fractal-server 2.18.0a5__py3-none-any.whl → 2.18.0a7__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.18.0a5"
+__VERSION__ = "2.18.0a7"

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

@@ -279,16 +279,6 @@ async def import_dataset(
             ),
         )
 
-    for image in dataset.images:
-        if not image.zarr_url.startswith(dataset.zarr_dir):
-            raise HTTPException(
-                status_code=status.HTTP_422_UNPROCESSABLE_CONTENT,
-                detail=(
-                    f"Cannot import dataset: zarr_url {image.zarr_url} is not "
-                    f"relative to zarr_dir={dataset.zarr_dir}."
-                ),
-            )
-
     # Create new Dataset
     db_dataset = DatasetV2(
         project_id=project_id,

fractal_server/app/schemas/v2/dataset.py

@@ -1,4 +1,5 @@
 from datetime import datetime
+from pathlib import Path
 
 from pydantic import BaseModel
 from pydantic import ConfigDict
@@ -100,6 +101,15 @@ class DatasetImport(BaseModel):
     zarr_dir: ZarrDirStr
     images: list[SingleImage] = Field(default_factory=list)
 
+    @model_validator(mode="after")
+    def validate_image_zarr_url(self):
+        for image in self.images:
+            if not Path(image.zarr_url).is_relative_to(self.zarr_dir):
+                raise ValueError(
+                    f"{image.zarr_url=} is not relative to {self.zarr_dir=}."
+                )
+        return self
+
 
 class DatasetExport(BaseModel):
     """

fractal_server/images/models.py

@@ -5,7 +5,6 @@ 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
 
 
@@ -21,7 +20,7 @@ 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)

fractal_server/main.py

@@ -135,14 +135,25 @@ async def lifespan(app: FastAPI):
 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):
-        # Filter out any non-http scope (e.g. `type="lifespan"`)
-        if scope["type"] != "http":
+        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
 

fractal_server/runner/config/_slurm.py

@@ -34,6 +34,10 @@ class SlurmConfigSet(BaseModel):
         account:
         extra_lines:
         gpus:
+        sleep_after_srun:
+            Add a `sleep` command in the SLURM submission script, after the
+            `srun .. &` lines, and before the `wait` one. This may mitigate
+            an issue observed on SLURM 25.05.4.
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -49,6 +53,7 @@ class SlurmConfigSet(BaseModel):
     account: NonEmptyStr | None = None
     extra_lines: list[NonEmptyStr] = Field(default_factory=list)
     gpus: NonEmptyStr | None = None
+    sleep_after_srun: int = 0
 
 
 class BatchingConfigSet(BaseModel):

fractal_server/runner/executors/slurm_common/base_slurm_runner.py

@@ -396,6 +396,8 @@ class BaseSlurmRunner(BaseRunner):
                 f"--mem={mem_per_task_MB}MB "
                 f"{cmd} &"
             )
+        if slurm_config.sleep_after_srun > 0:
+            script_lines.append(f"sleep {slurm_config.sleep_after_srun}\n")
         script_lines.append("wait\n\n")
         script_lines.append('echo "End time:   $(date +"%Y-%m-%dT%H:%M:%S%z")"')
         script = "\n".join(script_lines)

fractal_server/runner/executors/slurm_common/slurm_config.py

@@ -60,6 +60,10 @@ class SlurmConfig(BaseModel):
             Key-value pairs to be included as `export`-ed variables in SLURM
             submission script, after prepending values with the user's cache
             directory.
+        sleep_after_srun:
+            Add a `sleep` command in the SLURM submission script, after the
+            `srun .. &` lines, and before the `wait` one. This may mitigate
+            an issue observed on SLURM 25.05.4.
     """
 
     model_config = ConfigDict(extra="forbid")
@@ -99,6 +103,8 @@ class SlurmConfig(BaseModel):
     target_num_jobs: int
     max_num_jobs: int
 
+    sleep_after_srun: int = 0
+
     def _sorted_extra_lines(self) -> list[str]:
         """
         Return a copy of `self.extra_lines`, where lines starting with

{fractal_server-2.18.0a5.dist-info → fractal_server-2.18.0a7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: fractal-server
-Version: 2.18.0a5
+Version: 2.18.0a7
 Summary: Backend component of the Fractal analytics platform
 License-Expression: BSD-3-Clause
 License-File: LICENSE

