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params.R
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params.R
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knit_params_get <- function(input_lines, params) {
# check for recent enough knitr
if (utils::packageVersion("knitr") < "1.10") {
stop("knitr >= 1.10 required to use rmarkdown params")
}
# read the default parameters and extract them into a named list
knit_params <- mark_utf8(knitr::knit_params(input_lines))
default_params <- list()
for (param in knit_params) {
default_params[[param$name]] <- param$value
}
# validate params passed to render
if (!is.null(params)) {
if (identical(params, "ask")) {
if (!interactive()) {
stop("render parameter configuration only allowed in an interactive environment")
}
params <- knit_params_ask(input_lines = input_lines)
if (is.null(params)) {
stop("render parameter configuration canceled")
}
}
# verify they are a list
if (!is.list(params) || (length(names(params)) != length(params))) {
stop("render params argument must be a named list")
}
# verify that all parameters passed are also in the yaml
invalid_params <- setdiff(names(params), names(default_params))
if (length(invalid_params) > 0) {
stop("render params not declared in YAML: ",
paste(invalid_params, sep = ", "))
}
}
# merge explicitly provided params with defaults
merge_lists(default_params, params, recursive = FALSE)
}
params_label <- function(inputControlFn, param) {
label <- ifelse(is.null(param$label), param$name, param$label)
if (identical(inputControlFn, shiny::fileInput)) {
if (is.character(param$value)) {
label <- paste0(label, " (default: ", param$value, ")")
}
}
label
}
params_value_to_ui <- function(inputControlFn, value) {
if (identical(inputControlFn, shiny::fileInput)) {
NULL
} else if (identical(inputControlFn, shiny::textInput)) {
## TODO: if long input, maybe truncate textInput values for display
classes <- class(value)
if ("POSIXct" %in% classes) {
as.character(value)
} else {
value
}
} else if (is.null(value)) {
numerics <- c(shiny::numericInput,
shiny::sliderInput)
# The numerics can't deal with a NULL value, but everything else is fine.
if (identical(inputControlFn, shiny::numericInput) ||
identical(inputControlFn, shiny::sliderInput)) {
0
} else {
value
}
} else {
## A type/control that doesn't need special handling; just emit the value.
value
}
}
params_value_from_ui <- function(inputControlFn, value, uivalue) {
if (identical(inputControlFn, shiny::fileInput)) {
uivalue$datapath
} else if (identical(inputControlFn, shiny::textInput)) {
classes <- class(value)
if ("POSIXct" %in% classes) {
as.POSIXct(uivalue)
} else {
uivalue
}
} else {
## A type/control that doesn't need special handling; just emit the value.
uivalue
}
}
params_get_input <- function(param) {
# Maps between value types and input: XXX
default_inputs <- list(
logical = "checkbox",
## BUG: dateInput does not allow the user to not specify a value.
## https://github.com/rstudio/shiny/issues/896
Date = "date",
## BUG: shiny does not support datetime selectors
## https://github.com/rstudio/shiny/issues/897
## we ask for string input for now.
POSIXct = "datetime",
character = "text"
)
default_inputs$integer <- default_inputs$numeric <- {
## If min/max are specified, use a slider.
if (is.null(param$min) || is.null(param$max)) {
"numeric"
} else {
"slider"
}
}
input <- param$input
if (is.null(input)) {
if (!is.null(param$choices)) {
## radio buttons for a small number of choices, select otherwise.
if (length(param$choices) <= 4) {
input <- "radio"
} else {
input <- "select"
}
} else {
## Not choices. Look at the value type to find what input control we
## should use.
## A value might have multiple classes. Try: class(Sys.time())
## Try to find first class listed with a named control.
for (c in class(param$value)) {
default_input <- default_inputs[[c]]
if (!is.null(default_input)) {
input <- default_input
break
}
}
}
}
input
}
params_get_control <- function(param) {
input <- params_get_input(param)
if (is.null(input)) {
return(NULL)
}
# Maps between input: XXX and the various Shiny input controls
input_controls <- list(
checkbox = shiny::checkboxInput,
numeric = shiny::numericInput,
slider = shiny::sliderInput,
date = shiny::dateInput,
datetime = shiny::textInput, # placeholder for future datetime picker
text = shiny::textInput,
file = shiny::fileInput,
radio = shiny::radioButtons,
select = shiny::selectInput
)
control <- input_controls[[input]]
if (is.null(control)) {
stop(paste("could not determine what control to use for parameter", param$name, "with input:", input))
}
control
}
params_configurable <- function(param) {
length(param$value) <= 1 && !is.null(params_get_control(param))
}
# Returns a new empty named list.
params_namedList <- function() {
empty <- list()
names(empty) <- character()
empty
}
#' Run a shiny application asking for parameter configuration for the given document.
