tests/testthat/test-saveDataset.R

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

# This checks that saveDataset works as expected.
# library(testthat); library(scRNAseq); source("test-saveDataset.R")

sce <- SingleCellExperiment(list(counts=matrix(rpois(1000, lambda=1), 100, 10)))
sce$foo <- sample(letters, 10)
rownames(sce) <- sprintf("GENE_%i", seq_len(nrow(sce)))
colnames(sce) <- head(LETTERS, 10)

test_that("saveDataset works as expected", {
    meta <- list(
        title="My dataset",
        description="This is my dataset",
        taxonomy_id="10090",
        genome="GRCh38",
        sources=list(list(provider="GEO", id="GSE12345")),
        maintainer_name="Shizuka Mogami",
        maintainer_email="mogami.shizuka@765pro.com"
    )

    tmp <- tempfile()
    saveDataset(sce, tmp, meta)
    roundtrip <- alabaster.base::readObject(tmp)
    expect_identical(colData(roundtrip), colData(sce))
    expect_identical(as.matrix(counts(roundtrip)), assay(sce))

    meta <- jsonlite::fromJSON(file.path(tmp, "_bioconductor.json"), simplifyVector=FALSE)
    expect_identical(meta$bioconductor_version, as.character(BiocManager::version()))

    # Validation fails as expected.
    tmp <- tempfile()
    meta$title <- 1234
    expect_error(saveDataset(sce, tmp, meta), "title")
})

test_that("saveDataset works with ReloadedArray objects", {
    meta <- list(
        title="My dataset",
        description="This is my dataset",
        taxonomy_id="10090",
        genome="GRCh38",
        sources=list(list(provider="GEO", id="GSE12345")),
        maintainer_name="Shizuka Mogami",
        maintainer_email="mogami.shizuka@765pro.com"
    )

    # Saving something to link to.
    tmp <- tempfile()
    saveDataset(sce, tmp, meta)

    # Adding some ReloadedArray assays.
    sce2 <- sce
    assay(sce2, "foobar", withDimnames=FALSE) <- alabaster.matrix::ReloadedArray(path=file.path(tmp, "assays", "0"), seed=matrix(0, 100, 10))
    assay(sce2, "blah", withDimnames=FALSE) <- alabaster.matrix::ReloadedArray(path=file.path(tmp, "assays", "0"), seed=matrix(0, 100, 10))

    # Checking that the link targets are created correctly.
    tmp2 <- tempfile()
    saveDataset(sce2, tmp2, meta)
    expect_true(nchar(Sys.readlink(file.path(tmp2, "assays", "1", "array.h5"))) > 0L) # check that these are indeed symlinks.
    expect_true(nchar(Sys.readlink(file.path(tmp2, "assays", "2", "OBJECT"))) > 0L)

    roundtrip <- alabaster.base::readObject(tmp2)
    expect_identical(as.matrix(assay(roundtrip, 2)), assay(sce)) # all assays are just symlinked to the first save!
    expect_identical(as.matrix(assay(roundtrip, 3)), assay(sce))
})