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

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

@@ -6,14 +6,8 @@ from fastapi import HTTPException
 from fastapi import Response
 from fastapi import status
 
-from ....db import AsyncSession
-from ....db import get_async_db
-from ._aux_functions import _get_workflow_check_owner
-from ._aux_functions import _get_workflow_task_check_owner
-from ._aux_functions import _workflow_has_submitted_job
-from ._aux_functions import _workflow_insert_task
-from ._aux_functions_tasks import _check_type_filters_compatibility
-from ._aux_functions_tasks import _get_task_read_access
+from fractal_server.app.db import AsyncSession
+from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_user_act_ver_prof
 from fractal_server.app.schemas.v2 import TaskType
@@ -21,6 +15,13 @@ from fractal_server.app.schemas.v2 import WorkflowTaskCreateV2
 from fractal_server.app.schemas.v2 import WorkflowTaskReadV2
 from fractal_server.app.schemas.v2 import WorkflowTaskUpdateV2
 
+from ._aux_functions import _get_workflow_check_owner
+from ._aux_functions import _get_workflow_task_check_owner
+from ._aux_functions import _workflow_has_submitted_job
+from ._aux_functions import _workflow_insert_task
+from ._aux_functions_tasks import _check_type_filters_compatibility
+from ._aux_functions_tasks import _get_task_read_access
+
 router = APIRouter()
 
 
@@ -63,10 +64,7 @@ async def create_workflowtask(
                 ),
             )
     elif task.type == TaskType.NON_PARALLEL:
-        if (
-            wftask.meta_parallel is not None
-            or wftask.args_parallel is not None
-        ):
+        if wftask.meta_parallel is not None or wftask.args_parallel is not None:
             raise HTTPException(
                 status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
                 detail=(

fractal_server/app/routes/auth/__init__.py

@@ -12,7 +12,6 @@ from fractal_server.app.security import get_user_manager
 from fractal_server.config import get_settings
 from fractal_server.syringe import Inject
 
-
 bearer_transport = BearerTransport(tokenUrl="/auth/token/login")
 cookie_transport = CookieTransport(cookie_samesite="none")
 
@@ -71,8 +70,7 @@ async def current_user_act_ver_prof(
         raise HTTPException(
             status_code=status.HTTP_403_FORBIDDEN,
             detail=(
-                f"Forbidden access "
-                f"({user.is_verified=} {user.profile_id=})."
+                f"Forbidden access ({user.is_verified=} {user.profile_id=})."
             ),
         )
     return user

fractal_server/app/routes/auth/_aux_auth.py

@@ -13,7 +13,6 @@ from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
 
-
 logger = set_logger(__name__)
 
 
@@ -36,7 +35,7 @@ async def _get_single_user_with_groups(
 
     stm_groups = (
         select(UserGroup)
-        .join(LinkUserGroup)
+        .join(LinkUserGroup, LinkUserGroup.group_id == UserGroup.id)
         .where(LinkUserGroup.user_id == user.id)
         .order_by(asc(LinkUserGroup.timestamp_created))
     )

fractal_server/app/routes/auth/current_user.py

@@ -1,6 +1,7 @@
 """
 Definition of `/auth/current-user/` endpoints
 """
+
 import os
 
 from fastapi import APIRouter
@@ -23,8 +24,8 @@ from fractal_server.app.schemas import UserProfileInfo
 from fractal_server.app.schemas.user import UserRead
 from fractal_server.app.schemas.user import UserUpdate
 from fractal_server.app.schemas.user import UserUpdateStrict
-from fractal_server.app.security import get_user_manager
 from fractal_server.app.security import UserManager
+from fractal_server.app.security import get_user_manager
 from fractal_server.config import DataAuthScheme
 from fractal_server.config import get_data_settings
 from fractal_server.syringe import Inject
@@ -87,9 +88,8 @@ async def get_current_user_profile_info(
 ) -> UserProfileInfo:
     stm = (
         select(Resource, Profile)
-        .join(UserOAuth)
+        .join(UserOAuth, Profile.id == UserOAuth.profile_id)
         .where(Resource.id == Profile.resource_id)
-        .where(Profile.id == UserOAuth.profile_id)
         .where(UserOAuth.id == current_user.id)
     )
     res = await db.execute(stm)
@@ -146,8 +146,7 @@ async def get_current_user_allowed_viewer_paths(
         # Returns the union of `viewer_paths` for all user's groups
         cmd = (
             select(UserGroup.viewer_paths)
-            .join(LinkUserGroup)
-            .where(LinkUserGroup.group_id == UserGroup.id)
+            .join(LinkUserGroup, LinkUserGroup.group_id == UserGroup.id)
             .where(LinkUserGroup.user_id == current_user.id)
         )
         res = await db.execute(cmd)

fractal_server/app/routes/auth/group.py

@@ -1,6 +1,7 @@
 """
 Definition of `/auth/group/` routes
 """
+
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -9,11 +10,6 @@ from fastapi import status
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import select
 
