, str] | None = None,
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) -> GoalLedger:
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if interaction_kind not in _INTERACTION_KINDS:
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raise ValueError("interaction_kind is invalid")
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conversation = self.repository.get_conversation(turn.conversation_id)
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if conversation is None:
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raise ValueError("conversation is missing")
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self.repository.append_message(
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conversation_id=turn.conversation_id,
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message_id=str(uuid4()),
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role="assistant",
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content=assistant_message,
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expected_revision=conversation.revision,
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)
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current = self.repository.get_goal_ledger(turn.conversation_id)
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if current is None:
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raise ValueError("goal ledger is missing")
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active_goal = current.active_goal
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queued_goals = list(current.queued_goals)
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corrections = list(current.corrections)
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prior_terms = dict(current.user_terms)
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pending_proposal = prior_terms.get("pending_proposal")
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pending_proposal = (
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dict(pending_proposal)
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if isinstance(pending_proposal, Mapping)
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else None
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)
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confirmed_pending_proposal = bool(
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action == "propose_analysis"
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and pending_proposal is not None
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and str(pending_proposal.get("job_id") or turn.job_id)
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== turn.job_id
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and isinstance(proposal, Mapping)
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and str(proposal.get("proposal_id") or "")
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== str(pending_proposal.get("proposal_id") or "")
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)
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prior_stages = {
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str(stage)
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for stage in prior_terms.get("requested_stages", ())
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if isinstance(stage, str) and stage.strip()
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}
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current_stages = {
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str(stage)
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for stage in ((intent or {}).get("stages") or ())
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if isinstance(stage, str) and stage.strip()
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}
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prior_family = str(prior_terms.get("gene_family") or "").strip()
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current_family = str((intent or {}).get("gene_family") or "").strip()
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is_current_phase = bool(
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active_goal
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and action == "propose_analysis"
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and current_stages
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and prior_stages
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and current_stages < prior_stages
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and not (
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prior_family
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and current_family
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and prior_family != current_family
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)
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)
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if interaction_kind == "cancel":
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active_goal = None
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elif interaction_kind == "correction":
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active_goal = turn.query
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if turn.query not in corrections:
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corrections.append(turn.query)
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elif interaction_kind == "switch":
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active_goal = turn.query
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elif interaction_kind == "independent" and action in {
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"propose_analysis",
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"propose_utility",
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} and not is_current_phase and not (
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active_goal and is_short_acknowledgement(turn.query)
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):
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if active_goal and active_goal != turn.query and active_goal not in queued_goals:
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queued_goals.append(active_goal)
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active_goal = turn.query
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elif (
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interaction_kind == "supplement"
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and active_goal is None
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and action in {"propose_analysis", "propose_utility"}
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):
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active_goal = (
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str(pending_proposal.get("request") or turn.query)
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if pending_proposal
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and (
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is_short_acknowledgement(turn.query)
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or confirmed_pending_proposal
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)
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else turn.query
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)
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if active_goal in queued_goals:
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queued_goals.remove(active_goal)
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serialized = current.model_dump(mode="json")
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user_terms = dict(serialized["user_terms"])
