| 1 |
- #' Execute and validate `teal_data_module`+ # FilteredData ------ |
||
| 2 |
- #'+ |
||
| 3 |
- #' This is a low level module to handle `teal_data_module` execution and validation.+ #' Drive a `teal` application |
||
| 4 |
- #' [teal_transform_module()] inherits from [teal_data_module()] so it is handled by this module too.+ #' |
||
| 5 |
- #' [srv_teal()] accepts various `data` objects and eventually they are all transformed to `reactive`+ #' Extension of the `shinytest2::AppDriver` class with methods for |
||
| 6 |
- #' [teal_data()] which is a standard data class in whole `teal` framework.+ #' driving a teal application for performing interactions for `shinytest2` tests. |
||
| 8 |
- #' @section data validation:+ #' @keywords internal |
||
| 10 |
- #' Executed [teal_data_module()] is validated and output is validated for consistency.+ TealAppDriver <- R6::R6Class( # nolint: object_name. |
||
| 11 |
- #' Output `data` is invalid if:+ "TealAppDriver", |
||
| 12 |
- #' 1. [teal_data_module()] is invalid if server doesn't return `reactive`. **Immediately crashes an app!**+ inherit = {
|
||
| 13 |
- #' 2. `reactive` throws a `shiny.error` - happens when module creating [teal_data()] fails.+ if (!requireNamespace("shinytest2", quietly = TRUE)) {
|
||
| 14 |
- #' 3. `reactive` returns `qenv.error` - happens when [teal_data()] evaluates a failing code.+ stop("Please install 'shinytest2' package to use this class.")
|
||
| 15 |
- #' 4. `reactive` object doesn't return [teal_data()].+ } |
||
| 16 |
- #' 5. [teal_data()] object lacks any `datanames` specified in the `modules` argument.+ if (!requireNamespace("rvest", quietly = TRUE)) {
|
||
| 17 |
- #'+ stop("Please install 'rvest' package to use this class.")
|
||
| 18 |
- #' `teal` (observers in `srv_teal`) always waits to render an app until `reactive` `teal_data` is+ } |
||
| 19 |
- #' returned. If error 2-4 occurs, relevant error message is displayed to the app user. Once the issue is+ shinytest2::AppDriver |
||
| 20 |
- #' resolved, the app will continue to run. `teal` guarantees that errors in data don't crash the app+ }, |
||
| 21 |
- #' (except error 1).+ # public methods ---- |
||
| 22 |
- #'+ public = list( |
||
| 23 |
- #' @param id (`character(1)`) Module id+ #' @description |
||
| 24 |
- #' @param data (`reactive teal_data`)+ #' Initialize a `TealAppDriver` object for testing a `teal` application. |
||
| 25 |
- #' @param data_module (`teal_data_module`)+ #' |
||
| 26 |
- #' @param modules (`teal_modules` or `teal_module`) For `datanames` validation purpose+ #' @param data,modules,filter,title,header,footer,landing_popup arguments passed to `init` |
||
| 27 |
- #' @param validate_shiny_silent_error (`logical`) If `TRUE`, then `shiny.silent.error` is validated and+ #' @param timeout (`numeric`) Default number of milliseconds for any timeout or |
||
| 28 |
- #' @param is_transformer_failed (`reactiveValues`) contains `logical` flags named after each transformer.+ #' timeout_ parameter in the `TealAppDriver` class. |
||
| 29 |
- #' Help to determine if any previous transformer failed, so that following transformers can be disabled+ #' Defaults to 20s. |
||
| 30 |
- #' and display a generic failure message.+ #' |
||
| 31 |
- #'+ #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it |
||
| 32 |
- #' @return `reactive` `teal_data`+ #' via options or environment variables. |
||
| 33 |
- #'+ #' @param load_timeout (`numeric`) How long to wait for the app to load, in ms. |
||
| 34 |
- #' @rdname module_teal_data+ #' This includes the time to start R. Defaults to 100s. |
||
| 35 |
- #' @name module_teal_data+ #' |
||
| 36 |
- #' @keywords internal+ #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it |
||
| 37 |
- NULL+ #' via options or environment variables |
||
| 38 |
-
+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$new` |
||
| 39 |
- #' @rdname module_teal_data+ #' |
||
| 40 |
- ui_teal_data <- function(id, data_module = function(id) NULL) {
+ #' |
||
| 41 | -! | +
- checkmate::assert_string(id)+ #' @return Object of class `TealAppDriver` |
|
| 42 | -! | +
- checkmate::assert_function(data_module, args = "id")+ initialize = function(data, |
|
| 43 | -! | +
- ns <- NS(id)+ modules, |
|
| 44 |
-
+ filter = teal_slices(), |
||
| 45 | -! | +
- shiny::tagList(+ title = build_app_title(), |
|
| 46 | -! | +
- tags$div(id = ns("wrapper"), data_module(id = ns("data"))),
+ header = tags$p(), |
|
| 47 | -! | +
- ui_validate_reactive_teal_data(ns("validate"))
+ footer = tags$p(), |
|
| 48 |
- )+ landing_popup = NULL, |
||
| 49 |
- }+ timeout = rlang::missing_arg(), |
||
| 50 |
-
+ load_timeout = rlang::missing_arg(), |
||
| 51 |
- #' @rdname module_teal_data+ ...) {
|
||
| 52 | -+ | ! |
- srv_teal_data <- function(id,+ private$data <- data |
| 53 | -+ | ! |
- data_module = function(id) NULL,+ private$modules <- modules |
| 54 | -+ | ! |
- modules = NULL,+ private$filter <- filter |
| 55 | -+ | ! |
- validate_shiny_silent_error = TRUE,+ app <- init( |
| 56 | -+ | ! |
- is_transformer_failed = reactiveValues()) {
+ data = data, |
| 57 | -20x | +! |
- checkmate::assert_string(id)+ modules = modules, |
| 58 | -20x | +! |
- checkmate::assert_function(data_module, args = "id")+ filter = filter, |
| 59 | -20x | +! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ title = title, |
| 60 | -20x | +! |
- checkmate::assert_class(is_transformer_failed, "reactivevalues")+ header = header, |
| 61 | -+ | ! |
-
+ footer = footer, |
| 62 | -20x | +! |
- moduleServer(id, function(input, output, session) {
+ landing_popup = landing_popup, |
| 63 | -20x | +
- logger::log_debug("srv_teal_data initializing.")
+ ) |
|
| 64 | -20x | +
- is_transformer_failed[[id]] <- FALSE+ |
|
| 65 | -20x | +
- data_out <- data_module(id = "data")+ # Default timeout is hardcoded to 4s in shinytest2:::resolve_timeout |
|
| 66 | -20x | +
- data_handled <- reactive(tryCatch(data_out(), error = function(e) e))+ # It must be set as parameter to the AppDriver |
|
| 67 | -20x | +! |
- observeEvent(data_handled(), {
+ suppressWarnings( |
| 68 | -22x | +! |
- if (!inherits(data_handled(), "teal_data")) {
+ super$initialize( |
| 69 | -6x | +! |
- is_transformer_failed[[id]] <- TRUE+ app_dir = shinyApp(app$ui, app$server), |
| 70 | -+ | ! |
- } else {
+ name = "teal", |
| 71 | -16x | +! |
- is_transformer_failed[[id]] <- FALSE+ variant = shinytest2::platform_variant(), |
| 72 | -+ | ! |
- }+ timeout = rlang::maybe_missing(timeout, 20 * 1000), |
| 73 | -+ | ! |
- })+ load_timeout = rlang::maybe_missing(load_timeout, 100 * 1000), |
| 74 |
-
+ ... |
||
| 75 | -20x | +
- is_previous_failed <- reactive({
+ ) |
|
| 76 | -20x | +
- idx_this <- which(names(is_transformer_failed) == id)+ ) |
|
| 77 | -20x | +
- is_transformer_failed_list <- reactiveValuesToList(is_transformer_failed)+ |
|
| 78 | -20x | +
- idx_failures <- which(unlist(is_transformer_failed_list))+ # Check for minimum version of Chrome that supports the tests |
|
| 79 | -20x | +
- any(idx_failures < idx_this)+ # - Element.checkVisibility was added on 105 |
|
| 80 | -+ | ! |
- })+ chrome_version <- numeric_version( |
| 81 | -+ | ! |
-
+ gsub( |
| 82 | -20x | +! |
- observeEvent(is_previous_failed(), {
+ "[[:alnum:]_]+/", # Prefix that ends with forward slash |
| 83 | -20x | +
- if (is_previous_failed()) {
+ "", |
|
| 84 | ! |
- shinyjs::disable("wrapper")
+ self$get_chromote_session()$Browser$getVersion()$product |
|
| 85 |
- } else {
+ ), |
||
| 86 | -20x | +! |
- shinyjs::enable("wrapper")
+ strict = FALSE |
| 87 |
- }+ ) |
||
| 88 |
- })+ |
||
| 89 | -+ | ! |
-
+ required_version <- "121" |
| 90 | -20x | +
- srv_validate_reactive_teal_data(+ |
|
| 91 | -20x | +! |
- "validate",+ testthat::skip_if( |
| 92 | -20x | +! |
- data = data_handled,+ is.na(chrome_version), |
| 93 | -20x | +! |
- modules = modules,+ "Problem getting Chrome version, please contact the developers." |
| 94 | -20x | +
- validate_shiny_silent_error = validate_shiny_silent_error,+ ) |
|
| 95 | -20x | +! |
- hide_validation_error = is_previous_failed+ testthat::skip_if( |
| 96 | -+ | ! |
- )+ chrome_version < required_version, |
| 97 | -+ | ! |
- })+ sprintf( |
| 98 | -+ | ! |
- }+ "Chrome version '%s' is not supported, please upgrade to '%s' or higher", |
| 99 | -+ | ! |
-
+ chrome_version, |
| 100 | -+ | ! |
- #' @rdname module_teal_data+ required_version |
| 101 |
- ui_validate_reactive_teal_data <- function(id) {
+ ) |
||
| 102 | -82x | +
- ns <- NS(id)+ ) |
|
| 103 | -82x | +
- tagList(+ # end od check |
|
| 104 | -82x | +
- div(+ |
|
| 105 | -82x | +! |
- id = ns("validate_messages"),
+ private$set_active_ns() |
| 106 | -82x | +! |
- class = "teal_validated",+ self$wait_for_idle() |
| 107 | -82x | +
- ui_validate_error(ns("silent_error")),
+ }, |
|
| 108 | -82x | +
- ui_check_class_teal_data(ns("class_teal_data")),
+ #' @description |
|
| 109 | -82x | +
- ui_check_shiny_warnings(ns("shiny_warnings"))
+ #' Append parent [`shinytest2::AppDriver`] `click` method with a call to `waif_for_idle()` method. |
|
| 110 |
- ),+ #' @param ... arguments passed to parent [`shinytest2::AppDriver`] `click()` method. |
||
| 111 | -82x | +
- div(+ click = function(...) {
|
|
| 112 | -82x | +! |
- class = "teal_validated",+ super$click(...) |
| 113 | -82x | +! |
- uiOutput(ns("previous_failed"))
+ private$wait_for_page_stability() |
| 114 |
- )+ }, |
||
| 115 |
- )+ #' @description |
||
| 116 |
- }+ #' Check if the app has shiny errors. This checks for global shiny errors. |
||
| 117 |
-
+ #' Note that any shiny errors dependent on shiny server render will only be captured after the teal module tab |
||
| 118 |
- #' @rdname module_teal_data+ #' is visited because shiny will not trigger server computations when the tab is invisible. |
||
| 119 |
- srv_validate_reactive_teal_data <- function(id, # nolint: object_length+ #' So, navigate to the module tab you want to test before calling this function. |
||
| 120 |
- data,+ #' Although, this catches errors hidden in the other module tabs if they are already rendered. |
||
| 121 |
- modules = NULL,+ expect_no_shiny_error = function() {
|
||
| 122 | -+ | ! |
- validate_shiny_silent_error = FALSE,+ testthat::expect_null( |
| 123 | -+ | ! |
- hide_validation_error = reactive(FALSE)) {
+ self$get_html(".shiny-output-error:not(.shiny-output-error-validation)"),
|
| 124 | -183x | +! |
- checkmate::assert_string(id)+ info = "Shiny error is observed" |
| 125 | -183x | +
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
+ ) |
|
| 126 | -183x | +
- checkmate::assert_flag(validate_shiny_silent_error)+ }, |
|
| 127 |
-
+ #' @description |
||
| 128 | -183x | +
- moduleServer(id, function(input, output, session) {
+ #' Check if the app has no validation errors. This checks for global shiny validation errors. |
|
| 129 |
- # there is an empty reactive cycle on `init` and `data_rv` has `shiny.silent.error` class+ expect_no_validation_error = function() {
|
||
| 130 | -183x | +! |
- srv_validate_error("silent_error", data, validate_shiny_silent_error)
+ testthat::expect_null( |
| 131 | -183x | +! |
- srv_check_class_teal_data("class_teal_data", data)
+ self$get_html(".shiny-output-error-validation"),
|
| 132 | -183x | +! |
- srv_check_shiny_warnings("shiny_warnings", data, modules)
+ info = "No validation error is observed" |
| 133 | -183x | +
- output$previous_failed <- renderUI({
+ ) |
|
| 134 | -173x | +
- if (hide_validation_error()) {
+ }, |
|
| 135 | -! | +
- shinyjs::hide("validate_messages")
+ #' @description |
|
| 136 | -! | +
- tags$div("One of previous transformers failed. Please fix and continue.", class = "teal-output-warning")
+ #' Check if the app has validation errors. This checks for global shiny validation errors. |
|
| 137 |
- } else {
+ expect_validation_error = function() {
|
||
| 138 | -173x | +! |
- shinyjs::show("validate_messages")
+ testthat::expect_false( |
| 139 | -173x | +! |
- NULL+ is.null(self$get_html(".shiny-output-error-validation")),
|
| 140 | -+ | ! |
- }+ info = "Validation error is not observed" |
| 141 |
- })+ ) |
||
| 142 |
-
+ }, |
||
| 143 | -183x | +
- .trigger_on_success(data)+ #' @description |
|
| 144 |
- })+ #' Set the input in the `teal` app. |
||
| 145 |
- }+ #' |
||
| 146 |
-
+ #' @param input_id (character) The shiny input id with it's complete name space. |
||
| 147 |
- #' @keywords internal+ #' @param value The value to set the input to. |
||
| 148 |
- ui_validate_error <- function(id) {
+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
||
| 149 | -82x | +
- ns <- NS(id)+ #' |
|
| 150 | -82x | +
- uiOutput(ns("message"))
+ #' @return The `TealAppDriver` object invisibly. |
|
| 151 |
- }+ set_input = function(input_id, value, ...) {
|
||
| 152 | -+ | ! |
-
+ do.call( |
| 153 | -+ | ! |
- #' @keywords internal+ self$set_inputs, |
| 154 | -+ | ! |
- srv_validate_error <- function(id, data, validate_shiny_silent_error) {
+ c(setNames(list(value), input_id), list(...)) |
| 155 | -183x | +
- checkmate::assert_string(id)+ ) |
|
| 156 | -183x | +! |
- checkmate::assert_flag(validate_shiny_silent_error)+ invisible(self) |
| 157 | -183x | +
- moduleServer(id, function(input, output, session) {
+ }, |
|
| 158 | -183x | +
- output$message <- renderUI({
+ #' @description |
|
| 159 | -186x | +
- is_shiny_silent_error <- inherits(data(), "shiny.silent.error") && identical(data()$message, "")+ #' Navigate the teal tabs in the `teal` app. |
|
| 160 | -180x | +
- if (inherits(data(), "qenv.error")) {
+ #' |
|
| 161 | -2x | +
- validate(+ #' @param tabs (character) Labels of tabs to navigate to. The order of the tabs is important, |
|
| 162 | -2x | +
- need(+ #' and it should start with the most parent level tab. |
|
| 163 | -2x | +
- FALSE,+ #' Note: In case the teal tab group has duplicate names, the first tab will be selected, |
|
| 164 | -2x | +
- paste(+ #' If you wish to select the second tab with the same name, use the suffix "_1". |
|
| 165 | -2x | +
- "Error when executing the `data` module:",+ #' If you wish to select the third tab with the same name, use the suffix "_2" and so on. |
|
| 166 | -2x | +
- strip_style(paste(data()$message, collapse = "\n")),+ #' |
|
| 167 | -2x | +
- "\nCheck your inputs or contact app developer if error persists.",+ #' @return The `TealAppDriver` object invisibly. |
|
| 168 | -2x | +
- collapse = "\n"+ navigate_teal_tab = function(tabs) {
|
|
| 169 | -+ | ! |
- )+ checkmate::check_character(tabs, min.len = 1) |
| 170 | -+ | ! |
- )+ for (tab in tabs) {
|
| 171 | -+ | ! |
- )+ self$set_input( |
| 172 | -178x | +! |
- } else if (inherits(data(), "error")) {
+ "teal-teal_modules-active_tab", |
| 173 | -7x | +! |
- if (is_shiny_silent_error && !validate_shiny_silent_error) {
+ get_unique_labels(tab), |
| 174 | -1x | +! |
- return(NULL)+ wait_ = FALSE |
| 175 |
- }+ ) |
||
| 176 | -6x | +
- validate(+ } |
|
| 177 | -6x | +! |
- need(+ self$wait_for_idle() |
| 178 | -6x | +! |
- FALSE,+ private$set_active_ns() |
| 179 | -6x | +! |
- sprintf(+ invisible(self) |
| 180 | -6x | +
- "Shiny error when executing the `data` module.\n%s\n%s",+ }, |
|
| 181 | -6x | +
- data()$message,+ #' @description |
|
| 182 | -6x | +
- "Check your inputs or contact app developer if error persists."+ #' Get the active shiny name space for different components of the teal app. |
|
| 183 |
- )+ #' |
||
| 184 |
- )+ #' @return (`list`) The list of active shiny name space of the teal components. |
||
| 185 |
- )+ active_ns = function() {
|
||
| 186 | -+ | ! |
- }+ if (identical(private$ns$module, character(0))) {
|
| 187 | -+ | ! |
- })+ private$set_active_ns() |
| 188 |
- })+ } |
||
| 189 | -+ | ! |
- }+ private$ns |
| 190 |
-
+ }, |
||
| 191 |
-
+ #' @description |
||
| 192 |
- #' @keywords internal+ #' Get the active shiny name space for interacting with the module content. |
||
| 193 |
- ui_check_class_teal_data <- function(id) {
+ #' |
||
| 194 | -82x | +
- ns <- NS(id)+ #' @return (`string`) The active shiny name space of the component. |
|
| 195 | -82x | +
- uiOutput(ns("message"))
+ active_module_ns = function() {
|
|
| 196 | -+ | ! |
- }+ if (identical(private$ns$module, character(0))) {
|
| 197 | -+ | ! |
-
+ private$set_active_ns() |
| 198 |
- #' @keywords internal+ } |
||
| 199 | -+ | ! |
- srv_check_class_teal_data <- function(id, data) {
+ private$ns$module |
| 200 | -183x | +
- checkmate::assert_string(id)+ }, |
|
| 201 | -183x | +
- moduleServer(id, function(input, output, session) {
+ #' @description |
|
| 202 | -183x | +
- output$message <- renderUI({
+ #' Get the active shiny name space bound with a custom `element` name. |
|
| 203 | -186x | +
- validate(+ #' |
|
| 204 | -186x | +
- need(+ #' @param element `character(1)` custom element name. |
|
| 205 | -186x | +
- inherits(data(), c("teal_data", "error")),
+ #' |
|
| 206 | -186x | +
- "Did not receive `teal_data` object. Cannot proceed further."+ #' @return (`string`) The active shiny name space of the component bound with the input `element`. |
|
| 207 |
- )+ active_module_element = function(element) {
|
||
| 208 | -+ | ! |
- )+ checkmate::assert_string(element) |
| 209 | -+ | ! |
- })+ sprintf("#%s-%s", self$active_module_ns(), element)
|
| 210 |
- })+ }, |
||
| 211 |
- }+ #' @description |
||
| 212 |
-
+ #' Get the text of the active shiny name space bound with a custom `element` name. |
||
| 213 |
- #' @keywords internal+ #' |
||
| 214 |
- ui_check_shiny_warnings <- function(id) {
+ #' @param element `character(1)` the text of the custom element name. |
||
| 215 | -82x | +
- ns <- NS(id)+ #' |
|
| 216 | -82x | +
- uiOutput(NS(id, "message"))+ #' @return (`string`) The text of the active shiny name space of the component bound with the input `element`. |
|
| 217 |
- }+ active_module_element_text = function(element) {
|
||
| 218 | -+ | ! |
-
+ checkmate::assert_string(element) |
| 219 | -+ | ! |
- #' @keywords internal+ self$get_text(self$active_module_element(element)) |
| 220 |
- srv_check_shiny_warnings <- function(id, data, modules) {
+ }, |
||
| 221 | -183x | +
- checkmate::assert_string(id)+ #' @description |
|
| 222 | -183x | +
- moduleServer(id, function(input, output, session) {
+ #' Get the active shiny name space for interacting with the filter panel. |
|
| 223 | -183x | +
- output$message <- renderUI({
+ #' |
|
| 224 | -186x | +
- if (inherits(data(), "teal_data")) {
+ #' @return (`string`) The active shiny name space of the component. |
|
| 225 | -169x | +
- is_modules_ok <- check_modules_datanames_html(+ active_filters_ns = function() {
|
|
| 226 | -169x | +! |
- modules = modules, datanames = ls(teal.code::get_env(data()))+ if (identical(private$ns$filter_panel, character(0))) {
|
| 227 | -+ | ! |
- )+ private$set_active_ns() |
| 228 | -169x | +
- if (!isTRUE(is_modules_ok)) {
+ } |
|
| 229 | -15x | +! |
- tags$div(is_modules_ok, class = "teal-output-warning")+ private$ns$filter_panel |
| 230 |
- }+ }, |
||
| 231 |
- }+ #' @description |
||
| 232 |
- })+ #' Get the active shiny name space for interacting with the data-summary panel. |
||
| 233 |
- })+ #' |
||
| 234 |
- }+ #' @return (`string`) The active shiny name space of the data-summary component. |
||
| 235 |
-
+ active_data_summary_ns = function() {
|
||
| 236 | -+ | ! |
- .trigger_on_success <- function(data) {
+ if (identical(private$ns$data_summary, character(0))) {
|
| 237 | -183x | +! |
- out <- reactiveVal(NULL)+ private$set_active_ns() |
| 238 | -183x | +
- observeEvent(data(), {
+ } |
|
| 239 | -180x | +! |
- if (inherits(data(), "teal_data")) {
+ private$ns$data_summary |
| 240 | -169x | +
- if (!identical(data(), out())) {
+ }, |
|
| 241 | -169x | +
- out(data())+ #' @description |
|
| 242 |
- }+ #' Get the active shiny name space bound with a custom `element` name. |
||
| 243 |
- }+ #' |
||
| 244 |
- })+ #' @param element `character(1)` custom element name. |
||
| 245 |
-
+ #' |
||
| 246 | -183x | +
- out+ #' @return (`string`) The active shiny name space of the component bound with the input `element`. |
|
| 247 |
- }+ active_data_summary_element = function(element) {
+ |
+ ||
| 248 | +! | +
+ checkmate::assert_string(element)+ |
+ |
| 249 | +! | +
+ sprintf("#%s-%s", self$active_data_summary_ns(), element)
|
| 1 | +250 |
- #' Get client timezone+ }, |
|
| 2 | +251 |
- #'+ #' @description |
|
| 3 | +252 |
- #' User timezone in the browser may be different to the one on the server.+ #' Get the input from the module in the `teal` app. |
|
| 4 | +253 |
- #' This script can be run to register a `shiny` input which contains information about the timezone in the browser.+ #' This function will only access inputs from the name space of the current active teal module. |
|
| 5 | +254 |
- #'+ #' |
|
| 6 | +255 |
- #' @param ns (`function`) namespace function passed from the `session` object in the `shiny` server.+ #' @param input_id (character) The shiny input id to get the value from. |
|
| 7 | +256 |
- #' For `shiny` modules this will allow for proper name spacing of the registered input.+ #' |
|
| 8 | +257 |
- #'+ #' @return The value of the shiny input. |
|
| 9 | +258 |
- #' @return `NULL`, invisibly.+ get_active_module_input = function(input_id) {
+ |
+ |
| 259 | +! | +
+ checkmate::check_string(input_id)+ |
+ |
| 260 | +! | +
+ self$get_value(input = sprintf("%s-%s", self$active_module_ns(), input_id))
|
|
| 10 | +261 |
- #'+ }, |
|
| 11 | +262 |
- #' @keywords internal+ #' @description |
|
| 12 | +263 |
- #'+ #' Get the output from the module in the `teal` app. |
|
| 13 | +264 |
- get_client_timezone <- function(ns) {
+ #' This function will only access outputs from the name space of the current active teal module. |
|
| 14 | -83x | +||
| 265 | +
- script <- sprintf(+ #' |
||
| 15 | -83x | +||
| 266 | +
- "Shiny.setInputValue(`%s`, Intl.DateTimeFormat().resolvedOptions().timeZone)",+ #' @param output_id (character) The shiny output id to get the value from. |
||
| 16 | -83x | +||
| 267 | +
- ns("timezone")
+ #' |
||
| 17 | +268 |
- )+ #' @return The value of the shiny output. |
|
| 18 | -83x | +||
| 269 | +
- shinyjs::runjs(script) # function does not return anything+ get_active_module_output = function(output_id) {
|
||
| 19 | -83x | +||
| 270 | +! |
- invisible(NULL)+ checkmate::check_string(output_id) |
|
| 20 | -+ | ||
| 271 | +! |
- }+ self$get_value(output = sprintf("%s-%s", self$active_module_ns(), output_id))
|
|
| 21 | +272 |
-
+ }, |
|
| 22 | +273 |
- #' Resolve the expected bootstrap theme+ #' @description |
|
| 23 | +274 |
- #' @noRd+ #' Get the output from the module's `teal.widgets::table_with_settings` or `DT::DTOutput` in the `teal` app. |
|
| 24 | +275 |
- #' @keywords internal+ #' This function will only access outputs from the name space of the current active teal module. |
|
| 25 | +276 |
- get_teal_bs_theme <- function() {
+ #' |
|
| 26 | -4x | +||
| 277 | +
- bs_theme <- getOption("teal.bs_theme")
+ #' @param table_id (`character(1)`) The id of the table in the active teal module's name space. |
||
| 27 | +278 |
-
+ #' @param which (integer) If there is more than one table, which should be extracted. |
|
| 28 | -4x | +||
| 279 | +
- if (is.null(bs_theme)) {
+ #' By default it will look for a table that is built using `teal.widgets::table_with_settings`. |
||
| 29 | -1x | +||
| 280 | +
- return(NULL)+ #' |
||
| 30 | +281 |
- }+ #' @return The data.frame with table contents. |
|
| 31 | +282 |
-
+ get_active_module_table_output = function(table_id, which = 1) {
|
|
| 32 | -3x | +||
| 283 | +! |
- if (!checkmate::test_class(bs_theme, "bs_theme")) {
+ checkmate::check_number(which, lower = 1) |
|
| 33 | -2x | +||
| 284 | +! |
- warning(+ checkmate::check_string(table_id) |
|
| 34 | -2x | +||
| 285 | +! |
- "Assertion on 'teal.bs_theme' option value failed: ",+ table <- rvest::html_table( |
|
| 35 | -2x | +||
| 286 | +! |
- checkmate::check_class(bs_theme, "bs_theme"),+ self$get_html_rvest(self$active_module_element(table_id)), |
|
| 36 | -2x | +||
| 287 | +! |
- ". The default Shiny Bootstrap theme will be used."+ fill = TRUE |
|
| 37 | +288 |
- )+ ) |
|
| 38 | -2x | +||
| 289 | +! |
- return(NULL)+ if (length(table) == 0) {
|
|
| 39 | -+ | ||
| 290 | +! |
- }+ data.frame() |
|
| 40 | +291 |
-
+ } else {
|
|
| 41 | -1x | +||
| 292 | +! |
- bs_theme+ table[[which]] |
|
| 42 | +293 |
- }+ } |
|
| 43 | +294 |
-
+ }, |
|
| 44 | +295 |
- #' Return parentnames along with datanames.+ #' @description |
|
| 45 | +296 |
- #' @noRd+ #' Get the output from the module's `teal.widgets::plot_with_settings` in the `teal` app. |
|
| 46 | +297 |
- #' @keywords internal+ #' This function will only access plots from the name space of the current active teal module. |
|
| 47 | +298 |
- .include_parent_datanames <- function(datanames, join_keys) {
- |
- |
| 48 | -167x | -
- ordered_datanames <- datanames+ #' |
|
| 49 | -167x | +||
| 299 | +
- for (i in datanames) {
+ #' @param plot_id (`character(1)`) The id of the plot in the active teal module's name space. |
||
| 50 | -306x | +||
| 300 | +
- parents <- character(0)+ #' |
||
| 51 | -306x | +||
| 301 | +
- while (length(i) > 0) {
+ #' @return The `src` attribute as `character(1)` vector. |
||
| 52 | -319x | +||
| 302 | +
- parent_i <- teal.data::parent(join_keys, i)+ get_active_module_plot_output = function(plot_id) {
|
||
| 53 | -319x | +||
| 303 | +! |
- parents <- c(parent_i, parents)+ checkmate::check_string(plot_id) |
|
| 54 | -319x | +||
| 304 | +! |
- i <- parent_i+ self$get_attr( |
|
| 55 | -+ | ||
| 305 | +! |
- }+ self$active_module_element(sprintf("%s-plot_main > img", plot_id)),
|
|
| 56 | -306x | +||
| 306 | +! |
- ordered_datanames <- c(parents, ordered_datanames)+ "src" |
|
| 57 | +307 |
- }- |
- |
| 58 | -167x | -
- unique(ordered_datanames)+ ) |
|
| 59 | +308 |
- }+ }, |
|
| 60 | +309 |
-
+ #' @description |
|
| 61 | +310 |
- #' Return topologicaly sorted datanames+ #' Set the input in the module in the `teal` app. |
|
| 62 | +311 |
- #' @noRd+ #' This function will only set inputs in the name space of the current active teal module. |
|
| 63 | +312 |
- #' @keywords internal+ #' |
|
| 64 | +313 |
- .topologically_sort_datanames <- function(datanames, join_keys) {
- |
- |
| 65 | -135x | -
- datanames_with_parents <- .include_parent_datanames(datanames, join_keys)+ #' @param input_id (character) The shiny input id to get the value from. |
|
| 66 | -135x | +||
| 314 | +
- intersect(datanames, datanames_with_parents)+ #' @param value The value to set the input to. |
||
| 67 | +315 |
- }+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 68 | +316 |
-
+ #' |
|
| 69 | +317 |
- #' Create a `FilteredData`+ #' @return The `TealAppDriver` object invisibly. |
|
| 70 | +318 |
- #'+ set_active_module_input = function(input_id, value, ...) {
|
|
| 71 | -+ | ||
| 319 | +! |
- #' Create a `FilteredData` object from a `teal_data` object.+ checkmate::check_string(input_id) |
|
| 72 | -+ | ||
| 320 | +! |
- #'+ checkmate::check_string(value) |
|
| 73 | -+ | ||
| 321 | +! |
- #' @param x (`teal_data`) object+ self$set_input( |
|
| 74 | -+ | ||
| 322 | +! |
- #' @param datanames (`character`) vector of data set names to include; must be subset of `datanames(x)`+ sprintf("%s-%s", self$active_module_ns(), input_id),
|
|
| 75 | -+ | ||
| 323 | +! |
- #' @return A `FilteredData` object.+ value, |
|
| 76 | +324 |
- #' @keywords internal+ ... |
|
| 77 | +325 |
- teal_data_to_filtered_data <- function(x, datanames = ls(teal.code::get_env(x))) {
+ ) |
|
| 78 | -78x | -
- checkmate::assert_class(x, "teal_data")- |
- |
| 79 | -78x | -
- checkmate::assert_character(datanames, min.chars = 1L, any.missing = FALSE)- |
- |
| 80 | -- |
- # Otherwise, FilteredData will be created in the modules' scope later- |
- |
| 81 | -78x | -
- teal.slice::init_filtered_data(- |
- |
| 82 | -78x | +||
| 326 | +! |
- x = Filter(+ dots <- rlang::list2(...) |
|
| 83 | -78x | +||
| 327 | +! |
- length,+ if (!isFALSE(dots[["wait"]])) self$wait_for_idle() # Default behavior is to wait |
|
| 84 | -78x | +||
| 328 | +! |
- sapply(datanames, function(dn) x[[dn]], simplify = FALSE)+ invisible(self) |
|
| 85 | +329 |
- ),- |
- |
| 86 | -78x | -
- join_keys = teal.data::join_keys(x)+ }, |
|
| 87 | +330 |
- )+ #' @description |
|
| 88 | +331 |
- }+ #' Get the active datasets that can be accessed via the filter panel of the current active teal module. |
|
| 89 | +332 |
-
+ get_active_filter_vars = function() {
|
|
| 90 | -+ | ||
| 333 | +! |
-
+ displayed_datasets_index <- self$is_visible( |
|
| 91 | -+ | ||
| 334 | +! |
- #' Template function for `TealReportCard` creation and customization+ sprintf("#%s-filters-filter_active_vars_contents > span", self$active_filters_ns())
|
|
| 92 | +335 |
- #'+ ) |
|
| 93 | +336 |
- #' This function generates a report card with a title,+ |
|
| 94 | -+ | ||
| 337 | +! |
- #' an optional description, and the option to append the filter state list.+ available_datasets <- self$get_text( |
|
| 95 | -+ | ||
| 338 | +! |
- #'+ sprintf( |
|
| 96 | -+ | ||
| 339 | +! |
- #' @param title (`character(1)`) title of the card (unless overwritten by label)+ "#%s-filters-filter_active_vars_contents .filter_panel_dataname", |
|
| 97 | -+ | ||
| 340 | +! |
- #' @param label (`character(1)`) label provided by the user when adding the card+ self$active_filters_ns() |
|
| 98 | +341 |
- #' @param description (`character(1)`) optional, additional description+ ) |
|
| 99 | +342 |
- #' @param with_filter (`logical(1)`) flag indicating to add filter state+ ) |
|
| 100 | +343 |
- #' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation+ |
|
| 101 | -+ | ||
| 344 | +! |
- #' of the filter state in the report+ available_datasets[displayed_datasets_index] |
|
| 102 | +345 |
- #'+ }, |
|
| 103 | +346 |
- #' @return (`TealReportCard`) populated with a title, description and filter state.+ #' @description |
|
| 104 | +347 |
- #'+ #' Get the active data summary table |
|
| 105 | +348 |
- #' @export+ #' @return `data.frame` |
|
| 106 | +349 |
- report_card_template <- function(title, label, description = NULL, with_filter, filter_panel_api) {
- |
- |
| 107 | -2x | -
- checkmate::assert_string(title)+ get_active_data_summary_table = function() {
|
|
| 108 | -2x | +||
| 350 | +! |
- checkmate::assert_string(label)+ summary_table <- rvest::html_table( |
|
| 109 | -2x | +||
| 351 | +! |
- checkmate::assert_string(description, null.ok = TRUE)+ self$get_html_rvest(self$active_data_summary_element("table")),
|
|
| 110 | -2x | +||
| 352 | +! |
- checkmate::assert_flag(with_filter)+ fill = TRUE |
|
| 111 | -2x | +||
| 353 | +! |
- checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI")+ )[[1]] |
|
| 112 | +354 | ||
| 113 | -2x | -
- card <- teal::TealReportCard$new()- |
- |
| 114 | -2x | -
- title <- if (label == "") title else label- |
- |
| 115 | -2x | +||
| 355 | +! |
- card$set_name(title)+ col_names <- unlist(summary_table[1, ], use.names = FALSE) |
|
| 116 | -2x | +||
| 356 | +! |
- card$append_text(title, "header2")+ summary_table <- summary_table[-1, ] |
|
| 117 | -1x | +||
| 357 | +! |
- if (!is.null(description)) card$append_text(description, "header3")+ colnames(summary_table) <- col_names |
|
| 118 | -1x | +||
| 358 | +! |
- if (with_filter) card$append_fs(filter_panel_api$get_filter_state())+ if (nrow(summary_table) > 0) {
|
|
| 119 | -2x | +||
| 359 | +! |
- card+ summary_table |
|
| 120 | +360 |
- }+ } else {
|
|
| 121 | -+ | ||
| 361 | +! |
-
+ NULL |
|
| 122 | +362 |
-
+ } |
|
| 123 | +363 |
- #' Check `datanames` in modules+ }, |
|
| 124 | +364 |
- #'+ #' @description |
|
| 125 | +365 |
- #' These functions check if specified `datanames` in modules match those in the data object,+ #' Test if `DOM` elements are visible on the page with a JavaScript call. |
|
| 126 | +366 |
- #' returning error messages or `TRUE` for successful validation. Two functions return error message+ #' @param selector (`character(1)`) `CSS` selector to check visibility. |
|
| 127 | +367 |
- #' in different forms:+ #' A `CSS` id will return only one element if the UI is well formed. |
|
| 128 | +368 |
- #' - `check_modules_datanames` returns `character(1)` for basic assertion usage+ #' @param content_visibility_auto,opacity_property,visibility_property (`logical(1)`) See more information |
|
| 129 | +369 |
- #' - `check_modules_datanames_html` returns `shiny.tag.list` to display it in the app.+ #' on <https://developer.mozilla.org/en-US/docs/Web/API/Element/checkVisibility>. |
|
| 130 | +370 |
- #'+ #' |
|
| 131 | +371 |
- #' @param modules (`teal_modules`) object+ #' @return Logical vector with all occurrences of the selector. |
|
| 132 | +372 |
- #' @param datanames (`character`) names of datasets available in the `data` object+ is_visible = function(selector, |
|
| 133 | +373 |
- #'+ content_visibility_auto = FALSE, |
|
| 134 | +374 |
- #' @return `TRUE` if validation passes, otherwise `character(1)` or `shiny.tag.list`+ opacity_property = FALSE, |
|
| 135 | +375 |
- #' @keywords internal+ visibility_property = FALSE) {
|
|
| 136 | -+ | ||
| 376 | +! |
- check_modules_datanames <- function(modules, datanames) {
+ checkmate::assert_string(selector) |
|
| 137 | -9x | +||
| 377 | +! |
- out <- check_modules_datanames_html(modules, datanames)+ checkmate::assert_flag(content_visibility_auto) |
|
| 138 | -9x | +||
| 378 | +! |
- if (inherits(out, "shiny.tag.list")) {
+ checkmate::assert_flag(opacity_property) |
|
| 139 | -3x | +||
| 379 | +! |
- out_with_ticks <- gsub("<code>|</code>", "`", toString(out))
+ checkmate::assert_flag(visibility_property) |
|
| 140 | -3x | +||
| 380 | +
- out_text <- gsub("<[^<>]+>", "", toString(out_with_ticks))
+
|
||
| 141 | -3x | +||
| 381 | +! |
- trimws(gsub("[[:space:]]+", " ", out_text))
+ private$wait_for_page_stability() |
|
| 142 | +382 |
- } else {
- |
- |
| 143 | -6x | -
- out+ |
|
| 144 | -+ | ||
| 383 | +! |
- }+ testthat::skip_if_not( |
|
| 145 | -+ | ||
| 384 | +! |
- }+ self$get_js("typeof Element.prototype.checkVisibility === 'function'"),
|
|
| 146 | -+ | ||
| 385 | +! |
-
+ "Element.prototype.checkVisibility is not supported in the current browser." |
|
| 147 | +386 |
- #' @rdname check_modules_datanames+ ) |
|
| 148 | +387 |
- check_modules_datanames_html <- function(modules,+ |
|
| 149 | -+ | ||
| 388 | +! |
- datanames) {
+ unlist( |
|
| 150 | -178x | +||
| 389 | +! |
- check_datanames <- check_modules_datanames_recursive(modules, datanames)+ self$get_js( |
|
| 151 | -178x | +||
| 390 | +! |
- show_module_info <- inherits(modules, "teal_modules") # used in two contexts - module and app+ sprintf( |
|
| 152 | -178x | +||
| 391 | +! |
- if (!length(check_datanames)) {
+ "Array.from(document.querySelectorAll('%s')).map(el => el.checkVisibility({%s, %s, %s}))",
|
|
| 153 | -160x | +||
| 392 | +! |
- return(TRUE)+ selector, |
|
| 154 | +393 |
- }+ # Extra parameters |
|
| 155 | -18x | +||
| 394 | +! |
- shiny::tagList(+ sprintf("contentVisibilityAuto: %s", tolower(content_visibility_auto)),
|
|
| 156 | -18x | +||
| 395 | +! |
- lapply(+ sprintf("opacityProperty: %s", tolower(opacity_property)),
|
|
| 157 | -18x | +||
| 396 | +! |
- check_datanames,+ sprintf("visibilityProperty: %s", tolower(visibility_property))
|
|
| 158 | -18x | +||
| 397 | +
- function(mod) {
+ ) |
||
| 159 | -18x | +||
| 398 | +
- tagList(+ ) |
||
| 160 | -18x | +||
| 399 | +
- tags$span(+ ) |
||
| 161 | -18x | +||
| 400 | +
- tags$span(if (length(mod$missing_datanames) == 1) "Dataset" else "Datasets"),+ }, |
||
| 162 | -18x | +||
| 401 | +
- to_html_code_list(mod$missing_datanames),+ #' @description |
||
| 163 | -18x | +||
| 402 | +
- tags$span(+ #' Get the active filter variables from a dataset in the `teal` app. |
||
| 164 | -18x | +||
| 403 | +
- paste0(+ #' |
||
| 165 | -18x | +||
| 404 | +
- if (length(mod$missing_datanames) > 1) "are missing" else "is missing",+ #' @param dataset_name (character) The name of the dataset to get the filter variables from. |
||
| 166 | -18x | +||
| 405 | +
- if (show_module_info) sprintf(" for module '%s'.", mod$label) else "."
