fractal-server 2.17.0a3__tar.gz → 2.17.0a5__tar.gz

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.0a3
+Version: 2.17.0a5
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE
@@ -12,7 +12,6 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
 Requires-Dist: alembic (>=1.13.1,<2.0.0)
-Requires-Dist: cryptography (>=46.0.0,<47.0.0)
 Requires-Dist: fabric (>=3.2.2,<3.3.0)
 Requires-Dist: fastapi (>=0.118.0,<0.119.0)
 Requires-Dist: fastapi-users[oauth] (>=14,<15)

fractal_server-2.17.0a5/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.17.0a5"

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/__main__.py

@@ -62,14 +62,33 @@ init_db_data_parser = subparsers.add_parser(
 init_db_data_parser.add_argument(
     "--resource",
     type=str,
-    help=("Either `default` or path to the JSON file of the first resource."),
-    required=True,
+    help="Either `default` or path to the JSON file of the first resource.",
+    required=False,
 )
 init_db_data_parser.add_argument(
     "--profile",
     type=str,
-    help=("Either `default` or path to the JSON file of the first profile."),
-    required=True,
+    help="Either `default` or path to the JSON file of the first profile.",
+    required=False,
+)
+init_db_data_parser.add_argument(
+    "--admin-email",
+    type=str,
+    help="Email of the first admin user.",
+    required=False,
+)
+init_db_data_parser.add_argument(
+    "--admin-pwd",
+    type=str,
+    help="Password for the first admin user.",
+    required=False,
+)
+
+init_db_data_parser.add_argument(
+    "--admin-project-dir",
+    type=str,
+    help="Project_dir for the first admin user.",
+    required=False,
 )
 
 # fractalctl update-db-data
@@ -78,15 +97,6 @@ update_db_data_parser = subparsers.add_parser(
     description="Apply data-migration script to an existing database.",
 )
 
-# fractalctl encrypt-email-password
-encrypt_email_password_parser = subparsers.add_parser(
-    "encrypt-email-password",
-    description=(
-        "Generate valid values for environment variables "
-        "FRACTAL_EMAIL_PASSWORD and FRACTAL_EMAIL_PASSWORD_KEY."
-    ),
-)
-
 
 def save_openapi(dest="openapi.json"):
     from fractal_server.main import start_application
@@ -125,13 +135,14 @@ def set_db():
 
 def init_db_data(
     *,
-    resource: str,
-    profile: str,
+    resource: str | None = None,
+    profile: str | None = None,
+    admin_email: str | None = None,
+    admin_password: str | None = None,
+    admin_project_dir: str | None = None,
 ) -> None:
     from fractal_server.app.security import _create_first_user
     from fractal_server.app.security import _create_first_group
-    from fractal_server.syringe import Inject
-    from fractal_server.config import get_init_data_settings
     from fractal_server.app.db import get_sync_db
     from sqlalchemy import select, func
     from fractal_server.app.models.security import UserOAuth
@@ -139,104 +150,120 @@ def init_db_data(
     from fractal_server.app.schemas.v2.resource import cast_serialize_resource
     from fractal_server.app.schemas.v2.profile import cast_serialize_profile
 
-    init_data_settings = Inject(get_init_data_settings)
-
     # Create default group and user
     print()
     _create_first_group()
     print()
-    asyncio.run(
-        _create_first_user(
-            email=init_data_settings.FRACTAL_DEFAULT_ADMIN_EMAIL,
-            password=(
-                init_data_settings.FRACTAL_DEFAULT_ADMIN_PASSWORD.get_secret_value()  # noqa E501
-            ),
-            is_superuser=True,
-            is_verified=True,
-        )
-    )
-    print()
 
