fractal-server 2.14.15__py3-none-any.whl → 2.15.0__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.14.15"
+__VERSION__ = "2.15.0"

fractal_server/app/models/security.py

@@ -15,8 +15,8 @@ from typing import Optional
 from pydantic import ConfigDict
 from pydantic import EmailStr
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -124,5 +124,5 @@ class UserGroup(SQLModel, table=True):
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
     viewer_paths: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )

fractal_server/app/models/user_settings.py

@@ -1,5 +1,5 @@
 from sqlalchemy import Column
-from sqlalchemy.types import JSON
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
@@ -25,7 +25,7 @@ class UserSettings(SQLModel, table=True):
 
     id: int | None = Field(default=None, primary_key=True)
     slurm_accounts: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )
     ssh_host: str | None = None
     ssh_username: str | None = None

fractal_server/app/models/v2/dataset.py

@@ -3,8 +3,8 @@ from typing import Any
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -24,7 +24,7 @@ class DatasetV2(SQLModel, table=True):
     )
 
     history: list[dict[str, Any]] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )
 
     timestamp_created: datetime = Field(
@@ -34,7 +34,7 @@ class DatasetV2(SQLModel, table=True):
 
     zarr_dir: str
     images: list[dict[str, Any]] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )
 
     @property

fractal_server/app/models/v2/history.py

@@ -65,11 +65,13 @@ class HistoryImageCache(SQLModel, table=True):
         primary_key=True,
         foreign_key="datasetv2.id",
         ondelete="CASCADE",
+        index=True,
     )
     workflowtask_id: int = Field(
         primary_key=True,
         foreign_key="workflowtaskv2.id",
         ondelete="CASCADE",
+        index=True,
     )
 
     latest_history_unit_id: int = Field(

fractal_server/app/models/v2/job.py

@@ -3,8 +3,8 @@ from typing import Any
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
@@ -31,13 +31,13 @@ class JobV2(SQLModel, table=True):
     slurm_account: str | None = None
 
     dataset_dump: dict[str, Any] = Field(
-        sa_column=Column(JSON, nullable=False)
+        sa_column=Column(JSONB, nullable=False)
     )
     workflow_dump: dict[str, Any] = Field(
-        sa_column=Column(JSON, nullable=False)
+        sa_column=Column(JSONB, nullable=False)
     )
     project_dump: dict[str, Any] = Field(
-        sa_column=Column(JSON, nullable=False)
+        sa_column=Column(JSONB, nullable=False)
     )
 
     worker_init: str | None = None
@@ -57,8 +57,8 @@ class JobV2(SQLModel, table=True):
     log: str | None = None
 
     attribute_filters: AttributeFilters = Field(
-        sa_column=Column(JSON, nullable=False, server_default="{}")
+        sa_column=Column(JSONB, nullable=False, server_default="{}")
     )
     type_filters: dict[str, bool] = Field(
-        sa_column=Column(JSON, nullable=False, server_default="{}")
+        sa_column=Column(JSONB, nullable=False, server_default="{}")
     )

fractal_server/app/models/v2/task.py

@@ -1,7 +1,7 @@
 from typing import Any
 
 from sqlalchemy import Column
-from sqlalchemy.types import JSON
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field
 from sqlmodel import SQLModel
 
@@ -16,25 +16,29 @@ class TaskV2(SQLModel, table=True):
     source: str | None = None
 
     meta_non_parallel: dict[str, Any] = Field(
-        sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
+        sa_column=Column(
+            JSONB, server_default="{}", default={}, nullable=False
+        )
     )
     meta_parallel: dict[str, Any] = Field(
-        sa_column=Column(JSON, server_default="{}", default={}, nullable=False)
+        sa_column=Column(
+            JSONB, server_default="{}", default={}, nullable=False
+        )
     )
 
     version: str | None = None
     args_schema_non_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
     args_schema_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
     args_schema_version: str | None = None
     docs_info: str | None = None
     docs_link: str | None = None
 
