now error out on invalid config files

R/config.R

@@ -190,10 +190,15 @@ Config <- S7::new_class(
 #'
 #' @param config_path A string specifying the path to the JSON configuration
 #' file.
+#' @param optional_fields A list of strings specifying the optional fields in
+#' the JSON file. If a field is not present in the JSON file, and is marked as
+#' optional, it will be set to either the empty type (e.g. `chr(0)`), or NULL.
+#' If a field is not present in the JSON file, and is not marked as optional, an
+#' error will be thrown.
 #' @return An instance of the `Config` class populated with the data from the
 #' JSON file.
 #' @export
-read_json_into_config <- function(config_path) {
+read_json_into_config <- function(config_path, optional_fields) {
   # First, our hard coded, flattened, map from strings to Classes. If any new
   # subclasses are added above, they will also need to be added here. If we
   # create a more automated way to do this, we can remove this.
@@ -211,11 +216,19 @@ read_json_into_config <- function(config_path) {
 
   # Check what top level properties were not in the raw input
   missing_properties <- setdiff(S7::prop_names(Config()), names(raw_input))
+  # Remove any optional fields from the missing properties, give info message
+  # about what is being given a default arg.
+  not_need_but_missing <- intersect(optional_fields, missing_properties)
+  if (length(not_need_but_missing) > 0) {
+    cli::cli_alert_info(
+      "Optional field{?s} not in config file: {.var {not_need_but_missing}}"
+    )
+  }
+  missing_properties <- setdiff(missing_properties, optional_fields)
   # Error out if missing any fields
   if (length(missing_properties) > 0) {
-    cli::cli_alert_info(c(
-      "The following expected propert{?y/ies} were not in the config file:",
-      "{.var {missing_properties}}"
+    cli::cli_abort(c(
+      "Propert{?y/ies} not in the config file: {.var {missing_properties}}"
     ))
   }
 

R/pipeline.R

@@ -72,7 +72,7 @@ orchestrate_pipeline <- function(config_path,
                                  blob_storage_container = NULL,
                                  output_dir = "/") {
   config <- rlang::try_fetch(
-    read_json_into_config(config_path),
+    read_json_into_config(config_path, c("exclusions")),
     error = function(con) {
       cli::cli_warn("Bad config file",
         parent = con,

tests/testthat/data/sample_config_no_exclusion.json

@@ -46,5 +46,6 @@
         "iter_sampling": 50,
         "adapt_delta": 0.99,
         "max_treedepth": 12
-    }
+    },
+    "config_version": "0.1.0"
 }

tests/testthat/data/sample_config_with_exclusion.json

@@ -50,5 +50,6 @@
         "iter_sampling": 50,
         "adapt_delta": 0.99,
         "max_treedepth": 12
-    }
+    },
+    "config_version": "0.1.0"
 }

tests/testthat/data/v_bad_config.json

@@ -0,0 +1,4 @@
+{
+  "job_id": "6183da58-89bc-455f-8562-4f607257a876",
+  "task_id": "bc0c3eb3-7158-4631-a2a9-86b97357f97e"
+}

tests/testthat/test-pipeline.R

@@ -14,7 +14,7 @@ test_that("Bad config throws warning and returns failure", {
       blob_storage_container = blob_storage_container,
       output_dir = output_dir
     ),
-    class = "Run_failed"
+    class = "Bad_config"
   )
   expect_false(pipeline_success)
 })
@@ -71,7 +71,7 @@ test_that("Pipeline run produces expected outputs with exclusions", {
 test_that("Process pipeline produces expected outputs and returns success", {
   # Arrange
   config_path <- test_path("data", "sample_config_with_exclusion.json")
-  config <- read_json_into_config(config_path)
+  config <- read_json_into_config(config_path, c("exclusions"))
   # Read from locally
   output_dir <- "pipeline_test"
   on.exit(unlink(output_dir, recursive = TRUE))
@@ -95,7 +95,7 @@ test_that("Process pipeline produces expected outputs and returns success", {
 test_that("Runs on config from generator as of 2024-11-26", {
   # Arrange
   config_path <- test_path("data", "CA_COVID-19.json")
-  config <- read_json_into_config(config_path)
+  config <- read_json_into_config(config_path, c("exclusions"))
   # Read from locally
   output_dir <- "pipeline_test"
   on.exit(unlink(output_dir, recursive = TRUE))
@@ -115,3 +115,22 @@ test_that("Runs on config from generator as of 2024-11-26", {
     config@task_id
   )
 })
+
+test_that("Warning and exit for bad config file", {
+  # Arrange
+  config_path <- test_path("data", "v_bad_config.json")
+  # Read from locally
+  output_dir <- "pipeline_test"
+  on.exit(unlink(output_dir, recursive = TRUE))
+
+  # Act
+  expect_warning(
+    pipeline_success <- orchestrate_pipeline(
+      config_path = config_path,
+      blob_storage_container = NULL,
+      output_dir = output_dir
+    ),
+    class = "Bad_config"
+  )
+  expect_false(pipeline_success)
+})