Merge pull request #64 from hubverse-org/ak/v4-output-type-ids/63

Support v4 output type specification when creating schema

DESCRIPTION

@@ -15,7 +15,7 @@ Description: A set of utility functions for accessing and working with
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Config/testthat/edition: 3
 URL: https://github.com/hubverse-org/hubData
 BugReports: https://github.com/hubverse-org/hubData/issues

NEWS.md

@@ -1,5 +1,7 @@
 # hubData (development version)
 
+* Support the determination of hub schema from v4 configuration files (#63). Also fixes bug in `create_hub_schema()` where `output_type_id` data type was being incorrectly auto-determined as `logical` when only point estimate output types where being collected by a hub. Now `character` data type is returned for the `output_type_id` for all schema versions in such situations when auto-determined.
+
 # hubData 1.2.3
 
 * Fix bug in `create_hub_schema()` where `output_type_id` data type was being incorrectly determined as `Date` instead of `character` (Reported in https://github.com/reichlab/variant-nowcast-hub/pull/87#issuecomment-2387372238).

R/create_hub_schema.R

@@ -15,6 +15,9 @@
 #' the  `output_type_id` data type automatically from the `tasks.json`
 #' config file as the simplest data type required to represent all output
 #' type ID values across all output types in the hub.
+#' When only point estimate output types (where `output_type_id`s are `NA`,) are
+#' being collected by a hub, the `output_type_id` column is assigned a `character`
+#' data type when auto-determined.
 #' Other data type values can be used to override automatic determination.
 #' Note that attempting to coerce `output_type_id` to a data type that is
 #' not valid for the data (e.g. trying to coerce`"character"` values to
@@ -149,6 +152,8 @@ get_output_type_id_type <- function(config_tasks) {
   # retired
   config_tid <- hubUtils::get_config_tid(config_tasks = config_tasks)
 
+  # Get the values of all output type id values across all output types and rounds
+  # in the hub config
   values <- purrr::map(
     config_tasks[["rounds"]],
     function(x) {
@@ -203,7 +208,12 @@ get_output_type_id_type <- function(config_tasks) {
   # `get_data_type()` which checks characters for ISO date format.
   # Should Dates be introduced as output type id values in the future,
   # this will need to be revisited.
-  typeof(c(values, sample_values))
+  type <- typeof(c(values, sample_values))
+
+  if (type %in% c("NULL", "logical")) {
+    type <- "character"
+  }
+  type
 }
 
 

R/reexports-hubUtils.R

@@ -0,0 +1,15 @@
+#' @export
+#' @importFrom hubUtils as_model_out_tbl
+hubUtils::as_model_out_tbl
+
+#' @export
+#' @importFrom hubUtils validate_model_out_tbl
+hubUtils::validate_model_out_tbl
+
+#' @export
+#' @importFrom hubUtils model_id_merge
+hubUtils::model_id_merge
+
+#' @export
+#' @importFrom hubUtils model_id_split
+hubUtils::model_id_split

tests/testthat/test-create_hub_schema.R

@@ -61,6 +61,14 @@ test_that("create_hub_schema works correctly", {
       output_type_id = "character", value = "integer", model_id = "character"
     )
   )
+
+  # Validate that configs with only point estimate output types returns character (the default)
+  # not logical
+  config_tasks <- hubUtils::read_config_file(test_path("testdata/configs/v3-tasks-point.json"))
+  expect_equal(
+    create_hub_schema(config_tasks)$GetFieldByName("output_type_id")$ToString(),
+    "output_type_id: string"
+  )
 })
 
 test_that("create_hub_schema works with sample output types", {
@@ -135,3 +143,30 @@ test_that("create_hub_schema works with config output_type_id_datatype", {
     "nowcast_date: date32[day]\ntarget_date: date32[day]\nlocation: string\nclade: string\noutput_type: string\noutput_type_id: string\nvalue: double\nmodel_id: string"
   )
 })
+
+test_that("create_hub_schema works with v4 output_type_id configuration", {
+  config_tasks <- suppressWarnings(
+    hubUtils::read_config_file(test_path("testdata/configs/v4-tasks.json"))
+  )
+  expect_equal(
+    create_hub_schema(config_tasks)$ToString(),
+    "forecast_date: date32[day]\ntarget: string\nhorizon: int32\nlocation: string\ntarget_date: date32[day]\noutput_type: string\noutput_type_id: string\nvalue: double\nmodel_id: string"
+  )
+
+  # Validate that configs with only point estimate output types returns character (the default)
+  config_tasks <- suppressWarnings(
+    hubUtils::read_config_file(test_path("testdata/configs/v4-tasks-point.json"))
+  )
+  expect_equal(
+    create_hub_schema(config_tasks)$GetFieldByName("output_type_id")$ToString(),
+    "output_type_id: string"
+  )
+  # Ensure `output_type_id_datatype` arg works with v4 configs
+  expect_equal(
+    create_hub_schema(
+      config_tasks,
+      output_type_id_datatype = "double"
+    )$GetFieldByName("output_type_id")$ToString(),
+    "output_type_id: double"
+  )
+})