tests/testthat/test_ChrombackendMzR.R

In rformassspectrometry/Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

## test backendInitialize

test_that("ChromBackendMzR works", {
    expect_true(isReadOnly(be_mzr))
    expect_false(be_mzr@inMemory)
    expect_false(identical(peaksData(be_mzr), be_mzr@peaksData))
    expect_true(identical(length(peaksData(be_mzr)), length((be_mzr@peaksData))))
    expect_true(identical(chromData(be_mzr),
                          fillCoreChromVariables(be_mzr@chromData)))
    expect_false(supportsSetBackend(be_mzr))
})

test_that("backendInitialize works", {
    expect_equal(backendInitialize(ChromBackendMzR(), files = character()),
                 ChromBackendMzR())
    expect_error(backendInitialize(ChromBackendMzR(), files = numeric(2)),
                 "must be")
})

test_that("show method for ChromBackendMzR works correctly", {
    expect_output(show(be_mzr), "file")
    expect_output(show(be_mzr), "138 chromatograms")
    expect_output(show(be_mzr), "chromIndex")
    expect_output(show(be_mzr), "msLevel")
    expect_output(show(be_mzr), "mz")
    tmp <- be_mzr
    tmp@inMemory <- TRUE
    expect_output(show(tmp), "Peaks data is cached in memory")

})
test_that("replacement method works", {
    tmp <- be_mzr
    peaksData(tmp)[[1]] <- peaksData(be_mzr)[[1]] + 1
    expect_false(identical(peaksData(tmp)[[1]], peaksData(be_mzr)[[1]]))
    expect_true(identical(peaksData(tmp)[[1]], peaksData(be_mzr)[[1]] + 1))
    expect_true(tmp@inMemory)
    expect_false(be_mzr@inMemory)

    cd <- chromData(tmp)
    cd$mz <-  1
    expect_true(!identical(chromData(tmp), cd))
    chromData(tmp) <- cd
    expect_equal(chromData(tmp), cd)
})

test_that("backendParallelFactor works", {
    expect_equal(levels(backendParallelFactor(be_mzr)), unique(dataOrigin(be_mzr)))
})

test_that("error message work", {
    expect_error(peaksData(be_mzr, columns = "notacolumn"),
                 "requested peaks variables")
    })