register teal.logger handlers (#628)

close insightsengineering/coredev-tasks#502 test with insightsengineering/teal.logger#73 As a bonus, we can safely move `logger` to suggests (it's still used in tests) --------- Signed-off-by: Pawel Rucki <[email protected]>
insightsengineering · Mar 20, 2024 · 2892295 · 2892295
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -35,7 +35,6 @@ Imports:
     DT (>= 0.13),
     forcats (>= 1.0.0),
     grid,
-    logger (>= 0.2.0),
     scales,
     shinyjs,
     shinyTree (>= 0.2.8),
@@ -45,7 +44,7 @@ Imports:
     stringr (>= 1.4.1),
     teal.code (>= 0.5.0),
     teal.data (>= 0.5.0),
-    teal.logger (>= 0.1.1),
+    teal.logger (>= 0.1.3.9013),
     teal.reporter (>= 0.3.0),
     teal.widgets (>= 0.4.0),
     tern (>= 0.9.3),
@@ -66,6 +65,7 @@ Suggests:
     jsonlite,
     knitr (>= 1.42),
     lattice (>= 0.18-4),
+    logger (>= 0.2.0),
     MASS,
     nestcolor (>= 0.1.0),
     rlang (>= 1.0.0),
@@ -78,7 +78,7 @@ VignetteBuilder:
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, insightsengineering/teal,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
-    rstudio/DT, tidyverse/forcats, daroczig/logger, r-lib/scales,
+    rstudio/DT, tidyverse/forcats, r-lib/scales,
     daattali/shinyjs, shinyTree/shinyTree, rstudio/shinyvalidate,
     dreamRs/shinyWidgets, tidyverse/stringr,
     insightsengineering/teal.code, insightsengineering/teal.data,
@@ -87,7 +87,7 @@ Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     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,
+    jeroen/jsonlite, yihui/knitr, deepayan/lattice, daroczig/logger, MASS,
     insightsengineering/nestcolor, r-lib/rlang,
     insightsengineering/rtables, sparkline, insightsengineering/teal.data,
     r-lib/testthat, r-lib/withr

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
@@ -105,7 +105,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
                      size = c(2, 1, 8),
                      pre_output = NULL,
                      post_output = NULL) {
-  logger::log_info("Initializing tm_a_pca")
+  message("Initializing tm_a_pca")
 
   # Normalize the parameters
   if (inherits(dat, "data_extract_spec")) dat <- list(dat)

diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R
@@ -150,7 +150,7 @@ tm_a_regression <- function(label = "Regression Analysis",
                             default_plot_type = 1,
                             default_outlier_label = "USUBJID",
                             label_segment_threshold = c(0.5, 0, 10)) {
-  logger::log_info("Initializing tm_a_regression")
+  message("Initializing tm_a_regression")
 
   # Normalize the parameters
   if (inherits(regressor, "data_extract_spec")) regressor <- list(regressor)

diff --git a/R/tm_data_table.R b/R/tm_data_table.R
@@ -90,7 +90,7 @@ tm_data_table <- function(label = "Data Table",
                           server_rendering = FALSE,
                           pre_output = NULL,
                           post_output = NULL) {
-  logger::log_info("Initializing tm_data_table")
+  message("Initializing tm_data_table")
 
   # Start of assertions
   checkmate::assert_string(label)

diff --git a/R/tm_file_viewer.R b/R/tm_file_viewer.R
@@ -41,7 +41,7 @@
 #'
 tm_file_viewer <- function(label = "File Viewer Module",
                            input_path = list("Current Working Directory" = ".")) {
-  logger::log_info("Initializing tm_file_viewer")
+  message("Initializing tm_file_viewer")
 
   # Normalize the parameters
   if (length(label) == 0 || identical(label, "")) label <- " "

diff --git a/R/tm_front_page.R b/R/tm_front_page.R
@@ -67,7 +67,7 @@ tm_front_page <- function(label = "Front page",
                           additional_tags = tagList(),
                           footnotes = character(0),
                           show_metadata = FALSE) {
-  logger::log_info("Initializing tm_front_page")
+  message("Initializing tm_front_page")
 
   # Start of assertions
   checkmate::assert_string(label)

diff --git a/R/tm_g_association.R b/R/tm_g_association.R
@@ -132,7 +132,7 @@ tm_g_association <- function(label = "Association",
                              pre_output = NULL,
                              post_output = NULL,
                              ggplot2_args = teal.widgets::ggplot2_args()) {
-  logger::log_info("Initializing tm_g_association")
+  message("Initializing tm_g_association")
 
   # Normalize the parameters
   if (inherits(ref, "data_extract_spec")) ref <- list(ref)

diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
@@ -193,7 +193,7 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
                            ggplot2_args = teal.widgets::ggplot2_args(),
                            pre_output = NULL,
                            post_output = NULL) {
-  logger::log_info("Initializing tm_g_bivariate")
+  message("Initializing tm_g_bivariate")
 
   # Normalize the parameters
   if (inherits(x, "data_extract_spec")) x <- list(x)

diff --git a/R/tm_g_distribution.R b/R/tm_g_distribution.R
@@ -119,7 +119,7 @@ tm_g_distribution <- function(label = "Distribution Module",
                               plot_width = NULL,
                               pre_output = NULL,
                               post_output = NULL) {
-  logger::log_info("Initializing tm_g_distribution")
+  message("Initializing tm_g_distribution")
 
   # Requires Suggested packages
   extra_packages <- c("ggpmisc", "ggpp", "goftest", "MASS", "broom")

diff --git a/R/tm_g_response.R b/R/tm_g_response.R
@@ -151,7 +151,7 @@ tm_g_response <- function(label = "Response Plot",
                           ggplot2_args = teal.widgets::ggplot2_args(),
                           pre_output = NULL,
                           post_output = NULL) {
-  logger::log_info("Initializing tm_g_response")
+  message("Initializing tm_g_response")
 
   # Normalize the parameters
   if (inherits(response, "data_extract_spec")) response <- list(response)

diff --git a/R/tm_g_scatterplot.R b/R/tm_g_scatterplot.R
@@ -227,7 +227,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
                              post_output = NULL,
                              table_dec = 4,
                              ggplot2_args = teal.widgets::ggplot2_args()) {
-  logger::log_info("Initializing tm_g_scatterplot")
+  message("Initializing tm_g_scatterplot")
 
   # Requires Suggested packages
   extra_packages <- c("ggpmisc", "ggExtra", "colourpicker")

diff --git a/R/tm_g_scatterplotmatrix.R b/R/tm_g_scatterplotmatrix.R
@@ -162,7 +162,7 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
                                    plot_width = NULL,
                                    pre_output = NULL,
                                    post_output = NULL) {
-  logger::log_info("Initializing tm_g_scatterplotmatrix")
+  message("Initializing tm_g_scatterplotmatrix")
 
   # Requires Suggested packages
   if (!requireNamespace("lattice", quietly = TRUE)) {

diff --git a/R/tm_missing_data.R b/R/tm_missing_data.R
@@ -89,7 +89,7 @@ tm_missing_data <- function(label = "Missing data",
                             ),
                             pre_output = NULL,
                             post_output = NULL) {
-  logger::log_info("Initializing tm_missing_data")
+  message("Initializing tm_missing_data")
 
   # Requires Suggested packages
   if (!requireNamespace("gridExtra", quietly = TRUE)) {

diff --git a/R/tm_outliers.R b/R/tm_outliers.R
@@ -131,7 +131,7 @@ tm_outliers <- function(label = "Outliers Module",
                         plot_width = NULL,
                         pre_output = NULL,
                         post_output = NULL) {
-  logger::log_info("Initializing tm_outliers")
+  message("Initializing tm_outliers")
 
   # Normalize the parameters
   if (inherits(outlier_var, "data_extract_spec")) outlier_var <- list(outlier_var)

diff --git a/R/tm_t_crosstable.R b/R/tm_t_crosstable.R
@@ -138,7 +138,7 @@ tm_t_crosstable <- function(label = "Cross Table",
                             pre_output = NULL,
                             post_output = NULL,
                             basic_table_args = teal.widgets::basic_table_args()) {
-  logger::log_info("Initializing tm_t_crosstable")
+  message("Initializing tm_t_crosstable")
 
   # Requires Suggested packages
   if (!requireNamespace("rtables", quietly = TRUE)) {

diff --git a/R/tm_variable_browser.R b/R/tm_variable_browser.R
@@ -76,7 +76,7 @@ tm_variable_browser <- function(label = "Variable Browser",
                                 pre_output = NULL,
                                 post_output = NULL,
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
-  logger::log_info("Initializing tm_variable_browser")
+  message("Initializing tm_variable_browser")
 
   # Requires Suggested packages
   if (!requireNamespace("sparkline", quietly = TRUE)) {

diff --git a/R/zzz.R b/R/zzz.R
@@ -1,5 +1,6 @@
 .onLoad <- function(libname, pkgname) {
   teal.logger::register_logger(namespace = "teal.modules.general")
+  teal.logger::register_handlers("teal.modules.general")
 }
 
