fractal-server 2.5.0a1__py3-none-any.whl → 2.5.2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.5.0a1"
+__VERSION__ = "2.5.2"

fractal_server/app/routes/api/v2/submit.py

@@ -238,6 +238,18 @@ async def apply_workflow(
     await db.merge(job)
     await db.commit()
 
+    # User appropriate FractalSSH object
+    if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
+        ssh_credentials = dict(
+            user=settings.FRACTAL_SLURM_SSH_USER,
+            host=settings.FRACTAL_SLURM_SSH_HOST,
+            key_path=settings.FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH,
+        )
+        fractal_ssh_list = request.app.state.fractal_ssh_list
+        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
+    else:
+        fractal_ssh = None
+
     background_tasks.add_task(
         submit_workflow,
         workflow_id=workflow.id,
@@ -246,7 +258,7 @@ async def apply_workflow(
         worker_init=job.worker_init,
         slurm_user=user.slurm_user,
         user_cache_dir=user.cache_dir,
-        fractal_ssh=request.app.state.fractal_ssh,
+        fractal_ssh=fractal_ssh,
     )
     request.app.state.jobsV2.append(job.id)
     logger.info(

fractal_server/app/routes/api/v2/task_collection.py

@@ -124,11 +124,20 @@ async def collect_tasks_pip(
         db.add(state)
         await db.commit()
 
+        # User appropriate FractalSSH object
+        ssh_credentials = dict(
+            user=settings.FRACTAL_SLURM_SSH_USER,
+            host=settings.FRACTAL_SLURM_SSH_HOST,
+            key_path=settings.FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH,
+        )
+        fractal_ssh_list = request.app.state.fractal_ssh_list
+        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
+
         background_tasks.add_task(
             background_collect_pip_ssh,
             state.id,
             task_pkg,
-            request.app.state.fractal_ssh,
+            fractal_ssh,
         )
 
         response.status_code = status.HTTP_201_CREATED

fractal_server/app/routes/api/v2/task_collection_custom.py

@@ -20,12 +20,12 @@ from ....schemas.v2 import TaskCreateV2
 from ....schemas.v2 import TaskReadV2
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_verified_user
+from fractal_server.string_tools import validate_cmd
 from fractal_server.tasks.v2.background_operations import _insert_tasks
 from fractal_server.tasks.v2.background_operations import (
     _prepare_tasks_metadata,
 )
 
-
 router = APIRouter()
 
 logger = set_logger(__name__)
@@ -74,6 +74,7 @@ async def collect_task_custom(
         package_name_underscore = task_collect.package_name.replace("-", "_")
         # Note that python_command is then used as part of a subprocess.run
         # statement: be careful with mixing `'` and `"`.
+        validate_cmd(package_name_underscore)
         python_command = (
             "import importlib.util; "
             "from pathlib import Path; "

fractal_server/app/runner/compress_folder.py

@@ -48,7 +48,7 @@ def create_tar_archive(
         "."
     )
     logger.debug(f"cmd tar:\n{cmd_tar}")
-    run_subprocess(cmd=cmd_tar, logger_name=logger_name)
+    run_subprocess(cmd=cmd_tar, logger_name=logger_name, allow_char="*")
 
 
 def remove_temp_subfolder(subfolder_path_tmp_copy: Path, logger_name: str):

fractal_server/app/runner/executors/slurm/ssh/executor.py

@@ -163,17 +163,34 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         settings = Inject(get_settings)
         self.python_remote = settings.FRACTAL_SLURM_WORKER_PYTHON
         if self.python_remote is None:
+            self._stop_and_join_wait_thread()
             raise ValueError("FRACTAL_SLURM_WORKER_PYTHON is not set. Exit.")
 
         # Initialize connection and perform handshake
         self.fractal_ssh = fractal_ssh
         logger.warning(self.fractal_ssh)
-        self.handshake()
+        try:
+            self.handshake()
+        except Exception as e:
+            logger.warning(
+                "Stop/join waiting thread and then "
+                f"re-raise original error {str(e)}"
+            )
+            self._stop_and_join_wait_thread()
+            raise e
 
         # Set/validate parameters for SLURM submission scripts
         self.slurm_account = slurm_account
         self.common_script_lines = common_script_lines or []
-        self._validate_common_script_lines()
+        try:
+            self._validate_common_script_lines()
+        except Exception as e:
+            logger.warning(
+                "Stop/join waiting thread and then "
+                f"re-raise original error {str(e)}"
+            )
+            self._stop_and_join_wait_thread()
+            raise e
 
         # Set/initialize some more options
         self.keep_pickle_files = keep_pickle_files
@@ -1385,6 +1402,10 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
             self.fractal_ssh.run_command(cmd=scancel_command)
         logger.debug("Executor shutdown: end")
 
