tests/testthat/test-as-cff-reference.R

In cffr: Generate Citation File Format ('CFF') Metadata

# Coerce citation from BibTeX ----

test_that("article bibentries round-trip through cff references", {
  bib <- bibentry(
    "Article",
    key = "knuth:1984",
    author = person("R Core Team"),
    title = "Literate Programming",
    journal = "The Computer Journal",
    year = "1984",
    # Optional
    volume = "27",
    number = 2,
    pages = "97--111",
    month = "January",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- sort(names(unclass(bib)[[1]]))
  fld2 <- sort(names(unclass(tobib)[[1]]))
  expect_identical(fld1, fld2)
})

test_that("book bibentries round-trip through cff references", {
  bib <- bibentry(
    "Book",
    key = "latex:companion",
    author = "Frank Mittelbach and Michel Gossens
            and Johannes Braams and David Carlisle
            and Chris Rowley",
    editor = "{Barnes and Noble}",
    title = "The LaTeX Companion",
    publisher = "Addison-Wesley Professional",
    year = "2004",
    # Optional
    volume = "3",
    number = 7,
    series = "The LateX Books",
    address = "Santa Monica",
    edition = "Fourth",
    month = "August",
    note = "Example modified for testing purposes",
    keywords = c("Two, keyword")
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- sort(names(unclass(bib)[[1]]))
  fld2 <- sort(names(unclass(tobib)[[1]]))
  expect_identical(fld1, fld2)
})


test_that("booklet bibentries round-trip through cff references", {
  bib <- bibentry(
    "Booklet",
    key = "Mustermann2016",
    title = "Java Booklet",
    # Optional
    author = "Max Mustermann",
    howpublished = "Internet",
    address = "Stuttgart",
    month = "feb",
    year = "2016",
    note = "Example modified from Jabref",
    keywords = "java"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- sort(names(unclass(bib)[[1]]))
  fld2 <- sort(names(unclass(tobib)[[1]]))

  # Keyword is not coerced
  expect_identical(setdiff(fld1, fld2), "keywords")
})

test_that("conference bibentries round-trip through cff references", {
  bib <- bibentry(
    "InProceedings",
    key = "inproceedings-full",
    author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
    title = "On Notions of Information Transfer in {VLSI} Circuits",
    booktitle = "Proc. Fifteenth Annual ACM STOC",
    year = "1983",
    # Optional
    editor = "Wizard V. Oz and Mihalis Yannakakis",
    volume = "41",
    number = 17,
    series = "All ACM Conferences",
    pages = "133--139",
    address = "Boston",
    organization = "ACM",
    publisher = "Academic Press",
    note = "Example modified for testing purposes"
  )

  # Hack to convert to conference
  bib_un <- unclass(bib)[[1]]

  attr(bib_un, "bibtype") <- "Conference"

  bib <- list(bib_un)
  class(bib) <- "bibentry"

  bib_cff <- as_cff(bib)

  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "series")
})

test_that("inbook bibentries round-trip through cff references", {
  bib <- bibentry(
    "InBook",
    key = "1326",
    author = "A. King",
    editor = "E Tick and G Succi",
    title = "A Framework for Freeness Analysis",
    chapter = "7, 14",
    pages = "137--149",
    publisher = "Kluwer Academic Publishers",
    year = "1994",
    # Optional
    volume = "27",
    number = 2,
    series = "Implementations of Logic Programming Systems",
    type = "A chapter",
    address = "Dordrecht",
    edition = "Second",
    month = "January",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))
  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "type")
})

test_that("incollection bibentries round-trip through cff references", {
  bib <- bibentry(
    "InCollection",
    key = "Mihalcea:2006",
    author = "Rada Mihalcea",
    title = "Knowledge-Based Methods for {WSD}",
    booktitle = "Word Sense Disambiguation: Algorithms
               and Applications",
    publisher = "Springer",
    year = "2006",
    # Optional
    editor = "Eneko Agirre and Philip Edmonds",
    volume = "23",
    number = 3,
    series = "The Word Sense Series",
    type = "A random type",
    chapter = "1,2,3",
    pages = "24--57",
    address = "107--132",
    edition = "Third",
    month = "August",
    note = "A note"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), c("series", "type"))
})

