fractal-server 2.14.5__py3-none-any.whl → 2.14.6__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.14.5"
+__VERSION__ = "2.14.6"

fractal_server/app/db/__init__.py

@@ -2,8 +2,8 @@
 `db` module, loosely adapted from
 https://testdriven.io/blog/fastapi-sqlmodel/#async-sqlmodel
 """
-from typing import AsyncGenerator
-from typing import Generator
+from collections.abc import AsyncGenerator
+from collections.abc import Generator
 
 from sqlalchemy import create_engine
 from sqlalchemy.ext.asyncio import AsyncSession

fractal_server/app/models/security.py

@@ -46,13 +46,13 @@ class OAuthAccount(SQLModel, table=True):
 
     __tablename__ = "oauthaccount"
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id", nullable=False)
     user: Optional["UserOAuth"] = Relationship(back_populates="oauth_accounts")
     oauth_name: str = Field(index=True, nullable=False)
     access_token: str = Field(nullable=False)
-    expires_at: Optional[int] = Field(nullable=True, default=None)
-    refresh_token: Optional[str] = Field(nullable=True, default=None)
+    expires_at: int | None = Field(nullable=True, default=None)
+    refresh_token: str | None = Field(nullable=True, default=None)
     account_id: str = Field(index=True, nullable=False)
     account_email: str = Field(nullable=False)
     model_config = ConfigDict(from_attributes=True)
@@ -81,7 +81,7 @@ class UserOAuth(SQLModel, table=True):
 
     __tablename__ = "user_oauth"
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
 
     email: EmailStr = Field(
         sa_column_kwargs={"unique": True, "index": True}, nullable=False
@@ -91,17 +91,17 @@ class UserOAuth(SQLModel, table=True):
     is_superuser: bool = Field(default=False, nullable=False)
     is_verified: bool = Field(default=False, nullable=False)
 
-    username: Optional[str] = None
+    username: str | None = None
 
     oauth_accounts: list["OAuthAccount"] = Relationship(
         back_populates="user",
         sa_relationship_kwargs={"lazy": "joined", "cascade": "all, delete"},
     )
 
-    user_settings_id: Optional[int] = Field(
+    user_settings_id: int | None = Field(
         foreign_key="user_settings.id", default=None
     )
-    settings: Optional[UserSettings] = Relationship(
+    settings: UserSettings | None = Relationship(
         sa_relationship_kwargs=dict(lazy="selectin", cascade="all, delete")
     )
     model_config = ConfigDict(from_attributes=True)
@@ -117,7 +117,7 @@ class UserGroup(SQLModel, table=True):
         timestamp_created: Time of creation
     """
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     name: str = Field(unique=True)
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,

fractal_server/app/models/user_settings.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from sqlalchemy import Column
 from sqlalchemy.types import JSON
 from sqlmodel import Field
@@ -25,14 +23,14 @@ class UserSettings(SQLModel, table=True):
 
     __tablename__ = "user_settings"
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     slurm_accounts: list[str] = Field(
         sa_column=Column(JSON, server_default="[]", nullable=False)
     )
-    ssh_host: Optional[str] = None
-    ssh_username: Optional[str] = None
-    ssh_private_key_path: Optional[str] = None
-    ssh_tasks_dir: Optional[str] = None
-    ssh_jobs_dir: Optional[str] = None
-    slurm_user: Optional[str] = None
-    project_dir: Optional[str] = None
+    ssh_host: str | None = None
+    ssh_username: str | None = None
+    ssh_private_key_path: str | None = None
+    ssh_tasks_dir: str | None = None
+    ssh_jobs_dir: str | None = None
+    slurm_user: str | None = None
+    project_dir: str | None = None

fractal_server/app/models/v2/accounting.py

@@ -1,5 +1,4 @@
 from datetime import datetime
-from typing import Optional
 
 from sqlalchemy import Column
 from sqlalchemy import Integer
@@ -12,7 +11,7 @@ from ....utils import get_timestamp
 
 
 class AccountingRecord(SQLModel, table=True):
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id", nullable=False)
     timestamp: datetime = Field(
         default_factory=get_timestamp,
@@ -23,7 +22,7 @@ class AccountingRecord(SQLModel, table=True):
 
