fractal-server 2.3.7__tar.gz → 2.3.8__tar.gz

{fractal_server-2.3.7 → fractal_server-2.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.3.7
+Version: 2.3.8
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -23,7 +23,7 @@ Requires-Dist: bcrypt (==4.0.1)
 Requires-Dist: cloudpickle (>=3.0.0,<3.1.0)
 Requires-Dist: clusterfutures (>=0.5,<0.6)
 Requires-Dist: fabric (>=3.2.2,<4.0.0)
-Requires-Dist: fastapi (>=0.110.0,<0.111.0)
+Requires-Dist: fastapi (>=0.112.0,<0.113.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
 Requires-Dist: gunicorn (>=21.2,<23.0) ; extra == "gunicorn"
 Requires-Dist: packaging (>=23.2,<24.0)
@@ -35,6 +35,7 @@ Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
 Requires-Dist: sqlmodel (>=0.0.21,<0.0.22)
 Requires-Dist: uvicorn (>=0.29.0,<0.30.0)
+Requires-Dist: uvicorn-worker (>=0.2.0,<0.3.0)
 Project-URL: Changelog, https://github.com/fractal-analytics-platform/fractal-server/blob/main/CHANGELOG.md
 Project-URL: Documentation, https://fractal-analytics-platform.github.io/fractal-server
 Project-URL: Repository, https://github.com/fractal-analytics-platform/fractal-server
@@ -48,10 +49,9 @@ Description-Content-Type: text/markdown
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Benchmarks](https://img.shields.io/badge/Benchmarks-Done-blue)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/benchmark-api/benchmarks/bench.html)
 
-Fractal is a framework to process high content imaging data at scale and
-prepare it for interactive visualization.
+[Fractal](https://fractal-analytics-platform.github.io/) is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
 
-![Fractal_Overview](https://fractal-analytics-platform.github.io/assets/fractal_overview.jpg)
+![Fractal_overview](https://github.com/user-attachments/assets/286122d9-08cf-48e8-996d-3cf53e0a81c6)
 
 This is the server component of the fractal analytics platform.
 Find more information about Fractal in general and the other repositories at

{fractal_server-2.3.7 → fractal_server-2.3.8}/README.md

@@ -6,10 +6,9 @@
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Benchmarks](https://img.shields.io/badge/Benchmarks-Done-blue)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/benchmark-api/benchmarks/bench.html)
 
-Fractal is a framework to process high content imaging data at scale and
-prepare it for interactive visualization.
+[Fractal](https://fractal-analytics-platform.github.io/) is a framework developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) to process bioimaging data at scale in the OME-Zarr format and prepare the images for interactive visualization.
 
-![Fractal_Overview](https://fractal-analytics-platform.github.io/assets/fractal_overview.jpg)
+![Fractal_overview](https://github.com/user-attachments/assets/286122d9-08cf-48e8-996d-3cf53e0a81c6)
 
 This is the server component of the fractal analytics platform.
 Find more information about Fractal in general and the other repositories at

fractal_server-2.3.8/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.3.8"

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/admin/v1.py

@@ -18,6 +18,7 @@ from sqlmodel import select
 from ....config import get_settings
 from ....syringe import Inject
 from ....utils import get_timestamp
+from ....zip_tools import _zip_folder_to_byte_stream_iterator
 from ...db import AsyncSession
 from ...db import get_async_db
 from ...models.security import UserOAuth as User
@@ -34,7 +35,6 @@ from ...schemas.v1 import ProjectReadV1
 from ...schemas.v1 import WorkflowReadV1
 from ...security import current_active_superuser
 from ..aux._job import _write_shutdown_file
-from ..aux._job import _zip_folder_to_byte_stream
 from ..aux._runner import _check_shutdown_is_supported
 
 router_admin_v1 = APIRouter()
@@ -387,9 +387,8 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
-        iter([byte_stream.getvalue()]),
+        _zip_folder_to_byte_stream_iterator(folder=job.working_dir),
         media_type="application/x-zip-compressed",
         headers={"Content-Disposition": f"attachment;filename={zip_filename}"},
     )

