From 9e78bb4b4153e085006609742c2e5444fc284050 Mon Sep 17 00:00:00 2001
From: StijnVandenbulcke <vandenbulcke.stijn@gmail.com>
Date: Tue, 7 May 2024 20:04:31 +0200
Subject: [PATCH] Testing the temporary unit tests

---
 DESCRIPTION                    |  3 +-
 tests/testthat/test-msqrob.R   | 62 ++++++++++++++++++++++++++++++++++
 tests/testthat/test-testthat.R |  3 ++
 3 files changed, 67 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/test-msqrob.R
 create mode 100644 tests/testthat/test-testthat.R

diff --git a/DESCRIPTION b/DESCRIPTION
index 04e8e33..60e373a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -66,7 +66,7 @@ Suggests:
     RefManageR,
     sessioninfo,
     rmarkdown,
-    testthat,
+    testthat (>= 3.0.0),
     tidyverse,
     plotly,
     msdata,
@@ -97,3 +97,4 @@ biocViews:
     Preprocessing
 URL: https://github.com/statOmics/msqrob2
 BugReports: https://github.com/statOmics/msqrob2/issues
+Config/testthat/edition: 3
diff --git a/tests/testthat/test-msqrob.R b/tests/testthat/test-msqrob.R
new file mode 100644
index 0000000..34bbb39
--- /dev/null
+++ b/tests/testthat/test-msqrob.R
@@ -0,0 +1,62 @@
+#Create Data
+#One protein that can be fit and one that returns a fitError
+se_assay <- matrix(c(rnorm(n = 10,
+                         mean = rep(c(5,10),
+                                    each  =5),
+                         sd = 0.1),
+                   rep(NA,times=10)),
+                   nrow =2,
+                   byrow = TRUE,
+                   dimnames = list(c("Protein1","Protein2"), LETTERS[1:10]))
+se_cd <- DataFrame(treatment = rep(c("A","B"), each= 5),
+                   row.names = LETTERS[1:10])
+se <- SummarizedExperiment(assay = se_assay,
+                           colData = se_cd)
+qf <- QFeatures(List(se1 = se), colData = se_cd)
+#Testing with SummarizedExperiment class
+msqrob_output_se <- msqrob(object = se,
+                           formula = ~ treatment,
+                           robust = FALSE,
+                           ridge = FALSE)
+
+msqrob_output_qf <- msqrob(object = qf,
+                           i = "se1",
+                           formula = ~ treatment,
+                           robust = FALSE,
+                           ridge = FALSE)
+
+
+test_that("Testing classes of msqrob output", {
+  expect_s4_class(msqrob_output_se, "SummarizedExperiment")
+  expect_s4_class(msqrob_output_qf, "QFeatures")
+  expect_s4_class(msqrob_output_qf[["se1"]],"SummarizedExperiment")
+})
+
+
+#As the output of the SummarizedExperiment and QFeatures are made with
+#The same functions i will not be testing them separately
+#Todo: Testing all the functions separately
+
+test_that("Testing msqrob models", {
+  Protein1 <- rowData(msqrob_output_se)$msqrobModels$Protein1
+  Protein2 <- rowData(msqrob_output_se)$msqrobModels$Protein2
+
+  expect_s4_class(Protein1, "StatModel")
+  expect_s4_class(Protein2, "StatModel")
+
+  expect_equal(Protein1@type, expected = "lm")
+  expect_equal(Protein2@type, expected = "fitError")
+})
+
+
+
+#Todo:
+#Testing coldata
+# - Missing data
+# - Subsetted data
+# - levels (ordering as well, important for coefficient names)
+#Testing rowdata
+#Testing parameters
+# - correct naming (check ordering with levels of coldata!)
+# - correct values
+# ...
diff --git a/tests/testthat/test-testthat.R b/tests/testthat/test-testthat.R
new file mode 100644
index 0000000..8849056
--- /dev/null
+++ b/tests/testthat/test-testthat.R
@@ -0,0 +1,3 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})