Update app.py

app.py

@@ -1,180 +1,136 @@
 # app.py
-import os
 import gradio as gr
-from genesis.pipeline import (
-    run_literature_mode,
-    run_molecule_mode,
-    run_pathway_mode,
-    run_funding_mode,
-    run_image_mode
+from genesis.providers import (
+    run_pubmed_literature,
+    run_chembl_search,
+    run_bioportal_ontology,
+    run_ncbi_gene_lookup,
+    ai_generate_text,
+    ai_generate_image,
+    run_tts,
+    query_funding_network,
+    query_pathway_graph
 )
-from genesis.utils.pdf_export import export_pdf_report
-
-# Load CSS
-with open(os.path.join("genesis", "static", "style.css"), "r") as f:
-    custom_css = f.read()
-
-HF_SPACE = os.environ.get("HF_SPACE", "false").lower() == "true"
-
-# ---------------------------------------------------------
-# Wrappers to ensure click-to-run functionality
-# ---------------------------------------------------------
-
-def literature_tab(query, narration, export_pdf):
-    result = run_literature_mode(query, narration=narration)
-    pdf_path = None
-    if export_pdf:
-        pdf_path = export_pdf_report(result)
-    return (
-        result.get("summary", ""),
-        result.get("citations", []),
-        result.get("visuals", None),
-        result.get("audio_url", None),
-        pdf_path
-    )
-
-def molecule_tab(identifier, narration, export_pdf):
-    result = run_molecule_mode(identifier, narration=narration)
-    pdf_path = None
-    if export_pdf:
-        pdf_path = export_pdf_report(result)
-    return (
-        result.get("summary", ""),
-        result.get("structure_3d", None),
-        result.get("properties", ""),
-        result.get("audio_url", None),
-        pdf_path
-    )
-
-def pathway_tab(pathway_name, narration, export_pdf):
-    result = run_pathway_mode(pathway_name, narration=narration)
-    pdf_path = None
-    if export_pdf:
-        pdf_path = export_pdf_report(result)
-    return (
-        result.get("summary", ""),
-        result.get("graph_svg", None),
-        result.get("analysis", ""),
-        result.get("audio_url", None),
-        pdf_path
-    )
-
-def funding_tab(query, narration, export_pdf):
-    result = run_funding_mode(query, narration=narration)
-    pdf_path = None
-    if export_pdf:
-        pdf_path = export_pdf_report(result)
-    return (
-        result.get("summary", ""),
-        result.get("funding_graph", None),
-        result.get("top_investors", ""),
-        result.get("audio_url", None),
-        pdf_path
-    )
-
-def image_tab(image, narration, export_pdf):
-    result = run_image_mode(image, narration=narration)
-    pdf_path = None
-    if export_pdf:
-        pdf_path = export_pdf_report(result)
-    return (
-        result.get("summary", ""),
-        result.get("annotations", None),
-        result.get("enhanced_image", None),
-        result.get("audio_url", None),
-        pdf_path
-    )
-
-# ---------------------------------------------------------
-# Build Gradio Interface
-# ---------------------------------------------------------
-with gr.Blocks(css=custom_css, theme=gr.themes.Monochrome()) as demo:
-    gr.Markdown("# 🧬 GENESIS-AI — The Synthetic Biology OS")
-    gr.Markdown("Multi-modal AI for Literature, Molecules, Pathways, Funding, and Images.")
+from genesis.utils.pdf_export import export_pdf
+import tempfile, os
+
+# ========================
+# HELPER FUNCTIONS
+# ========================
+def search_literature(query):
+    results = run_pubmed_literature(query, max_results=5)
+    if not results:
+        return "No results found."
+    return results
+
+def molecule_lookup(molecule):
+    return run_chembl_search(molecule)
+
+def ontology_lookup(term):
+    return run_bioportal_ontology(term)
+
+def gene_lookup(gene_id):
+    return run_ncbi_gene_lookup(gene_id)
+
+def funding_map(keyword):
+    data = query_funding_network(keyword)
+    return data if data else "No funding connections found."
+
+def pathway_map(pathway):
+    data = query_pathway_graph(pathway)
+    return data if data else "No pathway data found."
