teal.logger: Logging Setup for the 'teal' Family of Packages

Description

Logging Setup for the teal Family of Packages.

Author(s)

Maintainer: Dawid Kaledkowski dawid.kaledkowski@roche.com

Authors:

• Konrad Pagacz

Other contributors:

• F. Hoffmann-La Roche AG [copyright holder, funder]

See Also

Useful links:

• https://insightsengineering.github.io/teal.logger/

• https://github.com/insightsengineering/teal.logger/

• Report bugs at https://github.com/insightsengineering/teal.logger/issues

Get value from environmental variable or R option or default in that order if the previous one is missing.

Description

Get value from environmental variable or R option or default in that order if the previous one is missing.

Usage

get_val(env_var_name, option_name, default = NULL)

Arguments

Value

an object of any class

Generate log layout function using common variables available via glue syntax including shiny session token

Description

Generate log layout function using common variables available via glue syntax including shiny session token

Usage

layout_teal_glue_generator(layout)

Arguments

Details

this function behaves in the same way as logger::layout_glue_generator() but allows the shiny session token (last 8 chars) to be included in the logging layout

Value

function taking level and msg arguments - keeping the original call creating the generator in the generator attribute that is returned when calling log_layout for the currently used layout

Auto logging input changes in Shiny app

Description

This is to be called in the server section of the Shiny app.

Usage

log_shiny_input_changes(
  input,
  namespace = NA_character_,
  excluded_inputs = character(),
  excluded_pattern = "_width$",
  session = shiny::getDefaultReactiveDomain()
)

Arguments

Details

Function having very similar behavior as logger::log_shiny_input_changes() but adjusted for teal needs.

Examples

## Not run: 
library(shiny)

ui <- bootstrapPage(
  numericInput("mean1", "mean1", 0),
  numericInput("mean2", "mean2", 0),
  numericInput("sd", "sd", 1),
  textInput("title", "title", "title"),
  textInput("foo", "This is not used at all, still gets logged", "foo"),
  passwordInput("password", "Password not to be logged", "secret"),
  plotOutput("plot")
)

server <- function(input, output) {
  log_shiny_input_changes(input, excluded_inputs = "password", excluded_pattern = "mean")

  output$plot <- renderPlot({
    hist(rnorm(1e3, input$mean1, input$sd), main = input$title)
  })
}

shinyApp(ui = ui, server = server)

## End(Not run)

Logs the basic information about the session.

Description

Logs the basic information about the session.

Usage

log_system_info()

Value

invisible(NULL)

Register handlers for logging messages, warnings and errors

Description

Register handlers for logging messages, warnings and errors

Usage

register_handlers(namespace, package = namespace)

Arguments

Details

This function registers global handlers for messages, warnings and errors. The handlers will investigate the call stack and if it contains a function from the package, the message, warning or error will be logged into the respective namespace.

The handlers are registered only once per package and type. Consecutive calls will no effect. Registering handlers for package base is not supported.

Use TEAL.LOG_MUFFLE environmental variable or teal.log_muffle R option to optionally control recover strategies. If TRUE (a default value) then the handler will jump to muffle restart for a given type of condition and doesn't continue (with output to the console). Applicable for message and warning types only. The errors won't be suppressed.

Value

NULL invisibly. Called for its side effects.

Note

Registering handlers is forbidden within tryCatch() or withCallingHandlers(). Because of this, handlers are registered only if it is possible.

See Also

globalCallingHandlers()

Examples

## Not run: 
register_handlers("teal.logger")
# see the outcome
globalCallingHandlers()

## End(Not run)

Registers a logger instance in a given logging namespace.

Description

Usage

register_logger(namespace = NA_character_, layout = NULL, level = NULL)

Arguments

Details

Creates a new logging namespace specified by the namespace argument. When the layout and level arguments are set to NULL (default), the function gets the values for them from system variables or R options. When deciding what to use (either argument, an R option or system variable), the function picks the first non NULL value, checking in order:

1. Function argument.

2. System variable.

3. R option.

layout and level can be set as system environment variables, respectively:

• teal.log_layout as TEAL.LOG_LAYOUT,

• teal.log_level as TEAL.LOG_LEVEL.

If neither the argument nor the environment variable is set the function uses the following R options:

• options(teal.log_layout), which is passed to logger::layout_glue_generator(),

• options(teal.log_level), which is passed to logger::log_threshold()

The logs are output to stdout by default. Check logger for more information about layouts and how to use logger.

Value

invisible(NULL)

Note

It's a thin wrapper around the logger package.

See Also

The package vignettes for more help: browseVignettes("teal.logger").

Examples

options(teal.log_layout = "{msg}")
options(teal.log_level = "ERROR")
register_logger(namespace = "new_namespace")

logger::log_info("Hello from new_namespace", namespace = "new_namespace")

Suppress logger logs

Description

This function suppresses logger when running tests via testthat. To suppress logs for a single test, add this function call within the testthat::test_that expression. To suppress logs for an entire test file, call this function at the start of the file.

Usage

suppress_logs()

Value

NULL invisible

Examples

testthat::test_that("An example test", {
  suppress_logs()
  testthat::expect_true(TRUE)
})

Teal log_formatter

Description

Custom log_formatter supporting atomic vectors. By default glue::glue returns n-element vector when vector is provided as an input. This function generates "[elem1, elem2, ...]" for atomic vectors. Function also handles NULL value which normally causes logger to return empty character.

Usage

teal_logger_formatter()

teal_logger_transformer(text, envir)

Arguments

Value

Nothing. Called for its side effects.