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/admin/v2.py

@@ -21,6 +21,7 @@ from sqlmodel import select
 from ....config import get_settings
 from ....syringe import Inject
 from ....utils import get_timestamp
+from ....zip_tools import _zip_folder_to_byte_stream_iterator
 from ...db import AsyncSession
 from ...db import get_async_db
 from ...models.security import UserOAuth as User
@@ -37,7 +38,6 @@ from ...schemas.v2 import JobUpdateV2
 from ...schemas.v2 import ProjectReadV2
 from ...security import current_active_superuser
 from ..aux._job import _write_shutdown_file
-from ..aux._job import _zip_folder_to_byte_stream
 from ..aux._runner import _check_shutdown_is_supported
 
 router_admin_v2 = APIRouter()
@@ -274,9 +274,8 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
-        iter([byte_stream.getvalue()]),
+        _zip_folder_to_byte_stream_iterator(folder=job.working_dir),
         media_type="application/x-zip-compressed",
         headers={"Content-Disposition": f"attachment;filename={zip_filename}"},
     )

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/_aux_functions.py

@@ -11,6 +11,8 @@ from fastapi import status
 from sqlmodel import select
 from sqlmodel.sql.expression import SelectOfScalar
 
+from .....config import get_settings
+from .....syringe import Inject
 from ....db import AsyncSession
 from ....models.v1 import ApplyWorkflow
 from ....models.v1 import Dataset
@@ -23,6 +25,15 @@ from ....schemas.v1 import JobStatusTypeV1
 from ....security import User
 
 
+def _raise_if_v1_is_read_only() -> None:
+    settings = Inject(get_settings)
+    if settings.FRACTAL_API_V1_MODE == "include_read_only":
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail="Legacy API is in read-only mode.",
+        )
+
+
 async def _get_project_check_owner(
     *,
     project_id: int,

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/dataset.py

@@ -33,7 +33,7 @@ from ._aux_functions import _get_dataset_check_owner
 from ._aux_functions import _get_project_check_owner
 from ._aux_functions import _get_submitted_jobs_statement
 from ._aux_functions import _get_workflow_check_owner
-
+from ._aux_functions import _raise_if_v1_is_read_only
 
 router = APIRouter()
 
@@ -52,6 +52,7 @@ async def create_dataset(
     """
     Add new dataset to current project
     """
+    _raise_if_v1_is_read_only()
     await _get_project_check_owner(
         project_id=project_id, user_id=user.id, db=db
     )
@@ -133,7 +134,7 @@ async def update_dataset(
     """
     Edit a dataset associated to the current project
     """
-
+    _raise_if_v1_is_read_only()
     if dataset_update.history is not None:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -170,6 +171,7 @@ async def delete_dataset(
     """
     Delete a dataset associated to the current project
     """
+    _raise_if_v1_is_read_only()
     output = await _get_dataset_check_owner(
         project_id=project_id,
         dataset_id=dataset_id,
@@ -243,6 +245,7 @@ async def create_resource(
     """
     Add resource to an existing dataset
     """
+    _raise_if_v1_is_read_only()
     output = await _get_dataset_check_owner(
         project_id=project_id,
         dataset_id=dataset_id,
@@ -299,6 +302,7 @@ async def update_resource(
     """
     Edit a resource of a dataset
     """
+    _raise_if_v1_is_read_only()
     output = await _get_dataset_check_owner(
         project_id=project_id,
         dataset_id=dataset_id,
@@ -339,6 +343,7 @@ async def delete_resource(
     """
     Delete a resource of a dataset
     """
+    _raise_if_v1_is_read_only()
     # Get the dataset DB entry
     output = await _get_dataset_check_owner(
         project_id=project_id,

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/job.py

@@ -8,6 +8,7 @@ from fastapi import status
 from fastapi.responses import StreamingResponse
 from sqlmodel import select
 
+from .....zip_tools import _zip_folder_to_byte_stream_iterator
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v1 import ApplyWorkflow
@@ -18,7 +19,6 @@ from ....schemas.v1 import ApplyWorkflowReadV1
 from ....security import current_active_user
 from ....security import User
 from ...aux._job import _write_shutdown_file
-from ...aux._job import _zip_folder_to_byte_stream
 from ...aux._runner import _check_shutdown_is_supported
 from ._aux_functions import _get_job_check_owner
 from ._aux_functions import _get_project_check_owner
@@ -128,9 +128,8 @@ async def download_job_logs(
     # Create and return byte stream for zipped log folder
     PREFIX_ZIP = Path(job.working_dir).name
     zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
     return StreamingResponse(
-        iter([byte_stream.getvalue()]),
+        _zip_folder_to_byte_stream_iterator(folder=job.working_dir),
         media_type="application/x-zip-compressed",
         headers={"Content-Disposition": f"attachment;filename={zip_filename}"},
     )

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/project.py

@@ -42,6 +42,7 @@ from ._aux_functions import _get_dataset_check_owner
 from ._aux_functions import _get_project_check_owner
 from ._aux_functions import _get_submitted_jobs_statement
 from ._aux_functions import _get_workflow_check_owner
+from ._aux_functions import _raise_if_v1_is_read_only
 from ._aux_functions import clean_app_job_list_v1
 
 router = APIRouter()
@@ -80,7 +81,7 @@ async def create_project(
     """
     Create new poject
     """
-
+    _raise_if_v1_is_read_only()
     # Check that there is no project with the same user and name
     await _check_project_exists(
         project_name=project.name, user_id=user.id, db=db
@@ -120,6 +121,7 @@ async def update_project(
     user: User = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
 ):
+    _raise_if_v1_is_read_only()
     project = await _get_project_check_owner(
         project_id=project_id, user_id=user.id, db=db
     )
@@ -148,6 +150,7 @@ async def delete_project(
     """
     Delete project
     """
+    _raise_if_v1_is_read_only()
     project = await _get_project_check_owner(
         project_id=project_id, user_id=user.id, db=db
     )
@@ -249,16 +252,8 @@ async def apply_workflow(
     user: User = Depends(current_active_verified_user),
     db: AsyncSession = Depends(get_async_db),
 ) -> Optional[ApplyWorkflowReadV1]:
-
+    _raise_if_v1_is_read_only()
     settings = Inject(get_settings)
-    if settings.FRACTAL_API_V1_MODE == "include_without_submission":
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                "Legacy API is still accessible, "
-                "but the submission of legacy jobs is not available."
-            ),
-        )
 
     # Remove non-submitted V1 jobs from the app state when the list grows
     # beyond a threshold

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/task.py

@@ -21,6 +21,7 @@ from ....security import current_active_user
 from ....security import current_active_verified_user
 from ....security import User
 from ._aux_functions import _get_task_check_owner
+from ._aux_functions import _raise_if_v1_is_read_only
 
 router = APIRouter()
 
@@ -75,7 +76,7 @@ async def patch_task(
     """
     Edit a specific task (restricted to superusers and task owner)
     """
-
+    _raise_if_v1_is_read_only()
     if task_update.source:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
@@ -121,6 +122,7 @@ async def create_task(
     """
     Create a new task
     """
+    _raise_if_v1_is_read_only()
     # Set task.owner attribute
     if user.username:
         owner = user.username
@@ -174,7 +176,7 @@ async def delete_task(
     """
     Delete a task
     """
-
+    _raise_if_v1_is_read_only()
     db_task = await _get_task_check_owner(task_id=task_id, user=user, db=db)
 
     # Check that the Task is not in relationship with some WorkflowTask

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/task_collection.py

@@ -25,6 +25,7 @@ from ....schemas.v1 import TaskCollectStatusV1
 from ....security import current_active_user
 from ....security import current_active_verified_user
 from ....security import User
+from ._aux_functions import _raise_if_v1_is_read_only
 from fractal_server.string_tools import slugify_task_name_for_source
 from fractal_server.tasks.utils import get_collection_log
 from fractal_server.tasks.v1._TaskCollectPip import _TaskCollectPip
@@ -71,7 +72,7 @@ async def collect_tasks_pip(
     Trigger the creation of a dedicated virtual environment, the installation
     of a package and the collection of tasks as advertised in the manifest.
     """
-
+    _raise_if_v1_is_read_only()
     logger = set_logger(logger_name="collect_tasks_pip")
 
     # Validate payload as _TaskCollectPip, which has more strict checks than

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/workflow.py

@@ -39,6 +39,7 @@ from ._aux_functions import _check_workflow_exists
 from ._aux_functions import _get_project_check_owner
 from ._aux_functions import _get_submitted_jobs_statement
 from ._aux_functions import _get_workflow_check_owner
+from ._aux_functions import _raise_if_v1_is_read_only
 from ._aux_functions import _workflow_insert_task
 
 
@@ -84,6 +85,7 @@ async def create_workflow(
     """
     Create a workflow, associate to a project
     """
+    _raise_if_v1_is_read_only()
     await _get_project_check_owner(
         project_id=project_id,
         user_id=user.id,
@@ -136,6 +138,7 @@ async def update_workflow(
     """
     Edit a workflow
     """
+    _raise_if_v1_is_read_only()
     workflow = await _get_workflow_check_owner(
         project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
     )
@@ -187,7 +190,7 @@ async def delete_workflow(
     """
     Delete a workflow
     """
-
+    _raise_if_v1_is_read_only()
     workflow = await _get_workflow_check_owner(
         project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
     )
@@ -275,7 +278,7 @@ async def import_workflow(
     Also create all required objects (i.e. Workflow and WorkflowTask's) along
     the way.
     """
-
+    _raise_if_v1_is_read_only()
     # Preliminary checks
     await _get_project_check_owner(
         project_id=project_id,

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v1/workflowtask.py

@@ -30,6 +30,7 @@ from ....security import current_active_user
 from ....security import User
 from ._aux_functions import _get_workflow_check_owner
 from ._aux_functions import _get_workflow_task_check_owner
+from ._aux_functions import _raise_if_v1_is_read_only
 from ._aux_functions import _workflow_insert_task
 
 router = APIRouter()
@@ -51,7 +52,7 @@ async def create_workflowtask(
     """
     Add a WorkflowTask to a Workflow
     """
-
+    _raise_if_v1_is_read_only()
     workflow = await _get_workflow_check_owner(
         project_id=project_id, workflow_id=workflow_id, user_id=user.id, db=db
     )
@@ -112,7 +113,7 @@ async def update_workflowtask(
     """
     Edit a WorkflowTask of a Workflow
     """
-
+    _raise_if_v1_is_read_only()
     db_workflow_task, db_workflow = await _get_workflow_task_check_owner(
         project_id=project_id,
         workflow_task_id=workflow_task_id,
@@ -167,7 +168,7 @@ async def delete_workflowtask(
     """
     Delete a WorkflowTask of a Workflow
     """
-
+    _raise_if_v1_is_read_only()
     db_workflow_task, db_workflow = await _get_workflow_task_check_owner(
         project_id=project_id,
         workflow_task_id=workflow_task_id,

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/api/v2/job.py

@@ -8,6 +8,7 @@ from fastapi import status
 from fastapi.responses import StreamingResponse
 from sqlmodel import select
 
+from .....zip_tools import _zip_folder_to_byte_stream_iterator
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import JobV2
@@ -18,7 +19,6 @@ from ....schemas.v2 import JobStatusTypeV2
 from ....security import current_active_user
 from ....security import User
 from ...aux._job import _write_shutdown_file
-from ...aux._job import _zip_folder_to_byte_stream
 from ...aux._runner import _check_shutdown_is_supported
 from ._aux_functions import _get_job_check_owner
 from ._aux_functions import _get_project_check_owner
@@ -118,7 +118,7 @@ async def download_job_logs(
     db: AsyncSession = Depends(get_async_db),
 ) -> StreamingResponse:
     """
-    Download job folder
+    Download zipped job folder
     """
     output = await _get_job_check_owner(
         project_id=project_id,
@@ -127,15 +127,11 @@ async def download_job_logs(
         db=db,
     )
     job = output["job"]
-
-    # Create and return byte stream for zipped log folder
-    PREFIX_ZIP = Path(job.working_dir).name
-    zip_filename = f"{PREFIX_ZIP}_archive.zip"
-    byte_stream = _zip_folder_to_byte_stream(folder=job.working_dir)
+    zip_name = f"{Path(job.working_dir).name}_archive.zip"
     return StreamingResponse(
-        iter([byte_stream.getvalue()]),
+        _zip_folder_to_byte_stream_iterator(folder=job.working_dir),
         media_type="application/x-zip-compressed",
-        headers={"Content-Disposition": f"attachment;filename={zip_filename}"},
+        headers={"Content-Disposition": f"attachment;filename={zip_name}"},
     )
 
 

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/routes/aux/_job.py

@@ -1,9 +1,5 @@
-import os
-from io import BytesIO
 from pathlib import Path
 from typing import Union
-from zipfile import ZIP_DEFLATED
-from zipfile import ZipFile
 
 from ...models.v1 import ApplyWorkflow
 from ...models.v2 import JobV2
@@ -24,22 +20,3 @@ def _write_shutdown_file(*, job: Union[ApplyWorkflow, JobV2]):
     shutdown_file = Path(job.working_dir) / SHUTDOWN_FILENAME
     with shutdown_file.open("w") as f:
         f.write(f"Trigger executor shutdown for {job.id=}.")
-
-
-def _zip_folder_to_byte_stream(*, folder: str) -> BytesIO:
-    """
-    Get byte stream with the zipped log folder of a job.
-
-    Args:
-        folder: the folder to zip
-    """
-
-    byte_stream = BytesIO()
-    with ZipFile(byte_stream, mode="w", compression=ZIP_DEFLATED) as zipfile:
-        for root, dirs, files in os.walk(folder):
-            for file in files:
-                file_path = os.path.join(root, file)
-                archive_path = os.path.relpath(file_path, folder)
-                zipfile.write(file_path, archive_path)
-
-    return byte_stream

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/app/runner/v2/__init__.py

@@ -5,7 +5,6 @@ This module is the single entry point to the runner backend subsystem V2.
 Other subystems should only import this module and not its submodules or
 the individual backends.
 """
-import logging
 import os
 import traceback
 from pathlib import Path
@@ -21,6 +20,7 @@ from ....logger import set_logger
 from ....ssh._fabric import FractalSSH
 from ....syringe import Inject
 from ....utils import get_timestamp
+from ....zip_tools import _zip_folder_to_file_and_remove
 from ...db import DB
 from ...models.v2 import DatasetV2
 from ...models.v2 import JobV2
@@ -114,9 +114,34 @@ async def submit_workflow(
 
     with next(DB.get_sync_db()) as db_sync:
 
-        job: JobV2 = db_sync.get(JobV2, job_id)
-        if not job:
+        try:
+            job: Optional[JobV2] = db_sync.get(JobV2, job_id)
+            dataset: Optional[DatasetV2] = db_sync.get(DatasetV2, dataset_id)
+            workflow: Optional[WorkflowV2] = db_sync.get(
+                WorkflowV2, workflow_id
+            )
+        except Exception as e:
+            logger.error(
+                f"Error conneting to the database. Original error: {str(e)}"
+            )
+            reset_logger_handlers(logger)
+            return
+
+        if job is None:
             logger.error(f"JobV2 {job_id} does not exist")
+            reset_logger_handlers(logger)
+            return
+        if dataset is None or workflow is None:
+            log_msg = ""
+            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"
+                )
+            fail_job(
+                db=db_sync, job=job, log_msg=log_msg, logger_name=logger_name
+            )
             return
 
         # Declare runner backend and set `process_workflow` function
@@ -137,21 +162,6 @@ async def submit_workflow(
             )
             return
 
-        dataset: DatasetV2 = db_sync.get(DatasetV2, dataset_id)
-        workflow: WorkflowV2 = db_sync.get(WorkflowV2, workflow_id)
-        if not (dataset and workflow):
-            log_msg = ""
-            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"
-                )
-            fail_job(
-                db=db_sync, job=job, log_msg=log_msg, logger_name=logger_name
-            )
-            return
-
         # Define and create server-side working folder
         WORKFLOW_DIR_LOCAL = Path(job.working_dir)
         if WORKFLOW_DIR_LOCAL.exists():
@@ -192,9 +202,9 @@ async def submit_workflow(
                 fractal_ssh.mkdir(
                     folder=str(WORKFLOW_DIR_REMOTE),
                 )
-                logging.info(f"Created {str(WORKFLOW_DIR_REMOTE)} via SSH.")
+                logger.info(f"Created {str(WORKFLOW_DIR_REMOTE)} via SSH.")
             else:
-                logging.error(
+                logger.error(
                     "Invalid FRACTAL_RUNNER_BACKEND="
                     f"{settings.FRACTAL_RUNNER_BACKEND}."
                 )
@@ -219,7 +229,7 @@ async def submit_workflow(
                         user=slurm_user,
                     )
                 else:
-                    logging.info("Skip remote-subfolder creation")
+                    logger.info("Skip remote-subfolder creation")
         except Exception as e:
             error_type = type(e).__name__
             fail_job(
@@ -448,3 +458,4 @@ async def submit_workflow(
     finally:
         reset_logger_handlers(logger)
         db_sync.close()
+        _zip_folder_to_file_and_remove(folder=job.working_dir)

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/config.py

@@ -547,7 +547,7 @@ class Settings(BaseSettings):
     """
 
     FRACTAL_API_V1_MODE: Literal[
-        "include", "include_without_submission", "exclude"
+        "include", "include_read_only", "exclude"
     ] = "include"
     """
     Whether to include the v1 API.

{fractal_server-2.3.7 → fractal_server-2.3.8}/fractal_server/gunicorn_fractal.py

@@ -3,7 +3,7 @@ import os
 import signal
 
 from gunicorn.glogging import Logger as GunicornLogger
-from uvicorn.workers import UvicornWorker
+from uvicorn_worker import UvicornWorker
 
 logger = logging.getLogger("uvicorn.error")