-    # Create resource and profile
-    with next(get_sync_db()) as db:
-        # Preliminary check
-        num_resources = db.execute(select(func.count(Resource.id))).scalar()
-        if num_resources != 0:
-            print(f"There exist already {num_resources=} resources. Exit.")
-            sys.exit(1)
-
-        # Get resource/profile data
-        if resource == "default":
-            _python_version = (
-                f"{sys.version_info.major}.{sys.version_info.minor}"
-            )
-            resource_data = {
-                "name": "Local resource",
-                "type": ResourceType.LOCAL,
-                "jobs_local_dir": (Path.cwd() / "data-jobs").as_posix(),
-                "tasks_local_dir": (Path.cwd() / "data-tasks").as_posix(),
-                "tasks_python_config": {
-                    "default_version": _python_version,
-                    "versions": {
-                        _python_version: sys.executable,
-                    },
-                },
-                "jobs_poll_interval": 0,
-                "jobs_runner_config": {},
-                "tasks_pixi_config": {},
-            }
-            print("Prepared default resource data.")
-        else:
-            with open(resource) as f:
-                resource_data = json.load(f)
-            print(f"Read resource data from {resource}.")
-        if profile == "default":
-            profile_data = {
-                "resource_type": "local",
-                "name": "Local profile",
-            }
-            print("Prepared default profile data.")
-        else:
-            with open(profile) as f:
-                profile_data = json.load(f)
-            print(f"Read profile data from {profile}.")
-
-        # Validate resource/profile data
-        try:
-            resource_data = cast_serialize_resource(resource_data)
-        except ValidationError as e:
-            sys.exit(
-                f"ERROR: Invalid resource data.\nOriginal error:\n{str(e)}"
-            )
-        try:
-            profile_data = cast_serialize_profile(profile_data)
-        except ValidationError as e:
-            sys.exit(
-                f"ERROR: Invalid profile data.\nOriginal error:\n{str(e)}"
+    # Create admin user if requested
+    if not (
+        (admin_email is None)
+        == (admin_password is None)
+        == (admin_project_dir is None)
+    ):
+        print(
+            "You must provide either or or none of `--admin-email`, "
+            "`--admin-pwd` and `--admin-project-dir`. Exit."
+        )
+        sys.exit(1)
+    if admin_password and admin_email:
+        asyncio.run(
+            _create_first_user(
+                email=admin_email,
+                password=admin_password,
+                project_dir=admin_project_dir,
+                is_superuser=True,
+                is_verified=True,
             )
-
-        # Create resource/profile db objects
-        resource_obj = Resource(**resource_data)
-        db.add(resource_obj)
-        db.commit()
-        db.refresh(resource_obj)
-        profile_data["resource_id"] = resource_obj.id
-        profile_obj = Profile(**profile_data)
-        db.add(profile_obj)
-        db.commit()
-        db.refresh(profile_obj)
-
-        # Associate profile to users
-        res = db.execute(select(UserOAuth))
-        users = res.unique().scalars().all()
-        for user in users:
-            print(f"Now set profile_id={profile_obj.id} for {user.email}.")
-            user.profile_id = profile_obj.id
-            db.add(user)
-        db.commit()
-        db.expunge_all()
+        )
         print()
 
