fractal-server 1.4.3a0__py3-none-any.whl → 1.4.3a1__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "1.4.3a0"
+__VERSION__ = "1.4.3a1"

fractal_server/app/db/__init__.py

@@ -21,6 +21,12 @@ from ...syringe import Inject
 print(__name__)
 logger = set_logger(__name__)
 
+SQLITE_WARNING_MESSAGE = (
+    "SQLite is supported (for version >=3.37) but discouraged in production. "
+    "Given its partial support for ForeignKey constraints, "
+    "database consistency cannot be guaranteed."
+)
+
 
 class DB:
     """
@@ -32,7 +38,7 @@ class DB:
         try:
             return cls._engine_async
         except AttributeError:
-            cls.set_db()
+            cls.set_async_db()
             return cls._engine_async
 
     @classmethod
@@ -40,32 +46,22 @@ class DB:
         try:
             return cls._engine_sync
         except AttributeError:
-            cls.set_db()
+            cls.set_sync_db()
             return cls._engine_sync
 
     @classmethod
-    def set_db(cls):
+    def set_async_db(cls):
         settings = Inject(get_settings)
         settings.check_db()
 
         if settings.DB_ENGINE == "sqlite":
-            logger.warning(
-                "SQLite is supported (for version >=3.37) but discouraged "
-                "in production. Given its partial support for ForeignKey "
-                "constraints, database consistency cannot be guaranteed."
-            )
-
+            logger.warning(SQLITE_WARNING_MESSAGE)
             # Set some sqlite-specific options
             engine_kwargs_async = dict(poolclass=StaticPool)
-            engine_kwargs_sync = dict(
-                poolclass=StaticPool,
-                connect_args={"check_same_thread": False},
-            )
         else:
             engine_kwargs_async = {
                 "pool_pre_ping": True,
             }
-            engine_kwargs_sync = {}
 
         cls._engine_async = create_async_engine(
             settings.DATABASE_URL,
@@ -73,13 +69,6 @@ class DB:
             future=True,
             **engine_kwargs_async,
         )
-        cls._engine_sync = create_engine(
-            settings.DATABASE_SYNC_URL,
-            echo=settings.DB_ECHO,
-            future=True,
-            **engine_kwargs_sync,
-        )
-
         cls._async_session_maker = sessionmaker(
             cls._engine_async,
             class_=AsyncSession,
@@ -87,6 +76,28 @@ class DB:
             future=True,
         )
 
+    @classmethod
+    def set_sync_db(cls):
+        settings = Inject(get_settings)
+        settings.check_db()
+
+        if settings.DB_ENGINE == "sqlite":
+            logger.warning(SQLITE_WARNING_MESSAGE)
+            # Set some sqlite-specific options
+            engine_kwargs_sync = dict(
+                poolclass=StaticPool,
+                connect_args={"check_same_thread": False},
+            )
+        else:
+            engine_kwargs_sync = {}
+
+        cls._engine_sync = create_engine(
+            settings.DATABASE_SYNC_URL,
+            echo=settings.DB_ECHO,
+            future=True,
+            **engine_kwargs_sync,
+        )
+
         cls._sync_session_maker = sessionmaker(
             bind=cls._engine_sync,
             autocommit=False,
@@ -102,14 +113,14 @@ class DB:
                 cursor.close()
 
     @classmethod
-    async def get_db(cls) -> AsyncGenerator[AsyncSession, None]:
+    async def get_async_db(cls) -> AsyncGenerator[AsyncSession, None]:
         """
         Get async database session
         """
         try:
             session_maker = cls._async_session_maker()
         except AttributeError:
-            cls.set_db()
+            cls.set_async_db()
             session_maker = cls._async_session_maker()
         async with session_maker as async_session:
             yield async_session
@@ -122,11 +133,11 @@ class DB:
         try:
             session_maker = cls._sync_session_maker()
         except AttributeError:
-            cls.set_db()
+            cls.set_sync_db()
             session_maker = cls._sync_session_maker()
         with session_maker as sync_session:
             yield sync_session
 
