308 lines
7.0 KiB
Markdown
Executable File
308 lines
7.0 KiB
Markdown
Executable File
# 根目录整理方案
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## 📊 当前状况
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| 类型 | 数量 | 示例 |
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| Markdown文档 | 59个 | CHANGELOG*.md, *_REPORT.md, *_PLAN.md |
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| 提取器 | 25个 | extractor_*.py |
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| Shell脚本 | 6个 | *.sh |
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| 其他 | 大量 | test_*.py, rule_base*.json, config文件 |
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---
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## 📁 建议目录结构
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```
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gene-family-mas-v2/
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├── docs/ # 📚 文档目录
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│ ├── changelogs/ # 变更日志
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│ ├── reports/ # 报告文档
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│ ├── plans/ # 计划文档
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│ ├── analysis/ # 分析文档
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│ └── guides/ # 指南文档
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├── extractors/ # 🔧 提取器目录
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│ ├── current/ # 当前使用
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│ │ ├── fusion/ # PC融合版
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│ │ └── llm/ # LLM提取器
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│ └── archive/ # 归档版本
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├── scripts/ # 📜 脚本目录
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│ ├── shell/ # Shell脚本
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│ └── utils/ # 工具脚本
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├── tests/ # 🧪 测试文件
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├── config/ # ⚙️ 配置文件
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├── data/ # 📊 数据文件
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│ ├── rule_bases/ # 规则库
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│ └── samples/ # 样本数据
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└── [根目录保留核心文件] # 精简后的根目录
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```
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---
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## 🗂️ 具体整理方案
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### 1. Markdown文档 → docs/
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#### changelogs/ (7个)
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```
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CHANGELOG.md
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CHANGELOG_2026-04-05.md
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CHANGELOG_2026-04-08.md
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CHANGELOG_2026-04-09.md
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CHANGELOG_2026-04-09-V12.1.md
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revision_log_0330.md
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revision_logs/
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```
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#### reports/ (15个)
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```
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COMPARISON_REPORT.md
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COMPARISON_RESULT.md
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DATA_QUALITY_REPORT.md
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FINAL_COMPLETE_REPORT.md
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FINAL_QUALITY_REPORT.md
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FINAL_STATUS_REPORT.md
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FINAL_SUMMARY.md
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FINAL_TEST_REPORT.md
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kg_completion_report.md
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kg_validation_report.md
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LLM_TEST_REPORT.md
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prompt_v2_evaluation_report.md
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QUALITY_COMPARISON_RESULT.md (假设存在)
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V12_1_FIX_SUMMARY.md
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V2_STATUS.md
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```
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#### plans/ (8个)
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```
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10DAY_DELIVERY_PLAN.md
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COMPLETE_PROJECT_PLAN.md
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INTEGRATION_PLAN.md
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OPTIMIZATION_PLAN.md
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PROJECT_ORGANIZE_STATUS.md
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PROJECT_RECORD.md
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PROJECT_STATUS.md
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PROJECT_STRUCTURE.md
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REVISION_PLAN.md
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```
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#### analysis/ (12个)
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```
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AUTOSKG_INSIGHTS.md
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COMPETITIVE_ANALYSIS.md
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CRITICAL_ANALYSIS.md
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DEEP_COMPARISON.md
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extract_phylogeny_v4_README.md
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kg_expression_solution.md
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KG_TYPE_STATUS.md
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multi_agent_analysis.md
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MULTI_AGENT_SUMMARY.md
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PC_COMPARISON_ANALYSIS.md
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PC_COMPARISON_PLAN.md
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PC_METHOD_SUMMARY.md
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pc_workflow_analysis.md
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PLANTSCIENCE_AI_STATUS.md
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PLANTSCIENCE_AI_TECH_ANALYSIS.md
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REVIEW_MECHANISM_ANALYSIS.md
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THREE_METHODS_COMPARISON.md
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```
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#### guides/ (5个)
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```
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EXTRACTOR_CATALOG.md
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EXTRACTOR_INVENTORY.md
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INTEGRATION_PLAN.md (如果偏指南)
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VALIDATION_GUIDE.md
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VALIDATION_METHODS.md
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```
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### 2. 提取器 → extractors/
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#### current/fusion/ (2个 - 保留)
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```
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extractor_fusion_complete.py # ✅ 当前主用
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extractor_fusion_v1.py # ✅ 备份
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```
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#### current/llm/ (3个 - 保留)
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```
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llm_extractor_dashscope.py # ✅ 当前主用
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llm_relation_extractor.py # ✅ 关系提取
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universal_extractor_v2.py # ✅ 通用版
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```
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#### archive/ (20个 - 归档)
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```
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# SUC5系列 (6个)
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extractor_suc5.py
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extractor_suc5_v2.py
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extractor_suc5_v3.py
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extractor_suc5_v4.py
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extractor_suc5_final.py
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extractor_suc5_pc_match.py
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# PC实验版 (8个)
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extractor_pc_122_types.py
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extractor_pc_based.py
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extractor_pc_complete.py
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extractor_pc_complete_types.py
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extractor_pc_entities.py
