fractal-server 2.17.0a11__py3-none-any.whl → 2.17.1__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.17.0a11"
+__VERSION__ = "2.17.1"

fractal_server/__main__.py

@@ -7,7 +7,6 @@ from pathlib import Path
 import uvicorn
 from pydantic import ValidationError
 
-from fractal_server.app.schemas.v2 import ResourceType
 
 parser = ap.ArgumentParser(description="fractal-server commands")
 
@@ -149,6 +148,7 @@ def init_db_data(
     from fractal_server.app.models import Resource, Profile
     from fractal_server.app.schemas.v2.resource import cast_serialize_resource
     from fractal_server.app.schemas.v2.profile import cast_serialize_profile
+    from fractal_server.app.schemas.v2 import ResourceType
 
     # Create default group and user
     print()

fractal_server/app/models/__init__.py

@@ -6,5 +6,4 @@ will not be picked up by alembic.
 from .linkusergroup import LinkUserGroup  # noqa: F401
 from .linkuserproject import LinkUserProjectV2  # noqa: F401
 from .security import *  # noqa
-from .user_settings import UserSettings  # noqa
 from .v2 import *  # noqa

fractal_server/app/models/security.py

@@ -95,24 +95,11 @@ class UserOAuth(SQLModel, table=True):
         ondelete="RESTRICT",
     )
 
-    # TODO-2.17.1: update to `project_dir: str`
-    project_dir: str = Field(
-        sa_column=Column(
-            String,
-            server_default="/PLACEHOLDER",
-            nullable=False,
-        )
-    )
+    project_dir: str
     slurm_accounts: list[str] = Field(
         sa_column=Column(ARRAY(String), server_default="{}"),
     )
 
-    # TODO-2.17.1: remove
-    user_settings_id: int | None = Field(
-        foreign_key="user_settings.id",
-        default=None,
-    )
-
 
 class UserGroup(SQLModel, table=True):
     """

fractal_server/app/models/v2/project.py

@@ -15,10 +15,7 @@ class ProjectV2(SQLModel, table=True):
     id: int | None = Field(default=None, primary_key=True)
     name: str
 
-    # TODO-2.17.1: make `resource_id` not nullable
-    resource_id: int | None = Field(
-        foreign_key="resource.id", default=None, ondelete="RESTRICT"
-    )
+    resource_id: int = Field(foreign_key="resource.id", ondelete="RESTRICT")
     timestamp_created: datetime = Field(
         default_factory=get_timestamp,
         sa_column=Column(DateTime(timezone=True), nullable=False),

fractal_server/app/models/v2/task_group.py

@@ -42,10 +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="RESTRICT"
-    )
+    resource_id: int = Field(foreign_key="resource.id", ondelete="RESTRICT")
 
     origin: str
     pkg_name: str

fractal_server/app/routes/admin/v2/job.py

@@ -7,6 +7,7 @@ from fastapi import Response
 from fastapi import status
 from fastapi.responses import StreamingResponse
 from pydantic.types import AwareDatetime
+from sqlalchemy import func
 from sqlmodel import select
 
 from fractal_server.app.db import AsyncSession
@@ -19,6 +20,9 @@ from fractal_server.app.models.v2 import ProjectV2
 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.routes.pagination import get_pagination_params
+from fractal_server.app.routes.pagination import PaginationRequest
+from fractal_server.app.routes.pagination import PaginationResponse
 from fractal_server.app.schemas.v2 import HistoryUnitStatus
 from fractal_server.app.schemas.v2 import JobReadV2
 from fractal_server.app.schemas.v2 import JobStatusTypeV2
@@ -30,7 +34,7 @@ from fractal_server.zip_tools import _zip_folder_to_byte_stream_iterator
 router = APIRouter()
 
 
-@router.get("/", response_model=list[JobReadV2])
+@router.get("/", response_model=PaginationResponse[JobReadV2])
 async def view_job(
     id: int | None = None,
     user_id: int | None = None,
@@ -43,9 +47,10 @@ async def view_job(
     end_timestamp_min: AwareDatetime | None = None,
     end_timestamp_max: AwareDatetime | None = None,
     log: bool = True,
+    pagination: PaginationRequest = Depends(get_pagination_params),
     user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
-) -> list[JobReadV2]:
+) -> PaginationResponse[JobReadV2]:
     """
     Query `ApplyWorkflow` table.
 
@@ -68,43 +73,74 @@ async def view_job(
             `job.log` is set to `None`.
     """
 
-    stm = select(JobV2)
+    # Assign pagination parameters
+    page = pagination.page
+    page_size = pagination.page_size
 
+    # Prepare statements
+    stm = select(JobV2).order_by(JobV2.start_timestamp.desc())
+    stm_count = select(func.count(JobV2.id))
     if id is not None:
         stm = stm.where(JobV2.id == id)
+        stm_count = stm_count.where(JobV2.id == id)
     if user_id is not None:
         stm = stm.join(ProjectV2).where(
             ProjectV2.user_list.any(UserOAuth.id == user_id)
         )
+        stm_count = stm_count.join(ProjectV2).where(
+            ProjectV2.user_list.any(UserOAuth.id == user_id)
+        )
     if project_id is not None:
         stm = stm.where(JobV2.project_id == project_id)
+        stm_count = stm_count.where(JobV2.project_id == project_id)
     if dataset_id is not None:
         stm = stm.where(JobV2.dataset_id == dataset_id)
+        stm_count = stm_count.where(JobV2.dataset_id == dataset_id)
     if workflow_id is not None:
         stm = stm.where(JobV2.workflow_id == workflow_id)
+        stm_count = stm_count.where(JobV2.workflow_id == workflow_id)
     if status is not None:
         stm = stm.where(JobV2.status == status)
+        stm_count = stm_count.where(JobV2.status == status)
     if start_timestamp_min is not None:
-        start_timestamp_min = start_timestamp_min
         stm = stm.where(JobV2.start_timestamp >= start_timestamp_min)
+        stm_count = stm_count.where(
+            JobV2.start_timestamp >= start_timestamp_min
+        )
     if start_timestamp_max is not None:
-        start_timestamp_max = start_timestamp_max
         stm = stm.where(JobV2.start_timestamp <= start_timestamp_max)
+        stm_count = stm_count.where(
+            JobV2.start_timestamp <= start_timestamp_max
+        )
     if end_timestamp_min is not None:
-        end_timestamp_min = end_timestamp_min
         stm = stm.where(JobV2.end_timestamp >= end_timestamp_min)
+        stm_count = stm_count.where(JobV2.end_timestamp >= end_timestamp_min)
     if end_timestamp_max is not None:
-        end_timestamp_max = end_timestamp_max
         stm = stm.where(JobV2.end_timestamp <= end_timestamp_max)
+        stm_count = stm_count.where(JobV2.end_timestamp <= end_timestamp_max)
 
+    # Find total number of elements
+    res_total_count = await db.execute(stm_count)
+    total_count = res_total_count.scalar()
+    if page_size is None:
+        page_size = total_count
+    else:
+        stm = stm.offset((page - 1) * page_size).limit(page_size)
+
+    # Get `page_size` rows
     res = await db.execute(stm)
     job_list = res.scalars().all()
-    await db.close()
+
     if not log:
         for job in job_list:
             setattr(job, "log", None)
 