-    input_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
-    output_types: dict[str, bool] = Field(sa_column=Column(JSON), default={})
+    input_types: dict[str, bool] = Field(sa_column=Column(JSONB), default={})
+    output_types: dict[str, bool] = Field(sa_column=Column(JSONB), default={})
 
     taskgroupv2_id: int = Field(foreign_key="taskgroupv2.id")
 
@@ -42,5 +46,5 @@ class TaskV2(SQLModel, table=True):
     modality: str | None = None
     authors: str | None = None
     tags: list[str] = Field(
-        sa_column=Column(JSON, server_default="[]", nullable=False)
+        sa_column=Column(JSONB, server_default="[]", nullable=False)
     )

fractal_server/app/models/v2/task_group.py

@@ -2,8 +2,8 @@ from datetime import datetime
 from datetime import timezone
 
 from sqlalchemy import Column
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
-from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -29,18 +29,19 @@ class TaskGroupV2(SQLModel, table=True):
     pkg_name: str
     version: str | None = None
     python_version: str | None = None
+    pixi_version: str | None = None
     path: str | None = None
-    wheel_path: str | None = None
+    archive_path: str | None = None
     pip_extras: str | None = None
     pinned_package_versions: dict[str, str] = Field(
         sa_column=Column(
-            JSON,
+            JSONB,
             server_default="{}",
             default={},
             nullable=True,
         ),
     )
-    pip_freeze: str | None = None
+    env_info: str | None = None
     venv_path: str | None = None
     venv_size_in_kB: int | None = None
     venv_file_number: int | None = None
@@ -66,15 +67,20 @@ class TaskGroupV2(SQLModel, table=True):
         """
         Prepare string to be used in `python -m pip install`.
         """
+        if self.origin == "pixi":
+            raise ValueError(
+                f"Cannot call 'pip_install_string' if {self.origin=}."
+            )
+
         extras = f"[{self.pip_extras}]" if self.pip_extras is not None else ""
 
-        if self.wheel_path is not None:
-            return f"{self.wheel_path}{extras}"
+        if self.archive_path is not None:
+            return f"{self.archive_path}{extras}"
         else:
             if self.version is None:
                 raise ValueError(
                     "Cannot run `pip_install_string` with "
-                    f"{self.pkg_name=}, {self.wheel_path=}, {self.version=}."
+                    f"{self.pkg_name=}, {self.archive_path=}, {self.version=}."
                 )
             return f"{self.pkg_name}{extras}=={self.version}"
 
@@ -83,6 +89,12 @@ class TaskGroupV2(SQLModel, table=True):
         """
         Prepare string to be used in `python -m pip install`.
         """
+        if self.origin == "pixi":
+            raise ValueError(
+                "Cannot call 'pinned_package_versions_string' if "
+                f"{self.origin=}."
+            )
+
         if self.pinned_package_versions is None:
             return ""
         output = " ".join(

fractal_server/app/models/v2/workflowtask.py

@@ -2,7 +2,7 @@ from typing import Any
 
 from pydantic import ConfigDict
 from sqlalchemy import Column
-from sqlalchemy.types import JSON
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -18,20 +18,20 @@ class WorkflowTaskV2(SQLModel, table=True):
     workflow_id: int = Field(foreign_key="workflowv2.id", ondelete="CASCADE")
     order: int | None = None
     meta_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
     meta_non_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
     args_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
     args_non_parallel: dict[str, Any] | None = Field(
-        sa_column=Column(JSON), default=None
+        sa_column=Column(JSONB), default=None
     )
 
     type_filters: dict[str, bool] = Field(
-        sa_column=Column(JSON, nullable=False, server_default="{}")
+        sa_column=Column(JSONB, nullable=False, server_default="{}")
     )
 
     # Task

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

@@ -2,7 +2,6 @@ from fastapi import APIRouter
 from fastapi import BackgroundTasks
 from fastapi import Depends
 from fastapi import HTTPException
-from fastapi import Request
 from fastapi import Response
 from fastapi import status
 
