mirror of
https://github.com/lllin000/PaperForge.git
synced 2026-07-22 17:00:23 +00:00
9b88c441b0
- Replace 6 scattered pf-*.md files with single SKILL.md router + 4 reference files - Add paper_resolver.py: deterministic key/DOI/field search (4 subcommands) - Remove pf-sync/ocr/status (CLI-only commands, no skill wrapper needed) - Move chart-reading/ into references/ for flat structure - Make ld_deep.py --vault optional (auto-detect from cwd) - Add 26 unit tests for paper_resolver - All paths dynamically resolved from paperforge.json, zero hardcoding
361 lines
12 KiB
Python
361 lines
12 KiB
Python
"""Tests for paperforge.worker.paper_resolver."""
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import json
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from pathlib import Path
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import pytest
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from paperforge.worker.paper_resolver import PaperResolver, PaperWorkspace
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# ---------------------------------------------------------------------------
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# Fixtures
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# ---------------------------------------------------------------------------
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def _make_index_entry(
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key="ABC12345",
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title="Test Paper Title",
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domain="骨科",
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year=2024,
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authors="Smith J; Doe J",
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doi="10.1234/test.2024",
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journal="Journal of Testing",
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note_path=None,
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ocr_status="done",
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deep_reading_status="pending",
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analyze=True,
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do_ocr=True,
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has_pdf=True,
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**overrides,
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):
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if note_path is None:
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note_path = f"Literature/{domain}/{key} - {title}.md"
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entry = {
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"zotero_key": key,
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"title": title,
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"domain": domain,
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"year": year,
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"authors": authors.split("; "),
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"doi": doi,
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"journal": journal,
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"note_path": note_path,
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"ocr_status": ocr_status,
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"deep_reading_status": deep_reading_status,
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"analyze": analyze,
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"do_ocr": do_ocr,
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"has_pdf": has_pdf,
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"fulltext_path": "",
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"collection_path": "",
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"first_author": authors.split("; ")[0] if authors else "",
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"abstract": "This is a test abstract.",
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"impact_factor": "5.0",
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"pmid": "",
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"collections": [],
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"collection_tags": [],
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"collection_group": [],
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"pdf_path": "",
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"ocr_job_id": "",
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"ocr_md_path": "",
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"ocr_json_path": "",
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"deep_reading_md_path": "",
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"paper_root": "",
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"main_note_path": "",
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"deep_reading_path": "",
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"ai_path": "",
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"lifecycle": "fulltext_ready",
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"health": {},
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"maturity": {},
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"next_step": "/pf-deep",
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}
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entry.update(overrides)
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return entry
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def _make_index_envelope(items):
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return {"schema_version": "2", "generated_at": "2026-01-01T00:00:00", "paper_count": len(items), "items": items}
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def _write_index(path: Path, envelope: dict):
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path.parent.mkdir(parents=True, exist_ok=True)
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path.write_text(json.dumps(envelope, ensure_ascii=False), encoding="utf-8")
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def _write_vault_config(vault: Path):
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(vault / "paperforge.json").write_text(
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json.dumps(
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{
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"vault_config": {
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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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}
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}
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),
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encoding="utf-8",
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)
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# ---------------------------------------------------------------------------
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# Patch PaperResolver to bypass real file system dependencies
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# ---------------------------------------------------------------------------
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@pytest.fixture
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def resolver_with_index(tmp_path):
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"""Create a PaperResolver preloaded with a test index."""
