solvated viewer file permission error corrected

js/script.js

@@ -1344,10 +1344,8 @@ echo "Analysis completed! Results saved in analysis/ directory"
                 throw new Error(data.error || 'Failed to load viewer PDB');
             }
 
-            // Wait a moment for the file to be written, then open the viewer
-            setTimeout(() => {
-                window.open('/viewer/viewer_protein_with_ligand.pdb', '_blank');
-            }, 1000);
+            // Open the dedicated viewer page (bypasses CSP issues)
+            window.open('/viewer/viewer_protein_with_ligand.pdb', '_blank');
 
         } catch (error) {
             console.error('Error previewing solvated protein:', error);

python/app.py

@@ -28,7 +28,7 @@ logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
 # Create output directory
-OUTPUT_DIR = Path("output")
+OUTPUT_DIR = Path(__file__).parent.parent / "output"
 
 def clean_and_create_output_folder():
     """Clean existing output folder and create a new one"""
@@ -893,6 +893,15 @@ def viewer(filename):
 @app.route('/output/<path:filename>')
 def serve_output(filename):
     """Serve output files"""
+    # Debug: print available files
+    print(f"Requested file: {filename}")
+    print(f"Full path: {OUTPUT_DIR / filename}")
+    print(f"File exists: {(OUTPUT_DIR / filename).exists()}")
+    print(f"Files in output dir: {list(OUTPUT_DIR.iterdir()) if OUTPUT_DIR.exists() else 'Directory not found'}")
+    
+    if not (OUTPUT_DIR / filename).exists():
+        abort(404)
+    
     return send_from_directory(OUTPUT_DIR, filename)
 
 @app.route('/')