I have a few Docker containers up and running. The main ones are RStudio (for the app that connects to the database) and a database that's been synced with github container registry (ghcr.io). The end goal will be transitioning the R Shiny app to a Dash app in Python. Right now I'm having trouble connecting the database to either the Shiny app in another container or Python (the Python app has yet to be developed). See below for the docker-compose.yml
version: '3'
services:
frontapp:
container_name: frontend
build:
context: .
dockerfile: shinyserver-dockerfile
ports:
- "3838:3838"
volumes:
- type: bind
source: ../
target: /XXXX/XX_front_end_R
networks:
- frontend
rstudio:
container_name: rstudio
build:
context: .
dockerfile: rstudio-dockerfile
ports:
- "8787:8787"
volumes:
- type: bind
source: ../
target: /home/rstudio
networks:
- frontend
db:
image: ghcr.io/XXXX/XX_db:main
container_name: db
ports:
- "3306:3306"
volumes:
- dbdata:/var/lib/mysql
phpmyadmin:
image: phpmyadmin/phpmyadmin
container_name: pma
links:
- db
environment:
PMA_HOST: db
PMA_PORT: 3306
PMA_ARBITRARY: 1
restart: always
ports:
- "8081:80"
networks:
- frontend
volumes:
dbdata:
networks:
frontend:
driver: bridge
Below is the result from docker ps
Then when I log into R Studio and try to run the app (in http://localhost:8787/), there's an error trying to connect to the database.
mydb <- dbConnect(MariaDB(), user = "XXXX", password = "YYYY",
dbname = "prototype", host = "db", port="3306")
I then get the following error:
Error: Failed to connect: Unknown MySQL server host 'db' (-2)
It looks like the app should be running on http://localhost:3838 although that page just returns an error.
Any help with connecting to the database is helpful. I'm not sure if there are other dependencies or installations that need to be done or if I'm not correcting in the right way. Thanks.
Note: I'm coming in fresh to this project. A previous developer has currently created what I have access to now.
Related
I have been trying to setup docker-compose for my application written in flask and connect it to msql database. Both containers are seems to be working fine and aplication starts properrly, but whenever there is any request to database, I am getting following error from my flask-app comtainer:
sqlalchemy.exc.OperationalError: (MySQLdb.OperationalError) (2002, "Can't connect to local MySQL server through socket '/run/mysqld/mysqld.sock' (2)")
For me it looks like my containers don't see each other. I am new to Docker, but I thought that my current docker-compose should work
version: '3.9'
networks:
backend:
volumes:
mysqldb:
services:
app:
restart: "no"
container_name: flask-app
build:
context: ./AEH_PAP
dockerfile: ./Dockerfile
ports:
- "9000:9000"
networks:
- backend
environment:
DATABASE_URI: mysql://user:password#db:9000/library3
links:
- 'db'
depends_on:
- db
volumes:
- /var/lib/mysql/mysql.sock:/mysql.sock
db:
container_name: mysql-db
image: "mysql:8.0.31"
ports:
- '3307:3306'
restart: "no"
environment:
MYSQL_ROOT_PASSWORD: root
MYSQL_DATABASE: library3
MYSQL_USER: user
MYSQL_PASSWORD: password
volumes:
- "mysqldb:/var/lib/mysql"
- "./init.sql:/docker-entrypoint-initdb.d/init.sql"
networks:
- backend
mysql-db logs
flask-app logs
Also I have been trying to connect to mysql-db container from flask-app container with command mysql --host localhost --port 3306 -u user -p but still getting the same error.
My Docker knowledge is very limited but should I have msql server installed also on flask-app?
I'm trying to connect my FASTAPI app container to a MySQL database container using the docker-compose file. In the Docker documentation it says that docker creates a default network for both containers. However, I would like to use a pre-existing network that I've created(app-net).
This is my docker-compose file:
version: '3.4'
services:
mysql:
image: mysql:latest
command: mysqld --default-authentication-plugin=mysql_native_password
container_name: mysql
restart: always
ports:
- 3307:3306
environment:
MYSQL_ROOT_PASSWORD: password
volumes:
- mysql-data:/var/lib/mysql
app:
build: .
image: app:1.0
container_name: app
ports:
- 8000:8000
environment:
PASSWORD: password
USERNAME: root
networks:
default:
external: true
name: app-net
volumes:
mysql-data:
driver: local
this is the output I get when i run docker inspect mysql -f "{{json .NetworkSettings.Networks }}":
{"app-net":{"IPAMConfig":null,"Links":null,"Aliases":["mysql","5e998f9fb646"],"NetworkID":"7f60c83e4c88d25e674461521446ec9fa98baca8639c782c79671c4fcb77ba88","EndpointID":"","Gateway":"","IPAddress":"","IPPrefixLen":0,"IPv6Gateway":"","GlobalIPv6Address":"","GlobalIPv6PrefixLen":0,"MacAddress":"","DriverOpts":null}}
However, when I run each container individually using CMD with the --network app-net the output is different:
{"app-net":{"IPAMConfig":null,"Links":null,"Aliases":["46157e588c87"],"NetworkID":"7f60c83e4c88d25e674461521446ec9fa98baca8639c782c79671c4fcb77ba88","EndpointID":"6a6922a9a6ea8f9d113447decbbb927cb93ddffd3b9563ee882fa2e44970cde5","Gateway":"172.20.0.1","IPAddress":"172.20.0.2","IPPrefixLen":16,"IPv6Gateway":"","GlobalIPv6Address":"","GlobalIPv6PrefixLen":0,"MacAddress":"02:42:ac:14:00:02","DriverOpts":null}}
In my app code in order to connect the mysql server, I specified the container name as the hostname since they are supposed to share the same network. But, as I mentioned it seems both containers can't talk to each other.
