mirror of
https://github.com/lllin000/PaperForge.git
synced 2026-07-22 06:50:53 +00:00
fix(wizard): auto-run pip install -e . and improve UX flow
- setup_wizard.py: _deploy() now calls pip install -e <repo_root> automatically - DoneStep: removes manual 'pip install -e .' instruction (wizard handles it) - README.md: removes separate pip install -r requirements.txt step - docs/INSTALLATION.md: same pip install simplification - pyproject.toml: add pytest ignore for nested sandbox vault - tests/sandbox/: remove old vault/ (replaced by 00_TestVault/) - tests/sandbox/README.md: update flow, wizard handles pip install
This commit is contained in:
Research Assistant
parent
31cce820e2
commit
1d8478ce9c
16 changed files with 30 additions and 319 deletions
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@ -20,15 +20,13 @@
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git clone https://github.com/LLLin000/PaperForge.git
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cd PaperForge
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# 2. 安装依赖
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pip install -r requirements.txt
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# 3. 运行向导（交互式，按步骤引导）
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# 2. 运行向导（交互式，按步骤引导）
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python setup_wizard.py --vault /path/to/your/vault
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```
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向导会自动完成：
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- 检测 Python 环境和依赖
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- 安装 PaperForge 工具包（`pip install -e .` 由向导自动执行）
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- 配置 Vault 目录结构（可自定义名称）
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- 链接 Zotero 数据目录
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- 检测 Better BibTeX 插件
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@ -9,10 +9,7 @@ PaperForge 提供图形化安装向导，引导你完成全部配置：
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git clone https://github.com/LLLin000/PaperForge.git
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cd PaperForge
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# 2. 安装依赖
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pip install -r requirements.txt
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# 3. 运行向导
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# 2. 运行向导（pip install -e . 由向导自动执行）
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python setup_wizard.py --vault /path/to/your/vault
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```
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@ -45,3 +45,6 @@ include = ["paperforge_lite*"]
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[tool.setuptools.package-data]
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paperforge_lite = ["py.typed"]
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[tool.pytest.ini_options]
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addopts = "--ignore=tests/sandbox/00_TestVault/"
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@ -1126,7 +1126,22 @@ ZOTERO_DATA_DIR={getattr(self.app, 'zotero_data_dir', '')}
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self.set_status(f"脚本测试警告: {result.stderr[:100]}", None)
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except Exception as e:
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self.set_status(f"脚本测试跳过: {e}", None)
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# 9. 安装 PaperForge 工具包（让 paperforge 命令全局可用）
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self.set_status("安装 PaperForge 工具包...", None)
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try:
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result = subprocess.run(
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[sys.executable, "-m", "pip", "install", "-e", str(repo_root)],
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capture_output=True, text=True, timeout=60,
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)
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if result.returncode == 0:
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self.set_status("PaperForge 工具包安装完成（paperforge 命令已全局注册）", True)
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else:
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stderr = result.stderr[:200] if result.stderr else ""
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self.set_status(f"pip install 警告（paperforge 命令可能需要手动注册）: {stderr}", None)
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except Exception as e:
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self.set_status(f"pip install 跳过: {e}", None)
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return True
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@ -1141,36 +1156,31 @@ class DoneStep(StepScreen):
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yield Markdown(f"""
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## 安装完成！
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所有前置条件已满足，你现在可以开始使用 PaperForge Lite。
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PaperForge Lite 已完成安装和初始化。以下是立即开始使用的步骤：
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### 首次使用步骤：
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**1. 安装 PaperForge 工具包**
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```bash
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pip install -e .
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```
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**2. 同步 Zotero 文献**
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**1. 同步 Zotero 文献**
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```bash
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paperforge selection-sync
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```
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**3. 生成正式笔记**
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**2. 生成正式笔记**
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```bash
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paperforge index-refresh
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```
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**4. 标记精读文献**
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**3. 标记精读文献**
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在 Obsidian 中打开 library-records 文件，设置：
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- `do_ocr: true`
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- `analyze: true`
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**5. 运行 OCR**
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**4. 运行 OCR**
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```bash
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paperforge ocr run
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```
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**6. 执行精读**
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**5. 执行精读**
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在 OpenCode Agent 中输入：
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```
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/LD-deep <zotero_key>
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@ -21,7 +21,7 @@ tests/sandbox/
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# 1. 进入仓库根目录
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cd D:\...\github-release
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# 2. 运行安装向导，指向空 vault
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# 2. 运行安装向导，指向空 vault（pip install -e . 由向导自动完成）
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python setup_wizard.py --vault D:\L\Med\Research\99_System\LiteraturePipeline\github-release\tests\sandbox\00_TestVault
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# 3. 安装向导中：
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@ -32,14 +32,10 @@ python setup_wizard.py --vault D:\L\Med\Research\99_System\LiteraturePipeline\gi
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# （向导会检测到 exports/ 下的 JSON 文件）
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# - 其他步骤默认即可
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# 4. 向导完成后，按提示运行（在同一终端窗口）：
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pip install -e .