-from . import current_superuser_act
-from ._aux_auth import _get_default_usergroup_id_or_none
-from ._aux_auth import _get_single_usergroup_with_user_ids
-from ._aux_auth import _user_or_404
-from ._aux_auth import _usergroup_or_404
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import LinkUserGroup
 from fractal_server.app.models import UserGroup
@@ -25,6 +21,12 @@ from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
 
+from . import current_superuser_act
+from ._aux_auth import _get_default_usergroup_id_or_none
+from ._aux_auth import _get_single_usergroup_with_user_ids
+from ._aux_auth import _user_or_404
+from ._aux_auth import _usergroup_or_404
+
 logger = set_logger(__name__)
 
 

fractal_server/app/routes/auth/login.py

@@ -1,6 +1,7 @@
 """
 Definition of `/auth/{login,logout}/`, `/auth/token/{login/logout}` routes.
 """
+
 from fastapi import APIRouter
 
 from . import cookie_backend

fractal_server/app/routes/auth/oauth.py

@@ -4,13 +4,14 @@ from httpx_oauth.clients.google import GoogleOAuth2
 from httpx_oauth.clients.openid import OpenID
 from httpx_oauth.clients.openid import OpenIDConfigurationError
 
-from . import cookie_backend
-from . import fastapi_users
+from fractal_server.config import OAuthSettings
 from fractal_server.config import get_oauth_settings
 from fractal_server.config import get_settings
-from fractal_server.config import OAuthSettings
 from fractal_server.syringe import Inject
 
+from . import cookie_backend
+from . import fastapi_users
+
 
 def _create_client_github(cfg: OAuthSettings) -> GitHubOAuth2:
     return GitHubOAuth2(

fractal_server/app/routes/auth/register.py

@@ -1,13 +1,15 @@
 """
 Definition of `/auth/register/` routes.
 """
+
 from fastapi import APIRouter
 from fastapi import Depends
 
+from fractal_server.app.schemas.user import UserCreate
+from fractal_server.app.schemas.user import UserRead
+
 from . import current_superuser_act
 from . import fastapi_users
-from ...schemas.user import UserCreate
-from ...schemas.user import UserRead
 
 router_register = APIRouter()
 

fractal_server/app/routes/auth/users.py

@@ -1,6 +1,7 @@
 """
 Definition of `/auth/users/` routes
 """
+
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -11,24 +12,24 @@ from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import func
 from sqlmodel import select
 
-from . import current_superuser_act
-from ...db import get_async_db
-from ...schemas.user import UserRead
-from ...schemas.user import UserUpdate
-from ._aux_auth import _get_default_usergroup_id_or_none
-from ._aux_auth import _get_single_user_with_groups
+from fractal_server.app.db import get_async_db
 from fractal_server.app.models import LinkUserGroup
 from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import Profile
 from fractal_server.app.routes.auth._aux_auth import _user_or_404
+from fractal_server.app.schemas.user import UserRead
+from fractal_server.app.schemas.user import UserUpdate
 from fractal_server.app.schemas.user import UserUpdateGroups
-from fractal_server.app.security import get_user_manager
 from fractal_server.app.security import UserManager
+from fractal_server.app.security import get_user_manager
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
 
+from . import current_superuser_act
+from ._aux_auth import _get_default_usergroup_id_or_none
+from ._aux_auth import _get_single_user_with_groups
 
 router_users = APIRouter()
 
@@ -197,13 +198,12 @@ async def set_user_groups(
     # Remove/create links as needed
     for link in links_to_remove:
         logger.info(
-            f"Removing LinkUserGroup with {link.user_id=} "
-            f"and {link.group_id=}."
+            f"Removing LinkUserGroup with {link.user_id=} and {link.group_id=}."
         )
         await db.delete(link)
     for group_id in ids_links_to_add:
         logger.info(
-            f"Creating new LinkUserGroup with {user_id=} " f"and {group_id=}."
+            f"Creating new LinkUserGroup with {user_id=} and {group_id=}."
         )
         db.add(LinkUserGroup(user_id=user_id, group_id=group_id))
     await db.commit()

fractal_server/app/routes/aux/_job.py

@@ -1,6 +1,6 @@
 from pathlib import Path
 
-from ...models.v2 import JobV2
+from fractal_server.app.models.v2 import JobV2
 from fractal_server.runner.filenames import SHUTDOWN_FILENAME
 
