fractal-server 2.17.1a0__py3-none-any.whl → 2.17.2__py3-none-any.whl

fractal_server/config/_main.py

@@ -11,68 +11,49 @@ from ._settings_config import SETTINGS_CONFIG_DICT
 
 class Settings(BaseSettings):
     """
-    Contains all the configuration variables for Fractal Server
-
-    The attributes of this class are set from the environment.
+    Contains the general configuration variables for Fractal Server.
+
+    Attributes:
+        JWT_EXPIRE_SECONDS:
+            JWT token lifetime, in seconds.
+        JWT_SECRET_KEY:
+            JWT secret.<br>
+            ⚠️ Set this variable to a secure string, and do not disclose it.
+        COOKIE_EXPIRE_SECONDS:
+            Cookie token lifetime, in seconds.
+        FRACTAL_RUNNER_BACKEND:
+            Select which runner backend to use.
+        FRACTAL_LOGGING_LEVEL:
+            Logging-level threshold for logging
+            Only logs of with this level (or higher) will appear in the console
+            logs.
+        FRACTAL_API_MAX_JOB_LIST_LENGTH:
+            Number of ids that can be stored in the `jobsV2` attribute of
+            `app.state`.
+        FRACTAL_GRACEFUL_SHUTDOWN_TIME:
+            Waiting time for the shutdown phase of executors, in seconds.
+        FRACTAL_HELP_URL:
+            The URL of an instance-specific Fractal help page.
+        FRACTAL_DEFAULT_GROUP_NAME:
+            Name of the default user group.
+
+            If set to `"All"`, then the user group with that name is a special
+            user group (e.g. it cannot be deleted, and new users are
+            automatically added to it). If set to `None` (the default value),
+            then user groups are all equivalent, independently on their name.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
 
     JWT_EXPIRE_SECONDS: int = 180
-    """
-    JWT token lifetime, in seconds.
-    """
-
     JWT_SECRET_KEY: SecretStr
-    """
-    JWT secret
-
-    ⚠️ **IMPORTANT**: set this variable to a secure string, and do not disclose
-    it.
-    """
-
     COOKIE_EXPIRE_SECONDS: int = 86400
-    """
-    Cookie token lifetime, in seconds.
-    """
-
     # Note: we do not use ResourceType here to avoid circular imports
-    FRACTAL_RUNNER_BACKEND: Literal[
-        "local", "slurm_ssh", "slurm_sudo"
-    ] = "local"
-    """
-    Select which runner backend to use.
-    """
-
+    FRACTAL_RUNNER_BACKEND: Literal["local", "slurm_ssh", "slurm_sudo"] = (
+        "local"
+    )
     FRACTAL_LOGGING_LEVEL: int = logging.INFO
-    """
-    Logging-level threshold for logging
-
-    Only logs of with this level (or higher) will appear in the console logs.
-    """
-
     FRACTAL_API_MAX_JOB_LIST_LENGTH: int = 25
-    """
-    Number of ids that can be stored in the `jobsV2` attribute of
-    `app.state`.
-    """
-
-    FRACTAL_GRACEFUL_SHUTDOWN_TIME: int = 30
-    """
-    Waiting time for the shutdown phase of executors
-    """
-
+    FRACTAL_GRACEFUL_SHUTDOWN_TIME: float = 30.0
     FRACTAL_HELP_URL: HttpUrl | None = None
-    """
-    The URL of an instance-specific Fractal help page.
-    """
-
     FRACTAL_DEFAULT_GROUP_NAME: Literal["All"] | None = None
-    """
-    Name of the default user group.
-
-    If set to `"All"`, then the user group with that name is a special user
-    group (e.g. it cannot be deleted, and new users are automatically added
-    to it). If set to `None` (the default value), then user groups are all
-    equivalent, independently on their name.
-    """

fractal_server/config/_oauth.py

@@ -1,20 +1,33 @@
 from typing import Annotated
 from typing import Self
 
-from pydantic import model_validator
 from pydantic import SecretStr
 from pydantic import StringConstraints
+from pydantic import model_validator
 from pydantic_settings import BaseSettings
 from pydantic_settings import SettingsConfigDict
 
-from ._settings_config import SETTINGS_CONFIG_DICT
 from fractal_server.types import NonEmptyStr
 
