From 2fe0db074ae01238cdfa12f6450dc6d4b1b99a70 Mon Sep 17 00:00:00 2001
From: Sean Hackett <sean@calicolabs.com>
Date: Mon, 19 Feb 2024 13:10:25 -1000
Subject: [PATCH] allow for testing design lists which are not in a tomic
 object

---
 NAMESPACE                    |  1 +
 R/data_classes.R             |  4 +--
 R/design.R                   | 56 +++++++++++++++++++++++++++++-------
 man/check_design.Rd          | 23 +++++++++++++++
 man/romic-package.Rd         |  9 ++++++
 tests/testthat/test-design.R |  2 +-
 6 files changed, 81 insertions(+), 14 deletions(-)
 create mode 100644 man/check_design.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 253f09c..a3e96c3 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/data_classes.R b/R/data_classes.R
index 75636ea..e4a9869 100644
--- a/R/data_classes.R
+++ b/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(
diff --git a/R/design.R b/R/design.R
index 517a737..ef5d0d1 100644
--- a/R/design.R
+++ b/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)
+
 }
+
diff --git a/man/check_design.Rd b/man/check_design.Rd
new file mode 100644
index 0000000..46c1b3c
--- /dev/null
+++ b/man/check_design.Rd
@@ -0,0 +1,23 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/design.R
+\name{check_design}
+\alias{check_design}
+\title{Check Design}
+\usage{
+check_design(tomic_design)
+}
+\arguments{
+\item{tomic_design}{a list with named attributes describing feature,
+sample, and measurement variables.}
+}
+\value{
+0, invisibly
+}
+\description{
+Check that the design list embedded in `tomic` objects is properly
+formatted.
+}
+\examples{
+check_design(brauer_2008_triple$design)
+
+}
diff --git a/man/romic-package.Rd b/man/romic-package.Rd
index d9db4ef..c905615 100644
--- a/man/romic-package.Rd
+++ b/man/romic-package.Rd
@@ -13,6 +13,15 @@
   manner. 'romic' takes advantage of these transformations to create
   interactive shiny apps for exploratory data analysis such as an
   interactive heatmap.
+}
+\seealso{
+Useful links:
+\itemize{
+  \item \url{https://calico.github.io/romic/}
+  \item \url{https://github.com/calico/romic}
+  \item Report bugs at \url{https://github.com/calico/romic/issues}
+}
+
 }
 \author{
 \strong{Maintainer}: Sean Hackett \email{sean@calicolabs.com} (\href{https://orcid.org/0000-0002-9553-4341}{ORCID})
diff --git a/tests/testthat/test-design.R b/tests/testthat/test-design.R
index a9483c5..da50d69 100644
--- a/tests/testthat/test-design.R
+++ b/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))
 })