+ #' If `NULL`, the filter variables for all the datasets will be returned in a list. |
||
| 167 | +406 |
- )+ get_active_data_filters = function(dataset_name = NULL) {
|
|
| 168 | -+ | ||
| 407 | +! |
- )+ checkmate::check_string(dataset_name, null.ok = TRUE) |
|
| 169 | -+ | ||
| 408 | +! |
- ),+ datasets <- self$get_active_filter_vars() |
|
| 170 | -18x | +||
| 409 | +! |
- if (length(datanames) >= 1) {
+ checkmate::assert_subset(dataset_name, datasets) |
|
| 171 | -16x | +||
| 410 | +! |
- tagList(+ active_filters <- lapply( |
|
| 172 | -16x | +||
| 411 | +! |
- tags$span(if (length(datanames) == 1) "Dataset" else "Datasets"),+ datasets, |
|
| 173 | -16x | +||
| 412 | +! |
- tags$span("available in data:"),
+ function(x) {
|
|
| 174 | -16x | +||
| 413 | +! |
- tagList(+ var_names <- gsub( |
|
| 175 | -16x | +||
| 414 | +! |
- tags$span(+ pattern = "\\s", |
|
| 176 | -16x | +||
| 415 | +! |
- to_html_code_list(datanames),+ replacement = "", |
|
| 177 | -16x | +||
| 416 | +! |
- tags$span(".", .noWS = "outside"),
+ self$get_text( |
|
| 178 | -16x | +||
| 417 | +! |
- .noWS = c("outside")
+ sprintf( |
|
| 179 | -+ | ||
| 418 | +! |
- )+ "#%s-filters-%s .filter-card-varname",+ |
+ |
| 419 | +! | +
+ self$active_filters_ns(),+ |
+ |
| 420 | +! | +
+ x |
|
| 180 | +421 |
) |
|
| 181 | +422 |
) |
|
| 182 | +423 |
- } else {
+ ) |
|
| 183 | -2x | +||
| 424 | +! |
- tags$span("No datasets are available in data.")
+ structure( |
|
| 184 | -+ | ||
| 425 | +! |
- },+ lapply(var_names, private$get_active_filter_selection, dataset_name = x), |
|
| 185 | -18x | +||
| 426 | +! |
- tags$br(.noWS = "before")+ names = var_names |
|
| 186 | +427 |
- )+ ) |
|
| 187 | +428 |
- }+ } |
|
| 188 | +429 |
- )+ ) |
|
| 189 | -+ | ||
| 430 | +! |
- )+ names(active_filters) <- datasets |
|
| 190 | -+ | ||
| 431 | +! |
- }+ if (is.null(dataset_name)) {
|
|
| 191 | -+ | ||
| 432 | +! |
-
+ return(active_filters) |
|
| 192 | +433 |
- #' Recursively checks modules and returns list for every datanames mismatch between module and data+ }+ |
+ |
| 434 | +! | +
+ active_filters[[dataset_name]] |
|
| 193 | +435 |
- #' @noRd+ }, |
|
| 194 | +436 |
- check_modules_datanames_recursive <- function(modules, datanames) { # nolint: object_name_length
+ #' @description |
|
| 195 | -277x | +||
| 437 | +
- checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
+ #' Add a new variable from the dataset to be filtered. |
||
| 196 | -277x | +||
| 438 | +
- checkmate::assert_character(datanames)+ #' |
||
| 197 | -277x | +||
| 439 | +
- if (inherits(modules, "teal_modules")) {
+ #' @param dataset_name (character) The name of the dataset to add the filter variable to. |
||
| 198 | -79x | +||
| 440 | +
- unlist(+ #' @param var_name (character) The name of the variable to add to the filter panel. |
||
| 199 | -79x | +||
| 441 | +
- lapply(modules$children, check_modules_datanames_recursive, datanames = datanames),+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
||
| 200 | -79x | +||
| 442 | +
- recursive = FALSE+ #' |
||
| 201 | +443 |
- )+ #' @return The `TealAppDriver` object invisibly. |
|
| 202 | +444 |
- } else {
+ add_filter_var = function(dataset_name, var_name, ...) {
|
|
| 203 | -198x | +||
| 445 | +! |
- missing_datanames <- setdiff(modules$datanames, c("all", datanames))
+ checkmate::check_string(dataset_name) |
|
| 204 | -198x | +||
| 446 | +! |
- if (length(missing_datanames)) {
+ checkmate::check_string(var_name) |
|
| 205 | -18x | +||
| 447 | +! |
- list(list(+ private$set_active_ns() |
|
| 206 | -18x | +||
| 448 | +! |
- label = modules$label,+ self$click( |
|
| 207 | -18x | +||
| 449 | +! |
- missing_datanames = missing_datanames+ selector = sprintf( |
|
| 208 | -+ | ||
| 450 | +! |
- ))+ "#%s-filters-%s-add_filter_icon", |
|
| 209 | -+ | ||
| 451 | +! |
- }+ private$ns$filter_panel, |
|
| 210 | -+ | ||
| 452 | +! |
- }+ dataset_name |
|
| 211 | +453 |
- }+ ) |
|
| 212 | +454 |
-
+ ) |
|
| 213 | -+ | ||
| 455 | +! |
- #' Convert character vector to html code separated with commas and "and"+ self$set_input( |
|
| 214 | -+ | ||
| 456 | +! |
- #' @noRd+ sprintf( |
|
| 215 | -+ | ||
| 457 | +! |
- to_html_code_list <- function(x) {
+ "%s-filters-%s-%s-filter-var_to_add", |
|
| 216 | -34x | +||
| 458 | +! |
- checkmate::assert_character(x)+ private$ns$filter_panel, |
|
| 217 | -34x | +||
| 459 | +! |
- do.call(+ dataset_name, |
|
| 218 | -34x | +||
| 460 | +! |
- tagList,+ dataset_name |
|
| 219 | -34x | +||
| 461 | +
- lapply(seq_along(x), function(.ix) {
+ ), |
||
| 220 | -47x | +||
| 462 | +! |
- tagList(+ var_name, |
|
| 221 | -47x | +||
| 463 | +
- tags$code(x[.ix]),+ ... |
||
| 222 | -47x | +||
| 464 | +
- if (.ix != length(x)) {
+ ) |
||
| 223 | -1x | +||
| 465 | +! |
- if (.ix == length(x) - 1) tags$span(" and ") else tags$span(", ", .noWS = "before")
+ invisible(self) |
|
| 224 | +466 |
- }+ }, |
|
| 225 | +467 |
- )+ #' @description |
|
| 226 | +468 |
- })+ #' Remove an active filter variable of a dataset from the active filter variables panel. |
|
| 227 | +469 |
- )+ #' |
|
| 228 | +470 |
- }+ #' @param dataset_name (character) The name of the dataset to remove the filter variable from. |
|
| 229 | +471 |
-
+ #' If `NULL`, all the filter variables will be removed. |
|
| 230 | +472 |
-
+ #' @param var_name (character) The name of the variable to remove from the filter panel. |
|
| 231 | +473 |
- #' Check `datanames` in filters+ #' If `NULL`, all the filter variables of the dataset will be removed. |
|
| 232 | +474 |
- #'+ #' |
|
| 233 | +475 |
- #' This function checks whether `datanames` in filters correspond to those in `data`,+ #' @return The `TealAppDriver` object invisibly. |
|
| 234 | +476 |
- #' returning character vector with error messages or `TRUE` if all checks pass.+ remove_filter_var = function(dataset_name = NULL, var_name = NULL) {
|
|
| 235 | -+ | ||
| 477 | +! |
- #'+ checkmate::check_string(dataset_name, null.ok = TRUE) |
|
| 236 | -+ | ||
| 478 | +! |
- #' @param filters (`teal_slices`) object+ checkmate::check_string(var_name, null.ok = TRUE) |
|
| 237 | -+ | ||
| 479 | +! |
- #' @param datanames (`character`) names of datasets available in the `data` object+ if (is.null(dataset_name)) {
|
|
| 238 | -+ | ||
| 480 | +! |
- #'+ remove_selector <- sprintf( |
|
| 239 | -+ | ||
| 481 | +! |
- #' @return A `character(1)` containing error message or TRUE if validation passes.+ "#%s-active-remove_all_filters", |
|
| 240 | -+ | ||
| 482 | +! |
- #' @keywords internal+ self$active_filters_ns() |
|
| 241 | +483 |
- check_filter_datanames <- function(filters, datanames) {
+ ) |
|
| 242 | -79x | +||
| 484 | +! |
- checkmate::assert_class(filters, "teal_slices")+ } else if (is.null(var_name)) {
|
|
| 243 | -79x | +||
| 485 | +! |
- checkmate::assert_character(datanames)+ remove_selector <- sprintf( |
|
| 244 | -+ | ||
| 486 | +! |
-
+ "#%s-active-%s-remove_filters", |
|
| 245 | -+ | ||
| 487 | +! |
- # check teal_slices against datanames+ self$active_filters_ns(), |
|
| 246 | -79x | +||
| 488 | +! |
- out <- unlist(sapply(+ dataset_name |
|
| 247 | -79x | +||
| 489 | +
- filters, function(filter) {
+ ) |
||
| 248 | -24x | +||
| 490 | +
- dataname <- shiny::isolate(filter$dataname)+ } else {
|
||
| 249 | -24x | +||
| 491 | +! |
- if (!dataname %in% datanames) {
+ remove_selector <- sprintf( |
|
| 250 | -3x | +||
| 492 | +! |
- sprintf(+ "#%s-active-%s-filter-%s_%s-remove", |
|
| 251 | -3x | +||
| 493 | +! |
- "- Filter '%s' refers to dataname not available in 'data':\n %s not in (%s)",+ self$active_filters_ns(), |
|
| 252 | -3x | +||
| 494 | +! |
- shiny::isolate(filter$id),+ dataset_name, |
|
| 253 | -3x | +||
| 495 | +! |
- dQuote(dataname, q = FALSE),+ dataset_name, |
|
| 254 | -3x | +||
| 496 | +! |
- toString(dQuote(datanames, q = FALSE))+ var_name |
|
| 255 | +497 |
) |
|
| 256 | +498 |
} |
|
| 257 | -+ | ||
| 499 | +! |
- }+ self$click( |
|
| 258 | -+ | ||
| 500 | +! |
- ))+ selector = remove_selector |
|
| 259 | +501 |
-
+ )+ |
+ |
| 502 | +! | +
+ invisible(self) |
|
| 260 | +503 |
-
+ }, |
|
| 261 | -79x | +||
| 504 | +
- if (length(out)) {
+ #' @description |
||
| 262 | -3x | +||
| 505 | +
- paste(out, collapse = "\n")+ #' Set the active filter values for a variable of a dataset in the active filter variable panel. |
||
| 263 | +506 |
- } else {
+ #' |
|
| 264 | -76x | +||
| 507 | +
- TRUE+ #' @param dataset_name (character) The name of the dataset to set the filter value for. |
||
| 265 | +508 |
- }+ #' @param var_name (character) The name of the variable to set the filter value for. |
|
| 266 | +509 |
- }+ #' @param input The value to set the filter to. |
|
| 267 | +510 |
-
+ #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs` |
|
| 268 | +511 |
- #' Function for validating the title parameter of `teal::init`+ #' |
|
| 269 | +512 |
- #'+ #' @return The `TealAppDriver` object invisibly. |
|
| 270 | +513 |
- #' Checks if the input of the title from `teal::init` will create a valid title and favicon tag.+ set_active_filter_selection = function(dataset_name, |
|
| 271 | +514 |
- #' @param shiny_tag (`shiny.tag`) Object to validate for a valid title.+ var_name, |
|
| 272 | +515 |
- #' @keywords internal+ input, |
|
| 273 | +516 |
- validate_app_title_tag <- function(shiny_tag) {
+ ...) {
|
|
| 274 | -7x | +||
| 517 | +! |
- checkmate::assert_class(shiny_tag, "shiny.tag")+ checkmate::check_string(dataset_name) |
|
| 275 | -7x | +||
| 518 | +! |
- checkmate::assert_true(shiny_tag$name == "head")+ checkmate::check_string(var_name) |
|
| 276 | -6x | +||
| 519 | +! |
- child_names <- vapply(shiny_tag$children, `[[`, character(1L), "name")+ checkmate::check_string(input) |
|
| 277 | -6x | +||
| 520 | +
- checkmate::assert_subset(c("title", "link"), child_names, .var.name = "child tags")
+
|
||
| 278 | -4x | +||
| 521 | +! |
- rel_attr <- shiny_tag$children[[which(child_names == "link")]]$attribs$rel+ input_id_prefix <- sprintf( |
|
| 279 | -4x | +||
| 522 | +! |
- checkmate::assert_subset(+ "%s-filters-%s-filter-%s_%s-inputs", |
|
| 280 | -4x | +||
| 523 | +! |
- rel_attr,+ self$active_filters_ns(), |
|
| 281 | -4x | +||
| 524 | +! |
- c("icon", "shortcut icon"),
+ dataset_name, |
|
| 282 | -4x | +||
| 525 | +! |
- .var.name = "Link tag's rel attribute",+ dataset_name, |
|
| 283 | -4x | +||
| 526 | +! |
- empty.ok = FALSE+ var_name |
|
| 284 | +527 |
- )+ ) |
|
| 285 | +528 |
- }+ |
|
| 286 | +529 |
-
+ # Find the type of filter (based on filter panel) |
|
| 287 | -+ | ||
| 530 | +! |
- #' Build app title with favicon+ supported_suffix <- c("selection", "selection_manual")
|
|
| 288 | -+ | ||
| 531 | +! |
- #'+ slices_suffix <- supported_suffix[ |
|
| 289 | -+ | ||
| 532 | +! |
- #' A helper function to create the browser title along with a logo.+ match( |
|
| 290 | -+ | ||
| 533 | +! |
- #'+ TRUE, |
|
| 291 | -+ | ||
| 534 | +! |
- #' @param title (`character`) The browser title for the `teal` app.+ vapply( |
|
| 292 | -+ | ||
| 535 | +! |
- #' @param favicon (`character`) The path for the icon for the title.+ supported_suffix, |
|
| 293 | -+ | ||
| 536 | +! |
- #' The image/icon path can be remote or the static path accessible by `shiny`, like the `www/`+ function(suffix) {
|
|
| 294 | -+ | ||
| 537 | +! |
- #'+ !is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))
|
|
| 295 | +538 |
- #' @return A `shiny.tag` containing the element that adds the title and logo to the `shiny` app.+ },+ |
+ |
| 539 | +! | +
+ logical(1) |
|
| 296 | +540 |
- #' @export+ ) |
|
| 297 | +541 |
- build_app_title <- function(+ ) |
|
| 298 | +542 |
- title = "teal app",+ ] |
|
| 299 | +543 |
- favicon = "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png") {
+
|
|
| 300 | -13x | +||
| 544 | +
- checkmate::assert_string(title, null.ok = TRUE)+ # Generate correct namespace |
||
| 301 | -13x | +||
| 545 | +! |
- checkmate::assert_string(favicon, null.ok = TRUE)+ slices_input_id <- sprintf( |
|
| 302 | -13x | +||
| 546 | +! |
- tags$head(+ "%s-filters-%s-filter-%s_%s-inputs-%s", |
|
| 303 | -13x | +||
| 547 | +! |
- tags$title(title),+ self$active_filters_ns(), |
|
| 304 | -13x | +||
| 548 | +! |
- tags$link(+ dataset_name, |
|
| 305 | -13x | +||
| 549 | +! |
- rel = "icon",+ dataset_name, |
|
| 306 | -13x | +||
| 550 | +! |
- href = favicon,+ var_name, |
|
| 307 | -13x | +||
| 551 | +! |
- sizes = "any"+ slices_suffix |
|
| 308 | +552 |
- )+ ) |
|
| 309 | +553 |
- )+ |
|
| 310 | -+ | ||
| 554 | +! |
- }+ if (identical(slices_suffix, "selection_manual")) {
+ |
+ |
| 555 | +! | +
+ checkmate::assert_numeric(input, len = 2) |
|
| 311 | +556 | ||
| 312 | -+ | ||
| 557 | +! |
- #' Application ID+ dots <- rlang::list2(...) |
|
| 313 | -+ | ||
| 558 | +! |
- #'+ checkmate::assert_choice(dots$priority_, formals(self$set_inputs)[["priority_"]], null.ok = TRUE) |
|
| 314 | -+ | ||
| 559 | +! |
- #' Creates App ID used to match filter snapshots to application.+ checkmate::assert_flag(dots$wait_, null.ok = TRUE) |
|
| 315 | +560 |
- #'+ |
|
| 316 | -+ | ||
| 561 | +! |
- #' Calculate app ID that will be used to stamp filter state snapshots.+ self$run_js( |
|
| 317 | -+ | ||
| 562 | +! |
- #' App ID is a hash of the app's data and modules.+ sprintf( |
|
| 318 | -+ | ||
| 563 | +! |
- #' See "transferring snapshots" section in ?snapshot.+ "Shiny.setInputValue('%s:sw.numericRange', [%f, %f], {priority: '%s'})",
|
|
| 319 | -+ | ||
| 564 | +! |
- #'+ slices_input_id, |
|
| 320 | -+ | ||
| 565 | +! |
- #' @param data (`teal_data` or `teal_data_module`) as accepted by `init`+ input[[1]], |
|
| 321 | -+ | ||
| 566 | +! |
- #' @param modules (`teal_modules`) object as accepted by `init`+ input[[2]], |
|
| 322 | -+ | ||
| 567 | +! |
- #'+ priority_ = ifelse(is.null(dots$priority_), "input", dots$priority_) |
|
| 323 | +568 |
- #' @return A single character string.+ ) |
|
| 324 | +569 |
- #'+ ) |
|
| 325 | +570 |
- #' @keywords internal+ |
|
| 326 | -+ | ||
| 571 | +! |
- create_app_id <- function(data, modules) {
+ if (isTRUE(dots$wait_) || is.null(dots$wait_)) {
|
|
| 327 | -21x | +||
| 572 | +! |
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
+ self$wait_for_idle( |
|
| 328 | -20x | +||
| 573 | +! |
- checkmate::assert_class(modules, "teal_modules")+ timeout = if (is.null(dots$timeout_)) rlang::missing_arg() else dots$timeout_ |
|
| 329 | +574 |
-
+ ) |
|
| 330 | -19x | +||
| 575 | +
- data <- if (inherits(data, "teal_data")) {
+ } |
||
| 331 | -17x | +||
| 576 | +! |
- as.list(teal.code::get_env(data))+ } else if (identical(slices_suffix, "selection")) {
|
|
| 332 | -19x | +||
| 577 | +! |
- } else if (inherits(data, "teal_data_module")) {
+ self$set_input( |
|
| 333 | -2x | +||
| 578 | +! |
- deparse1(body(data$server))+ slices_input_id,+ |
+ |
| 579 | +! | +
+ input, |
|
| 334 | +580 |
- }+ ... |
|
| 335 | -19x | +||
| 581 | +
- modules <- lapply(modules, defunction)+ ) |
||
| 336 | +582 |
-
+ } else {
|
|
| 337 | -19x | +||
| 583 | +! |
- rlang::hash(list(data = data, modules = modules))+ stop("Filter selection set not supported for this slice.")
|
|
| 338 | +584 |
- }+ } |
|
| 339 | +585 | ||
| 340 | -+ | ||
| 586 | +! |
- #' Go through list and extract bodies of encountered functions as string, recursively.+ invisible(self) |
|
| 341 | +587 |
- #' @keywords internal+ }, |
|
| 342 | +588 |
- #' @noRd+ #' @description |
|
| 343 | +589 |
- defunction <- function(x) {
- |
- |
| 344 | -229x | -
- if (is.list(x)) {
+ #' Extract `html` attribute (found by a `selector`). |
|
| 345 | -67x | +||
| 590 | +
- lapply(x, defunction)+ #' |
||
| 346 | -162x | +||
| 591 | +
- } else if (is.function(x)) {
+ #' @param selector (`character(1)`) specifying the selector to be used to get the content of a specific node. |
||
| 347 | -50x | +||
| 592 | +
- deparse1(body(x))+ #' @param attribute (`character(1)`) name of an attribute to retrieve from a node specified by `selector`. |
||
| 348 | +593 |
- } else {
+ #' |
|
| 349 | -112x | +||
| 594 | +
- x+ #' @return The `character` vector. |
||
| 350 | +595 |
- }+ get_attr = function(selector, attribute) {
|
|
| 351 | -+ | ||
| 596 | +! |
- }+ rvest::html_attr( |
|
| 352 | -+ | ||
| 597 | +! |
-
+ rvest::html_nodes(self$get_html_rvest("html"), selector),
|
|
| 353 | -+ | ||
| 598 | +! |
- #' Get unique labels+ attribute |
|
| 354 | +599 |
- #'+ ) |
|
| 355 | +600 |
- #' Get unique labels for the modules to avoid namespace conflicts.+ }, |
|
| 356 | +601 |
- #'+ #' @description |
|
| 357 | +602 |
- #' @param labels (`character`) vector of labels+ #' Wrapper around `get_html` that passes the output directly to `rvest::read_html`. |
|
| 358 | +603 |
- #'+ #' |
|
| 359 | +604 |
- #' @return (`character`) vector of unique labels+ #' @param selector `(character(1))` passed to `get_html`. |
|
| 360 | +605 |
- #'+ #' |
|
| 361 | +606 |
- #' @keywords internal+ #' @return An XML document. |
|
| 362 | +607 |
- get_unique_labels <- function(labels) {
+ get_html_rvest = function(selector) {
|
|
| 363 | -215x | +||
| 608 | +! |
- make.unique(gsub("[^[:alnum:]]", "_", tolower(labels)), sep = "_")
+ rvest::read_html(self$get_html(selector)) |
|
| 364 | +609 |
- }+ }, |
|
| 365 | +610 |
-
+ #' Wrapper around `get_url()` method that opens the app in the browser. |
|
| 366 | +611 |
- #' Remove ANSI escape sequences from a string+ #' |
|
| 367 | +612 |
- #' @noRd+ #' @return Nothing. Opens the underlying teal app in the browser. |
|
| 368 | +613 |
- strip_style <- function(string) {
+ open_url = function() {
|
|
| 369 | -2x | +||
| 614 | +! |
- checkmate::assert_string(string)+ browseURL(self$get_url()) |
|
| 370 | +615 | - - | -|
| 371 | -2x | -
- gsub(- |
- |
| 372 | -2x | -
- "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]",
+ }, |
|
| 373 | +616 |
- "",- |
- |
| 374 | -2x | -
- string,- |
- |
| 375 | -2x | -
- perl = TRUE,+ #' @description |
|
| 376 | -2x | +||
| 617 | +
- useBytes = TRUE+ #' Waits until a specified input, output, or export value. |
||
| 377 | +618 |
- )+ #' This function serves as a wrapper around the `wait_for_value` method, |
|
| 378 | +619 |
- }+ #' providing a more flexible interface for waiting on different types of values within the active module namespace. |
|
| 379 | +620 |
-
+ #' @param input,output,export A name of an input, output, or export value. |
|
| 380 | +621 |
- #' @keywords internal+ #' Only one of these parameters may be used. |
|
| 381 | +622 |
- #' @noRd+ #' @param ... Must be empty. Allows for parameter expansion. |
|
| 382 | -4x | +||
| 623 | +
- pasten <- function(...) paste0(..., "\n")+ #' Parameter with additional value to passed in `wait_for_value`. |
||
| 383 | +624 |
-
+ wait_for_active_module_value = function(input = rlang::missing_arg(), |
|
| 384 | +625 |
- #' Convert character list to human readable html with commas and "and"+ output = rlang::missing_arg(), |
|
| 385 | +626 |
- #' @noRd+ export = rlang::missing_arg(), |
|
| 386 | +627 |
- paste_datanames_character <- function(x,+ ...) {
|
|
| 387 | -+ | ||
| 628 | +! |
- tags = list(span = shiny::tags$span, code = shiny::tags$code),+ ns <- shiny::NS(self$active_module_ns()) |
|
| 388 | +629 |
- tagList = shiny::tagList) { # nolint: object_name.