+    def _stop_and_join_wait_thread(self):
+        self.wait_thread.stop()
+        self.wait_thread.join()
+
     def __exit__(self, *args, **kwargs):
         """
         See
@@ -1393,8 +1414,7 @@ class FractalSlurmSSHExecutor(SlurmExecutor):
         logger.debug(
             "[FractalSlurmSSHExecutor.__exit__] Stop and join `wait_thread`"
         )
-        self.wait_thread.stop()
-        self.wait_thread.join()
+        self._stop_and_join_wait_thread()
         logger.debug("[FractalSlurmSSHExecutor.__exit__] End")
 
     def run_squeue(self, job_ids):

fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py

@@ -20,6 +20,7 @@ import subprocess  # nosec
 from typing import Optional
 
 from ......logger import set_logger
+from fractal_server.string_tools import validate_cmd
 
 logger = set_logger(__name__)
 
@@ -47,6 +48,7 @@ def _run_command_as_user(
     Returns:
         res: The return value from `subprocess.run`.
     """
+    validate_cmd(cmd)
     logger.debug(f'[_run_command_as_user] {user=}, cmd="{cmd}"')
     if user:
         new_cmd = f"sudo --set-home --non-interactive -u {user} {cmd}"

fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -47,6 +47,7 @@ from ._subprocess_run_as_user import _path_exists_as_user
 from ._subprocess_run_as_user import _run_command_as_user
 from fractal_server import __VERSION__
 from fractal_server.app.runner.components import _COMPONENT_KEY_
+from fractal_server.string_tools import validate_cmd
 
 
 logger = set_logger(__name__)
@@ -65,6 +66,7 @@ def _subprocess_run_or_raise(full_command: str) -> Optional[CompletedProcess]:
     Returns:
         The actual `CompletedProcess` output of `subprocess.run`.
     """
+    validate_cmd(full_command)
     try:
         output = subprocess.run(  # nosec
             shlex.split(full_command),
@@ -257,6 +259,7 @@ class FractalSlurmExecutor(SlurmExecutor):
                 for line in self.common_script_lines
                 if line.startswith("#SBATCH --account=")
             )
+            self._stop_and_join_wait_thread()
             raise RuntimeError(
                 "Invalid line in `FractalSlurmExecutor.common_script_lines`: "
                 f"'{invalid_line}'.\n"
@@ -1266,6 +1269,7 @@ class FractalSlurmExecutor(SlurmExecutor):
             pre_command = f"sudo --non-interactive -u {self.slurm_user}"
             submit_command = f"scancel {scancel_string}"
             full_command = f"{pre_command} {submit_command}"
+            validate_cmd(full_command)
             logger.debug(f"Now execute `{full_command}`")
             try:
                 subprocess.run(  # nosec
@@ -1284,6 +1288,10 @@ class FractalSlurmExecutor(SlurmExecutor):
 
         logger.debug("Executor shutdown: end")
 
+    def _stop_and_join_wait_thread(self):
+        self.wait_thread.stop()
+        self.wait_thread.join()
+
     def __exit__(self, *args, **kwargs):
         """
         See
@@ -1292,6 +1300,5 @@ class FractalSlurmExecutor(SlurmExecutor):
         logger.debug(
             "[FractalSlurmExecutor.__exit__] Stop and join `wait_thread`"
         )
-        self.wait_thread.stop()
-        self.wait_thread.join()
+        self._stop_and_join_wait_thread()
         logger.debug("[FractalSlurmExecutor.__exit__] End")

fractal_server/app/runner/run_subprocess.py

@@ -3,11 +3,15 @@ import subprocess  # nosec
 from typing import Optional
 
 from fractal_server.logger import get_logger
+from fractal_server.string_tools import validate_cmd
 
 
 def run_subprocess(
-    cmd: str, logger_name: Optional[str] = None
+    cmd: str,
+    allow_char: Optional[str] = None,
+    logger_name: Optional[str] = None,
 ) -> subprocess.CompletedProcess:
+    validate_cmd(cmd, allow_char=allow_char)
     logger = get_logger(logger_name)
     try:
         res = subprocess.run(  # nosec

fractal_server/app/runner/v1/_common.py

@@ -31,6 +31,7 @@ from .common import write_args_file
 from fractal_server.app.runner.filenames import HISTORY_FILENAME
 from fractal_server.app.runner.filenames import METADATA_FILENAME
 from fractal_server.app.runner.task_files import get_task_file_paths
+from fractal_server.string_tools import validate_cmd
 
 
 def no_op_submit_setup_call(
@@ -77,6 +78,7 @@ def _call_command_wrapper(cmd: str, stdout: Path, stderr: Path) -> None:
                             TERM or KILL signal)
     """
 
