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9b746db452
Merge feature/admin-console: 管理后台 + 用户端鉴权(登录/授权/数据隔离/日志)
admin
2026-10-16 16:01:13 +08:00
d9abd0b86a
feat(auth): 用户端鉴权(登录/授权清单/逐次校验/功能门禁 + owner 数据隔离)
admin
2026-10-16 14:42:23 +08:00
282415fcb1
feat(admin): 行为日志记录 hub_id(便于区分不同中枢)
admin
2026-10-15 23:56:42 +08:00
1ca2241a97
feat(admin): 增加中枢设置(自定义 ID 与名称,右上角设置入口)
admin
2026-10-15 23:52:17 +08:00
8b5095f70f
Merge pull request 'feat(review): P5 科研汇报助手（论文 → PPT 大纲 → PPTX）' (#5 ) from wjq/PlantAI-rag-new:feature/p5-ppt-assistant into main
admin
2026-10-15 20:19:30 +08:00
f5a951f47a
docs: add P5 PR report
potaser
2026-10-15 19:35:51 +08:00
7ced30fa96
feat(review): P5 科研汇报助手 + 14 风格 + 真图嵌入
potaser
2026-10-15 18:05:29 +08:00
c78df3a6a6
feat(admin): 新增管理后台(登录/用户管理/日志查看) + 行为日志文件采集(请求中间件 + log_event)
admin
2026-10-15 18:43:19 +08:00
69e3f35a43
Merge pull request 'feat(review): P3b+P4 论文重排版支持编译 PDF（含 zip 项目）' (#4 ) from wjq/PlantAI-rag-new:feature/p3b-compile-ui into main
admin
2026-10-15 18:30:14 +08:00
de0b9f92be
fix(review): EPS batch conversion in zip compile (v2)
potaser
2026-10-14 09:47:49 +08:00
3c00e1675e
feat(bioflow): skill 编排续作 WIP checkpoint（多轮链续接/plan 回填/job_id 提取/历史 blocks 文本提取）
admin
2026-10-14 09:41:44 +08:00
2797145104
feat(review): P4 two-phase zip compile + XDV→PDF diagnostics + EPS fallback
potaser
2026-10-13 18:42:04 +08:00
8ab4279b04
fix(bioflow): sendCardResult 从 raw.bioflow 读 active_job_id(BFF 归一化剥离顶层 bioflow 导致订阅没建立)
admin
2026-10-13 14:39:33 +08:00
c943e8d363
fix(bioflow): sendCardResult 创建任务后补 connectJobEvents 订阅，恢复文件/参数引导等任务事件触发
admin
2026-10-13 12:34:27 +08:00
9ac36e99ba
fix(bioflow): 路径选择卡空状态文案「暂无候选路径」改为「正在检索可用分析路径....」
admin
2026-10-13 11:33:39 +08:00
9cb0bf2e35
feat(bioflow): stage_done 摘要从 manifest.metrics 提取关键指标(命中/比对率等) (#010 )
admin
2026-10-13 11:28:18 +08:00
4e19350115
docs: add P3b PR report
potaser
2026-10-13 11:23:01 +08:00
e036301e1a
feat(review): show format rules summary per target journal
potaser
2026-10-13 11:22:52 +08:00
da84dff9bb
fix(review): persist uploaded .tex file in reformat panel
potaser
2026-10-13 11:20:33 +08:00
6b4b5e571f
feat(bioflow): 就绪卡+版本化卡接线——工具结果经 payload.bioflow 下发前端渲染 (#009 )
admin
2026-10-13 11:18:53 +08:00
9797b1b414
feat(bioflow): 交付卡接线——job_done 构造 manifest 调 validate_delivery 下发交付清单 (#009-交付)
admin
2026-10-13 11:12:39 +08:00
b9bc90ffb0
feat(bioflow): 诊断卡接线——stage_failed 补 G13 错误对象+guidance，前端诊断卡渲染 (#009-诊断)
admin
2026-10-13 11:10:30 +08:00
821f3c1c4e
feat(bioflow): 引导帧——卡片环节补自然语言引导气泡(文件/参数/存档/进度) (#006/#007/#008/#010)
admin
2026-10-13 11:04:32 +08:00
da8f531bbc
fix(bioflow): check_disk_available 捕获 OSError 返回 PATH_NOT_EXIST，不再抛未捕获异常 (#004 )
admin
2026-10-13 11:01:17 +08:00
21c79582bf
fix(bioflow): QA 生信流加活跃任务续接分支，续接输入(提供文件/参数等)不再掉普通 QA (#011 )
admin
2026-10-13 10:59:54 +08:00
1ecc4cb29e
chore(deploy): 新增 bioflow_switch_restart.sh 切分支→重启→验证规范脚本
