From 26345f2ba32c8bcdce41c51e46031e46251e3456 Mon Sep 17 00:00:00 2001
From: Edgar Manukyan <edgar.manukyan@roche.com>
Date: Mon, 2 Dec 2024 01:18:46 +0000
Subject: [PATCH] #107 lintr

---
 R/generate_code.R                   | 12 ++++++------
 tests/testthat/test-generate_code.R | 18 ++++++++----------
 2 files changed, 14 insertions(+), 16 deletions(-)

diff --git a/R/generate_code.R b/R/generate_code.R
index 9e6c060e..183ae3ec 100644
--- a/R/generate_code.R
+++ b/R/generate_code.R
@@ -126,7 +126,7 @@ generate_code <- function(spec, domain, out_dir = ".") {
   ) |>
     unlist() |>
     remove_last_pipe() |>
-    append(cm_template_prefix, after = 0) |>
+    append(cm_template_prefix, after = 0L) |>
     styler::style_text()
 
   # Save the code to a file
@@ -165,7 +165,7 @@ generate_one_var_code <- function(spec_var) {
   }
 
   # Remove the arguments that are missing
-  args <- purrr::discard(args, \(x) is.vector(x) && any(is.na(x)))
+  args <- purrr::discard(args, \(x) is.vector(x) && anyNA(x))
 
   # Generate the function call
   generated_call <- rlang::call2(
@@ -200,7 +200,7 @@ parse_into_c_call <- function(str_in) {
   admiraldev::assert_character_scalar(str_in)
 
   str_out <- str_in |>
-    stringr::str_split(",") |>
+    stringr::str_split(stringr::fixed(",")) |>
     unlist() |>
     stringr::str_trim()
 
@@ -245,7 +245,7 @@ remove_last_pipe <- function(code_blocks) {
 
   # The last code block should not have a pipe operator
   code_blocks[len_code_block] <- code_blocks[len_code_block] |>
-    stringr::str_remove("%>%")
+    stringr::str_remove(stringr::fixed("%>%"))
 
   code_blocks
 }
@@ -296,12 +296,12 @@ get_domain_spec <- function(spec, domain) {
       entity_sub_algorithm_temp = dplyr::if_else(
         mapping_algorithm %in% "condition_add",
         mapping_algorithm,
-        entity_sub_algorithm,
+        entity_sub_algorithm
       ),
       mapping_algorithm = dplyr::if_else(
         mapping_algorithm %in% "condition_add",
         entity_sub_algorithm,
-        mapping_algorithm,
+        mapping_algorithm
       ),
       entity_sub_algorithm = entity_sub_algorithm_temp
     ) |>
diff --git a/tests/testthat/test-generate_code.R b/tests/testthat/test-generate_code.R
index 0aff91d9..98cd64fb 100644
--- a/tests/testthat/test-generate_code.R
+++ b/tests/testthat/test-generate_code.R
@@ -10,12 +10,10 @@ test_that("generate_code works", {
 
   # Convert all NA to NA_character_
   spec <- spec |>
-    dplyr::mutate(
-      dplyr::across(
-        .cols = dplyr::everything(),
-        .fns = ~dplyr::if_else(is.na(.x), NA_character_, .x)
-    )
-  )
+    dplyr::mutate(dplyr::across(
+      .cols = dplyr::everything(),
+      .fns = ~ dplyr::if_else(is.na(.x), NA_character_, .x)
+    ))
 
   domain <- "cm"
 
@@ -24,12 +22,12 @@ test_that("generate_code works", {
   unlink(out_dir, recursive = TRUE, force = TRUE)
   dir.create(out_dir, showWarnings = FALSE, recursive = TRUE)
 
-  withr::with_options(list(width = 20), {
+  withr::with_options(list(width = 20L), {
     generate_code(spec, domain, out_dir)
     observed <- readLines(file.path(out_dir,  paste0(domain, "_sdtm_oak_code.R")))
 
-    expect_true(length(observed) > 10L)
-    expect_true(grepl("generate_oak_id_vars", observed) |> any())
-    expect_true(grepl("assign_no_ct", observed) |> any())
+    expect_gt(length(observed), 10L)
+    expect_true(grepl("generate_oak_id_vars", observed, fixed = TRUE) |> any())
+    expect_true(grepl("assign_no_ct", observed, fixed = TRUE) |> any())
   })
 })