-    return job_list
+    return PaginationResponse[JobReadV2](
+        total_count=total_count,
+        page_size=page_size,
+        current_page=page,
+        items=[job.model_dump() for job in job_list],
+    )
 
 
 @router.get("/{job_id}/", response_model=JobReadV2)

fractal_server/app/routes/admin/v2/task.py

@@ -1,7 +1,5 @@
 from fastapi import APIRouter
 from fastapi import Depends
-from fastapi import HTTPException
-from fastapi import status
 from pydantic import BaseModel
 from pydantic import EmailStr
 from pydantic import Field
@@ -16,6 +14,10 @@ from fractal_server.app.models.v2 import TaskV2
 from fractal_server.app.models.v2 import WorkflowTaskV2
 from fractal_server.app.models.v2 import WorkflowV2
 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
+from fractal_server.app.schemas.v2.task import TaskType
 
 router = APIRouter()
 
@@ -49,75 +51,85 @@ class TaskV2Info(BaseModel):
     relationships: list[TaskV2Relationship]
 
 
-@router.get("/", response_model=list[TaskV2Info])
+@router.get("/", response_model=PaginationResponse[TaskV2Info])
 async def query_tasks(
     id: int | None = None,
     source: str | None = None,
     version: str | None = None,
     name: str | None = None,
-    max_number_of_results: int = 25,
+    task_type: TaskType | None = None,
     category: str | None = None,
     modality: str | None = None,
     author: str | None = None,
     resource_id: int | None = None,
+    pagination: PaginationRequest = Depends(get_pagination_params),
     user: UserOAuth = Depends(current_superuser_act),
     db: AsyncSession = Depends(get_async_db),
-) -> list[TaskV2Info]:
+) -> PaginationResponse[TaskV2Info]:
     """
-    Query `TaskV2` table and get information about related items
-    (WorkflowV2s and ProjectV2s)
-
-    Args:
-        id: If not `None`, query for matching `task.id`.
-        source: If not `None`, query for contained case insensitive
-            `task.source`.
-        version: If not `None`, query for matching `task.version`.
-        name: If not `None`, query for contained case insensitive `task.name`.
-        max_number_of_results: The maximum length of the response.
-        category:
-        modality:
-        author:
-        resource_id:
+    Query `TaskV2` and get information about related workflows and projects.
     """
 
-    stm = select(TaskV2)
+    # Assign pagination parameters
+    page = pagination.page
+    page_size = pagination.page_size
 
+    # Prepare statements
+    stm = select(TaskV2).order_by(TaskV2.id)
+    stm_count = select(func.count(TaskV2.id))
     if id is not None:
         stm = stm.where(TaskV2.id == id)
+        stm_count = stm_count.where(TaskV2.id == id)
     if source is not None:
         stm = stm.where(TaskV2.source.icontains(source))
+        stm_count = stm_count.where(TaskV2.source.icontains(source))
     if version is not None:
         stm = stm.where(TaskV2.version == version)
+        stm_count = stm_count.where(TaskV2.version == version)
     if name is not None:
         stm = stm.where(TaskV2.name.icontains(name))
+        stm_count = stm_count.where(TaskV2.name.icontains(name))
+    if task_type is not None:
+        stm = stm.where(TaskV2.type == task_type)
+        stm_count = stm_count.where(TaskV2.type == task_type)
     if category is not None:
         stm = stm.where(func.lower(TaskV2.category) == category.lower())
+        stm_count = stm_count.where(
+            func.lower(TaskV2.category) == category.lower()
+        )
     if modality is not None:
         stm = stm.where(func.lower(TaskV2.modality) == modality.lower())
+        stm_count = stm_count.where(
+            func.lower(TaskV2.modality) == modality.lower()
+        )
     if author is not None:
         stm = stm.where(TaskV2.authors.icontains(author))
+        stm_count = stm_count.where(TaskV2.authors.icontains(author))
     if resource_id is not None:
         stm = (
             stm.join(TaskGroupV2)
             .where(TaskGroupV2.id == TaskV2.taskgroupv2_id)
             .where(TaskGroupV2.resource_id == resource_id)
         )
+        stm_count = (
+            stm_count.join(TaskGroupV2)
+            .where(TaskGroupV2.id == TaskV2.taskgroupv2_id)
+            .where(TaskGroupV2.resource_id == resource_id)
+        )
+
+    # Find total number of elements
+    res_total_count = await db.execute(stm_count)
+    total_count = res_total_count.scalar()
+    if page_size is None:
+        page_size = total_count
+    else:
+        stm = stm.offset((page - 1) * page_size).limit(page_size)
 
-    stm = stm.order_by(TaskV2.id)
+    # Get `page_size` rows
     res = await db.execute(stm)
     task_list = res.scalars().all()
-    if len(task_list) > max_number_of_results:
-        await db.close()
-        raise HTTPException(
-            status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
-            detail=(
-                f"Too many Tasks ({len(task_list)} > {max_number_of_results})."
-                " Please add more query filters."
-            ),
-        )
 
     task_info_list = []
-
     for task in task_list:
         stm = (
             select(WorkflowV2)
@@ -147,4 +159,9 @@ async def query_tasks(
             )
         )
 
-    return task_info_list
+    return PaginationResponse[TaskV2Info](
+        total_count=total_count,
+        page_size=page_size,
+        current_page=page,
+        items=task_info_list,
+    )

fractal_server/app/schemas/v2/task_collection.py

@@ -51,9 +51,17 @@ class TaskCollectPipV2(BaseModel):
     package: NonEmptyStr | None = None
     package_version: NonEmptyStr | None = None
     package_extras: NonEmptyStr | None = None
-    python_version: Literal[
-        "3.9", "3.10", "3.11", "3.12", "3.13"
-    ] | None = None
+    python_version: (
+        Literal[
+            "3.9",
+            "3.10",
+            "3.11",
+            "3.12",
+            "3.13",
+            "3.14",
+        ]
+        | None
+    ) = None
     pinned_package_versions_pre: DictStrStr | None = None
     pinned_package_versions_post: DictStrStr | None = None
 

fractal_server/app/shutdown.py

@@ -12,44 +12,48 @@ from fractal_server.syringe import Inject
 
 
 async def cleanup_after_shutdown(*, jobsV2: list[int], logger_name: str):
+    settings = Inject(get_settings)
     logger = get_logger(logger_name)
     logger.info("Cleanup function after shutdown")
-    stm_v2 = (
+    stm_objects = (
         select(JobV2)
         .where(JobV2.id.in_(jobsV2))
         .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
     )
+    stm_ids = (
+        select(JobV2.id)
+        .where(JobV2.id.in_(jobsV2))
+        .where(JobV2.status == JobStatusTypeV2.SUBMITTED)
+    )
 
     async for session in get_async_db():
-        jobsV2_db = (await session.execute(stm_v2)).scalars().all()
-
-        for job in jobsV2_db:
+        # Write shutdown file for all jobs
+        jobs = (await session.execute(stm_objects)).scalars().all()
+        for job in jobs:
             _write_shutdown_file(job=job)
 
