fractal-server 2.14.4a0__py3-none-any.whl → 2.14.6__py3-none-any.whl

fractal_server/app/security/__init__.py

@@ -27,11 +27,9 @@ registers the client and the relative routes.
 All routes are registered under the `auth/` prefix.
 """
 import contextlib
+from collections.abc import AsyncGenerator
 from typing import Any
-from typing import AsyncGenerator
 from typing import Generic
-from typing import Optional
-from typing import Type
 
 from fastapi import Depends
 from fastapi import Request
@@ -82,24 +80,24 @@ class SQLModelUserDatabaseAsync(Generic[UP, ID], BaseUserDatabase[UP, ID]):
     """
 
     session: AsyncSession
-    user_model: Type[UP]
-    oauth_account_model: Optional[Type[OAuthAccount]] = None
+    user_model: type[UP]
+    oauth_account_model: type[OAuthAccount] | None = None
 
     def __init__(
         self,
         session: AsyncSession,
-        user_model: Type[UP],
-        oauth_account_model: Optional[Type[OAuthAccount]] = None,
+        user_model: type[UP],
+        oauth_account_model: type[OAuthAccount] | None = None,
     ):
         self.session = session
         self.user_model = user_model
         self.oauth_account_model = oauth_account_model
 
-    async def get(self, id: ID) -> Optional[UP]:
+    async def get(self, id: ID) -> UP | None:
         """Get a single user by id."""
         return await self.session.get(self.user_model, id)
 
-    async def get_by_email(self, email: str) -> Optional[UP]:
+    async def get_by_email(self, email: str) -> UP | None:
         """Get a single user by email."""
         statement = select(self.user_model).where(
             func.lower(self.user_model.email) == func.lower(email)
@@ -112,7 +110,7 @@ class SQLModelUserDatabaseAsync(Generic[UP, ID], BaseUserDatabase[UP, ID]):
 
     async def get_by_oauth_account(
         self, oauth: str, account_id: str
-    ) -> Optional[UP]:  # noqa
+    ) -> UP | None:  # noqa
         """Get a single user by OAuth account id."""
         if self.oauth_account_model is None:
             raise NotImplementedError()
@@ -212,7 +210,7 @@ class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
             )
 
     async def on_after_register(
-        self, user: UserOAuth, request: Optional[Request] = None
+        self, user: UserOAuth, request: Request | None = None
     ):
         logger.info(
             f"New-user registration completed ({user.id=}, {user.email=})."
@@ -290,7 +288,7 @@ async def _create_first_user(
     password: str,
     is_superuser: bool = False,
     is_verified: bool = False,
-    username: Optional[str] = None,
+    username: str | None = None,
 ) -> None:
     """
     Private method to create the first fractal-server user

fractal_server/config.py

@@ -18,7 +18,6 @@ from os import environ
 from os import getenv
 from pathlib import Path
 from typing import Literal
-from typing import Optional
 from typing import TypeVar
 
 from cryptography.fernet import Fernet
@@ -56,8 +55,8 @@ class MailSettings(BaseModel):
     recipients: list[EmailStr] = Field(min_length=1)
     smtp_server: str
     port: int
-    encrypted_password: Optional[SecretStr] = None
-    encryption_key: Optional[SecretStr] = None
+    encrypted_password: SecretStr | None = None
+    encryption_key: SecretStr | None = None
     instance_name: str
     use_starttls: bool
     use_login: bool
@@ -100,8 +99,8 @@ class OAuthClientConfig(BaseModel):
     CLIENT_NAME: str
     CLIENT_ID: str
     CLIENT_SECRET: SecretStr
-    OIDC_CONFIGURATION_ENDPOINT: Optional[str] = None
-    REDIRECT_URL: Optional[str] = None
+    OIDC_CONFIGURATION_ENDPOINT: str | None = None
+    REDIRECT_URL: str | None = None
 
     @model_validator(mode="before")
     @classmethod
@@ -139,7 +138,7 @@ class Settings(BaseSettings):
     JWT token lifetime, in seconds.
     """
 
-    JWT_SECRET_KEY: Optional[SecretStr] = None
+    JWT_SECRET_KEY: SecretStr | None = None
     """
     JWT secret
 
