fractal-server 2.14.0a27__py3-none-any.whl → 2.14.0a28__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.14.0a27"
+__VERSION__ = "2.14.0a28"

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

@@ -42,7 +42,7 @@ async def verify_unique_types(
             type_filters=query.type_filters,
         )
 
-    # Get all available types (#FIXME use aux function)
+    # NOTE: see issue 2486
     available_types = set(
         _type for _img in filtered_images for _type in _img["types"].keys()
     )

fractal_server/app/runner/executors/local/runner.py

@@ -25,7 +25,6 @@ class LocalRunner(BaseRunner):
         self,
         root_dir_local: Path,
     ):
-
         self.root_dir_local = root_dir_local
         self.root_dir_local.mkdir(parents=True, exist_ok=True)
         self.executor = ThreadPoolExecutor()
@@ -182,10 +181,6 @@ class LocalRunner(BaseRunner):
                                     db_sync=db,
                                 )
 
-                            # FIXME: what should happen here? Option 1: stop
-                            # all existing tasks and shutdown runner (for the
-                            # compound-task case)
-
-        logger.debug(f"[multisubmit] END, {results=}, {exceptions=}")
+        logger.debug(f"[multisubmit] END, {len(results)=}, {len(exceptions)=}")
 
         return results, exceptions

fractal_server/app/runner/executors/slurm_common/_slurm_config.py

@@ -368,9 +368,7 @@ class SlurmConfig(BaseModel):
             if value is not None:
                 # Handle the `time` parameter
                 if key == "time" and self.parallel_tasks_per_job > 1:
-                    # FIXME SSH: time setting must be handled better. Right now
-                    # we simply propagate `time`, but this is not enough when
-                    # several `srun` are combined in a single script.
+                    # NOTE: see issue #1632
                     logger.warning(
                         f"`time` SLURM parameter is set to {self.time}, "
                         "but this does not take into account the number of "

fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py

@@ -34,7 +34,7 @@ SHUTDOWN_EXCEPTION = JobExecutionError(SHUTDOWN_ERROR_MESSAGE)
 
 logger = set_logger(__name__)
 
-# FIXME: Transform several logger.info into logger.debug.
+# NOTE: see issue 2481.
 
 
 class BaseSlurmRunner(BaseRunner):
@@ -107,8 +107,7 @@ class BaseSlurmRunner(BaseRunner):
         raise NotImplementedError("Implement in child class.")
 
     def run_squeue(self, job_ids: list[str]) -> tuple[bool, str]:
-
-        # FIXME: review different cases (exception vs no job found)
+        # NOTE: see issue 2482
 
         if len(job_ids) == 0:
             return (False, "")
@@ -457,7 +456,6 @@ class BaseSlurmRunner(BaseRunner):
             "converter_compound",
         ],
     ) -> tuple[Any, Exception]:
-
         logger.info("[submit] START")
 
         workdir_local = task_files.wftask_subfolder_local
@@ -514,7 +512,7 @@ class BaseSlurmRunner(BaseRunner):
         )
         logger.info(f"[submit] END submission phase, {self.job_ids=}")
 
-        # FIXME: replace this sleep with a more precise check
+        # NOTE: see issue 2444
         settings = Inject(get_settings)
         sleep_time = settings.FRACTAL_SLURM_INTERVAL_BEFORE_RETRIEVAL
         logger.warning(f"[submit] Now sleep {sleep_time} seconds.")
@@ -524,7 +522,6 @@ class BaseSlurmRunner(BaseRunner):
         logger.info("[submit] START retrieval phase")
         scancelled_job_ids = []
         while len(self.jobs) > 0:
-
             # Look for finished jobs
             finished_job_ids = self._get_finished_jobs(job_ids=self.job_ids)
             logger.debug(f"[submit] {finished_job_ids=}")
@@ -664,9 +661,7 @@ class BaseSlurmRunner(BaseRunner):
                 )
             )
 
-        # FIXME: split parts 2 and 3
-        # Part 2/3. Transfer all relevant input files (for SSH)
-        # Part 3/3. Run all `sbatch`es and update `self.jobs`
+        # NOTE: see issue 2431
         logger.info("[multisubmit] Transfer files and submit jobs.")
         for slurm_job in jobs_to_submit:
             self._submit_single_sbatch(
@@ -677,19 +672,15 @@ class BaseSlurmRunner(BaseRunner):
 
         logger.info(f"END submission phase, {self.job_ids=}")
 
