Update app.py

app.py

@@ -504,22 +504,73 @@ def analyze_sequence_for_tree(sequence: str, matching_percentage: float) -> tupl
         
         logging.info(f"Found {len(matched_ids)} similar sequences at {actual_percentage:.2f}% similarity")
         
+        # Limit sequences for testing (optional)
+        matched_ids = matched_ids[:5]  # Remove this after confirming fix
+        
         # Build tree structure
         analyzer.build_tree_structure_with_ml_safe(matched_ids)
         
         # Create interactive tree
         fig = analyzer.create_interactive_tree(matched_ids, actual_percentage)
+        if fig is None or not hasattr(fig, 'write_html'):
+            logging.error("Failed to create valid Plotly figure")
+            return "❌ Error: Failed to create interactive tree (invalid Plotly figure)", None, None
         
         # Save tree to temporary file
         temp_dir = tempfile.gettempdir()
         query_id = analyzer.query_id or f"query_{int(time.time())}"
         tree_html_path = os.path.join(temp_dir, f'phylogenetic_tree_interactive_{query_id}.html')
-        fig.write_html(tree_html_path)
+        try:
+            fig.write_html(tree_html_path, include_plotlyjs=True)  # Embed Plotly.js
+            if not os.path.exists(tree_html_path) or os.path.getsize(tree_html_path) == 0:
+                logging.error(f"Tree HTML file is empty or not created: {tree_html_path}")
+                return "❌ Error: Failed to save interactive tree", None, None
+        except Exception as e:
+            logging.error(f"Failed to write tree HTML: {e}")
+            return f"❌ Error: Failed to save interactive tree: {str(e)}", None, None
+        
+        # Copy tree HTML to output directory
+        output_dir = "output"
+        os.makedirs(output_dir, exist_ok=True)
+        safe_seq_name = re.sub(r'[^a-zA-Z0-9_-]', '', sequence[:20])
+        timestamp = str(int(time.time()))
+        tree_html_filename = f"tree_{safe_seq_name}_{timestamp}.html"
+        tree_html_final_path = os.path.join(output_dir, tree_html_filename)
+        try:
+            shutil.copy2(tree_html_path, tree_html_final_path)
+            if not os.path.exists(tree_html_final_path):
+                logging.error(f"Failed to copy tree HTML to: {tree_html_final_path}")
+                return "❌ Error: Failed to copy interactive tree", None, None
+        except Exception as e:
+            logging.error(f"Failed to copy tree HTML: {e}")
+            return f"❌ Error: Failed to copy interactive tree: {str(e)}", None, None
+        
+        # Read tree HTML content from final path for display
+        try:
+            with open(tree_html_final_path, 'r', encoding='utf-8') as f:
+                tree_html_content = f.read()
+            if not tree_html_content.strip():
+                logging.error(f"Tree HTML content is empty: {tree_html_final_path}")
+                return "❌ Error: Tree HTML content is empty", None, None
+            logging.info(f"Tree HTML content length: {len(tree_html_content)}")
+            logging.debug(f"Tree HTML content preview: {tree_html_content[:200]}")
+            # Use iframe to isolate Plotly content
+            tree_html_content = f'<iframe srcdoc="{tree_html_content.replace('"', '&quot;')}" width="100%" height="600px" style="border:none;"></iframe>'
+        except Exception as e:
+            logging.error(f"Failed to read tree HTML: {e}")
+            return f"❌ Error: Failed to read interactive tree: {str(e)}", None, None
+        
+        # Clean up temporary tree file
+        try:
+            if os.path.exists(tree_html_path):
+                os.unlink(tree_html_path)
+        except Exception as e:
+            logging.warning(f"Failed to delete temporary tree file: {e}")
         
         # Ensure the analyzer has the correct user input threshold for the report
         analyzer.matching_percentage = matching_percentage
         
-        # Generate detailed report - FIXED: Only pass the two required parameters
+        # Generate detailed report
         report_success = analyzer.generate_detailed_report(matched_ids, actual_percentage)
         report_html_path = None
         if report_success:
@@ -533,15 +584,14 @@ def analyze_sequence_for_tree(sequence: str, matching_percentage: float) -> tupl
         
         success_msg = f"✅ Analysis complete! Found {len(matched_ids)} similar sequences with {actual_percentage:.2f}% average similarity."
         
-        return success_msg, tree_html_path, report_html_path
+        return success_msg, tree_html_final_path, report_html_path
         
     except Exception as e:
         error_msg = f"❌ Error during analysis: {str(e)}"
         logging.error(error_msg)
         import traceback
         logging.error(f"Full traceback: {traceback.format_exc()}")
-        return error_msg, None, None# --- Keras Prediction ---
-def predict_with_keras(sequence):
+        return error_msg, None, Nonedef predict_with_keras(sequence):
     try:
         if not keras_model or not kmer_to_index:
             return f"Keras model not available. Input sequence: {sequence[:100]}..."
@@ -948,7 +998,9 @@ def create_interface():
                 )
                 tree_html_display = gr.HTML(
                     label="Interactive Phylogenetic Tree",
-                    value="<div style='text-align: center; color: #6b7280; padding: 40px;'>No tree generated yet. Run analysis to create interactive tree.</div>"
+                    value="<div style='text-align: center; color: #6b7280; padding: 40px;'>No tree generated yet. Run analysis to create interactive tree.</div>",
+                    elem_id="tree_html_display",
+                    height=600
                 )
             
             with gr.TabItem("📝 Detailed Report"):