test

.gitignore

@@ -0,0 +1,2 @@
+.env
+__pycache__

app.py

@@ -1,915 +1,184 @@
-# 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 - AGGRESSIVE FIX: Minimal yields."""
-#     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})
-    
-#     # CRITICAL FIX: Only yield once at the start to show user message
-#     yield chatbot_history, None, None, None, None, "🔄 Processing..."
-    
-#     try:
-#         # CRITICAL FIX: Collect ALL steps without yielding
-#         step_count = 0
-#         collected_outputs = []
-        
-#         for step in agent.go_stream(prompt):
-#             step_count += 1
-#             output = step.get("output", "")
-            
-#             if output:
-#                 collected_outputs.append(output)
-        
-#         # CRITICAL FIX: Process ALL collected outputs at once
-#         for output in collected_outputs:
-#             parsed = parse_agent_output(output)
-#             formatted_message = format_message_for_display(parsed)
-            
-#             # Update or append to chatbot history
-#             if chatbot_history and chatbot_history[-1]["role"] == "assistant":
-#                 # Update the last assistant message
-#                 chatbot_history[-1]["content"] = formatted_message
-#             else:
-#                 # Add new assistant message
-#                 chatbot_history.append({
-#                     "role": "assistant",
-#                     "content": formatted_message
-#                 })
-        
-#         # CRITICAL FIX: Check files only ONCE after all processing
-#         images, data = check_for_output_files()
-        
-#         status_msg = f"✅ Complete ({step_count} steps)"
-#         if images:
-#             status_msg += f" | {len(images)} image(s)"
-#         if data:
-#             status_msg += f" | {len(data)} data file(s)"
-        
-#         # CRITICAL FIX: Final single yield with all results
-#         yield chatbot_history, images, data, None, None, status_msg
-        
-#     except Exception as e:
-#         error_trace = traceback.format_exc()
-#         error_msg = f"❌ **Error:** {str(e)}\n\n<details>\n<summary>Stack Trace</summary>\n\n```\n{error_trace}\n```\n</details>"
-        
-#         chatbot_history.append({
-#             "role": "assistant",
-#             "content": error_msg
-#         })
-        
-#         yield chatbot_history, None, None, None, None, f"❌ Error: {str(e)}"
-
-
-# def clear_chat():
-#     """Clear the chat history and outputs."""
-#     return [], None, None, None, None, "Ready"
-
-
-# def validate_passcode(input_passcode):
-#     """Validate the passcode and initialize the agent."""
-#     global agent
-    
-#     if input_passcode == PASSCODE:
-#         try:
-#             # Initialize the agent
-#             agent = A1(
-#                 path="./data",
-#                 llm="claude-sonnet-4-20250514",
-#                 use_tool_retriever=True,
-#                 timeout_seconds=600
-#             )
-#             return (
-#                 gr.update(visible=False),  # Hide passcode section
-#                 gr.update(visible=True),   # Show main interface
-#                 "✅ Access granted! Agent initialized successfully."
-#             )
-#         except Exception as e:
-#             error_msg = f"❌ Failed to initialize agent: {str(e)}"
-#             return (
-#                 gr.update(visible=True),
-#                 gr.update(visible=False),
-#                 error_msg
