Move duplicate functions (#145)

Fixes issue #131
*  Move custom expect_ functions out of dataset_test, into R/test_functions.R so that R CMD check warnings are removed (otherwise "no visible global function definition" warning comes up)
*  Rename prefixes to test_expect_ to differentiate between custom testthat functions and built-in testthat functions
*  I kept using expect_silent() from {testthat} instead of writing a custom function because I'm not sure how to rewrite the function to capture messages on top of errors and warnings

---------

Co-authored-by: ehwenk <ehwenk@gmail.com>

NAMESPACE

@@ -81,9 +81,7 @@ importFrom(stringr,str_remove_all)
 importFrom(stringr,str_replace_all)
 importFrom(stringr,str_squish)
 importFrom(styler,style_text)
-importFrom(testthat,compare)
 importFrom(testthat,context)
-importFrom(testthat,expect)
 importFrom(testthat,expect_silent)
 importFrom(testthat,local_edition)
 importFrom(testthat,test_that)

R/test_functions.R

@@ -0,0 +1,377 @@
+
+test_expect_no_error <- function(object, info) {
+
+  error <- tryCatch({
+    object
+    NULL
+  }, error = function(e) {
+    e
+  })
+  testthat::expect(
+    is.null(error),
+    sprintf("%s threw an error:\n\n" %+% red("%s"), info, paste(error, collapse = ",")))
+  invisible(object)
+}
+
+
+test_expect_no_warning <- function(object, info) {
+  warning <- tryCatch({
+    object
+    NULL
+  }, warning = function(w) {
+    w
+  })
+  testthat::expect(is.null(warning), info)
+}
+
+
+test_expect_is_in <- function(object, expected, info, label, na.rm = TRUE) {
+
+    if (na.rm)
+      object <- object[!is.na(object)]
+    i <- object %in% expected
+
+    comp <- testthat::compare(all(i), TRUE)
+    testthat::expect(
+      comp$equal,
+      sprintf(
+        "%s - %s should not contain: '%s'",
+        info, label,
+        paste(object[!i], collapse = "', '")
+      ))
+
+    invisible(object)
+  }
+
+
+test_expect_contains <- function(object, expected, info) {
+
+  i <- expected %in% object
+
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(
+    comp$equal,
+    sprintf("%s - does not contain: '%s'", info, paste(expected[!i], collapse = "', '"))
+  )
+
+  invisible(object)
+}
+
+
+test_expect_allowed <- function(object, allowed, info, label) {
+
+  i <- object %in% allowed
+
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(
+    comp$equal,
+    sprintf(
+      "%s - %s include(s) invalid terms: '%s'",
+      info, label,
+      paste(object[!i], collapse = "', '")
+    ))
+
+  invisible(object)
+}
+
+
+test_expect_equal <- function(object, expected, info) {
+  i <- object == expected
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(comp$equal, info)
+}
+
+
+test_expect_true <- function(object, info) {
+  i <- object == TRUE
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(comp$equal, info)
+}
+
+
+test_expect_false <- function(object, info) {
+  i <- object == FALSE
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(comp$equal, info)
+}
+
+
+test_expect_named <- function(object, expected_names, info, label) {
+
+  if (missing(expected_names)) {
+    testthat::expect(
+      !identical(names(object), NULL),
+      sprintf("%s - %s do not exist", info, label))
+  } else {
+    testthat::expect(
+      identical(names(object), expected_names),
+      sprintf(
+        "%s\tnames of %s (%s) don't match %s",
+        info,
+        label, paste0("'", names(object), "'", collapse = ", "),
+        paste0("'", expected_names, "'", collapse = ", ")
+      )
+    )
+  }
+}
+
+
+test_expect_type <- function(object, type, info, label) {
+  stopifnot(is.character(type), length(type) == 1)
+  testthat::expect(
+    identical(typeof(object), type),
+    sprintf("%s - %s has type %s, not %s", info, label, typeof(object), type)
+  )
+}
+
+
+test_expect_not_NA <- function(object, info, label) {
+  i <- !is.na(object)
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(comp$equal, sprintf("%s - %s contain(s) NAs", info, label))
