Update app.py

app.py

@@ -1,79 +1,79 @@
 # app.py
-import os
 import gradio as gr
-from genesis.pipeline import research_once
-from genesis.narration import narrate_text
+from genesis.pipeline import research_once, DEMO_QUERIES
 
 def run_pipeline_ui(query):
-    """Run the full synthetic biology research pipeline and handle flexible outputs."""
+    """Run the full GENESIS-AI pipeline for the given query."""
     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
+        result = research_once(query)
 
-        # Generate narration
-        audio_path = narrate_text(report) or None
-
-        # Citations
+        summary_md = f"### Research Summary\n{result['summary']}"
         cites_md = "### Citations\n"
-        if citations:
-            for cite in citations:
-                cites_md += f"- [{cite.get('type','Ref')} {cite.get('id','')}]({cite.get('url','#')})\n"
+        if result["citations"]:
+            for c in result["citations"]:
+                cites_md += f"- [{c['type']} {c['id'] or ''}]({c['url']})\n"
         else:
-            cites_md += "_No citations found._\n"
+            cites_md += "_No citations found._"
 
-        # 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"
+        if result["structures"]:
+            for s in result["structures"]:
+                struct_md += f"- **{s['name']}** — [View]({s['url']})\n"
         else:
-            struct_md += "_No structures found._\n"
+            struct_md += "_No structures found._"
 
-        # Image
-        img_md = "### Generated Visual\n"
-        if image_url:
-            img_md += f"![Diagram]({image_url})\n"
-        else:
-            img_md += "_No visual generated._\n"
+        img_md = ""
+        if result["visual_image_url"]:
+            img_md = f"### Visual Diagram\n![]({result['visual_image_url']})"
 
-        return report, cites_md, struct_md, graph_status, audio_path, img_md
+        audio_component = None
+        if result["audio_url"]:
+            audio_component = result["audio_url"]
+
+        return summary_md, cites_md, struct_md, img_md, audio_component
 
     except Exception as e:
-        return f"Error: {str(e)}", "", "", "", None, ""
+        return f"**Error:** {e}", "", "", "", None
+
+
+with gr.Blocks(title="GENESIS-AI — Synthetic Biology Research Engine", theme="default") as demo:
+    gr.Markdown("# 🧬 GENESIS-AI — Synthetic Biology Research Engine")
+    gr.Markdown("Ask about synthetic biology, drug design, CRISPR, biosensors, and more.")
 
-# 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.Textbox(label="Enter a Research Topic", placeholder="e.g. CRISPR-based probiotics for cancer therapy")
-        run_btn = gr.Button("🚀 Run Research", variant="primary")
+        query_input = gr.Textbox(label="Enter your research topic", placeholder="e.g., AI-driven biosensor design for early cancer detection")
+        run_btn = gr.Button("Run Research", variant="primary")
 
-    with gr.Tab("📄 Report"):
-        report_out = gr.Textbox(label="Full Research Report", lines=20)
-    with gr.Tab("📚 Citations"):
-        cites_out = gr.Markdown()
-    with gr.Tab("🔬 Structures"):
-        struct_out = gr.Markdown()
-    with gr.Tab("🕸 Graph"):
-        graph_status_out = gr.Textbox(label="Graph DB Status")
-    with gr.Tab("🔊 Narration"):
-        audio_out = gr.Audio(label="Narrated Summary")
-    with gr.Tab("🖼 Visual Diagram"):
-        img_out = gr.Markdown()
+    with gr.Row():
+        summary_output = gr.Markdown()
+    with gr.Row():
+        cites_output = gr.Markdown()
+    with gr.Row():
+        struct_output = gr.Markdown()
+    with gr.Row():
+        img_output = gr.Markdown()
+    with gr.Row():
+        audio_output = gr.Audio()
 
     run_btn.click(
-        fn=run_pipeline_ui,
-        inputs=[query_box],
-        outputs=[report_out, cites_out, struct_out, graph_status_out, audio_out, img_out]
+        run_pipeline_ui,
+        inputs=[query_input],
+        outputs=[summary_output, cites_output, struct_output, img_output, audio_output]
+    )
+
+    gr.Markdown("## Demo Queries")
+    demo_gallery = gr.Dataset(
+        components=[gr.Textbox()],
+        samples=[[q] for q in DEMO_QUERIES],
+        type="values",
+        label="Click a demo query to run it"
+    )
+
+    demo_gallery.click(
+        run_pipeline_ui,
+        inputs=[query_input],
+        outputs=[summary_output, cites_output, struct_output, img_output, audio_output]
     )
 
 if __name__ == "__main__":
-    demo.launch()
+    demo.launch(server_name="0.0.0.0", server_port=7860, share=True)