Update app.py

app.py

@@ -1,42 +1,95 @@
+# app.py
 import gradio as gr
-from genesis.pipeline import research_once, DEMO_QUERIES
+from genesis.pipeline import research_once
+from genesis.visualization import generate_pathway_graph, generate_funding_network
 
-def run_pipeline_ui(query):
-    """Run the full synthetic biology research pipeline."""
-    if not query.strip():
-        return "Please enter a research topic.", "", None, None
+# Predefined demo queries
+DEMO_QUERIES = [
+    "Map all CRISPR-based living therapeutics in clinical trials since 2020",
+    "Graph metabolic engineering pathways for bio-based drug production",
+    "Synthetic biology startups developing oncolytic viruses — funding + trials",
+    "3D bioprinting advances for organ transplantation with regulatory analysis",
+    "AI-driven biosensor design for early cancer detection"
+]
+
+def run_pipeline(query):
+    """Run GENESIS-AI pipeline and return all outputs for UI."""
     report = research_once(query)
-    summary = report["summary"]
-    citations_md = "\n".join(f"- [{c['type']}]({c['url']})" for c in report["citations"]) or "No citations found."
-    return summary, citations_md, report["visual_image_url"], report["audio_url"]
 
-with gr.Blocks(theme=gr.themes.Soft(primary_hue="green", secondary_hue="blue")) as demo:
+    # Markdown citations
+    cites_md = "### Citations\n"
+    if report["citations"]:
+        for c in report["citations"]:
+            cites_md += f"- [{c['type']}]({c['url']})\n"
+    else:
+        cites_md += "_No citations found_"
 
-    gr.Markdown("# 🧬 GENESIS-AI — Synthetic Biology Research Engine")
+    # Build pathway graph (demo: using expanded_terms as nodes)
+    pathway_fig = generate_pathway_graph(
+        entities=report["expanded_terms"],
+        relationships=[{"source": report["expanded_terms"][i],
+                        "target": report["expanded_terms"][i+1],
+                        "type": "related"}
+                       for i in range(len(report["expanded_terms"]) - 1)]
+    )
 
-    with gr.Row():
-        query_box = gr.Textbox(label="Enter Your Research Topic", scale=4)
-        run_btn = gr.Button("🚀 Run Research", variant="primary", scale=1)
+    # Funding graph (only demo; in real use, use data from pipeline)
+    funding_fig = generate_funding_network(
+        companies=[
+            {"name": "SynBioTech", "investors": "BioFund, HealthCapital"},
+            {"name": "GeneWorks", "investors": "BioFund, InnovationAngels"}
+        ]
+    )
+
+    return (
+        report["summary"],
+        cites_md,
+        report["visual_image_url"] or "No image generated",
+        pathway_fig,
+        funding_fig
+    )
 
-    gr.Markdown("**Or try one of these demo queries:**")
+# ---- Build UI ----
+with gr.Blocks(theme=gr.themes.Soft()) as demo:
+    gr.Markdown("# 🌱 GENESIS-AI — Synthetic Biology Intelligence Platform")
+    gr.Markdown("Cutting-edge research synthesis, citations, structures, and interactive graphs.")
 
-    # Outputs (must be defined before using in button.click)
-    summary_out = gr.Textbox(label="Executive Summary", lines=15, interactive=False)
-    cites_out = gr.Markdown()
-    img_out = gr.Image(type="filepath", label="Generated Research Diagram")
-    audio_out = gr.Audio(type="filepath", label="AI Narration")
+    with gr.Row():
+        query_input = gr.Textbox(label="Enter your research topic", placeholder="e.g., CRISPR gene therapy for cancer")
+        run_btn = gr.Button("Run Research", variant="primary")
 
-    # Create clickable buttons for demo queries
+    gr.Markdown("### Quick Demo Queries")
     with gr.Row():
+        demo_buttons = []
         for q in DEMO_QUERIES:
-            btn = gr.Button(q)
-            btn.click(fn=run_pipeline_ui,
-                      inputs=gr.Textbox(value=q, visible=False),
-                      outputs=[summary_out, cites_out, img_out, audio_out])
+            btn = gr.Button(q, variant="secondary")
+            demo_buttons.append((btn, q))
+
+    with gr.Tab("Summary"):
+        summary_output = gr.Markdown()
+    with gr.Tab("Citations"):
+        cites_output = gr.Markdown()
+    with gr.Tab("Image / Diagram"):
+        image_output = gr.Image(type="filepath")
+    with gr.Tab("Pathway Graph"):
+        pathway_output = gr.Plot()
+    with gr.Tab("Funding Network"):
+        funding_output = gr.Plot()
+
+    # Link run button
+    run_btn.click(
+        fn=run_pipeline,
+        inputs=query_input,
+        outputs=[summary_output, cites_output, image_output, pathway_output, funding_output]
+    )
 
-    # Main run button
-    run_btn.click(fn=run_pipeline_ui,
-                  inputs=query_box,
-                  outputs=[summary_out, cites_out, img_out, audio_out])
+    # Link each demo query button
+    for btn, q in demo_buttons:
+        btn.click(
+            fn=run_pipeline,
+            inputs=gr.Textbox(value=q, visible=False),
+            outputs=[summary_output, cites_output, image_output, pathway_output, funding_output]
+        )
 
-demo.launch()
+if __name__ == "__main__":
+    demo.launch()