app.py

from __future__ import annotations
import os, asyncio, json
import gradio as gr
from dotenv import load_dotenv

load_dotenv()

from genesis.pipeline import research_once

APP_TITLE = "GENESIS-AI — Synthetic Biology Deep Research (Safety-First)"
APP_DESC = "High-level synthetic biology literature synthesis with citations. This app **never** produces operational protocols."

async def run_research(query: str, fast: bool):
    out = await research_once(query, fast=fast)
    final_text = out.get("final_output") or "_No output_"
    cites = out.get("citations", [])
    cites_md = "\n".join([f"- [{c.get('title','link')}]({c.get('url','')})" for c in cites]) or "_None detected_"
    return final_text, cites_md, json.dumps(out, indent=2)

with gr.Blocks(theme=gr.themes.Soft(), fill_height=True) as demo:
    gr.Markdown(f"# {APP_TITLE}")
    gr.Markdown(APP_DESC)

    query = gr.Textbox(label="Your high-level research request", lines=4, placeholder="e.g., High-level synthesis of CRISPR base-editing trends in oncology (last 2 years).")
    fast = gr.Checkbox(label="Fast mode (o4-mini-deep-research)", value=False)
    go = gr.Button("Run Deep Research", variant="primary")

    with gr.Tabs():
        with gr.Tab("Research Report"):
            report = gr.Markdown()
        with gr.Tab("Citations"):
            citations = gr.Markdown()
        with gr.Tab("JSON Export"):
            json_out = gr.Code(language="json")

    go.click(fn=run_research, inputs=[query, fast], outputs=[report, citations, json_out])

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