From 5f8935653e5e3d64cf344a096f19d5e1f407fce3 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Fri, 14 Jul 2023 18:59:33 -0500
Subject: [PATCH 1/9] try readr for `checbox_choices()`

ref #500
---
 R/metadata-utilities.R | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/R/metadata-utilities.R b/R/metadata-utilities.R
index 0d4a2f4b..b99a8a4d 100644
--- a/R/metadata-utilities.R
+++ b/R/metadata-utilities.R
@@ -114,7 +114,12 @@ 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)"
-
-  regex_named_captures(pattern = pattern_checkboxes, text = select_choices)
+  strsplit(select_choices, split = "|", fixed = TRUE)[[1]] |>
+    I() |>
+    readr::read_csv(
+      col_names = c("id", "label"),
+      col_types = "cc"
+    )
+  # pattern_checkboxes <- "(?<=\\A| \\| |\\| )(?<id>\\d{1,}), (?<label>[^|]{1,}?)(?= \\| |\\| |\\Z)"
+  # regex_named_captures(pattern = pattern_checkboxes, text = select_choices)
 }

From 61dc0f8b08f126e961d6804bf9079a4b794dcb94 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Fri, 14 Jul 2023 19:08:48 -0500
Subject: [PATCH 2/9] use magrittr pipes for a little longer

ref #500
---
 R/metadata-utilities.R | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/R/metadata-utilities.R b/R/metadata-utilities.R
index b99a8a4d..a5c5c7a2 100644
--- a/R/metadata-utilities.R
+++ b/R/metadata-utilities.R
@@ -82,6 +82,7 @@
 #' choices_3  <- ds_metadata_3[ds_metadata_3$field_name=="race", "select_choices_or_calculations"]
 #' REDCapR::regex_named_captures(pattern = pattern_boxes, text = choices_3)
 
+#' @importFrom magrittr %>%
 #' @export
 regex_named_captures <- function(pattern, text, perl = TRUE) {
   checkmate::assert_character(pattern, any.missing = FALSE, len = 1, min.chars = 0L)
@@ -114,8 +115,10 @@ 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)
 
-  strsplit(select_choices, split = "|", fixed = TRUE)[[1]] |>
-    I() |>
+  select_choices %>%
+    strsplit(split = "|", fixed = TRUE) %>%
+    magrittr::extract2(1) %>%
+    I() %>%
     readr::read_csv(
       col_names = c("id", "label"),
       col_types = "cc"

From 0f207f146d7918a6707ed1bdb57fae12f5a50a2e Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Fri, 14 Jul 2023 19:26:03 -0500
Subject: [PATCH 3/9] test multiple scenarios with one expected  dataset

ref #500

cc: @BlairCooper
---
 tests/testthat/test-metadata-utilities.R | 65 +++++++++++++++++++-----
 1 file changed, 52 insertions(+), 13 deletions(-)

diff --git a/tests/testthat/test-metadata-utilities.R b/tests/testthat/test-metadata-utilities.R
index 7831bdce..c758ebce 100644
--- a/tests/testthat/test-metadata-utilities.R
+++ b/tests/testthat/test-metadata-utilities.R
@@ -19,21 +19,60 @@ test_that("Named Captures", {
   expect_s3_class(ds_boxes, "tbl")
 })
 
-test_that("checkbox choices", {
-  choices_1 <- "1, American Indian/Alaska Native | 2, Asian | 3, Native Hawaiian or Other Pacific Islander | 4, Black or African American | 5, White | 6, Unknown / Not Reported"
-  ds_boxes <- checkbox_choices(select_choices=choices_1)
+test_that("checkbox choices -digits", {
+  ds_expected <-
+    tibble::tribble(
+      ~id,                                      ~label,
+      "1",             "American Indian/Alaska Native",
+      "-2",                                    "Asian",
+      "3", "Native Hawaiian or Other Pacific Islander",
+      "4",                 "Black or African American",
+      "5",                                     "White",
+      "66",                   "Unknown / Not Reported"
+    )
 