 
 class AccountingRecordSlurm(SQLModel, table=True):
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id", nullable=False)
     timestamp: datetime = Field(
         default_factory=get_timestamp,

fractal_server/app/models/v2/dataset.py

@@ -1,6 +1,5 @@
 from datetime import datetime
 from typing import Any
-from typing import Optional
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
@@ -16,7 +15,7 @@ from ....utils import get_timestamp
 class DatasetV2(SQLModel, table=True):
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     name: str
 
     project_id: int = Field(foreign_key="projectv2.id", ondelete="CASCADE")

fractal_server/app/models/v2/history.py

@@ -1,6 +1,5 @@
 from datetime import datetime
 from typing import Any
-from typing import Optional
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
@@ -17,12 +16,12 @@ from ....utils import get_timestamp
 class HistoryRun(SQLModel, table=True):
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     dataset_id: int = Field(
         foreign_key="datasetv2.id",
         ondelete="CASCADE",
     )
-    workflowtask_id: Optional[int] = Field(
+    workflowtask_id: int | None = Field(
         foreign_key="workflowtaskv2.id",
         default=None,
         ondelete="SET NULL",
@@ -45,7 +44,7 @@ class HistoryRun(SQLModel, table=True):
 
 
 class HistoryUnit(SQLModel, table=True):
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     history_run_id: int = Field(
         foreign_key="historyrun.id",
         ondelete="CASCADE",

fractal_server/app/models/v2/job.py

@@ -1,6 +1,5 @@
 from datetime import datetime
 from typing import Any
-from typing import Optional
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
@@ -17,19 +16,19 @@ from fractal_server.types import AttributeFilters
 class JobV2(SQLModel, table=True):
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    id: Optional[int] = Field(default=None, primary_key=True)
-    project_id: Optional[int] = Field(
+    id: int | None = Field(default=None, primary_key=True)
+    project_id: int | None = Field(
         foreign_key="projectv2.id", default=None, ondelete="SET NULL"
     )
-    workflow_id: Optional[int] = Field(
+    workflow_id: int | None = Field(
         foreign_key="workflowv2.id", default=None, ondelete="SET NULL"
     )
-    dataset_id: Optional[int] = Field(
+    dataset_id: int | None = Field(
         foreign_key="datasetv2.id", default=None, ondelete="SET NULL"
     )
 
     user_email: str = Field(nullable=False)
-    slurm_account: Optional[str] = None
+    slurm_account: str | None = None
 
     dataset_dump: dict[str, Any] = Field(
         sa_column=Column(JSON, nullable=False)
@@ -41,9 +40,9 @@ class JobV2(SQLModel, table=True):
         sa_column=Column(JSON, nullable=False)
     )
 
-    worker_init: Optional[str] = None
-    working_dir: Optional[str] = None
-    working_dir_user: Optional[str] = None
+    worker_init: str | None = None
+    working_dir: str | None = None
+    working_dir_user: str | None = None
     first_task_index: int
     last_task_index: int
 
@@ -51,11 +50,11 @@ class JobV2(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
-    end_timestamp: Optional[datetime] = Field(
+    end_timestamp: datetime | None = Field(
         default=None, sa_column=Column(DateTime(timezone=True))
     )
     status: str = JobStatusTypeV2.SUBMITTED
-    log: Optional[str] = None
+    log: str | None = None
 
     attribute_filters: AttributeFilters = Field(
         sa_column=Column(JSON, nullable=False, server_default="{}")

fractal_server/app/models/v2/project.py

@@ -1,5 +1,4 @@
 from datetime import datetime
-from typing import Optional
 
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
@@ -14,7 +13,7 @@ from fractal_server.utils import get_timestamp
 
 class ProjectV2(SQLModel, table=True):
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     name: str
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,

fractal_server/app/models/v2/task.py

@@ -1,5 +1,4 @@
 from typing import Any
-from typing import Optional
 
 from sqlalchemy import Column
 from sqlalchemy.types import JSON
@@ -8,13 +7,13 @@ from sqlmodel import SQLModel
 
 
 class TaskV2(SQLModel, table=True):
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     name: str
 
     type: str
-    command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str] = None
-    source: Optional[str] = None
+    command_non_parallel: str | None = None
+    command_parallel: str | None = None
+    source: str | None = None
 
     meta_non_parallel: dict[str, Any] = Field(
         sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
@@ -23,25 +22,25 @@ class TaskV2(SQLModel, table=True):
         sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
     )
 
