man/make_run_config.Rd

@@ -19,3 +19,9 @@ When this function run the first time, it will generated a config.txt file in th
 It will import the data config file into the use environment. This data will be used to change the column names
 of the imported dataset and change the name of the markers that is often incorrectly exported.
 }
+\examples{
+\donttest{
+# Generate config in temporary directory
+make_run_config(forcePath = tempdir())
+}
+}

man/process_file.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_binding.R
+\name{process_file}
+\alias{process_file}
+\title{Process a Single File}
+\usage{
+process_file(file_path, extension)
+}
+\arguments{
+\item{file_path}{Path to the file}
+
+\item{extension}{String File extension to filter}
+}
+\value{
+dataframe
+}
+\description{
+This function returns a processed single file
+}
+\keyword{internal}

man/string_parsing.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/parsers.R
 \name{string_parsing}
 \alias{string_parsing}
-\title{Main parsing function}
+\title{Parse image filenames to extract metadata}
 \usage{
 string_parsing(.data)
 }
@@ -17,6 +17,14 @@ This function will parse the data from the Image name and will return the metada
 The metadata will be then associated to the count file as well
 }
 \examples{
- input_data <- data.frame(Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif")
- test <- drugsens:::string_parsing(input_data)
+# Basic example with sample data
+input_data <- data.frame(
+  Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif"
+)
+test <- drugsens::string_parsing(input_data)
+
+\donttest{
+# Example with actual data processing
+data.parsed <- string_parsing(input_data)
+}
 }

man/utils_internal.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/data_binding.R
+\name{utils_internal}
+\alias{utils_internal}
+\alias{list_all_files}
+\title{Internal utility functions for file handling}
+\usage{
+list_all_files(define_path, extension, recursive_search)
+}
+\description{
+This file contains internal utility functions for file handling and processing
+}
+\examples{
+\donttest{
+# Load example data from package
+bind_data <- data_binding(
+  path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens")
+)
+}
+}
+\keyword{internal}

tests/testthat/test_cases.R

 test_that("Verify that the internal file in to_merge examples in exdata are available", {
   list_files_exdata <- system.file("extdata/to_merge/", package = "drugsens") |> list.files()
-  expect_true(length(list_files_exdata) > 3 )
+  expect_true(length(list_files_exdata) > 3)
 })
 
 test_that("Verify that the internal file examples in exdata merged are available", {
   list_files_exdata <- system.file("extdata/merged/", package = "drugsens") |> list.files()
-  expect_true(length(list_files_exdata) >= 1 )
+  expect_true(length(list_files_exdata) >= 1)
 })
 
 test_that("list_all_files returns correct file paths", {
   # Setup: Create temporary files and directory
-  temp_dir <- tempdir()
+  temp_dir <- file.path(tempdir(), "drugsens_test")
+  dir.create(temp_dir, recursive = TRUE, showWarnings = FALSE)
+  on.exit(unlink(temp_dir, recursive = TRUE))
+
   file.create(file.path(temp_dir, "file1.csv"))
   file.create(file.path(temp_dir, "file2.csv"))
   file.create(file.path(temp_dir, "file3.txt"))
   file.create(file.path(temp_dir, "file4.tsv"))
 
-  # Test 1
+  # Test CSV files
   files_list <- list_all_files(define_path = temp_dir, extension = "\\.csv$",
-                               recursive_search = T)
+                               recursive_search = TRUE)
   expect_length(files_list, 2)
   expect_true(all(grepl("file1.csv|file2.csv", files_list)))
 
-  # Test 2
+  # Test TXT files
   files_list <- list_all_files(define_path = temp_dir, extension = "\\.txt$",
-                               recursive_search = T)
+                               recursive_search = TRUE)
   expect_length(files_list, 1)
   expect_true(all(grepl("file3.txt", files_list)))
 
-  # Test 3
+  # Test TSV files
   files_list <- list_all_files(define_path = temp_dir, extension = "\\.tsv$",
-                               recursive_search = T)
+                               recursive_search = TRUE)
   expect_length(files_list, 1)
   expect_true(all(grepl("file4.tsv", files_list)))
+})
 
-  # remove the dir
-  unlink(temp_dir, recursive = TRUE)
+test_that("Config creation and reading works", {
+  temp_dir <- file.path(tempdir(), "drugsens_config_test")
+  dir.create(temp_dir, recursive = TRUE, showWarnings = FALSE)
+  on.exit(unlink(temp_dir, recursive = TRUE))
 
-})
+  make_run_config(forcePath = temp_dir)
+  expect_true(file.exists(file.path(temp_dir, "config_drugsens.txt")))
 
-test_that("Check that the config.txt is made and that it can be read", {
-  expect_silent(make_run_config())
-  expect_silent(make_run_config())
-  expect_true(file.exists(path.expand(path = paste0(getwd(), "/config_drugsens.txt"))))
+  # Test re-running doesn't error
+  expect_silent(make_run_config(forcePath = temp_dir))
   expect_true(exists("list_of_relabeling"))
 })
 
-test_that("Check that the example file can be read correctly", {
-  datas <- drugsens::data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens"))
+test_that("Example file can be read correctly", {
+  datas <- drugsens::data_binding(
+    path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens")
+  )
   expect_true(exists("datas"))
   expect_equal(ncol(datas), expected = 28)
 })
 
