fractal-server 2.0.5__py3-none-any.whl → 2.0.6__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.5"
+__VERSION__ = "2.0.6"

fractal_server/app/models/__init__.py

@@ -1,7 +1,3 @@
-"""
-`models` module
-"""
-from .security import *  # noqa: F401, F403
 from .v1 import Project  # noqa: F401
 from .v2 import ProjectV2  # noqa: F401
 

fractal_server/app/models/security.py

@@ -18,9 +18,6 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
-from .linkuserproject import LinkUserProject
-from .linkuserproject import LinkUserProjectV2
-
 
 class OAuthAccount(SQLModel, table=True):
     """
@@ -103,16 +100,6 @@ class UserOAuth(SQLModel, table=True):
         back_populates="user",
         sa_relationship_kwargs={"lazy": "joined", "cascade": "all, delete"},
     )
-    project_list: list["Project"] = Relationship(  # noqa
-        back_populates="user_list",
-        link_model=LinkUserProject,
-        sa_relationship_kwargs={"lazy": "selectin"},
-    )
-    project_list_v2: list["ProjectV2"] = Relationship(  # noqa
-        back_populates="user_list",
-        link_model=LinkUserProjectV2,
-        sa_relationship_kwargs={"lazy": "selectin"},
-    )
 
     class Config:
         orm_mode = True

fractal_server/app/models/v1/__init__.py

@@ -1,12 +1,13 @@
 """
 `models` module
 """
-from .dataset import Dataset  # noqa: F401
-from .dataset import Resource  # noqa: F401
-from .job import ApplyWorkflow  # noqa: F403, F401
-from .job import JobStatusTypeV1  # noqa: F401, F403
-from .project import Project  # noqa: F403, F401
-from .state import State  # noqa: F403, F401
-from .task import Task  # noqa: F403, F401
-from .workflow import Workflow  # noqa: F401, F403
-from .workflow import WorkflowTask  # noqa: F401, F403
+from ..linkuserproject import LinkUserProject  # noqa F401
+from .dataset import Dataset  # noqa F401
+from .dataset import Resource  # noqa F401
+from .job import ApplyWorkflow  # noqa F401
+from .job import JobStatusTypeV1  # noqa F401
+from .project import Project  # noqa F401
+from .state import State  # noqa F401
+from .task import Task  # noqa F401
+from .workflow import Workflow  # noqa F401
+from .workflow import WorkflowTask  # noqa F401

fractal_server/app/models/v1/project.py

@@ -7,9 +7,9 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
+from . import LinkUserProject
 from ....utils import get_timestamp
 from ...schemas.v1.project import _ProjectBaseV1
-from ..linkuserproject import LinkUserProject
 from ..security import UserOAuth
 
 
@@ -23,7 +23,6 @@ class Project(_ProjectBaseV1, SQLModel, table=True):
 
     user_list: list[UserOAuth] = Relationship(
         link_model=LinkUserProject,
-        back_populates="project_list",
         sa_relationship_kwargs={
             "lazy": "selectin",
         },

fractal_server/app/models/v2/project.py

@@ -7,8 +7,8 @@ from sqlmodel import Field
 from sqlmodel import Relationship
 from sqlmodel import SQLModel
 
+from . import LinkUserProjectV2
 from ....utils import get_timestamp
-from ..linkuserproject import LinkUserProjectV2
 from ..security import UserOAuth
 
 
@@ -23,7 +23,6 @@ class ProjectV2(SQLModel, table=True):
 
     user_list: list[UserOAuth] = Relationship(
         link_model=LinkUserProjectV2,
-        back_populates="project_list_v2",
         sa_relationship_kwargs={
             "lazy": "selectin",
         },

fractal_server/app/routes/api/v1/_aux_functions.py

@@ -12,9 +12,9 @@ from sqlmodel import select
 from sqlmodel.sql.expression import SelectOfScalar
 
 from ....db import AsyncSession
-from ....models import LinkUserProject
 from ....models.v1 import ApplyWorkflow
 from ....models.v1 import Dataset
+from ....models.v1 import LinkUserProject
 from ....models.v1 import Project
 from ....models.v1 import Task
 from ....models.v1 import Workflow

