app_old.py

# import os
# import re
# import shutil
# import traceback
# import gradio as gr
# from pathlib import Path
# from histopath.agent import A1
# from dotenv import load_dotenv

# # Load environment variables
# load_dotenv()

# # Get passcode from environment
# PASSCODE = os.getenv("GRADIO_PASSWORD")

# # Initialize agent (will be created after passcode validation)
# agent = None


# def check_for_output_files():
#     """Check for all files in the output directory and return their paths."""
#     output_dir = Path("./output")
#     if not output_dir.exists():
#         return [], []
    
#     image_extensions = {".png", ".jpg", ".jpeg", ".svg", ".tif", ".tiff"}
#     data_extensions = {".csv", ".txt", ".json", ".npy"}
    
#     images = []
#     data_files = []
    
#     for file in output_dir.iterdir():
#         if file.is_file():
#             if file.suffix.lower() in image_extensions:
#                 images.append(str(file))
#             elif file.suffix.lower() in data_extensions:
#                 data_files.append(str(file))
    
#     return images, data_files


# def preview_uploaded_file(uploaded_file):
#     """Preview the uploaded file - show image or file info."""
#     if uploaded_file is None:
#         return None, None, "No file uploaded"
    
#     file_path = Path(uploaded_file.name)
#     file_ext = file_path.suffix.lower()
    
#     image_extensions = {".png", ".jpg", ".jpeg", ".svg", ".tif", ".tiff", ".svs"}
    
#     if file_ext in image_extensions:
#         # Show image preview
#         return uploaded_file.name, None, f"📷 Previewing: {file_path.name}"
#     else:
#         # Show file info
#         file_size = Path(uploaded_file.name).stat().st_size / 1024  # KB
#         return None, uploaded_file.name, f"📄 File: {file_path.name} ({file_size:.1f} KB)"


# def parse_agent_output(output):
#     """Parse agent output to extract code blocks, observations, and regular text."""
#     # Strip out the message divider bars
#     output = re.sub(r'={30,}\s*(Human|Ai)\s+Message\s*={30,}', '', output)
#     output = output.strip()
    
#     parsed = {
#         "type": "text",
#         "content": output,
#         "code": None,
#         "observation": None,
#         "thinking": None
#     }
    
#     # Check for code execution block
#     execute_match = re.search(r'<execute>(.*?)</execute>', output, re.DOTALL)
#     if execute_match:
#         parsed["type"] = "code"
#         parsed["code"] = execute_match.group(1).strip()
#         # Extract text before the code block (thinking/explanation)
#         text_before = output[:execute_match.start()].strip()
#         # Remove any think tags but keep the content
#         text_before = re.sub(r'<think>(.*?)</think>', r'\1', text_before, flags=re.DOTALL)
#         text_before = re.sub(r'={30,}.*?={30,}', '', text_before).strip()
#         parsed["thinking"] = text_before if text_before else None
#         return parsed
    
#     # Check for observation block
#     observation_match = re.search(r'<observation>(.*?)</observation>', output, re.DOTALL)
#     if observation_match:
#         parsed["type"] = "observation"
#         parsed["observation"] = observation_match.group(1).strip()
#         # Extract text before observation if any
#         text_before = output[:observation_match.start()].strip()
#         text_before = re.sub(r'<think>(.*?)</think>', r'\1', text_before, flags=re.DOTALL)
#         text_before = re.sub(r'={30,}.*?={30,}', '', text_before).strip()
#         parsed["thinking"] = text_before if text_before else None
#         return parsed
    
#     # Check for solution block
#     solution_match = re.search(r'<solution>(.*?)</solution>', output, re.DOTALL)
#     if solution_match:
#         parsed["type"] = "solution"
#         parsed["content"] = solution_match.group(1).strip()
#         # Get thinking before solution
#         text_before = output[:solution_match.start()].strip()
#         text_before = re.sub(r'<think>(.*?)</think>', r'\1', text_before, flags=re.DOTALL)
#         text_before = re.sub(r'={30,}.*?={30,}', '', text_before).strip()
#         parsed["thinking"] = text_before if text_before else None
#         return parsed
    
