amd-gaia 0.15.1__py3-none-any.whl → 0.15.2__py3-none-any.whl

gaia/agents/chat/agent.py

@@ -78,23 +78,6 @@ class ChatAgent(
     - MCP server integration
     """
 
-    # Define simple tools that can execute without requiring a multi-step plan
-    SIMPLE_TOOLS = [
-        "list_indexed_documents",
-        "rag_status",
-        "query_documents",
-        "query_specific_file",
-        "search_indexed_chunks",  # RAG: Search indexed document chunks
-        "dump_document",  # RAG: Export cached extracted text
-        "search_file_content",  # Shared: Grep-like disk search
-        "search_file",  # Shared: Find files by name
-        "search_directory",  # Shared: Find directories by name
-        "read_file",  # Shared: Read any file
-        "write_file",  # Shared: Write any file
-        "index_directory",  # RAG: Index directory
-        "run_shell_command",  # Shell: Execute commands
-    ]
-
     def __init__(self, config: Optional[ChatAgentConfig] = None):
         """
         Initialize Chat Agent.
@@ -109,6 +92,9 @@ class ChatAgent(
         # Initialize path validator
         self.path_validator = PathValidator(config.allowed_paths)
 
+        # Store config for access in other methods
+        self.config = config
+
         # Now use config for all initialization
         # Store RAG configuration from config
         self.rag_documents = config.rag_documents
@@ -148,6 +134,7 @@ class ChatAgent(
                 use_local_llm=not (config.use_claude or config.use_chatgpt),
                 use_llm_chunking=config.use_llm_chunking,  # Enable semantic chunking
                 base_url=config.base_url,  # Pass base_url to RAG for VLM client
+                allowed_paths=config.allowed_paths,  # Pass allowed paths to RAG SDK
             )
             self.rag = RAGSDK(rag_config)
         except ImportError as e:
@@ -267,10 +254,7 @@ No documents are currently indexed.
 """
 
         # Add indexed documents section
-        prompt = (
-            base_prompt
-            + indexed_docs_section
-            + """
+        prompt = base_prompt + indexed_docs_section + """
 **WHEN TO USE TOOLS VS DIRECT ANSWERS:**
 
 Use Format 1 (answer) for:
@@ -376,7 +360,6 @@ When user asks to "index my data folder" or similar:
 2. Show user the matches and ask which one (if multiple)
 3. Use index_directory on the chosen path
 4. Report indexing results"""
-        )
 
         return prompt
 
@@ -473,7 +456,7 @@ When user asks to "index my data folder" or similar:
     def _is_path_allowed(self, path: str) -> bool:
         """
         Check if a path is within allowed directories.
-        Uses real path resolution to prevent TOCTOU attacks.
+        Uses PathValidator for the actual check.
 
         Args:
             path: Path to validate
@@ -481,24 +464,7 @@ When user asks to "index my data folder" or similar:
         Returns:
             True if path is allowed, False otherwise
         """
-        try:
-            # Resolve path using os.path.realpath to follow symlinks
-            # This prevents TOCTOU attacks by resolving at check time
-            real_path = Path(os.path.realpath(path)).resolve()
-
-            # Check if real path is within any allowed directory
-            for allowed_path in self.allowed_paths:
-                try:
-                    # is_relative_to requires Python 3.9+, use alternative for compatibility
-                    real_path.relative_to(allowed_path)
-                    return True
-                except ValueError:
-                    continue
-
-            return False
-        except Exception as e:
-            logger.error(f"Error validating path {path}: {e}")
-            return False
+        return self.path_validator.is_path_allowed(path, prompt_user=False)
 
     def _validate_and_open_file(self, file_path: str, mode: str = "r"):
         """
@@ -647,9 +613,9 @@ When user asks to "index my data folder" or similar:
                 logger.error(f"Failed to index {doc}: {e}")
 
         # Update system prompt after indexing to include the new documents
-        self._update_system_prompt()
+        self.update_system_prompt()
 