-        settings = Inject(get_settings)
-
+        # Wait for completion of all job - with a timeout
+        interval = settings.FRACTAL_GRACEFUL_SHUTDOWN_TIME / 20
         t_start = time.perf_counter()
         while (
             time.perf_counter() - t_start
-        ) < settings.FRACTAL_GRACEFUL_SHUTDOWN_TIME:  # 30 seconds
-            logger.info("Waiting 3 seconds before checking")
-            time.sleep(3)
-            jobsV2_db = (await session.execute(stm_v2)).scalars().all()
-
-            if len(jobsV2_db) == 0:
-                logger.info(
-                    "All jobs associated to this app are "
-                    "either done or failed. Exit."
-                )
+        ) <= settings.FRACTAL_GRACEFUL_SHUTDOWN_TIME:
+            job_ids = (await session.execute(stm_ids)).scalars().all()
+            if len(job_ids) == 0:
+                logger.info("All jobs are either done or failed. Exit.")
                 return
             else:
-                logger.info(f"Some jobs are still 'submitted' {jobsV2_db=}")
+                logger.info(f"Some jobs are still 'submitted': {job_ids=}")
+                logger.info(f"Wait {interval:.4f} seconds before next check.")
+                time.sleep(interval)
         logger.info(
             "Graceful shutdown reached its maximum time, "
-            "but some jobs are still submitted"
+            "but some jobs are still submitted."
         )
 
-        for job in jobsV2_db:
+        # Mark jobs as failed and update their logs.
+        jobs = (await session.execute(stm_objects)).scalars().all()
+        for job in jobs:
             job.status = "failed"
             job.log = (job.log or "") + "\nJob stopped due to app shutdown\n"
             session.add(job)

fractal_server/config/_database.py

@@ -1,4 +1,5 @@
 from pydantic import SecretStr
+from pydantic.types import NonNegativeInt
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 from sqlalchemy.engine import URL
@@ -27,11 +28,11 @@ class DatabaseSettings(BaseSettings):
     """
     Password to use when connecting to the PostgreSQL database.
     """
-    POSTGRES_HOST: NonEmptyStr | None = "localhost"
+    POSTGRES_HOST: NonEmptyStr = "localhost"
     """
     URL to the PostgreSQL server or path to a UNIX domain socket.
     """
-    POSTGRES_PORT: NonEmptyStr | None = "5432"
+    POSTGRES_PORT: NonNegativeInt = 5432
     """
     Port number to use when connecting to the PostgreSQL server.
     """

fractal_server/config/_main.py

@@ -57,7 +57,7 @@ class Settings(BaseSettings):
     `app.state`.
     """
 
-    FRACTAL_GRACEFUL_SHUTDOWN_TIME: int = 30
+    FRACTAL_GRACEFUL_SHUTDOWN_TIME: float = 30.0
     """
     Waiting time for the shutdown phase of executors
     """

fractal_server/migrations/versions/45fbb391d7af_make_resource_id_fk_non_nullable.py

@@ -0,0 +1,46 @@
+"""Make resource_id FK non-nullable
+
+Revision ID: 45fbb391d7af
+Revises: caba9fb1ea5e
+Create Date: 2025-11-11 16:39:12.813766
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "45fbb391d7af"
+down_revision = "caba9fb1ea5e"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("projectv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "resource_id", existing_type=sa.INTEGER(), nullable=False
+        )
+
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "resource_id", existing_type=sa.INTEGER(), nullable=False
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("taskgroupv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "resource_id", existing_type=sa.INTEGER(), nullable=True
+        )
+
+    with op.batch_alter_table("projectv2", schema=None) as batch_op:
+        batch_op.alter_column(
+            "resource_id", existing_type=sa.INTEGER(), nullable=True
+        )
+
+    # ### end Alembic commands ###

fractal_server/migrations/versions/49d0856e9569_drop_table.py

@@ -0,0 +1,63 @@
+"""Drop  table
+
+Revision ID: 49d0856e9569
+Revises: 45fbb391d7af
+Create Date: 2025-11-11 16:39:41.497832
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision = "49d0856e9569"
+down_revision = "45fbb391d7af"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table("user_settings")
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table(
+        "user_settings",
+        sa.Column("id", sa.INTEGER(), autoincrement=True, nullable=False),
+        sa.Column(
+            "slurm_accounts",
+            postgresql.JSONB(astext_type=sa.Text()),
+            server_default=sa.text("'[]'::json"),
+            autoincrement=False,
+            nullable=False,
+        ),
+        sa.Column(
+            "ssh_host", sa.VARCHAR(), autoincrement=False, nullable=True
+        ),
+        sa.Column(
+            "ssh_username", sa.VARCHAR(), autoincrement=False, nullable=True
+        ),
+        sa.Column(
+            "ssh_private_key_path",
+            sa.VARCHAR(),
+            autoincrement=False,
+            nullable=True,
+        ),
+        sa.Column(
+            "ssh_tasks_dir", sa.VARCHAR(), autoincrement=False, nullable=True
+        ),
+        sa.Column(
+            "ssh_jobs_dir", sa.VARCHAR(), autoincrement=False, nullable=True
+        ),
+        sa.Column(
+            "slurm_user", sa.VARCHAR(), autoincrement=False, nullable=True
+        ),
+        sa.Column(
+            "project_dir", sa.VARCHAR(), autoincrement=False, nullable=True
+        ),
+        sa.PrimaryKeyConstraint("id", name=op.f("pk_user_settings")),
+    )
+    # ### end Alembic commands ###

fractal_server/migrations/versions/7673fe18c05d_remove_project_dir_server_default.py

@@ -0,0 +1,29 @@
+"""Remove project_dir server_default
+
+Revision ID: 7673fe18c05d
+Revises: 49d0856e9569
+Create Date: 2025-11-11 16:50:20.079193
+
+"""
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "7673fe18c05d"
+down_revision = "49d0856e9569"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    """
+    Remove `server_default` for `project_dir` column - see
+    https://alembic.sqlalchemy.org/en/latest/ops.html#alembic.operations.Operations.alter_column.params.server_default
+    """
+    with op.batch_alter_table("user_oauth") as batch_op:
+        batch_op.alter_column("project_dir", server_default=None)
+
+
+def downgrade() -> None:
+    with op.batch_alter_table("user_oauth") as batch_op:
+        batch_op.alter_column("project_dir", server_default="/PLACEHOLDER")

fractal_server/migrations/versions/caba9fb1ea5e_drop_useroauth_user_settings_id.py

