fractal-server 2.7.0a11__tar.gz → 2.8.0__tar.gz

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/PKG-INFO

@@ -1,35 +1,29 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.7.0a11
+Version: 2.8.0
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
 Author: Tommaso Comparin
 Author-email: tommaso.comparin@exact-lab.it
-Requires-Python: >=3.9,<4.0
+Requires-Python: >=3.10,<4.0
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Provides-Extra: gunicorn
-Provides-Extra: postgres
-Provides-Extra: postgres-psycopg-binary
 Requires-Dist: aiosqlite (>=0.19.0,<0.20.0)
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: asyncpg (>=0.29.0,<0.30.0) ; extra == "postgres"
 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 (>=0.115.0,<0.116.0)
 Requires-Dist: fastapi-users[oauth] (>=12.1.0,<13.0.0)
-Requires-Dist: gunicorn (>=21.2,<23.0) ; extra == "gunicorn"
+Requires-Dist: gunicorn (>=21.2,<23.0)
 Requires-Dist: packaging (>=23.2,<24.0)
 Requires-Dist: psutil (>=5.9.8,<6.0.0)
-Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
-Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0) ; extra == "postgres-psycopg-binary"
+Requires-Dist: psycopg[binary] (>=3.1.0,<4.0.0)
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=1.0.0,<2.0.0)
 Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
@@ -43,15 +37,20 @@ Description-Content-Type: text/markdown
 
 # Fractal Server
 
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/16e9cf11-d47d-4db8-a9b1-f5349e4175b7" alt="Fractal server" width="400">
+</p>
+
 [![PyPI version](https://img.shields.io/pypi/v/fractal-server?color=gree)](https://pypi.org/project/fractal-server/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![CI Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml?query=branch%3Amain)
 [![Coverage](https://raw.githubusercontent.com/fractal-analytics-platform/fractal-server/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/python-coverage-comment-action-data/htmlcov/index.html)
-[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![Documentation Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/documentation.yaml/badge.svg)](https://fractal-analytics-platform.github.io/fractal-server)
 [![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](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://github.com/user-attachments/assets/286122d9-08cf-48e8-996d-3cf53e0a81c6)
+![Fractal_overview](https://github.com/user-attachments/assets/666c8797-2594-4b8e-b1d2-b43fca66d1df)
 
 This is the server component of the fractal analytics platform.
 Find more information about Fractal in general and the other repositories at
@@ -64,14 +63,12 @@ See https://fractal-analytics-platform.github.io/fractal-server.
 
 # Contributors and license
 
-Unless otherwise stated in each individual module, all Fractal components are
-released according to a BSD 3-Clause License, and Copyright is with Friedrich
-Miescher Institute for Biomedical Research and University of Zurich.
+Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it).
+
+Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.
 
 The SLURM compatibility layer is based on
 [`clusterfutures`](https://github.com/sampsyo/clusterfutures), by
 [@sampsyo](https://github.com/sampsyo) and collaborators, and it is released
 under the terms of the MIT license.
 
-Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it/).
-

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/README.md

@@ -1,14 +1,19 @@
 # Fractal Server
 
+<p align="center">
+  <img src="https://github.com/user-attachments/assets/16e9cf11-d47d-4db8-a9b1-f5349e4175b7" alt="Fractal server" width="400">
+</p>
+
 [![PyPI version](https://img.shields.io/pypi/v/fractal-server?color=gree)](https://pypi.org/project/fractal-server/)
+[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![CI Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml?query=branch%3Amain)
 [![Coverage](https://raw.githubusercontent.com/fractal-analytics-platform/fractal-server/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/python-coverage-comment-action-data/htmlcov/index.html)
-[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
+[![Documentation Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/documentation.yaml/badge.svg)](https://fractal-analytics-platform.github.io/fractal-server)
 [![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](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://github.com/user-attachments/assets/286122d9-08cf-48e8-996d-3cf53e0a81c6)
+![Fractal_overview](https://github.com/user-attachments/assets/666c8797-2594-4b8e-b1d2-b43fca66d1df)
 
 This is the server component of the fractal analytics platform.
 Find more information about Fractal in general and the other repositories at
@@ -21,13 +26,11 @@ See https://fractal-analytics-platform.github.io/fractal-server.
 
