Remove unneeded files (#785)

* remove file not required in austraits.build

* Recover deleted files

* Update to run

---------

Co-authored-by: Daniel Falster <[email protected]>

tests/build/helper.R

@@ -1,10 +1,7 @@
 requireNamespace("testthat", quietly = TRUE)
 
-
-
-
 library(traits.build)
-source("../testthat/functions.R")
+source("../functions.R")
 
 root.dir <- rprojroot::find_package_root_file()
 source(file.path(root.dir, "R/custom_R_code.R"))

tests/build/test-axrxiv_constancy.R

@@ -10,9 +10,9 @@ build_comparison_set <- function(root.dir, definitions, unit_conversions, schema
 #  Tomlinson_2019 - complete taxonomic changes
 
   f_build <- function(x, definitions, unit_conversions, schema, resource_metadata, taxon_list) {
-    config <-  dataset_configure(file.path(root.dir, "data", x, "metadata.yml"), definitions, unit_conversions)
-    data <-  dataset_process(file.path(root.dir, "data", x, "data.csv"), config, schema, resource_metadata)
-    data <- build_update_taxonomy(data, taxon_list)
+    config <-  dataset_configure(file.path(root.dir, "data", x, "metadata.yml"), definitions)
+    data <- dataset_process(file.path(root.dir, "data", x, "data.csv"), config, schema, resource_metadata, unit_conversions)
+    data <- dataset_update_taxonomy(data, taxon_list)
 
     data
   }

tests/functions.R

@@ -0,0 +1,126 @@
+
+# Better than expect_silent as contains `info` and allows for complete failures
+expect_no_error <- function (object, regexp = NULL, ..., info = NULL, label = NULL)
+{
+  error <- tryCatch({
+    object
+    NULL
+  }, error = function(e) {
+    e
+  })
+  expect(is.null(error), sprintf("%s threw an error: %s", label, paste(error$message, collapse=",")), info = info)
+  invisible(NULL)
+}
+
+
+expect_unique <- function (object, info = NULL, label = NULL) {
+  x <- table(unlist(object))
+  i <- x==1
+  comp <- compare(all(i), TRUE)
+  expect(comp$equal,
+         sprintf("%s - not unique: %s", info, paste(names(x)[!i], collapse= ", ")))
+  invisible(object)
+}
+
+expect_isin <- function(object, expected, ..., info = NULL, label = NULL,
+                        expected.label = NULL, na.rm=TRUE) {
+
+  if(na.rm)
+    object <- object[!is.na(object)]
+  i <- object %in% expected
+
+  comp <- compare(all(i), TRUE, ...)
+  expect(
+    comp$equal,
+    sprintf("%s - should not contain: %s", info, paste(object[!i], collapse= ", "))
+  )
+
+  invisible(object)
+}
+
+expect_not_NA <- function (object, info = NULL, label = NULL) {
+  i <- !is.na(object)
+  comp <- compare(all(i), TRUE)
+  expect(comp$equal,
+         sprintf("%s - contains NAs: %s", info, label))
+  invisible(object)
+}
+
+test_list <- function(data, info) {
+  expect_true(class(data)=="list", info = info)
+}
+
+test_list_names_valid <- function(data, info) {
+  test_list(data, info)
+  expect_not_NA(names(data), info = info)
+#  expect_allowed_text(names(data), info = info)
+  expect_unique(names(data), info = info)
+}
+
+test_list_named <- function(data, expected_names, info) {
+  test_list_names_valid(data, info)
+  expect_named(data, expected_names, info= info)
+}
+
+test_list_named_contains <- function(data, expected_names, info) {
+  test_list_names_valid(data, info)
+  expect_isin(names(data), expected_names)
+}
+
+
+test_dataframe_valid <- function(data, info) {
+  expect_not_NA(colnames(data), info = info)
+#  expect_allowed_text(colnames(data), info = info)
+  expect_unique(colnames(data), info = info)
+  expect_true(is.data.frame(data), info = info)
+}
+
+test_dataframe_named <- function(data, expected_colnames, info) {
+  test_dataframe_valid(data, info)
+  expect_named(data, expected_colnames, 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
+  expect_no_error({
+    build_config <- dataset_configure(path_metadata, definitions, unit_conversions)
+  }, info = paste(info, " config"))
+
+  expect_no_error({
+    build_dataset_raw <- dataset_process(path_data, build_config, schema, resource_metadata)
+  }, info = paste(info, " dataset_process"))
+
+  expect_no_error({
+    build_dataset <- build_update_taxonomy(build_dataset_raw, taxon_list)
+  }, info = paste(info, " update taxonomy"))
+
+  test_structure(build_dataset, info, schema, definitions, single_dataset = TRUE)
+
+  build_dataset
+}
+
+test_structure <- function(data, info, schema, definitions, single_dataset = TRUE) {
+
+  vars_austraits <-
+    schema$austraits$elements %>% names()
+
+  vars_tables <- vars_austraits %>% subset(., !(. %in% c("dataset_id", "definitions", "schema", "sources", "metadata", "build_info")))
+
+  # test lists have the right objects
+  comparison <- vars_austraits
+
+  test_list_named(data, comparison, info = c(info, " - main elements"))
+
+  # test structure of tables
+  for(v in vars_tables) {
+
+    comparison <- schema$austraits$elements[[v]]$elements %>% names()
+
+    test_dataframe_named(data[[v]], comparison, info = paste(info, " - structure of ", v))
+  }
+
+  # contains allowed traits
+  expect_isin(data$traits$trait_name %>% unique(), definitions$elements %>% names(), info = paste("traits ", v))
+}