fractal-server 2.14.5__py3-none-any.whl → 2.14.7__py3-none-any.whl

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

@@ -30,6 +30,7 @@ from fractal_server.app.schemas.v2 import TaskGroupReadV2
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
+from fractal_server.ssh._fabric import SSHConfig
 from fractal_server.syringe import Inject
 from fractal_server.tasks.v2.local import deactivate_local
 from fractal_server.tasks.v2.local import reactivate_local
@@ -120,19 +121,17 @@ async def deactivate_task_group(
             user=user, backend=settings.FRACTAL_RUNNER_BACKEND, db=db
         )
         # User appropriate FractalSSH object
-        ssh_credentials = dict(
+        ssh_config = SSHConfig(
             user=user_settings.ssh_username,
             host=user_settings.ssh_host,
             key_path=user_settings.ssh_private_key_path,
         )
-        fractal_ssh_list = request.app.state.fractal_ssh_list
-        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
 
         background_tasks.add_task(
             deactivate_ssh,
             task_group_id=task_group.id,
             task_group_activity_id=task_group_activity.id,
-            fractal_ssh=fractal_ssh,
+            ssh_config=ssh_config,
             tasks_base_dir=user_settings.ssh_tasks_dir,
         )
     else:
@@ -238,19 +237,17 @@ async def reactivate_task_group(
             user=user, backend=settings.FRACTAL_RUNNER_BACKEND, db=db
         )
         # Use appropriate FractalSSH object
-        ssh_credentials = dict(
+        ssh_config = SSHConfig(
             user=user_settings.ssh_username,
             host=user_settings.ssh_host,
             key_path=user_settings.ssh_private_key_path,
         )
-        fractal_ssh_list = request.app.state.fractal_ssh_list
-        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
 
         background_tasks.add_task(
             reactivate_ssh,
             task_group_id=task_group.id,
             task_group_activity_id=task_group_activity.id,
-            fractal_ssh=fractal_ssh,
+            ssh_config=ssh_config,
             tasks_base_dir=user_settings.ssh_tasks_dir,
         )
     else:

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

@@ -16,6 +16,7 @@ from .task_collection import router as task_collection_router_v2
 from .task_collection_custom import router as task_collection_router_v2_custom
 from .task_group import router as task_group_router_v2
 from .task_group_lifecycle import router as task_group_lifecycle_router_v2
+from .task_version_update import router as task_version_update_router_v2
 from .workflow import router as workflow_router_v2
 from .workflow_import import router as workflow_import_router_v2
 from .workflowtask import router as workflowtask_router_v2
@@ -55,6 +56,7 @@ router_api_v2.include_router(
 )
 
 router_api_v2.include_router(task_router_v2, prefix="/task", tags=["V2 Task"])
+router_api_v2.include_router(task_version_update_router_v2, tags=["V2 Task"])
 router_api_v2.include_router(
     task_group_router_v2, prefix="/task-group", tags=["V2 TaskGroup"]
 )

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

@@ -3,8 +3,6 @@ Auxiliary functions to get object from the database or perform simple checks
 """
 from typing import Any
 from typing import Literal
-from typing import Optional
-from typing import Union
 
 from fastapi import HTTPException
 from fastapi import status
@@ -233,7 +231,7 @@ async def _get_dataset_check_owner(
     dataset_id: int,
     user_id: int,
     db: AsyncSession,
-) -> dict[Literal["dataset", "project"], Union[DatasetV2, ProjectV2]]:
+) -> dict[Literal["dataset", "project"], DatasetV2 | ProjectV2]:
     """
     Get a dataset and a project, after access control on the project
 
@@ -279,7 +277,7 @@ async def _get_job_check_owner(
     job_id: int,
     user_id: int,
     db: AsyncSession,
-) -> dict[Literal["job", "project"], Union[JobV2, ProjectV2]]:
+) -> dict[Literal["job", "project"], JobV2 | ProjectV2]:
     """
     Get a job and a project, after access control on the project
 
@@ -331,11 +329,11 @@ async def _workflow_insert_task(
     *,
     workflow_id: int,
     task_id: int,
-    meta_parallel: Optional[dict[str, Any]] = None,
-    meta_non_parallel: Optional[dict[str, Any]] = None,
-    args_non_parallel: Optional[dict[str, Any]] = None,
-    args_parallel: Optional[dict[str, Any]] = None,
-    type_filters: Optional[dict[str, bool]] = None,
+    meta_parallel: dict[str, Any] | None = None,
+    meta_non_parallel: dict[str, Any] | None = None,
+    args_non_parallel: dict[str, Any] | None = None,
+    args_parallel: dict[str, Any] | None = None,
+    type_filters: dict[str, bool] | None = None,
     db: AsyncSession,
 ) -> WorkflowTaskV2:
     """

