fractal-server 2.18.0a1__tar.gz → 2.18.0a3__tar.gz

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.0a1
+Version: 2.18.0a3
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

fractal_server-2.18.0a3/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.18.0a3"

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/__main__.py

@@ -167,7 +167,8 @@ def init_db_data(
             "`--admin-pwd` and `--admin-project-dir`. Exit."
         )
         sys.exit(1)
-    if admin_password and admin_email:
+
+    if admin_email:
         asyncio.run(
             _create_first_user(
                 email=admin_email,

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/models/security.py

@@ -6,7 +6,6 @@ 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
@@ -113,7 +112,13 @@ class UserOAuth(SQLModel, table=True):
         ondelete="RESTRICT",
     )
 
-    project_dir: str
+    # TODO-2.18.1: drop `project_dir`
+    project_dir: str | None = Field(default=None, nullable=True)
+    # TODO-2.18.1: `project_dirs: list[str] = Field(min_length=1)`
+    project_dirs: list[str] = Field(
+        sa_column=Column(ARRAY(String), nullable=False, server_default="{}"),
+    )
+
     slurm_accounts: list[str] = Field(
         sa_column=Column(ARRAY(String), server_default="{}"),
     )
@@ -135,6 +140,3 @@ class UserGroup(SQLModel, table=True):
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),
     )
-    viewer_paths: list[str] = Field(
-        sa_column=Column(JSONB, server_default="[]", nullable=False)
-    )

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/api/__init__.py

@@ -8,7 +8,6 @@ from fastapi import Depends
 import fractal_server
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_superuser_act
-from fractal_server.config import get_data_settings
 from fractal_server.config import get_db_settings
 from fractal_server.config import get_email_settings
 from fractal_server.config import get_oauth_settings
@@ -50,14 +49,6 @@ async def view_email_settings(
     return settings.model_dump()
 
 
-@router_api.get("/settings/data/")
-async def view_data_settings(
-    user: UserOAuth = Depends(current_superuser_act),
-):
-    settings = Inject(get_data_settings)
-    return settings.model_dump()
-
-
 @router_api.get("/settings/oauth/")
 async def view_oauth_settings(
     user: UserOAuth = Depends(current_superuser_act),

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/api/v2/dataset.py

@@ -1,3 +1,5 @@
+from pathlib import Path
+
 from fastapi import APIRouter
 from fastapi import Depends
 from fastapi import HTTPException
@@ -58,7 +60,7 @@ async def create_dataset(
         await db.commit()
         await db.refresh(db_dataset)
         path = (
-            f"{user.project_dir}/fractal/"
+            f"{user.project_dirs[0]}/fractal/"
             f"{project_id}_{sanitize_string(project.name)}/"
             f"{db_dataset.id}_{sanitize_string(db_dataset.name)}"
         )
@@ -69,6 +71,18 @@ async def create_dataset(
         await db.commit()
         await db.refresh(db_dataset)
     else:
+        if not any(
+            Path(dataset.zarr_dir).is_relative_to(project_dir)
+            for project_dir in user.project_dirs
+        ):
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
+                detail=(
+                    "Dataset zarr_dir is not relative to any of the user "
+                    "project directories."
+                ),
+            )
+
         db_dataset = DatasetV2(project_id=project_id, **dataset.model_dump())
         db.add(db_dataset)
         await db.commit()
@@ -154,14 +168,26 @@ async def update_dataset(
     )
     db_dataset = output["dataset"]
 
-    if (dataset_update.zarr_dir is not None) and (len(db_dataset.images) != 0):
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
-            detail=(
-                "Cannot modify `zarr_dir` because the dataset has a non-empty "
-                "image list."
-            ),
-        )
+    if dataset_update.zarr_dir is not None:
+        if db_dataset.images:
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
+                detail=(
+                    "Cannot modify `zarr_dir` because the dataset has a "
+                    "non-empty image list."
+                ),
+            )
+        if not any(
+            Path(dataset_update.zarr_dir).is_relative_to(project_dir)
+            for project_dir in user.project_dirs
+        ):
+            raise HTTPException(
+                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
+                detail=(
+                    "Dataset zarr_dir is not relative to any of the user "
+                    "project directories."
+                ),
+            )
 
     for key, value in dataset_update.model_dump(exclude_unset=True).items():
         setattr(db_dataset, key, value)

