Merge pull request usnavy13#43 from usnavy13/dev

Merge dev into main: File mounting, session management, and testing improvements

Author: usnavy13

docker/repl_server.py

@@ -291,7 +291,8 @@ def execute_code(
     timeout: int = 30,
     working_dir: str = "/mnt/data",
     initial_state: str = None,
-    capture_state: bool = False
+    capture_state: bool = False,
+    args: list = None
 ) -> dict:
     """Execute code in isolated namespace and capture output.
 
@@ -301,6 +302,7 @@ def execute_code(
         working_dir: Working directory for execution
         initial_state: Base64-encoded cloudpickle state to restore before execution
         capture_state: Whether to capture and return state after execution
+        args: Optional list of command line arguments
 
     Returns:
         Dict with exit_code, stdout, stderr, execution_time_ms, and optionally state/state_errors
@@ -330,6 +332,12 @@ def execute_code(
 
     exit_code = 0
 
+    # Save and set sys.argv if args provided
+    original_argv = sys.argv
+    if args is not None:
+        # Set sys.argv to [script_name] + args (matches file-based execution)
+        sys.argv = ['/mnt/data/code.py'] + list(args)
+
     # Set up timeout handler
     old_handler = signal.signal(signal.SIGALRM, timeout_handler)
     signal.alarm(timeout)
@@ -370,6 +378,9 @@ def execute_code(
         signal.alarm(0)
         signal.signal(signal.SIGALRM, old_handler)
 
+        # Restore sys.argv
+        sys.argv = original_argv
+
         # Restore working directory
         try:
             os.chdir(original_dir)
@@ -503,14 +514,16 @@ def main():
             working_dir = request.get("working_dir", "/mnt/data")
             initial_state = request.get("initial_state")
             capture_state = request.get("capture_state", False)
+            args = request.get("args")  # List of command line arguments
 
             # Execute code with optional state persistence
             response = execute_code(
                 code,
                 timeout,
                 working_dir,
                 initial_state=initial_state,
-                capture_state=capture_state
+                capture_state=capture_state,
+                args=args
             )
 
             # Send response

src/api/files.py

@@ -14,9 +14,9 @@
 
 # Local application imports
 from ..config import settings
-from ..dependencies import FileServiceDep
+from ..dependencies import FileServiceDep, SessionServiceDep
+from ..models import SessionCreate
 from ..services.execution.output import OutputProcessor
-from ..utils.id_generator import generate_session_id
 
 logger = structlog.get_logger(__name__)
 router = APIRouter()
@@ -55,6 +55,7 @@ async def upload_file(
     files: Optional[List[UploadFile]] = File(None),
     entity_id: Optional[str] = Form(None),
     file_service: FileServiceDep = None,
+    session_service: SessionServiceDep = None,
 ):
     """Upload files with multipart form handling - LibreChat compatible.
 
@@ -112,8 +113,17 @@ async def upload_file(
 
         uploaded_files = []
 
-        # Create a session ID for this upload
-        session_id = generate_session_id()
+        # Create a real session for file uploads
+        # This enables session reuse when files are referenced in /exec
+        metadata = {}
+        if entity_id:
+            metadata["entity_id"] = entity_id
+        session = await session_service.create_session(SessionCreate(metadata=metadata))
+        session_id = session.session_id
+
+        # Determine if this is an agent file (uploaded with entity_id)
+        # Agent files are read-only and cannot be modified by user code
+        is_agent_file = entity_id is not None and len(entity_id) > 0
 
         for file in upload_files:
             # Read file content
@@ -125,6 +135,7 @@ async def upload_file(
                 filename=file.filename,
                 content=content,
                 content_type=file.content_type,
+                is_agent_file=is_agent_file,
             )
 
             # Sanitize filename to match what will be used in container

src/models/exec.py

@@ -14,6 +14,7 @@ class FileRef(BaseModel):
     id: str
     name: str
     path: Optional[str] = None  # Make path optional
+    session_id: Optional[str] = None  # Session ID for cross-message file persistence
 
 
 class RequestFile(BaseModel):
@@ -22,6 +23,10 @@ class RequestFile(BaseModel):
     id: str
     session_id: str
     name: str
+    restore_state: bool = Field(
+        default=False,
+        description="If true, restore Python state from when this file was last used",
+    )
 
 
 class ExecRequest(BaseModel):

src/models/execution.py

@@ -79,6 +79,9 @@ class ExecuteCodeRequest(BaseModel):
     timeout: Optional[int] = Field(
         default=None, description="Execution timeout in seconds"
     )
+    args: Optional[List[str]] = Field(
+        default=None, description="Command line arguments to pass to the executed code"
+    )
 