{fractal_server-2.18.0a5.dist-info → fractal_server-2.18.0a7.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=JtUJqLV8j7pkQCJbYQv055n1eaT2cMBaPTLFzh3MTnU,25
+fractal_server/__init__.py,sha256=DuwF9p41_x2O2lnB3pphTsGrOZmbrzmtU02F_hsYOHo,25
 fractal_server/__main__.py,sha256=QeKoAgqoiozLJDa8kSVe-Aso1WWgrk1yLUYWS8RxZVM,11405
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -41,7 +41,7 @@ fractal_server/app/routes/api/v2/_aux_functions_task_lifecycle.py,sha256=qTJdKC3
 fractal_server/app/routes/api/v2/_aux_functions_task_version_update.py,sha256=PKjV7r8YsPRXoNiVSnOK4KBYVV3l_Yb_ZPrqAkMkXrQ,1182
 fractal_server/app/routes/api/v2/_aux_functions_tasks.py,sha256=Hrumknv0vH5VX7SFp8WZDzsJv_z7quvFyNoDYmYoD7A,13623
 fractal_server/app/routes/api/v2/_aux_task_group_disambiguation.py,sha256=vdvMTa3San1HMTzctN5Vk7zxpqe4ccByrFBQyHfgWW8,4889
-fractal_server/app/routes/api/v2/dataset.py,sha256=mM5jH9Ta06mHvgPfKl76kRwzd7e3_HO1lQ8PJkFwEqQ,8911
+fractal_server/app/routes/api/v2/dataset.py,sha256=HZGJezPqzbU1PYlFZfQSOj-ONmhtitCv6I7SDORGiPg,8515
 fractal_server/app/routes/api/v2/history.py,sha256=5IYb6m6vmXjNU7uatEmgdXhehyKdbK98T5wAjQpNH4g,18266
 fractal_server/app/routes/api/v2/images.py,sha256=k9wd44iwjCtEWSH9j6X6zToBwuOOo6J4FxSW7AGbPHA,8266
 fractal_server/app/routes/api/v2/job.py,sha256=05_uzX11wYWpGZLN159-7CFXGB9gnSDYdeLEvDAefpY,7250
@@ -80,7 +80,7 @@ fractal_server/app/schemas/user.py,sha256=qixLVZWeANxX5TIWoruLjYE_oh4DMZ2q3vMgMB
 fractal_server/app/schemas/user_group.py,sha256=irel29GbffKCXNcyrAYbNSN3pCgmoUQ1wG32_s6jvos,1082
 fractal_server/app/schemas/v2/__init__.py,sha256=6W1uSthuLGXs9oOYnjmScoqJYkWyUTT-9cNHFZoTmkM,4005
 fractal_server/app/schemas/v2/accounting.py,sha256=6EVUdPTkFY6Wb9-Vc0cIEZYVXwGEvJ3tP4YOXYE1hao,546
-fractal_server/app/schemas/v2/dataset.py,sha256=T1FkA66qvASds0DBWyxnc0rlmu7xS3qlsUzdhwTp-ag,2381
+fractal_server/app/schemas/v2/dataset.py,sha256=SBS3TwHxPRHtLvFu-Bm4eQlI96DIkCiFF7oKvfcfTOc,2736
 fractal_server/app/schemas/v2/dumps.py,sha256=UPtb1Rqkd48AFpWsVfcHcAjKGzF2ZoHLdYrAJzPdsSM,2276
 fractal_server/app/schemas/v2/history.py,sha256=pZiMKfh6nMWbTp5MUtrnGySPKbeRFf5tM1VLFaTgGcw,1784
 fractal_server/app/schemas/v2/job.py,sha256=YnnxnrbI_l7EgZNzk_KgnuEuh0COg-RPoph2foHUvZo,3308
@@ -111,11 +111,11 @@ fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyM
 fractal_server/exceptions.py,sha256=l6aZDk_6u_9PwDaQSoIFdI40ekpzqOJaxjx5rhW-HVI,141
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
 fractal_server/images/__init__.py,sha256=-_wjoKtSX02P1KjDxDP_EXKvmbONTRmbf7iGVTsyBpM,154
-fractal_server/images/models.py,sha256=dNcCW7XzRRbqL86LJ5aGc6LUAqIPsZXMq67IZyGbIpQ,1242
+fractal_server/images/models.py,sha256=5wtUmX3hRy8vyOb4SgezuIWcwUaB69HyXHg4zFMJkvk,1198
 fractal_server/images/status_tools.py,sha256=Is2QWThbLCrVJuI0NpGv7TcWs1T8z8q_8Qsidr3TdBU,4932
 fractal_server/images/tools.py,sha256=37jVIU6RiAGbiyucNDlKe9J3yN3Y47NOvv-RJor9Jm0,4154
 fractal_server/logger.py,sha256=9EhRdgPnGdbJ51vxhOD42K0iaDRhKx7wuikpHoh9kzY,5302
-fractal_server/main.py,sha256=ksCV8BCyxQnvF26IYSzwQFZNo74J4cBNkNzqgq6mdeE,6181
+fractal_server/main.py,sha256=vCDvUndmLIkxUX8EAtyA4Wu9YiIHGZge5J37Yn2U5R4,6537
 fractal_server/migrations/env.py,sha256=nfyBpMIOT3kny6t-b-tUjyRjZ4k906bb1_wCQ7me1BI,1353
 fractal_server/migrations/naming_convention.py,sha256=bSEMiMZeArmWKrUk-12lhnOw1pAFMg6LEl7yucohPqc,263
