tests/testthat/test_import-GMT.R

In Bioconductor/BiocSet: Representing Different Biological Sets

context("import-GMT")

test_that("'import.gmt()' works", {
    gmtFile <- system.file(package = "BiocSet", "extdata",
                           "hallmark.gene.symbol.gmt")
    es <- import.gmt(gmtFile)
    expect_true(.is_tbl_elementset(.elementset(es)))
    expect_identical(dim(.set(es)), c(50L, 2L))
    expect_identical(dim(.elementset(es)), c(7324L, 2L))
    expect_type(.set(es)$source, "character")
})

test_that("'import()' works", {
    gmtFile <- system.file(package = "BiocSet", "extdata",
                           "hallmark.gene.symbol.gmt")
    es <- import.gmt(gmtFile)
    fl <- tempfile(fileext = ".gmt")
    export(es, fl)
    expect_equal(es, import(fl))

    es <- BiocSet() %>% mutate_set(source = character(0))
    fl <- tempfile(fileext = ".gmt")
    export(es, fl)
    expect_identical(es, import(fl))

    es <- BiocSet(a = letters, b = LETTERS)
    fl <- tempfile(fileext = ".gmt")
    export(es, fl)
    expect_identical(es %>% mutate_set(source = NA_character_), import(fl))
})