Python FastAPI app runs in debugger, but crashes when run with docker compose

Created November 14, 2022 14:44

Hi everyone,

I wanted to share some upfront information; despite my years as a developer, I'm a relative noob when it comes to Docker.

At work, I'm building a new FastAPI application. I'm developing this to be deployed as a Docker container and am using Docker to develop locally on my M1 Macbook Pro. I'm using Python 3.10.8 and the latest FastAPI, etc., and the latest PyCharm.

Here's my simplified project directory structure:

payment

+-- < general project stuff, including my docker-compose.yml file >

+-- project

+-- < Dockerfile, pyproject.toml, etc >

+-- app

+-- < directories containing application code >

I've got a remote interpreter setup using the docker-compose.yml file, and it starts when I click the run or debug button in PyCharm. However, the application fails to start because the Python path is screwy. If open a bash shell into the container, my project is now in /opt/project/project. In the configuration file in PyCharm, to run the project, I need to set an environment variable PYTHONPATH=/opt/project/project to get the application to start correctly and allow me to debug it.

This works as I can debug the application in the Docker container in the PyCharm debugger, but it seems weird to me and took me some time to figure it out.

When I run docker compose -f docker-compose.yml up --build -d from the command line, that application crashes. If I open a bash shell in the container, the project is located at /project right at the root of the container file system.

Here is the output on the terminal when I run "docker compose...."

$ docker logs 36e4b6a84816
ENVIRONMENT: development
Starting development server
INFO: Will watch for changes in these directories: ['/project']
INFO: Uvicorn running on http://0.0.0.0:8000 (Press CTRL+C to quit)
INFO: Started reloader process [1] using StatReload
Process SpawnProcess-1:
Traceback (most recent call last):
File "/usr/local/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/usr/local/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/venv/lib/python3.10/site-packages/uvicorn/_subprocess.py", line 76, in subprocess_started
target(sockets=sockets)
File "/opt/venv/lib/python3.10/site-packages/uvicorn/server.py", line 60, in run
return asyncio.run(self.serve(sockets=sockets))
File "/usr/local/lib/python3.10/asyncio/runners.py", line 44, in run
return loop.run_until_complete(main)
File "/usr/local/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
return future.result()
File "/opt/venv/lib/python3.10/site-packages/uvicorn/server.py", line 67, in serve
config.load()
File "/opt/venv/lib/python3.10/site-packages/uvicorn/config.py", line 474, in load
self.loaded_app = import_from_string(self.app)
File "/opt/venv/lib/python3.10/site-packages/uvicorn/importer.py", line 24, in import_from_string
raise exc from None
File "/opt/venv/lib/python3.10/site-packages/uvicorn/importer.py", line 21, in import_from_string
module = importlib.import_module(module_str)
File "/usr/local/lib/python3.10/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1050, in _gcd_import
File "<frozen importlib._bootstrap>", line 1027, in _find_and_load
File "<frozen importlib._bootstrap>", line 1006, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 688, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 883, in exec_module
File "<frozen importlib._bootstrap>", line 241, in _call_with_frames_removed
File "/project/./app/main.py", line 20, in <module>
from .server import app
File "/project/./app/server.py", line 9, in <module>
from auth.routes import router as auth_router
ModuleNotFoundError: No module named 'auth'

Would you happen to have any insights about why this is happening?

I can send you my Dockerfile and docker-compose.yml file if that would be useful.

Thanks very much for taking a look at this,

Doug Farrell

7 comments

Daniil Bogdanov

Created November 15, 2022 15:41

Hello,

Dockerfile and docker-compose.yml are needed to understand better what might cause an issue.

Dfarrell

Created November 15, 2022 16:28

Hi Daniil,

I'll upload the Dockerfile and docker-compose.yml files using a link I've gotten from a direct email from Sergey.

Here is the upload ID from the above link: 2022_11_15_KgVJjhgp41r8Dh98LZisXF

Thanks!

Doug

Daniil Bogdanov

Created November 17, 2022 16:00

Hello Doug,

I've built an image with a dummy fastapi project and your Dockerfile and .yml files, and it's expected that /project will contain project files but /opt contains only venv, as it states in Dockerfile.

The interpreter was also added without any issues and ran test files without extra environment variables.

I'm a little bit confused, the only thing that bothers me is that there is an extra step between the project and app dirs in your log: /project/./app/main.py. But I can't find anything related to that "dot folder" in Dockerfile or docker-compose; those seem fine. Could it be a misconfiguration in other project files?

