fractal-server 2.17.1a0__py3-none-any.whl → 2.17.2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.17.1a0"
+__VERSION__ = "2.17.2"

fractal_server/__main__.py

@@ -7,7 +7,6 @@ from pathlib import Path
 import uvicorn
 from pydantic import ValidationError
 
-
 parser = ap.ArgumentParser(description="fractal-server commands")
 
 subparsers = parser.add_subparsers(title="Commands", dest="cmd", required=True)
@@ -48,9 +47,7 @@ openapi_parser.add_argument(
 # fractalctl set-db
 set_db_parser = subparsers.add_parser(
     "set-db",
-    description=(
-        "Initialise/upgrade database schemas and create first group&user."
-    ),
+    description="Initialise/upgrade database schemas.",
 )
 
 # fractalctl init-db-data
@@ -114,12 +111,13 @@ def set_db():
     Call alembic to upgrade to the latest migration.
     Ref: https://stackoverflow.com/a/56683030/283972
     """
-    from fractal_server.syringe import Inject
-    from fractal_server.config import get_db_settings
+    from pathlib import Path
 
     import alembic.config
-    from pathlib import Path
+
     import fractal_server
+    from fractal_server.config import get_db_settings
+    from fractal_server.syringe import Inject
 
     # Validate DB settings
     Inject(get_db_settings)
@@ -140,15 +138,18 @@ def init_db_data(
     admin_password: str | None = None,
     admin_project_dir: str | None = None,
 ) -> None:
-    from fractal_server.app.security import _create_first_user
-    from fractal_server.app.security import _create_first_group
+    from sqlalchemy import func
+    from sqlalchemy import select
+
     from fractal_server.app.db import get_sync_db
-    from sqlalchemy import select, func
+    from fractal_server.app.models import Profile
+    from fractal_server.app.models import Resource
     from fractal_server.app.models.security import UserOAuth
-    from fractal_server.app.models import Resource, Profile
-    from fractal_server.app.schemas.v2.resource import cast_serialize_resource
-    from fractal_server.app.schemas.v2.profile import cast_serialize_profile
     from fractal_server.app.schemas.v2 import ResourceType
+    from fractal_server.app.schemas.v2.profile import cast_serialize_profile
+    from fractal_server.app.schemas.v2.resource import cast_serialize_resource
+    from fractal_server.app.security import _create_first_group
+    from fractal_server.app.security import _create_first_user
 
     # Create default group and user
     print()
@@ -185,9 +186,7 @@ def init_db_data(
     if resource and profile:
         with next(get_sync_db()) as db:
             # Preliminary check
-            num_resources = db.execute(
-                select(func.count(Resource.id))
-            ).scalar()
+            num_resources = db.execute(select(func.count(Resource.id))).scalar()
             if num_resources != 0:
                 print(f"There exist already {num_resources=} resources. Exit.")
                 sys.exit(1)
@@ -270,10 +269,12 @@ def update_db_data():
     Apply data migrations.
     """
 
-    import fractal_server
+    import os
     from importlib import import_module
+
     from packaging.version import parse
-    import os
+
+    import fractal_server
 
     def _slugify_version(raw_version: str) -> str:
         v = parse(raw_version)

fractal_server/app/db/__init__.py

@@ -2,6 +2,7 @@
 `db` module, loosely adapted from
 https://testdriven.io/blog/fastapi-sqlmodel/#async-sqlmodel
 """
+
 from collections.abc import AsyncGenerator
 from collections.abc import Generator
 
@@ -15,7 +16,6 @@ from fractal_server.config import get_db_settings
 from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
 
-
 logger = set_logger(__name__)
 