#     # Clean up any remaining tags for display
#     cleaned = re.sub(r'<think>(.*?)</think>', r'\1', output, flags=re.DOTALL)
#     cleaned = re.sub(r'={30,}.*?={30,}', '', cleaned).strip()
#     parsed["content"] = cleaned
    
#     return parsed


# def format_message_for_display(parsed_output):
#     """Format parsed output into a readable message for the chatbot."""
#     msg_parts = []
    
#     # Add thinking/explanation text first if present
#     if parsed_output.get("thinking"):
#         msg_parts.append(parsed_output["thinking"])
    
#     if parsed_output["type"] == "code":
#         # Add separator if there was thinking text
#         if parsed_output.get("thinking"):
#             msg_parts.append("\n---\n")
        
#         msg_parts.append("### 💻 Executing Code\n")
#         msg_parts.append(f"```python\n{parsed_output['code']}\n```")
        
#     elif parsed_output["type"] == "observation":
#         # Add separator if there was thinking text
#         if parsed_output.get("thinking"):
#             msg_parts.append("\n---\n")
        
#         msg_parts.append("### 📊 Observation\n")
#         msg_parts.append(f"```\n{parsed_output['observation']}\n```")
        
#     elif parsed_output["type"] == "solution":
#         # Add separator if there was thinking text
#         if parsed_output.get("thinking"):
#             msg_parts.append("\n---\n")
        
#         msg_parts.append("### ✅ Solution\n")
#         msg_parts.append(parsed_output['content'])
        
#     else:
#         # For regular text, just add the content if thinking wasn't already set
#         if not parsed_output.get("thinking"):
#             msg_parts.append(parsed_output["content"])
    
#     return "\n\n".join(msg_parts)


# def process_agent_response(prompt, uploaded_file, chatbot_history):
#     """Process the agent response and update chatbot."""
#     global agent
    
#     if agent is None:
#         chatbot_history.append({
#             "role": "assistant",
#             "content": "⚠️ Please enter the passcode first to initialize the agent."
#         })
#         yield chatbot_history, None, None, None, None, "⚠️ Agent not initialized"
#         return
    
#     if not prompt.strip() and uploaded_file is None:
#         chatbot_history.append({
#             "role": "assistant",
#             "content": "⚠️ Please provide a prompt or upload a file."
#         })
#         yield chatbot_history, None, None, None, None, "⚠️ No input provided"
#         return
    
#     # Handle file upload
#     file_path = None
#     file_info = ""
#     if uploaded_file is not None:
#         try:
#             # Create data directory if it doesn't exist
#             data_dir = Path("./data")
#             data_dir.mkdir(exist_ok=True)
            
#             # Copy uploaded file to data directory
#             file_name = Path(uploaded_file.name).name
#             file_path = data_dir / file_name
#             shutil.copy(uploaded_file.name, file_path)
            
#             file_info = f"\n\n📎 **Uploaded file:** `{file_path}`\n"
            
#             # Augment prompt with file path
#             if prompt.strip():
#                 prompt = f"{prompt}\n\nUploaded file path: {file_path}"
#             else:
#                 prompt = f"I have uploaded a file at: {file_path}. Please analyze it."
                
#         except Exception as e:
#             error_msg = f"❌ Error handling file upload: {str(e)}"
#             chatbot_history.append({
#                 "role": "assistant",
#                 "content": error_msg
#             })
#             yield chatbot_history, None, None, None, None, error_msg
#             return
    
#     # Add user message to chat
#     user_message = prompt if not file_info else f"{prompt}{file_info}"
#     chatbot_history.append({"role": "user", "content": user_message})
#     yield chatbot_history, None, None, None, None, "🔄 Processing..."
    