fractal_server/app/routes/api/v1/project.py

@@ -18,9 +18,9 @@ from .....logger import set_logger
 from .....syringe import Inject
 from ....db import AsyncSession
 from ....db import get_async_db
-from ....models import LinkUserProject
 from ....models.v1 import ApplyWorkflow
 from ....models.v1 import Dataset
+from ....models.v1 import LinkUserProject
 from ....models.v1 import Project
 from ....models.v1 import Workflow
 from ....runner.set_start_and_last_task_index import (

fractal_server/app/runner/executors/slurm/_subprocess_run_as_user.py

@@ -141,7 +141,7 @@ def _glob_as_user_strict(
     new_output = []
     known_filenames = [
         f"{startswith}{suffix}"
-        for suffix in [".args.json", ".metadiff.json", ".err", ".out"]
+        for suffix in [".args.json", ".metadiff.json", ".err", ".out", ".log"]
     ]
     for filename in output:
         if filename in known_filenames:

fractal_server/config.py

@@ -361,6 +361,11 @@ class Settings(BaseSettings):
     attribute in their input-arguments JSON file.
     """
 
+    FRACTAL_API_V1_MODE: Literal["include", "exclude"] = "include"
+    """
+    Whether to include the v1 API.
+    """
+
     ###########################################################################
     # BUSINESS LOGIC
     ###########################################################################

fractal_server/{logger.py → logger/__init__.py}

@@ -17,8 +17,8 @@ from pathlib import Path
 from typing import Optional
 from typing import Union
 
-from .config import get_settings
-from .syringe import Inject
+from ..config import get_settings
+from ..syringe import Inject
 
 
 LOG_FORMAT = "%(asctime)s - %(name)s - %(levelname)s - %(message)s"
@@ -136,3 +136,29 @@ def reset_logger_handlers(logger: logging.Logger) -> None:
     """
     close_logger(logger)
     logger.handlers.clear()
+
+
+def config_uvicorn_loggers():
+    """
+    Change the formatter for the uvicorn access/error loggers.
+
+    This is similar to https://stackoverflow.com/a/68864979/19085332. See also
+    https://github.com/tiangolo/fastapi/issues/1508.
+
+    This function is meant to work in two scenarios:
+
+    1. The most relevant case is for a `gunicorn` startup command, with
+       `--access-logfile` and `--error-logfile` options set.
+    2. The case of `fractalctl start` (directly calling `uvicorn`).
+
+    Because of the second use case, we need to check whether uvicorn loggers
+    already have a handler. If not, we skip the formatting.
+    """
+
+    access_logger = logging.getLogger("uvicorn.access")
+    if len(access_logger.handlers) > 0:
+        access_logger.handlers[0].setFormatter(LOG_FORMATTER)
+
+    error_logger = logging.getLogger("uvicorn.error")
+    if len(error_logger.handlers) > 0:
+        error_logger.handlers[0].setFormatter(LOG_FORMATTER)

fractal_server/logger/gunicorn_logger.py

@@ -0,0 +1,19 @@
+"""
+This module (which is only executed if `gunicorn` can be imported) subclasses
+the gunicorn `Logger` class in order to slightly change its log formats.
+
+This class can be used by including this `gunicorn` command-line option:
+```
+--logger-class fractal_server.logger.gunicorn_logger.FractalGunicornLogger
+```
+"""
+
+try:
+    from gunicorn.glogging import Logger as GunicornLogger
+
+    class FractalGunicornLogger(GunicornLogger):
+        error_fmt = r"%(asctime)s   - gunicorn.error - %(levelname)s - [pid %(process)d] - %(message)s"  # noqa: E501
+        datefmt = r"%Y-%m-%d %H:%M:%S,%u"
+
+except (ModuleNotFoundError, ImportError):
+    pass

fractal_server/main.py

@@ -19,6 +19,7 @@ from fastapi import FastAPI
 
 from .app.security import _create_first_user
 from .config import get_settings
+from .logger import config_uvicorn_loggers
 from .logger import reset_logger_handlers
 from .logger import set_logger
 from .syringe import Inject
@@ -39,12 +40,15 @@ def collect_routers(app: FastAPI) -> None:
     from .app.routes.admin.v2 import router_admin_v2
     from .app.routes.auth import router_auth
 
