| import uuid |
| from src.models.paper import Paper |
| from src.models.claim import Claim, ClaimType, Polarity, StudyDesign, Entity, EntityType |
| from src.models.contradiction import ContradictionPair, ContradictionType |
| from src.synthesis.report_generator import detect_knowledge_gaps |
|
|
| def make_paper(pmid: str, author: str, year: int) -> Paper: |
| return Paper( |
| pmid=pmid, |
| title="Sample Paper Title", |
| authors=[author], |
| year=year, |
| journal="Sample Journal", |
| abstract_text="Abstract content", |
| full_text=None, |
| doi="10.1000/xyz" |
| ) |
|
|
| def make_claim(id_str: str, pmid: str, year: int, entities: list[Entity], claim_type: ClaimType = ClaimType.CAUSAL) -> Claim: |
| return Claim( |
| id=uuid.UUID(id_str), |
| text="Sample claim text", |
| paper_id=pmid, |
| section="Abstract", |
| year=year, |
| confidence_score=1.0, |
| claim_type=claim_type, |
| polarity=Polarity.POSITIVE, |
| population="humans", |
| context="general", |
| quote_anchor="anchor", |
| study_design=StudyDesign.RCT, |
| sample_size=100, |
| entities=entities |
| ) |
|
|
| def test_detect_knowledge_gaps(): |
| |
| paper_1 = make_paper("pmid1", "Author One", 2020) |
| paper_2 = make_paper("pmid2", "Author Two", 2021) |
| papers = [paper_1, paper_2] |
|
|
| |
| ent_a = Entity(text="Metformin", canonical_id="MeSH:D001241", entity_type=EntityType.DRUG) |
| ent_b = Entity(text="Breast Cancer", canonical_id="MeSH:D001943", entity_type=EntityType.DISEASE) |
| ent_c = Entity(text="Aspirin", canonical_id="MeSH:D001242", entity_type=EntityType.DRUG) |
| ent_d = Entity(text="Alzheimer", canonical_id="MeSH:D000544", entity_type=EntityType.DISEASE) |
|
|
| |
| claim_1 = make_claim("11111111-1111-1111-1111-111111111111", "pmid1", 2020, [ent_a, ent_b]) |
| |
| claim_2 = make_claim("22222222-2222-2222-2222-222222222222", "pmid2", 2021, [ent_c, ent_d]) |
| claims = [claim_1, claim_2] |
|
|
| |
| contradictions = [] |
|
|
| gaps = detect_knowledge_gaps(claims, contradictions, papers) |
| assert len(gaps) == 2 |
| assert any("Metformin" in g and "Breast Cancer" in g for g in gaps) |
| assert any("Aspirin" in g and "Alzheimer" in g for g in gaps) |
|
|
| |
| claim_3 = make_claim("33333333-3333-3333-3333-333333333333", "pmid2", 2021, [ent_a, ent_b]) |
| claims_replicated = [claim_1, claim_2, claim_3] |
| gaps_replicated = detect_knowledge_gaps(claims_replicated, contradictions, papers) |
| |
| |
| assert len(gaps_replicated) == 1 |
| assert "Aspirin" in gaps_replicated[0] |
| assert "Metformin" not in gaps_replicated[0] |
|
|
| |
| claim_4 = make_claim("44444444-4444-4444-4444-444444444444", "pmid1", 2020, [ent_c, ent_d]) |
| pair = ContradictionPair( |
| claim_a=claim_2, |
| claim_b=claim_4, |
| contradiction_score=0.9, |
| contradiction_type=ContradictionType.DIRECT_NEGATION, |
| explanation="Opposing findings", |
| scope_note="", |
| temporal_resolution=None, |
| is_genuine=True |
| ) |
| |
| |
| gaps_contradicted = detect_knowledge_gaps([claim_2, claim_4], [pair], papers) |
| assert len(gaps_contradicted) == 0 |
|
|
