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potaser db610031c1 修复轻量拓展分析 NL 触发第一轮测试反馈（PM 裁断） 
- P0 目录截断：_rough_candidates 关键词源扩展 extension_id token 与参数 flag；命中数降序排序；MAX_CATALOG_CHARS 12000→24000；截断时 reason 注明
- P1a 过滤缺失 extension_id 的记录，不再产出 None 候选
- P1b hmmsearch/hmmer/blast/blastp 不再全量触发，改为按关键词源匹配子集；仅「拓展分析/扩展分析/extension」允许全量候选
- P2 extension_name 改为 extension_id 紧凑形式（去尾缀时间戳截 30 字符）；message 中文模板（extension_id 为主、summary 括号补充）
- P2 nl-import-paths：目录同名冲突 _1/_2 后缀；多路径先整体校验后复制
2026-08-27 00:21:31 +08:00
.codegraph
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.local/meme-4.11.2-mpi
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.planning
feat: deepseek summary agent + clean old memory logs + merge prep
2026-08-09 09:04:27 +08:00
.recovery
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.revision-ppi-kaks-plan-pruning-v1
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.superpowers
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.tmp_meme_mpi
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.tmp_meme_parallel_test_out
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.worktrees/router-error-detail
chore: track worktree checkout, lightweight extension staging and wgs manifests
2026-08-21 11:49:48 +08:00
apps
修复轻量拓展分析 NL 触发第一轮测试反馈（PM 裁断）
2026-08-27 00:21:31 +08:00
assets
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
benchmarks/plantgenebench
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
codeMiaoshu
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
config
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
contrib/methodology-rag-substage-progress
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
docs
fix: integrate deployed reports with PPI KaKs handoff
2026-08-11 04:48:38 +08:00
enviroment
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
extension_code_data_staging/genome_shell_30
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
extension_stages
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
extension_stages_lightweight
全量扩展分析样本验证测试
2026-08-24 20:52:42 +08:00
gfa_core
修复轻量拓展分析 NL 触发第一轮测试反馈（PM 裁断）
2026-08-27 00:21:31 +08:00
graphify-out
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
manuscript/plantai_aiia_zh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
memory
fix: restore memory logs and keep absolute data symlink
2026-08-21 11:06:49 +08:00
models/bge-m3_from_web
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
prompts
feat: deepseek summary agent + clean old memory logs + merge prep
2026-08-09 09:04:27 +08:00
rollback_backups
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
scripts
fix(runtime): standardize 9000 startup and isolate project services
2026-08-10 10:57:49 +08:00
skills
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_integration
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test-results/completed-stage-pruning
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
tests
fix: preserve gene-family stage intent and completed results
2026-08-24 09:34:13 +08:00
tools
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
validation/rnaseq_design_20260719
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
w/final
chore: track worktree checkout, lightweight extension staging and wgs manifests
2026-08-21 11:49:48 +08:00
.env.example
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.gitignore
feat: deepseek summary agent + clean old memory logs + merge prep
2026-08-09 09:04:27 +08:00
.gitignore.opensource
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.revision_memory.json
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.run_ident_enhance.py.swp
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
.tmp_meme_parallel_test.fa
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
=1.0.0,
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
AGENTS.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
ANALYSIS_FLOW_ANALYSIS.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
At.HD-ZIP.short_names.subfamily.locus.tsv
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
At.HD-ZIP.short_names.subfamily.tsv
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
celery_app.py
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
2026-08-05 09:40:45 +08:00
CHANGELOG_2026-04-14.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
check_cost.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
CLAUDE.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
cleanup_agents.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
CONVERSATION_MANAGER_REPORT.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
data
fix: restore memory logs and keep absolute data symlink
2026-08-21 11:06:49 +08:00
download_prjna530826_rnaseq_aria2c.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
download_prjna530826_rnaseq_aria2c.sh.bak
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
enable_persistent_memory.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
example_task_with_wechat.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
Ft.SPL.expression.gene-cor.heatmap.pdf
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
Ft.SPL.expression.gene-cor.txt
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
Ft.SPL.expression.gene-exp.heatmap.pdf
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
Ft.SPL.expression.gene-exp.hist.pdf
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
Ft.SPL.expression.gene-exp.txt
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
get_wechat_id.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
IDENTIFY_AGENT_FLOW.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
input
chore: 清理旧 data 目录数据文件，新增 data/input/workspace 路径入口
2026-08-05 14:51:04 +08:00
input.shared_bbav5_7880_bak_link
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
interproscanpy311.yaml
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
manage_plantai.sh
feat:sync-report-workflows-and-migration-runtime
2026-08-10 11:40:20 +08:00
MEMORY.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
notify_integration.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
OPEN_SOURCE_EXCLUDE.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
Os.NAC_promoter_05_upset_data.csv
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
pipeline_backend_patch.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
PLAN-REVIEW-LOG.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
PLAN.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
PRJNA530826.aria2c.urls.txt
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
PRJNA530826.ena_fastq.tsv
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
PRJNA530826.fastq.md5
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
PROJECT_PLAN.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
pytest.ini
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
restart_plantai_9000.sh
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
REVISION_2026-04-13.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
rnaseq.before_salmon_downgrade.txt
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
rnaseq.before_salmon_downgrade.yml
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_kaks_manual.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
run_tests.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
SECRET_AUDIT.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
session_storage.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
start_celery_9000.sh
feat:sync-report-workflows-and-migration-runtime
2026-08-10 11:40:20 +08:00
start_plantai_9000.sh
feat:sync-report-workflows-and-migration-runtime
2026-08-10 11:40:20 +08:00
start_wechat_bot.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
start_wechat_service.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
tasks.py
feat: add gene family result reports
2026-08-09 04:32:28 +08:00
test_agent_manual.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_annotation_skill.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_full_integration.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_langgraph_state.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_rnaseq_align.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_router.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
test_tree_plot.sh
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
update_prompts.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
validate_js.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
VUE3_CONVERSATION_SIDEBAR_REPORT.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
wechat_bot.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
WECHAT_INTEGRATION.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
wechat_integration.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
wechat_service.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
wechat_task_bridge.py
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
WORKLINE.md
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
workspace
chore: 清理旧 data 目录数据文件，新增 data/input/workspace 路径入口
2026-08-05 14:51:04 +08:00
workspace.shared_bbav5_7880_bak_link
Initial commit: PlantAI-dev
2026-08-03 18:42:47 +08:00
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20260808展会版
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2026-08-10 17:25:25 +08:00
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