 

fractal_server/app/routes/aux/_runner.py

@@ -1,9 +1,9 @@
 from fastapi import HTTPException
 from fastapi import status
 
-from ....config import get_settings
-from ....syringe import Inject
 from fractal_server.app.schemas.v2 import ResourceType
+from fractal_server.config import get_settings
+from fractal_server.syringe import Inject
 
 
 def _backend_supports_shutdown(backend: str) -> bool:

fractal_server/app/routes/pagination.py

@@ -4,8 +4,8 @@ from typing import TypeVar
 from fastapi import HTTPException
 from pydantic import BaseModel
 from pydantic import Field
-from pydantic import model_validator
 from pydantic import ValidationError
+from pydantic import model_validator
 
 T = TypeVar("T")
 

fractal_server/app/schemas/user.py

@@ -74,9 +74,9 @@ class UserUpdate(schemas.BaseUserUpdate):
     is_superuser: bool = None
     is_verified: bool = None
     profile_id: int | None = None
-    project_dir: Annotated[
-        AbsolutePathStr, AfterValidator(_validate_cmd)
-    ] = None
+    project_dir: Annotated[AbsolutePathStr, AfterValidator(_validate_cmd)] = (
+        None
+    )
     slurm_accounts: ListUniqueNonEmptyString = None
 
 

fractal_server/app/schemas/v2/accounting.py

@@ -6,6 +6,17 @@ from pydantic.types import AwareDatetime
 
 
 class AccountingRecordRead(BaseModel):
+    """
+    AccountingRecordRead
+
+    Attributes:
+        id:
+        user_id:
+        timestamp:
+        num_tasks:
+        num_new_images:
+    """
+
     id: int
     user_id: int
     timestamp: AwareDatetime

fractal_server/app/schemas/v2/dataset.py

@@ -8,22 +8,38 @@ from pydantic.types import AwareDatetime
 
 from fractal_server.app.schemas.v2.project import ProjectReadV2
 from fractal_server.images import SingleImage
-from fractal_server.types import AttributeFilters
 from fractal_server.types import NonEmptyStr
 from fractal_server.types import ZarrDirStr
 
 
 class DatasetCreateV2(BaseModel):
+    """
+    DatasetCreateV2
+
+    Attributes:
+        name:
+        zarr_dir:
+    """
+
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
-
     zarr_dir: ZarrDirStr | None = None
 
-    attribute_filters: AttributeFilters = Field(default_factory=dict)
-
 
 class DatasetReadV2(BaseModel):
+    """
+    DatasetReadV2
+
+    Attributes:
+        id:
+        name:
+        project_id:
+        project:
+        timestamp_created:
+        zarr_dir:
+    """
+
     id: int
     name: str
 
@@ -40,6 +56,14 @@ class DatasetReadV2(BaseModel):
 
 
 class DatasetUpdateV2(BaseModel):
+    """
+    DatasetUpdateV2
+
+    Attributes:
+        name:
+        zarr_dir:
+    """
+
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None

fractal_server/app/schemas/v2/dumps.py

@@ -7,6 +7,7 @@ These models are used in at least two situations:
 1. In the "*_dump" attributes of Job models;
 2. In the history items, to trim their size.
 """
+
 from pydantic import BaseModel
 from pydantic import ConfigDict
 from pydantic import Field

fractal_server/app/schemas/v2/manifest.py

@@ -4,11 +4,12 @@ from pydantic import BaseModel
 from pydantic import Field
 from pydantic import model_validator
 
-from .task import TaskType
 from fractal_server.types import DictStrAny
 from fractal_server.types import HttpUrlStr
 from fractal_server.types import NonEmptyStr
 