-    def _update_system_prompt(self) -> None:
+    def update_system_prompt(self) -> None:
         """Update the system prompt with current indexed documents."""
         # Regenerate the system prompt with updated document list
         self.system_prompt = self._get_system_prompt()
@@ -732,18 +698,26 @@ When user asks to "index my data folder" or similar:
             )
             return
 
+        # Resolve to real path for consistent validation
+        real_file_path = os.path.realpath(file_path)
+
+        # Security check
+        if not self._is_path_allowed(real_file_path):
+            logger.warning(f"Re-indexing skipped: Path not allowed {real_file_path}")
+            return
+
         try:
-            logger.info(f"Reindexing: {file_path}")
+            logger.info(f"Reindexing: {real_file_path}")
             # Use the new reindex_document method which removes old chunks first
-            result = self.rag.reindex_document(file_path)
+            result = self.rag.reindex_document(real_file_path)
             if result.get("success"):
                 self.indexed_files.add(file_path)
-                logger.info(f"Successfully reindexed {file_path}")
+                logger.info(f"Successfully reindexed {real_file_path}")
             else:
                 error = result.get("error", "Unknown error")
-                logger.error(f"Failed to reindex {file_path}: {error}")
+                logger.error(f"Failed to reindex {real_file_path}: {error}")
         except Exception as e:
-            logger.error(f"Failed to reindex {file_path}: {e}")
+            logger.error(f"Failed to reindex {real_file_path}: {e}")
 
     def stop_watching(self) -> None:
         """Stop all file system observers."""

gaia/agents/chat/app.py

@@ -370,6 +370,10 @@ def interactive_mode(agent: ChatAgent):
                             f"\n📊 Summary: {success_count}/{len(doc_files)} documents indexed successfully"
                         )
 
+                        # Update system prompt to include newly indexed documents
+                        if success_count > 0:
+                            agent.update_system_prompt()
+
                     else:
                         # Single file
                         if not os.path.exists(arg):
@@ -417,6 +421,9 @@ def interactive_mode(agent: ChatAgent):
                                 )
                                 print(f"Total Chunks: {result.get('total_chunks', 0)}")
                                 print("=" * 60)
+
+                                # Update system prompt to include newly indexed document
+                                agent.update_system_prompt()
                             else:
                                 # Display error
                                 print("❌ INDEXING FAILED")

gaia/agents/chat/tools/rag_tools.py

@@ -73,6 +73,7 @@ class RAGToolsMixin:
         from gaia.agents.base.tools import tool
 
         @tool(
+            atomic=True,
             name="query_documents",
             description="Query indexed documents using RAG to find relevant information. Returns document chunks that the agent should use to answer the user's question.",
             parameters={
@@ -474,6 +475,7 @@ class RAGToolsMixin:
                 }
 
         @tool(
+            atomic=True,
             name="query_specific_file",
             description="Query a SPECIFIC file by name for targeted, fast retrieval. Use when user mentions a specific file or needs information from one document.",
             parameters={
@@ -865,6 +867,7 @@ class RAGToolsMixin:
                 }
 
         @tool(
+            atomic=True,
             name="search_indexed_chunks",
             description="Search for exact text patterns within RAG-indexed document chunks. Use for finding specific phrases in indexed documents.",
             parameters={
@@ -1070,12 +1073,20 @@ class RAGToolsMixin:
                 if not os.path.exists(file_path):
                     return {"status": "error", "error": f"File not found: {file_path}"}
 
-                # Validate path with user confirmation
-                if not self.session_manager.validate_path(file_path, operation="index"):
-                    return {"status": "error", "error": f"Access denied: {file_path}"}
+                # Resolve to real path for consistent validation
+                real_file_path = os.path.realpath(file_path)
+
+                # Validate path with ChatAgent's internal logic (which uses allowed_paths)
+                if hasattr(self, "_is_path_allowed"):
+                    if not self._is_path_allowed(real_file_path):
+                        return {
+                            "status": "error",
+                            "error": f"Access denied: {real_file_path} is not in allowed paths",
+                        }
 