#     try:
#         # Stream agent responses
#         step_count = 0
#         for step in agent.go_stream(prompt):
#             step_count += 1
#             output = step.get("output", "")
            
#             if output:
#                 # Parse the output
#                 parsed = parse_agent_output(output)
                
#                 # Add thinking text as separate message if present
#                 if parsed.get("thinking"):
#                     chatbot_history.append({
#                         "role": "assistant",
#                         "content": parsed["thinking"]
#                     })
                
#                 # Add the block (code/observation/solution) as separate message if present
#                 if parsed["type"] == "code" and parsed["code"]:
#                     chatbot_history.append({
#                         "role": "assistant",
#                         "content": f"### 💻 Executing Code\n\n```python\n{parsed['code']}\n```"
#                     })
#                 elif parsed["type"] == "observation" and parsed["observation"]:
#                     chatbot_history.append({
#                         "role": "assistant",
#                         "content": f"### 📊 Observation\n\n```\n{parsed['observation']}\n```"
#                     })
#                 elif parsed["type"] == "solution":
#                     chatbot_history.append({
#                         "role": "assistant",
#                         "content": f"### ✅ Solution\n\n{parsed['content']}"
#                     })
#                 elif parsed["type"] == "text" and parsed["content"]:
#                     # Only add if we haven't already added it as thinking
#                     if not parsed.get("thinking"):
#                         chatbot_history.append({
#                             "role": "assistant",
#                             "content": parsed["content"]
#                         })
                
#                 # Check for output files after each step
#                 images, data_files = check_for_output_files()
                
#                 # Create status message
#                 status = f"🔄 Step {step_count}"
#                 if parsed["type"] == "code":
#                     status += " - Executing code..."
#                 elif parsed["type"] == "observation":
#                     status += " - Processing results..."
#                 elif parsed["type"] == "solution":
#                     status += " - Finalizing solution..."
                
#                 yield (
#                     chatbot_history,
#                     images if images else None,
#                     data_files if data_files else None,
#                     None,
#                     None,
#                     status
#                 )
        
#         # Final check for files
#         final_images, final_data = check_for_output_files()
        
#         # Create download links message if files were generated
#         if final_images or final_data:
#             download_msg = "\n\n---\n\n### 📁 Generated Files Ready for Download\n\n"
            
#             if final_images:
#                 download_msg += f"**🖼️ Images ({len(final_images)})** - Available in the **Images** tab →\n"
#                 for img_path in final_images:
#                     img_name = Path(img_path).name
#                     download_msg += f"- `{img_name}`\n"
#                 download_msg += "\n"
            
#             if final_data:
#                 download_msg += f"**📄 Data Files ({len(final_data)})** - Available in the **Data** tab →\n"
#                 for data_path in final_data:
#                     data_name = Path(data_path).name
#                     download_msg += f"- `{data_name}`\n"
            
#             download_msg += "\n*Click the download button on each file in the respective tabs above.*"
            
#             # Add download message as separate bubble
#             chatbot_history.append({
#                 "role": "assistant",
#                 "content": download_msg
#             })
        
#         status = "✅ Complete"
#         if final_images:
#             status += f" | {len(final_images)} image(s)"
#         if final_data:
#             status += f" | {len(final_data)} data file(s)"
            
#         yield chatbot_history, final_images if final_images else None, final_data if final_data else None, None, None, status
        
#     except Exception as e:
#         error_msg = f"❌ Error: {str(e)}\n\n```\n{traceback.format_exc()}\n```"
#         chatbot_history.append({
#             "role": "assistant",
#             "content": error_msg
#         })
#         yield chatbot_history, None, None, None, None, "❌ Error occurred"


# def validate_passcode(passcode):
#     """Validate the passcode and initialize the agent."""
#     global agent
    
#     if passcode == PASSCODE:
#         # Initialize agent
#         try:
#             agent = A1()
#             return (
#                 gr.update(visible=False),  # Hide passcode section
#                 gr.update(visible=True),   # Show main interface
#                 "✅ Access granted! Agent initialized and ready."
#             )
#         except Exception as e:
#             error_trace = traceback.format_exc()
#             return (
#                 gr.update(visible=True),
#                 gr.update(visible=False),
#                 f"❌ Error initializing agent:\n{str(e)}\n\n{error_trace}"
#             )
#     else:
#         return (
#             gr.update(visible=True),
#             gr.update(visible=False),
#             "❌ Invalid passcode. Please try again."
#         )


