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feat(tests): add sealed sandbox vault for paperforge testing
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360
tests/sandbox/generate_sandbox.py
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360
tests/sandbox/generate_sandbox.py
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#!/usr/bin/env python3
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"""Generate a completely sealed test sandbox vault for PaperForge Lite.
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Run from repo root:
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python tests/sandbox/generate_sandbox.py
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This creates tests/sandbox/vault/ with:
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- Full vault directory structure
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- Mock Zotero storage with 3 PDFs
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- Better BibTeX JSON exports (2 domains)
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- Library records for all papers
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- paperforge.json with defaults
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- .env with dummy credentials
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Everything isolated — never touches real vault or Zotero.
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"""
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from __future__ import annotations
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import json
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import os
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from pathlib import Path
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ROOT = Path(__file__).parent
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SANDBOX_VAULT = ROOT / "vault"
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PAPERFORGE_CFG = {
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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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ZOTERO_JSON_ITEMS = {
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"骨科": [
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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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{"creatorType": "author", "firstName": "James", "lastName": "Burkhardt"},
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{"creatorType": "author", "firstName": "Maria", "lastName": "Chen"},
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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": ["骨科"],
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"attachments": [{"path": "storage:SANDBOX001/SANDBOX001.pdf", "contentType": "application/pdf"}],
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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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{"creatorType": "author", "firstName": "Wei", "lastName": "Zhang"},
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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": ["骨科"],
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"attachments": [{"path": "storage:SANDBOX002/SANDBOX002.pdf", "contentType": "application/pdf"}],
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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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{"creatorType": "author", "firstName": "Sarah", "lastName": "Johnson"},
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{"creatorType": "author", "firstName": "Ahmed", "lastName": "Hassan"},
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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": ["骨科"],
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"attachments": [],
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},
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],
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"运动医学": [
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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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{"creatorType": "author", "firstName": "Lisa", "lastName": "Park"},
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{"creatorType": "author", "firstName": "Tom", "lastName": "Nguyen"},
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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": ["运动医学"],
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"attachments": [{"path": "storage:SANDBOX004/SANDBOX004.pdf", "contentType": "application/pdf"}],
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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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{"creatorType": "author", "firstName": "Carlos", "lastName": "Rodriguez"},
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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": ["运动医学"],
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"attachments": [{"path": "storage:SANDBOX005/SANDBOX005.pdf", "contentType": "application/pdf"}],
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},
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],
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}
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OCR_STATUSES = {
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"SANDBOX001": "pending",
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"SANDBOX002": "pending",
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"SANDBOX003": "nopdf",
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"SANDBOX004": "pending",
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"SANDBOX005": "pending",
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}
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def write_minimal_pdf(path: Path) -> None:
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pdf_content = (
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b"%PDF-1.4\n"
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b"1 0 obj\n<< /Type /Catalog /Pages 2 0 R >>\nendobj\n"
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b"2 0 obj\n<< /Type /Pages /Kids [3 0 R] /Count 1 >>\nendobj\n"
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b"3 0 obj\n<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>\nendobj\n"
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b"xref\n0 4\n"
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b"0000000000 65535 f \n"
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b"0000000009 00000 n \n"