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# 5. 测试 pipeline：
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# 4. 测试 pipeline：
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cd D:\L\Med\Research\99_System\LiteraturePipeline\github-release\tests\sandbox\00_TestVault
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paperforge selection-sync
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paperforge index-refresh
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paperforge ocr run
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paperforge status
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```
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@ -1,13 +0,0 @@
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# GENERATED by PaperForge sandbox — test fixture
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name: Literature Hub
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type: ObsidianBase
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views:
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- name: 全记录
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type: table
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filters: ""
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order: title, year
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---
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# Literature Hub
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Cross-domain overview.
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@ -1,12 +0,0 @@
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# GENERATED by PaperForge sandbox — test fixture
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name: 运动医学
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type: ObsidianBase
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views:
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- name: 全记录
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type: table
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filters: ""
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order: title, year
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---
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# 运动医学 Literature Base
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@ -1,12 +0,0 @@
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# GENERATED by PaperForge sandbox — test fixture
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name: 骨科
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type: ObsidianBase
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views:
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- name: 全记录
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type: table
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filters: ""
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order: title, year
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---
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# 骨科 Literature Base
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@ -1,61 +0,0 @@
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{
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"items": [
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{
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"key": "SANDBOX004",
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"itemType": "journalArticle",
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"title": "Return to Sport Protocols After ACL Reconstruction: A Systematic Review",
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"creators": [
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{
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"creatorType": "author",
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"firstName": "Lisa",
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"lastName": "Park"
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},
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{
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"creatorType": "author",
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"firstName": "Tom",
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"lastName": "Nguyen"
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}
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],
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"date": "2024",
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"publicationTitle": "Sports Health",
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"DOI": "10.1177/19417381241234567",
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"PMID": "38876543",
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"abstractNote": "DATA SOURCES: PubMed, Embase, Cochrane. 23 studies included. Return-to-sport criteria varied widely.",
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"collections": [
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"运动医学"
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],
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"attachments": [
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{
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"path": "storage:SANDBOX004/SANDBOX004.pdf",
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"contentType": "application/pdf"
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}
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]
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},
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{
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"key": "SANDBOX005",
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"itemType": "journalArticle",
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"title": "Ultrasound-Guided Percutaneous Achilles Tendon Repair in Acute Ruptures",
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"creators": [
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{
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"creatorType": "author",
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"firstName": "Carlos",
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"lastName": "Rodriguez"
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}
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],
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"date": "2023",
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"publicationTitle": "Foot and Ankle International",
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"DOI": "10.1177/107110072311234",
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"PMID": "37234567",
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"abstractNote": "CASE SERIES: 28 patients. Primary outcomes: AOFAS score, time to weight-bearing, complications.",
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"collections": [
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"运动医学"
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],
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"attachments": [
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{
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"path": "storage:SANDBOX005/SANDBOX005.pdf",
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"contentType": "application/pdf"
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}
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]
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}
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]
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}
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@ -1,87 +0,0 @@
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{
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"items": [
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{
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"key": "SANDBOX001",
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"itemType": "journalArticle",
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"title": "Suture Anchor Fixation for Rotator Cuff Tears: A Biomechanical Analysis",
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"creators": [
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{
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"creatorType": "author",
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"firstName": "James",
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"lastName": "Burkhardt"
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},
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{
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"creatorType": "author",
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"firstName": "Maria",
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"lastName": "Chen"
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}
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],
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"date": "2024",
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"publicationTitle": "Journal of Shoulder and Elbow Surgery",
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"DOI": "10.1016/j.jses.2024.01.001",
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"PMID": "38234156",
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"abstractNote": "BACKGROUND: Suture anchor fixation is critical for rotator cuff repair. We compared pull-out strength across 3 anchor types.",
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"collections": [
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"骨科"
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],
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"attachments": [
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{
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"path": "storage:SANDBOX001/SANDBOX001.pdf",
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"contentType": "application/pdf"
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}
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]
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},
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{
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"key": "SANDBOX002",
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"itemType": "journalArticle",
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"title": "Machine Learning Prediction of Anterior Cruciate Ligament Injury Risk in Athletes",
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"creators": [
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{
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"creatorType": "author",
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"firstName": "Wei",
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"lastName": "Zhang"
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}
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],
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"date": "2023",
