Deploying mhealthannotator

Source: vignettes/deploying_mhealthannotator.Rmd

This vignette is applicable to Sage employees who are deploying the application on our Shiny Pro server. To learn about the server and how to get credentials, please read the Confluence documentation.

The app is deployed on the server through the following steps:

  1. ssh into the Shiny Pro server and navigate to /home/{user}/ShinyApps/mhealthannotator-app
  2. git pull changes from GitHub
  3. To ensure packages are up-to-date, open an R session and run renv::restore()
  4. Note: Make sure that you have Python Environment set up. Documentation: https://python-docs.synapse.org/build/html/reticulate.html

You may need to run touch restart.txt afterward to ensure the application is restarted.

If you want to deploy the app in a different location (e.g. because you want to stand up a new version that is customized for a different community):

  1. ssh into the Shiny Pro server
  2. Create a folder under /home/yourusername/ShinyApps
  3. git clone the repository into the folder you’ve created
  4. If needed, make any changes to the application’s behavior by editing the files, or check out a branch that contains your changes
  5. Create a .Renviron file with the verified OAuth client_name, client_id and client_secret and restrict permissions (chmod 600 .Renviron or chmod 400 .Renviron)
  6. To ensure packages are up-to-date, open an R session and run renv::restore()
  7. Note: Make sure that your Python environment is correctly configured using reticulate with synapseclient

Again, you may need to run touch restart.txt afterward to ensure the application is restarted.