+    validate_cmd(cmd)
     # Verify that task command is executable
     if shutil.which(shlex_split(cmd)[0]) is None:
         msg = (

fractal_server/app/runner/v2/runner_functions_low_level.py

@@ -12,6 +12,7 @@ from ..exceptions import JobExecutionError
 from ..exceptions import TaskExecutionError
 from fractal_server.app.models.v2 import WorkflowTaskV2
 from fractal_server.app.runner.task_files import get_task_file_paths
+from fractal_server.string_tools import validate_cmd
 
 
 def _call_command_wrapper(cmd: str, log_path: Path) -> None:
@@ -25,6 +26,10 @@ def _call_command_wrapper(cmd: str, log_path: Path) -> None:
                             exit code (e.g. due to the subprocess receiving a
                             TERM or KILL signal)
     """
+    try:
+        validate_cmd(cmd)
+    except ValueError as e:
+        raise TaskExecutionError(f"Invalid command. Original error: {str(e)}")
 
     # Verify that task command is executable
     if shutil.which(shlex_split(cmd)[0]) is None:

fractal_server/app/schemas/user.py

@@ -10,7 +10,7 @@ from pydantic.types import StrictStr
 from ._validators import val_absolute_path
 from ._validators import val_unique_list
 from ._validators import valstr
-
+from fractal_server.string_tools import validate_cmd
 
 __all__ = (
     "UserRead",
@@ -77,14 +77,16 @@ class UserUpdate(schemas.BaseUserUpdate):
         valstr("slurm_user")
     )
     _username = validator("username", allow_reuse=True)(valstr("username"))
-    _cache_dir = validator("cache_dir", allow_reuse=True)(
-        val_absolute_path("cache_dir")
-    )
 
     _slurm_accounts = validator("slurm_accounts", allow_reuse=True)(
         val_unique_list("slurm_accounts")
     )
 
+    @validator("cache_dir")
+    def cache_dir_validator(cls, value):
+        validate_cmd(value)
+        return val_absolute_path("cache_dir")(value)
+
     @validator(
         "is_active",
         "is_verified",
@@ -115,9 +117,10 @@ class UserUpdateStrict(BaseModel, extra=Extra.forbid):
         val_unique_list("slurm_accounts")
     )
 
-    _cache_dir = validator("cache_dir", allow_reuse=True)(
-        val_absolute_path("cache_dir")
-    )
+    @validator("cache_dir")
+    def cache_dir_validator(cls, value):
+        validate_cmd(value)
+        return val_absolute_path("cache_dir")(value)
 
 
 class UserUpdateWithNewGroupIds(UserUpdate):
@@ -157,6 +160,8 @@ class UserCreate(schemas.BaseUserCreate):
         valstr("slurm_user")
     )
     _username = validator("username", allow_reuse=True)(valstr("username"))
-    _cache_dir = validator("cache_dir", allow_reuse=True)(
-        val_absolute_path("cache_dir")
-    )
+
+    @validator("cache_dir")
+    def cache_dir_validator(cls, value):
+        validate_cmd(value)
+        return val_absolute_path("cache_dir")(value)

fractal_server/app/schemas/v2/dumps.py

@@ -39,14 +39,23 @@ class TaskDumpV2(BaseModel):
 
 
 class WorkflowTaskDumpV2(BaseModel):
+    """
+    Before v2.5.0, WorkflowTaskV2 could have `task_id=task=None` and
+    non-`None` `task_legacy_id` and `task_legacy`. Since these objects
+    may still exist in the database after version updates, we are setting
+    `task_id` and `task` to `Optional` to avoid response-validation errors
+    for the endpoints that GET datasets.
+    Ref issue #1783.
+    """
+
     id: int
     workflow_id: int
     order: Optional[int]
 
     input_filters: Filters
 
-    task_id: int
-    task: TaskDumpV2
+    task_id: Optional[int]
+    task: Optional[TaskDumpV2]
 
 
 class WorkflowDumpV2(BaseModel, extra=Extra.forbid):

fractal_server/app/schemas/v2/task.py

@@ -11,6 +11,7 @@ from pydantic import validator
 
 from .._validators import valdictkeys
 from .._validators import valstr
+from fractal_server.string_tools import validate_cmd
 
 
 class TaskCreateV2(BaseModel, extra=Extra.forbid):
@@ -43,6 +44,11 @@ class TaskCreateV2(BaseModel, extra=Extra.forbid):
                 "Task must have at least one valid command "
                 "(parallel and/or non_parallel)"
             )
+        if command_parallel is not None:
+            validate_cmd(command_parallel)
+        if command_non_parallel is not None:
+            validate_cmd(command_non_parallel)
+
         return values
 
     _name = validator("name", allow_reuse=True)(valstr("name"))

fractal_server/main.py

@@ -92,32 +92,34 @@ async def lifespan(app: FastAPI):
     settings = Inject(get_settings)
 
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-        from fractal_server.ssh._fabric import get_ssh_connection
-        from fractal_server.ssh._fabric import FractalSSH
 
-        connection = get_ssh_connection()
-        app.state.fractal_ssh = FractalSSH(connection=connection)
+        from fractal_server.ssh._fabric import FractalSSHList
+
+        app.state.fractal_ssh_list = FractalSSHList()
+
         logger.info(
-            f"Created SSH connection "
-            f"({app.state.fractal_ssh.is_connected=})."
+            "Added empty FractalSSHList to app.state "
+            f"(id={id(app.state.fractal_ssh_list)})."
         )
     else:
-        app.state.fractal_ssh = None
+        app.state.fractal_ssh_list = None
 
     config_uvicorn_loggers()
     logger.info("End application startup")
     reset_logger_handlers(logger)
+
     yield
+
     logger = get_logger("fractal_server.lifespan")
     logger.info("Start application shutdown")
 