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"publicationTitle": "American Journal of Sports Medicine",
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"DOI": "10.1177/03635465231123456",
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"PMID": "37123456",
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"abstractNote": "PURPOSE: To develop and validate an ML model for predicting ACL injury risk using biomechanical and demographic features.",
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"collections": [
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"骨科"
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],
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"attachments": [
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{
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"path": "storage:SANDBOX002/SANDBOX002.pdf",
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"contentType": "application/pdf"
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}
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]
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},
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{
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"key": "SANDBOX003",
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"itemType": "journalArticle",
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"title": "Platelet-Rich Plasma Injection for Knee Osteoarthritis: Randomized Controlled Trial",
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"creators": [
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{
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"creatorType": "author",
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"firstName": "Sarah",
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"lastName": "Johnson"
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},
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{
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"creatorType": "author",
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"firstName": "Ahmed",
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"lastName": "Hassan"
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}
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],
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"date": "2022",
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"publicationTitle": "Osteoarthritis and Cartilage",
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"DOI": "10.1016/j.joca.2022.03.012",
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"PMID": "35412345",
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"abstractNote": "OBJECTIVE: To evaluate the efficacy of PRP injections vs hyaluronic acid for symptomatic knee OA.",
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"collections": [
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"骨科"
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],
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"attachments": []
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}
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]
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}
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@ -1,21 +0,0 @@
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%PDF-1.4
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1 0 obj
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<< /Type /Catalog /Pages 2 0 R >>
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endobj
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2 0 obj
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<< /Type /Pages /Kids [3 0 R] /Count 1 >>
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endobj
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3 0 obj
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<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
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endobj
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xref
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0 4
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0000000000 65535 f
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0000000009 00000 n
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0000000058 00000 n
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0000000115 00000 n
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trailer
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<< /Size 4 /Root 1 0 R >>
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startxref
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199
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%%EOF
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@ -1,21 +0,0 @@
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%PDF-1.4
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1 0 obj
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<< /Type /Catalog /Pages 2 0 R >>
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endobj
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2 0 obj
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<< /Type /Pages /Kids [3 0 R] /Count 1 >>
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endobj
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3 0 obj
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<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
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endobj
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xref
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0 4
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0000000000 65535 f
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0000000009 00000 n
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0000000058 00000 n
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0000000115 00000 n
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trailer
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<< /Size 4 /Root 1 0 R >>
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startxref
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199
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%%EOF
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%PDF-1.4
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1 0 obj
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<< /Type /Catalog /Pages 2 0 R >>
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endobj
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2 0 obj
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<< /Type /Pages /Kids [3 0 R] /Count 1 >>
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endobj
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3 0 obj
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<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
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endobj
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xref
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0 4
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0000000000 65535 f
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0000000009 00000 n
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0000000058 00000 n
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0000000115 00000 n
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trailer
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<< /Size 4 /Root 1 0 R >>
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startxref
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199
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%%EOF
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%PDF-1.4
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1 0 obj
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<< /Type /Catalog /Pages 2 0 R >>
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endobj
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2 0 obj
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<< /Type /Pages /Kids [3 0 R] /Count 1 >>
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endobj
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3 0 obj
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<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
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endobj
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xref
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0 4
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0000000000 65535 f
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0000000009 00000 n
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0000000058 00000 n
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0000000115 00000 n
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trailer
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<< /Size 4 /Root 1 0 R >>
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startxref
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199
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%%EOF
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# Sandbox Vault
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This is a completely sealed test vault for PaperForge Lite testing.
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Do not use with a real Obsidian vault.
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- 5 mock papers across 2 domains (骨科, 运动医学)
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- 4 with PDFs, 1 without (no-pdf case)
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- paperforge.json configured with default paths
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- .env with dummy PaddleOCR credentials
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Zotero storage: 99_System/Zotero/storage/
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BBT exports: 99_System/PaperForge/exports/
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Library records: 03_Resources/LiteratureControl/library-records/
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Literature notes: 03_Resources/Literature/
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Bases: 05_Bases/
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DO NOT ADD REAL DATA HERE.
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{
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"system_dir": "99_System",
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"resources_dir": "03_Resources",
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"literature_dir": "Literature",
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"control_dir": "LiteratureControl",
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"base_dir": "05_Bases"
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}
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Loading…
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