+
|
|
| 389 | +630 | ! |
- checkmate::assert_character(x)+ if (!rlang::is_missing(input) && checkmate::test_string(input, min.chars = 1)) input <- ns(input) |
| 390 | +631 | ! |
- do.call(+ if (!rlang::is_missing(output) && checkmate::test_string(output, min.chars = 1)) output <- ns(output) |
| 391 | +632 | ! |
- tagList,+ if (!rlang::is_missing(export) && checkmate::test_string(export, min.chars = 1)) export <- ns(export) |
| 392 | -! | +||
| 633 | +
- lapply(seq_along(x), function(.ix) {
+
|
||
| 393 | +634 | ! |
- tagList(+ self$wait_for_value( |
| 394 | +635 | ! |
- tags$code(x[.ix]),+ input = input, |
| 395 | +636 | ! |
- if (.ix != length(x)) {
+ output = output, |
| 396 | +637 | ! |
- tags$span(ifelse(.ix == length(x) - 1, " and ", ", "))+ export = export, |
| 397 | +638 |
- }+ ... |
|
| 398 | +639 |
) |
|
| 399 | +640 |
- })+ } |
|
| 400 | +641 |
- )+ ), |
|
| 401 | +642 |
- }+ # private members ---- |
|
| 402 | +643 |
-
+ private = list( |
|
| 403 | +644 |
- #' Build datanames error string for error message+ # private attributes ---- |
|
| 404 | +645 |
- #'+ data = NULL, |
|
| 405 | +646 |
- #' tags and tagList are overwritten in arguments allowing to create strings for+ modules = NULL, |
|
| 406 | +647 |
- #' logging purposes+ filter = teal_slices(), |
|
| 407 | +648 |
- #' @noRd+ ns = list( |
|
| 408 | +649 |
- build_datanames_error_message <- function(label = NULL,+ module = character(0), |
|
| 409 | +650 |
- datanames,+ filter_panel = character(0) |
|
| 410 | +651 |
- extra_datanames,+ ), |
|
| 411 | +652 |
- tags = list(span = shiny::tags$span, code = shiny::tags$code),+ # private methods ---- |
|
| 412 | +653 |
- tagList = shiny::tagList) { # nolint: object_name.
+ set_active_ns = function() {
|
|
| 413 | +654 | ! |
- tags$span(+ all_inputs <- self$get_values()$input |
| 414 | +655 | ! |
- tags$span(ifelse(length(extra_datanames) > 1, "Datasets", "Dataset")),+ active_tab_inputs <- all_inputs[grepl("-active_tab$", names(all_inputs))]
+ |
+
| 656 | ++ | + | |
| 415 | +657 | ! |
- paste_datanames_character(extra_datanames, tags, tagList),+ tab_ns <- unlist(lapply(names(active_tab_inputs), function(name) {
|
| 416 | +658 | ! |
- tags$span(+ gsub( |
| 417 | +659 | ! |
- paste0(+ pattern = "-active_tab$", |
| 418 | +660 | ! |
- ifelse(length(extra_datanames) > 1, "are missing", "is missing"),+ replacement = sprintf("-%s", active_tab_inputs[[name]]),
|
| 419 | +661 | ! |
- ifelse(is.null(label), ".", sprintf(" for tab '%s'.", label))
+ name |
| 420 | +662 |
- )+ ) |
|
| 421 | +663 |
- ),+ })) |
|
| 422 | +664 | ! |
- if (length(datanames) >= 1) {
+ active_ns <- tab_ns[1] |
| 423 | +665 | ! |
- tagList(+ if (length(tab_ns) > 1) {
|
| 424 | +666 | ! |
- tags$span(ifelse(length(datanames) > 1, "Datasets", "Dataset")),+ for (i in 2:length(tab_ns)) {
|
| 425 | +667 | ! |
- tags$span("available in data:"),
+ next_ns <- tab_ns[i] |
| 426 | +668 | ! |
- tagList(+ if (grepl(pattern = active_ns, next_ns)) {
|
| 427 | +669 | ! |
- tags$span(+ active_ns <- next_ns+ |
+
| 670 | ++ |
+ }+ |
+ |
| 671 | ++ |
+ }+ |
+ |
| 672 | ++ |
+ } |
|
| 428 | +673 | ! |
- paste_datanames_character(datanames, tags, tagList),+ private$ns$module <- sprintf("%s-%s", active_ns, "module")
+ |
+
| 674 | ++ | + | |
| 429 | +675 | ! |
- tags$span(".", .noWS = "outside"),
+ components <- c("filter_panel", "data_summary")
|
| 430 | +676 | ! |
- .noWS = c("outside")
+ for (component in components) {
|
| 431 | +677 |
- )+ if ( |
|
| 432 | -+ | ||
| 678 | +! |
- )+ !is.null(self$get_html(sprintf("#%s-%s-panel", active_ns, component))) ||
|
|
| 433 | -+ | ||
| 679 | +! |
- )+ !is.null(self$get_html(sprintf("#%s-%s-table", active_ns, component)))
|
|
| 434 | +680 |
- } else {
+ ) {
|
|
| 435 | +681 | ! |
- tags$span("No datasets are available in data.")
+ private$ns[[component]] <- sprintf("%s-%s", active_ns, component)
|
| 436 | +682 |
- }+ } else {
+ |
+ |
| 683 | +! | +
+ private$ns[[component]] <- sprintf("%s-module_%s", active_ns, component)
|
|
| 437 | +684 |
- )+ } |
|
| 438 | +685 |
- }+ } |
|
| 439 | +686 |
-
+ }, |
|
| 440 | +687 |
- #' Smart `rbind`+ # @description |
|
| 441 | +688 |
- #'+ # Get the active filter values from the active filter selection of dataset from the filter panel. |
|
| 442 | +689 |
- #' Combine `data.frame` objects which have different columns+ # |
|
| 443 | +690 |
- #'+ # @param dataset_name (character) The name of the dataset to get the filter values from. |
|
| 444 | +691 |
- #' @param ... (`data.frame`)+ # @param var_name (character) The name of the variable to get the filter values from. |
|
| 445 | +692 |
- #' @keywords internal+ # |
|
| 446 | +693 |
- .smart_rbind <- function(...) {
+ # @return The value of the active filter selection. |
|
| 447 | -82x | +||
| 694 | +
- dots <- list(...)+ get_active_filter_selection = function(dataset_name, var_name) {
|
||
| 448 | -82x | +||
| 695 | +! |
- checkmate::assert_list(dots, "data.frame", .var.name = "...")+ checkmate::check_string(dataset_name) |
|
| 449 | -82x | +||
| 696 | +! |
- Reduce(+ checkmate::check_string(var_name) |
|
| 450 | -82x | +||
| 697 | +! |
- x = dots,+ input_id_prefix <- sprintf( |
|
| 451 | -82x | +||
| 698 | +! |
- function(x, y) {
+ "%s-filters-%s-filter-%s_%s-inputs", |
|
| 452 | -69x | +||
| 699 | +! |
- all_columns <- union(colnames(x), colnames(y))+ self$active_filters_ns(), |
|
| 453 | -69x | +||
| 700 | +! |
- x[setdiff(all_columns, colnames(x))] <- NA+ dataset_name, |
|
| 454 | -69x | +||
| 701 | +! |
- y[setdiff(all_columns, colnames(y))] <- NA+ dataset_name, |
|
| 455 | -69x | +||
| 702 | +! |
- rbind(x, y)+ var_name |
|
| 456 | +703 |
- }+ ) |
|
| 457 | +704 |
- )+ |
|
| 458 | +705 |
- }+ # Find the type of filter (categorical or range) |
| 1 | -+ | ||
| 706 | +! |
- #' Manage multiple `FilteredData` objects+ supported_suffix <- c("selection", "selection_manual")
|
|
| 2 | -+ | ||
| 707 | +! |
- #'+ for (suffix in supported_suffix) {
|
|
| 3 | -+ | ||
| 708 | +! |
- #' @description+ if (!is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))) {
|
|
| 4 | -+ | ||
| 709 | +! |
- #' Oversee filter states across the entire application.+ return(self$get_value(input = sprintf("%s-%s", input_id_prefix, suffix)))
|
|
| 5 | +710 |
- #'+ } |
|
| 6 | +711 |
- #' @section Slices global:+ } |
|
| 7 | +712 |
- #' The key role in maintaining the module-specific filter states is played by the `.slicesGlobal`+ |
|
| 8 | -+ | ||
| 713 | +! |
- #' object. It is a reference class that holds the following fields:+ NULL # If there are not any supported filters |
|
| 9 | +714 |
- #' - `all_slices` (`reactiveVal`) - reactive value containing all filters registered in an app.+ }, |
|
| 10 | +715 |
- #' - `module_slices_api` (`reactiveValues`) - reactive field containing references to each modules'+ # @description |
|
| 11 | +716 |
- #' `FilteredData` object methods. At this moment it is used only in `srv_filter_manager` to display+ # Check if the page is stable without any `DOM` updates in the body of the app. |
|
| 12 | +717 |
- #' the filter states in a table combining informations from `all_slices` and from+ # This is achieved by blocing the R process by sleeping until the page is unchanged till the `stability_period`. |
|
| 13 | +718 |
- #' `FilteredData$get_available_teal_slices()`.+ # @param stability_period (`numeric(1)`) The time in milliseconds to wait till the page to be stable. |
|
| 14 | +719 |
- #'+ # @param check_interval (`numeric(1)`) The time in milliseconds to check for changes in the page. |
|
| 15 | +720 |
- #' During a session only new filters are added to `all_slices` unless [`module_snapshot_manager`] is+ # The stability check is reset when a change is detected in the page after sleeping for check_interval. |
|
| 16 | +721 |
- #' used to restore previous state. Filters from `all_slices` can be activated or deactivated in a+ wait_for_page_stability = function(stability_period = 2000, check_interval = 200) {
|
|
| 17 | -+ | ||
| 722 | +! |
- #' module which is linked (both ways) by `attr(, "mapping")` so that:+ previous_content <- self$get_html("body")
|
|
| 18 | -+ | ||
| 723 | +! |
- #' - If module's filter is added or removed in its `FilteredData` object, this information is passed+ end_time <- Sys.time() + (stability_period / 1000) |
|
| 19 | +724 |
- #' to `SlicesGlobal` which updates `attr(, "mapping")` accordingly.+ |
|
| 20 | -+ | ||
| 725 | +! |
- #' - When mapping changes in a `SlicesGlobal`, filters are set or removed from module's+ repeat {
|
|
| 21 | -+ | ||
| 726 | +! |
- #' `FilteredData`.+ Sys.sleep(check_interval / 1000) |
|
| 22 | -+ | ||
| 727 | +! |
- #'+ current_content <- self$get_html("body")
|
|
| 23 | +728 |
- #' @section Filter manager:+ |
|
| 24 | -+ | ||
| 729 | +! |
- #' Filter-manager is split into two parts:+ if (!identical(previous_content, current_content)) {
|
|
| 25 | -+ | ||
| 730 | +! |
- #' 1. `ui/srv_filter_manager_panel` - Called once for the whole app. This module observes changes in+ previous_content <- current_content |
|
| 26 | -+ | ||
| 731 | +! |
- #' the filters in `slices_global` and displays them in a table utilizing information from `mapping`:+ end_time <- Sys.time() + (stability_period / 1000) |
|
| 27 | -+ | ||
| 732 | +! |
- #' - (`TRUE`) - filter is active in the module+ } else if (Sys.time() >= end_time) {
|
|
| 28 | -+ | ||
| 733 | +! |
- #' - (`FALSE`) - filter is inactive in the module+ break |
|
| 29 | +734 |
- #' - (`NA`) - filter is not available in the module+ } |
|
| 30 | +735 |
- #' 2. `ui/srv_module_filter_manager` - Called once for each `teal_module`. Handling filter states+ } |
|
| 31 | +736 |
- #' for of single module and keeping module `FilteredData` consistent with `slices_global`, so that+ }+ |
+ |
| 737 | ++ |
+ )+ |
+ |
| 738 | ++ |
+ )+ |
+
| 1 | ++ |
+ setOldClass("teal_module")
+ |
+ |
| 2 | ++ |
+ setOldClass("teal_modules")
+ |
+ |
| 3 | ++ | + + | +|
| 4 | ++ |
+ #' Create `teal_module` and `teal_modules` objects+ |
+ |
| 5 | ++ |
+ #'+ |
+ |
| 6 | ++ |
+ #' @description+ |
+ |
| 7 | ++ |
+ #' `r lifecycle::badge("stable")`
+ |
+ |
| 8 | ++ |
+ #' Create a nested tab structure to embed modules in a `teal` application.+ |
+ |
| 9 | ++ |
+ #'+ |
+ |
| 10 | ++ |
+ #' @details+ |
+ |
| 11 | ++ |
+ #' `module()` creates an instance of a `teal_module` that can be placed in a `teal` application.+ |
+ |
| 12 | ++ |
+ #' `modules()` shapes the structure of a the application by organizing `teal_module` within the navigation panel.+ |
+ |
| 13 | ++ |
+ #' It wraps `teal_module` and `teal_modules` objects in a `teal_modules` object,+ |
+ |
| 14 | ++ |
+ #' which results in a nested structure corresponding to the nested tabs in the final application.+ |
+ |
| 15 | ++ |
+ #'+ |
+ |
| 16 | ++ |
+ #' Note that for `modules()` `label` comes after `...`, so it must be passed as a named argument,+ |
+ |
| 17 | ++ |
+ #' otherwise it will be captured by `...`.+ |
+ |
| 18 | ++ |
+ #'+ |
+ |
| 19 | ++ |
+ #' The labels `"global_filters"` and `"Report previewer"` are reserved+ |
+ |
| 20 | ++ |
+ #' because they are used by the `mapping` argument of [teal_slices()]+ |
+ |
| 21 | ++ |
+ #' and the report previewer module [reporter_previewer_module()], respectively.+ |
+ |
| 22 | ++ |
+ #'+ |
+ |
| 23 | ++ |
+ #' # Restricting datasets used by `teal_module`:+ |
+ |
| 24 | ++ |
+ #' The `datanames` argument controls which datasets are used by the module’s server. These datasets,+ |
+ |
| 25 | ++ |
+ #' passed via server's `data` argument, are the only ones shown in the module's tab.+ |
+ |
| 26 | ++ |
+ #'+ |
+ |
| 27 | ++ |
+ #' When `datanames` is set to `"all"`, all datasets in the data object are treated as relevant.+ |
+ |
| 28 | ++ |
+ #' However, this may include unnecessary datasets, such as:+ |
+ |
| 29 | ++ |
+ #' - Proxy variables for column modifications+ |
+ |
| 30 | ++ |
+ #' - Temporary datasets used to create final versions+ |
+ |
| 31 | ++ |
+ #' - Connection objects |
|
| 32 |
- #' local filters are always reflected in the `slices_global` and its mapping and vice versa.+ #' |
||
| 33 |
- #'+ #' To exclude irrelevant datasets, use the [set_datanames()] function to change `datanames` from |
||
| 34 |
- #'+ #' `"all"` to specific names. Trying to modify non-`"all"` values with [set_datanames()] will result |
||
| 35 |
- #' @param id (`character(1)`)+ #' in a warning. Datasets with names starting with . are ignored globally unless explicitly listed |
||
| 36 |
- #' `shiny` module instance id.+ #' in `datanames`. |
||
| 38 |
- #' @param slices_global (`reactiveVal`)+ #' # `datanames` with `transformers` |
||
| 39 |
- #' containing `teal_slices`.+ #' When transformers are specified, their `datanames` are added to the module’s `datanames`, which |
||
| 40 |
- #'+ #' changes the behavior as follows: |
||
| 41 |
- #' @param module_fd (`FilteredData`)+ #' - If `module(datanames)` is `NULL` and the `transformers` have defined `datanames`, the sidebar |
||
| 42 |
- #' Object containing the data to be filtered in a single `teal` module.+ #' will appear showing the `transformers`' datasets, instead of being hidden. |
||
| 43 |
- #'+ #' - If `module(datanames)` is set to specific values and any `transformer` has `datanames = "all"`, |
||
| 44 |
- #' @return+ #' the module may receive extra datasets that could be unnecessary |
||
| 45 |
- #' Module returns a `slices_global` (`reactiveVal`) containing a `teal_slices` object with mapping.+ #' |
||
| 46 |
- #'+ #' @param label (`character(1)`) Label shown in the navigation item for the module or module group. |
||
| 47 |
- #' @encoding UTF-8+ #' For `modules()` defaults to `"root"`. See `Details`. |
||
| 48 |
- #'+ #' @param server (`function`) `shiny` module with following arguments: |
||
| 49 |
- #' @name module_filter_manager+ #' - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]). |
||
| 50 |
- #' @rdname module_filter_manager+ #' - `input`, `output`, `session` - (optional; not recommended) When provided, then [shiny::callModule()] |
||
| 51 |
- #'+ #' will be used to call a module. From `shiny` 1.5.0, the recommended way is to use |
||
| 52 |
- NULL+ #' [shiny::moduleServer()] instead which doesn't require these arguments. |
||
| 53 |
-
+ #' - `data` (optional) When provided, the module will be called with `teal_data` object (i.e. a list of |
||
| 54 |
- #' @rdname module_filter_manager+ #' reactive (filtered) data specified in the `filters` argument) as the value of this argument. |
||
| 55 |
- ui_filter_manager_panel <- function(id) {
+ #' - `datasets` (optional) When provided, the module will be called with `FilteredData` object as the |
||
| 56 | -! | +
- ns <- NS(id)+ #' value of this argument. (See [`teal.slice::FilteredData`]). |
|
| 57 | -! | +
- tags$button(+ #' - `reporter` (optional) When provided, the module will be called with `Reporter` object as the value |
|
| 58 | -! | +
- id = ns("show_filter_manager"),
+ #' of this argument. (See [`teal.reporter::Reporter`]). |
|
| 59 | -! | +
- class = "btn action-button wunder_bar_button",+ #' - `filter_panel_api` (optional) When provided, the module will be called with `FilterPanelAPI` object |
|
| 60 | -! | +
- title = "View filter mapping",+ #' as the value of this argument. (See [`teal.slice::FilterPanelAPI`]). |
|
| 61 | -! | +
- suppressMessages(icon("fas fa-grip"))
+ #' - `...` (optional) When provided, `server_args` elements will be passed to the module named argument |
|
| 62 |
- )+ #' or to the `...`. |
||
| 63 |
- }+ #' @param ui (`function`) `shiny` UI module function with following arguments: |
||
| 64 |
-
+ #' - `id` - `teal` will set proper `shiny` namespace for this module. |
||
| 65 |
- #' @rdname module_filter_manager+ #' - `...` (optional) When provided, `ui_args` elements will be passed to the module named argument |
||
| 66 |
- #' @keywords internal+ #' or to the `...`. |
||
| 67 |
- srv_filter_manager_panel <- function(id, slices_global) {
+ #' @param filters (`character`) Deprecated. Use `datanames` instead. |
||
| 68 | -82x | +
- checkmate::assert_string(id)+ #' @param datanames (`character`) Names of the datasets relevant to the item. |
|
| 69 | -82x | +
- checkmate::assert_class(slices_global, ".slicesGlobal")+ #' There are 2 reserved values that have specific behaviors: |
|
| 70 | -82x | +
- moduleServer(id, function(input, output, session) {
+ #' - The keyword `"all"` includes all datasets available in the data passed to the teal application. |
|
| 71 | -82x | +
- setBookmarkExclude(c("show_filter_manager"))
+ #' - `NULL` hides the sidebar panel completely. |
|
| 72 | -82x | +
- observeEvent(input$show_filter_manager, {
+ #' - If `transformers` are specified, their `datanames` are automatically added to this `datanames` |
|
| 73 | -! | +
- logger::log_debug("srv_filter_manager_panel@1 show_filter_manager button has been clicked.")
+ #' argument. |
|
| 74 | -! | +
- showModal(+ #' @param server_args (named `list`) with additional arguments passed on to the server function. |
|
| 75 | -! | +
- modalDialog(+ #' @param ui_args (named `list`) with additional arguments passed on to the UI function. |
|
| 76 | -! | +
- ui_filter_manager(session$ns("filter_manager")),
+ #' @param x (`teal_module` or `teal_modules`) Object to format/print. |
|
| 77 | -! | +
- class = "filter_manager_modal",+ #' @param indent (`integer(1)`) Indention level; each nested element is indented one level more. |
|
| 78 | -! | +
- size = "l",+ #' @param transformers (`list` of `teal_data_module`) that will be applied to transform the data. |
|
| 79 | -! | +
- footer = NULL,+ #' Each transform module UI will appear in the `teal`'s sidebar panel. |
|
| 80 | -! | +
- easyClose = TRUE+ #' Transformers' `datanames` are added to the `datanames`. See [teal_transform_module()]. |
|
| 81 |
- )+ #' |
||
| 82 |
- )+ #' @param ... |
||
| 83 |
- })+ #' - For `modules()`: (`teal_module` or `teal_modules`) Objects to wrap into a tab. |
||
| 84 | -82x | +
- srv_filter_manager("filter_manager", slices_global = slices_global)
+ #' - For `format()` and `print()`: Arguments passed to other methods. |
|
| 85 |
- })+ #' |
||
| 86 |
- }+ #' @return |
||
| 87 |
-
+ #' `module()` returns an object of class `teal_module`. |
||
| 88 |
- #' @rdname module_filter_manager+ #' |
||
| 89 |
- ui_filter_manager <- function(id) {
+ #' `modules()` returns a `teal_modules` object which contains following fields: |
||
| 90 | -! | +
- ns <- NS(id)+ #' - `label`: taken from the `label` argument. |
|
| 91 | -! | +
- actionButton(ns("filter_manager"), NULL, icon = icon("fas fa-filter"))
+ #' - `children`: a list containing objects passed in `...`. List elements are named after |
|
| 92 | -! | +
- tags$div(+ #' their `label` attribute converted to a valid `shiny` id. |
|
| 93 | -! | +
- class = "filter_manager_content",+ #' |
|
| 94 | -! | +
- tableOutput(ns("slices_table"))
+ #' @name teal_modules |
|
| 95 |
- )+ #' @aliases teal_module |
||
| 96 |
- }+ #' |
||
| 97 |
-
+ #' @examples |
||
| 98 |
- #' @rdname module_filter_manager+ #' library(shiny) |
||
| 99 |
- srv_filter_manager <- function(id, slices_global) {
+ #' |
||
| 100 | -82x | +
- checkmate::assert_string(id)+ #' module_1 <- module( |
|
| 101 | -82x | +
- checkmate::assert_class(slices_global, ".slicesGlobal")+ #' label = "a module", |
|
| 102 |
-
+ #' server = function(id, data) {
|
||
| 103 | -82x | +
- moduleServer(id, function(input, output, session) {
+ #' moduleServer( |
|
| 104 | -82x | +
- logger::log_debug("filter_manager_srv initializing.")
+ #' id, |
|
| 105 |
-
+ #' module = function(input, output, session) {
|
||
| 106 |
- # Bookmark slices global with mapping.+ #' output$data <- renderDataTable(data()[["iris"]]) |
||
| 107 | -82x | +
- session$onBookmark(function(state) {
+ #' } |
|
| 108 | -! | +
- logger::log_debug("filter_manager_srv@onBookmark: storing filter state")
+ #' ) |
|
| 109 | -! | +
- state$values$filter_state_on_bookmark <- as.list(+ #' }, |
|
| 110 | -! | +
- slices_global$all_slices(),+ #' ui = function(id) {
|
|
| 111 | -! | +
- recursive = TRUE+ #' ns <- NS(id) |
|
| 112 |
- )+ #' tagList(dataTableOutput(ns("data")))
|
||
| 113 |
- })+ #' }, |
||
| 114 |
-
+ #' datanames = "all" |
||
| 115 | -82x | +
- bookmarked_slices <- restoreValue(session$ns("filter_state_on_bookmark"), NULL)
+ #' ) |
|
| 116 | -82x | +
- if (!is.null(bookmarked_slices)) {
+ #' |
|
| 117 | -! | +
- logger::log_debug("filter_manager_srv: restoring filter state from bookmark.")
+ #' module_2 <- module( |
|
| 118 | -! | +
- slices_global$slices_set(bookmarked_slices)+ #' label = "another module", |
|
| 119 |
- }+ #' server = function(id) {
|
||
| 120 |
-
+ #' moduleServer( |
||
| 121 | -82x | +
- mapping_table <- reactive({
+ #' id, |
|
| 122 |
- # We want this to be reactive on slices_global$all_slices() only as get_available_teal_slices()+ #' module = function(input, output, session) {
|
||
| 123 |
- # is dependent on slices_global$all_slices().+ #' output$text <- renderText("Another Module")
|
||
| 124 | -91x | +
- module_labels <- setdiff(+ #' } |
|
| 125 | -91x | +
- names(attr(slices_global$all_slices(), "mapping")),+ #' ) |
|
| 126 | -91x | +
- "Report previewer"+ #' }, |
|
| 127 |
- )+ #' ui = function(id) {
|
||
| 128 | -91x | +
- isolate({
+ #' ns <- NS(id) |
|
| 129 | -91x | +
- mm <- as.data.frame(+ #' tagList(textOutput(ns("text")))
|
|
| 130 | -91x | +
- sapply(+ #' }, |
|
| 131 | -91x | +
- module_labels,+ #' datanames = NULL |
|
| 132 | -91x | +
- simplify = FALSE,+ #' ) |
|
| 133 | -91x | +
- function(module_label) {
+ #' |
|
| 134 | -104x | +
- available_slices <- slices_global$module_slices_api[[module_label]]$get_available_teal_slices()+ #' modules <- modules( |
|
| 135 | -96x | +
- global_ids <- sapply(slices_global$all_slices(), `[[`, "id", simplify = FALSE)+ #' label = "modules", |
|
| 136 | -96x | +
- module_ids <- sapply(slices_global$slices_get(module_label), `[[`, "id", simplify = FALSE)+ #' modules( |
|
| 137 | -96x | +
- allowed_ids <- vapply(available_slices, `[[`, character(1L), "id")+ #' label = "nested modules", |
|
| 138 | -96x | +
- active_ids <- global_ids %in% module_ids+ #' module_1 |
|
| 139 | -96x | +
- setNames(nm = global_ids, ifelse(global_ids %in% allowed_ids, active_ids, NA))+ #' ), |
|
| 140 |
- }+ #' module_2 |
||
| 141 |
- ),+ #' ) |
||
| 142 | -91x | +
- check.names = FALSE+ #' |
|
| 143 |
- )+ #' app <- init( |
||
| 144 | -83x | +
- colnames(mm)[colnames(mm) == "global_filters"] <- "Global filters"+ #' data = teal_data(iris = iris), |
|
| 145 |
-
+ #' modules = modules |
||
| 146 | -83x | +
- mm+ #' ) |
|
| 147 |
- })+ #' |
||
| 148 |
- })+ #' if (interactive()) {
|
||
| 149 |
-
+ #' shinyApp(app$ui, app$server) |
||
| 150 | -82x | +
- output$slices_table <- renderTable(+ #' } |
|
| 151 | -82x | +
- expr = {
+ #' @rdname teal_modules |
|
| 152 | -91x | +
- logger::log_debug("filter_manager_srv@1 rendering slices_table.")
+ #' @export |
|
| 153 | -91x | +
- mm <- mapping_table()+ #' |
|
| 154 |
-
+ module <- function(label = "module", |
||
| 155 |
- # Display logical values as UTF characters.+ server = function(id, data, ...) moduleServer(id, function(input, output, session) NULL), |
||
| 156 | -83x | +
- mm[] <- lapply(mm, ifelse, yes = intToUtf8(9989), no = intToUtf8(10060))+ ui = function(id, ...) tags$p(paste0("This module has no UI (id: ", id, " )")),
|
|
| 157 | -83x | +
- mm[] <- lapply(mm, function(x) ifelse(is.na(x), intToUtf8(128306), x))+ filters, |
|
| 158 |
-
+ datanames = "all", |
||
| 159 |
- # Display placeholder if no filters defined.+ server_args = NULL, |
||
| 160 | -83x | +
- if (nrow(mm) == 0L) {
+ ui_args = NULL, |
|
| 161 | -59x | +
- mm <- data.frame(`Filter manager` = "No filters specified.", check.names = FALSE)+ transformers = list()) {
|
|
| 162 | -59x | +
- rownames(mm) <- ""+ # argument checking (independent) |
|
| 163 |
- }+ ## `label` |
||
| 164 | -83x | +213x |
- mm+ checkmate::assert_string(label) |
| 165 | -+ | 210x |
- },+ if (label == "global_filters") {
|
| 166 | -82x | +1x |
- rownames = TRUE+ stop( |
| 167 | -+ | 1x |
- )+ sprintf("module(label = \"%s\", ...\n ", label),
|
| 168 | -+ | 1x |
-
+ "Label 'global_filters' is reserved in teal. Please change to something else.", |
| 169 | -82x | +1x |
- mapping_table # for testing purpose+ call. = FALSE |
| 170 |
- })+ ) |
||
| 171 |
- }+ } |
||
| 172 | -+ | 209x |
-
+ if (label == "Report previewer") {
|
| 173 | -+ | ! |
- #' @rdname module_filter_manager+ stop( |
| 174 | -+ | ! |
- srv_module_filter_manager <- function(id, module_fd, slices_global) {
+ sprintf("module(label = \"%s\", ...\n ", label),
|
| 175 | -107x | +! |
- checkmate::assert_string(id)+ "Label 'Report previewer' is reserved in teal. Please change to something else.", |
| 176 | -107x | +! |
- assert_reactive(module_fd)+ call. = FALSE |
| 177 | -107x | +
- checkmate::assert_class(slices_global, ".slicesGlobal")+ ) |
|
| 178 |
-
+ } |
||
| 179 | -107x | +
- moduleServer(id, function(input, output, session) {
+
|
|
| 180 | -107x | +
- logger::log_debug("srv_module_filter_manager initializing for module: { id }.")
+ ## server |
|
| 181 | -+ | 209x |
- # Track filter global and local states.+ checkmate::assert_function(server) |
| 182 | -107x | +209x |
- slices_global_module <- reactive({
+ server_formals <- names(formals(server)) |
| 183 | -193x | +209x |
- slices_global$slices_get(module_label = id)+ if (!( |
| 184 | -+ | 209x |
- })+ "id" %in% server_formals || |
| 185 | -107x | +209x |
- slices_module <- reactive(req(module_fd())$get_filter_state())+ all(c("input", "output", "session") %in% server_formals)
|
| 186 |
-
+ )) {
|
||
| 187 | -107x | +2x |
- module_fd_previous <- reactiveVal(NULL)+ stop( |
| 188 | -+ | 2x |
-
+ "\nmodule() `server` argument requires a function with following arguments:", |
| 189 | -+ | 2x |
- # Set (reactively) available filters for the module.+ "\n - id - `teal` will set proper `shiny` namespace for this module.", |
| 190 | -107x | +2x |
- obs1 <- observeEvent(module_fd(), priority = 1, {
+ "\n - input, output, session (not recommended) - then `shiny::callModule` will be used to call a module.", |
| 191 | -88x | +2x |
- logger::log_debug("srv_module_filter_manager@1 setting initial slices for module: { id }.")
+ "\n\nFollowing arguments can be used optionaly:", |
| 192 | -+ | 2x |
- # Filters relevant for the module in module-specific app.+ "\n - `data` - module will receive list of reactive (filtered) data specified in the `filters` argument", |
| 193 | -88x | +2x |
- slices <- slices_global_module()+ "\n - `datasets` - module will receive `FilteredData`. See `help(teal.slice::FilteredData)`", |
| 194 | -+ | 2x |
-
+ "\n - `reporter` - module will receive `Reporter`. See `help(teal.reporter::Reporter)`", |
| 195 | -+ | 2x |
- # Clean up previous filter states and refresh cache of previous module_fd with current+ "\n - `filter_panel_api` - module will receive `FilterPanelAPI`. (See [teal.slice::FilterPanelAPI]).", |
| 196 | -3x | +2x |
- if (!is.null(module_fd_previous())) module_fd_previous()$finalize()+ "\n - `...` server_args elements will be passed to the module named argument or to the `...`" |
| 197 | -88x | +
- module_fd_previous(module_fd())+ ) |
|
| 198 |
-
+ } |
||
| 199 | -+ | 207x |
- # Setting filter states from slices_global:+ if ("datasets" %in% server_formals) {
|
| 200 | -+ | 2x |
- # 1. when app initializes slices_global set to initial filters (specified by app developer)+ warning( |
| 201 | -+ | 2x |
- # 2. when data reinitializes slices_global reflects latest filter states+ sprintf("Called from module(label = \"%s\", ...)\n ", label),
|
| 202 | -+ | 2x |
-
+ "`datasets` argument in the server is deprecated and will be removed in the next release. ", |
| 203 | -88x | +2x |
- module_fd()$set_filter_state(slices)+ "Please use `data` instead.", |
| 204 | -+ | 2x |
-
+ call. = FALSE |
| 205 |
- # irrelevant filters are discarded in FilteredData$set_available_teal_slices+ ) |
||
| 206 |
- # it means we don't need to subset slices_global$all_slices() from filters refering to irrelevant datasets+ } |
||
| 207 | -88x | +
- module_fd()$set_available_teal_slices(slices_global$all_slices)+ |
|
| 209 |
- # this needed in filter_manager_srv+ ## UI |
||
| 210 | -88x | +207x |
- slices_global$module_slices_api_set(+ checkmate::assert_function(ui) |
| 211 | -88x | +207x |
- id,+ ui_formals <- names(formals(ui)) |
| 212 | -88x | +207x |
- list(+ if (!"id" %in% ui_formals) {
|
| 213 | -88x | +1x |
- get_available_teal_slices = module_fd()$get_available_teal_slices(),+ stop( |
| 214 | -88x | +1x |
- set_filter_state = module_fd()$set_filter_state, # for testing purpose+ "\nmodule() `ui` argument requires a function with following arguments:", |
| 215 | -88x | +1x |
- get_filter_state = module_fd()$get_filter_state # for testing purpose+ "\n - id - `teal` will set proper `shiny` namespace for this module.", |
| 216 | -+ | 1x |
- )+ "\n\nFollowing arguments can be used optionally:", |
| 217 | -+ | 1x |
- )+ "\n - `...` ui_args elements will be passed to the module argument of the same name or to the `...`" |
| 218 |
- })+ ) |
||
| 219 |
-
+ } |
||
| 220 | -+ | 206x |
- # Update global state and mapping matrix when module filters change.+ if (any(c("data", "datasets") %in% ui_formals)) {
|
| 221 | -107x | +2x |
- obs2 <- observeEvent(slices_module(), priority = 0, {
+ stop( |
| 222 | -110x | +2x |
- this_slices <- slices_module()+ sprintf("Called from module(label = \"%s\", ...)\n ", label),
|
| 223 | -110x | +2x |
- slices_global$slices_append(this_slices) # append new slices to the all_slices list+ "UI with `data` or `datasets` argument is no longer accepted.\n ", |
| 224 | -110x | +2x |
- mapping_elem <- setNames(nm = id, list(vapply(this_slices, `[[`, character(1L), "id")))+ "If some UI inputs depend on data, please move the logic to your server instead.\n ", |
| 225 | -110x | +2x |
- slices_global$slices_active(mapping_elem)+ "Possible solutions are renderUI() or updateXyzInput() functions." |
| 226 |
- })+ ) |
||
| 227 |
-
+ } |
||
| 228 | -107x | +
- obs3 <- observeEvent(slices_global_module(), {
+
|
|
| 229 | -130x | +
- global_vs_module <- setdiff_teal_slices(slices_global_module(), slices_module())+ |
|
| 230 | -130x | +
- module_vs_global <- setdiff_teal_slices(slices_module(), slices_global_module())+ ## `filters` |
|
| 231 | -121x | +204x |
- if (length(global_vs_module) || length(module_vs_global)) {
+ if (!missing(filters)) {
|
| 232 | -+ | ! |
- # Comment: (Nota Bene) Normally new filters for a module are added through module-filter-panel, and slices+ datanames <- filters |
| 233 | -+ | ! |
- # global are updated automatically so slices_module -> slices_global_module are equal.+ msg <- |
| 234 | -+ | ! |
- # this if is valid only when a change is made on the global level so the change needs to be propagated down+ "The `filters` argument is deprecated and will be removed in the next release. Please use `datanames` instead." |
| 235 | -+ | ! |
- # to the module (for example through snapshot manager). If it happens both slices are different+ warning(msg) |
| 236 | -13x | +
- logger::log_debug("srv_module_filter_manager@3 (N.B.) global state has changed for a module:{ id }.")
