fractal-server 2.15.2__py3-none-any.whl → 2.15.4__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.15.2"
+__VERSION__ = "2.15.4"

fractal_server/app/models/v2/project.py

@@ -12,7 +12,6 @@ from fractal_server.utils import get_timestamp
 
 
 class ProjectV2(SQLModel, table=True):
-
     id: int | None = Field(default=None, primary_key=True)
     name: str
     timestamp_created: datetime = Field(

fractal_server/app/models/v2/task_group.py

@@ -107,7 +107,6 @@ class TaskGroupV2(SQLModel, table=True):
 
 
 class TaskGroupActivityV2(SQLModel, table=True):
-
     id: int | None = Field(default=None, primary_key=True)
     user_id: int = Field(foreign_key="user_oauth.id")
     taskgroupv2_id: int | None = Field(

fractal_server/app/models/v2/workflow.py

@@ -12,7 +12,6 @@ from .workflowtask import WorkflowTaskV2
 
 
 class WorkflowV2(SQLModel, table=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/routes/admin/v2/accounting.py

@@ -82,7 +82,6 @@ async def query_accounting_slurm(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
-
     stm = select(AccountingRecordSlurm.slurm_job_ids)
     if query.user_id is not None:
         stm = stm.where(AccountingRecordSlurm.user_id == query.user_id)

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

@@ -111,7 +111,6 @@ async def view_single_job(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> JobReadV2:
-
     job = await db.get(JobV2, job_id)
     if not job:
         raise HTTPException(

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

@@ -20,7 +20,6 @@ router = APIRouter()
 
 
 class TaskV2Minimal(BaseModel):
-
     id: int
     name: str
     type: str
@@ -32,13 +31,11 @@ class TaskV2Minimal(BaseModel):
 
 
 class ProjectUser(BaseModel):
-
     id: int
     email: EmailStr
 
 
 class TaskV2Relationship(BaseModel):
-
     workflow_id: int
     workflow_name: str
     project_id: int
@@ -47,7 +44,6 @@ class TaskV2Relationship(BaseModel):
 
 
 class TaskV2Info(BaseModel):
-
     task: TaskV2Minimal
     relationships: list[TaskV2Relationship]
 

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

@@ -43,7 +43,6 @@ async def get_task_group_activity_list(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupActivityV2Read]:
-
     stm = select(TaskGroupActivityV2)
     if task_group_activity_id is not None:
         stm = stm.where(TaskGroupActivityV2.id == task_group_activity_id)
@@ -73,7 +72,6 @@ async def query_task_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:
-
     task_group = await db.get(TaskGroupV2, task_group_id)
     if task_group is None:
         raise HTTPException(
@@ -96,7 +94,6 @@ async def query_task_group_list(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupReadV2]:
-
     stm = select(TaskGroupV2)
 
     if user_group_id is not None and private is True:

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

@@ -6,6 +6,7 @@ from typing import Literal
 
 from fastapi import HTTPException
 from fastapi import status
+from sqlalchemy.exc import MultipleResultsFound
 from sqlalchemy.orm.attributes import flag_modified
 from sqlmodel import select
 from sqlmodel.sql.expression import SelectOfScalar
@@ -19,6 +20,9 @@ from ....models.v2 import TaskV2
 from ....models.v2 import WorkflowTaskV2
 from ....models.v2 import WorkflowV2
 from ....schemas.v2 import JobStatusTypeV2
+from fractal_server.logger import set_logger
+
+logger = set_logger(__name__)
 