-    version: Optional[str] = None
-    args_schema_non_parallel: Optional[dict[str, Any]] = Field(
+    version: str | None = None
+    args_schema_non_parallel: dict[str, Any] | None = Field(
         sa_column=Column(JSON), default=None
     )
-    args_schema_parallel: Optional[dict[str, Any]] = Field(
+    args_schema_parallel: dict[str, Any] | None = Field(
         sa_column=Column(JSON), default=None
     )
-    args_schema_version: Optional[str] = None
-    docs_info: Optional[str] = None
-    docs_link: Optional[str] = None
+    args_schema_version: str | None = None
+    docs_info: str | None = None
+    docs_link: str | None = None
 
     input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
     output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
 
     taskgroupv2_id: int = Field(foreign_key="taskgroupv2.id")
 
-    category: Optional[str] = None
-    modality: Optional[str] = None
-    authors: Optional[str] = None
+    category: str | None = None
+    modality: str | None = None
+    authors: str | None = None
     tags: list[str] = Field(
         sa_column=Column(JSON, server_default="[]", nullable=False)
     )

fractal_server/app/models/v2/task_group.py

@@ -1,6 +1,5 @@
 from datetime import datetime
 from datetime import timezone
-from typing import Optional
 
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
@@ -14,7 +13,7 @@ from fractal_server.utils import get_timestamp
 
 
 class TaskGroupV2(SQLModel, table=True):
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     task_list: list[TaskV2] = Relationship(
         sa_relationship_kwargs=dict(
             lazy="selectin", cascade="all, delete-orphan"
@@ -22,17 +21,17 @@ class TaskGroupV2(SQLModel, table=True):
     )
 
     user_id: int = Field(foreign_key="user_oauth.id")
-    user_group_id: Optional[int] = Field(
+    user_group_id: int | None = Field(
         foreign_key="usergroup.id", default=None, ondelete="SET NULL"
     )
 
     origin: str
     pkg_name: str
-    version: Optional[str] = None
-    python_version: Optional[str] = None
-    path: Optional[str] = None
-    wheel_path: Optional[str] = None
-    pip_extras: Optional[str] = None
+    version: str | None = None
+    python_version: str | None = None
+    path: str | None = None
+    wheel_path: str | None = None
+    pip_extras: str | None = None
     pinned_package_versions: dict[str, str] = Field(
         sa_column=Column(
             JSON,
@@ -41,10 +40,10 @@ class TaskGroupV2(SQLModel, table=True):
             nullable=True,
         ),
     )
-    pip_freeze: Optional[str] = None
-    venv_path: Optional[str] = None
-    venv_size_in_kB: Optional[int] = None
-    venv_file_number: Optional[int] = None
+    pip_freeze: str | None = None
+    venv_path: str | None = None
+    venv_size_in_kB: int | None = None
+    venv_file_number: int | None = None
 
     active: bool = True
     timestamp_created: datetime = Field(
@@ -97,9 +96,9 @@ class TaskGroupV2(SQLModel, table=True):
 
 class TaskGroupActivityV2(SQLModel, table=True):
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id")
-    taskgroupv2_id: Optional[int] = Field(
+    taskgroupv2_id: int | None = Field(
         default=None, foreign_key="taskgroupv2.id", ondelete="SET NULL"
     )
     timestamp_started: datetime = Field(
@@ -110,8 +109,8 @@ class TaskGroupActivityV2(SQLModel, table=True):
     version: str
     status: str
     action: str
-    log: Optional[str] = None
-    timestamp_ended: Optional[datetime] = Field(
+    log: str | None = None
+    timestamp_ended: datetime | None = Field(
         default=None,
         sa_column=Column(DateTime(timezone=True)),
     )

