Merge branch 'main' into 546-fix-verdepcheck@main

Signed-off-by: André Veríssimo <[email protected]>

.pre-commit-config.yaml

@@ -24,7 +24,6 @@ repos:
           - dplyr
           - DT
           - forcats
-          - ggrepel
           - grid
           - logger
           - scales

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.3.0.9030
-Date: 2024-05-10
+Version: 0.3.0.9034
+Date: 2024-05-16
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -35,6 +35,7 @@ Imports:
     DT (>= 0.13),
     forcats (>= 1.0.0),
     grid,
+    logger (>= 0.3.0),
     scales,
     shinyjs,
     shinyTree (>= 0.2.8),
@@ -65,8 +66,7 @@ Suggests:
     jsonlite,
     knitr (>= 1.42),
     lattice (>= 0.18-4),
-    logger (>= 0.2.0),
-    MASS,
+    MASS
     nestcolor (>= 0.1.0),
     pkgload,
     rlang (>= 1.0.0),
@@ -82,16 +82,16 @@ VignetteBuilder:
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, insightsengineering/teal,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
-    rstudio/DT, tidyverse/forcats, r-lib/scales, daattali/shinyjs,
-    shinyTree/shinyTree, rstudio/shinyvalidate, dreamRs/shinyWidgets,
-    tidyverse/stringr, insightsengineering/teal.code,
-    insightsengineering/teal.data, insightsengineering/teal.logger,
-    insightsengineering/teal.reporter, insightsengineering/teal.widgets,
-    insightsengineering/tern, tidyverse/tibble, tidyverse/tidyr,
-    tidymodels/broom, daattali/colourpicker, daattali/ggExtra,
-    aphalo/ggpmisc, aphalo/ggpp, slowkow/ggrepel, baddstats/goftest,
-    gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite, yihui/knitr,
-    deepayan/lattice, daroczig/logger, MASS,
+    rstudio/DT, tidyverse/forcats, daroczig/logger, r-lib/scales,
+    daattali/shinyjs, shinyTree/shinyTree, rstudio/shinyvalidate,
+    dreamRs/shinyWidgets, tidyverse/stringr,
+    insightsengineering/teal.code, insightsengineering/teal.data,
+    insightsengineering/teal.logger, insightsengineering/teal.reporter,
+    insightsengineering/teal.widgets, insightsengineering/tern,
+    tidyverse/tibble, tidyverse/tidyr, tidymodels/broom,
+    daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
+    slowkow/ggrepel, baddstats/goftest, gridExtra, ramnathv/htmlwidgets,
+    jeroen/jsonlite, yihui/knitr, deepayan/lattice, MASS,
     insightsengineering/nestcolor, r-lib/rlang, rstudio/rmarkdown,
     insightsengineering/rtables, tidyverse/rvest, sparkline,
     rstudio/shinytest2, insightsengineering/teal.data, r-lib/testthat,

NEWS.md

@@ -1,7 +1,10 @@
-# teal.modules.general 0.3.0.9030
+# teal.modules.general 0.3.0.9034
 
 * Removed `Show Warnings` modals from modules.
 
+### Enhancements
+* Added `logger` functionality for logging changes in shiny inputs in all modules. `logger` was added to Imports.
+
 # teal.modules.general 0.3.0
 
 ### Enhancements
@@ -38,6 +41,7 @@
 * Removed `scda` package dependency from examples.
 * Replaced deprecated `ggplot2` functions `..count..`, `..density..` and `..prop..`.
 * Version bump on `forcats` dependency.
+* Replaced `scda` data generation functions with `random.cdisc.data`
 
 # teal.modules.general 0.2.15
 

R/tm_a_pca.R

@@ -297,6 +297,8 @@ srv_a_pca <- function(id, data, reporter, filter_panel_api, dat, plot_height, pl
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     response <- dat
 
     for (i in seq_along(response)) {

R/tm_a_regression.R

@@ -371,6 +371,8 @@ srv_a_regression <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     rule_rvr1 <- function(value) {

R/tm_data_table.R

@@ -182,6 +182,8 @@ srv_page_data_table <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     if_filtered <- reactive(as.logical(input$if_filtered))
     if_distinct <- reactive(as.logical(input$if_distinct))
 

R/tm_file_viewer.R

@@ -124,6 +124,8 @@ ui_viewer <- function(id, ...) {
 # Server function for the file viewer module
 srv_viewer <- function(id, input_path) {
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     temp_dir <- tempfile()
     if (!dir.exists(temp_dir)) {
       dir.create(temp_dir, recursive = TRUE)

R/tm_front_page.R

@@ -137,6 +137,8 @@ srv_front_page <- function(id, data, tables, show_metadata) {
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     setBookmarkExclude("metadata_button")

R/tm_g_association.R

@@ -285,6 +285,8 @@ srv_tm_g_association <- function(id,
   checkmate::assert_class(isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(ref = ref, vars = vars),
       datasets = data,

R/tm_g_bivariate.R

@@ -459,6 +459,8 @@ srv_g_bivariate <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     data_extract <- list(

R/tm_g_distribution.R

@@ -356,6 +356,8 @@ srv_distribution <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     setBookmarkExclude("params_reset")
 
     ns <- session$ns

R/tm_g_response.R

@@ -313,6 +313,8 @@ srv_g_response <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     data_extract <- list(response = response, x = x, row_facet = row_facet, col_facet = col_facet)
 
     rule_diff <- function(other) {

R/tm_g_scatterplot.R

@@ -494,6 +494,8 @@ srv_g_scatterplot <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     data_extract <- list(
       x = x,
       y = y,

R/tm_g_scatterplotmatrix.R

@@ -266,6 +266,8 @@ srv_g_scatterplotmatrix <- function(id, data, reporter, filter_panel_api, variab
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(variables = variables),
       datasets = data,

R/tm_missing_data.R

@@ -170,6 +170,8 @@ srv_page_missing_data <- function(id, data, reporter, filter_panel_api, parent_d
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     datanames <- isolate(teal.data::datanames(data()))
     datanames <- Filter(function(name) {
       is.data.frame(isolate(data())[[name]])

R/tm_outliers.R

@@ -332,6 +332,8 @@ srv_outliers <- function(id, data, reporter, filter_panel_api, outlier_var,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     ns <- session$ns
 
     vars <- list(outlier_var = outlier_var, categorical_var = categorical_var)

R/tm_t_crosstable.R

@@ -241,6 +241,8 @@ srv_t_crosstable <- function(id, data, reporter, filter_panel_api, label, x, y,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     selector_list <- teal.transform::data_extract_multiple_srv(
       data_extract = list(x = x, y = y),
       datasets = data,

R/tm_variable_browser.R

@@ -201,6 +201,8 @@ srv_variable_browser <- function(id,
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(isolate(data()), "teal_data")
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.general")
+
     # if there are < this number of unique records then a numeric
     # variable can be treated as a factor and all factors with < this groups
     # have their values plotted

data-raw/data.R

@@ -1,16 +1,15 @@
 ## code to prepare `data` for testing examples
-library(scda)
-rADAE <- synthetic_cdisc_data("latest")$adae
+rADAE <- random.cdisc.data::cadae
 usethis::use_data(rADAE)
 
-rADLB <- synthetic_cdisc_data("latest")$adlb
+rADLB <- random.cdisc.data::cadlb
 usethis::use_data(rADLB)
 
-rADRS <- synthetic_cdisc_data("latest")$adrs
+rADRS <- random.cdisc.data::cadrs
 usethis::use_data(rADRS)
 
-rADSL <- synthetic_cdisc_data("latest")$adsl
+rADSL <- random.cdisc.data::cadsl
 usethis::use_data(rADSL)
 
-rADTTE <- synthetic_cdisc_data("latest")$adtte
+rADTTE <- random.cdisc.data::cadtte
 usethis::use_data(rADTTE)

tests/testthat/test-shinytest2-tm_file_viewer.R

@@ -1,3 +1,5 @@
+nest_logo_url <- "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png"
+
 app_driver_tm_file_viewer <- function() {
   init_teal_app_driver(
     data = simple_teal_data(),
@@ -7,7 +9,7 @@ app_driver_tm_file_viewer <- function() {
         folder = system.file("sample_files", package = "teal.modules.general"),
         png = system.file("sample_files/sample_file.png", package = "teal.modules.general"),
         txt = system.file("sample_files/sample_file.txt", package = "teal.modules.general"),
-        url = "https://fda.gov/files/drugs/published/Portable-Document-Format-Specifications.pdf"
+        url = nest_logo_url
       )
     ),
     timeout = 3000
@@ -84,9 +86,9 @@ test_that("e2e - tm_file_viewer: Shows selected url", {
   app_driver$click(selector = "[id= '6_anchor']")
   testthat::expect_true(app_driver$is_visible(selector = app_driver$active_module_element("output")))
 
-  testthat::expect_match(
+  testthat::expect_equal(
     attr(app_driver$get_active_module_input("tree")$url, "ancestry"),
-    "pdf$"
+    nest_logo_url
   )
 
   app_driver$stop()

tests/testthat/test-shinytest2-tm_misssing_data.R

@@ -1,7 +1,6 @@
 app_driver_tm_missing_data <- function() {
   data <- within(simple_teal_data(), {
     set.seed(123)
-    require(nestcolor)
 
     add_nas <- function(x) {
       x[sample(seq_along(x), floor(length(x) * runif(1, .05, .17)))] <- NA