+
+def generate_ai_summary(prompt, model_choice):
+    return ai_generate_text(prompt, model=model_choice)
+
+def generate_ai_image(prompt):
+    return ai_generate_image(prompt)
+
+def narrate_summary(text, voice):
+    audio = run_tts(text, voice=voice)
+    if audio:
+        temp_file = tempfile.NamedTemporaryFile(delete=False, suffix=".mp3")
+        with open(temp_file.name, "wb") as f:
+            f.write(audio)
+        return temp_file.name
+    return None
+
+def export_results_to_pdf(content):
+    pdf_path = export_pdf(content)
+    return pdf_path
+
+# ========================
+# UI DESIGN
+# ========================
+with gr.Blocks(css="static/style.css", theme=gr.themes.Soft()) as demo:
+    gr.HTML("<h1>🧬 GENESIS-AI — Synthetic Biology Research OS</h1>")
+    gr.HTML("<p>Multi-modal intelligence for scientists. Powered by AI + global biology databases.</p>")
 
     with gr.Tab("📚 Literature Review"):
-        with gr.Row():
-            query = gr.Textbox(label="Research Query")
-            narration = gr.Checkbox(label="Enable Narration", value=False)
-            export_pdf = gr.Checkbox(label="Export PDF", value=False)
-        run_btn = gr.Button("Run Literature Review 🚀")
-        summary = gr.Textbox(label="Summary", lines=10)
-        citations = gr.JSON(label="Citations")
-        visuals = gr.Image(label="Visuals")
-        audio_url = gr.Audio(label="Narration Audio")
-        pdf_out = gr.File(label="Download PDF")
-        run_btn.click(
-            literature_tab,
-            inputs=[query, narration, export_pdf],
-            outputs=[summary, citations, visuals, audio_url, pdf_out]
-        )
-
-    with gr.Tab("🧪 Molecule Explorer"):
-        identifier = gr.Textbox(label="Molecule Name / Gene ID")
-        narration2 = gr.Checkbox(label="Enable Narration", value=False)
-        export_pdf2 = gr.Checkbox(label="Export PDF", value=False)
-        run_btn2 = gr.Button("Run Molecule Analysis 🔍")
-        summary2 = gr.Textbox(label="Summary", lines=10)
-        structure_3d = gr.HTML(label="3D Structure Viewer")
-        properties = gr.Textbox(label="Properties")
-        audio_url2 = gr.Audio(label="Narration Audio")
-        pdf_out2 = gr.File(label="Download PDF")
-        run_btn2.click(
-            molecule_tab,
-            inputs=[identifier, narration2, export_pdf2],
-            outputs=[summary2, structure_3d, properties, audio_url2, pdf_out2]
-        )
-
-    with gr.Tab("🧬 Pathway Mapper"):
-        pathway_name = gr.Textbox(label="Pathway Name")
-        narration3 = gr.Checkbox(label="Enable Narration", value=False)
-        export_pdf3 = gr.Checkbox(label="Export PDF", value=False)
-        run_btn3 = gr.Button("Run Pathway Mapping 🧩")
-        summary3 = gr.Textbox(label="Summary", lines=10)
-        graph_svg = gr.HTML(label="Pathway Graph")
-        analysis = gr.Textbox(label="Analysis")
-        audio_url3 = gr.Audio(label="Narration Audio")
-        pdf_out3 = gr.File(label="Download PDF")
-        run_btn3.click(
-            pathway_tab,
-            inputs=[pathway_name, narration3, export_pdf3],
-            outputs=[summary3, graph_svg, analysis, audio_url3, pdf_out3]
-        )
-
-    with gr.Tab("💰 Funding Network"):
-        funding_query = gr.Textbox(label="Funding Query (global)")
-        narration4 = gr.Checkbox(label="Enable Narration", value=False)
-        export_pdf4 = gr.Checkbox(label="Export PDF", value=False)
-        run_btn4 = gr.Button("Run Funding Analysis 🌍")
-        summary4 = gr.Textbox(label="Summary", lines=10)
-        funding_graph = gr.HTML(label="Funding Network Graph")
-        top_investors = gr.Textbox(label="Top Investors")
-        audio_url4 = gr.Audio(label="Narration Audio")
-        pdf_out4 = gr.File(label="Download PDF")
-        run_btn4.click(
-            funding_tab,
-            inputs=[funding_query, narration4, export_pdf4],
-            outputs=[summary4, funding_graph, top_investors, audio_url4, pdf_out4]
