tcompa
commented
1 year ago (likely a consequence of https://github.com/fractal-analytics-platform/fractal-server/pull/651)
Closed tcompa closed 1 year ago
tcompa
commented
1 year ago (likely a consequence of https://github.com/fractal-analytics-platform/fractal-server/pull/651)
tcompa
commented
1 year ago (likely a consequence of #651)
I take it back. Tests pass with 1.2.3, so that this is a consequence of 1.2.4 (that is, https://github.com/fractal-analytics-platform/fractal-server/pull/657).
tcompa
commented
1 year ago The local CI (using sqlite) passes again after adding https://github.com/fractal-analytics-platform/fractal-server/pull/662/commits/d3661170b5a2296cfbce0ab505a0cbac8912e9fe (which was there in some older versions), but the reason is unclear (the rationale behind those few lines of code is not clear, and there is no useful comment).
We'll need to understand the issue better before merging.
gusqgm
commented
1 year ago I saw the same issue when testing things in WSL here.
tcompa
commented
1 year ago More info:
Based on some other failure examples (and on my experience), this bug is not fully reproducible - as it depends on the timing of two operations which can vary in different tests. This is why it was not clear to me what the latest working version of fractal-server is.
Still, it's most likely a consequence of #651, for the moment the latest working version (with sqlite) is 1.2.2. We are now looking for a reasonable fix.
tcompa
commented
1 year ago Other relevant references:
Notable quote (by fastapi maintainer):
You can just use the same session as in the path operation.
tcompa
commented
1 year ago Minimal failing example:
from fastapi import APIRouter
from fastapi import BackgroundTasks
from fastapi import Depends
from devtools import debug
from ...db import AsyncSession
from ...db import get_db
from ...models import State
from ....logger import set_logger
logger = set_logger(__name__)
router = APIRouter()
async def myfun(random: AsyncSession):
logger.critical("BGTASK START")
new_db = await get_db().__anext__()
state = await new_db.get(State, 1)
debug(state)
state.data = {"a": "b"}
logger.critical("BGTASK MERGE:")
await new_db.merge(state)
logger.critical("BGTASK COMMIT:")
await new_db.commit()
await new_db.close()
logger.critical("BGTASK END")
return
@router.post('/test')
async def dummy_endpoint(
background_tasks: BackgroundTasks,
db: AsyncSession = Depends(get_db),
):
logger.critical("ENDPOINT START")
debug(db)
sss = State()
db.add(sss)
await db.commit()
await db.close()
logger.critical("ENDPOINT END")
background_tasks.add_task(myfun, 1)
returnAs part of #664, we (me and @mfranzon) introduced a minimal test that captures the wrong behavior, namely an endpoint which submits a background task which acts on the db. The background task can act on the DB either through sync or async sessions, with the async ones being trickier.
Note that we currently have two background tasks, in fractal-server:
The difference in what kind of db sessions to use is due to no special reason, and in principle we could make them homogeneous.
After reproducing the bug, we introduced two main changes:
StaticPool of connections in sqlalchemy (instead of the default NullPool). Refs: https://stackoverflow.com/a/56145687/19085332 and https://docs.sqlalchemy.org/en/14/dialects/sqlite.html#threading-pooling-behavior. This change should greatly reduce the risk of closing connections from a different thread (reminder: sqlite and multithreading do not necessarily work nicely -- see #656)__anext__ with async for (as in 846cf544415cf8fc2969194247e1c9104a363dde), due to the fact that otherwise the new test would hang when using postgresql. We don't have full understanding on why the __anext__ option wouldn't work, but async for does work (and it is also used elsewhere in fractal-server tests) and for the moment it's enough.With these two changes, CI (including the new specific test) is passing both with sqlite and postgresql. We'll then test this by hand as soon as we have a patch release.
tcompa
commented
1 year ago I just tested 1.2.5a0 as part of fractal-demos, and got the following warnings:
sys:1: SAWarning: Identity map already had an identity for (<class 'fractal_server.app.models.task.Task'>, (3,), None), replacing it with newly flushed object. Are there load operations occurring inside of an event handler within the flush?
sys:1: SAWarning: Identity map already had an identity for (<class 'fractal_server.app.models.task.Task'>, (2,), None), replacing it with newly flushed object. Are there load operations occurring inside of an event handler within the flush?
sys:1: SAWarning: Identity map already had an identity for (<class 'fractal_server.app.models.task.Task'>, (1,), None), replacing it with newly flushed object. Are there load operations occurring inside of an event handler within the flush?
