Refactor: Unified pipeline execution, simplified UI, and fixed Docker config

- Backend: Refactored tasks.py to directly invoke run_single_fna_pipeline.py for consistency.
- Backend: Changed output format to ZIP and added auto-cleanup of intermediate files.
- Backend: Fixed language parameter passing in API and tasks.
- Frontend: Removed CRISPR Fusion UI elements from Submit and Monitor views.
- Frontend: Implemented simulated progress bar for better UX.
- Frontend: Restored One-click load button and added result file structure documentation.
- Docker: Fixed critical Restarting loop by removing incorrect image directive in docker-compose.yml.
- Docker: Optimized Dockerfile to correct .pixi environment path issues and prevent accidental deletion of frontend assets.

tools/crispr_cas_analysis/tests/test_fusion_analysis.py

@@ -0,0 +1,93 @@
+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()