Update app.py

app.py

@@ -1,46 +1,60 @@
 # app.py
 import os
 import gradio as gr
-
 from genesis.pipeline import research_once
 from genesis.narration import narrate_text
 
-# Preloaded demo queries for tomorrow
-demo_queries = [
-    "Designing synthetic gene circuits for targeted cancer therapy",
-    "CRISPR-based microbial engineering for biofuel production",
-    "Synthetic biology approaches to carbon capture and sequestration",
-    "Engineering probiotics for mental health treatments",
-    "DNA-based nanorobots for targeted drug delivery"
-]
-
 def run_pipeline_ui(query):
-    """Run the full synthetic biology research pipeline."""
-    report, citations, structures, graph_status, image_url = research_once(query)
+    """Run the full synthetic biology research pipeline and handle flexible outputs."""
+    try:
+        # Call pipeline
+        output = research_once(query)
+        
+        # Handle cases with more than 5 return values
+        report = output[0] if len(output) > 0 else "No report generated."
+        citations = output[1] if len(output) > 1 else []
+        structures = output[2] if len(output) > 2 else []
+        graph_status = output[3] if len(output) > 3 else "No graph status."
+        image_url = output[4] if len(output) > 4 else None
 
-    audio_path = narrate_text(report) or "Narration not available"
+        # Generate narration
+        audio_path = narrate_text(report) or None
 
-    cites_md = "### Citations\n"
-    for cite in citations:
-        cites_md += f"- [{cite['type']} {cite['id']}]({cite['url']})\n"
+        # Citations
+        cites_md = "### Citations\n"
+        if citations:
+            for cite in citations:
+                cites_md += f"- [{cite.get('type','Ref')} {cite.get('id','')}]({cite.get('url','#')})\n"
+        else:
+            cites_md += "_No citations found._\n"
 
-    struct_md = "### Molecular Structures\n"
-    for s in structures:
-        struct_md += f"- {s['term']}: [{s['pdb_id']}]({s['pdbe_url']}) ([RCSB]({s['rcsb_url']}))\n"
+        # Structures
+        struct_md = "### Molecular Structures\n"
+        if structures:
+            for s in structures:
+                struct_md += f"- {s.get('term','Unknown')}: [{s.get('pdb_id','')}]({s.get('pdbe_url','#')}) ([RCSB]({s.get('rcsb_url','#')}))\n"
+        else:
+            struct_md += "_No structures found._\n"
 
-    img_md = "### Generated Visual\n"
-    if image_url:
-        img_md += f"![Diagram]({image_url})\n"
+        # Image
+        img_md = "### Generated Visual\n"
+        if image_url:
+            img_md += f"![Diagram]({image_url})\n"
+        else:
+            img_md += "_No visual generated._\n"
 
-    return report, cites_md, struct_md, graph_status, audio_path, img_md
+        return report, cites_md, struct_md, graph_status, audio_path, img_md
 
+    except Exception as e:
+        return f"Error: {str(e)}", "", "", "", None, ""
 
+# Gradio UI
 with gr.Blocks(title="GENESIS-AI: Synthetic Biology Deep Research") as demo:
     gr.Markdown("# 🧬 GENESIS-AI\nThe most advanced synthetic biology research assistant ever built.")
     
     with gr.Row():
-        query_box = gr.Dropdown(choices=demo_queries, label="Select a Research Topic", value=demo_queries[0])
-        run_btn = gr.Button("🚀 Run Research")
+        query_box = gr.Textbox(label="Enter a Research Topic", placeholder="e.g. CRISPR-based probiotics for cancer therapy")
+        run_btn = gr.Button("🚀 Run Research", variant="primary")
 
     with gr.Tab("📄 Report"):
         report_out = gr.Textbox(label="Full Research Report", lines=20)