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Author SHA1 Message Date
potaser 7ced30fa96 feat(review): P5 科研汇报助手 + 14 风格 + 真图嵌入 2026-10-15 18:51:59 +08:00
potaser 2797145104 feat(review): P4 two-phase zip compile + XDV→PDF diagnostics + EPS fallback 
- inspect/upload zip then compile project (main-file detection, zip safety,
  single-slot queue, failed-envelope carries compile_id + log_url)
- keep failed project/ scene 24h (failed_project_ttl_s; KEEP_FAILED_PROJECTS=1
  forever), success deletes immediately; two-tier compile_jobs sweep
- add tectonic --print and persist full engine chatter to output.log so
  XDV→PDF (xdvipdfmx) errors are visible (MDPI: logo EPS inclusion failure)
- EPS fallback: swap X.eps refs for *-eps-converted-to.pdf when present and
  materialize X.pdf for extension-less graphicx lookup; friendly error when
  no converted PDF exists
- frontend: ReformatPanel zip upload/inspect/run flow; one-off
  scripts/debug_compile.py (gitignored)
- tests: backend 169 passed (22 zip_safety + 34 compile_zip + P3a regression),
  frontend edu vitest 43 passed
 2026-10-13 18:42:04 +08:00
admin 19fa12eb39 merge main: 解决 .gitignore 冲突（合并部署文档忽略规则） 2026-10-11 13:47:47 +08:00
admin 11337a788f 更新 .gitignore 
解决冲突

Signed-off-by: admin <jerryhaozhang@gmail.com>
 2026-10-11 13:29:35 +08:00
potaser 55410b663a feat(review): journal format-rule fetch scripts (offline CLI) 
- fetch_format_rules.py CLI: robots.txt-aware fetcher (httpx + bs4,
  >=2s per-host throttle) + DeepSeek quote-backed rule extractor
- Status: OUP/Wiley/Cell return 403 from this environment; the five
  featured journals' format_rules in journals.json were manually
  verified against official sites instead. Tooling kept for future
  re-runs; data/format_cache/ is runtime output and gitignored
- Service code never imports this toolchain (standalone CLI only)
 2026-10-11 12:19:18 +08:00
potaser 42aeb8fa4c feat(review): paper auto-reformat P1 (.tex rule engine + diff panel) 
- Rule engine: font/margin/line-spacing/bib-style transformers,
  tighten-only + structural guard + idempotency
- POST/GET /api/review/reformat with 200-envelope errors and job store
- ReformatPanel: journal dropdown (featured + directory search),
  source/diff tabs; compile tab is a dev placeholder for now
- journals.json format_rules_default kept as generic fallback
 2026-10-11 12:19:17 +08:00
admin 60375b04d7 chore: .gitignore 忽略含凭据的部署方案文档 DEPLOY_PAPER_176.md 2026-10-10 18:53:25 +08:00
potaser d43d30ee3f feat: add review_service with plant genomics presubmit, journals endpoint, and BFF proxy 2026-10-09 16:54:03 +08:00
admin 91f6a1c242 feat: 新增论文撰写功能 paper-writer（独立 MCP 服务 + BFF 大脑 + 前端三卡） 
- paper_writer_service(8097)：FastAPI + MCP streamable-http 单端点，9 工具
  （propose_paper_outline/write_paper_section/get_paper_progress/search_refs/
  revise_paper_section/revise_paper/get_paper/complete_paper/cancel_paper），
  SQLite 三表（papers/paper_sections/citations，WAL），GB/T 7714 引用协议
- BFF：services/paper/{mcp_client,agent}.py（裸 JSON-RPC 客户端 + 规则状态机）、
  routers/paper.py、schemas.py 4 个 Paper*Block + ArtifactBlock 加 paper_id/citation_count、
  config.py 开关、main.py 条件注册、docgen.py 抽 insert_artifact 公共 helper
- 前端：intent.js paperIntent 纯函数、Composer docgen 分支 sub-route、sendPaper/轮询、
  PaperBriefCard/PaperOutlineCard/PaperProgressCard、DocPane cite-chip
- deploy/paper_restart.sh + toggle_paper.sh；compile_sdk.sh 白名单追加 paper 文件
- tests/paper 26 条（工具逻辑 + MCP 协议 + BFF 状态机 + 块 schema + 前端 intent 单测）
 2026-09-30 22:29:22 +08:00
admin 0282cfeeeb feat(bioflow): 阶段进度条+滚动日志+点击定位全链;图片注入三修;QA启动就绪等待 
- 生信进度:后端新增 stage_progress 事件帧+进度解析白名单(rnaseq_qc/sample_qc),
  kernel 日志流式落盘(20行/1s flush+fsync),logs 分页端点(offset/limit/eof),
  事件 seq 跨重启扫描续增(2026-09-17 断流修复);前端 FlowProgressCard 确定性/
  不确定两态进度条+点击定位到生信任务 TAB,BioJobsPane DAG 行展开滚动日志区
  (3s 轮询),log_tail 4000 截断,重跑 stage_started 清零进度
- 图片注入:figures 三源重构(标准DOI图库主路径/遗留体系兜底/PMC兜底),
  [[FIG:]] 宽松归一化识别 PMC/PMID/DOI 三种形态,引文兜底扩展至
  [PMCID:]/[DOI:] 且标记未满配额继续注入,注入预算 90s/10篇(175 实测校准),
  PMC graphic 无 content-type 宽松正则,空结果不缓存(176 冷连接三连败修复)
- QA 启动自愈:start.sh 启动前等 Qdrant readyz(30min)+Neo4j TCP(10min);
  backend_guard 标签校验改子集判定
- 样本配对:同 inode 去重优先真实文件,R1/R2 归一配对一对一认领
- gitignore 新增 *.bak-*/*.before-*/bioflow_service/bioflow.db

