fractal-server 1.4.0a7__tar.gz → 1.4.0a9__tar.gz

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 1.4.0a7
+Version: 1.4.0a9
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -12,12 +12,13 @@ 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: slurm
 Requires-Dist: aiosqlite (>=0.17.0,<0.18.0)
 Requires-Dist: alembic (>=1.9.1,<2.0.0)
-Requires-Dist: asyncpg (>=0.27.0,<0.28.0) ; extra == "postgres"
+Requires-Dist: asyncpg (>=0.29.0,<0.30.0) ; extra == "postgres"
 Requires-Dist: cloudpickle (>=2.2.1,<2.3.0) ; extra == "slurm"
 Requires-Dist: clusterfutures (>=0.5,<0.6) ; extra == "slurm"
 Requires-Dist: fastapi (>=0.103.0,<0.104.0)
@@ -26,8 +27,8 @@ Requires-Dist: gunicorn (>=20.1.0,<21.0.0) ; extra == "gunicorn"
 Requires-Dist: psycopg2 (>=2.9.5,<3.0.0) ; extra == "postgres"
 Requires-Dist: pydantic (>=1.10.8,<2)
 Requires-Dist: python-dotenv (>=0.20.0,<0.21.0)
-Requires-Dist: sqlalchemy[asyncio] (>=1.4,<2.0)
-Requires-Dist: sqlmodel (>=0.0.11,<0.0.12)
+Requires-Dist: sqlalchemy[asyncio] (>=2.0.23,<2.1)
+Requires-Dist: sqlmodel (>=0.0.12,<0.0.13)
 Requires-Dist: uvicorn (>=0.20.0,<0.21.0)
 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

fractal_server-1.4.0a9/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "1.4.0a9"

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/db/__init__.py

@@ -63,7 +63,9 @@ class DB:
                 connect_args={"check_same_thread": False},
             )
         else:
-            engine_kwargs_async = {}
+            engine_kwargs_async = {
+                "pool_pre_ping": True,
+            }
             engine_kwargs_sync = {}
 
         cls._engine_async = create_async_engine(
@@ -80,11 +82,17 @@ class DB:
         )
 
         cls._async_session_maker = sessionmaker(
-            cls._engine_async, class_=AsyncSession, expire_on_commit=False
+            cls._engine_async,
+            class_=AsyncSession,
+            expire_on_commit=False,
+            future=True,
         )
 
         cls._sync_session_maker = sessionmaker(
-            bind=cls._engine_sync, autocommit=False, autoflush=False
+            bind=cls._engine_sync,
+            autocommit=False,
+            autoflush=False,
+            future=True,
         )
 
         @event.listens_for(cls._engine_sync, "connect")

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/routes/api/v1/job.py

@@ -15,8 +15,12 @@ from .....config import get_settings
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_db
+from ....models import ApplyWorkflow
 from ....runner._common import SHUTDOWN_FILENAME
 from ....schemas import ApplyWorkflowRead
+from ....schemas import ApplyWorkflowUpdate
+from ....schemas import JobStatusType
+from ....security import current_active_superuser
 from ....security import current_active_user
 from ....security import User
 from ._aux_functions import _get_job_check_owner
@@ -196,3 +200,39 @@ async def stop_job(
         f.write(f"Trigger executor shutdown for {job.id=}, {project_id=}.")
 
     return Response(status_code=status.HTTP_204_NO_CONTENT)
+
+
+@router.patch(
+    "/job/{job_id}/",
+    response_model=ApplyWorkflowRead,
+)
+async def update_job(
+    job_update: ApplyWorkflowUpdate,
+    job_id: int,
+    user: User = Depends(current_active_superuser),
+    db: AsyncSession = Depends(get_db),
+) -> Optional[ApplyWorkflowRead]:
+    """
+    Change the status of an existing job.
+
+    This endpoint is only open to superusers, and it does not apply
+    project-based access-control to jobs.
+    """
+    job = await db.get(ApplyWorkflow, job_id)
+    if job is None:
+        raise HTTPException(
+            status_code=status.HTTP_404_NOT_FOUND,
+            detail=f"Job {job_id} not found",
+        )
+
+    if job_update.status != JobStatusType.FAILED:
+        raise HTTPException(
+            status_code=status.HTTP_422_UNPROCESSABLE_ENTITY,
+            detail=f"Cannot set job status to {job_update.status}",
+        )
+
+    setattr(job, "status", job_update.status)
+    await db.commit()
+    await db.refresh(job)
+    await db.close()
+    return job