test_that("inproceedings bibentries round-trip through cff references", {
  bib <- bibentry(
    "InProceedings",
    key = "inproceedings-full",
    author = "Alfred V. Oaho and Jeffrey D. Ullman and Mihalis Yannakakis",
    title = "On Notions of Information Transfer in {VLSI} Circuits",
    booktitle = "Proc. Fifteenth Annual ACM STOC",
    year = "1983",
    # Optional
    editor = "Wizard V. Oz and Mihalis Yannakakis",
    volume = "41",
    number = 17,
    series = "All ACM Conferences",
    pages = "133--139",
    address = "Boston",
    organization = "ACM",
    publisher = "Academic Press",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "series")

  # If we remove collection title use conference
  bib_cff[[1]]$`collection-title` <- NULL
  bib_cff[[1]]$conference$name <- "I Am a conference"
  bib <- as_bibentry(bib_cff)
  expect_snapshot(toBibtex(bib))
})

test_that("manual bibentries round-trip through cff references", {
  bib <- bibentry(
    "Manual",
    title = "A Language and Environment for Statistical Computing",
    # Optional
    author = person("R Core Team"),
    organization = "R Foundation for Statistical Computing",
    address = "Vienna, Austria",
    edition = "Fourth",
    month = "August",
    year = "2021",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(fld1, fld2)
})

test_that("mastersthesis bibentries round-trip through cff references", {
  bib <- bibentry(
    "MastersThesis",
    key = "Master2006",
    author = "Eesa Alsolami",
    title = "An examination of keystroke dynamics
                for continuous user authentication",
    school = "Queensland University of Technology",
    year = "2012",
    # Optional
    type = "Final thesis",
    address = "Queensland, NZ",
    month = "August",
    note = "Example modified for testing purposes"
  )
  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "type")
})

test_that("misc bibentries round-trip through cff references", {
  bib <- bibentry(
    "Misc",
    # Optional
    author = person("R Core Team"),
    title = "A Language and Environment for Statistical Computing",
    howpublished = "CD-ROM",
    month = 1,
    year = "2021",
    note = "A note"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(fld1, fld2)
})


test_that("phdthesis bibentries round-trip through cff references", {
  bib <- bibentry(
    "PhdThesis",
    author = "Eesa Alsolami",
    title = "An examination of keystroke dynamics
                for continuous user authentication",
    school = "Queensland University of Technology",
    year = "2012",
    # Optional
    type = "Final PhD thesis",
    address = "Queensland, NZ",
    month = "August",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "type")
})


test_that("proceedings bibentries round-trip through cff references", {
  bib <- bibentry(
    "Proceedings",
    title = "Proc. Fifteenth Annual STOC",
    year = "1983",
    # Optional
    editor = "Wizard V. Oz and Mihalis Yannakakis",
    volume = 1,
    number = 17,
    series = "All ACM Conferences",
    address = "Boston, US",
    month = "August",
    organization = "The OX Association for Computing Machinery",
    publisher = "Academic Press",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(fld1, fld2)
})

test_that("techreport bibentries round-trip through cff references", {
  bib <- bibentry(
    "TechReport",
    author = "Matthew C. Jadud and Sally A. Fincher",
    title = "Naive tools for studying compilation histories",
    institution = "University of Kent Canterbury",
    year = "2003",
    # Optional
    type = "techreport",
    number = "3-03",
    address = paste(
      "Computing Laboratory, University of Kent,",
      "Canterbury, Kent, CT2 7NF"
    ),
    month = "mar",
    note = "Example modified for testing purposes"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "type")
})

test_that("unpublished bibentries round-trip through cff references", {
  bib <- bibentry(
    "Unpublished",
    author = "D. Kaplan",
    title = "Demonstratives",
    note = "Unpublished manuscript, UCLA",
    # Optional
    year = "1977",
    month = "aug"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(fld1, fld2)