@@ -0,0 +1,49 @@
+"""Drop UserOAuth.user_settings_id
+
+Revision ID: caba9fb1ea5e
+Revises: 83bc2ad3ffcc
+Create Date: 2025-11-11 16:38:27.243693
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+
+# revision identifiers, used by Alembic.
+revision = "caba9fb1ea5e"
+down_revision = "83bc2ad3ffcc"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_oauth", schema=None) as batch_op:
+        batch_op.drop_constraint(
+            batch_op.f("fk_user_oauth_user_settings_id_user_settings"),
+            type_="foreignkey",
+        )
+        batch_op.drop_column("user_settings_id")
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("user_oauth", schema=None) as batch_op:
+        batch_op.add_column(
+            sa.Column(
+                "user_settings_id",
+                sa.INTEGER(),
+                autoincrement=False,
+                nullable=True,
+            )
+        )
+        batch_op.create_foreign_key(
+            batch_op.f("fk_user_oauth_user_settings_id_user_settings"),
+            "user_settings",
+            ["user_settings_id"],
+            ["id"],
+        )
+
+    # ### end Alembic commands ###

fractal_server/runner/v2/runner.py

@@ -192,6 +192,30 @@ def execute_tasks_v2(
             job_db.executor_error_log = None
             db.merge(job_db)
             db.commit()
+            db.expunge_all()
+
+        # Fail when running a non-converter task on an empty image list
+        if (
+            wftask.task_type
+            in [
+                TaskType.COMPOUND,
+                TaskType.PARALLEL,
+                TaskType.NON_PARALLEL,
+            ]
+            and len(filtered_images) == 0
+        ):
+            error_msg = (
+                f"Cannot run task '{task.name}' for an empty image list "
+                f"(obtained after applying {type_filters=} and "
+                f"attribute_filters={job_attribute_filters})."
+            )
+            logger.info(error_msg)
+            update_status_of_history_run(
+                history_run_id=history_run_id,
+                status=HistoryUnitStatus.FAILED,
+                db_sync=db,
+            )
+            raise JobExecutionError(error_msg)
 
         # TASK EXECUTION (V2)
         try:

fractal_server/tasks/config/_python.py

@@ -45,7 +45,7 @@ class TasksPythonSettings(BaseModel):
         if self.default_version not in self.versions.keys():
             raise ValueError(
                 f"The default Python version ('{self.default_version}') is "
-                f"not available versions in {list(self.versions.keys())}."
+                f"not available in {list(self.versions.keys())}."
             )
 
         return self

fractal_server/tasks/v2/local/delete.py

@@ -51,8 +51,8 @@ def delete_local(
                 activity.log = get_current_log(log_file_path)
                 activity = add_commit_refresh(obj=activity, db=db)
 
-                db.commit()
                 db.delete(task_group)
+                db.commit()
                 logger.debug("Task group removed from database.")
 
                 if task_group.origin != TaskGroupV2OriginEnum.OTHER:

{fractal_server-2.17.0a11.dist-info → fractal_server-2.17.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.0a11
+Version: 2.17.1
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

