Merge pull request #499 from OuhscBbmc/dev

Handle leading space in REDCap checkbox options (into main branch)
OuhscBbmc · Jul 14, 2023 · 1bdde82 · 1bdde82
2 parents 0d69b0e + 53bc3e1
commit 1bdde82
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diff --git a/NEWS.md b/NEWS.md
@@ -89,6 +89,7 @@ This will help extract forms from longitudinal & repeating projects.
   * `validate_repeat_instance()`
   * `validate_no_logical()`
 * `redcap_read()` checks the `event` parameter and throws an error if a value is not recognized, or the project is not longitudinal (#493)
+* The regex in `regex_named_captures()` is forgiving if there's an unnecessary leading space (@BlairCooper, #495)
 
 Version 1.1.0 (released 2022-08-10)
 ==========================================================

diff --git a/R/constant.R b/R/constant.R
@@ -23,7 +23,7 @@
 #'
 #' The current constants relate to the 'complete' variable at the
 #' end of each form.
-#' * `form_incomplete`: 0L (*i.e.*, an integer)
+#' * `form_incomplete`: 0L (_i.e._, an integer)
 #' * `form_unverified`: 1L
 #' * `form_complete`: 2L
 #'

diff --git a/R/create-batch-glossary.R b/R/create-batch-glossary.R
@@ -71,12 +71,12 @@ create_batch_glossary <- function(row_count, batch_size) {
 
   start_index <- as.integer(base::seq.int(from=1L, to=row_count, by=batch_size))
 
-  ds_batch             <-
+  ds_batch <-
     tibble::tibble(
       id          = seq_along(start_index),
       start_index = start_index
     )
-  ds_batch$stop_index  <-
+  ds_batch$stop_index <-
     base::mapply(
       function(i) {
         base::ifelse(

diff --git a/R/kernel-api.R b/R/kernel-api.R
@@ -41,16 +41,16 @@
 #' token          <- "9A81268476645C4E5F03428B8AC3AA7B"
 #' post_body      <- list(
 #'   token    = token,
-#'   content  = 'project',
-#'   format   = 'csv'
+#'   content  = "project",
+#'   format   = "csv"
 #' )
 #' \dontrun{
 #' kernel <- REDCapR:::kernel_api(uri, post_body, config_options)
 #'
 #' # Consume the results in a few different ways.
 #' kernel$result
-#' read.csv(text=kernel$raw_text)
-#' as.list(read.csv(text=kernel$raw_text))
+#' read.csv(text = kernel$raw_text)
+#' as.list(read.csv(text = kernel$raw_text))
 #' }
 
 kernel_api <- function(
@@ -83,9 +83,9 @@ kernel_api <- function(
     httr::user_agent("OuhscBbmc/REDCapR")
   )
 
-  status_code           <- response$status
-  success               <- (status_code == 200L)
-  raw_text              <- httr::content(
+  status_code <- response$status
+  success     <- (status_code == 200L)
+  raw_text    <- httr::content(
     x           = response,
     as          = "text",
     encoding    = encoding,     # UTF-8 is the default parameter value
@@ -104,7 +104,7 @@ kernel_api <- function(
     any(grepl(regex_cannot_connect, raw_text)) #||
     # any(grepl(regex_empty         , raw_text))
   ) {
-    success     <- FALSE  # nocov
+    success <- FALSE  # nocov
   }
 
   return(list(
@@ -114,7 +114,6 @@ kernel_api <- function(
     elapsed_seconds     = elapsed_seconds,
     result              = response,
     result_headers      = response$headers,
-
     regex_empty         = regex_empty
   ))
 }
diff --git a/R/metadata-utilities.R b/R/metadata-utilities.R
@@ -84,9 +84,9 @@
 
 #' @export
 regex_named_captures <- function(pattern, text, perl = TRUE) {
-  checkmate::assert_character(pattern, any.missing=FALSE, min.chars=0L, len=1)
-  checkmate::assert_character(text   , any.missing=FALSE, min.chars=0L, len=1)
-  checkmate::assert_logical(  perl   , any.missing=FALSE)
+  checkmate::assert_character(pattern, any.missing = FALSE, len = 1, min.chars = 0L)
+  checkmate::assert_character(text   , any.missing = FALSE, len = 1, min.chars = 0L)
+  checkmate::assert_logical(  perl   , any.missing = FALSE, len = 1                )
 
   match <- gregexpr(pattern, text, perl = perl)[[1]]
   capture_names <- attr(match, "capture.names")
@@ -114,7 +114,7 @@ regex_named_captures <- function(pattern, text, perl = TRUE) {
 checkbox_choices <- function(select_choices) {
   checkmate::assert_character(select_choices, any.missing=FALSE, len=1, min.chars=1)
 