fractal_server/app/models/v2/workflow.py

@@ -1,5 +1,4 @@
 from datetime import datetime
-from typing import Optional
 
 from sqlalchemy import Column
 from sqlalchemy.ext.orderinglist import ordering_list
@@ -14,7 +13,7 @@ from .workflowtask import WorkflowTaskV2
 
 class WorkflowV2(SQLModel, table=True):
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
     name: str
     project_id: int = Field(foreign_key="projectv2.id", ondelete="CASCADE")
     project: "ProjectV2" = Relationship(  # noqa: F821

fractal_server/app/models/v2/workflowtask.py

@@ -1,5 +1,4 @@
 from typing import Any
-from typing import Optional
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
@@ -14,20 +13,20 @@ from .task import TaskV2
 class WorkflowTaskV2(SQLModel, table=True):
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
-    id: Optional[int] = Field(default=None, primary_key=True)
+    id: int | None = Field(default=None, primary_key=True)
 
     workflow_id: int = Field(foreign_key="workflowv2.id", ondelete="CASCADE")
-    order: Optional[int] = None
-    meta_parallel: Optional[dict[str, Any]] = Field(
+    order: int | None = None
+    meta_parallel: dict[str, Any] | None = Field(
         sa_column=Column(JSON), default=None
     )
-    meta_non_parallel: Optional[dict[str, Any]] = Field(
+    meta_non_parallel: dict[str, Any] | None = Field(
         sa_column=Column(JSON), default=None
     )
-    args_parallel: Optional[dict[str, Any]] = Field(
+    args_parallel: dict[str, Any] | None = Field(
         sa_column=Column(JSON), default=None
     )
-    args_non_parallel: Optional[dict[str, Any]] = Field(
+    args_non_parallel: dict[str, Any] | None = Field(
         sa_column=Column(JSON), default=None
     )
 

fractal_server/app/routes/admin/v2/accounting.py

@@ -1,5 +1,4 @@
 from itertools import chain
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -22,9 +21,9 @@ from fractal_server.app.schemas.v2 import AccountingRecordRead
 
 
 class AccountingQuery(BaseModel):
-    user_id: Optional[int] = None
-    timestamp_min: Optional[AwareDatetime] = None
-    timestamp_max: Optional[AwareDatetime] = None
+    user_id: int | None = None
+    timestamp_min: AwareDatetime | None = None
+    timestamp_max: AwareDatetime | None = None
 
 
 router = APIRouter()

fractal_server/app/routes/admin/v2/job.py

@@ -1,5 +1,4 @@
 from pathlib import Path
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -30,16 +29,16 @@ router = APIRouter()
 
 @router.get("/", response_model=list[JobReadV2])
 async def view_job(
-    id: Optional[int] = None,
-    user_id: Optional[int] = None,
-    project_id: Optional[int] = None,
-    dataset_id: Optional[int] = None,
-    workflow_id: Optional[int] = None,
-    status: Optional[JobStatusTypeV2] = None,
-    start_timestamp_min: Optional[AwareDatetime] = None,
-    start_timestamp_max: Optional[AwareDatetime] = None,
-    end_timestamp_min: Optional[AwareDatetime] = None,
-    end_timestamp_max: Optional[AwareDatetime] = None,
+    id: int | None = None,
+    user_id: int | None = None,
+    project_id: int | None = None,
+    dataset_id: int | None = None,
+    workflow_id: int | None = None,
+    status: JobStatusTypeV2 | None = None,
+    start_timestamp_min: AwareDatetime | None = None,
+    start_timestamp_max: AwareDatetime | None = None,
+    end_timestamp_min: AwareDatetime | None = None,
+    end_timestamp_max: AwareDatetime | None = None,
     log: bool = True,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
@@ -123,7 +122,7 @@ async def view_single_job(
 
     if show_tmp_logs and (job.status == JobStatusTypeV2.SUBMITTED):
         try:
-            with open(f"{job.working_dir}/{WORKFLOW_LOG_FILENAME}", "r") as f:
+            with open(f"{job.working_dir}/{WORKFLOW_LOG_FILENAME}") as f:
                 job.log = f.read()
         except FileNotFoundError:
             pass
@@ -137,7 +136,7 @@ async def update_job(
     job_id: int,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[JobReadV2]:
+) -> JobReadV2 | None:
     """
     Change the status of an existing job.
 