{fractal_server-2.17.0a11.dist-info → fractal_server-2.17.1.dist-info}/RECORD

@@ -1,23 +1,22 @@
-fractal_server/__init__.py,sha256=Pj-IcBWFE8pRiluuKSO6LdRI9wotfOFmP9J3PnyZ0GE,26
-fractal_server/__main__.py,sha256=68FlTuST3zbzVofFI8JSYsSBrBQ07Bv3Mu3PsZX9Fw0,11423
+fractal_server/__init__.py,sha256=CUZtFSmkfStuE3L_hKV87CswJmhI3gnUuekCrCEQ1Yk,23
+fractal_server/__main__.py,sha256=qLbUicU1Ulaob_Eo5pspi-IH2xAkLfifJTH9gYEhZss,11427
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/db/__init__.py,sha256=sttX0mHVV0ESI1SJ1kcxUKiuEwqeP-BWsst0o_9Yo44,2810
-fractal_server/app/models/__init__.py,sha256=xJWiGAwpXmCpnFMC4c_HTqoUCzMOXrakoGLUH_uMvdA,415
+fractal_server/app/models/__init__.py,sha256=93eFiAaiV6cU_Mf8WQDi_Ir7vqakAiS5H9Pl7qAb4JE,367
 fractal_server/app/models/linkusergroup.py,sha256=3KkkE4QIUAlTrBAZs_tVy0pGvAxUAq6yOEjflct_z2M,678
 fractal_server/app/models/linkuserproject.py,sha256=hvaxh3Lkiy2uUCwB8gvn8RorCpvxSSdzWdCS_U1GL7g,315
-fractal_server/app/models/security.py,sha256=VThWDEmzUP4SgLsAvd5WjJ1p2WVxBuc6D5TMQJaOyd8,3873
-fractal_server/app/models/user_settings.py,sha256=u0GOK1JdqDmXzA8hK2JV93rZxY_rF-0oKMkArRolnN8,1201
+fractal_server/app/models/security.py,sha256=f44hOx4Tro0-KLj5N70_gv1UsFrr5ygHY7W_XHFaOJE,3546
 fractal_server/app/models/v2/__init__.py,sha256=A668GF4z_UPar6kAOwC-o_qUo3CIRJ3SmBGYTs3Xc7k,923
 fractal_server/app/models/v2/accounting.py,sha256=i-2TsjqyuclxFQ21C-TeDoss7ZBTRuXdzIJfVr2UxwE,1081
 fractal_server/app/models/v2/dataset.py,sha256=P_zy4dPQAqrCALQ6737VkAFk1SvcgYjnslGUZhPI8sc,1226
 fractal_server/app/models/v2/history.py,sha256=CBN2WVg9vW5pHU1RP8TkB_nnJrwnuifCcxgnd53UtEE,2163
 fractal_server/app/models/v2/job.py,sha256=YYzt3ef2CU1WXFNjlltR3ft2kM9T0Hq8oskSipQSxuM,2042
 fractal_server/app/models/v2/profile.py,sha256=QqOE7XGeq-ckQAbGhcgzDN5zFFaTNrtcuWgOXy9psR8,440
-fractal_server/app/models/v2/project.py,sha256=oXNcuNVDeNYZ60fwAx-Y_vnkS3xd9pwFdoT2pZmnBNI,918
+fractal_server/app/models/v2/project.py,sha256=DJgTZG1NTA_pbLlY0Jy3WFBE8X8fBMkVALfDWK5ZuHY,832
 fractal_server/app/models/v2/resource.py,sha256=ReaBGtKb3e0_1PZOZncdGqrttkrC-bsgDCv3wPCGfOs,3512
 fractal_server/app/models/v2/task.py,sha256=iBIQB8POQE5MyKvLZhw7jZWlBhbrThzCDzRTcgiAczQ,1493
-fractal_server/app/models/v2/task_group.py,sha256=gHkuyIBw8hkoMCwHgo08SWVMc8T1MXC5xqoW2YNd5Sw,4753
+fractal_server/app/models/v2/task_group.py,sha256=v9hI-R8mXhm0LvE_I_YG3M8VHz0V9DohhGNykdEgcB8,4667
 fractal_server/app/models/v2/workflow.py,sha256=gBjDXO-RytVT81aAlesImBhmVHrwNUrmsF_UsGa1qLM,1057
 fractal_server/app/models/v2/workflowtask.py,sha256=qkTc-hcFLpJUVsEUbnDq2BJL0qg9jagy2doZeusF1ek,1266
 fractal_server/app/routes/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -26,11 +25,11 @@ fractal_server/app/routes/admin/v2/__init__.py,sha256=SzLurEzKBRWHcIFh2mpac2wrGA
 fractal_server/app/routes/admin/v2/_aux_functions.py,sha256=fqA5sUCFuD2iVANQt2WUUfVOEVz5egQA7inzUKYGCw0,1684
 fractal_server/app/routes/admin/v2/accounting.py,sha256=DjgMqzdrL8hYMn19cZj2pkwtLKl3QfBwxd473kH4KaI,3584
 fractal_server/app/routes/admin/v2/impersonate.py,sha256=ictDjuvBr3iLv3YtwkVRMNQRq5qtPAeAXbbC7STSsEg,1125
-fractal_server/app/routes/admin/v2/job.py,sha256=sFgMbOtUCIJ-ri6YD3ZWP7XETZZDQsLqPfT1kaH9RHQ,8577
+fractal_server/app/routes/admin/v2/job.py,sha256=CRt_a6tULsuzN5ojcClzVH3vd7OXT06jK81Qro9fuBk,10171
 fractal_server/app/routes/admin/v2/profile.py,sha256=0Y_1Qv-BA6cHVrxPTDDBOpttpfuJN8g1FqFlG6JiOD8,3164
 fractal_server/app/routes/admin/v2/project.py,sha256=rRq7ZDngr_29skASnte1xfycZCjK-WPdeTf7siBXiCU,1182
 fractal_server/app/routes/admin/v2/resource.py,sha256=UWimApUcL9HPu8NN0ccDbReuKly3aCqff2SA-Y1iEzs,6349
-fractal_server/app/routes/admin/v2/task.py,sha256=9MMUI2PnyHQx08Xmt93O5rM60C_tlic27mP6t7ljpYo,4655
+fractal_server/app/routes/admin/v2/task.py,sha256=tHWCPZRpfvu7k8sQA-634CUC7QbgdJa2RHiMXQL8a58,5599
 fractal_server/app/routes/admin/v2/task_group.py,sha256=EDY9oliXq_xYVJ2HgRuE4-5MbL85j-y4LbWwupZxy38,6249
 fractal_server/app/routes/admin/v2/task_group_lifecycle.py,sha256=W7LjIBAheyjrn0fEz0SsWINqcZK5HMB5GRGMjPrc6a4,9994
 fractal_server/app/routes/api/__init__.py,sha256=ewprevw6hZ0FWM-GPHoQZU0w-yfItqLeQT-Jr_Nbjnw,1658
@@ -88,21 +87,20 @@ fractal_server/app/schemas/v2/project.py,sha256=7UC0aZLgtmkaAiPykeUj-9OZXhMkoyi3
 fractal_server/app/schemas/v2/resource.py,sha256=4iXzZJeHVLcXYY08-okoJM_4gqpzhG4KglRPBm24Jwc,3718
 fractal_server/app/schemas/v2/status_legacy.py,sha256=eQT1zGxbkzSwd0EqclsOdZ60n1x6J3DB1CZ3m4LYyxc,955
 fractal_server/app/schemas/v2/task.py,sha256=IJv8loB4kx9FBkaIHoiMsswQyq02FxvyAnHK1u074fU,4364
-fractal_server/app/schemas/v2/task_collection.py,sha256=BzHQXq2_zLZTbigWauOR5Zi-mlsqCIF2NEF_z12Nqxg,4480
+fractal_server/app/schemas/v2/task_collection.py,sha256=S4fBQ3cbL4YmyL6ZTZYDbIBm6o8D-v5CuYQy4ng3nWU,4581
 fractal_server/app/schemas/v2/task_group.py,sha256=4hNZUXnWYSozpLXR3JqBvGzfZBG2TbjqydckHHu2Aq0,3506
 fractal_server/app/schemas/v2/workflow.py,sha256=L-dW6SzCH_VNoH6ENip44lTgGGqVYHHBk_3PtM-Ooy8,1772
 fractal_server/app/schemas/v2/workflowtask.py,sha256=6eweAMyziwaoMT-7R1fVJYunIeZKzT0-7fAVgPO_FEc,3639
 fractal_server/app/security/__init__.py,sha256=k-La8Da89C1hSUGsiidrWo6Az4u6dbe5PzN1Ctt1t34,18394
 fractal_server/app/security/signup_email.py,sha256=kphjq6TAygvPpYpg95QJWefyqmzdVrGz7fyRMctUJWE,1982
-fractal_server/app/shutdown.py,sha256=ViSNJyXWU_iWPSDOOMGNh_iQdUFrdPh_jvf8vVKLpAo,1950
+fractal_server/app/shutdown.py,sha256=QU4DfNvqwUXlHiLORtYJit4DxlFQo014SKTfs4dcE2U,2295
 fractal_server/config/__init__.py,sha256=ZCmroNB50sUxJiFtkW0a4fFtmfyPnL4LWhtKY5FbQfg,737
 fractal_server/config/_data.py,sha256=9Jyt83yrSsr_0_9ANWDAXz88_jjyFlcB5VWJGXq8aUY,2311
-fractal_server/config/_database.py,sha256=YOBi3xuJno5wLGw1hKsjLm-bftaxVWiBNIQWVTMX3Ag,1661
+fractal_server/config/_database.py,sha256=k1z__MrslQjmel34yFvge0sroPUs1vBtT_OSlPY8pN8,1690
 fractal_server/config/_email.py,sha256=j1QmZCyspNbD1xxkypc9Kv299tU3vTO1AqDFJ8-LZzQ,4201
-fractal_server/config/_main.py,sha256=9v64gJsvY1oGP70_AoJMnyMIeRo7FcIg6T8NDV-p9as,1992
+fractal_server/config/_main.py,sha256=NmpNuNezVI7MpuAiZ9AOlo3Fc-4x73FIaFm-UMhppEw,1996
 fractal_server/config/_oauth.py,sha256=7J4FphGVFfVmtQycCkas6scEJQJGZUGEzQ-t2PZiqSo,1934
 fractal_server/config/_settings_config.py,sha256=tsyXQOnn9QKCFJD6hRo_dJXlQQyl70DbqgHMJoZ1xnY,144
-fractal_server/data_migrations/2_17_0.py,sha256=ltMrezWWma-KPnZpOzQ12_yebBrjrdu0m7pQQh_RGWM,10894
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/exceptions.py,sha256=7ftpWwNsTQmNonWCynhH5ErUh1haPPhIaVPrNHla7-o,53
@@ -122,7 +120,9 @@ fractal_server/migrations/versions/19eca0dd47a9_user_settings_project_dir.py,sha
