update unit tests

waldronlab · Aug 8, 2023 · 4fcaa2e · 4fcaa2e
1 parent 3d65695
commit 4fcaa2e
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Showing 2 changed files with 46 additions and 5 deletions.
diff --git a/R/MultiAssayExperiment-class.R b/R/MultiAssayExperiment-class.R
@@ -373,16 +373,15 @@ MultiAssayExperiment <-
     sampMap <- sampleMap(object)
     assayCols <- mapToList(sampMap[, c("assay", "colname")])
     colNams <- Filter(function(x) !isEmpty(x), colnames(object))
+    msg <- NULL
     if (length(colNams)) {
         logicResult <- mapply(function(x, y) {
             identical(sort(x), sort(y))
         }, x = colNams, y = assayCols)
-    if (all(logicResult))
-        NULL
-    else
-        "not all samples in the ExperimentList are found in the sampleMap"
+        if (!all(logicResult))
+            msg <- "not all ExperimentList samples are found in the sampleMap"
     }
-    NULL
+    msg
 }
 
 ## COLDATA

diff --git a/tests/testthat/test-MultiAssayExperiment.R b/tests/testthat/test-MultiAssayExperiment.R
@@ -173,3 +173,45 @@ test_that("ExperimentList metadata and mcols are preserved", {
     expect_identical(mcols(experiments(mae0)), mcoldf)
     expect_identical(metadata(experiments(mae0)), metalist)
 })
+
+test_that("sampleMap inputs are checked in MultiAssayExperiment constructor", {
+    se <- matrix(runif(100), 10, 10)
+    ## empty sampleMap
+    expect_error(
+        MultiAssayExperiment(list(foo=se))
+    )
+    se <- matrix(runif(12), 3, 4, dimnames = list(letters[1:3], NULL))
+    asamp <- DataFrame(a = "a", b = "b", c = "c")
+    expect_error(
+        MultiAssayExperiment(list(foo=se), sampleMap = asamp)
+    )
+    asamp <- DataFrame(assay = factor("foo"), primary = "p1", colname = "col1")
+    expect_error(
+        new(
+            "MultiAssayExperiment",
+            ExperimentList = ExperimentList(list(foo = se, bar = se)),
+            sampleMap = asamp
+        )
+    )
+    se <- matrix(runif(100), 10, 10)
+    expect_error(
+        new(
+            "MultiAssayExperiment",
+            ExperimentList = ExperimentList(list(foo = se)),
+            sampleMap = DataFrame(
+                assay = factor(character(), levels = "foo"),
+                primary = character(),
+                colname = character()
+            )
+        )
+    )
+    se <- matrix(runif(2), 1, 2, dimnames = list(letters[1], LETTERS[1:2]))
+    cd <- DataFrame(score = 1, row.names = "patA")
+    asamp <- DataFrame(assay = factor("foo"), primary = "patA", colname = "A")
+        new(
+            "MultiAssayExperiment",
+            ExperimentList = ExperimentList(list(foo = se)),
+            colData = cd,
+            sampleMap = asamp
+        )
+})