-        # FIXME: replace this sleep with a more precise check
         settings = Inject(get_settings)
         sleep_time = settings.FRACTAL_SLURM_INTERVAL_BEFORE_RETRIEVAL
         logger.warning(f"[submit] Now sleep {sleep_time} seconds.")
         time.sleep(sleep_time)
 
-        # FIXME: Could we merge the submit/multisubmit retrieval phases?
-
         # Retrieval phase
         logger.info("[multisubmit] START retrieval phase")
         scancelled_job_ids = []
         while len(self.jobs) > 0:
-
             # Look for finished jobs
             finished_job_ids = self._get_finished_jobs(job_ids=self.job_ids)
             logger.debug(f"[multisubmit] {finished_job_ids=}")

fractal_server/app/runner/executors/slurm_ssh/runner.py

@@ -90,7 +90,7 @@ class SlurmSSHRunner(BaseSlurmRunner):
         ).as_posix()
 
         # Create file list
-        # # FIXME can we make this more efficient with iterators?
+        # NOTE: see issue 2483
         filelist = []
         for _slurm_job in finished_slurm_jobs:
             _single_job_filelist = [
@@ -168,7 +168,6 @@ class SlurmSSHRunner(BaseSlurmRunner):
         Transfer the jobs subfolder to the remote host.
         """
         for job in jobs:
-
             # Create local archive
             tarfile_path_local = compress_folder(
                 job.workdir_local,

fractal_server/app/runner/v2/db_tools.py

@@ -77,7 +77,7 @@ def bulk_upsert_image_cache_fast(
     See docs at
     https://docs.sqlalchemy.org/en/20/dialects/postgresql.html#insert-on-conflict-upsert
 
-    FIXME: we tried to replace `index_elements` with
+    NOTE: we tried to replace `index_elements` with
     `constraint="pk_historyimagecache"`, but it did not work as expected.
 
     Arguments:

fractal_server/app/runner/v2/runner_functions.py

@@ -50,6 +50,7 @@ class SubmissionOutcome(BaseModel):
     model_config = ConfigDict(arbitrary_types_allowed=True)
     task_output: TaskOutput | None = None
     exception: BaseException | None = None
+    invalid_output: bool = False
 
 
 class InitSubmissionOutcome(BaseModel):
@@ -66,6 +67,7 @@ def _process_task_output(
     result: dict[str, Any] | None = None,
     exception: BaseException | None = None,
 ) -> SubmissionOutcome:
+    invalid_output = False
     if exception is not None:
         task_output = None
     else:
@@ -75,13 +77,13 @@ def _process_task_output(
             try:
                 task_output = _cast_and_validate_TaskOutput(result)
             except TaskOutputValidationError as e:
-                # FIXME: This should correspond to some status="failed",
-                # but it does not
                 task_output = None
                 exception = e
+                invalid_output = True
     return SubmissionOutcome(
         task_output=task_output,
         exception=exception,
+        invalid_output=invalid_output,
     )
 
 
@@ -99,8 +101,6 @@ def _process_init_task_output(
             try:
                 task_output = _cast_and_validate_InitTaskOutput(result)
             except TaskOutputValidationError as e:
-                # FIXME: This should correspond to some status="failed",
-                # but it does not
                 task_output = None
                 exception = e
     return InitSubmissionOutcome(
@@ -225,6 +225,13 @@ def run_v2_task_non_parallel(
             exception=exception,
         )
     }
+    if outcome[0].invalid_output:
+        with next(get_sync_db()) as db:
+            update_status_of_history_unit(
+                history_unit_id=history_unit_id,
+                status=HistoryUnitStatus.FAILED,
+                db_sync=db,
+            )
     return outcome, num_tasks
 
 
@@ -331,7 +338,6 @@ def run_v2_task_parallel(
     outcome = {}
     for ind in range(len(list_function_kwargs)):
         if ind not in results.keys() and ind not in exceptions.keys():
-            # FIXME: Could we avoid this branch?
             error_msg = (
                 f"Invalid branch: {ind=} is not in `results.keys()` "
                 "nor in `exceptions.keys()`."
@@ -342,7 +348,13 @@ def run_v2_task_parallel(
             result=results.get(ind, None),
             exception=exceptions.get(ind, None),
         )
-
+        if outcome[ind].invalid_output:
+            with next(get_sync_db()) as db:
+                update_status_of_history_unit(
+                    history_unit_id=history_unit_ids[ind],
+                    status=HistoryUnitStatus.FAILED,
+                    db_sync=db,
+                )
     num_tasks = len(images)
     return outcome, num_tasks
 
