PermissionError: [Errno 1] Operation not permitted while a docker conatiner tries to connect to database

Question

I am trying to build docker containers from the following docker-compose file. All the containers are created and are connected to MySQL database except one container which is throwing an error. It is having same permissions as other containers and the same port is provided for the database but it doesn't connect to the database. Here is the error from the docker container logs

enabling audit logging
Waiting for database to be reachable 
Traceback (most recent call last):
  File "/usr/local/bin/celery", line 8, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.6/site-packages/celery/__main__.py", line 16, in main
    _main()
  File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 322, in main
    cmd.execute_from_commandline(argv)
  File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 499, in execute_from_commandline
    super(CeleryCommand, self).execute_from_commandline(argv)))
  File "/usr/local/lib/python3.6/site-packages/celery/bin/base.py", line 305, in execute_from_commandline
    return self.handle_argv(self.prog_name, argv[1:])
  File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 491, in handle_argv
    return self.execute(command, argv)
  File "/usr/local/lib/python3.6/site-packages/celery/bin/celery.py", line 419, in execute
    ).run_from_argv(self.prog_name, argv[1:], command=argv[0])
  File "/usr/local/lib/python3.6/site-packages/celery/bin/base.py", line 309, in run_from_argv
    sys.argv if argv is None else argv, command)
  File "/usr/local/lib/python3.6/site-packages/celery/bin/base.py", line 393, in handle_argv
    return self(*args, **options)
  File "/usr/local/lib/python3.6/site-packages/celery/bin/base.py", line 253, in __call__
    ret = self.run(*args, **kwargs)
  File "/usr/local/lib/python3.6/site-packages/celery/bin/beat.py", line 100, in run
    maybe_drop_privileges(uid=uid, gid=gid)
  File "/usr/local/lib/python3.6/site-packages/celery/platforms.py", line 543, in maybe_drop_privileges
    _setuid(uid, gid)
  File "/usr/local/lib/python3.6/site-packages/celery/platforms.py", line 564, in _setuid
    initgroups(uid, gid)
  File "/usr/local/lib/python3.6/site-packages/celery/platforms.py", line 507, in initgroups
    return os.initgroups(username, gid)
PermissionError: [Errno 1] Operation not permitted
wait-for-it.sh: waiting 30 seconds for mysql:3306
wait-for-it.sh: mysql:3306 is available after 0 seconds
uid=1001(defectdojo) gid=65534(nogroup) groups=65534(nogroup) 