@@ -51,7 +50,6 @@ async def deactivate_task_group(
     task_group_id: int,
     background_tasks: BackgroundTasks,
     response: Response,
-    request: Request,
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:
@@ -157,7 +155,6 @@ async def reactivate_task_group(
     task_group_id: int,
     background_tasks: BackgroundTasks,
     response: Response,
-    request: Request,
     superuser: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> TaskGroupReadV2:
@@ -207,12 +204,12 @@ async def reactivate_task_group(
         response.status_code = status.HTTP_202_ACCEPTED
         return task_group_activity
 
-    if task_group.pip_freeze is None:
+    if task_group.env_info is None:
         raise HTTPException(
             status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
             detail=(
                 "Cannot reactivate a task group with "
-                f"{task_group.pip_freeze=}."
+                f"{task_group.env_info=}."
             ),
         )
 

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

@@ -14,6 +14,7 @@ from .submit import router as submit_job_router_v2
 from .task import router as task_router_v2
 from .task_collection import router as task_collection_router_v2
 from .task_collection_custom import router as task_collection_router_v2_custom
+from .task_collection_pixi import router as task_collection_pixi_router_v2
 from .task_group import router as task_group_router_v2
 from .task_group_lifecycle import router as task_group_lifecycle_router_v2
 from .task_version_update import router as task_version_update_router_v2
@@ -49,6 +50,11 @@ router_api_v2.include_router(
     prefix="/task",
     tags=["V2 Task Lifecycle"],
 )
+router_api_v2.include_router(
+    task_collection_pixi_router_v2,
+    prefix="/task",
+    tags=["V2 Task Lifecycle"],
+)
 router_api_v2.include_router(
     task_group_lifecycle_router_v2,
     prefix="/task-group",

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

@@ -333,6 +333,28 @@ async def _verify_non_duplication_group_constraint(
         )
 
 
+async def _verify_non_duplication_group_path(
+    path: str | None,
+    db: AsyncSession,
+) -> None:
+    """
+    Verify uniqueness of non-`None` `TaskGroupV2.path`
+    """
+    if path is None:
+        return
+    stm = select(TaskGroupV2.id).where(TaskGroupV2.path == path)
+    res = await db.execute(stm)
+    duplicate_ids = res.scalars().all()
+    if duplicate_ids:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                f"Other TaskGroups already have {path=}: "
+                f"{sorted(duplicate_ids)}."
+            ),
+        )
+
+
 async def _add_warnings_to_workflow_tasks(
     wftask_list: list[WorkflowTaskV2], user_id: int, db: AsyncSession
 ) -> list[dict[str, Any]]:

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

@@ -34,7 +34,7 @@ from fractal_server.app.schemas.v2 import HistoryUnitRead
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
 from fractal_server.app.schemas.v2 import HistoryUnitStatusWithUnset
 from fractal_server.app.schemas.v2 import ImageLogsRequest
-from fractal_server.images.status_tools import enrich_images_async
+from fractal_server.images.status_tools import enrich_images_unsorted_async
 from fractal_server.images.status_tools import IMAGE_STATUS_KEY
 from fractal_server.images.tools import aggregate_attributes
 from fractal_server.images.tools import aggregate_types
@@ -334,7 +334,7 @@ async def get_history_images(
     types = aggregate_types(type_filtered_images)
 
     # (3) Enrich images with status attribute
-    type_filtered_images_with_status = await enrich_images_async(
+    type_filtered_images_with_status = await enrich_images_unsorted_async(
         dataset_id=dataset_id,
         workflowtask_id=workflowtask_id,
         images=type_filtered_images,

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

@@ -14,7 +14,7 @@ from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_user
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
 from fractal_server.app.schemas.v2 import TaskType
-from fractal_server.images.status_tools import enrich_images_async
+from fractal_server.images.status_tools import enrich_images_unsorted_async
 from fractal_server.images.status_tools import IMAGE_STATUS_KEY
 from fractal_server.images.tools import aggregate_types
 from fractal_server.images.tools import filter_image_list
@@ -46,7 +46,7 @@ async def verify_unique_types(
         filtered_images = dataset.images
     else:
         if IMAGE_STATUS_KEY in query.attribute_filters.keys():
-            images = await enrich_images_async(
+            images = await enrich_images_unsorted_async(
                 dataset_id=dataset_id,
                 workflowtask_id=workflowtask_id,
                 images=dataset.images,
@@ -134,7 +134,7 @@ async def check_non_processed_images(
         attribute_filters=filters.attribute_filters,
     )
 