2023-05-09 12:00:43,810 - fractal-tasks-core - INFO - Background collection failed. Original error: Instance '<Task at 0x7f96045b5300>' is not persistent within this SessionMore verbose logs:
This is the task-collection log:
2023-05-09 11:59:49,344 - fractal-tasks-core - DEBUG - Start background task collection
2023-05-09 11:59:49,345 - fractal-tasks-core - DEBUG - Task-collection status: installing
2023-05-09 11:59:49,347 - fractal-tasks-core - DEBUG - Creating venv and installing package
2023-05-09 11:59:50,604 - fractal-tasks-core - DEBUG - Subprocess call to: /home/tommaso/miniconda3/envs/fractal-server-1.2.5a0/bin/python3.9 -m venv venv
2023-05-09 11:59:50,604 - fractal-tasks-core - DEBUG -
2023-05-09 11:59:50,604 - fractal-tasks-core - DEBUG -
2023-05-09 11:59:51,764 - fractal-tasks-core - DEBUG - Subprocess call to: /home/tommaso/Fractal/fractal-demos/examples/server/FRACTAL_TASKS_DIR/.fractal/fractal-tasks-core0.9.4/venv/bin/pip install --upgrade pip
2023-05-09 11:59:51,765 - fractal-tasks-core - DEBUG - Collecting pip
Using cached pip-23.1.2-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 20.2.3
Uninstalling pip-20.2.3:
Successfully uninstalled pip-20.2.3
Successfully installed pip-23.1.2
2023-05-09 11:59:51,765 - fractal-tasks-core - DEBUG -
2023-05-09 12:00:42,688 - fractal-tasks-core - DEBUG - Subprocess call to: /home/tommaso/Fractal/fractal-demos/examples/server/FRACTAL_TASKS_DIR/.fractal/fractal-tasks-core0.9.4/venv/bin/pip install fractal-tasks-core==0.9.4
2023-05-09 12:00:42,689 - fractal-tasks-core - DEBUG - Collecting fractal-tasks-core==0.9.4
Using cached fractal_tasks_core-0.9.4-py3-none-any.whl (70 kB)
Collecting Pillow<10.0.0,>=9.1.1 (from fractal-tasks-core==0.9.4)
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Collecting rfc3339-validator (from jupyter-events>=0.4.0->jupyter-server>=1.8->nbclassic>=0.4.7->notebook->jupyter->napari-assistant->napari-segment-blobs-and-things-with-membranes<0.4.0,>=0.3.3->fractal-tasks-core==0.9.4)
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Using cached arrow-1.2.3-py3-none-any.whl (66 kB)
Installing collected packages: webencodings, wcwidth, snowballstemmer, pytz, pytomlpp, pyperclip, PyOpenGL, pure-eval, ptyprocess, pickleshare, mistune, ipython-genutils, heapdict, fastjsonschema, executing, backcall, asciitree, appdirs, zipp, wrapt, widgetsnbextension, websocket-client, webcolors, urllib3, uri-template, typing-extensions, traitlets, tqdm, tornado, toolz, tomli, toml, tinycss2, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, sniffio, six, Send2Trash, rfc3986-validator, pyzmq, pyyaml, python-json-logger, pyrsistent, pyparsing, pygments, pycparser, pycodestyle, psutil, prompt-toolkit, prometheus-client, platformdirs, pint, Pillow, pexpect, parso, pandocfilters, packaging, numpy, networkx, nest-asyncio, natsort, napari-plugin-engine, mypy-extensions, mdurl, MarkupSafe, lxml, loguru, locket, llvmlite, lazy_loader, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, in-n-out, imagesize, imageio-ffmpeg, idna, hsluv, fsspec, freetype-py, fqdn, fonttools, fasteners, entrypoints, docutils, docstring-parser, defusedxml, decorator, debugpy, cycler, cloudpickle, click, charset-normalizer, certifi, cachey, babel, attrs, alabaster, vispy, typer, torch, tifffile, terminado, scipy, rfc3339-validator, requests, qtpy, PyWavelets, python-dateutil, pyproject_hooks, pydantic, psygnal, partd, opencv-python-headless, numcodecs, numba, matplotlib-inline, markdown-it-py, jupyter-core, jsonschema, Jinja2, jedi, importlib-resources, importlib-metadata, imageio, imagecodecs, h5py, fastremap, contourpy, comm, cffi, bleach, beautifulsoup4, autopep8, asttokens, anyio, zarr, superqt, stack-data, sphinx, scikit-image, rich, pandas, nbformat, napari-svg, mdit-py-plugins, matplotlib, jupyter-server-terminals, jupyter-client, dask, cellpose, build, arrow, argon2-cffi-bindings, app-model, numpydoc, npe2, nbclient, magicgui, jupytext, isoduration, IPython, argon2-cffi, anndata, nbconvert, ipykernel, qtconsole, jupyter-events, jupyter-console, ipywidgets, napari-console, jupyter-server, ipyevents, ipycanvas, stackview, notebook-shim, napari, nbclassic, napari-workflows, napari-tools-menu, notebook, napari-time-slicer, napari-skimage-regionprops, jupyter, napari-assistant, napari-segment-blobs-and-things-with-membranes, fractal-tasks-core
Successfully installed IPython-8.13.2 Jinja2-3.1.2 MarkupSafe-2.1.2 Pillow-9.5.0 PyOpenGL-3.1.6 PyWavelets-1.4.1 Send2Trash-1.8.2 alabaster-0.7.13 anndata-0.8.0 anyio-3.6.2 app-model-0.1.4 appdirs-1.4.4 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 arrow-1.2.3 asciitree-0.3.3 asttokens-2.2.1 attrs-23.1.0 autopep8-2.0.2 babel-2.12.1 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 build-0.10.0 cachey-0.2.1 cellpose-2.2.1 certifi-2023.5.7 cffi-1.15.1 charset-normalizer-3.1.0 click-8.1.3 cloudpickle-2.2.1 comm-0.1.3 contourpy-1.0.7 cycler-0.11.0 dask-2023.1.1 debugpy-1.6.7 decorator-5.1.1 defusedxml-0.7.1 docstring-parser-0.15 docutils-0.17.1 entrypoints-0.4 executing-1.2.0 fasteners-0.18 fastjsonschema-2.16.3 fastremap-1.13.4 fonttools-4.39.3 fqdn-1.5.1 fractal-tasks-core-0.9.4 freetype-py-2.4.0 fsspec-2023.5.0 h5py-3.8.0 heapdict-1.0.1 hsluv-5.0.3 idna-3.4 imagecodecs-2023.3.16 imageio-2.28.1 imageio-ffmpeg-0.4.8 imagesize-1.4.1 importlib-metadata-6.6.0 importlib-resources-5.12.0 in-n-out-0.1.7 ipycanvas-0.13.1 ipyevents-2.0.1 ipykernel-6.23.0 ipython-genutils-0.2.0 ipywidgets-8.0.6 isoduration-20.11.0 jedi-0.18.2 jsonpointer-2.3 jsonschema-4.17.3 jupyter-1.0.0 jupyter-client-8.2.0 jupyter-console-6.6.3 jupyter-core-5.3.0 jupyter-events-0.6.3 jupyter-server-2.5.0 jupyter-server-terminals-0.4.4 jupyterlab-pygments-0.2.2 jupyterlab-widgets-3.0.7 jupytext-1.14.5 kiwisolver-1.4.4 lazy_loader-0.2 llvmlite-0.39.1 locket-1.0.0 loguru-0.7.0 lxml-4.9.2 magicgui-0.7.2 markdown-it-py-2.2.0 matplotlib-3.7.1 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.5 mdurl-0.1.2 mistune-2.0.5 mypy-extensions-1.0.0 napari-0.4.17 napari-assistant-0.4.5 napari-console-0.0.8 napari-plugin-engine-0.2.0 napari-segment-blobs-and-things-with-membranes-0.3.4 napari-skimage-regionprops-0.8.2 