 ### global variables

diff --git a/tests/testthat/helper-functions.R b/tests/testthat/helper-functions.R
@@ -1,13 +1,3 @@
-local_logger_threshold <- function(threshold, envir = parent.frame()) {
-  old <- logger::log_threshold(namespace = "teal.modules.general")
-
-  # Equivalent to withr::defer
-  thunk <- as.call(list(function() logger::log_threshold(old, namespace = "teal.modules.general")))
-  do.call(base::on.exit, list(thunk, TRUE, FALSE), envir = envir)
-  logger::log_threshold(threshold, namespace = "teal.modules.general")
-  invisible(old)
-}
-
 # Create a mock data extact spec for tests
 mock_data_extract_spec <- function(dataname = "MOCK_DATASET",
                                    select_choices = sample(LETTERS, sample(2:10, 1)),

diff --git a/tests/testthat/test-tm_g_bivariate.R b/tests/testthat/test-tm_g_bivariate.R
@@ -1,6 +1,4 @@
 testthat::test_that("tm_g_bivariate creates a `teal_module` object", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_s3_class(
     tm_g_bivariate(
       "a label",
@@ -23,8 +21,6 @@ testthat::test_that("tm_g_bivariate creates a `teal_module` object", {
 })
 
 testthat::test_that("tm_g_bivariate creates a `teal_module` object with default options", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_s3_class(
     tm_g_bivariate(
       "a label",
@@ -36,8 +32,6 @@ testthat::test_that("tm_g_bivariate creates a `teal_module` object with default
 })
 
 testthat::test_that("tm_g_bivariate creates a `teal_module` object with multiple data extract specs", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_s3_class(
     tm_g_bivariate(
       "a label",
@@ -51,8 +45,6 @@ testthat::test_that("tm_g_bivariate creates a `teal_module` object with multiple
 })
 
 testthat::test_that("tm_g_bivariate creates a module with datanames taken from data extracts", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   mod <- tm_g_bivariate(
     "a label",
     list(
@@ -71,8 +63,6 @@ testthat::test_that("tm_g_bivariate creates a module with datanames taken from d
 # Test `x` and `y` arguments with invalid data_extract_spec
 
 testthat::test_that("tm_g_bivariate fails when `x` contains a spec with multiple selection", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -86,8 +76,6 @@ testthat::test_that("tm_g_bivariate fails when `x` contains a spec with multiple
 })
 
 testthat::test_that("tm_g_bivariate fails when `x` contains multiple spec with (at least one ) multiple selection", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -102,8 +90,6 @@ testthat::test_that("tm_g_bivariate fails when `x` contains multiple spec with (
 })
 
 testthat::test_that("tm_g_bivariate fails when `x` contains multiple spec with (at least one ) multiple selection", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -118,8 +104,6 @@ testthat::test_that("tm_g_bivariate fails when `x` contains multiple spec with (
 })
 
 testthat::test_that("tm_g_bivariate fails when `y` contains multiple spec with (at least one ) multiple selection", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -136,8 +120,6 @@ testthat::test_that("tm_g_bivariate fails when `y` contains multiple spec with (
 # Test `plot_height` and `plot_width` arguments
 
 testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -150,8 +132,6 @@ testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
 })
 
 testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -164,8 +144,6 @@ testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
 })
 
 testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -178,8 +156,6 @@ testthat::test_that("tm_g_bivariate fails when `plot_height` is not valid", {
 })
 
 testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -192,8 +168,6 @@ testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
 })
 
 testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -206,8 +180,6 @@ testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
 })
 
 testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -222,8 +194,6 @@ testthat::test_that("tm_g_bivariate fails when `plot_width` is not valid", {
 # Test `color_settings` argument
 
 testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `color` is supplied", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -237,8 +207,6 @@ testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `col
 })
 
 testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `size` is supplied", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -252,8 +220,6 @@ testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `siz
 })
 
 testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `fill` is supplied", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   testthat::expect_error(
     tm_g_bivariate(
       "a label",
@@ -267,8 +233,6 @@ testthat::test_that("tm_g_bivariate fails when `color_setting` is FALSE and `fil
 })
 
 testthat::test_that("tm_g_bivariate determines `color`, `size` and `fill` when `color_setting` is TRUE", {
-  local_logger_threshold(logger::FATAL) # Suppress logger messages
-
   mod <- tm_g_bivariate(
     "a label",
     mock_data_extract_spec(select_multiple = FALSE),