Rename JoinKeys class to join_keys from upstream {teal.data} (#161)

All tests pass with exception of: ![image](https://github.com/insightsengineering/teal.transform/assets/211358/bd40791c-bc17-45c4-984d-7f4902a192d5)
insightsengineering · Nov 8, 2023 · dd6a003 · dd6a003
1 parent ed7aa88
commit dd6a003
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Showing 21 changed files with 29 additions and 29 deletions.
diff --git a/R/data_extract_module.R b/R/data_extract_module.R
@@ -421,7 +421,7 @@ data_extract_srv.FilteredData <- function(id, datasets, data_extract_spec, ...)
 }
 
 #' @rdname data_extract_srv
-#' @param join_keys (`JoinKeys` or `NULL`) of keys per dataset in `datasets`
+#' @param join_keys (`join_keys` or `NULL`) of keys per dataset in `datasets`
 #' @param select_validation_rule (`NULL` or `function`)
 #'   Should there be any `shinyvalidate` input validation of the select parts of the `data_extract_ui`.
 #'   You can use a validation function directly (i.e. `select_validation_rule = shinyvalidate::sv_required()`)
@@ -443,7 +443,7 @@ data_extract_srv.list <- function(id, datasets, data_extract_spec, join_keys = N
                                   },
                                   ...) {
   checkmate::assert_list(datasets, types = c("reactive", "data.frame"), names = "named")
-  checkmate::assert_class(join_keys, "JoinKeys", null.ok = TRUE)
+  checkmate::assert_class(join_keys, "join_keys", null.ok = TRUE)
   checkmate::assert_multi_class(select_validation_rule, classes = c("function", "formula"), null.ok = TRUE)
   checkmate::assert_multi_class(filter_validation_rule, classes = c("function", "formula"), null.ok = TRUE)
   checkmate::assert_multi_class(dataset_validation_rule, classes = c("function", "formula"), null.ok = TRUE)
@@ -681,7 +681,7 @@ data_extract_multiple_srv.FilteredData <- function(data_extract, datasets, ...)
 }
 
 #' @rdname data_extract_multiple_srv
-#' @param join_keys (`JoinKeys` or `NULL`) of join keys per dataset in `datasets`.
+#' @param join_keys (`join_keys` or `NULL`) of join keys per dataset in `datasets`.
 #' @param select_validation_rule (`NULL`, `function` or `named list` of `function`)
 #'   Should there be any `shinyvalidate` input validation of the select parts of the `data_extract_ui`
 #'   If all `data_extract` require the same validation function then this can be used directly (
@@ -702,7 +702,7 @@ data_extract_multiple_srv.list <- function(data_extract, datasets, join_keys = N
                                              shinyvalidate::sv_required("Please select a dataset")
                                            }, ...) {
   checkmate::assert_list(datasets, types = c("reactive", "data.frame"), names = "named")
-  checkmate::assert_class(join_keys, "JoinKeys", null.ok = TRUE)
+  checkmate::assert_class(join_keys, "join_keys", null.ok = TRUE)
   checkmate::assert(
     checkmate::check_multi_class(select_validation_rule, classes = c("function", "formula"), null.ok = TRUE),
     checkmate::check_list(select_validation_rule, types = c("function", "formula", "NULL"), null.ok = TRUE)

diff --git a/R/get_dplyr_call.R b/R/get_dplyr_call.R
@@ -9,7 +9,7 @@
 #' @keywords internal
 get_dplyr_call_data <- function(selector_list, join_keys = teal.data::join_keys()) {
   logger::log_trace("get_dplyr_call_data called with: { paste(names(selector_list), collapse = ', ') } selectors.")
-  checkmate::assert_class(join_keys, "JoinKeys")
+  checkmate::assert_class(join_keys, "join_keys")
   lapply(selector_list, check_selector)
 
   all_merge_key_list <- get_merge_key_grid(selector_list, join_keys)
@@ -211,7 +211,7 @@ get_dplyr_call <- function(selector_list,
     )
   )
   lapply(selector_list, check_selector)
-  checkmate::assert_class(join_keys, "JoinKeys", null.ok = TRUE)
+  checkmate::assert_class(join_keys, "join_keys", null.ok = TRUE)
   checkmate::assert_integer(idx, len = 1, any.missing = FALSE)
 
   n_selectors <- length(selector_list)

diff --git a/R/get_merge_call.R b/R/get_merge_call.R
@@ -4,7 +4,7 @@
 #' Returns list of calls depending on selector(s) and type of the merge
 #' Order of merge is the same as in selectors passed to the function.
 #' @inheritParams merge_datasets
-#' @param join_keys (`JoinKeys`) nested list of keys used for joining
+#' @param join_keys (`join_keys`) nested list of keys used for joining
 #' @param dplyr_call_data (`list`) simplified selectors with aggregated set of filters,
 #'
 #' @return (`list` with `call` elements)

