Update vignettes/credential-scraping.Rmd

Add option to get username from API_USER env var.
Add calling instructions.

Author: pbchase

vignettes/credential-scraping.Rmd

@@ -117,17 +117,35 @@ dbDisconnect(source_conn)
 
 ### Scraping one user's API tokens
 
-Scraping one user's API tokens and putting them in a new, local sqlite DB for use.
+Scraping one user's API tokens and putting them in a new, local sqlite DB for use. 
+
+You must provide the username in the API_USER environment variable or on the command line. To specify it on the command line via `Rscript` and specify a REDCap username. e.g.
+
+```sh
+Rscript scrape_one_user.R jane_doe
+```
 
 ```{r, eval = FALSE}
 library(redcapcustodian)
 library(DBI)
 library(tidyverse)
 library(dotenv)
 
-# get the username provided on the command line
+# Get the username provided on the command line if one is provided. 
+# Otherwise, get the username form the environment.
+# Otherwise, exit.
 args <- commandArgs(trailingOnly = TRUE)
-username <- args
+if (length(args) > 0) {
+  # Use the command line argument
+  username <- args
+} else if (Sys.getenv("API_USER") != "") {
+  # Use the environment variable
+  username <- Sys.getenv("API_USER")
+} else {
+  # Exit
+  warning("Please provide an username that whose API tokens you want to read either on the command line or via the API_USER environment variable. No action taken.")
+  quit()
+}
 
 # Creates the credentials file if one does not exists.
 # Otherwise it deletes the credentials file