 fractal_server/migrations/versions/1a83a5260664_rename.py,sha256=EkzTAjbJm7CfsLraIUbH9hkTj4M6XvmziVb4K9ZjKmQ,790
 fractal_server/migrations/versions/1eac13a26c83_drop_v1_tables.py,sha256=7OW3HmqAePHx53OWdEPzNxvtupxSR0lB_6tZF1b3JIM,1604
 fractal_server/migrations/versions/316140ff7ee1_remove_usersettings_cache_dir.py,sha256=lANgTox0rz459_yo1Rw7fGCT1qw5sUCUXTLUMc_Bzf8,911
+fractal_server/migrations/versions/45fbb391d7af_make_resource_id_fk_non_nullable.py,sha256=y9zr161YIWgnWbaMg1rahKN4b-vHjT3f5VSeoOAHaqI,1296
 fractal_server/migrations/versions/47351f8c7ebc_drop_dataset_filters.py,sha256=vePkVm1iUHiPNKLQ3KR7BBLdHruqBdl87j_tUCbMbEA,1414
+fractal_server/migrations/versions/49d0856e9569_drop_table.py,sha256=qoq7cGUQmrnUj_wpV2mRqVneyoKqglgbrgzW_8eS_5w,1835
 fractal_server/migrations/versions/4c308bcaea2b_add_task_args_schema_and_task_args_.py,sha256=-wHe-fOffmYeAm0JXVl_lxZ7hhDkaEVqxgxpHkb_uL8,954
 fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py,sha256=Mob8McGYAcmgvrseyyYOa54E6Gsgr-4SiGdC-r9O4_A,1157
 fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py,sha256=JOrVa6mGzqZ6H61YCFVOed64vFRjTWGWyN3z7NE3T08,3270
@@ -130,6 +130,7 @@ fractal_server/migrations/versions/50a13d6138fd_initial_schema.py,sha256=zwXegXs
 fractal_server/migrations/versions/5bf02391cfef_v2.py,sha256=axhNkr_H6R4rRbY7oGYazNbFvPXeSyBDWFVbKNmiqs8,8433
 fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_index_and_.py,sha256=Q-DsMzG3IcUV2Ol1dhJWosDvKERamBE6QvA2zzS5zpQ,1632
 fractal_server/migrations/versions/71eefd1dd202_add_slurm_accounts.py,sha256=mbWuCkTpRAdGbRhW7lhXs_e5S6O37UAcCN6JfoY5H8A,1353
+fractal_server/migrations/versions/7673fe18c05d_remove_project_dir_server_default.py,sha256=LAC1Uv4SeLkqjXPyqj5Mof8L0105gxqS1TYKzNVX4GE,795
 fractal_server/migrations/versions/791ce783d3d8_add_indices.py,sha256=gNE6AgJgeJZY99Fbd336Z9see3gRMQvuNBC0xDk_5sw,1154
 fractal_server/migrations/versions/83bc2ad3ffcc_2_17_0.py,sha256=U7t_8n58taRkd9sxCXOshrTr9M5AhlsQne8SGKa5Jt4,6377
 fractal_server/migrations/versions/84bf0fffde30_add_dumps_to_applyworkflow.py,sha256=NSCuhANChsg76vBkShBl-9tQ4VEHubOjtAv1etHhlvY,2684
@@ -149,6 +150,7 @@ fractal_server/migrations/versions/af8673379a5c_drop_old_filter_columns.py,sha25
 fractal_server/migrations/versions/b1e7f7a1ff71_task_group_for_pixi.py,sha256=loDrqBB-9U3vqLKePEeJy4gK4EuPs_1F345mdrnoCt0,1293
 fractal_server/migrations/versions/b3ffb095f973_json_to_jsonb.py,sha256=Q01lPlBNQgi3hpoUquWj2QUEF7cTsyQ7uikUhWunzWY,10035
 fractal_server/migrations/versions/c90a7c76e996_job_id_in_history_run.py,sha256=Y1cPwmFOZ4mx3v2XZM6adgu8u0L0VD_R4ADURyMb2ro,1102
+fractal_server/migrations/versions/caba9fb1ea5e_drop_useroauth_user_settings_id.py,sha256=8tlWVmux-c-fB9hMO4JEsaPMXRwLN_X3PpC0rUuFrYw,1320
 fractal_server/migrations/versions/d256a7379ab8_taskgroup_activity_and_venv_info_to_.py,sha256=HN3_Pk8G81SzdYjg4K1RZAyjKSlsZGvcYE2nWOUbwxQ,3861
 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
@@ -198,7 +200,7 @@ fractal_server/runner/v2/_slurm_sudo.py,sha256=f34B6KWtn1Wwm7Y-D95Ecub0vKpA03zYL
 fractal_server/runner/v2/db_tools.py,sha256=kLB0sGYNuCMPPoP4XDSClPIf7x5lSseTKUjzGk6gAfc,3318
 fractal_server/runner/v2/deduplicate_list.py,sha256=vidkd7K6u3w0A4zVgsGZkc9mwoP6ihTYJZQUhBNorfE,667
 fractal_server/runner/v2/merge_outputs.py,sha256=0ahaSwdMFAoEhxVaEaO9nSJuKIcWg9pDZ356ktSHcC0,897
-fractal_server/runner/v2/runner.py,sha256=1vj6m_ir6RrYNr3Ew98h5hnEAms_TaHPhee52swQ_gA,19404
+fractal_server/runner/v2/runner.py,sha256=PANeskwZpZbbaL8i5vk0voHfP-jli1sZaFKpiW1gq20,20245
 fractal_server/runner/v2/runner_functions.py,sha256=w_i74LCt_9f07w511wslTFhoDUtoE1R-IKcglEGWPIc,19618
 fractal_server/runner/v2/submit_workflow.py,sha256=s3mo5pLZH5x8V01IZjoJXcbpCl9geZwvISEr5StSBeI,11458
 fractal_server/runner/v2/task_interface.py,sha256=ftPPpOU16rbJD8q-QV7o_3ey8W7MQTFuWJiYUr4OmF4,2532
@@ -210,7 +212,7 @@ fractal_server/syringe.py,sha256=3YJeIALH-wibuJ9R5VMNYUWh7x1-MkWT0SqGcWG5MY8,279
 fractal_server/tasks/__init__.py,sha256=kadmVUoIghl8s190_Tt-8f-WBqMi8u8oU4Pvw39NHE8,23
 fractal_server/tasks/config/__init__.py,sha256=f1kARvKJPdM3b0HmJhIyMRxi8RCgPajUfS7RBhNfLKY,152
 fractal_server/tasks/config/_pixi.py,sha256=KVf0xYAf6hAnOKSrTmg_GYJ5VaA19kEMAydRJNHjeiA,3773
-fractal_server/tasks/config/_python.py,sha256=DKXHpSctTU0GJp4D9iF7DncAyrG6disMrECNX4Qu9_k,1362
+fractal_server/tasks/config/_python.py,sha256=uEBm4Z9Ah-7A7pXBcSTBhFgefSuJPwN8WrWQHoNdp9M,1353
 fractal_server/tasks/utils.py,sha256=V7dj8o2AnoHhGSTYlqJHcRFhCIpmOrMOUhtiE_DvRVA,291
 fractal_server/tasks/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/tasks/v2/local/__init__.py,sha256=2dJqJIwn9UEANg8lPFprxVLk3ug-4xYIb5pvIsqPb5s,353
@@ -219,7 +221,7 @@ fractal_server/tasks/v2/local/collect.py,sha256=2dvR90b57gCz8F_bmNoMLtnvlrW1ZLBz
 fractal_server/tasks/v2/local/collect_pixi.py,sha256=BTWwu07LZQB0zTvCpHJkyEHgUl8XlF1qSN5NsOC5MVo,11489
 fractal_server/tasks/v2/local/deactivate.py,sha256=cPJbB-zoHjmxL5goaNAUItkW0o_fg-YAd2YuXu_n8Rg,9925
 fractal_server/tasks/v2/local/deactivate_pixi.py,sha256=h1XdAwihACywC9qak5K2tlfz4y32zZJOA-OEkIVy67U,3627
-fractal_server/tasks/v2/local/delete.py,sha256=4uKf6WjbSy_KiJNm1ip8eXa9GgvZWiDbWQjlSKE4I20,2960
+fractal_server/tasks/v2/local/delete.py,sha256=rmAjZ5i8x0jAIqOjG7eH9XFtUZkeo172S2WyZRFIVq0,2960
 fractal_server/tasks/v2/local/reactivate.py,sha256=ZQTaqPquevpwdchUJIp59Lw01vErA3T2XN8g1jMBNAE,6013
 fractal_server/tasks/v2/local/reactivate_pixi.py,sha256=R0D3bUwrAo3uyDNZRYsQ65NMl7-nhqd1GefBAh9Hk5c,8159
 fractal_server/tasks/v2/ssh/__init__.py,sha256=dPK6BtEZVh1GiFP05j1RKTEnZvjJez8o2KkMC2hWXaw,339
@@ -255,8 +257,8 @@ fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=HL
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=SYVVUuXe_nWyrJLsy7QA-KJscwc5PHEXjvsW4TK7XQI,2180
 fractal_server/zip_tools.py,sha256=H0w7wS5yE4ebj7hw1_77YQ959dl2c-L0WX6J_ro1TY4,4884
-fractal_server-2.17.0a11.dist-info/METADATA,sha256=7ma0Jk6lM9eGlYkmJYO3Y_RTw3oVhJoNfVfGJ5Ex1Wk,4227
-fractal_server-2.17.0a11.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fractal_server-2.17.0a11.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.17.0a11.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.17.0a11.dist-info/RECORD,,
+fractal_server-2.17.1.dist-info/METADATA,sha256=fxvj3AoIvayiofwYRfl1dwAp2cQcdCZ0cZPnQoEoOBg,4224
+fractal_server-2.17.1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+fractal_server-2.17.1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.17.1.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.17.1.dist-info/RECORD,,

