Use containers for R development

Table of contents

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:

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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
    develop:
      watch:
        - action: rebuild
          path: .
  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

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.