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

@@ -81,7 +81,7 @@ def read_log_file(
         )
 
     try:
-        with open(logfile, "r") as f:
+        with open(logfile) as f:
             return f.read()
     except Exception as e:
         return (

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

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import HTTPException
 from fastapi import status
 from httpx import AsyncClient
@@ -23,7 +21,7 @@ logger = set_logger(__name__)
 
 async def get_package_version_from_pypi(
     name: str,
-    version: Optional[str] = None,
+    version: str | None = None,
 ) -> str:
     """
     Make a GET call to PyPI JSON API and get latest *compatible* version.

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

@@ -3,7 +3,6 @@ Auxiliary functions to get task and task-group object from the database or
 perform simple checks
 """
 from typing import Any
-from typing import Optional
 
 from fastapi import HTTPException
 from fastapi import status
@@ -191,11 +190,11 @@ async def _get_task_read_access(
 
 async def _get_valid_user_group_id(
     *,
-    user_group_id: Optional[int] = None,
+    user_group_id: int | None = None,
     private: bool,
     user_id: int,
     db: AsyncSession,
-) -> Optional[int]:
+) -> int | None:
     """
     Validate query parameters for endpoints that create some task(s).
 
@@ -257,7 +256,7 @@ async def _verify_non_duplication_user_constraint(
     db: AsyncSession,
     user_id: int,
     pkg_name: str,
-    version: Optional[str],
+    version: str | None,
 ):
     stm = (
         select(TaskGroupV2)
@@ -294,9 +293,9 @@ async def _verify_non_duplication_user_constraint(
 
 async def _verify_non_duplication_group_constraint(
     db: AsyncSession,
-    user_group_id: Optional[int],
+    user_group_id: int | None,
     pkg_name: str,
-    version: Optional[str],
+    version: str | None,
 ):
     if user_group_id is None:
         return

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

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -38,7 +36,7 @@ async def create_dataset(
     dataset: DatasetCreateV2,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[DatasetReadV2]:
+) -> DatasetReadV2 | None:
     """
     Add new dataset to current project
     """
@@ -92,7 +90,7 @@ async def read_dataset_list(
     project_id: int,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[list[DatasetReadV2]]:
+) -> list[DatasetReadV2] | None:
     """
     Get dataset list for given project
     """
@@ -120,7 +118,7 @@ async def read_dataset(
     dataset_id: int,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[DatasetReadV2]:
+) -> DatasetReadV2 | None:
     """
     Get info on a dataset associated to the current project
     """
@@ -145,7 +143,7 @@ async def update_dataset(
     dataset_update: DatasetUpdateV2,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[DatasetReadV2]:
+) -> DatasetReadV2 | None:
     """
     Edit a dataset associated to the current project
     """
@@ -247,7 +245,7 @@ async def export_dataset(
     dataset_id: int,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[DatasetExportV2]:
+) -> DatasetExportV2 | None:
     """
     Export an existing dataset
     """
@@ -274,7 +272,7 @@ async def import_dataset(
     dataset: DatasetImportV2,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[DatasetReadV2]:
+) -> DatasetReadV2 | None:
     """
     Import an existing dataset into a project
     """

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

@@ -1,6 +1,5 @@
 from copy import deepcopy
 from typing import Any
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -123,19 +122,17 @@ async def get_workflow_tasks_statuses(
                 .where(
                     HistoryImageCache.latest_history_unit_id == HistoryUnit.id
                 )
-                .where(HistoryUnit.status == target_status.value)
+                .where(HistoryUnit.status == target_status)
             )
             res = await db.execute(stm)
             num_images = res.scalar()
-            response[wftask.id][
-                f"num_{target_status.value}_images"
-            ] = num_images
+            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.value}_images"]
+                value[f"num_{target_status}_images"]
                 for target_status in HistoryUnitStatus
             )
             if num_total_images > value["num_available_images"]:
@@ -213,7 +210,7 @@ async def get_history_run_units(
     dataset_id: int,
     workflowtask_id: int,
     history_run_id: int,
-    unit_status: Optional[HistoryUnitStatus] = None,
+    unit_status: HistoryUnitStatus | None = None,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
     pagination: PaginationRequest = Depends(get_pagination_params),
@@ -274,7 +271,7 @@ async def get_history_images(
     dataset_id: int,
     workflowtask_id: int,
     request_body: ImageQuery,
-    unit_status: Optional[HistoryUnitStatusQuery] = None,
+    unit_status: HistoryUnitStatusQuery | None = None,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
     pagination: PaginationRequest = Depends(get_pagination_params),

