import pytest
import json
from pathlib import Path
import sys

# Add project root to path to allow importing modules
sys.path.insert(0, str(Path(__file__).parents[2]))

from crispr_cas.scripts.fusion_analysis import calculate_distance, perform_fusion_analysis

def test_calculate_distance():
    """Test genomic distance calculation"""
    # Same contig, no overlap
    # Range1: 100-200, Range2: 300-400 -> Dist 100
    assert calculate_distance("c1:100-200", "c1:300-400") == 100

    # Same contig, overlap
    # Range1: 100-300, Range2: 200-400 -> Dist 0
    assert calculate_distance("c1:100-300", "c1:200-400") == 0

    # Different contig
    assert calculate_distance("c1:100-200", "c2:300-400") == -1

    # Invalid format
    assert calculate_distance("invalid", "c1:100-200") == -1

def test_fusion_analysis_logic(tmp_path):
    """Test main analysis logic with mock data"""

    # Mock CRISPR data
    crispr_data = {
        "strain_id": "test_strain",
        "arrays": [
            {
                "id": "A1",
                "contig": "contig_1",
                "start": 1000,
                "end": 2000,
                "spacers": [{"sequence": "ATGC"}]
            }
        ]
    }

    # Mock toxin file (just a placeholder for path)
    toxin_file = tmp_path / "toxins.txt"
    toxin_file.touch()

    # Run analysis in mock mode
    # In mock mode, the script generates its own toxin list:
    # {"name": "Cry1Ac1", "position": "contig_1:10000-12000"}
    # Distance: 10000 - 2000 = 8000 (< 10000 threshold) -> Should match

    results = perform_fusion_analysis(crispr_data, toxin_file, mock=True)

    assert results["strain_id"] == "test_strain"
    assert len(results["associations"]) > 0

    # Check for proximity match
    proximity_matches = [a for a in results["associations"] if a["type"] == "proximity"]
    assert len(proximity_matches) > 0
    assert proximity_matches[0]["distance"] == 8000

def test_script_execution(tmp_path):
    """Test full script execution via subprocess"""

    # Create input files
    crispr_file = tmp_path / "crispr.json"
    with open(crispr_file, 'w') as f:
        json.dump({"strain_id": "test", "arrays": []}, f)

    toxin_file = tmp_path / "toxins.txt"
    toxin_file.touch()

    genome_file = tmp_path / "genome.fna"
    genome_file.touch()

    output_file = tmp_path / "output.json"

    script_path = Path("crispr_cas/scripts/fusion_analysis.py").absolute()

    import subprocess
    cmd = [
        "python3", str(script_path),
        "--crispr-results", str(crispr_file),
        "--toxin-results", str(toxin_file),
        "--genome", str(genome_file),
        "--output", str(output_file),
        "--mock"
    ]

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