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
         logger.info(
-            f"Closing SSH connection "
-            f"(current: {app.state.fractal_ssh.is_connected=})."
+            "Close FractalSSH connections "
+            f"(current size: {app.state.fractal_ssh_list.size})."
         )
 
-        app.state.fractal_ssh.close()
+        app.state.fractal_ssh_list.close_all()
 
     logger.info(
         f"Current worker with pid {os.getpid()} is shutting down. "

fractal_server/ssh/_fabric.py

@@ -16,19 +16,21 @@ from paramiko.ssh_exception import NoValidConnectionsError
 
 from ..logger import get_logger
 from ..logger import set_logger
-from fractal_server.config import get_settings
-from fractal_server.syringe import Inject
+from fractal_server.string_tools import validate_cmd
 
 
 class FractalSSHTimeoutError(RuntimeError):
     pass
 
 
+class FractalSSHListTimeoutError(RuntimeError):
+    pass
+
+
 logger = set_logger(__name__)
 
 
 class FractalSSH(object):
-
     """
     FIXME SSH: Fix docstring
 
@@ -110,7 +112,6 @@ class FractalSSH(object):
     def run(
         self, *args, lock_timeout: Optional[float] = None, **kwargs
     ) -> Any:
-
         actual_lock_timeout = self.default_lock_timeout
         if lock_timeout is not None:
             actual_lock_timeout = lock_timeout
@@ -137,12 +138,25 @@ class FractalSSH(object):
                 )
 
     def close(self) -> None:
-        return self._connection.close()
+        """
+        Aggressively close `self._connection`.
+
+        When `Connection.is_connected` is `False`, `Connection.close()` does
+        not call `Connection.client.close()`. Thus we do this explicitly here,
+        because we observed cases where `is_connected=False` but the underlying
+        `Transport` object was not closed.
+        """
+
+        self._connection.close()
+
+        if self._connection.client is not None:
+            self._connection.client.close()
 
     def run_command(
         self,
         *,
         cmd: str,
+        allow_char: Optional[str] = None,
         max_attempts: Optional[int] = None,
         base_interval: Optional[int] = None,
         lock_timeout: Optional[int] = None,
@@ -152,6 +166,7 @@ class FractalSSH(object):
 
         Args:
             cmd: Command to be run
+            allow_char: Forbidden chars to allow for this command
             max_attempts:
             base_interval:
             lock_timeout:
@@ -159,6 +174,9 @@ class FractalSSH(object):
         Returns:
             Standard output of the command, if successful.
         """
+
+        validate_cmd(cmd, allow_char=allow_char)
+
         actual_max_attempts = self.default_max_attempts
         if max_attempts is not None:
             actual_max_attempts = max_attempts
@@ -329,36 +347,169 @@ class FractalSSH(object):
                 f.write(content)
 
 
-def get_ssh_connection(
-    *,
-    host: Optional[str] = None,
-    user: Optional[str] = None,
-    key_filename: Optional[str] = None,
-) -> Connection:
+class FractalSSHList(object):
     """
-    Create a `fabric.Connection` object based on fractal-server settings
-    or explicit arguments.
+    Collection of `FractalSSH` objects
 
-    Args:
-        host:
-        user:
-        key_filename:
+    Attributes are all private, and access to this collection must be
+    through methods (mostly the `get` one).
 
