"""
Shared pytest fixtures for zotero-chunk-rag tests.
All fixtures that need to be shared across test modules should be defined here.
"""
from __future__ import annotations
import csv
import sqlite3
from pathlib import Path
import pytest
_FIXTURES_DIR = Path(__file__).parent / "fixtures" / "papers"
_PAPER_NAMES = ["noname1.pdf", "noname2.pdf", "noname3.pdf"]
# =============================================================================
# Path fixtures
# =============================================================================
@pytest.fixture
def real_papers_dir() -> Path:
"""Path to the directory containing real academic papers for testing."""
path = _FIXTURES_DIR
assert path.exists(), f"Real papers directory not found: {path}"
return path
# =============================================================================
# Session-scoped extraction fixtures (run once, shared by all tests)
# =============================================================================
@pytest.fixture(scope="session")
def extracted_papers():
"""Extract all fixture PDFs once per session. Returns dict keyed by filename."""
from zotero_chunk_rag.pdf_processor import extract_document
return {
name: extract_document(_FIXTURES_DIR / name)
for name in _PAPER_NAMES
}
@pytest.fixture(scope="session")
def chunked_papers(extracted_papers):
"""Chunk all fixture PDFs once per session. Returns dict keyed by filename."""
from zotero_chunk_rag.chunker import Chunker
chunker = Chunker(chunk_size=400, overlap=100)
return {
name: chunker.chunk(ex.full_markdown, ex.pages, ex.sections)
for name, ex in extracted_papers.items()
}
# =============================================================================
# Database fixtures
# =============================================================================
@pytest.fixture
def temp_db_path(tmp_path: Path) -> Path:
"""Temporary directory for ChromaDB during tests."""
db_path = tmp_path / "chroma"
db_path.mkdir(parents=True, exist_ok=True)
return db_path
@pytest.fixture
def mock_zotero_db(tmp_path: Path) -> Path:
"""Create a mock Zotero database with sample data for testing.
This creates a minimal Zotero SQLite schema with the tables needed
for full-text search testing.
"""
db_path = tmp_path / "zotero.sqlite"
conn = sqlite3.connect(db_path)
# Create minimal Zotero schema
conn.executescript("""
-- Core item tables
CREATE TABLE items (
itemID INTEGER PRIMARY KEY,
itemTypeID INTEGER,
key TEXT UNIQUE,
libraryID INTEGER,
dateAdded TEXT,
dateModified TEXT
);
-- Attachment relationship
CREATE TABLE itemAttachments (
itemID INTEGER PRIMARY KEY,
parentItemID INTEGER,
path TEXT,
contentType TEXT,
FOREIGN KEY (itemID) REFERENCES items(itemID),
FOREIGN KEY (parentItemID) REFERENCES items(itemID)
);
-- Full-text search tables (Zotero's custom FTS)
CREATE TABLE fulltextWords (
wordID INTEGER PRIMARY KEY,
word TEXT UNIQUE
);
CREATE TABLE fulltextItemWords (
wordID INTEGER,
itemID INTEGER,
PRIMARY KEY (wordID, itemID)
);
CREATE TABLE fulltextItems (
itemID INTEGER PRIMARY KEY,
indexedPages INTEGER,
totalPages INTEGER,
indexedChars INTEGER,
version INTEGER
);
-- Item metadata
CREATE TABLE itemData (
itemID INTEGER,
fieldID INTEGER,
valueID INTEGER,
PRIMARY KEY (itemID, fieldID)
);
CREATE TABLE itemDataValues (
valueID INTEGER PRIMARY KEY,
value TEXT
);
CREATE TABLE fields (
fieldID INTEGER PRIMARY KEY,
fieldName TEXT
);
-- Creators
CREATE TABLE creators (
creatorID INTEGER PRIMARY KEY,
firstName TEXT,
lastName TEXT
);
CREATE TABLE itemCreators (
itemID INTEGER,
creatorID INTEGER,
orderIndex INTEGER
);
-- Insert some test data
INSERT INTO items (itemID, key) VALUES (1, 'ABC12345');
INSERT INTO items (itemID, key) VALUES (2, 'DEF67890');
INSERT INTO items (itemID, key) VALUES (3, 'GHI11111');
-- Attachment items
INSERT INTO items (itemID, key) VALUES (101, 'ATT00001');
INSERT INTO items (itemID, key) VALUES (102, 'ATT00002');
INSERT INTO itemAttachments (itemID, parentItemID, path)
