Nothing
test_that("trim works", {
x = trim_dataset(mx_sample,"slide_id","image_id",c("marker1_vals"),c("metadata1_vals"))
y = trim_dataset(mx_sample,"slide_id","image_id",c("marker1_vals"),NULL)
## trims correctly
expect_equal(any(c("marker2_vals","marker_3_vals") %in% colnames(x)),FALSE)
## trims correctly with metadata
expect_equal(any(c("marker2_vals","marker_3_vals","metadata1_vals") %in% colnames(y)),FALSE)
})
test_that("trim error messages work", {
## catches columns that DNE
expect_error(trim_dataset(mx_sample,"slide_id","image_id",c("marker5_vals"),c("metadata1_vals")))
## catches columns that DNE without metadata
expect_error(trim_dataset(mx_sample,"slide_id","image_id",c("marker5_vals"),NULL))
})
test_that("object works", {
x = mx_dataset(mx_sample, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals"))
## s3 object creation works
expect_equal(class(x),"mx_dataset")
## attributes work
expect_equal(attributes(x)$names, c("data","slide_id","image_id","marker_cols","metadata_cols"))
})
test_that("object error messages works", {
## catches incorrect slide_id
expect_error(new_mx_dataset(mx_sample, 1, "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
## catches incorrect image_id
expect_error(new_mx_dataset(mx_sample, "slide_id", 1, c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
## catches incorrect structure of mx_sample
expect_error(new_mx_dataset(matrix(mx_sample), "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
})
test_that("validate works", {
x <- mx_sample
y <- mx_sample
z <- mx_sample
x$marker1_vals[5] = Inf
y$marker1_vals[6] = "7"
z$marker1_vals[7] = NA
## catches Inf
expect_error(mx_dataset(x, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
## catches character
expect_error(mx_dataset(y, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
## catches NAs
expect_error(mx_dataset(z, "slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals")))
})
test_that("metadata catch works",{
x = mx_dataset(mx_sample,"slide_id", "image_id", c("marker1_vals","marker2_vals","marker3_vals"), c("metadata1_vals"))
x$data = x$data[,-6]
expect_error(validate_mx_dataset(x))
})
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