docker-compose.yml

    ---
version: '3.7'
services:
  nginx:
    build:
      context: ./jamshaid
      dockerfile: Dockerfile.nginx
    image: defectdojo/defectdojo-nginx:${NGINX_VERSION:-latest}
    restart: always
    depends_on:
      - uwsgi
    ports:
      - target: ${DD_PORT:-8080}
        published: ${DD_PORT:-9092}
        protocol: tcp
        mode: host
  uwsgi:
    build:
      context: ./jamshaid
      dockerfile: Dockerfile.django
    image: defectdojo/defectdojo-django:${DJANGO_VERSION:-latest}
    restart: always
    depends_on:
      - mysql
    entrypoint: ['/wait-for-it.sh', 'mysql:3306', '-t', '30', '--', '/entrypoint-uwsgi.sh']
    environment:
      DD_DEBUG: 'False'
      DD_ALLOWED_HOSTS: ${DD_ALLOWED_HOSTS:-*}
      DD_DATABASE_URL: ${DD_DATABASE_URL:-mysql://defectdojo:defectdojo@mysql:3306/defectdojo}
      DD_CELERY_BROKER_USER: ${DD_CELERY_BROKER_USER:-guest}
      DD_CELERY_BROKER_PASSWORD: ${DD_CELERY_BROKER_USER:-guest}
      DD_SECRET_KEY: ${DD_SECRET_KEY:-hhZCp@D28z!n@NED*yB!ROMt+WzsY*iq}
      DD_CREDENTIAL_AES_256_KEY: ${DD_CREDENTIAL_AES_256_KEY:-&91a*agLqesc*0DJ+2*bAbsUZfR*4nLw}
  celerybeat:
    image: defectdojo/defectdojo-django:latest
    restart: always
    depends_on:
      - mysql
      - rabbitmq
    entrypoint: ['/wait-for-it.sh', 'mysql:3306', '-t', '30', '--', '/entrypoint-celery-beat.sh']
    environment:
      DD_DATABASE_URL: ${DD_DATABASE_URL:-mysql://defectdojo:defectdojo@mysql:3306/defectdojo}
      DD_CELERY_BROKER_USER: ${DD_CELERY_BROKER_USER:-guest}
      DD_CELERY_BROKER_PASSWORD: ${DD_CELERY_BROKER_USER:-guest}
      DD_SECRET_KEY: ${DD_SECRET_KEY:-hhZCp@D28z!n@NED*yB!ROMt+WzsY*iq}
      DD_CREDENTIAL_AES_256_KEY: ${DD_CREDENTIAL_AES_256_KEY:-&91a*agLqesc*0DJ+2*bAbsUZfR*4nLw}
  celeryworker:
    image: defectdojo/defectdojo-django:latest
    restart: always
    depends_on:
      - mysql
      - rabbitmq
    entrypoint: ['/wait-for-it.sh', 'mysql:3306', '-t', '30', '--', '/entrypoint-celery-worker.sh']
    environment:
      DD_DATABASE_URL: ${DD_DATABASE_URL:-mysql://defectdojo:defectdojo@mysql:3306/defectdojo}
      DD_CELERY_BROKER_USER: ${DD_CELERY_BROKER_USER:-guest}
      DD_CELERY_BROKER_PASSWORD: ${DD_CELERY_BROKER_USER:-guest}
      DD_SECRET_KEY: ${DD_SECRET_KEY:-hhZCp@D28z!n@NED*yB!ROMt+WzsY*iq}
      DD_CREDENTIAL_AES_256_KEY: ${DD_CREDENTIAL_AES_256_KEY:-&91a*agLqesc*0DJ+2*bAbsUZfR*4nLw}
  initializer:
    image: defectdojo/defectdojo-django:latest
    restart: always
    depends_on:
      - mysql
    entrypoint: ['/wait-for-it.sh', 'mysql:3306', '--', '/entrypoint-initializer.sh']
    environment:
      DD_DATABASE_URL: ${DD_DATABASE_URL:-mysql://defectdojo:defectdojo@mysql:3306/defectdojo}
      DD_ADMIN_USER: ${DD_ADMIN_USER:-admin}
      DD_ADMIN_MAIL: ${DD_ADMIN_USER:-admin@defectdojo.local}
      DD_ADMIN_FIRST_NAME: ${DD_ADMIN_FIRST_NAME:-Admin}
      DD_ADMIN_LAST_NAME: ${DD_ADMIN_LAST_NAME:-User}
      DD_INITIALIZE: ${DD_INITIALIZE:-true}
      DD_SECRET_KEY: ${DD_SECRET_KEY:-hhZCp@D28z!n@NED*yB!ROMt+WzsY*iq}
      DD_CREDENTIAL_AES_256_KEY: ${DD_CREDENTIAL_AES_256_KEY:-&91a*agLqesc*0DJ+2*bAbsUZfR*4nLw}
  mysql:
    image: mysql:5.7.27@sha256:540488d8f0e04c1077d17934d1c1511fe417e2221dff508ce4621f5efe6131db
    restart: always
    environment:
      MYSQL_RANDOM_ROOT_PASSWORD: 'yes'
      DD_DATABASE_URL: ${DD_DATABASE_URL:-mysql://defectdojo:defectdojo@mysql:3306/defectdojo}
      MYSQL_USER: ${DD_DATABASE_USER:-defectdojo}
      MYSQL_PASSWORD: ${DD_DATABASE_PASSWORD:-defectdojo}
      MYSQL_DATABASE: ${DD_DATABASE_NAME:-defectdojo}
    command: ['mysqld', '--character-set-server=utf8mb4', '--collation-server=utf8mb4_unicode_ci']
    volumes:
       - defectdojo_data:/var/lib/mysql
    ports:
       - 3306:3306
  rabbitmq:
    image: rabbitmq:3.7.17@sha256:12202c13c8e1d7f5688e733e04f3713cf25c4478dde62be691e0a1d2c9346d1c
    restart: always
volumes:
  defectdojo_data: {} 

The error is being thrown by celerybeat: container. I am unable to understand the cause because all the containers are connecting successfully except this one. What might be the issues? thanks a lot
Dockerfile.nginx

    #
# Nginx Dockerfile
#
# https://github.com/dockerfile/nginx
#

# Pull base image.
FROM ubuntu:18.04

# Install Nginx.
RUN \
  add-apt-repository -y ppa:nginx/stable && \
  apt-get update && \
  apt-get install -y nginx && \
  rm -rf /var/lib/apt/lists/* && \
  echo "\ndaemon off;" >> /etc/nginx/nginx.conf && \
  chown -R www-data:www-data /var/lib/nginx

# Define mountable directories.
VOLUME ["/etc/nginx/sites-enabled", "/etc/nginx/certs", "/etc/nginx/conf.d", "/var/log/nginx", "/var/www/html"]

# Define working directory.
WORKDIR /etc/nginx

# Define default command.
CMD ["nginx"]

# Expose ports.
EXPOSE 80
EXPOSE 443
 

Dockerfile.django

    FROM python:3.4-slim

RUN apt-get update && apt-get install -y \
        gcc \
        gettext \
        mysql-client libmysqlclient-dev \
        postgresql-client libpq-dev \
        sqlite3 \
    --no-install-recommends && rm -rf /var/lib/apt/lists/*

ENV DJANGO_VERSION 1.10.4

RUN pip install mysqlclient psycopg2 django=="$DJANGO_VERSION"
 

Answer 1

you should try by running docker-compose using sudo. (if not already using):

sudo docker-compose up