Dfarrell

Created November 18, 2022 18:51

Daniil,

Thanks for getting back to me. I'm also seeing that strange /project/./app/main.py behavior, and don't understand it.

Right now, I can run the app from the debugger in PyCharm and the terminal command line. If I run this command:

docker compose -f docker-compose.yml up -d --build

I get a running application inside the docker container. If open a bash shell into the container, I get this information with some command line stuff:

appuser@20bb48f9148a:/project$ ls -la /
total 80
drwxr-xr-x 1 root root 4096 Nov 18 18:41 .
drwxr-xr-x 1 root root 4096 Nov 18 18:41 ..
-rwxr-xr-x 1 root root 0 Nov 18 18:41 .dockerenv
drwxr-xr-x 1 root root 4096 Nov 15 09:32 bin
drwxr-xr-x 2 root root 4096 Sep 3 12:10 boot
drwxr-xr-x 5 root root 360 Nov 18 18:42 dev
drwxr-xr-x 1 root root 4096 Nov 18 18:41 etc
drwxr-xr-x 2 root root 4096 Sep 3 12:10 home
drwxr-xr-x 1 root root 4096 Nov 15 09:32 lib
drwxr-xr-x 2 root root 4096 Nov 14 00:00 media
drwxr-xr-x 2 root root 4096 Nov 14 00:00 mnt
drwxr-xr-x 1 root root 4096 Nov 16 22:03 opt
dr-xr-xr-x 217 root root 0 Nov 18 18:42 proc
drwxr-xr-x 15 appuser appuser 480 Nov 14 18:43 project
drwx------ 1 root root 4096 Nov 18 18:41 root
drwxr-xr-x 3 root root 4096 Nov 14 00:00 run
drwxr-xr-x 2 root root 4096 Nov 14 00:00 sbin
drwxr-xr-x 2 root root 4096 Nov 14 00:00 srv
dr-xr-xr-x 13 root root 0 Nov 18 18:42 sys
drwxr-xr-x 9 root root 288 Nov 10 18:15 tests
drwxrwxrwt 1 root root 4096 Nov 16 22:04 tmp
drwxr-xr-x 1 root root 4096 Nov 14 00:00 usr
drwxr-xr-x 1 root root 4096 Nov 14 00:00 var
appuser@20bb48f9148a:/project$ pwd
/project
appuser@20bb48f9148a:/project$ ls -la
total 84
drwxr-xr-x 15 appuser appuser 480 Nov 14 18:43 .
drwxr-xr-x 1 root root 4096 Nov 18 18:41 ..
-rw-r--r-- 1 appuser appuser 385 Oct 21 15:05 .dockerignore
drwxr-xr-x 6 appuser appuser 192 Nov 10 17:59 .pytest_cache
drwxr-xr-x 6 appuser appuser 192 Nov 14 16:05 .venv
-rw-r--r-- 1 appuser appuser 232 Nov 16 17:52 BUILD
-rw-r--r-- 1 appuser appuser 1739 Nov 14 18:43 Dockerfile
-rw-r--r-- 1 appuser appuser 0 Oct 31 14:28 __init__.py
drwxr-xr-x 3 appuser appuser 96 Oct 31 14:34 __pycache__
drwxr-xr-x 2 appuser appuser 64 Sep 29 21:12 alembic
-rw-r--r-- 1 appuser appuser 1591 Oct 6 19:58 alembic.ini
drwxr-xr-x 18 appuser appuser 576 Nov 18 18:42 app
-rw-r--r-- 1 appuser appuser 54975 Nov 16 22:01 poetry.lock
-rw-r--r-- 1 appuser appuser 1344 Nov 16 22:01 pyproject.toml
-rwxr-xr-x 1 appuser appuser 381 Nov 11 22:44 startup.sh
appuser@20bb48f9148a:/project$

If I run the application from the PyCharm debugger and open a bash shell in the container and run the same set of command line tools, I get this:

