Merge pull request #35 from RMI-PACTA/logger-updates

Logger updates

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: pacta.workflow.utils
 Title: Utility functions for PACTA workflows
-Version: 0.0.0.9014
+Version: 0.0.0.9015
 Authors@R: 
     c(person(given = "Alex",
              family = "Axthelm",

tests/testthat/setup.R

@@ -0,0 +1,13 @@
+## save current settings so that we can reset later
+
+## Logger Settings
+# Set threshold to OFF, and capture previous state
+logger_threshold <- logger::log_threshold("OFF")
+
+## Tear down function
+withr::defer(
+  expr = {
+    logger::log_threshold(logger_threshold)
+  },
+  envir = teardown_env()
+)

tests/testthat/test-check_dir_writable.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 # TESTS BEGIN
 
 test_that("check_dir_writable correctly registers writable directory", {

tests/testthat/test-check_file.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("check_dir_writable correctly identifies missing files", {
   test_file <- withr::local_tempfile()
   expect_warning(

tests/testthat/test-check_io.R

@@ -1,19 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
-
 missing_file <- withr::local_tempfile()
 file_is_dir <- withr::local_tempdir()
 empty_file <- withr::local_tempfile()

tests/testthat/test-create_manifest.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("create_manifest with minimal arguments", {
   suppressWarnings({
     manifest <- create_manifest(

tests/testthat/test-export_manifest.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("export_manifest with minimal arguments", {
   manifest_file <- withr::local_tempfile(fileext = ".json")
   suppressWarnings({

tests/testthat/test-get_environment.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("get_r_session_info returns expected values", {
   expect_identical(
     get_r_session_info(),

tests/testthat/test-get_file_metadata.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 # setup
 test_time <- as.POSIXct("2020-01-01T12:34:56+00:00")
 

tests/testthat/test-get_git_info.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 # TESTS BEGIN
 test_that("get_git_info processes non-git-repo correctly", {
   test_dir <- withr::local_tempdir()

tests/testthat/test-get_individual_package_info.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 expect_package_info <- function(
   package_info,
   package_identical,

tests/testthat/test-get_package_info.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 expect_warning_if_any_pkgload <- function(object, regexp) {
   attached_pkgs <- names(utils::sessionInfo()[["otherPkgs"]])
   has_pkgload <- any(

tests/testthat/test-get_single_file_metadata.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("get_single_file_metadata processes CSV tables correctly", {
   testfile <- withr::local_tempfile(fileext = ".csv")
   write.csv(mtcars, testfile, row.names = FALSE)

tests/testthat/test-inherit_config.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("No inheritence", {
   params <- list(
     foo = 1L,

tests/testthat/test-is_git_path.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 # # TESTS BEGIN
 test_that("is_git_path processes non-existing directory correctly", {
   test_dir <- withr::local_tempdir()

tests/testthat/test-merge_lists.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 simple_list <- list(
   a = 1L,
   b = "base string",

tests/testthat/test-modify_list_element.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("modify_list_element correctly modifies a flat list", {
   test_list <- list(a = 1L, b = 2.2, c = "a")
   results <- modify_list_element(

tests/testthat/test-modify_single_list_element.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("modify_single_list_element correctly modifies a flat list", {
   test_list <- list(a = 1L, b = 2.2, c = "a")
   results <- modify_single_list_element(

tests/testthat/test-parse_params.R

@@ -1,19 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
-
 test_that("No inheritence, pass as string", {
   json_string <- '{
     "id": 1,

tests/testthat/test-parse_raw_params.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("No inheritence, no raw param validation, pass as string", {
   json_string <- '{
     "id": 1,

tests/testthat/test-un_asis.R

@@ -1,18 +1,3 @@
-## save current settings so that we can reset later
-threshold <- logger::log_threshold()
-appender  <- logger::log_appender()
-layout    <- logger::log_layout()
-on.exit({
-  ## reset logger settings
-  logger::log_threshold(threshold)
-  logger::log_layout(layout)
-  logger::log_appender(appender)
-})
-
-logger::log_appender(logger::appender_stdout)
-logger::log_threshold(logger::FATAL)
-logger::log_layout(logger::layout_simple)
-
 test_that("un_asis does not alter objects without AsIs class", {
   x <- rnorm(10L)
   results <- un_asis(x)