fractal-server 2.4.0a0__py3-none-any.whl → 2.4.0a2__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.4.0a0"
+__VERSION__ = "2.4.0a2"

fractal_server/app/routes/auth/group.py

@@ -5,8 +5,10 @@ from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
 from fastapi import status
+from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import col
+from sqlmodel import func
 from sqlmodel import select
 
 from . import current_active_superuser
@@ -18,7 +20,9 @@ from ._aux_auth import _get_single_group_with_user_ids
 from fractal_server.app.models import LinkUserGroup
 from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
+from fractal_server.logger import set_logger
 
+logger = set_logger(__name__)
 
 router_group = APIRouter()
 
@@ -31,9 +35,6 @@ async def get_list_user_groups(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[UserGroupRead]:
-    """
-    FIXME docstring
-    """
 
     # Get all groups
     stm_all_groups = select(UserGroup)
@@ -46,7 +47,8 @@ async def get_list_user_groups(
         res = await db.execute(stm_all_links)
         links = res.scalars().all()
 
-        # FIXME GROUPS: this must be optimized
+        # TODO: possible optimizations for this construction are listed in
+        # https://github.com/fractal-analytics-platform/fractal-server/issues/1742
         for ind, group in enumerate(groups):
             groups[ind] = dict(
                 group.model_dump(),
@@ -68,9 +70,6 @@ async def get_single_user_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-    """
-    FIXME docstring
-    """
     group = await _get_single_group_with_user_ids(group_id=group_id, db=db)
     return group
 
@@ -85,9 +84,6 @@ async def create_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-    """
-    FIXME docstring
-    """
 
     # Check that name is not already in use
     existing_name_str = select(UserGroup).where(
@@ -119,24 +115,21 @@ async def update_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-    """
-    FIXME docstring
-    """
 
     # Check that all required users exist
     # Note: The reason for introducing `col` is as in
     # https://sqlmodel.tiangolo.com/tutorial/where/#type-annotations-and-errors,
-    stm = select(UserOAuth).where(
+    stm = select(func.count()).where(
         col(UserOAuth.id).in_(group_update.new_user_ids)
     )
     res = await db.execute(stm)
-    matching_users = res.scalars().unique().all()
-    if not len(matching_users) == len(group_update.new_user_ids):
+    number_matching_users = res.scalar()
+    if number_matching_users != len(group_update.new_user_ids):
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,
             detail=(
-                f"At least user with IDs {group_update.new_user_ids} "
-                "does not exist."
+                f"Not all requested users (IDs {group_update.new_user_ids}) "
+                "exist."
             ),
         )
 
@@ -144,7 +137,20 @@ async def update_single_group(
     for user_id in group_update.new_user_ids:
         link = LinkUserGroup(user_id=user_id, group_id=group_id)
         db.add(link)
-    await db.commit()
+    try:
+        await db.commit()
+    except IntegrityError as e:
+        error_msg = (
+            f"Cannot link users with IDs {group_update.new_user_ids} "
+            f"to group {group_id}. "
+            "Likely reason: one of these links already exists.\n"
+            f"Original error: {str(e)}"
+        )
+        logger.info(error_msg)
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=error_msg,
+        )
 
     updated_group = await _get_single_group_with_user_ids(
         group_id=group_id, db=db
@@ -161,9 +167,6 @@ async def delete_single_group(
     user: UserOAuth = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_async_db),
 ) -> UserGroupRead:
-    """
-    FIXME docstring
-    """
     raise HTTPException(
         status_code=status.HTTP_405_METHOD_NOT_ALLOWED,
         detail=(

fractal_server/app/routes/auth/users.py

@@ -8,23 +8,32 @@ from fastapi import status
 from fastapi_users import exceptions
 from fastapi_users import schemas
 from fastapi_users.router.common import ErrorCode
+from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.asyncio import AsyncSession
+from sqlmodel import col
+from sqlmodel import func
 from sqlmodel import select
 
 from . import current_active_superuser
 from ...db import get_async_db
 from ...schemas.user import UserRead
 from ...schemas.user import UserUpdate
+from ...schemas.user import UserUpdateWithNewGroupIds
 from ._aux_auth import _get_single_user_with_group_ids
 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.routes.auth._aux_auth import _user_or_404
 from fractal_server.app.security import get_user_manager
 from fractal_server.app.security import UserManager
+from fractal_server.logger import set_logger
 
 router_users = APIRouter()
 
