covid_ireland_shiny

Shiny application visualising the Covid Situation in the Republic of Ireland. The app is currently published on the RStudio shinyapps.io platform

https://iboboburo.shinyapps.io/coviddash/

Data Source

Initially I was pulling data from Ireland Covid Data Hub and specifically from here. However this proved to be buggy and often times didn't return the full data dataset

TODO: Write some test for this based on the return the count and comparing with the downloaded data ?

I changed the data pull to Irelands Open Data Portal and grabbed the csv data. This has proved to be more stable.

Development

Use renv to manage the environment for use in Docker.

renv::init()
renv::install("package_name")
renv::snapshot()

Installation & Dev

If you want to run local or extend you can do so by pulling the repo, then either setup the project for development locally

install.packages("renv")
renv::restore()

TODO: Create a Dockerfile fo development

The app can be run in online or offline mode. Offline is typically used in development and connect to local stored version of the data. The option can be changed the R/global.R file.

TODO: Find nicer way of passing this argument.

This requires creating a SQLite db with grab of the data. This is detailed in the DATA/create_db_table.md file.

Testing

There are a number of tests provided. To run

shiny::runTests()

Deployment

For all deployment, the R/global.R file mode should be set to online - alternatively you need to upload the SQLite db.

RStudio ShinyApps

The app can deployed directly from within R Studio to shinyapps.io

Github Actions

There a Github Action setup in the repo, this pushes to shinyapps.io on a pull request to the master branch. It can also be activated manually. The structure of the workflow is below. You need to add the secrets in the github repo.

jobs:
  deploy-shiny:
    runs-on: macOS-latest
    steps:
      - uses: actions/checkout@v2
      - uses: r-lib/actions/setup-r@master
      - name: install-packages
        run: |
         Rscript -e "install.packages(c('renv'), type  = 'binary')"
         Rscript -e "renv::restore()"
      - name: authorise-shiny
        run: |
<<<<<<< Updated upstream
         Rscript -e "rsconnect::setAccountInfo(name='yourAccount', token=${{secrets.SHINYAPPS_TOKEN}}, secret=${{secrets.SHINYAPPS_SECRET}})"
         Rscript -e "rsconnect::deployApp(appName = 'yourAppName')"

Docker

There is a nice guide to dockerising shiny apps here. A Dockerfile is provided.

Create the docker image

docker build -t covid-irl-image . 

Run the image

docker run -d --rm -p 3838:3838 covid-irl-image

TODO

• add tests
• add Ireland as a "county"
• write up installation.
• add data in sqlite for Docker container
• update dockerFile
• create Docker ignore file
• create docker image and publish ?
• add other countries ?
• reduce dependencies
• add test check to GA

Blog write up points

• project template
• start with plots
• then modules
• then stick it together
• move to tests - note on naming convention, need to change the test file, helper functions.
• docker file vs shiny apps.
• discuss golem as option vs https://shiny.rstudio.com/reference/shiny/1.5.0/shinyAppTemplate.html
• make sure that the secrets are setup with '', you have a unique secret for this computer ? will it work a second time