pre-release updates

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

NEWS.md

@@ -13,7 +13,7 @@ Version 1.1.0 (Released 2024-03-28)
 
 - `read_redcap()` now supports instruments that follow a mixed repeating/non-repeating structure with the `allow_mixed_structure` parameter
 - Mixed structure instruments (those with both repeating and nonrepeating elements) can be supported by setting `allow_mixed_structure` to `TRUE` or `getOption("redcaptidier.allow.mixed.structure", FALSE)`.
-   - When allowed, nonrepeating elements of mixed structure insturments will be treated as repeating elements with a single instance.
+   - When allowed, nonrepeating elements of mixed structure instruments will be treated as repeating elements with a single instance.
 - Missing data codes from REDCap additional customization settings are now handled. Non-logical values are converted to `NA` in `yesno`, `truefalse`, and `checkbox` fields with a warning. 
    - Warnings for MDCs can be silenced with `options(redcaptidier.allow.mdc = TRUE)`.
 - `raw_or_label` now accepts `"haven"` as an option, converting categorical fields to `haven_labelled` vectors instead of factors.

R/checks.R

@@ -624,23 +624,23 @@ check_field_is_logical <- function(x) {
 #'
 #' @keywords internal
 check_extra_field_values <- function(x, values) {
-  extra_vals <- setdiff(as.character(x), values) |> na.omit()
+  extra_vals <- setdiff(as.character(x), values) %>% na.omit()
   if (length(extra_vals) == 0) {
     return(NULL)
   }
   as.character(extra_vals)
 }
 
 check_extra_field_values_message <- function(extra_field_values, call = caller_env()) {
-  extra_field_values <- extra_field_values |>
+  extra_field_values <- extra_field_values %>%
     discard(is.null)
 
   if (length(extra_field_values) == 0) {
     return(NULL)
   }
 
   fields <- names(extra_field_values)
-  values <- flatten_chr(extra_field_values) |> unique()
+  values <- flatten_chr(extra_field_values) %>% unique()
 
   msg <- c(
     `!` = "{.code {fields}} contain{?s/} values with no labels: {values}",

R/utils.R

@@ -514,13 +514,13 @@ parse_logical_cols <- function(db_data, db_metadata, call = caller_env()) {
   out[logical_cols$field_name_updated] <- map(parsed, "parsed")
 
   if (!getOption("redcaptidier.allow.mdc", FALSE)) {
-    problems <- parsed |>
-      map("problems") |>
+    problems <- parsed %>%
+      map("problems") %>%
       discard(is.null)
 
     if (length(problems) > 0) {
       fields <- names(problems)
-      values <- flatten_chr(problems) |> unique()
+      values <- flatten_chr(problems) %>% unique()
 
       msg <- c(
         `!` = "{.code {fields}} {?is/are} logical but contain{?s/} non-logical values: {values}",

utility/cli_message_examples_reprex.md

@@ -34,9 +34,13 @@ read_redcap(letters[1:3], classic_token)
 read_redcap("https://www.google.com", classic_token)
 #> Error in `read_redcap()`:
 #> ✖ The REDCapR export operation was not successful.
-#> ! The URL returned the HTTP error code 405 (POST Method not allowed).
-#> ℹ Are you sure the URI points to an active REDCap API endpoint?
-#> ℹ URI: `https://www.google.com`
+#> ! An unexpected error occured.
+#> ℹ This means that you probably discovered a bug!
+#> ℹ Please consider submitting a bug report here:
+#>   <https://github.com/CHOP-CGTInformatics/REDCapTidieR/issues>.
+#> Caused by error in `redcap_metadata_read()`:
+#> ! The REDCapR metadata export operation was not successful.  The error message was:
+#> <html><body><h1>404 Not Found</h1></body></html>
 
 read_redcap("https://www.google.comm", classic_token)
 #> Error in `read_redcap()`:
@@ -255,7 +259,7 @@ withr::with_tempdir({
 })
 #> Error:
 #> ✖ File
-#>   ''/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/RtmpQi1Xne/file52d750f31b3f/temp.csv''
+#>   ''/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c744dd73619/temp.csv''
 #>   already exists.
 #> ℹ Overwriting files is disabled by default. Set `overwrite = TRUE` to overwrite
 #>   existing file.
@@ -296,7 +300,7 @@ withr::with_tempdir({
     write_redcap_xlsx(file = filepath)
 })
 #> Warning in write_redcap_xlsx(., file = filepath): ! No extension provided for `file`:
-#>   '/private/var/folders/qc/mmjjyjq50530z9r_7mfqcqfhxkkk67/T/RtmpQi1Xne/file52d72e91eb7b/temp'
+#>   '/private/var/folders/9c/k1m0bzys7gb1v32g86hfn5sn5k86h1/T/Rtmp1QPC0p/file5c7456597c2b/temp'
 #> ℹ The extension '.xlsx' will be appended to the file name.
 
 # Printed supertibble
@@ -339,4 +343,4 @@ read_redcap(redcap_uri, Sys.getenv("REDCAPTIDIER_MDC_API"))
 #> #   data_na_pct <formttbl>, form_complete_pct <formttbl>
 ```
 
-<sup>Created on 2024-03-27 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>
+<sup>Created on 2024-04-10 with [reprex v2.1.0](https://reprex.tidyverse.org)</sup>