fractal-server 2.17.1a1__py3-none-any.whl → 2.17.2__py3-none-any.whl

fractal_server/app/schemas/v2/task.py

@@ -14,7 +14,6 @@ from fractal_server.types import ListUniqueNonEmptyString
 from fractal_server.types import NonEmptyStr
 from fractal_server.types import TypeFilters
 
-
 logger = set_logger(__name__)
 
 

fractal_server/app/schemas/v2/task_collection.py

@@ -86,7 +86,7 @@ class TaskCollectPipV2(BaseModel):
     def validate_pinned_package_versions(cls, value):
         if value is not None:
             for pkg, version in value.items():
-                validate_cmd(pkg)
+                validate_cmd(pkg, allow_char="[]")
                 validate_cmd(version)
         return value
 

fractal_server/app/schemas/v2/workflowtask.py

@@ -5,14 +5,15 @@ from pydantic import ConfigDict
 from pydantic import Field
 from pydantic import model_validator
 
+from fractal_server.types import DictStrAny
+from fractal_server.types import TypeFilters
+from fractal_server.types import WorkflowTaskArgument
+
 from .task import TaskExportV2
 from .task import TaskImportV2
 from .task import TaskImportV2Legacy
 from .task import TaskReadV2
 from .task import TaskType
-from fractal_server.types import DictStrAny
-from fractal_server.types import TypeFilters
-from fractal_server.types import WorkflowTaskArgument
 
 
 class WorkflowTaskCreateV2(BaseModel):

fractal_server/app/security/__init__.py

@@ -15,6 +15,7 @@ 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
@@ -39,7 +40,7 @@ from sqlalchemy.orm import selectinload
 from sqlmodel import func
 from sqlmodel import select
 
-from ..db import get_async_db
+from fractal_server.app.db import get_async_db
 from fractal_server.app.db import get_sync_db
 from fractal_server.app.models import LinkUserGroup
 from fractal_server.app.models import OAuthAccount
@@ -275,9 +276,7 @@ class UserManager(IntegerIDMixin, BaseUserManager[UserOAuth, int]):
                 )
             except exceptions.UserNotExists:
                 # (0) Log
-                logger.warning(
-                    f"Self-registration attempt by {account_email}."
-                )
+                logger.warning(f"Self-registration attempt by {account_email}.")
 
                 # (1) Prepare user-facing error message
                 error_msg = (
@@ -459,9 +458,7 @@ def _create_first_group():
         )
         return
 
-    function_logger.info(
-        f"START, name '{settings.FRACTAL_DEFAULT_GROUP_NAME}'"
-    )
+    function_logger.info(f"START, name '{settings.FRACTAL_DEFAULT_GROUP_NAME}'")
     with next(get_sync_db()) as db:
         group_all = db.execute(
             select(UserGroup).where(

fractal_server/app/security/signup_email.py

@@ -36,9 +36,9 @@ def send_fractal_email_or_log_failure(
                 for recipient in email_settings.recipients
             ]
         )
-        mail_msg[
-            "Subject"
-        ] = f"[Fractal, {email_settings.instance_name}] {subject}"
+        mail_msg["Subject"] = (
+            f"[Fractal, {email_settings.instance_name}] {subject}"
+        )
         with smtplib.SMTP(
             email_settings.smtp_server,
             email_settings.port,
@@ -61,6 +61,5 @@ def send_fractal_email_or_log_failure(
 
     except Exception as e:
         logger.error(
-            "Could not send self-registration email, "
-            f"original error: {str(e)}."
+            f"Could not send self-registration email, original error: {str(e)}."
         )

fractal_server/config/_data.py

@@ -5,9 +5,10 @@ from pydantic import model_validator
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 
-from ._settings_config import SETTINGS_CONFIG_DICT
 from fractal_server.types import AbsolutePathStr
 
+from ._settings_config import SETTINGS_CONFIG_DICT
+
 
 class DataAuthScheme(StrEnum):
     VIEWER_PATHS = "viewer-paths"
@@ -18,37 +19,47 @@ class DataAuthScheme(StrEnum):
 class DataSettings(BaseSettings):
     """
     Settings for the `fractal-data` integration.
-    """
 
-    model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
-
-    FRACTAL_DATA_AUTH_SCHEME: DataAuthScheme = "none"
-    """
-    Defines how the list of allowed viewer paths is built.
+    See https://github.com/fractal-analytics-platform/fractal-data.
 