+ } |
|
| 237 | -13x | +
- module_fd()$clear_filter_states()+ |
|
| 238 | -13x | +
- module_fd()$set_filter_state(slices_global_module())+ ## `datanames` (also including deprecated `filters`) |
|
| 239 |
- }+ # please note a race condition between datanames set when filters is not missing and data arg in server function |
||
| 240 | -+ | 204x |
- })+ if (!is.element("data", server_formals) && !is.null(datanames)) {
|
| 241 | -+ | 12x |
-
+ message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
|
| 242 | -107x | +12x |
- slices_module # returned for testing purpose+ datanames <- NULL |
| 243 |
- })+ } |
||
| 244 | -+ | 204x |
- }+ checkmate::assert_character(datanames, min.len = 1, null.ok = TRUE, any.missing = FALSE) |
| 246 |
- #' @importFrom shiny reactiveVal reactiveValues+ ## `server_args` |
||
| 247 | -+ | 203x |
- methods::setOldClass("reactiveVal")
+ checkmate::assert_list(server_args, null.ok = TRUE, names = "named") |
| 248 | -+ | 201x |
- methods::setOldClass("reactivevalues")
+ srv_extra_args <- setdiff(names(server_args), server_formals) |
| 249 | -+ | 201x |
-
+ if (length(srv_extra_args) > 0 && !"..." %in% server_formals) {
|
| 250 | -+ | 1x |
- #' @importFrom methods new+ stop( |
| 251 | -+ | 1x |
- #' @rdname module_filter_manager+ "\nFollowing `server_args` elements have no equivalent in the formals of the server:\n", |
| 252 | -+ | 1x |
- .slicesGlobal <- methods::setRefClass(".slicesGlobal", # nolint: object_name.
+ paste(paste(" -", srv_extra_args), collapse = "\n"),
|
| 253 | -+ | 1x |
- fields = list(+ "\n\nUpdate the server arguments by including above or add `...`" |
| 254 |
- all_slices = "reactiveVal",+ ) |
||
| 255 |
- module_slices_api = "reactivevalues"+ } |
||
| 256 |
- ),+ |
||
| 257 |
- methods = list(+ ## `ui_args` |
||
| 258 | -+ | 200x |
- initialize = function(slices = teal_slices(), module_labels) {
+ checkmate::assert_list(ui_args, null.ok = TRUE, names = "named") |
| 259 | -82x | +198x |
- shiny::isolate({
+ ui_extra_args <- setdiff(names(ui_args), ui_formals) |
| 260 | -82x | +198x |
- checkmate::assert_class(slices, "teal_slices")+ if (length(ui_extra_args) > 0 && !"..." %in% ui_formals) {
|
| 261 | -+ | 1x |
- # needed on init to not mix "global_filters" with module-specific-slots+ stop( |
| 262 | -82x | +1x |
- if (isTRUE(attr(slices, "module_specific"))) {
+ "\nFollowing `ui_args` elements have no equivalent in the formals of UI:\n", |
| 263 | -11x | +1x |
- old_mapping <- attr(slices, "mapping")+ paste(paste(" -", ui_extra_args), collapse = "\n"),
|
| 264 | -11x | +1x |
- new_mapping <- sapply(module_labels, simplify = FALSE, function(module_label) {
+ "\n\nUpdate the UI arguments by including above or add `...`" |
| 265 | -20x | +
- unique(unlist(old_mapping[c(module_label, "global_filters")]))+ ) |
|
| 266 |
- })+ } |
||
| 267 | -11x | +
- attr(slices, "mapping") <- new_mapping+ |
|
| 268 |
- }+ ## `transformers` |
||
| 269 | -82x | +197x |
- .self$all_slices <<- shiny::reactiveVal(slices)+ if (inherits(transformers, "teal_transform_module")) {
|
| 270 | -82x | +1x |
- .self$module_slices_api <<- shiny::reactiveValues()+ transformers <- list(transformers) |
| 271 | -82x | +
- .self$slices_append(slices)+ } |
|
| 272 | -82x | +197x |
- .self$slices_active(attr(slices, "mapping"))+ checkmate::assert_list(transformers, types = "teal_transform_module") |
| 273 | -82x | +197x |
- invisible(.self)+ transformer_datanames <- unlist(lapply(transformers, attr, "datanames")) |
| 274 | -+ | 197x |
- })+ combined_datanames <- if (identical(datanames, "all")) {
|
| 275 | -+ | 144x |
- },+ "all" |
| 276 |
- is_module_specific = function() {
+ } else {
|
||
| 277 | -283x | +53x |
- isTRUE(attr(.self$all_slices(), "module_specific"))+ union(datanames, transformer_datanames) |
| 278 |
- },+ } |
||
| 279 |
- module_slices_api_set = function(module_label, functions_list) {
+
|
||
| 280 | -88x | +197x |
- shiny::isolate({
+ structure( |
| 281 | -88x | +197x |
- if (!.self$is_module_specific()) {
+ list( |
| 282 | -72x | +197x |
- module_label <- "global_filters"+ label = label, |
| 283 | -+ | 197x |
- }+ server = server, |
| 284 | -88x | +197x |
- if (!identical(.self$module_slices_api[[module_label]], functions_list)) {
+ ui = ui, |
| 285 | -88x | +197x |
- .self$module_slices_api[[module_label]] <- functions_list+ datanames = combined_datanames, |
| 286 | -+ | 197x |
- }+ server_args = server_args, |
| 287 | -88x | +197x |
- invisible(.self)+ ui_args = ui_args, |
| 288 | -+ | 197x |
- })+ transformers = transformers |
| 289 |
- },+ ), |
||
| 290 | -+ | 197x |
- slices_deactivate_all = function(module_label) {
+ class = "teal_module" |
| 291 | -! | +
- shiny::isolate({
+ ) |
|
| 292 | -! | +
- new_slices <- .self$all_slices()+ } |
|
| 293 | -! | +
- old_mapping <- attr(new_slices, "mapping")+ |
|
| 294 |
-
+ #' @rdname teal_modules |
||
| 295 | -! | +
- new_mapping <- if (.self$is_module_specific()) {
+ #' @export |
|
| 296 | -! | +
- new_module_mapping <- setNames(nm = module_label, list(character(0)))+ #' |
|
| 297 | -! | +
- modifyList(old_mapping, new_module_mapping)+ modules <- function(..., label = "root") {
|
|
| 298 | -! | +137x |
- } else if (missing(module_label)) {
+ checkmate::assert_string(label) |
| 299 | -! | +135x |
- lapply(+ submodules <- list(...) |
| 300 | -! | +135x |
- attr(.self$all_slices(), "mapping"),+ if (any(vapply(submodules, is.character, FUN.VALUE = logical(1)))) {
|
| 301 | -! | +2x |
- function(x) character(0)+ stop( |
| 302 | -+ | 2x |
- )+ "The only character argument to modules() must be 'label' and it must be named, ", |
| 303 | -+ | 2x |
- } else {
+ "change modules('lab', ...) to modules(label = 'lab', ...)"
|
| 304 | -! | +
- old_mapping[[module_label]] <- character(0)+ ) |
|
| 305 | -! | +
- old_mapping+ } |
|
| 306 |
- }+ |
||
| 307 | -+ | 133x |
-
+ checkmate::assert_list(submodules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
|
| 308 | -! | +
- if (!identical(new_mapping, old_mapping)) {
+ # name them so we can more easily access the children |
|
| 309 | -! | +
- logger::log_debug(".slicesGlobal@slices_deactivate_all: deactivating all slices.")
+ # beware however that the label of the submodules should not be changed as it must be kept synced |
|
| 310 | -! | +130x |
- attr(new_slices, "mapping") <- new_mapping+ labels <- vapply(submodules, function(submodule) submodule$label, character(1)) |
| 311 | -! | +130x |
- .self$all_slices(new_slices)+ names(submodules) <- get_unique_labels(labels) |
| 312 | -+ | 130x |
- }+ structure( |
| 313 | -! | +130x |
- invisible(.self)+ list( |
| 314 | -+ | 130x |
- })+ label = label, |
| 315 | -+ | 130x |
- },+ children = submodules |
| 316 |
- slices_active = function(mapping_elem) {
+ ), |
||
| 317 | -195x | +130x |
- shiny::isolate({
+ class = "teal_modules" |
| 318 | -195x | +
- if (.self$is_module_specific()) {
+ ) |
|
| 319 | -36x | +
- new_mapping <- modifyList(attr(.self$all_slices(), "mapping"), mapping_elem)+ } |
|
| 320 |
- } else {
+
|
||
| 321 | -159x | +
- new_mapping <- setNames(nm = "global_filters", list(unique(unlist(mapping_elem))))+ # printing methods ---- |
|
| 322 |
- }+ |
||
| 323 |
-
+ #' @rdname teal_modules |
||
| 324 | -195x | +
- if (!identical(new_mapping, attr(.self$all_slices(), "mapping"))) {
+ #' @param is_last (`logical(1)`) Whether this is the last item in its parent's children list. |
|
| 325 | -138x | +
- mapping_modules <- toString(names(new_mapping))+ #' Affects the tree branch character used (L- vs |-) |
|
| 326 | -138x | +
- logger::log_debug(".slicesGlobal@slices_active: changing mapping for module(s): { mapping_modules }.")
+ #' @param parent_prefix (`character(1)`) The prefix inherited from parent nodes, |
|
| 327 | -138x | +
- new_slices <- .self$all_slices()+ #' used to maintain the tree structure in nested levels |
|
| 328 | -138x | +
- attr(new_slices, "mapping") <- new_mapping+ #' @param is_root (`logical(1)`) Whether this is the root node of the tree. Only used in |
|
| 329 | -138x | +
- .self$all_slices(new_slices)+ #' format.teal_modules(). Determines whether to show "TEAL ROOT" header |
|
| 330 |
- }+ #' @param what (`character`) Specifies which metadata to display. |
||
| 331 |
-
+ #' Possible values: "datasets", "properties", "ui_args", "server_args", "transformers" |
||
| 332 | -195x | +
- invisible(.self)+ #' @examples |
|
| 333 |
- })+ #' mod <- module( |
||
| 334 |
- },+ #' label = "My Custom Module", |
||
| 335 |
- # - only new filters are appended to the $all_slices+ #' server = function(id, data, ...) {},
|
||
| 336 |
- # - mapping is not updated here+ #' ui = function(id, ...) {},
|
||
| 337 |
- slices_append = function(slices, activate = FALSE) {
+ #' datanames = c("ADSL", "ADTTE"),
|
||
| 338 | -195x | +
- shiny::isolate({
+ #' transformers = list(), |
|
| 339 | -195x | +
- if (!is.teal_slices(slices)) {
+ #' ui_args = list(a = 1, b = "b"), |
|
| 340 | -! | +
- slices <- as.teal_slices(slices)+ #' server_args = list(x = 5, y = list(p = 1)) |
|
| 341 |
- }+ #' ) |
||
| 342 |
-
+ #' cat(format(mod)) |
||
| 343 |
- # to make sure that we don't unnecessary trigger $all_slices <reactiveVal>+ #' @export |
||
| 344 | -195x | +
- new_slices <- setdiff_teal_slices(slices, .self$all_slices())+ format.teal_module <- function( |
|
| 345 | -195x | +
- old_mapping <- attr(.self$all_slices(), "mapping")+ x, indent = 0, is_last = FALSE, parent_prefix = "", |
|
| 346 | -195x | +
- if (length(new_slices)) {
+ what = c("datasets", "properties", "ui_args", "server_args", "transformers"), ...) {
|
|
| 347 | -6x | +3x |
- new_ids <- vapply(new_slices, `[[`, character(1L), "id")+ empty_text <- "" |
| 348 | -6x | +3x |
- logger::log_debug(".slicesGlobal@slices_append: appending new slice(s): { new_ids }.")
+ branch <- if (is_last) "L-" else "|-" |
| 349 | -6x | +3x |
- slices_ids <- vapply(.self$all_slices(), `[[`, character(1L), "id")+ current_prefix <- paste0(parent_prefix, branch, " ") |
| 350 | -6x | +3x |
- lapply(new_slices, function(slice) {
+ content_prefix <- paste0(parent_prefix, if (is_last) " " else "| ") |
| 351 |
- # In case the new state has the same id as an existing one, add a suffix+ |
||
| 352 | -6x | +3x |
- if (slice$id %in% slices_ids) {
+ format_list <- function(lst, empty = empty_text, label_width = 0) {
|
| 353 | -1x | +6x |
- slice$id <- utils::tail(make.unique(c(slices_ids, slice$id), sep = "_"), 1)+ if (is.null(lst) || length(lst) == 0) {
|
| 354 | -+ | 6x |
- }+ empty |
| 355 |
- })+ } else {
|
||
| 356 | -+ | ! |
-
+ colon_space <- paste(rep(" ", label_width), collapse = "")
|
| 357 | -6x | +
- new_slices_all <- c(.self$all_slices(), new_slices)+ |
|
| 358 | -6x | +! |
- attr(new_slices_all, "mapping") <- old_mapping+ first_item <- sprintf("%s (%s)", names(lst)[1], crayon::silver(class(lst[[1]])[1]))
|
| 359 | -6x | +! |
- .self$all_slices(new_slices_all)+ rest_items <- if (length(lst) > 1) {
|
| 360 | -+ | ! |
- }+ paste( |
| 361 | -+ | ! |
-
+ vapply( |
| 362 | -195x | +! |
- invisible(.self)+ names(lst)[-1], |
| 363 | -+ | ! |
- })+ function(name) {
|
| 364 | -+ | ! |
- },+ sprintf( |
| 365 | -+ | ! |
- slices_get = function(module_label) {
+ "%s%s (%s)", |
| 366 | -289x | +! |
- if (missing(module_label)) {
+ paste0(content_prefix, "| ", colon_space), |
| 367 | ! |
- .self$all_slices()+ name, |
|
| 368 | -+ | ! |
- } else {
+ crayon::silver(class(lst[[name]])[1]) |
| 369 | -289x | +
- module_ids <- unlist(attr(.self$all_slices(), "mapping")[c(module_label, "global_filters")])+ ) |
|
| 370 | -289x | +
- Filter(+ }, |
|
| 371 | -289x | +! |
- function(slice) slice$id %in% module_ids,+ character(1) |
| 372 | -289x | +
- .self$all_slices()+ ), |
|
| 373 | -+ | ! |
- )+ collapse = "\n" |
| 374 |
- }+ ) |
||
| 375 |
- },+ } |
||
| 376 | -+ | ! |
- slices_set = function(slices) {
+ if (length(lst) > 1) paste0(first_item, "\n", rest_items) else first_item |
| 377 | -7x | +
- shiny::isolate({
+ } |
|
| 378 | -7x | +
- if (!is.teal_slices(slices)) {
+ } |
|
| 379 | -! | +
- slices <- as.teal_slices(slices)+ |
|
| 380 | -+ | 3x |
- }+ bookmarkable <- isTRUE(attr(x, "teal_bookmarkable")) |
| 381 | -7x | +3x |
- .self$all_slices(slices)+ reportable <- "reporter" %in% names(formals(x$server)) |
| 382 | -7x | +
- invisible(.self)+ |
|
| 383 | -+ | 3x |
- })+ transformers <- if (length(x$transformers) > 0) {
|
| 384 | -+ | ! |
- },+ paste(sapply(x$transformers, function(t) attr(t, "label")), collapse = ", ") |
| 385 |
- show = function() {
+ } else {
|
||
| 386 | -! | +3x |
- shiny::isolate(print(.self$all_slices()))+ empty_text |
| 387 | -! | +
- invisible(.self)+ } |
|
| 388 |
- }+ |
||
| 389 | -+ | 3x |
- )+ output <- pasten(current_prefix, crayon::bgWhite(x$label)) |
| 390 |
- )+ |
||
| 391 | -+ | 3x |
- # todo: prevent any teal_slices attribute except mapping+ if ("datasets" %in% what) {
|
| 1 | -+ | ||
| 392 | +3x |
- # FilteredData ------+ output <- paste0( |
|
| 2 | -+ | ||
| 393 | +3x |
-
+ output, |
|
| 3 | -+ | ||
| 394 | +3x |
- #' Drive a `teal` application+ content_prefix, "|- ", crayon::yellow("Datasets : "), paste(x$datanames, collapse = ", "), "\n"
|
|
| 4 | +395 |
- #'+ ) |
|
| 5 | +396 |
- #' Extension of the `shinytest2::AppDriver` class with methods for+ } |
|
| 6 | -+ | ||
| 397 | +3x |
- #' driving a teal application for performing interactions for `shinytest2` tests.+ if ("properties" %in% what) {
|
|
| 7 | -+ | ||
| 398 | +3x |
- #'+ output <- paste0( |
|
| 8 | -+ | ||
| 399 | +3x |
- #' @keywords internal+ output, |
|
| 9 | -+ | ||
| 400 | +3x |
- #'+ content_prefix, "|- ", crayon::blue("Properties:"), "\n",
|
|
| 10 | -+ | ||
| 401 | +3x |
- TealAppDriver <- R6::R6Class( # nolint: object_name.+ content_prefix, "| |- ", crayon::cyan("Bookmarkable : "), bookmarkable, "\n",
|
|
| 11 | -+ | ||
| 402 | +3x |
- "TealAppDriver",+ content_prefix, "| L- ", crayon::cyan("Reportable : "), reportable, "\n"
|
|
| 12 | +403 |
- inherit = {
+ ) |
|
| 13 | +404 |
- if (!requireNamespace("shinytest2", quietly = TRUE)) {
+ } |
|
| 14 | -+ | ||
| 405 | +3x |
- stop("Please install 'shinytest2' package to use this class.")
+ if ("ui_args" %in% what) {
|
|
| 15 | -+ | ||
| 406 | +3x |
- }+ ui_args_formatted <- format_list(x$ui_args, label_width = 19) |
|
| 16 | -+ | ||
| 407 | +3x |
- if (!requireNamespace("rvest", quietly = TRUE)) {
+ output <- paste0( |
|
| 17 | -+ | ||
| 408 | +3x |
- stop("Please install 'rvest' package to use this class.")
+ output, |
|
| 18 | -+ | ||
| 409 | +3x |
- }+ content_prefix, "|- ", crayon::green("UI Arguments : "), ui_args_formatted, "\n"
|
|
| 19 | +410 |
- shinytest2::AppDriver+ ) |
|
| 20 | +411 |
- },+ } |
|
| 21 | -+ | ||
| 412 | +3x |
- # public methods ----+ if ("server_args" %in% what) {
|
|
| 22 | -+ | ||
| 413 | +3x |
- public = list(+ server_args_formatted <- format_list(x$server_args, label_width = 19) |
|
| 23 | -+ | ||
| 414 | +3x |
- #' @description+ output <- paste0( |
|
| 24 | -+ | ||
| 415 | +3x |
- #' Initialize a `TealAppDriver` object for testing a `teal` application.+ output, |
|
| 25 | -+ | ||
| 416 | +3x |
- #'+ content_prefix, "|- ", crayon::green("Server Arguments : "), server_args_formatted, "\n"
|
|
| 26 | +417 |
- #' @param data,modules,filter,title,header,footer,landing_popup arguments passed to `init`+ ) |
|
| 27 | +418 |
- #' @param timeout (`numeric`) Default number of milliseconds for any timeout or+ } |
|
| 28 | -+ | ||
| 419 | +3x |
- #' timeout_ parameter in the `TealAppDriver` class.+ if ("transformers" %in% what) {
|
|
| 29 | -+ | ||
| 420 | +3x |
- #' Defaults to 20s.+ output <- paste0( |
|
| 30 | -+ | ||
| 421 | +3x |
- #'+ output, |
|
| 31 | -+ | ||
| 422 | +3x |
- #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it+ content_prefix, "L- ", crayon::magenta("Transformers : "), transformers, "\n"
|
|
| 32 | +423 |
- #' via options or environment variables.+ ) |
|
| 33 | +424 |
- #' @param load_timeout (`numeric`) How long to wait for the app to load, in ms.+ } |
|
| 34 | +425 |
- #' This includes the time to start R. Defaults to 100s.+ |
|
| 35 | -+ | ||
| 426 | +3x |
- #'+ output |
|
| 36 | +427 |
- #' See [`shinytest2::AppDriver`] `new` method for more details on how to change it+ } |
|
| 37 | +428 |
- #' via options or environment variables+ |
|
| 38 | +429 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$new`+ #' @rdname teal_modules |
|
| 39 | +430 |
- #'+ #' @examples |
|
| 40 | +431 |
- #'+ #' custom_module <- function( |
|
| 41 | +432 |
- #' @return Object of class `TealAppDriver`+ #' label = "label", ui_args = NULL, server_args = NULL, |
|
| 42 | +433 |
- initialize = function(data,+ #' datanames = "all", transformers = list(), bk = FALSE) {
|
|
| 43 | +434 |
- modules,+ #' ans <- module( |
|
| 44 | +435 |
- filter = teal_slices(),+ #' label, |
|
| 45 | +436 |
- title = build_app_title(),+ #' server = function(id, data, ...) {},
|
|
| 46 | +437 |
- header = tags$p(),+ #' ui = function(id, ...) {
|
|
| 47 | +438 |
- footer = tags$p(),+ #' }, |
|
| 48 | +439 |
- landing_popup = NULL,+ #' datanames = datanames, |
|
| 49 | +440 |
- timeout = rlang::missing_arg(),+ #' transformers = transformers, |
|
| 50 | +441 |
- load_timeout = rlang::missing_arg(),+ #' ui_args = ui_args, |
|
| 51 | +442 |
- ...) {
+ #' server_args = server_args |
|
| 52 | -! | +||
| 443 | +
- private$data <- data+ #' ) |
||
| 53 | -! | +||
| 444 | +
- private$modules <- modules+ #' attr(ans, "teal_bookmarkable") <- bk |
||
| 54 | -! | +||
| 445 | +
- private$filter <- filter+ #' ans |
||
| 55 | -! | +||
| 446 | +
- app <- init(+ #' } |
||
| 56 | -! | +||
| 447 | +
- data = data,+ #' |
||
| 57 | -! | +||
| 448 | +
- modules = modules,+ #' dummy_transformer <- teal_transform_module( |
||
| 58 | -! | +||
| 449 | +
- filter = filter,+ #' label = "Dummy Transform", |
||
| 59 | -! | +||
| 450 | +
- title = title,+ #' ui = function(id) div("(does nothing)"),
|
||
| 60 | -! | +||
| 451 | +
- header = header,+ #' server = function(id, data) {
|
||
| 61 | -! | +||
| 452 | +
- footer = footer,+ #' moduleServer(id, function(input, output, session) data) |
||
| 62 | -! | +||
| 453 | +
- landing_popup = landing_popup,+ #' } |
||
| 63 | +454 |
- )+ #' ) |
|
| 64 | +455 |
-
+ #' |
|
| 65 | +456 |
- # Default timeout is hardcoded to 4s in shinytest2:::resolve_timeout+ #' plot_transformer <- teal_transform_module( |
|
| 66 | +457 |
- # It must be set as parameter to the AppDriver+ #' label = "Plot Settings", |
|
| 67 | -! | +||
| 458 | +
- suppressWarnings(+ #' ui = function(id) div("(does nothing)"),
|
||
| 68 | -! | +||
| 459 | +
- super$initialize(+ #' server = function(id, data) {
|
||
| 69 | -! | +||
| 460 | +
- app_dir = shinyApp(app$ui, app$server),+ #' moduleServer(id, function(input, output, session) data) |
||
| 70 | -! | +||
| 461 | +
- name = "teal",+ #' } |
||
| 71 | -! | +||
| 462 | +
- variant = shinytest2::platform_variant(),+ #' ) |
||
| 72 | -! | +||
| 463 | +
- timeout = rlang::maybe_missing(timeout, 20 * 1000),+ #' |
||
| 73 | -! | +||
| 464 | +
- load_timeout = rlang::maybe_missing(load_timeout, 100 * 1000),+ #' complete_modules <- modules( |
||
| 74 | +465 |
- ...+ #' custom_module( |
|
| 75 | +466 |
- )+ #' label = "Data Overview", |
|
| 76 | +467 |
- )+ #' datanames = c("ADSL", "ADAE", "ADVS"),
|
|
| 77 | +468 |
-
+ #' ui_args = list( |
|
| 78 | +469 |
- # Check for minimum version of Chrome that supports the tests+ #' view_type = "table", |
|
| 79 | +470 |
- # - Element.checkVisibility was added on 105+ #' page_size = 10, |
|
| 80 | -! | +||
| 471 | +
- chrome_version <- numeric_version(+ #' filters = c("ARM", "SEX", "RACE")
|
||
| 81 | -! | +||
| 472 | +
- gsub(+ #' ), |
||
| 82 | -! | +||
| 473 | +
- "[[:alnum:]_]+/", # Prefix that ends with forward slash+ #' server_args = list( |
||
| 83 | +474 |
- "",+ #' cache = TRUE, |
|
| 84 | -! | +||
| 475 | +
- self$get_chromote_session()$Browser$getVersion()$product+ #' debounce = 1000 |
||
| 85 | +476 |
- ),+ #' ), |
|
| 86 | -! | +||
| 477 | +
- strict = FALSE+ #' transformers = list(dummy_transformer), |
||
| 87 | +478 |
- )+ #' bk = TRUE |
|
| 88 | +479 |
-
+ #' ), |
|
| 89 | -! | +||
| 480 | +
- required_version <- "121"+ #' modules( |
||
| 90 | +481 |
-
+ #' label = "Nested 1", |
|
| 91 | -! | +||
| 482 | +
- testthat::skip_if(+ #' custom_module( |
||
| 92 | -! | +||
| 483 | +
- is.na(chrome_version),+ #' label = "Interactive Plots", |
||
| 93 | -! | +||
| 484 | +
- "Problem getting Chrome version, please contact the developers."+ #' datanames = c("ADSL", "ADVS"),
|
||
| 94 | +485 |
- )+ #' ui_args = list( |
|
| 95 | -! | +||
| 486 | +
- testthat::skip_if(+ #' plot_type = c("scatter", "box", "line"),
|
||
| 96 | -! | +||
| 487 | +
- chrome_version < required_version,+ #' height = 600, |
||
| 97 | -! | +||
| 488 | +
- sprintf(+ #' width = 800, |
||
| 98 | -! | +||
| 489 | +
- "Chrome version '%s' is not supported, please upgrade to '%s' or higher",+ #' color_scheme = "viridis" |
||
| 99 | -! | +||
| 490 | +
- chrome_version,+ #' ), |
||
| 100 | -! | +||
| 491 | +
- required_version+ #' server_args = list( |
||
| 101 | +492 |
- )+ #' render_type = "svg", |
|
| 102 | +493 |
- )+ #' cache_plots = TRUE |
|
| 103 | +494 |
- # end od check+ #' ), |
|
| 104 | +495 |
-
+ #' transformers = list(dummy_transformer, plot_transformer), |
|
| 105 | -! | +||
| 496 | +
- private$set_active_ns()+ #' bk = TRUE |
||
| 106 | -! | +||
| 497 | +
- self$wait_for_idle()+ #' ), |
||
| 107 | +498 |
- },+ #' modules( |
|
| 108 | +499 |
- #' @description+ #' label = "Nested 2", |
|
| 109 | +500 |
- #' Append parent [`shinytest2::AppDriver`] `click` method with a call to `waif_for_idle()` method.+ #' custom_module( |
|
| 110 | +501 |
- #' @param ... arguments passed to parent [`shinytest2::AppDriver`] `click()` method.+ #' label = "Summary Statistics", |
|
| 111 | +502 |
- click = function(...) {
+ #' datanames = "ADSL", |
|
| 112 | -! | +||
| 503 | +
- super$click(...)+ #' ui_args = list( |
||
| 113 | -! | +||
| 504 | +
- private$wait_for_page_stability()+ #' stats = c("mean", "median", "sd", "range"),
|
||
| 114 | +505 |
- },+ #' grouping = c("ARM", "SEX")
|
|
| 115 | +506 |
- #' @description+ #' ) |
|
| 116 | +507 |
- #' Check if the app has shiny errors. This checks for global shiny errors.+ #' ), |
|
| 117 | +508 |
- #' Note that any shiny errors dependent on shiny server render will only be captured after the teal module tab+ #' modules( |
|
| 118 | +509 |
- #' is visited because shiny will not trigger server computations when the tab is invisible.+ #' label = "Labeled nested modules", |
|
| 119 | +510 |
- #' So, navigate to the module tab you want to test before calling this function.+ #' custom_module( |
|
| 120 | +511 |
- #' Although, this catches errors hidden in the other module tabs if they are already rendered.+ #' label = "Subgroup Analysis", |
|
| 121 | +512 |
- expect_no_shiny_error = function() {
- |
- |
| 122 | -! | -
- testthat::expect_null(- |
- |
| 123 | -! | -
- self$get_html(".shiny-output-error:not(.shiny-output-error-validation)"),
- |
- |
| 124 | -! | -
- info = "Shiny error is observed"+ #' datanames = c("ADSL", "ADAE"),
|
|
| 125 | +513 |
- )+ #' ui_args = list( |
|
| 126 | +514 |
- },+ #' subgroups = c("AGE", "SEX", "RACE"),
|
|
| 127 | +515 |
- #' @description+ #' analysis_type = "stratified" |
|
| 128 | +516 |
- #' Check if the app has no validation errors. This checks for global shiny validation errors.+ #' ), |
|
| 129 | +517 |
- expect_no_validation_error = function() {
- |
- |
| 130 | -! | -
- testthat::expect_null(- |
- |
| 131 | -! | -
- self$get_html(".shiny-output-error-validation"),
- |
- |
| 132 | -! | -
- info = "No validation error is observed"+ #' bk = TRUE |
|
| 133 | +518 |
- )+ #' ) |
|
| 134 | +519 |
- },+ #' ), |
|
| 135 | +520 |
- #' @description+ #' modules(custom_module(label = "Subgroup Analysis in non-labled modules")) |
|
| 136 | +521 |
- #' Check if the app has validation errors. This checks for global shiny validation errors.+ #' ) |
|
| 137 | +522 |
- expect_validation_error = function() {
- |
- |
| 138 | -! | -
- testthat::expect_false(- |
- |
| 139 | -! | -
- is.null(self$get_html(".shiny-output-error-validation")),
+ #' ), |
|
| 140 | -! | +||
| 523 | +
- info = "Validation error is not observed"+ #' custom_module("Non-nested module")
|
||
| 141 | +524 |
- )+ #' ) |
|
| 142 | +525 |
- },+ #' |
|
| 143 | +526 |
- #' @description+ #' cat(format(complete_modules)) |
|
| 144 | +527 |
- #' Set the input in the `teal` app.+ #' cat(format(complete_modules, what = c("ui_args", "server_args", "transformers")))
|
|
| 145 | +528 |
- #'+ #' @export |
|
| 146 | +529 |
- #' @param input_id (character) The shiny input id with it's complete name space.+ format.teal_modules <- function(x, indent = 0, is_root = TRUE, is_last = FALSE, parent_prefix = "", ...) {
|
|
| 147 | -+ | ||
| 530 | +1x |
- #' @param value The value to set the input to.+ if (is_root) {
|
|
| 148 | -+ | ||
| 531 | +1x |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ header <- pasten(crayon::bold("TEAL ROOT"))
|
|
| 149 | -+ | ||
| 532 | +1x |
- #'+ new_parent_prefix <- " " #' Initial indent for root level |
|
| 150 | +533 |
- #' @return The `TealAppDriver` object invisibly.+ } else {
|
|
| 151 | -+ | ||
| 534 | +! |
- set_input = function(input_id, value, ...) {
+ if (!is.null(x$label)) {
|
|
| 152 | +535 | ! |
- do.call(+ branch <- if (is_last) "L-" else "|-" |
| 153 | +536 | ! |
- self$set_inputs,+ header <- pasten(parent_prefix, branch, " ", crayon::bold(x$label)) |
| 154 | +537 | ! |
- c(setNames(list(value), input_id), list(...))+ new_parent_prefix <- paste0(parent_prefix, if (is_last) " " else "| ") |
| 155 | +538 |
- )+ } else {
|
|
| 156 | +539 | ! |
- invisible(self)+ header <- "" |
| 157 | -+ | ||
| 540 | +! |
- },+ new_parent_prefix <- parent_prefix |
|
| 158 | +541 |
- #' @description+ } |
|
| 159 | +542 |
- #' Navigate the teal tabs in the `teal` app.+ } |
|
| 160 | +543 |
- #'+ |
|
| 161 | -+ | ||
| 544 | +1x |
- #' @param tabs (character) Labels of tabs to navigate to. The order of the tabs is important,+ if (length(x$children) > 0) {
|
|
| 162 | -+ | ||
| 545 | +1x |
- #' and it should start with the most parent level tab.+ children_output <- character(0) |
|
| 163 | -+ | ||
| 546 | +1x |