                 # Index the document (now returns dict with stats)
-                result = self.rag.index_document(file_path)
+                # Use real_file_path to ensure consistency in RAG index
+                result = self.rag.index_document(real_file_path)
 
                 if result.get("success"):
                     self.indexed_files.add(file_path)
@@ -1087,8 +1098,8 @@ class RAGToolsMixin:
                             self.session_manager.save_session(self.current_session)
 
                     # Update system prompt to include the new document
-                    if hasattr(self, "_update_system_prompt"):
-                        self._update_system_prompt()
+                    if hasattr(self, "update_system_prompt"):
+                        self.update_system_prompt()
 
                     # Return detailed stats from RAG SDK
                     return {
@@ -1123,6 +1134,7 @@ class RAGToolsMixin:
                 }
 
         @tool(
+            atomic=True,
             name="list_indexed_documents",
             description="List all currently indexed documents",
             parameters={},
@@ -1147,6 +1159,7 @@ class RAGToolsMixin:
                 }
 
         @tool(
+            atomic=True,
             name="rag_status",
             description="Get the status of the RAG system",
             parameters={},
@@ -1511,6 +1524,7 @@ Use the {summary_type} style. Ensure page references from section summaries are
         # This provides shared file search functionality across all agents
 
         @tool(
+            atomic=True,
             name="dump_document",
             description="Export the cached extracted text from an indexed document to a markdown file. Useful for reviewing extracted content or debugging.",
             parameters={
@@ -1620,6 +1634,7 @@ Use the {summary_type} style. Ensure page references from section summaries are
                 }
 
         @tool(
+            atomic=True,
             name="index_directory",
             description="Index all supported files in a directory. Supports PDF, TXT, CSV, JSON, and code files.",
             parameters={
@@ -1704,8 +1719,8 @@ Use the {summary_type} style. Ensure page references from section summaries are
                         skipped_files.append(str(file_path))
 
                 # Update system prompt after indexing directory
-                if indexed_files and hasattr(self, "_update_system_prompt"):
-                    self._update_system_prompt()
+                if indexed_files and hasattr(self, "update_system_prompt"):
+                    self.update_system_prompt()
 
                 return {
                     "status": "success",

gaia/agents/chat/tools/shell_tools.py

@@ -102,6 +102,7 @@ class ShellToolsMixin:
         from gaia.agents.base.tools import tool
 
         @tool(
+            atomic=True,
             name="run_shell_command",
             description="Execute a shell/terminal command. Useful for listing directories (ls/dir), checking files (cat, stat), finding files (find), text processing (grep, head, tail), and navigation (pwd).",
             parameters={

gaia/agents/code/prompts/code_patterns.py

@@ -1278,8 +1278,7 @@ def generate_field_display(fields: dict, max_fields: int = 3) -> str:
     # Generate checkbox + title combo for boolean fields (e.g., completed todo)
     if boolean_field and title_field:
         # Render checkbox with title that has strikethrough when boolean is true
-        display_fields.append(
-            f"""<div className="flex items-center gap-4">
+        display_fields.append(f"""<div className="flex items-center gap-4">
                     <div className="relative">
                       <input
                         type="checkbox"
@@ -1296,8 +1295,7 @@ def generate_field_display(fields: dict, max_fields: int = 3) -> str:
                     <h3 className={{`font-semibold text-lg ${{item.{boolean_field} ? "line-through text-slate-500" : "text-slate-100"}}`}}>
                       {{item.{title_field}}}
                     </h3>
-                  </div>"""
-        )
+                  </div>""")
     elif title_field:
         # Just render title without checkbox
         display_fields.append(

gaia/agents/docker/agent.py

@@ -7,6 +7,7 @@ Docker Agent for GAIA.
 This agent provides an intelligent interface for containerizing applications,
 generating Dockerfiles, and managing Docker containers through natural language commands.
 """
+
 import json
 import logging
 import subprocess