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b"0000000058 00000 n \n"
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b"0000000115 00000 n \n"
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b"trailer\n<< /Size 4 /Root 1 0 R >>\n"
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b"startxref\n199\n"
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b"%%EOF\n"
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)
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path.write_bytes(pdf_content)
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def build_vault() -> None:
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print(f"Generating sandbox vault at: {SANDBOX_VAULT}")
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vault = SANDBOX_VAULT
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if vault.exists():
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import shutil
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shutil.rmtree(vault)
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vault.mkdir(parents=True)
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system = vault / "99_System"
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pf = system / "PaperForge"
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exports = pf / "exports"
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ocr = pf / "ocr"
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zotero_link = system / "Zotero"
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resources = vault / "03_Resources"
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literature = resources / "Literature"
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control = resources / "LiteratureControl"
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records_root = control / "library-records"
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bases = vault / "05_Bases"
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opencode = vault / ".opencode"
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skills = opencode / "skills"
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cmd_dir = opencode / "command"
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dirs = [
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exports, ocr, zotero_link,
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literature, control, records_root,
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bases, skills, cmd_dir,
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]
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for d in dirs:
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d.mkdir(parents=True, exist_ok=True)
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(vault / "paperforge.json").write_text(
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json.dumps(PAPERFORGE_CFG, ensure_ascii=False, indent=2),
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encoding="utf-8",
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)
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(vault / ".env").write_text(
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"PADDLEOCR_API_TOKEN=sandbox_dummy_token_do_not_use\n"
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"PADDLEOCR_API_TOKEN_USER=\n"
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"PADDLEOCR_JOB_URL=https://api.paddleocr.com/v1/job\n"
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"PADDLEOCR_MODEL=docThinking\n"
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"PADDLEOCR_MAX_ITEMS=10\n",
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encoding="utf-8",
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)
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zotero_storage = zotero_link / "storage"
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zotero_storage.mkdir(exist_ok=True)
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for domain, items in ZOTERO_JSON_ITEMS.items():
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domain_records = records_root / domain
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domain_records.mkdir(exist_ok=True)
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export_items = []
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for item in items:
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key = item["key"]
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export_items.append(item)
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attachments = item.get("attachments", [])
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for att in attachments:
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att_path = att["path"]
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if att_path.startswith("storage:"):
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storage_rel = att_path[len("storage:") :]
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storage_path = zotero_storage / storage_rel
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storage_path.parent.mkdir(parents=True, exist_ok=True)
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write_minimal_pdf(storage_path)
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doi = item.get("DOI", "")
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year = item.get("date", "")
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title = item.get("title", "")
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ocr_status = OCR_STATUSES.get(key, "pending")
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has_pdf = "true" if attachments else "false"
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pdf_path_val = f"storage:{key}/{key}.pdf" if attachments else ""
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record_text = f"""---
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zotero_key: "{key}"
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domain: "{domain}"
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title: "{title}"
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year: "{year}"
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doi: "{doi}"
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has_pdf: {has_pdf}
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pdf_path: "{pdf_path_val}"
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fulltext_md_path: ""
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recommend_analyze: true
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analyze: false
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do_ocr: false
