fractal-server 2.7.0a2__py3-none-any.whl → 2.7.0a4__py3-none-any.whl

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

@@ -7,8 +7,6 @@ from fastapi import Response
 from fastapi import status
 from sqlmodel import select
 
-from .....logger import reset_logger_handlers
-from .....logger import set_logger
 from ....db import AsyncSession
 from ....db import get_async_db
 from ....models.v2 import JobV2
@@ -27,7 +25,7 @@ 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 _workflow_insert_task
-from ._aux_functions_tasks import _get_task_group_read_access
+from ._aux_functions_tasks import _add_warnings_to_workflow_tasks
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_active_user
 
@@ -110,31 +108,21 @@ async def read_workflow(
         db=db,
     )
 
+    wftask_list_with_warnings = await _add_warnings_to_workflow_tasks(
+        wftask_list=workflow.task_list, user_id=user.id, db=db
+    )
     workflow_data = dict(
         **workflow.model_dump(),
         project=workflow.project,
+        task_list=wftask_list_with_warnings,
     )
-    task_list_with_warnings = []
-    for wftask in workflow.task_list:
-        wftask_data = dict(wftask.model_dump(), task=wftask.task)
-        try:
-            task_group = await _get_task_group_read_access(
-                task_group_id=wftask.task.taskgroupv2_id,
-                user_id=user.id,
-                db=db,
-            )
-            if not task_group.active:
-                wftask_data["warning"] = "Task is not active."
-        except HTTPException:
-            wftask_data["warning"] = "Current user has no access to this task."
-        task_list_with_warnings.append(wftask_data)
-    workflow_data["task_list"] = task_list_with_warnings
+
     return workflow_data
 
 
 @router.patch(
     "/project/{project_id}/workflow/{workflow_id}/",
-    response_model=WorkflowReadV2,
+    response_model=WorkflowReadV2WithWarnings,
 )
 async def update_workflow(
     project_id: int,
@@ -142,7 +130,7 @@ async def update_workflow(
     patch: WorkflowUpdateV2,
     user: UserOAuth = Depends(current_active_user),
     db: AsyncSession = Depends(get_async_db),
-) -> Optional[WorkflowReadV2]:
+) -> Optional[WorkflowReadV2WithWarnings]:
     """
     Edit a workflow
     """
@@ -184,7 +172,16 @@ async def update_workflow(
     await db.refresh(workflow)
     await db.close()
 
-    return workflow
+    wftask_list_with_warnings = await _add_warnings_to_workflow_tasks(
+        wftask_list=workflow.task_list, user_id=user.id, db=db
+    )
+    workflow_data = dict(
+        **workflow.model_dump(),
+        project=workflow.project,
+        task_list=wftask_list_with_warnings,
+    )
+
+    return workflow_data
 
 
 @router.delete(
@@ -259,19 +256,6 @@ async def export_worfklow(
         user_id=user.id,
         db=db,
     )
-    # Emit a warning when exporting a workflow with custom tasks
-    logger = set_logger(None)
-    for wftask in workflow.task_list:
-        if wftask.task.owner is not None:
-            logger.warning(
-                f"Custom tasks (like the one with id={wftask.task_id} and "
-                f'source="{wftask.task.source}") are not meant to be '
-                "portable; re-importing this workflow may not work as "
-                "expected."
-            )
-    reset_logger_handlers(logger)
-
-    await db.close()
     return workflow
 
 

fractal_server/app/routes/auth/_aux_auth.py

@@ -66,7 +66,7 @@ async def _get_single_user_with_groups(
     )
 
 
-async def _get_single_group_with_user_ids(
+async def _get_single_usergroup_with_user_ids(
     group_id: int, db: AsyncSession
 ) -> UserGroupRead:
     """
@@ -80,15 +80,7 @@ async def _get_single_group_with_user_ids(
         `UserGroupRead` object, with `user_ids` attribute populated
         from database.
     """
-    # Get the UserGroup object from the database
-    stm_group = select(UserGroup).where(UserGroup.id == group_id)
-    res = await db.execute(stm_group)
-    group = res.scalars().one_or_none()
-    if group is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"Group {group_id} not found.",
-        )
+    group = await _usergroup_or_404(group_id, db)
 
