fractal-server 1.2.3a0__tar.gz → 1.2.3a2__tar.gz

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fractal-server
-Version: 1.2.3a0
+Version: 1.2.3a2
 Summary: Server component of the Fractal analytics platform
 Home-page: https://github.com/fractal-analytics-platform/fractal-server
 License: BSD-3-Clause

fractal_server-1.2.3a2/fractal_server/__init__.py

@@ -0,0 +1 @@
+__VERSION__ = "1.2.3a2"

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/fractal_server/app/api/v1/project.py

@@ -216,7 +216,6 @@ async def apply_workflow(
     project = output["project"]
 
     workflow = db_sync.get(Workflow, apply_workflow.workflow_id)
-    db_sync.close()
     if not workflow:
         raise HTTPException(
             status_code=status.HTTP_404_NOT_FOUND,
@@ -295,7 +294,6 @@ async def apply_workflow(
     db.add(job)
     await db.commit()
     await db.refresh(job)
-    await db.close()
 
     background_tasks.add_task(
         submit_workflow,
@@ -308,6 +306,9 @@ async def apply_workflow(
         user_cache_dir=user.cache_dir,
     )
 
+    await db.close()
+    db_sync.close()
+
     return job
 
 
@@ -408,7 +409,7 @@ async def get_job_list(
     stm = select(ApplyWorkflow).where(ApplyWorkflow.project_id == project_id)
     res = await db.execute(stm)
     job_list = res.scalars().all()
-
+    await db.close()
     return job_list
 
 

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/fractal_server/app/api/v1/task.py

@@ -48,7 +48,9 @@ router = APIRouter()
 
 
 async def _background_collect_pip(
-    state: State, venv_path: Path, task_pkg: _TaskCollectPip, db: AsyncSession
+    state_id: int,
+    venv_path: Path,
+    task_pkg: _TaskCollectPip,
 ) -> None:
     """
     Install package and collect tasks
@@ -59,6 +61,12 @@ async def _background_collect_pip(
     In case of error, copy the log into the state and delete the package
     directory.
     """
+
+    # Note: anext(get_db()) is only available for python>=3.10
+    db = await get_db().__anext__()
+
+    state: State = await db.get(State, state_id)
+
     logger_name = task_pkg.package.replace("/", "_")
     logger = set_logger(
         logger_name=logger_name,
@@ -110,6 +118,7 @@ async def _background_collect_pip(
         logger.debug("Task-collection status: OK")
         logger.info("Background task collection completed successfully")
         close_logger(logger)
+        await db.close()
 
     except Exception as e:
         # Write last logs to file
@@ -124,6 +133,7 @@ async def _background_collect_pip(
         state.data = data.sanitised_dict()
         await db.merge(state)
         await db.commit()
+        await db.close()
 
         # Delete corrupted package dir
         shell_rmtree(venv_path)
@@ -240,10 +250,9 @@ async def collect_tasks_pip(
 
     background_tasks.add_task(
         _background_collect_pip,
-        state=state,
+        state_id=state.id,
         venv_path=venv_path,
         task_pkg=task_pkg,
-        db=db,
     )
     logger.debug(
         "Task-collection endpoint: start background collection "

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/fractal_server/app/runner/__init__.py

@@ -207,6 +207,10 @@ async def submit_workflow(
             worker_init=worker_init,
         )
 
+        logger.info(
+            f'End execution of workflow "{workflow.name}"; '
+            f"more logs at {str(log_file_path)}"
+        )
         logger.debug(f'END workflow "{workflow.name}"')
 
         db_sync.merge(output_dataset)

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/fractal_server/app/security/__init__.py

@@ -173,6 +173,7 @@ async def list_users(
     stm = select(User)
     res = await db.execute(stm)
     user_list = res.scalars().all()
+    await db.close()
     return user_list
 
 

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "fractal-server"
-version = "1.2.3a0"
+version = "1.2.3a2"
 description = "Server component of the Fractal analytics platform"
 authors = [
     "Jacopo Nespolo <jacopo.nespolo@exact-lab.it>",
@@ -75,7 +75,7 @@ filterwarnings = [
 ]
 
 [tool.bumpver]
-current_version = "1.2.3a0"
+current_version = "1.2.3a2"
 version_pattern = "MAJOR.MINOR.PATCH[PYTAGNUM]"
 commit_message = "bump version {old_version} -> {new_version}"
 commit = true

{fractal_server-1.2.3a0 → fractal_server-1.2.3a2}/setup.py

@@ -44,7 +44,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'fractal-server',
-    'version': '1.2.3a0',
+    'version': '1.2.3a2',
     'description': 'Server component of the Fractal analytics platform',
     'long_description': '# Fractal Server\n\n[![PyPI version](https://img.shields.io/pypi/v/fractal-server?color=gree)](https://pypi.org/project/fractal-server/)\n[![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)\n[![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)\n[![License](https://img.shields.io/badge/License-BSD_3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)\n\nFractal is a framework to process high content imaging data at scale and\nprepare it for interactive visualization.\n\n![Fractal_Overview](https://fractal-analytics-platform.github.io/assets/fractal_overview.jpg)\n\nThis is the server component of the fractal analytics platform.\nFind more information about Fractal in general and the other repositories at\nthe [Fractal home page](https://fractal-analytics-platform.github.io).\n\n\n## Documentation\n\nSee https://fractal-analytics-platform.github.io/fractal-server.\n\n# Contributors and license\n\nUnless otherwise stated in each individual module, all Fractal components are\nreleased according to a BSD 3-Clause License, and Copyright is with Friedrich\nMiescher Institute for Biomedical Research and University of Zurich.\n\nThe SLURM compatibility layer is based on\n[`clusterfutures`](https://github.com/sampsyo/clusterfutures), by\n[@sampsyo](https://github.com/sampsyo) and collaborators, and it is released\nunder the terms of the MIT license.\n\nFractal was conceived in the Liberali Lab at the Friedrich Miescher Institute\nfor Biomedical Research and in the Pelkmans Lab at the University of Zurich\n(both in Switzerland). The project lead is with\n[@gusqgm](https://github.com/gusqgm) & [@jluethi](https://github.com/jluethi).\nThe core development is done under contract by\n[@mfranzon](https://github.com/mfranzon), [@tcompa](https://github.com/tcompa)\n& [@japs](https://github.com/japs) of [eXact lab S.r.l.](exact-lab.it).\n',
     'author': 'Jacopo Nespolo',

fractal_server-1.2.3a0/fractal_server/__init__.py

@@ -1 +0,0 @@
-__VERSION__ = "1.2.3a0"