+  invisible(object)
+}
+
+
+test_expect_length_zero <- function(object, info, label) {
+  comp <- testthat::compare(length(object), 0)
+  testthat::expect(comp$equal, sprintf("%s: %s", info, label))
+  invisible(object)
+}
+
+
+test_expect_unique <- function(object, info, label) {
+  x <- table(unlist(object))
+  i <- x == 1
+  comp <- testthat::compare(all(i), TRUE)
+  testthat::expect(comp$equal, sprintf("%s - %s not unique: '%s'", info, label, paste(names(x)[!i], collapse = "', '")))
+  invisible(object)
+}
+
+
+test_expect_allowed_text <- function(object, is_data = FALSE, is_col_names = FALSE, info, label) {
+
+  if (length(object) > 0) {
+
+    if (is_data) {
+      disallowed <-
+        object %>% lapply(check_disallowed_chars, exceptions = c("")) %>% simplify2array()
+    } else {
+      disallowed <-
+        object %>% lapply(check_disallowed_chars) %>% simplify2array()
+    }
+
+    check <- disallowed %>% lapply(any) %>% unlist()
+
+    txt <- "\n"
+    for (i in which(check)) {
+      if (is_col_names) {
+        txt <- sprintf(
+          "%s\t- col %s: %s\n",
+          txt, i, colour_characters(object[[i]], which(disallowed[[i]])))
+      } else {
+        txt <- sprintf(
+          "%s\t- ln %s: %s\n",
+          txt, i, colour_characters(object[[i]], which(disallowed[[i]])))
+      }
+
+    }
+
+    if (is_data) {
+      testthat::expect(
+        identical(as.vector(all(!check)), TRUE),
+        sprintf(
+          "%s\tdisallowed characters in data detected: %s\n\tPlease replace using `custom_R_code`",
+          info, txt
+        )
+      )
+    } else {
+      testthat::expect(
+        identical(as.vector(all(!check)), TRUE),
+        sprintf("%s - disallowed characters in %s detected: \n%s", info, label, txt)
+      )
+    }
+
+  }
+
+  invisible(object)
+
+}
+
+
+colour_characters <- function(x, i = NULL) {
+
+  chars <- x %>% charToRaw() %>% lapply(rawToChar) %>% unlist()
+
+  # Wrapper around characters to print as colour
+  # obtained from crayon::red(x)
+  if (!is.null(i))
+    chars[i] <- sprintf("\033[31m%s\033[39m", chars[i])
+
+  paste0(chars, collapse = "")
+}
+
+
+check_disallowed_chars <- function(x, exceptions = c("ÁÅÀÂÄÆÃĀâíåæäãàáíÇčóöøéèłńl°êÜüùúû±µµ“”‘’-–—≈˜×≥≤")) {
+
+  i <- charToRaw(x)
+  # Allow all ascii text
+  is_ascii <- i < 0x7F
+
+  # Allow some utf8 characters, those with accents over letters for foreign names
+  # List of codes is here: http://www.utf8-chartable.de/
+  # Note c3 is needed because this is prefix for allowed UTF8 chars
+  # Warning: Portable packages must use only ASCII characters in their R code
+  # Sophie - could replace these with unicode like Lizzy did before?
+  exceptions <- exceptions
+
+  is_allowed <- i %in% charToRaw(exceptions)
+  !(is_ascii | is_allowed)
+}
+
+
+test_expect_list_elements_contains_names <- function(object, expected, info) {
+  for (i in seq_along(object))
+    test_expect_contains(names(object[[i]]), expected, info = paste(info, i))
+  invisible(object)
+}
+
+
+test_expect_list_elements_allowed_names <- function(object, allowed, info, label) {
+  for (i in seq_along(object))
+    test_expect_allowed(names(object[[i]]), allowed, info = paste(info, i), label = "field names")
+  invisible(object)
+}
+
+
+test_expect_list_elements_exact_names <- function(object, expected, info) {
+  for (i in seq_along(object)) {
+    test_expect_contains(names(object[[i]]), expected, info = paste(info, i))
+    test_expect_allowed(names(object[[i]]), expected, info = paste(info, i), label = "field names")
+  }
+  invisible(object)
+}
+
+
+test_expect_dataframe_valid <- function(data, info, label) {
+  test_expect_not_NA(colnames(data), info, label)
+  test_expect_allowed_text(colnames(data), is_col_names = TRUE, info = info, label = label)
+  test_expect_unique(colnames(data), info, label)