fractal_server/app/models/user_settings.py

@@ -1,37 +0,0 @@
-from sqlalchemy import Column
-from sqlalchemy.dialects.postgresql import JSONB
-from sqlmodel import Field
-from sqlmodel import SQLModel
-
-
-# TODO-2.17.1: Drop `UserSettings`
-class UserSettings(SQLModel, table=True):
-    """
-    Comprehensive list of user settings.
-
-    Attributes:
-        id: ID of database object
-        slurm_accounts:
-            List of SLURM accounts, to be used upon Fractal job submission.
-        ssh_host: SSH-reachable host where a SLURM client is available.
-        ssh_username: User on `ssh_host`.
-        ssh_private_key_path: Path of private SSH key for `ssh_username`.
-        slurm_user: Local user, to be impersonated via `sudo -u`
-        project_dir: Folder where `slurm_user` can write.
-    """
-
-    __tablename__ = "user_settings"
-
-    id: int | None = Field(default=None, primary_key=True)
-    slurm_accounts: list[str] = Field(
-        sa_column=Column(JSONB, server_default="[]", nullable=False)
-    )
-    ssh_host: str | None = None
-    ssh_username: str | None = None
-    ssh_private_key_path: str | None = None
-
-    slurm_user: str | None = None
-    project_dir: str | None = None
-
-    ssh_tasks_dir: str | None = None
-    ssh_jobs_dir: str | None = None

