tests/test_demo.py

"""Regression tests for CLI/reporting helper utilities."""

from pathlib import Path

import pytest
import yaml

from sentinel.models import (
    CancerRiskAssessment,
    ContributingFactor,
    ContributionStrength,
    DxRecommendation,
    InitialAssessment,
    RiskFactor,
    RiskFactorCategory,
)
from sentinel.reporting import generate_excel_report, generate_pdf_report
from sentinel.user_input import (
    AlcoholConsumption,
    Anthropometrics,
    CancerType,
    Demographics,
    Ethnicity,
    FamilyMemberCancer,
    FamilyRelation,
    FamilySide,
    Lifestyle,
    PersonalMedicalHistory,
    RelationshipDegree,
    Sex,
    SmokingHistory,
    SmokingStatus,
    UserInput,
)
from sentinel.utils import load_user_file


def test_load_user_file_yaml(tmp_path):
    """Ensure YAML user profiles load into a ``UserInput`` instance.

    Args:
        tmp_path: Pytest-managed temporary directory path.
    """

    data = {
        "demographics": {
            "age_years": 30,
            "sex": "male",
            "anthropometrics": {"height_cm": 175, "weight_kg": 70},
        },
        "lifestyle": {
            "smoking": {"status": "never"},
            "alcohol_consumption": "none",
        },
        "personal_medical_history": {},
        "family_history": [],
    }
    path = tmp_path / "user.yaml"
    path.write_text(yaml.dump(data))

    user = load_user_file(str(path))
    assert isinstance(user, UserInput)
    assert user.demographics.age_years == 30
    assert user.lifestyle.smoking.status == SmokingStatus.NEVER
    assert user.symptoms == []


@pytest.mark.parametrize("save_files", [True, False])
def test_generate_reports(tmp_path, save_files):
    """Generate PDF and Excel reports and assert the outputs exist.

    Args:
        tmp_path: Pytest-managed temporary directory path.
        save_files: Whether to write outputs to repo path or temporary path.
    """
    # 1. Create mock UserInput data with all fields
    user = UserInput(
        demographics=Demographics(
            age_years=45,
            sex=Sex.FEMALE,
            ethnicity=Ethnicity.WHITE,
            anthropometrics=Anthropometrics(height_cm=165, weight_kg=70),
        ),
        lifestyle=Lifestyle(
            smoking=SmokingHistory(
                status=SmokingStatus.FORMER,
                pack_years=10,
            ),
            alcohol_consumption=AlcoholConsumption.LIGHT,
        ),
        personal_medical_history=PersonalMedicalHistory(
            previous_cancers=[CancerType.MELANOMA],
        ),
        family_history=[
            FamilyMemberCancer(
                relation=FamilyRelation.MOTHER,
                cancer_type=CancerType.BREAST,
                age_at_diagnosis=50,
                degree=RelationshipDegree.FIRST,
                side=FamilySide.MATERNAL,
            )
        ],
    )

