Update app.py

app.py

@@ -5,23 +5,15 @@ from multiprocessing import freeze_support
 import importlib
 import inspect
 
-# === Fix path to include src/txagent
 sys.path.insert(0, os.path.join(os.path.dirname(__file__), "src"))
-
-# === Import and reload to ensure correct file
 import txagent.txagent
 importlib.reload(txagent.txagent)
 from txagent.txagent import TxAgent
 
-print(">>> TxAgent loaded from:", inspect.getfile(TxAgent))
-print(">>> TxAgent has run_gradio_chat:", hasattr(TxAgent, "run_gradio_chat"))
-
-# === Environment
 current_dir = os.path.abspath(os.path.dirname(__file__))
 os.environ["MKL_THREADING_LAYER"] = "GNU"
 os.environ["TOKENIZERS_PARALLELISM"] = "false"
 
-# === Configs
 model_name = "mims-harvard/TxAgent-T1-Llama-3.1-8B"
 rag_model_name = "mims-harvard/ToolRAG-T1-GTE-Qwen2-1.5B"
 new_tool_files = {
@@ -29,23 +21,25 @@ new_tool_files = {
 }
 
 question_examples = [
-    ["Given a patient with WHIM syndrome on prophylactic antibiotics, is it advisable to co-administer Xolremdi with fluconazole?"],
+    ["Given a patient with WHIM syndrome on antibiotics, is Xolremdi + fluconazole advisable?"],
     ["What treatment options exist for HER2+ breast cancer resistant to trastuzumab?"]
 ]
 
-# === Format output in collapsible panels
-def format_collapsible_response(content):
-    return (
-        f"<details open style='border: 1px solid #ccc; padding: 8px; margin-top: 8px; border-radius: 6px;'>"
-        f"<summary style='font-weight: bold; font-size: 16px;'>Answer</summary>"
-        f"<div style='margin-top: 10px; line-height: 1.6;'>{content.strip()}</div></details>"
-    )
+def extract_sections(content):
+    """
+    Example extractor splitting into sections. You should improve it to parse actual keys.
+    """
+    return {
+        "Summary": content[:1000],  # simulate
+        "Clinical Studies": content[1000:2500],
+        "Drug Interactions": "See CYP3A4 interactions...",
+        "Pharmacokinetics": "- Absorption: Oral\n- Half-life: ~24h\n- Metabolized by CYP3A4"
+    }
 
-# === UI
 def create_ui(agent):
     with gr.Blocks() as demo:
         gr.Markdown("<h1 style='text-align: center;'>TxAgent: Therapeutic Reasoning</h1>")
-        gr.Markdown("Ask biomedical or therapeutic questions. Powered by step-by-step reasoning and tools.")
+        gr.Markdown("Ask therapeutic or biomedical questions. Results are categorized for readability.")
 
         temperature = gr.Slider(0, 1, value=0.3, label="Temperature")
         max_new_tokens = gr.Slider(128, 4096, value=1024, label="Max New Tokens")
@@ -54,56 +48,65 @@ def create_ui(agent):
         multi_agent = gr.Checkbox(label="Enable Multi-agent Reasoning", value=False)
         conversation_state = gr.State([])
 
-        chatbot = gr.Chatbot(label="TxAgent", height=600, type="messages")
+        chatbot = gr.Tabs()
+        summary_box = gr.Markdown(label="Summary")
+        studies_box = gr.Markdown(label="Clinical Studies")
+        interactions_box = gr.Markdown(label="Drug Interactions")
+        kinetics_box = gr.Markdown(label="Pharmacokinetics")
+
+        with chatbot:
+            with gr.TabItem("Summary"):
+                summary_display = summary_box
+            with gr.TabItem("Clinical Studies"):
+                studies_display = studies_box
+            with gr.TabItem("Drug Interactions"):
+                interactions_display = interactions_box
+            with gr.TabItem("Pharmacokinetics"):
+                kinetics_display = kinetics_box
+
         message_input = gr.Textbox(placeholder="Ask your biomedical question...", show_label=False)
         send_button = gr.Button("Send", variant="primary")
 