I'm pretty sure that is the reason I can't connect the database through my app and get that error when I run:
docker-compose -f docker-compose.yml up
I get this error:
sqlalchemy.exc.OperationalError: (_mysql_exceptions.OperationalError) (2005, "Unknown MySQL server host 'mysql' (0)")
What am I missing?
If the error you're getting is specifically "unknown host" or something similar, this can happen if your application container starts before the database container exists. You can work around this situation by telling Compose about the dependency:
version: '3.8'
services:
mysql: { ... }
app:
depends_on:
- mysql
This has two key effects. If you try to start only the application container docker-compose up app, it will also start the mysql container, following the depends_on: chain. When Compose does start containers, it at least creates the mysql container before creating the app container.
Note that this doesn't guarantee the database will actually be running by the time your application starts up. If you do encounter this, you will get a different error like "connection refused". You can work around this by embedding a script in your image that waits for the database to be available, or by using a version 2 Compose file with health-check support; see Docker Compose wait for container X before starting Y for more details on this specific problem.
You could add the key networks to both containers, this way:
version: '3.4'
services:
mysql:
image: mysql:latest
command: mysqld --default-authentication-plugin=mysql_native_password
container_name: mysql
restart: always
ports:
- 3307:3306
environment:
MYSQL_ROOT_PASSWORD: password
volumes:
- mysql-data:/var/lib/mysql
networks:
- app-net
app:
build: .
image: app:1.0
container_name: app
ports:
- 8000:8000
environment:
PASSWORD: password
USERNAME: root
networks:
- app-net
networks:
default:
external: true
name: app-net
volumes:
mysql-data:
driver: local
I'm trying to create a docker-compose.yml file that will bring up JIRA and MySQL. Here's my file:
version: '3'
services:
jira:
depends_on:
- mysql
container_name: jira
restart: always
networks:
- jiranet
build:
context: .
dockerfile: Dockerfile.jira
environment:
- ATL_DB_TYPE=mysql
- ATL_DB_DRIVER=com.mysql.cj.jdbc.Driver
- ATL_JDBC_URL=jdbc:mysql://mysql:3306/jiradb
- ATL_JDBC_USER=jira
- ATL_JDBC_PASSWORD=jellyfish
ports:
- 8080:8080
volumes:
- jira-data:/var/atlassian-data/jira
mysql:
container_name: mysql
restart: always
image: mysql:5.7
networks:
- jiranet
environment:
- MYSQL_ROOT_PASSWORD=ChangeMe!
- MYSQL_DATABASE=jiradb
- MYSQL_USER=jira
- MYSQL_PASSWORD=jellyfish
command: [mysqld, --character-set-server=utf8, --collation-server=utf8_bin, --default-storage-engine=INNODB, --max_allowed_packet=256M, --innodb_log_file_size=2GB, --transaction-isolation=READ-COMMITTED, --binlog_format=row]
volumes:
- mysql-data:/var/lib/mysql
networks:
jiranet: {}
volumes:
jira-data:
mysql-data:
Unfortunately, I'm getting JIRA startup errors when it tried to initialize the database, of the form:
CREATE command denied to user 'jira'#'172.22.0.3' for table 'jiraaction'
I'm guessing it's because the mysql container is creating user jira, but only allowing it to connect from localhost. But, the JIRA container is being seen as coming from an an external IP.
Any ideas on how I can get the jiradb database in mysql to be accessible by the JIRA container by user jira?
I figured out the problem -- I was missing an environment variable in the jira container:
ATL_DB_SCHEMA_NAME=jiradb
After that, things worked fine!