  # With custom note
  bib_cff[[1]]$notes <- NULL
  bib <- as_bibentry(bib_cff)
  expect_snapshot(toBibtex(bib))
})

test_that("inbook bibentries preserve book titles", {
  bib <- bibentry(
    "InBook",
    title = "Bibliographies and citations",
    year = "2020",
    author = "Yihui Xie and Christophe Dervieux and Emily Riederer",
    booktitle = "{R} Markdown Cookbook",
    publisher = "Chapman and Hall/CRC",
    address = "Boca Raton, Florida",
    series = "The {R} Series",
    isbn = "9780367563837",
    url = "https://yihui.org/rmarkdown-cookbook/",
    chapter = "4.5"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))

  # Should be an incollection now
  res <- as_bibentry(bib_cff)
  init_type <- attr(unclass(res)[[1]], "bibtype")
  expect_identical(tolower(init_type), "incollection")

  # Back to bibtex and check names
  tobib <- as_bibentry(bib_cff)

  fld1 <- unique(sort(names(unclass(bib)[[1]])))
  fld2 <- unique(sort(names(unclass(tobib)[[1]])))

  expect_identical(setdiff(fld1, fld2), "series")
})

test_that("references support entries without authors", {
  bib <- bibentry(
    "Proceedings",
    editor = "Yolande Berbers and Willy Zwaenepoel",
    title = "Proceedings of the 6th European Conference on Computer Systems",
    booktitle = paste(
      "Proceedings of the 6th European",
      "
                      Conference on Computer Systems"
    ),
    publisher = "ACM",
    venue = "Leuven, Belgium",
    month = "apr",
    year = 2006,
    isbn = "1-59593-322-02"
  )

  bib_cff <- as_cff(bib)

  expect_identical(bib_cff[[1]]$authors[[1]]$name, "anonymous")

  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))
})


test_that("references preserve keys when authors are absent", {
  bib <- bibentry(
    "Misc",
    key = "I am the key",
    title = "Proceedings of the 6th European Conference on Computer Systems",
    booktitle = paste(
      "Proceedings of the 6th European Conference",
      "on Computer Systems"
    ),
    publisher = "ACM",
    venue = "Leuven, Belgium",
    month = "apr",
    year = 2006,
    isbn = "1-59593-322-02"
  )

  bib_cff <- as_cff(bib)

  expect_identical(bib_cff[[1]]$authors[[1]]$name, "anonymous")

  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))
})


test_that("references support entries without authors or keys", {
  bib <- bibentry(
    "Misc",
    title = "Proceedings of the 6th European Conference on Computer Systems",
    booktitle = paste(
      "Proceedings of the 6th European",
      "
                      Conference on Computer Systems"
    ),
    publisher = "ACM",
    venue = "Leuven, Belgium",
    month = "apr",
    year = 2006,
    isbn = "1-59593-322-02"
  )

  bib_cff <- as_cff(bib)

  expect_identical(bib_cff[[1]]$authors[[1]]$name, "anonymous")

  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))
})


test_that("references skip misc entries without titles", {
  bib <- bibentry(
    bibtype = "misc",
    author = c(person("SHERPA/RoMEO")),
    url = "http://www.sherpa.ac.uk/romeo/",
    year = 2018
  )

  expect_message(bib_cff <- as_cff(bib), "Skipping")

  expect_null(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_snapshot(cffobj)

  expect_true(cff_validate(cffobj, verbose = FALSE))
})


test_that("invalid references do not remove valid references", {
  bib <- c(
    bibentry(
      bibtype = "misc",
      author = c(person("SHERPA/RoMEO")),
      url = "http://www.sherpa.ac.uk/romeo/",
      year = 2018
    ),
    bibentry(
      bibtype = "misc",
      title = "{rromeo}: An {R} Client for {SHERPA/RoMEO} {API}",
      author = c(person("Matthias", "Grenié"), person("Hugo", "Gruson")),
      year = 2019,
      header = "To cite this package in publications, please use:",
      url = "https://CRAN.R-project.org/package=rromeo"
    )
  )

  expect_message(bib_cff <- as_cff(bib), "SHERPA/RoMEO")

  expect_length(bib_cff, 1)

  expect_s3_class(bib_cff[[1]], "cff")