# def clear_chat():
#     """Clear the chat history and output files."""
#     # Clean up output directory
#     output_dir = Path("./output")
#     if output_dir.exists():
#         shutil.rmtree(output_dir)
#     output_dir.mkdir(exist_ok=True)
    
#     # Clean up data directory
#     data_dir = Path("./data")
#     if data_dir.exists():
#         for file in data_dir.iterdir():
#             if file.is_file():
#                 file.unlink()
    
#     return [], None, None, None, None, "🗑️ Chat cleared"


# # Create Gradio interface with custom theme
# custom_theme = gr.themes.Soft(
#     primary_hue="blue",
#     secondary_hue="slate",
#     spacing_size="sm",
#     radius_size="md",
# ).set(
#     button_primary_background_fill="*primary_500",
#     button_primary_background_fill_hover="*primary_600",
#     block_label_text_weight="600",
#     block_title_text_weight="600",
# )

# with gr.Blocks(title="HistoPath Agent", theme=custom_theme, css="""
#     .gradio-container {
#         max-width: 100% !important;
#     }
#     .main-header {
#         text-align: center;
#         padding: 1.5rem 0;
#         background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
#         color: white;
#         border-radius: 8px;
#         margin-bottom: 1.5rem;
#     }
#     .main-header h1 {
#         margin: 0;
#         font-size: 2.2rem;
#         font-weight: 700;
#     }
#     .main-header p {
#         margin: 0.5rem 0 0 0;
#         opacity: 0.95;
#         font-size: 1.1rem;
#     }
#     .file-upload-box .wrap {
#         min-width: 0 !important;
#     }
#     .file-upload-box .file-name {
#         word-break: break-word !important;
#         white-space: normal !important;
#         overflow-wrap: break-word !important;
#     }
#     .tab-nav {
#         margin-bottom: 0.5rem;
#     }
#     /* Better styling for code and observation blocks */
#     .message.bot pre {
#         background-color: #f6f8fa !important;
#         border: 1px solid #d0d7de !important;
#         border-radius: 6px !important;
#         padding: 12px !important;
#         margin: 8px 0 !important;
#     }
#     .message.bot h3 {
#         margin-top: 12px !important;
#         margin-bottom: 8px !important;
#         font-weight: 600 !important;
#     }
#     .message.bot hr {
#         border: none !important;
#         border-top: 2px solid #e1e4e8 !important;
#         margin: 16px 0 !important;
#     }
# """) as demo:
    
#     # Header
#     gr.HTML("""
#         <div class="main-header">
#             <h1>🔬 HistoPath Agent</h1>
#             <p>AI-Powered Histopathology Analysis Assistant</p>
#         </div>
#     """)
    
#     # Passcode section
#     with gr.Group(visible=True) as passcode_section:
#         gr.Markdown("### 🔐 Authentication Required")
        
#         with gr.Row():
#             passcode_input = gr.Textbox(
#                 label="Passcode",
#                 type="password",
#                 placeholder="Enter your passcode...",
#                 scale=3
#             )
#             passcode_btn = gr.Button("🔓 Unlock", variant="primary", scale=1, size="lg")
        
#         passcode_status = gr.Textbox(
#             label="Status",
#             interactive=False,
#             lines=2
#         )
    
#     # Main interface (hidden initially)
#     with gr.Group(visible=False) as main_interface:
#         with gr.Row(equal_height=True):
#             # Left column - Chat interface
#             with gr.Column(scale=3):
#                 chatbot = gr.Chatbot(
#                     label="💬 Conversation",
#                     height=550,
#                     # type="messages",
#                     show_label=True,
#                     render_markdown=True,
#                 )
                