 
 class ExecuteCodeResponse(BaseModel):

src/models/files.py

@@ -40,6 +40,18 @@ class FileInfo(BaseModel):
     content_type: str
     created_at: datetime
     path: str = Field(..., description="File path in the session")
+    # State restoration fields (for Python state-file linking)
+    execution_id: Optional[str] = Field(
+        default=None, description="ID of the execution that created/last used this file"
+    )
+    state_hash: Optional[str] = Field(
+        default=None,
+        description="SHA256 hash of the Python state when this file was last used",
+    )
+    last_used_at: Optional[datetime] = Field(
+        default=None,
+        description="Timestamp of when this file was last used in an execution",
+    )
 
     class Config:
         json_encoders = {datetime: lambda v: v.isoformat()}

src/services/container/manager.py

@@ -365,7 +365,7 @@ async def copy_to_container(
             return False
 
     async def copy_content_to_container(
-        self, container: Container, content: bytes, dest_path: str
+        self, container: Container, content: bytes, dest_path: str, language: str = "py"
     ) -> bool:
         """Copy content directly to container without tempfiles.
 
@@ -376,19 +376,25 @@ async def copy_content_to_container(
             container: Target container
             content: File content as bytes
             dest_path: Destination path in container (e.g., /mnt/data/file.py)
+            language: Programming language (used to set correct file ownership)
 
         Returns:
             True if successful, False otherwise
         """
         try:
             loop = asyncio.get_event_loop()
 
+            # Get user ID for this language's container
+            user_id = self.get_user_id_for_language(language)
+
             # Build in-memory tar archive
             tar_buffer = io.BytesIO()
             with tarfile.open(fileobj=tar_buffer, mode="w") as tar:
                 tarinfo = tarfile.TarInfo(name=dest_path.split("/")[-1])
                 tarinfo.size = len(content)
                 tarinfo.mode = 0o644
+                tarinfo.uid = user_id
+                tarinfo.gid = user_id
                 tar.addfile(tarinfo, io.BytesIO(content))
 
             tar_buffer.seek(0)

src/services/container/repl_executor.py

@@ -43,6 +43,7 @@ async def execute(
         code: str,
         timeout: int = None,
         working_dir: str = "/mnt/data",
+        args: Optional[List[str]] = None,
     ) -> Tuple[int, str, str]:
         """Execute code in running REPL.
 
@@ -51,6 +52,7 @@ async def execute(
             code: Python code to execute
             timeout: Maximum execution time in seconds
             working_dir: Working directory for code execution
+            args: Optional list of command line arguments
 
         Returns:
             Tuple of (exit_code, stdout, stderr)
@@ -62,6 +64,8 @@ async def execute(
 
         # Build request
         request = {"code": code, "timeout": timeout, "working_dir": working_dir}
+        if args:
+            request["args"] = args
         request_json = json.dumps(request)
         request_bytes = request_json.encode("utf-8") + DELIMITER
 
@@ -109,6 +113,7 @@ async def execute_with_state(
         working_dir: str = "/mnt/data",
         initial_state: Optional[str] = None,
         capture_state: bool = False,
+        args: Optional[List[str]] = None,
     ) -> Tuple[int, str, str, Optional[str], List[str]]:
         """Execute code in running REPL with optional state persistence.
 
@@ -119,6 +124,7 @@ async def execute_with_state(
             working_dir: Working directory for code execution
             initial_state: Base64-encoded state to restore before execution
             capture_state: Whether to capture state after execution
+            args: Optional list of command line arguments
 
         Returns:
             Tuple of (exit_code, stdout, stderr, new_state, state_errors)
@@ -138,6 +144,9 @@ async def execute_with_state(
         if capture_state:
             request["capture_state"] = True
 
+        if args:
+            request["args"] = args
+
         request_json = json.dumps(request)
         request_bytes = request_json.encode("utf-8") + DELIMITER
 

src/services/execution/runner.py

@@ -1,6 +1,7 @@
 """Code execution runner - core execution logic."""
 
 import asyncio
+import shlex
 from datetime import datetime, timedelta
 from pathlib import Path
 from typing import Any, Dict, List, Optional, Tuple
@@ -152,7 +153,7 @@ async def execute(
 
             # Mount files if provided
             if files:
-                await self._mount_files_to_container(container, files)
+                await self._mount_files_to_container(container, files, request.language)
 
             # Execute the code
             start_time = datetime.utcnow()
@@ -185,11 +186,16 @@ async def execute(
                     request.timeout or settings.max_execution_time,
                     initial_state=initial_state,
                     capture_state=capture_state,
+                    args=request.args,
                 )
             else:
                 # Standard execution (no state persistence)
                 exit_code, stdout, stderr = await self._execute_code_in_container(
-                    container, request.code, request.language, request.timeout
+                    container,
+                    request.code,
+                    request.language,
+                    request.timeout,
+                    args=request.args,
                 )
             end_time = datetime.utcnow()
 
@@ -435,12 +441,20 @@ async def _execute_code_in_container(
         code: str,
         language: str,
         timeout: Optional[int] = None,
+        args: Optional[List[str]] = None,
     ) -> Tuple[int, str, str]:
         """Execute code in the container.
 