     # Get all user/group links
     stm_links = select(LinkUserGroup).where(LinkUserGroup.group_id == group_id)
@@ -110,12 +102,23 @@ async def _user_or_404(user_id: int, db: AsyncSession) -> UserOAuth:
     user = await db.get(UserOAuth, user_id, populate_existing=True)
     if user is None:
         raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND, detail="User not found."
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"User {user_id} not found.",
+        )
+    return user
+
+
+async def _usergroup_or_404(usergroup_id: int, db: AsyncSession) -> UserGroup:
+    user = await db.get(UserGroup, usergroup_id)
+    if user is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"UserGroup {usergroup_id} not found.",
         )
     return user
 
 
-async def _get_default_user_group_id(db: AsyncSession) -> int:
+async def _get_default_usergroup_id(db: AsyncSession) -> int:
     stm = select(UserGroup.id).where(
         UserGroup.name == FRACTAL_DEFAULT_GROUP_NAME
     )

fractal_server/app/routes/auth/group.py

@@ -4,6 +4,7 @@ Definition of `/auth/group/` routes
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
+from fastapi import Response
 from fastapi import status
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.asyncio import AsyncSession
@@ -12,14 +13,17 @@ from sqlmodel import func
 from sqlmodel import select
 
 from . import current_active_superuser
-from ...db import get_async_db
-from ...schemas.user_group import UserGroupCreate
-from ...schemas.user_group import UserGroupRead
-from ...schemas.user_group import UserGroupUpdate
-from ._aux_auth import _get_single_group_with_user_ids
+from ._aux_auth import _get_single_usergroup_with_user_ids
+from ._aux_auth import _usergroup_or_404
+from fractal_server.app.db import get_async_db
 from fractal_server.app.models import LinkUserGroup
 from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
+from fractal_server.app.models.v2 import TaskGroupV2
+from fractal_server.app.schemas.user_group import UserGroupCreate
+from fractal_server.app.schemas.user_group import UserGroupRead
+from fractal_server.app.schemas.user_group import UserGroupUpdate
+from fractal_server.app.security import FRACTAL_DEFAULT_GROUP_NAME
 from fractal_server.logger import set_logger
 
 logger = set_logger(__name__)
@@ -70,7 +74,7 @@ async def get_single_user_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-    group = await _get_single_group_with_user_ids(group_id=group_id, db=db)
+    group = await _get_single_usergroup_with_user_ids(group_id=group_id, db=db)
     return group
 
 
@@ -118,12 +122,7 @@ async def update_single_group(
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
 
-    group = await db.get(UserGroup, group_id)
-    if group is None:
-        raise HTTPException(
-            status_code=status.HTTP_404_NOT_FOUND,
-            detail=f"UserGroup {group_id} not found.",
-        )
+    group = await _usergroup_or_404(group_id, db)
 
     # Check that all required users exist
     # Note: The reason for introducing `col` is as in
@@ -167,25 +166,49 @@ async def update_single_group(
         db.add(group)
         await db.commit()
 
-    updated_group = await _get_single_group_with_user_ids(
+    updated_group = await _get_single_usergroup_with_user_ids(
         group_id=group_id, db=db
     )
 
     return updated_group
 
 
-@router_group.delete(
-    "/group/{group_id}/", status_code=status.HTTP_405_METHOD_NOT_ALLOWED
-)
+@router_group.delete("/group/{group_id}/", status_code=204)
 async def delete_single_group(
     group_id: int,
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
-) -> UserGroupRead:
-    raise HTTPException(
-        status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
-        detail=(
-            "Deleting a user group is not allowed, as it may restrict "
-            "previously-granted access.",
-        ),
+) -> Response:
+
+    group = await _usergroup_or_404(group_id, db)
+
+    if group.name == FRACTAL_DEFAULT_GROUP_NAME:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "Cannot delete default UserGroup "
+                f"'{FRACTAL_DEFAULT_GROUP_NAME}'."
+            ),
+        )
+
+    # Cascade operations
+
+    res = await db.execute(
+        select(LinkUserGroup).where(LinkUserGroup.group_id == group_id)
+    )
+    for link in res.scalars().all():
+        await db.delete(link)
+
+    res = await db.execute(
+        select(TaskGroupV2).where(TaskGroupV2.user_group_id == group_id)
     )
+    for task_group in res.scalars().all():
+        task_group.user_group_id = None
+        db.add(task_group)
+
+    # Delete
+
+    await db.delete(group)
+    await db.commit()
+
+    return Response(status_code=status.HTTP_204_NO_CONTENT)

fractal_server/app/runner/v2/task_interface.py

@@ -1,6 +1,7 @@
 from typing import Any
 
 from pydantic import BaseModel
+from pydantic import Extra
 from pydantic import Field
 from pydantic import validator
 