- #' Note: In case the teal tab group has duplicate names, the first tab will be selected,+ n_children <- length(x$children) |
|
| 164 | +547 |
- #' If you wish to select the second tab with the same name, use the suffix "_1".+ |
|
| 165 | -+ | ||
| 548 | +1x |
- #' If you wish to select the third tab with the same name, use the suffix "_2" and so on.+ for (i in seq_along(x$children)) {
|
|
| 166 | -+ | ||
| 549 | +3x |
- #'+ child <- x$children[[i]] |
|
| 167 | -+ | ||
| 550 | +3x |
- #' @return The `TealAppDriver` object invisibly.+ is_last_child <- (i == n_children) |
|
| 168 | +551 |
- navigate_teal_tab = function(tabs) {
- |
- |
| 169 | -! | -
- checkmate::check_character(tabs, min.len = 1)+ |
|
| 170 | -! | +||
| 552 | +3x |
- for (tab in tabs) {
+ if (inherits(child, "teal_modules")) {
|
|
| 171 | +553 | ! |
- self$set_input(+ children_output <- c( |
| 172 | +554 | ! |
- "teal-teal_modules-active_tab",+ children_output, |
| 173 | +555 | ! |
- get_unique_labels(tab),+ format(child, |
| 174 | +556 | ! |
- wait_ = FALSE- |
-
| 175 | -- |
- )- |
- |
| 176 | -- |
- }+ indent = indent, |
|
| 177 | +557 | ! |
- self$wait_for_idle()+ is_root = FALSE, |
| 178 | +558 | ! |
- private$set_active_ns()+ is_last = is_last_child, |
| 179 | +559 | ! |
- invisible(self)+ parent_prefix = new_parent_prefix, |
| 180 | +560 |
- },+ ... |
|
| 181 | +561 |
- #' @description+ ) |
|
| 182 | +562 |
- #' Get the active shiny name space for different components of the teal app.+ ) |
|
| 183 | +563 |
- #'+ } else {
|
|
| 184 | -+ | ||
| 564 | +3x |
- #' @return (`list`) The list of active shiny name space of the teal components.+ children_output <- c( |
|
| 185 | -+ | ||
| 565 | +3x |
- active_ns = function() {
+ children_output, |
|
| 186 | -! | +||
| 566 | +3x |
- if (identical(private$ns$module, character(0))) {
+ format(child, |
|
| 187 | -! | +||
| 567 | +3x |
- private$set_active_ns()+ indent = indent, |
|
| 188 | -+ | ||
| 568 | +3x |
- }+ is_last = is_last_child, |
|
| 189 | -! | +||
| 569 | +3x |
- private$ns+ parent_prefix = new_parent_prefix, |
|
| 190 | +570 |
- },+ ... |
|
| 191 | +571 |
- #' @description+ ) |
|
| 192 | +572 |
- #' Get the active shiny name space for interacting with the module content.+ ) |
|
| 193 | +573 |
- #'+ } |
|
| 194 | +574 |
- #' @return (`string`) The active shiny name space of the component.+ } |
|
| 195 | +575 |
- active_module_ns = function() {
- |
- |
| 196 | -! | -
- if (identical(private$ns$module, character(0))) {
+
|
|
| 197 | -! | +||
| 576 | +1x |
- private$set_active_ns()+ paste0(header, paste(children_output, collapse = "")) |
|
| 198 | +577 |
- }+ } else {
|
|
| 199 | +578 | ! |
- private$ns$module- |
-
| 200 | -- |
- },- |
- |
| 201 | -- |
- #' @description+ header |
|
| 202 | +579 |
- #' Get the active shiny name space bound with a custom `element` name.+ } |
|
| 203 | +580 |
- #'+ } |
|
| 204 | +581 |
- #' @param element `character(1)` custom element name.+ |
|
| 205 | +582 |
- #'+ #' @rdname teal_modules |
|
| 206 | +583 |
- #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ #' @export |
|
| 207 | +584 |
- active_module_element = function(element) {
+ print.teal_module <- function(x, ...) {
|
|
| 208 | +585 | ! |
- checkmate::assert_string(element)+ cat(format(x, ...)) |
| 209 | +586 | ! |
- sprintf("#%s-%s", self$active_module_ns(), element)
+ invisible(x) |
| 210 | +587 |
- },+ } |
|
| 211 | +588 |
- #' @description+ |
|
| 212 | +589 |
- #' Get the text of the active shiny name space bound with a custom `element` name.+ #' @rdname teal_modules |
|
| 213 | +590 |
- #'+ #' @export |
|
| 214 | +591 |
- #' @param element `character(1)` the text of the custom element name.+ print.teal_modules <- function(x, ...) {
|
|
| 215 | -+ | ||
| 592 | +! |
- #'+ cat(format(x, ...)) |
|
| 216 | -+ | ||
| 593 | +! |
- #' @return (`string`) The text of the active shiny name space of the component bound with the input `element`.+ invisible(x) |
|
| 217 | +594 |
- active_module_element_text = function(element) {
+ } |
|
| 218 | -! | +||
| 595 | +
- checkmate::assert_string(element)+ |
||
| 219 | -! | +||
| 596 | +
- self$get_text(self$active_module_element(element))+ #' @param modules (`teal_module` or `teal_modules`) |
||
| 220 | +597 |
- },+ #' @rdname teal_modules |
|
| 221 | +598 |
- #' @description+ #' @examples |
|
| 222 | +599 |
- #' Get the active shiny name space for interacting with the filter panel.+ #' # change the module's datanames |
|
| 223 | +600 |
- #'+ #' set_datanames(module(datanames = "all"), "a") |
|
| 224 | +601 |
- #' @return (`string`) The active shiny name space of the component.+ #' |
|
| 225 | +602 |
- active_filters_ns = function() {
+ #' # change modules' datanames |
|
| 226 | -! | +||
| 603 | +
- if (identical(private$ns$filter_panel, character(0))) {
+ #' set_datanames( |
||
| 227 | -! | +||
| 604 | +
- private$set_active_ns()+ #' modules( |
||
| 228 | +605 |
- }+ #' module(datanames = "all"), |
|
| 229 | -! | +||
| 606 | +
- private$ns$filter_panel+ #' module(datanames = "a") |
||
| 230 | +607 |
- },+ #' ), |
|
| 231 | +608 |
- #' @description+ #' "b" |
|
| 232 | +609 |
- #' Get the active shiny name space for interacting with the data-summary panel.+ #' ) |
|
| 233 | +610 |
- #'+ #' @export |
|
| 234 | +611 |
- #' @return (`string`) The active shiny name space of the data-summary component.+ set_datanames <- function(modules, datanames) {
|
|
| 235 | -+ | ||
| 612 | +! |
- active_data_summary_ns = function() {
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
|
| 236 | +613 | ! |
- if (identical(private$ns$data_summary, character(0))) {
+ if (inherits(modules, "teal_modules")) {
|
| 237 | +614 | ! |
- private$set_active_ns()+ modules$children <- lapply(modules$children, set_datanames, datanames) |
| 238 | +615 |
- }+ } else {
|
|
| 239 | +616 | ! |
- private$ns$data_summary+ if (identical(modules$datanames, "all")) {
|
| 240 | -+ | ||
| 617 | +! |
- },+ modules$datanames <- datanames |
|
| 241 | +618 |
- #' @description+ } else {
|
|
| 242 | -+ | ||
| 619 | +! |
- #' Get the active shiny name space bound with a custom `element` name.+ warning( |
|
| 243 | -+ | ||
| 620 | +! |
- #'+ "Not possible to modify datanames of the module ", modules$label, |
|
| 244 | -+ | ||
| 621 | +! |
- #' @param element `character(1)` custom element name.+ ". set_datanames() can only change datanames if it was set to \"all\".",+ |
+ |
| 622 | +! | +
+ call. = FALSE |
|
| 245 | +623 |
- #'+ ) |
|
| 246 | +624 |
- #' @return (`string`) The active shiny name space of the component bound with the input `element`.+ } |
|
| 247 | +625 |
- active_data_summary_element = function(element) {
+ } |
|
| 248 | +626 | ! |
- checkmate::assert_string(element)+ modules |
| 249 | -! | +||
| 627 | +
- sprintf("#%s-%s", self$active_data_summary_ns(), element)
+ } |
||
| 250 | +628 |
- },+ |
|
| 251 | +629 |
- #' @description+ # utilities ---- |
|
| 252 | +630 |
- #' Get the input from the module in the `teal` app.+ ## subset or modify modules ---- |
|
| 253 | +631 |
- #' This function will only access inputs from the name space of the current active teal module.+ |
|
| 254 | +632 |
- #'+ #' Append a `teal_module` to `children` of a `teal_modules` object |
|
| 255 | +633 |
- #' @param input_id (character) The shiny input id to get the value from.+ #' @keywords internal |
|
| 256 | +634 |
- #'+ #' @param modules (`teal_modules`) |
|
| 257 | +635 |
- #' @return The value of the shiny input.+ #' @param module (`teal_module`) object to be appended onto the children of `modules` |
|
| 258 | +636 |
- get_active_module_input = function(input_id) {
+ #' @return A `teal_modules` object with `module` appended. |
|
| 259 | -! | +||
| 637 | +
- checkmate::check_string(input_id)+ append_module <- function(modules, module) {
|
||
| 260 | -! | +||
| 638 | +8x |
- self$get_value(input = sprintf("%s-%s", self$active_module_ns(), input_id))
+ checkmate::assert_class(modules, "teal_modules") |
|
| 261 | -+ | ||
| 639 | +6x |
- },+ checkmate::assert_class(module, "teal_module")+ |
+ |
| 640 | +4x | +
+ modules$children <- c(modules$children, list(module))+ |
+ |
| 641 | +4x | +
+ labels <- vapply(modules$children, function(submodule) submodule$label, character(1))+ |
+ |
| 642 | +4x | +
+ names(modules$children) <- get_unique_labels(labels)+ |
+ |
| 643 | +4x | +
+ modules |
|
| 262 | +644 |
- #' @description+ } |
|
| 263 | +645 |
- #' Get the output from the module in the `teal` app.+ |
|
| 264 | +646 |
- #' This function will only access outputs from the name space of the current active teal module.+ #' Extract/Remove module(s) of specific class |
|
| 265 | +647 |
- #'+ #' |
|
| 266 | +648 |
- #' @param output_id (character) The shiny output id to get the value from.+ #' Given a `teal_module` or a `teal_modules`, return the elements of the structure according to `class`. |
|
| 267 | +649 |
- #'+ #' |
|
| 268 | +650 |
- #' @return The value of the shiny output.+ #' @param modules (`teal_modules`) |
|
| 269 | +651 |
- get_active_module_output = function(output_id) {
+ #' @param class The class name of `teal_module` to be extracted or dropped. |
|
| 270 | -! | +||
| 652 | +
- checkmate::check_string(output_id)+ #' @keywords internal |
||
| 271 | -! | +||
| 653 | +
- self$get_value(output = sprintf("%s-%s", self$active_module_ns(), output_id))
+ #' @return |
||
| 272 | +654 |
- },+ #' - For `extract_module`, a `teal_module` of class `class` or `teal_modules` containing modules of class `class`. |
|
| 273 | +655 |
- #' @description+ #' - For `drop_module`, the opposite, which is all `teal_modules` of class other than `class`. |
|
| 274 | +656 |
- #' Get the output from the module's `teal.widgets::table_with_settings` or `DT::DTOutput` in the `teal` app.+ #' @rdname module_management |
|
| 275 | +657 |
- #' This function will only access outputs from the name space of the current active teal module.+ extract_module <- function(modules, class) {
+ |
+ |
| 658 | +24x | +
+ if (inherits(modules, class)) {
+ |
+ |
| 659 | +! | +
+ modules+ |
+ |
| 660 | +24x | +
+ } else if (inherits(modules, "teal_module")) {
+ |
+ |
| 661 | +13x | +
+ NULL+ |
+ |
| 662 | +11x | +
+ } else if (inherits(modules, "teal_modules")) {
+ |
+ |
| 663 | +11x | +
+ Filter(function(x) length(x) > 0L, lapply(modules$children, extract_module, class)) |
|
| 276 | +664 |
- #'+ } |
|
| 277 | +665 |
- #' @param table_id (`character(1)`) The id of the table in the active teal module's name space.+ } |
|
| 278 | +666 |
- #' @param which (integer) If there is more than one table, which should be extracted.+ |
|
| 279 | +667 |
- #' By default it will look for a table that is built using `teal.widgets::table_with_settings`.+ #' @keywords internal |
|
| 280 | +668 |
- #'+ #' @return `teal_modules` |
|
| 281 | +669 |
- #' @return The data.frame with table contents.+ #' @rdname module_management |
|
| 282 | +670 |
- get_active_module_table_output = function(table_id, which = 1) {
+ drop_module <- function(modules, class) {
|
|
| 283 | +671 | ! |
- checkmate::check_number(which, lower = 1)+ if (inherits(modules, class)) {
|
| 284 | +672 | ! |
- checkmate::check_string(table_id)+ NULL |
| 285 | +673 | ! |
- table <- rvest::html_table(+ } else if (inherits(modules, "teal_module")) {
|
| 286 | +674 | ! |
- self$get_html_rvest(self$active_module_element(table_id)),+ modules |
| 287 | +675 | ! |
- fill = TRUE+ } else if (inherits(modules, "teal_modules")) {
|
| 288 | -+ | ||
| 676 | +! |
- )+ do.call( |
|
| 289 | +677 | ! |
- if (length(table) == 0) {
+ "modules", |
| 290 | +678 | ! |
- data.frame()+ c(Filter(function(x) length(x) > 0L, lapply(modules$children, drop_module, class)), label = modules$label) |
| 291 | +679 |
- } else {
+ ) |
|
| 292 | -! | +||
| 680 | +
- table[[which]]+ } |
||
| 293 | +681 |
- }+ } |
|
| 294 | +682 |
- },+ |
|
| 295 | +683 |
- #' @description+ ## read modules ---- |
|
| 296 | +684 |
- #' Get the output from the module's `teal.widgets::plot_with_settings` in the `teal` app.+ |
|
| 297 | +685 |
- #' This function will only access plots from the name space of the current active teal module.+ #' Does the object make use of the `arg` |
|
| 298 | +686 |
- #'+ #' |
|
| 299 | +687 |
- #' @param plot_id (`character(1)`) The id of the plot in the active teal module's name space.+ #' @param modules (`teal_module` or `teal_modules`) object |
|
| 300 | +688 |
- #'+ #' @param arg (`character(1)`) names of the arguments to be checked against formals of `teal` modules. |
|
| 301 | +689 |
- #' @return The `src` attribute as `character(1)` vector.+ #' @return `logical` whether the object makes use of `arg`. |
|
| 302 | +690 |
- get_active_module_plot_output = function(plot_id) {
+ #' @rdname is_arg_used |
|
| 303 | -! | +||
| 691 | +
- checkmate::check_string(plot_id)+ #' @keywords internal |
||
| 304 | -! | +||
| 692 | +
- self$get_attr(+ is_arg_used <- function(modules, arg) {
|
||
| 305 | -! | +||
| 693 | +486x |
- self$active_module_element(sprintf("%s-plot_main > img", plot_id)),
+ checkmate::assert_string(arg) |
|
| 306 | -! | +||
| 694 | +483x |
- "src"+ if (inherits(modules, "teal_modules")) {
+ |
+ |
| 695 | +18x | +
+ any(unlist(lapply(modules$children, is_arg_used, arg)))+ |
+ |
| 696 | +465x | +
+ } else if (inherits(modules, "teal_module")) {
+ |
+ |
| 697 | +30x | +
+ is_arg_used(modules$server, arg) || is_arg_used(modules$ui, arg)+ |
+ |
| 698 | +435x | +
+ } else if (is.function(modules)) {
+ |
+ |
| 699 | +433x | +
+ isTRUE(arg %in% names(formals(modules))) |
|
| 307 | +700 |
- )+ } else {
+ |
+ |
| 701 | +2x | +
+ stop("is_arg_used function not implemented for this object")
|
|
| 308 | +702 |
- },+ } |
|
| 309 | +703 |
- #' @description+ } |
|
| 310 | +704 |
- #' Set the input in the module in the `teal` app.+ |
|
| 311 | +705 |
- #' This function will only set inputs in the name space of the current active teal module.+ |
|
| 312 | +706 |
- #'+ #' Get module depth |
|
| 313 | +707 |
- #' @param input_id (character) The shiny input id to get the value from.+ #' |
|
| 314 | +708 |
- #' @param value The value to set the input to.+ #' Depth starts at 0, so a single `teal.module` has depth 0. |
|
| 315 | +709 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ #' Nesting it increases overall depth by 1. |
|
| 316 | +710 |
- #'+ #' |
|
| 317 | +711 |
- #' @return The `TealAppDriver` object invisibly.+ #' @inheritParams init |
|
| 318 | +712 |
- set_active_module_input = function(input_id, value, ...) {
+ #' @param depth optional integer determining current depth level |
|
| 319 | -! | +||
| 713 | +
- checkmate::check_string(input_id)+ #' |
||
| 320 | -! | +||
| 714 | +
- checkmate::check_string(value)+ #' @return Depth level for given module. |
||
| 321 | -! | +||
| 715 | +
- self$set_input(+ #' @keywords internal |
||
| 322 | -! | +||
| 716 | +
- sprintf("%s-%s", self$active_module_ns(), input_id),
+ modules_depth <- function(modules, depth = 0L) {
|
||
| 323 | -! | +||
| 717 | +12x |
- value,+ checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
|
|
| 324 | -+ | ||
| 718 | +12x |
- ...+ checkmate::assert_int(depth, lower = 0)+ |
+ |
| 719 | +11x | +
+ if (inherits(modules, "teal_modules")) {
+ |
+ |
| 720 | +4x | +
+ max(vapply(modules$children, modules_depth, integer(1), depth = depth + 1L)) |
|
| 325 | +721 |
- )+ } else {
|
|
| 326 | -! | +||
| 722 | +7x |
- dots <- rlang::list2(...)+ depth |
|
| 327 | -! | +||
| 723 | +
- if (!isFALSE(dots[["wait"]])) self$wait_for_idle() # Default behavior is to wait+ } |
||
| 328 | -! | +||
| 724 | +
- invisible(self)+ } |
||
| 329 | +725 |
- },+ |
|
| 330 | +726 |
- #' @description+ #' Retrieve labels from `teal_modules` |
|
| 331 | +727 |
- #' Get the active datasets that can be accessed via the filter panel of the current active teal module.+ #' |
|
| 332 | +728 |
- get_active_filter_vars = function() {
+ #' @param modules (`teal_modules`) |
|
| 333 | -! | +||
| 729 | +
- displayed_datasets_index <- self$is_visible(+ #' @return A `list` containing the labels of the modules. If the modules are nested, |
||
| 334 | -! | +||
| 730 | +
- sprintf("#%s-filters-filter_active_vars_contents > span", self$active_filters_ns())
+ #' the function returns a nested `list` of labels. |
||
| 335 | +731 |
- )+ #' @keywords internal |
|
| 336 | +732 |
-
+ module_labels <- function(modules) {
|
|
| 337 | -! | +||
| 733 | +189x |
- available_datasets <- self$get_text(+ if (inherits(modules, "teal_modules")) {
|
|
| 338 | -! | +||
| 734 | +82x |
- sprintf(+ lapply(modules$children, module_labels) |
|
| 339 | -! | +||
| 735 | +
- "#%s-filters-filter_active_vars_contents .filter_panel_dataname",+ } else {
|
||
| 340 | -! | +||
| 736 | +107x |
- self$active_filters_ns()+ modules$label |
|
| 341 | +737 |
- )+ } |
|
| 342 | +738 |
- )+ } |
|
| 343 | +739 | ||
| 344 | -! | +||
| 740 | +
- available_datasets[displayed_datasets_index]+ #' Retrieve `teal_bookmarkable` attribute from `teal_modules` |
||
| 345 | +741 |
- },+ #' |
|
| 346 | +742 |
- #' @description+ #' @param modules (`teal_modules` or `teal_module`) object |
|
| 347 | +743 |
- #' Get the active data summary table+ #' @return named list of the same structure as `modules` with `TRUE` or `FALSE` values indicating |
|
| 348 | +744 |
- #' @return `data.frame`+ #' whether the module is bookmarkable. |
|
| 349 | +745 |
- get_active_data_summary_table = function() {
+ #' @keywords internal |
|
| 350 | -! | +||
| 746 | +
- summary_table <- rvest::html_table(+ modules_bookmarkable <- function(modules) {
|
||
| 351 | -! | +||
| 747 | +189x |
- self$get_html_rvest(self$active_data_summary_element("table")),
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
|
| 352 | -! | +||
| 748 | +189x |
- fill = TRUE+ if (inherits(modules, "teal_modules")) {
|
|
| 353 | -! | +||
| 749 | +82x |
- )[[1]]+ setNames( |
|
| 354 | -+ | ||
| 750 | +82x |
-
+ lapply(modules$children, modules_bookmarkable), |
|
| 355 | -! | +||
| 751 | +82x |
- col_names <- unlist(summary_table[1, ], use.names = FALSE)+ vapply(modules$children, `[[`, "label", FUN.VALUE = character(1)) |
|
| 356 | -! | +||
| 752 | +
- summary_table <- summary_table[-1, ]+ ) |
||
| 357 | -! | +||
| 753 | +
- colnames(summary_table) <- col_names+ } else {
|
||
| 358 | -! | +||
| 754 | +107x |
- if (nrow(summary_table) > 0) {
+ attr(modules, "teal_bookmarkable", exact = TRUE) |
|
| 359 | -! | +||
| 755 | +
- summary_table+ } |
||
| 360 | +756 |
- } else {
+ } |
|
| 361 | -! | +
| 1 | +
- NULL+ #' Generate lockfile for application's environment reproducibility |
||
| 362 | +2 |
- }+ #' |
|
| 363 | +3 |
- },+ #' @param lockfile_path (`character`) path to the lockfile. |
|
| 364 | +4 |
- #' @description+ #' |
|
| 365 | +5 |
- #' Test if `DOM` elements are visible on the page with a JavaScript call.+ #' @section Different ways of creating lockfile: |
|
| 366 | +6 |
- #' @param selector (`character(1)`) `CSS` selector to check visibility.+ #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation. |
|
| 367 | +7 |
- #' A `CSS` id will return only one element if the UI is well formed.+ #' |
|
| 368 | +8 |
- #' @param content_visibility_auto,opacity_property,visibility_property (`logical(1)`) See more information+ #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses |
|
| 369 | +9 |
- #' on <https://developer.mozilla.org/en-US/docs/Web/API/Element/checkVisibility>.+ #' `renv::dependencies()` to detect all R packages in the current project's working directory. |
|
| 370 | +10 |
- #'+ #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working |
|
| 371 | +11 |
- #' @return Logical vector with all occurrences of the selector.+ #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows
|
|
| 372 | +12 |
- is_visible = function(selector,+ #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the |
|
| 373 | +13 |
- content_visibility_auto = FALSE,+ #' `DESCRIPTION` fields included in the lockfile. |
|
| 374 | +14 |
- opacity_property = FALSE,+ #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set |
|
| 375 | +15 |
- visibility_property = FALSE) {
+ #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option.
|
|
| 376 | -! | +||
| 16 | +
- checkmate::assert_string(selector)+ #' |
||
| 377 | -! | +||
| 17 | +
- checkmate::assert_flag(content_visibility_auto)+ #' @section lockfile usage: |
||
| 378 | -! | +||
| 18 | +
- checkmate::assert_flag(opacity_property)+ #' After creating the lockfile, you can restore the application's environment using `renv::restore()`. |
||
| 379 | -! | +||
| 19 | +
- checkmate::assert_flag(visibility_property)+ #' |
||
| 380 | +20 |
-
+ #' @seealso [renv::snapshot()], [renv::restore()]. |
|
| 381 | -! | +||
| 21 | +
- private$wait_for_page_stability()+ #' |
||
| 382 | +22 |
-
+ #' @return `NULL` |
|
| 383 | -! | +||
| 23 | +
- testthat::skip_if_not(- |
- ||
| 384 | -! | -
- self$get_js("typeof Element.prototype.checkVisibility === 'function'"),
- |
- |
| 385 | -! | -
- "Element.prototype.checkVisibility is not supported in the current browser."+ #' |
|
| 386 | +24 |
- )+ #' @name module_teal_lockfile |
|
| 387 | +25 |
-
+ #' @rdname module_teal_lockfile |
|
| 388 | -! | +||
| 26 | +
- unlist(+ #' |
||
| 389 | -! | +||
| 27 | +
- self$get_js(+ #' @keywords internal |
||
| 390 | -! | +||
| 28 | +
- sprintf(+ NULL |
||
| 391 | -! | +||
| 29 | +
- "Array.from(document.querySelectorAll('%s')).map(el => el.checkVisibility({%s, %s, %s}))",
+
|
||
| 392 | -! | +||
| 30 | +
- selector,+ #' @rdname module_teal_lockfile |
||
| 393 | +31 |
- # Extra parameters+ ui_teal_lockfile <- function(id) {
|
|
| 394 | +32 | ! |
- sprintf("contentVisibilityAuto: %s", tolower(content_visibility_auto)),
+ ns <- NS(id) |
| 395 | +33 | ! |
- sprintf("opacityProperty: %s", tolower(opacity_property)),
+ shiny::tagList( |
| 396 | +34 | ! |
- sprintf("visibilityProperty: %s", tolower(visibility_property))
- |
-
| 397 | -- |
- )- |
- |
| 398 | -- |
- )- |
- |
| 399 | -- |
- )+ tags$span("", id = ns("lockFileStatus")),
|
|
| 400 | -+ | ||
| 35 | +! |
- },+ shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile"))
|
|
| 401 | +36 |
- #' @description+ ) |
|
| 402 | +37 |
- #' Get the active filter variables from a dataset in the `teal` app.+ } |
|
| 403 | +38 |
- #'+ |
|
| 404 | +39 |
- #' @param dataset_name (character) The name of the dataset to get the filter variables from.+ #' @rdname module_teal_lockfile |
|
| 405 | +40 |
- #' If `NULL`, the filter variables for all the datasets will be returned in a list.+ srv_teal_lockfile <- function(id) {
|
|
| 406 | -+ | ||
| 41 | +83x |
- get_active_data_filters = function(dataset_name = NULL) {
+ moduleServer(id, function(input, output, session) {
|
|
| 407 | -! | +||
| 42 | +83x |
- checkmate::check_string(dataset_name, null.ok = TRUE)+ logger::log_debug("Initialize srv_teal_lockfile.")
|
|
| 408 | -! | +||
| 43 | +83x |
- datasets <- self$get_active_filter_vars()+ enable_lockfile_download <- function() {
|
|
| 409 | +44 | ! |
- checkmate::assert_subset(dataset_name, datasets)+ shinyjs::html("lockFileStatus", "Application lockfile ready.")
|
| 410 | +45 | ! |
- active_filters <- lapply(+ shinyjs::hide("lockFileStatus", anim = TRUE)
|
| 411 | +46 | ! |
- datasets,+ shinyjs::enable("lockFileLink")
|
| 412 | +47 | ! |
- function(x) {
+ output$lockFileLink <- shiny::downloadHandler( |
| 413 | +48 | ! |
- var_names <- gsub(+ filename = function() {
|
| 414 | +49 | ! |
- pattern = "\\s",+ "renv.lock" |
| 415 | -! | +||
| 50 | +
- replacement = "",+ }, |
||
| 416 | +51 | ! |
- self$get_text(+ content = function(file) {
|
| 417 | +52 | ! |
- sprintf(+ file.copy(lockfile_path, file) |
| 418 | +53 | ! |
- "#%s-filters-%s .filter-card-varname",+ file |
| 419 | -! | +||
| 54 | +
- self$active_filters_ns(),+ }, |
||
| 420 | +55 | ! |
- x+ contentType = "application/json" |
| 421 | +56 |
- )+ ) |
|
| 422 | +57 |
- )+ } |
|
| 423 | -+ | ||
| 58 | +83x |
- )+ disable_lockfile_download <- function() {
|
|
| 424 | +59 | ! |
- structure(+ warning("Lockfile creation failed.", call. = FALSE)
|
| 425 | +60 | ! |
- lapply(var_names, private$get_active_filter_selection, dataset_name = x),+ shinyjs::html("lockFileStatus", "Lockfile creation failed.")
|
| 426 | +61 | ! |
- names = var_names+ shinyjs::hide("lockFileLink")
|
| 427 | +62 |
- )+ } |
|
| 428 | +63 |
- }+ |
|
| 429 | -+ | ||
| 64 | +83x |
- )+ shiny::onStop(function() {
|
|
| 430 | -! | +||
| 65 | +83x |
- names(active_filters) <- datasets+ if (file.exists(lockfile_path) && !shiny::isRunning()) {
|
|
| 431 | -! | +||
| 66 | +1x |
- if (is.null(dataset_name)) {
+ logger::log_debug("Removing lockfile after shutting down the app")
|
|
| 432 | -! | +||
| 67 | +1x |
- return(active_filters)+ file.remove(lockfile_path) |
|
| 433 | +68 |
} |
|
| 434 | -! | +||
| 69 | +
- active_filters[[dataset_name]]+ }) |
||
| 435 | +70 |
- },+ |
|
| 436 | -+ | ||
| 71 | +83x |
- #' @description+ lockfile_path <- "teal_app.lock" |
|
| 437 | -+ | ||
| 72 | +83x |
- #' Add a new variable from the dataset to be filtered.+ mode <- getOption("teal.lockfile.mode", default = "")
|
|
| 438 | +73 |
- #'+ |
|
| 439 | -+ | ||
| 74 | +83x |
- #' @param dataset_name (character) The name of the dataset to add the filter variable to.+ if (!(mode %in% c("auto", "enabled", "disabled"))) {
|
|
| 440 | -+ | ||
| 75 | +! |
- #' @param var_name (character) The name of the variable to add to the filter panel.+ stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ")
|
|
| 441 | +76 |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ } |
|
| 442 | +77 |
- #'+ |
|
| 443 | -+ | ||
| 78 | +83x |
- #' @return The `TealAppDriver` object invisibly.+ if (mode == "disabled") {
|
|
| 444 | -+ | ||
| 79 | +1x |
- add_filter_var = function(dataset_name, var_name, ...) {
+ logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.")
|
|
| 445 | -! | +||
| 80 | +1x |
- checkmate::check_string(dataset_name)+ shinyjs::hide("lockFileLink")
|
|
| 446 | -! | +||
| 81 | +1x |
- checkmate::check_string(var_name)+ return(NULL) |
|
| 447 | -! | +||
| 82 | +
- private$set_active_ns()+ } |
||
| 448 | -! | +||
| 83 | +
- self$click(+ |
||
| 449 | -! | +||
| 84 | +82x |
- selector = sprintf(+ if (file.exists(lockfile_path)) {
|
|
| 450 | +85 | ! |
- "#%s-filters-%s-add_filter_icon",+ logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.")
