fractal-server 2.17.1a0__tar.gz → 2.17.1a1__tar.gz

{fractal_server-2.17.1a0 → fractal_server-2.17.1a1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.17.1a0
+Version: 2.17.1a1
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

fractal_server-2.17.1a1/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.17.1a1"

{fractal_server-2.17.1a0 → fractal_server-2.17.1a1}/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-2.17.1a0 → fractal_server-2.17.1a1}/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-2.17.1a0 → fractal_server-2.17.1a1}/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-2.17.1a0 → fractal_server-2.17.1a1}/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-2.17.1a0 → fractal_server-2.17.1a1}/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-2.17.1a0 → fractal_server-2.17.1a1}/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-2.17.1a1/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-2.17.1a1/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-2.17.1a1/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-2.17.1a1/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-2.17.1a0 → fractal_server-2.17.1a1}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.17.1a0"
+version = "2.17.1a1"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -94,7 +94,7 @@ filterwarnings = [
 markers = ["container", "ssh", "fails_on_macos", "oauth"]
 
 [tool.bumpver]
-current_version = "2.17.1a0"
+current_version = "2.17.1a1"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true
@@ -130,5 +130,5 @@ POSTGRES_USER="postgres"
 POSTGRES_PASSWORD="postgres"
 POSTGRES_DB="fractal_test"
 FRACTAL_API_MAX_JOB_LIST_LENGTH=1
-FRACTAL_GRACEFUL_SHUTDOWN_TIME=1
+FRACTAL_GRACEFUL_SHUTDOWN_TIME=0.05
 FRACTAL_DEFAULT_GROUP_NAME="All"

fractal_server-2.17.1a0/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.17.1a0"

fractal_server-2.17.1a0/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