gaia/agents/emr/agent.py

@@ -155,8 +155,7 @@ class MedicalIntakeAgent(Agent, DatabaseMixin, FileWatcherMixin):
         """
         try:
             # Get aggregate stats from patients table
-            result = self.query(
-                """
+            result = self.query("""
                 SELECT
                     COUNT(*) as total_patients,
                     COALESCE(SUM(processing_time_seconds), 0) as total_processing_time,
@@ -164,8 +163,7 @@ class MedicalIntakeAgent(Agent, DatabaseMixin, FileWatcherMixin):
                     SUM(CASE WHEN is_new_patient = 1 THEN 1 ELSE 0 END) as new_patients,
                     SUM(CASE WHEN is_new_patient = 0 THEN 1 ELSE 0 END) as returning_patients
                 FROM patients
-                """
-            )
+                """)
 
             if result and result[0]:
                 stats = result[0]
@@ -327,7 +325,7 @@ class MedicalIntakeAgent(Agent, DatabaseMixin, FileWatcherMixin):
         """Get or create VLM client (lazy initialization)."""
         if self._vlm is None:
             try:
-                from gaia.llm.vlm_client import VLMClient
+                from gaia.llm import VLMClient
 
                 self.console.print_model_loading(self._vlm_model)
                 self._vlm = VLMClient(vlm_model=self._vlm_model)

gaia/agents/emr/cli.py

@@ -636,7 +636,7 @@ def cmd_test(args):
 
     from PIL import Image
 
-    from gaia.llm.vlm_client import VLMClient
+    from gaia.llm import VLMClient
 
     file_path = Path(args.file)
     if not file_path.exists():

gaia/agents/emr/dashboard/server.py

@@ -595,8 +595,7 @@ def create_app(
             """
             if search:
                 results = _agent_instance.query(
-                    base_query
-                    + """
+                    base_query + """
                     WHERE p.first_name LIKE :search OR p.last_name LIKE :search
                     ORDER BY p.created_at DESC
                     LIMIT :limit OFFSET :offset
@@ -605,8 +604,7 @@ def create_app(
                 )
             else:
                 results = _agent_instance.query(
-                    base_query
-                    + """
+                    base_query + """
                     ORDER BY p.created_at DESC
                     LIMIT :limit OFFSET :offset
                     """,

gaia/apps/llm/app.py

@@ -82,6 +82,10 @@ def main(
         stream: Whether to stream the response
         base_url: Base URL for local LLM server (defaults to LEMONADE_BASE_URL env var)
     """
+    from rich.console import Console
+
+    console = Console()
+
     if not query:
         raise ValueError("Query is required")
 
@@ -91,14 +95,21 @@ def main(
     )
 
     if stream:
-        # Handle streaming response
+        # Handle streaming response with Rich formatting
+        console.print()
+        console.print("[bold cyan]🤖 gaia:[/bold cyan] ", end="")
         full_response = ""
         for chunk in response:
-            print(chunk, end="", flush=True)
-            full_response += chunk
+            if chunk:  # Skip None chunks
+                print(chunk, end="", flush=True)
+                full_response += chunk
         print()  # Add newline
+        console.print()
         return full_response
     else:
+        console.print()
+        console.print(f"[bold cyan]🤖 gaia:[/bold cyan] {response}")
+        console.print()
         return response
 
 

gaia/chat/app.py

@@ -212,8 +212,7 @@ def print_integration_examples():
     print("INTEGRATION EXAMPLES")
     print("=" * 60)
 
-    print(
-        """
+    print("""
 Basic Integration:
 ```python
 from gaia.chat.sdk import ChatSDK, ChatConfig
@@ -297,8 +296,7 @@ responses = quick_chat_with_memory([
     "What's my name?"
 ], assistant_name="Gaia")
 ```
-"""
-    )
+""")
 
 
 async def main():