Update proofr.Rmd

R/utils.R

@@ -1,7 +1,7 @@
 
 make_url <- function(...) {
   proof_base <- Sys.getenv("PROOF_API_BASE_URL",
-    "https://proof-api.fredhutch.org")
+                           "https://proof-api.fredhutch.org")
   file.path(proof_base, ...)
 }
 

vignettes/proofr.Rmd

@@ -29,23 +29,24 @@ my_proof_token
 
 (note: the above token is not a real token)
 
-On your computer, save your API token as an environment variable named `PROOF_TOKEN`.
+Alternatively, save your API token directly as an environment variable named `PROOF_TOKEN` so that it can be used by other `proofr` functions without exposing your token in your code.  To do so, run the following: 
 
-If you've saved your `PROOF_TOKEN` env var, then you can use the other `proofr` functions.
-
-Otherwise, you can pass your PROOF token to the `proofr` functions. If you pass your token to the functions, only do so by passing the call to `Sys.getenv` like `proof_status(token = Sys.getenv("MY_TOKEN"))`.
 
+```r
+Sys.setenv("PROOF_TOKEN" = proof_authenticate("username", "password"))
+```
 
-## Start a Cromwell Server
+## Start a PROOF Server
 
-Start the server
+Start a PROOF server using the `proof_start()` function:
 
 
 ```r
 proof_start()
 ```
+Note: `proofr` assumes you only have one server running; if you've started a server using the app, you'll need to stop that server before starting one in R via `proofr`. 
 
-Get the URL, using `wait=TRUE` so that it doesn't return data until the server is fully ready to use
+Get metadata about the PROOF server you have started, including the URL of the API, using `wait=TRUE` so that it doesn't return data until the server is fully ready to use.  
 
 
 ```r

vignettes/proofr.Rmd.og

@@ -33,22 +33,22 @@ my_proof_token
 
 (note: the above token is not a real token)
 
-On your computer, save your API token as an environment variable named `PROOF_TOKEN`.
-
-If you've saved your `PROOF_TOKEN` env var, then you can use the other `proofr` functions.
-
-Otherwise, you can pass your PROOF token to the `proofr` functions. If you pass your token to the functions, only do so by passing the call to `Sys.getenv` like `proof_status(token = Sys.getenv("MY_TOKEN"))`.
+Alternatively, save your API token directly as an environment variable named `PROOF_TOKEN` so that it can be used by other `proofr` functions without exposing your token in your code.  To do so, run the following: 
 
+```{r set-env-token}
+Sys.setenv("PROOF_TOKEN" = proof_authenticate("username", "password"))
+```
 
-## Start a Cromwell Server
+## Start a PROOF Server
 
-Start the server
+Start a PROOF server using the `proof_start()` function:
 
 ```{r start}
 proof_start()
 ```
+Note: `proofr` assumes you only have one server running; if you've started a server using the app, you'll need to stop that server before starting one in R via `proofr`. 
 
-Get the URL, using `wait=TRUE` so that it doesn't return data until the server is fully ready to use
+Get metadata about the PROOF server you have started, including the URL of the API, using `wait=TRUE` so that it doesn't return data until the server is fully ready to use.  
 
 ```{r cromwell-url}
 metadata <- proof_status(wait = TRUE)