Update app.py

app.py

@@ -730,7 +730,6 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
             None, None, None, error_msg
         )
 
-# --- Gradio Interface ---
 # --- Gradio Interface ---
 def create_interface():
     """Create the Gradio interface with enhanced layout and features"""
@@ -863,10 +862,10 @@ def create_interface():
                     )
             
             # Tree visualization
-            gr.Markdown("### 🌲 Phylogenetic Tree Visualization")
+            gr.Markdown("### 🌲 Phylogenetic Tree Visualization (ML Simplified Tree)")
             tree_html = gr.HTML(
                 label="Interactive Tree",
-                value="<p>Click 'Open Tree' to view the phylogenetic tree in your browser after running analysis.</p>"
+                value="<p>Click 'Open Tree' to view the ML Simplified Tree in your browser after running analysis.</p>"
             )
             open_tree_btn = gr.Button("🌳 Open Tree", variant="secondary")
 
@@ -884,7 +883,7 @@ def create_interface():
                 )
                 
                 html_file = gr.File(
-                    label="Interactive Tree (HTML)",
+                    label="Interactive Tree (HTML) - ML Simplified Tree",
                     interactive=False
                 )
         
@@ -940,7 +939,7 @@ def create_interface():
             ### Output Files
             - **Aligned FASTA**: Multiple sequence alignment in FASTA format
             - **Tree File**: Newick format phylogenetic tree
-            - **HTML Tree**: Interactive visualization for web browsers
+            - **HTML Tree**: Interactive visualization for web browsers (ML Simplified Tree)
             
             ### Troubleshooting
             
@@ -980,11 +979,21 @@ def create_interface():
         def open_tree(html_file):
             if html_file and os.path.exists(html_file):
                 try:
-                    # Serve the file via Gradio's static file serving (temporary URL)
-                    return gr.File.update(value=html_file, visible=True), gr.update(value=f"<script>window.open('{html_file}', '_blank');</script>")
+                    # Generate a temporary URL for the file using Gradio's file serving in a Space
+                    from gradio.utils import get_space
+                    space_url = get_space()  # Gets the Space URL if running in a Space
+                    if space_url:
+                        # Construct a URL to the file (relative path from the Space root)
+                        import os
+                        file_path = os.path.relpath(html_file, os.getcwd())
+                        file_url = f"{space_url}/file={file_path}"
+                        return gr.update(value=f"<script>window.open('{file_url}', '_blank');</script>")
+                    else:
+                        # Fallback for local testing or if space_url fails
+                        return gr.update(value=f"<p>Please download the file and open it in your browser: <a href='/file={html_file}' download>Download</a></p>")
                 except Exception as e:
-                    return gr.File.update(value=None, visible=False), gr.update(value=f"<p>Error opening tree: {str(e)}. Please download and open the file manually.</p>")
-            return gr.File.update(value=None, visible=False), gr.update(value="<p>No tree file available. Run analysis to generate one.</p>")
+                    return gr.update(value=f"<p>Error opening tree: {str(e)}. Please download and open the file manually: <a href='/file={html_file}' download>Download</a></p>")
+            return gr.update(value="<p>No tree file available. Run analysis to generate one.</p>")
         
         # Connect events
         run_btn.click(
@@ -1005,7 +1014,7 @@ def create_interface():
         open_tree_btn.click(
             fn=open_tree,
             inputs=[html_file],
-            outputs=[html_file, tree_html]
+            outputs=[tree_html]
         )
         
         # Example data loading