@@ -545,7 +557,7 @@ def run_v2_task_compound(
     failure = False
     for ind in range(len(list_function_kwargs)):
         if ind not in results.keys() and ind not in exceptions.keys():
-            # FIXME: Could we avoid this branch?
+            # NOTE: see issue 2484
             error_msg = (
                 f"Invalid branch: {ind=} is not in `results.keys()` "
                 "nor in `exceptions.keys()`."
@@ -556,7 +568,7 @@ def run_v2_task_compound(
             result=results.get(ind, None),
             exception=exceptions.get(ind, None),
         )
-        if compute_outcomes[ind].exception is not None:
+        if compute_outcomes[ind].invalid_output:
             failure = True
 
     # NOTE: For compound tasks, we update `HistoryUnit.status` from here,

fractal_server/app/runner/v2/runner_functions_low_level.py

@@ -84,13 +84,12 @@ def run_single_task(
     logger.debug(f"Now start running {command=}")
 
     # Write arguments to args.json file
-    # FIXME: this could be done backend-side, with an additional
-    # file transfer if needed (e.g. on SSH)
+    # NOTE: see issue 2346
     with open(args_file_remote, "w") as f:
         json.dump(parameters, f, indent=2)
 
     # Assemble full command
-    # FIXME: this could be assembled backend-side
+    # NOTE: this could be assembled backend-side
     full_command = (
         f"{command} "
         f"--args-json {args_file_remote} "

fractal_server/config.py

@@ -494,7 +494,7 @@ class Settings(BaseSettings):
 
     FRACTAL_SLURM_INTERVAL_BEFORE_RETRIEVAL: int = 2
     """
-    FIXME: this is a workaround, we are still investigating.
+    NOTE: see issue 2444
     """
 
     FRACTAL_SLURM_SBATCH_SLEEP: float = 0

{fractal_server-2.14.0a27.dist-info → fractal_server-2.14.0a28.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.0a27
+Version: 2.14.0a28
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

