tests/testthat/test-write_tsv.R

In and3k/dtutils: Convenience Functions for the R Package data.table

test_that("write_tsv() writes data.tables", {
  dt <- data.table::as.data.table(mtcars, keep.rownames = "row names")

  tf <- tempfile(fileext = ".tsv")
  write_tsv(dt, tf)

  # this makes sure the output is absolutely identical to the reference,
  # as readLines does some processing (i.e., doesn’t care about EOL)
  expect_identical(
    digest::digest(tf, file = TRUE),
    digest::digest(test_path("TSVs/mtcars_with_row_names.tsv"), file = TRUE)
  )
  # once more, because EOL is so unpredictable
  expect_identical(digest::digest(tf, file = TRUE), "749a7bfc1e4492f1e5adc77fa7349455")
  # however, this has a better output for debugging than comparing digests
  expect_known_output(
    writeLines(readLines(tf)),
    test_path("TSVs/mtcars_with_row_names.tsv"),
    update = FALSE
  )
})

test_that("write_tsv() works with special cases", {
  tf <- paste0(tempfile(), ".tsv")
  dt <- data.table::data.table(
    Number = 1:7,
    String = c(
      "foo", "bar, baz",
      "Lorem ipsum dolor sit amet,\nconsectetur adipiscing elit",
      "", NA,
      "single quote 'hello world' test",
      "double quote \"hello world\" test"
    )
  )
  write_tsv(dt, tf)

  # KNOWN ISSUE: fread() with quoted double-quotes does not work
  # see https://github.com/Rdatatable/data.table/issues/1109
  # that is why the last row is not compared
  expect_equal(
    head(data.table::fread(tf, sep = "\t", na.strings = ""), -1),
    head(dt, -1)
  )

  res <- readLines(tf)

  i <- 1
  # no quotations around normal strings
  expect_equal(
    res[i],
    paste0(colnames(dt)[1], "\t", colnames(dt)[2])
  )
  i <- i + 1
  expect_equal(
    res[i],
    paste0(dt$Number[1], "\t", dt$String[1])
  )
  i <- i + 1
  expect_equal(
    res[i],
    paste0(dt$Number[2], "\t", dt$String[2])
  )
  i <- i + 1
  expect_equal(
    paste0(res[i], "\n", res[i + 1]),
    paste0(dt$Number[3], "\t", "\"", dt$String[3], "\"")
  )
  i <- i + 2
  # empty strings are exported as empty quoted strings
  expect_equal(
    res[i],
    "4\t\"\""
  )
  i <- i + 1
  # NAs exported as empty
  expect_equal(
    res[i],
    "5\t"
  )
  i <- i + 1
  expect_equal(
    res[i],
    paste0(dt$Number[6], "\t", dt$String[6])
  )
  i <- i + 1
  expect_equal(
    res[i],
    paste0(dt$Number[7], "\t", "\"", gsub("\"", "\"\"", dt$String[7]), "\"")
  )
})

test_that("write_tsv() warns about wrong extensions", {
  tf_tsv <- paste0(tempfile(), ".tsv")
  tf_tab <- paste0(tempfile(), ".tab")
  tf_txt <- paste0(tempfile(), ".txt")
  tf_csv <- paste0(tempfile(), ".csv") # wrong!
  dt <- data.table::data.table(x = 1:9)

  expect_warning(write_tsv(dt, tf_tsv), NA)
  expect_warning(write_tsv(dt, tf_tab), NA)
  expect_warning(write_tsv(dt, tf_txt), NA)
  expect_warning(write_tsv(dt, tf_csv), "extension ‘.tsv’")
  expect_error(expect_warning(
    write_tsv(dt, c(tf_tsv, tf_txt)),
    NA
  ))
  expect_error(expect_warning(
    write_tsv(dt, c(tf_tsv, tf_csv)),
    "extension ‘.tsv’"
  ))
  expect_error(expect_warning(
    write_tsv(dt, c(tf_csv, tf_tsv)),
    "extension ‘.tsv’"
  ))
})