-#             )
-#     else:
-#         return (
-#             gr.update(visible=True),
-#             gr.update(visible=False),
-#             "❌ Invalid passcode. Please try again."
-#         )
-# # batched streaming instead
-# def process_agent_response_batched(prompt, uploaded_file, chatbot_history, batch_size=5):
-#     """Process agent response with BATCHED updates (every N steps)."""
-#     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:
-#             data_dir = Path("./data")
-#             data_dir.mkdir(exist_ok=True)
-            
-#             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"
-            
-#             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 with batching
-#         step_count = 0
-#         batch_count = 0
-        
-#         for step in agent.go_stream(prompt):
-#             step_count += 1
-#             output = step.get("output", "")
-            
-#             if output:
-#                 parsed = parse_agent_output(output)
-#                 formatted_message = format_message_for_display(parsed)
-                
-#                 # Update chatbot history
-#                 if chatbot_history and chatbot_history[-1]["role"] == "assistant":
-#                     chatbot_history[-1]["content"] = formatted_message
-#                 else:
-#                     chatbot_history.append({
-#                         "role": "assistant",
-#                         "content": formatted_message
-#                     })
-                
-#                 # Only yield every batch_size steps
-#                 if step_count % batch_size == 0:
-#                     batch_count += 1
-#                     yield chatbot_history, None, None, None, None, f"🔄 Step {step_count}..."
-        
-#         # Final yield with files
-#         images, data = check_for_output_files()
-        
-#         status_msg = f"✅ Complete ({step_count} steps)"
-#         if images:
-#             status_msg += f" | {len(images)} image(s)"
-#         if data:
-#             status_msg += f" | {len(data)} data file(s)"
-        
-#         yield chatbot_history, images, data, None, None, status_msg
-        
-#     except Exception as e:
-#         error_trace = traceback.format_exc()
-#         error_msg = f"❌ **Error:** {str(e)}\n\n<details>\n<summary>Stack Trace</summary>\n\n```\n{error_trace}\n```\n</details>"
-        
-#         chatbot_history.append({
-#             "role": "assistant",
-#             "content": error_msg
-#         })
-        
-#         yield chatbot_history, None, None, None, None, f"❌ Error: {str(e)}"
-
-
-# # Custom theme
-# custom_theme = gr.themes.Soft(
-#     primary_hue="indigo",
-#     secondary_hue="purple",
-#     neutral_hue="slate",
-#     font=["Inter", "system-ui", "sans-serif"],
-#     text_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",
-#                     type="messages",
-#                     height=550,
-#                     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("Starting server...")
-#     print("=" * 60)
-    
-#     # Launch the app
-#     demo.launch(show_api=False)
+"""
+SIMPLIFIED VERSION - No monkey patching, just clean type hints
+"""
 import os
 import re
 import shutil
 import traceback
 import gradio as gr
 from pathlib import Path
+from typing import List, Dict, Any, Tuple, Optional
 from histopath.agent import A1
 from dotenv import load_dotenv
-from typing import List, Dict, Any, Optional, Tuple
 