-    This variable affects the `GET /auth/current-user/allowed-viewer-paths/`
-    response, which is then consumed by
-    [fractal-data](https://github.com/fractal-analytics-platform/fractal-data).
+    Attributes:
+        FRACTAL_DATA_AUTH_SCHEME:
+            Defines how the list of allowed viewer paths is built.
 
-    Options:
+            This variable affects the
+            `GET /auth/current-user/allowed-viewer-paths/` response, which is
+            then consumed by
+            [fractal-data](https://github.com/fractal-analytics-platform/fractal-data).
 
-    - "viewer-paths": The list of allowed viewer paths will include the user's
-      `project_dir` along with any path defined in user groups' `viewer_paths`
-      attributes.
-    - "users-folders": The list will consist of the user's `project_dir` and a
-       user-specific folder. The user folder is constructed by concatenating
-       the base folder `FRACTAL_DATA_BASE_FOLDER` with the user's profile
-       `username`.
-    - "none": An empty list will be returned, indicating no access to
-       viewer paths. Useful when vizarr viewer is not used.
+            Options:
+                <ul>
+                <li> `"viewer-paths"`: The list of allowed viewer paths will
+                    include the user's `project_dir` along with any path
+                    defined in  UserGroups `viewer_paths` attributes.
+                </li>
+                <li> `"users-folders"`: The list will consist of the user's
+                    `project_dir` and a user-specific folder. The user folder
+                    is constructed by concatenating the base folder
+                    `FRACTAL_DATA_BASE_FOLDER` with the user's profile
+                    `username`.
+                </li>
+                <li> `"none"`: An empty list will be returned, indicating no
+                    access to viewer paths. Useful when vizarr viewer is not
+                    used.
+                </li>
+                </ul>
+        FRACTAL_DATA_BASE_FOLDER:
+            Base path to Zarr files that will be served by
+            fractal-vizarr-viewer.
+            This variable is required and used only when
+            `FRACTAL_DATA_AUTHORIZATION_SCHEME` is set to `"users-folders"`.
     """
 
+    model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
+
+    FRACTAL_DATA_AUTH_SCHEME: DataAuthScheme = "none"
+
     FRACTAL_DATA_BASE_FOLDER: AbsolutePathStr | None = None
-    """
-    Base path to Zarr files that will be served by fractal-vizarr-viewer;
-    This variable is required and used only when
-    FRACTAL_DATA_AUTHORIZATION_SCHEME is set to "users-folders".
-    """
 
     @model_validator(mode="after")
     def check(self: Self) -> Self:

fractal_server/config/_database.py

@@ -1,45 +1,44 @@
+from typing import Literal
+
 from pydantic import SecretStr
 from pydantic.types import NonNegativeInt
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 from sqlalchemy.engine import URL
 
-from ._settings_config import SETTINGS_CONFIG_DICT
 from fractal_server.types import NonEmptyStr
 
+from ._settings_config import SETTINGS_CONFIG_DICT
+
 
 class DatabaseSettings(BaseSettings):
     """
     Minimal set of configurations needed for operating on the database (e.g
     for schema migrations).
+
+    Attributes:
+        DB_ECHO:
+            If `"true"`, make database operations verbose.
+        POSTGRES_USER:
+            User to use when connecting to the PostgreSQL database.
+        POSTGRES_PASSWORD:
+            Password to use when connecting to the PostgreSQL database.
+        POSTGRES_HOST:
+            URL to the PostgreSQL server or path to a UNIX domain socket.
+        POSTGRES_PORT:
+            Port number to use when connecting to the PostgreSQL server.
+        POSTGRES_DB:
+            Name of the PostgreSQL database to connect to.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
 