 
 async def _get_project_check_owner(
@@ -329,7 +333,6 @@ async def _workflow_has_submitted_job(
     workflow_id: int,
     db: AsyncSession,
 ) -> bool:
-
     res = await db.execute(
         select(JobV2.id)
         .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
@@ -499,3 +502,39 @@ async def _get_workflowtask_or_404(
         )
     else:
         return wftask
+
+
+async def _get_submitted_job_or_none(
+    *,
+    dataset_id: int,
+    workflow_id: int,
+    db: AsyncSession,
+) -> JobV2 | None:
+    """
+    Get the submitted job for given dataset/workflow, if any.
+
+    This function also handles the invalid branch where more than one job
+    is found.
+
+    Args:
+        dataset_id:
+        workflow_id:
+        db:
+    """
+    res = await db.execute(
+        _get_submitted_jobs_statement()
+        .where(JobV2.dataset_id == dataset_id)
+        .where(JobV2.workflow_id == workflow_id)
+    )
+    try:
+        return res.scalars().one_or_none()
+    except MultipleResultsFound as e:
+        error_msg = (
+            "Multiple running jobs found for "
+            f"{dataset_id=} and {workflow_id=}."
+        )
+        logger.error(f"{error_msg} Original error: {str(e)}.")
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=error_msg,
+        )

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

@@ -224,7 +224,6 @@ async def _get_collection_task_group_activity_status_message(
     task_group_id: int,
     db: AsyncSession,
 ) -> str:
-
     res = await db.execute(
         select(TaskGroupActivityV2)
         .where(TaskGroupActivityV2.taskgroupv2_id == task_group_id)

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

@@ -1,5 +1,3 @@
-from copy import deepcopy
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -9,6 +7,7 @@ from sqlmodel import func
 from sqlmodel import select
 
 from ._aux_functions import _get_dataset_check_owner
+from ._aux_functions import _get_submitted_job_or_none
 from ._aux_functions import _get_workflow_check_owner
 from ._aux_functions_history import _verify_workflow_and_dataset_access
 from ._aux_functions_history import get_history_run_or_404
@@ -86,6 +85,19 @@ async def get_workflow_tasks_statuses(
         db=db,
     )
 
+    running_job = await _get_submitted_job_or_none(
+        db=db,
+        dataset_id=dataset_id,
+        workflow_id=workflow_id,
+    )
+    if running_job is not None:
+        running_wftasks = workflow.task_list[
+            running_job.first_task_index : running_job.last_task_index + 1
+        ]
+        running_wftask_ids = [wft.id for wft in running_wftasks]
+    else:
+        running_wftask_ids = []
+
     response: dict[int, dict[str, int | str] | None] = {}
     for wftask in workflow.task_list:
         res = await db.execute(
@@ -95,17 +107,37 @@ async def get_workflow_tasks_statuses(
             .order_by(HistoryRun.timestamp_started.desc())
             .limit(1)
         )
-        latest_history_run = res.scalar_one_or_none()
-        if latest_history_run is None:
-            logger.debug(
-                f"No HistoryRun found for {dataset_id=} and {wftask.id=}."
-            )
-            response[wftask.id] = None
+        latest_run = res.scalar_one_or_none()
+
+        if latest_run is None:
+            if wftask.id in running_wftask_ids:
+                logger.debug(f"A1: No HistoryRun for {wftask.id=}.")
+                response[wftask.id] = dict(status=HistoryUnitStatus.SUBMITTED)
+            else:
+                logger.debug(f"A2: No HistoryRun for {wftask.id=}.")
+                response[wftask.id] = None
             continue
-        response[wftask.id] = dict(
-            status=latest_history_run.status,
-            num_available_images=latest_history_run.num_available_images,
-        )
+        else:
+            if wftask.id in running_wftask_ids:
+                if latest_run.job_id == running_job.id:
+                    logger.debug(
+                        f"B1 for {wftask.id} and {latest_run.job_id=}."
+                    )
+                    response[wftask.id] = dict(status=latest_run.status)
+                else:
+                    logger.debug(
+                        f"B2 for {wftask.id} and {latest_run.job_id=}."
+                    )
+                    response[wftask.id] = dict(
+                        status=HistoryUnitStatus.SUBMITTED
+                    )
+            else:
+                logger.debug(f"C1: {wftask.id=} not in {running_wftask_ids=}.")
+                response[wftask.id] = dict(status=latest_run.status)
+
+        response[wftask.id][
+            "num_available_images"
+        ] = latest_run.num_available_images
 
         for target_status in HistoryUnitStatus:
             stm = (
@@ -122,18 +154,24 @@ async def get_workflow_tasks_statuses(
             num_images = res.scalar()
             response[wftask.id][f"num_{target_status}_images"] = num_images
 