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/api/v2/submit.py

@@ -238,7 +238,7 @@ async def apply_workflow(
     )
 
     # Define user-side job directory
-    cache_dir = Path(user.project_dir, FRACTAL_CACHE_DIR)
+    cache_dir = Path(user.project_dirs[0], FRACTAL_CACHE_DIR)
     match resource.type:
         case ResourceType.LOCAL:
             WORKFLOW_DIR_REMOTE = WORKFLOW_DIR_LOCAL

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/api/v2/workflowtask.py

@@ -5,12 +5,10 @@ from fastapi import Depends
 from fastapi import HTTPException
 from fastapi import Response
 from fastapi import status
-from sqlmodel import select
 
 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.linkuserproject import LinkUserProjectV2
 from fractal_server.app.routes.auth import current_user_act_ver_prof
 from fractal_server.app.schemas.v2 import TaskType
 from fractal_server.app.schemas.v2 import WorkflowTaskCreateV2
@@ -53,31 +51,6 @@ async def create_workflowtask(
         db=db,
     )
 
-    res = await db.execute(
-        select(UserOAuth.id)
-        .join(LinkUserProjectV2, LinkUserProjectV2.user_id == UserOAuth.id)
-        .where(LinkUserProjectV2.project_id == project_id)
-        .where(LinkUserProjectV2.is_owner.is_(True))
-    )
-    project_owner_id = res.scalar_one()
-    if project_owner_id != user.id:
-        try:
-            await _get_task_read_access(
-                task_id=task_id,
-                user_id=project_owner_id,
-                db=db,
-                require_active=True,
-            )
-        except HTTPException as e:
-            raise (
-                HTTPException(
-                    status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
-                    detail="The task must be accessible to the project owner.",
-                )
-                if e.status_code == 403
-                else e
-            )
-
     task = await _get_task_read_access(
         task_id=task_id, user_id=user.id, db=db, require_active=True
     )

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/auth/current_user.py

@@ -2,21 +2,16 @@
 Definition of `/auth/current-user/` endpoints
 """
 
-import os
-
 from fastapi import APIRouter
 from fastapi import Depends
 from sqlalchemy.ext.asyncio import AsyncSession
 from sqlmodel import select
 
 from fractal_server.app.db import get_async_db
-from fractal_server.app.models import LinkUserGroup
 from fractal_server.app.models import Profile
 from fractal_server.app.models import Resource
-from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
 from fractal_server.app.routes.auth import current_user_act
-from fractal_server.app.routes.auth import current_user_act_ver
 from fractal_server.app.routes.auth._aux_auth import (
     _get_single_user_with_groups,
 )
@@ -26,9 +21,6 @@ from fractal_server.app.schemas.user import UserUpdate
 from fractal_server.app.schemas.user import UserUpdateStrict
 from fractal_server.app.security import UserManager
 from fractal_server.app.security import get_user_manager
-from fractal_server.config import DataAuthScheme
-from fractal_server.config import get_data_settings
-from fractal_server.syringe import Inject
 
 router_current_user = APIRouter()
 
@@ -106,58 +98,3 @@ async def get_current_user_profile_info(
         )
 