napari-svg-0.1.6 napari-time-slicer-0.4.9 napari-tools-menu-0.1.19 napari-workflows-0.2.8 natsort-8.3.1 nbclassic-1.0.0 nbclient-0.7.4 nbconvert-7.4.0 nbformat-5.8.0 nest-asyncio-1.5.6 networkx-3.1 notebook-6.5.4 notebook-shim-0.2.3 npe2-0.7.0 numba-0.56.4 numcodecs-0.11.0 numpy-1.23.5 numpydoc-1.5.0 opencv-python-headless-4.7.0.72 packaging-23.1 pandas-1.5.3 pandocfilters-1.5.0 parso-0.8.3 partd-1.4.0 pexpect-4.8.0 pickleshare-0.7.5 pint-0.21 platformdirs-3.5.0 prometheus-client-0.16.0 prompt-toolkit-3.0.38 psutil-5.9.5 psygnal-0.9.0 ptyprocess-0.7.0 pure-eval-0.2.2 pycodestyle-2.10.0 pycparser-2.21 pydantic-1.10.7 pygments-2.15.1 pyparsing-3.0.9 pyperclip-1.8.2 pyproject_hooks-1.0.0 pyrsistent-0.19.3 python-dateutil-2.8.2 python-json-logger-2.0.7 pytomlpp-1.0.13 pytz-2023.3 pyyaml-6.0 pyzmq-25.0.2 qtconsole-5.4.3 qtpy-2.3.1 requests-2.30.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rich-13.3.5 scikit-image-0.20.0 scipy-1.9.1 six-1.16.0 sniffio-1.3.0 snowballstemmer-2.2.0 soupsieve-2.4.1 sphinx-4.5.0 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 stack-data-0.6.2 stackview-0.6.3 superqt-0.4.1 terminado-0.17.1 tifffile-2023.4.12 tinycss2-1.2.1 toml-0.10.2 tomli-2.0.1 toolz-0.12.0 torch-1.12.1 tornado-6.3.1 tqdm-4.65.0 traitlets-5.9.0 typer-0.9.0 typing-extensions-4.5.0 uri-template-1.2.0 urllib3-2.0.2 vispy-0.11.0 wcwidth-0.2.6 webcolors-1.13 webencodings-0.5.1 websocket-client-1.5.1 widgetsnbextension-4.0.7 wrapt-1.15.0 zarr-2.13.6 zipp-3.15.0
2023-05-09 12:00:42,689 - fractal-tasks-core - DEBUG -
2023-05-09 12:00:43,778 - fractal-tasks-core - DEBUG - Subprocess call to: /home/tommaso/Fractal/fractal-demos/examples/server/FRACTAL_TASKS_DIR/.fractal/fractal-tasks-core0.9.4/venv/bin/pip show fractal-tasks-core
2023-05-09 12:00:43,778 - fractal-tasks-core - DEBUG - Name: fractal-tasks-core
Version: 0.9.4
Summary:
Home-page: https://github.com/fractal-analytics-platform/fractal-tasks-core
Author: Jacopo Nespolo
Author-email: jacopo.nespolo@exact-lab.it
License: BSD-3-Clause
Location: /home/tommaso/Fractal/fractal-demos/examples/server/FRACTAL_TASKS_DIR/.fractal/fractal-tasks-core0.9.4/venv/lib/python3.9/site-packages
Requires: anndata, cellpose, dask, defusedxml, imageio-ffmpeg, llvmlite, lxml, napari-segment-blobs-and-things-with-membranes, napari-skimage-regionprops, napari-tools-menu, napari-workflows, numpy, pandas, Pillow, pydantic, scikit-image, torch, zarr
Required-by:
2023-05-09 12:00:43,778 - fractal-tasks-core - DEBUG -
2023-05-09 12:00:43,778 - fractal-tasks-core - DEBUG - Loading task manifest
2023-05-09 12:00:43,779 - fractal-tasks-core - DEBUG - Loaded task manifest
2023-05-09 12:00:43,779 - fractal-tasks-core - DEBUG - Task-collection status: collecting
2023-05-09 12:00:43,810 - fractal-tasks-core - DEBUG - Task-collection status: fail
2023-05-09 12:00:43,810 - fractal-tasks-core - INFO - Background collection failed. Original error: Instance '<Task at 0x7f96045b5300>' is not persistent within this Session
Version
1.2.4seems to introduce an issue with task collection, when using sqlite: