import pytest
import json
import shutil
from pathlib import Path
from crispr_cas.scripts.detect_crispr import generate_mock_results

def test_generate_mock_results(tmp_path):
    """Test mock result generation"""
    input_file = tmp_path / "test_genome.fna"
    input_file.touch()

    results = generate_mock_results(input_file)

    assert results["strain_id"] == "test_genome"
    assert "cas_systems" in results
    assert "arrays" in results
    assert results["summary"]["has_cas"] is True
    assert len(results["arrays"]) > 0

def test_script_execution(tmp_path):
    """Test full script execution via subprocess"""
    # Create dummy input
    input_file = tmp_path / "genome.fna"
    input_file.touch()
    output_file = tmp_path / "results.json"
    script_path = Path("crispr_cas/scripts/detect_crispr.py").absolute()

    import subprocess
    cmd = [
        "python3", str(script_path),
        "--input", str(input_file),
        "--output", str(output_file),
        "--mock"
    ]

    result = subprocess.run(cmd, capture_output=True, text=True)
    assert result.returncode == 0
    assert output_file.exists()

    with open(output_file) as f:
        data = json.load(f)
        assert data["strain_id"] == "genome"