{fractal_server-2.14.0a27.dist-info → fractal_server-2.14.0a28.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=CloicZW6sLyhonlS5tDSm-UfO9_zirGQq16Kn8P5ek0,26
+fractal_server/__init__.py,sha256=7UElp_oL26Xzwy0fazO-_dZcH0gdX29TdHAqVARp7O8,26
 fractal_server/__main__.py,sha256=rkM8xjY1KeS3l63irB8yCrlVobR-73uDapC4wvrIlxI,6957
 fractal_server/alembic.ini,sha256=MWwi7GzjzawI9cCAK1LW7NxIBQDUqD12-ptJoq5JpP0,3153
 fractal_server/app/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -47,7 +47,7 @@ fractal_server/app/routes/api/v2/task_collection.py,sha256=IDNF6sjDuU37HIQ0TuQA-
 fractal_server/app/routes/api/v2/task_collection_custom.py,sha256=totsl0DOC2DFLw8vgqOFivvftpEk3KbFDeOHT0UVQUs,5997
 fractal_server/app/routes/api/v2/task_group.py,sha256=62zcVTdheXM5V3WmFuqisIqgETjXmZaRpNMcDX5bXS0,7408
 fractal_server/app/routes/api/v2/task_group_lifecycle.py,sha256=3o9bCC8ubMwffQPPaxQZy-CjH9IB2RkIReIecI6L2_w,9300
-fractal_server/app/routes/api/v2/verify_image_types.py,sha256=IOB96X3_FYBd9L_QiyVSEoV13ZP7YGS4WlBIDA1Op4I,1979
+fractal_server/app/routes/api/v2/verify_image_types.py,sha256=zGT1el58P-E7dVttyuo6MdCC0DtsxiP-NqMawl6EpGE,1950
 fractal_server/app/routes/api/v2/workflow.py,sha256=sW6Nm7dfzUY354hawyEkpQHy7rUvV2FCV8DPorH-TDU,10270
 fractal_server/app/routes/api/v2/workflow_import.py,sha256=INmnhlMEBJp-vHPR0f940DANPmIidts3OfcooeM_aNA,11205
 fractal_server/app/routes/api/v2/workflowtask.py,sha256=7_syX2EO7ibF6Xkm7HBPhsUYq6aYnKNeC5iSaafQhG4,11342
@@ -73,18 +73,18 @@ fractal_server/app/runner/executors/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQ
 fractal_server/app/runner/executors/base_runner.py,sha256=knWOERUwRLhsd9eq5GwGxH2ZVsvPOZRRjQPGbiExqcU,5052
 fractal_server/app/runner/executors/local/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/local/get_local_config.py,sha256=KiakXxOahaLgWvQJ1LVGYGXht6DMGR9x8Xu-TuT9aY4,3628
-fractal_server/app/runner/executors/local/runner.py,sha256=5SVNWnCfj2D5hIw_KNf8VchC0czLhmfqmqdHM0kWsuY,7159
+fractal_server/app/runner/executors/local/runner.py,sha256=pcwQ-ow4pJk4mkUg6mODMmfzGiMWX18vPxybrly_evY,6962
 fractal_server/app/runner/executors/slurm_common/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_common/_batching.py,sha256=ZY020JZlDS5mfpgpWTChQkyHU7iLE5kx2HVd57_C6XA,8850
 fractal_server/app/runner/executors/slurm_common/_job_states.py,sha256=nuV-Zba38kDrRESOVB3gaGbrSPZc4q7YGichQaeqTW0,238
-fractal_server/app/runner/executors/slurm_common/_slurm_config.py,sha256=qzWsMFUbcgxo2p5BltTlxDBLgGa6Z4gDKDdZioK3MB0,15979
-fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py,sha256=vF2lAUgO7vbK9pR1Jd2dFsimO45ccw2OeJTJ0z1YWwQ,30729
+fractal_server/app/runner/executors/slurm_common/_slurm_config.py,sha256=_feRRnVVnvQa3AsOQqfULfOgaoj2o6Ze0-fwXwic8p4,15795
+fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py,sha256=3LHrNmJ8VuBSeFI07q4tq41DWtcYTzYJfHvsaezDyoI,30355
 fractal_server/app/runner/executors/slurm_common/get_slurm_config.py,sha256=BW6fDpPyB0VH5leVxvwzkVH3r3hC7DuSyoWmRzHITWg,7305
 fractal_server/app/runner/executors/slurm_common/remote.py,sha256=FS_F8EaPp-A5eQT5_ZH3ICCHt0-C8b_2OSYcyRkXnb4,5851
 fractal_server/app/runner/executors/slurm_common/slurm_job_task_models.py,sha256=RoxHLKOn0_wGjnY0Sv0a9nDSiqxYZHKRoMkT3p9_G1E,3607
 fractal_server/app/runner/executors/slurm_common/utils_executors.py,sha256=naPyJI0I3lD-sYHbSXbMFGUBK4h_SggA5V91Z1Ch1Xg,1416
 fractal_server/app/runner/executors/slurm_ssh/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=ULQYW8A12BwC4GK2_2RhS33DFOFJewZoxS6vn_80z8c,7187
+fractal_server/app/runner/executors/slurm_ssh/runner.py,sha256=LeEt8a4knm9OCULxhhLkMPBanMW_65ZvL1O-HEA9QMw,7151
 fractal_server/app/runner/executors/slurm_sudo/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 fractal_server/app/runner/executors/slurm_sudo/_subprocess_run_as_user.py,sha256=O1bNg1DiSDJmQE0RmOk2Ii47DagiXp5ryd0R6KxO2OM,3177