+    # Create resource and profile if requested
+    if (resource is None) != (profile is None):
+        print("You must provide both --resource and --profile. Exit.")
+        sys.exit(1)
+    if resource and profile:
+        with next(get_sync_db()) as db:
+            # Preliminary check
+            num_resources = db.execute(
+                select(func.count(Resource.id))
+            ).scalar()
+            if num_resources != 0:
+                print(f"There exist already {num_resources=} resources. Exit.")
+                sys.exit(1)
+
+            # Get resource/profile data
+            if resource == "default":
+                _python_version = (
+                    f"{sys.version_info.major}.{sys.version_info.minor}"
+                )
+                resource_data = {
+                    "name": "Local resource",
+                    "type": ResourceType.LOCAL,
+                    "jobs_local_dir": (Path.cwd() / "data-jobs").as_posix(),
+                    "tasks_local_dir": (Path.cwd() / "data-tasks").as_posix(),
+                    "tasks_python_config": {
+                        "default_version": _python_version,
+                        "versions": {
+                            _python_version: sys.executable,
+                        },
+                    },
+                    "jobs_poll_interval": 0,
+                    "jobs_runner_config": {},
+                    "tasks_pixi_config": {},
+                }
+                print("Prepared default resource data.")
+            else:
+                with open(resource) as f:
+                    resource_data = json.load(f)
+                print(f"Read resource data from {resource}.")
+            if profile == "default":
+                profile_data = {
+                    "resource_type": "local",
+                    "name": "Local profile",
+                }
+                print("Prepared default profile data.")
+            else:
+                with open(profile) as f:
+                    profile_data = json.load(f)
+                print(f"Read profile data from {profile}.")
+
+            # Validate resource/profile data
+            try:
+                resource_data = cast_serialize_resource(resource_data)
+            except ValidationError as e:
+                sys.exit(
+                    f"ERROR: Invalid resource data.\nOriginal error:\n{str(e)}"
+                )
+            try:
+                profile_data = cast_serialize_profile(profile_data)
+            except ValidationError as e:
+                sys.exit(
+                    f"ERROR: Invalid profile data.\nOriginal error:\n{str(e)}"
+                )
+
+            # Create resource/profile db objects
+            resource_obj = Resource(**resource_data)
+            db.add(resource_obj)
+            db.commit()
+            db.refresh(resource_obj)
+            profile_data["resource_id"] = resource_obj.id
+            profile_obj = Profile(**profile_data)
+            db.add(profile_obj)
+            db.commit()
+            db.refresh(profile_obj)
+
+            # Associate profile to users
+            res = db.execute(select(UserOAuth))
+            users = res.unique().scalars().all()
+            for user in users:
+                print(f"Now set profile_id={profile_obj.id} for {user.email}.")
+                user.profile_id = profile_obj.id
+                db.add(user)
+            db.commit()
+            db.expunge_all()
+            print()
+
 
 def update_db_data():
     """
@@ -306,17 +333,6 @@ def update_db_data():
     current_update_db_data_module.fix_db()
 
 
-def print_encrypted_password():
-    from cryptography.fernet import Fernet
-
-    password = input("Insert email password: ").encode("utf-8")
-    key = Fernet.generate_key().decode("utf-8")
-    encrypted_password = Fernet(key).encrypt(password).decode("utf-8")
-
-    print(f"\nFRACTAL_EMAIL_PASSWORD={encrypted_password}")
-    print(f"FRACTAL_EMAIL_PASSWORD_KEY={key}")
-
-
 def run():
     args = parser.parse_args(sys.argv[1:])
 
@@ -328,6 +344,9 @@ def run():
         init_db_data(
             resource=args.resource,
             profile=args.profile,
+            admin_email=args.admin_email,
+            admin_password=args.admin_pwd,
+            admin_project_dir=args.admin_project_dir,
         )
     elif args.cmd == "update-db-data":
         update_db_data()
@@ -338,8 +357,6 @@ def run():
             port=args.port,
             reload=args.reload,
         )
-    elif args.cmd == "encrypt-email-password":
-        print_encrypted_password()
     else:
         sys.exit(f"Error: invalid command '{args.cmd}'.")
 

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/models/security.py

@@ -1,27 +1,17 @@
-# This is based on fastapi_users_db_sqlmodel
-# <https://github.com/fastapi-users/fastapi-users-db-sqlmodel>
-# Original Copyright
-# Copyright 2022 François Voron
-# License: MIT
-#
-# Modified by:
-# Tommaso Comparin <tommaso.comparin@exact-lab.it>
-#
-# Copyright 2022 (C) Friedrich Miescher Institute for Biomedical Research and
-# University of Zurich
 from datetime import datetime
 from typing import Optional
 
 from pydantic import ConfigDict
 from pydantic import EmailStr
 from sqlalchemy import Column
+from sqlalchemy import String
+from sqlalchemy.dialects.postgresql import ARRAY
 from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.types import DateTime
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from .user_settings import UserSettings
 from fractal_server.utils import get_timestamp
 
