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OHDSI Analysis Viewer Demo (2024)

Usage

This README assumes you are familiar with Docker concepts. An overview of Docker can be found here.

Since this container is designed to work with the OHDSI Shiny Proxy Deploy, it will require some modficiations if you'd like to use it on your machine. Here are the steps if you'd like to try it out:

  • Clone this repository
  • Add a file called .env to the root of the project to hold sensitive information. Specifically, you'll want to add your GitHub Personal Access Token to the .env file so it looks like this:
build_github_pat="ghp_<secret>"
  • Edit app.R to include the details to connect to your database. Specifically this section:
cli::cli_h1("Starting shiny server")
serverStr <- paste0(Sys.getenv("shinydbServer"), "/", Sys.getenv("shinydbDatabase"))
cli::cli_alert_info("Connecting to {serverStr}")
connectionDetails <- DatabaseConnector::createConnectionDetails(
  dbms = "postgresql",
  server = serverStr,
  port = Sys.getenv("shinydbPort"),
  user = "shinyproxy",
  password = Sys.getenv("shinydbPw")
)


cli::cli_h2("Loading schema")
ShinyAppBuilder::createShinyApp(
   config = shinyConfig,
   connectionDetails = connectionDetails,
   resultDatabaseSettings = createDefaultResultDatabaseSettings(schema = "viewerdemo2024"),
   title = "OHDSI Analysis Viewer Demo (2024)"
)

In the code above, you'll want to replace the DatabaseConnector::createConnectionDetails with the details to connect to your PostgreSQL database with the study results. Additionally, you'll want to change the schema parameter in: resultDatabaseSettings = createDefaultResultDatabaseSettings(schema = "viewerdemo2024") to match the schema where you have the study results.

  • Once the changes above are complete, you can build the container by running:

docker-compose build

  • Once the docker container is built, you can run it:

docker-compose up

The application will be available on http://localhost:3838