fractal-server 2.17.1a0__py3-none-any.whl → 2.17.1a1__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.17.1a0"
+__VERSION__ = "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/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/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/_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-2.17.1a0.dist-info → fractal_server-2.17.1a1.dist-info}/METADATA

@@ -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-2.17.1a0.dist-info → fractal_server-2.17.1a1.dist-info}/RECORD

@@ -1,23 +1,22 @@
-fractal_server/__init__.py,sha256=DW4yg1QyP_AsgqW1m4v28pnbhBE5KzkBv39LnIslJnE,25
+fractal_server/__init__.py,sha256=q8l8BntWJPUSkWbFRN9cZn0xrmXCLBoe5spKmWSrjxM,25
 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
@@ -94,15 +93,14 @@ fractal_server/app/schemas/v2/workflow.py,sha256=L-dW6SzCH_VNoH6ENip44lTgGGqVYHH
 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=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=DGxrQ5JSiJW5tzpfydCjYKjX7FsiF3y_k34b0mo_RaY,11757
 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
@@ -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-2.17.1a0.dist-info/METADATA,sha256=XJQY23pLEp0LL8hg0EN9kPh7P6wfJLD9GwcHq8psXQo,4226
-fractal_server-2.17.1a0.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fractal_server-2.17.1a0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.17.1a0.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.17.1a0.dist-info/RECORD,,
+fractal_server-2.17.1a1.dist-info/METADATA,sha256=PTysEV2k6eEa799QPMn2C9pTxTL2jR0wn1luvcrCCPM,4226
+fractal_server-2.17.1a1.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+fractal_server-2.17.1a1.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.17.1a1.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.17.1a1.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

@@ -1,339 +0,0 @@
-import json
-import logging
-import sys
-from pathlib import Path
-from typing import Any
-
-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 JobRunnerConfigLocal
-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
-
-logging.basicConfig(level=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 == "local":
-                username = None
-            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,
-            )
-            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:
-                    error_msg = (
-                        "Profile data mismatch.\n"
-                        f"{profiles_and_users[username].data=}\n"
-                        f"{new_profile_data=}"
-                    )
-                    logging.error(error_msg)
-                    sys.exit(error_msg)
-                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_JobRunnerConfigLocal(
-    old_config: dict[str, str | None]
-) -> dict[str, Any]:
-    local_file = old_config.get("FRACTAL_LOCAL_CONFIG_FILE", None)
-    if local_file is None or not Path(local_file).exists():
-        return JobRunnerConfigLocal().model_dump()
-    else:
-        with open(local_file) as f:
-            old_local_config = json.load(f)
-        JobRunnerConfigLocal(**old_local_config)
-        return old_local_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),
-        tasks_local_dir=old_config["FRACTAL_TASKS_DIR"],
-        jobs_local_dir=old_config["FRACTAL_RUNNER_WORKING_BASE_DIR"],
-        jobs_poll_interval=int(
-            old_config.get("FRACTAL_SLURM_POLL_INTERVAL", 15)
-        ),
-    )
-    if settings.FRACTAL_RUNNER_BACKEND == "local":
-        resource_data["jobs_runner_config"] = get_JobRunnerConfigLocal(
-            old_config
-        )
-    elif settings.FRACTAL_RUNNER_BACKEND == "slurm_sudo":
-        resource_data["jobs_slurm_python_worker"] = old_config[
-            "FRACTAL_SLURM_WORKER_PYTHON"
-        ]
-        resource_data["jobs_runner_config"] = get_JobRunnerConfigSLURM(
-            old_config
-        )
-    else:
-        resource_data["jobs_slurm_python_worker"] = old_config[
-            "FRACTAL_SLURM_WORKER_PYTHON"
-        ]
-        resource_data["jobs_runner_config"] = get_JobRunnerConfigSLURM(
-            old_config
-        )
-        resource_data["host"] = get_ssh_host()
-
-    resource_data = cast_serialize_resource(resource_data)
-
-    return resource_data
-
-
-def fix_db():
-    logging.info("START preliminary checks.")
-
-    # Read old env file
-    old_config = get_old_dotenv_variables()
-
-    # Prepare resource data
-    logging.info("START prepare_resource_data")
-    resource_data = prepare_resource_data(old_config)
-    logging.info("END prepare_resource_data")
-
-    # Prepare profile/users data
-    logging.info("START prepare_profile_and_user_updates")
-    profile_and_user_updates = prepare_profile_and_user_updates()
-    logging.info("END prepare_profile_and_user_updates")
-
-    logging.info("END preliminary checks.")
-    print()
-
-    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
-        logging.info(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()
-        logging.info(f"Set {resource_id=} foreign key for all task groups.")
-
-        # 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()
-        logging.info(f"Set {resource_id=} foreign key for all projects.")
-        print()
-
-        db.expunge_all()
-
-        for _, info in profile_and_user_updates.items():
-            # 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
-            logging.info(
-                f"Created profile '{profile.name}', with {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)
-                logging.info(f"Updated {user.email} with {user.project_dir=}.")
-                logging.info(
-                    f"Associated {user.email} to profile {profile.name}."
-                )
-            print()
-            db.commit()
-
-    logging.info("END - all ok.")