+from ._settings_config import SETTINGS_CONFIG_DICT
+
 
 class OAuthSettings(BaseSettings):
     """
-    Minimal set of configurations needed for operating on the database (e.g
-    for schema migrations).
+    Settings for integration with an OAuth identity provider.
+
+    Attributes:
+        OAUTH_CLIENT_NAME: Name of the client.
+        OAUTH_CLIENT_ID: ID of client.
+        OAUTH_CLIENT_SECRET:
+            Secret to authorise against the identity provider.
+        OAUTH_OIDC_CONFIG_ENDPOINT:
+            OpenID Connect configuration endpoint, for autodiscovery of
+            relevant endpoints.
+        OAUTH_REDIRECT_URL:
+            String to be used as `redirect_url` argument in
+            `fastapi_users.get_oauth_router`, and then in
+            `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`.
     """
 
     model_config = SettingsConfigDict(**SETTINGS_CONFIG_DICT)
@@ -26,27 +39,10 @@ class OAuthSettings(BaseSettings):
         ]
         | None
     ) = None
-    """
-    The name of the client.
-    """
     OAUTH_CLIENT_ID: SecretStr | None = None
-    """
-    ID of client.
-    """
     OAUTH_CLIENT_SECRET: SecretStr | None = None
-    """
-    Secret to authorise against the identity provider.
-    """
     OAUTH_OIDC_CONFIG_ENDPOINT: SecretStr | None = None
-    """
-    OpenID configuration endpoint, for autodiscovery of relevant endpoints.
-    """
     OAUTH_REDIRECT_URL: str | None = None
-    """
-    String to be used as `redirect_url` argument in
-    `fastapi_users.get_oauth_router`, and then in
-    `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`
-    """
 
     @model_validator(mode="after")
     def check_configuration(self: Self) -> Self:

fractal_server/exceptions.py

@@ -1,2 +1,6 @@
 class UnreachableBranchError(RuntimeError):
+    """
+    Exception marking a code branch that should have not been reached.
+    """
+
     pass

fractal_server/images/models.py

@@ -9,7 +9,7 @@ from fractal_server.types import ZarrDirStr
 from fractal_server.types import ZarrUrlStr
 
 
-class _SingleImageBase(BaseModel):
+class SingleImageBase(BaseModel):
     """
     Base for SingleImage and SingleImageTaskOutput.
 
@@ -27,7 +27,7 @@ class _SingleImageBase(BaseModel):
     types: ImageTypes = Field(default_factory=dict)
 
 
-class SingleImageTaskOutput(_SingleImageBase):
+class SingleImageTaskOutput(SingleImageBase):
     """
     `SingleImageBase`, with scalar `attributes` values (`None` included).
     """
@@ -35,7 +35,7 @@ class SingleImageTaskOutput(_SingleImageBase):
     attributes: ImageAttributesWithNone = Field(default_factory=dict)
 
 
-class SingleImage(_SingleImageBase):
+class SingleImage(SingleImageBase):
     """
     `SingleImageBase`, with scalar `attributes` values (`None` excluded).
     """

fractal_server/images/status_tools.py

@@ -37,10 +37,12 @@ def _prepare_query(
     """
     stm = (
         select(HistoryImageCache.zarr_url, HistoryUnit.status)
-        .join(HistoryUnit)
+        .join(
+            HistoryUnit,
+            HistoryImageCache.latest_history_unit_id == HistoryUnit.id,
+        )
         .where(HistoryImageCache.dataset_id == dataset_id)
         .where(HistoryImageCache.workflowtask_id == workflowtask_id)
-        .where(HistoryImageCache.latest_history_unit_id == HistoryUnit.id)
     )
     return stm
 

fractal_server/logger.py

@@ -12,13 +12,13 @@
 """
 This module provides logging utilities
 """
+
 import logging
 from pathlib import Path
 
 from .config import get_settings
 from .syringe import Inject
 
-
 LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
 LOG_FORMATTER = logging.Formatter(LOG_FORMAT)
 

fractal_server/main.py

@@ -4,6 +4,9 @@ from itertools import chain
 
 from fastapi import FastAPI
 
+from fractal_server import __VERSION__
+from fractal_server.app.schemas.v2 import ResourceType
+
 from .app.routes.aux._runner import _backend_supports_shutdown
 from .app.shutdown import cleanup_after_shutdown
 from .config import get_data_settings
@@ -15,8 +18,6 @@ from .logger import get_logger
 from .logger import reset_logger_handlers
 from .logger import set_logger
 from .syringe import Inject
-from fractal_server import __VERSION__
-from fractal_server.app.schemas.v2 import ResourceType
 
 
 def collect_routers(app: FastAPI) -> None:
@@ -27,9 +28,9 @@ def collect_routers(app: FastAPI) -> None:
         app:
             The application to register the routers to.
     """
+    from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.api import router_api
     from .app.routes.api.v2 import router_api_v2
-    from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.auth.router import router_auth
 