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

@@ -1,5 +1,4 @@
 from typing import Any
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -44,7 +43,7 @@ class ImageQuery(BaseModel):
 
 
 class ImageQueryWithZarrUrl(ImageQuery):
-    zarr_url: Optional[str] = None
+    zarr_url: str | None = None
 
 
 @router.post(
@@ -106,7 +105,7 @@ async def post_new_image(
 async def query_dataset_images(
     project_id: int,
     dataset_id: int,
-    query: Optional[ImageQueryWithZarrUrl] = None,
+    query: ImageQueryWithZarrUrl | None = None,
     pagination: PaginationRequest = Depends(get_pagination_params),
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),

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

@@ -1,7 +1,6 @@
 import asyncio
+from collections.abc import Iterator
 from pathlib import Path
-from typing import Iterator
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -71,7 +70,7 @@ async def get_workflow_jobs(
     workflow_id: int,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[list[JobReadV2]]:
+) -> list[JobReadV2] | None:
     """
     Returns all the jobs related to a specific workflow
     """
@@ -123,7 +122,7 @@ async def read_job(
     show_tmp_logs: bool = False,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[JobReadV2]:
+) -> JobReadV2 | None:
     """
     Return info on an existing job
     """
@@ -139,7 +138,7 @@ async def read_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
@@ -187,7 +186,7 @@ async def get_job_list(
     user: UserOAuth = Depends(current_active_user),
     log: bool = True,
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[list[JobReadV2]]:
+) -> list[JobReadV2] | None:
     """
     Get job list for given project
     """

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

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import status
@@ -32,7 +30,7 @@ router = APIRouter()
 async def verify_unique_types(
     project_id: int,
     dataset_id: int,
-    query: Optional[ImageQuery] = None,
+    query: ImageQuery | None = None,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[str]:

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

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -50,7 +48,7 @@ async def create_project(
     project: ProjectCreateV2,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[ProjectReadV2]:
+) -> ProjectReadV2 | None:
     """
     Create new project
     """
@@ -76,7 +74,7 @@ async def read_project(
     project_id: int,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[ProjectReadV2]:
+) -> ProjectReadV2 | None:
     """
     Return info on an existing project
     """

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

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -32,7 +30,7 @@ async def get_workflowtask_status(
     workflow_id: int,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[LegacyStatusReadV2]:
+) -> LegacyStatusReadV2 | None:
     """
     Extract the status of all `WorkflowTaskV2` of a given `WorkflowV2` that ran
     on a given `DatasetV2`.
@@ -119,7 +117,7 @@ async def get_workflowtask_status(
         except ValueError:
             logger.warning(
                 f"Job {running_job.id} is submitted but its task list does not"
-                f" contain a {WorkflowTaskStatusTypeV2.SUBMITTED.value} task."
+                f" contain a {WorkflowTaskStatusTypeV2.SUBMITTED} task."
             )
             first_submitted_index = 0
 

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

@@ -1,7 +1,6 @@
 import json
 import os
 from pathlib import Path
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import BackgroundTasks
@@ -57,7 +56,7 @@ async def apply_workflow(
     request: Request,
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[JobReadV2]:
+) -> JobReadV2 | None:
 
     # Remove non-submitted V2 jobs from the app state when the list grows
     # beyond a threshold
@@ -223,13 +222,13 @@ async def apply_workflow(
 
     # User appropriate FractalSSH object
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-        ssh_credentials = dict(
+        ssh_config = dict(
             user=user_settings.ssh_username,
             host=user_settings.ssh_host,
             key_path=user_settings.ssh_private_key_path,
         )
         fractal_ssh_list = request.app.state.fractal_ssh_list
-        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
+        fractal_ssh = fractal_ssh_list.get(**ssh_config)
     else:
         fractal_ssh = None
 

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

@@ -1,5 +1,4 @@
 from copy import deepcopy  # noqa
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -37,9 +36,9 @@ logger = set_logger(__name__)
 @router.get("/", response_model=list[TaskReadV2])
 async def get_list_task(
     args_schema: bool = True,
-    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_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskReadV2]:
@@ -98,7 +97,7 @@ async def patch_task(
     task_update: TaskUpdateV2,
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[TaskReadV2]:
+) -> TaskReadV2 | None:
     """
     Edit a specific task (restricted to task owner)
     """
@@ -135,11 +134,11 @@ async def patch_task(
 )
 async def create_task(
     task: TaskCreateV2,
-    user_group_id: Optional[int] = None,
+    user_group_id: int | None = None,
     private: bool = False,
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[TaskReadV2]:
+) -> TaskReadV2 | None:
     """
     Create a new task
     """

