R/global.R

In Sage-Bionetworks/release_administrator: Data Flow App Demo

## SET GLOBAL VARS
# READ IN BRANCH NAME
ref <- Sys.getenv("DFA_REF")

# SET FAVICON URL
FAVICON_URL <- file.path(
  "https://raw.githubusercontent.com/Sage-Bionetworks/data_flow",
  ref,
  "inst/app/www/favicon.ico"
)

# READ IN TENANTS.JSON
tenants_config_path <- Sys.getenv("DFA_DCC_CONFIG")
if (is.null(tenants_config_path) || nchar(tenants_config_path) == 0) stop("missing DFA_DCC_CONFIG environmental variable")
message("Tenants.json path: ", tenants_config_path)

# GET SCHEMATIC API URL
schematic_api_url <- Sys.getenv("DFA_SCHEMATIC_API_URL")
message("Schematic base URL: ", schematic_api_url)

# SET UP OAUTH
client_id <- Sys.getenv("DFA_CLIENT_ID")
client_secret <- Sys.getenv("DFA_CLIENT_SECRET")
app_url <- Sys.getenv("DFA_APP_URL")

if (is.null(client_id) | nchar(client_id) == 0) stop("missing DFA_CLIENT_ID environmental variable")
if (is.null(client_secret) | nchar(client_secret) == 0) stop("missing DFA_CLIENT_SECRET environmental variable")
if (is.null(app_url) | nchar(app_url) == 0) stop("missing DFA_APP_URL environmental variable")

# update port if running app locally
if (interactive()) {
  port <- httr::parse_url(app_url)$port
  if (is.null(port)) stop("running locally requires a TCP port that the application should listen on")
  options(shiny.port = as.numeric(port))
}

has_auth_code <- function(params) {
  # params is a list object containing the parsed URL parameters. Return TRUE if
  # based on these parameters, it looks like auth code is present that we can
  # use to get an access token. If not, it means we need to go through the OAuth
  # flow.
  return(!is.null(params$code))
}

app <- httr::oauth_app("shinysynapse",
                       key = client_id,
                       secret = client_secret,
                       redirect_uri = app_url
)

# These are the user info details ('claims') requested from Synapse:
claims <- list(
  family_name = NULL,
  given_name = NULL,
  email = NULL,
  email_verified = NULL,
  userid = NULL,
  orcid = NULL,
  is_certified = NULL,
  is_validated = NULL,
  validated_given_name = NULL,
  validated_family_name = NULL,
  validated_location = NULL,
  validated_email = NULL,
  validated_company = NULL,
  validated_at = NULL,
  validated_orcid = NULL,
  company = NULL
)

claimsParam <- jsonlite::toJSON(list(id_token = claims, userinfo = claims))
api <- httr::oauth_endpoint(
  authorize = paste0("https://signin.synapse.org?claims=", claimsParam),
  access = "https://repo-prod.prod.sagebase.org/auth/v1/oauth2/token"
)

# The 'openid' scope is required by the protocol for retrieving user information.
scope <- "openid view download modify"