     return response_data
-
-
-@router_current_user.get(
-    "/current-user/allowed-viewer-paths/", response_model=list[str]
-)
-async def get_current_user_allowed_viewer_paths(
-    current_user: UserOAuth = Depends(current_user_act_ver),
-    db: AsyncSession = Depends(get_async_db),
-) -> list[str]:
-    """
-    Returns the allowed viewer paths for current user, according to the
-    selected FRACTAL_DATA_AUTH_SCHEME
-    """
-
-    data_settings = Inject(get_data_settings)
-
-    authorized_paths = []
-
-    if data_settings.FRACTAL_DATA_AUTH_SCHEME == DataAuthScheme.NONE:
-        return authorized_paths
-
-    # Append `project_dir` to the list of authorized paths
-    authorized_paths.append(current_user.project_dir)
-
-    # If auth scheme is "users-folders" and `slurm_user` is set,
-    # build and append the user folder
-    if (
-        data_settings.FRACTAL_DATA_AUTH_SCHEME == DataAuthScheme.USERS_FOLDERS
-        and current_user.profile_id is not None
-    ):
-        profile = await db.get(Profile, current_user.profile_id)
-        if profile is not None and profile.username is not None:
-            base_folder = data_settings.FRACTAL_DATA_BASE_FOLDER
-            user_folder = os.path.join(base_folder, profile.username)
-            authorized_paths.append(user_folder)
-
-    if data_settings.FRACTAL_DATA_AUTH_SCHEME == DataAuthScheme.VIEWER_PATHS:
-        # Returns the union of `viewer_paths` for all user's groups
-        cmd = (
-            select(UserGroup.viewer_paths)
-            .join(LinkUserGroup, LinkUserGroup.group_id == UserGroup.id)
-            .where(LinkUserGroup.user_id == current_user.id)
-        )
-        res = await db.execute(cmd)
-        viewer_paths_nested = res.scalars().all()
-
-        # Flatten a nested object and make its elements unique
-        all_viewer_paths_set = {
-            path
-            for _viewer_paths in viewer_paths_nested
-            for path in _viewer_paths
-        }
-        authorized_paths.extend(all_viewer_paths_set)
-
-    return authorized_paths

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/auth/group.py

@@ -16,7 +16,6 @@ from fractal_server.app.models import UserGroup
 from fractal_server.app.models import UserOAuth
 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.config import get_settings
 from fractal_server.logger import set_logger
 from fractal_server.syringe import Inject
@@ -101,41 +100,13 @@ async def create_single_group(
         )
 
     # Create and return new group
-    new_group = UserGroup(
-        name=group_create.name, viewer_paths=group_create.viewer_paths
-    )
+    new_group = UserGroup(name=group_create.name)
     db.add(new_group)
     await db.commit()
 
     return dict(new_group.model_dump(), user_ids=[])
 
 
-@router_group.patch(
-    "/group/{group_id}/",
-    response_model=UserGroupRead,
-    status_code=status.HTTP_200_OK,
-)
-async def update_single_group(
-    group_id: int,
-    group_update: UserGroupUpdate,
-    user: UserOAuth = Depends(current_superuser_act),
-    db: AsyncSession = Depends(get_async_db),
-) -> UserGroupRead:
-    group = await _usergroup_or_404(group_id, db)
-
-    # Patch `viewer_paths`
-    if group_update.viewer_paths is not None:
-        group.viewer_paths = group_update.viewer_paths
-        db.add(group)
-        await db.commit()
-
-    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=204)
 async def delete_single_group(
     group_id: int,

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/routes/auth/router.py

@@ -6,6 +6,7 @@ from .login import router_login
 from .oauth import get_oauth_router
 from .register import router_register
 from .users import router_users
+from .viewer_paths import router_viewer_paths
 
 router_auth = APIRouter()
 
@@ -14,6 +15,7 @@ router_auth.include_router(router_current_user)
 router_auth.include_router(router_login)
 router_auth.include_router(router_users)
 router_auth.include_router(router_group)
+router_auth.include_router(router_viewer_paths)
 router_oauth = get_oauth_router()
 if router_oauth is not None:
     router_auth.include_router(router_oauth)