@@ -154,7 +153,7 @@ async def update_job(
     if job_update.status != JobStatusTypeV2.FAILED:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=f"Cannot set job status to {job_update.status.value}",
+            detail=f"Cannot set job status to {job_update.status}",
         )
 
     setattr(job, "status", job_update.status)

fractal_server/app/routes/admin/v2/project.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from sqlmodel import select
@@ -16,8 +14,8 @@ router = APIRouter()
 
 @router.get("/", response_model=list[ProjectReadV2])
 async def view_project(
-    id: Optional[int] = None,
-    user_id: Optional[int] = None,
+    id: int | None = None,
+    user_id: int | None = None,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[ProjectReadV2]:

fractal_server/app/routes/admin/v2/task.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -27,10 +25,10 @@ class TaskV2Minimal(BaseModel):
     name: str
     type: str
     taskgroupv2_id: int
-    command_non_parallel: Optional[str] = None
-    command_parallel: Optional[str] = None
-    source: Optional[str] = None
-    version: Optional[str] = None
+    command_non_parallel: str | None = None
+    command_parallel: str | None = None
+    source: str | None = None
+    version: str | None = None
 
 
 class ProjectUser(BaseModel):
@@ -56,14 +54,14 @@ class TaskV2Info(BaseModel):
 
 @router.get("/", response_model=list[TaskV2Info])
 async def query_tasks(
-    id: Optional[int] = None,
-    source: Optional[str] = None,
-    version: Optional[str] = None,
-    name: Optional[str] = None,
+    id: int | None = None,
+    source: str | None = None,
+    version: str | None = None,
+    name: str | None = None,
     max_number_of_results: int = 25,
-    category: Optional[str] = None,
-    modality: Optional[str] = None,
-    author: Optional[str] = None,
+    category: str | None = None,
+    modality: str | None = None,
+    author: str | None = None,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskV2Info]:

fractal_server/app/routes/admin/v2/task_group.py

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -35,13 +33,13 @@ logger = set_logger(__name__)
 
 @router.get("/activity/", response_model=list[TaskGroupActivityV2Read])
 async def get_task_group_activity_list(
-    task_group_activity_id: Optional[int] = None,
-    user_id: Optional[int] = None,
-    taskgroupv2_id: Optional[int] = None,
-    pkg_name: Optional[str] = None,
-    status: Optional[TaskGroupActivityStatusV2] = None,
-    action: Optional[TaskGroupActivityActionV2] = None,
-    timestamp_started_min: Optional[AwareDatetime] = None,
+    task_group_activity_id: int | None = None,
+    user_id: int | None = None,
+    taskgroupv2_id: int | None = None,
+    pkg_name: str | None = None,
+    status: TaskGroupActivityStatusV2 | None = None,
+    action: TaskGroupActivityActionV2 | None = None,
+    timestamp_started_min: AwareDatetime | None = None,
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupActivityV2Read]:
@@ -87,14 +85,14 @@ async def query_task_group(
 
 @router.get("/", response_model=list[TaskGroupReadV2])
 async def query_task_group_list(
-    user_id: Optional[int] = None,
-    user_group_id: Optional[int] = None,
-    private: Optional[bool] = None,
-    active: Optional[bool] = None,
-    pkg_name: Optional[str] = None,
-    origin: Optional[TaskGroupV2OriginEnum] = None,
-    timestamp_last_used_min: Optional[AwareDatetime] = None,
-    timestamp_last_used_max: Optional[AwareDatetime] = None,
+    user_id: int | None = None,
+    user_group_id: int | None = None,
+    private: bool | None = None,
+    active: bool | None = None,
+    pkg_name: str | None = None,
+    origin: TaskGroupV2OriginEnum | None = None,
+    timestamp_last_used_min: AwareDatetime | None = None,
+    timestamp_last_used_max: AwareDatetime | None = None,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupReadV2]: