fractal-server 2.18.0__py3-none-any.whl → 2.18.0a1__py3-none-any.whl

fractal_server/config/_data.py

@@ -0,0 +1,79 @@
+from enum import StrEnum
+from typing import Self
+
+from pydantic import model_validator
+from pydantic_settings import BaseSettings
+from pydantic_settings import SettingsConfigDict
+
+from fractal_server.types import AbsolutePathStr
+
+from ._settings_config import SETTINGS_CONFIG_DICT
+
+
+class DataAuthScheme(StrEnum):
+    VIEWER_PATHS = "viewer-paths"
+    USERS_FOLDERS = "users-folders"
+    NONE = "none"
+
+
+class DataSettings(BaseSettings):
+    """
+    Settings for the `fractal-data` integration.
+
+    See https://github.com/fractal-analytics-platform/fractal-data.
+
+    Attributes:
+        FRACTAL_DATA_AUTH_SCHEME:
+            Defines how the list of allowed viewer paths is built.
+
+            This variable affects the
+            `GET /auth/current-user/allowed-viewer-paths/` response, which is
+            then consumed by
+            [fractal-data](https://github.com/fractal-analytics-platform/fractal-data).
+
+            Options:
+                <ul>
+                <li> `"viewer-paths"`: The list of allowed viewer paths will
+                    include the user's `project_dir` along with any path
+                    defined in  UserGroups `viewer_paths` attributes.
+                </li>
+                <li> `"users-folders"`: The list will consist of the user's
+                    `project_dir` and a user-specific folder. The user folder
+                    is constructed by concatenating the base folder
+                    `FRACTAL_DATA_BASE_FOLDER` with the user's profile
+                    `username`.
+                </li>
+                <li> `"none"`: An empty list will be returned, indicating no
+                    access to viewer paths. Useful when vizarr viewer is not
+                    used.
+                </li>
+                </ul>
+        FRACTAL_DATA_BASE_FOLDER:
+            Base path to Zarr files that will be served by
+            fractal-vizarr-viewer.
+            This variable is required and used only when
+            `FRACTAL_DATA_AUTHORIZATION_SCHEME` is set to `"users-folders"`.
+    """
+
+    model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
+
+    FRACTAL_DATA_AUTH_SCHEME: DataAuthScheme = "none"
+
+    FRACTAL_DATA_BASE_FOLDER: AbsolutePathStr | None = None
+
+    @model_validator(mode="after")
+    def check(self: Self) -> Self:
+        """
+        `FRACTAL_DATA_BASE_FOLDER` is required when
+        `FRACTAL_DATA_AUTHORIZATION_SCHEME` is set to `"users-folders"`.
+        """
+        if (
+            self.FRACTAL_DATA_AUTH_SCHEME == DataAuthScheme.USERS_FOLDERS
+            and self.FRACTAL_DATA_BASE_FOLDER is None
+        ):
+            raise ValueError(
+                "FRACTAL_DATA_BASE_FOLDER is required when "
+                "FRACTAL_DATA_AUTH_SCHEME is set to "
+                "users-folders"
+            )
+        return self

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 `jobs` attribute of
+            Number of ids that can be stored in the `jobsV2` attribute of
             `app.state`.
         FRACTAL_GRACEFUL_SHUTDOWN_TIME:
             Waiting time for the shutdown phase of executors, in seconds.
@@ -41,10 +41,6 @@ class Settings(BaseSettings):
             user group (e.g. it cannot be deleted, and new users are
             automatically added to it). If set to `None` (the default value),
             then user groups are all equivalent, independently on their name.
-        FRACTAL_LONG_REQUEST_TIME:
-            Time limit beyond which the execution of an API request is
-            considered *slow* and an appropriate warning is logged by the
-            middleware.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -61,4 +57,3 @@ class Settings(BaseSettings):
     FRACTAL_GRACEFUL_SHUTDOWN_TIME: float = 30.0
     FRACTAL_HELP_URL: HttpUrl | None = None
     FRACTAL_DEFAULT_GROUP_NAME: Literal["All"] | None = None
-    FRACTAL_LONG_REQUEST_TIME: float = 30.0

fractal_server/images/models.py

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

fractal_server/main.py

@@ -1,20 +1,15 @@
 import os
-import time
 from contextlib import asynccontextmanager
-from datetime import datetime
 from itertools import chain
 
 from fastapi import FastAPI
-from starlette.types import Message
-from starlette.types import Receive
-from starlette.types import Scope
-from starlette.types import Send
 
 from fractal_server import __VERSION__
 from fractal_server.app.schemas.v2 import ResourceType
 
 from .app.routes.aux._runner import _backend_supports_shutdown
 from .app.shutdown import cleanup_after_shutdown
+from .config import get_data_settings
 from .config import get_db_settings
 from .config import get_email_settings
 from .config import get_settings
@@ -33,14 +28,16 @@ def collect_routers(app: FastAPI) -> None:
         app:
             The application to register the routers to.
     """
-    from .app.routes.admin.v2 import router_admin
+    from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.api import router_api
-    from .app.routes.api.v2 import router_api as router_api_v2
+    from .app.routes.api.v2 import 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, prefix="/admin/v2", tags=["Admin area"])
+    app.include_router(
+        router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
+    )
     app.include_router(router_auth, prefix="/auth", tags=["Authentication"])
 
 
@@ -57,12 +54,14 @@ def check_settings() -> None:
     settings = Inject(get_settings)
     db_settings = Inject(get_db_settings)
     email_settings = Inject(get_email_settings)
+    data_settings = Inject(get_data_settings)
     logger = set_logger("fractal_server_settings")
     logger.debug("Fractal Settings:")
     for key, value in chain(
         db_settings.model_dump().items(),
         settings.model_dump().items(),
         email_settings.model_dump().items(),
+        data_settings.model_dump().items(),
     ):
         if any(s in key.upper() for s in ["PASSWORD", "SECRET", "KEY"]):
             value = "*****"
@@ -72,7 +71,7 @@ def check_settings() -> None:
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
-    app.state.jobs = []
+    app.state.jobsV2 = []
     logger = set_logger("fractal_server.lifespan")
     logger.info(f"[startup] START (fractal-server {__VERSION__})")
     check_settings()
@@ -109,12 +108,12 @@ async def lifespan(app: FastAPI):
 
     logger.info(
         f"[teardown] Current worker with pid {os.getpid()} is shutting down. "
-        f"Current jobs: {app.state.jobs=}"
+        f"Current jobs: {app.state.jobsV2=}"
     )
     if _backend_supports_shutdown(settings.FRACTAL_RUNNER_BACKEND):
         try:
             await cleanup_after_shutdown(
-                jobs=app.state.jobs,
+                jobsV2=app.state.jobsV2,
                 logger_name="fractal_server.lifespan",
             )
         except Exception as e:
@@ -132,59 +131,6 @@ async def lifespan(app: FastAPI):
     reset_logger_handlers(logger)
 
 
-slow_response_logger = set_logger("slow-response")
-
-
-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:
-    def __init__(self, app: FastAPI, time_threshold: float):
-        self.app = app
-        self.time_threshold = time_threshold
-
-    async def __call__(self, scope: Scope, receive: Receive, send: Send):
-        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
-
-        # Mutable variable which can be updated from within `send_wrapper`
-        context = {"status_code": None}
-
-        async def send_wrapper(message: Message):
-            if message["type"] == "http.response.start":
-                context["status_code"] = message["status"]
-            await send(message)
-
-        # Measure request time
-        start_timestamp = datetime.now()
-        start_time = time.perf_counter()
-        await self.app(scope, receive, send_wrapper)
-        stop_time = time.perf_counter()
-        request_time = stop_time - start_time
-
-        # Log if process time is too high
-        if request_time > self.time_threshold:
-            end_timestamp = datetime.now()
-            slow_response_logger.warning(
-                f"{scope['method']} {scope['route'].path}"
-                f"?{scope['query_string'].decode('utf-8')}, "
-                f"{context['status_code']}, "
-                f"{request_time:.2f}, "
-                f"{start_timestamp.isoformat(timespec='milliseconds')}, "
-                f"{end_timestamp.isoformat(timespec='milliseconds')}"
-            )
-
-
 def start_application() -> FastAPI:
     """
     Create the application, initialise it and collect all available routers.
@@ -194,13 +140,6 @@ def start_application() -> FastAPI:
             The fully initialised application.
     """
     app = FastAPI(lifespan=lifespan)
-
-    settings = Inject(get_settings)
-    app.add_middleware(
-        SlowResponseMiddleware,
-        time_threshold=settings.FRACTAL_LONG_REQUEST_TIME,
-    )
-
     collect_routers(app)
     return app
 

fractal_server/runner/config/_slurm.py

@@ -34,7 +34,6 @@ class SlurmConfigSet(BaseModel):
         account:
         extra_lines:
         gpus:
-        shebang_line: The shell shebang to use for SLURM jobs.
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -50,7 +49,6 @@ class SlurmConfigSet(BaseModel):
     account: NonEmptyStr | None = None
     extra_lines: list[NonEmptyStr] = Field(default_factory=list)
     gpus: NonEmptyStr | None = None
-    shebang_line: str = "#!/bin/sh"
 
 
 class BatchingConfigSet(BaseModel):

fractal_server/runner/executors/slurm_common/slurm_config.py

@@ -60,7 +60,6 @@ class SlurmConfig(BaseModel):
             Key-value pairs to be included as `export`-ed variables in SLURM
             submission script, after prepending values with the user's cache
             directory.
-
     """
 
     model_config = ConfigDict(extra="forbid")

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
+from .runner import execute_tasks_v2
 
 
 def process_workflow(
@@ -59,7 +59,7 @@ def process_workflow(
         resource: Computational resource for running this job.
         profile: Computational profile for running this job.
         user_cache_dir:
-            User-writeable folder (typically a subfolder of `project_dirs`).
+            User-writeable folder (typically a subfolder of `project_dir`).
             Only relevant for `slurm_sudo` and `slurm_ssh` backends.
         fractal_ssh:
             `FractalSSH` object, only relevant for the `slurm_ssh` backend.
@@ -90,7 +90,7 @@ def process_workflow(
         resource=resource,
         profile=profile,
     ) as runner:
-        execute_tasks(
+        execute_tasks_v2(
             wf_task_list=workflow.task_list[
                 first_task_index : (last_task_index + 1)
             ],
@@ -104,5 +104,4 @@ 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
+from .runner import execute_tasks_v2
 
 logger = set_logger(__name__)
 
@@ -80,7 +80,7 @@ def process_workflow(
         resource: Computational resource for running this job.
         profile: Computational profile for running this job.
         user_cache_dir:
-            User-writeable folder (typically a subfolder of `project_dirs`).
+            User-writeable folder (typically a subfolder of `project_dir`).
             Only relevant for `slurm_sudo` and `slurm_ssh` backends.
         fractal_ssh:
             `FractalSSH` object, only relevant for the `slurm_ssh` backend.
@@ -113,7 +113,7 @@ def process_workflow(
         common_script_lines=worker_init,
         user_cache_dir=user_cache_dir,
     ) as runner:
-        execute_tasks(
+        execute_tasks_v2(
             wf_task_list=workflow.task_list[
                 first_task_index : (last_task_index + 1)
             ],
@@ -127,5 +127,4 @@ 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
+from .runner import execute_tasks_v2
 
 
 def process_workflow(
@@ -77,7 +77,7 @@ def process_workflow(
         resource: Computational resource for running this job.
         profile: Computational profile for running this job.
         user_cache_dir:
-            User-writeable folder (typically a subfolder of `project_dirs`).
+            User-writeable folder (typically a subfolder of `project_dir`).
             Only relevant for `slurm_sudo` and `slurm_ssh` backends.
         fractal_ssh:
             `FractalSSH` object, only relevant for the `slurm_ssh` backend.
@@ -109,7 +109,7 @@ def process_workflow(
         user_cache_dir=user_cache_dir,
         slurm_account=slurm_account,
     ) as runner:
-        execute_tasks(
+        execute_tasks_v2(
             wf_task_list=workflow.task_list[
                 first_task_index : (last_task_index + 1)
             ],
@@ -123,5 +123,4 @@ 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

@@ -14,12 +14,11 @@ 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 TaskDump
-from fractal_server.app.schemas.v2 import TaskGroupDump
+from fractal_server.app.schemas.v2 import TaskDumpV2
+from fractal_server.app.schemas.v2 import TaskGroupDumpV2
 from fractal_server.app.schemas.v2 import TaskType
 from fractal_server.images import SingleImage
 from fractal_server.images.status_tools import IMAGE_STATUS_KEY
@@ -36,9 +35,9 @@ 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_task_compound
-from .runner_functions import run_task_non_parallel
-from .runner_functions import run_task_parallel
+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 .task_interface import TaskOutput
 
 
@@ -83,7 +82,7 @@ def get_origin_attribute_and_types(
     return updated_attributes, updated_types
 
 
-def execute_tasks(
+def execute_tasks_v2(
     *,
     wf_task_list: list[WorkflowTaskV2],
     dataset: DatasetV2,
@@ -96,7 +95,6 @@ def execute_tasks(
     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)
 
@@ -167,10 +165,10 @@ def execute_tasks(
             # Create dumps for workflowtask and taskgroup
             workflowtask_dump = dict(
                 **wftask.model_dump(exclude={"task"}),
-                task=TaskDump(**wftask.task.model_dump()).model_dump(),
+                task=TaskDumpV2(**wftask.task.model_dump()).model_dump(),
             )
             task_group = db.get(TaskGroupV2, wftask.task.taskgroupv2_id)
-            task_group_dump = TaskGroupDump(
+            task_group_dump = TaskGroupDumpV2(
                 **task_group.model_dump()
             ).model_dump()
             # Create HistoryRun
@@ -213,37 +211,20 @@ def execute_tasks(
                 f"attribute_filters={job_attribute_filters})."
             )
             logger.info(error_msg)
-            with next(get_sync_db()) as db:
-                update_status_of_history_run(
-                    history_run_id=history_run_id,
-                    status=HistoryUnitStatus.FAILED,
-                    db_sync=db,
-                )
+            update_status_of_history_run(
+                history_run_id=history_run_id,
+                status=HistoryUnitStatus.FAILED,
+                db_sync=db,
+            )
             raise JobExecutionError(error_msg)
 
-        # 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
+        # TASK EXECUTION (V2)
         try:
             if task.type in [
                 TaskType.NON_PARALLEL,
                 TaskType.CONVERTER_NON_PARALLEL,
             ]:
-                outcomes_dict, num_tasks = run_task_non_parallel(
+                outcomes_dict, num_tasks = run_v2_task_non_parallel(
                     images=filtered_images,
                     zarr_dir=zarr_dir,
                     wftask=wftask,
@@ -258,7 +239,7 @@ def execute_tasks(
                     user_id=user_id,
                 )
             elif task.type == TaskType.PARALLEL:
-                outcomes_dict, num_tasks = run_task_parallel(
+                outcomes_dict, num_tasks = run_v2_task_parallel(
                     images=filtered_images,
                     wftask=wftask,
                     task=task,
@@ -274,7 +255,7 @@ def execute_tasks(
                 TaskType.COMPOUND,
                 TaskType.CONVERTER_COMPOUND,
             ]:
-                outcomes_dict, num_tasks = run_task_compound(
+                outcomes_dict, num_tasks = run_v2_task_compound(
                     images=filtered_images,
                     zarr_dir=zarr_dir,
                     wftask=wftask,

fractal_server/runner/v2/runner_functions.py

@@ -64,9 +64,9 @@ GetRunnerConfigType = GetRunnerConfigTypeLocal | GetRunnerConfigTypeSLURM
 
 
 __all__ = [
-    "run_task_parallel",
-    "run_task_non_parallel",
-    "run_task_compound",
+    "run_v2_task_parallel",
+    "run_v2_task_non_parallel",
+    "run_v2_task_compound",
 ]
 
 
@@ -145,7 +145,7 @@ def _check_parallelization_list_size(my_list):
         )
 
 
-def run_task_non_parallel(
+def run_v2_task_non_parallel(
     *,
     images: list[dict[str, Any]],
     zarr_dir: str,
@@ -168,7 +168,9 @@ def run_task_non_parallel(
         TaskType.NON_PARALLEL,
         TaskType.CONVERTER_NON_PARALLEL,
     ]:
-        raise ValueError(f"Invalid {task_type=} for `run_task_non_parallel`.")
+        raise ValueError(
+            f"Invalid {task_type=} for `run_v2_task_non_parallel`."
+        )
 
     # Get TaskFiles object
     task_files = TaskFiles(
@@ -211,7 +213,7 @@ def run_task_non_parallel(
         db.commit()
         db.refresh(history_unit)
         logger.debug(
-            "[run_task_non_parallel] Created `HistoryUnit` with "
+            "[run_v2_task_non_parallel] Created `HistoryUnit` with "
             f"{history_run_id=}."
         )
         history_unit_id = history_unit.id
@@ -263,7 +265,7 @@ def run_task_non_parallel(
     return outcome, num_tasks
 
 
-def run_task_parallel(
+def run_v2_task_parallel(
     *,
     images: list[dict[str, Any]],
     task: TaskV2,
@@ -324,7 +326,7 @@ def run_task_parallel(
         db.add_all(history_units)
         db.commit()
         logger.debug(
-            f"[run_task_non_parallel] Created {len(history_units)} "
+            f"[run_v2_task_non_parallel] Created {len(history_units)} "
             "`HistoryUnit`s."
         )
 
@@ -386,7 +388,7 @@ def run_task_parallel(
     return outcome, num_tasks
 
 
-def run_task_compound(
+def run_v2_task_compound(
     *,
     images: list[dict[str, Any]],
     zarr_dir: str,
@@ -443,7 +445,7 @@ def run_task_compound(
         db.refresh(history_unit)
         init_history_unit_id = history_unit.id
         logger.debug(
-            "[run_task_compound] Created `HistoryUnit` with "
+            "[run_v2_task_compound] Created `HistoryUnit` with "
             f"{init_history_unit_id=}."
         )
         # Create one `HistoryImageCache` for each input image
@@ -555,7 +557,8 @@ def run_task_compound(
         for history_unit in history_units:
             db.refresh(history_unit)
         logger.debug(
-            f"[run_task_compound] Created {len(history_units)} `HistoryUnit`s."
+            f"[run_v2_task_compound] Created {len(history_units)} "
+            "`HistoryUnit`s."
         )
         history_unit_ids = [history_unit.id for history_unit in history_units]
 

fractal_server/runner/v2/submit_workflow.py

@@ -20,7 +20,7 @@ from fractal_server.app.models.v2 import JobV2
 from fractal_server.app.models.v2 import Profile
 from fractal_server.app.models.v2 import Resource
 from fractal_server.app.models.v2 import WorkflowV2
-from fractal_server.app.schemas.v2 import JobStatusType
+from fractal_server.app.schemas.v2 import JobStatusTypeV2
 from fractal_server.app.schemas.v2 import ResourceType
 from fractal_server.logger import get_logger
 from fractal_server.logger import reset_logger_handlers
@@ -71,7 +71,7 @@ def fail_job(
         logger.error(log_msg)
     reset_logger_handlers(logger)
     job = db.get(JobV2, job.id)  # refetch, in case it was updated
-    job.status = JobStatusType.FAILED
+    job.status = JobStatusTypeV2.FAILED
     job.end_timestamp = get_timestamp()
     job.log = log_msg
     db.merge(job)
@@ -145,27 +145,14 @@ def submit_workflow(
             return
         if dataset is None or workflow is None:
             log_msg = ""
-            if dataset is None:
-                current_log_msg = (
-                    f"Cannot fetch dataset {dataset_id} from database "
-                    f"(as part of job {job_id})."
+            if not dataset:
+                log_msg += f"Cannot fetch dataset {dataset_id} from database\n"
+            if not workflow:
+                log_msg += (
+                    f"Cannot fetch workflow {workflow_id} from database\n"
                 )
-                logger.error(current_log_msg)
-                log_msg += f"{current_log_msg}\n"
-            if workflow is None:
-                current_log_msg += (
-                    f"Cannot fetch workflow {workflow_id} from database "
-                    f"(as part of job {job_id})."
-                )
-                logger.error(current_log_msg)
-                log_msg += f"{current_log_msg}\n"
-
             fail_job(
-                db=db_sync,
-                job=job,
-                log_msg=log_msg,
-                logger_name=logger_name,
-                emit_log=False,
+                db=db_sync, job=job, log_msg=log_msg, logger_name=logger_name
             )
             return
 
@@ -286,7 +273,7 @@ def submit_workflow(
         # Update job DB entry
         with next(DB.get_sync_db()) as db_sync:
             job = db_sync.get(JobV2, job_id)
-            job.status = JobStatusType.DONE
+            job.status = JobStatusTypeV2.DONE
             job.end_timestamp = get_timestamp()
             with log_file_path.open("r") as f:
                 logs = f.read()