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ocr_status: "{ocr_status}"
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deep_reading_status: "pending"
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analysis_note: ""
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---
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# {title}
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DOI: {doi}
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Year: {year}
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Abstract:
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{item.get('abstractNote', '')}
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---
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*Generated sandbox record — not a real citation*
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"""
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record_file = domain_records / f"{key}.md"
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record_file.write_text(record_text, encoding="utf-8")
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literature_note = f"""---
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title: "{title}"
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year: {year}
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type: journal
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category: "{domain}"
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tags:
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- sandbox
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- test
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pdf_link: "99_System/Zotero/storage/{key}/{key}.pdf"
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---
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# {title}
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{item.get('abstractNote', '')}
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---
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*Generated sandbox literature note*
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"""
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lit_dir = literature / domain
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lit_dir.mkdir(exist_ok=True)
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lit_file = lit_dir / f"{key} - {title[:30]}.md"
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lit_file.write_text(literature_note, encoding="utf-8")
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bbt_export = exports / f"{domain}.json"
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bbt_export.write_text(
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json.dumps({"items": export_items}, ensure_ascii=False, indent=2),
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encoding="utf-8",
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)
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for domain in ZOTERO_JSON_ITEMS:
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base_file = bases / f"{domain}.base"
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base_file.write_text(
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f"""# GENERATED by PaperForge sandbox — test fixture
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name: {domain}
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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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# {domain} Literature Base
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""",
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encoding="utf-8",
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)
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lit_hub = bases / "Literature Hub.base"
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lit_hub.write_text(
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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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""",
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encoding="utf-8",
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)
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readme = vault / "README.md"
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readme.write_text(
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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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encoding="utf-8",
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)
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print(f" vault/ — root")
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print(f" 99_System/ — system dir (Zotero junction, PaperForge)")
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print(f" Zotero/storage/ — 4 mock PDFs")
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print(f" PaperForge/exports/ — 2 BBT JSON files (骨科.json, 运动医学.json)")
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print(f" PaperForge/ocr/ — OCR output dir")
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print(f" 03_Resources/ — resources dir")
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print(f" Literature/ — formal literature notes (5)")
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print(f" LiteratureControl/ — control dir")
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print(f" library-records/ — 5 library records")
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print(f" 05_Bases/ — 3 Base files")
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print(f" .opencode/ — skills + command stubs")
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print(f" .env — dummy credentials")
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print(f" paperforge.json — default config")
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print(f"\nTotal: 5 papers, 4 PDFs, 2 domains")
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print(f"Sandbox vault ready at: {SANDBOX_VAULT}")
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if __name__ == "__main__":
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build_vault()
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13
tests/sandbox/vault/05_Bases/Literature Hub.base
Normal file
13
tests/sandbox/vault/05_Bases/Literature Hub.base
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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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12
tests/sandbox/vault/05_Bases/运动医学.base
Normal file
12
tests/sandbox/vault/05_Bases/运动医学.base
Normal file