 
@@ -74,17 +64,20 @@ class UserOAuth(SQLModel, table=True):
         is_superuser:
         is_verified:
         oauth_accounts:
-        user_settings_id:
         profile_id:
-        settings:
+        project_dir:
+        slurm_accounts:
     """
 
+    model_config = ConfigDict(from_attributes=True)
+
     __tablename__ = "user_oauth"
 
     id: int | None = Field(default=None, primary_key=True)
 
     email: EmailStr = Field(
-        sa_column_kwargs={"unique": True, "index": True}, nullable=False
+        sa_column_kwargs={"unique": True, "index": True},
+        nullable=False,
     )
     hashed_password: str
     is_active: bool = Field(default=True, nullable=False)
@@ -96,18 +89,23 @@ class UserOAuth(SQLModel, table=True):
         sa_relationship_kwargs={"lazy": "joined", "cascade": "all, delete"},
     )
 
-    user_settings_id: int | None = Field(
-        foreign_key="user_settings.id", default=None
-    )
     profile_id: int | None = Field(
         foreign_key="profile.id",
         default=None,
         ondelete="SET NULL",
     )
-    settings: UserSettings | None = Relationship(
-        sa_relationship_kwargs=dict(lazy="selectin", cascade="all, delete")
+
+    # TODO-2.17.1: update to `project_dir: str`
+    project_dir: str = Field(
+        sa_column=Column(
+            String,
+            server_default="/PLACEHOLDER",
+            nullable=False,
+        )
+    )
+    slurm_accounts: list[str] = Field(
+        sa_column=Column(ARRAY(String), server_default="{}"),
     )
-    model_config = ConfigDict(from_attributes=True)
 
 
 class UserGroup(SQLModel, table=True):

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/models/user_settings.py

@@ -4,6 +4,7 @@ from sqlmodel import Field
 from sqlmodel import SQLModel
 
 
+# TODO-2.17.1: Drop `UserSettings`
 class UserSettings(SQLModel, table=True):
     """
     Comprehensive list of user settings.

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/models/v2/task_group.py

@@ -42,6 +42,7 @@ class TaskGroupV2(SQLModel, table=True):
     user_group_id: int | None = Field(
         foreign_key="usergroup.id", default=None, ondelete="SET NULL"
     )
+    # TODO-2.17.1: make `resource_id` not nullable
     resource_id: int | None = Field(
         foreign_key="resource.id", default=None, ondelete="SET NULL"
     )

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/routes/admin/v2/accounting.py

@@ -13,7 +13,7 @@ from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import AccountingRecord
 from fractal_server.app.models.v2 import AccountingRecordSlurm
-from fractal_server.app.routes.auth import current_active_superuser
+from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.routes.pagination import get_pagination_params
 from fractal_server.app.routes.pagination import PaginationRequest
 from fractal_server.app.routes.pagination import PaginationResponse
@@ -34,7 +34,7 @@ async def query_accounting(
     query: AccountingQuery,
     # Dependencies
     pagination: PaginationRequest = Depends(get_pagination_params),
-    superuser: UserOAuth = Depends(current_active_superuser),
+    superuser: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> PaginationResponse[AccountingRecordRead]:
     page = pagination.page
@@ -79,7 +79,7 @@ async def query_accounting(
 async def query_accounting_slurm(
     query: AccountingQuery,
     # dependencies
-    superuser: UserOAuth = Depends(current_active_superuser),
+    superuser: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
     stm = select(AccountingRecordSlurm.slurm_job_ids)

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/routes/admin/v2/impersonate.py

@@ -6,7 +6,7 @@ from fastapi_users.authentication import JWTStrategy
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
-from fractal_server.app.routes.auth import current_active_superuser
+from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.routes.auth._aux_auth import _user_or_404
 from fractal_server.config import get_settings
 from fractal_server.syringe import Inject
@@ -17,7 +17,7 @@ router = APIRouter()
 @router.get("/{user_id}/")
 async def impersonate_user(
     user_id: int,
-    superuser: UserOAuth = Depends(current_active_superuser),
+    superuser: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> JSONResponse:
     user = await _user_or_404(user_id, db)

