Use containers for R development
Prerequisites
Complete Containerize a R application.
Overview
In this section, you'll learn how to set up a development environment for your containerized application. This includes:
- Adding a local database and persisting data
- Configuring Compose to automatically update your running Compose services as you edit and save your code
Get the sample application
You'll need to clone a new repository to get a sample application that includes logic to connect to the database.
Change to a directory where you want to clone the repository and run the following command.
$ git clone https://github.com/mfranzon/r-docker-dev.git
Configure the application to use the database
To try the connection between the Shiny application and the local database you have to modify the Dockerfile
changing the COPY
instruction:
-COPY src/ .
+COPY src_db/ .
Add a local database and persist data
You can use containers to set up local services, like a database. In this section, you'll update the compose.yaml
file to define a database service and a volume to persist data.
In the cloned repository's directory, open the compose.yaml
file in an IDE or text editor.
In the compose.yaml
file, you need to un-comment the properties for configuring the database. You must also mount the database password file and set an environment variable on the shiny-app
service pointing to the location of the file in the container.
The following is the updated compose.yaml
file.
services:
shiny-app:
build:
context: .
dockerfile: Dockerfile
ports:
- 3838:3838
environment:
- POSTGRES_PASSWORD_FILE=/run/secrets/db-password
depends_on:
db:
condition: service_healthy
secrets:
- db-password
db:
image: postgres
restart: always
user: postgres
secrets:
- db-password
volumes:
- db-data:/var/lib/postgresql/data
environment:
- POSTGRES_DB=example
- POSTGRES_PASSWORD_FILE=/run/secrets/db-password
expose:
- 5432
healthcheck:
test: [ "CMD", "pg_isready" ]
interval: 10s
timeout: 5s
retries: 5
volumes:
db-data:
secrets:
db-password:
file: db/password.txt
Note
To learn more about the instructions in the Compose file, see Compose file reference.
Before you run the application using Compose, notice that this Compose file specifies a password.txt
file to hold the database's password. You must create this file as it's not included in the source repository.
In the cloned repository's directory, create a new directory named db
and inside that directory create a file named password.txt
that contains the password for the database. Using your favorite IDE or text editor, add the following contents to the password.txt
file.
mysecretpassword
Save and close the password.txt
file.
You should now have the following contents in your r-docker-dev
directory.
├── r-docker-dev/
│ ├── db/
│ │ └── password.txt
│ ├── src/
│ │ └── app.R
│ ├── src_db/
│ │ └── app_db.R
│ ├── requirements.txt
│ ├── .dockerignore
│ ├── compose.yaml
│ ├── Dockerfile
│ ├── README.Docker.md
│ └── README.md
Now, run the following docker compose up
command to start your application.
$ docker compose up --build
Now test your DB connection opening a browser at:
http://localhost:3838
You should see a pop-up message:
DB CONNECTED
Press ctrl+c
in the terminal to stop your application.
Automatically update services
Use Compose Watch to automatically update your running Compose services as you edit and save your code. For more details about Compose Watch, see Use Compose Watch.
Lines 15 to 18 in the compose.yaml
file contain properties that trigger Docker
to rebuild the image when a file in the current working directory is changed:
|
|
Run the following command to run your application with Compose Watch.
$ docker compose watch
Now, if you modify your app.R
you will see the changes in real time without re-building the image!
Press ctrl+c
in the terminal to stop your application.
Summary
In this section, you took a look at setting up your Compose file to add a local database and persist data. You also learned how to use Compose Watch to automatically rebuild and run your container when you update your code.
Related information:
Next steps
In the next section, you'll take a look at how to set up a CI/CD pipeline using GitHub Actions.