-  pattern_checkboxes <- "(?<=\\A| \\| )(?<id>\\d{1,}), (?<label>[^|]{1,})(?= \\| |\\Z)"
+  pattern_checkboxes <- "(?<=\\A| \\| |\\| )(?<id>\\d{1,}), (?<label>[^|]{1,}?)(?= \\| |\\| |\\Z)"
 
   regex_named_captures(pattern = pattern_checkboxes, text = select_choices)
 }
diff --git a/R/redcap-metadata-coltypes.R b/R/redcap-metadata-coltypes.R
@@ -306,15 +306,15 @@ redcap_metadata_internal <- function(
 
   if (is.na(d_proj$has_repeating_instruments_or_events[1])) { # nocov start
     # Don't test coverage for this block b/c it only executes for old versions of REDCap
-    stop(
+    error_message <-
       sprintf(
         paste(
           "The REDCap instance at %s failed to report if the",
           "current project uses repeatable instruments or events."
         ),
         redcap_uri
       )
-    )
+    stop(error_message)
   } # nocov end
 
   if (d_proj$has_repeating_instruments_or_events[1]) {

diff --git a/R/validate.R b/R/validate.R
@@ -272,8 +272,8 @@ validate_record_id_name <- function(
       suggestion         = character(0)
     )
   } else if (stop_on_error) {
-    "The field called `%s` is not found in the dataset.\nAdjust the value passed to the `record_id_name` if this isn't the correct named used by your specific REDCap project." |>
-      sprintf(record_id_name) |>
+    "The field called `%s` is not found in the dataset.\nAdjust the value passed to the `record_id_name` if this isn't the correct named used by your specific REDCap project." %>%
+      sprintf(record_id_name) %>%
       stop()
   } else {
     tibble::tibble(
@@ -335,11 +335,11 @@ validate_uniqueness <- function(d, record_id_name = "record_id", stop_on_error =
   variables <- intersect(colnames(d), plumbing)
 
   d_replicates <-
-    d |>
+    d %>%
     dplyr::count(
       !!!rlang::parse_exprs(variables),
       name  = "count_of_records"
-    ) |>
+    ) %>%
     dplyr::filter(1L < count_of_records)
 
   if (nrow(d_replicates) == 0L) {
@@ -359,8 +359,8 @@ validate_uniqueness <- function(d, record_id_name = "record_id", stop_on_error =
         paste(d_replicates, collapse = "\n")  # nocov
       }
 
-    "There are %i record(s) that violate the uniqueness requirement:\n%s" |>
-      sprintf(nrow(d_replicates), m) |>
+    "There are %i record(s) that violate the uniqueness requirement:\n%s" %>%
+      sprintf(nrow(d_replicates), m) %>%
       stop()
   } else {
     indices <- paste(which(colnames(d) == variables), collapse = ", ")

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,55 +1,61 @@
 Description
 ===============================================
 
-This submission is primarily to address a recent change in the REDCap server.
+This submission is primarily to address a change in the REDCap server.  A lot of packages additions in the meantime were building up.
 
 Thank you for taking the time to review my submission, and please tell me if there's something else I should do for CRAN.  -Will Beasley
 
 Test environments
 -----------------------------------------------
 
 1. Local Ubuntu, R 4.2.2
-2. Local Win10, R 4.2.3 patched
+2. Local Win11, R 4.3.1 patched
 3. R-hub
-    1. [Ubuntu Linux 20.04 LTS, R-release, GCC](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-aa1d5ab8d07d453db1f07927d1ad23f4)
-    2. [Fedora Linux, R-devel, clang, gfortran](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-a56bc6477bbb48d2a4aa5d1872481dac)
-    3. [Windows Server](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-34917c524b674b82860b920d177844f1)
-4. [win-builder](https://win-builder.r-project.org/eG6x3HZ9ITqN), development version.
-5. [GiHub Actions](https://github.com/OuhscBbmc/REDCapR/actions), Ubuntu 20.04 LTS
+    1. [Ubuntu Linux, R-release, GCC](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-746e237d11914129b4410114fbfa2c83)
+    2. [Fedora Linux, R-devel, clang, gfortran](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-e695d8a48601419e8059863cc80964b7)
+    3. [Windows Server](https://builder.r-hub.io/status/REDCapR_1.1.9005.tar.gz-c30d344462dc43a4b03e68a33be664d9)
+4. [win-builder](https://win-builder.r-project.org/0u5J1JiksFZg/), development version.
+5. [GiHub Actions](https://github.com/OuhscBbmc/REDCapR/actions), Ubuntu 22.04 LTS
 
 R CMD check results
 -----------------------------------------------
 
 * No ERRORs or WARNINGs on any builds.
 