-    Returns:
-        Fabric connection object
+    Attributes:
+        _data:
+            Mapping of unique keys (the SSH-credentials tuples) to
+            `FractalSSH` objects.
+        _lock:
+            A `threading.Lock object`, to be acquired when changing `_data`.
+        _timeout: Timeout for `_lock` acquisition.
+        _logger_name: Logger name.
     """
-    settings = Inject(get_settings)
-    if host is None:
-        host = settings.FRACTAL_SLURM_SSH_HOST
-    if user is None:
-        user = settings.FRACTAL_SLURM_SSH_USER
-    if key_filename is None:
-        key_filename = settings.FRACTAL_SLURM_SSH_PRIVATE_KEY_PATH
-
-    connection = Connection(
-        host=host,
-        user=user,
-        forward_agent=False,
-        connect_kwargs={"key_filename": key_filename},
-    )
-    return connection
+
+    _data: dict[tuple[str, str, str], FractalSSH]
+    _lock: Lock
+    _timeout: float
+    _logger_name: str
+
+    def __init__(
+        self,
+        *,
+        timeout: float = 5.0,
+        logger_name: str = "fractal_server.FractalSSHList",
+    ):
+        self._lock = Lock()
+        self._data = {}
+        self._timeout = timeout
+        self._logger_name = logger_name
+        set_logger(self._logger_name)
+
+    @property
+    def logger(self) -> logging.Logger:
+        """
+        This property exists so that we never have to propagate the
+        `Logger` object.
+        """
+        return get_logger(self._logger_name)
+
+    @property
+    def size(self) -> int:
+        """
+        Number of current key-value pairs in `self._data`.
+        """
+        return len(self._data.values())
+
+    def get(self, *, host: str, user: str, key_path: str) -> FractalSSH:
+        """
+        Get the `FractalSSH` for the current credentials, or create one.
+
+        Note: Changing `_data` requires acquiring `_lock`.
+
+        Arguments:
+            host:
+            user:
+            key_path:
+        """
+        key = (host, user, key_path)
+        fractal_ssh = self._data.get(key, None)
+        if fractal_ssh is not None:
+            self.logger.info(
+                f"Return existing FractalSSH object for {user}@{host}"
+            )
+            return fractal_ssh
+        else:
+            self.logger.info(f"Add new FractalSSH object for {user}@{host}")
+            connection = Connection(
+                host=host,
+                user=user,
+                forward_agent=False,
+                connect_kwargs={
+                    "key_filename": key_path,
+                    "look_for_keys": False,
+                },
+            )
+            with self.acquire_lock_with_timeout():
+                self._data[key] = FractalSSH(connection=connection)
+                return self._data[key]
+
+    def contains(
+        self,
+        *,
+        host: str,
+        user: str,
+        key_path: str,
+    ) -> bool:
+        """
+        Return whether a given key is present in the collection.
+
+        Arguments:
+            host:
+            user:
+            key_path:
+        """
+        key = (host, user, key_path)
+        return key in self._data.keys()
+
+    def remove(
+        self,
+        *,
+        host: str,
+        user: str,
+        key_path: str,
+    ) -> None:
+        """
+        Remove a key from `_data` and close the corresponding connection.
+
+        Note: Changing `_data` requires acquiring `_lock`.
+
+        Arguments:
+            host:
+            user:
+            key_path:
+        """
+        key = (host, user, key_path)
+        with self.acquire_lock_with_timeout():
+            self.logger.info(
+                f"Removing FractalSSH object for {user}@{host} "
+                "from collection."
+            )
+            fractal_ssh_obj = self._data.pop(key)
+            self.logger.info(
+                f"Closing FractalSSH object for {user}@{host} "
+                f"({fractal_ssh_obj.is_connected=})."
+            )
+            fractal_ssh_obj.close()
+
+    def close_all(self, *, timeout: float = 5.0):
+        """
+        Close all `FractalSSH` objects in the collection.
+
+        Arguments:
+            timeout:
+                Timeout for `FractalSSH._lock` acquisition, to be obtained
+                before closing.
+        """
+        for key, fractal_ssh_obj in self._data.items():
+            host, user, _ = key[:]
+            self.logger.info(
+                f"Closing FractalSSH object for {user}@{host} "
+                f"({fractal_ssh_obj.is_connected=})."
+            )
+            with fractal_ssh_obj.acquire_timeout(timeout=timeout):
+                fractal_ssh_obj.close()
+
+    @contextmanager
+    def acquire_lock_with_timeout(self) -> Generator[Literal[True], Any, None]:
+        self.logger.debug(
+            f"Trying to acquire lock, with timeout {self._timeout} s"
+        )
+        result = self._lock.acquire(timeout=self._timeout)
+        try:
+            if not result:
+                self.logger.error("Lock was *NOT* acquired.")
+                raise FractalSSHListTimeoutError(
+                    f"Failed to acquire lock within {self._timeout} ss"
+                )
+            self.logger.debug("Lock was acquired.")
+            yield result
+        finally:
+            if result:
+                self._lock.release()
+                self.logger.debug("Lock was released")

fractal_server/string_tools.py

@@ -1,7 +1,12 @@
 import string
+from typing import Optional
 
 __SPECIAL_CHARACTERS__ = f"{string.punctuation}{string.whitespace}"
 
+# List of invalid characters discussed here:
+# https://github.com/fractal-analytics-platform/fractal-server/issues/1647
+__NOT_ALLOWED_FOR_COMMANDS__ = r"`#$&*()\|[]{};<>?!"
+
 
 def sanitize_string(value: str) -> str:
     """
@@ -43,3 +48,23 @@ def slugify_task_name_for_source(task_name: str) -> str:
         Slug-ified task name.
     """
     return task_name.replace(" ", "_").lower()
+
+
+def validate_cmd(command: str, allow_char: Optional[str] = None):
+    """
+    Assert that the provided `command` does not contain any of the forbidden
+    characters for commands
+    (fractal_server.string_tools.__NOT_ALLOWED_FOR_COMMANDS__)
+
+    Args:
+        command: command to validate.
+        allow_char: chars to accept among the forbidden ones
+    """
+    forbidden = set(__NOT_ALLOWED_FOR_COMMANDS__)
+    if allow_char is not None:
+        forbidden = forbidden - set(allow_char)
+    if not forbidden.isdisjoint(set(command)):
+        raise ValueError(
+            f"Command must not contain any of this characters: '{forbidden}'\n"
+            f"Provided command: '{command}'."
+        )

