fractal-server 2.0.2__py3-none-any.whl → 2.0.4__py3-none-any.whl

fractal_server/__init__.py

@@ -1 +1 @@
-__VERSION__ = "2.0.2"
+__VERSION__ = "2.0.4"

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

@@ -489,6 +489,10 @@ class FractalSlurmExecutor(SlurmExecutor):
         if len(args_batches) != math.ceil(tot_tasks / tasks_per_job):
             raise RuntimeError("Something wrong here while batching tasks")
 
+        # Fetch configuration variable
+        settings = Inject(get_settings)
+        FRACTAL_SLURM_SBATCH_SLEEP = settings.FRACTAL_SLURM_SBATCH_SLEEP
+
         # Construct list of futures (one per SLURM job, i.e. one per batch)
         fs = []
         current_component_index = 0
@@ -508,6 +512,7 @@ class FractalSlurmExecutor(SlurmExecutor):
                 )
             )
             current_component_index += batch_size
+            time.sleep(FRACTAL_SLURM_SBATCH_SLEEP)
 
         # Yield must be hidden in closure so that the futures are submitted
         # before the first iterator value is required.

fractal_server/config.py

@@ -331,6 +331,12 @@ class Settings(BaseSettings):
     [`clusterfutures`](https://github.com/sampsyo/clusterfutures/blob/master/cfut/__init__.py)).
     """
 
+    FRACTAL_SLURM_SBATCH_SLEEP: int = 0
+    """
+    Interval to wait (in seconds) between two subsequent `sbatch` calls, when
+    running a task that produces multiple SLURM jobs.
+    """
+
     FRACTAL_SLURM_ERROR_HANDLING_INTERVAL: int = 5
     """
     Interval to wait (in seconds) when the SLURM backend does not find an

fractal_server/data_migrations/2_0_3.py

@@ -0,0 +1,79 @@
+import logging
+
+from packaging.version import parse
+from sqlalchemy import select
+from sqlalchemy.orm.attributes import flag_modified
+
+import fractal_server
+from fractal_server.app.db import get_sync_db
+from fractal_server.app.models.v1 import ApplyWorkflow
+from fractal_server.app.models.v2 import JobV2
+from fractal_server.app.schemas.v1 import ApplyWorkflowReadV1
+from fractal_server.app.schemas.v2 import JobReadV2
+
+
+def fix_db():
+    logger = logging.getLogger("fix_db")
+    logger.warning("START execution of fix_db function")
+
+    # Check that this module matches with the current version
+    module_version = parse("2.0.3")
+    current_version = parse(fractal_server.__VERSION__)
+    if (
+        current_version.major != module_version.major
+        or current_version.minor != module_version.minor
+        or current_version.micro != module_version.micro
+    ):
+        raise RuntimeError(
+            f"{fractal_server.__VERSION__=} not matching with {__file__=}"
+        )
+
+    with next(get_sync_db()) as db:
+
+        # V1 jobs
+        stm = select(ApplyWorkflow)
+        jobs_v1 = db.execute(stm).scalars().all()
+        for job_v1 in sorted(jobs_v1, key=lambda x: x.id):
+            for KEY in ["history"]:
+                logger.warning(
+                    f"Now removing {KEY} from `input/output_dataset_dump`, "
+                    f"for appplyworkflow.id={job_v1.id}."
+                )
+                if KEY in job_v1.input_dataset_dump.keys():
+                    job_v1.input_dataset_dump.pop(KEY)
+                if KEY in job_v1.output_dataset_dump.keys():
+                    job_v1.output_dataset_dump.pop(KEY)
+            flag_modified(job_v1, "input_dataset_dump")
+            flag_modified(job_v1, "output_dataset_dump")
+            db.add(job_v1)
+            db.commit()
+            db.refresh(job_v1)
+            db.expunge(job_v1)
+            logger.warning(
+                f"Now validating applyworkflow.id={job_v1.id} with "
+                "ApplyWorkflowReadV1."
+            )
+            ApplyWorkflowReadV1(**job_v1.model_dump())
+
+        # V2 jobs
+        stm = select(JobV2)
+        jobs_v2 = db.execute(stm).scalars().all()
+        for job_v2 in sorted(jobs_v2, key=lambda x: x.id):
+            for KEY in ["history", "images"]:
+                logger.warning(
+                    f"Now removing {KEY} from `dataset_dump`, "
+                    f"for jobv2.id={job_v2.id}."
+                )
+                if KEY in job_v2.dataset_dump.keys():
+                    job_v2.dataset_dump.pop(KEY)
+            flag_modified(job_v2, "dataset_dump")
+            db.add(job_v2)
+            db.commit()
+            db.refresh(job_v2)
+            db.expunge(job_v2)
+            logger.warning(
+                f"Now validating jobv2.id={job_v2.id} with JobReadV2."
+            )
+            JobReadV2(**job_v2.model_dump())
+
+    logger.warning("END of execution of fix_db function")