@@ -9,9 +10,7 @@ from fractal_server.images import Filters
 from fractal_server.urls import normalize_url
 
 
-class TaskOutput(BaseModel):
-    class Config:
-        extra = "forbid"
+class TaskOutput(BaseModel, extra=Extra.forbid):
 
     image_list_updates: list[SingleImageTaskOutput] = Field(
         default_factory=list
@@ -43,9 +42,7 @@ class TaskOutput(BaseModel):
         return [normalize_url(zarr_url) for zarr_url in v]
 
 
-class InitArgsModel(BaseModel):
-    class Config:
-        extra = "forbid"
+class InitArgsModel(BaseModel, extra=Extra.forbid):
 
     zarr_url: str
     init_args: dict[str, Any] = Field(default_factory=dict)
@@ -55,8 +52,6 @@ class InitArgsModel(BaseModel):
         return normalize_url(v)
 
 
-class InitTaskOutput(BaseModel):
-    class Config:
-        extra = "forbid"
+class InitTaskOutput(BaseModel, extra=Extra.forbid):
 
     parallelization_list: list[InitArgsModel] = Field(default_factory=list)

fractal_server/app/schemas/v2/dataset.py

@@ -66,9 +66,7 @@ class DatasetReadV2(BaseModel):
     )
 
 
-class DatasetUpdateV2(BaseModel):
-    class Config:
-        extra = "forbid"
+class DatasetUpdateV2(BaseModel, extra=Extra.forbid):
 
     name: Optional[str]
     zarr_dir: Optional[str]
@@ -84,7 +82,7 @@ class DatasetUpdateV2(BaseModel):
     _name = validator("name", allow_reuse=True)(valstr("name"))
 
 
-class DatasetImportV2(BaseModel):
+class DatasetImportV2(BaseModel, extra=Extra.forbid):
     """
     Class for `Dataset` import.
 
@@ -95,9 +93,6 @@ class DatasetImportV2(BaseModel):
         filters:
     """
 
-    class Config:
-        extra = "forbid"
-
     name: str
     zarr_dir: str
     images: list[SingleImage] = Field(default_factory=[])

fractal_server/app/schemas/v2/dumps.py

@@ -30,7 +30,7 @@ class TaskDumpV2(BaseModel):
 
     command_non_parallel: Optional[str]
     command_parallel: Optional[str]
-    source: str
+    source: Optional[str] = None
     owner: Optional[str]
     version: Optional[str]
 

fractal_server/app/schemas/v2/job.py

@@ -109,6 +109,6 @@ class JobReadV2(BaseModel):
     )
 
 
-class JobUpdateV2(BaseModel):
+class JobUpdateV2(BaseModel, extra=Extra.forbid):
 
     status: JobStatusTypeV2

fractal_server/app/schemas/v2/project.py

@@ -27,7 +27,7 @@ class ProjectReadV2(BaseModel):
     )
 
 
-class ProjectUpdateV2(BaseModel):
+class ProjectUpdateV2(BaseModel, extra=Extra.forbid):
 
     name: Optional[str]
     # Validators

fractal_server/app/schemas/v2/task.py

@@ -21,7 +21,7 @@ class TaskCreateV2(BaseModel, extra=Extra.forbid):
 
     command_non_parallel: Optional[str] = None
     command_parallel: Optional[str] = None
-    source: str
+    source: Optional[str] = None
 
     meta_non_parallel: Optional[dict[str, Any]] = None
     meta_parallel: Optional[dict[str, Any]] = None
@@ -111,7 +111,7 @@ class TaskReadV2(BaseModel):
     id: int
     name: str
     type: Literal["parallel", "non_parallel", "compound"]
-    source: str
+    source: Optional[str] = None
     version: Optional[str] = None
 
     command_non_parallel: Optional[str] = None
@@ -134,7 +134,7 @@ class TaskReadV2(BaseModel):
     tags: list[str]
 
 
-class TaskUpdateV2(BaseModel):
+class TaskUpdateV2(BaseModel, extra=Extra.forbid):
 
     name: Optional[str] = None
     version: Optional[str] = None
@@ -189,7 +189,7 @@ class TaskUpdateV2(BaseModel):
         return val_unique_list("tags")(value)
 
 
-class TaskImportV2(BaseModel):
+class TaskImportV2(BaseModel, extra=Extra.forbid):
 
     source: str
     _source = validator("source", allow_reuse=True)(valstr("source"))
@@ -197,5 +197,5 @@ class TaskImportV2(BaseModel):
 
 class TaskExportV2(BaseModel):
 