admin
2026-10-13 10:28:06 +08:00
3a72d3a861
feat(review): P3b enable compile PDF in reformat panel
potaser
2026-10-13 10:24:55 +08:00
75eb489fc3
fix(bioflow): main.py 加 load_dotenv 把 .env 注入 os.environ，修复规划 LLM 配置断层
admin
2026-10-13 10:03:00 +08:00
ac07cb2008
Merge pull request 'feat(review): AI 预审稿修复 + 审稿回复助手 Phase 1' (#3 ) from wjq/PlantAI-rag-new:feature/presubmit-explainable-engine into main
admin
2026-10-13 09:34:41 +08:00
d077a5b930
test(docs): rebuttal + tracker tests + PR reports
potaser
2026-10-12 16:38:28 +08:00
c4dc344a31
feat(edu): presubmit UI + rebuttal assistant + tracker removal
potaser
2026-10-12 16:38:28 +08:00
cf5ccb3a37
feat(review): presubmit 4-bug fix + rebuttal Phase 1 backend
potaser
2026-10-12 16:38:28 +08:00
e4ed3589d5
fix(bioflow): INCOMPLETE_DELIVERY 错误分类映射到 input/diagnosed (G14 补漏)
admin
2026-10-12 12:20:52 +08:00
d99d5ef74a
fix(review): replace presubmit recommendation quota with explainable rule engine
potaser
2026-10-12 09:55:07 +08:00
4add9f176b
Merge pull request 'feat(review): journal_directory 启动自动 seed（部署即运行）' (#2 ) from wjq/PlantAI-rag-new:feature/journal-seed-autoload into main
admin
2026-10-11 21:12:56 +08:00
1319328b85
feat(review): auto-seed journal_directory on startup when empty
potaser
2026-10-11 20:41:05 +08:00
2d0e3a4858
fix(build): compile_sdk 白名单加入 review_proxy.py（科研审稿反代断流高危点）
admin
2026-10-11 16:40:24 +08:00
f27336e961
feat(bioflow): 生信 Skill 化改造 (CLI工具层+MCP薄适配+11分析工具+SKILL, G1-G23)
admin
2026-10-11 16:03:19 +08:00
ea0f2b3fad
Merge pull request 'feat(review): 教育科研工作台 + 论文自动重排版 + journals v4 数据集' (#1 ) from wjq/PlantAI-rag-new:feature/academic-review-assistant into main
admin
2026-10-11 13:49:12 +08:00
19fa12eb39
merge main: 解决 .gitignore 冲突（合并部署文档忽略规则）
admin
2026-10-11 13:47:47 +08:00
11337a788f
更新 .gitignore
admin
2026-10-11 13:29:35 +08:00
55410b663a
feat(review): journal format-rule fetch scripts (offline CLI)
potaser
2026-10-11 12:19:18 +08:00
dddb70ff6f
fix(review): directory partition source shown as constant note
potaser
2026-10-11 12:19:18 +08:00
649e66f41d
feat(review): tectonic PDF compile API (P3a) + rename journals panel
potaser
2026-10-11 12:19:18 +08:00
42aeb8fa4c
feat(review): paper auto-reformat P1 (.tex rule engine + diff panel)
potaser
2026-10-11 12:19:17 +08:00
c747ebd77a
feat(review): official format rules for 5 featured journals
potaser
2026-10-11 12:19:17 +08:00
963a87855c
feat(bioflow): 生信模块对话式改造 + MCP 外挂化 (S0-S6)
admin
2026-09-30 22:56:06 +08:00
60375b04d7
chore: .gitignore 忽略含凭据的部署方案文档 DEPLOY_PAPER_176.md
admin
2026-10-10 18:53:25 +08:00
1bd4aea5fd
fix(build): render_active_library_env 输出 GENE_FAMILY_ROOT 而非未定义的 QA_ROOT
admin
2026-10-10 18:52:15 +08:00
51532a30bc
fix(ui): 工作台「提取任务」tab 与离线提示改为「上传文献」
admin
2026-10-10 18:27:06 +08:00
5a71e29cf7
feat(edu): complete 7-panel academic assistant + journals v4 dataset
potaser
2026-10-10 16:05:08 +08:00
d43d30ee3f
feat: add review_service with plant genomics presubmit, journals endpoint, and BFF proxy
potaser
2026-10-09 16:54:03 +08:00
d37e0d9c3a
fix(paper): 确认大纲后即时 seed 进度卡并逐节刷新
admin
2026-10-08 17:10:50 +08:00
c923419d2d
fix(paper): 大纲阶段修改意见路由回 sendPaper + 用原始 brief 重新生成大纲
admin
2026-10-08 16:23:28 +08:00
43a7c6c132
feat(paper): UI 优化(卡片文字颜色/去模式按钮) + 模板下拉加论文选项并接线渲染
admin
2026-10-08 15:17:44 +08:00
8b228923bd
fix(paper): 取消路径(cancel_paper) + 引用元数据清洗(丢弃杜撰 DOI/PMID)
admin
2026-10-08 14:59:16 +08:00
2e5372cf90
fix(paper): 论文产物渲染为 HTML + 文末追加参考文献列表/disclaimer
admin
2026-10-08 14:54:00 +08:00
99bd86e535
feat(bioflow): 生信模块对话式改造 + MCP 外挂化 (S0-S6)
admin
2026-09-30 22:56:06 +08:00
91f6a1c242
feat: 新增论文撰写功能 paper-writer（独立 MCP 服务 + BFF 大脑 + 前端三卡）
admin
2026-09-30 22:29:22 +08:00
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
admin
2026-09-24 16:48:52 +08:00
0f6e16ce79
fix(sdk): run.sh 读取 PORT/PYTHON/BIND 移到 source .env 之后
admin and Claude Fable 5
2026-09-17 14:47:38 +08:00
964346dc77
fix(sdk): run.sh source .env + BIND host env 化(BFF_BIND_HOST)
admin and Claude Fable 5
2026-09-17 14:45:01 +08:00
f10b86c088
feat(deploy): start_all 生信段尊重 BIOFLOW_ENABLED(默认 false=无生信版)
admin and Claude Fable 5
2026-09-17 07:56:49 +08:00
d0e6c76ec1
feat(ui): 无生信启动时隐藏扩展按钮
admin and Claude Fable 5
2026-09-17 07:37:32 +08:00
16bde32020
feat(ui): 右上角生信跳转按钮+四按钮文字标签
admin and Claude Fable 5
2026-09-16 20:44:23 +08:00
ba43ba90bf
feat(bioflow): 样本配置 LLM 兜底——规则无法归纳时 DeepSeek 生成描述
admin and Claude Fable 5
2026-09-16 20:13:32 +08:00
36d3d8d62a
fix(bioflow): 描述文件候选择优+去除登记文件数上限
admin and Claude Fable 5
2026-09-16 20:03:49 +08:00
f2c101ec65
feat(bioflow): 样本配置智能分析——描述文件优先+实况分析+解压
admin and Claude Fable 5
2026-09-16 19:54:21 +08:00
750e218541
fix(bioflow): 卡片防误操作+暂停立即生效+确认幂等
admin and Claude Fable 5
2026-09-16 18:01:24 +08:00
becf76ecd9
feat(bioflow): 分析路径规划中提示——planning 帧+前端思考中状态
admin and Claude Fable 5
2026-09-16 16:15:17 +08:00
dcb810a758
feat(bioflow): wgs/pop/gwas 26 阶段参数契约(与 rnaseq 同款机制)
admin and Claude Fable 5
2026-09-16 15:33:43 +08:00
3b512fffd0
fix(bioflow): rnaseq/wgs 阶段参数契约——CLI 参数注入+样本配置自动生成+产物路径对齐
admin and Claude Fable 5
2026-09-16 15:23:50 +08:00
04fb306624
fix(bioflow): 内核树运行时挂载——非 gf 阶段镜像缺 cli 模块
admin and Claude Fable 5
2026-09-15 23:22:06 +08:00
2ee9af4bd0
fix(bioflow): 路径登记目录展开+黑名单+自动挂载
admin and Claude Fable 5
2026-09-15 23:11:27 +08:00
957f3cb062
feat(ui): 导航按钮迁移右上角+删除会话栏底部工具栏
admin and Claude Fable 5
2026-09-15 22:49:41 +08:00
e3870d19de
fix(extension): run 方法守卫与 trial 统一——适配器 _real 非 None 即执行
admin
2026-09-15 12:35:48 +08:00
a008fbba2a
fix(extension): 产物收割排除代码副本+删 work 目录——输出契约校验语义不变
admin and Claude Fable 5
2026-09-15 11:59:42 +08:00
3989dd3c3a
fix(extension): 容器入口可写工作目录——代码复制进 run_dir 执行+产物收割输出
admin and Claude Fable 5
2026-09-15 11:58:17 +08:00
8a58703d61