-  ds_expected <- structure(
-    list(
-      id = c("1", "2", "3", "4", "5", "6"),
-      label = c("American Indian/Alaska Native", "Asian", "Native Hawaiian or Other Pacific Islander", "Black or African American", "White", "Unknown / Not Reported")
-    ),
-    class = c("tbl_df", "tbl", "data.frame"),
-    row.names = c(NA, -6L)
-  )
+  # well-behaved
+  "1, American Indian/Alaska Native | -2, Asian | 3, Native Hawaiian or Other Pacific Islander | 4, Black or African American | 5, White | 66, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "well-behaved:")
 
-  expect_equal(ds_boxes, expected=ds_expected, label="The returned data.frame should be correct") #dput(ds_boxes)
-  expect_s3_class(ds_boxes, "tbl")
+  # no leading spaces
+  "1, American Indian/Alaska Native |-2, Asian |3, Native Hawaiian or Other Pacific Islander |4, Black or African American |5, White |66, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no leading spaces:")
+
+  # no trailing spaces
+  "1, American Indian/Alaska Native| -2, Asian| 3, Native Hawaiian or Other Pacific Islander| 4, Black or African American| 5, White| 66, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no trailing spaces:")
+})
+
+test_that("checkbox choices -letters", {
+  ds_expected <-
+    tibble::tribble(
+      ~id,                                      ~label,
+      "a",             "American Indian/Alaska Native",
+      "b",                                     "Asian",
+      "c", "Native Hawaiian or Other Pacific Islander",
+      "dd",                "Black or African American",
+      "eee",                                   "White",
+      "f",                    "Unknown / Not Reported"
+    )
+
+  # well-behaved
+  "a, American Indian/Alaska Native | b, Asian | c, Native Hawaiian or Other Pacific Islander | dd, Black or African American | eee, White | f, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "well-behaved:")
+
+  # no leading spaces
+  "a, American Indian/Alaska Native |b, Asian |c, Native Hawaiian or Other Pacific Islander |dd, Black or African American |eee, White |f, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no leading spaces:")
+
+  # no trailing spaces
+  "a, American Indian/Alaska Native| b, Asian| c, Native Hawaiian or Other Pacific Islander| dd, Black or African American| eee, White| f, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no trailing spaces:")
 })
 
 

From a8a9ac20f662f0cde359e10a402d6a8aae398846 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Fri, 14 Jul 2023 19:34:25 -0500
Subject: [PATCH 4/9] better structure to maintain

ref #500

cc: @BlairCooper
---
 tests/testthat/test-metadata-utilities.R | 72 ++++++++++++------------
 1 file changed, 37 insertions(+), 35 deletions(-)

diff --git a/tests/testthat/test-metadata-utilities.R b/tests/testthat/test-metadata-utilities.R
index c758ebce..d6e73d07 100644
--- a/tests/testthat/test-metadata-utilities.R
+++ b/tests/testthat/test-metadata-utilities.R
@@ -3,18 +3,20 @@ library(testthat)
 test_that("Named Captures", {
   pattern_checkboxes <- "(?<=\\A| \\| )(?<id>\\d{1,}), (?<label>[\x20-\x7B\x7D-\x7E]{1,})(?= \\| |\\Z)"
 
+  ds_expected <-
+    tibble::tribble(
+      ~id,                                      ~label,
+      "1",             "American Indian/Alaska Native",
+      "2",                                     "Asian",
+      "3", "Native Hawaiian or Other Pacific Islander",
+      "4",                 "Black or African American",
+      "5",                                     "White",
+      "6",                    "Unknown / Not Reported"
+    )
+
   choices_1 <- "1, American Indian/Alaska Native | 2, Asian | 3, Native Hawaiian or Other Pacific Islander | 4, Black or African American | 5, White | 6, Unknown / Not Reported"
   ds_boxes <- regex_named_captures(pattern=pattern_checkboxes, text=choices_1)
 
