fractal-server 2.18.0a4__py3-none-any.whl → 2.18.0a6__py3-none-any.whl

fractal_server/app/schemas/v2/workflow.py

@@ -5,29 +5,29 @@ from pydantic import ConfigDict
 from pydantic import field_serializer
 from pydantic.types import AwareDatetime
 
-from fractal_server.app.schemas.v2.project import ProjectReadV2
-from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskExportV2
-from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskImportV2
-from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskReadV2
+from fractal_server.app.schemas.v2.project import ProjectRead
+from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskExport
+from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskImport
+from fractal_server.app.schemas.v2.workflowtask import WorkflowTaskRead
 from fractal_server.app.schemas.v2.workflowtask import (
-    WorkflowTaskReadV2WithWarning,
+    WorkflowTaskReadWithWarning,
 )
 from fractal_server.types import ListUniqueNonNegativeInt
 from fractal_server.types import NonEmptyStr
 
 
-class WorkflowCreateV2(BaseModel):
+class WorkflowCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
 
 
-class WorkflowReadV2(BaseModel):
+class WorkflowRead(BaseModel):
     id: int
     name: str
     project_id: int
-    task_list: list[WorkflowTaskReadV2]
-    project: ProjectReadV2
+    task_list: list[WorkflowTaskRead]
+    project: ProjectRead
     timestamp_created: AwareDatetime
 
     @field_serializer("timestamp_created")
@@ -35,18 +35,18 @@ class WorkflowReadV2(BaseModel):
         return v.isoformat()
 
 
-class WorkflowReadV2WithWarnings(WorkflowReadV2):
-    task_list: list[WorkflowTaskReadV2WithWarning]
+class WorkflowReadWithWarnings(WorkflowRead):
+    task_list: list[WorkflowTaskReadWithWarning]
 
 
-class WorkflowUpdateV2(BaseModel):
+class WorkflowUpdate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr = None
     reordered_workflowtask_ids: ListUniqueNonNegativeInt | None = None
 
 
-class WorkflowImportV2(BaseModel):
+class WorkflowImport(BaseModel):
     """
     Class for `Workflow` import.
 
@@ -56,10 +56,10 @@ class WorkflowImportV2(BaseModel):
 
     model_config = ConfigDict(extra="forbid")
     name: NonEmptyStr
-    task_list: list[WorkflowTaskImportV2]
+    task_list: list[WorkflowTaskImport]
 
 
-class WorkflowExportV2(BaseModel):
+class WorkflowExport(BaseModel):
     """
     Class for `Workflow` export.
 
@@ -68,4 +68,4 @@ class WorkflowExportV2(BaseModel):
     """
 
     name: str
-    task_list: list[WorkflowTaskExportV2]
+    task_list: list[WorkflowTaskExport]

fractal_server/app/schemas/v2/workflowtask.py

@@ -9,14 +9,14 @@ from fractal_server.types import DictStrAny
 from fractal_server.types import TypeFilters
 from fractal_server.types import WorkflowTaskArgument
 
-from .task import TaskExportV2
-from .task import TaskImportV2
-from .task import TaskImportV2Legacy
-from .task import TaskReadV2
+from .task import TaskExport
+from .task import TaskImport
+from .task import TaskImportLegacy
+from .task import TaskRead
 from .task import TaskType
 
 
-class WorkflowTaskCreateV2(BaseModel):
+class WorkflowTaskCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: DictStrAny | None = None
@@ -26,14 +26,14 @@ class WorkflowTaskCreateV2(BaseModel):
     type_filters: TypeFilters = Field(default_factory=dict)
 
 
-class WorkflowTaskReplaceV2(BaseModel):
+class WorkflowTaskReplace(BaseModel):
     """Used by 'replace-task' endpoint"""
 
     args_non_parallel: dict[str, Any] | None = None
     args_parallel: dict[str, Any] | None = None
 
 
-class WorkflowTaskReadV2(BaseModel):
+class WorkflowTaskRead(BaseModel):
     id: int
 
     workflow_id: int
@@ -48,14 +48,14 @@ class WorkflowTaskReadV2(BaseModel):
 
     task_type: TaskType
     task_id: int
-    task: TaskReadV2
+    task: TaskRead
 
 
-class WorkflowTaskReadV2WithWarning(WorkflowTaskReadV2):
+class WorkflowTaskReadWithWarning(WorkflowTaskRead):
     warning: str | None = None
 