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

@@ -1,6 +1,5 @@
 import json
 from pathlib import Path
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import BackgroundTasks
@@ -41,6 +40,7 @@ from fractal_server.app.schemas.v2 import (
     TaskGroupActivityActionV2,
 )
 from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
+from fractal_server.ssh._fabric import SSHConfig
 from fractal_server.tasks.v2.local.collect import (
     collect_local,
 )
@@ -65,7 +65,7 @@ class CollectionRequestData(BaseModel):
     """
 
     task_collect: TaskCollectPipV2
-    file: Optional[UploadFile] = None
+    file: UploadFile | None = None
     origin: TaskGroupV2OriginEnum
 
     @model_validator(mode="before")
@@ -105,12 +105,12 @@ class CollectionRequestData(BaseModel):
 
 
 def parse_request_data(
-    package: Optional[str] = Form(None),
-    package_version: Optional[str] = Form(None),
-    package_extras: Optional[str] = Form(None),
-    python_version: Optional[str] = Form(None),
-    pinned_package_versions: Optional[str] = Form(None),
-    file: Optional[UploadFile] = File(None),
+    package: str | None = Form(None),
+    package_version: str | None = Form(None),
+    package_extras: str | None = Form(None),
+    python_version: str | None = Form(None),
+    pinned_package_versions: str | None = Form(None),
+    file: UploadFile | None = File(None),
 ) -> CollectionRequestData:
     """
     Expand the parsing/validation of `parse_form_data`, based on `file`.
@@ -156,7 +156,7 @@ async def collect_tasks_pip(
     background_tasks: BackgroundTasks,
     request_data: CollectionRequestData = Depends(parse_request_data),
     private: bool = False,
-    user_group_id: Optional[int] = None,
+    user_group_id: int | None = None,
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupActivityV2Read:
@@ -342,19 +342,17 @@ async def collect_tasks_pip(
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
         # SSH task collection
         # Use appropriate FractalSSH object
-        ssh_credentials = dict(
+        ssh_config = SSHConfig(
             user=user_settings.ssh_username,
             host=user_settings.ssh_host,
             key_path=user_settings.ssh_private_key_path,
         )
-        fractal_ssh_list = request.app.state.fractal_ssh_list
-        fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
 
         background_tasks.add_task(
             collect_ssh,
             task_group_id=task_group.id,
             task_group_activity_id=task_group_activity.id,
-            fractal_ssh=fractal_ssh,
+            ssh_config=ssh_config,
             tasks_base_dir=user_settings.ssh_tasks_dir,
             wheel_file=wheel_file,
         )

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

@@ -2,7 +2,6 @@ import os
 import shlex
 import subprocess  # nosec
 from pathlib import Path
-from typing import Optional
 
 from fastapi import APIRouter
 from fastapi import Depends
@@ -44,7 +43,7 @@ logger = set_logger(__name__)
 async def collect_task_custom(
     task_collect: TaskCollectCustomV2,
     private: bool = False,
-    user_group_id: Optional[int] = None,
+    user_group_id: int | None = None,
     user: UserOAuth = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskReadV2]:
@@ -152,6 +151,7 @@ async def collect_task_custom(
         pkg_name=task_collect.label,
         user_id=user.id,
         user_group_id=user_group_id,
+        version=task_collect.version,
     )
     TaskGroupCreateV2(**task_group_attrs)
 
@@ -159,13 +159,13 @@ async def collect_task_custom(
     await _verify_non_duplication_user_constraint(
         user_id=user.id,
         pkg_name=task_group_attrs["pkg_name"],
-        version=None,
+        version=task_group_attrs["version"],
         db=db,
     )
     await _verify_non_duplication_group_constraint(
         user_group_id=task_group_attrs["user_group_id"],
         pkg_name=task_group_attrs["pkg_name"],
-        version=None,
+        version=task_group_attrs["version"],
         db=db,
     )
 

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

@@ -1,5 +1,3 @@
-from typing import Optional
-
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -37,12 +35,12 @@ 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,
-    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,
+    taskgroupv2_id: int | None = None,
+    pkg_name: str | None = None,
+    status: TaskGroupActivityStatusV2 | None = None,
+    action: TaskGroupActivityActionV2 | None = None,
+    timestamp_started_min: AwareDatetime | None = None,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupActivityV2Read]: