Fix merge conflicts

Merge commit '8c143f108778c5a03364747d5f6b6aaac5a252d7'

#Conflicts:
#	tests/testthat/test-module_teal.R

.github/workflows/check.yaml

@@ -50,6 +50,9 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+
   r-cmd-non-cran:
     name: R CMD Check (non-CRAN) 🧬
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
@@ -79,6 +82,9 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
+
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -95,6 +101,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️
@@ -114,6 +122,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main

.github/workflows/docs.yaml

@@ -50,3 +50,5 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer

.github/workflows/release.yaml

@@ -24,6 +24,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   validation:
     name: R Package Validation report 📃
     needs: release
@@ -39,6 +41,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   release:
     name: Create release 🎉
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
@@ -71,6 +75,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   coverage:
     name: Coverage 📔
     needs: [release, docs]
@@ -88,6 +94,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   wasm:
     name: Build WASM packages 🧑‍🏭
     needs: release

.github/workflows/scheduled.yaml

@@ -64,6 +64,8 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer
   rhub:
     if: >
       github.event_name == 'schedule' || (
@@ -80,3 +82,5 @@ jobs:
         insightsengineering/teal.logger
         insightsengineering/teal.reporter
         insightsengineering/teal.widgets
+        insightsengineering/rtables
+        insightsengineering/rtables.officer

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal
 Title: Exploratory Web Apps for Analyzing Clinical Trials Data
-Version: 0.15.2.9086
-Date: 2024-11-15
+Version: 0.15.2.9089
+Date: 2024-11-20
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
@@ -38,7 +38,7 @@ Depends:
     R (>= 4.0),
     shiny (>= 1.8.1),
     teal.data (>= 0.6.0.9017),
-    teal.slice (>= 0.5.1.9009)
+    teal.slice (>= 0.5.1.9015)
 Imports:
     checkmate (>= 2.1.0),
     crayon,

NEWS.md

@@ -1,4 +1,4 @@
-# teal 0.15.2.9086
+# teal 0.15.2.9089
 
 ### New features
 
@@ -8,6 +8,7 @@
 * Possibility to download lockfile to restore app session for reproducibility. #479
 * Introduced a function `set_datanames()` to change a `datanames` of the `teal_module`.
 * Datasets which name starts with `.` are ignored when `module`'s `datanames` is set as `"all"`.
+* Added warning when reserved `datanames`, such as `all` and `.raw_data` are being used. 
 
 ### Breaking changes
 

R/utils.R

@@ -134,31 +134,58 @@ check_modules_datanames <- function(modules, datanames) {
 }
 