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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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12
tests/sandbox/vault/05_Bases/骨科.base
Normal file
12
tests/sandbox/vault/05_Bases/骨科.base
Normal file
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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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61
tests/sandbox/vault/99_System/PaperForge/exports/运动医学.json
Normal file
61
tests/sandbox/vault/99_System/PaperForge/exports/运动医学.json
Normal file
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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",
|
||||
"contentType": "application/pdf"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
87
tests/sandbox/vault/99_System/PaperForge/exports/骨科.json
Normal file
87
tests/sandbox/vault/99_System/PaperForge/exports/骨科.json
Normal file
|
|
@ -0,0 +1,87 @@
|
|||
{
|
||||
"items": [
|
||||
{
|
||||
"key": "SANDBOX001",
|
||||
"itemType": "journalArticle",
|
||||
"title": "Suture Anchor Fixation for Rotator Cuff Tears: A Biomechanical Analysis",
|
||||
"creators": [
|
||||
{
|
||||
"creatorType": "author",
|
||||
"firstName": "James",
|
||||
"lastName": "Burkhardt"
|
||||
},
|
||||
{
|
||||
"creatorType": "author",
|
||||
"firstName": "Maria",
|
||||
"lastName": "Chen"
|
||||
}
|
||||
],
|
||||
"date": "2024",
|
||||
"publicationTitle": "Journal of Shoulder and Elbow Surgery",
|
||||
"DOI": "10.1016/j.jses.2024.01.001",
|
||||
"PMID": "38234156",
|
||||
"abstractNote": "BACKGROUND: Suture anchor fixation is critical for rotator cuff repair. We compared pull-out strength across 3 anchor types.",
|
||||
"collections": [
|
||||
"骨科"
|
||||
],
|
||||
"attachments": [
|
||||
{
|
||||
"path": "storage:SANDBOX001/SANDBOX001.pdf",
|
||||
"contentType": "application/pdf"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"key": "SANDBOX002",
|
||||
"itemType": "journalArticle",
|
||||
"title": "Machine Learning Prediction of Anterior Cruciate Ligament Injury Risk in Athletes",
|
||||
"creators": [
|
||||
{
|
||||
"creatorType": "author",
|
||||
"firstName": "Wei",
|
||||
"lastName": "Zhang"
|
||||
}
|
||||
],
|
||||
"date": "2023",
|
||||
"publicationTitle": "American Journal of Sports Medicine",
|
||||
"DOI": "10.1177/03635465231123456",
|
||||
"PMID": "37123456",
|
||||
"abstractNote": "PURPOSE: To develop and validate an ML model for predicting ACL injury risk using biomechanical and demographic features.",
|
||||
"collections": [
|
||||
"骨科"
|
||||
],
|
||||
"attachments": [
|
||||
{
|
||||
"path": "storage:SANDBOX002/SANDBOX002.pdf",
|
||||
"contentType": "application/pdf"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"key": "SANDBOX003",
|
||||
"itemType": "journalArticle",
|
||||
"title": "Platelet-Rich Plasma Injection for Knee Osteoarthritis: Randomized Controlled Trial",
|
||||
"creators": [
|
||||
{
|
||||
"creatorType": "author",
|
||||
"firstName": "Sarah",
|
||||
"lastName": "Johnson"
|
||||
},
|
||||
{
|
||||
"creatorType": "author",
|
||||
"firstName": "Ahmed",
|
||||
"lastName": "Hassan"
|
||||
}
|
||||
],
|
||||
"date": "2022",
|
||||
"publicationTitle": "Osteoarthritis and Cartilage",
|
||||
"DOI": "10.1016/j.joca.2022.03.012",
|
||||
"PMID": "35412345",
|
||||
"abstractNote": "OBJECTIVE: To evaluate the efficacy of PRP injections vs hyaluronic acid for symptomatic knee OA.",
|
||||
"collections": [
|
||||
"骨科"
|
||||
],
|
||||
"attachments": []
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
%PDF-1.4
|
||||
1 0 obj
|
||||
<< /Type /Catalog /Pages 2 0 R >>
|
||||
endobj
|
||||
2 0 obj
|
||||
<< /Type /Pages /Kids [3 0 R] /Count 1 >>
|
||||
endobj
|
||||
3 0 obj
|
||||
<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
|
||||
endobj
|
||||
xref
|
||||
0 4
|
||||
0000000000 65535 f
|
||||
0000000009 00000 n
|
||||
0000000058 00000 n
|
||||
0000000115 00000 n
|
||||
trailer
|
||||
<< /Size 4 /Root 1 0 R >>
|
||||
startxref
|
||||
199
|
||||
%%EOF
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
%PDF-1.4
|
||||
1 0 obj
|
||||
<< /Type /Catalog /Pages 2 0 R >>
|
||||
endobj
|
||||
2 0 obj
|
||||
<< /Type /Pages /Kids [3 0 R] /Count 1 >>
|
||||
endobj
|
||||
3 0 obj
|
||||
<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
|
||||
endobj
|
||||
xref
|
||||
0 4
|
||||
0000000000 65535 f
|
||||
0000000009 00000 n
|
||||
0000000058 00000 n
|
||||
0000000115 00000 n
|
||||
trailer
|
||||
<< /Size 4 /Root 1 0 R >>
|
||||
startxref
|
||||
199
|
||||
%%EOF
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
%PDF-1.4
|
||||
1 0 obj
|
||||
<< /Type /Catalog /Pages 2 0 R >>
|
||||
endobj
|
||||
2 0 obj
|
||||
<< /Type /Pages /Kids [3 0 R] /Count 1 >>
|
||||
endobj
|
||||
3 0 obj
|
||||
<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
|
||||
endobj
|
||||
xref
|
||||
0 4
|
||||
0000000000 65535 f
|
||||
0000000009 00000 n
|
||||
0000000058 00000 n
|
||||
0000000115 00000 n
|
||||
trailer
|
||||
<< /Size 4 /Root 1 0 R >>
|
||||
startxref
|
||||
199
|
||||
%%EOF
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
%PDF-1.4
|
||||
1 0 obj
|
||||
<< /Type /Catalog /Pages 2 0 R >>
|
||||
endobj
|
||||
2 0 obj
|
||||
<< /Type /Pages /Kids [3 0 R] /Count 1 >>
|
||||
endobj
|
||||
3 0 obj
|
||||
<< /Type /Page /Parent 2 0 R /MediaBox [0 0 612 792] >>
|
||||
endobj
|
||||
xref
|
||||
0 4
|
||||
0000000000 65535 f
|
||||
0000000009 00000 n
|
||||
0000000058 00000 n
|
||||
0000000115 00000 n
|
||||
trailer
|
||||
<< /Size 4 /Root 1 0 R >>
|
||||
startxref
|
||||
199
|
||||
%%EOF
|
||||
17
tests/sandbox/vault/README.md
Normal file
17
tests/sandbox/vault/README.md
Normal file
|
|
@ -0,0 +1,17 @@
|
|||
# Sandbox Vault
|
||||
|
||||
This is a completely sealed test vault for PaperForge Lite testing.
|
||||
Do not use with a real Obsidian vault.
|
||||
|
||||
- 5 mock papers across 2 domains (骨科, 运动医学)
|
||||
- 4 with PDFs, 1 without (no-pdf case)
|
||||
- paperforge.json configured with default paths
|
||||
- .env with dummy PaddleOCR credentials
|
||||
|
||||
Zotero storage: 99_System/Zotero/storage/
|
||||
BBT exports: 99_System/PaperForge/exports/
|
||||
Library records: 03_Resources/LiteratureControl/library-records/
|
||||
Literature notes: 03_Resources/Literature/
|
||||
Bases: 05_Bases/
|
||||
|
||||
DO NOT ADD REAL DATA HERE.
|
||||
7
tests/sandbox/vault/paperforge.json
Normal file
7
tests/sandbox/vault/paperforge.json
Normal file
|
|
@ -0,0 +1,7 @@
|
|||
{
|
||||
"system_dir": "99_System",
|
||||
"resources_dir": "03_Resources",
|
||||
"literature_dir": "Literature",
|
||||
"control_dir": "LiteratureControl",
|
||||
"base_dir": "05_Bases"
|
||||
}
|
||||
Loading…
Reference in a new issue