 
+logger = set_logger(__name__)
+
+
 @router_users.get("/users/{user_id}/", response_model=UserRead)
 async def get_user(
     user_id: int,
@@ -43,31 +52,110 @@ async def get_user(
 @router_users.patch("/users/{user_id}/", response_model=UserRead)
 async def patch_user(
     user_id: int,
-    user_update: UserUpdate,
+    user_update: UserUpdateWithNewGroupIds,
     current_superuser: UserOAuth = Depends(current_active_superuser),
     user_manager: UserManager = Depends(get_user_manager),
     db: AsyncSession = Depends(get_async_db),
 ):
     """
     Custom version of the PATCH-user route from `fastapi-users`.
+
+    In order to keep the fastapi-users logic in place (which is convenient to
+    update user attributes), we split the endpoint into two branches. We either
+    go through the fastapi-users-based attribute-update branch, or through the
+    branch where we establish new user/group relationships.
+
+    Note that we prevent making both changes at the same time, since it would
+    be more complex to guarantee that endpoint error would leave the database
+    in the same state as before the API call.
     """
 
+    # We prevent simultaneous editing of both user attributes and user/group
+    # associations
+    user_update_dict_without_groups = user_update.dict(
+        exclude_unset=True, exclude={"new_group_ids"}
+    )
+    edit_attributes = user_update_dict_without_groups != {}
+    edit_groups = user_update.new_group_ids is not None
+    if edit_attributes and edit_groups:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=(
+                "Cannot modify both user attributes and group membership. "
+                "Please make two independent PATCH calls"
+            ),
+        )
+
+    # Check that user exists
     user_to_patch = await _user_or_404(user_id, db)
 
-    try:
-        user = await user_manager.update(
-            user_update, user_to_patch, safe=False, request=None
-        )
-        patched_user = schemas.model_validate(UserOAuth, user)
-    except exceptions.InvalidPasswordException as e:
-        raise HTTPException(
-            status_code=status.HTTP_400_BAD_REQUEST,
-            detail={
-                "code": ErrorCode.UPDATE_USER_INVALID_PASSWORD,
-                "reason": e.reason,
-            },
+    if edit_groups:
+        # Establish new user/group relationships
+
+        # Check that all required groups exist
+        # Note: The reason for introducing `col` is as in
+        # https://sqlmodel.tiangolo.com/tutorial/where/#type-annotations-and-errors,
+        stm = select(func.count()).where(
+            col(UserGroup.id).in_(user_update.new_group_ids)
         )
+        res = await db.execute(stm)
+        number_matching_groups = res.scalar()
+        if number_matching_groups != len(user_update.new_group_ids):
+            raise HTTPException(
+                status_code=status.HTTP_404_NOT_FOUND,
+                detail=(
+                    "Not all requested groups (IDs: "
+                    f"{user_update.new_group_ids}) exist."
+                ),
+            )
+
+        for new_group_id in user_update.new_group_ids:
+            link = LinkUserGroup(user_id=user_id, group_id=new_group_id)
+            db.add(link)
+
+        try:
+            await db.commit()
+        except IntegrityError as e:
+            error_msg = (
+                f"Cannot link groups with IDs {user_update.new_group_ids} "
+                f"to user {user_id}. "
+                "Likely reason: one of these links already exists.\n"
+                f"Original error: {str(e)}"
+            )
+            logger.info(error_msg)
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+                detail=error_msg,
+            )
+
+        patched_user = user_to_patch
+
+    elif edit_attributes:
+        # Modify user attributes
+        try:
+            user_update_without_groups = UserUpdate(
+                **user_update_dict_without_groups
+            )
+            user = await user_manager.update(
+                user_update_without_groups,
+                user_to_patch,
+                safe=False,
+                request=None,
+            )
+            patched_user = schemas.model_validate(UserOAuth, user)
+        except exceptions.InvalidPasswordException as e:
+            raise HTTPException(
+                status_code=status.HTTP_400_BAD_REQUEST,
+                detail={
+                    "code": ErrorCode.UPDATE_USER_INVALID_PASSWORD,
+                    "reason": e.reason,
+                },
+            )
+    else:
+        # Nothing to do, just continue
+        patched_user = user_to_patch
 
+    # Enrich user object with `group_ids` attribute
     patched_user_with_group_ids = await _get_single_user_with_group_ids(
         patched_user, db
     )
@@ -92,7 +180,8 @@ async def list_users(
     res = await db.execute(stm_all_links)
     links = res.scalars().all()
 
