resolved issue #22. Yes/No will not be converted to booleans

CHANGELOG.md

@@ -4,6 +4,12 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.6.1
+
+### Fixes
+
+- Improved the read_params function by enforcing the params.yaml to be read as is. "Yes", "No" will not be converted to booleans anymore. Related to issue #22
+
 ## v0.6
 
 ### New Features

DESCRIPTION

@@ -19,7 +19,8 @@ Imports:
     stringr,
     methods,
     rlang,
-    rstudioapi (>= 0.11)
+    rstudioapi (>= 0.11),
+    purrr
 RoxygenNote: 7.3.2
 Suggests:
     testthat (>= 3.0.0)

NAMESPACE

@@ -10,6 +10,7 @@ export(dso_repro_stage_addin)
 export(dso_repro_stage_w_dependencies_addin)
 export(init)
 export(read_params)
+export(read_safe_yaml)
 export(reload)
 export(repro)
 export(safe_get)
@@ -22,6 +23,7 @@ importFrom(glue,glue)
 importFrom(here,here)
 importFrom(here,i_am)
 importFrom(methods,show)
+importFrom(purrr,modify_tree)
 importFrom(rlang,caller_env)
 importFrom(rstudioapi,viewer)
 importFrom(stringr,coll)

R/read_params.R

@@ -11,7 +11,6 @@
 #' @param return_list returns a list if TRUE, by default it return `dsoParams` class which is a list with secure access
 #'
 #' @return parameters as list of list as `dsoParams` or conventional list when `return_list` is set.
-#' @importFrom yaml read_yaml
 #' @export
 read_params <- function(stage_path = NULL, return_list = FALSE) {
   if (!is.logical(return_list)) {
@@ -73,7 +72,7 @@ read_params <- function(stage_path = NULL, return_list = FALSE) {
     }
   )
 
-  yaml <- read_yaml(tmp_config_file)
+  yaml <- read_clean_yaml(tmp_config_file)
   unlink(tmp_config_file)
 
   if (return_list) {
@@ -125,3 +124,38 @@ set_stage <- function(stage_path) {
 stage_here <- function(...) {
   file.path(config_env$stage_dir, ...)
 }
+
+#' @title read_safe_yaml
+#' @description
+#' Safely reads in yaml files
+#' @export
+#' @return a list
+#' @importFrom yaml read_yaml
+#' @importFrom purrr modify_tree
+#' @export
+read_safe_yaml <- function(params_file) {
+  yaml <- read_yaml(params_file,
+    handlers = list(
+      "bool#yes" = \(x) {
+        attr(x, "yaml_bool") <- TRUE
+        x
+      },
+      "bool#no" = \(x) {
+        attr(x, "yaml_bool") <- FALSE
+        x
+      }
+    )
+  ) |>
+    purrr::modify_tree(leaf = \(x) {
+      if (is.character(x) && is.logical(attr(x, "yaml_bool"))) {
+        if (x %in% c("true", "false")) {
+          return(attr(x, "yaml_bool"))
+        } else {
+          attr(x, "yaml_bool") <- NULL
+          return(x)
+        }
+      } else {
+        return(x)
+      }
+    })
+}

tests/testthat/test-read_params.R

@@ -0,0 +1,51 @@
+library(yaml)
+test_that("read_params: yes and no parameters are correctly loaded", {
+  ### Create Test Data
+  # Create a temporary YAML file
+  temp_file <- file.path("temp.yaml")
+  # Define the data
+  data <- list(
+    correct_true = "true",
+    correct_false = "false",
+    false_true = "Y",
+    false_false = "N",
+    false_true2 = "yes",
+    false_false2 = "no"
+  )
+  write_yaml(data, temp_file)
+
+  ### Removal of quotes necessary
+  # Read the file
+  file_content <- readLines(temp_file)
+
+  # Apply noquote to each line
+  file_content <- gsub("'", "", file_content)
+
+  # Write the modified content back to a file
+  writeLines(as.character(file_content), temp_file)
+
+  ### Load temp params.yaml
+  # Load in temporary YAML file using read_safe_yaml
+  safe_yaml <- read_safe_yaml(temp_file)
+
+  # Load in temporary YAML file using default read_yaml
+  yaml <- read_yaml(temp_file)
+
+  # Test default read_yaml function
+  expect_false(yaml$false_true == data$false_true)
+  expect_false(yaml$false_false == data$false_false)
+  expect_false(yaml$false_true2 == data$false_true2)
+  expect_false(yaml$false_false2 == data$false_false2)
+  expect_true(yaml$correct_true == TRUE)
+  expect_true(yaml$correct_false == FALSE)
+
+  # Test read_safe_yaml function
+  expect_true(safe_yaml$false_true == safe_yaml$false_true)
+  expect_true(safe_yaml$false_false == safe_yaml$false_false)
+  expect_true(safe_yaml$false_true2 == safe_yaml$false_true2)
+  expect_true(safe_yaml$false_false2 == safe_yaml$false_false2)
+  expect_true(safe_yaml$correct_true == TRUE)
+  expect_true(safe_yaml$correct_false == FALSE)
+
+  file.remove(temp_file)
+})