-    new_response = deepcopy(response)
-    for key, value in response.items():
-        if value is not None:
-            num_total_images = sum(
-                value[f"num_{target_status}_images"]
-                for target_status in HistoryUnitStatus
-            )
-            if num_total_images > value["num_available_images"]:
-                value["num_available_images"] = None
-        new_response[key] = value
+    # Set `num_available_images=None` for cases where it would be
+    # smaller than `num_total_images`
+    values_to_skip = (None, {"status": HistoryUnitStatus.SUBMITTED})
+    response_update = {}
+    for wftask_id, status_value in response.items():
+        if status_value in values_to_skip:
+            # Skip cases where status has no image counters
+            continue
+        num_total_images = sum(
+            status_value[f"num_{target_status}_images"]
+            for target_status in HistoryUnitStatus
+        )
+        if num_total_images > status_value["num_available_images"]:
+            status_value["num_available_images"] = None
+            response_update[wftask_id] = status_value
+    response.update(response_update)
 
-    return JSONResponse(content=new_response, status_code=200)
+    return JSONResponse(content=response, status_code=200)
 
 
 @router.get("/project/{project_id}/status/run/")
@@ -296,7 +334,6 @@ async def get_history_images(
     db: AsyncSession = Depends(get_async_db),
     pagination: PaginationRequest = Depends(get_pagination_params),
 ) -> ImagePage:
-
     # Access control and object retrieval
     wftask = await get_wftask_check_owner(
         project_id=project_id,

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

@@ -31,7 +31,6 @@ router = APIRouter()
 
 
 class ImagePage(PaginationResponse[SingleImage]):
-
     attributes: dict[str, list[ImageAttributeValue]]
     types: list[str]
 
@@ -64,7 +63,6 @@ async def post_new_image(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
-
     output = await _get_dataset_check_owner(
         project_id=project_id, dataset_id=dataset_id, user_id=user.id, db=db
     )
@@ -117,7 +115,6 @@ async def query_dataset_images(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> ImagePage:
-
     page = pagination.page
     page_size = pagination.page_size
 
@@ -131,7 +128,6 @@ async def query_dataset_images(
     types = aggregate_types(images)
 
     if query is not None:
-
         if query.zarr_url is not None:
             image = next(
                 (
@@ -190,7 +186,6 @@ async def delete_dataset_images(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
-
     output = await _get_dataset_check_owner(
         project_id=project_id, dataset_id=dataset_id, user_id=user.id, db=db
     )

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

@@ -96,7 +96,6 @@ async def check_non_processed_images(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
-
     db_workflow_task, db_workflow = await _get_workflow_task_check_owner(
         project_id=project_id,
         workflow_task_id=workflowtask_id,

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

@@ -57,7 +57,6 @@ async def apply_workflow(
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> JobReadV2 | None:
-
     # Remove non-submitted V2 jobs from the app state when the list grows
     # beyond a threshold
     settings = Inject(get_settings)

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

@@ -47,7 +47,6 @@ async def collect_task_custom(
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskReadV2]:
-
     settings = Inject(get_settings)
 
     # Validate query parameters related to user-group ownership
@@ -97,7 +96,6 @@ async def collect_task_custom(
                 )
 
     if task_collect.package_root is None:
-
         package_name_underscore = task_collect.package_name.replace("-", "_")
         # Note that python_command is then used as part of a subprocess.run
         # statement: be careful with mixing `'` and `"`.

