Docker

Table of contents

1. Error response from daemon: driver failed programming external connectivity on endpoint mariadb_container (XXX): Error starting userland proxy: listen tcp4 0.0.0.0:3306: bind: address already in use
   1. Identify the process using port 3306
   2. Kill process
   3. Disable MariaDB
2. docker.errors.DockerException: Error while fetching server API version: (‘Connection aborted.’, FileNotFoundError(2, ‘No such file or directory’))
   1. How features are selected
   2. Solution 1: deploy with the webhook compose file
   3. Solution 2: drop the feature from your deployment

Error response from daemon: driver failed programming external connectivity on endpoint mariadb_container (XXX): Error starting userland proxy: listen tcp4 0.0.0.0:3306: bind: address already in use

This occurs because there is already a process on port 3306 (typically because MariaDB has been installed manually).

Identify the process using port 3306

sudo lsof -i :3306

With this we find out the PID identifier of the process running on 3306

Kill process

sudo kill -9 <PID>

Disable MariaDB

If you have installed uvlhub manually and you are not going to use this deployment anymore, it is convenient to disable the MariaDB process:

sudo systemctl stop mariadb
sudo systemctl disable mariadb

docker.errors.DockerException: Error while fetching server API version: (‘Connection aborted.’, FileNotFoundError(2, ‘No such file or directory’))

This is the webhook feature failing to import. app/features/webhook/services.py calls docker.from_env() at module level, so the exception is raised while the feature is being registered and the application never finishes booting.

That call needs two things the plain production container does not have: the Docker CLI, which is installed only in docker/images/Dockerfile.dev and docker/images/Dockerfile.webhook, and the Docker socket bind-mounted at /var/run/docker.sock.

How features are selected

Which features get loaded is declared in the root pyproject.toml (see Feature selection):

[tool.splent]
features = [
    "auth",
    "dataset",
    "explore",
    "featuremodel",
    "flamapy",
    "hubfile",
    "profile",
    "public",
    "team",
    "zenodo",
]
features_dev = [
    "webhook",
]
features_prod = [
    "webhook",
]

app/feature_loader.py walks app/features/, and loads a feature only if it appears in features or in the list for the current environment (features_dev or features_prod). webhook is declared in both environment lists: its test suite needs it in development, and the CD pipeline posts to it in production.

The filter needs pyproject.toml to be present

app/feature_loader.py reads pyproject.toml from the directory above app/. If the file is not there, it falls back to loading every package it finds under app/features/. The production images (Dockerfile.prod, Dockerfile.render) copy it for exactly this reason; if you maintain a custom image, copy it too or the declarative filter is silently inactive.

Solution 1: deploy with the webhook compose file

If you want the webhook-driven deployment, use the compose file that was built for it:

docker compose -f docker/docker-compose.prod.webhook.yml up -d --build

It builds docker/images/Dockerfile.webhook, which installs the Docker CLI, bind-mounts the repository at /workspace and mounts /var/run/docker.sock into the container. With those in place docker.from_env() succeeds. This is the only production compose file with a build: section, which is why --build appears here.

Solution 2: drop the feature from your deployment

If you do not need continuous deployment through the webhook, remove "webhook" from both features_dev and features_prod in pyproject.toml. Images that carry pyproject.toml honour the lists; if yours does not, copy it in or delete app/features/webhook/ from your fork.

After that, bring the containers back up. These compose files pull the image instead of building it, so there is no --build:

docker compose -f docker/docker-compose.prod.yml up -d

If you are deploying using the SSL option:

docker compose -f docker/docker-compose.prod.ssl.yml up -d

Both files ship with the placeholder image: <your_dockerhub_name>/uvlhub:latest. If you have not replaced it yet, see Deployment in server.