fractal-server 2.0.6__py3-none-any.whl → 2.1.0__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.6"
+__VERSION__ = "2.1.0"

fractal_server/app/routes/api/v2/submit.py

@@ -195,21 +195,16 @@ async def apply_workflow(
 
     # Define server-side job directory
     timestamp_string = get_timestamp().strftime("%Y%m%d_%H%M%S")
-    WORKFLOW_DIR = (
-        settings.FRACTAL_RUNNER_WORKING_BASE_DIR
-        / (
-            f"proj_v2_{project_id:07d}_wf_{workflow_id:07d}_job_{job.id:07d}"
-            f"_{timestamp_string}"
-        )
-    ).resolve()
+    WORKFLOW_DIR = settings.FRACTAL_RUNNER_WORKING_BASE_DIR / (
+        f"proj_v2_{project_id:07d}_wf_{workflow_id:07d}_job_{job.id:07d}"
+        f"_{timestamp_string}"
+    )
 
     # Define user-side job directory
     if FRACTAL_RUNNER_BACKEND == "local":
         WORKFLOW_DIR_USER = WORKFLOW_DIR
     elif FRACTAL_RUNNER_BACKEND == "slurm":
-        WORKFLOW_DIR_USER = (
-            Path(user.cache_dir) / f"{WORKFLOW_DIR.name}"
-        ).resolve()
+        WORKFLOW_DIR_USER = Path(user.cache_dir) / f"{WORKFLOW_DIR.name}"
 
     # Update job folders in the db
     job.working_dir = WORKFLOW_DIR.as_posix()

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

@@ -1188,3 +1188,15 @@ class FractalSlurmExecutor(SlurmExecutor):
                 raise JobExecutionError(info=error_msg)
 
         logger.debug("Executor shutdown: end")
+
+    def __exit__(self, *args, **kwargs):
+        """
+        See
+        https://github.com/fractal-analytics-platform/fractal-server/issues/1508
+        """
+        logger.debug(
+            "[FractalSlurmExecutor.__exit__] Stop and join `wait_thread`"
+        )
+        self.wait_thread.stop()
+        self.wait_thread.join()
+        logger.debug("[FractalSlurmExecutor.__exit__] End")

fractal_server/app/runner/v1/__init__.py

@@ -137,13 +137,10 @@ async def submit_workflow(
         # Define and create server-side working folder
         project_id = workflow.project_id
         timestamp_string = get_timestamp().strftime("%Y%m%d_%H%M%S")
-        WORKFLOW_DIR = (
-            settings.FRACTAL_RUNNER_WORKING_BASE_DIR
-            / (
-                f"proj_{project_id:07d}_wf_{workflow_id:07d}_job_{job_id:07d}"
-                f"_{timestamp_string}"
-            )
-        ).resolve()
+        WORKFLOW_DIR = settings.FRACTAL_RUNNER_WORKING_BASE_DIR / (
+            f"proj_{project_id:07d}_wf_{workflow_id:07d}_job_{job_id:07d}"
+            f"_{timestamp_string}"
+        )
 
         if WORKFLOW_DIR.exists():
             raise RuntimeError(f"Workflow dir {WORKFLOW_DIR} already exists.")
@@ -162,9 +159,7 @@ async def submit_workflow(
                 _mkdir_as_user,
             )
 
-            WORKFLOW_DIR_USER = (
-                Path(user_cache_dir) / f"{WORKFLOW_DIR.name}"
-            ).resolve()
+            WORKFLOW_DIR_USER = Path(user_cache_dir) / f"{WORKFLOW_DIR.name}"
             _mkdir_as_user(folder=str(WORKFLOW_DIR_USER), user=slurm_user)
         else:
             raise ValueError(f"{FRACTAL_RUNNER_BACKEND=} not supported")

fractal_server/app/security/__init__.py

@@ -57,9 +57,8 @@ from sqlmodel import select
 from ...config import get_settings
 from ...syringe import Inject
 from ..db import get_async_db
-from ..models.security import OAuthAccount
-from ..models.security import UserOAuth as User
-from fractal_server.app.models.security import UserOAuth
+from fractal_server.app.models.security import OAuthAccount
+from fractal_server.app.models.security import UserOAuth as User
 from fractal_server.app.schemas.user import UserCreate
 from fractal_server.logger import get_logger
 
@@ -287,8 +286,8 @@ async def _create_first_user(
 
             if is_superuser is True:
                 # If a superuser already exists, exit
-                stm = select(UserOAuth).where(
-                    UserOAuth.is_superuser == True  # noqa: E712
+                stm = select(User).where(
+                    User.is_superuser == True  # noqa E712
                 )
                 res = await session.execute(stm)
                 existing_superuser = res.scalars().first()

fractal_server/config.py

@@ -289,6 +289,27 @@ class Settings(BaseSettings):
             )
         return FRACTAL_TASKS_DIR_path
 