fix(extension): converted_code 镜像保留嵌套结构(与 raw_code 落盘一致)
admin
2026-09-15 11:51:27 +08:00
4266a89872
fix(extension): 容器入口默认 cwd 改为代码目录(run.sh 相对脚本路径语义)
admin
2026-09-15 11:43:16 +08:00
1bce4bf587
fix(extension): context 接线改用 _default_exec_config(entry_script_dir 空串致 trial 入口缺失)
admin
2026-09-15 11:37:39 +08:00
9bbe2c83f6
fix(extension): 入口脚本目录解析——176 部署树路径深度不同致 trial 报入口缺失
admin and Claude Fable 5
2026-09-15 11:24:05 +08:00
82b954b957
docs(deploy): BFF 手动重启 venv 绝对路径陷阱(2026-09-15 实测)
admin and Claude Fable 5
2026-09-15 10:54:10 +08:00
d12071a4d7
feat(extension): 上传支持 zip/tar/目录三形态+结构自适应分类
admin and Claude Fable 5
2026-09-15 10:34:52 +08:00
76529f78ab
docs(deploy): 环境镜像全量同步原则固化
admin and Claude Fable 5
2026-09-14 22:15:47 +08:00
835d55cb5b
docs(images): bioflow-pan 镜像 panfamily 模块修复记录\n\n- 根因: conda activate.d 注入的 PYTHONPATH 指向宿主路径,容器内断链,\n 所有 from panfamily.io import 失败\n- 修复: panfamily 模块(68K)COPY 进 site-packages + 删断链脚本;\n 新镜像已 load 176,panfamily.io read_fasta 端到端通过(49432 序列)\n\nCo-Authored-By: Claude Fable 5 <noreply@anthropic.com >
admin
2026-09-14 22:05:45 +08:00
653d2211cf
fix(extension): inject_executor 废弃——曾把生信 stage runner 函数塞进扩展 store
admin and Claude Fable 5
2026-09-14 17:30:09 +08:00
4128fbf3bf
fix(extension): 执行器守卫与注入修复——active_store 不存在+占位误判已注入适配器
admin and Claude Fable 5
2026-09-14 17:27:49 +08:00
68b45c60a0
fix(extension): 扩展意图检测提前到 route_intent 之前
admin and Claude Fable 5
2026-09-14 17:24:27 +08:00
c0b3026209
fix(extension): docker 镜像引用双后缀拼接——已含 tag 的自动镜像再补 suffix
admin and Claude Fable 5
2026-09-14 16:01:28 +08:00
bb560d7bea
fix(extension): 自动镜像生成两缺陷——Dockerfile FROM 顺序+timeout 参数名
admin and Claude Fable 5
2026-09-14 15:59:33 +08:00
2a6315e615
docs(extension): 测试报告——TL 接管测试循环,B1-B4 缺陷修复,全量测试绿
admin and Claude Fable 5
2026-09-14 15:10:10 +08:00
812decf310
fix(extension): 测试隔离+注入惰性适配+chat_stream 意图接线
admin and Claude Fable 5
2026-09-14 15:09:15 +08:00
3b16397baf
feat(extension): TL 接线——executor 适配/validate 帧/form_defaults/context 注入
admin and Claude Fable 5
2026-09-14 13:53:44 +08:00
4fa758d602
Merge branch 'dev/extension-backend' into feature/bioflow-conversation-orchestration
admin
2026-09-14 13:49:25 +08:00
d95c2b5761
Merge branch 'dev/extension-frontend' into feature/bioflow-conversation-orchestration
admin
2026-09-14 13:49:18 +08:00
4866b0408a
feat(bioflow): extension lifecycle backend (P0) - spec whitelist, state machine, AI build, intent layers
admin and Claude Fable 5
2026-09-14 13:48:37 +08:00
03e6ff508a
feat(extension-frontend): 扩展分析前端引导卡 + 事件分派(Dev-C)
admin and Claude Fable 5
2026-09-14 13:43:20 +08:00
79b4c7c52c
feat(extension): docker 执行内核入口 + 176 本地自动镜像生成(并行链路)
admin and Claude Fable 5
2026-09-14 13:36:18 +08:00
f0a1711ebc
fix(aqua): batch_runner path sanitize, loader batch embed, alias expansion
admin and Claude Fable 5
2026-09-13 01:06:38 +08:00
admin
potaser