|
| 451 | +86 | ! |
- private$ns$filter_panel,+ enable_lockfile_download() |
| 452 | +87 | ! |
- dataset_name+ return(NULL) |
| 453 | +88 |
- )+ } |
|
| 454 | +89 |
- )+ |
|
| 455 | -! | +||
| 90 | +82x |
- self$set_input(+ if (mode == "auto" && .is_disabled_lockfile_scenario()) {
|
|
| 456 | -! | +||
| 91 | +81x |
- sprintf(+ logger::log_debug( |
|
| 457 | -! | +||
| 92 | +81x |
- "%s-filters-%s-%s-filter-var_to_add",+ "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()." |
|
| 458 | -! | +||
| 93 | +
- private$ns$filter_panel,+ ) |
||
| 459 | -! | +||
| 94 | +81x |
- dataset_name,+ shinyjs::hide("lockFileLink")
|
|
| 460 | -! | +||
| 95 | +81x |
- dataset_name+ return(NULL) |
|
| 461 | +96 |
- ),+ } |
|
| 462 | -! | +||
| 97 | +
- var_name,+ |
||
| 463 | -+ | ||
| 98 | +1x |
- ...+ if (!.is_lockfile_deps_installed()) {
|
|
| 464 | -+ | ||
| 99 | +! |
- )+ warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.")
|
|
| 465 | +100 | ! |
- invisible(self)+ shinyjs::hide("lockFileLink")
|
| 466 | -+ | ||
| 101 | +! |
- },+ return(NULL) |
|
| 467 | +102 |
- #' @description+ } |
|
| 468 | +103 |
- #' Remove an active filter variable of a dataset from the active filter variables panel.+ |
|
| 469 | +104 |
- #'+ # - Will be run only if the lockfile doesn't exist (see the if-s above) |
|
| 470 | +105 |
- #' @param dataset_name (character) The name of the dataset to remove the filter variable from.- |
- |
| 471 | -- |
- #' If `NULL`, all the filter variables will be removed.- |
- |
| 472 | -- |
- #' @param var_name (character) The name of the variable to remove from the filter panel.- |
- |
| 473 | -- |
- #' If `NULL`, all the filter variables of the dataset will be removed.- |
- |
| 474 | -- |
- #'+ # - We render to the tempfile because the process might last after session is closed and we don't |
|
| 475 | +106 |
- #' @return The `TealAppDriver` object invisibly.+ # want to make a "teal_app.renv" then. This is why we copy only during active session. |
|
| 476 | -+ | ||
| 107 | +1x |
- remove_filter_var = function(dataset_name = NULL, var_name = NULL) {
+ process <- .teal_lockfile_process_invoke(lockfile_path) |
|
| 477 | -! | +||
| 108 | +1x |
- checkmate::check_string(dataset_name, null.ok = TRUE)+ observeEvent(process$status(), {
|
|
| 478 | +109 | ! |
- checkmate::check_string(var_name, null.ok = TRUE)+ if (process$status() %in% c("initial", "running")) {
|
| 479 | +110 | ! |
- if (is.null(dataset_name)) {
+ shinyjs::html("lockFileStatus", "Creating lockfile...")
|
| 480 | +111 | ! |
- remove_selector <- sprintf(+ } else if (process$status() == "success") {
|
| 481 | +112 | ! |
- "#%s-active-remove_all_filters",+ result <- process$result() |
| 482 | +113 | ! |
- self$active_filters_ns()- |
-
| 483 | -- |
- )+ if (any(grepl("Lockfile written to", result$out))) {
|
|
| 484 | +114 | ! |
- } else if (is.null(var_name)) {
+ logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.")
|
| 485 | +115 | ! |
- remove_selector <- sprintf(+ if (any(grepl("(WARNING|ERROR):", result$out))) {
|
| 486 | +116 | ! |
- "#%s-active-%s-remove_filters",+ warning("Lockfile created with warning(s) or error(s):", call. = FALSE)
|
| 487 | +117 | ! |
- self$active_filters_ns(),+ for (i in result$out) {
|
| 488 | +118 | ! |
- dataset_name+ warning(i, call. = FALSE) |
| 489 | +119 |
- )+ } |
|
| 490 | +120 |
- } else {
+ } |
|
| 491 | +121 | ! |
- remove_selector <- sprintf(+ enable_lockfile_download() |
| 492 | -! | +||
| 122 | +
- "#%s-active-%s-filter-%s_%s-remove",+ } else {
|
||
| 493 | +123 | ! |
- self$active_filters_ns(),+ disable_lockfile_download() |
| 494 | -! | +||
| 124 | +
- dataset_name,+ } |
||
| 495 | +125 | ! |
- dataset_name,+ } else if (process$status() == "error") {
|
| 496 | +126 | ! |
- var_name+ disable_lockfile_download() |
| 497 | +127 |
- )+ } |
|
| 498 | +128 |
- }+ }) |
|
| 499 | -! | +||
| 129 | +
- self$click(+ |
||
| 500 | -! | +||
| 130 | +1x |
- selector = remove_selector+ NULL |
|
| 501 | +131 |
- )- |
- |
| 502 | -! | -
- invisible(self)+ }) |
|
| 503 | +132 |
- },+ } |
|
| 504 | +133 |
- #' @description+ |
|
| 505 | +134 |
- #' Set the active filter values for a variable of a dataset in the active filter variable panel.+ utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call
|
|
| 506 | +135 |
- #'+ #' @rdname module_teal_lockfile |
|
| 507 | +136 |
- #' @param dataset_name (character) The name of the dataset to set the filter value for.+ .teal_lockfile_process_invoke <- function(lockfile_path) {
|
|
| 508 | -+ | ||
| 137 | +1x |
- #' @param var_name (character) The name of the variable to set the filter value for.+ mirai_obj <- NULL |
|
| 509 | -+ | ||
| 138 | +1x |
- #' @param input The value to set the filter to.+ process <- shiny::ExtendedTask$new(function() {
|
|
| 510 | -+ | ||
| 139 | +1x |
- #' @param ... Additional arguments to be passed to `shinytest2::AppDriver$set_inputs`+ m <- mirai::mirai( |
|
| 511 | +140 |
- #'+ {
|
|
| 512 | -+ | ||
| 141 | +1x |
- #' @return The `TealAppDriver` object invisibly.+ options(opts) |
|
| 513 | -+ | ||
| 142 | +1x |
- set_active_filter_selection = function(dataset_name,+ do.call(Sys.setenv, sysenv) |
|
| 514 | -+ | ||
| 143 | +1x |
- var_name,+ .libPaths(libpaths) |
|
| 515 | -+ | ||
| 144 | +1x |
- input,+ setwd(wd) |
|
| 516 | -+ | ||
| 145 | +1x |
- ...) {
+ run(lockfile_path = lockfile_path) |
|
| 517 | -! | +||
| 146 | +
- checkmate::check_string(dataset_name)+ }, |
||
| 518 | -! | +||
| 147 | +1x |
- checkmate::check_string(var_name)+ run = .renv_snapshot, |
|
| 519 | -! | +||
| 148 | +1x |
- checkmate::check_string(input)+ lockfile_path = lockfile_path, |
|
| 520 | -+ | ||
| 149 | +1x |
-
+ opts = options(), |
|
| 521 | -! | +||
| 150 | +1x |
- input_id_prefix <- sprintf(+ libpaths = .libPaths(), |
|
| 522 | -! | +||
| 151 | +1x |
- "%s-filters-%s-filter-%s_%s-inputs",+ sysenv = as.list(Sys.getenv()), |
|
| 523 | -! | +||
| 152 | +1x |
- self$active_filters_ns(),+ wd = getwd() |
|
| 524 | -! | +||
| 153 | +
- dataset_name,+ ) |
||
| 525 | -! | +||
| 154 | +1x |
- dataset_name,+ mirai_obj <<- m |
|
| 526 | -! | +||
| 155 | +1x |
- var_name+ m |
|
| 527 | +156 |
- )+ }) |
|
| 528 | +157 | ||
| 529 | -+ | ||
| 158 | +1x |
- # Find the type of filter (based on filter panel)+ shiny::onStop(function() {
|
|
| 530 | -! | +||
| 159 | +1x |
- supported_suffix <- c("selection", "selection_manual")
+ if (mirai::unresolved(mirai_obj)) {
|
|
| 531 | +160 | ! |
- slices_suffix <- supported_suffix[+ logger::log_debug("Terminating a running lockfile process...")
|
| 532 | +161 | ! |
- match(+ mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed |
| 533 | -! | +||
| 162 | +
- TRUE,+ } |
||
| 534 | -! | +||
| 163 | +
- vapply(+ }) |
||
| 535 | -! | +||
| 164 | +
- supported_suffix,+ |
||
| 536 | -! | +||
| 165 | +1x |
- function(suffix) {
+ suppressWarnings({ # 'package:stats' may not be available when loading
|
|
| 537 | -! | +||
| 166 | +1x |
- !is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))
+ process$invoke() |
|
| 538 | +167 |
- },+ }) |
|
| 539 | -! | +||
| 168 | +
- logical(1)+ |
||
| 540 | -+ | ||
| 169 | +1x |
- )+ logger::log_debug("Lockfile creation started based on { getwd() }.")
|
|
| 541 | +170 |
- )+ + |
+ |
| 171 | +1x | +
+ process |
|
| 542 | +172 |
- ]+ } |
|
| 543 | +173 | ||
| 544 | +174 |
- # Generate correct namespace+ #' @rdname module_teal_lockfile |
|
| 545 | -! | +||
| 175 | +
- slices_input_id <- sprintf(+ .renv_snapshot <- function(lockfile_path) {
|
||
| 546 | -! | +||
| 176 | +1x |
- "%s-filters-%s-filter-%s_%s-inputs-%s",+ out <- utils::capture.output( |
|
| 547 | -! | +||
| 177 | +1x |
- self$active_filters_ns(),+ res <- renv::snapshot( |
|
| 548 | -! | +||
| 178 | +1x |
- dataset_name,+ lockfile = lockfile_path, |
|
| 549 | -! | +||
| 179 | +1x |
- dataset_name,+ prompt = FALSE, |
|
| 550 | -! | +||
| 180 | +1x |
- var_name,+ force = TRUE, |
|
| 551 | -! | +||
| 181 | +1x |
- slices_suffix+ type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here |
|
| 552 | +182 |
- )+ ) |
|
| 553 | +183 | ++ |
+ )+ |
+
| 184 | |||
| 554 | -! | +||
| 185 | +1x |
- if (identical(slices_suffix, "selection_manual")) {
+ list(out = out, res = res) |
|
| 555 | -! | +||
| 186 | +
- checkmate::assert_numeric(input, len = 2)+ } |
||
| 556 | +187 | ||
| 557 | -! | +||
| 188 | +
- dots <- rlang::list2(...)+ #' @rdname module_teal_lockfile |
||
| 558 | -! | +||
| 189 | +
- checkmate::assert_choice(dots$priority_, formals(self$set_inputs)[["priority_"]], null.ok = TRUE)+ .is_lockfile_deps_installed <- function() {
|
||
| 559 | -! | +||
| 190 | +1x |
- checkmate::assert_flag(dots$wait_, null.ok = TRUE)+ requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE)
|
|
| 560 | +191 | ++ |
+ }+ |
+
| 192 | |||
| 561 | -! | +||
| 193 | +
- self$run_js(+ #' @rdname module_teal_lockfile |
||
| 562 | -! | +||
| 194 | +
- sprintf(+ .is_disabled_lockfile_scenario <- function() {
|
||
| 563 | -! | +||
| 195 | +81x |
- "Shiny.setInputValue('%s:sw.numericRange', [%f, %f], {priority: '%s'})",
+ identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process
|
|
| 564 | -! | +||
| 196 | +81x |
- slices_input_id,+ identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test
|
|
| 565 | -! | +||
| 197 | +81x |
- input[[1]],+ !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process
|
|
| 566 | -! | +||
| 198 | +
- input[[2]],+ ( |
||
| 567 | -! | +||
| 199 | +81x |
- priority_ = ifelse(is.null(dots$priority_), "input", dots$priority_)+ ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
+ |
+ |
| 200 | +81x | +
+ ) # inside R CMD CHECK |
|
| 568 | +201 |
- )+ } |
| 569 | +1 |
- )+ #' Calls all `modules` |
|
| 570 | +2 |
-
+ #' |
|
| 571 | -! | +||
| 3 | +
- if (isTRUE(dots$wait_) || is.null(dots$wait_)) {
+ #' On the UI side each `teal_modules` is translated to a `tabsetPanel` and each `teal_module` is a |
||
| 572 | -! | +||
| 4 | +
- self$wait_for_idle(+ #' `tabPanel`. Both, UI and server are called recursively so that each tab is a separate module and |
||
| 573 | -! | +||
| 5 | +
- timeout = if (is.null(dots$timeout_)) rlang::missing_arg() else dots$timeout_+ #' reflect nested structure of `modules` argument. |
||
| 574 | +6 |
- )+ #' |
|
| 575 | +7 |
- }+ #' @name module_teal_module |
|
| 576 | -! | +||
| 8 | +
- } else if (identical(slices_suffix, "selection")) {
+ #' |
||
| 577 | -! | +||
| 9 | +
- self$set_input(+ #' @inheritParams module_teal |
||
| 578 | -! | +||
| 10 | +
- slices_input_id,+ #' |
||
| 579 | -! | +||
| 11 | +
- input,+ #' @param data_rv (`reactive` returning `teal_data`) |
||
| 580 | +12 |
- ...+ #' |
|
| 581 | +13 |
- )+ #' @param slices_global (`reactiveVal` returning `modules_teal_slices`) |
|
| 582 | +14 |
- } else {
+ #' see [`module_filter_manager`] |
|
| 583 | -! | +||
| 15 | +
- stop("Filter selection set not supported for this slice.")
+ #' |
||
| 584 | +16 |
- }+ #' @param depth (`integer(1)`) |
|
| 585 | +17 |
-
+ #' number which helps to determine depth of the modules nesting. |
|
| 586 | -! | +||
| 18 | +
- invisible(self)+ #' |
||
| 587 | +19 |
- },+ #' @param datasets (`reactive` returning `FilteredData` or `NULL`) |
|
| 588 | +20 |
- #' @description+ #' When `datasets` is passed from the parent module (`srv_teal`) then `dataset` is a singleton |
|
| 589 | +21 |
- #' Extract `html` attribute (found by a `selector`).+ #' which implies in filter-panel to be "global". When `NULL` then filter-panel is "module-specific". |
|
| 590 | +22 |
- #'+ #' |
|
| 591 | +23 |
- #' @param selector (`character(1)`) specifying the selector to be used to get the content of a specific node.+ #' @param data_load_status (`reactive` returning `character`) |
|
| 592 | +24 |
- #' @param attribute (`character(1)`) name of an attribute to retrieve from a node specified by `selector`.+ #' Determines action dependent on a data loading status: |
|
| 593 | +25 |
- #'+ #' - `"ok"` when `teal_data` is returned from the data loading. |
|
| 594 | +26 |
- #' @return The `character` vector.+ #' - `"teal_data_module failed"` when [teal_data_module()] didn't return `teal_data`. Disables tabs buttons. |
|
| 595 | +27 |
- get_attr = function(selector, attribute) {
+ #' - `"external failed"` when a `reactive` passed to `srv_teal(data)` didn't return `teal_data`. Hides the whole tab |
|
| 596 | -! | +||
| 28 | +
- rvest::html_attr(+ #' panel. |
||
| 597 | -! | +||
| 29 | +
- rvest::html_nodes(self$get_html_rvest("html"), selector),
+ #' |
||
| 598 | -! | +||
| 30 | +
- attribute+ #' @return |
||
| 599 | +31 |
- )+ #' output of currently active module. |
|
| 600 | +32 |
- },+ #' - `srv_teal_module.teal_module` returns `reactiveVal` containing output of the called module. |
|
| 601 | +33 |
- #' @description+ #' - `srv_teal_module.teal_modules` returns output of module selected by `input$active_tab`. |
|
| 602 | +34 |
- #' Wrapper around `get_html` that passes the output directly to `rvest::read_html`.+ #' |
|
| 603 | +35 |
- #'+ #' @keywords internal |
|
| 604 | +36 |
- #' @param selector `(character(1))` passed to `get_html`.+ NULL |
|
| 605 | +37 |
- #'+ |
|
| 606 | +38 |
- #' @return An XML document.+ #' @rdname module_teal_module |
|
| 607 | +39 |
- get_html_rvest = function(selector) {
+ ui_teal_module <- function(id, modules, depth = 0L) {
|
|
| 608 | +40 | ! |
- rvest::read_html(self$get_html(selector))+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module", "shiny.tag"))
|
| 609 | -+ | ||
| 41 | +! |
- },+ checkmate::assert_count(depth) |
|
| 610 | -+ | ||
| 42 | +! |
- #' Wrapper around `get_url()` method that opens the app in the browser.+ UseMethod("ui_teal_module", modules)
|
|
| 611 | +43 |
- #'+ } |
|
| 612 | +44 |
- #' @return Nothing. Opens the underlying teal app in the browser.+ |
|
| 613 | +45 |
- open_url = function() {
- |
- |
| 614 | -! | -
- browseURL(self$get_url())+ #' @rdname module_teal_module |
|
| 615 | +46 |
- },+ #' @export |
|
| 616 | +47 |
- #' @description+ ui_teal_module.default <- function(id, modules, depth = 0L) {
|
|
| 617 | -+ | ||
| 48 | +! |
- #' Waits until a specified input, output, or export value.+ stop("Modules class not supported: ", paste(class(modules), collapse = " "))
|
|
| 618 | +49 |
- #' This function serves as a wrapper around the `wait_for_value` method,+ } |
|
| 619 | +50 |
- #' providing a more flexible interface for waiting on different types of values within the active module namespace.+ |
|
| 620 | +51 |
- #' @param input,output,export A name of an input, output, or export value.+ #' @rdname module_teal_module |
|
| 621 | +52 |
- #' Only one of these parameters may be used.+ #' @export |
|
| 622 | +53 |
- #' @param ... Must be empty. Allows for parameter expansion.+ ui_teal_module.teal_modules <- function(id, modules, depth = 0L) {
|
|
| 623 | -+ | ||
| 54 | +! |
- #' Parameter with additional value to passed in `wait_for_value`.+ ns <- NS(id) |
|
| 624 | -+ | ||
| 55 | +! |
- wait_for_active_module_value = function(input = rlang::missing_arg(),+ tags$div( |
|
| 625 | -+ | ||
| 56 | +! |
- output = rlang::missing_arg(),+ id = ns("wrapper"),
|
|
| 626 | -+ | ||
| 57 | +! |
- export = rlang::missing_arg(),+ do.call( |
|
| 627 | -+ | ||
| 58 | +! |
- ...) {
+ tabsetPanel, |
|
| 628 | +59 | ! |
- ns <- shiny::NS(self$active_module_ns())+ c( |
| 629 | +60 |
-
+ # by giving an id, we can reactively respond to tab changes |
|
| 630 | +61 | ! |
- if (!rlang::is_missing(input) && checkmate::test_string(input, min.chars = 1)) input <- ns(input)+ list( |
| 631 | +62 | ! |
- if (!rlang::is_missing(output) && checkmate::test_string(output, min.chars = 1)) output <- ns(output)+ id = ns("active_tab"),
|
| 632 | +63 | ! |
- if (!rlang::is_missing(export) && checkmate::test_string(export, min.chars = 1)) export <- ns(export)+ type = if (modules$label == "root") "pills" else "tabs" |
| 633 | +64 |
-
+ ), |
|
| 634 | +65 | ! |
- self$wait_for_value(+ lapply( |
| 635 | +66 | ! |
- input = input,+ names(modules$children), |
| 636 | +67 | ! |
- output = output,+ function(module_id) {
|
| 637 | +68 | ! |
- export = export,+ module_label <- modules$children[[module_id]]$label |
| 638 | -+ | ||
| 69 | +! |
- ...+ if (is.null(module_label)) {
|
|
| 639 | -+ | ||
| 70 | +! |
- )+ module_label <- icon("fas fa-database")
|
|
| 640 | +71 |
- }+ } |
|
| 641 | -+ | ||
| 72 | +! |
- ),+ tabPanel(+ |
+ |
| 73 | +! | +
+ title = module_label,+ |
+ |
| 74 | +! | +
+ value = module_id, # when clicked this tab value changes input$<tabset panel id>+ |
+ |
| 75 | +! | +
+ ui_teal_module(+ |
+ |
| 76 | +! | +
+ id = ns(module_id),+ |
+ |
| 77 | +! | +
+ modules = modules$children[[module_id]],+ |
+ |
| 78 | +! | +
+ depth = depth + 1L |
|
| 642 | +79 |
- # private members ----+ ) |
|
| 643 | +80 |
- private = list(+ ) |
|
| 644 | +81 |
- # private attributes ----+ } |
|
| 645 | +82 |
- data = NULL,+ ) |
|
| 646 | +83 |
- modules = NULL,+ ) |
|
| 647 | +84 |
- filter = teal_slices(),+ ) |
|
| 648 | +85 |
- ns = list(+ ) |
|
| 649 | +86 |
- module = character(0),+ } |
|
| 650 | +87 |
- filter_panel = character(0)+ |
|
| 651 | +88 |
- ),+ #' @rdname module_teal_module |
|
| 652 | +89 |
- # private methods ----+ #' @export |
|
| 653 | +90 |
- set_active_ns = function() {
+ ui_teal_module.teal_module <- function(id, modules, depth = 0L) {
|
|
| 654 | +91 | ! |
- all_inputs <- self$get_values()$input+ ns <- NS(id) |
| 655 | +92 | ! |
- active_tab_inputs <- all_inputs[grepl("-active_tab$", names(all_inputs))]
+ args <- c(list(id = ns("module")), modules$ui_args)
|
| 656 | +93 | ||
| 657 | -! | -
- tab_ns <- unlist(lapply(names(active_tab_inputs), function(name) {
- |
- |
| 658 | +94 | ! |
- gsub(+ ui_teal <- tagList( |
| 659 | +95 | ! |
- pattern = "-active_tab$",+ div( |
| 660 | +96 | ! |
- replacement = sprintf("-%s", active_tab_inputs[[name]]),
+ id = ns("validate_datanames"),
|
| 661 | +97 | ! |
- name+ ui_validate_reactive_teal_data(ns("validate_datanames"))
|
| 662 | +98 |
- )+ ), |
|
| 663 | -+ | ||
| 99 | +! |
- }))+ shinyjs::hidden( |
|
| 664 | +100 | ! |
- active_ns <- tab_ns[1]+ tags$div( |
| 665 | +101 | ! |
- if (length(tab_ns) > 1) {
+ id = ns("transformer_failure_info"),
|
| 666 | +102 | ! |
- for (i in 2:length(tab_ns)) {
+ class = "teal_validated", |
| 667 | +103 | ! |
- next_ns <- tab_ns[i]+ div( |
| 668 | +104 | ! |
- if (grepl(pattern = active_ns, next_ns)) {
+ class = "teal-output-warning", |
| 669 | +105 | ! |
- active_ns <- next_ns+ "One of transformers failed. Please fix and continue." |
| 670 | +106 |
- }+ ) |
|
| 671 | +107 |
- }+ ) |
|
| 672 | +108 |
- }+ ), |
|
| 673 | +109 | ! |
- private$ns$module <- sprintf("%s-%s", active_ns, "module")
- |
-
| 674 | -- |
-
+ tags$div( |
|
| 675 | +110 | ! |
- components <- c("filter_panel", "data_summary")
+ id = ns("teal_module_ui"),
|
| 676 | +111 | ! |
- for (component in components) {
+ do.call(modules$ui, args) |
| 677 | +112 |
- if (- |
- |
| 678 | -! | -
- !is.null(self$get_html(sprintf("#%s-%s-panel", active_ns, component))) ||
- |
- |
| 679 | -! | -
- !is.null(self$get_html(sprintf("#%s-%s-table", active_ns, component)))
+ ) |
|
| 680 | +113 |
- ) {
- |
- |
| 681 | -! | -
- private$ns[[component]] <- sprintf("%s-%s", active_ns, component)
+ ) |
|
| 682 | +114 |
- } else {
+
|
|
| 683 | +115 | ! |
- private$ns[[component]] <- sprintf("%s-module_%s", active_ns, component)
- |
-
| 684 | -- |
- }- |
- |
| 685 | -- |
- }- |
- |
| 686 | -- |
- },- |
- |
| 687 | -- |
- # @description- |
- |
| 688 | -- |
- # Get the active filter values from the active filter selection of dataset from the filter panel.+ div( |
|
| 689 | -+ | ||
| 116 | +! |
- #+ id = id, |
|
| 690 | -+ | ||
| 117 | +! |
- # @param dataset_name (character) The name of the dataset to get the filter values from.+ class = "teal_module", |
|
| 691 | -+ | ||
| 118 | +! |
- # @param var_name (character) The name of the variable to get the filter values from.+ uiOutput(ns("data_reactive"), inline = TRUE),
|
|
| 692 | -+ | ||
| 119 | +! |
- #+ tagList( |
|
| 693 | -+ | ||
| 120 | +! |
- # @return The value of the active filter selection.+ if (depth >= 2L) tags$div(style = "mt-6"), |
|
| 694 | -+ | ||
| 121 | +! |
- get_active_filter_selection = function(dataset_name, var_name) {
+ if (!is.null(modules$datanames)) {
|
|
| 695 | +122 | ! |
- checkmate::check_string(dataset_name)+ fluidRow( |
| 696 | +123 | ! |
- checkmate::check_string(var_name)+ column(width = 9, ui_teal, class = "teal_primary_col"), |
| 697 | +124 | ! |
- input_id_prefix <- sprintf(+ column( |
| 698 | +125 | ! |
- "%s-filters-%s-filter-%s_%s-inputs",+ width = 3, |
| 699 | +126 | ! |
- self$active_filters_ns(),+ ui_data_summary(ns("data_summary")),
|
| 700 | +127 | ! |
- dataset_name,+ ui_filter_data(ns("filter_panel")),
|
| 701 | +128 | ! |
- dataset_name,+ ui_transform_data(ns("data_transform"), transformers = modules$transformers, class = "well"),
|
| 702 | +129 | ! |
- var_name+ class = "teal_secondary_col" |
| 703 | +130 |
- )+ ) |
|
| 704 | +131 |
-
+ ) |
|
| 705 | +132 |
- # Find the type of filter (categorical or range)+ } else {
|
|
| 706 | +133 | ! |
- supported_suffix <- c("selection", "selection_manual")
+ div( |
| 707 | +134 | ! |
- for (suffix in supported_suffix) {
+ div( |
| 708 | +135 | ! |
- if (!is.null(self$get_html(sprintf("#%s-%s", input_id_prefix, suffix)))) {
+ class = "teal_validated", |
| 709 | +136 | ! |
- return(self$get_value(input = sprintf("%s-%s", input_id_prefix, suffix)))
+ uiOutput(ns("data_input_error"))
|
| 710 | +137 |
- }+ ),+ |
+ |
| 138 | +! | +
+ ui_teal |
|
| 711 | +139 |
- }+ ) |
|
| 712 | +140 |
-
+ } |
|
| 713 | -! | +||
| 141 | +
- NULL # If there are not any supported filters+ ) |
||
| 714 | +142 |
- },+ ) |
|
| 715 | +143 |
- # @description+ } |
|
| 716 | +144 |
- # Check if the page is stable without any `DOM` updates in the body of the app.+ |
|
| 717 | +145 |
- # This is achieved by blocing the R process by sleeping until the page is unchanged till the `stability_period`.+ #' @rdname module_teal_module |
|
| 718 | +146 |
- # @param stability_period (`numeric(1)`) The time in milliseconds to wait till the page to be stable.+ srv_teal_module <- function(id, |
|
| 719 | +147 |
- # @param check_interval (`numeric(1)`) The time in milliseconds to check for changes in the page.+ data_rv, |
|
| 720 | +148 |
- # The stability check is reset when a change is detected in the page after sleeping for check_interval.+ modules, |
|
| 721 | +149 |
- wait_for_page_stability = function(stability_period = 2000, check_interval = 200) {
+ datasets = NULL, |
|
| 722 | -! | +||
| 150 | +
- previous_content <- self$get_html("body")
+ slices_global, |
||
| 723 | -! | +||
| 151 | +
- end_time <- Sys.time() + (stability_period / 1000)+ reporter = teal.reporter::Reporter$new(), |
||
| 724 | +152 |
-
+ data_load_status = reactive("ok"),
|
|
| 725 | -! | +||
| 153 | +
- repeat {
+ is_active = reactive(TRUE)) {
|
||
| 726 | -! | +||
| 154 | +189x |
- Sys.sleep(check_interval / 1000)+ checkmate::assert_string(id) |
|
| 727 | -! | +||
| 155 | +189x |
- current_content <- self$get_html("body")
+ assert_reactive(data_rv) |
|
| 728 | -+ | ||
| 156 | +189x |
-
+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
|
|
| 729 | -! | +||
| 157 | +189x |
- if (!identical(previous_content, current_content)) {
+ assert_reactive(datasets, null.ok = TRUE) |
|
| 730 | -! | +||
| 158 | +189x |
- previous_content <- current_content+ checkmate::assert_class(slices_global, ".slicesGlobal") |
|
| 731 | -! | +||
| 159 | +189x |
- end_time <- Sys.time() + (stability_period / 1000)+ checkmate::assert_class(reporter, "Reporter") |
|
| 732 | -! | +||
| 160 | +189x |
- } else if (Sys.time() >= end_time) {
+ assert_reactive(data_load_status) |
|
| 733 | -! | +||
| 161 | +189x |
- break+ UseMethod("srv_teal_module", modules)
|
|
| 734 | +162 |
- }+ } |
|
| 735 | +163 |
- }+ |
|
| 736 | +164 |
- }+ #' @rdname module_teal_module |
|
| 737 | +165 |
- )+ #' @export |
|
| 738 | +166 |
- )+ srv_teal_module.default <- function(id, |
| 1 | +167 |
- setOldClass("teal_module")
+ data_rv, |
||
| 2 | +168 |
- setOldClass("teal_modules")
+ modules, |
||
| 3 | +169 |
-
+ datasets = NULL, |
||
| 4 | +170 |
- #' Create `teal_module` and `teal_modules` objects+ slices_global, |
||
| 5 | +171 |
- #'+ reporter = teal.reporter::Reporter$new(), |
||
| 6 | +172 |
- #' @description+ data_load_status = reactive("ok"),
|
||
| 7 | +173 |
- #' `r lifecycle::badge("stable")`
+ is_active = reactive(TRUE)) {
|
||
| 8 | -+ | |||
| 174 | +! |
- #' Create a nested tab structure to embed modules in a `teal` application.+ stop("Modules class not supported: ", paste(class(modules), collapse = " "))
|
||
| 9 | +175 |
- #'+ } |
||
| 10 | +176 |
- #' @details+ |
||
| 11 | +177 |
- #' `module()` creates an instance of a `teal_module` that can be placed in a `teal` application.+ #' @rdname module_teal_module |
||
| 12 | +178 |
- #' `modules()` shapes the structure of a the application by organizing `teal_module` within the navigation panel.+ #' @export |
||
| 13 | +179 |
- #' It wraps `teal_module` and `teal_modules` objects in a `teal_modules` object,+ srv_teal_module.teal_modules <- function(id, |
||
| 14 | +180 |
- #' which results in a nested structure corresponding to the nested tabs in the final application.+ data_rv, |
||
| 15 | +181 |
- #'+ modules, |
||
| 16 | +182 |
- #' Note that for `modules()` `label` comes after `...`, so it must be passed as a named argument,+ datasets = NULL, |
||
| 17 | +183 |
- #' otherwise it will be captured by `...`.+ slices_global, |
||
| 18 | +184 |
- #'+ reporter = teal.reporter::Reporter$new(), |
||
| 19 | +185 |
- #' The labels `"global_filters"` and `"Report previewer"` are reserved+ data_load_status = reactive("ok"),
|
||
| 20 | +186 |
- #' because they are used by the `mapping` argument of [teal_slices()]+ is_active = reactive(TRUE)) {
|
||
| 21 | -+ | |||
| 187 | +82x |
- #' and the report previewer module [reporter_previewer_module()], respectively.+ moduleServer(id = id, module = function(input, output, session) {
|
||
| 22 | -+ | |||
| 188 | +82x |
- #'+ logger::log_debug("srv_teal_module.teal_modules initializing the module { deparse1(modules$label) }.")
|
||
| 23 | +189 |
- #' # Restricting datasets used by `teal_module`:+ |
||
| 24 | -+ | |||
| 190 | +82x |
- #' The `datanames` argument controls which datasets are used by the module’s server. These datasets,+ observeEvent(data_load_status(), {
|
||
| 25 | -+ | |||
| 191 | +75x |
- #' passed via server's `data` argument, are the only ones shown in the module's tab.+ tabs_selector <- sprintf("#%s li a", session$ns("active_tab"))
|
||
| 26 | -+ | |||
| 192 | +75x |
- #'+ if (identical(data_load_status(), "ok")) {
|
||
| 27 | -+ | |||
| 193 | +70x |
- #' When `datanames` is set to `"all"`, all datasets in the data object are treated as relevant.+ logger::log_debug("srv_teal_module@1 enabling modules tabs.")
|
||
| 28 | -+ | |||
| 194 | +70x |
- #' However, this may include unnecessary datasets, such as:+ shinyjs::show("wrapper")
|
||
| 29 | -+ | |||
| 195 | +70x |
- #' - Proxy variables for column modifications+ shinyjs::enable(selector = tabs_selector) |
||
| 30 | -+ | |||
| 196 | +5x |
- #' - Temporary datasets used to create final versions+ } else if (identical(data_load_status(), "teal_data_module failed")) {
|
||
| 31 | -+ | |||
| 197 | +5x |
- #' - Connection objects+ logger::log_debug("srv_teal_module@1 disabling modules tabs.")
