fractal-server 2.17.1a1__py3-none-any.whl → 2.18.0__py3-none-any.whl

fractal_server/images/models.py

@@ -5,11 +5,10 @@ from fractal_server.types import DictStrAny
 from fractal_server.types import ImageAttributes
 from fractal_server.types import ImageAttributesWithNone
 from fractal_server.types import ImageTypes
-from fractal_server.types import ZarrDirStr
 from fractal_server.types import ZarrUrlStr
 
 
-class _SingleImageBase(BaseModel):
+class SingleImageBase(BaseModel):
     """
     Base for SingleImage and SingleImageTaskOutput.
 
@@ -21,13 +20,13 @@ class _SingleImageBase(BaseModel):
     """
 
     zarr_url: ZarrUrlStr
-    origin: ZarrDirStr | None = None
+    origin: ZarrUrlStr | None = None
 
     attributes: DictStrAny = Field(default_factory=dict)
     types: ImageTypes = Field(default_factory=dict)
 
 
-class SingleImageTaskOutput(_SingleImageBase):
+class SingleImageTaskOutput(SingleImageBase):
     """
     `SingleImageBase`, with scalar `attributes` values (`None` included).
     """
@@ -35,7 +34,7 @@ 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

@@ -1,12 +1,20 @@
 import os
+import time
 from contextlib import asynccontextmanager
+from datetime import datetime
 from itertools import chain
 
 from fastapi import FastAPI
+from starlette.types import Message
+from starlette.types import Receive
+from starlette.types import Scope
+from starlette.types import Send
+
+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
 from .config import get_db_settings
 from .config import get_email_settings
 from .config import get_settings
@@ -15,8 +23,6 @@ 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:
@@ -27,16 +33,14 @@ def collect_routers(app: FastAPI) -> None:
         app:
             The application to register the routers to.
     """
+    from .app.routes.admin.v2 import router_admin
     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.api.v2 import router_api as router_api_v2
     from .app.routes.auth.router import router_auth
 
     app.include_router(router_api, prefix="/api")
     app.include_router(router_api_v2, prefix="/api/v2")
-    app.include_router(
-        router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
-    )
+    app.include_router(router_admin, prefix="/admin/v2", tags=["Admin area"])
     app.include_router(router_auth, prefix="/auth", tags=["Authentication"])
 
 
@@ -53,14 +57,12 @@ def check_settings() -> None:
     settings = Inject(get_settings)
     db_settings = Inject(get_db_settings)
     email_settings = Inject(get_email_settings)
-    data_settings = Inject(get_data_settings)
     logger = set_logger("fractal_server_settings")
     logger.debug("Fractal Settings:")
     for key, value in chain(
         db_settings.model_dump().items(),
         settings.model_dump().items(),
         email_settings.model_dump().items(),
-        data_settings.model_dump().items(),
     ):
         if any(s in key.upper() for s in ["PASSWORD", "SECRET", "KEY"]):
             value = "*****"
@@ -70,7 +72,7 @@ def check_settings() -> None:
 
 @asynccontextmanager
 async def lifespan(app: FastAPI):
-    app.state.jobsV2 = []
+    app.state.jobs = []
     logger = set_logger("fractal_server.lifespan")
     logger.info(f"[startup] START (fractal-server {__VERSION__})")
     check_settings()
@@ -107,12 +109,12 @@ async def lifespan(app: FastAPI):
 
     logger.info(
         f"[teardown] Current worker with pid {os.getpid()} is shutting down. "
-        f"Current jobs: {app.state.jobsV2=}"
+        f"Current jobs: {app.state.jobs=}"
     )
     if _backend_supports_shutdown(settings.FRACTAL_RUNNER_BACKEND):
         try:
             await cleanup_after_shutdown(
-                jobsV2=app.state.jobsV2,
+                jobs=app.state.jobs,
                 logger_name="fractal_server.lifespan",
             )
         except Exception as e:
@@ -130,6 +132,59 @@ async def lifespan(app: FastAPI):
     reset_logger_handlers(logger)
 
