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Update proofr.Rmd #21

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Aug 5, 2024
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Update proofr.Rmd #21

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Update proofr.Rmd
vortexing May 20, 2024
0725d9b
Removing token sentence and adding small wording fixes
tefirman Aug 5, 2024
bd92662
Fixing spacing issue identified by linting GH Action
tefirman Aug 5, 2024
e6e68d3
Porting changes to proofr.Rmd.og and remade proofr.Rmd
tefirman Aug 5, 2024
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21 changes: 13 additions & 8 deletions vignettes/proofr.Rmd
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Expand Up @@ -18,7 +18,7 @@ library(proofr)

## Authenticate with the PROOF API

Run the function `proof_authenticate()`, which calls the PROOF API with your username and password, and returns an API token (an alphanumeric string).
Run the function `proof_authenticate()`, which calls the PROOF API with your username and password, and returns an API token (an alphanumeric string). A new token is created when a new PROOF server is created, thus this API token will need to be reset.
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This is not what happens. The token does not change. We can/should discuss whether it should, but currently it does not.

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@vortexing can you undo this text change, or change the wording to explain that the same token is returned when calling proof_authenticate



```r
Expand All @@ -29,23 +29,25 @@ 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


```r
proof_start()
```
Note: `proofr` assumes you only have one server running and 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
Expand All @@ -54,6 +56,9 @@ cromwell_url <- metadata$cromwellUrl
cromwell_url
```




## rcromwell setup

Load `rcromwell`
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