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import pytest
import uuid
import tempfile
from src.models.paper import Paper
from src.models.claim import Claim, Entity, ClaimType, Polarity, StudyDesign, EntityType
from src.models.contradiction import ContradictionPair, ContradictionType
from src.storage.database import init_db, save_papers, save_claims, save_contradictions, get_paper, get_claim, get_claims_for_run, get_contradictions_for_run
@pytest.fixture
def temp_db():
# Create a temporary SQLite database file path
fd, path = tempfile.mkstemp(suffix=".db")
os.close(fd)
# Initialize the database
init_db(db_path=path)
yield path
# Cleanup after test
if os.path.exists(path):
os.remove(path)
def test_paper_round_trip(temp_db):
original_paper = Paper(
pmid="12345",
title="Impact of Metformin on Cancer Cells",
authors=["John Smith", "Jane Doe"],
year=2024,
journal="Journal of Medicine",
abstract_text="Metformin reduces breast cancer risk.",
doi="10.1234/med.2024.1"
)
save_papers([original_paper], db_path=temp_db)
retrieved_paper = get_paper("12345", db_path=temp_db)
assert retrieved_paper is not None
assert retrieved_paper.pmid == original_paper.pmid
assert retrieved_paper.title == original_paper.title
assert retrieved_paper.authors == original_paper.authors
assert retrieved_paper.year == original_paper.year
assert retrieved_paper.journal == original_paper.journal
assert retrieved_paper.abstract_text == original_paper.abstract_text
assert retrieved_paper.doi == original_paper.doi
def test_claim_round_trip(temp_db):
paper = Paper(
pmid="98765",
title="Study on Metformin",
authors=["Dr. Who"],
year=2023,
journal="Journal of Time",
abstract_text="Metformin does things.",
doi="10.1000/time.1"
)
save_papers([paper], db_path=temp_db)
claim_id = uuid.uuid4()
claim = Claim(
id=claim_id,
text="Metformin reduces cell growth.",
normalized_text="metformin reduces cell growth",
paper_id="98765",
section="Abstract",
authors=["Dr. Who"],
year=2023,
confidence_score=1.0,
claim_type=ClaimType.CAUSAL,
polarity=Polarity.POSITIVE,
entities=[Entity(text="metformin", entity_type=EntityType.DRUG)],
population="in vitro HeLa cells",
context="10mM for 24h",
quote_anchor="Metformin reduces cell growth",
study_design=StudyDesign.IN_VITRO,
is_primary_finding=True
)
save_claims([claim], db_path=temp_db)
retrieved_claim = get_claim(str(claim_id), db_path=temp_db)
assert retrieved_claim is not None
assert retrieved_claim.id == claim.id
assert retrieved_claim.text == claim.text
assert retrieved_claim.normalized_text == claim.normalized_text
assert retrieved_claim.paper_id == claim.paper_id
assert retrieved_claim.confidence_score == claim.confidence_score
assert retrieved_claim.claim_type == claim.claim_type
assert retrieved_claim.polarity == claim.polarity
assert len(retrieved_claim.entities) == 1
assert retrieved_claim.entities[0].text == "metformin"
assert retrieved_claim.entities[0].entity_type == EntityType.DRUG
# Test batch retrieval
claims = get_claims_for_run(["98765"], db_path=temp_db)
assert len(claims) == 1
assert claims[0].id == claim.id
def test_contradiction_saving(temp_db):
paper = Paper(
pmid="55555",
title="Double Study",
authors=["Author A"],
year=2022,
journal="Double Journal",
abstract_text="Abstract content.",
doi="10.1000/double"
)
save_papers([paper], db_path=temp_db)
claim_a = Claim(
id=uuid.uuid4(),
text="Drug A is good.",
normalized_text="drug a is good",
paper_id="55555",
year=2022,
confidence_score=1.0,
claim_type=ClaimType.CAUSAL,
polarity=Polarity.POSITIVE,
population="humans",
context="none",
quote_anchor="Drug A is good.",
study_design=StudyDesign.RCT,
)
claim_b = Claim(
id=uuid.uuid4(),
text="Drug A is bad.",
normalized_text="drug a is bad",
paper_id="55555",
year=2022,
confidence_score=1.0,
claim_type=ClaimType.CAUSAL,
polarity=Polarity.NEGATIVE,
population="humans",
context="none",
quote_anchor="Drug A is bad.",
study_design=StudyDesign.RCT,
)
save_claims([claim_a, claim_b], db_path=temp_db)
pair = ContradictionPair(
claim_a=claim_a,
claim_b=claim_b,
contradiction_score=0.9,
contradiction_type=ContradictionType.DIRECT_NEGATION,
explanation="Opposite efficacy statements",
scope_note="Same population",
is_genuine=True
)
assigned_ids = save_contradictions([pair], db_path=temp_db)
assert len(assigned_ids) == 1
assert isinstance(assigned_ids[0], str)
# Test retrieving contradictions
retrieved_pairs = get_contradictions_for_run(["55555"], db_path=temp_db)
assert len(retrieved_pairs) == 1
assert retrieved_pairs[0].contradiction_score == 0.9
assert retrieved_pairs[0].claim_a.id == claim_a.id
assert retrieved_pairs[0].claim_b.id == claim_b.id
def test_package_exports():
import src.storage as storage
import src.storage.database as db
assert storage.get_connection is db.get_connection
assert storage.init_db is db.init_db
assert storage.save_papers is db.save_papers
assert storage.save_claims is db.save_claims
assert storage.save_contradictions is db.save_contradictions
assert storage.save_pipeline_run is db.save_pipeline_run
assert storage.get_pipeline_run is db.get_pipeline_run
assert storage.get_paper is db.get_paper
assert storage.get_claim is db.get_claim
assert storage.get_contradictions_for_run is db.get_contradictions_for_run
assert storage.get_claims_for_run is db.get_claims_for_run
assert storage.get_papers_for_run is db.get_papers_for_run
def test_save_pipeline_run_preserves_started_at(temp_db):
from src.storage.database import save_pipeline_run, get_pipeline_run
run_id = "test_run_123"
query = "metformin cancer"
started_at = "2026-06-12T12:00:00Z"
# 1. Start the run
save_pipeline_run(
run_id=run_id,
query=query,
status="RUNNING",
started_at=started_at,
db_path=temp_db
)
run = get_pipeline_run(run_id, db_path=temp_db)
assert run is not None
assert run["status"] == "RUNNING"
assert run["started_at"] == started_at
# 2. Update the run (e.g. intermediate save without started_at)
save_pipeline_run(
run_id=run_id,
query=query,
status="COMPLETED",
completed_at="2026-06-12T12:05:00Z",
db_path=temp_db
)
run = get_pipeline_run(run_id, db_path=temp_db)
assert run is not None
assert run["status"] == "COMPLETED"
assert run["started_at"] == started_at # Should be preserved!
assert run["completed_at"] == "2026-06-12T12:05:00Z"
def test_seed_demo_script(temp_db):
from scripts.seed_demo import seed_demo_data
from src.storage.database import get_pipeline_run
# Run the seeding script targeting our temp database
seed_demo_data(db_path=temp_db)
# Verify the demo runs exist in the database
run_metformin = get_pipeline_run("demo_metformin", db_path=temp_db)
assert run_metformin is not None
assert run_metformin["status"] == "COMPLETED"
assert run_metformin["query"] == "Does metformin reduce cancer risk?"
run_fasting = get_pipeline_run("demo_fasting", db_path=temp_db)
assert run_fasting is not None
run_ssri = get_pipeline_run("demo_ssri", db_path=temp_db)
assert run_ssri is not None
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