-        )
-
-    with gr.Tab("🖼️ Image Analysis"):
-        img_input = gr.Image(type="filepath", label="Upload Microscopy or Diagram")
-        narration5 = gr.Checkbox(label="Enable Narration", value=False)
-        export_pdf5 = gr.Checkbox(label="Export PDF", value=False)
-        run_btn5 = gr.Button("Run Image Analysis 🖼️")
-        summary5 = gr.Textbox(label="Summary", lines=10)
-        annotations = gr.Image(label="Annotated Image")
-        enhanced_image = gr.Image(label="Enhanced Image")
-        audio_url5 = gr.Audio(label="Narration Audio")
-        pdf_out5 = gr.File(label="Download PDF")
-        run_btn5.click(
-            image_tab,
-            inputs=[img_input, narration5, export_pdf5],
-            outputs=[summary5, annotations, enhanced_image, audio_url5, pdf_out5]
-        )
-
-# ---------------------------------------------------------
-# Launch
-# ---------------------------------------------------------
+        lit_query = gr.Textbox(label="Enter Search Query")
+        lit_btn = gr.Button("Search Literature")
+        lit_output = gr.JSON(label="Results")
+        lit_btn.click(search_literature, inputs=lit_query, outputs=lit_output)
+
+    with gr.Tab("🧪 Molecule & Gene Lookup"):
+        mol_input = gr.Textbox(label="Molecule Name")
+        mol_btn = gr.Button("Search Molecule")
+        mol_output = gr.JSON()
+
+        gene_input = gr.Textbox(label="Gene ID")
+        gene_btn = gr.Button("Lookup Gene")
+        gene_output = gr.JSON()
+
+        mol_btn.click(molecule_lookup, inputs=mol_input, outputs=mol_output)
+        gene_btn.click(gene_lookup, inputs=gene_input, outputs=gene_output)
+
+    with gr.Tab("🔬 Ontology & Pathway Mapping"):
+        term_input = gr.Textbox(label="Ontology Term")
+        term_btn = gr.Button("Search Ontology")
+        term_output = gr.JSON()
+
+        pathway_input = gr.Textbox(label="Pathway Name")
+        pathway_btn = gr.Button("Map Pathway")
+        pathway_output = gr.JSON()
+
+        term_btn.click(ontology_lookup, inputs=term_input, outputs=term_output)
+        pathway_btn.click(pathway_map, inputs=pathway_input, outputs=pathway_output)
+
+    with gr.Tab("💰 Funding Networks"):
+        fund_input = gr.Textbox(label="Keyword (Company / Topic)")
+        fund_btn = gr.Button("Find Funding Connections")
+        fund_output = gr.JSON()
+        fund_btn.click(funding_map, inputs=fund_input, outputs=fund_output)
+
+    with gr.Tab("🎨 AI Tools"):
+        # AI Text
+        ai_prompt = gr.Textbox(label="Prompt for AI")
+        ai_model = gr.Dropdown(choices=["gemini", "openai", "claude", "deepseek"], value="gemini", label="Model")
+        ai_btn = gr.Button("Generate Summary")
+        ai_output = gr.Textbox(label="AI Summary")
+        ai_btn.click(generate_ai_summary, inputs=[ai_prompt, ai_model], outputs=ai_output)
+
+        # AI Image
+        img_prompt = gr.Textbox(label="Prompt for Image")
+        img_btn = gr.Button("Generate Image")
+        img_output = gr.Image()
+        img_btn.click(generate_ai_image, inputs=img_prompt, outputs=img_output)
+
+        # Narration
+        narr_text = gr.Textbox(label="Text to Narrate")
+        narr_voice = gr.Dropdown(choices=["Rachel", "Bella", "Antoni"], value="Rachel", label="Voice")
+        narr_btn = gr.Button("Narrate")
+        narr_output = gr.Audio()
+        narr_btn.click(narrate_summary, inputs=[narr_text, narr_voice], outputs=narr_output)
+
+    with gr.Row():
+        pdf_text = gr.Textbox(label="Enter text/content for PDF export")
+        pdf_btn = gr.Button("Export PDF")
+        pdf_file = gr.File(label="Download PDF")
+        pdf_btn.click(export_results_to_pdf, inputs=pdf_text, outputs=pdf_file)
+
+# ========================
+# APP LAUNCH
+# ========================
 if __name__ == "__main__":
-    demo.launch(server_name="0.0.0.0", server_port=7860, share=HF_SPACE)
+    demo.launch(server_name="0.0.0.0", server_port=7860)