 
-get_db = DB.get_db
+get_async_db = DB.get_async_db
 get_sync_db = DB.get_sync_db

fractal_server/app/routes/admin.py

@@ -16,7 +16,7 @@ from sqlmodel import select
 
 from ...utils import get_timestamp
 from ..db import AsyncSession
-from ..db import get_db
+from ..db import get_async_db
 from ..models import ApplyWorkflow
 from ..models import Dataset
 from ..models import JobStatusType
@@ -41,7 +41,7 @@ async def view_project(
     id: Optional[int] = None,
     user_id: Optional[int] = None,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[ProjectRead]:
     """
     Query `project` table.
@@ -73,7 +73,7 @@ async def view_workflow(
     project_id: Optional[int] = None,
     name_contains: Optional[str] = None,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[WorkflowRead]:
     """
     Query `workflow` table.
@@ -115,7 +115,7 @@ async def view_dataset(
     name_contains: Optional[str] = None,
     type: Optional[str] = None,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[DatasetRead]:
     """
     Query `dataset` table.
@@ -166,7 +166,7 @@ async def view_job(
     end_timestamp_min: Optional[datetime] = None,
     end_timestamp_max: Optional[datetime] = None,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[ApplyWorkflowRead]:
     """
     Query `ApplyWorkflow` table.
@@ -231,7 +231,7 @@ async def update_job(
     job_update: ApplyWorkflowUpdate,
     job_id: int,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ApplyWorkflowRead]:
     """
     Change the status of an existing job.
@@ -264,7 +264,7 @@ async def update_job(
 async def stop_job(
     job_id: int,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
     Stop execution of a workflow job.
@@ -293,7 +293,7 @@ async def stop_job(
 async def download_job_logs(
     job_id: int,
     user: User = Depends(current_active_superuser),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> StreamingResponse:
     """
     Download job folder

fractal_server/app/routes/api/v1/_aux_functions.py

@@ -368,16 +368,14 @@ async def _get_task_check_owner(
     return task
 
 
-def _get_active_jobs_statement() -> SelectOfScalar:
+def _get_submitted_jobs_statement() -> SelectOfScalar:
     """
     Returns:
         A sqlmodel statement that selects all `ApplyWorkflow`s with
-        `ApplyWorkflow.status` equal to `submitted` or `running`.
+        `ApplyWorkflow.status` equal to `submitted`.
     """
     stm = select(ApplyWorkflow).where(
-        ApplyWorkflow.status.in_(
-            [JobStatusType.SUBMITTED, JobStatusType.RUNNING]
-        )
+        ApplyWorkflow.status == JobStatusType.SUBMITTED
     )
     return stm
 

fractal_server/app/routes/api/v1/dataset.py

@@ -11,7 +11,7 @@ from sqlmodel import or_
 from sqlmodel import select
 
 from ....db import AsyncSession
-from ....db import get_db
+from ....db import get_async_db
 from ....models import ApplyWorkflow
 from ....models import Dataset
 from ....models import Project
@@ -28,9 +28,9 @@ from ....schemas import WorkflowExport
 from ....schemas import WorkflowTaskExport
 from ....security import current_active_user
 from ....security import User
-from ._aux_functions import _get_active_jobs_statement
 from ._aux_functions import _get_dataset_check_owner
 from ._aux_functions import _get_project_check_owner
+from ._aux_functions import _get_submitted_jobs_statement
 from ._aux_functions import _get_workflow_check_owner
 
 
@@ -46,7 +46,7 @@ async def create_dataset(
     project_id: int,
     dataset: DatasetCreate,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[DatasetRead]:
     """
     Add new dataset to current project
@@ -70,7 +70,7 @@ async def create_dataset(
 async def read_dataset_list(
     project_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[list[DatasetRead]]:
     """
     Get dataset list for given project
@@ -96,7 +96,7 @@ async def read_dataset(
     project_id: int,
     dataset_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[DatasetRead]:
     """
     Get info on a dataset associated to the current project
@@ -121,7 +121,7 @@ async def update_dataset(
     dataset_id: int,
     dataset_update: DatasetUpdate,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[DatasetRead]:
     """
     Edit a dataset associated to the current project
@@ -158,7 +158,7 @@ async def delete_dataset(
     project_id: int,
     dataset_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
     Delete a dataset associated to the current project
@@ -171,9 +171,9 @@ async def delete_dataset(
     )
     dataset = output["dataset"]
 