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

@@ -89,7 +89,6 @@ async def collect_task_pixi(
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupActivityV2Read:
-
     settings = Inject(get_settings)
     # Check if Pixi is available
     if settings.pixi is None:

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

@@ -72,7 +72,6 @@ async def get_task_group_activity_list(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupActivityV2Read]:
-
     stm = select(TaskGroupActivityV2).where(
         TaskGroupActivityV2.user_id == user.id
     )
@@ -105,7 +104,6 @@ async def get_task_group_activity(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupActivityV2Read:
-
     activity = await db.get(TaskGroupActivityV2, task_group_activity_id)
 
     if activity is None:

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

@@ -115,7 +115,6 @@ async def deactivate_task_group(
     # Submit background task
     settings = Inject(get_settings)
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-
         # Validate user settings (backend-specific)
         user_settings = await validate_user_settings(
             user=user, backend=settings.FRACTAL_RUNNER_BACKEND, db=db
@@ -242,7 +241,6 @@ async def reactivate_task_group(
     # Submit background task
     settings = Inject(get_settings)
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-
         # Validate user settings (backend-specific)
         user_settings = await validate_user_settings(
             user=user, backend=settings.FRACTAL_RUNNER_BACKEND, db=db

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

@@ -78,7 +78,6 @@ async def get_workflow_version_update_candidates(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[list[TaskVersionRead]]:
-
     workflow = await _get_workflow_check_owner(
         project_id=project_id,
         workflow_id=workflow_id,
@@ -181,7 +180,6 @@ async def replace_workflowtask(
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> WorkflowTaskReadV2:
-
     # Get objects from database
     workflow_task, workflow = await _get_workflow_task_check_owner(
         project_id=project_id,

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

@@ -147,7 +147,6 @@ async def update_workflow(
 
     for key, value in patch.model_dump(exclude_unset=True).items():
         if key == "reordered_workflowtask_ids":
-
             if await _workflow_has_submitted_job(
                 workflow_id=workflow_id, db=db
             ):
@@ -329,7 +328,6 @@ async def get_workflow_type_filters(
 
     response_items = []
     for wftask in workflow.task_list:
-
         # Compute input_type_filters, based on wftask and task manifest
         input_type_filters = merge_type_filters(
             wftask_type_filters=wftask.type_filters,

fractal_server/app/routes/auth/group.py

@@ -39,7 +39,6 @@ async def get_list_user_groups(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[UserGroupRead]:
-
     # Get all groups
     stm_all_groups = select(UserGroup)
     res = await db.execute(stm_all_groups)
@@ -88,7 +87,6 @@ async def create_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-
     # Check that name is not already in use
     existing_name_str = select(UserGroup).where(
         UserGroup.name == group_create.name
@@ -121,7 +119,6 @@ async def update_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-
     group = await _usergroup_or_404(group_id, db)
 
     # Patch `viewer_paths`
@@ -143,7 +140,6 @@ async def delete_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
-
     group = await _usergroup_or_404(group_id, db)
 
     if group.name == FRACTAL_DEFAULT_GROUP_NAME:
@@ -219,7 +215,6 @@ async def remove_user_from_group(
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-
     # Check that user and group exist
     await _usergroup_or_404(group_id, db)
     user = await _user_or_404(user_id, db)

fractal_server/app/routes/pagination.py

@@ -11,7 +11,6 @@ T = TypeVar("T")
 
 
 class PaginationRequest(BaseModel):
-
     page: int = Field(ge=1)
     page_size: int | None = Field(ge=1)
 
@@ -38,7 +37,6 @@ def get_pagination_params(
 
 
 class PaginationResponse(BaseModel, Generic[T]):
-
     current_page: int = Field(ge=1)
     page_size: int = Field(ge=0)
     total_count: int = Field(ge=0)

fractal_server/app/runner/executors/local/runner.py

@@ -28,7 +28,6 @@ def run_single_task(
     parameters: dict[str, Any],
     task_files: TaskFiles,
 ):
-
     # Write args.json file
     with open(task_files.args_file_local, "w") as f:
         json.dump(parameters, f)
@@ -169,7 +168,6 @@ class LocalRunner(BaseRunner):
         exceptions: dict[int, BaseException] = {}
 
         try:
-
             self.validate_multisubmit_parameters(
                 list_parameters=list_parameters,
                 task_type=task_type,
@@ -208,7 +206,6 @@ class LocalRunner(BaseRunner):
 
