 wtx
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7399b0bf14
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Merge origin/master before analysis handoff push
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2026-08-08 10:41:45 +08:00 |
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wtx
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5f240d1eec
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fix: delegate analysis planning from main agent
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2026-08-08 10:40:01 +08:00 |
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potaserandClaude Opus 5
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d66a5f9378
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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>
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2026-08-07 20:51:27 +08:00 |
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potaserandClaude Opus 5
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842455dd78
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Add gfa_core/mas/memory module
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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2026-08-07 09:52:43 +08:00 |
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potaser
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822baab367
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fix: preserve species roles through confirmation
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2026-08-07 08:57:22 +08:00 |
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wtx
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8c3d601072
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fix: allow reordered subfamily member records
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2026-08-06 21:32:49 +08:00 |
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potaser
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35fbee8c85
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fix: preserve confirmed species roles in agent planning
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2026-08-05 15:42:32 +08:00 |
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potaserandClaude Opus 5
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e641c8b9ab
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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>
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2026-08-05 09:40:45 +08:00 |
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potaser
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f745ee9d7e
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Initial commit: PlantAI-dev
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2026-08-03 18:42:47 +08:00 |
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