-    # FIXME GROUPS: this must be optimized
+    # TODO: possible optimizations for this construction are listed in
+    # https://github.com/fractal-analytics-platform/fractal-server/issues/1742
     for ind, user in enumerate(user_list):
         user_list[ind] = dict(
             user.model_dump(),

fractal_server/app/schemas/user.py

@@ -16,6 +16,7 @@ __all__ = (
     "UserRead",
     "UserUpdate",
     "UserCreate",
+    "UserUpdateWithNewGroupIds",
 )
 
 
@@ -102,6 +103,14 @@ class UserUpdateStrict(BaseModel, extra=Extra.forbid):
     )
 
 
+class UserUpdateWithNewGroupIds(UserUpdate):
+    new_group_ids: Optional[list[int]] = None
+
+    _val_unique = validator("new_group_ids", allow_reuse=True)(
+        val_unique_list("new_group_ids")
+    )
+
+
 class UserCreate(schemas.BaseUserCreate):
     """
     Schema for `User` creation.

fractal_server/app/schemas/user_group.py

@@ -4,6 +4,10 @@ from typing import Optional
 from pydantic import BaseModel
 from pydantic import Extra
 from pydantic import Field
+from pydantic import validator
+
+from ._validators import val_unique_list
+
 
 __all__ = (
     "UserGroupRead",
@@ -55,3 +59,7 @@ class UserGroupUpdate(BaseModel, extra=Extra.forbid):
     """
 
     new_user_ids: list[int] = Field(default_factory=list)
+
+    _val_unique = validator("new_user_ids", allow_reuse=True)(
+        val_unique_list("new_user_ids")
+    )

fractal_server/app/security/__init__.py

@@ -43,7 +43,6 @@ from fastapi_users.exceptions import UserAlreadyExists
 from fastapi_users.models import ID
 from fastapi_users.models import OAP
 from fastapi_users.models import UP
-from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlalchemy.orm import selectinload
 from sqlmodel import func
@@ -295,12 +294,6 @@ async def _create_first_user(
                     user = await user_manager.create(UserCreate(**kwargs))
                     logger.info(f"User {user.email} created")
 
-    except IntegrityError:
-        logger.warning(
-            f"Creation of user {email} failed with IntegrityError "
-            "(likely due to concurrent attempts from different workers)."
-        )
-
     except UserAlreadyExists:
         logger.warning(f"User {email} already exists")
 