 fractal_server/app/runner/executors/slurm_sudo/runner.py,sha256=WGGVHX_juqyC6OVhln9yg-YKjLiuAoWZhAGxBjhNkWw,5873
@@ -98,12 +98,12 @@ fractal_server/app/runner/v2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NM
 fractal_server/app/runner/v2/_local.py,sha256=DK8yagbvd6HHjcDVhUzTy0f7MURlTkQha-NM6OZKgJc,3044
 fractal_server/app/runner/v2/_slurm_ssh.py,sha256=_bytOf8z9sdrhI03D6eqg-aQPnJ7V2-qnqpcHAYizns,3278
 fractal_server/app/runner/v2/_slurm_sudo.py,sha256=DBCNxifXmMkpu71Wnk5u9-wKT7PV1WROQuY_4DYoZRI,2993
-fractal_server/app/runner/v2/db_tools.py,sha256=Ots6-Da7A_5yetSYrUGi-_yV-2r21Nc6XUBK3bv2mTM,2967
+fractal_server/app/runner/v2/db_tools.py,sha256=BfwDhIDssBmEu6HDRj1RSvDYLaoLSWFByro1Ca70aA8,2966
 fractal_server/app/runner/v2/deduplicate_list.py,sha256=IVTE4abBU1bUprFTkxrTfYKnvkNTanWQ-KWh_etiT08,645
 fractal_server/app/runner/v2/merge_outputs.py,sha256=D1L4Taieq9i71SPQyNc1kMokgHh-sV_MqF3bv7QMDBc,907
 fractal_server/app/runner/v2/runner.py,sha256=sbBOH5gCErxK0fCPPGBWtLtqsSwtmrhTth5OLUGMeZQ,15658
-fractal_server/app/runner/v2/runner_functions.py,sha256=FsUkgnVC2Wb_YJzzMf_pAgVAwjfEGi6p6r4WLHtv-sw,17807
-fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=9t1CHN3EyfsGRWfG257YPY5WjQ6zuztsw_KZrpEAFPo,3703
+fractal_server/app/runner/v2/runner_functions.py,sha256=2im4gskJRLN4SQ6jhfgbU-U0-nEz5r7YtrpC10S2aWg,18209
+fractal_server/app/runner/v2/runner_functions_low_level.py,sha256=_h_OOffq3d7V0uHa8Uvs0mj31y1GSZBUXjDDF3WjVjY,3620
 fractal_server/app/runner/v2/submit_workflow.py,sha256=EDUyUuIPwZHb2zm7SCRRoFsGq2cN-b5OKw6CYkZ8kWk,13048
 fractal_server/app/runner/v2/task_interface.py,sha256=IXdQTI8rXFgXv1Ez0js4CjKFf3QwO2GCHRTuwiFtiTQ,2891
 fractal_server/app/runner/versions.py,sha256=dSaPRWqmFPHjg20kTCHmi_dmGNcCETflDtDLronNanU,852
@@ -130,7 +130,7 @@ fractal_server/app/schemas/v2/workflowtask.py,sha256=rVbmNihDAJL_Sckbt1hBK2JEcb-
 fractal_server/app/security/__init__.py,sha256=e2cveg5hQpieGD3bSPd5GTOMthvJ-HXH3buSb9WVfEU,14096
 fractal_server/app/security/signup_email.py,sha256=Xd6QYxcdmg0PHpDwmUE8XQmPcOj3Xjy5oROcIMhmltM,1472
 fractal_server/app/user_settings.py,sha256=OP1yiYKtPadxwM51_Q0hdPk3z90TCN4z1BLpQsXyWiU,1316
-fractal_server/config.py,sha256=RQmM9IGlT3K7jpWolwVPVe9KoDgFY3abk9IjEmmtvhs,28570
+fractal_server/config.py,sha256=83dHIuZMdMiu4LAtzVGBe_iD1nWEYOiKmeC-HHZ0nhw,28534
 fractal_server/data_migrations/README.md,sha256=_3AEFvDg9YkybDqCLlFPdDmGJvr6Tw7HRI14aZ3LOIw,398
 fractal_server/data_migrations/tools.py,sha256=LeMeASwYGtEqd-3wOLle6WARdTGAimoyMmRbbJl-hAM,572
 fractal_server/gunicorn_fractal.py,sha256=u6U01TLGlXgq1v8QmEpLih3QnsInZD7CqphgJ_GrGzc,1230
@@ -208,8 +208,8 @@ fractal_server/tasks/v2/utils_templates.py,sha256=Kc_nSzdlV6KIsO0CQSPs1w70zLyENP
 fractal_server/urls.py,sha256=QjIKAC1a46bCdiPMu3AlpgFbcv6a4l3ABcd5xz190Og,471
 fractal_server/utils.py,sha256=PMwrxWFxRTQRl1b9h-NRIbFGPKqpH_hXnkAT3NfZdpY,3571
 fractal_server/zip_tools.py,sha256=GjDgo_sf6V_DDg6wWeBlZu5zypIxycn_l257p_YVKGc,4876
-fractal_server-2.14.0a27.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.14.0a27.dist-info/METADATA,sha256=C4cH5dZP3XZ1XpieeG5pOdYq24CGuSRrMkwXeUN6_BY,4563
-fractal_server-2.14.0a27.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
-fractal_server-2.14.0a27.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.14.0a27.dist-info/RECORD,,
+fractal_server-2.14.0a28.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.14.0a28.dist-info/METADATA,sha256=bSrvv3snGeMW_3fQ2zdtKvoGU2SZm5J0-EZPxEcy43c,4563
+fractal_server-2.14.0a28.dist-info/WHEEL,sha256=7dDg4QLnNKTvwIDR9Ac8jJaAmBC_owJrckbC0jjThyA,88
+fractal_server-2.14.0a28.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.14.0a28.dist-info/RECORD,,