-    source: str
+    source: Optional[str] = None
     _source = validator("source", allow_reuse=True)(valstr("source"))

fractal_server/app/schemas/v2/task_collection.py

@@ -6,6 +6,7 @@ from typing import Literal
 from typing import Optional
 
 from pydantic import BaseModel
+from pydantic import Extra
 from pydantic import root_validator
 from pydantic import validator
 
@@ -24,7 +25,7 @@ class CollectionStatusV2(str, Enum):
     OK = "OK"
 
 
-class TaskCollectPipV2(BaseModel):
+class TaskCollectPipV2(BaseModel, extra=Extra.forbid):
     """
     TaskCollectPipV2 class
 
@@ -70,7 +71,7 @@ class TaskCollectPipV2(BaseModel):
 
     @validator("package")
     def package_validator(cls, value):
-        if "/" in value:
+        if "/" in value or value.endswith(".whl"):
             if not value.endswith(".whl"):
                 raise ValueError(
                     "Local-package path must be a wheel file "
@@ -92,14 +93,15 @@ class TaskCollectPipV2(BaseModel):
         return v
 
 
-class TaskCollectCustomV2(BaseModel):
+class TaskCollectCustomV2(BaseModel, extra=Extra.forbid):
     """
     Attributes:
         manifest: Manifest of a Fractal task package (this is typically the
             content of `__FRACTAL_MANIFEST__.json`).
         python_interpreter: Absolute path to the Python interpreter to be used
             for running tasks.
-        source: A common label identifying this package.
+        name: A name identifying this package, that will fill the
+            `TaskGroupV2.pkg_name` column.
         package_root: The folder where the package is installed.
             If not provided, it will be extracted via `pip show`
             (requires `package_name` to be set).
@@ -111,7 +113,7 @@ class TaskCollectCustomV2(BaseModel):
 
     manifest: ManifestV2
     python_interpreter: str
-    source: str
+    label: str
     package_root: Optional[str]
     package_name: Optional[str]
     version: Optional[str]
@@ -120,7 +122,7 @@ class TaskCollectCustomV2(BaseModel):
     _python_interpreter = validator("python_interpreter", allow_reuse=True)(
         valstr("python_interpreter")
     )
-    _source = validator("source", allow_reuse=True)(valstr("source"))
+    _label = validator("label", allow_reuse=True)(valstr("label"))
     _package_root = validator("package_root", allow_reuse=True)(
         valstr("package_root", accept_none=True)
     )

fractal_server/app/schemas/v2/task_group.py

@@ -3,12 +3,19 @@ from typing import Literal
 from typing import Optional
 
 from pydantic import BaseModel
+from pydantic import Extra
+from pydantic import Field
 from pydantic import validator
 
+from .._validators import val_absolute_path
+from .._validators import valdictkeys
+from .._validators import valstr
 from .task import TaskReadV2
 
 
-class TaskGroupCreateV2(BaseModel):
+class TaskGroupCreateV2(BaseModel, extra=Extra.forbid):
+    user_id: int
+    user_group_id: Optional[int] = None
     active: bool = True
     origin: Literal["pypi", "wheel-file", "other"]
     pkg_name: str
@@ -16,11 +23,30 @@ class TaskGroupCreateV2(BaseModel):
     python_version: Optional[str] = None
     path: Optional[str] = None
     venv_path: Optional[str] = None
+    wheel_path: Optional[str] = None
     pip_extras: Optional[str] = None
+    pinned_package_versions: dict[str, str] = Field(default_factory=dict)
 
+    # Validators
+    _path = validator("path", allow_reuse=True)(val_absolute_path("path"))
+    _venv_path = validator("venv_path", allow_reuse=True)(
+        val_absolute_path("venv_path")
+    )
+    _wheel_path = validator("wheel_path", allow_reuse=True)(
+        val_absolute_path("wheel_path")
+    )
+    _pinned_package_versions = validator(
+        "pinned_package_versions", allow_reuse=True
+    )(valdictkeys("pinned_package_versions"))
+    _pip_extras = validator("pip_extras", allow_reuse=True)(
+        valstr("pip_extras")
+    )
+    _python_version = validator("python_version", allow_reuse=True)(
+        valstr("python_version")
+    )
 
-class TaskGroupReadV2(BaseModel):
 
+class TaskGroupReadV2(BaseModel):
     id: int
     task_list: list[TaskReadV2]
 