 fractal_server/migrations/versions/034a469ec2eb_task_groups.py,sha256=uuf0sJibC4Am1HDb_dX_Jdj2oinptlg2ojiHwCpjDCY,6155
@@ -177,7 +177,7 @@ fractal_server/runner/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3h
 fractal_server/runner/components.py,sha256=-Ii5l8d_V6f5DFOd-Zsr8VYmOsyqw0Hox9fEFQiuqxY,66
 fractal_server/runner/config/__init__.py,sha256=a-vSrvWBeMVnxTtYoy-f5Ibt_mM8MM3F7jqnPvvjHSY,108
 fractal_server/runner/config/_local.py,sha256=IHWtxpKuJDdsQNpk8Q5bNL4DEJunNkNJkLfetfnwmQM,788
-fractal_server/runner/config/_slurm.py,sha256=iC4gBolGaYD8SX5FMZu7mq9xI6-kepzeZ6bETrFf0pg,3636
+fractal_server/runner/config/_slurm.py,sha256=FtWQi74e_9nolpKF07zMsOr3R1_yZKqNhC_cIo9MTUk,3892
 fractal_server/runner/config/slurm_mem_to_MB.py,sha256=6KmrIC-NymQjb9-bIQjNYQx6mE0OoKoZxdi6WQnWOHw,2003
 fractal_server/runner/exceptions.py,sha256=N8DLn7tuV8zMSdr8xdJN0aIdytPveSCeQ1Y5IoxXW-8,1778
 fractal_server/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -189,10 +189,10 @@ fractal_server/runner/executors/local/runner.py,sha256=0s0u5ONasXdsvS2WD5zxksQgv
 fractal_server/runner/executors/slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/runner/executors/slurm_common/_batching.py,sha256=YQjWRTDI1e6NeLe1R-1QWlt49i42M9ILeExEjdjgy48,8348
 fractal_server/runner/executors/slurm_common/_job_states.py,sha256=nuV-Zba38kDrRESOVB3gaGbrSPZc4q7YGichQaeqTW0,238
-fractal_server/runner/executors/slurm_common/base_slurm_runner.py,sha256=pU2Szcg3tv7vinLJXbzSgYlfEPLY_b0R0YDR-FSYLc8,41873
+fractal_server/runner/executors/slurm_common/base_slurm_runner.py,sha256=vHm5wjZ-VkRUuVIhbrpUJqtpxOZDlFHwTT0OmTv3CAw,41995
 fractal_server/runner/executors/slurm_common/get_slurm_config.py,sha256=B6EKjob8Y-DiJ8YbXf2CeoY7B8cwvkpKvlW8Ce6bbx0,7115
 fractal_server/runner/executors/slurm_common/remote.py,sha256=8pTMTRp_LjzoUr3FtFTfdvDhuLnqzY6HT-T9pzrVLw4,3845
-fractal_server/runner/executors/slurm_common/slurm_config.py,sha256=VSow-JfxBkdmkMnTBeZ01nnMXXtlqV8ysaSYcdE-_PU,7896
+fractal_server/runner/executors/slurm_common/slurm_config.py,sha256=rF-9Q1gWDBqtNbs9hji6oTvIQ2uV36FqCc04DdAqtHA,8153
 fractal_server/runner/executors/slurm_common/slurm_job_task_models.py,sha256=VeX40CvU5fckUpSyXlzb3EDE9xxPXkT2sZKLXq_6Ooc,3493
 fractal_server/runner/executors/slurm_ssh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/runner/executors/slurm_ssh/run_subprocess.py,sha256=SyW6t4egvbiARph2YkFjc88Hj94fCamZVi50L7ph8VM,996
@@ -268,8 +268,8 @@ fractal_server/types/validators/_workflow_task_arguments_validators.py,sha256=zt
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=-rjg8QTXQcKweXjn0NcmETFs1_uM9PGnbl0Q7c4ERPM,2181
 fractal_server/zip_tools.py,sha256=Uhn-ax4_9g1PJ32BdyaX30hFpAeVOv2tZYTUK-zVn1E,5719
-fractal_server-2.18.0a5.dist-info/METADATA,sha256=ifDV_PyTlPG8dTwRyUcr7fHpCcDvCEFlGUlCMujQB2s,4277
-fractal_server-2.18.0a5.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-fractal_server-2.18.0a5.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.18.0a5.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.18.0a5.dist-info/RECORD,,
+fractal_server-2.18.0a7.dist-info/METADATA,sha256=8gfu8aos4ki_fVT2imS8dopTKPdsTnGzSQa0ah-kU1o,4277
+fractal_server-2.18.0a7.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
+fractal_server-2.18.0a7.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.18.0a7.dist-info/licenses/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.18.0a7.dist-info/RECORD,,