-    DB_ECHO: bool = False
-    """
-    If `True`, make database operations verbose.
-    """
+    DB_ECHO: Literal["true", "false"] = "false"
     POSTGRES_USER: NonEmptyStr | None = None
-    """
-    User to use when connecting to the PostgreSQL database.
-    """
     POSTGRES_PASSWORD: SecretStr | None = None
-    """
-    Password to use when connecting to the PostgreSQL database.
-    """
     POSTGRES_HOST: NonEmptyStr = "localhost"
-    """
-    URL to the PostgreSQL server or path to a UNIX domain socket.
-    """
     POSTGRES_PORT: NonNegativeInt = 5432
-    """
-    Port number to use when connecting to the PostgreSQL server.
-    """
     POSTGRES_DB: NonEmptyStr
-    """
-    Name of the PostgreSQL database to connect to.
-    """
 
     @property
     def DATABASE_URL(self) -> URL:

fractal_server/config/_email.py

@@ -4,8 +4,8 @@ from typing import Self
 from pydantic import BaseModel
 from pydantic import EmailStr
 from pydantic import Field
-from pydantic import model_validator
 from pydantic import SecretStr
+from pydantic import model_validator
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 
@@ -17,14 +17,14 @@ class PublicEmailSettings(BaseModel):
     Schema for `EmailSettings.public`, namely the ready-to-use settings.
 
     Attributes:
-        sender: Sender email address
-        recipients: List of recipients email address
-        smtp_server: SMTP server address
-        port: SMTP server port
-        password: Sender password
-        instance_name: Name of SMTP server instance
-        use_starttls: Whether to use the security protocol
-        use_login: Whether to use login
+        sender: Sender email address.
+        recipients: List of recipients email address.
+        smtp_server: SMTP server address.
+        port: SMTP server port.
+        password: Sender password.
+        instance_name: Name of SMTP server instance.
+        use_starttls: Whether to use the security protocol.
+        use_login: Whether to use login.
     """
 
     sender: EmailStr
@@ -40,50 +40,42 @@ class PublicEmailSettings(BaseModel):
 class EmailSettings(BaseSettings):
     """
     Class with settings for email-sending feature.
+
+    Attributes:
+        FRACTAL_EMAIL_SENDER:
+            Address of the OAuth-signup email sender.
+        FRACTAL_EMAIL_PASSWORD:
+            Password for the OAuth-signup email sender.
+        FRACTAL_EMAIL_SMTP_SERVER:
+            SMTP server for the OAuth-signup emails.
+        FRACTAL_EMAIL_SMTP_PORT:
+            SMTP server port for the OAuth-signup emails.
+        FRACTAL_EMAIL_INSTANCE_NAME:
+            Fractal instance name, to be included in the OAuth-signup emails.
+        FRACTAL_EMAIL_RECIPIENTS:
+            Comma-separated list of recipients of the OAuth-signup emails.
+        FRACTAL_EMAIL_USE_STARTTLS:
+            Whether to use StartTLS when using the SMTP server.
+        FRACTAL_EMAIL_USE_LOGIN:
+            Whether to use login when using the SMTP server.
+            If 'true', FRACTAL_EMAIL_PASSWORD  must be provided.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
 