-        # === Chat handler
         def handle_chat(message, history, temperature, max_new_tokens, max_tokens, multi_agent, conversation, max_round):
-            try:
-                generator = agent.run_gradio_chat(
-                    message=message,
-                    history=history,
-                    temperature=temperature,
-                    max_new_tokens=max_new_tokens,
-                    max_token=max_tokens,
-                    call_agent=multi_agent,
-                    conversation=conversation,
-                    max_round=max_round
-                )
-
-                for update in generator:
-                    formatted_messages = []
-                    for m in update:
-                        role = m["role"] if isinstance(m, dict) else getattr(m, "role", "assistant")
-                        content = m["content"] if isinstance(m, dict) else getattr(m, "content", "")
-                        if role == "assistant":
-                            content = format_collapsible_response(content)
-                        formatted_messages.append({"role": role, "content": content})
-                    yield formatted_messages
-            except Exception as e:
-                print("⚠️ Error in chat handler:", e)
-                yield history + [{"role": "assistant", "content": f"An error occurred: {str(e)}"}]
-
-        # === Actions
+            generator = agent.run_gradio_chat(
+                message=message,
+                history=history,
+                temperature=temperature,
+                max_new_tokens=max_new_tokens,
+                max_token=max_tokens,
+                call_agent=multi_agent,
+                conversation=conversation,
+                max_round=max_round
+            )
+
+            final_output = ""
+            for update in generator:
+                for m in update:
+                    role = m["role"] if isinstance(m, dict) else getattr(m, "role", "assistant")
+                    content = m["content"] if isinstance(m, dict) else getattr(m, "content", "")
+                    if role == "assistant":
+                        final_output += content + "\n"
+
+            sections = extract_sections(final_output)
+            return sections["Summary"], sections["Clinical Studies"], sections["Drug Interactions"], sections["Pharmacokinetics"]
+
         send_button.click(
             fn=handle_chat,
-            inputs=[message_input, chatbot, temperature, max_new_tokens, max_tokens, multi_agent, conversation_state, max_round],
-            outputs=chatbot
+            inputs=[message_input, [], temperature, max_new_tokens, max_tokens, multi_agent, conversation_state, max_round],
+            outputs=[summary_box, studies_box, interactions_box, kinetics_box]
         )
 
         message_input.submit(
             fn=handle_chat,
-            inputs=[message_input, chatbot, temperature, max_new_tokens, max_tokens, multi_agent, conversation_state, max_round],
-            outputs=chatbot
+            inputs=[message_input, [], temperature, max_new_tokens, max_tokens, multi_agent, conversation_state, max_round],
+            outputs=[summary_box, studies_box, interactions_box, kinetics_box]
         )
 
         gr.Examples(examples=question_examples, inputs=message_input)
-        gr.Markdown("**DISCLAIMER**: This demo is for research purposes only and does not provide medical advice.")
+        gr.Markdown("**DISCLAIMER**: For research only. Not medical advice.")
 
     return demo
 
-# === Entry point
 if __name__ == "__main__":
     freeze_support()
     try:
@@ -115,16 +118,16 @@ if __name__ == "__main__":
             enable_checker=True,
             step_rag_num=10,
             seed=100,
-            additional_default_tools=[]  # Avoid broken tools
+            additional_default_tools=[]
         )
         agent.init_model()
 
         if not hasattr(agent, "run_gradio_chat"):
-            raise AttributeError("❌ TxAgent is missing `run_gradio_chat`.")
+            raise AttributeError("❌ TxAgent missing `run_gradio_chat`")
 
         demo = create_ui(agent)
         demo.launch(show_error=True)
 
     except Exception as e:
-        print(f"❌ Failed to launch app: {e}")
+        print(f"❌ App failed to start: {e}")
         raise