fractal_server-2.18.0a3/fractal_server/app/routes/auth/viewer_paths.py

@@ -0,0 +1,43 @@
+from fastapi import APIRouter
+from fastapi import Depends
+from sqlalchemy.ext.asyncio import AsyncSession
+from sqlmodel import select
+
+from fractal_server.app.db import get_async_db
+from fractal_server.app.models import UserOAuth
+from fractal_server.app.models.linkuserproject import LinkUserProjectV2
+from fractal_server.app.models.v2.dataset import DatasetV2
+from fractal_server.app.models.v2.project import ProjectV2
+from fractal_server.app.routes.auth import current_user_act_ver
+
+router_viewer_paths = APIRouter()
+
+
+@router_viewer_paths.get(
+    "/current-user/allowed-viewer-paths/", response_model=list[str]
+)
+async def get_current_user_allowed_viewer_paths(
+    include_shared_projects: bool = True,
+    current_user: UserOAuth = Depends(current_user_act_ver),
+    db: AsyncSession = Depends(get_async_db),
+) -> list[str]:
+    """
+    Returns the allowed viewer paths for current user.
+    """
+    authorized_paths = current_user.project_dirs.copy()
+
+    if include_shared_projects:
+        res = await db.execute(
+            select(DatasetV2.zarr_dir)
+            .join(ProjectV2, ProjectV2.id == DatasetV2.project_id)
+            .join(
+                LinkUserProjectV2, LinkUserProjectV2.project_id == ProjectV2.id
+            )
+            .where(LinkUserProjectV2.user_id == current_user.id)
+            .where(LinkUserProjectV2.is_owner.is_(False))
+        )
+        authorized_paths.extend(res.unique().scalars().all())
+        # Note that `project_dirs` and the `db.execute` result may have some
+        # common elements, and then this list may have non-unique items.
+
+    return authorized_paths

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/schemas/user.py

@@ -8,12 +8,18 @@ from pydantic import EmailStr
 from pydantic import Field
 
 from fractal_server.string_tools import validate_cmd
-from fractal_server.types import AbsolutePathStr
+from fractal_server.types import ListUniqueAbsolutePathStr
 from fractal_server.types import ListUniqueNonEmptyString
 from fractal_server.types import ListUniqueNonNegativeInt
 from fractal_server.types import NonEmptyStr
 
 
+def _validate_cmd_list(value: list[str]) -> list[str]:
+    for v in value:
+        validate_cmd(v)
+    return value
+
+
 class OAuthAccountRead(BaseModel):
     """
     Schema for storing essential `OAuthAccount` information within
@@ -38,20 +44,17 @@ class UserRead(schemas.BaseUser[int]):
         group_ids_names:
         oauth_accounts:
         profile_id:
+        project_dirs:
+        slurm_accounts:
     """
 
     group_ids_names: list[tuple[int, str]] | None = None
     oauth_accounts: list[OAuthAccountRead]
     profile_id: int | None = None
-    project_dir: str
+    project_dirs: list[str]
     slurm_accounts: list[str]
 
 
-def _validate_cmd(value: str) -> str:
-    validate_cmd(value)
-    return value
-
-
 class UserUpdate(schemas.BaseUserUpdate):
     """
     Schema for `User` update.
@@ -63,7 +66,7 @@ class UserUpdate(schemas.BaseUserUpdate):
         is_superuser:
         is_verified:
         profile_id:
-        project_dir:
+        project_dirs:
         slurm_accounts:
     """
 
@@ -74,9 +77,9 @@ class UserUpdate(schemas.BaseUserUpdate):
     is_superuser: bool = None
     is_verified: bool = None
     profile_id: int | None = None
-    project_dir: Annotated[AbsolutePathStr, AfterValidator(_validate_cmd)] = (
-        None
-    )
+    project_dirs: Annotated[
+        ListUniqueAbsolutePathStr, AfterValidator(_validate_cmd_list)
+    ] = None
     slurm_accounts: ListUniqueNonEmptyString = None
 
 
@@ -98,10 +101,14 @@ class UserCreate(schemas.BaseUserCreate):
 
     Attributes:
         profile_id:
+        project_dirs:
+        slurm_accounts:
     """
 
     profile_id: int | None = None
-    project_dir: Annotated[AbsolutePathStr, AfterValidator(_validate_cmd)]
+    project_dirs: Annotated[
+        ListUniqueAbsolutePathStr, AfterValidator(_validate_cmd_list)
+    ] = Field(min_length=1)
     slurm_accounts: list[str] = Field(default_factory=list)
 
 
@@ -109,6 +116,8 @@ class UserUpdateGroups(BaseModel):
     """
     Schema for `POST /auth/users/{user_id}/set-groups/`
 
+    Attributes:
+        group_ids:
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -117,6 +126,14 @@ class UserUpdateGroups(BaseModel):
 
 
 class UserProfileInfo(BaseModel):
+    """
+    Attributes:
+        has_profile:
+        resource_name:
+        profile_name:
+        username:
+    """
+
     has_profile: bool
     resource_name: str | None = None
     profile_name: str | None = None