I'm developing Backend server with prisma 2, MySQL, Docker-compose, GraphQL-Yoga server
My OS is Windows 10, docker compose use debian-openssl-1.1.x
problem is prisma 2 container can't connect MySQL container
docker-compose.yml
version: "3.7"
services:
mysql:
image: mysql:8.0.19
container_name: mysql
ports:
- 3306:3306
restart: always
environment:
MYSQL_DATABASE: $${MYSQL_DATABASE}
MYSQL_ROOT_PASSWORD: $${MYSQL_ROOT_PASSWORD}
volumes:
- /var/lib/mysql
prisma:
links:
- mysql
depends_on:
- mysql
container_name: prisma
ports:
- "5555:5555"
build:
context: back/prisma
dockerfile: Dockerfile
environment:
MYSQL_URL: $${MYSQL_URL}
MYSQL_ROOT_PASSWORD: $${MYSQL_ROOT_PASSWORD}
volumes:
- /app/prisma
backend:
links:
- mysql
depends_on:
- mysql
container_name: backend
ports:
- "4000:4000"
build:
context: back
dockerfile: Dockerfile
environment:
MYSQL_URL: $${MYSQL_URL}
FRONTEND_URL: $${FRONTEND_URL}
volumes:
- ./back:/app
- ./back/node_modules:/app/node_modules
- ./back/prisma:/app/prisma
frontend:
container_name: frontend
ports:
- "3000:3000"
build:
context: front
dockerfile: Dockerfile
environment:
BACKEND_URL: $${BACKEND_URL}
volumes:
- ./front:/app
- ./front/node_modules:/app/node_modules
.env
MYSQL_URL="mysql://root:prisma#mysql:3306/prisma"
BACKEND_URL=http://localhost:4000
FRONTEND_URL=http://localhost:3000
MYSQL_DATABASE:"prisma"
MYSQL_ROOT_PASSWORD:"prisma"
-schema.prisma
generator client {
provider = "prisma-client-js"
binaryTargets = ["native", "debian-openssl-1.1.x"]
}
datasource db {
provider = "mysql"
url = env("DATABASE_URL")
}
.env in prisma folder
DATABASE_URL="mysql://root:prisma#mysql:3306/prisma"
when i run docker-compose (docker-compose up), prisma container (prisma 2 studio) show this logs
Error in Prisma Client request:
Error:
Invalid `prisma.user.count()` invocation:
Authentication failed against database server at `mysql`, the provided database credentials for `root` are not valid.
Please make sure to provide valid database credentials for the database server at `mysql`.
at PrismaClientFetcher.request (/root/.cache/prisma/studio/app/runtime/index.js:1:52273)
at processTicksAndRejections (internal/process/task_queues.js:97:5)
enter image description here
I think this error occurred because MySQL container has a password different from MYSQL_ROOT_PASSWORD which I wrote in the doctor-compose.yml.
But, i think there seems to be no problem with the setup, why is this error happening?
And if i did not set up MYSQL_ROOT_PASSWORD, what is the default password value generated by MySQL container?
I searched for days to find the answer to this problem, but I could not get the answer. please give me some advices. thank you
I want to run two instances of mysql using docker-compose.
I'm running MySQL in a Docker container and I have another Docker container running a python script to access the MySQL database.
One works fine on port 3306. In order to get two working, I thought I would just run the other one on a different port. But when I change it to a different port (e.g. 6603), but when I do, I get the below error:
mysql.connector.errors.InterfaceError: 2003: Can't connect to MySQL server on 'mysql:6603' (111 Connection refused)
I have read every question on s.o. I can find that seems relevant but none of the solutions work. I feel certain the fix will involve changing a line or two of configuration but I've spent many hours on this so far so any help would be greatly appreciated.
The docker-compose script is below (works fine if 6603 is replaced with 3306).
server:
build:
context: ../
dockerfile: Docker/ServerDockerfile
ports:
- "8080:8080"
links:
- mysql:mysql
volumes:
- ../py:/app
tty: true
mysql:
image: mysql
expose:
- "6603"
environment:
MYSQL_ROOT_PASSWORD: password
MYSQL_DATABASE: project
volumes:
- ./MySQL:/docker-entrypoint-initdb.d
- ./MySQL/data:/var/lib/mysql
And it is being accessed like this:
cnx = mysql.connector.connect(user='root', password='password',
host='mysql',
port="6603",
database='project')
Try to specify another port for MySQL by modifying its my.cnf file.
Have eventually found a couple of ways that work. The neatest one is for each app to create a network and connect the containers to it.
If each app uses a different network then mysql can run on 3306 on that Docker network and can be accessed on mysql://3306 from app1 and mysql2://3306 from app2. (Assuming you name you give the mysql service for app 2 is mysql2).
The Docker file with the new lines is below:
server:
build:
context: ../
dockerfile: Docker/ServerDockerfile
ports:
- "8080:8080"
volumes:
- ../py:/app
tty: true
networks:
-net
mysql2:
image: mysql
environment:
MYSQL_ROOT_PASSWORD: password
MYSQL_DATABASE: project
volumes:
- ./MySQL:/docker-entrypoint-initdb.d
- ./MySQL/data:/var/lib/mysql
networks:
-net
networks:
net:
driver: bridge
The Docker file for the second app is identical except the names are different (I put a 2 after each for simplicity).
server2:
build:
context: ../
dockerfile: Docker/ServerDockerfile
ports:
- "8081:8080"
volumes:
- ../py:/app
tty: true
networks:
-net2
mysql2:
image: mysql
environment:
MYSQL_ROOT_PASSWORD: password
MYSQL_DATABASE: project
volumes:
- ./MySQL:/docker-entrypoint-initdb.d
- ./MySQL/data:/var/lib/mysql
networks:
-net2
networks:
net2:
driver: bridge