Update app.py

app.py

@@ -3,7 +3,7 @@ import gradio as gr
 from genesis.pipeline import research_once
 from genesis.visualization import generate_pathway_graph, generate_funding_network
 
-# Predefined demo queries
+# Demo queries for fast testing
 DEMO_QUERIES = [
     "Map all CRISPR-based living therapeutics in clinical trials since 2020",
     "Graph metabolic engineering pathways for bio-based drug production",
@@ -12,19 +12,27 @@ DEMO_QUERIES = [
     "AI-driven biosensor design for early cancer detection"
 ]
 
+# Store past results for quick access
+history_store = {}
+
 def run_pipeline(query):
-    """Run GENESIS-AI pipeline and return all outputs for UI."""
+    """Run the GENESIS-AI research pipeline and return formatted outputs."""
+    if not query.strip():
+        return "⚠️ Please enter a topic", "", None, None, None
+
     report = research_once(query)
+    history_store[query] = report  # save to session
 
-    # Markdown citations
-    cites_md = "### Citations\n"
+    # Build citations markdown
+    cites_md = ""
     if report["citations"]:
-        for c in report["citations"]:
-            cites_md += f"- [{c['type']}]({c['url']})\n"
+        cites_md = "### 📚 Citations\n" + "\n".join(
+            [f"- [{c['type']}]({c['url']})" for c in report["citations"]]
+        )
     else:
-        cites_md += "_No citations found_"
+        cites_md = "⚠️ _No citations found_"
 
-    # Build pathway graph (demo: using expanded_terms as nodes)
+    # Build pathway & funding visualizations
     pathway_fig = generate_pathway_graph(
         entities=report["expanded_terms"],
         relationships=[{"source": report["expanded_terms"][i],
@@ -33,7 +41,6 @@ def run_pipeline(query):
                        for i in range(len(report["expanded_terms"]) - 1)]
     )
 
-    # Funding graph (only demo; in real use, use data from pipeline)
     funding_fig = generate_funding_network(
         companies=[
             {"name": "SynBioTech", "investors": "BioFund, HealthCapital"},
@@ -44,52 +51,89 @@ def run_pipeline(query):
     return (
         report["summary"],
         cites_md,
-        report["visual_image_url"] or "No image generated",
+        report["visual_image_url"],
         pathway_fig,
         funding_fig
     )
 
-# ---- 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.")
+def load_history(query):
+    """Load past research result instantly."""
+    report = history_store.get(query)
+    if not report:
+        return "", "", None, None, None
 
-    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")
+    cites_md = "### 📚 Citations\n" + "\n".join(
+        [f"- [{c['type']}]({c['url']})" for c in report["citations"]]
+    )
+    return (
+        report["summary"],
+        cites_md,
+        report["visual_image_url"],
+        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)]
+        ),
+        generate_funding_network(
+            companies=[
+                {"name": "SynBioTech", "investors": "BioFund, HealthCapital"},
+                {"name": "GeneWorks", "investors": "BioFund, InnovationAngels"}
+            ]
+        )
+    )
+
+with gr.Blocks(theme=gr.themes.Soft(primary_hue="emerald", secondary_hue="gray")) as demo:
+    gr.Markdown(
+        """
+        # 🌱 **GENESIS-AI** — Synthetic Biology Intelligence Platform
+        _AI-powered research, visualization, and synthesis for the future of life sciences._
+        """
+    )
 
-    gr.Markdown("### Quick Demo Queries")
     with gr.Row():
-        demo_buttons = []
-        for q in DEMO_QUERIES:
-            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
+        with gr.Column(scale=3):
+            query_box = gr.Textbox(
+                label="🔍 Enter a research topic",
+                placeholder="e.g., CRISPR gene therapy for cancer",
+                lines=2
+            )
+            run_btn = gr.Button("🚀 Run Research", variant="primary")
+            gr.Markdown("### 🔬 Quick Research Chips")
+            with gr.Row():
+                for q in DEMO_QUERIES:
+                    gr.Button(q, elem_classes="chip").click(
+                        run_pipeline, inputs=gr.Textbox(value=q, visible=False),
+                        outputs=["summary_out", "cites_out", "image_out", "pathway_out", "funding_out"]
+                    )
+
+            gr.Markdown("### 🕘 History")
+            history_list = gr.Dropdown(
+                choices=[], label="Past Research Queries", interactive=True
+            )
+            history_list.change(
+                load_history, inputs=history_list,
+                outputs=["summary_out", "cites_out", "image_out", "pathway_out", "funding_out"]
+            )
+
+        with gr.Column(scale=7):
+            with gr.Accordion("📄 Summary", open=True):
+                summary_out = gr.Markdown(elem_id="summary_out")
+            with gr.Accordion("📚 Citations", open=False):
+                cites_out = gr.Markdown(elem_id="cites_out")
+            with gr.Accordion("🖼️ Image / Diagram", open=False):
+                image_out = gr.Image(type="filepath", elem_id="image_out")
+            with gr.Accordion("🔗 Pathway Graph", open=False):
+                pathway_out = gr.Plot(elem_id="pathway_out")
+            with gr.Accordion("💰 Funding Network", open=False):
+                funding_out = gr.Plot(elem_id="funding_out")
+
     run_btn.click(
         fn=run_pipeline,
-        inputs=query_input,
-        outputs=[summary_output, cites_output, image_output, pathway_output, funding_output]
+        inputs=query_box,
+        outputs=[summary_out, cites_out, image_out, pathway_out, funding_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]
-        )
-
 if __name__ == "__main__":
     demo.launch()