 # Contributors and license
 
-Unless otherwise stated in each individual module, all Fractal components are
-released according to a BSD 3-Clause License, and Copyright is with Friedrich
-Miescher Institute for Biomedical Research and University of Zurich.
+Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it).
+
+Unless otherwise specified, Fractal components are released under the BSD 3-Clause License, and copyright is with the BioVisionCenter at the University of Zurich.
 
 The SLURM compatibility layer is based on
 [`clusterfutures`](https://github.com/sampsyo/clusterfutures), by
 [@sampsyo](https://github.com/sampsyo) and collaborators, and it is released
 under the terms of the MIT license.
-
-Fractal was conceived in the Liberali Lab at the Friedrich Miescher Institute for Biomedical Research and in the Pelkmans Lab at the University of Zurich by [@jluethi](https://github.com/jluethi) and [@gusqgm](https://github.com/gusqgm). The Fractal project is now developed at the [BioVisionCenter](https://www.biovisioncenter.uzh.ch/en.html) at the University of Zurich and the project lead is with [@jluethi](https://github.com/jluethi). The core development is done under contract by [eXact lab S.r.l.](https://www.exact-lab.it/).

fractal_server-2.8.0/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.8.0"

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/models/user_settings.py

@@ -36,3 +36,4 @@ class UserSettings(SQLModel, table=True):
     ssh_jobs_dir: Optional[str] = None
     slurm_user: Optional[str] = None
     cache_dir: Optional[str] = None
+    project_dir: Optional[str] = None

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/models/v2/task.py

@@ -29,7 +29,6 @@ class TaskV2(SQLModel, table=True):
         sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
     )
 
-    owner: Optional[str] = None
     version: Optional[str] = None
     args_schema_non_parallel: Optional[dict[str, Any]] = Field(
         sa_column=Column(JSON), default=None
@@ -44,7 +43,7 @@ class TaskV2(SQLModel, table=True):
     input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
     output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
 
-    taskgroupv2_id: Optional[int] = Field(foreign_key="taskgroupv2.id")
+    taskgroupv2_id: int = Field(foreign_key="taskgroupv2.id")
 
     category: Optional[str] = None
     modality: Optional[str] = None
@@ -104,3 +103,18 @@ class TaskGroupV2(SQLModel, table=True):
                     f"{self.pkg_name=}, {self.wheel_path=}, {self.version=}."
                 )
             return f"{self.pkg_name}{extras}=={self.version}"
+
+    @property
+    def pinned_package_versions_string(self) -> str:
+        """
+        Prepare string to be used in `python -m pip install`.
+        """
+        if self.pinned_package_versions is None:
+            return ""
+        output = " ".join(
+            [
+                f"{key}=={value}"
+                for key, value in self.pinned_package_versions.items()
+            ]
+        )
+        return output

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/routes/admin/v2/task_group.py

@@ -21,6 +21,7 @@ from fractal_server.app.routes.auth._aux_auth import (
 )
 from fractal_server.app.schemas.v2 import TaskGroupReadV2
 from fractal_server.app.schemas.v2 import TaskGroupUpdateV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.logger import set_logger
 
 router = APIRouter()
@@ -50,6 +51,8 @@ async def query_task_group_list(
     user_group_id: Optional[int] = None,
     private: Optional[bool] = None,
     active: Optional[bool] = None,
+    pkg_name: Optional[str] = None,
+    origin: Optional[TaskGroupV2OriginEnum] = None,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[TaskGroupReadV2]:
@@ -75,6 +78,10 @@ async def query_task_group_list(
             stm = stm.where(is_(TaskGroupV2.active, True))
         else:
             stm = stm.where(is_(TaskGroupV2.active, False))
+    if origin is not None:
+        stm = stm.where(TaskGroupV2.origin == origin)
+    if pkg_name is not None:
+        stm = stm.where(TaskGroupV2.pkg_name.icontains(pkg_name))
 
     res = await db.execute(stm)
     task_groups_list = res.scalars().all()

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/routes/api/v2/dataset.py

@@ -22,6 +22,8 @@ from ._aux_functions import _get_project_check_owner
 from ._aux_functions import _get_submitted_jobs_statement
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_user
+from fractal_server.string_tools import sanitize_string
+from fractal_server.urls import normalize_url
 
 router = APIRouter()
 
@@ -40,14 +42,45 @@ async def create_dataset(
     """
     Add new dataset to current project
     """
-    await _get_project_check_owner(
+    project = await _get_project_check_owner(
         project_id=project_id, user_id=user.id, db=db
     )
-    db_dataset = DatasetV2(project_id=project_id, **dataset.dict())
-    db.add(db_dataset)
-    await db.commit()
-    await db.refresh(db_dataset)
-    await db.close()
+
+    if dataset.zarr_dir is None:
+
+        if user.settings.project_dir is None:
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail=(
+                    "Both 'dataset.zarr_dir' and 'user.settings.project_dir' "
+                    "are null"
+                ),
+            )
+
+        db_dataset = DatasetV2(
+            project_id=project_id,
+            zarr_dir="__PLACEHOLDER__",
+            **dataset.dict(exclude={"zarr_dir"}),
+        )
+        db.add(db_dataset)
+        await db.commit()
+        await db.refresh(db_dataset)
+        path = (
+            f"{user.settings.project_dir}/fractal/"
+            f"{project_id}_{sanitize_string(project.name)}/"
+            f"{db_dataset.id}_{sanitize_string(db_dataset.name)}"
+        )
+        normalized_path = normalize_url(path)
+        db_dataset.zarr_dir = normalized_path
+
+        db.add(db_dataset)
+        await db.commit()
+        await db.refresh(db_dataset)
+    else:
+        db_dataset = DatasetV2(project_id=project_id, **dataset.dict())
+        db.add(db_dataset)
+        await db.commit()
+        await db.refresh(db_dataset)
 
     return db_dataset
 

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/routes/api/v2/task.py

@@ -24,6 +24,7 @@ from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.routes.auth import current_active_user
 from fractal_server.app.routes.auth import current_active_verified_user
 from fractal_server.app.schemas.v2 import TaskCreateV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2 import TaskReadV2
 from fractal_server.app.schemas.v2 import TaskUpdateV2
 from fractal_server.logger import set_logger
@@ -35,8 +36,7 @@ logger = set_logger(__name__)
 
 @router.get("/", response_model=list[TaskReadV2])
 async def get_list_task(
-    args_schema_parallel: bool = True,
-    args_schema_non_parallel: bool = True,
+    args_schema: bool = True,
     category: Optional[str] = None,
     modality: Optional[str] = None,
     author: Optional[str] = None,
@@ -71,11 +71,9 @@ async def get_list_task(
     res = await db.execute(stm)
     task_list = res.scalars().all()
     await db.close()
-    if args_schema_parallel is False:
+    if args_schema is False:
         for task in task_list:
             setattr(task, "args_schema_parallel", None)
-    if args_schema_non_parallel is False:
-        for task in task_list:
             setattr(task, "args_schema_non_parallel", None)
 
     return task_list
@@ -200,7 +198,7 @@ async def create_task(
         user_group_id=user_group_id,
         active=True,
         task_list=[db_task],
-        origin="other",
+        origin=TaskGroupV2OriginEnum.OTHER,
         version=db_task.version,
         pkg_name=pkg_name,
     )

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/routes/api/v2/task_collection.py

@@ -24,22 +24,22 @@ from ....schemas.v2 import CollectionStatusV2
 from ....schemas.v2 import TaskCollectPipV2
 from ....schemas.v2 import TaskGroupCreateV2
 from ...aux.validate_user_settings import validate_user_settings
+from ._aux_functions_task_collection import get_package_version_from_pypi
 from ._aux_functions_tasks import _get_valid_user_group_id
 from ._aux_functions_tasks import _verify_non_duplication_group_constraint
 from ._aux_functions_tasks import _verify_non_duplication_user_constraint
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_user
 from fractal_server.app.routes.auth import current_active_verified_user
-from fractal_server.tasks.utils import _normalize_package_name
-from fractal_server.tasks.utils import get_collection_log_v2
-from fractal_server.tasks.v2.background_operations import (
-    background_collect_pip,
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
+from fractal_server.tasks.v2.collection_local import (
+    collect_package_local,
 )
-from fractal_server.tasks.v2.endpoint_operations import (
-    get_package_version_from_pypi,
+from fractal_server.tasks.v2.utils_package_names import _parse_wheel_filename
+from fractal_server.tasks.v2.utils_package_names import normalize_package_name
+from fractal_server.tasks.v2.utils_python_interpreter import (
+    get_python_interpreter_v2,
 )
-from fractal_server.tasks.v2.utils import _parse_wheel_filename
-from fractal_server.tasks.v2.utils import get_python_interpreter_v2
 
 router = APIRouter()
 
@@ -117,15 +117,15 @@ async def collect_tasks_pip(
                     f"Original error: {str(e)}",
                 ),
             )
-        task_group_attrs["pkg_name"] = _normalize_package_name(
+        task_group_attrs["pkg_name"] = normalize_package_name(
             wheel_info["distribution"]
         )
         task_group_attrs["version"] = wheel_info["version"]
-        task_group_attrs["origin"] = "wheel-file"
+        task_group_attrs["origin"] = TaskGroupV2OriginEnum.WHEELFILE
     else:
         pkg_name = task_collect.package
-        task_group_attrs["pkg_name"] = _normalize_package_name(pkg_name)
-        task_group_attrs["origin"] = "pypi"
+        task_group_attrs["pkg_name"] = normalize_package_name(pkg_name)
+        task_group_attrs["origin"] = TaskGroupV2OriginEnum.PYPI
         latest_version = await get_package_version_from_pypi(
             task_collect.package,
             task_collect.package_version,
@@ -248,8 +248,8 @@ async def collect_tasks_pip(
     if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
         # SSH task collection
 
-        from fractal_server.tasks.v2.background_operations_ssh import (
-            background_collect_pip_ssh,
+        from fractal_server.tasks.v2.collection_ssh import (
+            collect_package_ssh,
         )
 
         # User appropriate FractalSSH object
@@ -262,7 +262,7 @@ async def collect_tasks_pip(
         fractal_ssh = fractal_ssh_list.get(**ssh_credentials)
 
         background_tasks.add_task(
-            background_collect_pip_ssh,
+            collect_package_ssh,
             state_id=state.id,
             task_group=task_group,
             fractal_ssh=fractal_ssh,
@@ -272,7 +272,7 @@ async def collect_tasks_pip(
     else:
         # Local task collection
         background_tasks.add_task(
-            background_collect_pip,
+            collect_package_local,
             state_id=state.id,
             task_group=task_group,
         )
@@ -295,42 +295,15 @@ async def collect_tasks_pip(
 async def check_collection_status(
     state_id: int,
     user: UserOAuth = Depends(current_active_user),
-    verbose: bool = False,
     db: AsyncSession = Depends(get_async_db),
 ) -> CollectionStateReadV2:  # State[TaskCollectStatus]
     """
     Check status of background task collection
     """
-
-    logger = set_logger(logger_name="check_collection_status")
-    logger.debug(f"Querying state for state.id={state_id}")
     state = await db.get(CollectionStateV2, state_id)
-    if not state:
-        await db.close()
+    if state is None:
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,
             detail=f"No task collection info with id={state_id}",
         )
-
-    settings = Inject(get_settings)
-    if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-        # FIXME SSH: add logic for when data.state["log"] is empty
-        pass
-    else:
-        # Non-SSH mode
-        # In some cases (i.e. a successful or ongoing task collection),
-        # state.data["log"] is not set; if so, we collect the current logs.
-        if verbose and not state.data.get("log"):
-            if "path" not in state.data.keys():
-                await db.close()
-                raise HTTPException(
-                    status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-                    detail=(
-                        f"No 'path' in CollectionStateV2[{state_id}].data"
-                    ),
-                )
-            state.data["log"] = get_collection_log_v2(Path(state.data["path"]))
-
-    reset_logger_handlers(logger)
-    await db.close()
     return state