test_that("write_tsv() works with data.frame and row_names = FALSE", {
  tf <- paste0(tempfile(), ".tsv")
  write_tsv(mtcars, tf, row_names = FALSE)
  df <- read.delim(tf)
  rownames(mtcars) <- NULL
  expect_equal(df, mtcars)
})

test_that("write_tsv() works with data.frame and row_names = TRUE", {
  tf <- paste0(tempfile(), ".tsv")
  write_tsv(mtcars, tf, row_names = TRUE)
  df <- read.delim(tf, row.names = 1)
  expect_equal(df, mtcars)
})

test_that("write_tsv() and non-boolean row_names values", {
  tf <- paste0(tempfile(), ".tsv")
  df <- data.frame(
    number = 1:3,
    string = c("foo", "bar, baz", "Lorem ipsum dolor sit amet"),
    stringsAsFactors = FALSE
  )
  dt <- data.table::as.data.table(df)

  # automatic row names are not written
  write_tsv(df, tf)
  expect_equal(data.table::fread(tf, sep = "\t"), dt)

  rn <- letters[1:3]
  row.names(df) <- rn

  # explicit row names are written
  write_tsv(df, tf)
  expect_equal(
    data.table::fread(tf, sep = "\t"),
    data.table::data.table(rn = rn, dt)
  )

  # row names name can be given
  write_tsv(df, tf, row_names = "these_are_the_row_names")
  expect_equal(
    data.table::fread(tf, sep = "\t"),
    data.table::data.table(these_are_the_row_names = rn, dt)
  )
})

test_that("write_tsv() works with matrix", {
  tf <- paste0(tempfile(), ".tsv")

  first_row_plain <- "101\t111\t121\t131\t141"

  # PLAIN MATRIX

  m0 <- matrix(101:150, ncol = 5)
  first_row_named <- "V1\tV2\tV3\tV4\tV5"

  write_tsv(m0, tf)
  expect_identical(readLines(tf, 1), first_row_plain)
  expect_equal(
    data.table::fread(tf, sep = "\t", header = FALSE),
    data.table::as.data.table(m0)
  )

  write_tsv(m0, tf, col_names = TRUE)
  expect_identical(readLines(tf, 1), first_row_named)
  expect_equal(
    data.table::fread(tf, sep = "\t", header = TRUE),
    data.table::as.data.table(m0)
  )

  write_tsv(m0, tf, col_names = TRUE, row_names = TRUE)
  expect_identical(readLines(tf, 1), paste0("rn\t", first_row_named))

  write_tsv(m0, tf, col_names = TRUE, row_names = "these_are_the_row_names")
  expect_identical(
    readLines(tf, 1),
    paste0("these_are_the_row_names\t", first_row_named)
  )

  # MATRIX WITH COLUM NAMES

  m1 <- m0
  cn <- paste0("col_", letters[1:5])
  colnames(m1) <- cn
  first_row_named <- paste0(cn, collapse = "\t")

  write_tsv(m1, tf)
  expect_identical(readLines(tf, 1), first_row_named)
  expect_equal(
    data.table::fread(tf, sep = "\t", header = TRUE),
    data.table::as.data.table(m1, keep.rownames = FALSE)
  )

  write_tsv(m1, tf, col_names = FALSE)
  expect_identical(readLines(tf, 1), first_row_plain)
  expect_equal(
    data.table::fread(tf, sep = "\t", header = FALSE),
    data.table::as.data.table(m0, keep.rownames = FALSE)
  )

  # MATRIX WITH COLUM AND ROW NAMES

  m2 <- m1
  rownames(m2) <- paste0("row_", letters[1:10])

  write_tsv(m2, tf)
  expect_identical(readLines(tf, 1), paste0("rn\t", first_row_named))
  expect_equal(
    data.table::fread(tf, sep = "\t", header = TRUE),
    data.table::as.data.table(m2, keep.rownames = TRUE)
  )

  write_tsv(m2, tf, row_names = FALSE)
  expect_identical(readLines(tf, 1), first_row_named)
  expect_equal(
    data.table::fread(tf, sep = "\t", header = TRUE),
    data.table::as.data.table(m2, keep.rownames = FALSE)
  )
})