     app.include_router(router_api, prefix="/api")

fractal_server/migrations/versions/034a469ec2eb_task_groups.py

@@ -5,6 +5,7 @@ Revises: da2cb2ac4255
 Create Date: 2024-10-10 16:14:13.976231
 
 """
+
 from datetime import datetime
 from datetime import timezone
 
@@ -12,7 +13,6 @@ import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "034a469ec2eb"
 down_revision = "da2cb2ac4255"
@@ -26,15 +26,11 @@ def upgrade() -> None:
         sa.Column("id", sa.Integer(), nullable=False),
         sa.Column("user_id", sa.Integer(), nullable=False),
         sa.Column("user_group_id", sa.Integer(), nullable=True),
-        sa.Column(
-            "origin", sqlmodel.sql.sqltypes.AutoString(), nullable=False
-        ),
+        sa.Column("origin", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column(
             "pkg_name", sqlmodel.sql.sqltypes.AutoString(), nullable=False
         ),
-        sa.Column(
-            "version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
-        ),
+        sa.Column("version", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
         sa.Column(
             "python_version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
         ),
@@ -123,8 +119,8 @@ def upgrade() -> None:
     except BaseException as e:
         if op.get_bind().dialect.name != "sqlite":
             raise e
-        import sqlite3
         import logging
+        import sqlite3
 
         logger = logging.getLogger("alembic.runtime.migration")
         logger.warning(

fractal_server/migrations/versions/091b01f51f88_add_usergroup_and_linkusergroup_table.py

@@ -5,11 +5,11 @@ Revises: 5bf02391cfef
 Create Date: 2024-09-09 13:17:51.008231
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "091b01f51f88"
 down_revision = "5bf02391cfef"

fractal_server/migrations/versions/0f5f85bb2ae7_add_pre_pinned_packages.py

@@ -5,6 +5,7 @@ Revises: 1a83a5260664
 Create Date: 2025-09-10 14:36:06.028179
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 from sqlalchemy.dialects import postgresql

fractal_server/migrations/versions/19eca0dd47a9_user_settings_project_dir.py

@@ -5,11 +5,11 @@ Revises: 8e8f227a3e36
 Create Date: 2024-10-30 14:34:28.219355
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "19eca0dd47a9"
 down_revision = "8e8f227a3e36"

fractal_server/migrations/versions/1a83a5260664_rename.py

@@ -5,8 +5,8 @@ Revises: b3ffb095f973
 Create Date: 2025-09-10 14:16:51.202765
 
 """
-from alembic import op
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "1a83a5260664"

fractal_server/migrations/versions/1eac13a26c83_drop_v1_tables.py

@@ -5,6 +5,7 @@ Revises: af8673379a5c
 Create Date: 2025-01-10 13:17:47.838607
 
 """
+
 import logging
 
 from alembic import op

fractal_server/migrations/versions/316140ff7ee1_remove_usersettings_cache_dir.py

@@ -5,10 +5,10 @@ Revises: d256a7379ab8
 Create Date: 2024-12-03 10:15:53.255958
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "316140ff7ee1"
 down_revision = "d256a7379ab8"

fractal_server/migrations/versions/40d6d6511b20_add_index_to_history_models.py

@@ -0,0 +1,47 @@
+"""add index to history models
+
+Revision ID: 40d6d6511b20
+Revises: 7673fe18c05d
+Create Date: 2025-11-14 10:34:12.300920
+
+"""
+
+from alembic import op
+
+# revision identifiers, used by Alembic.
+revision = "40d6d6511b20"
+down_revision = "7673fe18c05d"
+branch_labels = None
+depends_on = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("historyimagecache", schema=None) as batch_op:
+        batch_op.create_index(
+            batch_op.f("ix_historyimagecache_latest_history_unit_id"),
+            ["latest_history_unit_id"],
+            unique=False,
+        )
+
+    with op.batch_alter_table("historyunit", schema=None) as batch_op:
+        batch_op.create_index(
+            batch_op.f("ix_historyunit_history_run_id"),
+            ["history_run_id"],
+            unique=False,
+        )
+
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    with op.batch_alter_table("historyunit", schema=None) as batch_op:
+        batch_op.drop_index(batch_op.f("ix_historyunit_history_run_id"))
+
+    with op.batch_alter_table("historyimagecache", schema=None) as batch_op:
+        batch_op.drop_index(
+            batch_op.f("ix_historyimagecache_latest_history_unit_id")
+        )
+
+    # ### end Alembic commands ###

