Merge pull request #14 from Infectious-Disease-Modeling-Hubs/enhancem…

…ent/handle-null-taskids Enhancement/handle null taskids
hubverse-org · Apr 2, 2024 · 1194ab2 · 1194ab2
2 parents 4fb92c3 + 6d9cd6a
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: hubAdmin
 Title: Utilities for administering hubverse Hubs
-Version: 0.0.1
+Version: 0.1.0
 Authors@R: 
     c(person("Anna", "Krystalli", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-2378-4915")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# hubAdmin 0.1.0
+
+* Allow task ID `create_task_id()` arguments `required` and `optional` to both be set to `NULL`, facilitating the encoding of `NA` task IDs in modeling tasks where no value is expected for a given task ID.  
+
 # hubAdmin 0.0.1
 
 * Initial package release resulting from split of `hubUtils` package. See [`hubUtils` NEWS.md](https://github.com/Infectious-Disease-Modeling-Hubs/hubUtils/blob/main/NEWS.md) for details including previous release notes.
diff --git a/R/create_config.R b/R/create_config.R
@@ -10,7 +10,7 @@
 #' @seealso [create_rounds()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #'
 #' @examples
 #' rounds <- create_rounds(

diff --git a/R/create_output_type.R b/R/create_output_type.R
@@ -10,7 +10,7 @@
 #' [create_output_type_pmf()], [create_output_type_sample()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #' @examples
 #' create_output_type(
 #'   create_output_type_mean(

diff --git a/R/create_output_type_item.R b/R/create_output_type_item.R
@@ -13,7 +13,7 @@
 #'
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #' @return a named list of class `output_type_item` representing a `mean` or
 #' `median` output type.
 #' @inheritParams create_task_id
@@ -156,7 +156,7 @@ create_output_type_point <- function(output_type = c("mean", "median"),
 #' @inheritParams create_output_type_mean
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #'
 #' @return a named list of class `output_type_item` representing a `quantile`,
 #' `cdf`, `pmf` or `sample` output type.

diff --git a/R/create_round.R b/R/create_round.R
@@ -33,13 +33,13 @@
 #'  of file format in `admin.json`. For more details on whether this argument can
 #'  be used as well as available formats, please consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #' @return a named list of class `round`.
 #' @export
 #' @seealso [create_rounds()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #' @examples
 #' model_tasks <- create_model_tasks(
 #'   create_model_task(

diff --git a/R/create_rounds.R b/R/create_rounds.R
@@ -8,7 +8,7 @@
 #' @seealso [create_round()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #'
 #' @examples
 #' model_tasks <- create_model_tasks(

diff --git a/R/create_target_metadata.R b/R/create_target_metadata.R
@@ -8,7 +8,7 @@
 #' @seealso [create_target_metadata_item()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #'
 #' @examples
 #' create_target_metadata(

diff --git a/R/create_target_metadata_item.R b/R/create_target_metadata_item.R
@@ -32,7 +32,7 @@
 #' @seealso [create_target_metadata()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #' @return a named list of class `target_metadata_item`.
 #' @export
 #'

diff --git a/R/create_task_id.R b/R/create_task_id.R
@@ -20,7 +20,7 @@
 #' @details `required` and `optional` vectors for standard task_ids defined in a Hub schema
 #' must match data types and formats specified in the schema. For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file)
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html)
 #'
 #' JSON schema data type names differ to those in R. Use the following mappings to
 #' create vectors of appropriate data types which will correspond to correct JSON
@@ -32,7 +32,7 @@
 #'            row.names = NULL))
 #' ```
 #' Values across `required` and `optional` arguments must be unique. `required`
-#' and `optional` must be of the same type (unless `NULL`) and both cannot be `NULL`.
+#' and `optional` must be of the same type (unless `NULL`).
 #' Task_ids that represent dates must be supplied as character strings in ISO 8601
 #' date format (YYYY-MM-DD). If working with date objects, please convert to character
 #' (e.g. using `as.character()`) before supplying as arguments.
@@ -87,7 +87,6 @@ create_task_id <- function(name, required, optional,
     )
   }
 
-  check_prop_not_all_null(required, optional)
   check_prop_type_const(required, optional)
   check_prop_dups(required, optional)
 
@@ -187,7 +186,7 @@ check_prop_type_const <- function(required, optional) {
   ) %>%
     unique()
 
-  if (length(prop_types) != 1L && !"NULL" %in% prop_types) {
+  if (length(prop_types) > 1L && !"NULL" %in% prop_types) {
     cli::cli_abort(c(
       "x" = "Arguments {.arg required} and {.arg optional}
               must be of same type.",

diff --git a/R/create_task_ids.R b/R/create_task_ids.R
@@ -7,7 +7,7 @@
 #' @seealso [create_task_id()]
 #' @details For more details consult
 #' the [documentation on `tasks.json` Hub config files](
-#' https://hubdocs.readthedocs.io/en/latest/format/hub-metadata.html#hub-model-task-metadata-tasks-json-file).
+#' https://hubdocs.readthedocs.io/en/latest/quickstart-hub-admin/tasks-config.html).
 #'
 #' @examples
 #' create_task_ids(

diff --git a/man/create_config.Rd b/man/create_config.Rd
diff --git a/man/create_output_type.Rd b/man/create_output_type.Rd
diff --git a/man/create_output_type_mean.Rd b/man/create_output_type_mean.Rd
diff --git a/man/create_output_type_quantile.Rd b/man/create_output_type_quantile.Rd
diff --git a/man/create_round.Rd b/man/create_round.Rd
diff --git a/man/create_rounds.Rd b/man/create_rounds.Rd
diff --git a/man/create_target_metadata.Rd b/man/create_target_metadata.Rd
diff --git a/man/create_target_metadata_item.Rd b/man/create_target_metadata_item.Rd
diff --git a/man/create_task_id.Rd b/man/create_task_id.Rd
diff --git a/man/create_task_ids.Rd b/man/create_task_ids.Rd
diff --git a/tests/testthat/_snaps/create_task_id.md b/tests/testthat/_snaps/create_task_id.md
@@ -72,15 +72,25 @@
       attr(,"schema_id")
       [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.1/tasks-schema.json"
 
-# create_task_id errors correctly
+---
 
     Code
       create_task_id("horizon", required = NULL, optional = NULL)
-    Condition
-      Error in `check_prop_not_all_null()`:
-      x Both arguments `required` and `optional` cannot be NULL.
+    Output
+      $horizon
+      $horizon$required
+      NULL
+      
+      $horizon$optional
+      NULL
+      
+      
+      attr(,"class")
+      [1] "task_id" "list"   
+      attr(,"schema_id")
+      [1] "https://raw.githubusercontent.com/Infectious-Disease-Modeling-Hubs/schemas/main/v2.0.1/tasks-schema.json"
 
----
+# create_task_id errors correctly
 
     Code
       create_task_id("origin_date", required = NULL, optional = c("01/20/2023"))

diff --git a/tests/testthat/test-create_task_id.R b/tests/testthat/test-create_task_id.R
@@ -26,18 +26,16 @@ test_that("create_task_id works correctly", {
       2L
     )
   ))
-})
-
-
-test_that("create_task_id errors correctly", {
   expect_snapshot(
     create_task_id("horizon",
       required = NULL,
       optional = NULL
-    ),
-    error = TRUE
+    )
   )
+})
 
+
+test_that("create_task_id errors correctly", {
   expect_snapshot(
     create_task_id("origin_date",
       required = NULL,