Allow configuring timeout #1
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Not really necessary tbh
|
Looks great thanks! |
|
Looks like this is now failing due to something off between python/flask/sqlalchemy based on some quick googles. |
|
This issue may be relevant? Looks like this was an issue in one version of sqlalchemy that may have been fixed in a later version?
pallets-eco/flask-sqlalchemy#1122
Jason.
From: Helena ***@***.***>
Sent: Thursday, September 21, 2023 10:03 AM
To: galaxy-genome-annotation/apolpi ***@***.***>
Cc: jasonjgill ***@***.***>; State change ***@***.***>
Subject: Re: [galaxy-genome-annotation/apolpi] Allow configuring timeout (PR #1)
Looks like this is now failing due to something off between python/flask/sqlalchemy based on some quick googles. [2023-09-21 15: 01: 21 +0000] [1] [INFO] Starting gunicorn 21. 2. 0 [2023-09-21 15: 01: 21 +0000] [1] [INFO] Listening at: http: //0. 0. 0. 0: 80
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
ZjQcmQRYFpfptBannerEnd
Looks like this is now failing due to something off between python/flask/sqlalchemy based on some quick googles.
[2023-09-21 15:01:21 +0000] [1] [INFO] Starting gunicorn 21.2.0
[2023-09-21 15:01:21 +0000] [1] [INFO] Listening at: http://0.0.0.0:80 (1)
[2023-09-21 15:01:21 +0000] [1] [INFO] Using worker: sync
[2023-09-21 15:01:21 +0000] [9] [INFO] Booting worker with pid: 9
[2023-09-21 15:01:21 +0000] [9] [ERROR] Exception in worker process
Traceback (most recent call last):
File "/usr/local/lib/python3.8/site-packages/gunicorn/arbiter.py", line 609, in spawn_worker
worker.init_process()
File "/usr/local/lib/python3.8/site-packages/gunicorn/workers/base.py", line 134, in init_process
self.load_wsgi()
File "/usr/local/lib/python3.8/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
self.wsgi = self.app.wsgi()
File "/usr/local/lib/python3.8/site-packages/gunicorn/app/base.py", line 67, in wsgi
self.callable = self.load()
File "/usr/local/lib/python3.8/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
return self.load_wsgiapp()
File "/usr/local/lib/python3.8/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
return util.import_app(self.app_uri)
File "/usr/local/lib/python3.8/site-packages/gunicorn/util.py", line 371, in import_app
mod = importlib.import_module(module)
File "/usr/local/lib/python3.8/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
File "<frozen importlib._bootstrap>", line 991, in _find_and_load
File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 843, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/apolpi/apolpi.py", line 30, in <module>
db = SQLAlchemy(app)
File "/usr/local/lib/python3.8/site-packages/flask_sqlalchemy/__init__.py", line 758, in __init__
_include_sqlalchemy(self, query_class)
File "/usr/local/lib/python3.8/site-packages/flask_sqlalchemy/__init__.py", line 112, in _include_sqlalchemy
for key in module.__all__:
AttributeError: module 'sqlalchemy' has no attribute '__all__'
[2023-09-21 15:01:21 +0000] [9] [INFO] Worker exiting (pid: 9)
[2023-09-21 15:01:21 +0000] [1] [ERROR] Worker (pid:9) exited with code 3
[2023-09-21 15:01:21 +0000] [1] [ERROR] Shutting down: Master
[2023-09-21 15:01:21 +0000] [1] [ERROR] Reason: Worker failed to boot.
—
Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https:/github.com/galaxy-genome-annotation/apolpi/pull/1*issuecomment-1729766619__;Iw!!KwNVnqRv!BM2eku_rdWOxrwyOkhhBF0iFHyVOr3IAfq9CFzWmEQ_nGVKCTk0ndBiMbxYXYGBcc9Cd5uuzKo5NGoMgjA80hL40Vgw$>, or unsubscribe<https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AKIFQTQX6MOYXDP6FTXO2K3X3RJKRANCNFSM6AAAAAA44NQCUA__;!!KwNVnqRv!BM2eku_rdWOxrwyOkhhBF0iFHyVOr3IAfq9CFzWmEQ_nGVKCTk0ndBiMbxYXYGBcc9Cd5uuzKo5NGoMgjA80LVEiXuw$>.
You are receiving this because you modified the open/close state.Message ID: ***@***.******@***.***>>
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
@jasonjgill is having issues creating an organism, I suspect due to failing read-after-write. Since apollo uses POSTs for both because they don't use a proper authentication header and GET for queries, we can't expire the cache that way. Thus we are stuck manually changing the timeout (I'm not entirely sure why the tools don't experience this, but CPT could be using some custom script triggering this.)