 
-class WorkflowTaskUpdateV2(BaseModel):
+class WorkflowTaskUpdate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: DictStrAny | None = None
@@ -65,7 +65,7 @@ class WorkflowTaskUpdateV2(BaseModel):
     type_filters: TypeFilters = None
 
 
-class WorkflowTaskImportV2(BaseModel):
+class WorkflowTaskImport(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     meta_non_parallel: DictStrAny | None = None
@@ -75,7 +75,7 @@ class WorkflowTaskImportV2(BaseModel):
     type_filters: TypeFilters | None = None
     input_filters: dict[str, Any] | None = None
 
-    task: TaskImportV2 | TaskImportV2Legacy
+    task: TaskImport | TaskImportLegacy
 
     @model_validator(mode="before")
     @classmethod
@@ -106,11 +106,11 @@ class WorkflowTaskImportV2(BaseModel):
         return values
 
 
-class WorkflowTaskExportV2(BaseModel):
+class WorkflowTaskExport(BaseModel):
     meta_non_parallel: dict[str, Any] | None = None
     meta_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] = Field(default_factory=dict)
 
-    task: TaskExportV2
+    task: TaskExport

fractal_server/app/shutdown.py

@@ -4,26 +4,26 @@ from sqlmodel import select
 
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models.v2 import JobV2
-from fractal_server.app.models.v2.job import JobStatusTypeV2
+from fractal_server.app.models.v2.job import JobStatusType
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.config import get_settings
 from fractal_server.logger import get_logger
 from fractal_server.syringe import Inject
 
 
-async def cleanup_after_shutdown(*, jobsV2: list[int], logger_name: str):
+async def cleanup_after_shutdown(*, jobs: list[int], logger_name: str):
     settings = Inject(get_settings)
     logger = get_logger(logger_name)
     logger.info("Cleanup function after shutdown")
     stm_objects = (
         select(JobV2)
-        .where(JobV2.id.in_(jobsV2))
-        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
+        .where(JobV2.id.in_(jobs))
+        .where(JobV2.status == JobStatusType.SUBMITTED)
     )
     stm_ids = (
         select(JobV2.id)
-        .where(JobV2.id.in_(jobsV2))
-        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
+        .where(JobV2.id.in_(jobs))
+        .where(JobV2.status == JobStatusType.SUBMITTED)
     )
 
     async for session in get_async_db():

fractal_server/config/_main.py

@@ -28,7 +28,7 @@ class Settings(BaseSettings):
             Only logs of with this level (or higher) will appear in the console
             logs.
         FRACTAL_API_MAX_JOB_LIST_LENGTH:
-            Number of ids that can be stored in the `jobsV2` attribute of
+            Number of ids that can be stored in the `jobs` attribute of
             `app.state`.
         FRACTAL_GRACEFUL_SHUTDOWN_TIME:
             Waiting time for the shutdown phase of executors, in seconds.

fractal_server/data_migrations/2_18_0.py

@@ -1,5 +1,6 @@
 import logging
 import sys
+from os.path import normpath
 
 from sqlalchemy.orm.attributes import flag_modified
 from sqlmodel import select
@@ -21,7 +22,7 @@ def fix_db():
             logging.info(f"Now handling user {user.email}.")
             if user.project_dirs != []:
                 sys.exit(f"Non empty `project_dirs` for User[{user.id}]")
-            user.project_dirs.append(user.project_dir)
+            user.project_dirs.append(normpath(user.project_dir))
             flag_modified(user, "project_dirs")
 
         db.commit()

fractal_server/images/models.py

@@ -5,7 +5,6 @@ from fractal_server.types import DictStrAny
 from fractal_server.types import ImageAttributes
 from fractal_server.types import ImageAttributesWithNone
 from fractal_server.types import ImageTypes
-from fractal_server.types import ZarrDirStr
 from fractal_server.types import ZarrUrlStr
 