{fractal_server-2.0.2.dist-info → fractal_server-2.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 2.0.2
+Version: 2.0.4
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause
@@ -39,7 +39,7 @@ Description-Content-Type: text/markdown
 # Fractal Server
 
 [![PyPI version](https://img.shields.io/pypi/v/fractal-server?color=gree)](https://pypi.org/project/fractal-server/)
-[![CI Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml)
+[![CI Status](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml/badge.svg)](https://github.com/fractal-analytics-platform/fractal-server/actions/workflows/ci.yml?query=branch%3Amain)
 [![Coverage](https://raw.githubusercontent.com/fractal-analytics-platform/fractal-server/python-coverage-comment-action-data/badge.svg)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/python-coverage-comment-action-data/htmlcov/index.html)
 [![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)
 [![Benchmarks](https://img.shields.io/badge/Benchmarks-Done-blue)](https://htmlpreview.github.io/?https://github.com/fractal-analytics-platform/fractal-server/blob/benchmark-api/benchmarks/bench.html)

{fractal_server-2.0.2.dist-info → fractal_server-2.0.4.dist-info}/RECORD

@@ -1,4 +1,4 @@
-fractal_server/__init__.py,sha256=gs_vt2BGew5iMLZDjM9dN_UiSCo9swvJzExXe0z6N7w,22
+fractal_server/__init__.py,sha256=dHp8YqTkoz9qO-fmbD43kqbzj_u4UgsCauJnWEM4z0k,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
@@ -64,7 +64,7 @@ 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=8CCtxWCuB5UDst3C_WJxBU77xwPrpDyq7iMCZMnodXU,5123
-fractal_server/app/runner/executors/slurm/executor.py,sha256=O9h6ZPAKM95BUJrZkHCdFJZrw2zR2XmxeB5fCoGp97w,44451
+fractal_server/app/runner/executors/slurm/executor.py,sha256=267YTDvyeA0yX2n2HffxP8OAu_CQF5uB9K-_AaUG3iU,44655
 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
@@ -121,7 +121,8 @@ fractal_server/app/schemas/v2/task_collection.py,sha256=sY29NQfJrbjiidmVkVjSIH-2
 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=2vw5M78aAogELsWut9X5sxxUz2lirNFpgqP6OynmKOQ,14859
+fractal_server/config.py,sha256=lXofyyyMdRQoK39yTBUwVotRT8ptSb5LceHlZrUuK2o,15048
+fractal_server/data_migrations/2_0_3.py,sha256=7EhwLCZTk1yHD_dlU-HIf2uvx6jUIgfDaA5np27QEEM,2918
 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
@@ -162,8 +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-2.0.2.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
-fractal_server-2.0.2.dist-info/METADATA,sha256=ykUREKoZndksb0goOo27hM14j41SvTljFa5P7eR9zTU,4202
-fractal_server-2.0.2.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
-fractal_server-2.0.2.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
-fractal_server-2.0.2.dist-info/RECORD,,
+fractal_server-2.0.4.dist-info/LICENSE,sha256=QKAharUuhxL58kSoLizKJeZE3mTCBnX6ucmz8W0lxlk,1576
+fractal_server-2.0.4.dist-info/METADATA,sha256=4irspCdC-GXbBTPYtUiQ8FIAaFeRfJBlYnuGWYGdKBo,4222
+fractal_server-2.0.4.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+fractal_server-2.0.4.dist-info/entry_points.txt,sha256=8tV2kynvFkjnhbtDnxAqImL6HMVKsopgGfew0DOp5UY,58
+fractal_server-2.0.4.dist-info/RECORD,,