|
||
| 32 | -+ | |||
| 198 | +5x |
- #'+ shinyjs::disable(selector = tabs_selector) |
||
| 33 | -+ | |||
| 199 | +! |
- #' To exclude irrelevant datasets, use the [set_datanames()] function to change `datanames` from+ } else if (identical(data_load_status(), "external failed")) {
|
||
| 34 | -+ | |||
| 200 | +! |
- #' `"all"` to specific names. Trying to modify non-`"all"` values with [set_datanames()] will result+ logger::log_debug("srv_teal_module@1 hiding modules tabs.")
|
||
| 35 | -+ | |||
| 201 | +! |
- #' in a warning. Datasets with names starting with . are ignored globally unless explicitly listed+ shinyjs::hide("wrapper")
|
||
| 36 | +202 |
- #' in `datanames`.+ } |
||
| 37 | +203 |
- #'+ }) |
||
| 38 | +204 |
- #' # `datanames` with `transformers`+ |
||
| 39 | -+ | |||
| 205 | +82x |
- #' When transformers are specified, their `datanames` are added to the module’s `datanames`, which+ modules_output <- sapply( |
||
| 40 | -+ | |||
| 206 | +82x |
- #' changes the behavior as follows:+ names(modules$children), |
||
| 41 | -+ | |||
| 207 | +82x |
- #' - If `module(datanames)` is `NULL` and the `transformers` have defined `datanames`, the sidebar+ function(module_id) {
|
||
| 42 | -+ | |||
| 208 | +107x |
- #' will appear showing the `transformers`' datasets, instead of being hidden.+ srv_teal_module( |
||
| 43 | -+ | |||
| 209 | +107x |
- #' - If `module(datanames)` is set to specific values and any `transformer` has `datanames = "all"`,+ id = module_id, |
||
| 44 | -+ | |||
| 210 | +107x |
- #' the module may receive extra datasets that could be unnecessary+ data_rv = data_rv, |
||
| 45 | -+ | |||
| 211 | +107x |
- #'+ modules = modules$children[[module_id]], |
||
| 46 | -+ | |||
| 212 | +107x |
- #' @param label (`character(1)`) Label shown in the navigation item for the module or module group.+ datasets = datasets, |
||
| 47 | -+ | |||
| 213 | +107x |
- #' For `modules()` defaults to `"root"`. See `Details`.+ slices_global = slices_global, |
||
| 48 | -+ | |||
| 214 | +107x |
- #' @param server (`function`) `shiny` module with following arguments:+ reporter = reporter, |
||
| 49 | -+ | |||
| 215 | +107x |
- #' - `id` - `teal` will set proper `shiny` namespace for this module (see [shiny::moduleServer()]).+ is_active = reactive( |
||
| 50 | -+ | |||
| 216 | +107x |
- #' - `input`, `output`, `session` - (optional; not recommended) When provided, then [shiny::callModule()]+ is_active() && |
||
| 51 | -+ | |||
| 217 | +107x |
- #' will be used to call a module. From `shiny` 1.5.0, the recommended way is to use+ input$active_tab == module_id && |
||
| 52 | -+ | |||
| 218 | +107x |
- #' [shiny::moduleServer()] instead which doesn't require these arguments.+ identical(data_load_status(), "ok") |
||
| 53 | +219 |
- #' - `data` (optional) When provided, the module will be called with `teal_data` object (i.e. a list of+ ) |
||
| 54 | +220 |
- #' reactive (filtered) data specified in the `filters` argument) as the value of this argument.+ ) |
||
| 55 | +221 |
- #' - `datasets` (optional) When provided, the module will be called with `FilteredData` object as the+ }, |
||
| 56 | -+ | |||
| 222 | +82x |
- #' value of this argument. (See [`teal.slice::FilteredData`]).+ simplify = FALSE |
||
| 57 | +223 |
- #' - `reporter` (optional) When provided, the module will be called with `Reporter` object as the value+ ) |
||
| 58 | +224 |
- #' of this argument. (See [`teal.reporter::Reporter`]).+ |
||
| 59 | -+ | |||
| 225 | +82x |
- #' - `filter_panel_api` (optional) When provided, the module will be called with `FilterPanelAPI` object+ modules_output |
||
| 60 | +226 |
- #' as the value of this argument. (See [`teal.slice::FilterPanelAPI`]).+ }) |
||
| 61 | +227 |
- #' - `...` (optional) When provided, `server_args` elements will be passed to the module named argument+ } |
||
| 62 | +228 |
- #' or to the `...`.+ |
||
| 63 | +229 |
- #' @param ui (`function`) `shiny` UI module function with following arguments:+ #' @rdname module_teal_module |
||
| 64 | +230 |
- #' - `id` - `teal` will set proper `shiny` namespace for this module.+ #' @export |
||
| 65 | +231 |
- #' - `...` (optional) When provided, `ui_args` elements will be passed to the module named argument+ srv_teal_module.teal_module <- function(id, |
||
| 66 | +232 |
- #' or to the `...`.+ data_rv, |
||
| 67 | +233 |
- #' @param filters (`character`) Deprecated. Use `datanames` instead.+ modules, |
||
| 68 | +234 |
- #' @param datanames (`character`) Names of the datasets relevant to the item.+ datasets = NULL, |
||
| 69 | +235 |
- #' There are 2 reserved values that have specific behaviors:+ slices_global, |
||
| 70 | +236 |
- #' - The keyword `"all"` includes all datasets available in the data passed to the teal application.+ reporter = teal.reporter::Reporter$new(), |
||
| 71 | +237 |
- #' - `NULL` hides the sidebar panel completely.+ data_load_status = reactive("ok"),
|
||
| 72 | +238 |
- #' - If `transformers` are specified, their `datanames` are automatically added to this `datanames`+ is_active = reactive(TRUE)) {
|
||
| 73 | -+ | |||
| 239 | +107x |
- #' argument.+ logger::log_debug("srv_teal_module.teal_module initializing the module: { deparse1(modules$label) }.")
|
||
| 74 | -+ | |||
| 240 | +107x |
- #' @param server_args (named `list`) with additional arguments passed on to the server function.+ moduleServer(id = id, module = function(input, output, session) {
|
||
| 75 | -+ | |||
| 241 | +107x |
- #' @param ui_args (named `list`) with additional arguments passed on to the UI function.+ module_out <- reactiveVal() |
||
| 76 | +242 |
- #' @param x (`teal_module` or `teal_modules`) Object to format/print.+ |
||
| 77 | -+ | |||
| 243 | +107x |
- #' @param indent (`integer(1)`) Indention level; each nested element is indented one level more.+ active_datanames <- reactive({
|
||
| 78 | -+ | |||
| 244 | +84x |
- #' @param transformers (`list` of `teal_data_module`) that will be applied to transform the data.+ .resolve_module_datanames(data = data_rv(), modules = modules) |
||
| 79 | +245 |
- #' Each transform module UI will appear in the `teal`'s sidebar panel.+ }) |
||
| 80 | -+ | |||
| 246 | +107x |
- #' Transformers' `datanames` are added to the `datanames`. See [teal_transform_module()].+ if (is.null(datasets)) {
|
||
| 81 | -+ | |||
| 247 | +20x |
- #'+ datasets <- eventReactive(data_rv(), {
|
||
| 82 | -+ | |||
| 248 | +16x |
- #' @param ...+ req(inherits(data_rv(), "teal_data")) |
||
| 83 | -+ | |||
| 249 | +16x |
- #' - For `modules()`: (`teal_module` or `teal_modules`) Objects to wrap into a tab.+ logger::log_debug("srv_teal_module@1 initializing module-specific FilteredData")
|
||
| 84 | -+ | |||
| 250 | +16x |
- #' - For `format()` and `print()`: Arguments passed to other methods.+ teal_data_to_filtered_data(data_rv(), datanames = active_datanames()) |
||
| 85 | +251 |
- #'+ }) |
||
| 86 | +252 |
- #' @return+ } |
||
| 87 | +253 |
- #' `module()` returns an object of class `teal_module`.+ |
||
| 88 | +254 |
- #'+ # manage module filters on the module level |
||
| 89 | +255 |
- #' `modules()` returns a `teal_modules` object which contains following fields:+ # important: |
||
| 90 | +256 |
- #' - `label`: taken from the `label` argument.+ # filter_manager_module_srv needs to be called before filter_panel_srv |
||
| 91 | +257 |
- #' - `children`: a list containing objects passed in `...`. List elements are named after+ # Because available_teal_slices is used in FilteredData$srv_available_slices (via srv_filter_panel) |
||
| 92 | +258 |
- #' their `label` attribute converted to a valid `shiny` id.+ # and if it is not set, then it won't be available in the srv_filter_panel |
||
| 93 | -+ | |||
| 259 | +107x |
- #'+ srv_module_filter_manager(modules$label, module_fd = datasets, slices_global = slices_global) |
||
| 94 | +260 |
- #' @name teal_modules+ |
||
| 95 | -+ | |||
| 261 | +107x |
- #' @aliases teal_module+ call_once_when(is_active(), {
|
||
| 96 | -+ | |||
| 262 | +81x |
- #'+ filtered_teal_data <- srv_filter_data( |
||
| 97 | -+ | |||
| 263 | +81x |
- #' @examples+ "filter_panel", |
||
| 98 | -+ | |||
| 264 | +81x |
- #' library(shiny)+ datasets = datasets, |
||
| 99 | -+ | |||
| 265 | +81x |
- #'+ active_datanames = active_datanames, |
||
| 100 | -+ | |||
| 266 | +81x |
- #' module_1 <- module(+ data_rv = data_rv, |
||
| 101 | -+ | |||
| 267 | +81x |
- #' label = "a module",+ is_active = is_active |
||
| 102 | +268 |
- #' server = function(id, data) {
+ ) |
||
| 103 | -+ | |||
| 269 | +81x |
- #' moduleServer(+ is_transformer_failed <- reactiveValues() |
||
| 104 | -+ | |||
| 270 | +81x |
- #' id,+ transformed_teal_data <- srv_transform_data( |
||
| 105 | -+ | |||
| 271 | +81x |
- #' module = function(input, output, session) {
+ "data_transform", |
||
| 106 | -+ | |||
| 272 | +81x |
- #' output$data <- renderDataTable(data()[["iris"]])+ data = filtered_teal_data, |
||
| 107 | -+ | |||
| 273 | +81x |
- #' }+ transformers = modules$transformers, |
||
| 108 | -+ | |||
| 274 | +81x |
- #' )+ modules = modules, |
||
| 109 | -+ | |||
| 275 | +81x |
- #' },+ is_transformer_failed = is_transformer_failed |
||
| 110 | +276 |
- #' ui = function(id) {
+ ) |
||
| 111 | -+ | |||
| 277 | +81x |
- #' ns <- NS(id)+ any_transformer_failed <- reactive({
|
||
| 112 | -+ | |||
| 278 | +81x |
- #' tagList(dataTableOutput(ns("data")))
+ any(unlist(reactiveValuesToList(is_transformer_failed))) |
||
| 113 | +279 |
- #' },+ }) |
||
| 114 | +280 |
- #' datanames = "all"+ |
||
| 115 | -+ | |||
| 281 | +81x |
- #' )+ observeEvent(any_transformer_failed(), {
|
||
| 116 | -+ | |||
| 282 | +81x |
- #'+ if (isTRUE(any_transformer_failed())) {
|
||
| 117 | -+ | |||
| 283 | +6x |
- #' module_2 <- module(+ shinyjs::hide("teal_module_ui")
|
||
| 118 | -+ | |||
| 284 | +6x |
- #' label = "another module",+ shinyjs::hide("validate_datanames")
|
||
| 119 | -+ | |||
| 285 | +6x |
- #' server = function(id) {
+ shinyjs::show("transformer_failure_info")
|
||
| 120 | +286 |
- #' moduleServer(+ } else {
|
||
| 121 | -+ | |||
| 287 | +75x |
- #' id,+ shinyjs::show("teal_module_ui")
|
||
| 122 | -+ | |||
| 288 | +75x |
- #' module = function(input, output, session) {
+ shinyjs::show("validate_datanames")
|
||
| 123 | -+ | |||
| 289 | +75x |
- #' output$text <- renderText("Another Module")
+ shinyjs::hide("transformer_failure_info")
|
||
| 124 | +290 |
- #' }+ } |
||
| 125 | +291 |
- #' )+ }) |
||
| 126 | +292 |
- #' },+ |
||
| 127 | -+ | |||
| 293 | +81x |
- #' ui = function(id) {
+ module_teal_data <- reactive({
|
||
| 128 | -+ | |||
| 294 | +89x |
- #' ns <- NS(id)+ req(inherits(transformed_teal_data(), "teal_data")) |
||
| 129 | -+ | |||
| 295 | +83x |
- #' tagList(textOutput(ns("text")))
+ all_teal_data <- transformed_teal_data() |
||
| 130 | -+ | |||
| 296 | +83x |
- #' },+ module_datanames <- .resolve_module_datanames(data = all_teal_data, modules = modules) |
||
| 131 | -+ | |||
| 297 | +83x |
- #' datanames = NULL+ .subset_teal_data(all_teal_data, module_datanames) |
||
| 132 | +298 |
- #' )+ }) |
||
| 133 | +299 |
- #'+ |
||
| 134 | -+ | |||
| 300 | +81x |
- #' modules <- modules(+ srv_validate_reactive_teal_data( |
||
| 135 | -+ | |||
| 301 | +81x |
- #' label = "modules",+ "validate_datanames", |
||
| 136 | -+ | |||
| 302 | +81x |
- #' modules(+ data = module_teal_data, |
||
| 137 | -+ | |||
| 303 | +81x |
- #' label = "nested modules",+ modules = modules |
||
| 138 | +304 |
- #' module_1+ ) |
||
| 139 | +305 |
- #' ),+ |
||
| 140 | -+ | |||
| 306 | +81x |
- #' module_2+ summary_table <- srv_data_summary("data_summary", module_teal_data)
|
||
| 141 | +307 |
- #' )+ |
||
| 142 | +308 |
- #'+ # Call modules. |
||
| 143 | -+ | |||
| 309 | +81x |
- #' app <- init(+ if (!inherits(modules, "teal_module_previewer")) {
|
||
| 144 | -+ | |||
| 310 | +81x |
- #' data = teal_data(iris = iris),+ obs_module <- call_once_when( |
||
| 145 | -+ | |||
| 311 | +81x |
- #' modules = modules+ !is.null(module_teal_data()), |
||
| 146 | -+ | |||
| 312 | +81x |
- #' )+ ignoreNULL = TRUE, |
||
| 147 | -+ | |||
| 313 | +81x |
- #'+ handlerExpr = {
|
||
| 148 | -+ | |||
| 314 | +75x |
- #' if (interactive()) {
+ module_out(.call_teal_module(modules, datasets, module_teal_data, reporter)) |
||
| 149 | +315 |
- #' shinyApp(app$ui, app$server)+ } |
||
| 150 | +316 |
- #' }+ ) |
||
| 151 | +317 |
- #' @rdname teal_modules+ } else {
|
||
| 152 | +318 |
- #' @export+ # Report previewer must be initiated on app start for report cards to be included in bookmarks. |
||
| 153 | +319 |
- #'+ # When previewer is delayed, cards are bookmarked only if previewer has been initiated (visited). |
||
| 154 | -+ | |||
| 320 | +! |
- module <- function(label = "module",+ module_out(.call_teal_module(modules, datasets, module_teal_data, reporter)) |
||
| 155 | +321 |
- server = function(id, data, ...) moduleServer(id, function(input, output, session) NULL),+ } |
||
| 156 | +322 |
- ui = function(id, ...) tags$p(paste0("This module has no UI (id: ", id, " )")),
+
|
||
| 157 | +323 |
- filters,+ # todo: (feature request) add a ReporterCard to the reporter as an output from the teal_module |
||
| 158 | +324 |
- datanames = "all",+ # how to determine if module returns a ReporterCard so that reportPreviewer is needed? |
||
| 159 | +325 |
- server_args = NULL,+ # Should we insertUI of the ReportPreviewer then? |
||
| 160 | +326 |
- ui_args = NULL,+ # What about attr(module, "reportable") - similar to attr(module, "bookmarkable") |
||
| 161 | -+ | |||
| 327 | +81x |
- transformers = list()) {
+ if ("report" %in% names(module_out)) {
|
||
| 162 | +328 |
- # argument checking (independent)+ # (reactively) add card to the reporter |
||
| 163 | +329 |
- ## `label`- |
- ||
| 164 | -213x | -
- checkmate::assert_string(label)- |
- ||
| 165 | -210x | -
- if (label == "global_filters") {
- |
- ||
| 166 | -1x | -
- stop(- |
- ||
| 167 | -1x | -
- sprintf("module(label = \"%s\", ...\n ", label),
- |
- ||
| 168 | -1x | -
- "Label 'global_filters' is reserved in teal. Please change to something else.",- |
- ||
| 169 | -1x | -
- call. = FALSE+ } |
||
| 170 | +330 |
- )+ }) |
||
| 171 | +331 |
- }+ |
||
| 172 | -209x | -
- if (label == "Report previewer") {
- |
- ||
| 173 | -! | -
- stop(- |
- ||
| 174 | -! | -
- sprintf("module(label = \"%s\", ...\n ", label),
- |
- ||
| 175 | -! | -
- "Label 'Report previewer' is reserved in teal. Please change to something else.",- |
- ||
| 176 | -! | +332 | +107x |
- call. = FALSE+ module_out |
| 177 | +333 |
- )+ }) |
||
| 178 | +334 |
- }+ } |
||
| 179 | +335 | |||
| 180 | +336 |
- ## server+ # This function calls a module server function. |
||
| 181 | -209x | +|||
| 337 | +
- checkmate::assert_function(server)+ .call_teal_module <- function(modules, datasets, filtered_teal_data, reporter) {
|
|||
| 182 | -209x | +|||
| 338 | +
- server_formals <- names(formals(server))+ # collect arguments to run teal_module |
|||
| 183 | -209x | +339 | +75x |
- if (!(+ args <- c(list(id = "module"), modules$server_args) |
| 184 | -209x | +340 | +75x |
- "id" %in% server_formals ||+ if (is_arg_used(modules$server, "reporter")) {
|
| 185 | -209x | +341 | +1x |
- all(c("input", "output", "session") %in% server_formals)
+ args <- c(args, list(reporter = reporter)) |
| 186 | +342 |
- )) {
- |
- ||
| 187 | -2x | -
- stop(- |
- ||
| 188 | -2x | -
- "\nmodule() `server` argument requires a function with following arguments:",+ } |
||
| 189 | -2x | +|||
| 343 | +
- "\n - id - `teal` will set proper `shiny` namespace for this module.",+ |
|||
| 190 | -2x | +344 | +75x |
- "\n - input, output, session (not recommended) - then `shiny::callModule` will be used to call a module.",+ if (is_arg_used(modules$server, "datasets")) {
|
| 191 | -2x | +345 | +1x |
- "\n\nFollowing arguments can be used optionaly:",+ args <- c(args, datasets = datasets()) |
| 192 | -2x | +346 | +1x |
- "\n - `data` - module will receive list of reactive (filtered) data specified in the `filters` argument",+ warning("datasets argument is not reactive and therefore it won't be updated when data is refreshed.")
|
| 193 | -2x | +|||
| 347 | +
- "\n - `datasets` - module will receive `FilteredData`. See `help(teal.slice::FilteredData)`",+ } |
|||
| 194 | -2x | +|||
| 348 | +
- "\n - `reporter` - module will receive `Reporter`. See `help(teal.reporter::Reporter)`",+ |
|||
| 195 | -2x | +349 | +75x |
- "\n - `filter_panel_api` - module will receive `FilterPanelAPI`. (See [teal.slice::FilterPanelAPI]).",+ if (is_arg_used(modules$server, "data")) {
|
| 196 | -2x | +350 | +71x |
- "\n - `...` server_args elements will be passed to the module named argument or to the `...`"+ args <- c(args, data = list(filtered_teal_data)) |
| 197 | +351 |
- )+ } |
||
| 198 | +352 |
- }+ |
||
| 199 | -207x | +353 | +75x |
- if ("datasets" %in% server_formals) {
+ if (is_arg_used(modules$server, "filter_panel_api")) {
|
| 200 | -2x | +354 | +1x |
- warning(+ args <- c(args, filter_panel_api = teal.slice::FilterPanelAPI$new(datasets())) |
| 201 | -2x | +|||
| 355 | +
- sprintf("Called from module(label = \"%s\", ...)\n ", label),
+ } |
|||
| 202 | -2x | +|||
| 356 | +
- "`datasets` argument in the server is deprecated and will be removed in the next release. ",+ |
|||
| 203 | -2x | +357 | +75x |
- "Please use `data` instead.",+ if (is_arg_used(modules$server, "id")) {
|
| 204 | -2x | +358 | +75x |
- call. = FALSE+ do.call(modules$server, args) |
| 205 | +359 |
- )+ } else {
+ |
+ ||
| 360 | +! | +
+ do.call(callModule, c(args, list(module = modules$server))) |
||
| 206 | +361 |
} |
||
| 207 | +362 |
-
+ } |
||
| 208 | +363 | |||
| 209 | +364 |
- ## UI- |
- ||
| 210 | -207x | -
- checkmate::assert_function(ui)+ .resolve_module_datanames <- function(data, modules) {
|
||
| 211 | -207x | +365 | +167x |
- ui_formals <- names(formals(ui))+ stopifnot("data_rv must be teal_data object." = inherits(data, "teal_data"))
|
| 212 | -207x | +366 | +167x |
- if (!"id" %in% ui_formals) {
+ if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
|
| 213 | -1x | +367 | +135x |
- stop(+ names(data) |
| 214 | -1x | +|||
| 368 | +
- "\nmodule() `ui` argument requires a function with following arguments:",+ } else {
|
|||
| 215 | -1x | +369 | +32x |
- "\n - id - `teal` will set proper `shiny` namespace for this module.",+ intersect( |
| 216 | -1x | +370 | +32x |
- "\n\nFollowing arguments can be used optionally:",+ names(data), # Keep topological order from teal.data::names() |
| 217 | -1x | +371 | +32x |
- "\n - `...` ui_args elements will be passed to the module argument of the same name or to the `...`"+ .include_parent_datanames(modules$datanames, teal.data::join_keys(data)) |
| 218 | +372 |
) |
||
| 219 | +373 |
} |
||
| 220 | -206x | +|||
| 374 | +
- if (any(c("data", "datasets") %in% ui_formals)) {
+ } |
|||
| 221 | -2x | +|||
| 375 | +
- stop(+ |
|||
| 222 | -2x | +|||
| 376 | +
- sprintf("Called from module(label = \"%s\", ...)\n ", label),
+ #' Calls expression when condition is met |
|||
| 223 | -2x | +|||
| 377 | +
- "UI with `data` or `datasets` argument is no longer accepted.\n ",+ #' |
|||
| 224 | -2x | +|||
| 378 | +
- "If some UI inputs depend on data, please move the logic to your server instead.\n ",+ #' Function postpones `handlerExpr` to the moment when `eventExpr` (condition) returns `TRUE`, |
|||
| 225 | -2x | +|||
| 379 | +
- "Possible solutions are renderUI() or updateXyzInput() functions."+ #' otherwise nothing happens. |
|||
| 226 | +380 |
- )+ #' @param eventExpr A (quoted or unquoted) logical expression that represents the event; |
||
| 227 | +381 |
- }+ #' this can be a simple reactive value like input$click, a call to a reactive expression |
||
| 228 | +382 |
-
+ #' like dataset(), or even a complex expression inside curly braces. |
||
| 229 | +383 |
-
+ #' @param ... additional arguments passed to `observeEvent` with the exception of `eventExpr` that is not allowed. |
||
| 230 | +384 |
- ## `filters`+ #' @inheritParams shiny::observeEvent |
||
| 231 | -204x | +|||
| 385 | +
- if (!missing(filters)) {
+ #' |
|||
| 232 | -! | +|||
| 386 | +
- datanames <- filters+ #' @return An observer. |
|||
| 233 | -! | +|||
| 387 | +
- msg <-+ #' |
|||
| 234 | -! | +|||
| 388 | +
- "The `filters` argument is deprecated and will be removed in the next release. Please use `datanames` instead."+ #' @keywords internal |
|||
| 235 | -! | +|||
| 389 | +
- warning(msg)+ call_once_when <- function(eventExpr, # nolint: object_name. |
|||
| 236 | +390 |
- }+ handlerExpr, # nolint: object_name. |
||
| 237 | +391 |
-
+ event.env = parent.frame(), # nolint: object_name. |
||
| 238 | +392 |
- ## `datanames` (also including deprecated `filters`)+ handler.env = parent.frame(), # nolint: object_name. |
||
| 239 | +393 |
- # please note a race condition between datanames set when filters is not missing and data arg in server function+ ...) {
|
||
| 240 | -204x | +394 | +188x |
- if (!is.element("data", server_formals) && !is.null(datanames)) {
+ event_quo <- rlang::new_quosure(substitute(eventExpr), env = event.env) |
| 241 | -12x | +395 | +188x |
- message(sprintf("module \"%s\" server function takes no data so \"datanames\" will be ignored", label))
+ handler_quo <- rlang::new_quosure(substitute(handlerExpr), env = handler.env) |
| 242 | -12x | +|||
| 396 | +
- datanames <- NULL+ |
|||
| 243 | +397 |
- }+ # When `condExpr` is TRUE, then `handlerExpr` is evaluated once. |
||
| 244 | -204x | +398 | +188x |
- checkmate::assert_character(datanames, min.len = 1, null.ok = TRUE, any.missing = FALSE)+ activator <- reactive({
+ |
+
| 399 | +188x | +
+ if (isTRUE(rlang::eval_tidy(event_quo))) {
+ |
+ ||
| 400 | +156x | +
+ TRUE |
||
| 245 | +401 |
-
+ } |
||
| 246 | +402 |
- ## `server_args`+ }) |
||
| 247 | -203x | +|||
| 403 | +
- checkmate::assert_list(server_args, null.ok = TRUE, names = "named")+ |
|||
| 248 | -201x | +404 | +188x |
- srv_extra_args <- setdiff(names(server_args), server_formals)+ observeEvent( |
| 249 | -201x | +405 | +188x |
- if (length(srv_extra_args) > 0 && !"..." %in% server_formals) {
+ eventExpr = activator(), |
| 250 | -1x | +406 | +188x |
- stop(+ once = TRUE, |
| 251 | -1x | +407 | +188x |
- "\nFollowing `server_args` elements have no equivalent in the formals of the server:\n",+ handlerExpr = rlang::eval_tidy(handler_quo), |
| 252 | -1x | +|||
| 408 | +
- paste(paste(" -", srv_extra_args), collapse = "\n"),
+ ... |
|||
| 253 | -1x | +|||
| 409 | +
- "\n\nUpdate the server arguments by including above or add `...`"+ ) |
|||
| 254 | +410 |
- )+ } |
| 255 | +1 |
- }+ #' Get client timezone |
||
| 256 | +2 |
-
+ #' |
||
| 257 | +3 |
- ## `ui_args`+ #' User timezone in the browser may be different to the one on the server. |
||
| 258 | -200x | +|||
| 4 | +
- checkmate::assert_list(ui_args, null.ok = TRUE, names = "named")+ #' This script can be run to register a `shiny` input which contains information about the timezone in the browser. |
|||
| 259 | -198x | +|||
| 5 | +
- ui_extra_args <- setdiff(names(ui_args), ui_formals)+ #' |
|||
| 260 | -198x | +|||
| 6 | +
- if (length(ui_extra_args) > 0 && !"..." %in% ui_formals) {
+ #' @param ns (`function`) namespace function passed from the `session` object in the `shiny` server. |
|||
| 261 | -1x | +|||
| 7 | +
- stop(+ #' For `shiny` modules this will allow for proper name spacing of the registered input. |
|||
| 262 | -1x | +|||
| 8 | +
- "\nFollowing `ui_args` elements have no equivalent in the formals of UI:\n",+ #' |
|||
| 263 | -1x | +|||
| 9 | +
- paste(paste(" -", ui_extra_args), collapse = "\n"),
+ #' @return `NULL`, invisibly. |
|||
| 264 | -1x | +|||
| 10 | +
- "\n\nUpdate the UI arguments by including above or add `...`"+ #' |
|||
| 265 | +11 |
- )+ #' @keywords internal |
||
| 266 | +12 |
- }+ #' |
||
| 267 | +13 |
-
+ get_client_timezone <- function(ns) {
|
||
| 268 | -+ | |||
| 14 | +83x |
- ## `transformers`+ script <- sprintf( |
||
| 269 | -197x | +15 | +83x |
- if (inherits(transformers, "teal_transform_module")) {
+ "Shiny.setInputValue(`%s`, Intl.DateTimeFormat().resolvedOptions().timeZone)", |
| 270 | -1x | +16 | +83x |
- transformers <- list(transformers)+ ns("timezone")
|
| 271 | +17 |
- }+ ) |
||
| 272 | -197x | +18 | +83x |
- checkmate::assert_list(transformers, types = "teal_transform_module")+ shinyjs::runjs(script) # function does not return anything |
| 273 | -197x | +19 | +83x |
- transformer_datanames <- unlist(lapply(transformers, attr, "datanames"))+ invisible(NULL) |
| 274 | -197x | +|||
| 20 | +
- combined_datanames <- if (identical(datanames, "all")) {
+ } |
|||
| 275 | -144x | +|||
| 21 | +
- "all"+ |
|||
| 276 | +22 |
- } else {
+ #' Resolve the expected bootstrap theme |
||
| 277 | -53x | +|||
| 23 | +
- union(datanames, transformer_datanames)+ #' @noRd |
|||
| 278 | +24 |
- }+ #' @keywords internal |
||
| 279 | +25 |
-
+ get_teal_bs_theme <- function() {
|
||
| 280 | -197x | +26 | +4x |
- structure(+ bs_theme <- getOption("teal.bs_theme")
|
| 281 | -197x | +|||
| 27 | +
- list(+ |
|||
| 282 | -197x | +28 | +4x |
- label = label,+ if (is.null(bs_theme)) {
|
| 283 | -197x | +29 | +1x |
- server = server,+ return(NULL)+ |
+
| 30 | ++ |
+ }+ |
+ ||
| 31 | ++ | + | ||
| 284 | -197x | +32 | +3x |
- ui = ui,+ if (!checkmate::test_class(bs_theme, "bs_theme")) {
|
| 285 | -197x | +33 | +2x |
- datanames = combined_datanames,+ warning( |
| 286 | -197x | +34 | +2x |
- server_args = server_args,+ "Assertion on 'teal.bs_theme' option value failed: ", |
| 287 | -197x | +35 | +2x |
- ui_args = ui_args,+ checkmate::check_class(bs_theme, "bs_theme"), |
| 288 | -197x | +36 | +2x |
- transformers = transformers+ ". The default Shiny Bootstrap theme will be used." |
| 289 | +37 |
- ),+ ) |
||
| 290 | -197x | +38 | +2x |
- class = "teal_module"+ return(NULL) |
| 291 | +39 |
- )+ } |
||
| 292 | +40 | ++ | + + | +|
| 41 | +1x | +
+ bs_theme+ |
+ ||
| 42 |
} |
|||
| 293 | +43 | |||
| 294 | +44 |
- #' @rdname teal_modules+ #' Return parentnames along with datanames. |
||
| 295 | +45 |
- #' @export+ #' @noRd |
||
| 296 | +46 |
- #'+ #' @keywords internal |
||
| 297 | +47 |
- modules <- function(..., label = "root") {
+ .include_parent_datanames <- function(datanames, join_keys) {
|
||
| 298 | -137x | +48 | +32x |
- checkmate::assert_string(label)+ ordered_datanames <- datanames |
| 299 | -135x | +49 | +32x |
- submodules <- list(...)+ for (current in datanames) {
|
| 300 | -135x | +50 | +62x |
- if (any(vapply(submodules, is.character, FUN.VALUE = logical(1)))) {
+ parents <- character(0L) |
| 301 | -2x | +51 | +62x |
- stop(+ while (length(current) > 0) {
|
| 302 | -2x | +52 | +64x |
- "The only character argument to modules() must be 'label' and it must be named, ",+ current <- teal.data::parent(join_keys, current) |
| 303 | -2x | +53 | +64x |
- "change modules('lab', ...) to modules(label = 'lab', ...)"