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/routes/api/v2/task_collection_custom.py

@@ -21,17 +21,18 @@ from fractal_server.app.routes.auth import current_active_verified_user
 from fractal_server.app.schemas.v2 import TaskCollectCustomV2
 from fractal_server.app.schemas.v2 import TaskCreateV2
 from fractal_server.app.schemas.v2 import TaskGroupCreateV2
+from fractal_server.app.schemas.v2 import TaskGroupV2OriginEnum
 from fractal_server.app.schemas.v2 import TaskReadV2
 from fractal_server.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.string_tools import validate_cmd
 from fractal_server.syringe import Inject
-from fractal_server.tasks.v2.background_operations import (
-    _prepare_tasks_metadata,
-)
 from fractal_server.tasks.v2.database_operations import (
     create_db_tasks_and_update_task_group,
 )
+from fractal_server.tasks.v2.utils_background import (
+    _prepare_tasks_metadata,
+)
 
 router = APIRouter()
 
@@ -140,7 +141,7 @@ async def collect_task_custom(
 
     # Prepare task-group attributes
     task_group_attrs = dict(
-        origin="other",
+        origin=TaskGroupV2OriginEnum.OTHER,
         pkg_name=task_collect.label,
         user_id=user.id,
         user_group_id=user_group_id,

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/schemas/user_settings.py

@@ -19,6 +19,10 @@ __all__ = (
 
 
 class UserSettingsRead(BaseModel):
+    """
+    Schema reserved for superusers
+    """
+
     id: int
     ssh_host: Optional[str] = None
     ssh_username: Optional[str] = None
@@ -28,6 +32,7 @@ class UserSettingsRead(BaseModel):
     slurm_user: Optional[str] = None
     slurm_accounts: list[str]
     cache_dir: Optional[str] = None
+    project_dir: Optional[str] = None
 
 
 class UserSettingsReadStrict(BaseModel):
@@ -35,9 +40,14 @@ class UserSettingsReadStrict(BaseModel):
     slurm_accounts: list[str]
     cache_dir: Optional[str] = None
     ssh_username: Optional[str] = None
+    project_dir: Optional[str] = None
 
 
 class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
+    """
+    Schema reserved for superusers
+    """
+
     ssh_host: Optional[str] = None
     ssh_username: Optional[str] = None
     ssh_private_key_path: Optional[str] = None
@@ -46,6 +56,7 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
     slurm_user: Optional[str] = None
     slurm_accounts: Optional[list[StrictStr]] = None
     cache_dir: Optional[str] = None
+    project_dir: Optional[str] = None
 
     _ssh_host = validator("ssh_host", allow_reuse=True)(
         valstr("ssh_host", accept_none=True)
@@ -83,6 +94,13 @@ class UserSettingsUpdate(BaseModel, extra=Extra.forbid):
         validate_cmd(value)
         return val_absolute_path("cache_dir")(value)
 
+    @validator("project_dir")
+    def project_dir_validator(cls, value):
+        if value is None:
+            return None
+        validate_cmd(value)
+        return val_absolute_path("project_dir")(value)
+
 
 class UserSettingsUpdateStrict(BaseModel, extra=Extra.forbid):
     slurm_accounts: Optional[list[StrictStr]] = None

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/schemas/v2/__init__.py

@@ -30,6 +30,7 @@ from .task_collection import TaskCollectPipV2  # noqa F401
 from .task_group import TaskGroupCreateV2  # noqa F401
 from .task_group import TaskGroupReadV2  # noqa F401
 from .task_group import TaskGroupUpdateV2  # noqa F401
+from .task_group import TaskGroupV2OriginEnum  # noqa F401
 from .workflow import WorkflowCreateV2  # noqa F401
 from .workflow import WorkflowExportV2  # noqa F401
 from .workflow import WorkflowImportV2  # noqa F401

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/schemas/v2/dataset.py

@@ -33,14 +33,16 @@ class DatasetCreateV2(BaseModel, extra=Extra.forbid):
 
     name: str
 
-    zarr_dir: str
+    zarr_dir: Optional[str] = None
 
     filters: Filters = Field(default_factory=Filters)
 
     # Validators
     @validator("zarr_dir")
     def normalize_zarr_dir(cls, v: str) -> str:
-        return normalize_url(v)
+        if v is not None:
+            return normalize_url(v)
+        return v
 
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
@@ -95,7 +97,7 @@ class DatasetImportV2(BaseModel, extra=Extra.forbid):
 
     name: str
     zarr_dir: str
-    images: list[SingleImage] = Field(default_factory=[])
+    images: list[SingleImage] = Field(default_factory=list)
     filters: Filters = Field(default_factory=Filters)
 
     # Validators

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/schemas/v2/task_collection.py

@@ -10,7 +10,6 @@ from pydantic import Extra
 from pydantic import root_validator
 from pydantic import validator
 
-from .._validators import valdictkeys
 from .._validators import valstr
 from fractal_server.app.schemas._validators import valutc
 from fractal_server.app.schemas.v2 import ManifestV2
@@ -62,13 +61,30 @@ class TaskCollectPipV2(BaseModel, extra=Extra.forbid):
     _package_version = validator("package_version", allow_reuse=True)(
         valstr("package_version")
     )
-    _pinned_package_versions = validator(
-        "pinned_package_versions", allow_reuse=True
-    )(valdictkeys("pinned_package_versions"))
     _package_extras = validator("package_extras", allow_reuse=True)(
         valstr("package_extras")
     )
 
+    @validator("pinned_package_versions")
+    def pinned_package_validator(cls, value):
+        if value is None:
+            return value
+        old_keys = list(value.keys())
+        new_keys = [
+            valstr(f"pinned_package_versions[{key}]")(key) for key in old_keys
+        ]
+        if len(new_keys) != len(set(new_keys)):
+            raise ValueError(
+                f"Dictionary contains multiple identical keys: {value}."
+            )
+        for old_key, new_key in zip(old_keys, new_keys):
+            if new_key != old_key:
+                value[new_key] = value.pop(old_key)
+        for pkg, version in value.items():
+            validate_cmd(pkg)
+            validate_cmd(version)
+        return value
+
     @validator("package")
     def package_validator(cls, value):
         if "/" in value or value.endswith(".whl"):

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/schemas/v2/task_group.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from enum import Enum
 from typing import Literal
 from typing import Optional
 
@@ -13,11 +14,17 @@ from .._validators import valstr
 from .task import TaskReadV2
 
 
+class TaskGroupV2OriginEnum(str, Enum):
+    PYPI = "pypi"
+    WHEELFILE = "wheel-file"
+    OTHER = "other"
+
+
 class TaskGroupCreateV2(BaseModel, extra=Extra.forbid):
     user_id: int
     user_group_id: Optional[int] = None
     active: bool = True
-    origin: Literal["pypi", "wheel-file", "other"]
+    origin: TaskGroupV2OriginEnum
     pkg_name: str
     version: Optional[str] = None
     python_version: Optional[str] = None

{fractal_server-2.7.0a11 → fractal_server-2.8.0}/fractal_server/app/security/__init__.py

@@ -315,13 +315,20 @@ async def _create_first_user(
 
 
 def _create_first_group():
+    """
+    Create a `UserGroup` with `name=FRACTAL_DEFAULT_GROUP_NAME`, if missing.
+    """
     function_logger = set_logger("fractal_server.create_first_group")
 
     function_logger.info(
         f"START _create_first_group, with name '{FRACTAL_DEFAULT_GROUP_NAME}'"
     )
     with next(get_sync_db()) as db:
-        group_all = db.execute(select(UserGroup))
+        group_all = db.execute(
+            select(UserGroup).where(
+                UserGroup.name == FRACTAL_DEFAULT_GROUP_NAME
+            )
+        )
         if group_all.scalars().one_or_none() is None:
             first_group = UserGroup(name=FRACTAL_DEFAULT_GROUP_NAME)
             db.add(first_group)