{fractal_server-2.5.0a1.dist-info → fractal_server-2.5.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.5.0a1
+Version: 2.5.2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.5.0a1.dist-info → fractal_server-2.5.2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=1fM-hrX8GvZ3DcdEUtfHmLjQ5GtgW0uU1Sqd6Va9Mbo,24
+fractal_server/__init__.py,sha256=zW_UoRr0gmuphO3yp_Nmzq1qV6ZNQIt_3zHJMXwFtIM,22
 fractal_server/__main__.py,sha256=upYBkGYrkBnkS1rp4D_nb_1LS37QT4j-wxGX1ZMvR4A,5704
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -43,10 +43,10 @@ fractal_server/app/routes/api/v2/images.py,sha256=JR1rR6qEs81nacjriOXAOBQjAbCXF4
 fractal_server/app/routes/api/v2/job.py,sha256=Bga2Kz1OjvDIdxZObWaaXVhNIhC_5JKhKRjEH2_ayEE,5157
 fractal_server/app/routes/api/v2/project.py,sha256=eWYFJ7F2ZYQcpi-_n-rhPF-Q4gJhzYBsVGYFhHZZXAE,6653
 fractal_server/app/routes/api/v2/status.py,sha256=6N9DSZ4iFqbZImorWfEAPoyoFUgEruo4Hweqo0x0xXU,6435
-fractal_server/app/routes/api/v2/submit.py,sha256=iTGCYbxiZNszHQa8r3gmAR4QcF6QhVrb8ktzste2Ovc,8775
+fractal_server/app/routes/api/v2/submit.py,sha256=tyaeEpGMEkazdmltlnJxJYfD9Y9_t9mP2MUmx3s1Ato,9223
 fractal_server/app/routes/api/v2/task.py,sha256=XgRnGBvSoI9VNJHtWZQ2Ide99f6elo7a2FN3GQkf0dU,8376
-fractal_server/app/routes/api/v2/task_collection.py,sha256=wEwP8VfsxhKPZ6K3v1Bnput_Zw0Cjhlaal0-e50feIQ,12337
-fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=6MW-l7xTCTbWKDSYDw8e_hnm5jFCJpgFL3UdvrHAaBk,6029
+fractal_server/app/routes/api/v2/task_collection.py,sha256=SirU4yiE4pGfW68cyopMLgHSevIzaepQXLZJeIdaoDE,12697
+fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=CbeC7xYYF8K9JVOOunL3Y_3wXBEGGGoiJcoPa2hEftI,6127
 fractal_server/app/routes/api/v2/workflow.py,sha256=rMCcclz9aJAMSVLncUdSDGrgkKbn4KOCZTqZtqs2HDY,10428
 fractal_server/app/routes/api/v2/workflowtask.py,sha256=-3-c8DDnxGjMwWbX_h5V5OLaC_iCLXYzwWKBUaL-5wE,7060
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
@@ -66,7 +66,7 @@ fractal_server/app/runner/.gitignore,sha256=ytzN_oyHWXrGU7iFAtoHSTUbM6Rn6kG0Zkdd
 fractal_server/app/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/async_wrap.py,sha256=_O6f8jftKYXG_DozkmlrDBhoiK9QhE9MablOyECq2_M,829
 fractal_server/app/runner/components.py,sha256=ZF8ct_Ky5k8IAcrmpYOZ-bc6OBgdELEighYVqFDEbZg,119
-fractal_server/app/runner/compress_folder.py,sha256=zmxo2EFkSaO4h3GnMRi9DYaf62bxy4zznZZGfmq-n68,3975
+fractal_server/app/runner/compress_folder.py,sha256=HSc1tv7x2DBjBoXwugZlC79rm9GNBIWtQKK9yWn5ZBI,3991
 fractal_server/app/runner/exceptions.py,sha256=_qZ_t8O4umAdJ1ikockiF5rDJuxnEskrGrLjZcnQl7A,4159
 fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -76,20 +76,20 @@ fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77
 fractal_server/app/runner/executors/slurm/ssh/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/ssh/_executor_wait_thread.py,sha256=bKo5Ja0IGxJWpPWyh9dN0AG-PwzTDZzD5LyaEHB3YU4,3742
 fractal_server/app/runner/executors/slurm/ssh/_slurm_job.py,sha256=rwlqZzoGo4SAb4nSlFjsQJdaCgfM1J6YGcjb8yYxlqc,4506
-fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=oCc5cLZoNmJ3ENV0VaYRiIKayVClKDoEnjgZjHU864Y,57052
+fractal_server/app/runner/executors/slurm/ssh/executor.py,sha256=K1lKsn40PqQb-GZKwJkzeJk2Q8OGqy6YR-IxcV0E0Pw,57705
 fractal_server/app/runner/executors/slurm/sudo/__init__.py,sha256=Cjn1rYvljddi96tAwS-qqGkNfOcfPzjChdaEZEObCcM,65
 fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py,sha256=wAgwpVcr6JIslKHOuS0FhRa_6T1KCManyRJqA-fifzw,1909
 fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=z5LlhaiqAb8pHsF1WwdzXN39C5anQmwjo1rSQgtRAYE,4422
-fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py,sha256=0wRA-hg0JxVrFw4rBXAu6P2L2dbwzx2N_kUmpil1ErU,5143
-fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=6D83o4BE5D-1LZ3BhfEmhWJ1DZrk3Vzg-b3tB5TWMAU,48471
+fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py,sha256=g8wqUjSicN17UZVXlfaMomYZ-xOIbBu1oE7HdJTzfvw,5218
+fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=6OPe9t70gLyuC2JhWt2o1f0e7zhQPBtrbMHQkDd6RAQ,48725
 fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
-fractal_server/app/runner/run_subprocess.py,sha256=KTkJnWLrLQdR2WRJ3jGu0RBu4330L3mtCAE_B0wDx3M,818
+fractal_server/app/runner/run_subprocess.py,sha256=c3JbYXq3hX2aaflQU19qJ5Xs6J6oXGNvnTEoAfv2bxc,959
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/shutdown.py,sha256=I_o2iYKJwzku0L3E85ETjrve3QPECygR5xhhsAo5huM,2910
 fractal_server/app/runner/task_files.py,sha256=sd_MpJ01C8c9QTO8GzGMidFGdlq_hXX_ARDRhd_YMnI,3762
 fractal_server/app/runner/v1/__init__.py,sha256=VvJFk4agX2X3fQfDcoNmOB2ouNCaQU7dAqaFmpcdP8I,15063
-fractal_server/app/runner/v1/_common.py,sha256=rF9IsOo_h_UyeCZ2hkHYPHsdgTjqLlGGig4wyrDS5CQ,21544
+fractal_server/app/runner/v1/_common.py,sha256=EiSfp-PvhtTD3uijSec5CNKxe50ITts2DyGCFcjfVBw,21619
 fractal_server/app/runner/v1/_local/__init__.py,sha256=KlSML4LqF4p1IfhSd8tAkiu3aeDzifeanuNXjATDsYE,6929
 fractal_server/app/runner/v1/_local/_local_config.py,sha256=hM7SPxR07luXPcXdrWXRpEB2uOyjSSRUdqW3QBKJn9c,3147
 fractal_server/app/runner/v1/_local/_submit_setup.py,sha256=XyBDPb4IYdKEEnzLYdcYteIHWVWofJxKMmQCyRkn5Bc,1509
@@ -119,12 +119,12 @@ fractal_server/app/runner/v2/handle_failed_job.py,sha256=fipRJT5Y8UY0US4bXUX-4OR
 fractal_server/app/runner/v2/merge_outputs.py,sha256=IHuHqbKmk97K35BFvTrKVBs60z3e_--OzXTnsvmA02c,1281
 fractal_server/app/runner/v2/runner.py,sha256=nw9oYt3cFItHWVoevJyMI63K0kWHCTAriAQ_KINo_F8,13039
 fractal_server/app/runner/v2/runner_functions.py,sha256=BLREIcQaE6FSc2AEJyZuiYk6rGazEz_9gprUqUZDljs,9488
-fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=hXRjaPjBVWQ2HK7s2yhvqKC5Uc_K41MvW9kUm4KajTA,3453
+fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=1fWvQ6YZUUnDhO_mipXC5hnaT-zK-GHxg8ayoxZX82k,3648
 fractal_server/app/runner/v2/task_interface.py,sha256=myS-kT0DsJ8xIJZBVEzgD8g54VbiwL6i7Im3e1zcVHQ,1866
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=jiIf54owztXupv3PO6Ilh0qcrkh2RUzKq4bcEFqEfc4,40
 fractal_server/app/schemas/_validators.py,sha256=1dTOYr1IZykrxuQSV2-zuEMZbKe_nGwrfS7iUrsh-sE,3461
-fractal_server/app/schemas/user.py,sha256=PP0xU42hKeOGQLjOw5DnjaIISXrlbf2CHzCqAtv2_Bk,3889
+fractal_server/app/schemas/user.py,sha256=OJutfwMR1JPEmdFzqA4vHMZO-mhB4Mb9Yyx_G24XTCM,4081
 fractal_server/app/schemas/user_group.py,sha256=2f9XQ6kIar6NMY4UCN0yOnve6ZDHUVZaHv1dna1Vfjg,1446
 fractal_server/app/schemas/v1/__init__.py,sha256=CrBGgBhoemCvmZ70ZUchM-jfVAICnoa7AjZBAtL2UB0,1852
 fractal_server/app/schemas/v1/applyworkflow.py,sha256=uuIh7fHlHEL4yLqL-dePI6-nfCsqgBYATmht7w_KITw,4302
@@ -138,12 +138,12 @@ fractal_server/app/schemas/v1/task_collection.py,sha256=uvq9bcMaGD_qHsh7YtcpoSAk
 fractal_server/app/schemas/v1/workflow.py,sha256=tuOs5E5Q_ozA8if7YPZ07cQjzqB_QMkBS4u92qo4Ro0,4618