#'
#' @param file Path to the R Markdown document with configurable parameters.
#' @param input_lines Content of the R Markdown document. If \code{NULL}, the contents of \code{file} will be read.
#' @param params A named list of optional parameter overrides used in place of the document defaults.
#' @param shiny_args Additional arguments to \code{\link[shiny:runApp]{runApp}}.
#' @param save_caption Caption to use use for button that saves/confirms parameters.
#' @param encoding The encoding of the input file; see \code{\link{file}}.
#'
#' @return named list with overridden parameter names and value.
#'
#' @export
knit_params_ask <- function(file = NULL,
input_lines = NULL,
params = NULL,
shiny_args = NULL,
save_caption = "Save",
encoding = getOption("encoding")) {
if (utils::packageVersion("knitr") < "1.10.18") {
stop("knitr >= 1.10.18 required to use rmarkdown::knit_params_ask")
}
if (is.null(input_lines)) {
if (is.null(file)) {
stop("knit_params_ask must have a non-NULL file or input_lines parameter")
}
input_lines <- read_lines_utf8(file, encoding)
}
knit_params <- mark_utf8(knitr::knit_params(input_lines))
## Input validation on params (checks shared with render)
if (!is.null(params)) {
## Must be a named list
if (!is.list(params) || (length(names(params)) != length(params))) {
stop("knit_params_ask params argument must be a named list")
}
## We do not validate names(params) because the document may have changed
## but we're loading parameters that were configured with an older
## version.
}
## If we happen to not have any knit_params, just return an empty named list
## and don't fire up the Shiny app.
if (length(knit_params) == 0) {
return(params_namedList())
}
configurable <- Filter(params_configurable, knit_params)
unconfigurable <- Filter(Negate(params_configurable), knit_params)
## This set of published values is the raw set that came from the user.
## It does not include those values that cannot be configured or are
## left to use the default.
values <- params_namedList()
server <- function(input, output) {
param.ui <- function(param) {
inputControlFn <- params_get_control(param)
inputControlFnFormals <- names(formals(inputControlFn))
inputId <- param$name
label <- params_label(inputControlFn, param)
arguments = list(
inputId = inputId,
label = label
)
# We MUST process the "value" name even if it is not present (due to
# NULL values).
attrib_names <- unique(c(names(param), "value"))
lapply(attrib_names, function(name) {
if (name %in% c("name", "input", "expr")) {
} else if (name == "label") {
arguments$label <<- label
} else if (name == "value") {
## The current value for this parameter is either `params` when
## overridden by our caller or `param$value` otherwise.
current_value <- param$value
if (!is.null(params)) {
override <- params[[param$name]]
if (!is.null(override)) {
current_value <- override
}
}
# Now, transform into something that the input control can handle.
current_value <- params_value_to_ui(inputControlFn, current_value)
# value maps to either "value" or "selected" depending on the control.
if ("value" %in% inputControlFnFormals) {
arguments$value <<- current_value
} else if ("selected" %in% inputControlFnFormals) {
arguments$selected <<- current_value
}
} else {
## Not a special field. Blindly promote to the input control.
arguments[[name]] <<- param[[name]]
}
})
## This is based on param$value not current_value because we want to
## understand deviation from the report default, not any (optional)
## call-time override.
uidefault <- params_value_to_ui(inputControlFn, param$value)
hasDefaultValue <- function(value) {
identical(uidefault, value)
}
inputControl <- NULL
unsupported <- setdiff(names(arguments), inputControlFnFormals)
if (length(unsupported) > 0) {
inputControl <- shiny::div(class = "form-group",
tags$label(class="control-label",param$name),
shiny::div(paste('Cannot customize the parameter "', param$name, '" ',
'because the "', params_get_input(param), '" ',
'Shiny control does not support: ',
paste(unsupported, collapse = ', '), sep = '')))
} else {
inputControl <- do.call(inputControlFn, arguments)
}
showSelectControl <- NULL
selectControl <- NULL
selectInputId <- paste0("select_", param$name)
