fractal-server 2.0.5__tar.gz → 2.0.6__tar.gz

{fractal_server-2.0.5 → fractal_server-2.0.6}/PKG-INFO

@@ -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-2.0.6/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.0.6"

{fractal_server-2.0.5 → fractal_server-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-2.0.5 → fractal_server-2.0.6}/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-2.0.6/fractal_server/app/models/v1/__init__.py

@@ -0,0 +1,13 @@
+"""
+`models` module
+"""
+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-2.0.5 → fractal_server-2.0.6}/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-2.0.5 → fractal_server-2.0.6}/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-2.0.5 → fractal_server-2.0.6}/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-2.0.5 → fractal_server-2.0.6}/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-2.0.5 → fractal_server-2.0.6}/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-2.0.5 → fractal_server-2.0.6}/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-2.0.5/fractal_server/logger.py → fractal_server-2.0.6/fractal_server/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-2.0.6/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-2.0.5 → fractal_server-2.0.6}/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 → fractal_server-2.0.6}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.0.5"
+version = "2.0.6"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -49,16 +49,16 @@ gunicorn = ["gunicorn"]
 
 [tool.poetry.group.dev.dependencies]
 asgi-lifespan = "^2"
-pytest = "^7.2"
+pytest = "8.1.*"
 httpx = "^0.23"
 devtools = "^0.12"
 pytest-asyncio = "^0.21"
 bumpver = "^2022.1120"
 pre-commit = "^2.19"
-coverage = {extras = ["toml"], version = "^6.4.4"}
-pytest-docker = {version = "^2.0"}
+coverage = {extras = ["toml"], version = "7.5.*"}
+pytest-docker = {version = "3.1.*"}
 mypy = "^1.9"
-pytest-subprocess = "^1.4"
+pytest-subprocess = "^1.5"
 pyyaml="^6.0.1"
 a2wsgi = "^1.10.0"
 jinja2 = "^3.1.3"
@@ -87,7 +87,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.0.5"
+current_version = "2.0.6"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.0.5/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.0.5"

fractal_server-2.0.5/fractal_server/app/models/v1/__init__.py

@@ -1,12 +0,0 @@
-"""
-`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