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vault = tmp_path / "test_vault"
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vault.mkdir(parents=True)
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_write_vault_config(vault)
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# Create index path structure
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indexes_dir = vault / "99_System" / "PaperForge" / "indexes"
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indexes_dir.mkdir(parents=True)
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items = [
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_make_index_entry(key="ABC12345", title="TGF-beta in Bone Regeneration", domain="骨科", year=2024, authors="Smith J; Lee K", doi="10.1234/tgf.2024"),
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_make_index_entry(key="DEF67890", title="MRI Predictive Findings in Rotator Cuff", domain="运动医学", year=2023, authors="Chen W; Wang L", doi="10.5678/mri.2023"),
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_make_index_entry(key="GHI11111", title="Another Bone Study", domain="骨科", year=2024, authors="Smith J; Zhang Y", doi="10.9999/bone.2024"),
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]
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_write_index(indexes_dir / "formal-library.json", _make_index_envelope(items))
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# Create literature dirs and minimal formal notes
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for item in items:
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note_dir = vault / Path(item["note_path"]).parent
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note_dir.mkdir(parents=True, exist_ok=True)
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frontmatter = f"""---
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zotero_key: "{item['zotero_key']}"
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domain: "{item['domain']}"
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title: "{item['title']}"
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year: {item['year']}
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doi: "{item['doi']}"
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ocr_status: "{item['ocr_status']}"
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deep_reading_status: "{item['deep_reading_status']}"
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analyze: {str(item['analyze']).lower()}
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do_ocr: {str(item['do_ocr']).lower()}
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has_pdf: {str(item['has_pdf']).lower()}
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---
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"""
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(vault / item["note_path"]).write_text(frontmatter, encoding="utf-8")
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# Create OCR dir for ABC12345
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ocr_dir = vault / "99_System" / "PaperForge" / "ocr" / "ABC12345"
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ocr_dir.mkdir(parents=True)
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(ocr_dir / "fulltext.md").write_text("# Fulltext\nTest content.", encoding="utf-8")
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resolver = PaperResolver(vault)
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resolver._ensure_loaded()
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return resolver
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@pytest.fixture
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def empty_resolver(tmp_path):
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"""Create a PaperResolver with no index data."""
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vault = tmp_path / "empty_vault"
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vault.mkdir(parents=True)
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_write_vault_config(vault)
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return PaperResolver(vault)
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# ---------------------------------------------------------------------------
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# resolve_key tests
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# ---------------------------------------------------------------------------
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class TestResolveKey:
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def test_exact_match(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("ABC12345")
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assert ws is not None
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assert ws.key == "ABC12345"
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assert ws.title == "TGF-beta in Bone Regeneration"
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assert ws.domain == "骨科"
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assert ws.year == "2024"
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def test_case_insensitive(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("abc12345")
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assert ws is not None
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assert ws.key == "ABC12345"
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def test_no_match(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("ZZZZZZZZ")
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assert ws is None
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def test_empty_key(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("")
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assert ws is None
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def test_whitespace_trimmed(self, resolver_with_index):
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ws = resolver_with_index.resolve_key(" ABC12345 ")
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assert ws is not None
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assert ws.key == "ABC12345"
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# ---------------------------------------------------------------------------
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# resolve_doi tests
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# ---------------------------------------------------------------------------
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class TestResolveDoi:
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def test_exact_match(self, resolver_with_index):
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ws = resolver_with_index.resolve_doi("10.1234/tgf.2024")
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assert ws is not None
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assert ws.key == "ABC12345"
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def test_case_insensitive(self, resolver_with_index):
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ws = resolver_with_index.resolve_doi("10.1234/TGF.2024")
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assert ws is not None
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assert ws.key == "ABC12345"
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def test_with_url_prefix(self, resolver_with_index):
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ws = resolver_with_index.resolve_doi("https://doi.org/10.1234/tgf.2024")
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assert ws is not None
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assert ws.key == "ABC12345"
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def test_with_dx_prefix(self, resolver_with_index):
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ws = resolver_with_index.resolve_doi("http://dx.doi.org/10.1234/tgf.2024")
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assert ws is not None
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assert ws.key == "ABC12345"
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def test_no_match(self, resolver_with_index):
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ws = resolver_with_index.resolve_doi("10.0000/nonexistent")
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assert ws is None
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def test_empty_doi_entries_handled(self, resolver_with_index):
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items = resolver_with_index._items
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for item in items:
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if item["zotero_key"] == "GHI11111":
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break
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ws = resolver_with_index.resolve_doi("10.9999/bone.2024")
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assert ws is not None
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assert ws.key == "GHI11111"
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# ---------------------------------------------------------------------------
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# search tests
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# ---------------------------------------------------------------------------