@@ -33,13 +59,15 @@ class TaskGroupReadV2(BaseModel):
     python_version: Optional[str] = None
     path: Optional[str] = None
     venv_path: Optional[str] = None
+    wheel_path: Optional[str] = None
     pip_extras: Optional[str] = None
+    pinned_package_versions: dict[str, str] = Field(default_factory=dict)
 
     active: bool
     timestamp_created: datetime
 
 
-class TaskGroupUpdateV2(BaseModel):
+class TaskGroupUpdateV2(BaseModel, extra=Extra.forbid):
     user_group_id: Optional[int] = None
     active: Optional[bool] = None
 

fractal_server/app/schemas/v2/workflow.py

@@ -40,7 +40,7 @@ class WorkflowReadV2WithWarnings(WorkflowReadV2):
     task_list: list[WorkflowTaskReadV2WithWarning]
 
 
-class WorkflowUpdateV2(BaseModel):
+class WorkflowUpdateV2(BaseModel, extra=Extra.forbid):
 
     name: Optional[str]
     reordered_workflowtask_ids: Optional[list[int]]
@@ -57,7 +57,7 @@ class WorkflowUpdateV2(BaseModel):
         return value
 
 
-class WorkflowImportV2(BaseModel):
+class WorkflowImportV2(BaseModel, extra=Extra.forbid):
     """
     Class for `Workflow` import.
 

fractal_server/app/schemas/v2/workflowtask.py

@@ -106,7 +106,7 @@ class WorkflowTaskReadV2WithWarning(WorkflowTaskReadV2):
     warning: Optional[str] = None
 
 
-class WorkflowTaskUpdateV2(BaseModel):
+class WorkflowTaskUpdateV2(BaseModel, extra=Extra.forbid):
 
     meta_non_parallel: Optional[dict[str, Any]]
     meta_parallel: Optional[dict[str, Any]]
@@ -151,7 +151,7 @@ class WorkflowTaskUpdateV2(BaseModel):
         return value
 
 
-class WorkflowTaskImportV2(BaseModel):
+class WorkflowTaskImportV2(BaseModel, extra=Extra.forbid):
 
     meta_non_parallel: Optional[dict[str, Any]] = None
     meta_parallel: Optional[dict[str, Any]] = None

fractal_server/data_migrations/2_7_0.py

@@ -110,7 +110,6 @@ def prepare_task_groups(
     user_mapping: dict[str, int],
     default_user_group_id: int,
     default_user_id: int,
-    dry_run: bool,
     db: Session,
 ):
     stm_tasks = select(TaskV2).order_by(TaskV2.id)
@@ -236,14 +235,6 @@ def prepare_task_groups(
 
         print()
 
-        if dry_run:
-            print(
-                "End dry-run of handling task group with key "
-                f"'{task_group_key}"
-            )
-            print("-" * 80)
-            continue
-
         task_group = TaskGroupV2(**task_group_attributes)
         db.add(task_group)
         db.commit()
@@ -254,7 +245,7 @@ def prepare_task_groups(
     return
 
 
-def fix_db(dry_run: bool = False):
+def fix_db():
     logger.warning("START execution of fix_db function")
     _check_current_version("2.7.0")
 
@@ -268,7 +259,6 @@ def fix_db(dry_run: bool = False):
             default_user_id=default_user_id,
             default_user_group_id=default_user_group_id,
             db=db,
-            dry_run=dry_run,
         )
 
     logger.warning("END of execution of fix_db function")

fractal_server/images/models.py

@@ -3,6 +3,7 @@ from typing import Optional
 from typing import Union
 
 from pydantic import BaseModel
+from pydantic import Extra
 from pydantic import Field
 from pydantic import validator
 
@@ -109,13 +110,10 @@ class SingleImageUpdate(BaseModel):
     _types = validator("types", allow_reuse=True)(valdictkeys("types"))
 
 
-class Filters(BaseModel):
+class Filters(BaseModel, extra=Extra.forbid):
     attributes: dict[str, Any] = Field(default_factory=dict)
     types: dict[str, bool] = Field(default_factory=dict)
 
-    class Config:
-        extra = "forbid"
-
     # Validators
     _attributes = validator("attributes", allow_reuse=True)(
         valdictkeys("attributes")

fractal_server/main.py

@@ -20,7 +20,7 @@ from contextlib import asynccontextmanager
 
 from fastapi import FastAPI
 
-from .app.routes.aux._runner import _backend_supports_shutdown  # FIXME: change
+from .app.routes.aux._runner import _backend_supports_shutdown
 from .app.runner.shutdown import cleanup_after_shutdown
 from .config import get_settings
 from .logger import config_uvicorn_loggers