+    settings = Inject(get_settings)
+
     app.include_router(router_api, prefix="/api")
-    app.include_router(router_api_v1, prefix="/api/v1")
+    if settings.FRACTAL_API_V1_MODE == "include":
+        app.include_router(router_api_v1, prefix="/api/v1")
+        app.include_router(
+            router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
+        )
     app.include_router(router_api_v2, prefix="/api/v2")
-    app.include_router(
-        router_admin_v1, prefix="/admin/v1", tags=["V1 Admin area"]
-    )
     app.include_router(
         router_admin_v2, prefix="/admin/v2", tags=["V2 Admin area"]
     )
@@ -81,6 +85,7 @@ async def __on_startup() -> None:
     callable.
     """
     check_settings()
+    config_uvicorn_loggers()
 
 
 def start_application() -> FastAPI:

{fractal_server-2.0.5.dist-info → fractal_server-2.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.5
+Version: 2.0.6
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

{fractal_server-2.0.5.dist-info → fractal_server-2.0.6.dist-info}/RECORD

@@ -1,15 +1,15 @@
-fractal_server/__init__.py,sha256=iemtcbFq1-Ut2bx94D5rbhyNac6WTU--MpGgUfTDdXI,22
+fractal_server/__init__.py,sha256=S5hrGn9zHoCPoN-w6jqLkqipFDSl7JkGHq3amd7eoVE,22
 fractal_server/__main__.py,sha256=CocbzZooX1UtGqPi55GcHGNxnrJXFg5tUU5b3wyFCyo,4958
 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=WZEVfdJAX7ZyBM1ngfEGeqWWcjK_NygtCbawpmbwGpU,4042
-fractal_server/app/models/__init__.py,sha256=FRRDJkx7LgPaUqSp8IV7qevu_VE2dt0-fQtQruHFaVo,267
+fractal_server/app/models/__init__.py,sha256=QGRjxBgk6GzHyyXh_7RuHvpLoe5PTl1g5KLkGqhFYMQ,199
 fractal_server/app/models/linkuserproject.py,sha256=eQaourbGRshvlMVlKzLYJKHEjfsW1CbWws9yW4eHXhA,567
-fractal_server/app/models/security.py,sha256=UG9wCVA5GRSyHrYEFhH8lIF1hXykxsr9LSi8_dFToMY,3378
-fractal_server/app/models/v1/__init__.py,sha256=qUlUGnWFaIm3aBXfUuLdhcW9f_s1VzAEuypr31zvHGo,458
+fractal_server/app/models/security.py,sha256=0oYj_cqPcQFsPFDyN4OTsqbXsLlXRcweawjP_iSiRI0,2900
+fractal_server/app/models/v1/__init__.py,sha256=hUI7dEbPaiZGN0IbHW4RSmSicyvtn_xeuevoX7zvUwI,466
 fractal_server/app/models/v1/dataset.py,sha256=99GDgt7njx8yYQApkImqp_7bHA5HH3ElvbR6Oyj9kVI,2017
 fractal_server/app/models/v1/job.py,sha256=QLGXcWdVRHaUHQNDapYYlLpEfw4K7QyD8TmcwhrWw2o,3304
-fractal_server/app/models/v1/project.py,sha256=sDmAFLOBK5o4dLrwsIN681JcT5J1rzoUNTV9QVqwnA8,859
+fractal_server/app/models/v1/project.py,sha256=tf6fniyBH-sb6rBvGiqNl2wgN9ipR4hDEE3OKvxKaoo,804
 fractal_server/app/models/v1/state.py,sha256=ew7xw3iPzBwUnPlzmsOEMiPbPEMsJn_TyZ5cK93jBRQ,1095
 fractal_server/app/models/v1/task.py,sha256=3xZqNeFYUqslh8ddMSXF2nO4nIiOD8T5Ij37wY20kss,2782
 fractal_server/app/models/v1/workflow.py,sha256=dnY5eMaOe3oZv8arn00RNX9qVkBtTLG-vYdWXcQuyo4,3950
@@ -17,7 +17,7 @@ fractal_server/app/models/v2/__init__.py,sha256=uLzdInqATSwi0bS_V4vKB-TqFrOFaXux
