180 lines
6.2 KiB
Markdown
Executable File
180 lines
6.2 KiB
Markdown
Executable File
# 项目整理状态报告
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> 整理时间: 2026-04-01
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> 整理范围: 全面整理所有新旧版本文件
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---
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## ✅ 已完成的整理
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### 1. 核心提取器文件 (保留最新版本)
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- ✅ `extract_phylogeny_v5_universal_v3.py` → `scripts/extractors/` ⭐
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- ✅ `batch_extract.py` → `scripts/extractors/`
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- ✅ `kg_import.py` → `scripts/extractors/`
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- ✅ `kg_schema.py` → `scripts/extractors/`
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- ✅ `gene_family_keywords_v3.json` → `scripts/extractors/`
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### 2. 旧版本提取器归档 (37个文件)
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- ✅ 全部移入 `archive/old_extractors/`
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- 包括: v1-v4版本, v5实验版本, ICL版本等
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### 3. 旧版本API归档 (4个文件)
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- ✅ `api_server.py` → `archive/old_api/`
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- ✅ `api_server_v2.py` → `archive/old_api/`
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- ✅ `api_server_v3.py` → `archive/old_api/`
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- ✅ `api_server_v3_complete.py` → `archive/old_api/`
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### 4. 工具脚本整理 (14个文件)
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- ✅ `add_missing_genes.py` → `scripts/utils/`
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- ✅ `apply_locus_mapping.py` → `scripts/utils/`
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- ✅ `chunk_by_section.py` → `scripts/utils/`
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- ✅ `expand_*.py` → `scripts/utils/`
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- ✅ `fetch_supplementary_data.py` → `scripts/utils/`
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- ✅ `final_merge*.py` → `scripts/utils/`
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- ✅ `generate_validation_report.py` → `scripts/utils/`
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- ✅ `kg_sqlite.py` → `scripts/utils/`
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- ✅ `merge_all_extractions.py` → `scripts/utils/`
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- ✅ `post_process_*.py` → `scripts/utils/`
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- ✅ `reasoning_engine.py` → `scripts/utils/`
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- ✅ `universal_supplementary_fetcher.py` → `scripts/utils/`
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- ✅ `validate_extraction.py` → `scripts/utils/`
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### 5. 测试脚本整理 (5个文件)
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- ✅ `rag_test_100.py` → `tests/`
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- ✅ `test_europe_pmc_api.py` → `tests/`
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- ✅ `test_ocr_only.py` → `tests/`
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- ✅ `test_phylo_inference.py` → `tests/`
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### 6. 配置文件整理
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- ✅ `docker-compose*.yml` → `config/`
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- ✅ `Dockerfile*` → `config/`
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- ✅ `.env*` → `config/`
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- ✅ `prometheus.yml` → `config/`
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- ✅ `nginx.conf` → `config/`
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### 7. 文档文件整理 (13个文件)
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- ✅ 旧版本文档 → `archive/old_docs/`
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- ✅ `PROJECT_STRUCTURE.md` → 根目录
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- ✅ `PROJECT_ORGANIZE_STATUS.md` → 根目录
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### 8. 临时数据文件归档
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- ✅ `tair_data.txt` → `archive/`
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- ✅ `tair_parsed.json` → `archive/`
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### 9. 整理脚本归档
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- ✅ `archive_old_versions.sh` → `scripts/`
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- ✅ `organize.py` → `scripts/`
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---
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## 📁 最终目录结构
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```
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gene-family-mas-v2/
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├── 📁 api/ # FastAPI接口
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│ ├── main.py
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│ ├── rag_routes.py
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│ ├── kg_routes.py
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│ └── ...