 
@@ -46,7 +46,7 @@ class DB:
 
         cls._engine_async = create_async_engine(
             db_settings.DATABASE_URL,
-            echo=db_settings.DB_ECHO,
+            echo=(db_settings.DB_ECHO == "true"),
             future=True,
             pool_pre_ping=True,
         )
@@ -63,7 +63,7 @@ class DB:
 
         cls._engine_sync = create_engine(
             db_settings.DATABASE_URL,
-            echo=db_settings.DB_ECHO,
+            echo=(db_settings.DB_ECHO == "true"),
             future=True,
             pool_pre_ping=True,
         )

fractal_server/app/models/__init__.py

@@ -3,8 +3,8 @@ Note that this module is imported from `fractal_server/migrations/env.py`,
 thus we should always export all relevant database models from here or they
 will not be picked up by alembic.
 """
+
 from .linkusergroup import LinkUserGroup  # noqa: F401
 from .linkuserproject import LinkUserProjectV2  # noqa: F401
 from .security import *  # noqa
-from .user_settings import UserSettings  # noqa
 from .v2 import *  # noqa

fractal_server/app/models/linkuserproject.py

@@ -7,5 +7,7 @@ class LinkUserProjectV2(SQLModel, table=True):
     Crossing table between User and ProjectV2
     """
 
-    project_id: int = Field(foreign_key="projectv2.id", primary_key=True)
+    project_id: int = Field(
+        foreign_key="projectv2.id", primary_key=True, ondelete="CASCADE"
+    )
     user_id: int = Field(foreign_key="user_oauth.id", primary_key=True)

fractal_server/app/models/security.py

@@ -52,21 +52,39 @@ class UserOAuth(SQLModel, table=True):
     """
     ORM model for the `user_oauth` database table.
 
-    This class is a modification of SQLModelBaseUserDB from from
-    fastapi_users_db_sqlmodel. Original Copyright: 2022 François Voron,
-    released under MIT licence.
+    This class is a modification of
+    [`SQLModelBaseUserDB`](https://github.com/fastapi-users/fastapi-users-db-sqlmodel/blob/83980d7f20886120f4636a102ab1822b4c366f63/fastapi_users_db_sqlmodel/__init__.py#L15-L32)
+    from `fastapi_users_db_sqlmodel`.
+    Original Copyright: 2022 François Voron, released under MIT licence.
+
+    Note that several class attributes are
+    [the default ones from `fastapi-users`
+    ](https://fastapi-users.github.io/fastapi-users/latest/configuration/schemas/).
 
     Attributes:
         id:
         email:
         hashed_password:
         is_active:
+            If this is `False`, the user has no access to the `/api/v2/`
+            endpoints.
         is_superuser:
         is_verified:
+            If this is `False`, the user has no access to the `/api/v2/`
+            endpoints.
         oauth_accounts:
         profile_id:
+            Foreign key linking the user to a `Profile`. If this is unset,
+            the user has no access to the `/api/v2/` endpoints.
         project_dir:
+            Absolute path of the user's project directory. This is used (A) as
+            a default base folder for the `zarr_dir` of new datasets (where
+            the output Zarr are located), and (B) as a folder which is included
+            by default in the paths that a user is allowed to stream (if the
+            `fractal-data` integration is set up).
+            two goals:
         slurm_accounts:
+            List of SLURM accounts that the user can select upon running a job.
     """
 
     model_config = ConfigDict(from_attributes=True)
@@ -95,24 +113,11 @@ class UserOAuth(SQLModel, table=True):
         ondelete="RESTRICT",
     )
 
-    # TODO-2.17.1: update to `project_dir: str`
-    project_dir: str = Field(
-        sa_column=Column(
-            String,
-            server_default="/PLACEHOLDER",
-            nullable=False,
-        )
-    )
+    project_dir: str
     slurm_accounts: list[str] = Field(
         sa_column=Column(ARRAY(String), server_default="{}"),
     )
 