@@ -202,23 +201,23 @@ class Settings(BaseSettings):
     """
     If `True`, make database operations verbose.
     """
-    POSTGRES_USER: Optional[str] = None
+    POSTGRES_USER: str | None = None
     """
     User to use when connecting to the PostgreSQL database.
     """
-    POSTGRES_PASSWORD: Optional[SecretStr] = None
+    POSTGRES_PASSWORD: SecretStr | None = None
     """
     Password to use when connecting to the PostgreSQL database.
     """
-    POSTGRES_HOST: Optional[str] = "localhost"
+    POSTGRES_HOST: str | None = "localhost"
     """
     URL to the PostgreSQL server or path to a UNIX domain socket.
     """
-    POSTGRES_PORT: Optional[str] = "5432"
+    POSTGRES_PORT: str | None = "5432"
     """
     Port number to use when connecting to the PostgreSQL server.
     """
-    POSTGRES_DB: Optional[str] = None
+    POSTGRES_DB: str | None = None
     """
     Name of the PostgreSQL database to connect to.
     """
@@ -275,13 +274,13 @@ class Settings(BaseSettings):
     default admin credentials.
     """
 
-    FRACTAL_TASKS_DIR: Optional[Path] = None
+    FRACTAL_TASKS_DIR: Path | None = None
     """
     Directory under which all the tasks will be saved (either an absolute path
     or a path relative to current working directory).
     """
 
-    FRACTAL_RUNNER_WORKING_BASE_DIR: Optional[Path] = None
+    FRACTAL_RUNNER_WORKING_BASE_DIR: Path | None = None
     """
     Base directory for job files (either an absolute path or a path relative to
     current working directory).
@@ -293,7 +292,7 @@ class Settings(BaseSettings):
         mode="after",
     )
     @classmethod
-    def make_paths_absolute(cls, path: Optional[Path]) -> Optional[Path]:
+    def make_paths_absolute(cls, path: Path | None) -> Path | None:
         if path is None or path.is_absolute():
             return path
         else:
@@ -319,7 +318,7 @@ class Settings(BaseSettings):
     Only logs of with this level (or higher) will appear in the console logs.
     """
 
-    FRACTAL_LOCAL_CONFIG_FILE: Optional[Path] = None
+    FRACTAL_LOCAL_CONFIG_FILE: Path | None = None
     """
     Path of JSON file with configuration for the local backend.
     """
@@ -335,27 +334,27 @@ class Settings(BaseSettings):
     Waiting time for the shutdown phase of executors
     """
 
-    FRACTAL_SLURM_CONFIG_FILE: Optional[Path] = None
+    FRACTAL_SLURM_CONFIG_FILE: Path | None = None
     """
     Path of JSON file with configuration for the SLURM backend.
     """
 
-    FRACTAL_SLURM_WORKER_PYTHON: Optional[AbsolutePathStr] = None
+    FRACTAL_SLURM_WORKER_PYTHON: AbsolutePathStr | None = None
     """
     Absolute path to Python interpreter that will run the jobs on the SLURM
     nodes. If not specified, the same interpreter that runs the server is used.
     """
 
-    FRACTAL_TASKS_PYTHON_DEFAULT_VERSION: Optional[
+    FRACTAL_TASKS_PYTHON_DEFAULT_VERSION: None | (
         Literal["3.9", "3.10", "3.11", "3.12"]
-    ] = None
+    ) = None
     """
     Default Python version to be used for task collection. Defaults to the
     current version. Requires the corresponding variable (e.g
     `FRACTAL_TASKS_PYTHON_3_10`) to be set.
     """
 
-    FRACTAL_TASKS_PYTHON_3_9: Optional[str] = None
+    FRACTAL_TASKS_PYTHON_3_9: str | None = None
     """
     Absolute path to the Python 3.9 interpreter that serves as base for virtual
     environments tasks. Note that this interpreter must have the `venv` module
@@ -364,17 +363,17 @@ class Settings(BaseSettings):
     unset, `sys.executable` is used as a default.
     """
 
-    FRACTAL_TASKS_PYTHON_3_10: Optional[str] = None
+    FRACTAL_TASKS_PYTHON_3_10: str | None = None
     """
     Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.10.
     """
 
-    FRACTAL_TASKS_PYTHON_3_11: Optional[str] = None
+    FRACTAL_TASKS_PYTHON_3_11: str | None = None
     """
     Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.11.
     """
 
-    FRACTAL_TASKS_PYTHON_3_12: Optional[str] = None
+    FRACTAL_TASKS_PYTHON_3_12: str | None = None
     """
     Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.12.
     """
@@ -460,16 +459,7 @@ class Settings(BaseSettings):
     running a task that produces multiple SLURM jobs.
     """
 
