tests/testthat/test_Chromatograms-processingQueue.R

In rformassspectrometry/Chromatograms: Infrastructure for Chromatographic Mass Spectrometry Data

test_that("addProcessing adds processing steps correctly", {
    c_queued <- addProcessing(c_full, filterPeaksData,
                              variables = c("rtime"), ranges = c(12.5, 45.5))
    queue <- c_queued@processingQueue
    expect_length(queue, 1)
    expect_equal(queue[[1]]@FUN, filterPeaksData)
    expect_equal(queue[[1]]@ARGS, list(variables = c("rtime"),
                                       ranges = c(12.5, 45.5)))
    c_queued <- addProcessing(c_queued, filterPeaksData,
                              variables = c("intensity"), ranges = c(100, 200))
    queue <- c_queued@processingQueue
    expect_length(queue, 2)

    ## Missing FUN
    c_queued <- addProcessing(c_mzr,
                              variables = c("rtime"), ranges = c(12.5, 45.5))
    expect_equal(c_queued, c_mzr)
})

test_that("processingChunkFactor is handled correctly in peaksData", {
    f <- processingChunkFactor(c_full, chunkSize = 2)
    factorized_peaks <- peaksData(c_full, f = f)
    non_factorized_peaks <- peaksData(c_full, f = f())
    expect_equal(factorized_peaks, non_factorized_peaks)

    f <- processingChunkFactor(c_mzr, chunkSize = 100)
    factorized_peaks <- peaksData(c_mzr, f = f)
    non_factorized_peaks <- peaksData(c_mzr, f = f())
    expect_equal(factorized_peaks, non_factorized_peaks)
})

test_that("applyProcessing applies all queued processing steps", {
    c_queued <- filterPeaksData(c_full, variables = c("rtime"),
                                ranges = c(12.5, 45.5))
    c_queued <- filterPeaksData(c_queued, variables = c("intensity"),
                                ranges = c(100, 200), keep = FALSE)
    c_applied <- applyProcessing(c_queued)
    expect_length(c_applied@processingQueue, 0)
    expect_equal(peaksData(c_applied), peaksData(c_applied@backend))

    ## empty queue
    c_queued@processingQueue <- list()
    c_applied <- applyProcessing(c_queued)
    expect_equal(c_applied, c_queued)

    c_queued <- filterPeaksData(c_mzr, variables = c("rtime"),
                                ranges = c(12.5, 45.5))
    expect_error(applyProcessing(c_queued), "Cannot apply")
})