app.py

import os
import gradio as gr

from genesis.pipeline import (
    run_literature_review,
    run_molecule_lookup,
    run_pathway_analysis,
    run_funding_analysis,
    run_image_analysis
)
from genesis.visualization import generate_pathway_graph, generate_funding_network
from genesis.utils.pdf_export import export_report_to_pdf

# Load custom CSS
with open("genesis/static/style.css", "r") as f:
    custom_css = f.read()

# App Title
APP_TITLE = "🧬 GENESIS-AI — The Synthetic Biology OS"
APP_DESCRIPTION = """
Your **multi-modal synthetic biology intelligence suite**.
Explore molecules, pathways, funding, literature, and images — with real-time AI insights.
"""

# =========================
# TAB FUNCTIONS
# =========================

def literature_tab(query):
    """Run literature review (PubMed, ChEMBL, BioPortal, UMLS)"""
    summary, citations = run_literature_review(query)
    pdf_path = export_report_to_pdf(
        filename="literature_report.pdf",
        title="Literature Review",
        summary=summary,
        citations=citations
    )
    return summary, citations, pdf_path


def molecule_tab(molecule_name):
    """Fetch molecule data from ChEMBL/NCBI & visualize"""
    mol_data, mol_img = run_molecule_lookup(molecule_name)
    pdf_path = export_report_to_pdf(
        filename="molecule_report.pdf",
        title="Molecule Report",
        summary=mol_data
    )
    return mol_data, mol_img, pdf_path


def pathway_tab(pathway_name):
    """Run pathway analysis & generate graph"""
    analysis = run_pathway_analysis(pathway_name)
    graph_fig = generate_pathway_graph(pathway_name)
    pdf_path = export_report_to_pdf(
        filename="pathway_report.pdf",
        title="Pathway Analysis",
        summary=analysis
    )
    return analysis, graph_fig, pdf_path


def funding_tab(keyword):
    """Run funding analysis & generate investor graph"""
    funding_info = run_funding_analysis(keyword)
    funding_graph = generate_funding_network(keyword)
    pdf_path = export_report_to_pdf(
        filename="funding_report.pdf",
        title="Funding Analysis",
        summary=funding_info
    )
    return funding_info, funding_graph, pdf_path


def image_tab(image_file):
    """Run microscopy/image analysis"""
    analysis_text = run_image_analysis(image_file)
    pdf_path = export_report_to_pdf(
        filename="image_report.pdf",
        title="Image Analysis",
        summary=analysis_text
    )
    return analysis_text, pdf_path


# =========================
# GRADIO UI
# =========================

with gr.Blocks(css=custom_css, theme="default") as demo:
    gr.HTML(f"<h1>{APP_TITLE}</h1><p>{APP_DESCRIPTION}</p>")

    with gr.Tabs():
        # Literature Tab
        with gr.Tab("📚 Literature Review"):
            lit_query = gr.Textbox(label="Enter research question")
            lit_summary = gr.Textbox(label="Summary", lines=8)
            lit_citations = gr.Textbox(label="Citations", lines=5)
            lit_pdf = gr.File(label="Download PDF")
            lit_btn = gr.Button("Run Literature Review", variant="primary")
            lit_btn.click(literature_tab, inputs=lit_query, outputs=[lit_summary, lit_citations, lit_pdf])

        # Molecule Lookup
        with gr.Tab("🧪 Molecule Viewer"):
            mol_name = gr.Textbox(label="Enter molecule name / ChEMBL ID")
            mol_info = gr.Textbox(label="Molecule Information", lines=8)
            mol_img = gr.Image(label="Structure")
            mol_pdf = gr.File(label="Download PDF")
            mol_btn = gr.Button("Lookup Molecule", variant="primary")
            mol_btn.click(molecule_tab, inputs=mol_name, outputs=[mol_info, mol_img, mol_pdf])

        # Pathway Analysis
        with gr.Tab("🔬 Pathway Analysis"):
            path_name = gr.Textbox(label="Enter pathway name")
            path_analysis = gr.Textbox(label="Pathway Analysis", lines=8)
            path_graph = gr.Plot(label="Pathway Graph")
            path_pdf = gr.File(label="Download PDF")
            path_btn = gr.Button("Analyze Pathway", variant="primary")
            path_btn.click(pathway_tab, inputs=path_name, outputs=[path_analysis, path_graph, path_pdf])

        # Funding Network
        with gr.Tab("💰 Funding Explorer"):
            fund_keyword = gr.Textbox(label="Enter biotech keyword")
            fund_info = gr.Textbox(label="Funding Information", lines=8)
            fund_graph = gr.Plot(label="Funding Network")
            fund_pdf = gr.File(label="Download PDF")
            fund_btn = gr.Button("Analyze Funding", variant="primary")
            fund_btn.click(funding_tab, inputs=fund_keyword, outputs=[fund_info, fund_graph, fund_pdf])

        # Image Analysis
        with gr.Tab("🖼️ Image Analysis"):
            img_upload = gr.Image(type="filepath", label="Upload microscopy or bio-image")
            img_analysis = gr.Textbox(label="Image Analysis", lines=8)
            img_pdf = gr.File(label="Download PDF")
            img_btn = gr.Button("Analyze Image", variant="primary")
            img_btn.click(image_tab, inputs=img_upload, outputs=[img_analysis, img_pdf])

demo.queue().launch(server_name="0.0.0.0", server_port=7860)