-# Load environment variables
-load_dotenv()
+# Load environment
+if os.path.exists(".env"):
+    load_dotenv()
 
-# Get passcode from environment
-PASSCODE = os.getenv("GRADIO_PASSWORD")
-
-# Initialize agent (will be created after passcode validation)
+PASSCODE = os.getenv("GRADIO_PASSWORD", "TESTING")
 agent = None
 
 
 def check_for_output_files():
-    """Check for all files in the output directory and return their paths."""
+    """Check output directory for files."""
     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 = []
+    images = [str(f) for f in output_dir.glob("*") if f.suffix.lower() in {".png", ".jpg", ".jpeg", ".svg", ".tif", ".tiff"}]
+    data = [str(f) for f in output_dir.glob("*") if f.suffix.lower() in {".csv", ".txt", ".json", ".npy"}]
     
-    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
+    return images, data
 
 
-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()
+def preview_file(file):
+    """Preview uploaded file."""
+    if file is None:
+        return None, None, "No file"
     
-    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}"
+    path = Path(file.name)
+    if path.suffix.lower() in {".png", ".jpg", ".jpeg", ".svg", ".tif", ".tiff", ".svs"}:
+        return file.name, None, f"Preview: {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'])
-        
+        size = path.stat().st_size / 1024
+        return None, file.name, f"File: {path.name} ({size:.1f} KB)"
+
+
+def parse_output(text):
+    """Parse agent output."""
+    text = re.sub(r'={30,}.*?={30,}', '', text, flags=re.DOTALL).strip()
+    
+    result = {"type": "text", "content": text, "code": None, "obs": None, "think": None}
+    
+    code_match = re.search(r'<execute>(.*?)</execute>', text, re.DOTALL)
+    if code_match:
+        result["type"] = "code"
+        result["code"] = code_match.group(1).strip()
+        before = text[:code_match.start()].strip()
+        before = re.sub(r'<think>(.*?)</think>', r'\1', before, flags=re.DOTALL)
+        result["think"] = before or None
+        return result
+    
+    obs_match = re.search(r'<observation>(.*?)</observation>', text, re.DOTALL)
+    if obs_match:
+        result["type"] = "obs"
+        result["obs"] = obs_match.group(1).strip()
+        before = text[:obs_match.start()].strip()
+        before = re.sub(r'<think>(.*?)</think>', r'\1', before, flags=re.DOTALL)
+        result["think"] = before or None
+        return result
+    
+    sol_match = re.search(r'<solution>(.*?)</solution>', text, re.DOTALL)
+    if sol_match:
+        result["type"] = "solution"
+        result["content"] = sol_match.group(1).strip()
+        before = text[:sol_match.start()].strip()
+        before = re.sub(r'<think>(.*?)</think>', r'\1', before, flags=re.DOTALL)
+        result["think"] = before or None
+        return result
+    
+    result["content"] = re.sub(r'<think>(.*?)</think>', r'\1', text, flags=re.DOTALL)
+    return result
+
+
+def format_display(parsed):
+    """Format for display."""
+    parts = []
+    
+    if parsed.get("think"):
+        parts.append(parsed["think"])
+    
+    if parsed["type"] == "code":
+        if parsed.get("think"):
+            parts.append("\n---\n")
+        parts.append("### 💻 Code\n")
+        parts.append(f"```python\n{parsed['code']}\n```")
+    elif parsed["type"] == "obs":
+        if parsed.get("think"):
+            parts.append("\n---\n")
+        parts.append("### 📊 Output\n")
+        parts.append(f"```\n{parsed['obs']}\n```")
+    elif parsed["type"] == "solution":
+        if parsed.get("think"):
+            parts.append("\n---\n")
+        parts.append("### ✅ Solution\n")
+        parts.append(parsed['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"])
+        if not parsed.get("think"):
+            parts.append(parsed["content"])
     
-    return "\n\n".join(msg_parts)
+    return "\n\n".join(parts)
 
 
-# CRITICAL FIX: Wrap the main processing function to simplify type signatures
-def process_agent_response_wrapper(prompt: str, uploaded_file, chatbot_history: List[Dict[str, str]]):
-    """
-    Wrapper function with simplified type hints to avoid Gradio API introspection issues.
-    
-    Args:
-        prompt: User query string
-        uploaded_file: Uploaded file object (or None)
-        chatbot_history: List of message dictionaries
-        
-    Returns:
-        Tuple of (chatbot_history, images, data_files, preview_image, preview_file, status)
-    """
+# CRITICAL: Simple types only
+def process_query(prompt: str, file: Any, history: List[Dict[str, str]]):
+    """Process user query - SIMPLE TYPES ONLY."""
     global agent
     
+    # Initialize history if None
+    if history is None:
+        history = []
+    
+    # Check 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"
+        history.append({"role": "assistant", "content": "⚠️ Enter passcode first"})
+        yield history, None, None, None, None, "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"
+    # Check input
+    if not prompt.strip() and file is None:
+        history.append({"role": "assistant", "content": "⚠️ Provide prompt or file"})
+        yield history, None, None, None, None, "No input"
         return
     
-    # Handle file upload
-    file_path = None
-    file_info = ""
-    if uploaded_file is not None:
+    # Handle file
+    if 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."
-                
+            Path("./data").mkdir(exist_ok=True)
+            fname = Path(file.name).name
+            fpath = Path("./data") / fname
+            shutil.copy(file.name, fpath)
+            prompt = f"{prompt}\n\nFile: {fpath}" if prompt.strip() else f"File at: {fpath}"
         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
+            history.append({"role": "assistant", "content": f"❌ File error: {e}"})
+            yield history, None, None, None, None, str(e)
             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})
-    
-    # CRITICAL FIX: Only yield once at the start to show user message
-    yield chatbot_history, None, None, None, None, "🔄 Processing..."
+    # Add user message
+    history.append({"role": "user", "content": prompt})
+    yield history, None, None, None, None, "Processing..."
     