+    @validator("FRACTAL_RUNNER_WORKING_BASE_DIR", always=True)
+    def make_FRACTAL_RUNNER_WORKING_BASE_DIR_absolute(cls, v):
+        """
+        (Copy of make_FRACTAL_TASKS_DIR_absolute)
+        If `FRACTAL_RUNNER_WORKING_BASE_DIR` is a non-absolute path,
+        make it absolute (based on the current working directory).
+        """
+        if v is None:
+            return None
+        FRACTAL_RUNNER_WORKING_BASE_DIR_path = Path(v)
+        if not FRACTAL_RUNNER_WORKING_BASE_DIR_path.is_absolute():
+            FRACTAL_RUNNER_WORKING_BASE_DIR_path = (
+                FRACTAL_RUNNER_WORKING_BASE_DIR_path.resolve()
+            )
+            logging.warning(
+                f'FRACTAL_RUNNER_WORKING_BASE_DIR="{v}" is not an absolute '
+                "path; converting it to "
+                f'"{str(FRACTAL_RUNNER_WORKING_BASE_DIR_path)}"'
+            )
+        return FRACTAL_RUNNER_WORKING_BASE_DIR_path
+
     FRACTAL_RUNNER_BACKEND: Literal["local", "slurm"] = "local"
     """
     Select which runner backend to use.

fractal_server/main.py

@@ -15,6 +15,8 @@
 
 This module sets up the FastAPI application that serves the Fractal Server.
 """
+from contextlib import asynccontextmanager
+
 from fastapi import FastAPI
 
 from .app.security import _create_first_user
@@ -77,15 +79,27 @@ def check_settings() -> None:
     reset_logger_handlers(logger)
 
 
-async def __on_startup() -> None:
-    """
-    Private wrapper for routines that need to be executed at server start-up.
-
-    It should only be called from a `@app.on_event("startup")`-decorated
-    callable.
-    """
+@asynccontextmanager
+async def lifespan(app: FastAPI):
+    logger = set_logger("fractal_server.lifespan")
+    logger.info("Start application startup")
     check_settings()
+    settings = Inject(get_settings)
+    await _create_first_user(
+        email=settings.FRACTAL_DEFAULT_ADMIN_EMAIL,
+        password=settings.FRACTAL_DEFAULT_ADMIN_PASSWORD,
+        username=settings.FRACTAL_DEFAULT_ADMIN_USERNAME,
+        is_superuser=True,
+        is_verified=True,
+    )
     config_uvicorn_loggers()
+    logger.info("End application startup")
+    reset_logger_handlers(logger)
+    yield
+    logger = set_logger("fractal_server.lifespan")
+    logger.info("Start application shutdown")
+    logger.info("End application shutdown")
+    reset_logger_handlers(logger)
 
 
 def start_application() -> FastAPI:
@@ -96,27 +110,9 @@ def start_application() -> FastAPI:
         app:
             The fully initialised application.
     """
-    app = FastAPI()
+    app = FastAPI(lifespan=lifespan)
     collect_routers(app)
     return app
 
 
 app = start_application()
-
-
-@app.on_event("startup")
-async def on_startup() -> None:
-    """
-    Register the starup calls
-
-    If the calls raise any error, the application startup is aborted.
-    """
-    settings = Inject(get_settings)
-    await _create_first_user(
-        email=settings.FRACTAL_DEFAULT_ADMIN_EMAIL,
-        password=settings.FRACTAL_DEFAULT_ADMIN_PASSWORD,
-        username=settings.FRACTAL_DEFAULT_ADMIN_USERNAME,
-        is_superuser=True,
-        is_verified=True,
-    )
-    await __on_startup()