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│
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├── 📁 scripts/ # Python脚本
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│ ├── 📁 extractors/ # ⭐ 核心提取器 (5个文件)
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│ │ ├── extract_phylogeny_v5_universal_v3.py
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│ │ ├── batch_extract.py
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│ │ ├── kg_import.py
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│ │ ├── kg_schema.py
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│ │ └── gene_family_keywords_v3.json
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│ │
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│ ├── 📁 utils/ # 工具脚本 (14个文件)
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│ │ ├── add_missing_genes.py
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│ │ ├── apply_locus_mapping.py
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│ │ ├── chunk_by_section.py
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│ │ └── ...
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│ │
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│ └── 📁 legacy/ # 旧版本
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│ └── ...
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│
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├── 📁 tests/ # 测试脚本 (5个文件)
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│ ├── rag_test_100.py
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│ └── test_*.py
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│
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├── 📁 docs/ # 文档
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│ ├── 📁 reports/ # 分析报告
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│ ├── 📁 plans/ # 计划文档
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│ └── ORGANIZE_REPORT.json # 整理报告
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│
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├── 📁 config/ # 配置文件
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│ ├── docker-compose.yml
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│ ├── docker-compose.neo4j.yml
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│ ├── Dockerfile
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│ └── .env*
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│
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├── 📁 data/ # 数据目录
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│ ├── raw/
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│ ├── processed/
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│ └── neo4j/
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│
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├── 📁 archive/ # ⭐ 归档文件
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│ ├── 📁 old_extractors/ # 37个旧版本提取器
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│ ├── 📁 old_api/ # 4个旧版本API
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│ ├── 📁 old_docs/ # 13个旧版本文档
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│ ├── tair_data.txt
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│ └── tair_parsed.json
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│
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├── 📁 frontend/ # 前端代码
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├── 📁 skills/ # 技能模块
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├── 📁 evaluation/ # 评估结果
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├── 📁 paper/ # 论文PDF
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├── 📁 extracted/ # 提取结果
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├── 📁 prompts/ # Prompt模板
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├── 📁 project_memory/ # 项目记忆 (24个文件)
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├── 📁 batch_results/ # 批量结果
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│
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├── 📄 README.md # 项目说明
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├── 📄 CHANGELOG.md # 变更日志
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├── 📄 PROJECT_STRUCTURE.md # 结构说明
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└── 📄 PROJECT_ORGANIZE_STATUS.md # 本文件
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```
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---
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## 📊 整理统计
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| 类别 | 数量 | 位置 |
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|:---|:---:|:---|
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| 核心提取器 | 5 | `scripts/extractors/` |
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| 工具脚本 | 14 | `scripts/utils/` |
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| 测试脚本 | 5 | `tests/` |
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| 旧版本提取器 | 37 | `archive/old_extractors/` |
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| 旧版本API | 4 | `archive/old_api/` |
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| 旧版本文档 | 13 | `archive/old_docs/` |
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| 配置文件 | 6 | `config/` |
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| 项目记忆 | 24 | `project_memory/` |
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**总计**: 108个文件已分类整理 ✅
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---
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## 🎯 核心文件快速定位
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| 功能 | 路径 |
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|:---|:---|
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| **v5.2提取器** | `scripts/extractors/extract_phylogeny_v5_universal_v3.py` |
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| **批量提取** | `scripts/extractors/batch_extract.py` |
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| **关键词库** | `scripts/extractors/gene_family_keywords_v3.json` |
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| **知识图谱导入** | `scripts/extractors/kg_import.py` |
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| **知识图谱Schema** | `scripts/extractors/kg_schema.py` |
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| **API路由** | `api/rag_routes.py`, `api/kg_routes.py` |
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| **Docker配置** | `config/docker-compose.yml` |
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| **Neo4j配置** | `config/docker-compose.neo4j.yml` |
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| **项目记忆** | `project_memory/2026-04-01.md` |
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| **项目结构** | `PROJECT_STRUCTURE.md` |
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---
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## ✅ 整理完成
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项目已全面整理完毕！所有文件都在标准位置，根目录保持整洁。
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如需查看旧版本文件，请访问 `archive/` 目录。
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