 
+slow_response_logger = set_logger("slow-response")
+
+
+def _endpoint_has_background_task(method: str, path: str) -> bool:
+    has_background_task = (method == "POST") and (
+        "/job/submit/" in path
+        or "/task/collect/pi" in path  # "/pip" and "/pixi"
+        or "/task-group/" in path
+    )
+    return has_background_task
+
+
+class SlowResponseMiddleware:
+    def __init__(self, app: FastAPI, time_threshold: float):
+        self.app = app
+        self.time_threshold = time_threshold
+
+    async def __call__(self, scope: Scope, receive: Receive, send: Send):
+        if (
+            scope["type"] != "http"  # e.g. `scope["type"] == "lifespan"`
+            or _endpoint_has_background_task(scope["method"], scope["path"])
+        ):
+            await self.app(scope, receive, send)
+            return
+
+        # Mutable variable which can be updated from within `send_wrapper`
+        context = {"status_code": None}
+
+        async def send_wrapper(message: Message):
+            if message["type"] == "http.response.start":
+                context["status_code"] = message["status"]
+            await send(message)
+
+        # Measure request time
+        start_timestamp = datetime.now()
+        start_time = time.perf_counter()
+        await self.app(scope, receive, send_wrapper)
+        stop_time = time.perf_counter()
+        request_time = stop_time - start_time
+
+        # Log if process time is too high
+        if request_time > self.time_threshold:
+            end_timestamp = datetime.now()
+            slow_response_logger.warning(
+                f"{scope['method']} {scope['route'].path}"
+                f"?{scope['query_string'].decode('utf-8')}, "
+                f"{context['status_code']}, "
+                f"{request_time:.2f}, "
+                f"{start_timestamp.isoformat(timespec='milliseconds')}, "
+                f"{end_timestamp.isoformat(timespec='milliseconds')}"
+            )
+
+
 def start_application() -> FastAPI:
     """
     Create the application, initialise it and collect all available routers.
@@ -139,6 +194,13 @@ def start_application() -> FastAPI:
             The fully initialised application.
     """
     app = FastAPI(lifespan=lifespan)
+
+    settings = Inject(get_settings)
+    app.add_middleware(
+        SlowResponseMiddleware,
+        time_threshold=settings.FRACTAL_LONG_REQUEST_TIME,
+    )
+
     collect_routers(app)
     return app
 

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

@@ -5,10 +5,10 @@ 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"

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

@@ -5,6 +5,7 @@ Revises: 45fbb391d7af
 Create Date: 2025-11-11 16:39:41.497832
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 from sqlalchemy.dialects import postgresql
@@ -34,9 +35,7 @@ def downgrade() -> None:
             autoincrement=False,
             nullable=False,
         ),
-        sa.Column(
-            "ssh_host", sa.VARCHAR(), autoincrement=False, nullable=True
-        ),
+        sa.Column("ssh_host", sa.VARCHAR(), autoincrement=False, nullable=True),
         sa.Column(
             "ssh_username", sa.VARCHAR(), autoincrement=False, nullable=True
         ),

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")

fractal_server/migrations/versions/5bf02391cfef_v2.py

@@ -5,11 +5,11 @@ Revises: 9fd26a2b0de4
 Create Date: 2024-04-18 10:35:19.067833
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "5bf02391cfef"
 down_revision = "9fd26a2b0de4"
@@ -50,9 +50,7 @@ def upgrade() -> None:
             sqlmodel.sql.sqltypes.AutoString(),
             nullable=True,
         ),
-        sa.Column(
-            "source", sqlmodel.sql.sqltypes.AutoString(), nullable=False
-        ),
+        sa.Column("source", sqlmodel.sql.sqltypes.AutoString(), nullable=False),
         sa.Column(
             "meta_non_parallel", sa.JSON(), server_default="{}", nullable=False
         ),
@@ -60,9 +58,7 @@ def upgrade() -> None:
             "meta_parallel", sa.JSON(), server_default="{}", 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.Column("args_schema_non_parallel", sa.JSON(), nullable=True),
         sa.Column("args_schema_parallel", sa.JSON(), nullable=True),
         sa.Column(
@@ -166,9 +162,7 @@ def upgrade() -> None:
             "start_timestamp", sa.DateTime(timezone=True), nullable=False
         ),
         sa.Column("end_timestamp", sa.DateTime(timezone=True), 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(
             ["dataset_id"],

fractal_server/migrations/versions/70e77f1c38b0_add_applyworkflow_first_task_index_and_.py

@@ -5,6 +5,7 @@ Revises: f384e1c0cf5d
 Create Date: 2023-07-17 11:39:47.679582
 
 """
+
 import sqlalchemy as sa
 from alembic import op
 from sqlalchemy.sql import column

fractal_server/migrations/versions/71eefd1dd202_add_slurm_accounts.py

@@ -5,11 +5,11 @@ Revises: d4fe3708d309
 Create Date: 2023-12-05 12:36:44.100065
 
 """
+
 import sqlalchemy as sa
 import sqlmodel
 from alembic import op
 
-
 # revision identifiers, used by Alembic.
 revision = "71eefd1dd202"
 down_revision = "d4fe3708d309"

fractal_server/migrations/versions/7673fe18c05d_remove_project_dir_server_default.py

@@ -5,8 +5,8 @@ Revises: 49d0856e9569
 Create Date: 2025-11-11 16:50:20.079193
 
 """
-from alembic import op
 
+from alembic import op
 
 # revision identifiers, used by Alembic.
 revision = "7673fe18c05d"