fractal-server 2.6.2__tar.gz → 2.6.3__tar.gz

{fractal_server-2.6.2 → fractal_server-2.6.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.6.2
+Version: 2.6.3
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-2.6.3/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.6.3"

{fractal_server-2.6.2 → fractal_server-2.6.3}/fractal_server/app/models/security.py

@@ -15,6 +15,7 @@ from typing import Optional
 from pydantic import EmailStr
 from sqlalchemy import Column
 from sqlalchemy.types import DateTime
+from sqlalchemy.types import JSON
 from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
@@ -126,3 +127,6 @@ 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(JSON, server_default="[]", nullable=False)
+    )

{fractal_server-2.6.2 → fractal_server-2.6.3}/fractal_server/app/routes/auth/current_user.py

@@ -5,6 +5,7 @@ from fastapi import APIRouter
 from fastapi import Depends
 from fastapi_users import schemas
 from sqlalchemy.ext.asyncio import AsyncSession
+from sqlmodel import select
 
 from . import current_active_user
 from ...db import get_async_db
@@ -13,6 +14,8 @@ from ...schemas.user import UserUpdate
 from ...schemas.user import UserUpdateStrict
 from ..aux.validate_user_settings import verify_user_has_settings
 from ._aux_auth import _get_single_user_with_group_names
+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 import UserSettings
 from fractal_server.app.schemas import UserSettingsReadStrict
@@ -103,3 +106,29 @@ async def patch_current_user_settings(
     await db.refresh(current_user_settings)
 
     return current_user_settings
+
+
+@router_current_user.get(
+    "/current-user/viewer-paths/", response_model=list[str]
+)
+async def get_current_user_viewer_paths(
+    current_user: UserOAuth = Depends(current_active_user),
+    db: AsyncSession = Depends(get_async_db),
+) -> list[str]:
+    """Returns the union of `viewer_paths` for all user's groups"""
+    cmd = (
+        select(UserGroup.viewer_paths)
+        .join(LinkUserGroup)
+        .where(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 = set(
+        path for _viewer_paths in viewer_paths_nested for path in _viewer_paths
+    )
+    all_viewer_paths = list(all_viewer_paths_set)
+
+    return all_viewer_paths

{fractal_server-2.6.2 → fractal_server-2.6.3}/fractal_server/app/routes/auth/group.py

@@ -97,7 +97,9 @@ async def create_single_group(
         )
 
     # Create and return new group
-    new_group = UserGroup(name=group_create.name)
+    new_group = UserGroup(
+        name=group_create.name, viewer_paths=group_create.viewer_paths
+    )
     db.add(new_group)
     await db.commit()
 
@@ -116,6 +118,13 @@ 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.",
+        )
+
     # 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,
@@ -152,6 +161,12 @@ async def update_single_group(
             detail=error_msg,
         )
 
+    # 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_group_with_user_ids(
         group_id=group_id, db=db
     )

{fractal_server-2.6.2 → fractal_server-2.6.3}/fractal_server/app/runner/executors/slurm/sudo/executor.py

@@ -246,6 +246,11 @@ class FractalSlurmExecutor(SlurmExecutor):
 
         super().__init__(*args, **kwargs)
 
+        # Assign `wait_thread.shutdown_callback` early, since it may be called
+        # from within `_stop_and_join_wait_thread` (e.g. if an exception is
+        # raised within `__init__`).
+        self.wait_thread.shutdown_callback = self.shutdown
+
         self.keep_pickle_files = keep_pickle_files
         self.slurm_user = slurm_user
         self.slurm_account = slurm_account
@@ -291,7 +296,6 @@ class FractalSlurmExecutor(SlurmExecutor):
             shutdown_file
             or (self.workflow_dir_local / SHUTDOWN_FILENAME).as_posix()
         )
-        self.wait_thread.shutdown_callback = self.shutdown
 
     def _cleanup(self, jobid: str) -> None:
         """

{fractal_server-2.6.2 → fractal_server-2.6.3}/fractal_server/app/schemas/user_group.py

@@ -6,9 +6,9 @@ from pydantic import Extra
 from pydantic import Field
 from pydantic import validator
 
+from ._validators import val_absolute_path
 from ._validators import val_unique_list
 
-
 __all__ = (
     "UserGroupRead",
     "UserGroupUpdate",
@@ -34,6 +34,7 @@ class UserGroupRead(BaseModel):
     name: str
     timestamp_created: datetime
     user_ids: Optional[list[int]] = None
+    viewer_paths: list[str]
 
 
 class UserGroupCreate(BaseModel, extra=Extra.forbid):
@@ -45,6 +46,14 @@ class UserGroupCreate(BaseModel, extra=Extra.forbid):
     """
 
     name: str
+    viewer_paths: list[str] = Field(default_factory=list)
+
+    @validator("viewer_paths")
+    def viewer_paths_validator(cls, value):
+        for i, path in enumerate(value):
+            value[i] = val_absolute_path(f"viewer_paths[{i}]")(path)
+        value = val_unique_list("viewer_paths")(value)
+        return value
 
 
 class UserGroupUpdate(BaseModel, extra=Extra.forbid):
@@ -59,7 +68,15 @@ class UserGroupUpdate(BaseModel, extra=Extra.forbid):
     """
 
     new_user_ids: list[int] = Field(default_factory=list)
+    viewer_paths: Optional[list[str]] = None
 
     _val_unique = validator("new_user_ids", allow_reuse=True)(
         val_unique_list("new_user_ids")
     )
+
+    @validator("viewer_paths")
+    def viewer_paths_validator(cls, value):
+        for i, path in enumerate(value):
+            value[i] = val_absolute_path(f"viewer_paths[{i}]")(path)
+        value = val_unique_list("viewer_paths")(value)
+        return value

fractal_server-2.6.3/fractal_server/migrations/versions/da2cb2ac4255_user_group_viewer_paths.py

@@ -0,0 +1,36 @@
+"""user group viewer paths
+
+Revision ID: da2cb2ac4255
+Revises: 94a47ea2d3ff
+Create Date: 2024-09-26 14:39:26.135101
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "da2cb2ac4255"
+down_revision = "94a47ea2d3ff"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("usergroup", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "viewer_paths", sa.JSON(), server_default="[]", nullable=False
+            )
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("usergroup", schema=None) as batch_op:
+        batch_op.drop_column("viewer_paths")
+
+    # ### end Alembic commands ###

{fractal_server-2.6.2 → fractal_server-2.6.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.6.2"
+version = "2.6.3"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -92,7 +92,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.6.2"
+current_version = "2.6.3"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.6.2/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.6.2"