Diagnostics Explorer Shiny App

The DiagnosticsExplorer Shiny application is designed to be the primary method for exploring CohortDiagnostics results. See the CohortDiagnostics documentation for guidance on running CohortDiagnostics and generating the required results.

This application directory is designed to be a stand-alone shiny application. To install the required packages for this app we recommend using renv to create an isolated environment. Assuming your working directory is the DiagnosticsExplorer shiny app, run the following:

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

The shiny app can now be launched:

shiny::runApp()

The default data is file is intended to be placed in data/MergedCohortDiagnosticsData.sqlite. This can be changed to use a different database engine.

Configuration using other

The default YAML file contains the following options

# Alter these configuration settings for usage with remote databases
connectionDetails:
  dbms: "sqlite"
  server: "data/MergedCohortDiagnosticsData.sqlite"
  user: ""
  password: ""
  port: ""

# Store connection details as a json string in keyring
# Store with keyring::key_set_with_value("KEYNAME", jsonlite::toJSON(myConnectionDetails))
connectionDetailsSecureKey: ~

# If you used a table prefix to store the results (e.g. cd_)
tablePrefix: ""

# Results schema being used
resultsDatabaseSchema: "main"

# Vocabulary schemas. Should include the reuslts schema and optional custom vocabularies
vocabularyDatabaseSchemas: ["main"]

# Custom table name for cohorts and cdm databases (probably not needed, ignores table prefix)
cohortTableName: "cohort"
databaseTableName: "database"

# If you wish to enable annotation - not currently reccomended in multi-user environments
enableAnnotation: TRUE
enableAuthorization: TRUE

### if you need a way to authorize users
### generate hash using code like digest::digest("diagnostics",algo = "sha512")
### store in external file called UserCredentials.csv - with fields userId, hashCode
### place the file in the root folder
userCredentialsFile: UserCredentials.csv

Setting connection details

Connection details should conform to a standard DatabaseConnector connection details object, in yaml format. Optionally, this object can be saved to a secure secret using the keyring package as follows:

myConnectionDetails <- list(
    user = "myusername",
    password = "someSecretPassword",
    server = "my-server-address.com/cohort_diagnostics",
    dbms = "postgresql",
    port = 5432
)
keyring::key_set_with_value("KEYNAME", jsonlite::toJSON(myConnectionDetails))

This list will then be loaded at runtime, meaning that secure credentails don't need to be saved in plain text.

OHDSI shiny server instructions

To use this shiny app on the (OHDSI ShinyServer)['https://github.com/OHDSI/ShinyDeploy'] use the environment variable configuration settings included in the file config-ohdsi-shiny.yml. The following settings can be reconfigured if environment variables differ:

# Alter these configuration settings for usage with remote databases


# store connection details with environment variables
# Note - if dbms and port vars are unset in environment variables they will default to above connectionDetails settings
# See above for postgresql 
connectionEnvironmentVariables:
  dbms: ~
  database: "shinydbDatabase"
  server: "shinydbServer"
  user: "shinydbUser"
  password: "shinydbPw"
  port: "shinydbPort"
  extraSettings: ~

connectionDetails:
  dbms: "postgresql"
  port: 5432

# This must be set up by a system administrator
resultsDatabaseSchema: "some_schema"
vocabularyDatabaseSchemas: ["some_schema"]

This file makes use of system set environment variables with a read-only account. Please contact the system administrator for creating a schema that can be accessed by the applications.