fractal_server/data_migrations/2_17_0.py

@@ -1,321 +0,0 @@
-"""
-
-PRELIMINARY CHECKS (TO DO WITH 2.16)
-* All users who are meant to actually use Fractal must be marked as active and verified.
-* All users who are not active and verified will still be able to log in, but they won't have access to the rest of the API.
-* All active users must have `project_dir` set, in their user settings.
-* `FRACTAL_SLURM_WORKER_PYTHON` must be included explicitly in the old env file.
-
-DATA-MIGRATION REQUIREMENTS
-* Old `.fractal_server.env`, renamed into `.fractal_server.env.old`.
-* New `.fractal_server.env` - see XXX for list of changes.
-* Old JSON file with SLURM configuration.
-* Old JSON file with pixi configuration - if applicable.
-
-
-MANUAL FIXES POST DATA MIGRATION:
-* Rename resource
-* Rename profiles - if needed
-"""
-import json
-import logging
-import sys
-from typing import Any
-
-from devtools import debug
-from dotenv.main import DotEnv
-from pydantic import BaseModel
-from sqlalchemy.orm import Session
-from sqlalchemy.sql.operators import is_
-from sqlalchemy.sql.operators import is_not
-from sqlmodel import select
-
-from fractal_server.app.db import get_sync_db
-from fractal_server.app.models import Profile
-from fractal_server.app.models import ProjectV2
-from fractal_server.app.models import Resource
-from fractal_server.app.models import TaskGroupV2
-from fractal_server.app.models import UserOAuth
-from fractal_server.app.models import UserSettings
-from fractal_server.app.schemas.v2.profile import cast_serialize_profile
-from fractal_server.app.schemas.v2.resource import cast_serialize_resource
-from fractal_server.config import get_settings
-from fractal_server.runner.config import JobRunnerConfigSLURM
-from fractal_server.tasks.config import TasksPixiSettings
-from fractal_server.tasks.config import TasksPythonSettings
-from fractal_server.types import AbsolutePathStr
-from fractal_server.types import ListUniqueNonEmptyString
-from fractal_server.urls import normalize_url
-
-logger = logging.getLogger("fix_db")
-logger.setLevel(logging.INFO)
-
-
-class UserUpdateInfo(BaseModel):
-    user_id: int
-    project_dir: AbsolutePathStr
-    slurm_accounts: ListUniqueNonEmptyString
-
-
-class ProfileUsersUpdateInfo(BaseModel):
-    data: dict[str, Any]
-    user_updates: list[UserUpdateInfo]
-
-
-def _get_user_settings(user: UserOAuth, db: Session) -> UserSettings:
-    if user.user_settings_id is None:
-        sys.exit(f"User {user.email} is active but {user.user_settings_id=}.")
-    user_settings = db.get(UserSettings, user.user_settings_id)
-    return user_settings
-
-
-def assert_user_setting_key(
-    user: UserOAuth,
-    user_settings: UserSettings,
-    keys: list[str],
-) -> None:
-    for key in keys:
-        if getattr(user_settings, key) is None:
-            sys.exit(
-                f"User {user.email} is active and verified but their "
-                f"user settings have {key}=None."
-            )
-
-
-def prepare_profile_and_user_updates() -> dict[str, ProfileUsersUpdateInfo]:
-    settings = get_settings()
-    profiles_and_users: dict[str, ProfileUsersUpdateInfo] = {}
-    with next(get_sync_db()) as db:
-        # Get active&verified users
-        res = db.execute(
-            select(UserOAuth)
-            .where(is_(UserOAuth.is_active, True))
-            .where(is_(UserOAuth.is_verified, True))
-            .order_by(UserOAuth.id)
-        )
-        for user in res.unique().scalars().all():
-            # Get user settings
-            user_settings = _get_user_settings(user=user, db=db)
-            assert_user_setting_key(user, user_settings, ["project_dir"])
-
-            # Prepare profile data and user update
-            new_profile_data = dict()
-            if settings.FRACTAL_RUNNER_BACKEND == "slurm_sudo":
-                assert_user_setting_key(user, user_settings, ["slurm_user"])
-                username = user_settings.slurm_user
-            elif settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-                assert_user_setting_key(
-                    user,
-                    user_settings,
-                    [
-                        "ssh_username",
-                        "ssh_private_key_path",
-                        "ssh_tasks_dir",
-                        "ssh_jobs_dir",
-                    ],
-                )
-                username = user_settings.ssh_username
-                new_profile_data.update(
-                    ssh_key_path=user_settings.ssh_private_key_path,
-                    tasks_remote_dir=normalize_url(
-                        user_settings.ssh_tasks_dir
-                    ),
-                    jobs_remote_dir=normalize_url(user_settings.ssh_jobs_dir),
-                )
-
-            new_profile_data.update(
-                name=f"Profile {username}",
-                username=username,
-                resource_type=settings.FRACTAL_RUNNER_BACKEND,
-            )
-            debug(new_profile_data)
-            cast_serialize_profile(new_profile_data)
-
-            user_update_info = UserUpdateInfo(
-                user_id=user.id,
-                project_dir=normalize_url(user_settings.project_dir),
-                slurm_accounts=user_settings.slurm_accounts or [],
-            )
-
-            if username in profiles_and_users.keys():
-                if profiles_and_users[username].data != new_profile_data:
-                    # FIXME
-                    debug(new_profile_data)
-                    debug(profiles_and_users[username].data)
-                    raise ValueError()
-                profiles_and_users[username].user_updates.append(
-                    user_update_info
-                )
-            else:
-                profiles_and_users[username] = ProfileUsersUpdateInfo(
-                    data=new_profile_data,
-                    user_updates=[user_update_info],
-                )
-
-    return profiles_and_users
-
-
-def get_old_dotenv_variables() -> dict[str, str | None]:
-    """
-    See
-    https://github.com/fractal-analytics-platform/fractal-server/blob/2.16.x/fractal_server/config.py
-    """
-    OLD_DOTENV_FILE = ".fractal_server.env.old"
-    return dict(
-        **DotEnv(
-            dotenv_path=OLD_DOTENV_FILE,
-            override=False,
-        ).dict()
-    )
-
-
-def get_TasksPythonSettings(
-    old_config: dict[str, str | None]
-) -> dict[str, Any]:
-    versions = {}
-    for version_underscore in ["3_9", "3_10", "3_11", "3_12"]:
-        key = f"FRACTAL_TASKS_PYTHON_{version_underscore}"
-        version_dot = version_underscore.replace("_", ".")
-        value = old_config.get(key, None)
-        if value is not None:
-            versions[version_dot] = value
-    obj = TasksPythonSettings(
-        default_version=old_config["FRACTAL_TASKS_PYTHON_DEFAULT_VERSION"],
-        versions=versions,
-        pip_cache_dir=old_config.get("FRACTAL_PIP_CACHE_DIR", None),
-    )
-    return obj.model_dump()
-
-
-def get_TasksPixiSettings(old_config: dict[str, str | None]) -> dict[str, Any]:
-    pixi_file = old_config.get("FRACTAL_PIXI_CONFIG_FILE", None)
-    if pixi_file is None:
-        return {}
-    with open(pixi_file) as f:
-        old_pixi_config = json.load(f)
-    TasksPixiSettings(**old_pixi_config)
-    return old_pixi_config
-
-
-def get_JobRunnerConfigSLURM(
-    old_config: dict[str, str | None]
-) -> dict[str, Any]:
-    slurm_file = old_config["FRACTAL_SLURM_CONFIG_FILE"]
-    with open(slurm_file) as f:
-        old_slurm_config = json.load(f)
-    JobRunnerConfigSLURM(**old_slurm_config)
-    return old_slurm_config
-
-
-def get_ssh_host() -> str:
-    with next(get_sync_db()) as db:
-        res = db.execute(
-            select(UserSettings.ssh_host).where(
-                is_not(UserSettings.ssh_host, None)
-            )
-        )
-        hosts = res.scalars().all()
-    if len(set(hosts)) > 1:
-        host = max(set(hosts), key=hosts.count)
-        print(f"MOST FREQUENT HOST: {host}")
-    else:
-        host = hosts[0]
-    return host
-
-
-def prepare_resource_data(old_config: dict[str, str | None]) -> dict[str, Any]:
-    settings = get_settings()
-
-    resource_data = dict(
-        type=settings.FRACTAL_RUNNER_BACKEND,
-        name="Resource Name",
-        tasks_python_config=get_TasksPythonSettings(old_config),
-        tasks_pixi_config=get_TasksPixiSettings(old_config),
-        jobs_runner_config=get_JobRunnerConfigSLURM(old_config),
-        tasks_local_dir=old_config["FRACTAL_TASKS_DIR"],
-        jobs_local_dir=old_config["FRACTAL_RUNNER_WORKING_BASE_DIR"],
-        jobs_slurm_python_worker=old_config["FRACTAL_SLURM_WORKER_PYTHON"],
-        jobs_poll_interval=int(
-            old_config.get("FRACTAL_SLURM_POLL_INTERVAL", 15)
-        ),
-    )
-    if settings.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
-        resource_data["host"] = get_ssh_host()
-
-    resource_data = cast_serialize_resource(resource_data)
-
-    return resource_data
-
-
-def fix_db():
-    # READ-ONLY CHECK
-
-    settings = get_settings()
-
-    # Verify that we are in a SLURM instance
-    if settings.FRACTAL_RUNNER_BACKEND == "local":
-        sys.exit(
-            "ERROR: FRACTAL_RUNNER_BACKEND='local' is not "
-            "supported for this data migration."
-        )
-
-    # Read old env file
-    old_config = get_old_dotenv_variables()
-
-    # Prepare resource data
-    resource_data = prepare_resource_data(old_config)
-
-    # Prepare profile/users data
-    profile_and_user_updates = prepare_profile_and_user_updates()
-
-    # ---------------------------------------
-
-    # WRITES
-
-    with next(get_sync_db()) as db:
-        # Create new resource
-        resource = Resource(**resource_data)
-        db.add(resource)
-        db.commit()
-        db.refresh(resource)
-        db.expunge(resource)
-        resource_id = resource.id
-        debug(f"CREATED RESOURCE with {resource_id=}")
-
-        # Update task groups
-        res = db.execute(select(TaskGroupV2).order_by(TaskGroupV2.id))
-        for taskgroup in res.scalars().all():
-            taskgroup.resource_id = resource_id
-            db.add(taskgroup)
-        db.commit()
-
-        # Update projects
-        res = db.execute(select(ProjectV2).order_by(ProjectV2.id))
-        for project in res.scalars().all():
-            project.resource_id = resource_id
-            db.add(project)
-        db.commit()
-
-        db.expunge_all()
-
-        for _, info in profile_and_user_updates.items():
-            debug(info)
-
-            # Create profile
-            profile_data = info.data
-            profile_data["resource_id"] = resource_id
-            profile = Profile(**profile_data)
-            db.add(profile)
-            db.commit()
-            db.refresh(profile)
-            db.expunge(profile)
-            profile_id = profile.id
-
-            # Update users
-            for user_update in info.user_updates:
-                user = db.get(UserOAuth, user_update.user_id)
-                user.profile_id = profile_id
-                user.project_dir = user_update.project_dir
-                user.slurm_accounts = user_update.slurm_accounts
-                db.add(user)
-            db.commit()