 
@@ -21,7 +20,7 @@ class SingleImageBase(BaseModel):
     """
 
     zarr_url: ZarrUrlStr
-    origin: ZarrDirStr | None = None
+    origin: ZarrUrlStr | None = None
 
     attributes: DictStrAny = Field(default_factory=dict)
     types: ImageTypes = Field(default_factory=dict)

fractal_server/main.py

@@ -33,16 +33,14 @@ def collect_routers(app: FastAPI) -> None:
         app:
             The application to register the routers to.
     """
-    from .app.routes.admin.v2 import router_admin_v2
+    from .app.routes.admin.v2 import router_admin
     from .app.routes.api import router_api
-    from .app.routes.api.v2 import router_api_v2
+    from .app.routes.api.v2 import router_api as router_api_v2
     from .app.routes.auth.router import router_auth
 
     app.include_router(router_api, prefix="/api")
     app.include_router(router_api_v2, prefix="/api/v2")
-    app.include_router(
-        router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
-    )
+    app.include_router(router_admin, prefix="/admin/v2", tags=["Admin area"])
     app.include_router(router_auth, prefix="/auth", tags=["Authentication"])
 
 
@@ -74,7 +72,7 @@ def check_settings() -> None:
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
-    app.state.jobsV2 = []
+    app.state.jobs = []
     logger = set_logger("fractal_server.lifespan")
     logger.info(f"[startup] START (fractal-server {__VERSION__})")
     check_settings()
@@ -111,12 +109,12 @@ async def lifespan(app: FastAPI):
 
     logger.info(
         f"[teardown] Current worker with pid {os.getpid()} is shutting down. "
-        f"Current jobs: {app.state.jobsV2=}"
+        f"Current jobs: {app.state.jobs=}"
     )
     if _backend_supports_shutdown(settings.FRACTAL_RUNNER_BACKEND):
         try:
             await cleanup_after_shutdown(
-                jobsV2=app.state.jobsV2,
+                jobs=app.state.jobs,
                 logger_name="fractal_server.lifespan",
             )
         except Exception as e:
@@ -136,7 +134,14 @@ async def lifespan(app: FastAPI):
 
 slow_response_logger = set_logger("slow-response")
 
-MIDDLEWARE_DATETIME_FORMAT = "%Y-%m-%d %H:%M:%S.%f"
+
+def _endpoint_has_background_task(method: str, path: str) -> bool:
+    has_background_task = (method == "POST") and (
+        "/job/submit/" in path
+        or "/task/collect/pi" in path  # "/pip" and "/pixi"
+        or "/task-group/" in path
+    )
+    return has_background_task
 
 
 class SlowResponseMiddleware:
@@ -145,8 +150,10 @@ class SlowResponseMiddleware:
         self.time_threshold = time_threshold
 
     async def __call__(self, scope: Scope, receive: Receive, send: Send):
-        # Filter out any non-http scope (e.g. `type="lifespan"`)
-        if scope["type"] != "http":
+        if (
+            scope["type"] != "http"  # e.g. `scope["type"] == "lifespan"`
+            or _endpoint_has_background_task(scope["method"], scope["path"])
+        ):
             await self.app(scope, receive, send)
             return
 
@@ -173,8 +180,8 @@ class SlowResponseMiddleware:
                 f"?{scope['query_string'].decode('utf-8')}, "
                 f"{context['status_code']}, "
                 f"{request_time:.2f}, "
-                f"{start_timestamp.strftime(MIDDLEWARE_DATETIME_FORMAT)}, "
-                f"{end_timestamp.strftime(MIDDLEWARE_DATETIME_FORMAT)}"
+                f"{start_timestamp.isoformat(timespec='milliseconds')}, "
+                f"{end_timestamp.isoformat(timespec='milliseconds')}"
             )
 
 

fractal_server/migrations/versions/88270f589c9b_add_prevent_new_submissions.py

@@ -0,0 +1,39 @@
+"""add_prevent_new_submissions
+
+Revision ID: 88270f589c9b
+Revises: f0702066b007
+Create Date: 2025-12-02 12:34:11.028259
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "88270f589c9b"
+down_revision = "f0702066b007"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("resource", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "prevent_new_submissions",
+                sa.BOOLEAN(),
+                server_default="false",
+                nullable=False,
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("resource", schema=None) as batch_op:
+        batch_op.drop_column("prevent_new_submissions")
+
+    # ### end Alembic commands ###