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/47351f8c7ebc_drop_dataset_filters.py

@@ -5,6 +5,7 @@ Revises: fbce16ff4e47
 Create Date: 2025-03-26 11:10:17.869028
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 from sqlalchemy.dialects import postgresql

fractal_server/migrations/versions/49d0856e9569_drop_table.py

@@ -0,0 +1,62 @@
+"""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/4c308bcaea2b_add_task_args_schema_and_task_args_.py

@@ -5,11 +5,11 @@ Revises: 50a13d6138fd
 Create Date: 2023-05-29 17:09:02.492639
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "4c308bcaea2b"
 down_revision = "50a13d6138fd"

fractal_server/migrations/versions/4cedeb448a53_workflowtask_foreign_keys_not_nullables.py

@@ -5,10 +5,10 @@ Revises: efa89c30e0a4
 Create Date: 2024-01-16 13:57:47.891931
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "4cedeb448a53"
 down_revision = "efa89c30e0a4"

fractal_server/migrations/versions/501961cfcd85_remove_link_between_v1_and_v2_tasks_.py

@@ -5,6 +5,7 @@ Revises: 5bf02391cfef
 Create Date: 2024-09-09 14:15:34.415926
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 
@@ -36,8 +37,8 @@ def upgrade() -> None:
     # NOTE: in sqlite, the `drop_index` command fails if the existing table
     # has zero rows, while it succeeds if there are already some rows
     if op.get_bind().dialect.name == "sqlite":
-        import sqlite3
         import logging
+        import sqlite3
 
         logger = logging.getLogger("alembic.runtime.migration")
         logger.warning(

fractal_server/migrations/versions/50a13d6138fd_initial_schema.py

@@ -5,11 +5,11 @@ Revises:
 Create Date: 2023-05-29 12:14:56.670243
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "50a13d6138fd"
 down_revision = None
@@ -37,9 +37,7 @@ def upgrade() -> None:
         "task",
         sa.Column("default_args", sa.JSON(), nullable=True),
         sa.Column("meta", sa.JSON(), nullable=True),
-        sa.Column(
-            "source", sqlmodel.sql.sqltypes.AutoString(), nullable=False
-        ),
+        sa.Column("source", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column("id", sa.Integer(), nullable=False),
         sa.Column("name", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column(
@@ -52,9 +50,7 @@ def upgrade() -> None:
             "output_type", sqlmodel.sql.sqltypes.AutoString(), nullable=False
         ),
         sa.Column("owner", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
-        sa.Column(
-            "version", sqlmodel.sql.sqltypes.AutoString(), nullable=True
-        ),
+        sa.Column("version", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
         sa.PrimaryKeyConstraint("id"),
         sa.UniqueConstraint("source"),
     )
@@ -163,9 +159,7 @@ def upgrade() -> None:
     )
     op.create_table(
         "applyworkflow",
-        sa.Column(
-            "start_timestamp", sa.DateTime(timezone=True), nullable=True
-        ),
+        sa.Column("start_timestamp", sa.DateTime(timezone=True), nullable=True),
         sa.Column("end_timestamp", sa.DateTime(timezone=True), nullable=True),
         sa.Column(
             "worker_init", sqlmodel.sql.sqltypes.AutoString(), nullable=True
@@ -183,9 +177,7 @@ def upgrade() -> None:
             sqlmodel.sql.sqltypes.AutoString(),
             nullable=True,
         ),
-        sa.Column(
-            "status", sqlmodel.sql.sqltypes.AutoString(), nullable=False
-        ),
+        sa.Column("status", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column("log", sqlmodel.sql.sqltypes.AutoString(), nullable=True),
         sa.ForeignKeyConstraint(
             ["input_dataset_id"],
@@ -243,12 +235,8 @@ def downgrade() -> None:
     op.drop_table("resource")
     op.drop_table("applyworkflow")
     op.drop_table("workflow")
-    op.drop_index(
-        op.f("ix_oauthaccount_oauth_name"), table_name="oauthaccount"
-    )
-    op.drop_index(
-        op.f("ix_oauthaccount_account_id"), table_name="oauthaccount"
-    )
+    op.drop_index(op.f("ix_oauthaccount_oauth_name"), table_name="oauthaccount")
+    op.drop_index(op.f("ix_oauthaccount_account_id"), table_name="oauthaccount")
     op.drop_table("oauthaccount")
     op.drop_table("linkuserproject")
     op.drop_table("dataset")