-    FRACTAL_SLURM_ERROR_HANDLING_INTERVAL: int = 5
-    """
-    Interval to wait (in seconds) when the SLURM backend does not find an
-    output pickle file - which could be due to several reasons (e.g. the SLURM
-    job was cancelled or failed, or writing the file is taking long). If the
-    file is still missing after this time interval, this leads to a
-    `JobExecutionError`.
-    """
-
-    FRACTAL_PIP_CACHE_DIR: Optional[AbsolutePathStr] = None
+    FRACTAL_PIP_CACHE_DIR: AbsolutePathStr | None = None
     """
     Absolute path to the cache directory for `pip`; if unset,
     `--no-cache-dir` is used.
@@ -516,7 +506,7 @@ class Settings(BaseSettings):
        viewer paths. Useful when vizarr viewer is not used.
     """
 
-    FRACTAL_VIEWER_BASE_FOLDER: Optional[str] = None
+    FRACTAL_VIEWER_BASE_FOLDER: str | None = None
     """
     Base path to Zarr files that will be served by fractal-vizarr-viewer;
     This variable is required and used only when
@@ -527,31 +517,31 @@ class Settings(BaseSettings):
     # SMTP SERVICE
     ###########################################################################
 
-    FRACTAL_EMAIL_SENDER: Optional[EmailStr] = None
+    FRACTAL_EMAIL_SENDER: EmailStr | None = None
     """
     Address of the OAuth-signup email sender.
     """
-    FRACTAL_EMAIL_PASSWORD: Optional[SecretStr] = None
+    FRACTAL_EMAIL_PASSWORD: SecretStr | None = None
     """
     Password for the OAuth-signup email sender.
     """
-    FRACTAL_EMAIL_PASSWORD_KEY: Optional[SecretStr] = None
+    FRACTAL_EMAIL_PASSWORD_KEY: SecretStr | None = None
     """
     Key value for `cryptography.fernet` decrypt
     """
-    FRACTAL_EMAIL_SMTP_SERVER: Optional[str] = None
+    FRACTAL_EMAIL_SMTP_SERVER: str | None = None
     """
     SMTP server for the OAuth-signup emails.
     """
-    FRACTAL_EMAIL_SMTP_PORT: Optional[int] = None
+    FRACTAL_EMAIL_SMTP_PORT: int | None = None
     """
     SMTP server port for the OAuth-signup emails.
     """
-    FRACTAL_EMAIL_INSTANCE_NAME: Optional[str] = None
+    FRACTAL_EMAIL_INSTANCE_NAME: str | None = None
     """
     Fractal instance name, to be included in the OAuth-signup emails.
     """
-    FRACTAL_EMAIL_RECIPIENTS: Optional[str] = None
+    FRACTAL_EMAIL_RECIPIENTS: str | None = None
     """
     Comma-separated list of recipients of the OAuth-signup emails.
     """
@@ -567,7 +557,7 @@ class Settings(BaseSettings):
     provided.
     Accepted values: 'true', 'false'.
     """
-    email_settings: Optional[MailSettings] = None
+    email_settings: MailSettings | None = None
 
     @model_validator(mode="after")
     def validate_email_settings(self):

fractal_server/images/models.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from pydantic import BaseModel
 from pydantic import Field
 
@@ -23,7 +21,7 @@ class _SingleImageBase(BaseModel):
     """
 
     zarr_url: ZarrUrlStr
-    origin: Optional[ZarrDirStr] = None
+    origin: ZarrDirStr | None = None
 
     attributes: DictStrAny = Field(default_factory=dict)
     types: ImageTypes = Field(default_factory=dict)
@@ -48,4 +46,4 @@ class SingleImage(_SingleImageBase):
 class SingleImageUpdate(BaseModel):
     zarr_url: ZarrUrlStr
     attributes: ImageAttributes = None
-    types: Optional[ImageTypes] = None
+    types: ImageTypes | None = None

fractal_server/images/tools.py

@@ -1,7 +1,6 @@
 from copy import copy
 from typing import Any
 from typing import Literal
-from typing import Optional
 from typing import Union
 
 from fractal_server.types import AttributeFilters
@@ -13,7 +12,7 @@ def find_image_by_zarr_url(
     *,
     images: list[dict[str, Any]],
     zarr_url: str,
-) -> Optional[ImageSearch]:
+) -> ImageSearch | None:
     """
     Return a copy of the image with a given zarr_url, and its positional index.
 