-  ds_expected <- structure(
-    list(
-      id = c("1", "2", "3", "4", "5", "6"),
-      label = c("American Indian/Alaska Native", "Asian", "Native Hawaiian or Other Pacific Islander", "Black or African American", "White", "Unknown / Not Reported")
-    ),
-    class = c("tbl_df", "tbl", "data.frame"),
-    row.names = c(NA, -6L)
-  )
-
   expect_equal(ds_boxes, expected=ds_expected, label="The returned data.frame should be correct") #dput(ds_boxes)
   expect_s3_class(ds_boxes, "tbl")
 })
@@ -48,7 +50,7 @@ test_that("checkbox choices -digits", {
 })
 
 test_that("checkbox choices -letters", {
-  ds_expected <-
+  ds_expected <- # datapasta::tribble_paste(ds_expected)
     tibble::tribble(
       ~id,                                      ~label,
       "a",             "American Indian/Alaska Native",
@@ -77,20 +79,21 @@ test_that("checkbox choices -letters", {
 
 
 test_that("checkbox choices with special characters", {
-  choices_1 <- "1, Hospital A | 2, Hospitäl B | 3, Hospital Ç | 4, Hospítal D"
+
   ds_boxes <- checkbox_choices(select_choices=choices_1)
 
-  ds_expected <- structure(
-    list(
-      id = c("1", "2", "3", "4"),
-      label = c("Hospital A", "Hospitäl B", "Hospital Ç", "Hospítal D")
-    ),
-    class = c("tbl_df", "tbl", "data.frame"),
-    row.names = c(NA, -4L)
-  )
+  ds_expected <- # datapasta::tribble_paste(ds_expected)
+    tibble::tribble(
+      ~id,       ~label,
+      "1", "Hospital A",
+      "2", "Hospitäl B",
+      "3", "Hospital Ç",
+      "4", "Hospítal D"
+    )
 
-  expect_equal(ds_boxes, expected=ds_expected, label="The returned data.frame should be correct")
-  expect_s3_class(ds_boxes, "tbl")
+  "1, Hospital A | 2, Hospitäl B | 3, Hospital Ç | 4, Hospítal D" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected)
 })
 
 ###############################################################################
@@ -111,18 +114,17 @@ test_that("checkbox choices with special characters", {
 # REDCap versions
 ###############################################################################
 test_that("checkbox choices with errant space", {
-  choices_1 <- "1, Depressive mood disorder | 2, Adjustment disorder| 3, Personality disorder | 4, Anxiety | 0, Not Noted"
-  ds_boxes <- checkbox_choices(select_choices=choices_1)
-
-  ds_expected <- structure(
-    list(
-      id = c("1", "2", "3", "4", "0"),
-      label = c("Depressive mood disorder", "Adjustment disorder", "Personality disorder", "Anxiety", "Not Noted")
-    ),
-    class = c("tbl_df", "tbl", "data.frame"),
-    row.names = c(NA, -5L)
-  )
-
-  expect_equal(ds_boxes, expected=ds_expected, label="The returned data.frame should be correct")
-  expect_s3_class(ds_boxes, "tbl")
+  ds_expected <-
+    tibble::tribble(
+      ~id,                     ~label,
+      "1", "Depressive mood disorder",
+      "2",      "Adjustment disorder",
+      "3",     "Personality disorder",
+      "4",                  "Anxiety",
+      "0",                "Not Noted"
+     )
+
+  "1, Depressive mood disorder | 2, Adjustment disorder| 3, Personality disorder | 4, Anxiety | 0, Not Noted" |>
+    checkbox_choices() |> # datapasta::tribble_paste()
+    expect_equal(ds_expected)
 })