-    filtered_images_with_status = await enrich_images_async(
+    filtered_images_with_status = await enrich_images_unsorted_async(
         dataset_id=dataset_id,
         workflowtask_id=previous_wft.id,
         images=filtered_images,

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

@@ -7,14 +7,12 @@ from fastapi import Depends
 from fastapi import File
 from fastapi import Form
 from fastapi import HTTPException
-from fastapi import Request
 from fastapi import Response
 from fastapi import status
 from fastapi import UploadFile
 from pydantic import BaseModel
 from pydantic import model_validator
 from pydantic import ValidationError
-from sqlmodel import select
 
 from .....config import get_settings
 from .....logger import reset_logger_handlers
@@ -23,15 +21,16 @@ from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import TaskGroupV2
+from ....schemas.v2 import FractalUploadedFile
 from ....schemas.v2 import TaskCollectPipV2
 from ....schemas.v2 import TaskGroupActivityStatusV2
 from ....schemas.v2 import TaskGroupActivityV2Read
 from ....schemas.v2 import TaskGroupCreateV2Strict
-from ....schemas.v2 import WheelFile
 from ...aux.validate_user_settings import validate_user_settings
 from ._aux_functions_task_lifecycle 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_group_path
 from ._aux_functions_tasks import _verify_non_duplication_user_constraint
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import TaskGroupActivityV2
@@ -151,7 +150,6 @@ def parse_request_data(
     response_model=TaskGroupActivityV2Read,
 )
 async def collect_tasks_pip(
-    request: Request,
     response: Response,
     background_tasks: BackgroundTasks,
     request_data: CollectionRequestData = Depends(parse_request_data),
@@ -208,13 +206,13 @@ async def collect_tasks_pip(
     # Initialize wheel_file_content as None
     wheel_file = None
 
-    # Set pkg_name, version, origin and wheel_path
+    # Set pkg_name, version, origin and archive_path
     if request_data.origin == TaskGroupV2OriginEnum.WHEELFILE:
         try:
             wheel_filename = request_data.file.filename
             wheel_info = _parse_wheel_filename(wheel_filename)
             wheel_file_content = await request_data.file.read()
-            wheel_file = WheelFile(
+            wheel_file = FractalUploadedFile(
                 filename=wheel_filename,
                 contents=wheel_file_content,
             )
@@ -293,18 +291,10 @@ async def collect_tasks_pip(
         version=task_group_attrs["version"],
         db=db,
     )
-
-    # Verify that task-group path is unique
-    stm = select(TaskGroupV2).where(TaskGroupV2.path == task_group_path)
-    res = await db.execute(stm)
-    for conflicting_task_group in res.scalars().all():
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
-            detail=(
-                f"Another task-group already has path={task_group_path}.\n"
-                f"{conflicting_task_group=}"
-            ),
-        )
+    await _verify_non_duplication_group_path(
+        path=task_group_attrs["path"],
+        db=db,
+    )
 
     # On-disk checks
 

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

@@ -26,7 +26,7 @@ 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.utils_background import (
-    _prepare_tasks_metadata,
+    prepare_tasks_metadata,
 )
 from fractal_server.tasks.v2.utils_database import (
     create_db_tasks_and_update_task_group_async,
@@ -138,7 +138,7 @@ async def collect_task_custom(
     else:
         package_root = Path(task_collect.package_root)
 
-    task_list: list[TaskCreateV2] = _prepare_tasks_metadata(
+    task_list: list[TaskCreateV2] = prepare_tasks_metadata(
         package_manifest=task_collect.manifest,
         python_bin=Path(task_collect.python_interpreter),
         package_root=package_root,