test_minify.R
In RaMS: R Access to Mass-Spec Data

# mzML tests ----
filename <- mzML_filenames[2]
output_dir <- tempdir()
output_filename <- paste0(output_dir, "\\mini_mzML.mzML")


# Test blacklist
exclude_mzs <- c(118.0865, 138.0555)
minifyMzml(filename, output_filename, mz_exclude=exclude_mzs, ppm=5, warn = FALSE)
mini_msdata <- grabMSdata(output_filename)


test_that("minified file is smaller", {
  expect_lt(nrow(mini_msdata$MS1),
            nrow(mzML_data$MS1[filename==basename(mzML_filenames[2])]))
})
test_that("blacklisted file has no data within bounds", {
  for(i in exclude_mzs){
    expect_equal(0, nrow(mini_msdata$MS1[mz%between%pmppm(i, ppm = 5)]))
  }
})
# # Don't want to deal with MSnbase dependencies, but these are good to run personally
# test_that("blacklist file opens in MSnbase", {
#   library(xcms)
#   raw_data <- readMSData(output_filename, pdata = NULL, msLevel. = 1)
#   bpis <- chromatogram(raw_data, aggregationFun = "max")
#   expect_s4_class(bpis, "MChromatograms")
#   plot(bpis)
# })




# Test whitelist
include_mzs <- c(118.0865, 138.0555)
minifyMzml(filename, output_filename, mz_include=include_mzs, ppm=5, warn = FALSE)
mini_msdata <- grabMSdata(output_filename)

test_that("minified file is smaller", {
  expect_lt(nrow(mini_msdata$MS1),
            nrow(mzML_data$MS1[filename==basename(filename)]))
})
test_that("whitelisted file has data only within bounds", {
  expect_lte(max(mini_msdata$MS1$mz), max(pmppm(max(exclude_mzs))))
  expect_gte(min(mini_msdata$MS1$mz), min(pmppm(min(exclude_mzs))))

  mini_list <- lapply(include_mzs, function(mz_i){
    mini_msdata$MS1[mz%between%pmppm(mz_i, ppm = 5)]
  })
  eic_mini <- do.call(rbind, mini_list)
  eic_mini <- eic_mini[order(eic_mini$rt),]
  expect_equal(eic_mini, mini_msdata$MS1)

  full_list <- lapply(include_mzs, function(mz_i){
    eic_start <- mzML_data$MS1[mz%between%pmppm(mz_i, ppm = 5)]
    chosen_filename <- basename(filename)
    eic_start[filename==chosen_filename]
  })
  eic_full <- do.call(rbind, full_list)
  eic_full <- eic_full[order(eic_full$rt),]

  expect_equal(eic_full$rt, mini_msdata$MS1$rt)
  expect_equal(eic_full$mz, mini_msdata$MS1$mz)
  expect_equal(eic_full$int, mini_msdata$MS1$int)
})
# # Don't want to deal with MSnbase dependencies, but these are good to run personally
# test_that("whitelist file opens in MSnbase", {
#   library(xcms)
#   raw_data <- readMSData(output_filename, pdata = NULL, msLevel. = 1)
#   bpis <- chromatogram(raw_data, aggregationFun = "max")
#   expect_s4_class(bpis, "MChromatograms")
# })



unlink(output_filename)
unlink(output_dir)



# mzXML tests ----
filename <- mzXML_filenames[2]
output_dir <- tempdir()
output_filename <- paste0(output_dir, "\\mini_mzXML.mzXML")


# Test blacklist
exclude_mzs <- c(118.0865, 138.0555)
minifyMzxml(filename, output_filename, mz_exclude=exclude_mzs, ppm=5, warn = FALSE)
mini_msdata <- grabMSdata(output_filename, grab_what = c("MS1", "MS2", "BPC", "TIC", "metadata"))


test_that("minified file is smaller", {
  expect_lt(nrow(mini_msdata$MS1),
            nrow(mzXML_data$MS1[filename==basename(mzXML_filenames[2])]))
})
test_that("blacklisted file has no data within bounds", {
  for(i in exclude_mzs){
    expect_equal(0, nrow(mini_msdata$MS1[mz%between%pmppm(i, ppm = 5)]))
  }
})
# # Don't want to deal with MSnbase dependencies, but these are good to run personally
# test_that("blacklist file opens in MSnbase", {
#   library(xcms)
#   raw_data <- MSnbase::readMSData(output_filename, pdata = NULL, msLevel. = 1)
#   bpis <- xcms::chromatogram(raw_data, aggregationFun = "max")
#   expect_s4_class(bpis, "MChromatograms")
# })