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/routes/admin/v2/job.py

@@ -16,7 +16,7 @@ from fractal_server.app.models.v2 import HistoryRun
 from fractal_server.app.models.v2 import HistoryUnit
 from fractal_server.app.models.v2 import JobV2
 from fractal_server.app.models.v2 import ProjectV2
-from fractal_server.app.routes.auth import current_active_superuser
+from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.routes.aux._job import _write_shutdown_file
 from fractal_server.app.routes.aux._runner import _check_shutdown_is_supported
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
@@ -43,7 +43,7 @@ async def view_job(
     end_timestamp_min: AwareDatetime | None = None,
     end_timestamp_max: AwareDatetime | None = None,
     log: bool = True,
-    user: UserOAuth = Depends(current_active_superuser),
+    user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[JobReadV2]:
     """
@@ -111,7 +111,7 @@ async def view_job(
 async def view_single_job(
     job_id: int,
     show_tmp_logs: bool = False,
-    user: UserOAuth = Depends(current_active_superuser),
+    user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> JobReadV2:
     job = await db.get(JobV2, job_id)
@@ -136,7 +136,7 @@ async def view_single_job(
 async def update_job(
     job_update: JobUpdateV2,
     job_id: int,
-    user: UserOAuth = Depends(current_active_superuser),
+    user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> JobReadV2 | None:
     """
@@ -200,7 +200,7 @@ async def update_job(
 @router.get("/{job_id}/stop/", status_code=202)
 async def stop_job(
     job_id: int,
-    user: UserOAuth = Depends(current_active_superuser),
+    user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> Response:
     """
@@ -224,7 +224,7 @@ async def stop_job(
 @router.get("/{job_id}/download/", response_class=StreamingResponse)
 async def download_job_logs(
     job_id: int,
-    user: UserOAuth = Depends(current_active_superuser),
+    user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> StreamingResponse:
     """

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/routes/admin/v2/profile.py

@@ -11,7 +11,7 @@ from ._aux_functions import _get_profile_or_404
 from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
-from fractal_server.app.routes.auth import current_active_superuser
+from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.schemas.v2 import ProfileCreate
 from fractal_server.app.schemas.v2 import ProfileRead
 
@@ -21,7 +21,7 @@ router = APIRouter()
 @router.get("/{profile_id}/", response_model=ProfileRead, status_code=200)
 async def get_single_profile(
     profile_id: int,
-    superuser: UserOAuth = Depends(current_active_superuser),
+    superuser: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> ProfileRead:
     """
@@ -35,7 +35,7 @@ async def get_single_profile(
 async def put_profile(
     profile_id: int,
     profile_update: ProfileCreate,
-    superuser: UserOAuth = Depends(current_active_superuser),
+    superuser: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> ProfileRead:
     """
@@ -56,7 +56,7 @@ async def put_profile(
 @router.delete("/{profile_id}/", status_code=204)
 async def delete_profile(
     profile_id: int,
-    superuser: UserOAuth = Depends(current_active_superuser),
+    superuser: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ):
     """

{fractal_server-2.17.0a3 → fractal_server-2.17.0a5}/fractal_server/app/routes/admin/v2/project.py

@@ -6,7 +6,7 @@ from fractal_server.app.db import AsyncSession
 from fractal_server.app.db import get_async_db
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.models.v2 import ProjectV2
-from fractal_server.app.routes.auth import current_active_superuser
+from fractal_server.app.routes.auth import current_superuser_act
 from fractal_server.app.schemas.v2 import ProjectReadV2
 
 router = APIRouter()
@@ -16,7 +16,7 @@ router = APIRouter()
 async def view_project(
     id: int | None = None,
     user_id: int | None = None,
-    user: UserOAuth = Depends(current_active_superuser),
+    user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
 ) -> list[ProjectReadV2]:
     """