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_snapshot(cffobj)

  expect_equal(
    cffobj$references[[1]]$title,
    "rromeo: An R Client for SHERPA/RoMEO API"
  )

  expect_true(cff_validate(cffobj, verbose = FALSE))
})


test_that("references preserve extended BibLaTeX fields", {
  bib <- bibentry(
    "Article",
    author = "M. A. Kastenholz, and Philippe H. Hünenbergerb",
    title = "Computation of methodology hyphen independent ionic solvation
                  free energies from molecular simulations",
    journal = "J. Chem. Phys.",
    year = 2006,
    note = "Example modified for testing purposes",
    pages = "55--65",

    # Additional BibLatex Fields
    date = "2006-03-15",
    file = "a_file.pdf",
    issuetitle = "Semantic {3D} Media and Content",
    translator = "Wicksteed, P. H. and Cornford, F. M.",
    urldate = "2006-10-01",
    pagetotal = 528,
    abstract = "The computation of ionic solvation free energies from
                  atomistic simulations is a surprisingly difficult problem that
                  has found no satisfactory solution for more than 15 years.",
    doi = "10.1063/1.2172593",
    isbn = "0-816-52066-6",
    issn = "0097-8493",
    url = "http://www.ctan.org"
  )

  bib_cff <- as_cff(bib)
  expect_snapshot(bib_cff)

  cffobj <- cff_create(cff(), keys = list(references = bib_cff))

  expect_true(cff_validate(cffobj, verbose = FALSE))
})

test_that("references remove duplicate entries", {
  bib <- bibentry(
    "InBook",
    title = "Bibliographies and citations",
    year = "2020",
    author = "Yihui Xie and Christophe Dervieux and Emily Riederer",
    booktitle = "{R} Markdown Cookbook",
    publisher = "Chapman and Hall/CRC",
    address = "Boca Raton, Florida",
    series = "The {R} Series",
    isbn = "9780367563837",
    url = "https://yihui.org/rmarkdown-cookbook/",
    chapter = "4.5"
  )

  expect_snapshot(bib_cff <- as_cff(rep(bib, 2)))
  expect_length(bib_cff, 1)
})

test_that("references normalize identifiers and DOIs", {
  # jarl-ignore-start duplicated_arguments: Testing edge case.
  bib <- bibentry(
    bibtype = "Manual",
    title = "A Language and Environment for Statistical Computing",
    year = "2022",
    year = "2023",
    author = person("R Core Team"),
    version = NULL,
    error = "",
    url = "https://www.R-project.org/",
    url = "https://google.com/",
    doi = "10.5281/zenodo.5366600",
    doi = "10.5281/zenodo.5366601",
    doi = "10.5281/zenodo.5366602",
    identifiers = "a,b"
  )
  # jarl-ignore-end duplicated_arguments

  bib_cff <- as_cff(bib)
  sin <- bib_cff[[1]]
  checf <- sin[names(sin) %in% c("url", "doi", "identifiers")]
  expect_snapshot(as_cff(checf))

  cffobj <- cff_modify(cff(), references = bib_cff)

  expect_snapshot(cffobj)
  expect_true(cff_validate(cffobj, verbose = FALSE))
})

test_that("references support R 4.6 bibentry output", {
  rvers <- getRversion()
  skip_if(!grepl("^4.6", rvers), "Snapshot created with R 4.6.*")

  # https://github.com/wch/r-source/blob/trunk/src/library/base/inst/CITATION

  bib <- bibentry(
    "Manual",
    title = "R: A Language and Environment for Statistical Computing",
    author = person("R Core Team", comment = c(ROR = "02zz1nj61")),
    organization = person(
      "R Foundation for Statistical Computing",
      comment = c(ROR = "05qewa988")
    ),
    address = "Vienna, Austria",
    year = 2026,
    doi = "10.32614/R.manuals",
    url = "https://www.R-project.org/"
  )

  bib_cff <- as_cff(bib)
  sin <- bib_cff[[1]]
  expect_snapshot(as_cff(sin))

  cffobj <- cff_modify(cff(), references = bib_cff)

  expect_snapshot(cffobj)
  expect_true(cff_validate(cffobj, verbose = FALSE))
})