    # 2. Create mock InitialAssessment data
    assessment = InitialAssessment(
        response="This is a summary response.",
        thinking="The user is a 45-year-old female with a BRCA2 mutation...",
        reasoning="1. Assessed breast cancer risk as high due to BRCA2...",
        overall_summary="This assessment indicates a significant and immediate need...",
        overall_risk_score=68,
        identified_risk_factors=[
            RiskFactor(
                description="Positive for BRCA2 genetic mutation",
                category=RiskFactorCategory.PERSONAL_MEDICAL,
            ),
            RiskFactor(
                description="Personal history of Skin Cancer",
                category=RiskFactorCategory.PERSONAL_MEDICAL,
            ),
            RiskFactor(
                description="First-degree relative (Mother) with Breast Cancer",
                category=RiskFactorCategory.FAMILY_HISTORY,
            ),
            RiskFactor(
                description="Age of 45", category=RiskFactorCategory.DEMOGRAPHICS
            ),
            RiskFactor(
                description="Former smoker (10 pack-years)",
                category=RiskFactorCategory.LIFESTYLE,
            ),
        ],
        llm_risk_interpretations=[
            CancerRiskAssessment(
                cancer_type="Breast Cancer",
                risk_level=4,
                explanation="Risk is high due to the combination of a known BRCA2 mutation and a first-degree relative with breast cancer.",
                recommended_steps=[
                    "Annual mammogram",
                    "Annual breast MRI",
                    "Consultation with a high-risk breast specialist",
                ],
                contributing_factors=[
                    ContributingFactor(
                        description="Positive for BRCA2 genetic mutation",
                        category=RiskFactorCategory.PERSONAL_MEDICAL,
                        strength=ContributionStrength.MAJOR,
                    ),
                    ContributingFactor(
                        description="First-degree relative (Mother) with Breast Cancer",
                        category=RiskFactorCategory.FAMILY_HISTORY,
                        strength=ContributionStrength.MAJOR,
                    ),
                    ContributingFactor(
                        description="Age of 45",
                        category=RiskFactorCategory.DEMOGRAPHICS,
                        strength=ContributionStrength.MINOR,
                    ),
                ],
            ),
            CancerRiskAssessment(
                cancer_type="Ovarian Cancer",
                risk_level=4,
                explanation="Risk is significantly elevated due to the known BRCA2 mutation.",
                recommended_steps=[
                    "Consider risk-reducing surgery",
                    "Transvaginal ultrasound and CA-125 blood test for surveillance",
                ],
                contributing_factors=[
                    ContributingFactor(
                        description="Positive for BRCA2 genetic mutation",
                        category=RiskFactorCategory.PERSONAL_MEDICAL,
                        strength=ContributionStrength.MAJOR,
                    )
                ],
            ),
            CancerRiskAssessment(
                cancer_type="Skin Cancer",
                risk_level=3,
                explanation="Risk is moderate-to-high due to a personal history of skin cancer, which is a strong predictor of future risk.",
                recommended_steps=[
                    "Annual full-body dermatological examination.",
                    "Vigilant use of broad-spectrum sunscreen.",
                ],
                contributing_factors=[
                    ContributingFactor(
                        description="Personal history of Skin Cancer",
                        category=RiskFactorCategory.PERSONAL_MEDICAL,
                        strength=ContributionStrength.MAJOR,
                    )
                ],
            ),
            CancerRiskAssessment(
                cancer_type="Colorectal Cancer",
                risk_level=3,
                explanation="Risk is moderate as you have reached the standard screening age. Some studies suggest a minor increased risk with BRCA2 mutations.",
                recommended_steps=[
                    "Begin regular colonoscopy screenings as per standard guidelines (age 45)."
                ],
                contributing_factors=[
                    ContributingFactor(
                        description="Age of 45",
                        category=RiskFactorCategory.DEMOGRAPHICS,
                        strength=ContributionStrength.MODERATE,
                    ),
                    ContributingFactor(
                        description="Positive for BRCA2 genetic mutation",
                        category=RiskFactorCategory.PERSONAL_MEDICAL,
                        strength=ContributionStrength.MINOR,
                    ),
                ],
            ),
            CancerRiskAssessment(
                cancer_type="Lung Cancer",
                risk_level=2,
                explanation="A history of smoking, even as a former smoker, confers a residual risk for lung cancer, though it is not high enough to warrant screening at this time.",
                recommended_steps=["Monitor for symptoms like persistent cough."],
                lifestyle_advice="Continue to avoid smoking.",
                contributing_factors=[
                    ContributingFactor(
                        description="Former smoker (10 pack-years)",
                        category=RiskFactorCategory.LIFESTYLE,
                        strength=ContributionStrength.MODERATE,
                    )
                ],
            ),
        ],
        dx_recommendations=[
            DxRecommendation(
                test_name="Mammogram",
                frequency="Annually",
                rationale="High risk for breast cancer due to BRCA2 and family history.",
                recommendation_level=5,
            ),
            DxRecommendation(
                test_name="MRI",  # Breast MRI
                frequency="Annually",
                rationale="Supplemental screening for high-risk individuals with BRCA mutations.",
                recommendation_level=5,
            ),
            DxRecommendation(
                test_name="Colonoscopy",
                frequency="Every 5-10 years",
                rationale="Standard screening age reached; commence screening.",
                recommendation_level=4,
            ),
        ],
    )

    # 3. Define output path
    if save_files:
        output_path = Path("outputs")
        output_path.mkdir(exist_ok=True)
    else:
        output_path = tmp_path

    # 4. Define output filenames
    pdf_filename = output_path / "report.pdf"
    excel_filename = output_path / "report.xlsx"

    # 5. Generate and check PDF report
    try:
        generate_pdf_report(assessment, user, str(pdf_filename))
        assert pdf_filename.exists()
        assert pdf_filename.stat().st_size > 0  # Check file is not empty
    except Exception as e:
        # The test environment might not have PDF generation dependencies
        print(f"PDF generation failed, likely due to missing dependencies: {e}")
        pytest.fail(f"PDF generation failed with an unexpected error: {e}")

    # 6. Generate and check Excel report
    generate_excel_report(assessment, user, str(excel_filename))
    assert excel_filename.exists()
    assert excel_filename.stat().st_size > 0