tests/testthat/test-drop_name.R

In nucleic-acid/namedropR: Create Visual Citations for Presentations and Posters

# CHECK INPUTS
test_that("Bibliographies are correctly read ", {
  new <- tempdir(check = TRUE)

  empty_bib <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI
  )
  withr::with_dir(
    new = new,
    code = {
      expect_error(drop_name(bib = empty_bib, cite_key = "Eschrich1983"), "is empty")
    }
  )

  bib_path <- system.file("testdata", "sample.bib", package = "namedropR")
  withr::with_dir(
    new = new,
    code = {
      expect_error(drop_name(bib = "wrong_file_path", cite_key = "Eschrich1983"), "file not found")
      expect_error(drop_name(bib = 123), "Inappropriate type of bibliography")
      expect_error(drop_name(cite_key = "Eschrich1983"), "No bibliography")
    }
  )

  good_bib <- system.file("testdata", "good.bib", package = "namedropR")
  withr::with_dir(
    new = new,
    code = {
      expect_message(
        expect_message(
          drop_name(bib = good_bib, cite_key = "Eschrich1983"),
          "Years coerced to string format."
        ),
        "Bibliography file successfully read."
      )
    }
  )
})

test_that("compact mode returns a correct file path", {
  new <- tempdir(check = TRUE)
  slim_bib <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~DATE,
    "Some 2022", c("Alice", "Bob", "Charlie"), "Journal of Unnecessary R Packages", "Alice2022", "2022"
  )

  withr::with_dir(
    new = new,
    code = {
      expect_equal(
        drop_name(bib = slim_bib, cite_key = "Alice2022", output_dir = "drop_name01", style = "compact"),
        file.path("drop_name01", "Alice2022.html")
      )
    }
  )
})

test_that("biblatex files produce an output", {
  new <- tempdir(check = TRUE)

  bib_tbl <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNALTITLE, ~BIBTEXKEY, ~DATE, ~URL,
    "Some 2022", c("Alice", "Bob", "Charlie"), "Journal of Unnecessary R Packages", "Alice2022", "2022", "https://en.wikipedia.org"
  )

  withr::with_dir(
    new = new,
    code = {
      expect_equal(
        drop_name(bib = bib_tbl, cite_key = "Alice2022", output_dir = "drop_name02"),
        file.path("drop_name02", "Alice2022.html")
      )
    }
  )


  bib_tbl2 <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNALTITLE, ~BIBTEXKEY, ~DATE, ~YEAR, ~URL,
    "Some 2022", c("Alice", "Bob", "Charlie"), "Journal of Unnecessary R Packages", "Alice2022", "2022-01-01", NA, "https://en.wikipedia.org",
    "Some 2023", c("Alice", "Bob", "Charlie"), "Journal of Unnecessary R Packages", "Alice2023", NA, "2023", "https://en.wikipedia.org"
  )

  new <- tempdir(check = TRUE)
  withr::with_dir(
    new = new,
    code = {
      expect_equal(
        suppressMessages(drop_name(bib = bib_tbl2, output_dir = "drop_name03")),
        c(
          file.path("drop_name03", "Alice2022.html"),
          file.path("drop_name03", "Alice2023.html")
        )
      )
    }
  )
})

test_that("missing DOI and URL columns are properly handled", {
  new <- tempdir(check = TRUE)
  slim_bib <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~DATE,
    "Some 2022", c("Alice", "Bob", "Charlie"), "Journal of Unnecessary R Packages", "Alice2022", "2022"
  )

  withr::with_dir(
    new = new,
    code = {
      expect_equal(
        drop_name(bib = slim_bib, cite_key = "Alice2022", output_dir = "drop_name04"),
        file.path("drop_name04", "Alice2022.html")
      )
    }
  )
})

test_that("all required columns are enforced", {
  new <- tempdir()
  missing_cols <- dplyr::tribble(
    ~TITLE, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI,
    "One", "Three", "Four", "2021", "Six"
  )

  # Authors missing
  withr::with_dir(
    new = new,
    code = {
      expect_error(drop_name(missing_cols, cite_key = "Four"))
    })

})



test_that("bulk operations work properly", {
  new <- tempdir()

  bulk_data <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI,
    "Title1", c("Alice1", "Bob1", "Charlie1"), "JoURP1", "Alice2021", "2021", "someDOI1",
    "Title2", c("Alice2", "Bob2", "Charlie2"), "JoURP2", "Alice2022", "2022", "someDOI2",
    "Title3", c("Alice3", "Bob3", "Charlie3"), "JoURP3", "Alice2023", "2023", "someDOI3",
    "Title4", c("Alice4", "Bob4", "Charlie4"), "JoURP4", "Alice2024", "2024", "someDOI4"
  )

  withr::with_dir(
    new = new,
    code = {
      # no cite_key given, 4 VCs should be created/4 paths returned
      bulk_res1 <- evaluate_promise(drop_name(bib = bulk_data, output_dir = "drop_name05"))
      expect_equal(length(bulk_res1$result), 4)
      expect_message(drop_name(bib = bulk_data, output_dir = "drop_name05"), "No cite_key specified.")