@@ -65,8 +64,8 @@ def match_filter(
 
 def filter_image_list(
     images: list[dict[str, Any]],
-    type_filters: Optional[dict[str, bool]] = None,
-    attribute_filters: Optional[AttributeFilters] = None,
+    type_filters: dict[str, bool] | None = None,
+    attribute_filters: AttributeFilters | None = None,
 ) -> list[dict[str, Any]]:
     """
     Compute a sublist with images that match a filter set.
@@ -141,6 +140,4 @@ def aggregate_types(images: list[dict[str, Any]]) -> list[str]:
     """
     Given a list of images, this function returns a list of all image types.
     """
-    return list(
-        set(type for image in images for type in image["types"].keys())
-    )
+    return list({type for image in images for type in image["types"].keys()})

fractal_server/logger.py

@@ -14,8 +14,6 @@ This module provides logging utilities
 """
 import logging
 from pathlib import Path
-from typing import Optional
-from typing import Union
 
 from .config import get_settings
 from .syringe import Inject
@@ -25,7 +23,7 @@ LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 LOG_FORMATTER = logging.Formatter(LOG_FORMAT)
 
 
-def get_logger(logger_name: Optional[str] = None) -> logging.Logger:
+def get_logger(logger_name: str | None = None) -> logging.Logger:
     """
     Wrap the
     [`logging.getLogger`](https://docs.python.org/3/library/logging.html#logging.getLogger)
@@ -57,8 +55,8 @@ def get_logger(logger_name: Optional[str] = None) -> logging.Logger:
 def set_logger(
     logger_name: str,
     *,
-    log_file_path: Optional[Union[str, Path]] = None,
-    default_logging_level: Optional[int] = None,
+    log_file_path: str | Path | None = None,
+    default_logging_level: int | None = None,
 ) -> logging.Logger:
     """
     Set up a `fractal-server` logger

fractal_server/ssh/_fabric.py

@@ -1,18 +1,18 @@
 import json
 import logging
 import time
+from collections.abc import Generator
 from contextlib import contextmanager
 from pathlib import Path
 from threading import Lock
 from typing import Any
-from typing import Generator
 from typing import Literal
-from typing import Optional
 
 import paramiko.sftp_client
 from fabric import Connection
 from invoke import UnexpectedExit
 from paramiko.ssh_exception import NoValidConnectionsError
+from pydantic import BaseModel
 
 from ..logger import get_logger
 from ..logger import set_logger
@@ -35,6 +35,12 @@ class FractalSSHUnknownError(RuntimeError):
     pass
 
 
+class SSHConfig(BaseModel):
+    host: str
+    user: str
+    key_path: str
+
+
 logger = set_logger(__name__)
 
 
@@ -56,6 +62,7 @@ def _acquire_lock_with_timeout(
     """
     logger = get_logger(logger_name)
     logger.info(f"Trying to acquire lock for '{label}', with {timeout=}")
+    t_start_lock_acquire = time.perf_counter()
     result = lock.acquire(timeout=timeout)
     try:
         if not result:
@@ -64,7 +71,9 @@ def _acquire_lock_with_timeout(
                 f"Failed to acquire lock for '{label}' within "
                 f"{timeout} seconds"
             )
-        logger.info(f"Lock for '{label}' was acquired.")
+        t_end_lock_acquire = time.perf_counter()
+        elapsed = t_end_lock_acquire - t_start_lock_acquire
+        logger.info(f"Lock for '{label}' was acquired - {elapsed=:.4f} s")
         yield result
     finally:
         if result:
@@ -72,7 +81,7 @@ def _acquire_lock_with_timeout(
             logger.info(f"Lock for '{label}' was released.")
 
 
-class FractalSSH(object):
+class FractalSSH:
     """
     Wrapper of `fabric.Connection` object, enriched with locks.
 
