fractal-server 2.0.2__tar.gz → 2.0.4__tar.gz

{fractal_server-2.0.2 → fractal_server-2.0.4}/PKG-INFO

@@ -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 → fractal_server-2.0.4}/README.md

@@ -1,7 +1,7 @@
 # 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-2.0.4/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "2.0.4"

{fractal_server-2.0.2 → fractal_server-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-2.0.2 → fractal_server-2.0.4}/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-2.0.4/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 → fractal_server-2.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "2.0.2"
+version = "2.0.4"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Tommaso Comparin <tommaso.comparin@exact-lab.it>",
@@ -87,7 +87,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "2.0.2"
+current_version = "2.0.4"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

fractal_server-2.0.2/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "2.0.2"