         For REPL-enabled containers (Python with REPL mode), uses the fast
         REPL executor which communicates with the pre-warmed Python interpreter.
         For other containers, uses the standard execution path.
+
+        Args:
+            container: Docker container to execute in
+            code: Code to execute
+            language: Programming language
+            timeout: Execution timeout in seconds
+            args: Optional list of command line arguments
         """
         language = language.lower()
         lang_config = get_language(language)
@@ -454,7 +468,9 @@ async def _execute_code_in_container(
             logger.debug(
                 "Using REPL executor", container_id=container.id[:12], language=language
             )
-            return await self._execute_via_repl(container, code, execution_timeout)
+            return await self._execute_via_repl(
+                container, code, execution_timeout, args=args
+            )
 
         # Standard execution path for non-REPL containers
         exec_command = lang_config.execution_command
@@ -480,13 +496,20 @@ async def _execute_code_in_container(
         # Direct memory-to-container transfer (no tempfiles)
         dest_path = f"/mnt/data/{code_filename}"
         if not await self.container_manager.copy_content_to_container(
-            container, code.encode("utf-8"), dest_path
+            container, code.encode("utf-8"), dest_path, language=language
         ):
             return 1, "", "Failed to write code file to container"
 
+        # Build execution command with args if provided
+        final_command = exec_command
+        if args:
+            # Safely quote each argument to prevent shell injection
+            quoted_args = " ".join(shlex.quote(arg) for arg in args)
+            final_command = f"{exec_command} {quoted_args}"
+
         return await self.container_manager.execute_command(
             container,
-            exec_command,
+            final_command,
             timeout=execution_timeout,
             language=language,
             working_dir="/mnt/data",
@@ -521,21 +544,26 @@ def _is_repl_container(self, container: Container, language: str) -> bool:
             return False
 
     async def _execute_via_repl(
-        self, container: Container, code: str, timeout: int
+        self,
+        container: Container,
+        code: str,
+        timeout: int,
+        args: Optional[List[str]] = None,
     ) -> Tuple[int, str, str]:
         """Execute code via REPL server in container.
 
         Args:
             container: Docker container with REPL server running
             code: Python code to execute
             timeout: Maximum execution time in seconds
+            args: Optional list of command line arguments
 
         Returns:
             Tuple of (exit_code, stdout, stderr)
         """
         repl_executor = REPLExecutor(self.container_manager.client)
         return await repl_executor.execute(
-            container, code, timeout=timeout, working_dir="/mnt/data"
+            container, code, timeout=timeout, working_dir="/mnt/data", args=args
         )
 
     async def _execute_via_repl_with_state(
@@ -545,6 +573,7 @@ async def _execute_via_repl_with_state(
         timeout: int,
         initial_state: Optional[str] = None,
         capture_state: bool = True,
+        args: Optional[List[str]] = None,
     ) -> Tuple[int, str, str, Optional[str], List[str]]:
         """Execute code via REPL server with state persistence.
 
@@ -554,6 +583,7 @@ async def _execute_via_repl_with_state(
             timeout: Maximum execution time in seconds
             initial_state: Base64-encoded state to restore before execution
             capture_state: Whether to capture state after execution
+            args: Optional list of command line arguments
 
         Returns:
             Tuple of (exit_code, stdout, stderr, new_state, state_errors)
@@ -566,10 +596,11 @@ async def _execute_via_repl_with_state(
             working_dir="/mnt/data",
             initial_state=initial_state,
             capture_state=capture_state,
+            args=args,
         )
 
     async def _mount_files_to_container(
-        self, container: Container, files: List[Dict[str, Any]]
+        self, container: Container, files: List[Dict[str, Any]], language: str = "py"
     ) -> None:
         """Mount files to container workspace."""
         try:
@@ -599,7 +630,7 @@ async def _mount_files_to_container(
                         dest_path = f"/mnt/data/{normalized_filename}"
 
                         if await self.container_manager.copy_content_to_container(
-                            container, file_content, dest_path
+                            container, file_content, dest_path, language=language
                         ):
                             logger.info(
                                 "Mounted file",