tests/testthat/test_utils.R

In pepkit/pepr: Reading Portable Encapsulated Projects

# get data ----------------------------------------------------------------

branch = "master"

DF = mtcars

p = Project(file = system.file(
    "extdata",
    paste0("example_peps-", branch),
    "example_basic",
    "project_config.yaml",
    package = "pepr"
))


# tests -------------------------------------------------------------------

test_that("listifyDF returns correct object type and throws errors", {
    expect_is(.listifyDF(DF = DF), 'data.frame')
    expect_is(.listifyDF(DF = DF)[[1]], 'list')
    expect_error(.listifyDF(DF = 1))
})

test_that("listifyDF does not change the dimensions", {
    expect_equal(dim(.listifyDF(DF)), dim(DF))
})

test_that(".makeAbsPath throws errors", {
    expect_error(expect_warning(.makeAbsPath("path", "test")))
})

test_that(".makeAbsPath returns NULL and NA if these are subject to test", {
    expect_null(.makeAbsPath(NULL, "test"))
    expect_true(is.na(.makeAbsPath(NA, "test")))
})
test_that(".expandPath returns correct object type", {
    expect_is(.expandPath(path = "~/UVA/"), 'character')
    expect_is(.expandPath(1), 'numeric')
})
test_that(".expandPath does not throw an error when when non-existent 
          environment variable is found. Just a warning.", {
    expect_warning(.expandPath("~/$HOME/test/$NonExistentVar"))
})

test_that("strformat returns correct object type and throws errors", {
    expect_is(.strformat("{VAR1}{VAR2}_file", list(VAR1 = "hi", VAR2 = "hello")), "character")
    expect_error(.strformat("{VAR1}{VAR2}_file", list(VAR1 = "hi")))
    expect_error(.strformat(1))
})

test_that(".isAbsolute returns correct object type and throws errors", {
    expect_is(.isAbsolute("/home/mjs5kd"), 'logical')
    expect_error(.isAbsolute(1))
})

test_that(".isAbsolute works properly", {
    expect_true(.isAbsolute("/home/mjs5kd"))
    expect_false(.isAbsolute("UVA/data"))
})

test_that("printNestedList throws errors", {
    expect_error(.printNestedList(1))
})

test_that("fetchSamples throws errors", {
    expect_error(
        fetchSamples(
            samples = sampleTable(p),
            attr = "test",
            func = function(x) {
                
            },
            action = "include"
        )
    )
    expect_error(
        fetchSamples(
            samples = sampleTable(p),
            attr = "file",
            func = function(x) {
                stop("test")
            },
            action = "include"
        )
    )
    expect_error(fetchSamples("test"))
    expect_error(fetchSamples(sampleTable(p), action = "test"))
    expect_error(fetchSamples(
        samples(p),
        func = function(x) {
            return(0)
        }
    ))
    expect_equal(NROW(
        fetchSamples(
            samples = sampleTable(p),
            attr = "sample_name",
            func = function(x) {
                which(x == "frog_1")
            },
            action = "include"
        )
    ), 1)
    expect_error(
        fetchSamples(
            samples = sampleTable(p),
            attr = "sample_name",
            func = "faulty function",
            action = "include"
        )
    )
})

test_that("fetchSamples returns correct rows count", {
    expect_equal(NROW(
        fetchSamples(
            samples = sampleTable(p),
            attr = "file",
            func = function(x) {
                grep("frog1", x)
            },
            action = "include"
        )
    ), 1)
    expect_equal(NROW(
        fetchSamples(
            samples = sampleTable(p),
            attr = "sample_name",
            func = function(x) {
                which(x == "frog_1")
            },
            action = "include"
        )
    ), 1)
})

test_that(".expandPath work with both curly braced and non-curly braced 
          env vars", {
    expect_equal(.expandPath("$HOME/my/path/string.txt"),
                 .expandPath("${HOME}/my/path/string.txt"))
})

test_that(".strformat returns an object of correct class", {
    expect_is(.strformat("~/{VAR1}{VAR2}_file", list(VAR1="var1a", VAR2="var2a")), "character")
})

test_that(".strformat works with multiple values", {
    expect_equal(length(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2="var2a"))), 2)
    expect_equal(length(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2=c("var2a", "var2b")))), 2)
    expect_equal(length(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2="var2a"))), 2)
})

test_that(".strformat fails when multiple multi-replacemenets of different lengths are used", {
    expect_error(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2=c("var2a", "var2b","var2c"))))
})

test_that(".printNestedList produces an output", {
    expect_output(.printNestedList(config(p)))
})