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if turn.job_id:
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user_terms["active_job_id"] = turn.job_id
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if action == "clarify" and isinstance(proposal, dict):
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normalized_proposal = {
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key: str(proposal.get(key) or "").strip()
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for key in ("proposal_id", "request", "subject")
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}
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if all(normalized_proposal.values()):
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workflow_id = str(proposal.get("workflow_id") or "").strip()
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if workflow_id in {
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"data_preparation",
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"gene_family",
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"rnaseq_whole_genome",
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"rnaseq_family_member",
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}:
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normalized_proposal["workflow_id"] = workflow_id
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normalized_proposal["job_id"] = turn.job_id
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user_terms["pending_proposal"] = normalized_proposal
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if (
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action == "propose_analysis"
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and (
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is_short_acknowledgement(turn.query)
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or confirmed_pending_proposal
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)
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and pending_proposal is not None
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and str(pending_proposal.get("job_id") or turn.job_id)
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== turn.job_id
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) or interaction_kind in {"cancel", "correction", "switch"}:
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user_terms.pop("pending_proposal", None)
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if (
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action == "clarify"
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or is_current_phase
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or (
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action == "propose_analysis"
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and interaction_kind == "supplement"
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and active_goal is not None
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)
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):
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user_terms["current_action"] = turn.query
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if isinstance(intent, dict):
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scalar_fields = {
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"gene_family": ("gene_family",),
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"species": ("species",),
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"scope_mode": ("scope_mode", "scopeMode"),
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"primary_stage": ("primary_stage", "stage"),
|
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"task_kind": ("task_kind", "taskType"),
|
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"prefix": ("prefix",),
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"rna_route": ("rna_route", "rnaRoute", "analysis_route"),
|
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"foreground_mode": ("foreground_mode", "foregroundMode"),
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}
|
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for target, sources in scalar_fields.items():
|
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value = next(
|
||
(
|
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intent.get(source)
|
||
for source in sources
|
||
if isinstance(intent.get(source), str)
|
||
and intent[source].strip()
|
||
),
|
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None,
|
||
)
|
||
if value is not None:
|
||
user_terms[target] = value
|
||
|
||
sequence_fields = {
|
||
"target_species": ("target_species", "targetSpecies"),
|
||
"reference_species": ("reference_species", "referenceSpecies"),
|
||
"comparative_species": (
|
||
"comparative_species",
|
||
"comparativeSpecies",
|
||
),
|
||
"requested_stages": ("stages",),
|
||
}
|
||
params = intent.get("params")
|
||
params = params if isinstance(params, dict) else {}
|
||
for target, sources in sequence_fields.items():
|
||
raw = next(
|
||
(
|
||
intent.get(source, params.get(source))
|
||
for source in sources
|
||
if isinstance(intent.get(source, params.get(source)), (list, tuple))
|
||
),
|
||
None,
|
||
)
|
||
if (
|
||
raw is not None
|
||
and (
|
||
target == "requested_stages"
|
||
or bool(raw)
|
||
or target not in user_terms
|
||
)
|
||
and all(
|
||
isinstance(item, str) and item.strip() for item in raw
|
||
)
|
||
):
|
||
user_terms[target] = list(raw)
|
||
changed = (
|
||
active_goal != current.active_goal
|
||
or tuple(queued_goals) != current.queued_goals
|
||
or tuple(corrections) != current.corrections
|
||
or user_terms != dict(current.user_terms)
|
||
)
|
||
if not changed:
|
||
return current
|
||
updated = GoalLedger(
|
||
**{
|
||
**serialized,
|
||
"revision": current.revision + 1,
|
||
"active_goal": active_goal,
|
||
"queued_goals": tuple(queued_goals),
|
||
"corrections": tuple(corrections),
|
||
"user_terms": user_terms,
|
||
}
|
||
)
|
||
return self.repository.put_goal_ledger(
|
||
updated,
|
||
expected_revision=current.revision,
|
||
)
|
||
|
||
def record_config_confirmation(
|
||
self,
|
||
*,
|
||
session_id: str,
|
||
job_id: str,
|
||
evidence_id: str,
|
||
) -> GoalLedger | None:
|
||
"""Attach a confirmed config to an existing conversation goal."""
|
||
conversation_id = _conversation_id(session_id)
|
||
if self.repository.get_conversation(conversation_id) is None:
|
||
return None
|
||
bound_job_id = self.resolve_job_binding(
|
||
session_id=conversation_id,
|
||
requested_job_id=job_id,
|
||
)
|
||
current = self.repository.get_goal_ledger(conversation_id)
|
||
if current is None:
|
||
return None
|
||
|
||
approved_decisions = list(current.approved_decisions)
|
||
if "config.xlsx 已确认" not in approved_decisions:
|
||
approved_decisions.append("config.xlsx 已确认")
|
||
evidence_ids = list(current.evidence_ids)
|
||
if evidence_id not in evidence_ids:
|
||
evidence_ids.append(evidence_id)
|
||
serialized = current.model_dump(mode="json")
|
||
user_terms = dict(serialized["user_terms"])
|
||
user_terms["config_confirmed"] = True
|
||
if bound_job_id:
|
||
user_terms["active_job_id"] = bound_job_id
|
||
unresolved_blockers = tuple(
|
||
blocker
|
||
for blocker in current.unresolved_blockers
|
||
if "config" not in blocker.lower() and "配置" not in blocker
|
||
)
|
||
|
||
updated = GoalLedger(
|
||
**{
|
||
**serialized,
|
||
"revision": current.revision + 1,
|
||
"approved_decisions": tuple(approved_decisions),
|
||
"unresolved_blockers": unresolved_blockers,
|
||
"user_terms": user_terms,
|
||
"evidence_ids": tuple(evidence_ids),
|
||
}
|
||
)
|
||
return self.repository.put_goal_ledger(
|
||
updated,
|
||
expected_revision=current.revision,
|
||
)
|