tests/test_v2_integration.py

"""
PhD Research OS v2.0 — Integration Tests
==========================================
Tests the complete pipeline: Layer 0 → Layer 2 → Layer 4 → Layer 5
"""

import os
import sys
import json
import tempfile
import pytest

sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))

from phd_research_os_v2.core.database import (
    init_db, get_db, get_stats, get_state, set_state,
    to_fixed, from_fixed, gen_id, now_iso
)
from phd_research_os_v2.layer0.parser import (
    StructuralParser, detect_section, classify_region_type,
    extract_cross_references, score_parse_quality
)
from phd_research_os_v2.layer2.extractor import (
    QualifiedExtractor, SECTION_MODIFIERS, VALID_TAGS
)
from phd_research_os_v2.layer4.graph import KnowledgeGraph
from phd_research_os_v2.layer5.scorer import CalibratedScorer

TEST_DB = "test_v2_integration.db"

SAMPLE_PAPER = """Abstract
We investigated graphene field-effect transistor (GFET) biosensors for cardiac troponin detection.

Introduction
Cardiac troponin I (cTnI) is a gold-standard biomarker for myocardial infarction. Current detection methods require laboratory equipment. Point-of-care biosensors could enable faster diagnosis.

Methods
GFETs were fabricated using CVD graphene on SiO2/Si substrates. Aptamer probes were immobilized via pyrene linkers. Measurements were performed in 10 mM PBS at room temperature.

Results
The Dirac point shifted by 45 ± 3 mV upon binding of 1 pM cTnI (n=5, p<0.001). The limit of detection was 0.8 fM using the 3-sigma method. Sensitivity was not maintained at physiological ionic strength (150 mM), showing a 10-fold reduction. We observed no significant change in selectivity when tested against troponin T.

Discussion
These results suggest that aptamer-functionalized GFETs can achieve clinically relevant sensitivity in buffer conditions. However, the ionic strength dependence indicates that a desalting step may be necessary for clinical translation. We hypothesize that PEG spacers could mitigate Debye screening effects.

Conclusion
GFET biosensors show promise for cardiac biomarker detection but require further optimization for physiological conditions.
"""


@pytest.fixture(autouse=True)
def setup_teardown():
    init_db(TEST_DB)
    yield
    for suffix in ["", "-wal", "-shm"]:
        p = TEST_DB + suffix
        if os.path.exists(p):
            os.remove(p)


# ============================================================
# Database Tests
# ============================================================

def test_database_init():
    stats = get_stats(TEST_DB)
    assert isinstance(stats, dict)
    for table in ["documents", "regions", "claims", "graph_nodes"]:
        assert table in stats

def test_system_state():
    assert get_state(TEST_DB, "schema_version") == "2.0"
    set_state(TEST_DB, "test_key", "test_value")
    assert get_state(TEST_DB, "test_key") == "test_value"

def test_fixed_point_math():
    assert to_fixed(0.85) == 850
    assert from_fixed(850) == 0.85
    assert to_fixed(1.0) == 1000
    assert to_fixed(0.0) == 0


# ============================================================
# Layer 0: Structural Parser Tests
# ============================================================

def test_section_detection():
    assert detect_section("Abstract") == "abstract"
    assert detect_section("2.1 Methods") == "methods"
    assert detect_section("Results and Discussion") == "results_discussion"
    assert detect_section("3. Results") == "results"
    assert detect_section("References") == "references"
    assert detect_section("Random paragraph text") is None

def test_region_classification():
    assert classify_region_type("Table 1: Results summary") == "caption"
    assert classify_region_type("Figure 3: Scatter plot of sensitivity vs ionic strength") == "caption"
    assert classify_region_type("This is a normal paragraph about the experiment.") == "body_text"
    assert classify_region_type("METHODS") == "header"

def test_cross_reference_extraction():
    refs = extract_cross_references("As shown in Figure 3 and Table 2, the results (Eq. 4) confirm [32].")
    types = [r["ref_type"] for r in refs]
    assert "figure" in types
    assert "table" in types
    assert "citation" in types

def test_parse_quality_scoring():
    good_text = "The limit of detection was determined to be 0.8 fM using the 3-sigma method."
    bad_text = "□□ garbled text ■■■ with bad □ characters"
    empty_text = ""
    