 fractal_server/app/models/v2/collection_state.py,sha256=nxb042i8tt8rCpmgbFJoBCYWU-34m0HdUfO9YurTp8k,588
 fractal_server/app/models/v2/dataset.py,sha256=-7sxHEw4IIAvF_uSan7tA3o8hvoakBkQ0SRvqS2iOQU,1455
 fractal_server/app/models/v2/job.py,sha256=ypJmN-qspkKBGhBG7Mt-HypSQqcQ2EmB4Bzzb2-y550,1535
-fractal_server/app/models/v2/project.py,sha256=CqDEKzdVxmFDMee6DnVOyX7WGmdn-dQSLSekzw_OLUc,817
+fractal_server/app/models/v2/project.py,sha256=CRBnZ8QITNp6u1f5bMxvi1_mcvEfXpWyitsWB5f7gn8,759
 fractal_server/app/models/v2/task.py,sha256=9ZPhug3VWyeqgT8wQ9_8ZXQ2crSiiicRipxrxTslOso,3257
 fractal_server/app/models/v2/workflow.py,sha256=YBgFGCziUgU0aJ5EM3Svu9W2c46AewZO9VBlFCHiSps,1069
 fractal_server/app/models/v2/workflowtask.py,sha256=3jEkObsSnlI05Pur_dSsXYdJxRqPL60Z7tK5-EJLOks,1532
@@ -27,10 +27,10 @@ fractal_server/app/routes/admin/v1.py,sha256=uMupmRkicaoWazX8qSX5fgh00O3MbuSfim8
 fractal_server/app/routes/admin/v2.py,sha256=e0A6RMWfmTO5dVL95XO-P2EljdEwR00FErxahEPzODQ,13757
 fractal_server/app/routes/api/__init__.py,sha256=EVyZrEq3I_1643QGTPCC5lgCp4xH_auYbrFfogTm4pc,315
 fractal_server/app/routes/api/v1/__init__.py,sha256=Y2HQdG197J0a7DyQEE2jn53IfxD0EHGhzK1I2JZuEck,958
-fractal_server/app/routes/api/v1/_aux_functions.py,sha256=KoSefKiBXximu0df4fJ3l9bKsGaLO8rb3z6xhD8PWj4,11973
+fractal_server/app/routes/api/v1/_aux_functions.py,sha256=lFfGJxbJc-Ryah_pPkiTH2SBncWQ15n0iqVFolzIOCM,11976
 fractal_server/app/routes/api/v1/dataset.py,sha256=HRE-8vPmVkeXf7WFYkI19mDtbY-iJZeJ7PmMiV0LMgY,16923
 fractal_server/app/routes/api/v1/job.py,sha256=NwXyhvvzdPDor0ts8Im__9-I0P1H943s4NXIRgaz7PM,5436
-fractal_server/app/routes/api/v1/project.py,sha256=tb1M2hhAKyHeToV0RwAQQx0ptIDeX6sEjM7dkfjCpXQ,15799
+fractal_server/app/routes/api/v1/project.py,sha256=DKQ6n1CPmHqsKieBaJlKnOhKaHWgQTZIA_asJTT9Uxo,15802
 fractal_server/app/routes/api/v1/task.py,sha256=udbKnenzc-Q10elYCVB9JmOPWATraa9tZi0AaByvWo0,6129
 fractal_server/app/routes/api/v1/task_collection.py,sha256=mFaYyCWtCPRqvs3j6zx_zaiDXn31Uzoa7UHZS-Lu_L0,8882
 fractal_server/app/routes/api/v1/workflow.py,sha256=7r9IoIevg_rvYCrerMOsIsUabSOQatxdPCfLdkP0dRs,10942
@@ -63,7 +63,7 @@ fractal_server/app/runner/executors/slurm/_batching.py,sha256=1P6CgrAOCK9u_EvNFT
 fractal_server/app/runner/executors/slurm/_check_jobs_status.py,sha256=8d29a7DQ2xoWxoFQCnFfTpHER-qBX8mEatl4Dw5HU_o,1908
 fractal_server/app/runner/executors/slurm/_executor_wait_thread.py,sha256=J3tjAx33nBgW4eHAXDte7hDs7Oe9FLEZaElEt8inrbg,4421
 fractal_server/app/runner/executors/slurm/_slurm_config.py,sha256=rF37XDImX1QoWx37MC5hSM9AuY_KfHU5gaWwN4vl4Zk,15552
-fractal_server/app/runner/executors/slurm/_subprocess_run_as_user.py,sha256=8CCtxWCuB5UDst3C_WJxBU77xwPrpDyq7iMCZMnodXU,5123
+fractal_server/app/runner/executors/slurm/_subprocess_run_as_user.py,sha256=YwfJzZr_y4FL_hirHJdWK0vWzrldjoZZhXVFlO2AOMU,5131