-    # TODO-2.17.1: remove
-    user_settings_id: int | None = Field(
-        foreign_key="user_settings.id",
-        default=None,
-    )
-
 
 class UserGroup(SQLModel, table=True):
     """

fractal_server/app/models/v2/__init__.py

@@ -1,7 +1,9 @@
 """
 v2 `models` module
 """
-from ..linkuserproject import LinkUserProjectV2
+
+from fractal_server.app.models.linkuserproject import LinkUserProjectV2
+
 from .accounting import AccountingRecord
 from .accounting import AccountingRecordSlurm
 from .dataset import DatasetV2

fractal_server/app/models/v2/accounting.py

@@ -7,10 +7,14 @@ from sqlalchemy.types import DateTime
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
-from ....utils import get_timestamp
+from fractal_server.utils import get_timestamp
 
 
 class AccountingRecord(SQLModel, table=True):
+    """
+    AccountingRecord table.
+    """
+
     id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id", nullable=False)
     timestamp: datetime = Field(
@@ -22,6 +26,10 @@ class AccountingRecord(SQLModel, table=True):
 
 
 class AccountingRecordSlurm(SQLModel, table=True):
+    """
+    AccountingRecordSlurm table.
+    """
+
     id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id", nullable=False)
     timestamp: datetime = Field(

fractal_server/app/models/v2/dataset.py

@@ -9,10 +9,14 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from ....utils import get_timestamp
+from fractal_server.utils import get_timestamp
 
 
 class DatasetV2(SQLModel, table=True):
+    """
+    Dataset table.
+    """
+
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
     id: int | None = Field(default=None, primary_key=True)

fractal_server/app/models/v2/history.py

@@ -10,10 +10,14 @@ from sqlalchemy.types import DateTime
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
-from ....utils import get_timestamp
+from fractal_server.utils import get_timestamp
 
 
 class HistoryRun(SQLModel, table=True):
+    """
+    HistoryRun table.
+    """
+
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
     id: int | None = Field(default=None, primary_key=True)
@@ -45,10 +49,15 @@ class HistoryRun(SQLModel, table=True):
 
 
 class HistoryUnit(SQLModel, table=True):
+    """
+    HistoryUnit table.
+    """
+
     id: int | None = Field(default=None, primary_key=True)
     history_run_id: int = Field(
         foreign_key="historyrun.id",
         ondelete="CASCADE",
+        index=True,
     )
 
     logfile: str
@@ -60,6 +69,10 @@ class HistoryUnit(SQLModel, table=True):
 
 
 class HistoryImageCache(SQLModel, table=True):
+    """
+    HistoryImageCache table.
+    """
+
     zarr_url: str = Field(primary_key=True)
     dataset_id: int = Field(
         primary_key=True,
@@ -77,4 +90,5 @@ class HistoryImageCache(SQLModel, table=True):
     latest_history_unit_id: int = Field(
         foreign_key="historyunit.id",
         ondelete="CASCADE",
+        index=True,
     )

fractal_server/app/models/v2/job.py

@@ -13,6 +13,10 @@ from fractal_server.utils import get_timestamp
 
 
 class JobV2(SQLModel, table=True):
+    """
+    Job table.
+    """
+
     model_config = ConfigDict(arbitrary_types_allowed=True)
 
     id: int | None = Field(default=None, primary_key=True)

fractal_server/app/models/v2/profile.py

@@ -3,14 +3,43 @@ from sqlmodel import SQLModel
 
 
 class Profile(SQLModel, table=True):
+    """
+    Profile table.
+    """
+
     id: int | None = Field(default=None, primary_key=True)
+
     resource_id: int = Field(foreign_key="resource.id", ondelete="RESTRICT")
+
     resource_type: str
+    """
+    Type of resource (either `local`, `slurm_sudo` or `slurm_ssh`).
+    """
 
     name: str = Field(unique=True)
+    """
+    Profile name.
+    """
 
     username: str | None = None
+    """
+    Username to be impersonated, either via `sudo -u` or via `ssh`.
+    """
+
     ssh_key_path: str | None = None
+    """
+    Path to the private SSH key of user `username` (only relevant if
+    `resource_type="slurm_ssh"`).
+    """
 
     jobs_remote_dir: str | None = None
+    """
+    Remote path of the job folder (only relevant if
+    `resource_type="slurm_ssh"`).
+    """
+
     tasks_remote_dir: str | None = None
+    """
+    Remote path of the task folder (only relevant if
+    `resource_type="slurm_ssh"`).
+    """

fractal_server/app/models/v2/project.py

@@ -3,30 +3,21 @@ from datetime import datetime
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
 from sqlmodel import Field
-from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from .. import LinkUserProjectV2
-from fractal_server.app.models import UserOAuth
 from fractal_server.utils import get_timestamp
 
 
 class ProjectV2(SQLModel, table=True):
+    """
+    Project table.
+    """
+
     id: int | None = Field(default=None, primary_key=True)
     name: str
 