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/routes/auth.py

@@ -3,6 +3,11 @@ Definition of `/auth` routes.
 """
 from fastapi import APIRouter
 from fastapi import Depends
+from fastapi import HTTPException
+from fastapi import status
+from fastapi_users import exceptions
+from fastapi_users import schemas
+from fastapi_users.router.common import ErrorCode
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import select
 
@@ -13,12 +18,14 @@ from ..models.security import UserOAuth as User
 from ..schemas.user import UserCreate
 from ..schemas.user import UserRead
 from ..schemas.user import UserUpdate
+from ..schemas.user import UserUpdateStrict
 from ..security import cookie_backend
 from ..security import current_active_superuser
 from ..security import current_active_user
 from ..security import fastapi_users
+from ..security import get_user_manager
 from ..security import token_backend
-
+from ..security import UserManager
 
 router_auth = APIRouter()
 
@@ -33,18 +40,22 @@ router_auth.include_router(
     fastapi_users.get_register_router(UserRead, UserCreate),
     dependencies=[Depends(current_active_superuser)],
 )
-router_auth.include_router(
-    fastapi_users.get_reset_password_router(),
-)
-router_auth.include_router(
-    fastapi_users.get_verify_router(UserRead),
-)
 
-# Include users routes, after removing DELETE endpoint (ref
-# https://github.com/fastapi-users/fastapi-users/discussions/606)
 users_router = fastapi_users.get_users_router(UserRead, UserUpdate)
+
+# We remove `/auth/users/me` endpoints to implement our own
+# at `/auth/current-user/`.
+# We also remove `DELETE /auth/users/{user_id}`
+# (ref https://github.com/fastapi-users/fastapi-users/discussions/606)
 users_router.routes = [
-    route for route in users_router.routes if route.name != "users:delete_user"
+    route
+    for route in users_router.routes
+    if route.name
+    not in [
+        "users:current_user",
+        "users:delete_user",
+        "users:patch_current_user",
+    ]
 ]
 router_auth.include_router(
     users_router,
@@ -53,17 +64,37 @@ router_auth.include_router(
 )
 
 
-@router_auth.get("/whoami", response_model=UserRead)
-async def whoami(
-    user: User = Depends(current_active_user),
+@router_auth.patch("/current-user/", response_model=UserRead)
+async def patch_current_user(
+    user_update: UserUpdateStrict,
+    current_user: User = Depends(current_active_user),
+    user_manager: UserManager = Depends(get_user_manager),
 ):
+
+    update = UserUpdate(**user_update.dict(exclude_unset=True))
+
+    try:
+        user = await user_manager.update(update, current_user, safe=True)
+    except exceptions.InvalidPasswordException as e:
+        raise HTTPException(
+            status_code=status.HTTP_400_BAD_REQUEST,
+            detail={
+                "code": ErrorCode.UPDATE_USER_INVALID_PASSWORD,
+                "reason": e.reason,
+            },
+        )
+    return schemas.model_validate(User, user)
+
+
+@router_auth.get("/current-user/", response_model=UserRead)
+async def get_current_user(user: User = Depends(current_active_user)):
     """
     Return current user
     """
     return user
 
 
-@router_auth.get("/userlist", response_model=list[UserRead])
+@router_auth.get("/users/", response_model=list[UserRead])
 async def list_users(
     user: User = Depends(current_active_superuser),
     db: AsyncSession = Depends(get_db),

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/schemas/__init__.py

@@ -3,6 +3,7 @@ Schemas for API request/response bodies
 """
 from .applyworkflow import ApplyWorkflowCreate  # noqa: F401
 from .applyworkflow import ApplyWorkflowRead  # noqa: F401
+from .applyworkflow import ApplyWorkflowUpdate  # noqa: F401
 from .applyworkflow import JobStatusType  # noqa: F401
 from .dataset import DatasetCreate  # noqa: F401
 from .dataset import DatasetRead  # noqa: F401

