diff --git a/DESCRIPTION b/DESCRIPTION
index d29dd9e7b9de49b52faf4c7ca0d6fb5c8b28fb4d..73b4d468ea1ba4c6418b5b910d1f5b1b0aee1b8a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,6 @@
Package: DRUGSENS
-Title: Get Data From QuPath For Data Analysis
+Title: DRUGSENS is a R-package that allows users to automatically analyze QuPathâ„¢'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
diff --git a/tests/testthat/test_cases.R b/tests/testthat/test_cases.R
index 6e696da11617734df3b8d0e38577af4f69fb7788..6a79e388bc49b951db8a4d168a69091fc98b9bde 100644
--- a/tests/testthat/test_cases.R
+++ b/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"
+})
+