239 utilize logger::log_shiny_input_change

.pre-commit-config.yaml

@@ -24,6 +24,7 @@ repos:
           - forcats
           - bioc::hermes
           - lifecycle
+          - logger
           - bioc::MultiAssayExperiment
           - rtables
           - S4Vectors

DESCRIPTION

@@ -40,6 +40,7 @@ Imports:
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
+    logger (>= 0.3.0),
     MultiAssayExperiment,
     rtables (>= 0.5.1),
     S4Vectors,
@@ -60,7 +61,6 @@ Suggests:
     dplyr,
     globals,
     knitr,
-    logger (>= 0.2.0),
     matrixStats,
     R6,
     rmarkdown,

NEWS.md

@@ -8,6 +8,7 @@
 ### Enhancements
 
 * Updated the documentation and vignettes with the new way of specifying data for `teal::init()`. The `data` argument accepts `teal_data` object.
+* Added `logger` functionality for logging changes in shiny inputs in all modules. `logger` was added to Imports.
 
 # teal.modules.hermes 0.1.5
 

R/adtteSpec.R

@@ -263,6 +263,7 @@ adtteSpecServer <- function(id, # nolint
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     # Join ADTTE with gene data.
     adtte_joined <- reactive({
       experiment_data <- experiment_data()

R/assaySpec.R

@@ -106,6 +106,7 @@ assaySpecServer <- function(id, # nolint
   assert_character(exclude_assays, any.missing = FALSE)
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     # When the assay names change, update the choices for assay.
     choices <- reactive({
       assays <- assays()

R/barplot.R

@@ -132,6 +132,7 @@ srv_g_barplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
   assert_flag(.test)
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/boxplot.R

@@ -128,6 +128,7 @@ srv_g_boxplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/experimentSpec.R

@@ -221,6 +221,7 @@ experimentSpecServer <- function(id, # nolint
   assert_flag(with_mae_col_data)
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     # When the filtered data set of the chosen experiment changes, update the
     # experiment data object.
     data_return <- reactive({

R/forestplot.R

@@ -155,6 +155,7 @@ srv_g_forest_tte <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/geneSpec.R

@@ -300,6 +300,7 @@ geneSpecServer <- function(id, # nolint
   assert_character(label_modal_footer)
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     # The `reactiveValues` object for storing current gene text input.
     # This will also be a data frame with id and name columns.
     parsed_genes <- reactiveVal(NULL, label = "Parsed genes")

R/km.R

@@ -159,6 +159,7 @@ srv_g_km <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/pca.R

@@ -168,6 +168,7 @@ srv_g_pca <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/quality.R

@@ -211,6 +211,7 @@ srv_g_quality <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/sampleVarSpec.R

@@ -288,6 +288,7 @@ sampleVarSpecServer <- function(id, # nolint
   assert_string(label_modal_title)
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     to_observe <- reactive({
       list(experiment_name(), original_data())
     })

R/scatterplot.R

@@ -130,6 +130,7 @@ srv_g_scatterplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })

R/volcanoplot.R

@@ -116,6 +116,7 @@ srv_g_volcanoplot <- function(id,
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
 
   moduleServer(id, function(input, output, session) {
+    if (shiny::isRunning()) logger::log_shiny_input_changes(input, namespace = "teal.modules.hermes")
     output$experiment_ui <- renderUI({
       experimentSpecInput(session$ns("experiment"), data, mae_name)
     })