Update app.py

app.py

@@ -1,29 +1,67 @@
-
-from __future__ import annotations
-import os, asyncio, json
+rom __future__ import annotations
+import os, json, asyncio, io
 import gradio as gr
 from dotenv import load_dotenv
 
 load_dotenv()
 
 from genesis.pipeline import research_once
+from genesis.providers import postprocess_summary
+from genesis.graph import build_preview_graph_html
 
 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."
+APP_DESC = (
+    "High-level synthetic biology literature synthesis with citations. "
+    "This app **never** produces operational protocols."
+)
+
+DEFAULT_POST = os.getenv("POSTPROCESSOR_DEFAULT", "none").lower()
+DEFAULT_RERANK_MODEL = os.getenv("RERANK_MODEL", "mixedbread-ai/mxbai-rerank-large-v1")
+
+async def run_pipeline(query: str, fast: bool, postprocessor: str, want_graph: bool) -> tuple:
+    out = await research_once(query, fast=fast, rerank_model=DEFAULT_RERANK_MODEL)
+
+    # Optional post-processing (Gemini/DeepSeek) for polish ONLY (no lab steps)
+    if postprocessor and postprocessor != "none":
+        out["final_output"] = await postprocess_summary(
+            base_text=out.get("final_output") or "",
+            citations=out.get("citations", []),
+            engine=postprocessor,
+        )
+
+    # Optional graph preview
+    graph_html = None
+    if want_graph:
+        graph_html = build_preview_graph_html(out.get("citations", []))
 
-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)
+    final_md = out.get("final_output") or "_No output_"
+    cites_md = "
+".join([f"- [{c.get('title','link')}]({c.get('url','')})" for c in out.get("citations", [])]) or "_None detected_"
+    json_blob = json.dumps(out, indent=2)
+    return final_md, cites_md, json_blob, graph_html
 
 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)
+    with gr.Row():
+        query = gr.Textbox(
+            label="Your high-level research request",
+            lines=5,
+            placeholder=(
+                "e.g., High-level synthesis of CRISPR base-editing trends in oncology (last 2 years). "
+                "Summarize mechanisms, targets, ethics, and provide citations."
+            ),
+        )
+    with gr.Row():
+        fast = gr.Checkbox(label="Fast mode (o4-mini-deep-research)", value=False)
+        post = gr.Dropdown(
+            label="Post-processor",
+            choices=["none", "gemini", "deepseek"],
+            value=DEFAULT_POST,
+            allow_custom_value=False,
+        )
+        want_graph = gr.Checkbox(label="Build graph preview", value=False)
     go = gr.Button("Run Deep Research", variant="primary")
 
     with gr.Tabs():
@@ -33,8 +71,14 @@ with gr.Blocks(theme=gr.themes.Soft(), fill_height=True) as demo:
             citations = gr.Markdown()
         with gr.Tab("JSON Export"):
             json_out = gr.Code(language="json")
+        with gr.Tab("Graph Preview"):
+            graph_html = gr.HTML()
 
-    go.click(fn=run_research, inputs=[query, fast], outputs=[report, citations, json_out])
+    go.click(
+        fn=run_pipeline,
+        inputs=[query, fast, post, want_graph],
+        outputs=[report, citations, json_out, graph_html],
+    )
 
 if __name__ == "__main__":
-    demo.launch()
+    demo.launch()