@@ -156,7 +165,7 @@ class FractalSSH(object):
         raise e
 
     def _run(
-        self, *args, label: str, lock_timeout: Optional[float] = None, **kwargs
+        self, *args, label: str, lock_timeout: float | None = None, **kwargs
     ) -> Any:
         actual_lock_timeout = self.default_lock_timeout
         if lock_timeout is not None:
@@ -272,10 +281,10 @@ class FractalSSH(object):
         self,
         *,
         cmd: str,
-        allow_char: Optional[str] = None,
-        max_attempts: Optional[int] = None,
-        base_interval: Optional[float] = None,
-        lock_timeout: Optional[int] = None,
+        allow_char: str | None = None,
+        max_attempts: int | None = None,
+        base_interval: float | None = None,
+        lock_timeout: int | None = None,
     ) -> str:
         """
         Run a command within an open SSH connection.
@@ -372,7 +381,7 @@ class FractalSSH(object):
         *,
         local: str,
         remote: str,
-        lock_timeout: Optional[float] = None,
+        lock_timeout: float | None = None,
     ) -> None:
         """
         Transfer a file via SSH
@@ -412,7 +421,7 @@ class FractalSSH(object):
         *,
         local: str,
         remote: str,
-        lock_timeout: Optional[float] = None,
+        lock_timeout: float | None = None,
     ) -> None:
         """
         Transfer a file via SSH
@@ -503,7 +512,7 @@ class FractalSSH(object):
         *,
         path: str,
         content: str,
-        lock_timeout: Optional[float] = None,
+        lock_timeout: float | None = None,
     ) -> None:
         """
         Open a remote file via SFTP and write it.
@@ -557,7 +566,7 @@ class FractalSSH(object):
                 )
 
 
-class FractalSSHList(object):
+class FractalSSHList:
     """
     Collection of `FractalSSH` objects
 
@@ -711,3 +720,22 @@ class FractalSSHList(object):
                 f"({fractal_ssh_obj.is_connected=})."
             )
             fractal_ssh_obj.close()
+
+
+@contextmanager
+def SingleUseFractalSSH(
+    *,
+    ssh_config: SSHConfig,
+    logger_name: str,
+) -> Generator[FractalSSH, Any, None]:
+    """
+    Get a new FractalSSH object (with a fresh connection).
+
+    Args:
+        ssh_config:
+        logger_name:
+    """
+    _fractal_ssh_list = FractalSSHList(logger_name=logger_name)
+    _fractal_ssh = _fractal_ssh_list.get(**ssh_config.model_dump())
+    yield _fractal_ssh
+    _fractal_ssh.close()

fractal_server/string_tools.py

@@ -1,5 +1,5 @@
 import string
-from typing import Optional
+
 
 __SPECIAL_CHARACTERS__ = f"{string.punctuation}{string.whitespace}"
 
@@ -36,7 +36,7 @@ def sanitize_string(value: str) -> str:
 def validate_cmd(
     command: str,
     *,
-    allow_char: Optional[str] = None,
+    allow_char: str | None = None,
     attribute_name: str = "Command",
 ):
     """

fractal_server/syringe.py

@@ -34,8 +34,8 @@ or popped from the directory.
     >>> bar()
     42
 """
+from collections.abc import Callable
 from typing import Any
-from typing import Callable
 from typing import TypeVar
 
 

fractal_server/tasks/v2/local/collect.py

@@ -4,7 +4,6 @@ import shutil
 import time
 from pathlib import Path
 from tempfile import TemporaryDirectory
-from typing import Optional
 
 from ..utils_database import create_db_tasks_and_update_task_group_sync
 from ._utils import _customize_and_run_template
@@ -39,7 +38,7 @@ def collect_local(
     *,
     task_group_activity_id: int,
     task_group_id: int,
-    wheel_file: Optional[WheelFile] = None,
+    wheel_file: WheelFile | None = None,
 ) -> None:
     """
     Collect a task package.
@@ -132,7 +131,7 @@ def collect_local(
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.COLLECT.value}_"
+                        f"{TaskGroupActivityActionV2.COLLECT}_"
                     ),
                     logger_name=LOGGER_NAME,
                 )

fractal_server/tasks/v2/local/deactivate.py

@@ -107,7 +107,7 @@ def deactivate_local(
                         ).as_posix(),
                         prefix=(
                             f"{int(time.time())}_"
-                            f"{TaskGroupActivityActionV2.DEACTIVATE.value}_"
+                            f"{TaskGroupActivityActionV2.DEACTIVATE}_"
                         ),
                         logger_name=LOGGER_NAME,
                     )

fractal_server/tasks/v2/local/reactivate.py

@@ -107,7 +107,7 @@ def reactivate_local(
                     ).as_posix(),
                     prefix=(
                         f"{int(time.time())}_"
-                        f"{TaskGroupActivityActionV2.REACTIVATE.value}_"
+                        f"{TaskGroupActivityActionV2.REACTIVATE}_"
                     ),
                     logger_name=LOGGER_NAME,
                 )