      # vector of 2 cite_keys returns 2 paths
      bulk_res2 <- evaluate_promise(drop_name(bib = bulk_data, cite_key = c("Alice2021", "Alice2023"), output_dir = "drop_name05"))
      expect_equal(length(bulk_res2$result), 2)

      # vector of 3 cite_keys with one false key returns 2, throws warning
      bulk_res3 <- evaluate_promise(drop_name(bib = bulk_data, cite_key = c("Alice2022", "Alice2024", "Bob2019"), output_dir = "drop_name05"))
      expect_equal(length(bulk_res3$result), 2)
      expect_true(bulk_res3$warnings == "The following cite_key items were not found in the provided library: Bob2019")

      # vector of only 3 false keys is supplied
      bulk_res4 <- evaluate_promise(drop_name(bib = bulk_data, cite_key = c("Bob1", "Bob2", "Bob3"), output_dir = "drop_name05"))
      expect_equal(bulk_res4$warnings[2], "No reference matches the given cite_keys. Please check that citation key(s) are correct.")

      # vector of type 'numerical' throws an error
      expect_error(drop_name(bib = bulk_data, cite_key = c(1, 1, 2, 3, 5, 8), output_dir = "drop_name05"), "cite_key must be of type 'caracter'")

      # library with non-unique BIBTEXKEYs
      bulk_data_dup <- dplyr::tribble(
        ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI,
        "Title1", c("Alice1", "Bob1", "Charlie1"), "JoURP1", "Alice2021", "2021", "someDOI1",
        "Title1", c("Alice2", "Bob2", "Charlie2"), "JoURP1", "Alice2021", "2021", "someDOI3",
      )

      expect_warning(drop_name(bib = bulk_data_dup, cite_key = "Alice2021", output_dir = "drop_name05"), "There are duplicated bibtex keys")
    }
  )

})

test_that("output_dir is properly checked", {
  sample_data <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI,
    "Title1", c("Alice1", "Bob1", "Charlie1"), "JoURP1", "Alice2021", "2021", "someDOI1",
  )

  # test wrong input formats
  expect_error(drop_name(bib = sample_data, output_dir = TRUE))
  expect_error(drop_name(bib = sample_data, output_dir = 5))
})

test_that("use_xaringan is properly checked", {
  sample_data <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI,
    "Title1", c("Alice1", "Bob1", "Charlie1"), "JoURP1", "Alice2021", "2021", "someDOI1",
  )
  expect_error(drop_name(bib = sample_data, use_xaringan = 987))
})

test_that("use_xaringan creates the correct folders (qr/ in working dir)", {
  new <- tempdir(check = TRUE)

  sample_data <- dplyr::tribble(
    ~TITLE, ~AUTHOR, ~JOURNAL, ~BIBTEXKEY, ~YEAR, ~DOI,
    "Title1", c("Alice1", "Bob1", "Charlie1"), "JoURP1", "Alice2021", "2021", "someDOI1",
  )
  withr::with_dir(
    new = new,
    code = {
      # remove possibly preexisting qr and visual_citations folders within tempdir
      unlink("qr", recursive = TRUE, force = TRUE)
      unlink("visual_citations", recursive = TRUE, force = TRUE)

      # run function
      drop_name(bib = sample_data, export_as = "html", cite_key = "Alice2021", use_xaringan = TRUE)
      # check if folders were correctly created
      expect_true(dir.exists("visual_citations"))
      expect_true(dir.exists("qr"))
    }
  )

  withr::with_dir(
    new = new,
    code = {
      # remove possibly preexisting qr and visual_citations folders within tempdir
      unlink("qr", recursive = TRUE, force = TRUE)
      unlink("visual_citations", recursive = TRUE, force = TRUE)

      # run function
      drop_name(bib = sample_data, export_as = "html_full", cite_key = "Alice2021", use_xaringan = TRUE)
      # check if folders were correctly created
      expect_true(dir.exists("visual_citations"))
      expect_true(dir.exists("qr"))
    }
  )
})