     FRACTAL_EMAIL_SENDER: EmailStr | None = None
-    """
-    Address of the OAuth-signup email sender.
-    """
     FRACTAL_EMAIL_PASSWORD: SecretStr | None = None
-    """
-    Password for the OAuth-signup email sender.
-    """
     FRACTAL_EMAIL_SMTP_SERVER: str | None = None
-    """
-    SMTP server for the OAuth-signup emails.
-    """
     FRACTAL_EMAIL_SMTP_PORT: int | None = None
-    """
-    SMTP server port for the OAuth-signup emails.
-    """
     FRACTAL_EMAIL_INSTANCE_NAME: str | None = None
-    """
-    Fractal instance name, to be included in the OAuth-signup emails.
-    """
     FRACTAL_EMAIL_RECIPIENTS: str | None = None
-    """
-    Comma-separated list of recipients of the OAuth-signup emails.
-    """
     FRACTAL_EMAIL_USE_STARTTLS: Literal["true", "false"] = "true"
-    """
-    Whether to use StartTLS when using the SMTP server.
-    Accepted values: 'true', 'false'.
-    """
     FRACTAL_EMAIL_USE_LOGIN: Literal["true", "false"] = "true"
-    """
-    Whether to use login when using the SMTP server.
-    If 'true', FRACTAL_EMAIL_PASSWORD  must be provided.
-    Accepted values: 'true', 'false'.
-    """
 
     public: PublicEmailSettings | None = None
     """
-    The validated field which is actually used in `fractal-server
-    (automatically populated upon creation).
+    The validated field which is actually used in `fractal-server`,
+    automatically populated upon creation.
     """
 
     @model_validator(mode="after")

fractal_server/config/_main.py

@@ -11,68 +11,49 @@ from ._settings_config import SETTINGS_CONFIG_DICT
 
 class Settings(BaseSettings):
     """
-    Contains all the configuration variables for Fractal Server
-
-    The attributes of this class are set from the environment.
+    Contains the general configuration variables for Fractal Server.
+
+    Attributes:
+        JWT_EXPIRE_SECONDS:
+            JWT token lifetime, in seconds.
+        JWT_SECRET_KEY:
+            JWT secret.<br>
+            ⚠️ Set this variable to a secure string, and do not disclose it.
+        COOKIE_EXPIRE_SECONDS:
+            Cookie token lifetime, in seconds.
+        FRACTAL_RUNNER_BACKEND:
+            Select which runner backend to use.
+        FRACTAL_LOGGING_LEVEL:
+            Logging-level threshold for logging
+            Only logs of with this level (or higher) will appear in the console
+            logs.
+        FRACTAL_API_MAX_JOB_LIST_LENGTH:
+            Number of ids that can be stored in the `jobsV2` attribute of
+            `app.state`.
+        FRACTAL_GRACEFUL_SHUTDOWN_TIME:
+            Waiting time for the shutdown phase of executors, in seconds.
+        FRACTAL_HELP_URL:
+            The URL of an instance-specific Fractal help page.
+        FRACTAL_DEFAULT_GROUP_NAME:
+            Name of the default user group.
+
+            If set to `"All"`, then the user group with that name is a special
+            user group (e.g. it cannot be deleted, and new users are
+            automatically added to it). If set to `None` (the default value),
+            then user groups are all equivalent, independently on their name.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
 
     JWT_EXPIRE_SECONDS: int = 180
-    """
-    JWT token lifetime, in seconds.
-    """
-
     JWT_SECRET_KEY: SecretStr
-    """
-    JWT secret
-
-    ⚠️ **IMPORTANT**: set this variable to a secure string, and do not disclose
-    it.
-    """
-
     COOKIE_EXPIRE_SECONDS: int = 86400
-    """
-    Cookie token lifetime, in seconds.
-    """
-
     # Note: we do not use ResourceType here to avoid circular imports
-    FRACTAL_RUNNER_BACKEND: Literal[
-        "local", "slurm_ssh", "slurm_sudo"
-    ] = "local"
-    """
-    Select which runner backend to use.
-    """
-
+    FRACTAL_RUNNER_BACKEND: Literal["local", "slurm_ssh", "slurm_sudo"] = (
+        "local"
+    )
     FRACTAL_LOGGING_LEVEL: int = logging.INFO
-    """
-    Logging-level threshold for logging
-
-    Only logs of with this level (or higher) will appear in the console logs.
-    """
-
     FRACTAL_API_MAX_JOB_LIST_LENGTH: int = 25
-    """
-    Number of ids that can be stored in the `jobsV2` attribute of
-    `app.state`.
-    """
-
     FRACTAL_GRACEFUL_SHUTDOWN_TIME: float = 30.0
-    """
-    Waiting time for the shutdown phase of executors
-    """
-
     FRACTAL_HELP_URL: HttpUrl | None = None
-    """
-    The URL of an instance-specific Fractal help page.
-    """
-
     FRACTAL_DEFAULT_GROUP_NAME: Literal["All"] | None = None
-    """
-    Name of the default user group.
-
-    If set to `"All"`, then the user group with that name is a special user
-    group (e.g. it cannot be deleted, and new users are automatically added
-    to it). If set to `None` (the default value), then user groups are all
-    equivalent, independently on their name.
-    """