From 982662bddd7f788d52d8b0ac06bccdf4fedcde58 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Fri, 14 Jul 2023 21:21:40 -0500
Subject: [PATCH 5/9] remove vestigial line of  test code

ref #500
---
 tests/testthat/test-metadata-utilities.R | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/tests/testthat/test-metadata-utilities.R b/tests/testthat/test-metadata-utilities.R
index d6e73d07..132860ea 100644
--- a/tests/testthat/test-metadata-utilities.R
+++ b/tests/testthat/test-metadata-utilities.R
@@ -79,9 +79,6 @@ test_that("checkbox choices -letters", {
 
 
 test_that("checkbox choices with special characters", {
-
-  ds_boxes <- checkbox_choices(select_choices=choices_1)
-
   ds_expected <- # datapasta::tribble_paste(ds_expected)
     tibble::tribble(
       ~id,       ~label,

From de881e348a40e42105faa576d104bc060cbb8338 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Sat, 15 Jul 2023 11:26:31 -0500
Subject: [PATCH 6/9] extra lines

raied by @BlairCooper in #501
---
 tests/testthat/test-metadata-utilities.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/testthat/test-metadata-utilities.R b/tests/testthat/test-metadata-utilities.R
index 132860ea..a9fbc891 100644
--- a/tests/testthat/test-metadata-utilities.R
+++ b/tests/testthat/test-metadata-utilities.R
@@ -47,6 +47,11 @@ test_that("checkbox choices -digits", {
   "1, American Indian/Alaska Native| -2, Asian| 3, Native Hawaiian or Other Pacific Islander| 4, Black or African American| 5, White| 66, Unknown / Not Reported" |>
     checkbox_choices() |>
     expect_equal(ds_expected, label = "no trailing spaces:")
+
+  # extra lines
+  "| | 1, American Indian/Alaska Native | | | -2, Asian | 3, Native Hawaiian or Other Pacific Islander | 4, Black or African American | 5, White | 66, Unknown / Not Reported | | | " |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "extra lines:")
 })
 
 test_that("checkbox choices -letters", {

From 86fe7a2f357157af394193025cb0bed136a1ac65 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Sat, 15 Jul 2023 15:05:53 -0500
Subject: [PATCH 7/9] new test: labels contain commas

ref #504
---
 tests/testthat/test-metadata-utilities.R | 27 ++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/tests/testthat/test-metadata-utilities.R b/tests/testthat/test-metadata-utilities.R
index a9fbc891..4b7e9744 100644
--- a/tests/testthat/test-metadata-utilities.R
+++ b/tests/testthat/test-metadata-utilities.R
@@ -82,6 +82,33 @@ test_that("checkbox choices -letters", {
     expect_equal(ds_expected, label = "no trailing spaces:")
 })
 
+test_that("checkbox choices -commas in labels", {
+  ds_expected <- # datapasta::tribble_paste(ds_expected)
+    tibble::tribble(
+      ~id   , ~label,
+      "a"   , "American Indian, Native American, or Alaska Native",
+      "b"   , "Asian",
+      "c"   , "Native Hawaiian, Samoan, or Other Pacific Islander",
+      "dd"  , "Black or African American",
+      "eee" , "White",
+      "f"   , "Unknown / Not Reported"
+    )
+
+  # well-behaved
+  "a, American Indian, Native American, or Alaska Native | b, Asian | c, Native Hawaiian, Samoan, or Other Pacific Islander | dd, Black or African American | eee, White | f, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "well-behaved:")
+
+  # no leading spaces
+  "a, American Indian, Native American, or Alaska Native |b, Asian |c, Native Hawaiian, Samoan, or Other Pacific Islander |dd, Black or African American |eee, White |f, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no leading spaces:")
+
+  # no trailing spaces
+  "a, American Indian, Native American, or Alaska Native| b, Asian| c, Native Hawaiian, Samoan, or Other Pacific Islander| dd, Black or African American| eee, White| f, Unknown / Not Reported" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no trailing spaces:")
+})
 
 test_that("checkbox choices with special characters", {
   ds_expected <- # datapasta::tribble_paste(ds_expected)