#                 # Input area
#                 with gr.Row():
#                     with gr.Column(scale=7):
#                         prompt_input = gr.Textbox(
#                             label="Your Query",
#                             placeholder="E.g., 'Caption the uploaded whole slide image' or 'Segment cells using instanseg model'",
#                             lines=2,
#                             max_lines=5,
#                             show_label=False,
#                         )
#                     with gr.Column(scale=3):
#                         file_upload = gr.File(
#                             label="📎 Upload File",
#                             file_types=[".svs", ".png", ".jpg", ".jpeg", ".tif", ".tiff", ".csv", ".txt", ".json", ".npy"],
#                             height=75,
#                             elem_classes="file-upload-box",
#                         )
                
#                 with gr.Row():
#                     submit_btn = gr.Button("🚀 Submit", variant="primary", scale=3, size="lg")
#                     clear_btn = gr.Button("🗑️ Clear", scale=1, size="lg", variant="secondary")
                
#                 status_text = gr.Textbox(
#                     label="Status",
#                     interactive=False,
#                     value="Ready",
#                     show_label=False,
#                     container=False,
#                 )
            
#             # Right column - Outputs
#             with gr.Column(scale=2):
#                 with gr.Tabs():
#                     with gr.Tab("📥 Input"):
#                         with gr.Column():
#                             input_image_preview = gr.Image(
#                                 label="Input Image",
#                                 height=400,
#                                 show_label=False,
#                                 container=True,
#                             )
#                             input_file_preview = gr.File(
#                                 label="Input File",
#                                 interactive=False,
#                                 height=100,
#                                 show_label=False,
#                                 container=True,
#                             )
#                             input_status = gr.Textbox(
#                                 value="Upload a file to preview",
#                                 show_label=False,
#                                 interactive=False,
#                                 container=False,
#                             )
                    
#                     with gr.Tab("🖼️ Images"):
#                         output_gallery = gr.Gallery(
#                             label="Generated Visualizations",
#                             columns=1,
#                             height=600,
#                             object_fit="contain",
#                             show_label=False,
#                             show_download_button=True,
#                         )
                    
#                     with gr.Tab("📄 Data"):
#                         data_files = gr.File(
#                             label="Generated Data Files",
#                             file_count="multiple",
#                             interactive=False,
#                             height=600,
#                             show_label=False,
#                         )
    
#     # Event handlers
#     passcode_btn.click(
#         fn=validate_passcode,
#         inputs=[passcode_input],
#         outputs=[passcode_section, main_interface, passcode_status]
#     )
    
#     # File upload preview
#     file_upload.change(
#         fn=preview_uploaded_file,
#         inputs=[file_upload],
#         outputs=[input_image_preview, input_file_preview, input_status]
#     )
    
#     submit_btn.click(
#         fn=process_agent_response,
#         inputs=[prompt_input, file_upload, chatbot],
#         outputs=[chatbot, output_gallery, data_files, input_image_preview, input_file_preview, status_text]
#     )
    
#     clear_btn.click(
#         fn=clear_chat,
#         outputs=[chatbot, output_gallery, data_files, input_image_preview, input_file_preview, status_text]
#     )
    
#     # Allow enter key to submit
#     prompt_input.submit(
#         fn=process_agent_response,
#         inputs=[prompt_input, file_upload, chatbot],
#         outputs=[chatbot, output_gallery, data_files, input_image_preview, input_file_preview, status_text]
#     )


# if __name__ == "__main__":
#     # Create necessary directories
#     Path("./data").mkdir(exist_ok=True)
#     Path("./output").mkdir(exist_ok=True)
    
#     print("=" * 60)
#     print("🔬 HistoPath Agent - Gradio Interface")
#     print("=" * 60)
#     # print(f"Passcode: {PASSCODE}")
#     print("Starting server...")
#     print("=" * 60)
    
#     # Launch the app
#     #demo.launch(
#         # server_name="0.0.0.0",
#         # server_port=7860,  # Let Gradio auto-pick an available port
#         # share=True,
#         # show_error=True,
#     #)
#     demo.launch()