Update vignette and GH Action (#514)

* Probably won't fix, but add new line to Windows file and fix spacing

* Add missing `client_name` in vignette info

* Add missing login, remove print from some logins, add missing skip

* Fix check

.github/workflows/R-CMD-check.yaml

@@ -99,14 +99,14 @@ jobs:
           cat > "$OUTPUT_FILE" << EOM
           [authentication]
           username = "${{ secrets.SYNAPSE_USER }}"
-          apikey = "${{ secrets.SYNAPSE_APIKEY}}"
+          apikey = "${{ secrets.SYNAPSE_APIKEY }}"
           EOM
           chmod +x "$OUTPUT_FILE"
           
       - name: Setup Synapse config file for testing (Windows)
         if: runner.os == 'Windows'
         run: |
-          "[authentication]`nusername = ${{ secrets.SYNAPSE_USER }}`napikey = ${{ secrets.SYNAPSE_APIKEY}}" | Out-File -FilePath "$HOME\.synapseConfig"
+          "[authentication]`nusername = ${{ secrets.SYNAPSE_USER }}`napikey = ${{ secrets.SYNAPSE_APIKEY }}`n" | Out-File -FilePath "$HOME\.synapseConfig"
 
       - name: Check
         run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")

R/df-helpers.R

@@ -81,11 +81,11 @@ gather_template_id_biospecimen <- function(templates, species,
     return(NA)
   }
   if (species %in% names(templates[["biospecimen_templates"]])) {
-    if (any(
+    if (any(c(
       length(biospecimen_type) < 0,
       is.na(biospecimen_type),
-      biospecimen_type %in% ""
-    )) {
+      biospecimen_type %in% c("", "NaN")
+    ))) {
       # Grab based on species
       return(templates[["biospecimen_templates"]][[species]])
     } else {

tests/testthat/test-check-all.R

@@ -491,6 +491,7 @@ test_that("check_all doesn't run check_cols if missing template col", {
 })
 
 test_that("check_all runs check_cols if not missing template col", {
+  skip_if_not(logged_in(syn))
   data <- tibble::tibble(
     metadataType = c(
       "manifest",

tests/testthat/test-get-template.R

@@ -1,6 +1,12 @@
 context("test-get-template.R")
 
 syn <- attempt_instantiate()
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 
 test_that("get_template fails when not logged in to Synapse", {
   skip_if(is.null(syn))
@@ -14,8 +20,12 @@ test_that("get_template fails when not logged in to Synapse", {
   )
 })
 
-attempt_login(syn)
-
+tryCatch(
+  attempt_login(syn),
+  error = function(e) {
+    print(glue::glue("Did not log into Synapse: {e$message}"))
+  }
+)
 
 test_that("get_template errors for files from synID that are not xlsx or csv", {
   skip_if_not(logged_in(syn = syn))

vignettes/customizing-dccvalidator.Rmd

@@ -48,7 +48,7 @@ To create a custom version of the app, you'll need to follow these steps:
    [example of how to create a project with appropriate permissions](https://github.com/Sage-Bionetworks/dccvalidator/blob/master/inst/app/create_project.R).
 1. Fork the [dccvalidator](https://github.com/Sage-Bionetworks/dccvalidator/blob/master/config.yml)
    GitHub repository.
-1. (For a production version): register a Synapse OAuth client (see [Synapse Docs](https://help.synapse.org/docs/Using-Synapse-as-an-OAuth-Server.2048327904.html#UsingSynapseasanOAuthServer-RegisteringandLinkinganOAuth2.0Client)) and store the `client_id` and `client_secret` in a .Renviron file within the repository. Ensure you are the only person who has access to this file (e.g. `chmod 600 .Renviron` or `chmod 400 .Renviron`).
+1. (For a production version): register a Synapse OAuth client (see [Synapse Docs](https://help.synapse.org/docs/Using-Synapse-as-an-OAuth-Server.2048327904.html#UsingSynapseasanOAuthServer-RegisteringandLinkinganOAuth2.0Client)) and store the `client_name`, `client_id` and `client_secret` in a .Renviron file within the repository. Ensure you are the only person who has access to this file (e.g. `chmod 600 .Renviron` or `chmod 400 .Renviron`).
 1. (For running locally only): create a .synapseConfig file in your home directory with your Synapse authentication credentials (see the [synapser docs for an example](https://r-docs.synapse.org/articles/manageSynapseCredentials.html#use-synapseconfig)).
 1. Create a new configuration in the `config.yml` file. Note that any values you
    do not customize will be inherited from the default configuration. The configuration file must have a `default` configuration.

vignettes/deploying-dccvalidator.Rmd

@@ -36,7 +36,7 @@ stand up a new version that is customized for a different community):
 1. `git clone` the repository into the folder you've created
 1. If needed, make any changes to the application's behavior by editing the
    files, or check out a branch that contains your changes
-1. Create a .Renviron file with the [verified OAuth](https://help.synapse.org/docs/Using-Synapse-as-an-OAuth-Server.2048327904.html#UsingSynapseasanOAuthServer-RegisteringandLinkinganOAuth2.0Client) `client_id` and `client_secret`
+1. Create a .Renviron file with the [verified OAuth](https://help.synapse.org/docs/Using-Synapse-as-an-OAuth-Server.2048327904.html#UsingSynapseasanOAuthServer-RegisteringandLinkinganOAuth2.0Client) `client_name`, `client_id` and `client_secret`
 and restrict permissions (`chmod 600 .Renviron` or `chmod 400 .Renviron`)
 1. To ensure packages are up-to-date, open an R session and run `renv::restore()`
 1. To ensure each connection has its own R process, the Sage Shiny Server administrator must configure the utilization scheduler. This is not necessary for the app to function, but might improve performance.