 fractal_server/app/schemas/v2/__init__.py,sha256=kmM4NfSGIL0I4xVtnmMST20kfVo3nBBG-Ssk8vJAvLs,1979
 fractal_server/app/schemas/v2/dataset.py,sha256=dLT52tV4dSf2HrFNak4vdQEn8PT_04IUrGnd2z-AXIU,2599
-fractal_server/app/schemas/v2/dumps.py,sha256=_iVgV98jb3gaKcOxX_halQFureKE81KTRIqbJsefw1s,1332
+fractal_server/app/schemas/v2/dumps.py,sha256=ZrJCHTv9oU2QMNjPUSBO3DIPRO3qDvbxpAGpernpf-Q,1720
 fractal_server/app/schemas/v2/job.py,sha256=zfF9K3v4jWUJ7M482ta2CkqUJ4tVT4XfVt60p9IRhP0,3250
 fractal_server/app/schemas/v2/manifest.py,sha256=N37IWohcfO3_y2l8rVM0h_1nZq7m4Izxk9iL1vtwBJw,6243
 fractal_server/app/schemas/v2/project.py,sha256=u7S4B-bote1oGjzAGiZ-DuQIyeRAGqJsI71Tc1EtYE0,736
 fractal_server/app/schemas/v2/status.py,sha256=SQaUpQkjFq5c5k5J4rOjNhuQaDOEg8lksPhkKmPU5VU,332
-fractal_server/app/schemas/v2/task.py,sha256=xQfQxL2h-Vw0YL3yEiYvVIXTybE1lyRE0pPUu59nZes,4574
+fractal_server/app/schemas/v2/task.py,sha256=XsN8w1Szs8BrxxRtKyWCHKjN4Od-Kmlhi769JEplL-M,4804
 fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHDmijt0bBW-mZsF7cSxUs,6129
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=TN-mdkuE_EWet9Wk-xFrUwIt_tXYcw88WOKMnUcchKk,5665
@@ -156,7 +156,7 @@ fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQ
 fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLiY,2209
 fractal_server/logger.py,sha256=56wfka6fHaa3Rx5qO009nEs_y8gx5wZ2NUNZZ1I-uvc,5130
-fractal_server/main.py,sha256=NUvMd8C8kosulAcQ8pCFLnOGdLw7j-6RzcHxoNvSB7k,5003
+fractal_server/main.py,sha256=68rVybnviF28yFgRhfHZXwnf6LyzkcmeYYZZppboU4M,4925
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=mEiX0TRa_8KAYBrUGJTx1cFJ5YAq_oNHHsFCp1raegk,2543
 fractal_server/migrations/naming_convention.py,sha256=htbKrVdetx3pklowb_9Cdo5RqeF0fJ740DNecY5de_M,265
@@ -181,8 +181,8 @@ fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
 fractal_server/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/ssh/__init__.py,sha256=sVUmzxf7_DuXG1xoLQ1_00fo5NPhi2LJipSmU5EAkPs,124
-fractal_server/ssh/_fabric.py,sha256=9xcsOEwbCgbJtupkIeG8OOtT8ct8c7_ruIehhNmD4wc,11379
-fractal_server/string_tools.py,sha256=KThgTLn_FHNSuEUGLabryJAP6DaFd7bpi-hF5FgkBjw,1268
+fractal_server/ssh/_fabric.py,sha256=B9C7Cj9ibrT1_OGlu38Jz94elNofLvkP1pxf0Tv8Eic,16140
+fractal_server/string_tools.py,sha256=YyopB2ZZ8iL9JLDXUA8PI0hahivqLiohir2HsAlEzqE,2170
 fractal_server/syringe.py,sha256=3qSMW3YaMKKnLdgnooAINOPxnCOxP7y2jeAQYB21Gdo,2786
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
 fractal_server/tasks/utils.py,sha256=wucz57I7G0Vd8hvtmvonlryACx9zIVlqfxG5I87MJ80,1820
@@ -207,8 +207,8 @@ fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kq
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
 fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
-fractal_server-2.5.0a1.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.5.0a1.dist-info/METADATA,sha256=qMNa2O2LVr-uNvS2djtZyio4-mk3FOHbIY_7N6Mh31k,4630
-fractal_server-2.5.0a1.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.5.0a1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.5.0a1.dist-info/RECORD,,
+fractal_server-2.5.2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.5.2.dist-info/METADATA,sha256=Q_lBgfC8qNcsp8ll6WrxkYOvt8P0YAVJCaWPuOIgFTY,4628
+fractal_server-2.5.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.5.2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.5.2.dist-info/RECORD,,