Update app.py

app.py

@@ -785,60 +785,6 @@ def run_pipeline(dna_input, similarity_score=95.0, build_ml_tree=False):
         return error_msg, "", "", "", "", None, None, None, None, error_msg, error_msg
 
 
-def run_pipeline(dna_sequence: str, similarity_threshold: float, do_phylogeny: bool):
-    try:
-        # Step 1: F Gene Extraction
-        f_gene_seq = boundary_model.predict_sequence(dna_sequence)
-        if not f_gene_seq:
-            return "❌ No F gene found", "", "", "", "F gene extraction failed", None, None, None, None, "", ""
-        
-        # Step 2: F Gene Validation
-        is_valid = keras_model.validate_sequence(f_gene_seq)
-        keras_result = "✅ Valid F gene" if is_valid else "❌ Not an F gene"
-
-        # Step 3: Save input to temp FASTA
-        temp_fasta_path = os.path.join(BASE_DIR, "input_temp.fasta")
-        SeqIO.write(SeqRecord(Seq(f_gene_seq), id="query", description=""), temp_fasta_path, "fasta")
-
-        # Step 4: Phylogenetic Placement (if enabled)
-        tree_result = ""
-        analysis_status = ""
-        summary_text = ""
-        align_file = tree_file = html_file = report_file = None
-        tree_html = report_html = "<div style='color:gray'>Skipped</div>"
-
-        if do_phylogeny:
-            # Run analyzer (wraps MAFFT + IQ-TREE + HTML visualizer)
-            outputs = analyzer.analyze(
-                input_fasta=temp_fasta_path,
-                similarity=similarity_threshold / 100.0,
-                output_dir=BASE_DIR
-            )
-            tree_result = outputs["tree_info"]
-            analysis_status = outputs["tree_status"]
-            summary_text = outputs["summary"]
-            align_file = outputs["alignment"]
-            tree_file = outputs["tree"]
-            html_file = outputs["tree_html"]
-            report_file = outputs["report"]
-            tree_html = Path(html_file).read_text() if html_file else tree_html
-            report_html = Path(report_file).read_text() if report_file else report_html
-
-        return f_gene_seq, keras_result, tree_result, analysis_status, summary_text, align_file, tree_file, html_file, report_file, tree_html, report_html
-
-    except Exception as e:
-        logging.error(f"Pipeline Error: {e}")
-        return "❌ Error during processing", "", "", "", f"Error: {e}", None, None, None, None, "", ""
-
-def run_pipeline_from_file(fasta_path, similarity_threshold: float, do_phylogeny: bool):
-    try:
-        seq_record = next(SeqIO.parse(fasta_path, "fasta"))
-        dna_sequence = str(seq_record.seq)
-        return run_pipeline(dna_sequence, similarity_threshold, do_phylogeny)
-    except Exception as e:
-        logging.error(f"File Pipeline Error: {e}")
-        return "❌ Invalid FASTA", "", "", "", f"Error: {e}", None, None, None, None, "", ""
-
 # --- Gradio Interface ---
 def create_interface():
     """Create and configure the Gradio interface"""
@@ -1104,12 +1050,11 @@ if __name__ == "__main__":
         
         # Create and launch interface
         iface = create_interface()
-        iface.queue().launch(
+        iface.launch(
             share=False,            # Set to True if you want to create a public link
             server_name="0.0.0.0",  # Allow connections from any IP
             server_port=7860,       # Default Gradio port
-            show_error=True,        # Show errors in the interface
-            ssr_mode=False          # Disable experimental SSR (prevents 405 error)
+            show_error=True         # Show errors in the interface
         )
         
     except Exception as e: