app.py

# app.py
import os
import gradio as gr
from genesis.pipeline import research_once
from genesis.narration import narrate_text

def run_pipeline_ui(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

        # Generate narration
        audio_path = narrate_text(report) or None

        # 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"

        # 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"

        # 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

    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.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)
    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()

    run_btn.click(
        fn=run_pipeline_ui,
        inputs=[query_box],
        outputs=[report_out, cites_out, struct_out, graph_status_out, audio_out, img_out]
    )

if __name__ == "__main__":
    demo.launch()