## Helper to materialize a "default/customize" control.
makeSelectControl <- function(default_name, custom_name) {
showSelectControl <<- function(current) {
(is.null(current) || identical(current, "default"))
}
hasDefaultValue <<- function(value) { FALSE }
choices <- list()
choices[[default_name]] <- "default"
choices[[custom_name]] <- "custom"
selectControl <<- shiny::selectInput(inputId = selectInputId,
label = label,
choices = choices)
}
if (is.null(params[[param$name]])) { # prior value; implicit customization
## Dates and times with expressions that mean "now" or "today" are first
## materialized as selects. If the user chooses to customize the field,
## we then show the type-specific picker.
if (identical("Sys.time()", param$expr)) {
makeSelectControl(paste0("now (", param$value, ")"),
"Use a custom time")
} else if (identical("Sys.Date()", param$expr)) {
makeSelectControl(paste0("today (", param$value, ")"),
"Use a custom date")
} else if (is.null(param$value)) {
# fileInput defaults to null, but for other null values, ask the
# user to explicitly choose to override (ie. we cannot use value
# comparison).
if (!identical(inputControlFn, shiny::fileInput)) {
makeSelectControl("Unspecified (NULL)",
"Use a custom value")
}
}
}
output[[paste0("ui_", param$name)]] <- shiny::renderUI({
# For most parameters, the selectInputId input will be NULL.
if (!is.null(showSelectControl) && showSelectControl(input[[selectInputId]])) {
selectControl
} else {
inputControl
}
})
shiny::observe({
# A little reactive magic to keep in mind. If you're in one of the
# "default/custom" selector scenarios, this will never fire until the
# user selects "custom" because hte value-producing input control is
# not rendered until that point.
uivalue <- input[[param$name]]
if (is.null(uivalue)) {
# ignore startup NULLs
} else if (hasDefaultValue(uivalue)) {
values[[param$name]] <<- NULL
} else {
values[[param$name]] <<- params_value_from_ui(inputControlFn, param$value, uivalue)
}
})
}
lapply(configurable, function(param) {
param.ui(param)
})
shiny::observeEvent(input$save, {
shiny::stopApp(values)
})
shiny::observeEvent(input$cancel, {
shiny::stopApp(NULL)
})
}
contents <- shiny::tags$div(
shiny::fluidRow(shiny::column(12, lapply(configurable, function(param) {
shiny::uiOutput(paste0("ui_", param$name))
}))), class = "container-fluid")
if (length(unconfigurable) > 0) {
skipped <- shiny::tags$div(shiny::tags$strong("Note:"),
"The following parameters cannot be customized:",
paste(lapply(unconfigurable, function(param) { param$name }), collapse = ", "))
contents <- shiny::tagAppendChildren(contents, shiny::fluidRow(shiny::column(12, skipped)))
}
footer <- shiny::tags$div(
shiny::tags$div(
shiny::fluidRow(shiny::column(12,
shiny::actionButton("save", save_caption, class = "btn-primary navbar-btn pull-right"),
shiny::actionButton("cancel","Cancel", class = "navbar-btn pull-right"))),
class = "container-fluid"),
class = "navbar navbar-default navbar-fixed-bottom")
style <- shiny::tags$style(
# Our controls are wiiiiide.
".container-fluid .shiny-input-container { width: auto; }",
# Prevent the save/cancel buttons from squashing together.
".navbar button { margin-left: 10px; }",
# Style for the navbar footer.
# http://getbootstrap.com/components/#navbar-fixed-bottom
"body { padding-bottom: 70px; }"
)
## Escape is "cancel" and Enter is "save".
script <- shiny::tags$script(shiny::HTML("$(document).keyup(function(e) {\n",
"if (e.which == 13) { $('#save').click(); } // enter\n",
"if (e.which == 27) { $('#cancel').click(); } // esc\n",
"});"
))
ui <- shiny::bootstrapPage(
shiny::tags$head(style, script),
contents,
footer)
shiny_app <- shiny::shinyApp(ui = ui, server = server)
shiny_args <- merge_lists(list(appDir = shiny_app), shiny_args)
do.call(shiny::runApp, shiny_args)
}