tests/testthat/test_PlainTextParam.R

In sneumann/xcms: LC-MS and GC-MS Data Analysis

xmse_full <- loadXcmsData("xmse")

test_that("storeResults,PlainTextParam,MsExperiment works", {
    pth <- file.path(tempdir(), "test")
    param <- PlainTextParam(path = pth)
    param2 <- PlainTextParam()
    expect_false(is.null(param2))
    expect_error(new("PlainTextParam", path = c(tempdir(), tempdir())))
    mse <- filterMzRange(mse, c(200, 500))
    storeResults(mse, param = param)
    expect_true(dir.exists(pth))
    expect_true(file.exists(file.path(param@path, "sample_data.txt")))
    expect_true(file.exists(file.path(param@path, "spectra_files.txt")))
    expect_true(file.exists(file.path(param@path, "spectra_processing_queue.json")))
})

test_that("storeResults,PlainTextParam,XcmsExperiment works", {
    pth = file.path(tempdir(), "test")
    param <- PlainTextParam(path = pth)
    param2 <- PlainTextParam()
    expect_false(is.null(param2))
    mse <- filterMzRange(xmse_full, c(200, 500))
    storeResults(xmse_full, param = param)
    expect_true(dir.exists(pth))
    expect_true(file.exists(file.path(param@path, "sample_data.txt")))
    expect_true(file.exists(file.path(param@path, "spectra_files.txt")))
    expect_true(file.exists(file.path(param@path, "spectra_processing_queue.json")))
    expect_true(file.exists(file.path(param@path, "process_history.json")))
    expect_true(file.exists(file.path(param@path, "chrom_peaks.txt")))
    expect_true(file.exists(file.path(param@path, "chrom_peak_data.txt")))
    expect_true(file.exists(file.path(param@path, "rtime_adjusted.txt")))
    expect_true(file.exists(file.path(param@path, "feature_definitions.txt")))
    expect_true(file.exists(file.path(param@path, "feature_peak_index.txt")))
})