Convert "# nolint" to specific rule exception (#178)

# Pull Request

<!--- Replace `#nnn` with your issue link for reference. -->

Part of #172

#### Changes description

- Add new regex style to object_name_linter to account for ADaM
variables.
  - See `.lintr` file
- `regexes = c(ANL = "^ANL_?[0-9]*$", ADaM =
"^r?ADSL|ADTTE|ADLB|ADRS|ADAE$"))`
- Allows for variables named `ANL` with optional underscore and numbers
after.
- note: can't use groups (`(rule_within_parenthesis)`) due to
[r-lib/lintr/issues/2188](r-lib/lintr#2188)
not being released yet.
- Convert other `# nolint` to specific `# nolint: <rule name>.` for
specificity

---------

Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
Co-authored-by: m7pr <marcin.kosinski.mk1@roche.com>

Author: averissimo

.lintr

@@ -1,5 +1,6 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
   cyclocomp_linter = NULL,
-  object_usage_linter = NULL
+  object_usage_linter = NULL,
+  object_name_linter = object_name_linter(styles = c("snake_case", "symbols"), regexes = c(ANL = "^ANL_?[0-9]*$", ADaM = "^r?AD[A-Z]{2,3}_?[0-9]*$"))
   )

R/Queue.R

@@ -17,7 +17,7 @@
 #' @name Queue
 #' @keywords internal
 #'
-Queue <- R6::R6Class( # nolint
+Queue <- R6::R6Class( # nolint: object_name_linter.
   classname = "Queue",
   # public methods ----
   public = list(

R/choices_labeled.R

@@ -191,8 +191,7 @@ variable_choices.character <- function(data, subset = NULL, fill = FALSE, key =
 
 #' @rdname variable_choices
 #' @export
-variable_choices.data.frame <- function(data, subset = NULL, fill = TRUE, key = NULL) { # nolint
-
+variable_choices.data.frame <- function(data, subset = NULL, fill = TRUE, key = NULL) {
   checkmate::assert(
     checkmate::check_character(subset, null.ok = TRUE),
     checkmate::check_function(subset, null.ok = TRUE)
@@ -316,7 +315,7 @@ value_choices.character <- function(data,
 
 #' @rdname value_choices
 #' @export
-value_choices.data.frame <- function(data, # nolint
+value_choices.data.frame <- function(data,
                                      var_choices,
                                      var_label = NULL,
                                      subset = NULL,

R/choices_selected.R

@@ -191,7 +191,7 @@ choices_selected <- function(choices,
 #'
 #' @export
 #'
-is.choices_selected <- function(x) { # nolint
+is.choices_selected <- function(x) { # nolint: object_name_linter.
   inherits(x, "choices_selected")
 }
 
@@ -231,7 +231,7 @@ add_no_selected_choices <- function(x, multiple = FALSE) {
 #'
 #' @export
 #'
-no_selected_as_NULL <- function(x) { # nolint
+no_selected_as_NULL <- function(x) { # nolint: object_name_linter.
   if (is.null(x) || identical(x, no_select_keyword) || x == "") {
     NULL
   } else {

R/data_extract_module.R

@@ -457,10 +457,16 @@ data_extract_srv.FilteredData <- function(id, datasets, data_extract_spec, ...)
 #' `select_validation_rule` but for the choose dataset part of the `data_extract_ui`
 #' @export
 #'
-data_extract_srv.list <- function(id, datasets, data_extract_spec, join_keys = NULL,
+data_extract_srv.list <- function(id,
+                                  datasets,
+                                  data_extract_spec,
+                                  join_keys = NULL,
                                   select_validation_rule = NULL,
                                   filter_validation_rule = NULL,
-                                  dataset_validation_rule = if (is.null(select_validation_rule) && is.null(filter_validation_rule)) { # nolint
+                                  dataset_validation_rule = if (
+                                    is.null(select_validation_rule) &&
+                                      is.null(filter_validation_rule)
+                                  ) {
                                     NULL
                                   } else {
                                     shinyvalidate::sv_required("Please select a dataset")
@@ -738,14 +744,20 @@ data_extract_multiple_srv.FilteredData <- function(data_extract, datasets, ...)
 #'
 #' @export
 #'
-data_extract_multiple_srv.list <- function(data_extract, datasets, join_keys = NULL,
+data_extract_multiple_srv.list <- function(data_extract,
+                                           datasets,
+                                           join_keys = NULL,
                                            select_validation_rule = NULL,
                                            filter_validation_rule = NULL,
-                                           dataset_validation_rule = if (is.null(select_validation_rule) && is.null(filter_validation_rule)) { # nolint
+                                           dataset_validation_rule = if (
+                                             is.null(select_validation_rule) &&
+                                               is.null(filter_validation_rule)
+                                           ) {
                                              NULL
                                            } else {
                                              shinyvalidate::sv_required("Please select a dataset")
-                                           }, ...) {
+                                           },
+                                           ...) {
   checkmate::assert_list(datasets, types = c("reactive", "data.frame"), names = "named")
   checkmate::assert_class(join_keys, "join_keys", null.ok = TRUE)
   checkmate::assert(

R/filter_spec.R

@@ -285,7 +285,7 @@ filter_spec_internal <- function(vars_choices,
 
 #' @rdname filter_spec_internal
 #' @export
-filter_spec_internal.delayed_data <- function(vars_choices, # nolint
+filter_spec_internal.delayed_data <- function(vars_choices,
                                               vars_selected = NULL,
                                               vars_label = NULL,
                                               vars_fixed = FALSE,

R/get_dplyr_call.R

@@ -82,7 +82,7 @@ get_dplyr_call_data <- function(selector_list, join_keys = teal.data::join_keys(
       all_cols
     )
 
-    pivot_longer_unite_cols_renamed <- if (rlang::is_empty(unite_vals)) { # nolint
+    pivot_longer_unite_cols_renamed <- if (rlang::is_empty(unite_vals)) { # nolint: object_length_linter.
       pivot_longer_cols_renamed
     } else {
       Reduce(

R/get_merge_call.R

@@ -57,7 +57,7 @@ get_merge_call <- function(selector_list,
     anl_merge_call_i <- call(
       "<-",
       as.name(anl_name),
-      { # nolint
+      {
         merge_key_i <- get_merge_key_i(idx = idx, dplyr_call_data = dplyr_call_data)
         is_merge_key_pair <- vapply(merge_key_i, function(x) length(names(x)) == 1, logical(1))
 

R/select_spec.R

@@ -109,7 +109,7 @@ select_spec <- function(choices,
 #' @rdname select_spec
 #' @export
 #'
-select_spec.delayed_data <- function(choices, # nolint
+select_spec.delayed_data <- function(choices, # nolint: object_name_linter.
                                      selected = NULL,
                                      multiple = length(selected) > 1,
                                      fixed = FALSE,
@@ -144,7 +144,7 @@ select_spec.delayed_data <- function(choices, # nolint
 #' @rdname select_spec
 #' @export
 #'
-select_spec.default <- function(choices, # nolint
+select_spec.default <- function(choices, # nolint: object_name_linter.
                                 selected = choices[1],
                                 multiple = length(selected) > 1,
                                 fixed = FALSE,

R/zzz.R

@@ -1,4 +1,4 @@
-.onLoad <- function(libname, pkgname) { # nolint
+.onLoad <- function(libname, pkgname) {
   teal.logger::register_logger("teal.transform")
   invisible()
 }