fractal_server/migrations/versions/f0702066b007_one_submitted_job_per_dataset.py

@@ -0,0 +1,40 @@
+"""One submitted Job per Dataset
+
+Revision ID: f0702066b007
+Revises: 7910eed4cf97
+Create Date: 2025-12-01 20:54:03.137093
+
+"""
+
+import sqlalchemy as sa
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "f0702066b007"
+down_revision = "7910eed4cf97"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("jobv2", schema=None) as batch_op:
+        batch_op.create_index(
+            "ix_jobv2_one_submitted_job_per_dataset",
+            ["dataset_id"],
+            unique=True,
+            postgresql_where=sa.text("status = 'submitted'"),
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("jobv2", schema=None) as batch_op:
+        batch_op.drop_index(
+            "ix_jobv2_one_submitted_job_per_dataset",
+            postgresql_where=sa.text("status = 'submitted'"),
+        )
+
+    # ### end Alembic commands ###

fractal_server/runner/v2/_local.py

@@ -14,7 +14,7 @@ from fractal_server.runner.set_start_and_last_task_index import (
 from fractal_server.ssh._fabric import FractalSSH
 from fractal_server.types import AttributeFilters
 
-from .runner import execute_tasks_v2
+from .runner import execute_tasks
 
 
 def process_workflow(
@@ -90,7 +90,7 @@ def process_workflow(
         resource=resource,
         profile=profile,
     ) as runner:
-        execute_tasks_v2(
+        execute_tasks(
             wf_task_list=workflow.task_list[
                 first_task_index : (last_task_index + 1)
             ],
@@ -104,4 +104,5 @@ def process_workflow(
             job_attribute_filters=job_attribute_filters,
             job_type_filters=job_type_filters,
             user_id=user_id,
+            resource_id=resource.id,
         )

fractal_server/runner/v2/_slurm_ssh.py

@@ -33,7 +33,7 @@ from fractal_server.runner.set_start_and_last_task_index import (
 from fractal_server.ssh._fabric import FractalSSH
 from fractal_server.types import AttributeFilters
 
-from .runner import execute_tasks_v2
+from .runner import execute_tasks
 
 logger = set_logger(__name__)
 
@@ -113,7 +113,7 @@ def process_workflow(
         common_script_lines=worker_init,
         user_cache_dir=user_cache_dir,
     ) as runner:
-        execute_tasks_v2(
+        execute_tasks(
             wf_task_list=workflow.task_list[
                 first_task_index : (last_task_index + 1)
             ],
@@ -127,4 +127,5 @@ def process_workflow(
             job_attribute_filters=job_attribute_filters,
             job_type_filters=job_type_filters,
             user_id=user_id,
+            resource_id=resource.id,
         )

fractal_server/runner/v2/_slurm_sudo.py

@@ -32,7 +32,7 @@ from fractal_server.runner.set_start_and_last_task_index import (
 from fractal_server.ssh._fabric import FractalSSH
 from fractal_server.types import AttributeFilters
 
-from .runner import execute_tasks_v2
+from .runner import execute_tasks
 
 
 def process_workflow(
@@ -109,7 +109,7 @@ def process_workflow(
         user_cache_dir=user_cache_dir,
         slurm_account=slurm_account,
     ) as runner:
-        execute_tasks_v2(
+        execute_tasks(
             wf_task_list=workflow.task_list[
                 first_task_index : (last_task_index + 1)
             ],
@@ -123,4 +123,5 @@ def process_workflow(
             job_attribute_filters=job_attribute_filters,
             job_type_filters=job_type_filters,
             user_id=user_id,
+            resource_id=resource.id,
         )

fractal_server/runner/v2/runner.py

@@ -14,11 +14,12 @@ from fractal_server.app.models.v2 import HistoryImageCache
 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 Resource
 from fractal_server.app.models.v2 import TaskGroupV2
 from fractal_server.app.models.v2 import WorkflowTaskV2
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
-from fractal_server.app.schemas.v2 import TaskDumpV2
-from fractal_server.app.schemas.v2 import TaskGroupDumpV2
+from fractal_server.app.schemas.v2 import TaskDump
+from fractal_server.app.schemas.v2 import TaskGroupDump
 from fractal_server.app.schemas.v2 import TaskType
 from fractal_server.images import SingleImage
 from fractal_server.images.status_tools import IMAGE_STATUS_KEY
@@ -35,9 +36,9 @@ from fractal_server.types import AttributeFilters
 from .merge_outputs import merge_outputs
 from .runner_functions import GetRunnerConfigType
 from .runner_functions import SubmissionOutcome
-from .runner_functions import run_v2_task_compound
-from .runner_functions import run_v2_task_non_parallel
-from .runner_functions import run_v2_task_parallel
+from .runner_functions import run_task_compound
+from .runner_functions import run_task_non_parallel
+from .runner_functions import run_task_parallel
 from .task_interface import TaskOutput
 