-    # Fail if there exist jobs that are active (that is, pending or running)
-    # and in relation with the current dataset.
-    stm = _get_active_jobs_statement().where(
+    # Fail if there exist jobs that are submitted and in relation with the
+    # current dataset.
+    stm = _get_submitted_jobs_statement().where(
         or_(
             ApplyWorkflow.input_dataset_id == dataset_id,
             ApplyWorkflow.output_dataset_id == dataset_id,
@@ -231,7 +231,7 @@ async def create_resource(
     dataset_id: int,
     resource: ResourceCreate,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ResourceRead]:
     """
     Add resource to an existing dataset
@@ -259,7 +259,7 @@ async def get_resource_list(
     project_id: int,
     dataset_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[list[ResourceRead]]:
     """
     Get resources from a dataset
@@ -287,7 +287,7 @@ async def update_resource(
     resource_id: int,
     resource_update: ResourceUpdate,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ResourceRead]:
     """
     Edit a resource of a dataset
@@ -327,7 +327,7 @@ async def delete_resource(
     dataset_id: int,
     resource_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
     Delete a resource of a dataset
@@ -360,7 +360,7 @@ async def export_history_as_workflow(
     project_id: int,
     dataset_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[WorkflowExport]:
     """
     Extract a reproducible workflow from the dataset history.
@@ -374,11 +374,12 @@ async def export_history_as_workflow(
     )
     dataset = output["dataset"]
 
-    # Check whether there exists an active job such that `job.output_dataset_id
-    # == dataset_id`. If at least one such job exists, then this endpoint will
-    # fail. We do not support the use case of exporting a reproducible workflow
-    # when job execution is in progress; this may change in the future.
-    stm = _get_active_jobs_statement().where(
+    # Check whether there exists a submitted job such that
+    # `job.output_dataset_id==dataset_id`.
+    # If at least one such job exists, then this endpoint will fail.
+    # We do not support the use case of exporting a reproducible workflow when
+    # job execution is in progress; this may change in the future.
+    stm = _get_submitted_jobs_statement().where(
         ApplyWorkflow.output_dataset_id == dataset_id
     )
     res = await db.execute(stm)
@@ -427,7 +428,7 @@ async def get_workflowtask_status(
     project_id: int,
     dataset_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[DatasetStatusRead]:
     """
     Extract the status of all `WorkflowTask`s that ran on a given `Dataset`.
@@ -449,7 +450,7 @@ async def get_workflowtask_status(
     # Note: see
     # https://sqlmodel.tiangolo.com/tutorial/where/#type-annotations-and-errors
     # regarding the type-ignore in this code block
-    stm = _get_active_jobs_statement().where(
+    stm = _get_submitted_jobs_statement().where(
         ApplyWorkflow.output_dataset_id == dataset_id
     )
     res = await db.execute(stm)
@@ -516,7 +517,7 @@ async def get_workflowtask_status(
 @router.get("/dataset/", response_model=list[DatasetRead])
 async def get_user_datasets(
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[DatasetRead]:
     """
     Returns all the datasets of the current user

fractal_server/app/routes/api/v1/job.py

@@ -9,7 +9,7 @@ from fastapi.responses import StreamingResponse
 from sqlmodel import select
 
 from ....db import AsyncSession
-from ....db import get_db
+from ....db import get_async_db
 from ....models import ApplyWorkflow
 from ....models import Project
 from ....schemas import ApplyWorkflowRead
@@ -29,7 +29,7 @@ router = APIRouter()
 @router.get("/job/", response_model=list[ApplyWorkflowRead])
 async def get_user_jobs(
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[ApplyWorkflowRead]:
     """
     Returns all the jobs of the current user
@@ -51,7 +51,7 @@ async def get_workflow_jobs(
     project_id: int,
     workflow_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[list[ApplyWorkflowRead]]:
     """
     Returns all the jobs related to a specific workflow
@@ -73,7 +73,7 @@ async def read_job(
     project_id: int,
     job_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ApplyWorkflowRead]:
     """
     Return info on an existing job
@@ -99,7 +99,7 @@ async def download_job_logs(
     project_id: int,
     job_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> StreamingResponse:
     """
     Download job folder
@@ -132,7 +132,7 @@ async def download_job_logs(
 async def get_job_list(
     project_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[list[ApplyWorkflowRead]]:
     """
     Get job list for given project
@@ -156,7 +156,7 @@ async def stop_job(
     project_id: int,
     job_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
     Stop execution of a workflow job (only available for slurm backend)

fractal_server/app/routes/api/v1/project.py

@@ -14,7 +14,7 @@ from .....logger import close_logger
 from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
-from ....db import get_db
+from ....db import get_async_db
 from ....models import ApplyWorkflow
 from ....models import Dataset
 from ....models import LinkUserProject
@@ -33,9 +33,9 @@ from ....security import current_active_user
 from ....security import current_active_verified_user
 from ....security import User
 from ._aux_functions import _check_project_exists
-from ._aux_functions import _get_active_jobs_statement
 from ._aux_functions import _get_dataset_check_owner
 from ._aux_functions import _get_project_check_owner
+from ._aux_functions import _get_submitted_jobs_statement
 from ._aux_functions import _get_workflow_check_owner
 