+  test_expect_true(is.data.frame(data), info = sprintf("%s - is not a dataframe", info))
+}
+
+
+test_expect_dataframe_named <- function(data, expected_colnames, info, label) {
+  test_expect_dataframe_valid(data, info, label)
+  test_expect_named(data, expected_colnames, info = info, label = label)
+}
+
+
+test_expect_dataframe_names_contain <- function(data, expected_colnames, info, label) {
+  test_expect_dataframe_valid(data, info, label)
+  test_expect_contains(names(data), expected_colnames, info = info)
+}
+
+
+
+test_expect_list <- function(data, info) {
+  test_expect_true("list" %in% class(data), info = sprintf("%s - is not a list", info))
+}
+
+
+test_expect_list_names_valid <- function(data, info, label) {
+  test_expect_list(data, info)
+  test_expect_not_NA(names(data), info = info, label = paste0("names of ", label))
+  test_expect_unique(names(data), info = info, label = paste0("names of ", label))
+}
+
+
+test_expect_list_names_exact <- function(data, expected_names, info, label) {
+  test_expect_list_names_valid(data, info, label = label)
+  test_expect_named(data, expected_names, info = info, label = label)
+}
+
+
+test_expect_list_names_allowed <- function(data, allowed_names, info, label) {
+  test_expect_list_names_valid(data, info, label = label)
+  test_expect_named(data, info = info, label = label)
+  test_expect_allowed(names(data), allowed_names, info = info, label = label)
+}
+
+
+test_expect_list_names_contain <- function(data, expected_names, info, label) {
+  test_expect_list_names_valid(data, info, label = label)
+  test_expect_named(data, info = info, label = label)
+  test_expect_contains(names(data), expected_names, info = info)
+}
+
+
+test_build_dataset <- function(
+  path_metadata, path_data, info, definitions, unit_conversions, schema, resource_metadata, taxon_list) {
+
+  # Test it builds with no errors
+  test_expect_no_error(
+    build_config <- dataset_configure(path_metadata, definitions),
+    info = "`dataset_configure`"
+  )
+
+  test_expect_no_error(
+    build_dataset_raw <- dataset_process(path_data, build_config, schema, resource_metadata, unit_conversions),
+    info = "`dataset_process`"
+  )
+
+  test_expect_no_error(
+    build_dataset <- dataset_update_taxonomy(build_dataset_raw, taxon_list),
+    info = "`dataset_update_taxonomy`"
+  )
+
+  test_expect_structure(build_dataset, info, schema, definitions, single_dataset = TRUE)
+
+  build_dataset
+}
+
+
+test_expect_structure <- function(data, info, schema, definitions, single_dataset = TRUE) {
+
+  vars_austraits <- schema$austraits$elements %>% names()
+
+  vars_tables <-
+    vars_austraits %>%
+    subset(., !(. %in% c(
+      "definitions", "schema", "sources", "metadata",
+      "build_info", "taxonomic_updates", "taxa")))
+
+  # Test lists have the right objects
+  comparison <- vars_austraits
+
+  test_expect_list_names_exact(data, comparison, info, label = "output tables")
+
+  # Test structure of tables
+  for (v in vars_tables) {
+    comparison <- schema$austraits$elements[[v]]$elements %>% names()
+    test_expect_dataframe_named(data[[v]], comparison, info = info, label = paste0(v, " table column names"))
+  }
+
+  # Test that minimum expected columns are in `taxa` and `taxonomic_updates` tables
+  test_expect_contains(names(data[["taxa"]]), c("taxon_name", "taxon_rank"), info = paste0(info, "\tnames of `taxa` table"))
+  test_expect_contains(
+    names(data[["taxonomic_updates"]]),
+    c("dataset_id", "original_name", "aligned_name", "taxon_name", "taxonomic_resolution"),
+    info = paste0(info, "\tnames of `taxonomic_updates` table")
+  )
+
+}
+
+
+## A helper function to determine if this is being run as part of a test
+is_testing_env <- function() {
+  # Calling scope
+  tb <- .traceback(x = 0)
+
+  # Check if called in `testthat` or interactive
+  if (any(unlist(lapply(tb, function(x) any(grepl("test_env", x)))))) {
+    return(TRUE)
+  } else {
+    return(FALSE)
+  }
+}