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/schemas/user_group.py

@@ -2,16 +2,13 @@ from datetime import datetime
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
-from pydantic import Field
 from pydantic import field_serializer
 from pydantic.types import AwareDatetime
 
-from fractal_server.types import ListUniqueAbsolutePathStr
 from fractal_server.types import NonEmptyStr
 
 __all__ = (
     "UserGroupRead",
-    "UserGroupUpdate",
     "UserGroupCreate",
 )
 
@@ -34,7 +31,6 @@ class UserGroupRead(BaseModel):
     name: str
     timestamp_created: AwareDatetime
     user_ids: list[int] | None = None
-    viewer_paths: list[str]
 
     @field_serializer("timestamp_created")
     def serialize_datetime(v: datetime) -> str:
@@ -52,14 +48,3 @@ class UserGroupCreate(BaseModel):
     model_config = ConfigDict(extra="forbid")
 
     name: NonEmptyStr
-    viewer_paths: ListUniqueAbsolutePathStr = Field(default_factory=list)
-
-
-class UserGroupUpdate(BaseModel):
-    """
-    Schema for `UserGroup` update
-    """
-
-    model_config = ConfigDict(extra="forbid")
-
-    viewer_paths: ListUniqueAbsolutePathStr = None

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/app/security/__init__.py

@@ -425,7 +425,7 @@ async def _create_first_user(
                     kwargs = dict(
                         email=email,
                         password=password,
-                        project_dir=project_dir,
+                        project_dirs=[project_dir],
                         profile_id=profile_id,
                         is_superuser=is_superuser,
                         is_verified=is_verified,

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/config/__init__.py

@@ -1,5 +1,3 @@
-from ._data import DataAuthScheme  # noqa F401
-from ._data import DataSettings
 from ._database import DatabaseSettings
 from ._email import EmailSettings
 from ._email import PublicEmailSettings  # noqa F401
@@ -21,7 +19,3 @@ def get_email_settings(email_settings=EmailSettings()) -> EmailSettings:
 
 def get_oauth_settings(oauth_settings=OAuthSettings()) -> OAuthSettings:
     return oauth_settings
-
-
-def get_data_settings(data_settings=DataSettings()) -> DataSettings:
-    return data_settings

{fractal_server-2.18.0a1 → fractal_server-2.18.0a3}/fractal_server/config/_main.py

@@ -41,6 +41,10 @@ class Settings(BaseSettings):
             user group (e.g. it cannot be deleted, and new users are
             automatically added to it). If set to `None` (the default value),
             then user groups are all equivalent, independently on their name.
+        FRACTAL_LONG_REQUEST_TIME:
+            Time limit beyond which the execution of an API request is
+            considered *slow* and an appropriate warning is logged by the
+            middleware.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -57,3 +61,4 @@ class Settings(BaseSettings):
     FRACTAL_GRACEFUL_SHUTDOWN_TIME: float = 30.0
     FRACTAL_HELP_URL: HttpUrl | None = None
     FRACTAL_DEFAULT_GROUP_NAME: Literal["All"] | None = None
+    FRACTAL_LONG_REQUEST_TIME: float = 30.0

fractal_server-2.18.0a3/fractal_server/data_migrations/2_18_1.py

@@ -0,0 +1,29 @@
+import logging
+import sys
+
+from sqlalchemy.orm.attributes import flag_modified
+from sqlmodel import select
+
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models import UserOAuth
+
+logging.basicConfig(level=logging.INFO)
+
+
+def fix_db():
+    logging.info("START - fix db")
+
+    with next(get_sync_db()) as db:
+        res = db.execute(select(UserOAuth).order_by(UserOAuth.email))
+        user_list = res.scalars().unique().all()
+
+        for user in user_list:
+            logging.info(f"Now handling user {user.email}.")
+            if user.project_dirs != []:
+                sys.exit(f"Non empty `project_dirs` for User[{user.id}]")
+            user.project_dirs.append(user.project_dir)
+            flag_modified(user, "project_dirs")
+
+        db.commit()
+
+    logging.info("END - fix db")