fractal-server 2.6.2__py3-none-any.whl → 2.6.3__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.6.2"
+__VERSION__ = "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/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/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/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/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/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.dist-info → fractal_server-2.6.3.dist-info}/METADATA

@@ -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-2.6.2.dist-info → fractal_server-2.6.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=zk2Mr_vPWXiYjT0KF9CbddwUnuJ011NmmqEbItcDUz4,22
+fractal_server/__init__.py,sha256=Xl00aUdi67dqYV36pJ6CjXHphNon7e48hzkQAE3HlRQ,22
 fractal_server/__main__.py,sha256=WcBAkmVE9aH5mDI6wGkVmPAql2N5Vyk0A-7zuUl8WX0,6122
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -6,7 +6,7 @@ fractal_server/app/db/__init__.py,sha256=81rK9w1__Z6PJ5cEcChPVc-wI9YOK4fN--_5Opr
 fractal_server/app/models/__init__.py,sha256=aG7mf1zZbsgzDSp7GHEcZhdjHfW3TGPOLCI8MrvYhPw,500
 fractal_server/app/models/linkusergroup.py,sha256=ufthlbLFAWMU_dJmsVZzVlQa_D9C9SmgydxypQ2Xq1U,309
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
-fractal_server/app/models/security.py,sha256=xeR_3Wb5Epn2fvNgEuTKibzMkMybVogACpUvrP1J1b8,3625
+fractal_server/app/models/security.py,sha256=2npjgRKBZ7OAnhAXNbYxjtuOsSm1P4kak__qfk2SpeM,3770
 fractal_server/app/models/user_settings.py,sha256=0YXCAwoAVGqI2irRLdXgr9-JS0STtHhSaoFENigAnrk,1312
 fractal_server/app/models/v1/__init__.py,sha256=hUI7dEbPaiZGN0IbHW4RSmSicyvtn_xeuevoX7zvUwI,466
 fractal_server/app/models/v1/dataset.py,sha256=99GDgt7njx8yYQApkImqp_7bHA5HH3ElvbR6Oyj9kVI,2017
@@ -52,8 +52,8 @@ fractal_server/app/routes/api/v2/workflow.py,sha256=rMCcclz9aJAMSVLncUdSDGrgkKbn
 fractal_server/app/routes/api/v2/workflowtask.py,sha256=-3-c8DDnxGjMwWbX_h5V5OLaC_iCLXYzwWKBUaL-5wE,7060
 fractal_server/app/routes/auth/__init__.py,sha256=fao6CS0WiAjHDTvBzgBVV_bSXFpEAeDBF6Z6q7rRkPc,1658
 fractal_server/app/routes/auth/_aux_auth.py,sha256=a3DCj6_tekf4Bfu8Kax9uxVGbTuVsONgki7E6AJUN_8,3269
-fractal_server/app/routes/auth/current_user.py,sha256=kJk6bONS8bwPoJh40mpmVGM2bb5qRrJ6Rf_p1_flvgI,3480
-fractal_server/app/routes/auth/group.py,sha256=az8kRJJU5rA0L8GCX5kvRNuQhrsoGWPuvQ26z7iFQ3E,5388
+fractal_server/app/routes/auth/current_user.py,sha256=s3R1O53Qnow1LqDW-UpkYvfKKSJwLrDWGeMtsIEMUNs,4462
+fractal_server/app/routes/auth/group.py,sha256=eT-1c0Ow8KbYkKEMQ5ebhEAeRixwJs2kQW45UIutH5w,5833
 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
@@ -83,7 +83,7 @@ fractal_server/app/runner/executors/slurm/sudo/__init__.py,sha256=Cjn1rYvljddi96
 fractal_server/app/runner/executors/slurm/sudo/_check_jobs_status.py,sha256=wAgwpVcr6JIslKHOuS0FhRa_6T1KCManyRJqA-fifzw,1909
 fractal_server/app/runner/executors/slurm/sudo/_executor_wait_thread.py,sha256=z5LlhaiqAb8pHsF1WwdzXN39C5anQmwjo1rSQgtRAYE,4422
 fractal_server/app/runner/executors/slurm/sudo/_subprocess_run_as_user.py,sha256=g8wqUjSicN17UZVXlfaMomYZ-xOIbBu1oE7HdJTzfvw,5218
-fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=6OPe9t70gLyuC2JhWt2o1f0e7zhQPBtrbMHQkDd6RAQ,48725
+fractal_server/app/runner/executors/slurm/sudo/executor.py,sha256=mTqTSvoRukvocyMLvlGuGWMaL6hy3McYLx_7bUW1pEM,48918
 fractal_server/app/runner/extract_archive.py,sha256=tLpjDrX47OjTNhhoWvm6iNukg8KoieWyTb7ZfvE9eWU,2483
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
 fractal_server/app/runner/run_subprocess.py,sha256=c3JbYXq3hX2aaflQU19qJ5Xs6J6oXGNvnTEoAfv2bxc,959
@@ -127,7 +127,7 @@ fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtD
 fractal_server/app/schemas/__init__.py,sha256=stURAU_t3AOBaH0HSUbV-GKhlPKngnnIMoqWc3orFyI,135
 fractal_server/app/schemas/_validators.py,sha256=XKEGEHxp3H6YSJewtFWXe_2Nh7SDdNtAXmlEmJO6Vb0,3606
 fractal_server/app/schemas/user.py,sha256=VNnAPnAVK6X0PZlw7XehocAshVNuUHdDwiZVWCCor6Y,2156
-fractal_server/app/schemas/user_group.py,sha256=2f9XQ6kIar6NMY4UCN0yOnve6ZDHUVZaHv1dna1Vfjg,1446
+fractal_server/app/schemas/user_group.py,sha256=YwJvYgj-PI66LWy38CEd_FIZPsBV1_2N5zJPGFcFvBw,2143
 fractal_server/app/schemas/user_settings.py,sha256=UEST1MSmd9w2YypCji3SONSFlJcr2u4uG3bTczZy_Pk,3102
 fractal_server/app/schemas/v1/__init__.py,sha256=CrBGgBhoemCvmZ70ZUchM-jfVAICnoa7AjZBAtL2UB0,1852
 fractal_server/app/schemas/v1/applyworkflow.py,sha256=uuIh7fHlHEL4yLqL-dePI6-nfCsqgBYATmht7w_KITw,4302
@@ -182,6 +182,7 @@ fractal_server/migrations/versions/9c5ae74c9b98_add_user_settings_table.py,sha25
 fractal_server/migrations/versions/9fd26a2b0de4_add_workflow_timestamp_created.py,sha256=4l1AHGUsa0ONoJVZlr3fTXw_xbbQ8O7wlD92Az2aRfM,1849
 fractal_server/migrations/versions/a7f4d6137b53_add_workflow_dump_to_applyworkflow.py,sha256=ekDUML7ILpmdoqEclKbEUdyLi4uw9HSG_sTjG2hp_JE,867
 fractal_server/migrations/versions/d4fe3708d309_make_applyworkflow_workflow_dump_non_.py,sha256=6cHEZFuTXiQg9yu32Y3RH1XAl71av141WQ6UMbiITIg,949
+fractal_server/migrations/versions/da2cb2ac4255_user_group_viewer_paths.py,sha256=yGWSA2HIHUybcVy66xBITk08opV2DFYSCIIrulaUZhI,901
 fractal_server/migrations/versions/e75cac726012_make_applyworkflow_start_timestamp_not_.py,sha256=lOggSvzGWqQvnxxFuSM6W50Ui49R918A-uBuiZJ0pNM,963
 fractal_server/migrations/versions/efa89c30e0a4_add_project_timestamp_created.py,sha256=jilQW3QIqYQ4Q6hCnUiG7UtNMpA41ujqrB3tPFiPM1Q,1221
 fractal_server/migrations/versions/f384e1c0cf5d_drop_task_default_args_columns.py,sha256=9BwqUS9Gf7UW_KjrzHbtViC880qhD452KAytkHWWZyk,746
@@ -213,8 +214,8 @@ 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-2.6.2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.6.2.dist-info/METADATA,sha256=hlWGMOKcA-SXQpW1tlXMo9zfn6lKs31rl-byf88u8Bs,4628
-fractal_server-2.6.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.6.2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.6.2.dist-info/RECORD,,
+fractal_server-2.6.3.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.6.3.dist-info/METADATA,sha256=hlZ8xt1P6qEjNO4ySIUzSMfqgQv6RilEJfaWaS5fqBs,4628
+fractal_server-2.6.3.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.6.3.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.6.3.dist-info/RECORD,,