{fractal_server-2.4.0a0.dist-info → fractal_server-2.4.0a2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.4.0a0
+Version: 2.4.0a2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.4.0a0.dist-info → fractal_server-2.4.0a2.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=3YbyR1dRXTwVjPcWPQWD72VIhMYsj-Cqwfmnwjo80JM,24
+fractal_server/__init__.py,sha256=LqB8PB8-x2CZLC5OUrNdxwSPLBLIrriGxEQXweZeNSc,24
 fractal_server/__main__.py,sha256=I9hF_SYc-GTZWDZZhihwyUBK7BMU5GAecbPLTjkpW4U,5830
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -53,13 +53,13 @@ fractal_server/app/routes/api/v2/workflowtask.py,sha256=HoHFnVRDa0Cw1oqTea1Of6A5
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
 fractal_server/app/routes/auth/_aux_auth.py,sha256=Kpgiw5q1eiCYLFkfhTT7XJGBu1d08YM71CEHhNtfJ5g,3126
 fractal_server/app/routes/auth/current_user.py,sha256=LK0Z13NgaXYQ3FaQ3MNec0p2RRiKxKN31XIt2g9mcGk,2003
-fractal_server/app/routes/auth/group.py,sha256=ZVXeUisf0gUzHXHMINbaPXwXnzXtbcX01AuWXBvNdrA,4871
+fractal_server/app/routes/auth/group.py,sha256=az8kRJJU5rA0L8GCX5kvRNuQhrsoGWPuvQ26z7iFQ3E,5388
 fractal_server/app/routes/auth/group_names.py,sha256=zvYDfhxKlDmbSr-oLXYy6WUVkPPTvzH6ZJtuoNdGZbE,960
 fractal_server/app/routes/auth/login.py,sha256=tSu6OBLOieoBtMZB4JkBAdEgH2Y8KqPGSbwy7NIypIo,566
 fractal_server/app/routes/auth/oauth.py,sha256=AnFHbjqL2AgBX3eksI931xD6RTtmbciHBEuGf9YJLjU,1895
 fractal_server/app/routes/auth/register.py,sha256=DlHq79iOvGd_gt2v9uwtsqIKeO6i_GKaW59VIkllPqY,587
 fractal_server/app/routes/auth/router.py,sha256=zWoZWiO69U48QFQf5tLRYQDWu8PUCj7GacnaFeW1n_I,618
-fractal_server/app/routes/auth/users.py,sha256=G9lFJ5zk-lAXDT1oDXXS66B_AxIlfnG35Sg7U44BdU4,3171
+fractal_server/app/routes/auth/users.py,sha256=hNTIR0e3QFbUUDvkzKNXJt4uKwONlI36i6UjjMPCgAA,6672
 fractal_server/app/routes/aux/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/routes/aux/_job.py,sha256=q-RCiW17yXnZKAC_0La52RLvhqhxuvbgQJ2MlGXOj8A,702
 fractal_server/app/routes/aux/_runner.py,sha256=FdCVla5DxGAZ__aB7Z8dEJzD_RIeh5tftjrPyqkr8N8,895
@@ -126,8 +126,8 @@ fractal_server/app/runner/v2/v1_compat.py,sha256=t0ficzAHUFaaeI56nqTb4YEKxfARF7L
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
 fractal_server/app/schemas/__init__.py,sha256=jiIf54owztXupv3PO6Ilh0qcrkh2RUzKq4bcEFqEfc4,40
 fractal_server/app/schemas/_validators.py,sha256=1dTOYr1IZykrxuQSV2-zuEMZbKe_nGwrfS7iUrsh-sE,3461
-fractal_server/app/schemas/user.py,sha256=ImNoZH7uqDkFuajVd0h9cDzJQ7D9YwYkluNuWtpk5_o,3199
-fractal_server/app/schemas/user_group.py,sha256=CgW38Ett-DuRvN4tFEjG1jfX1csCFJIhVu5mjVlGEyI,1262
+fractal_server/app/schemas/user.py,sha256=jRMUd3v7kmnOdHhGSoljKbCk6xyaJuGHRXkaxAxI8RA,3437
+fractal_server/app/schemas/user_group.py,sha256=2f9XQ6kIar6NMY4UCN0yOnve6ZDHUVZaHv1dna1Vfjg,1446
 fractal_server/app/schemas/v1/__init__.py,sha256=CrBGgBhoemCvmZ70ZUchM-jfVAICnoa7AjZBAtL2UB0,1852
 fractal_server/app/schemas/v1/applyworkflow.py,sha256=uuIh7fHlHEL4yLqL-dePI6-nfCsqgBYATmht7w_KITw,4302
 fractal_server/app/schemas/v1/dataset.py,sha256=n71lNUO3JLy2K3IM9BZM2Fk1EnKQOTU7pm2s2rJ1FGY,3444
@@ -149,7 +149,7 @@ fractal_server/app/schemas/v2/task.py,sha256=7IfxiZkaVqlARy7WYE_H8m7j_IEcuQaZORU
 fractal_server/app/schemas/v2/task_collection.py,sha256=8PG1bOqkfQqORMN0brWf6mHDmijt0bBW-mZsF7cSxUs,6129
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
-fractal_server/app/security/__init__.py,sha256=a-UEm1bdjgxLt88wmMyurf3X64UwxVw57yM9I8I2JYg,11687
+fractal_server/app/security/__init__.py,sha256=FBxdrMvn2s3Gdmp1orqOpYji87JojLBzr9TMfblj1SI,11441
 fractal_server/config.py,sha256=R0VezSe2PEDjQjHEX2V29A1jMdoomdyECBjWNY15v_0,25049
 fractal_server/data_migrations/2_4_0.py,sha256=T1HRRWp9ZuXeVfBY6NRGxQ8aNIHVSftOMnB-CMrfvi8,2117
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
@@ -207,8 +207,8 @@ fractal_server/tasks/v2/utils.py,sha256=JOyCacb6MNvrwfLNTyLwcz8y79J29YuJeJ2MK5kq
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
 fractal_server/zip_tools.py,sha256=xYpzBshysD2nmxkD5WLYqMzPYUcCRM3kYy-7n9bJL-U,4426
-fractal_server-2.4.0a0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.4.0a0.dist-info/METADATA,sha256=sZdr0mUMZvRpXhgArOMw16lfa282uBrl90dY_7QG4WU,4630
-fractal_server-2.4.0a0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.4.0a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.4.0a0.dist-info/RECORD,,
+fractal_server-2.4.0a2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.4.0a2.dist-info/METADATA,sha256=ujcw0RxpRcxYPLLI1NdkZ8v0IaKQP3d3D_CXsaxua4U,4630
+fractal_server-2.4.0a2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.4.0a2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.4.0a2.dist-info/RECORD,,