测试:bioflow_service pytest 358/358,前端 bioflow vitest 205/205
 2026-09-24 16:48:52 +08:00
adminandClaude Fable 5 812decf310 fix(extension): 测试隔离+注入惰性适配+chat_stream 意图接线 
TL 测试循环修复:
- conftest 两处 Settings 补 extensions_dir=tmp 隔离(此前测试扩展
  落仓库默认目录,跨测试污染致列表排序断言失败)
- inject_real_executor 惰性创建适配器(store.executor 默认 None)
- chat_stream 接扩展意图两层判定:create→extension_upload 帧、
  run→extension_candidates 帧、create_ambiguous→引导帧;
  扩展链路异常不回退生信主链
- .gitignore 排除 tests/extension_cases_18/(2.6G 测试数据不入库)

验证:bioflow_service 324/324、内核 15/15、ui 122/122+373/373、
真实 docker 冒烟 SMOKE_OK。

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-09-14 15:09:15 +08:00
admin afa7cce938 feat(aqua): unlock normalized KB identity via env with plant fallback 
- normalized_release EXPECTED_RELEASE defaults to NORMALIZED_RELEASE_ID (plant value)
- from_env falls back to constant on empty env; backend_guard uses env-or-constant
- start.sh sources env/active_library.env after prod.env (qa + legacy-rag)
- build_all.sh --library <name|dir> renders library identity (no name whitelist)
- add kb-libraries skeleton (plant/aqua identity cards) and tooling/aqua_kb
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-09-12 19:10:08 +08:00
adminandClaude Fable 5 e151f675f1 feat(qa-db): QA数据库裸进程标准(deploy/qa-db五脚本+守卫去版本锁定+打包/文档/Excel同步) 
- deploy/qa-db/: qdrant/neo4j systemd 裸进程安装脚本+unit模板+整库替换(replace_db.sh)
  * 数据双制品模型: <部署根>/qa-db 与 install 分开传输, 支持频繁整库替换
  * 免编译(官方静态二进制/tarball)+本地 bin/ 离线分发+国内镜像回退
  * 端口 27433/27434+19888/19885(127.0.0.1), 175 docker 容器(27333/19788)为其他项目共享不动
- backend_guard.py: 移除精确计数相等校验(数据库会整库替换/持续更新, 不得锁死版本)
  保留身份校验(release/collection/kb_version/标签/关系类型), 计数仅随 health 返回
- qa/scripts/start.sh: reranker 模型路径回退(install/models/bge-reranker-base)
- build_all.sh: qa-db 脚本+reranker 模型入包; .gitignore: qa-db/bin 离线载体
- DEPLOY_FLOW.md: §0/§5.0/§5.0b/§6.0b/§7 QA 数据库裸进程标准

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-09-08 17:59:53 +08:00
adminandClaude Fable 5 a3142d2a05 test(bioflow): T2 R1 轮次报告+TL 用例修订——catalog 口径与权威数据一致(75/21)、INTENT-044 交互式补充转 P7 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-09-06 08:18:20 +08:00
adminandClaude Fable 5 35bf6889a4 fix(bioflow): 部署期 P1 双缺陷修复——context 值导入脱钩 init_context 重绑定(路由层动态取模块全局)+BFF 反代非 SSE 透传 bytes 500(改纯透传 Response) 
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-09-06 07:22:01 +08:00
jerryandClaude Fable 5 0875bb036c P0/M1: 四部分重构——frontend→ui、backend→sdk 改名 + 引用修复 + 骨架 
- git mv 保留历史：ui/(Vue3+Vite)、sdk/(BFF 中间层)
- 路径语义修正：db_path/figures_cache 改相对 sdk/(BFF cwd)，
  历史库 sdk/backend/data 迁移至 sdk/data/(会话/图片缓存无损)
- 引用修复 ~15 处：config.py、deploy/*.sh、vitest/playwright 配置、
  单测导入路径、docs、README、gitignore、.env.example
- 骨架：agent/{qa,methodology,legacy-rag,vendor}、knowledge/manifest.yaml、
  tooling/{compile,kb,crypto,assemble,audit,tools,scripts} + README
- 门禁验证：sdk pytest 125 通过、ui vitest 158 通过、
  生产 BFF 脚本重启四上游全绿 + 静态托管 + 会话库无损

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-31 12:56:47 +08:00
jerry f456969a45 清理 .DS_Store 并加入忽略 2026-08-25 20:57:20 +08:00
jerryandClaude Fable 5 1e94de7464 PlantAI-rag-new 首次提交：文献知识工作台 
- BFF 薄适配层（FastAPI，8090）：QA 代理/SSE 中继/Neo4j 直连/抽取代理/会话持久化
- Vue3 前端：五相位检索流水线、文献来源与证据链、知识图谱、提取任务四 tab
- 四档响应式（桌面/笔记本/平板/手机）、深浅主题
- 81 个 FR 全部实现，测试追溯矩阵 81/81，后端 121 测/前端 156 测
- 真实凭据已脱敏，运行时配置在 backend/.env（不入 git）

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 2026-08-25 20:47:52 +08:00