Closes #2184 check _keys renaming scheme (#2200)

* feat: #2184 rename check_keys * chore: #2184 cleanup news * code typo * styler/lintr * feat: #2184 add appropriate deprecation test --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]>
pharmaverse · Nov 7, 2023 · 708d232 · 708d232
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commit 708d232
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Showing 4 changed files with 74 additions and 7 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -54,6 +54,8 @@ for the event number, which can be used in `order`. (#2140)
 
 - The default value for the `false_value` argument in `derive_extreme_records()` was changed to `NA_character_` (#2125)
 
+- For the function `consolidate_metadata()`, the argument `check_keys` was renamed to `check_type` to align with other functions (#2184)
+
 - In `filter_joined()` and `derive_var_joined_exist_flag()` (#2126)
     - the `first_cond` argument was deprecated in favor of `first_cond_upper` and
     - the `filter` argument was deprecated in favor of `filter_join`.

diff --git a/R/consolidate_metadata.R b/R/consolidate_metadata.R
@@ -30,12 +30,21 @@
 #'
 #' @param check_keys Check keys?
 #'
+#'  `r lifecycle::badge("deprecated")` Please use `check_type` instead.
+#'
 #'   If `"warning"` or `"error"` is specified, a message is issued if the key
 #'   variables (`key_vars`) are not a unique key in all of the input datasets
 #'   (`datasets`).
 #'
 #'   *Permitted Values*: `"none"`, `"warning"`, `"error"`
 #'
+#' @param check_type Check uniqueness?
+#'
+#'   If `"warning"` or `"error"` is specified, a message is issued if the key
+#'   variables (`key_vars`) are not a unique key in all of the input datasets
+#'   (`datasets`).
+#'
+#'   *Permitted Values*: `"none"`, `"warning"`, `"error"`
 #'
 #' @details All observations of the input datasets are put together into a
 #'   single dataset. If a by group (defined by `key_vars`) exists in more than
@@ -80,7 +89,8 @@ consolidate_metadata <- function(datasets,
                                  key_vars,
                                  source_var = SOURCE,
                                  check_vars = "warning",
-                                 check_keys = "error") {
+                                 check_keys,
+                                 check_type = "error") {
   assert_list_of(datasets, class = "data.frame", named = TRUE)
   assert_vars(key_vars)
   source_var <- assert_symbol(enexpr(source_var))
@@ -90,9 +100,23 @@ consolidate_metadata <- function(datasets,
       values = c("none", "message", "warning", "error"),
       case_sensitive = FALSE
     )
-  check_keys <-
+  if (!is_missing(check_keys)) {
+    deprecate_warn(
+      "1.0.0",
+      "consolidate_metadata(check_keys = )",
+      "consolidate_metadata(check_type = )"
+    )
+    check_type <-
+      assert_character_scalar(
+        check_keys,
+        values = c("none", "warning", "error"),
+        case_sensitive = FALSE,
+        optional = TRUE
+      )
+  }
+  check_type <-
     assert_character_scalar(
-      check_keys,
+      check_type,
       values = c("none", "warning", "error"),
       case_sensitive = FALSE
     )
@@ -118,7 +142,7 @@ consolidate_metadata <- function(datasets,
       by_vars = key_vars,
       order = exprs(!!tmp_source_ord),
       mode = "last",
-      check_type = check_keys
+      check_type = check_type
     ) %>%
     remove_tmp_vars()
 }
diff --git a/man/consolidate_metadata.Rd b/man/consolidate_metadata.Rd
diff --git a/tests/testthat/test-consolidate_metadata.R b/tests/testthat/test-consolidate_metadata.R
@@ -60,8 +60,38 @@ test_that("consolidate_metadata Test 2: error if key vars are not unique", {
   )
 })
 
-## Test 3: warn if variables differ ----
-test_that("consolidate_metadata Test 3: warn if variables differ", {
+
+## Test 3: check_keys deprecation test ----
+test_that("consolidate_metadata Test 3: check_keys deprecation test", {
+  glob <- tibble::tribble(
+    ~id, ~val,
+    1,   "glob_val_1a",
+    1,   "glob_val_1b",
+    2,   "glob_val_2"
+  )
+  stud <- tibble::tribble(
+    ~id, ~val,
+    3,   "stud_val_3"
+  )
+
+  expect_warning(
+    try(
+      consolidate_metadata(
+        datasets = list(
+          global = glob,
+          study = stud
+        ),
+        key_vars = exprs(id),
+        check_keys = "error"
+      ),
+      silent = TRUE
+    ),
+    class = "lifecycle_warning_deprecated"
+  )
+})
+
+## Test 4: warn if variables differ ----
+test_that("consolidate_metadata Test 4: warn if variables differ", {
   glob <- tibble::tribble(
     ~id, ~val,
     1,   "glob_val_1",