+    # Run agent
     try:
-        # CRITICAL FIX: Collect ALL steps without yielding
-        step_count = 0
-        collected_outputs = []
-        
+        outputs = []
         for step in agent.go_stream(prompt):
-            step_count += 1
-            output = step.get("output", "")
-            collected_outputs.append(output)
+            outputs.append(step.get("output", ""))
         
-        # Now process all collected outputs
-        for output in collected_outputs:
-            if not output or output.strip() == "":
+        # Format outputs
+        for out in outputs:
+            if not out.strip():
                 continue
-            
-            parsed = parse_agent_output(output)
-            formatted_msg = format_message_for_display(parsed)
-            
-            if formatted_msg and formatted_msg.strip():
-                chatbot_history.append({
-                    "role": "assistant",
-                    "content": formatted_msg
-                })
+            parsed = parse_output(out)
+            msg = format_display(parsed)
+            if msg.strip():
+                history.append({"role": "assistant", "content": msg})
         
-        # CRITICAL: Single final yield with all results
-        images, data = check_for_output_files()
-        final_status = f"✅ Complete! Processed {step_count} steps"
-        
-        yield chatbot_history, images, data, None, None, final_status
+        # Get results
+        imgs, data = check_for_output_files()
+        yield history, imgs, data, None, None, f"✅ Done ({len(outputs)} steps)"
         
     except Exception as e:
-        error_trace = traceback.format_exc()
-        error_msg = f"❌ **Error occurred:**\n\n```\n{str(e)}\n\n{error_trace}\n```"
-        chatbot_history.append({
-            "role": "assistant",
-            "content": error_msg
-        })
-        yield chatbot_history, None, None, None, None, f"❌ Error: {str(e)}"
+        err = f"❌ Error:\n```\n{traceback.format_exc()}\n```"
+        history.append({"role": "assistant", "content": err})
+        yield history, None, None, None, None, str(e)
 
 
-def validate_passcode(input_passcode: str) -> Tuple:
-    """Validate the passcode and initialize the agent."""
+def validate_pass(pwd: str):
+    """Validate passcode."""
     global agent
     
-    if input_passcode == PASSCODE:
+    if pwd == PASSCODE:
         try:
-            # Initialize the agent
             agent = A1(
                 path="./data",
                 llm="claude-sonnet-4-20250514",
@@ -917,264 +186,71 @@ def validate_passcode(input_passcode: str) -> Tuple:
                 use_tool_retriever=True,
                 timeout_seconds=600
             )
-            
-            return (
-                gr.update(visible=False),  # Hide passcode section
-                gr.update(visible=True),   # Show main interface
-                "✅ Authentication successful! Agent initialized."
-            )
+            return gr.update(visible=False), gr.update(visible=True), "✅ Authenticated"
         except Exception as e:
-            return (
-                gr.update(visible=True),   # Keep passcode section visible
-                gr.update(visible=False),  # Keep main interface hidden
-                f"❌ Error initializing agent: {str(e)}"
-            )
+            return gr.update(visible=True), gr.update(visible=False), f"❌ Init error: {e}"
     else:
-        return (
-            gr.update(visible=True),   # Keep passcode section visible
-            gr.update(visible=False),  # Keep main interface hidden
-            "❌ Invalid passcode. Please try again."
-        )
+        return gr.update(visible=True), gr.update(visible=False), "❌ Invalid passcode"
 
 
-def clear_chat():
-    """Clear the chat and reset outputs."""
-    # Clean output directory
-    output_dir = Path("./output")
-    if output_dir.exists():
-        for file in output_dir.iterdir():
-            if file.is_file():
-                file.unlink()
-    
-    return [], None, None, None, None, "Chat cleared"
-
+def clear_all():
+    """Clear everything."""
+    out_dir = Path("./output")
+    if out_dir.exists():
+        for f in out_dir.iterdir():
+            if f.is_file():
+                f.unlink()
+    return [], None, None, None, None, "Cleared"
 
-# Custom theme
-custom_theme = gr.themes.Soft(
-    primary_hue="indigo",
-    secondary_hue="purple",
-    neutral_hue="slate",
-    font=["Inter", "system-ui", "sans-serif"],
-    text_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:
+# UI
+with gr.Blocks(title="HistoPath") as demo:
+    gr.HTML("<h1 style='text-align:center'>🔬 HistoPath Agent</h1>")
     
-    # 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.Group(visible=True) as pass_section:
+        gr.Markdown("### 🔐 Enter Passcode")
         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
-        )
+            pass_input = gr.Textbox(label="Passcode", type="password", scale=3)
+            pass_btn = gr.Button("Unlock", variant="primary", scale=1)
+        pass_status = gr.Textbox(label="Status", interactive=False)
     
-    # Main interface (hidden initially)
-    with gr.Group(visible=False) as main_interface:
-        with gr.Row(equal_height=True):
-            # Left column - Chat interface
+    with gr.Group(visible=False) as main_section:
+        with gr.Row():
             with gr.Column(scale=3):
-                chatbot = gr.Chatbot(
-                    label="💬 Conversation",
-                    type="messages",
-                    height=550,
-                    show_label=True,
-                    render_markdown=True,
-                )
-                
-                # Input area
+                chat = gr.Chatbot(type="messages", height=500)
                 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",
-                        )
-                
+                    msg = gr.Textbox(label="Query", placeholder="Enter query...", scale=4)
+                    upload = gr.File(label="Upload", scale=1)
                 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,
-                )
+                    send = gr.Button("Send", variant="primary", scale=2)
+                    clear = gr.Button("Clear", scale=1)
+                status = gr.Textbox(value="Ready", interactive=False, show_label=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_wrapper,
-        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_wrapper,
-        inputs=[prompt_input, file_upload, chatbot],
-        outputs=[chatbot, output_gallery, data_files, input_image_preview, input_file_preview, status_text]
-    )
+                    with gr.Tab("Input"):
+                        in_img = gr.Image(height=300)
+                        in_file = gr.File(interactive=False)
+                        in_stat = gr.Textbox(value="No file", interactive=False, show_label=False)
+                    with gr.Tab("Images"):
+                        out_imgs = gr.Gallery(height=500)
+                    with gr.Tab("Data"):
+                        out_data = gr.File(file_count="multiple", interactive=False)
+    
+    # Events
+    pass_btn.click(validate_pass, [pass_input], [pass_section, main_section, pass_status])
+    upload.change(preview_file, [upload], [in_img, in_file, in_stat])
+    send.click(process_query, [msg, upload, chat], [chat, out_imgs, out_data, in_img, in_file, status])
+    clear.click(clear_all, None, [chat, out_imgs, out_data, in_img, in_file, status])
+    msg.submit(process_query, [msg, upload, chat], [chat, out_imgs, out_data, in_img, in_file, status])
 
 
 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("Starting server...")
-    print("=" * 60)
+    print("=" * 50)
+    print("🔬 HistoPath Agent - Simplified")
+    print("=" * 50)
     
-    # Launch the app with API documentation completely disabled
-    demo.launch(
-        show_api=False,
-    )
+    demo.launch(show_api=False, show_error=True)

test_gradio.py

@@ -0,0 +1,25 @@
+"""
+MINIMAL TEST VERSION - Diagnose what's wrong
+Run this first to see if basic Gradio works
+"""
+import gradio as gr
+from typing import List, Dict
+
+def simple_echo(message: str, history: List[Dict[str, str]]):
+    """Simplest possible function."""
+    history = history or []
+    history.append({"role": "user", "content": message})
+    history.append({"role": "assistant", "content": f"Echo: {message}"})
+    return history
+
+with gr.Blocks() as demo:
+    gr.Markdown("# Minimal Test")
+    chatbot = gr.Chatbot(type="messages")
+    msg = gr.Textbox(label="Message")
+    btn = gr.Button("Send")
+    
+    btn.click(simple_echo, [msg, chatbot], [chatbot])
+
+if __name__ == "__main__":
+    print("Testing minimal Gradio setup...")
+    demo.launch(show_api=False)