Minor fixes

NEWS.md

@@ -2,6 +2,8 @@
 
 -   fix bug in `check_df_values_required()` dealing with model task containing
     multiple output types.
+-   minor fixes: read partition of one file, improve output error message 
+    of invalid or missing variables combination. 
 
 # SMHvalidation 1.1.0
 

R/imports-hubValidations.R

@@ -82,6 +82,7 @@ check_tbl_values <- function(tbl, round_id, file_path, hub_path) {
   if (check) {
     details <- NULL
   } else {
+    valid_tbl <- dplyr::filter(valid_tbl, is.na(.data[["valid"]]))
     valid_tbl <- tibble::rowid_to_column(valid_tbl)
     error_summary <- summarise_invalid_values(valid_tbl, config_tasks, round_id)
     details <- error_summary$msg

R/plot_utils.R

@@ -94,8 +94,8 @@ print_table <- function(data, tab_title, metric = "prctdiff_gt", #"median",
     dplyr::select(tidyr::all_of(c("scenario_id", "state", "outcome",
                                   "ground truth")),
                   value = tidyr::all_of(metric)) |>
-    tidyr::pivot_wider(names_from = .data[["scenario_id"]],
-                       values_from = .data[["value"]])
+    tidyr::pivot_wider(names_from = dplyr::matches("scenario_id"),
+                       values_from = dplyr::matches("value"))
 
   # Cells to highlight
   nas <- na_cells(tab_data, sel_group)

R/test_req_value.R

@@ -115,7 +115,7 @@ check_df_values_required <- function(test_df, model_task, file_path) {
       req_targ <- NULL
     } else {
       req_targ <- purrr::map(x$task_ids, "required")
-      opt_targ <- purrr::map(x$task_ids, "optional")
+      opt_targ <- purrr::map(x$task_ids, unlist)
     }
     outtype_df <- extract_output_type(x)
 

R/validate_submission.R

@@ -296,7 +296,7 @@ validate_submission <- function(path, hub_path, js_def = NULL,
     return(check)
   } else {
     # Read file
-    if (length(file_path) == 1) {
+    if (length(file_path) == 1 && is.null(partition)) {
       df <- read_files(paste0(hub_path, "/", path))
     } else if (!is.null(partition)) {
       schema <- make_schema(js_def0, js_def, round_id,

tests/testthat/test_visualization.R

@@ -26,6 +26,8 @@ test_that("Test visualization", {
                                                           "target")))
 
   df <- dplyr::filter(df0, .data[["output_type"]] == "sample")
+  if (!dir.exists(basename(path_f)))
+    dir.create(basename(path_f), recursive = TRUE)
   arrow::write_parquet(df, path_f)
   rm(df)