merge main

Merge branch 'main' into remove_backticks_cdisc@main

# Conflicts:
#	R/default_cdisc_join_keys.R
#	man/build_cdisc_join_keys.Rd
#	man/default_cdisc_join_keys.Rd

DESCRIPTION

@@ -1,13 +1,16 @@
 Type: Package
 Package: teal.data
 Title: Data Model for 'teal' Applications
-Version: 0.3.0.9042
-Date: 2024-01-24
+Version: 0.4.0.9001
+Date: 2024-02-02
 Authors@R: c(
-    person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
-    person("Aleksander", "Chlebowski", , "[email protected]", role = "aut"),
+    person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-9533-457X")),
+    person("Aleksander", "Chlebowski", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0001-5018-6294")),
     person("Marcin", "Kosinski", , "[email protected]", role = "aut"),
-    person("Andre", "Verissimo", , "[email protected]", role = "aut"),
+    person("Andre", "Verissimo", , "[email protected]", role = "aut",
+           comment = c(ORCID = "0000-0002-2212-339X")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
     person("Mahmoud", "Hallal", , "[email protected]", role = "aut"),
     person("Nikolas", "Burkoff", role = "aut"),
@@ -18,8 +21,8 @@ Authors@R: c(
     person("Dony", "Unardi", , "[email protected]", role = "rev"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
-Description: Utilities for data transformations compatible with 'teal'
-    applications.
+Description: Provides a 'teal_data' class as a unified data model for
+    'teal' applications focusing on reproducibility and relational data.
 License: Apache License 2.0
 URL: https://insightsengineering.github.io/teal.data/,
     https://github.com/insightsengineering/teal.data/
@@ -33,8 +36,7 @@ Imports:
     methods,
     rlang (>= 1.1.0),
     stats,
-    utils,
-    yaml
+    utils
 Suggests:
     knitr (>= 1.42),
     rmarkdown (>= 2.19),
@@ -44,18 +46,17 @@ VignetteBuilder:
 RdMacros:
     lifecycle
 Config/Needs/verdepcheck: mllg/checkmate, r-lib/lifecycle, r-lib/rlang,
-    yaml=vubiostat/r-yaml, yihui/knitr, rstudio/rmarkdown,
-    insightsengineering/teal.code, r-lib/testthat
+    yihui/knitr, rstudio/rmarkdown, insightsengineering/teal.code,
+    r-lib/testthat
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
-Collate: 
+Collate:
     'cdisc_data.R'
     'data.R'
-    'default_cdisc_join_keys.R'
     'formatters_var_labels.R'
     'deprecated.R'
     'dummy_function.R'

NAMESPACE

@@ -44,7 +44,6 @@ export(dataset)
 export(dataset_connector)
 export(dataset_connector_file)
 export(dataset_file)
-export(default_cdisc_join_keys)
 export(example_cdisc_data)
 export(fun_cdisc_dataset_connector)
 export(fun_dataset_connector)

NEWS.md

@@ -1,4 +1,6 @@
-# teal.data 0.3.0.9042
+# teal.data 0.4.0.9001
+
+# teal.data 0.4.0
 
 ### Enhancements
 

R/cdisc_data.R

@@ -34,6 +34,6 @@
 cdisc_data <- function(...,
                        join_keys = teal.data::default_cdisc_join_keys[names(rlang::list2(...))],
                        code = character(0),
-                       check = FALSE) {
+                       check) {
   teal_data(..., join_keys = join_keys, code = code, check = check)
 }

R/data.R

@@ -80,3 +80,13 @@
 #' @source internal
 #' @name rADVS
 "rADVS"
+
+#' List containing default joining keys for `CDISC` datasets
+#'
+#' This data object is created at loading time from `cdisc_datasets/cdisc_datasets.yaml`.
+#'
+#' @name default_cdisc_join_keys
+#' @usage default_cdisc_join_keys
+#' @docType data
+#' @source internal
+"default_cdisc_join_keys"

R/deprecated.R

@@ -17,7 +17,7 @@ NULL
 
 .deprecate_function <- function(what, details) {
   lifecycle::deprecate_stop(
-    when = "0.3.1",
+    when = "0.4.0",
     what = what,
     details = details
   )
@@ -338,7 +338,7 @@ get_join_keys <- function(...) {
 #' `r lifecycle::badge("deprecated")`
 #'
 #' In previous versions of `teal.data` labels were managed with `get_labels()`.
-#' This function is deprecated as of `0.3.1`, use `col_labels` instead.
+#' This function is deprecated as of `0.4.0`, use `col_labels` instead.
 #' @export
 get_labels <- function(...) {
   .deprecate_function("get_labels()", "Use col_labels(data)")

