allow for testing design lists which are not in a tomic object

NAMESPACE

@@ -5,6 +5,7 @@ export(app_flow)
 export(app_heatmap)
 export(app_pcs)
 export(center_tomic)
+export(check_design)
 export(check_tomic)
 export(convert_wide_to_tidy_omic)
 export(create_tidy_omic)

R/data_classes.R

@@ -166,7 +166,7 @@ check_tidy_omic <- function(tidy_omic, fast_check = TRUE) {
   checkmate::assertClass(tidy_omic, "tidy_omic")
   checkmate::assertLogical(fast_check, len = 1)
   # check design
-  check_design(tidy_omic)
+  check_design_in_tomic(tidy_omic)
 
   feature_pk <- tidy_omic$design$feature_pk
   sample_pk <- tidy_omic$design$sample_pk
@@ -475,7 +475,7 @@ check_triple_omic <- function(triple_omic, fast_check = TRUE) {
   checkmate::assertClass(triple_omic, "triple_omic")
   checkmate::assertLogical(fast_check, len = 1)
   # check design
-  check_design(triple_omic)
+  check_design_in_tomic(triple_omic)
 
   # variables are same as design
   checkmate::assertNames(

R/design.R

@@ -20,17 +20,51 @@ get_design_tbl <- function(tomic) {
     dplyr::bind_rows()
 }
 
-check_design <- function(tomic) {
+#' Check Design
+#'
+#' Check that the design list embedded in `tomic` objects is properly
+#' formatted.
+#'
+#' @param tomic_design a list with named attributes describing feature,
+#'   sample, and measurement variables.
+#'
+#' @return 0, invisibly
+#'
+#' @examples
+#' check_design(brauer_2008_triple$design)
+#'
+#' @export
+check_design <- function(tomic_design) {
+
+  checkmate::assertList(tomic_design)
+
+  EXPECTED_ATTRIBUTES <- c("feature_pk", "features", "measurements", "sample_pk", "samples")
+  extra_elements <- setdiff(names(tomic_design), EXPECTED_ATTRIBUTES)
+  if (length(extra_elements) > 0) {
+    cli::cli_abort(
+      "The following unexpected attributes were found in the design: {.field {extra_elements}}"
+    )
+  }
+
+  missing_elements <- setdiff(EXPECTED_ATTRIBUTES, names(tomic_design))
+  if (length(missing_elements) > 0) {
+    cli::cli_abort(
+      "The following attributes were missing in the design: {.field {missing_elements}}"
+    )
+  }
+
+  checkmate::assertString(tomic_design$feature_pk)
+  checkmate::assertDataFrame(tomic_design$features)
+  checkmate::assertDataFrame(tomic_design$measurements)
+  checkmate::assertString(tomic_design$sample_pk)
+  checkmate::assertDataFrame(tomic_design$samples)
+}
+
+check_design_in_tomic <- function(tomic) {
+
   checkmate::assertClass(tomic, "tomic")
   stopifnot("design" %in% names(tomic))
-  stopifnot(all(
-    sort(names(tomic$design)) ==
-      c("feature_pk", "features", "measurements", "sample_pk", "samples")
-  ))
-
-  checkmate::assertString(tomic$design$feature_pk)
-  checkmate::assertDataFrame(tomic$design$features)
-  checkmate::assertDataFrame(tomic$design$measurements)
-  checkmate::assertString(tomic$design$sample_pk)
-  checkmate::assertDataFrame(tomic$design$samples)
+  check_design(tomic$design)
+
 }
+

tests/testthat/test-design.R

@@ -2,6 +2,6 @@ test_that("extract design as a table", {
   get_design_tbl(brauer_2008_tidy) %>%
     expect_snapshot()
 
-  expect_invisible(check_design(brauer_2008_tidy))
+  expect_invisible(check_design_in_tomic(brauer_2008_tidy))
 })