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class TestSearch:
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def test_search_by_title_exact(self, resolver_with_index):
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results = resolver_with_index.search(title="TGF-beta in Bone Regeneration")
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assert len(results) == 1
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assert results[0].key == "ABC12345"
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def test_search_by_title_substring(self, resolver_with_index):
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results = resolver_with_index.search(title="Bone")
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assert len(results) == 2 # ABC12345 + GHI11111
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keys = {r.key for r in results}
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assert "ABC12345" in keys
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assert "GHI11111" in keys
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def test_search_by_author(self, resolver_with_index):
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results = resolver_with_index.search(author="Smith")
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assert len(results) == 2 # ABC12345 + GHI11111
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def test_search_by_year(self, resolver_with_index):
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results = resolver_with_index.search(year=2023)
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assert len(results) == 1
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assert results[0].key == "DEF67890"
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def test_search_by_domain(self, resolver_with_index):
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results = resolver_with_index.search(domain="运动医学")
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assert len(results) == 1
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assert results[0].key == "DEF67890"
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def test_search_combined_and_logic(self, resolver_with_index):
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results = resolver_with_index.search(title="Bone", author="Smith", year=2024)
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assert len(results) == 2 # Both ABC and GHI match all three
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def test_search_no_match_combined(self, resolver_with_index):
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results = resolver_with_index.search(title="Bone", year=2023)
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assert len(results) == 0 # No bone papers in 2023
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def test_search_ranked_by_relevance(self, resolver_with_index):
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results = resolver_with_index.search(title="Bone")
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assert len(results) >= 1
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# Exact match (TGF-beta in Bone Regeneration) should rank higher
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# than substring match (Another Bone Study)
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assert results[0].key in ("ABC12345", "GHI11111")
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def test_search_returns_workspace_fields(self, resolver_with_index):
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results = resolver_with_index.search(title="TGF-beta")
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ws = results[0]
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assert isinstance(ws, PaperWorkspace)
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assert ws.key == "ABC12345"
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assert ws.formal_note_path
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assert ws.frontmatter
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assert ws.frontmatter["zotero_key"] == "ABC12345"
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# ---------------------------------------------------------------------------
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# PaperWorkspace tests
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# ---------------------------------------------------------------------------
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class TestPaperWorkspace:
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def test_has_all_fields(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("ABC12345")
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assert ws is not None
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assert ws.key == "ABC12345"
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assert ws.title
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assert ws.domain
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assert ws.year
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assert ws.authors
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assert ws.doi
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assert ws.journal
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assert ws.formal_note_path
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assert ws.ocr_status == "done"
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assert ws.deep_reading_status == "pending"
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assert ws.analyze is True
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assert ws.do_ocr is True
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assert ws.has_pdf is True
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def test_ocr_path_when_ocr_dir_exists(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("ABC12345")
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assert ws is not None
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assert ws.ocr_path
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assert "ABC12345" in ws.ocr_path
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def test_frontmatter_loaded(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("ABC12345")
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assert ws is not None
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fm = ws.frontmatter
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assert fm["zotero_key"] == "ABC12345"
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assert fm["domain"] == "骨科"
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assert fm["title"] == "TGF-beta in Bone Regeneration"
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# ---------------------------------------------------------------------------
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# Edge cases
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# ---------------------------------------------------------------------------
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class TestEdgeCases:
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def test_empty_index(self, empty_resolver):
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empty_resolver._ensure_loaded()
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assert empty_resolver.resolve_key("ABC12345") is None
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assert empty_resolver.resolve_doi("10.1234/test") is None
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assert empty_resolver.search(title="anything") == []
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def test_authors_as_list(self, resolver_with_index):
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ws = resolver_with_index.resolve_key("ABC12345")
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assert ws is not None
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assert "Smith" in ws.authors
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assert "Lee" in ws.authors
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def test_missing_optional_fields(self, resolver_with_index):
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items = resolver_with_index._items
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extra = _make_index_entry(
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key="XXX00000",
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title="Minimal Paper",
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domain="测试",
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year="",
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authors="",
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doi="",
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note_path="Literature/测试/XXX00000 - Minimal Paper.md",
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)
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items.append(extra)
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ws = resolver_with_index.resolve_key("XXX00000")
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assert ws is not None
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assert ws.year == ""
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assert ws.doi == ""
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