Fix: layout indeed can be longer the samples (#109)

* Fix: layout indeed can be longer the samples

* Update docs

R/classes-model.R

@@ -296,6 +296,7 @@ create_standard_curve_model_analyte <- function(plate, analyte_name, data_type =
 
   mfi_source <- ifelse(source_mfi_range_from_all_analytes, "ALL", analyte_name)
 
+
   mfi_min <- min(plate$get_data(mfi_source, "STANDARD CURVE", data_type = data_type), na.rm = TRUE)
   mfi_max <- max(plate$get_data(mfi_source, "STANDARD CURVE", data_type = data_type), na.rm = TRUE)
 

R/classes-plate_builder.R

@@ -433,13 +433,14 @@ convert_dilutions_to_numeric <- function(dilutions) {
 #'
 #' Otherwise, the returned SampleType is `TEST`
 #'
-#' @param sample_names (`character`)\cr
+#' @param sample_names (`character()`)\cr
 #' Vector of sample names from Luminex file
 #'
-#' @param sample_names_from_layout (`character`)\cr
+#' @param sample_names_from_layout (`character()`)\cr
 #' Vector of sample names from Layout file
 #' values in this vector may be different than `sample_names` and may
-#' contain additional information about the sample type like dilution
+#' contain additional information about the sample type like dilution.
+#' This vector when set has to have at least the length of `sample_names`.
 #'
 #' @return A vector of valid sample_type strings of length equal to the length of `sample_names`
 #'
@@ -448,12 +449,15 @@ convert_dilutions_to_numeric <- function(dilutions) {
 #' translate_sample_names_to_sample_types(c("S", "CP3"))
 #'
 #' @export
-translate_sample_names_to_sample_types <- function(sample_names, sample_names_from_layout = "") {
+translate_sample_names_to_sample_types <- function(sample_names, sample_names_from_layout = NULL) {
+  stopifnot(is.character(sample_names))
   # Handle case when sample name from layout is not provided
-  # Ensure sample_names_from_layout is a character vector of the same length as sample_names
-  if (length(sample_names_from_layout) != length(sample_names)) {
+  if (is.null(sample_names_from_layout)) {
     sample_names_from_layout <- rep("", length(sample_names))
   }
+  # Ensure sample_names_from_layout is a character vector at least as long as sample_names
+  stopifnot(length(sample_names) <= length(sample_names_from_layout))
+
   # Initialize the result vector
   sample_types <- vector("character", length(sample_names))
   # Iterate over each sample

R/parser.R

@@ -190,7 +190,6 @@ read_luminex_data <- function(plate_filepath,
   plate_builder$set_dilutions(use_layout_dilutions, dilutions)
 
 
-
   plate <- plate_builder$build(validate = TRUE)
 
   verbose_cat(color_codes$green_start, "\nNew plate object has been created with name: ",

tests/testthat/test-plate_builder.R

@@ -70,6 +70,16 @@ test_that("Sample type is correctly identified as POSITIVE CONTROL", {
   )
 })
 
+test_that("Test translating samples with only proportions", {
+  expect_equal(
+    translate_sample_names_to_sample_types(
+      c("BLANK", "1/50", "1/100", "1/1000"),
+      c("BLANK", "1/50", "1/100", "1/1000")
+    ),
+    c("BLANK", "STANDARD CURVE", "STANDARD CURVE", "STANDARD CURVE")
+  )
+})
+
 test_that("Sample type defaults to TEST when no special conditions are met", {
   expect_equal(
     translate_sample_names_to_sample_types(
@@ -88,14 +98,6 @@ test_that("Handling of missing layout names", {
     ),
     c("BLANK", "STANDARD CURVE", "POSITIVE CONTROL", "NEGATIVE CONTROL")
   )
-
-  expect_equal(
-    translate_sample_names_to_sample_types(
-      c("BLANK", "S", "POS 1/10", "NEGATIVE CONTROL"),
-      NA
-    ),
-    c("BLANK", "STANDARD CURVE", "POSITIVE CONTROL", "NEGATIVE CONTROL")
-  )
 })
 
 test_that("Handling of empty layout names", {