Add more unit testing, fix typos

DESCRIPTION

 Package: DRUGSENS
-Title: Get Data From QuPath For Data Analysis
+Title: DRUGSENS is a R-package that allows users to automatically analyze QuPath™'s output data from imaging analysis.
+       In addition, it will automatically extract metadata from the QuPath's data.
 Version: 0.1.0
 BugReports: https://git.scicore.unibas.ch/ovca-research/DRUGSENS/issues
 Authors@R: c(
@@ -9,7 +10,7 @@ Authors@R: c(
     person("University of Basel and University Hospital Basel", role = c("cph"))   
     )
 URL: https://git.scicore.unibas.ch/ovca-research/DRUGSENS/
-Maintainer: Flavio C. Lombardo <flavio.lombardo@unibas.cht>
+Maintainer: Flavio Lombardo <flavio.lombardo@unibas.ch>
 Description: This package simplifies the analysis of QuPath data is complementary to the STAR Protocol: 
     "DRUG-SENS: Quantification of Drug Sensitivity in 3D Patient-derived Ovarian Cancer Models"
 License: MIT + file LICENSE

tests/testthat/test_cases.R

@@ -39,28 +39,68 @@ test_that("list_all_files returns correct file paths", {
 
 })
 
-test_that("Check that the config.txt is made and can be read", {
+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"))))
   expect_true(exists("list_of_relabeling"))
 })
 
-# WIP add for the regex in processing the data
-# test_that("Check that parsig does work", {
-#
-#   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"
-#
-#   # make a dataframe of those images examples
-#   dt <- data.frame(
-#     Image = c(Image1, Image2, Image3, Image4),
-#     Example = c("Protocol", "Fake", "Fake", "Fake")
-#   )
-#
-#   # run parser
-#   dt1 <- DRUGSENS:::string_parsing(dt)
-#
-#   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"))
+  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("Config file was there and removed correctly", {
+  expect_silent( file.remove(path.expand(paste0(getwd(), "/config_DRUGSENS.txt"))) )
+})
+
+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_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"
+})
+