# Test whitelist
include_mzs <- c(118.0865, 138.0555)
minifyMzxml(filename, output_filename, mz_include=include_mzs, ppm=5, warn = FALSE)
mini_msdata <- grabMSdata(output_filename, grab_what = c("MS1", "MS2", "BPC", "TIC", "metadata"))

test_that("minified file is smaller", {
  expect_lt(nrow(mini_msdata$MS1),
            nrow(mzXML_data$MS1[filename==basename(filename)]))
})
test_that("whitelisted file has data only within bounds", {
  expect_lte(max(mini_msdata$MS1$mz), max(pmppm(max(exclude_mzs))))
  expect_gte(min(mini_msdata$MS1$mz), min(pmppm(min(exclude_mzs))))

  mini_list <- lapply(include_mzs, function(mz_i){
    mini_msdata$MS1[mz%between%pmppm(mz_i, ppm = 5)]
  })
  eic_mini <- do.call(rbind, mini_list)
  eic_mini <- eic_mini[order(eic_mini$rt),]
  expect_equal(eic_mini, mini_msdata$MS1)

  full_list <- lapply(include_mzs, function(mz_i){
    eic_start <- mzXML_data$MS1[mz%between%pmppm(mz_i, ppm = 5)]
    chosen_filename <- basename(filename)
    eic_start[filename==chosen_filename]
  })
  eic_full <- do.call(rbind, full_list)
  eic_full <- eic_full[order(eic_full$rt),]

  expect_equal(eic_full$rt, mini_msdata$MS1$rt)
  expect_equal(eic_full$mz, mini_msdata$MS1$mz)
  expect_equal(eic_full$int, mini_msdata$MS1$int)
})
# # Don't want to deal with MSnbase dependencies, but these are good to run personally
# test_that("whitelist file opens in MSnbase", {
#   raw_data <- MSnbase::readMSData(output_filename, pdata = NULL, msLevel. = 1)
#   bpis <- xcms::chromatogram(raw_data, aggregationFun = "max")
#   expect_s4_class(bpis, "MChromatograms")
# })



unlink(output_filename)
unlink(output_dir)


# Multifile tests ----
output_dir <- tempdir()

# Test errors_n_messes
test_that("Error when file not found", {
  expect_error(minifyMSdata(files = "banana"))
})

test_that("Fancy error when many files not found", {
  expect_error(minifyMSdata(files = letters[1:5]))
})

# test_that("Warn on overwrite", {
#   # Create initial files
#   output_files <- paste(output_dir, basename(mzML_filenames[2:4]), sep="/")
#   minifyMSdata(files = mzML_filenames[2:4], output_files = output_files,
#                ppm = 5, mz_include=include_mzs)
#   expect_warning(minifyMSdata(files = mzML_filenames[2:4],
#                               output_files = output_files,
#                               ppm = 5, mz_include=include_mzs))
# })


test_that("Stop if lengths not equal", {
  expect_error(minifyMSdata(files = mzML_filenames[2:4],
                            output_files = "banana"))
})
test_that("Stop if types not same", {
  acc_files <- gsub("mzML", "mzXML", mzML_filenames[2:4])
  expect_error(
    minifyMSdata(mzML_filenames[2:4], acc_files)
  )
})

unlink(output_dir)

# DDA tests ----
output_dir <- tempdir()

### mzML
filename <- mzML_filenames[1]
output_filename <- paste0(output_dir, "\\mini_DDA.mzML")
mz_include <- 118.0865
minifyMSdata(filename, output_files = output_filename,
             mz_include = mz_include, ppm = 5, warn = FALSE)

full_data <- grabMSdata(filename)
mini_data <- grabMSdata(output_filename)

test_that("Minified file has MS2", {
  expect_gt(nrow(mini_data$MS2), 0)
})

test_that("Mini data smaller than full data", {
  expect_gt(nrow(full_data$MS1), nrow(mini_data$MS1))
  expect_gt(nrow(full_data$MS2), nrow(mini_data$MS2))
})

test_that("Mini data has points only within bounds", {
  expect_gte(min(mini_data$MS2$premz), min(pmppm(mz_include)))
  expect_lte(max(mini_data$MS2$premz), max(pmppm(mz_include)))
})

unlink(output_filename)
unlink(output_dir)