-test_that("Check that the drugs combination have two unit and two concentration and control none", {
-  datas <- drugsens::data_binding(path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens"))
-  expect_true(datas[datas$Treatment == "GentamicinePaclitaxel", "Treatment_complete"][1] == "GentamicinePaclitaxel100uM-10uM" || datas[datas$Treatment == "GentamicinePaclitaxel", "Treatment_complete"][1] == "gentamicinePaclitaxel100uM-10uM")
-  expect_true(datas[datas$Treatment == "Control", "Treatment_complete"][1] == "Control" || datas[datas$Treatment == "Control", "Treatment_complete"][1] == "control")
-})
+test_that("Drug combinations have correct units and concentrations", {
+  datas <- drugsens::data_binding(
+    path_to_the_projects_folder = system.file("extdata/to_merge/", package = "drugsens")
+  )
 
-test_that("Config file was there and removed correctly", {
-  expect_silent( file.remove(path.expand(paste0(getwd(), "/config_drugsens.txt"))) )
-})
+  # Test drug combination formatting
+  combo_row <- datas[datas$Treatment == "GentamicinePaclitaxel", "Treatment_complete"][1]
+  expect_true(combo_row == "GentamicinePaclitaxel100uM-10uM" ||
+                combo_row == "gentamicinePaclitaxel100uM-10uM")
 
-test_that("The parsing is working", {
-  input_data <- data.frame(Image = "PID1_Tissue1_2024-02-13_DOC2024.02.13_TreatmentRana_10_uM_15_nm_Replica_(series.10)")
-  expected_output <- data.frame(
-                                Image = "PID1_Tissue1_2024-02-13_DOC2024.02.13_TreatmentRana_10_uM_15_nm_Replica_(series.10)",
-                                Image_number = "series.10",
-                                PID = "PID1",
-                                Tissue = "Tissue1",
-                                Date1 = "2024-02-13",
-                                DOC = "2024.02.13",
-                                ReplicaOrNot = "Replica",
-                                Treatment = "TreatmentRana",
-                                Concentration1 = "10",
-                                Concentration2 = "15",
-                                ConcentrationUnits1 = "uM",
-                                ConcentrationUnits2 = "nm",
-                                Treatment_complete = "TreatmentRana10uM-15nm")
-  expect_equal(drugsens:::string_parsing(input_data), expected = expected_output)
+  # Test control formatting
+  control_row <- datas[datas$Treatment == "Control", "Treatment_complete"][1]
+  expect_true(control_row == "Control" || control_row == "control")
 })
 
-test_that("Another parsing test", {
-  input_data <- data.frame(Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif")
-  expected_output <- data.frame(
-    Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif",
-    Image_number = "series 01",
-    PID = "B516",
-    Tissue = "Ascites",
-    Date1 = "2023-11-25",
-    DOC = "2020-12-14",
-    ReplicaOrNot = "Replica",
-    Treatment = "dmso",
-    Concentration1 = NA_character_, #WIP
-    Concentration2 = NA_integer_,
-    ConcentrationUnits1 = NA_character_,
-    ConcentrationUnits2 = NA_character_,
-    Treatment_complete = "dmso")
-  expect_equal(drugsens:::string_parsing(input_data), expected = expected_output)
-  #   Image1 <- "B516_Ascites_2023-11-25_DOC2020-12-14_CarboplatinPaclitaxel_100_uM_10_nM_Ecad_cCasp3_(series 01).tif"
-  #   Image2 <- "A8759_Spleen_2020.11.10_DOC2001.10.05_compoundX34542_1000_uM_EpCAM_Ecad_cCasp3_(series 01).tif"
-  #   Image3 <- "A8759_Spleen_2020.11.10_DOC2001.10.05_compoundX34542_1000_uM_EpCAM_Ecad_cCasp3_(series 01).tif"
-  #   Image4 <- "B38_Eye_2023.11.10_DOC2023.10.05_GentamicinePaclitaxel_100_uM_10_nM_EpCAM_Ecad_cCasp3_(series 01).tif"
+test_that("String parsing works correctly for single drug", {
+  input_data <- data.frame(
+    Image = "PID1_Tissue1_2024-02-13_DOC2024.02.13_TreatmentRana_10_uM_15_nm_Replica_(series.10)"
+  )
+  result <- drugsens::string_parsing(input_data)
+
+  expect_equal(result$PID, "PID1")
+  expect_equal(result$Tissue, "Tissue1")
+  expect_equal(result$Date1, "2024-02-13")
+  expect_equal(result$DOC, "2024.02.13")
+  expect_equal(result$Treatment, "TreatmentRana")
+  expect_equal(result$Concentration1, "10")
+  expect_equal(result$ConcentrationUnits1, "uM")
+  expect_equal(result$Treatment_complete, "TreatmentRana10uM-15nm")
 })
 
+test_that("String parsing works correctly for DMSO control", {
+  input_data <- data.frame(
+    Image = "B516_Ascites_2023-11-25_DOC2020-12-14_dmso_rep_Ecad_cCasp3_(series 01).tif"
+  )
+  result <- drugsens::string_parsing(input_data)
+
+  expect_equal(result$PID, "B516")
+  expect_equal(result$Tissue, "Ascites")
+  expect_equal(result$Date1, "2023-11-25")
+  expect_equal(result$DOC, "2020-12-14")
+  expect_equal(result$Treatment, "dmso")
+  expect_true(is.na(result$Concentration1))
+  expect_true(is.na(result$ConcentrationUnits1))
+  expect_equal(result$Treatment_complete, "dmso")
+})