appuser@be88621182fa:/opt/project/project/app$ ls -la /
total 76
drwxr-xr-x 1 root root 4096 Nov 18 18:48 .
drwxr-xr-x 1 root root 4096 Nov 18 18:48 ..
-rwxr-xr-x 1 root root 0 Nov 18 18:48 .dockerenv
drwxr-xr-x 1 root root 4096 Nov 15 09:32 bin
drwxr-xr-x 2 root root 4096 Sep 3 12:10 boot
drwxr-xr-x 5 root root 360 Nov 18 18:48 dev
drwxr-xr-x 1 root root 4096 Nov 18 18:48 etc
drwxr-xr-x 2 root root 4096 Sep 3 12:10 home
drwxr-xr-x 1 root root 4096 Nov 15 09:32 lib
drwxr-xr-x 2 root root 4096 Nov 14 00:00 media
drwxr-xr-x 2 root root 4096 Nov 14 00:00 mnt
drwxr-xr-x 1 root root 4096 Nov 18 18:48 opt
dr-xr-xr-x 214 root root 0 Nov 18 18:48 proc
drwxr-xr-x 15 appuser appuser 480 Nov 14 18:43 project
drwx------ 1 root root 4096 Nov 18 18:48 root
drwxr-xr-x 3 root root 4096 Nov 14 00:00 run
drwxr-xr-x 2 root root 4096 Nov 14 00:00 sbin
drwxr-xr-x 2 root root 4096 Nov 14 00:00 srv
dr-xr-xr-x 13 root root 0 Nov 18 18:48 sys
drwxr-xr-x 9 root root 288 Nov 10 18:15 tests
drwxrwxrwt 1 root root 4096 Nov 16 22:04 tmp
drwxr-xr-x 1 root root 4096 Nov 14 00:00 usr
drwxr-xr-x 1 root root 4096 Nov 14 00:00 var
appuser@be88621182fa:/opt/project/project/app$ pwd
/opt/project/project/app
appuser@be88621182fa:/opt/project/project/app$ ls -la
total 32
drwxr-xr-x 18 appuser appuser 576 Nov 18 18:42 .
drwxr-xr-x 15 appuser appuser 480 Nov 14 18:43 ..
-rw-r--r-- 1 appuser appuser 341 Nov 16 21:58 .env
-rw-r--r-- 1 appuser appuser 233 Nov 10 21:37 .env.template
drwxr-xr-x 5 appuser appuser 160 Nov 9 13:38 .mypy_cache
-rw-r--r-- 1 appuser appuser 17 Nov 9 20:17 BUILD
-rw-r--r-- 1 appuser appuser 0 Nov 16 18:22 __init__.py
drwxr-xr-x 7 appuser appuser 224 Nov 10 17:22 __pycache__
drwxr-xr-x 7 appuser appuser 224 Nov 18 18:36 auth
drwxr-xr-x 7 appuser appuser 224 Nov 16 19:07 common
-rw-r--r-- 1 appuser appuser 3723 Nov 16 17:50 config.py
-rw-r--r-- 1 appuser appuser 858 Nov 16 17:50 main.py
-rw-r--r-- 1 appuser appuser 0 Nov 16 17:50 models.py
drwxr-xr-x 6 appuser appuser 192 Nov 16 17:50 patients
drwxr-xr-x 6 appuser appuser 192 Nov 16 16:10 schedules
-rw-r--r-- 1 appuser appuser 2280 Nov 16 22:04 server.py
-rw-r--r-- 1 appuser appuser 925 Nov 18 18:42 settings.toml
-rw-r--r-- 1 appuser appuser 377 Nov 16 16:01 tags_metadata.json

So things are working, but I don't understand why they're set up this way. Like why does my application end up in /opt/project/project when run from the PyCharm debugger? I still need to add this:

PYTHONPATH=/opt/project/project

To the Run/Debug environment in order to run the app from PyCharm.

Doug

Daniil Bogdanov

Created November 21, 2022 15:46

This is indeed very odd.

Could you please try to edit docker-compose.yml and change the following:

dockerfile: ./Dockerfile

dockerfile: Dockerfile

Also, I mocked the last part of the docker building process with a dummy startup.sh with only one echo command. Could it be an issue inside that script?

Dfarrell

Created November 22, 2022 19:32

Hi Daniil,

I changed the docker-compose.yml file as you suggested:

dockerfile: ./Dockerfile => dockerfile: Dockerfile

And everything runs as it did before. The application runs from the command line, and the project is in (from the root) /project.

When run from the PyCharm debugger, it runs, and the project is in (from the root) /opt/project/project.

So effectively no change in behavior.

Doug

Daniil Bogdanov

Created November 23, 2022 14:37

Hi Doug,

I'm very sorry; I was able to reproduce the issue after deleting all previously created images and found where the problem is.

At the moment, PyCharm creates a docker-compose.override.yml file which overrides your docker-compose.yml and makes an unexpected /opt/project dir with your project.

To mitigate this issue, please turn off Help | Find Action | Registry | python.use.targets.api (as I remember from our other conversation, it should be turned off already) and re-create the interpreter. There should be a new option called Path mappings in the Project interpreter window, and the paths in the container should be correct.

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