diff --git a/R/merge_datasets.R b/R/merge_datasets.R
@@ -51,7 +51,7 @@ merge_datasets <- function(selector_list, datasets, join_keys, merge_function =
   checkmate::assert_list(selector_list, min.len = 1)
   checkmate::assert_string(anl_name)
   checkmate::assert_list(datasets, names = "named")
-  checkmate::assert_class(join_keys, "JoinKeys")
+  checkmate::assert_class(join_keys, "join_keys")
   stopifnot(attr(regexec("[A-Za-z0-9\\_]*", anl_name)[[1]], "match.length") == nchar(anl_name))
   lapply(selector_list, check_selector)
   merge_selectors_out <- merge_selectors(selector_list)
@@ -241,7 +241,7 @@ check_data_merge_selectors <- function(selector_list) {
 #' `merged_selector_list` come from datasets, which don't have the
 #' appropriate join keys in `join_keys`.
 #'
-#' @param join_keys (`JoinKeys`) the provided join keys
+#' @param join_keys (`join_keys`) the provided join keys
 #' @param merged_selector_list (`list`) the specification of datasets' slices to merge
 #'
 #' @return `TRUE` if the provided keys meet the requirements; the `shiny`

diff --git a/R/merge_expression_module.R b/R/merge_expression_module.R
@@ -9,7 +9,7 @@
 #' @param datasets (named `list` of `reactive` or non-`reactive` `data.frame`)\cr
 #'  object containing data as a list of `data.frame`. When passing a list of non-reactive `data.frame` objects, they are
 #'  converted to reactive `data.frame` objects internally.
-#' @param join_keys (`JoinKeys`)\cr
+#' @param join_keys (`join_keys`)\cr
 #'  of variables used as join keys for each of the datasets in `datasets`.
 #'  This will be used to extract the `keys` of every dataset.
 #' @param data_extract (named `list` of `data_extract_spec`)\cr
@@ -171,7 +171,7 @@ merge_expression_module <- function(datasets,
 #' @param datasets (named `list` of `reactive` or non-`reactive` `data.frame`)\cr
 #'  object containing data as a list of `data.frame`. When passing a list of non-reactive `data.frame` objects, they are
 #'  converted to reactive `data.frame` objects internally.
-#' @param join_keys (`JoinKeys`)\cr
+#' @param join_keys (`join_keys`)\cr
 #'  of variables used as join keys for each of the datasets in `datasets`.
 #'  This will be used to extract the `keys` of every dataset.
 #' @param selector_list (`reactive`)\cr
@@ -315,7 +315,7 @@ merge_expression_srv <- function(id = "merge_id",
   stopifnot(make.names(anl_name) == anl_name)
   checkmate::assert_class(selector_list, "reactive")
   checkmate::assert_list(datasets, types = c("reactive", "data.frame"), names = "named")
-  checkmate::assert_class(join_keys, "JoinKeys")
+  checkmate::assert_class(join_keys, "join_keys")
 
   moduleServer(
     id,

diff --git a/man/are_needed_keys_provided.Rd b/man/are_needed_keys_provided.Rd
diff --git a/man/data_extract_multiple_srv.Rd b/man/data_extract_multiple_srv.Rd
diff --git a/man/data_extract_srv.Rd b/man/data_extract_srv.Rd
diff --git a/man/get_dplyr_call.Rd b/man/get_dplyr_call.Rd
diff --git a/man/get_dplyr_call_data.Rd b/man/get_dplyr_call_data.Rd
diff --git a/man/get_merge_call.Rd b/man/get_merge_call.Rd
diff --git a/man/get_merge_key_grid.Rd b/man/get_merge_key_grid.Rd
diff --git a/man/get_rename_call.Rd b/man/get_rename_call.Rd
diff --git a/man/get_reshape_call.Rd b/man/get_reshape_call.Rd
diff --git a/man/merge_datasets.Rd b/man/merge_datasets.Rd
diff --git a/man/merge_expression_module.Rd b/man/merge_expression_module.Rd
diff --git a/man/merge_expression_srv.Rd b/man/merge_expression_srv.Rd
diff --git a/man/validate_keys_sufficient.Rd b/man/validate_keys_sufficient.Rd
diff --git a/tests/testthat/test-data_extract_multiple_srv.R b/tests/testthat/test-data_extract_multiple_srv.R
@@ -154,7 +154,7 @@ testthat::test_that(
 )
 
 testthat::test_that(
-  desc = "data_extract_multiple_srv accepts throws error when join_keys argument is not JoinKeys object",
+  desc = "data_extract_multiple_srv accepts throws error when join_keys argument is not join_keys object",
   code = {
     shiny::withReactiveDomain(
       domain = shiny::MockShinySession$new(),

diff --git a/tests/testthat/test-data_extract_srv.R b/tests/testthat/test-data_extract_srv.R
@@ -110,7 +110,7 @@ testthat::test_that(
 )
 
 testthat::test_that(
-  desc = "data_extract_srv accepts throws error when join_keys argument is not a JoinKeys object",
+  desc = "data_extract_srv accepts throws error when join_keys argument is not a join_keys object",
   code = {
     shiny::withReactiveDomain(
       domain = shiny::MockShinySession$new(),

diff --git a/tests/testthat/test-merge_expression_srv.R b/tests/testthat/test-merge_expression_srv.R
@@ -242,14 +242,14 @@ testthat::test_that("merge_expression_srv throws error if datasets is not a name
   )
 })
 
-testthat::test_that("merge_expression_srv throws error if join_keys is not a JoinKeys object", {
+testthat::test_that("merge_expression_srv throws error if join_keys is not a join_keys object", {
   testthat::expect_error(
     shiny::testServer(
       merge_expression_srv,
       args = list(selector_list = selector_list, datasets = data_list, join_keys = list("USUBJID")),
       expr = NULL
     ),
-    "class 'JoinKeys', but has class 'list'"
+    "class 'join_keys', but has class 'list'"
   )
 })