VALUES (101, 1, 'storage:test1.pdf');
INSERT INTO itemAttachments (itemID, parentItemID, path)
VALUES (102, 2, 'storage:test2.pdf');
-- Full-text words for testing boolean search
INSERT INTO fulltextWords (wordID, word) VALUES (1, 'heart');
INSERT INTO fulltextWords (wordID, word) VALUES (2, 'rate');
INSERT INTO fulltextWords (wordID, word) VALUES (3, 'variability');
INSERT INTO fulltextWords (wordID, word) VALUES (4, 'ecg');
INSERT INTO fulltextWords (wordID, word) VALUES (5, 'electrode');
-- Item 1 (ABC12345) contains: heart, rate, variability, ecg
INSERT INTO fulltextItemWords (wordID, itemID) VALUES (1, 101);
INSERT INTO fulltextItemWords (wordID, itemID) VALUES (2, 101);
INSERT INTO fulltextItemWords (wordID, itemID) VALUES (3, 101);
INSERT INTO fulltextItemWords (wordID, itemID) VALUES (4, 101);
-- Item 2 (DEF67890) contains: heart, electrode
INSERT INTO fulltextItemWords (wordID, itemID) VALUES (1, 102);
INSERT INTO fulltextItemWords (wordID, itemID) VALUES (5, 102);
INSERT INTO fulltextItems (itemID, indexedPages, totalPages) VALUES (101, 10, 10);
INSERT INTO fulltextItems (itemID, indexedPages, totalPages) VALUES (102, 5, 5);
""")
conn.commit()
conn.close()
return db_path
# =============================================================================
# Config fixtures
# =============================================================================
@pytest.fixture
def mock_config(temp_db_path: Path, tmp_path: Path):
"""Create a test configuration.
Uses local embeddings to avoid needing API keys in tests.
"""
from zotero_chunk_rag.config import Config
# Create minimal Zotero directory structure for config validation
zotero_dir = tmp_path / "zotero"
zotero_dir.mkdir(exist_ok=True)
(zotero_dir / "zotero.sqlite").touch()
return Config(
zotero_data_dir=zotero_dir,
chroma_db_path=temp_db_path,
embedding_model="all-MiniLM-L6-v2",
embedding_dimensions=384,
chunk_size=400,
chunk_overlap=100,
gemini_api_key=None,
embedding_provider="local",
embedding_timeout=120.0,
embedding_max_retries=3,
rerank_alpha=0.7,
rerank_section_weights=None,
rerank_journal_weights=None,
rerank_enabled=True,
oversample_multiplier=3,
oversample_topic_factor=5,
stats_sample_limit=10000,
ocr_language="eng",
openalex_email=None,
)
# =============================================================================
# Journal ranker fixtures
# =============================================================================
@pytest.fixture
def test_scimago_csv(tmp_path: Path) -> Path:
"""Create a test SCImago CSV file with known journals."""
csv_path = tmp_path / "test_scimago.csv"
with open(csv_path, "w", newline="", encoding="utf-8") as f:
writer = csv.writer(f)
writer.writerow(["title_normalized", "quartile"])
# Q1 journals
writer.writerow(["nature", "Q1"])
writer.writerow(["science", "Q1"])
writer.writerow(["cell", "Q1"])
writer.writerow(["the lancet", "Q1"])
writer.writerow(["new england journal of medicine", "Q1"])
writer.writerow(["ieee transactions on biomedical engineering", "Q1"])
writer.writerow(["circulation", "Q1"])
writer.writerow(["plos one", "Q1"])
# Q2 journals
writer.writerow(["journal of physiology", "Q2"])
writer.writerow(["physiological measurement", "Q2"])
writer.writerow(["medical engineering physics", "Q2"])
# Q3 journals
writer.writerow(["journal of medical systems", "Q3"])
writer.writerow(["biomedical signal processing and control", "Q3"])
# Q4 journals
writer.writerow(["medical hypotheses", "Q4"])
writer.writerow(["journal of low power electronics", "Q4"])
return csv_path
@pytest.fixture
def test_overrides_csv(tmp_path: Path) -> Path:
"""Create a test journal overrides CSV file."""
csv_path = tmp_path / "journal_overrides.csv"
with open(csv_path, "w", encoding="utf-8") as f:
f.write("# Manual corrections for fuzzy matching mistakes\n")
f.write("# Format: input_title,correct_quartile\n")
f.write("IEEE Transactions on Biomedical Circuits and Systems,Q1\n")
f.write("Journal of Neural Engineering,Q1\n")
return csv_path