-    # TODO-2.17.1: make `resource_id` not nullable
-    resource_id: int | None = Field(
-        foreign_key="resource.id", default=None, ondelete="RESTRICT"
-    )
+    resource_id: int = Field(foreign_key="resource.id", ondelete="RESTRICT")
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
-
-    user_list: list[UserOAuth] = Relationship(
-        link_model=LinkUserProjectV2,
-        sa_relationship_kwargs={
-            "lazy": "selectin",
-        },
-    )

fractal_server/app/models/v2/resource.py

@@ -13,6 +13,10 @@ from fractal_server.utils import get_timestamp
 
 
 class Resource(SQLModel, table=True):
+    """
+    Resource table.
+    """
+
     id: int | None = Field(default=None, primary_key=True)
 
     type: str

fractal_server/app/models/v2/task_group.py

@@ -8,9 +8,10 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from .task import TaskV2
 from fractal_server.utils import get_timestamp
 
+from .task import TaskV2
+
 
 def _check_origin_not_pixi(origin: str):
     """
@@ -22,10 +23,10 @@ def _check_origin_not_pixi(origin: str):
 
 def _create_dependency_string(pinned_versions: dict[str, str]) -> str:
     """
-    Expand e.g. `{"a": "1.2", "b": "3"}` into `"a==1.2 b==3"`.
+    Expand e.g. `{"a": "1.2", "b": "3"}` into `'"a==1.2" "b==3"'`.
     """
     output = " ".join(
-        [f"{key}=={value}" for key, value in pinned_versions.items()]
+        [f'"{key}=={value}"' for key, value in pinned_versions.items()]
     )
     return output
 
@@ -42,10 +43,7 @@ class TaskGroupV2(SQLModel, table=True):
     user_group_id: int | None = Field(
         foreign_key="usergroup.id", default=None, ondelete="SET NULL"
     )
-    # TODO-2.17.1: make `resource_id` not nullable
-    resource_id: int | None = Field(
-        foreign_key="resource.id", default=None, ondelete="RESTRICT"
-    )
+    resource_id: int = Field(foreign_key="resource.id", ondelete="RESTRICT")
 
     origin: str
     pkg_name: str

fractal_server/app/models/v2/workflow.py

@@ -7,7 +7,8 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from ....utils import get_timestamp
+from fractal_server.utils import get_timestamp
+
 from .workflowtask import WorkflowTaskV2
 
 

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

@@ -1,13 +1,13 @@
 """
 `admin/v2` module
 """
+
 from fastapi import APIRouter
 
 from .accounting import router as accounting_router
 from .impersonate import router as impersonate_router
 from .job import router as job_router
 from .profile import router as profile_router
-from .project import router as project_router
 from .resource import router as resource_router
 from .task import router as task_router
 from .task_group import router as task_group_router
@@ -17,7 +17,6 @@ router_admin_v2 = APIRouter()
 
 router_admin_v2.include_router(accounting_router, prefix="/accounting")
 router_admin_v2.include_router(job_router, prefix="/job")
-router_admin_v2.include_router(project_router, prefix="/project")
 router_admin_v2.include_router(task_router, prefix="/task")
 router_admin_v2.include_router(task_group_router, prefix="/task-group")
 router_admin_v2.include_router(