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/schemas/applyworkflow.py

@@ -146,3 +146,14 @@ class ApplyWorkflowRead(_ApplyWorkflowBase):
         d["start_timestamp"] = str(self.start_timestamp)
         d["end_timestamp"] = str(self.end_timestamp)
         return d
+
+
+class ApplyWorkflowUpdate(BaseModel):
+    """
+    Class for updating a job status.
+
+    Attributes:
+        status: New job status.
+    """
+
+    status: JobStatusType

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/schemas/user.py

@@ -1,6 +1,8 @@
 from typing import Optional
 
 from fastapi_users import schemas
+from pydantic import BaseModel
+from pydantic import Extra
 from pydantic import validator
 
 from ._validators import val_absolute_path
@@ -52,6 +54,31 @@ class UserUpdate(schemas.BaseUserUpdate):
         val_absolute_path("cache_dir")
     )
 
+    @validator(
+        "is_active",
+        "is_verified",
+        "is_superuser",
+        "email",
+        "password",
+        always=False,
+    )
+    def cant_set_none(cls, v, field):
+        if v is None:
+            raise ValueError(f"Cannot set {field.name}=None")
+        return v
+
+
+class UserUpdateStrict(BaseModel, extra=Extra.forbid):
+    """
+    Attributes that every user can self-edit
+    """
+
+    cache_dir: Optional[str]
+
+    _cache_dir = validator("cache_dir", allow_reuse=True)(
+        val_absolute_path("cache_dir")
+    )
+
 
 class UserCreate(schemas.BaseUserCreate):
     """

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/fractal_server/app/security/__init__.py

@@ -35,8 +35,6 @@ from typing import Type
 
 from fastapi import Depends
 from fastapi import HTTPException
-from fastapi import Request
-from fastapi import Response
 from fastapi import status
 from fastapi_users import BaseUserManager
 from fastapi_users import FastAPIUsers
@@ -46,6 +44,7 @@ from fastapi_users.authentication import BearerTransport
 from fastapi_users.authentication import CookieTransport
 from fastapi_users.authentication import JWTStrategy
 from fastapi_users.db.base import BaseUserDatabase
+from fastapi_users.exceptions import InvalidPasswordException
 from fastapi_users.models import ID
 from fastapi_users.models import OAP
 from fastapi_users.models import UP
@@ -176,17 +175,17 @@ async def get_user_db(
 
 
 class UserManager(IntegerIDMixin, BaseUserManager[User, int]):
-    async def on_after_login(
-        self,
-        user: User,
-        request: Optional[Request] = None,
-        response: Optional[Response] = None,
-    ) -> None:
-        """
-        Perform logic after user login.
-        *You should overload this method to add your own logic.*
-        """
-        pass
+    async def validate_password(self, password: str, user: User) -> None:
+        # check password length
+        min_length, max_length = 4, 100
+        if len(password) < min_length:
+            raise InvalidPasswordException(
+                f"The password is too short (minimum length: {min_length})."
+            )
+        elif len(password) > max_length:
+            raise InvalidPasswordException(
+                f"The password is too long (maximum length: {min_length})."
+            )
 
 
 async def get_user_manager(

{fractal_server-1.4.0a7 → fractal_server-1.4.0a9}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "1.4.0a7"
+version = "1.4.0a9"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Jacopo Nespolo <jacopo.nespolo@exact-lab.it>",
@@ -24,18 +24,18 @@ exclude = [
 python = "^3.9"
 python-dotenv = "^0.20.0"
 fastapi = "^0.103.0"
-sqlmodel = "^0.0.11"
+sqlmodel = "^0.0.12"
+sqlalchemy = {extras = ["asyncio"], version = ">=2.0.23,<2.1"}
 aiosqlite = "^0.17.0"
 fastapi-users = {extras = ["oauth"], version = "^12.1.0"}
 alembic = "^1.9.1"
 uvicorn = "^0.20.0"
-sqlalchemy = {extras = ["asyncio"], version = "^1.4"}
 pydantic = ">=1.10.8,<2"
 
 clusterfutures = { version = "^0.5", optional = true}
 cloudpickle = {version = ">=2.2.1,<2.3.0", optional = true}
 
-asyncpg = { version = "^0.27.0", optional = true }
+asyncpg = { version = "^0.29.0", optional = true }
 psycopg2 = { version = "^2.9.5", optional = true }
 gunicorn = { version = "^20.1.0", optional = true }
 
@@ -82,7 +82,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "1.4.0a7"
+current_version = "1.4.0a9"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-1.4.0a7/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "1.4.0a7"