         # Execute tasks, in chunks of size `parallel_tasks_per_job`
         for ind_chunk in range(0, n_elements, parallel_tasks_per_job):
-
             list_parameters_chunk = list_parameters[
                 ind_chunk : ind_chunk + parallel_tasks_per_job
             ]

fractal_server/app/runner/v2/db_tools.py

@@ -50,7 +50,6 @@ def bulk_update_status_of_history_unit(
     status: HistoryUnitStatus,
     db_sync: Session,
 ) -> None:
-
     len_history_unit_ids = len(history_unit_ids)
     logger.debug(
         f"[bulk_update_status_of_history_unit] {len_history_unit_ids=}."

fractal_server/app/runner/v2/merge_outputs.py

@@ -3,7 +3,6 @@ from fractal_server.app.runner.v2.task_interface import TaskOutput
 
 
 def merge_outputs(task_outputs: list[TaskOutput]) -> TaskOutput:
-
     if len(task_outputs) == 0:
         return TaskOutput()
 
@@ -11,7 +10,6 @@ def merge_outputs(task_outputs: list[TaskOutput]) -> TaskOutput:
     final_image_list_removals = []
 
     for task_output in task_outputs:
-
         final_image_list_updates.extend(task_output.image_list_updates)
         final_image_list_removals.extend(task_output.image_list_removals)
 

fractal_server/app/runner/v2/runner.py

@@ -415,7 +415,6 @@ def execute_tasks_v2(
             # Write current dataset images into the database.
             db_dataset = db.get(DatasetV2, dataset.id)
             if ENRICH_IMAGES_WITH_STATUS:
-
                 db_dataset.images = _remove_status_from_attributes(tmp_images)
             else:
                 db_dataset.images = tmp_images

fractal_server/app/runner/v2/task_interface.py

@@ -11,7 +11,6 @@ from fractal_server.types import ZarrUrlStr
 
 
 class TaskOutput(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     image_list_updates: list[SingleImageTaskOutput] = Field(
@@ -40,7 +39,6 @@ class TaskOutput(BaseModel):
 
 
 class InitArgsModel(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     zarr_url: ZarrUrlStr
@@ -48,14 +46,13 @@ class InitArgsModel(BaseModel):
 
 
 class InitTaskOutput(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     parallelization_list: list[InitArgsModel] = Field(default_factory=list)
 
 
 def _cast_and_validate_TaskOutput(
-    task_output: dict[str, Any]
+    task_output: dict[str, Any],
 ) -> TaskOutput | None:
     try:
         validated_task_output = TaskOutput(**task_output)

fractal_server/app/schemas/v2/accounting.py

@@ -6,7 +6,6 @@ from pydantic.types import AwareDatetime
 
 
 class AccountingRecordRead(BaseModel):
-
     id: int
     user_id: int
     timestamp: AwareDatetime

fractal_server/app/schemas/v2/project.py

@@ -9,14 +9,12 @@ from fractal_server.types import NonEmptyStr
 
 
 class ProjectCreateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
 class ProjectReadV2(BaseModel):
-
     id: int
     name: str
     timestamp_created: AwareDatetime
@@ -27,7 +25,6 @@ class ProjectReadV2(BaseModel):
 
 
 class ProjectUpdateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None

fractal_server/app/schemas/v2/workflow.py

@@ -17,14 +17,12 @@ from fractal_server.types import NonEmptyStr
 
 
 class WorkflowCreateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
 class WorkflowReadV2(BaseModel):
-
     id: int
     name: str
     project_id: int
@@ -42,7 +40,6 @@ class WorkflowReadV2WithWarnings(WorkflowReadV2):
 
 
 class WorkflowUpdateV2(BaseModel):
-
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None