tests/testthat/test-database-functions.R

In USEPA/LUMA: LCMS-Based Untargeted Metabolomics Assistant

context("test-database-functions")

test_that("filebases are generated", {
  file <- system.file("extdata","Sample_Data.csv", package =  "LUMA")
  sample_data <- read.table(file, header = TRUE, sep = ",")
  mzdatafiles <- sample_data$CT.ID
  test.spos <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode = "Positive", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos"
  test.sneg <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode = "Negative", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos"
  test.bpos <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = TRUE, IonMode = "Positive", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos"
  test.bneg <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = TRUE, IonMode = "Negative", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos"
  expect_equal(test.spos, "Peaklist_Pos")
  expect_equal(test.sneg, "Peaklist_Neg")
  expect_equal(test.bpos, "Blanks_Pos")
  expect_equal(test.bneg, "Blanks_Neg")
})

test_that("valid databases are created", {
  if(require(RSQLite, quietly = TRUE)) {
    file <- system.file("extdata","Sample_Data.csv", package =  "LUMA")
    sample_data <- read.table(file, header = TRUE, sep = ",")
    mzdatafiles <- sample_data$CT.ID
    file.base <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode = "Positive", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos"
    peak_db <- connect_peakdb(file.base = file.base, mem = TRUE)
    mydf <- Peaklist_Pos$From_CAMERA
    write_tbl(mydf = mydf, myname = "From_CAMERA", peak.db = peak_db)
    test <- read_tbl(mytable = "From_CAMERA", peak.db = peak_db)

    lib_db <- connect_libdb(mem = TRUE)
    samples.pos <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode = "Positive", ion.id = c("Pos","Neg")) #Returns "Peaklist_Pos"
    samples.neg <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = FALSE, IonMode = "Negative", ion.id = c("Pos","Neg")) #Returns "Peaklist_Neg"
    blanks.pos <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = TRUE, IonMode = "Positive", ion.id = c("Pos","Neg")) #Returns "Blanks_Pos"
    blanks.neg <- gen_filebase(mzdatafiles = mzdatafiles, BLANK = TRUE, IonMode = "Negative", ion.id = c("Pos","Neg")) #Returns "Blanks_Neg"

    spos_db <- connect_peakdb(file.base = samples.pos, mem = TRUE)
    sneg_db <- connect_peakdb(file.base = samples.neg, mem = TRUE)
    bpos_db <- connect_peakdb(file.base = blanks.pos, mem = TRUE)
    bneg_db <- connect_peakdb(file.base = blanks.neg, mem = TRUE)
    new_db.list <- connect_lumadb(db.list = c("spos_db","sneg_db","bpos_db","bneg_db"), mem = TRUE)

    expect_true(dbIsValid(peak_db))
    expect_equal(dbListTables(peak_db)[[1]],"From_CAMERA")
    expect_equal(test,mydf)
    expect_true(dbIsValid(lib_db))
    expect_true(all(sapply(new_db.list, function(x) { #All valid databases are created
      dbIsValid(x) })))
    lapply(list(peak_db, lib_db), function(x) dbDisconnect(x))
    lapply(new_db.list, function(x) dbDisconnect(x))
  }

})