-* A NOTE is returned for a few websites.  All are accessible by browser.
-  * <https://community.projectredcap.org> is a site accessible only to REDCap administrators
-  * <https://grantome.com/grant/NIH/P01-AG043362>
-  * <https://grantome.com/grant/NIH/U54-GM104938>
-  * <https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=U54GM104938&arg_ProgOfficeCode=127>
-  * <https://www.researchgate.net/profile/William-Beasley-5>
-
-* There is one NOTE that is only found on R-hub Windows (Server 2022, R-devel 64-bit):
+* There are two NOTEs across the R-hub builds:
 
   ```txt
   * checking for detritus in the temp directory ... NOTE
   Found the following files/directories:
     'lastMiKTeXException'
-  As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this could be due to a bug/crash in MiKTeX and can likely be ignored.
   ```
-
-* There is one NOTE that is only found on the R-hub Fedora:
+  As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this could be due to a bug/crash in MiKTeX and can likely be ignored.
 
   ```txt
   * checking HTML version of manual ... NOTE
   Skipping checking HTML validation: no command 'tidy' found
   ```
 
-  Based on [this discussion](https://groups.google.com/g/r-sig-mac/c/7u_ivEj4zhM?pli=1), it sounds like a problem with the testing environment, and not the package code.
+  Based on [this discussion](https://groups.google.com/g/r-sig-mac/c/7u_ivEj4zhM?pli=1)
+  and [this SO answer](https://stackoverflow.com/a/75007979/1082435),
+  it sounds like a problem with the testing environment and not the package code.
 
 Downstream dependencies
 -----------------------------------------------
 
-No downstream packages are affected.  The package that depends/imports/suggests REDCapR passes checks with `revdepcheck::revdep_check()`.  Results: <https://github.com/OuhscBbmc/REDCapR/blob/main/revdep/cran.md>
+With one exception,
+packages that depend/import/suggest REDCapR pass checks with `revdepcheck::revdep_check()`.
+
+I worked with **tidyREDCap** team and they accepted a PR that fixes the problem:
+<https://github.com/RaymondBalise/tidyREDCap/pull/61>.
+
+package                                  | E        | W        | N
+-------                                  | -        | -        | -
+codified 0.3.0                           | E: 0     | W: 0     | N: 0
+REDCapDM 0.7.0                           | E: 0     | W: 0     | N: 1
+REDCapCAST 23.6.2                        | E: 0     | W: 0     | N: 0
+REDCapTidieR 0.4.0                       | E: 1     | W: 0     | N: 0
+tidyREDCap 1.1.1                         | E: 0  +1 | W: 0     | N: 0
+ReviewR 2.3.8                            | E: 0     | W: 0     | N: 1
 
-* [ReviewR](https://CRAN.R-project.org/package=ReviewR)
+Results: <https://github.com/OuhscBbmc/REDCapR/blob/main/revdep/cran.md>
diff --git a/man/kernel_api.Rd b/man/kernel_api.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -2,17 +2,17 @@
 
 |field    |value                                            |
 |:--------|:------------------------------------------------|
-|version  |R version 4.2.3 Patched (2023-03-29 r84127 ucrt) |
-|os       |Windows 10 x64 (build 22621)                     |
+|version  |R version 4.3.1 Patched (2023-07-06 r84647 ucrt) |
+|os       |Windows 11 x64 (build 22621)                     |
 |system   |x86_64, mingw32                                  |
 |ui       |RStudio                                          |
 |language |(EN)                                             |
 |collate  |English_United States.utf8                       |
 |ctype    |English_United States.utf8                       |
 |tz       |America/Chicago                                  |
-|date     |2023-04-21                                       |
-|rstudio  |2023.03.0+386 Cherry Blossom (desktop)           |
-|pandoc   |NA                                               |
+|date     |2023-07-14                                       |
+|rstudio  |2023.06.1+524 Mountain Hydrangea (desktop)       |
+|pandoc   |3.1.5 @ C:\PROGRA~1\Pandoc\pandoc.exe            |
 