From 16fbe86d8beca97bad64c324f453716e185ddab4 Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Sat, 15 Jul 2023 15:06:05 -0500
Subject: [PATCH 8/9] back to regexes

ref #504
---
 R/metadata-utilities.R | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/R/metadata-utilities.R b/R/metadata-utilities.R
index a5c5c7a2..9ebff6c9 100644
--- a/R/metadata-utilities.R
+++ b/R/metadata-utilities.R
@@ -111,18 +111,25 @@ regex_named_captures <- function(pattern, text, perl = TRUE) {
 }
 
 #' @rdname metadata_utilities
+#' @importFrom rlang .data
 #' @export
 checkbox_choices <- function(select_choices) {
   checkmate::assert_character(select_choices, any.missing=FALSE, len=1, min.chars=1)
 
+  pattern <- "^(.+?),\\s*+(.*)$"
+
   select_choices %>%
     strsplit(split = "|", fixed = TRUE) %>%
     magrittr::extract2(1) %>%
-    I() %>%
-    readr::read_csv(
-      col_names = c("id", "label"),
-      col_types = "cc"
+    base::trimws() %>%
+    tibble::as_tibble() %>% # default column name is `value`
+    dplyr::filter(.data$value != "") %>%
+    dplyr::transmute(
+      id    = sub(pattern, "\\1", .data$value, perl = TRUE),
+      label = sub(pattern, "\\2", .data$value, perl = TRUE),
     )
+
   # 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)
 }

From 5f75564e9e20fb50cdfe8500f2577fed07081a4e Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Sat, 15 Jul 2023 16:40:18 -0500
Subject: [PATCH 9/9] incorporate another test scenario from @BlairCooper

ref #504

@BlairCooper wrote https://github.com/OuhscBbmc/REDCapR/pull/502/files
---
 NEWS.md                                  |  2 +-
 tests/testthat/test-metadata-utilities.R | 31 ++++++++++++++++++++++++
 2 files changed, 32 insertions(+), 1 deletion(-)

diff --git a/NEWS.md b/NEWS.md
index f5877ae2..76dba7c4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -89,7 +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)
+* The regex in `regex_named_captures()` is forgiving if there's an unnecessary leading space (@BlairCooper, #495, #501)
 
 Version 1.1.0 (released 2022-08-10)
 ==========================================================
diff --git a/tests/testthat/test-metadata-utilities.R b/tests/testthat/test-metadata-utilities.R
index 4b7e9744..6ceed0f3 100644
--- a/tests/testthat/test-metadata-utilities.R
+++ b/tests/testthat/test-metadata-utilities.R
@@ -110,6 +110,37 @@ test_that("checkbox choices -commas in labels", {
     expect_equal(ds_expected, label = "no trailing spaces:")
 })
 
+test_that("checkbox choices -digits only", {
+  ds_expected <- # datapasta::tribble_paste(ds_expected)
+    tibble::tribble(
+      ~id   , ~label,
+      "1"   , "1",
+      "2"   , "2",
+      "3"   , "3",
+      "4"   , "4"
+    )
+
+  # well-behaved
+  "1, 1 | 2, 2 | 3, 3 | 4, 4" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "well-behaved:")
+
+  # missing leading space
+  "1, 1 | 2,2 | 3, 3 | 4, 4" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "missing leading space:")
+
+  # missing trailing spaces
+  "1, 1 | 2, 2| 3, 3| 4, 4" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "no leading spaces:")
+
+  # extra lines
+  "|1, 1 | 2, 2 | 3, 3 || 4, 4| |" |>
+    checkbox_choices() |>
+    expect_equal(ds_expected, label = "well-behaved:")
+})
+
 test_that("checkbox choices with special characters", {
   ds_expected <- # datapasta::tribble_paste(ds_expected)
     tibble::tribble(