 fractal_server/app/runner/executors/slurm/executor.py,sha256=267YTDvyeA0yX2n2HffxP8OAu_CQF5uB9K-_AaUG3iU,44655
 fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77JRK82g_2hx0iBKTiMghuIo,5852
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
@@ -121,13 +121,14 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-2
 fractal_server/app/schemas/v2/workflow.py,sha256=Zzx3e-qgkH8le0FUmAx9UrV5PWd7bj14PPXUh_zgZXM,1827
 fractal_server/app/schemas/v2/workflowtask.py,sha256=atVuVN4aXsVEOmSd-vyg-8_8OnPmqx-gT75rXcn_AlQ,6552
 fractal_server/app/security/__init__.py,sha256=wxosoHc3mJYPCdPMyWnRD8w_2OgnKYp2aDkdmwrZh5k,11203
-fractal_server/config.py,sha256=lXofyyyMdRQoK39yTBUwVotRT8ptSb5LceHlZrUuK2o,15048
+fractal_server/config.py,sha256=19CnX1Jyw_zYjEvfXJTaypB7Ape7qfFzKX4B1LZmOe0,15167
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/images/__init__.py,sha256=xO6jTLE4EZKO6cTDdJsBmK9cdeh9hFTaSbSuWgQg7y4,196
 fractal_server/images/models.py,sha256=9ipU5h4N6ogBChoB-2vHoqtL0TXOHCv6kRR-fER3mkM,4167
 fractal_server/images/tools.py,sha256=gxeniYy4Z-cp_ToK2LHPJUTVVUUrdpogYdcBUvBuLiY,2209
-fractal_server/logger.py,sha256=AuCmrwIydaFWpotMTM_tGRNJbExQO5fP8Xolo82Vdbg,4178
-fractal_server/main.py,sha256=u_MngsZWI-1uKrBpNDUYXKyLgaYodyAEw2dKZrIzS_U,3381
+fractal_server/logger/__init__.py,sha256=Q_e03Lj30VWdCqGBJrKw9A2QEeDbCKC_OOkDQVW9Dyw,5132
+fractal_server/logger/gunicorn_logger.py,sha256=vb5s7mruCHPkKWGrTTOPyrB_658Y2Z05ECdHhCCBhp0,644
+fractal_server/main.py,sha256=OostfB8nyFKCySDTnIR64WlHg82eHkoykJgQg6se9xc,3556
 fractal_server/migrations/README,sha256=4rQvyDfqodGhpJw74VYijRmgFP49ji5chyEemWGHsuw,59
 fractal_server/migrations/env.py,sha256=bsl0HGZpjhommztgcs7wQ94sJzI1Orgnij97K8P_uyo,2630
 fractal_server/migrations/script.py.mako,sha256=oMXw9LC3zRbinWWPPDgeZ4z9FJrV2zhRWiYdS5YgNbI,526
@@ -162,8 +163,8 @@ fractal_server/tasks/v2/background_operations.py,sha256=MAMBn6W2bhkdK59kfUGiD7a1
 fractal_server/tasks/v2/get_collection_data.py,sha256=Qhf2T_aaqAfqu9_KpUSlXsS7EJoZQbEPEreHHa2jco8,502
 fractal_server/urls.py,sha256=5o_qq7PzKKbwq12NHSQZDmDitn5RAOeQ4xufu-2v9Zk,448
 fractal_server/utils.py,sha256=b7WwFdcFZ8unyT65mloFToYuEDXpQoHRcmRNqrhd_dQ,2115
-fractal_server-2.0.5.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.5.dist-info/METADATA,sha256=cJupXGRdWtFkGReZMLccMSwEAXunkgL2TQoZZ1pesmM,4222
-fractal_server-2.0.5.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.0.5.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.5.dist-info/RECORD,,
+fractal_server-2.0.6.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.6.dist-info/METADATA,sha256=id7WLlUPHEi6TAgIVSDxZJacFhTvriBOdX86QLLbqPM,4222
+fractal_server-2.0.6.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.0.6.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.6.dist-info/RECORD,,