 
@@ -82,7 +83,7 @@ def get_origin_attribute_and_types(
     return updated_attributes, updated_types
 
 
-def execute_tasks_v2(
+def execute_tasks(
     *,
     wf_task_list: list[WorkflowTaskV2],
     dataset: DatasetV2,
@@ -95,6 +96,7 @@ def execute_tasks_v2(
     get_runner_config: GetRunnerConfigType,
     job_type_filters: dict[str, bool],
     job_attribute_filters: AttributeFilters,
+    resource_id: int,
 ) -> None:
     logger = get_logger(logger_name=logger_name)
 
@@ -165,10 +167,10 @@ def execute_tasks_v2(
             # Create dumps for workflowtask and taskgroup
             workflowtask_dump = dict(
                 **wftask.model_dump(exclude={"task"}),
-                task=TaskDumpV2(**wftask.task.model_dump()).model_dump(),
+                task=TaskDump(**wftask.task.model_dump()).model_dump(),
             )
             task_group = db.get(TaskGroupV2, wftask.task.taskgroupv2_id)
-            task_group_dump = TaskGroupDumpV2(
+            task_group_dump = TaskGroupDump(
                 **task_group.model_dump()
             ).model_dump()
             # Create HistoryRun
@@ -211,20 +213,37 @@ def execute_tasks_v2(
                 f"attribute_filters={job_attribute_filters})."
             )
             logger.info(error_msg)
-            update_status_of_history_run(
-                history_run_id=history_run_id,
-                status=HistoryUnitStatus.FAILED,
-                db_sync=db,
-            )
+            with next(get_sync_db()) as db:
+                update_status_of_history_run(
+                    history_run_id=history_run_id,
+                    status=HistoryUnitStatus.FAILED,
+                    db_sync=db,
+                )
             raise JobExecutionError(error_msg)
 
-        # TASK EXECUTION (V2)
+        # Fail if the resource is not open for new submissions
+        with next(get_sync_db()) as db:
+            resource = db.get(Resource, resource_id)
+            if resource.prevent_new_submissions:
+                error_msg = (
+                    f"Cannot run '{task.name}', since the '{resource.name}' "
+                    "resource is not currently active."
+                )
+                logger.info(error_msg)
+                update_status_of_history_run(
+                    history_run_id=history_run_id,
+                    status=HistoryUnitStatus.FAILED,
+                    db_sync=db,
+                )
+                raise JobExecutionError(error_msg)
+
+        # TASK EXECUTION
         try:
             if task.type in [
                 TaskType.NON_PARALLEL,
                 TaskType.CONVERTER_NON_PARALLEL,
             ]:
-                outcomes_dict, num_tasks = run_v2_task_non_parallel(
+                outcomes_dict, num_tasks = run_task_non_parallel(
                     images=filtered_images,
                     zarr_dir=zarr_dir,
                     wftask=wftask,
@@ -239,7 +258,7 @@ def execute_tasks_v2(
                     user_id=user_id,
                 )
             elif task.type == TaskType.PARALLEL:
-                outcomes_dict, num_tasks = run_v2_task_parallel(
+                outcomes_dict, num_tasks = run_task_parallel(
                     images=filtered_images,
                     wftask=wftask,
                     task=task,
@@ -255,7 +274,7 @@ def execute_tasks_v2(
                 TaskType.COMPOUND,
                 TaskType.CONVERTER_COMPOUND,
             ]:
-                outcomes_dict, num_tasks = run_v2_task_compound(
+                outcomes_dict, num_tasks = run_task_compound(
                     images=filtered_images,
                     zarr_dir=zarr_dir,
                     wftask=wftask,