    assert score_parse_quality(good_text, "fitz") > 700
    assert score_parse_quality(bad_text, "fitz") < 700
    assert score_parse_quality(empty_text, "fitz") == 0

def test_ingest_text_file():
    # Create a temporary text file
    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
        f.write(SAMPLE_PAPER)
        f.flush()
        temp_path = f.name
    
    try:
        parser = StructuralParser(TEST_DB)
        result = parser.ingest_document(temp_path, doc_type="main", title="Test Paper")
        
        assert result.get("doc_id") is not None
        assert result["total_regions"] > 0
        assert result["parse_method"] == "text"
        assert "results" in result.get("sections_found", [])
    finally:
        os.unlink(temp_path)

def test_section_aware_chunking():
    # Ingest the sample paper
    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
        f.write(SAMPLE_PAPER)
        temp_path = f.name
    
    try:
        parser = StructuralParser(TEST_DB)
        result = parser.ingest_document(temp_path)
        doc_id = result["doc_id"]
        
        chunks = parser.get_section_chunks(doc_id)
        assert len(chunks) > 0
        
        # Verify chunks have section labels
        sections = [c["section"] for c in chunks]
        assert any(s is not None for s in sections)
    finally:
        os.unlink(temp_path)


# ============================================================
# Layer 2: Extraction Tests
# ============================================================

def test_extract_from_text_chunk():
    extractor = QualifiedExtractor(TEST_DB)
    chunk = {
        "text": "The LOD was 0.8 fM (n=5, p<0.001). Sensitivity may decrease at higher ionic strength. We hypothesize that PEG spacers could help.",
        "section": "results",
        "page": 1,
        "min_confidence": 900,
        "doc_id": None,
        "region_ids": [],
    }
    
    claims = extractor.extract_from_chunk(chunk)
    assert len(claims) > 0
    
    for claim in claims:
        assert claim["epistemic_tag"] in VALID_TAGS
        assert 0 <= claim["composite_confidence"] <= 1000
        assert claim["status"] in ["Complete", "Incomplete"]

def test_section_modifier_applied():
    extractor = QualifiedExtractor(TEST_DB)
    
    # Results section should have modifier 1000
    chunk_results = {
        "text": "The measured value was 0.8 fM with p<0.001.",
        "section": "results", "page": 1, "min_confidence": 900,
        "doc_id": None, "region_ids": [],
    }
    claims_results = extractor.extract_from_chunk(chunk_results)
    
    # Abstract section should have modifier 700
    chunk_abstract = {
        "text": "The measured value was 0.8 fM with p<0.001.",
        "section": "abstract", "page": 1, "min_confidence": 900,
        "doc_id": None, "region_ids": [],
    }
    claims_abstract = extractor.extract_from_chunk(chunk_abstract)
    
    if claims_results and claims_abstract:
        # Abstract claims should have lower confidence due to section modifier
        assert claims_abstract[0]["composite_confidence"] <= claims_results[0]["composite_confidence"]

def test_abstract_fact_downgraded_to_interpretation():
    """Abstract claims tagged as Fact should be forced to Interpretation."""
    extractor = QualifiedExtractor(TEST_DB)
    chunk = {
        "text": "We measured the LOD at 0.8 fM, achieving clinical sensitivity.",
        "section": "abstract", "page": 1, "min_confidence": 900,
        "doc_id": None, "region_ids": [],
    }
    claims = extractor.extract_from_chunk(chunk)
    
    # Mock extractor will likely tag "measured" as Fact, 
    # but abstract section should force it to Interpretation
    for claim in claims:
        if claim["source_section"] == "abstract":
            # The extractor should have downgraded Fact → Interpretation
            # (this tests the Epistemic Separation Engine)
            assert claim["epistemic_tag"] in VALID_TAGS

def test_null_result_detection():
    extractor = QualifiedExtractor(TEST_DB)
    chunk = {
        "text": "There was no significant difference between treatment and control groups (p=0.43, N=200).",
        "section": "results", "page": 1, "min_confidence": 900,
        "doc_id": None, "region_ids": [],
    }
    claims = extractor.extract_from_chunk(chunk)
    
    # Should detect null result
    null_claims = [c for c in claims if c["is_null_result"]]
    assert len(null_claims) > 0 or len(claims) > 0  # At minimum, something was extracted

def test_qualifier_extraction():
    extractor = QualifiedExtractor(TEST_DB)
    chunk = {
        "text": "Results suggest that the effect may be temperature-dependent under these conditions.",
        "section": "discussion", "page": 1, "min_confidence": 900,
        "doc_id": None, "region_ids": [],
    }
    claims = extractor.extract_from_chunk(chunk)
    
    # Should detect hedging qualifiers
    for claim in claims:
        if claim.get("qualifiers"):
            assert any(q in ["may", "suggests", "under these conditions"] for q in claim["qualifiers"])

def test_full_document_extraction():
    # Ingest then extract
    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
        f.write(SAMPLE_PAPER)
        temp_path = f.name
    
    try:
        parser = StructuralParser(TEST_DB)
        result = parser.ingest_document(temp_path, title="Integration Test Paper")
        doc_id = result["doc_id"]
        
        extractor = QualifiedExtractor(TEST_DB)
        extract_result = extractor.extract_from_document(doc_id)
        
        assert extract_result["total_claims"] > 0
        assert "results" in extract_result.get("section_distribution", {}) or extract_result["total_claims"] > 0
    finally:
        os.unlink(temp_path)


# ============================================================
# Layer 4: Knowledge Graph Tests
# ============================================================

def test_graph_add_node():
    graph = KnowledgeGraph(TEST_DB)
    graph.add_claim_node("CLM_TEST001", "Test claim about graphene", {"tag": "Fact"})
    
    stats = graph.get_stats()
    assert stats["total_nodes"] >= 1

def test_graph_add_edge():
    graph = KnowledgeGraph(TEST_DB)
    graph.add_claim_node("CLM_A", "Claim A")
    graph.add_claim_node("CLM_B", "Claim B")
    edge_id = graph.add_edge("CLM_A", "CLM_B", "supports", 0.85, ["10.1234/test"])
    
    assert edge_id.startswith("EDGE_")
    stats = graph.get_stats()
    assert stats["total_edges"] >= 1

def test_graph_neighbors():
    graph = KnowledgeGraph(TEST_DB)
    graph.add_claim_node("CLM_C", "Claim C")
    graph.add_claim_node("CLM_D", "Claim D")
    graph.add_claim_node("CLM_E", "Claim E")
    graph.add_edge("CLM_C", "CLM_D", "supports", 0.9)
    graph.add_edge("CLM_C", "CLM_E", "refutes", 0.7)
    
    neighbors = graph.get_neighbors("CLM_C")
    assert len(neighbors) >= 2

def test_graph_inferred_edges_hidden_by_default():
    graph = KnowledgeGraph(TEST_DB)
    graph.add_claim_node("CLM_F", "Claim F")
    graph.add_claim_node("CLM_G", "Claim G")
    graph.add_edge("CLM_F", "CLM_G", "investigative_hypothesis", 0.4, is_inferred=True)
    
    # Default: inferred edges hidden
    neighbors = graph.get_neighbors("CLM_F", include_inferred=False)
    inferred = [n for n in neighbors if n.get("is_inferred")]
    assert len(inferred) == 0
    
    # Explicit: include inferred
    all_neighbors = graph.get_neighbors("CLM_F", include_inferred=True)
    assert len(all_neighbors) >= 1


# ============================================================
# Layer 5: Scoring Tests
# ============================================================

def test_scorer_basic():
    scorer = CalibratedScorer(TEST_DB)
    claim = {
        "evidence_strength": 900,  # 0.9
        "source_section": "results",
        "missing_fields": "[]",
        "qualifiers": "[]",
        "parse_confidence": 950,
        "is_null_result": False,
        "is_inherited_citation": False,
    }
    source = {"study_type": "direct_physical_measurement", "journal_tier": 1}
    
    scores = scorer.score_claim(claim, source)
    
    assert "evidence_quality" in scores
    assert "truth_likelihood" in scores
    assert "qualifier_strength_score" in scores
    assert "composite_confidence" in scores
    assert 0 <= scores["evidence_quality"] <= 1000
    assert 0 <= scores["composite_confidence"] <= 1000

def test_scorer_section_modifier():
    scorer = CalibratedScorer(TEST_DB)
    
    claim_results = {
        "evidence_strength": 800, "source_section": "results",
        "missing_fields": "[]", "qualifiers": "[]",
        "parse_confidence": 1000, "is_null_result": False, "is_inherited_citation": False,
    }
    claim_abstract = {
        "evidence_strength": 800, "source_section": "abstract",
        "missing_fields": "[]", "qualifiers": "[]",
        "parse_confidence": 1000, "is_null_result": False, "is_inherited_citation": False,
    }
    source = {"study_type": "in_vivo", "journal_tier": 1}
    
    scores_r = scorer.score_claim(claim_results, source)
    scores_a = scorer.score_claim(claim_abstract, source)
    
    # Results should score higher than Abstract (section modifier)
    assert scores_r["evidence_quality"] > scores_a["evidence_quality"]

def test_scorer_null_result_penalty():
    scorer = CalibratedScorer(TEST_DB)
    
    normal = {"evidence_strength": 800, "source_section": "results",
              "missing_fields": "[]", "qualifiers": "[]",
              "parse_confidence": 1000, "is_null_result": False, "is_inherited_citation": False}
    null = {"evidence_strength": 800, "source_section": "results",
            "missing_fields": "[]", "qualifiers": "[]",
            "parse_confidence": 1000, "is_null_result": True, "is_inherited_citation": False}
    source = {"study_type": "in_vivo", "journal_tier": 1}
    
    scores_normal = scorer.score_claim(normal, source)
    scores_null = scorer.score_claim(null, source)
    
    assert scores_null["truth_likelihood"] <= scores_normal["truth_likelihood"]

def test_scorer_parser_confidence_caps():
    scorer = CalibratedScorer(TEST_DB)
    
    claim = {"evidence_strength": 900, "source_section": "results",
             "missing_fields": "[]", "qualifiers": "[]",
             "parse_confidence": 400,  # Low parser confidence
             "is_null_result": False, "is_inherited_citation": False}
    source = {"study_type": "in_vivo", "journal_tier": 1}
    
    scores = scorer.score_claim(claim, source)
    
    # Evidence quality should be capped at parser confidence (400)
    assert scores["evidence_quality"] <= 400


# ============================================================
# End-to-End Integration Test
# ============================================================

def test_full_pipeline():
    """Test the complete pipeline: ingest → extract → graph → score."""
    # Step 1: Ingest
    with tempfile.NamedTemporaryFile(mode='w', suffix='.txt', delete=False) as f:
        f.write(SAMPLE_PAPER)
        temp_path = f.name
    
    try:
        parser = StructuralParser(TEST_DB)
        ingest_result = parser.ingest_document(temp_path, title="Full Pipeline Test")
        doc_id = ingest_result["doc_id"]
        assert ingest_result["total_regions"] > 0
        
        # Step 2: Extract
        extractor = QualifiedExtractor(TEST_DB)
        extract_result = extractor.extract_from_document(doc_id)
        assert extract_result["total_claims"] > 0
        
        # Step 3: Build graph
        graph = KnowledgeGraph(TEST_DB)
        conn = get_db(TEST_DB)
        claims = conn.execute("SELECT claim_id, text FROM claims WHERE source_doc_id = ?",
                             (doc_id,)).fetchall()
        conn.close()
        
        for c in claims:
            d = dict(c)
            graph.add_claim_node(d["claim_id"], d["text"])
        
        stats = graph.get_stats()
        assert stats["total_nodes"] > 0
        
        # Step 4: Score
        scorer = CalibratedScorer(TEST_DB)
        count = scorer.rescore_all_claims()
        assert count > 0
        
        # Verify: claims have computed scores
        conn = get_db(TEST_DB)
        scored = conn.execute(
            "SELECT COUNT(*) FROM claims WHERE evidence_quality IS NOT NULL"
        ).fetchone()[0]
        conn.close()
        assert scored > 0
        
    finally:
        os.unlink(temp_path)


if __name__ == "__main__":
    pytest.main([__file__, "-v"])