 
@@ -45,7 +45,7 @@ router = APIRouter()
 @router.get("/", response_model=list[ProjectRead])
 async def get_list_project(
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[Project]:
     """
     Return list of projects user is member of
@@ -65,7 +65,7 @@ async def get_list_project(
 async def create_project(
     project: ProjectCreate,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ProjectRead]:
     """
     Create new poject
@@ -100,7 +100,7 @@ async def create_project(
 async def read_project(
     project_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ProjectRead]:
     """
     Return info on an existing project
@@ -117,7 +117,7 @@ async def update_project(
     project_id: int,
     project_update: ProjectUpdate,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ):
     project = await _get_project_check_owner(
         project_id=project_id, user_id=user.id, db=db
@@ -142,7 +142,7 @@ async def update_project(
 async def delete_project(
     project_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
     Delete project
@@ -151,9 +151,9 @@ async def delete_project(
         project_id=project_id, user_id=user.id, db=db
     )
 
-    # Fail if there exist jobs that are active (that is, pending or running)
-    # and in relation with the current project.
-    stm = _get_active_jobs_statement().where(
+    # Fail if there exist jobs that are submitted and in relation with the
+    # current project.
+    stm = _get_submitted_jobs_statement().where(
         ApplyWorkflow.project_id == project_id
     )
     res = await db.execute(stm)
@@ -245,7 +245,7 @@ async def apply_workflow(
     input_dataset_id: int,
     output_dataset_id: int,
     user: User = Depends(current_active_verified_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ApplyWorkflowRead]:
 
     output = await _get_dataset_check_owner(
@@ -352,16 +352,11 @@ async def apply_workflow(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY, detail=str(e)
         )
 
-    # Check that no other job with the same output_dataset_id is either
-    # SUBMITTED or RUNNING
+    # Check that no other job with the same output_dataset_id is SUBMITTED
     stm = (
         select(ApplyWorkflow)
         .where(ApplyWorkflow.output_dataset_id == output_dataset_id)
-        .where(
-            ApplyWorkflow.status.in_(
-                [JobStatusType.SUBMITTED, JobStatusType.RUNNING]
-            )
-        )
+        .where(ApplyWorkflow.status == JobStatusType.SUBMITTED)
     )
     res = await db.execute(stm)
     if res.scalars().all():
@@ -369,7 +364,7 @@ async def apply_workflow(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=(
                 f"Output dataset {output_dataset_id} is already in use "
-                "in pending/running job(s)."
+                "in submitted job(s)."
             ),
         )
 

fractal_server/app/routes/api/v1/task.py

@@ -10,7 +10,7 @@ from sqlmodel import select
 
 from .....logger import set_logger
 from ....db import AsyncSession
-from ....db import get_db
+from ....db import get_async_db
 from ....models import Task
 from ....models import WorkflowTask
 from ....schemas import TaskCreate
@@ -29,7 +29,7 @@ logger = set_logger(__name__)
 @router.get("/", response_model=list[TaskRead])
 async def get_list_task(
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskRead]:
     """
     Get list of available tasks
@@ -45,7 +45,7 @@ async def get_list_task(
 async def get_task(
     task_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> TaskRead:
     """
     Get info on a specific task
@@ -64,7 +64,7 @@ async def patch_task(
     task_id: int,
     task_update: TaskUpdate,
     user: User = Depends(current_active_verified_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[TaskRead]:
     """
     Edit a specific task (restricted to superusers and task owner)
@@ -108,7 +108,7 @@ async def patch_task(
 async def create_task(
     task: TaskCreate,
     user: User = Depends(current_active_verified_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Optional[TaskRead]:
     """
     Create a new task
@@ -154,7 +154,7 @@ async def create_task(
 async def delete_task(
     task_id: int,
     user: User = Depends(current_active_user),
-    db: AsyncSession = Depends(get_db),
+    db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
     Delete a task