fractal_server/config/_oauth.py

@@ -1,20 +1,33 @@
 from typing import Annotated
 from typing import Self
 
-from pydantic import model_validator
 from pydantic import SecretStr
 from pydantic import StringConstraints
+from pydantic import model_validator
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 
-from ._settings_config import SETTINGS_CONFIG_DICT
 from fractal_server.types import NonEmptyStr
 
+from ._settings_config import SETTINGS_CONFIG_DICT
+
 
 class OAuthSettings(BaseSettings):
     """
-    Minimal set of configurations needed for operating on the database (e.g
-    for schema migrations).
+    Settings for integration with an OAuth identity provider.
+
+    Attributes:
+        OAUTH_CLIENT_NAME: Name of the client.
+        OAUTH_CLIENT_ID: ID of client.
+        OAUTH_CLIENT_SECRET:
+            Secret to authorise against the identity provider.
+        OAUTH_OIDC_CONFIG_ENDPOINT:
+            OpenID Connect configuration endpoint, for autodiscovery of
+            relevant endpoints.
+        OAUTH_REDIRECT_URL:
+            String to be used as `redirect_url` argument in
+            `fastapi_users.get_oauth_router`, and then in
+            `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -26,27 +39,10 @@ class OAuthSettings(BaseSettings):
         ]
         | None
     ) = None
-    """
-    The name of the client.
-    """
     OAUTH_CLIENT_ID: SecretStr | None = None
-    """
-    ID of client.
-    """
     OAUTH_CLIENT_SECRET: SecretStr | None = None
-    """
-    Secret to authorise against the identity provider.
-    """
     OAUTH_OIDC_CONFIG_ENDPOINT: SecretStr | None = None
-    """
-    OpenID configuration endpoint, for autodiscovery of relevant endpoints.
-    """
     OAUTH_REDIRECT_URL: str | None = None
-    """
-    String to be used as `redirect_url` argument in
-    `fastapi_users.get_oauth_router`, and then in
-    `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`
-    """
 
     @model_validator(mode="after")
     def check_configuration(self: Self) -> Self:

fractal_server/exceptions.py

@@ -1,2 +1,6 @@
 class UnreachableBranchError(RuntimeError):
+    """
+    Exception marking a code branch that should have not been reached.
+    """
+
     pass

fractal_server/images/models.py

@@ -9,7 +9,7 @@ from fractal_server.types import ZarrDirStr
 from fractal_server.types import ZarrUrlStr
 
 
-class _SingleImageBase(BaseModel):
+class SingleImageBase(BaseModel):
     """
     Base for SingleImage and SingleImageTaskOutput.
 