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extractor_pc_entities_v2.py
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extractor_pc_full_types.py
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extractor_pc_style.py
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extractor_pc_v2.py
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# 其他旧版 (6个)
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extractor_complete_v1.py
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extractor_enhanced.py
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extractor_final.py
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extractor_hybrid.py
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extractor_hybrid_v3.py
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extractor_llm_v1.py
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extractor_production_v1.py
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extractor_v2_pro.py
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universal_extractor_v1.py
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```
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### 3. Shell脚本 → scripts/shell/
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```
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archive_old_versions.sh
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run_layer1_evaluation.sh
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RUN_V2_EXTRACTION.sh
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setup_docker_mirror.sh
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start_api.sh
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stop_api.sh
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```
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### 4. 测试文件 → tests/
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```
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test_api.py
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test_improved_quick.py
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test_litchi_v12.py
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test_llm_extraction.py
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test_phylo_result.json
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test_rag_prompt_v2.py
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test_rag_prompt_v2_real.py
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test_sentence_extraction.py
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test_v12_1_final.py
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test_v12_1_fixed_v2.py
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test_v12_1_full.py
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test_v12_1_lite.py
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test_v12_1_quality_report.md
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test_v12_1_quick.py
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test_v12_1_step_by_step.py
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test_v2_core.py
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```
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### 5. 规则库 → data/rule_bases/
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```
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rule_base_complete.py
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rule_base_full.json
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rule_base_loader.py
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rule_base_priority.json
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```
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### 6. 配置文件 → config/
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```
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config.py (如果存在)
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nginx.conf
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prometheus.yml
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pyproject.toml
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poetry.lock
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```
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---
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## 📋 根目录保留文件
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整理后根目录只保留：
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```
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README.md # 项目说明
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LICENSE # 许可证 (如果不存在需创建)
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.gitignore # Git忽略
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requirements.txt # Python依赖
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requirements-rag.txt # RAG依赖
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# 核心提取器 (软链接或保留)
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extractor_fusion_complete.py # 主提取器
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# 核心文档 (软链接)
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EXTRACTOR_CATALOG.md -> docs/guides/EXTRACTOR_CATALOG.md
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# 目录
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docs/
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extractors/
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scripts/
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tests/
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config/
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data/
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src/
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archive/ (如果保留)
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paper/
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output/
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supplementary_files/
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```
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---
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## 🔧 执行命令
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```bash
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# 1. 创建目录结构
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cd /home/xia-lab/gene-family-mas-v2
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mkdir -p docs/{changelogs,reports,plans,analysis,guides}
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mkdir -p extractors/{current/{fusion,llm},archive}
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mkdir -p scripts/shell
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mkdir -p config
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mkdir -p data/rule_bases
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# 2. 移动文档
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mv CHANGELOG*.md docs/changelogs/
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mv revision_log_0330.md docs/changelogs/
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mv *_REPORT.md docs/reports/
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mv *_PLAN.md docs/plans/
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mv *_ANALYSIS.md docs/analysis/
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mv EXTRACTOR_*.md docs/guides/
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# 3. 移动提取器
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mv extractor_fusion*.py extractors/current/fusion/
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mv llm_extractor*.py llm_relation_extractor.py universal_extractor_v2.py extractors/current/llm/
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mv extractor_suc5*.py extractor_pc_*.py extractor_complete_v1.py extractor_enhanced.py extractor_final.py extractor_hybrid*.py extractor_llm_v1.py extractor_production_v1.py extractor_v2_pro.py universal_extractor_v1.py extractors/archive/
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# 4. 移动脚本
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mv *.sh scripts/shell/
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# 5. 移动测试文件
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mv test_*.py tests/
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mv test_*.json tests/
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mv test_*.md tests/
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# 6. 移动规则库
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mv rule_base*.py rule_base*.json data/rule_bases/
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# 7. 移动配置
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mv nginx.conf prometheus.yml pyproject.toml poetry.lock config/
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# 8. 创建根目录核心文件软链接
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ln -s extractors/current/fusion/extractor_fusion_complete.py extractor.py
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ln -s docs/guides/EXTRACTOR_CATALOG.md EXTRACTOR_CATALOG.md
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```
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---
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## ⚠️ 注意事项
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1. **先备份**：执行前确保有git提交或备份
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2. **检查引用**：移动后检查其他文件中的import路径
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3. **软链接**：根目录保留软链接方便访问
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4. **archive目录**：如果已存在archive_old_versions，考虑合并
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---
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*整理方案创建时间：2026-04-12*
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