 # Dependencies
 
@@ -23,19 +23,19 @@
 |backports   |1.4.1  |1.4.1    |   |
 |bit         |4.0.5  |4.0.5    |   |
 |bit64       |4.0.5  |4.0.5    |   |
-|checkmate   |2.1.0  |2.1.0    |   |
+|checkmate   |2.2.0  |2.2.0    |   |
 |cli         |3.6.1  |3.6.1    |   |
 |clipr       |0.8.0  |0.8.0    |   |
-|cpp11       |0.4.3  |0.4.3    |   |
+|cpp11       |0.4.4  |0.4.4    |   |
 |crayon      |1.5.2  |1.5.2    |   |
-|curl        |5.0.0  |5.0.0    |   |
+|curl        |5.0.1  |5.0.1    |   |
 |dplyr       |1.1.2  |1.1.2    |   |
 |fansi       |1.0.4  |1.0.4    |   |
 |generics    |0.1.3  |0.1.3    |   |
 |glue        |1.6.2  |1.6.2    |   |
 |hms         |1.1.3  |1.1.3    |   |
-|httr        |1.4.5  |1.4.5    |   |
-|jsonlite    |1.8.4  |1.8.4    |   |
+|httr        |1.4.6  |1.4.6    |   |
+|jsonlite    |1.8.7  |1.8.7    |   |
 |lifecycle   |1.0.3  |1.0.3    |   |
 |magrittr    |2.0.3  |2.0.3    |   |
 |mime        |0.12   |0.12     |   |
@@ -47,17 +47,17 @@
 |purrr       |1.0.1  |1.0.1    |   |
 |R6          |2.5.1  |2.5.1    |   |
 |readr       |2.1.4  |2.1.4    |   |
-|rlang       |1.1.0  |1.1.0    |   |
+|rlang       |1.1.1  |1.1.1    |   |
 |stringi     |1.7.12 |1.7.12   |   |
 |stringr     |1.5.0  |1.5.0    |   |
-|sys         |3.4.1  |3.4.1    |   |
+|sys         |3.4.2  |3.4.2    |   |
 |tibble      |3.2.1  |3.2.1    |   |
 |tidyr       |1.3.0  |1.3.0    |   |
 |tidyselect  |1.2.0  |1.2.0    |   |
-|tzdb        |0.3.0  |0.3.0    |   |
+|tzdb        |0.4.0  |0.4.0    |   |
 |utf8        |1.2.3  |1.2.3    |   |
-|vctrs       |0.6.2  |0.6.2    |   |
-|vroom       |1.6.1  |1.6.1    |   |
+|vctrs       |0.6.3  |0.6.3    |   |
+|vroom       |1.6.3  |1.6.3    |   |
 |withr       |2.5.0  |2.5.0    |   |
 
 # Revdeps
@@ -66,5 +66,5 @@
 
 |package    |version |error  |warning |note |
 |:----------|:-------|:------|:-------|:----|
-|[tidyREDCap](problems.md#tidyredcap)|1.1.0   |__+1__ |        |     |
+|[tidyREDCap](problems.md#tidyredcap)|1.1.1   |__+1__ |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,6 +1,6 @@
 ## revdepcheck results
 
-We checked 5 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 6 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 1 new problems
  * We failed to check 0 packages

diff --git a/revdep/problems.md b/revdep/problems.md
@@ -2,11 +2,11 @@
 
 <details>
 
-* Version: 1.1.0
-* GitHub: <https://github.com/RaymondBalise/tidyREDCap>
-* Source code: <https://github.com/cran/tidyREDCap>
-* Date/Publication: 2023-02-18 18:10:02 UTC
-* Number of recursive dependencies: 82
+* Version: 1.1.1
+* GitHub: https://github.com/RaymondBalise/tidyREDCap
+* Source code: https://github.com/cran/tidyREDCap
+* Date/Publication: 2023-05-29 16:30:02 UTC
+* Number of recursive dependencies: 88
 
 Run `revdepcheck::revdep_details(, "tidyREDCap")` for more info
 
@@ -31,8 +31,9 @@ Run `revdepcheck::revdep_details(, "tidyREDCap")` for more info
        16.                   └─vctrs:::stop_names(...)
        17.                     └─vctrs:::stop_vctrs(...)
        18.                       └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
-
-      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 4 ]
+      
+      [ FAIL 1 | WARN 8 | SKIP 0 | PASS 13 ]
       Error: Test failures
       Execution halted
     ```
+
diff --git a/tests/testthat/test-arm-export.R b/tests/testthat/test-arm-export.R
@@ -9,7 +9,7 @@ read_arms <- function(path) {
     arm_num = readr::col_integer(),
     name    = readr::col_character()
   )
-  full_path |>
+  full_path %>%
     readr::read_csv(col_types = col_types) %>%
     dplyr::select(
       arm_number  = "arm_num",

diff --git a/tests/testthat/test-event-read.R b/tests/testthat/test-event-read.R
@@ -13,7 +13,7 @@ retrieve_expected_events <- function(path) {
     event_id           = readr::col_integer()
   )
 
-  full_path |>
+  full_path %>%
     readr::read_csv(col_types = col_types)
 }