@@ -27,7 +27,7 @@ class _SingleImageBase(BaseModel):
     types: ImageTypes = Field(default_factory=dict)
 
 
-class SingleImageTaskOutput(_SingleImageBase):
+class SingleImageTaskOutput(SingleImageBase):
     """
     `SingleImageBase`, with scalar `attributes` values (`None` included).
     """
@@ -35,7 +35,7 @@ class SingleImageTaskOutput(_SingleImageBase):
     attributes: ImageAttributesWithNone = Field(default_factory=dict)
 
 
-class SingleImage(_SingleImageBase):
+class SingleImage(SingleImageBase):
     """
     `SingleImageBase`, with scalar `attributes` values (`None` excluded).
     """

fractal_server/images/status_tools.py

@@ -37,10 +37,12 @@ def _prepare_query(
     """
     stm = (
         select(HistoryImageCache.zarr_url, HistoryUnit.status)
-        .join(HistoryUnit)
+        .join(
+            HistoryUnit,
+            HistoryImageCache.latest_history_unit_id == HistoryUnit.id,
+        )
         .where(HistoryImageCache.dataset_id == dataset_id)
         .where(HistoryImageCache.workflowtask_id == workflowtask_id)
-        .where(HistoryImageCache.latest_history_unit_id == HistoryUnit.id)
     )
     return stm
 

fractal_server/logger.py

@@ -12,13 +12,13 @@
 """
 This module provides logging utilities
 """
+
 import logging
 from pathlib import Path
 
 from .config import get_settings
 from .syringe import Inject
 
-
 LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 LOG_FORMATTER = logging.Formatter(LOG_FORMAT)
 

fractal_server/main.py

@@ -4,6 +4,9 @@ from itertools import chain
 
 from fastapi import FastAPI
 
+from fractal_server import __VERSION__
+from fractal_server.app.schemas.v2 import ResourceType
+
 from .app.routes.aux._runner import _backend_supports_shutdown
 from .app.shutdown import cleanup_after_shutdown
 from .config import get_data_settings
@@ -15,8 +18,6 @@ from .logger import get_logger
 from .logger import reset_logger_handlers
 from .logger import set_logger
 from .syringe import Inject
-from fractal_server import __VERSION__
-from fractal_server.app.schemas.v2 import ResourceType
 
 
 def collect_routers(app: FastAPI) -> None:
@@ -27,9 +28,9 @@ def collect_routers(app: FastAPI) -> None:
         app:
             The application to register the routers to.
     """
+    from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.api import router_api
     from .app.routes.api.v2 import router_api_v2
-    from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.auth.router import router_auth
 
     app.include_router(router_api, prefix="/api")

fractal_server/migrations/versions/034a469ec2eb_task_groups.py

@@ -5,6 +5,7 @@ Revises: da2cb2ac4255
 Create Date: 2024-10-10 16:14:13.976231
 
 """
+
 from datetime import datetime
 from datetime import timezone
 
@@ -12,7 +13,6 @@ import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "034a469ec2eb"
 down_revision = "da2cb2ac4255"
@@ -26,15 +26,11 @@ def upgrade() -> None:
         sa.Column("id", sa.Integer(), nullable=False),
         sa.Column("user_id", sa.Integer(), nullable=False),
         sa.Column("user_group_id", sa.Integer(), nullable=True),
-        sa.Column(
-            "origin", sqlmodel.sql.sqltypes.AutoString(), nullable=False
-        ),
+        sa.Column("origin", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column(
             "pkg_name", sqlmodel.sql.sqltypes.AutoString(), nullable=False
         ),
-        sa.Column(
-            "version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
-        ),
+        sa.Column("version", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
         sa.Column(
             "python_version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
         ),
@@ -123,8 +119,8 @@ def upgrade() -> None:
     except BaseException as e:
         if op.get_bind().dialect.name != "sqlite":
             raise e
-        import sqlite3
         import logging
+        import sqlite3
 
         logger = logging.getLogger("alembic.runtime.migration")
         logger.warning(

fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py

@@ -5,11 +5,11 @@ Revises: 5bf02391cfef
 Create Date: 2024-09-09 13:17:51.008231
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "091b01f51f88"
 down_revision = "5bf02391cfef"