tests/testthat/test-util_map_all.R

In dataquieR: Data Quality in Epidemiological Research

test_that("util_map_all works", {
  skip_if_not_installed("withr")
  withr::local_options(dataquieR.CONDITIONS_WITH_STACKTRACE = TRUE,
                   dataquieR.ERRORS_WITH_CALLER = TRUE,
                   dataquieR.WARNINGS_WITH_CALLER = TRUE,
                   dataquieR.MESSAGES_WITH_CALLER = TRUE)
  md <- prep_create_meta(
    VAR_NAMES = letters,
    DATA_TYPE = DATA_TYPES$FLOAT,
    LABEL = LETTERS,
    MISSING_LIST = "",
    nums = seq_along(letters)
  )
  sd <- as.data.frame(lapply(setNames(nm = letters), paste, 1:10),
                      stringsAsFactors = FALSE)
  mapped <- util_map_all(
    label_col = LABEL,
    study_data = sd,
    meta_data = md
  )

  expect_equal(colnames(mapped$df), LETTERS)

  mapped <- util_map_all(
    label_col = "nums",
    study_data = sd,
    meta_data = md
  )

  expect_error(util_map_all(
      label_col = c("nums", "kkk"),
      study_data = sd,
      meta_data = md
    ),
    regexp =
      paste("label_col must be exactly 1 metadata attribute,",
            "neither a vector nor NULL.")
  )

  expect_error(util_map_all(
    label_col = c(),
    study_data = sd,
    meta_data = md
  ),
  regexp =
    paste("label_col must be exactly 1 metadata attribute,",
          "neither a vector nor NULL.")
  )

  expect_error(util_map_all(
    label_col = "NO NO NO NO NO",
    study_data = sd,
    meta_data = md
  ), regexp = paste("label_col .+NO NO NO NO NO.+ not found in metadata.",
                    "Did you mean .+VAR_NAMES.+"))

  expect_error(util_map_all(
    label_col = "speed",
    study_data = sd,
    meta_data = cars
  ), regexp = paste(".*VAR_NAMES not found in metadata."))

  expect_error(util_map_all(
    label_col = "DATA_TYPE",
    study_data = sd,
    meta_data = md
  ), regexp =
    paste("The following .+DATA_TYPE.+ are duplicated in the",
          "metadata and cannot be used as label therefore: .+float.+"))

  mdx <- md
  mdx$VAR_NAMES[[5]] <- mdx$VAR_NAMES[[1]]
  expect_error(util_map_all(
    label_col = LABEL,
    study_data = sd,
    meta_data = mdx
  ), regexp =
    paste("The following variable names are duplicated in the",
          "metadata and cannot be used as label therefore: .+a.+"))

  mdx <- md
  mdx$VAR_NAMES[[5]] <- NA
  expect_error(util_map_all(
    label_col = LABEL,
    study_data = sd,
    meta_data = mdx
  ), regexp = paste("For the following variables, some variable names are",
                    "missing in the metadata: Variable No. #5"))

  mdx <- md
  mdx$LABEL[[5]] <- NA
  expect_error(util_map_all(
    label_col = LABEL,
    study_data = sd,
    meta_data = mdx
  ), regexp = paste("For the following variables, some .+LABEL.+ are missing",
                    "in the metadata and cannot be used as label therefore:",
                    "Variable No. #5"))

  mdx <- md
  mdx$VAR_NAMES[[1]] <- "xxx"
  mdx$VAR_NAMES[[4]] <- "yyy"
  expect_message(
    expect_warning(util_map_all(
      label_col = LABEL,
      study_data = sd,
      meta_data = mdx
    ), regexp =
      sprintf("(%s|%s|%s)",
              paste("Lost 7.7% of the study data because",
                    "of missing/not assignable metadata"),
              paste("Did not find any metadata for the following",
                    "variables from the study data: .+a.+, .+d.+"),
              paste("Lost 7.7% of the metadata because of",
                    "missing/not assignable study data")
      ),
      perl = TRUE,
      all = TRUE
    ), regexp =
      sprintf("(%s|%s)",
              paste("Did not find any metadata for the following",
                    "variables from the study data: .+a.+, .+d.+"),
              paste("Found metadata for the following variables not",
                    "found in the study data: .+xxx.+, .+yyy.+")
      ),
    all = TRUE,
    perl = TRUE
  )

  mdx <- md
  mdx$LABEL[[5]] <- "    "
  expect_error(util_map_all(
    label_col = LABEL,
    study_data = sd,
    meta_data = mdx
  ), regexp = paste("Mapping of metadata on study data yielded invalid",
                    "variable labels: .+    .+"))

  expect_equal(colnames(mapped$df), as.character(seq_along(letters)))

})