R/teal_data.R

@@ -15,9 +15,8 @@
 #' @param code (`character`, `language`) optional code to reproduce the datasets provided in `...`.
 #'  Note this code is not executed and the `teal_data` may not be reproducible
 #'
-#' @param check (`logical`) reproducibility check - whether to perform a check that the pre-processing
-#'  code included in the object definitions actually produces those objects.
-#'  If `check` is true and preprocessing code is empty an error will be thrown.
+#' @param check (`logical`) `r lifecycle::badge("deprecated")`
+#'  Use [verify()] to verify code reproducibility .
 #'
 #' @return A `teal_data` object.
 #'
@@ -29,11 +28,21 @@
 teal_data <- function(...,
                       join_keys = teal.data::join_keys(),
                       code = character(0),
-                      check = FALSE) {
+                      check) {
   data_objects <- rlang::list2(...)
   if (inherits(join_keys, "join_key_set")) {
     join_keys <- teal.data::join_keys(join_keys)
   }
+  if (!missing(check)) {
+    lifecycle::deprecate_stop(
+      when = "0.4.0",
+      "teal_data(
+        check = 'check argument is deprecated. Use `verify()` to verify code reproducibility.
+        Find more information on https://github.com/insightsengineering/teal/discussions/945'
+      )"
+    )
+  }
+
   if (
     checkmate::test_list(
       data_objects,
@@ -42,7 +51,7 @@ teal_data <- function(...,
     )
   ) {
     lifecycle::deprecate_stop(
-      when = "0.3.1",
+      when = "0.4.0",
       "teal_data(
         data_objects = 'should use data directly. Using TealDatasetConnector and TealDataset is deprecated.
         Find more information on https://github.com/insightsengineering/teal/discussions/945'

R/utils-get_code_dependency.R

@@ -154,17 +154,27 @@ fix_shifted_comments <- function(calls) {
 #' @keywords internal
 #' @noRd
 fix_arrows <- function(calls) {
-  lapply(
-    calls,
-    function(call) {
-      call[call$token == "SYMBOL_FUNCTION_CALL" & call$text == "`<-`", c("token", "text")] <- c("LEFT_ASSIGN", "<-")
-      call[call$token == "SYMBOL_FUNCTION_CALL" & call$text == "`->`", c("token", "text")] <- c("RIGHT_ASSIGN", "->")
-      call[call$token == "SYMBOL_FUNCTION_CALL" & call$text == "`<<-`", c("token", "text")] <- c("LEFT_ASSIGN", "<-")
-      call[call$token == "SYMBOL_FUNCTION_CALL" & call$text == "`->>`", c("token", "text")] <- c("RIGHT_ASSIGN", "->")
-      call[call$token == "SYMBOL_FUNCTION_CALL" & call$text == "`=`", c("token", "text")] <- c("LEFT_ASSIGN", "<-")
-      call
-    }
+  checkmate::assert_list(calls)
+  lapply(calls, function(call) {
+    sym_fun <- call$token == "SYMBOL_FUNCTION_CALL"
+    call[sym_fun, ] <- sub_arrows(call[sym_fun, ])
+    call
+  })
+}
+
+#' Execution of assignment operator substitutions for a call.
+#' @keywords internal
+#' @noRd
+sub_arrows <- function(call) {
+  checkmate::assert_data_frame(call)
+  map <- data.frame(
+    row.names = c("`<-`", "`<<-`", "`=`"),
+    token = rep("LEFT_ASSIGN", 3),
+    text = rep("<-", 3)
   )
+  sub_ids <- call$text %in% rownames(map)
+  call[sub_ids, c("token", "text")] <- map[call$text[sub_ids], ]
+  call
 }
 
 # code_graph ----

R/zzz.R

@@ -1,20 +1,2 @@
-.onLoad <- function(libname, pkgname) {
-  # expose default CDISC dataset names
-  # copy from excel file
-  default_cdisc_keys <- yaml::yaml.load_file(
-    system.file("cdisc_datasets/cdisc_datasets.yaml", package = "teal.data")
-  )
-  assign("default_cdisc_keys", default_cdisc_keys, envir = parent.env(environment()))
-
-  # update default_cdisc_join_keys
-  assign(
-    "default_cdisc_join_keys",
-    build_cdisc_join_keys(default_cdisc_keys),
-    envir = parent.env(environment())
-  )
-
-  invisible()
-}
-
 # use non-exported function from teal.code
 lang2calls <- getFromNamespace("lang2calls", "teal.code")

data-raw/data.R

@@ -26,3 +26,25 @@ usethis::use_data(rADTTE)
 
 rADVS <- synthetic_cdisc_data("latest")$advs # nolint: object_name_linter.
 usethis::use_data(rADVS)
+
+## Code to prepare default CDISC datasets for `teal.data`
+default_cdisc_keys <- yaml::yaml.load_file(file.path("data-raw", "cdisc_datasets.yaml"))
+
+default_cdisc_join_keys <- teal.data::join_keys()
+for (name in names(default_cdisc_keys)) {
+  # Set default primary keys
+  keys_list <- default_cdisc_keys[[name]]
+
+  if (!is.null(keys_list[["primary"]])) {
+    default_cdisc_join_keys[[name]][[name]] <- keys_list[["primary"]]
+  }
+
+  if (!is.null(keys_list[["parent"]])) {
+    if (!is.null(keys_list[["foreign"]])) {
+      default_cdisc_join_keys[[name]][[keys_list[["parent"]]]] <- keys_list[["foreign"]]
+    }
+    teal.data::parents(default_cdisc_join_keys)[[name]] <- keys_list[["parent"]]
+  }
+}
+
+usethis::use_data(default_cdisc_join_keys)

inst/WORDLIST

@@ -3,6 +3,7 @@ CDISC
 Forkers
 Getter
 Hoffmann
+ORCID
 Reproducibility
 formatters
 funder