 #' @rdname check_modules_datanames
-check_modules_datanames_html <- function(modules,
-                                         datanames) {
+check_reserved_datanames <- function(datanames) {
+  reserved_datanames <- datanames[datanames %in% c("all", ".raw_data")]
+  if (length(reserved_datanames) == 0L) {
+    return(NULL)
+  }
+
+  tags$span(
+    to_html_code_list(reserved_datanames),
+    sprintf(
+      "%s reserved for internal use. Please avoid using %s as %s.",
+      pluralize(reserved_datanames, "is", "are"),
+      pluralize(reserved_datanames, "it", "them"),
+      pluralize(reserved_datanames, "a dataset name", "dataset names")
+    )
+  )
+}
+
+#' @rdname check_modules_datanames
+check_modules_datanames_html <- function(modules, datanames) {
   check_datanames <- check_modules_datanames_recursive(modules, datanames)
   show_module_info <- inherits(modules, "teal_modules") # used in two contexts - module and app
+
+  reserved_datanames <- check_reserved_datanames(datanames)
+
   if (!length(check_datanames)) {
-    return(TRUE)
+    out <- if (is.null(reserved_datanames)) {
+      TRUE
+    } else {
+      shiny::tagList(reserved_datanames)
+    }
+    return(out)
   }
   shiny::tagList(
+    reserved_datanames,
     lapply(
       check_datanames,
       function(mod) {
         tagList(
           tags$span(
-            tags$span(if (length(mod$missing_datanames) == 1) "Dataset" else "Datasets"),
+            tags$span(pluralize(mod$missing_datanames, "Dataset")),
             to_html_code_list(mod$missing_datanames),
             tags$span(
-              paste0(
-                if (length(mod$missing_datanames) > 1) "are missing" else "is missing",
-                if (show_module_info) sprintf(" for module '%s'.", mod$label) else "."
+              sprintf(
+                "%s missing%s.",
+                pluralize(mod$missing_datanames, "is", "are"),
+                if (show_module_info) sprintf(" for module '%s'", mod$label) else ""
               )
             )
           ),
           if (length(datanames) >= 1) {
             tagList(
-              tags$span(if (length(datanames) == 1) "Dataset" else "Datasets"),
+              tags$span(pluralize(datanames, "Dataset")),
               tags$span("available in data:"),
               tagList(
                 tags$span(
@@ -382,7 +409,7 @@ paste_datanames_character <- function(x,
       tagList(
         tags$code(x[.ix]),
         if (.ix != length(x)) {
-          tags$span(ifelse(.ix == length(x) - 1, " and ", ", "))
+          tags$span(if (.ix == length(x) - 1) " and " else ", ")
         }
       )
     })
@@ -400,17 +427,18 @@ build_datanames_error_message <- function(label = NULL,
                                           tags = list(span = shiny::tags$span, code = shiny::tags$code),
                                           tagList = shiny::tagList) { # nolint: object_name.
   tags$span(
-    tags$span(ifelse(length(extra_datanames) > 1, "Datasets", "Dataset")),
+    tags$span(pluralize(extra_datanames, "Dataset")),
     paste_datanames_character(extra_datanames, tags, tagList),
     tags$span(
-      paste0(
-        ifelse(length(extra_datanames) > 1, "are missing", "is missing"),
-        ifelse(is.null(label), ".", sprintf(" for tab '%s'.", label))
+      sprintf(
+        "%s missing%s",
+        pluralize(extra_datanames, "is", "are"),
+        if (is.null(label)) "" else sprintf(" for tab '%s'", label)
       )
     ),
     if (length(datanames) >= 1) {
       tagList(
-        tags$span(ifelse(length(datanames) > 1, "Datasets", "Dataset")),
+        tags$span(pluralize(datanames, "Dataset")),
         tags$span("available in data:"),
         tagList(
           tags$span(
@@ -445,3 +473,26 @@ build_datanames_error_message <- function(label = NULL,
     }
   )
 }
+
+#' Pluralize a word depending on the size of the input
+#'
+#' @param x (`object`) to check length for plural.
+#' @param singular (`character`) singular form of the word.
+#' @param plural (optional `character`) plural form of the word. If not given an "s"
+#' is added to the singular form.
+#'
+#' @return A `character` that correctly represents the size of the `x` argument.
+#' @keywords internal
+pluralize <- function(x, singular, plural = NULL) {
+  checkmate::assert_string(singular)
+  checkmate::assert_string(plural, null.ok = TRUE)
+  if (length(x) == 1L) { # Zero length object should use plural form.
+    singular
+  } else {
+    if (is.null(plural)) {
+      sprintf("%ss", singular)
+    } else {
+      plural
+    }
+  }
+}

tests/testthat/test-init.R

@@ -108,6 +108,33 @@ testthat::test_that(
   }
 )
 
+testthat::describe("init throws warning when datanames in modules has reserved name", {
+  testthat::it("`all`", {
+    testthat::expect_warning(
+      init(
+        data = teal.data::teal_data(all = mtcars),
+        modules = list(example_module())
+      ),
+      "`all` is reserved for internal use\\. Please avoid using it as a dataset name\\."
+    )
+  })
+
+  testthat::it("`.raw_data` and `all`", {
+    td <-
+      testthat::expect_warning(
+        init(
+          data = teal.data::teal_data(
+            all = mtcars,
+            .raw_data = iris,
+            join_keys = teal.data::join_keys(teal.data::join_key(".raw_data", "all", "a_key"))
+          ),
+          modules = list(example_module())
+        ),
+        "`.raw_data` and `all` are reserved for internal use\\. Please avoid using them as dataset names\\."
+      )
+  })
+})
+
 testthat::test_that("init throws when dataname in filter incompatible w/ datanames in data", {
   testthat::expect_warning(
     init(