Merge pull request #102 from pharmaverse/99-create-var-from-codelist-bugfix

99 create var from codelist bugfix

Author: LiamHobby

R/codelists.R

@@ -191,10 +191,11 @@ type is {typeof(code_translation)}. Check the structure of the codelist in the \
   codelist <- code_translation |> pull(ref_var)
 
   miss <- setdiff(values, codelist)
-  if (strict == TRUE && length(miss) > 0) {
+  n_miss <- length(miss)
+  if (strict == TRUE && n_miss > 0) {
     cli_warn(
-      "In {.fn create_var_from_codelist}: The following value{?s} present in the
-input dataset {?is/are} not present in the codelist: {miss}"
+      "In {.fn create_var_from_codelist}: The following {qty(n_miss)}value{?s}
+present in the input dataset {qty(n_miss)}{?is/are} not present in the codelist: {miss}"
     )
   }
 

tests/testthat/test-codelist.R

@@ -84,7 +84,23 @@ test_that("create_var_from_codelist", {
     select(PARAMCD, PARAM) |>
     expect_equal(compare)
 
-  # Test warning where arg `strict == TRUE`
+  # Test character variable warning where arg `strict == TRUE` / single issue case
+  create_var_from_codelist(
+    data = data,
+    metacore = adlb_spec,
+    input_var = PARAMCD,
+    out_var = PARAM,
+    codelist = metacore::get_control_term(adlb_spec, PARAMCD),
+    decode_to_code = FALSE,
+    strict = TRUE
+  ) |>
+    expect_warning()
+
+  # Test character variable warning where arg `strict == TRUE` / multiple issue case
+  data <- tibble::tibble(
+    PARAMCD = c("ALB", "ALP", "ALT", "DUMMY", "DUMMY2")
+  )
+
   create_var_from_codelist(
     data = data,
     metacore = adlb_spec,
@@ -117,7 +133,7 @@ test_that("create_var_from_codelist", {
     select(PARAMN, PARAM) |>
     expect_equal(compare2)
 
-  # Test numeric variable used as input_var (strict == TRUE)
+  # Test numeric variable used as input_var / single issue case (strict == TRUE)
   create_var_from_codelist(
     data = data2,
     metacore = adlb_spec,
@@ -129,8 +145,27 @@ test_that("create_var_from_codelist", {
   ) |>
     expect_warning()
 
+  # Test numeric variable used as input_var / multiple issue case (strict == TRUE)
+  data3 <- tibble::tibble(
+    PARAMN = c(18, 19, 20, 99, 999)
+  )
+
+  create_var_from_codelist(
+    data = data3,
+    metacore = adlb_spec,
+    input_var = PARAMN,
+    out_var = PARAM,
+    codelist = get_control_term(adlb_spec, PARAMN),
+    decode_to_code = FALSE,
+    strict = TRUE
+  ) |>
+    expect_warning()
+
   # Test for Variable not in specs
-  expect_error(create_var_from_codelist(data, spec, VAR2, FOO))
+  expect_error(
+    create_var_from_codelist(data, adlb_spec, VAR2, FOO),
+    regexp = cli_inform(c("!" = "FOO not found in the value_spec table. Please check the variable name"))
+  )
 })
 
 test_that("create_cat_var", {