handle v3 samples when checking required values

hubverse-org · May 20, 2024 · 8285a60 · 8285a60
1 parent 2957a82
commit 8285a60
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Showing 4 changed files with 95 additions and 6 deletions.
diff --git a/R/check_tbl_values_required.R b/R/check_tbl_values_required.R
@@ -8,6 +8,9 @@
 check_tbl_values_required <- function(tbl, round_id, file_path, hub_path) {
   tbl[["value"]] <- NULL
   config_tasks <- hubUtils::read_config(hub_path, "tasks")
+  if (hubUtils::is_v3_config(config_tasks)) {
+    tbl[tbl$output_type == "sample", "output_type_id"] <- NA
+  }
   req <- hubData::expand_model_out_val_grid(
     config_tasks,
     round_id = round_id,

diff --git a/inst/testhubs/samples/hub-config/tasks.json b/inst/testhubs/samples/hub-config/tasks.json
@@ -32,10 +32,11 @@
                             "optional": [0, 1, 2, 3]
                         },
                         "location": {
-                            "required": null,
-                            "optional": [
+                            "required": [
                                 "US",
-                                "01",
+                                "01"
+                            ],
+                            "optional": [
                                 "02",
                                 "04",
                                 "05"
@@ -120,10 +121,11 @@
                             "optional": [0, 1, 2, 3]
                         },
                         "location": {
-                            "required": null,
-                            "optional": [
+                            "required": [
                                 "US",
-                                "01",
+                                "01"
+                            ],
+                            "optional": [
                                 "02",
                                 "04",
                                 "05"

diff --git a/tests/testthat/_snaps/check_tbl_values_required.md b/tests/testthat/_snaps/check_tbl_values_required.md
@@ -130,3 +130,44 @@
        $ use_cli_format: logi TRUE
        - attr(*, "class")= chr [1:5] "check_failure" "hub_check" "rlang_warning" "warning" ...
 
+# check_tbl_values_required works with v3 spec samples
+
+    Code
+      check_tbl_values_required(tbl = tbl, round_id = round_id, file_path = file_path,
+        hub_path = hub_path)
+    Output
+      <message/check_success>
+      Message:
+      Required task ID/output type/output type ID combinations all present.
+
+---
+
+    Code
+      check_tbl_values_required(tbl = tbl, round_id = round_id, file_path = file_path,
+        hub_path = hub_path)
+    Output
+      <warning/check_failure>
+      Warning:
+      Required task ID/output type/output type ID combinations missing.  See `missing` attribute for details.
+
+---
+
+    Code
+      missing
+    Output
+      # A tibble: 21 x 7
+         location reference_date horizon target_end_date target            output_type
+         <chr>    <date>           <int> <date>          <chr>             <chr>      
+       1 US       2022-10-22           0 2022-10-22      wk flu hosp rate~ pmf        
+       2 US       2022-10-22           0 2022-10-22      wk flu hosp rate~ pmf        
+       3 US       2022-10-22           0 2022-10-22      wk flu hosp rate~ pmf        
+       4 US       2022-10-22           0 2022-10-22      wk flu hosp rate~ pmf        
+       5 US       2022-10-22           1 2022-10-29      wk flu hosp rate~ pmf        
+       6 US       2022-10-22           1 2022-10-29      wk flu hosp rate~ pmf        
+       7 US       2022-10-22           1 2022-10-29      wk flu hosp rate~ pmf        
+       8 US       2022-10-22           1 2022-10-29      wk flu hosp rate~ pmf        
+       9 US       2022-10-22           2 2022-11-05      wk flu hosp rate~ pmf        
+      10 US       2022-10-22           2 2022-11-05      wk flu hosp rate~ pmf        
+      # i 11 more rows
+      # i 1 more variable: output_type_id <chr>
+
diff --git a/tests/testthat/test-check_tbl_values_required.R b/tests/testthat/test-check_tbl_values_required.R
@@ -181,3 +181,46 @@ test_that(
     )
   }
 )
+
+test_that("check_tbl_values_required 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_required(
+      tbl = tbl,
+      round_id = round_id,
+      file_path = file_path,
+      hub_path = hub_path
+    )
+  )
+  # Remove US location to test missing required values identified and reported
+  # correctly.
+  tbl <- tbl[tbl$location != "US", ]
+  expect_snapshot(
+    check_tbl_values_required(
+      tbl = tbl,
+      round_id = round_id,
+      file_path = file_path,
+      hub_path = hub_path
+    )
+  )
+  missing <- check_tbl_values_required(
+    tbl = tbl,
+    round_id = round_id,
+    file_path = file_path,
+    hub_path = hub_path
+  )$missing
+  expect_snapshot(missing)
+  expect_equal(
+    unique(missing$output_type),
+    c("pmf", "sample", "mean", "median")
+  )
+  expect_true(all(missing$location == "US"))
+
+})