tests/testthat/test_loading.R

In BodenmillerGroup/imcdatasets: Collection of publicly available imaging mass cytometry (IMC) datasets

# Checking all the getter functions.

check_sce <- function(sce) {
    expect_true(all(dim(sce) > 0))
    expect_true(length(assayNames(sce)) > 0)
}

check_images <- function(img) {
    expect_true(all(channelNames(img) > 0))
    expect_true(length(img) > 0)
}

check_masks <- function(msk) {
    expect_true(length(msk) > 0)
}

check_intersect <- function(sce, img, msk) {
    mappingcols <- Reduce(intersect, list(colnames(colData(sce)),
        colnames(mcols(img)),
        colnames(mcols(msk))))
    expect_true(length(mappingcols) > 0)
}

datasets <- list(
    "Damond_2019_Pancreas",
    "HochSchulz_2022_Melanoma",
    "JacksonFischer_2020_BreastCancer",
    "Zanotelli_2020_Spheroids",
    "IMMUcan_2022_CancerExample"
)

testDatasetWorks <- function(x) {
    test_that(paste(x, "works"), {
        sce <- do.call(x, args = list(data_type = "sce"))
        images <- do.call(x, args = list(data_type = "images"))
        masks <- do.call(x, args = list(data_type = "masks"))
        
        check_sce(sce)
        check_images(images)
        check_masks(masks)
        check_intersect(sce, images, masks)
        
        # On disk storage works
        cur_path <- tempdir()
        on.exit(unlink(cur_path))
        
        # Fail
        expect_error(
            do.call(x, args = list(data_type = "test")),
            regexp = 'The data_type argument should be "sce", "spe", "images", or "masks".'
        )
        expect_error(
            do.call(x, args = list(data_type = c("sce", "images"))),
            regexp = 'The data_type argument should be of length 1.'
        )
        expect_error(
            do.call(x, args = list(data_type = "sce", metadata = NA)),
            regexp = '"metadata" should be either TRUE or FALSE'
        )
        expect_error(
            do.call(x, args = list(data_type = "sce", version = "1")),
            regexp = '"version" should be "latest" or one of the available dataset versions, e.g., "v1".'
        )
        expect_error(
            do.call(x, args = list(data_type = "spe", version = "v0")),
            regexp = 'It is only possible to retrieve SPE objects with dataset versions >= v1.'
        )
        expect_error(do.call(x, args = list(metadata = TRUE)))
        expect_error(do.call(x, args = list(data_type = "masks",
            on_disk = TRUE)))
    }
)}

lapply(datasets, testDatasetWorks)