tests/testthat/test-struc-parser-wrapper.R

In glyparse: Parsing Glycan Structure Text Representations

test_that("struc_parser_wrapper returns glyrepr-compatible vectors", {
  skip_on_old_win()

  parsed <- parse_strucgp_struc(
    "A2B2C1D1E2F1G3gfF5fedD1E2F1feE2F1fedcba"
  )
  reconstructed <- glyrepr::as_glycan_structure(
    glyrepr::get_structure_graphs(parsed)
  )

  expect_identical(typeof(parsed), typeof(reconstructed))

  parsed_tbl <- dplyr::tibble(glycan_structure = parsed)
  unique_tbl <- dplyr::distinct(parsed_tbl, .data$glycan_structure)

  expect_error(
    dplyr::left_join(parsed_tbl, unique_tbl, by = "glycan_structure"),
    NA
  )
})

test_that("struc_parser_wrapper treats invalid parsed arrays as failures", {
  parser <- function(x) {
    list(
      mono = "Hex",
      sub = "",
      anomer = "??",
      edges = if (x == "invalid") c(1L, 1L) else integer(),
      linkage = if (x == "invalid") "??-?" else character()
    )
  }

  result <- struc_parser_wrapper(
    c("valid", "invalid"),
    parser,
    on_failure = "na"
  )

  expect_identical(as.character(result), c("Hex(??-", NA_character_))
})

test_that("struc_parser_wrapper preserves mixed monosaccharide types", {
  input <- c(
    generic = "Hex(??-",
    concrete = "Glc(?1-",
    generic_duplicate = "Hex(??-",
    mixed = "Gal(?1-?)HexNAc(?1-",
    missing = NA_character_
  )

  result <- normalized_struc_parser_wrapper(input)

  expect_identical(
    as.character(result),
    c(
      generic = "Hex(??-",
      concrete = "Glc(?1-",
      generic_duplicate = "Hex(??-",
      mixed = "Gal(?1-?)HexNAc(?1-",
      missing = NA_character_
    )
  )
  expect_identical(
    glyrepr::get_mono_type(result),
    c(
      generic = "generic",
      concrete = "concrete",
      generic_duplicate = "generic",
      mixed = "mixed",
      missing = NA_character_
    )
  )
})