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

@@ -14,9 +14,9 @@ from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import AccountingRecord
 from fractal_server.app.models.v2 import AccountingRecordSlurm
 from fractal_server.app.routes.auth import current_superuser_act
-from fractal_server.app.routes.pagination import get_pagination_params
 from fractal_server.app.routes.pagination import PaginationRequest
 from fractal_server.app.routes.pagination import PaginationResponse
+from fractal_server.app.routes.pagination import get_pagination_params
 from fractal_server.app.schemas.v2 import AccountingRecordRead
 
 

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

@@ -12,17 +12,17 @@ from sqlmodel import select
 
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
+from fractal_server.app.models import LinkUserProjectV2
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import HistoryRun
 from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.models.v2 import JobV2
-from fractal_server.app.models.v2 import ProjectV2
 from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.app.routes.aux._runner import _check_shutdown_is_supported
-from fractal_server.app.routes.pagination import get_pagination_params
 from fractal_server.app.routes.pagination import PaginationRequest
 from fractal_server.app.routes.pagination import PaginationResponse
+from fractal_server.app.routes.pagination import get_pagination_params
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
 from fractal_server.app.schemas.v2 import JobReadV2
 from fractal_server.app.schemas.v2 import JobStatusTypeV2
@@ -52,7 +52,7 @@ async def view_job(
     db: AsyncSession = Depends(get_async_db),
 ) -> PaginationResponse[JobReadV2]:
     """
-    Query `ApplyWorkflow` table.
+    Query `JobV2` table.
 
     Args:
         id: If not `None`, select a given `applyworkflow.id`.
@@ -84,12 +84,12 @@ async def view_job(
         stm = stm.where(JobV2.id == id)
         stm_count = stm_count.where(JobV2.id == id)
     if user_id is not None:
-        stm = stm.join(ProjectV2).where(
-            ProjectV2.user_list.any(UserOAuth.id == user_id)
-        )
-        stm_count = stm_count.join(ProjectV2).where(
-            ProjectV2.user_list.any(UserOAuth.id == user_id)
-        )
+        stm = stm.join(
+            LinkUserProjectV2, LinkUserProjectV2.project_id == JobV2.project_id
+        ).where(LinkUserProjectV2.user_id == user_id)
+        stm_count = stm_count.join(
+            LinkUserProjectV2, LinkUserProjectV2.project_id == JobV2.project_id
+        ).where(LinkUserProjectV2.user_id == user_id)
     if project_id is not None:
         stm = stm.where(JobV2.project_id == project_id)
         stm_count = stm_count.where(JobV2.project_id == project_id)

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

@@ -6,8 +6,6 @@ from fastapi import status
 from sqlmodel import func
 from sqlmodel import select
 
-from ._aux_functions import _check_profile_name
-from ._aux_functions import _get_profile_or_404
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import Profile
@@ -16,6 +14,9 @@ from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.schemas.v2 import ProfileCreate
 from fractal_server.app.schemas.v2 import ProfileRead
 
+from ._aux_functions import _check_profile_name
+from ._aux_functions import _get_profile_or_404
+
 router = APIRouter()
 
 

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

@@ -6,9 +6,6 @@ from fastapi import status
 from sqlalchemy.exc import IntegrityError
 from sqlmodel import select
 
-from ._aux_functions import _check_resource_name
-from ._aux_functions import _get_resource_or_404
-from .profile import _check_profile_name
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
@@ -22,6 +19,10 @@ from fractal_server.app.schemas.v2 import ResourceRead
 from fractal_server.config import get_settings
 from fractal_server.syringe import Inject
 
+from ._aux_functions import _check_resource_name
+from ._aux_functions import _get_resource_or_404
+from .profile import _check_profile_name
+
 router = APIRouter()
 
 
@@ -47,8 +48,7 @@ def _check_type_match_or_422(new_resource: ResourceCreate) -> None:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
             detail=(
-                f"{settings.FRACTAL_RUNNER_BACKEND=} != "
-                f"{new_resource.type=}"
+                f"{settings.FRACTAL_RUNNER_BACKEND=} != {new_resource.type=}"
             ),
         )