Update app.py

app.py

@@ -58,7 +58,6 @@ def extract_text_from_excel(file_obj: Union[str, Dict[str, Any]]) -> str:
     """Handle Gradio file upload object which is a dictionary with 'name' and other keys"""
     all_text = []
     try:
-        # Handle Gradio file upload object
         if isinstance(file_obj, dict) and 'name' in file_obj:
             file_path = file_obj['name']
         elif isinstance(file_obj, str):
@@ -120,6 +119,37 @@ Please analyze these clinical notes and provide:
 Provide a structured response with clear medical reasoning.
 """
 
+def validate_tool_file(tool_name: str, tool_path: str) -> None:
+    """Validate the structure of a tool JSON file."""
+    try:
+        if not os.path.exists(tool_path):
+            raise FileNotFoundError(f"Tool file not found: {tool_path}")
+        
+        with open(tool_path, 'r') as f:
+            tool_data = json.load(f)
+        
+        logger.info(f"Contents of {tool_name} ({tool_path}): {tool_data}")
+        
+        if isinstance(tool_data, list):
+            for item in tool_data:
+                if not isinstance(item, dict) or 'name' not in item:
+                    raise ValueError(f"Invalid tool format in {tool_name}: each item must be a dict with a 'name' key, got {item}")
+        elif isinstance(tool_data, dict):
+            if 'tools' in tool_data:
+                if not isinstance(tool_data['tools'], list):
+                    raise ValueError(f"'tools' field in {tool_name} must be a list, got {type(tool_data['tools'])}")
+                for item in tool_data['tools']:
+                    if not isinstance(item, dict) or 'name' not in item:
+                        raise ValueError(f"Invalid tool format in {tool_name}: each tool must be a dict with a 'name' key, got {item}")
+            else:
+                if 'name' not in tool_data:
+                    raise ValueError(f"Invalid tool format in {tool_name}: dict must have a 'name' key or 'tools' field, got {tool_data}")
+        else:
+            raise ValueError(f"Invalid tool file {tool_name}: must be a list or dict, got {type(tool_data)}")
+    except Exception as e:
+        logger.error(f"Error validating tool file {tool_name} ({tool_path}): {str(e)}")
+        raise
+
 def init_agent() -> TxAgent:
     tool_path = os.path.join(tool_cache_dir, "new_tool.json")
     logger.info(f"Checking for tool file at: {tool_path}")
@@ -130,32 +160,34 @@ def init_agent() -> TxAgent:
             "name": "new_tool",
             "description": "Default tool configuration",
             "version": "1.0",
-            "tools": []
+            "tools": [
+                {"name": "dummy_tool", "description": "Dummy tool for testing", "version": "1.0"}
+            ]
         }
         logger.info(f"Creating default tool file at: {tool_path}")
         with open(tool_path, 'w') as f:
             json.dump(default_tool, f)
     
-    # Validate tool file
-    try:
-        with open(tool_path, 'r') as f:
-            tool_data = json.load(f)
-            logger.info(f"Tool file contents: {tool_data}")
-            if not isinstance(tool_data, dict):
-                raise ValueError(f"Tool file {tool_path} must contain a JSON object")
-            if 'tools' not in tool_data or not isinstance(tool_data['tools'], (list, dict)):
-                raise ValueError(f"'tools' field in {tool_path} must be a list or dict, got {type(tool_data.get('tools'))}")
-    except Exception as e:
-        logger.error(f"Error validating tool file {tool_path}: {str(e)}")
-        raise
-
+    # Define tool files
+    tool_files_dict = {
+        'opentarget': '/home/user/.pyenv/versions/3.10.17/lib/python3.10/site-packages/tooluniverse/data/opentarget_tools.json',
+        'fda_drug_label': '/home/user/.pyenv/versions/3.10.17/lib/python3.10/site-packages/tooluniverse/data/fda_drug_labeling_tools.json',
+        'special_tools': '/home/user/.pyenv/versions/3.10.17/lib/python3.10/site-packages/tooluniverse/data/special_tools.json',
+        'monarch': '/home/user/.pyenv/versions/3.10.17/lib/python3.10/site-packages/tooluniverse/data/monarch_tools.json',
+        'new_tool': tool_path
+    }
+    
+    # Validate all tool files
+    for tool_name, tool_path in tool_files_dict.items():
+        validate_tool_file(tool_name, tool_path)
+    
     # Initialize TxAgent
     try:
-        logger.info("Initializing TxAgent with tool_files_dict: {'new_tool': tool_path}")
+        logger.info(f"Initializing TxAgent with tool_files_dict: {tool_files_dict}")
         agent = TxAgent(
             model_name="mims-harvard/TxAgent-T1-Llama-3.1-8B",
             rag_model_name="mims-harvard/ToolRAG-T1-GTE-Qwen2-1.5B",
-            tool_files_dict={"new_tool": tool_path},
+            tool_files_dict=tool_files_dict,
             force_finish=True,
             enable_checker=True,
             step_rag_num=4,