{fractal_server-2.0.6.dist-info → fractal_server-2.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.6
+Version: 2.1.0
 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.dist-info → fractal_server-2.1.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=S5hrGn9zHoCPoN-w6jqLkqipFDSl7JkGHq3amd7eoVE,22
+fractal_server/__init__.py,sha256=M-UCl3baEQIODOL7Zae_0jXfPyeyyPZypKzTHK83oM0,22
 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
@@ -42,7 +42,7 @@ fractal_server/app/routes/api/v2/images.py,sha256=4r_HblPWyuKSZSJZfn8mbDaLv1ncwZ
 fractal_server/app/routes/api/v2/job.py,sha256=BtaxErBDbLwjY2zgGD1I6eRpsffoMonifcS1CMEXmLU,5325
 fractal_server/app/routes/api/v2/project.py,sha256=qyvizYZ4aUFgF3tGdfp4z8AwWgfo19N_KbFEljfUaC8,5594
 fractal_server/app/routes/api/v2/status.py,sha256=osLexiMOSqmYcEV-41tlrwt9ofyFbtRm5HmPS5BU0t4,6394
-fractal_server/app/routes/api/v2/submit.py,sha256=su512HjafuD_lyiLswyxN4T8xwKaMpWOhGsYVPh94sI,7672
+fractal_server/app/routes/api/v2/submit.py,sha256=mdY1fN9VA8-8DkqeAGrzHa4n37QSPP-gN3sc4z-c-wc,7592
 fractal_server/app/routes/api/v2/task.py,sha256=bRTtGgL8BBGbT7csVeRB-a54clgU2xHydi5XpcByDxg,8297
 fractal_server/app/routes/api/v2/task_collection.py,sha256=eN3NkZaZHkrqnLGRKE7Xd5mo0cHc8aK2lojCt26ErOQ,8988
 fractal_server/app/routes/api/v2/task_legacy.py,sha256=P_VJv9v0yzFUBuS-DQHhMVSOe20ecGJJcFBqiiFciOM,1628
@@ -64,12 +64,12 @@ fractal_server/app/runner/executors/slurm/_check_jobs_status.py,sha256=8d29a7DQ2
 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=YwfJzZr_y4FL_hirHJdWK0vWzrldjoZZhXVFlO2AOMU,5131
-fractal_server/app/runner/executors/slurm/executor.py,sha256=267YTDvyeA0yX2n2HffxP8OAu_CQF5uB9K-_AaUG3iU,44655
+fractal_server/app/runner/executors/slurm/executor.py,sha256=z2MbI9He1lPhKBPMs0pqoQ9wUiAsxOIZY62s5VFHs-0,45044
 fractal_server/app/runner/executors/slurm/remote.py,sha256=wLziIsGdSMiO-jIXM8x77JRK82g_2hx0iBKTiMghuIo,5852
 fractal_server/app/runner/filenames.py,sha256=9lwu3yB4C67yiijYw8XIKaLFn3mJUt6_TCyVFM_aZUQ,206
 fractal_server/app/runner/set_start_and_last_task_index.py,sha256=-q4zVybAj8ek2XlbENKlfOAJ39hT_zoJoZkqzDqiAMY,1254
 fractal_server/app/runner/task_files.py,sha256=b5aRDi35QemBQnHT_AU6L_IPJJU_k_f5sJn-JXzkzy0,3180
-fractal_server/app/runner/v1/__init__.py,sha256=Uqf9smd4G9JCunXOsJ0U_DJyhYvl8TwItY3TbDLBLMc,13620
+fractal_server/app/runner/v1/__init__.py,sha256=kMiQJJ-XUp2ecI0tUAUYD_Em1vcct9iXULMoI5SGdU4,13520
 fractal_server/app/runner/v1/_common.py,sha256=2-NScI-7qCIw14Od90so1onw-psIt8x1kx6EXq489Vk,21246
 fractal_server/app/runner/v1/_local/__init__.py,sha256=ZcWftuGRLmN8-S6QZXm6FhNehsxwmwZRhuRv-a7zA6s,6839
 fractal_server/app/runner/v1/_local/_local_config.py,sha256=hM7SPxR07luXPcXdrWXRpEB2uOyjSSRUdqW3QBKJn9c,3147
@@ -120,15 +120,15 @@ fractal_server/app/schemas/v2/task.py,sha256=7IfxiZkaVqlARy7WYE_H8m7j_IEcuQaZORU
 fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-20wIsmh7G1QOdr05KoDQ,3171
 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=19CnX1Jyw_zYjEvfXJTaypB7Ape7qfFzKX4B1LZmOe0,15167
+fractal_server/app/security/__init__.py,sha256=2-QbwuR-nsuHM_uwKS_WzYvkhnuhO5jUv8UVROetyVk,11169
+fractal_server/config.py,sha256=7fF_lTGH_mH_16aYr8m3E5Dv81jH9wdJuGu-2p1x9H0,16081
 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/__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/main.py,sha256=faQfINM4k3G7Oakkn8R_EfHLma6Dd-U_TeyWesjs0js,3613
 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
@@ -163,8 +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-2.0.6.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,,
+fractal_server-2.1.0.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.1.0.dist-info/METADATA,sha256=kyfeNStKB16vegug3_OV6wxtnxDT1Mo1pqj5HKKXG1w,4222
+fractal_server-2.1.0.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.1.0.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.1.0.dist-info/RECORD,,