+from .task import TaskType
+
 
 class TaskManifestV2(BaseModel):
     """
@@ -119,9 +120,9 @@ class ManifestV2(BaseModel):
             manifests as the schema evolves. This is for instance used by
             Fractal to determine which subclass of the present base class needs
             be used to read and validate the input.
-        task_list : list[TaskManifestType]
+        task_list:
             The list of tasks, represented as specified by subclasses of the
-            _TaskManifestBase (a.k.a. TaskManifestType)
+            `_TaskManifestBase` (a.k.a. `TaskManifestType`)
         has_args_schemas:
             `True` if the manifest includes JSON Schemas for the arguments of
             each task.

fractal_server/app/schemas/v2/profile.py

@@ -6,12 +6,21 @@ from pydantic import Discriminator
 from pydantic import Tag
 from pydantic import validate_call
 
-from .resource import ResourceType
 from fractal_server.types import AbsolutePathStr
 from fractal_server.types import NonEmptyStr
 
+from .resource import ResourceType
+
 
 class ValidProfileLocal(BaseModel):
+    """
+    Valid local profile.
+
+    Attributes:
+        name: Profile name.
+        resource_type: Type of the corresponding resource.
+    """
+
     name: NonEmptyStr
     resource_type: ResourceType
     username: None = None
@@ -21,6 +30,17 @@ class ValidProfileLocal(BaseModel):
 
 
 class ValidProfileSlurmSudo(BaseModel):
+    """
+    Valid SLURM/sudo profile.
+
+    Attributes:
+        name: Profile name.
+        resource_type: Type of the corresponding resource.
+        username:
+            SLURM user to impersonate (e.g. as in
+            `sudo -u username sbatch /some/script.sh`).
+    """
+
     name: NonEmptyStr
     resource_type: ResourceType
     username: NonEmptyStr
@@ -30,6 +50,23 @@ class ValidProfileSlurmSudo(BaseModel):
 
 
 class ValidProfileSlurmSSH(BaseModel):
+    """
+    Valid SLURM/sudo profile.
+
+    Attributes:
+        name: Profile name.
+        resource_type: Type of the corresponding resource.
+        username:
+            SLURM user to impersonate (e.g. as in
+            `ssh username@cluster sbatch /some/script.sh`).
+        ssh_key_path:
+            Local path of SSH private key for user `username`.
+        tasks_remote_dir:
+            Base folder for task environments on the remote SLURM cluster.
+        jobs_remote_dir:
+            Base folder for job directories on the remote SLURM cluster.
+    """
+
     name: NonEmptyStr
     resource_type: ResourceType
     username: NonEmptyStr
@@ -54,6 +91,20 @@ ProfileCreate = Annotated[
 
 
 class ProfileRead(BaseModel):
+    """
+    Profile schema for GET endpoints.
+
+    Attributes:
+        id:
+        name:
+        resource_id:
+        resource_type:
+        username:
+        ssh_key_path:
+        jobs_remote_dir:
+        tasks_remote_dir:
+    """
+
     id: int
     name: str
     resource_id: int
@@ -69,7 +120,7 @@ def cast_serialize_profile(_data: ProfileCreate) -> dict[str, Any]:
     """
     Cast/serialize round-trip for `Profile` data.
 
-    We use `@validate_call` because `ProfileeCreate` is a `Union` type and it
+    We use `@validate_call` because `ProfileCreate` is a `Union` type and it
     cannot be instantiated directly.
 
     Return:

fractal_server/app/schemas/v2/resource.py

@@ -7,8 +7,8 @@ from typing import Self
 from pydantic import AfterValidator
 from pydantic import BaseModel
 from pydantic import Discriminator
-from pydantic import model_validator
 from pydantic import Tag
+from pydantic import model_validator
 from pydantic import validate_call
 from pydantic.types import AwareDatetime
 
@@ -21,23 +21,46 @@ from fractal_server.types import NonEmptyStr
 
 
 class ResourceType(StrEnum):
+    """
+    Enum for the possible resource types.
+    """
+
     SLURM_SUDO = "slurm_sudo"
+    """
+    Enum entry for resource type `slurm_sudo`.
+    """
+
     SLURM_SSH = "slurm_ssh"
+    """
+    Enum entry for resource type `slurm_ssh`.
+    """
+
     LOCAL = "local"
+    """
+    Enum entry for resource type `local`.
+    """
 
 
 def cast_serialize_pixi_settings(
-    v: dict[NonEmptyStr, Any],
+    value: dict[NonEmptyStr, Any],
 ) -> dict[NonEmptyStr, Any]:
     """
-    Validate current value, and enrich it with default values.
+    Cast/serialize round trip for `tasks_pixi_config` through the
+    `TasksPixiSettings` schema.
+
+    Arguments:
+        value: Current `tasks_pixi_config` value.
     """
-    if v != {}:
-        v = TasksPixiSettings(**v).model_dump()
-    return v
+    if value != {}:
+        value = TasksPixiSettings(**value).model_dump()
+    return value
 
