Dockerizing Fishbase Api

Dockerized MySQL background

Figuring out using an external MySQL docker container for the in-development fishbase API.

docker run --name some-mysql -e MYSQL_ROOT_PASSWORD=mysecretpassword -d mysql
docker run --rm -ti --link some-mysql:mysql ubuntu:latest bash

Now that we’re inside the ubuntu container we can see linked environment:



LESSOPEN=| /usr/bin/lesspipe %s
LESSCLOSE=/usr/bin/lesspipe %s %s

Great. Now we need a mysql client to access the host:

apt-get update && apt-get install -y mysql-client-core-5.6

Note that we cannot simply do:


which gives the error:

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

Instead, we must also specify the protocol and port of the server:

mysql --host=$MYSQL_PORT_3306_TCP_ADDR --protocol=$MYSQL_PORT_3306_TCP_PROTO --password=$MYSQL_ENV_MYSQL_ROOT_PASSWORD

EDIT It’s much better to use the hostname provided by the linked container in /etc/hosts. This automatically binds the name used in the link mysql to the linked container’s IP address, so we can simply do: mysql =--host=mysql --password=$MYSQL_ENV_MYSQL_ROOT_PASSWORD (protocol, like the port, is guessed implicitly from host). Unlike the env var solution, the /etc/hosts file is updated if the mysql container restarts.

and we’re good to go:

Warning: Using a password on the command line interface can be insecure.
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 5
Server version: 5.6.22 MySQL Community Server (GPL)

Copyright (c) 2000, 2014, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.


Applying this in fishbaseapi

Scott has put together a nice start to the fishbase API built on Ruby’s sinatra gem.

First step is to import the SQL database archive.

For our database to persist even if our container is destroyed, we link it to a local volume. So we start a mysql container with a local volume link, e.g. to /opt/fishbase/data on the server:

sudo mkdir -p /opt/fishbase/data
docker run --name mysql -e MYSQL_ROOT_PASSWORD=mysecretpassword -d -v /opt/fishbase/data:/var/lib/mysql mysql

We now need to import the data from the fbapp.sql file as a one-off event. We’ll use a temporary mysql container to do this, linked to the persistent image we just launched. For this container, we’ll start a bash container that is linked to the fbapp.sql file directly (note that docker volume linking works for files too):

docker run --rm -ti --link mysql:mysql -v /path/to/fbapp.sql:/data/fbapp.sql -w /data mysql bash

This drops us into a bash session on the container where we can launch a linked mysql session and import our tables:

mysql --host=$MYSQL_PORT_3306_TCP_ADDR --protocol=$MYSQL_PORT_3306_TCP_PROTO --password=$MYSQL_ENV_MYSQL_ROOT_PASSWORD fbapp < fbapp.sql

Note: if this gives us an error about being unable to write the table, we may need to adjust the permissions of the linked file appropriately.

docker exec -ti mysql bash
chown -R mysql:mysql /var/lib/mysql

From here, the database is set up and ready to be linked to our app.

Dockerizing the Sinatra app

This is straight-forward, noting only that we need to again use the environmental variables shown for the mysql credentials inside our ruby script:

  client = => ENV['MYSQL_PORT_3306_TCP_ADDR'], 
                             :port => ENV['MYSQL_PORT_3306_TCP_PORT'], 
                             :password => ENV['MYSQL_ENV_MYSQL_ROOT_PASSWORD'],
                             :username => "root", 
                             :database => "fbapp")

and that we need to execute our ruby app with host instead of the default localhost so that the port will be accessible outside the docker container, like so:

ruby api.rb -o

We could get away with just a 2-line Dockerfile using the onbuild flavor of the official Ruby containers, which has rather clever triggers for installing dependencies listed in the Gemfile when the image is built, see DockerHub/ruby.

Since one still needs to build a new Docker image either way, I’ve opted for a slightly more explicit (and smaller) Dockerfile based on Debian instead. This installs the ruby dependencies (including gems and associated libraries, which would all have been automated by the Ruby Dockerfile), and sets up a default run command to launch the app running the sinatra API.

Just run this container linked to the database and we’re good to go:

docker run -d -p 4567:4567 --link mysql:mysql ropensci/rfishbase