fractal-server 2.14.0a25__tar.gz → 2.14.0a27__tar.gz

{fractal_server-2.14.0a25 → fractal_server-2.14.0a27}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: fractal-server
-Version: 2.14.0a25
+Version: 2.14.0a27
 Summary: Backend component of the Fractal analytics platform
 License: BSD-3-Clause
 Author: Tommaso Comparin

fractal_server-2.14.0a27/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.14.0a27"

{fractal_server-2.14.0a25 → fractal_server-2.14.0a27}/fractal_server/app/runner/executors/slurm_common/base_slurm_runner.py

@@ -248,7 +248,7 @@ class BaseSlurmRunner(BaseRunner):
 
         # Always print output of `uname -n` and `pwd`
         script_lines.append('\necho "Hostname: $(uname -n)"')
-        script_lines.append('echo "Current directory : $(pwd)"')
+        script_lines.append('echo "Current directory: $(pwd)"')
         script_lines.append(
             'echo "Start time: $(date +"%Y-%m-%dT%H:%M:%S%z")"'
         )

{fractal_server-2.14.0a25 → fractal_server-2.14.0a27}/fractal_server/app/runner/executors/slurm_ssh/runner.py

@@ -137,7 +137,7 @@ class SlurmSSHRunner(BaseSlurmRunner):
         self.fractal_ssh.run_command(cmd=tar_command)
         t_1_tar = time.perf_counter()
         logger.info(
-            f"Remote archive {tarfile_path_remote} created"
+            f"[_fetch_artifacts] Remote archive {tarfile_path_remote} created"
             f" - elapsed: {t_1_tar - t_0_tar:.3f} s"
         )
 
@@ -149,7 +149,8 @@ class SlurmSSHRunner(BaseSlurmRunner):
         )
         t_1_get = time.perf_counter()
         logger.info(
-            f"Subfolder archive transferred back to {tarfile_path_local}"
+            "[_fetch_artifacts] Subfolder archive transferred back "
+            f"to {tarfile_path_local}"
             f" - elapsed: {t_1_get - t_0_get:.3f} s"
         )
 
@@ -160,7 +161,7 @@ class SlurmSSHRunner(BaseSlurmRunner):
         Path(tarfile_path_local).unlink(missing_ok=True)
 
         t_1 = time.perf_counter()
-        logger.info(f"[_get_subfolder_sftp] End - elapsed: {t_1 - t_0:.3f} s")
+        logger.info(f"[_fetch_artifacts] End - elapsed: {t_1 - t_0:.3f} s")
 
     def _send_inputs(self, jobs: list[SlurmJob]) -> None:
         """

{fractal_server-2.14.0a25 → fractal_server-2.14.0a27}/fractal_server/app/runner/v2/runner_functions.py

@@ -406,7 +406,7 @@ def run_v2_task_compound(
         db.add(history_unit)
         db.commit()
         db.refresh(history_unit)
-        history_unit_id = history_unit.id
+        init_history_unit_id = history_unit.id
         # Create one `HistoryImageCache` for each input image
         bulk_upsert_image_cache_fast(
             db=db,
@@ -415,7 +415,7 @@ def run_v2_task_compound(
                     workflowtask_id=wftask.id,
                     dataset_id=dataset_id,
                     zarr_url=zarr_url,
-                    latest_history_unit_id=history_unit_id,
+                    latest_history_unit_id=init_history_unit_id,
                 )
                 for zarr_url in input_image_zarr_urls
             ],
@@ -431,7 +431,7 @@ def run_v2_task_compound(
         parameters=function_kwargs,
         task_type=task_type,
         task_files=task_files_init,
-        history_unit_id=history_unit_id,
+        history_unit_id=init_history_unit_id,
         config=runner_config_init,
     )
 
@@ -459,7 +459,7 @@ def run_v2_task_compound(
     # Mark the init-task `HistoryUnit` as "done"
     with next(get_sync_db()) as db:
         update_status_of_history_unit(
-            history_unit_id=history_unit_id,
+            history_unit_id=init_history_unit_id,
             status=HistoryUnitStatus.DONE,
             db_sync=db,
         )
@@ -470,7 +470,7 @@ def run_v2_task_compound(
     if len(parallelization_list) == 0:
         with next(get_sync_db()) as db:
             update_status_of_history_unit(
-                history_unit_id=history_unit_id,
+                history_unit_id=init_history_unit_id,
                 status=HistoryUnitStatus.DONE,
                 db_sync=db,
             )
@@ -525,30 +525,6 @@ def run_v2_task_compound(
         for history_unit in history_units:
             db.refresh(history_unit)
         history_unit_ids = [history_unit.id for history_unit in history_units]
-    # Create one `HistoryImageCache` per `zarr_url`.
-    with next(get_sync_db()) as db:
-        visited_zarr_urls = set()
-        history_image_caches = []
-        for ind, history_unit in enumerate(history_units):
-            _zarr_url = history_unit.zarr_urls[0]
-            if _zarr_url in visited_zarr_urls:
-                # Note: This `HistoryUnit` won't be associated to any
-                # `HistoryImageCache`.
-                pass
-            else:
-                visited_zarr_urls.add(_zarr_url)
-                history_image_caches.append(
-                    dict(
-                        workflowtask_id=wftask.id,
-                        dataset_id=dataset_id,
-                        zarr_url=_zarr_url,
-                        latest_history_unit_id=history_unit.id,
-                    )
-                )
-        bulk_upsert_image_cache_fast(
-            db=db,
-            list_upsert_objects=history_image_caches,
-        )
 
     results, exceptions = runner.multisubmit(
         functools.partial(
@@ -565,7 +541,7 @@ def run_v2_task_compound(
         config=runner_config_compute,
     )
 
-    init_outcome = {}
+    compute_outcomes: dict[int, SubmissionOutcome] = {}
     failure = False
     for ind in range(len(list_function_kwargs)):
         if ind not in results.keys() and ind not in exceptions.keys():
@@ -576,10 +552,12 @@ def run_v2_task_compound(
             )
             logger.error(error_msg)
             raise RuntimeError(error_msg)
-        init_outcome[ind] = _process_task_output(
+        compute_outcomes[ind] = _process_task_output(
             result=results.get(ind, None),
             exception=exceptions.get(ind, None),
         )
+        if compute_outcomes[ind].exception is not None:
+            failure = True
 
     # NOTE: For compound tasks, we update `HistoryUnit.status` from here,
     # rather than within the submit/multisubmit runner methods. This is
@@ -588,7 +566,7 @@ def run_v2_task_compound(
     with next(get_sync_db()) as db:
         if failure:
             bulk_update_status_of_history_unit(
-                history_unit_ids=history_unit_ids,
+                history_unit_ids=history_unit_ids + [init_history_unit_id],
                 status=HistoryUnitStatus.FAILED,
                 db_sync=db,
             )
@@ -599,4 +577,4 @@ def run_v2_task_compound(
                 db_sync=db,
             )
 
-    return init_outcome, num_tasks
+    return compute_outcomes, num_tasks

{fractal_server-2.14.0a25 → fractal_server-2.14.0a27}/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "fractal-server"
-version = "2.14.0a25"
+version = "2.14.0a27"
 description = "Backend component of the Fractal analytics platform"
 authors = [
     { name="Tommaso Comparin", email="tommaso.comparin@exact-lab.it" },
@@ -95,7 +95,7 @@ filterwarnings = [
 markers = ["container", "ssh"]
 
 [tool.bumpver]
-current_version = "2.14.0a25"
+current_version = "2.14.0a27"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.14.0a25/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.14.0a25"