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Author SHA1 Message Date
potaser da8001ab2a Merge branch 'master' of http://192.168.0.175:3000/admin/PlantAI-dev 2026-08-19 20:23:24 +08:00
potaserandClaude Opus 5 a2e8cbae86 fix(lightweight-extension): 环境激活、前缀重命名、数据复制与上传进度 
- service.py: _make_env 用 conda run 激活环境（执行 activate.d，补 PYTHONPATH）
- index_ml.html: 环境下拉框动态加载 + 补传 runtime_env
- runtime_binding.py: 前缀误判修复、放宽 ambiguous、can_rename 判断、子目录数据复制补 mkdir
- api.py: 缺输出目录时友好提示
- main.py + lightWeightExtensionTest.js: run.sh 环境声明 # lightweight-env
- index.html/index_ml.html: 拖拽上传进度条

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 2026-08-19 20:17:43 +08:00
potaser 77011a21b7 fix: resume confirmed analysis handoff 2026-08-11 06:37:24 +08:00
potaser 4a80793b4a fix: integrate deployed reports with PPI KaKs handoff 2026-08-11 04:48:38 +08:00
potaser 8b61269d3f Merge remote-tracking branch 'origin/master' into fix/ppi-kaks-enable 
# Conflicts:
#	tests/unit/test_router_analysis_handoff_boundary.py
 2026-08-10 23:24:47 +08:00
potaser 7b7e334213 fix: complete PPI and KaKs reference handoff 2026-08-10 23:13:05 +08:00
potaser 7228b586c8 fix(runtime): standardize 9000 startup and isolate project services 20260808展会版 2026-08-10 10:57:49 +08:00
potaser fe5f7b9d6e 多语言散落补全 2026-08-10 00:31:32 +08:00
potaser 87c158efe5 多语言散落补全 2026-08-09 22:58:26 +08:00
potaser 963e4ddc73 多语言散落补全 2026-08-09 22:24:06 +08:00
potaser 9dbd87696b 多语言散落补全 2026-08-09 22:20:36 +08:00
potaser 39a2c969de docs: design reference download progress indicator 2026-08-09 16:18:53 +08:00
wtx 9b9c88b18e merge: preserve latest report refinements 2026-08-09 16:06:20 +08:00
wtx b8dcb63fa1 fix: preserve raw intent across language switching 2026-08-09 16:03:13 +08:00
wtx 1252c41661 merge: preserve multilingual UI with main-agent fixes 2026-08-09 15:54:56 +08:00
wtx 0e5cece447 feat: refine gene family result report 2026-08-09 14:28:41 +08:00
wtx dc9d44f95b feat: refine RNA-seq result report 2026-08-09 14:21:26 +08:00
wtx 0f81b5140c fix: restore main-agent routing and workflow handoff 2026-08-09 13:50:35 +08:00
potaser 55d320586a 多语言散落补全 2026-08-09 12:54:48 +08:00
potaser 53966e03b5 多语言散落位置补全 2026-08-09 12:45:13 +08:00
potaser e22da1879d Agent language switching 2026-08-09 11:38:03 +08:00
potaser 774490b47f 多语言首页 2026-08-09 06:38:53 +08:00
potaser cd3e9a5f22 多语言+拓展包拖拽上传 2026-08-09 06:17:22 +08:00
potaser e9f006351d 多语言+拓展包拖拽上传 2026-08-09 06:04:53 +08:00
potaser 8f7e992b84 多语言首页与首页引用页 2026-08-09 06:03:39 +08:00
wtx cb122fd088 feat: add gene family result reports 2026-08-09 04:32:28 +08:00
wtx 65f79207f0 feat: add evidence-bound RNA-seq result reports 2026-08-09 01:37:00 +08:00
wtx 7399b0bf14 Merge origin/master before analysis handoff push 2026-08-08 10:41:45 +08:00
wtx 5f240d1eec fix: delegate analysis planning from main agent 2026-08-08 10:40:01 +08:00
sj bfbddb544c docs: define main agent analysis handoff boundary 2026-08-07 21:15:00 +08:00
potaserandClaude Opus 5 d66a5f9378 fix: output prefix handling for tools without shared filename prefix 
15 changes to resolve the validation chain for extensions where
output files lack a common filename prefix (MEME, MCScanX, etc):

1. _output_has_prefix: match directory components, not just filenames
2. _replace_output_prefix: rename directory when prefix matches dir
3. _shared_output_prefix: fallback to deepest shared directory prefix
4. _fallback_dir_prefix (NEW): extract prefix from common dir
5. _is_dir_prefix (NEW): detect directory-style prefix
6. _replace_positional_prefix (NEW): rewrite positional args (MCScanX)
7. _symlink_prefix_data_files (NEW): create data file symlinks
8. _inject_dir_prefix_override (NEW): inject -oc flag (MEME family)
9. _root_prefix_pair (NEW): extract old/new root from renamed outputs
10. covered_by_patched_root: accept '/' as delimiter boundary
11. _requested_substitutions: auto-register unpatchable output roots
12. render_runtime_package: positional + -oc rewrite + locked data copy + symlink
13. _load_and_validate_render_record: exempt prefix overrides from ENTRY_COMMAND_CHANGED
14. _render_script_updates: tolerate count > expected (allow over-replace)
15. record schema: add _prefix_binding and actual_command fields

Fixes: s2-t02-f series, s4-t01-f series, s6-t02-f series, s8-v01-f
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 2026-08-07 20:51:27 +08:00
potaserandClaude Opus 5 842455dd78 Add gfa_core/mas/memory module 
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 2026-08-07 09:52:43 +08:00
potaser c389e90e64 Merge branch 'master' of http://192.168.31.232:3000/admin/PlantAI-dev 2026-08-07 09:41:18 +08:00
potaserandClaude Opus 5 7097ecdec5 Add memory directory 
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 2026-08-07 09:39:30 +08:00
potaser 822baab367 fix: preserve species roles through confirmation 2026-08-07 08:57:22 +08:00
wtx 8c3d601072 fix: allow reordered subfamily member records 2026-08-06 21:32:49 +08:00
sj 941673519f Merge branch 'master' of http://192.168.31.232:3000/admin/PlantAI-dev 2026-08-06 20:29:03 +08:00
sj 2623d3114c feat: update header and hide extension 2026-08-06 20:12:18 +08:00
potaser 4750bcc76f 增加了启动时可以指定web端口的功能；将主页运行结果按钮挪到了拓展分析title的后方 2026-08-06 19:34:11 +08:00
potaser 7b011da264 1. main.py 指向了新extension_stage_lightweight.api接口 
2. 优化了start_*_9000.sh启动时优先根据env配置启动的逻辑
3. 增加了一键启动脚本manage_plantai.sh，可以由Agent通过promot直接说启动、重启等进行服务的启动和关闭及重启
 2026-08-05 20:15:29 +08:00
potaser 35fbee8c85 fix: preserve confirmed species roles in agent planning 2026-08-05 15:42:32 +08:00
potaserandClaude Opus 5 231aa4517d chore: 清理旧 data 目录数据文件，新增 data/input/workspace 路径入口 
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
 2026-08-05 14:51:04 +08:00
potaserandClaude Opus 5 e641c8b9ab feat: 轻量拓展分析 + WGS2GWAS 阶段支持 + 结果区域重构 + 物种角色解析增强 + 会话 Job 隔离 
【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>
 2026-08-05 09:40:45 +08:00
potaser f745ee9d7e Initial commit: PlantAI-dev 2026-08-03 18:42:47 +08:00