 
-class _ValidResourceBase(BaseModel):
+class ValidResourceBase(BaseModel):
+    """
+    Base resource schema.
+    """
+
     type: ResourceType
     name: NonEmptyStr
 
@@ -61,27 +84,90 @@ class _ValidResourceBase(BaseModel):
             and self.type == ResourceType.SLURM_SSH
             and self.tasks_pixi_config["SLURM_CONFIG"] is None
         ):
-            raise ValueError(
-                "`tasks_pixi_config` must include `SLURM_CONFIG`."
-            )
+            raise ValueError("`tasks_pixi_config` must include `SLURM_CONFIG`.")
         return self
 
 
-class ValidResourceLocal(_ValidResourceBase):
+class ValidResourceLocal(ValidResourceBase):
+    """
+    Valid local resource.
+
+    Attributes:
+        name: Resource name.
+        type: Resource type.
+        tasks_python_config:
+            Configuration of Python interpreters used for task collection.
+        tasks_pixi_config:
+            Configuration of `pixi` interpreters used for task collection.
+        tasks_local_dir:
+            Local base folder for task environments.
+        jobs_local_dir:
+            Local base folder for job folders.
+        jobs_runner_config:
+            Runner configuration.
+
+    """
+
     type: Literal[ResourceType.LOCAL]
     jobs_runner_config: JobRunnerConfigLocal
     jobs_slurm_python_worker: None = None
     host: None = None
 
 
-class ValidResourceSlurmSudo(_ValidResourceBase):
+class ValidResourceSlurmSudo(ValidResourceBase):
+    """
+    Valid SLURM-sudo resource.
+
+    Attributes:
+        name: Resource name.
+        type: Resource type.
+        tasks_python_config:
+            Configuration of Python interpreters used for task collection.
+        tasks_pixi_config:
+            Configuration of `pixi` interpreters used for task collection.
+        tasks_local_dir:
+            Local base folder for task environments.
+        jobs_local_dir:
+            Local base folder for job folders.
+        jobs_runner_config:
+            Runner configuration.
+        jobs_poll_interval:
+            `squeue` polling interval.
+        jobs_slurm_python_worker:
+            Python worker to be used in SLURM jobs.
+    """
+
     type: Literal[ResourceType.SLURM_SUDO]
     jobs_slurm_python_worker: AbsolutePathStr
     jobs_runner_config: JobRunnerConfigSLURM
     host: None = None
 
 
-class ValidResourceSlurmSSH(_ValidResourceBase):
+class ValidResourceSlurmSSH(ValidResourceBase):
+    """
+    Valid SLURM-SSH resource.
+
+    Attributes:
+        name: Resource name
+        type: Resource type.
+        tasks_python_config:
+            Configuration of Python interpreters used for task collection.
+        tasks_pixi_config:
+            Configuration of `pixi` interpreters used for task collection.
+        tasks_local_dir:
+            Local base folder for task environments.
+        jobs_local_dir:
+            Local base folder for job folders.
+        jobs_runner_config:
+            Runner configuration.
+        jobs_poll_interval:
+            `squeue` polling interval.
+        jobs_slurm_python_worker:
+            Python worker to be used in SLURM jobs.
+        host:
+            Hostname or IP address of remote SLURM cluster.
+    """
+
     type: Literal[ResourceType.SLURM_SSH]
     host: NonEmptyStr
     jobs_slurm_python_worker: AbsolutePathStr
@@ -101,9 +187,16 @@ ResourceCreate = Annotated[
     | Annotated[ValidResourceSlurmSSH, Tag(ResourceType.SLURM_SSH)],
     Discriminator(get_discriminator_value),
 ]
+"""
+Schema for resources in API request bodies.
+"""
 
 
 class ResourceRead(BaseModel):
+    """
+    Schema for resources in API response bodies.
+    """
+
     id: int
 
     type: str
@@ -131,6 +224,9 @@ def cast_serialize_resource(_data: ResourceCreate) -> dict[str, Any]:
     We use `@validate_call` because `ResourceCreate` is a `Union` type and it
     cannot be instantiated directly.
 
+    Args:
+        _data:
+
     Return:
         Serialized version of a valid resource object.
     """