handle v3 samples when checking valid values

R/check_tbl_values.R

@@ -20,6 +20,11 @@ check_tbl_values <- function(tbl, round_id, file_path, hub_path) {
   # This approach uses dplyr to identify tbl rows that don't have a complete match
   # in accepted_vals.
   accepted_vals$valid <- TRUE
+  if (hubUtils::is_v3_config(config_tasks)) {
+    out_type_ids <- tbl[["output_type_id"]]
+    tbl[tbl$output_type == "sample", "output_type_id"] <- NA
+  }
+
   valid_tbl <- dplyr::left_join(
     tbl, accepted_vals,
     by = names(tbl)[names(tbl) != "value"]
@@ -36,6 +41,9 @@ check_tbl_values <- function(tbl, round_id, file_path, hub_path) {
     if (length(error_summary$invalid_combs_idx) == 0L) {
       error_tbl <- NULL
     } else {
+      if (hubUtils::is_v3_config(config_tasks)) {
+        tbl[["output_type_id"]] <- out_type_ids
+      }
       error_tbl <- tbl[
         error_summary$invalid_combs_idx,
         names(tbl) != "value"
@@ -125,7 +133,7 @@ coerce_num_output_type_ids <- function(tbl, file_path, hub_path) {
   )
 
   if (any(tbl[["output_type"]] %in% num_output_types) &&
-        inherits(tbl[["output_type_id"]], "character")) {
+    inherits(tbl[["output_type_id"]], "character")) {
     type_coerce <- tbl[["output_type"]] %in% num_output_types
     num_output_type_id <- suppressWarnings(
       as.numeric(tbl$output_type_id[type_coerce])

tests/testthat/_snaps/check_tbl_values.md

@@ -18,3 +18,23 @@
       Error:
       ! `tbl` contains invalid values/value combinations.  Column `horizon` contains invalid value "11".
 
+# check_tbl_values works with v3 spec samples
+
+    Code
+      check_tbl_values(tbl = tbl, round_id = round_id, file_path = file_path,
+        hub_path = hub_path)
+    Output
+      <message/check_success>
+      Message:
+      `tbl` contains valid values/value combinations.
+
+---
+
+    Code
+      check_tbl_values(tbl = tbl, round_id = round_id, file_path = file_path,
+        hub_path = hub_path)
+    Output
+      <error/check_error>
+      Error:
+      ! `tbl` contains invalid values/value combinations.  Column `horizon` contains invalid values "11" and "12".
+

tests/testthat/test-check_tbl_values.R

@@ -166,3 +166,32 @@ test_that("check_tbl_values consistent across numeric & character output type id
     exact = TRUE
   )
 })
+
+test_that("check_tbl_values works with v3 spec samples", {
+  hub_path <- system.file("testhubs/samples", package = "hubValidations")
+  file_path <- "Flusight-baseline/2022-10-22-Flusight-baseline.csv"
+  round_id <- "2022-10-22"
+  tbl <- read_model_out_file(
+    file_path = file_path,
+    hub_path = hub_path,
+    coerce_types = "chr"
+  )
+  expect_snapshot(
+    check_tbl_values(
+      tbl = tbl,
+      round_id = round_id,
+      file_path = file_path,
+      hub_path = hub_path
+    )
+  )
+
+  tbl[head(which(tbl$output_type == "sample"), 2), "horizon"] <- c("11", "12")
+  expect_snapshot(
+    check_tbl_values(
+      tbl = tbl,
+      round_id = round_id,
+      file_path = file_path,
+      hub_path = hub_path
+    )
+  )
+})