+ parents <- c(current, parents) |
| 304 | +54 |
- )+ }+ |
+ ||
| 55 | +62x | +
+ ordered_datanames <- c(parents, ordered_datanames) |
||
| 305 | +56 |
} |
||
| 306 | +57 | |||
| 307 | -133x | +58 | +32x |
- checkmate::assert_list(submodules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ unique(ordered_datanames) |
| 308 | +59 |
- # name them so we can more easily access the children+ } |
||
| 309 | +60 |
- # beware however that the label of the submodules should not be changed as it must be kept synced+ |
||
| 310 | -130x | +|||
| 61 | +
- labels <- vapply(submodules, function(submodule) submodule$label, character(1))+ #' Create a `FilteredData` |
|||
| 311 | -130x | +|||
| 62 | +
- names(submodules) <- get_unique_labels(labels)+ #' |
|||
| 312 | -130x | +|||
| 63 | +
- structure(+ #' Create a `FilteredData` object from a `teal_data` object. |
|||
| 313 | -130x | +|||
| 64 | +
- list(+ #' |
|||
| 314 | -130x | +|||
| 65 | +
- label = label,+ #' @param x (`teal_data`) object |
|||
| 315 | -130x | +|||
| 66 | +
- children = submodules+ #' @param datanames (`character`) vector of data set names to include; must be subset of `names(x)` |
|||
| 316 | +67 |
- ),+ #' @return A `FilteredData` object. |
||
| 317 | -130x | +|||
| 68 | +
- class = "teal_modules"+ #' @keywords internal |
|||
| 318 | +69 |
- )+ teal_data_to_filtered_data <- function(x, datanames = names(x)) {
|
||
| 319 | -+ | |||
| 70 | +78x |
- }+ checkmate::assert_class(x, "teal_data") |
||
| 320 | -+ | |||
| 71 | +78x |
-
+ checkmate::assert_character(datanames, min.chars = 1L, any.missing = FALSE) |
||
| 321 | +72 |
- # printing methods ----+ # Otherwise, FilteredData will be created in the modules' scope later |
||
| 322 | -+ | |||
| 73 | +78x |
-
+ teal.slice::init_filtered_data( |
||
| 323 | -+ | |||
| 74 | +78x |
- #' @rdname teal_modules+ x = Filter(length, sapply(datanames, function(dn) x[[dn]], simplify = FALSE)), |
||
| 324 | -+ | |||
| 75 | +78x |
- #' @param is_last (`logical(1)`) Whether this is the last item in its parent's children list.+ join_keys = teal.data::join_keys(x) |
||
| 325 | +76 |
- #' Affects the tree branch character used (L- vs |-)+ ) |
||
| 326 | +77 |
- #' @param parent_prefix (`character(1)`) The prefix inherited from parent nodes,+ } |
||
| 327 | +78 |
- #' used to maintain the tree structure in nested levels+ |
||
| 328 | +79 |
- #' @param is_root (`logical(1)`) Whether this is the root node of the tree. Only used in+ |
||
| 329 | +80 |
- #' format.teal_modules(). Determines whether to show "TEAL ROOT" header+ #' Template function for `TealReportCard` creation and customization |
||
| 330 | +81 |
- #' @param what (`character`) Specifies which metadata to display.+ #' |
||
| 331 | +82 |
- #' Possible values: "datasets", "properties", "ui_args", "server_args", "transformers"+ #' This function generates a report card with a title, |
||
| 332 | +83 |
- #' @examples+ #' an optional description, and the option to append the filter state list. |
||
| 333 | +84 |
- #' mod <- module(+ #' |
||
| 334 | +85 |
- #' label = "My Custom Module",+ #' @param title (`character(1)`) title of the card (unless overwritten by label) |
||
| 335 | +86 |
- #' server = function(id, data, ...) {},
+ #' @param label (`character(1)`) label provided by the user when adding the card |
||
| 336 | +87 |
- #' ui = function(id, ...) {},
+ #' @param description (`character(1)`) optional, additional description |
||
| 337 | +88 |
- #' datanames = c("ADSL", "ADTTE"),
+ #' @param with_filter (`logical(1)`) flag indicating to add filter state |
||
| 338 | +89 |
- #' transformers = list(),+ #' @param filter_panel_api (`FilterPanelAPI`) object with API that allows the generation |
||
| 339 | +90 |
- #' ui_args = list(a = 1, b = "b"),+ #' of the filter state in the report |
||
| 340 | +91 |
- #' server_args = list(x = 5, y = list(p = 1))+ #' |
||
| 341 | +92 |
- #' )+ #' @return (`TealReportCard`) populated with a title, description and filter state. |
||
| 342 | +93 |
- #' cat(format(mod))+ #' |
||
| 343 | +94 |
#' @export |
||
| 344 | -- |
- format.teal_module <- function(- |
- ||
| 345 | +95 |
- x, indent = 0, is_last = FALSE, parent_prefix = "",+ report_card_template <- function(title, label, description = NULL, with_filter, filter_panel_api) {
|
||
| 346 | -+ | |||
| 96 | +2x |
- what = c("datasets", "properties", "ui_args", "server_args", "transformers"), ...) {
+ checkmate::assert_string(title) |
||
| 347 | -3x | +97 | +2x |
- empty_text <- ""+ checkmate::assert_string(label) |
| 348 | -3x | +98 | +2x |
- branch <- if (is_last) "L-" else "|-"+ checkmate::assert_string(description, null.ok = TRUE) |
| 349 | -3x | +99 | +2x |
- current_prefix <- paste0(parent_prefix, branch, " ")+ checkmate::assert_flag(with_filter) |
| 350 | -3x | +100 | +2x |
- content_prefix <- paste0(parent_prefix, if (is_last) " " else "| ")+ checkmate::assert_class(filter_panel_api, classes = "FilterPanelAPI") |
| 351 | +101 | |||
| 352 | -3x | +102 | +2x |
- format_list <- function(lst, empty = empty_text, label_width = 0) {
+ card <- teal::TealReportCard$new() |
| 353 | -6x | +103 | +2x |
- if (is.null(lst) || length(lst) == 0) {
+ title <- if (label == "") title else label |
| 354 | -6x | -
- empty- |
- ||
| 355 | -- |
- } else {
- |
- ||
| 356 | -! | -
- colon_space <- paste(rep(" ", label_width), collapse = "")
- |
- ||
| 357 | -- | - - | -||
| 358 | -! | +104 | +2x |
- first_item <- sprintf("%s (%s)", names(lst)[1], crayon::silver(class(lst[[1]])[1]))
+ card$set_name(title) |
| 359 | -! | +|||
| 105 | +2x |
- rest_items <- if (length(lst) > 1) {
+ card$append_text(title, "header2") |
||
| 360 | -! | +|||
| 106 | +1x |
- paste(+ if (!is.null(description)) card$append_text(description, "header3") |
||
| 361 | -! | +|||
| 107 | +1x |
- vapply(+ if (with_filter) card$append_fs(filter_panel_api$get_filter_state()) |
||
| 362 | -! | +|||
| 108 | +2x |
- names(lst)[-1],+ card |
||
| 363 | -! | +|||
| 109 | +
- function(name) {
+ } |
|||
| 364 | -! | +|||
| 110 | +
- sprintf(+ |
|||
| 365 | -! | +|||
| 111 | +
- "%s%s (%s)",+ |
|||
| 366 | -! | +|||
| 112 | +
- paste0(content_prefix, "| ", colon_space),+ #' Check `datanames` in modules |
|||
| 367 | -! | +|||
| 113 | +
- name,+ #' |
|||
| 368 | -! | +|||
| 114 | +
- crayon::silver(class(lst[[name]])[1])+ #' These functions check if specified `datanames` in modules match those in the data object, |
|||
| 369 | +115 |
- )+ #' returning error messages or `TRUE` for successful validation. Two functions return error message |
||
| 370 | +116 |
- },+ #' in different forms: |
||
| 371 | -! | +|||
| 117 | +
- character(1)+ #' - `check_modules_datanames` returns `character(1)` for basic assertion usage |
|||
| 372 | +118 |
- ),+ #' - `check_modules_datanames_html` returns `shiny.tag.list` to display it in the app. |
||
| 373 | -! | +|||
| 119 | +
- collapse = "\n"+ #' |
|||
| 374 | +120 |
- )+ #' @param modules (`teal_modules`) object |
||
| 375 | +121 |
- }+ #' @param datanames (`character`) names of datasets available in the `data` object |
||
| 376 | -! | +|||
| 122 | +
- if (length(lst) > 1) paste0(first_item, "\n", rest_items) else first_item+ #' |
|||
| 377 | +123 |
- }+ #' @return `TRUE` if validation passes, otherwise `character(1)` or `shiny.tag.list` |
||
| 378 | +124 |
- }+ #' @keywords internal |
||
| 379 | +125 |
-
+ check_modules_datanames <- function(modules, datanames) {
|
||
| 380 | -3x | +126 | +9x |
- bookmarkable <- isTRUE(attr(x, "teal_bookmarkable"))+ out <- check_modules_datanames_html(modules, datanames) |
| 381 | -3x | +127 | +9x |
- reportable <- "reporter" %in% names(formals(x$server))+ if (inherits(out, "shiny.tag.list")) {
|
| 382 | -+ | |||
| 128 | +3x |
-
+ out_with_ticks <- gsub("<code>|</code>", "`", toString(out))
|
||
| 383 | +129 | 3x |
- transformers <- if (length(x$transformers) > 0) {
+ out_text <- gsub("<[^<>]+>", "", toString(out_with_ticks))
|
|
| 384 | -! | +|||
| 130 | +3x |
- paste(sapply(x$transformers, function(t) attr(t, "label")), collapse = ", ")+ trimws(gsub("[[:space:]]+", " ", out_text))
|
||
| 385 | +131 |
} else {
|
||
| 386 | -3x | +132 | +6x |
- empty_text+ out |
| 387 | +133 |
} |
||
| 388 | +134 | ++ |
+ }+ |
+ |
| 135 | ||||
| 389 | -3x | +|||
| 136 | +
- output <- pasten(current_prefix, crayon::bgWhite(x$label))+ #' @rdname check_modules_datanames |
|||
| 390 | +137 |
-
+ check_modules_datanames_html <- function(modules, |
||
| 391 | -3x | +|||
| 138 | +
- if ("datasets" %in% what) {
+ datanames) {
|
|||
| 392 | -3x | +139 | +178x |
- output <- paste0(+ check_datanames <- check_modules_datanames_recursive(modules, datanames) |
| 393 | -3x | +140 | +178x |
- output,+ show_module_info <- inherits(modules, "teal_modules") # used in two contexts - module and app |
| 394 | -3x | +141 | +178x |
- content_prefix, "|- ", crayon::yellow("Datasets : "), paste(x$datanames, collapse = ", "), "\n"
+ if (!length(check_datanames)) {
|
| 395 | -+ | |||
| 142 | +160x |
- )+ return(TRUE) |
||
| 396 | +143 |
} |
||
| 397 | -3x | +144 | +18x |
- if ("properties" %in% what) {
+ shiny::tagList( |
| 398 | -3x | +145 | +18x |
- output <- paste0(+ lapply( |
| 399 | -3x | +146 | +18x |
- output,+ check_datanames, |
| 400 | -3x | +147 | +18x |
- content_prefix, "|- ", crayon::blue("Properties:"), "\n",
+ function(mod) {
|
| 401 | -3x | +148 | +18x |
- content_prefix, "| |- ", crayon::cyan("Bookmarkable : "), bookmarkable, "\n",
+ tagList( |
| 402 | -3x | -
- content_prefix, "| L- ", crayon::cyan("Reportable : "), reportable, "\n"
- |
- ||
| 403 | -+ | 149 | +18x |
- )+ tags$span( |
| 404 | -+ | |||
| 150 | +18x |
- }+ tags$span(if (length(mod$missing_datanames) == 1) "Dataset" else "Datasets"), |
||
| 405 | -3x | +151 | +18x |
- if ("ui_args" %in% what) {
+ to_html_code_list(mod$missing_datanames), |
| 406 | -3x | +152 | +18x |
- ui_args_formatted <- format_list(x$ui_args, label_width = 19)+ tags$span( |
| 407 | -3x | +153 | +18x |
- output <- paste0(+ paste0( |
| 408 | -3x | +154 | +18x |
- output,+ if (length(mod$missing_datanames) > 1) "are missing" else "is missing", |
| 409 | -3x | +155 | +18x |
- content_prefix, "|- ", crayon::green("UI Arguments : "), ui_args_formatted, "\n"
+ if (show_module_info) sprintf(" for module '%s'.", mod$label) else "."
|
| 410 | +156 |
- )+ ) |
||
| 411 | +157 |
- }+ ) |
||
| 412 | -3x | +|||
| 158 | +
- if ("server_args" %in% what) {
+ ), |
|||
| 413 | -3x | +159 | +18x |
- server_args_formatted <- format_list(x$server_args, label_width = 19)+ if (length(datanames) >= 1) {
|
| 414 | -3x | +160 | +16x |
- output <- paste0(+ tagList( |
| 415 | -3x | +161 | +16x |
- output,+ tags$span(if (length(datanames) == 1) "Dataset" else "Datasets"), |
| 416 | -3x | +162 | +16x |
- content_prefix, "|- ", crayon::green("Server Arguments : "), server_args_formatted, "\n"
+ tags$span("available in data:"),
|
| 417 | -+ | |||
| 163 | +16x |
- )+ tagList( |
||
| 418 | -+ | |||
| 164 | +16x |
- }+ tags$span( |
||
| 419 | -3x | +165 | +16x |
- if ("transformers" %in% what) {
+ to_html_code_list(datanames), |
| 420 | -3x | +166 | +16x |
- output <- paste0(+ tags$span(".", .noWS = "outside"),
|
| 421 | -3x | +167 | +16x |
- output,+ .noWS = c("outside")
|
| 422 | -3x | +|||
| 168 | +
- content_prefix, "L- ", crayon::magenta("Transformers : "), transformers, "\n"
+ ) |
|||
| 423 | +169 |
- )+ ) |
||
| 424 | +170 |
- }+ ) |
||
| 425 | +171 |
-
+ } else {
|
||
| 426 | -3x | +172 | +2x |
- output+ tags$span("No datasets are available in data.")
|
| 427 | +173 |
- }+ }, |
||
| 428 | -+ | |||
| 174 | +18x |
-
+ tags$br(.noWS = "before") |
||
| 429 | +175 |
- #' @rdname teal_modules+ ) |
||
| 430 | +176 |
- #' @examples+ } |
||
| 431 | +177 |
- #' custom_module <- function(+ ) |
||
| 432 | +178 |
- #' label = "label", ui_args = NULL, server_args = NULL,+ ) |
||
| 433 | +179 |
- #' datanames = "all", transformers = list(), bk = FALSE) {
+ } |
||
| 434 | +180 |
- #' ans <- module(+ |
||
| 435 | +181 |
- #' label,+ #' Recursively checks modules and returns list for every datanames mismatch between module and data |
||
| 436 | +182 |
- #' server = function(id, data, ...) {},
+ #' @noRd |
||
| 437 | +183 |
- #' ui = function(id, ...) {
+ check_modules_datanames_recursive <- function(modules, datanames) { # nolint: object_name_length
|
||
| 438 | -+ | |||
| 184 | +277x |
- #' },+ checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
|
||
| 439 | -+ | |||
| 185 | +277x |
- #' datanames = datanames,+ checkmate::assert_character(datanames) |
||
| 440 | -+ | |||
| 186 | +277x |
- #' transformers = transformers,+ if (inherits(modules, "teal_modules")) {
|
||
| 441 | -+ | |||
| 187 | +79x |
- #' ui_args = ui_args,+ unlist( |
||
| 442 | -+ | |||
| 188 | +79x |
- #' server_args = server_args+ lapply(modules$children, check_modules_datanames_recursive, datanames = datanames), |
||
| 443 | -+ | |||
| 189 | +79x |
- #' )+ recursive = FALSE |
||
| 444 | +190 |
- #' attr(ans, "teal_bookmarkable") <- bk+ ) |
||
| 445 | +191 |
- #' ans+ } else {
|
||
| 446 | -+ | |||
| 192 | +198x |
- #' }+ missing_datanames <- setdiff(modules$datanames, c("all", datanames))
|
||
| 447 | -+ | |||
| 193 | +198x |
- #'+ if (length(missing_datanames)) {
|
||
| 448 | -+ | |||
| 194 | +18x |
- #' dummy_transformer <- teal_transform_module(+ list(list( |
||
| 449 | -+ | |||
| 195 | +18x |
- #' label = "Dummy Transform",+ label = modules$label, |
||
| 450 | -+ | |||
| 196 | +18x |
- #' ui = function(id) div("(does nothing)"),
+ missing_datanames = missing_datanames |
||
| 451 | +197 |
- #' server = function(id, data) {
+ )) |
||
| 452 | +198 |
- #' moduleServer(id, function(input, output, session) data)+ } |
||
| 453 | +199 |
- #' }+ } |
||
| 454 | +200 |
- #' )+ } |
||
| 455 | +201 |
- #'+ |
||
| 456 | +202 |
- #' plot_transformer <- teal_transform_module(+ #' Convert character vector to html code separated with commas and "and" |
||
| 457 | +203 |
- #' label = "Plot Settings",+ #' @noRd |
||
| 458 | +204 |
- #' ui = function(id) div("(does nothing)"),
+ to_html_code_list <- function(x) {
|
||
| 459 | -+ | |||
| 205 | +34x |
- #' server = function(id, data) {
+ checkmate::assert_character(x) |
||
| 460 | -+ | |||
| 206 | +34x |
- #' moduleServer(id, function(input, output, session) data)+ do.call( |
||
| 461 | -+ | |||
| 207 | +34x |
- #' }+ tagList, |
||
| 462 | -+ | |||
| 208 | +34x |
- #' )+ lapply(seq_along(x), function(.ix) {
|
||
| 463 | -+ | |||
| 209 | +47x |
- #'+ tagList( |
||
| 464 | -+ | |||
| 210 | +47x |
- #' complete_modules <- modules(+ tags$code(x[.ix]), |
||
| 465 | -+ | |||
| 211 | +47x |
- #' custom_module(+ if (.ix != length(x)) {
|
||
| 466 | -+ | |||
| 212 | +1x |
- #' label = "Data Overview",+ if (.ix == length(x) - 1) tags$span(" and ") else tags$span(", ", .noWS = "before")
|
||
| 467 | +213 |
- #' datanames = c("ADSL", "ADAE", "ADVS"),
+ } |
||
| 468 | +214 |
- #' ui_args = list(+ ) |
||
| 469 | +215 |
- #' view_type = "table",+ }) |
||
| 470 | +216 |
- #' page_size = 10,+ ) |
||
| 471 | +217 |
- #' filters = c("ARM", "SEX", "RACE")
+ } |
||
| 472 | +218 |
- #' ),+ |
||
| 473 | +219 |
- #' server_args = list(+ |
||
| 474 | +220 |
- #' cache = TRUE,+ #' Check `datanames` in filters |
||
| 475 | +221 |
- #' debounce = 1000+ #' |
||
| 476 | +222 |
- #' ),+ #' This function checks whether `datanames` in filters correspond to those in `data`, |
||
| 477 | +223 |
- #' transformers = list(dummy_transformer),+ #' returning character vector with error messages or `TRUE` if all checks pass. |
||
| 478 | +224 |
- #' bk = TRUE+ #' |
||
| 479 | +225 |
- #' ),+ #' @param filters (`teal_slices`) object |
||
| 480 | +226 |
- #' modules(+ #' @param datanames (`character`) names of datasets available in the `data` object |
||
| 481 | +227 |
- #' label = "Nested 1",+ #' |
||
| 482 | +228 |
- #' custom_module(+ #' @return A `character(1)` containing error message or TRUE if validation passes. |
||
| 483 | +229 |
- #' label = "Interactive Plots",+ #' @keywords internal |
||
| 484 | +230 |
- #' datanames = c("ADSL", "ADVS"),
+ check_filter_datanames <- function(filters, datanames) {
|
||
| 485 | -+ | |||
| 231 | +79x |
- #' ui_args = list(+ checkmate::assert_class(filters, "teal_slices") |
||
| 486 | -+ | |||
| 232 | +79x |
- #' plot_type = c("scatter", "box", "line"),
+ checkmate::assert_character(datanames) |
||
| 487 | +233 |
- #' height = 600,+ |
||
| 488 | +234 |
- #' width = 800,+ # check teal_slices against datanames |
||
| 489 | -+ | |||
| 235 | +79x |
- #' color_scheme = "viridis"+ out <- unlist(sapply( |
||
| 490 | -+ | |||
| 236 | +79x |
- #' ),+ filters, function(filter) {
|
||
| 491 | -+ | |||
| 237 | +24x |
- #' server_args = list(+ dataname <- shiny::isolate(filter$dataname) |
||
| 492 | -+ | |||
| 238 | +24x |
- #' render_type = "svg",+ if (!dataname %in% datanames) {
|
||
| 493 | -+ | |||
| 239 | +3x |
- #' cache_plots = TRUE+ sprintf( |
||
| 494 | -+ | |||
| 240 | +3x |
- #' ),+ "- Filter '%s' refers to dataname not available in 'data':\n %s not in (%s)", |
||
| 495 | -+ | |||
| 241 | +3x |
- #' transformers = list(dummy_transformer, plot_transformer),+ shiny::isolate(filter$id), |
||
| 496 | -+ | |||
| 242 | +3x |
- #' bk = TRUE+ dQuote(dataname, q = FALSE), |
||
| 497 | -+ | |||
| 243 | +3x |
- #' ),+ toString(dQuote(datanames, q = FALSE)) |
||
| 498 | +244 |
- #' modules(+ ) |
||
| 499 | +245 |
- #' label = "Nested 2",+ } |
||
| 500 | +246 |
- #' custom_module(+ } |
||
| 501 | +247 |
- #' label = "Summary Statistics",+ )) |
||
| 502 | +248 |
- #' datanames = "ADSL",+ |
||
| 503 | +249 |
- #' ui_args = list(+ |
||
| 504 | -+ | |||
| 250 | +79x |
- #' stats = c("mean", "median", "sd", "range"),
+ if (length(out)) {
|
||
| 505 | -+ | |||
| 251 | +3x |
- #' grouping = c("ARM", "SEX")
+ paste(out, collapse = "\n") |
||
| 506 | +252 |
- #' )+ } else {
|
||
| 507 | -+ | |||
| 253 | +76x |
- #' ),+ TRUE |
||
| 508 | +254 |
- #' modules(+ } |
||
| 509 | +255 |
- #' label = "Labeled nested modules",+ } |
||
| 510 | +256 |
- #' custom_module(+ |
||
| 511 | +257 |
- #' label = "Subgroup Analysis",+ #' Function for validating the title parameter of `teal::init` |
||
| 512 | +258 |
- #' datanames = c("ADSL", "ADAE"),
+ #' |
||
| 513 | +259 |
- #' ui_args = list(+ #' Checks if the input of the title from `teal::init` will create a valid title and favicon tag. |
||
| 514 | +260 |
- #' subgroups = c("AGE", "SEX", "RACE"),
+ #' @param shiny_tag (`shiny.tag`) Object to validate for a valid title. |
||
| 515 | +261 |
- #' analysis_type = "stratified"+ #' @keywords internal |
||
| 516 | +262 |
- #' ),+ validate_app_title_tag <- function(shiny_tag) {
+ |
+ ||
| 263 | +7x | +
+ checkmate::assert_class(shiny_tag, "shiny.tag")+ |
+ ||
| 264 | +7x | +
+ checkmate::assert_true(shiny_tag$name == "head")+ |
+ ||
| 265 | +6x | +
+ child_names <- vapply(shiny_tag$children, `[[`, character(1L), "name")+ |
+ ||
| 266 | +6x | +
+ checkmate::assert_subset(c("title", "link"), child_names, .var.name = "child tags")
+ |
+ ||
| 267 | +4x | +
+ rel_attr <- shiny_tag$children[[which(child_names == "link")]]$attribs$rel+ |
+ ||
| 268 | +4x | +
+ checkmate::assert_subset(+ |
+ ||
| 269 | +4x | +
+ rel_attr,+ |
+ ||
| 270 | +4x | +
+ c("icon", "shortcut icon"),
+ |
+ ||
| 271 | +4x | +
+ .var.name = "Link tag's rel attribute",+ |
+ ||
| 272 | +4x | +
+ empty.ok = FALSE |
||
| 517 | +273 |
- #' bk = TRUE+ ) |
||
| 518 | +274 |
- #' )+ } |
||
| 519 | +275 |
- #' ),+ |
||
| 520 | +276 |
- #' modules(custom_module(label = "Subgroup Analysis in non-labled modules"))+ #' Build app title with favicon |
||
| 521 | +277 |
- #' )+ #' |
||
| 522 | +278 |
- #' ),+ #' A helper function to create the browser title along with a logo. |
||
| 523 | +279 |
- #' custom_module("Non-nested module")
+ #' |
||
| 524 | +280 |
- #' )+ #' @param title (`character`) The browser title for the `teal` app. |
||
| 525 | +281 |
- #'+ #' @param favicon (`character`) The path for the icon for the title. |
||
| 526 | +282 |
- #' cat(format(complete_modules))+ #' The image/icon path can be remote or the static path accessible by `shiny`, like the `www/` |
||
| 527 | +283 |
- #' cat(format(complete_modules, what = c("ui_args", "server_args", "transformers")))
+ #' |
||
| 528 | +284 | ++ |
+ #' @return A `shiny.tag` containing the element that adds the title and logo to the `shiny` app.+ |
+ |
| 285 |
#' @export |
|||
| 529 | +286 |
- format.teal_modules <- function(x, indent = 0, is_root = TRUE, is_last = FALSE, parent_prefix = "", ...) {
+ build_app_title <- function( |
||
| 530 | -1x | +|||
| 287 | +
- if (is_root) {
+ title = "teal app", |
|||
| 531 | -1x | +|||
| 288 | +
- header <- pasten(crayon::bold("TEAL ROOT"))
+ favicon = "https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/PNG/nest.png") {
|
|||
| 532 | -1x | +289 | +13x |
- new_parent_prefix <- " " #' Initial indent for root level+ checkmate::assert_string(title, null.ok = TRUE) |
| 533 | -+ | |||
| 290 | +13x |
- } else {
+ checkmate::assert_string(favicon, null.ok = TRUE) |
||
| 534 | -! | +|||
| 291 | +13x |
- if (!is.null(x$label)) {
+ tags$head( |
||
| 535 | -! | +|||
| 292 | +13x |
- branch <- if (is_last) "L-" else "|-"+ tags$title(title), |
||
| 536 | -! | +|||
| 293 | +13x |
- header <- pasten(parent_prefix, branch, " ", crayon::bold(x$label))+ tags$link( |
||
| 537 | -! | +|||
| 294 | +13x |
- new_parent_prefix <- paste0(parent_prefix, if (is_last) " " else "| ")+ rel = "icon", |
||
| 538 | -+ | |||
| 295 | +13x |
- } else {
+ href = favicon, |
||
| 539 | -! | +|||
| 296 | +13x |
- header <- ""+ sizes = "any" |
||
| 540 | -! | +|||
| 297 | +
- new_parent_prefix <- parent_prefix+ ) |
|||
| 541 | +298 |
- }+ ) |
||
| 542 | +299 |
- }+ } |
||
| 543 | +300 | |||
| 544 | -1x | +|||
| 301 | +
- if (length(x$children) > 0) {
+ #' Application ID |
|||
| 545 | -1x | +|||
| 302 | +
- children_output <- character(0)+ #' |
|||
| 546 | -1x | +|||
| 303 | +
- n_children <- length(x$children)+ #' Creates App ID used to match filter snapshots to application. |
|||
| 547 | +304 |
-
+ #' |
||
| 548 | -1x | +|||
| 305 | +
- for (i in seq_along(x$children)) {
+ #' Calculate app ID that will be used to stamp filter state snapshots. |
|||
| 549 | -3x | +|||
| 306 | +
- child <- x$children[[i]]+ #' App ID is a hash of the app's data and modules. |
|||
| 550 | -3x | +|||
| 307 | +
- is_last_child <- (i == n_children)+ #' See "transferring snapshots" section in ?snapshot. |
|||
| 551 | +308 |
-
+ #' |
||
| 552 | -3x | +|||
| 309 | +
- if (inherits(child, "teal_modules")) {
+ #' @param data (`teal_data` or `teal_data_module`) as accepted by `init` |
|||
| 553 | -! | +|||
| 310 | +
- children_output <- c(+ #' @param modules (`teal_modules`) object as accepted by `init` |
|||
| 554 | -! | +|||
| 311 | +
- children_output,+ #' |
|||
| 555 | -! | +|||
| 312 | +
- format(child,+ #' @return A single character string. |
|||
| 556 | -! | +|||
| 313 | +
- indent = indent,+ #' |
|||
| 557 | -! | +|||
| 314 | +
- is_root = FALSE,+ #' @keywords internal |
|||
| 558 | -! | +|||
| 315 | +
- is_last = is_last_child,+ create_app_id <- function(data, modules) {
|
|||
| 559 | -! | +|||
| 316 | +21x |
- parent_prefix = new_parent_prefix,+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
|
||
| 560 | -+ | |||
| 317 | +20x |
- ...+ checkmate::assert_class(modules, "teal_modules") |
||
| 561 | +318 |
- )+ |
||
| 562 | -+ | |||
| 319 | +19x |
- )+ data <- if (inherits(data, "teal_data")) {
|
||
| 563 | -+ | |||
| 320 | +17x |
- } else {
+ as.list(data) |
||
| 564 | -3x | +321 | +19x |
- children_output <- c(+ } else if (inherits(data, "teal_data_module")) {
|
| 565 | -3x | +322 | +2x |
- children_output,+ deparse1(body(data$server)) |
| 566 | -3x | +|||
| 323 | +
- format(child,+ } |
|||
| 567 | -3x | +324 | +19x |
- indent = indent,+ modules <- lapply(modules, defunction) |
| 568 | -3x | +|||
| 325 | +
- is_last = is_last_child,+ |
|||
| 569 | -3x | +326 | +19x |
- parent_prefix = new_parent_prefix,+ rlang::hash(list(data = data, modules = modules)) |
| 570 | +327 |
- ...+ } |
||
| 571 | +328 |
- )+ |
||
| 572 | +329 |
- )+ #' Go through list and extract bodies of encountered functions as string, recursively. |
||
| 573 | +330 |
- }+ #' @keywords internal |
||
| 574 | +331 |
- }+ #' @noRd |
||
| 575 | +332 |
-
+ defunction <- function(x) {
|
||
| 576 | -1x | +333 | +229x |
- paste0(header, paste(children_output, collapse = ""))+ if (is.list(x)) {
+ |
+
| 334 | +67x | +
+ lapply(x, defunction)+ |
+ ||
| 335 | +162x | +
+ } else if (is.function(x)) {
+ |
+ ||
| 336 | +50x | +
+ deparse1(body(x)) |
||
| 577 | +337 |
} else {
|
||
| 578 | -! | +|||
| 338 | +112x |
- header+ x |
||
| 579 | +339 |
} |
||
| 580 | +340 |
} |
||
| 581 | +341 | |||
| 582 | +342 |
- #' @rdname teal_modules+ #' Get unique labels |
||
| 583 | +343 |
- #' @export+ #' |
||
| 584 | +344 |
- print.teal_module <- function(x, ...) {
- |
- ||
| 585 | -! | -
- cat(format(x, ...))+ #' Get unique labels for the modules to avoid namespace conflicts. |
||
| 586 | -! | +|||
| 345 | +
- invisible(x)+ #' |
|||
| 587 | +346 |
- }+ #' @param labels (`character`) vector of labels |
||
| 588 | +347 |
-
+ #' |
||
| 589 | +348 |
- #' @rdname teal_modules+ #' @return (`character`) vector of unique labels |
||
| 590 | +349 |
- #' @export+ #' |
||
| 591 | +350 |
- print.teal_modules <- function(x, ...) {
+ #' @keywords internal |
||
| 592 | -! | +|||
| 351 | +
- cat(format(x, ...))+ get_unique_labels <- function(labels) {
|
|||
| 593 | -! | +|||
| 352 | +215x |
- invisible(x)+ make.unique(gsub("[^[:alnum:]]", "_", tolower(labels)), sep = "_")
|
||
| 594 | +353 |
} |
||
| 595 | +354 | |||
| 596 | +355 |
- #' @param modules (`teal_module` or `teal_modules`)+ #' Remove ANSI escape sequences from a string |
||
| 597 | +356 |
- #' @rdname teal_modules+ #' @noRd |
||
| 598 | +357 |
- #' @examples+ strip_style <- function(string) {
+ |
+ ||
| 358 | +2x | +
+ checkmate::assert_string(string) |
||
| 599 | +359 |
- #' # change the module's datanames+ + |
+ ||
| 360 | +2x | +
+ gsub(+ |
+ ||
| 361 | +2x | +
+ "(?:(?:\\x{001b}\\[)|\\x{009b})(?:(?:[0-9]{1,3})?(?:(?:;[0-9]{0,3})*)?[A-M|f-m])|\\x{001b}[A-M]",
|
||
| 600 | +362 |
- #' set_datanames(module(datanames = "all"), "a")+ "",+ |
+ ||
| 363 | +2x | +
+ string,+ |
+ ||
| 364 | +2x | +
+ perl = TRUE,+ |
+ ||
| 365 | +2x | +
+ useBytes = TRUE |
||
| 601 | +366 |
- #'+ ) |
||
| 602 | +367 |
- #' # change modules' datanames+ } |
||
| 603 | +368 |
- #' set_datanames(+ |
||
| 604 | +369 |
- #' modules(+ #' @keywords internal |
||
| 605 | +370 |
- #' module(datanames = "all"),+ #' @noRd+ |
+ ||
| 371 | +4x | +
+ pasten <- function(...) paste0(..., "\n") |
||
| 606 | +372 |
- #' module(datanames = "a")+ |
||
| 607 | +373 |
- #' ),+ #' Convert character list to human readable html with commas and "and" |
||
| 608 | +374 |
- #' "b"+ #' @noRd |
||
| 609 | +375 |
- #' )+ paste_datanames_character <- function(x, |
||
| 610 | +376 |
- #' @export+ tags = list(span = shiny::tags$span, code = shiny::tags$code), |
||
| 611 | +377 |
- set_datanames <- function(modules, datanames) {
+ tagList = shiny::tagList) { # nolint: object_name.
|
||
| 612 | +378 | ! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ checkmate::assert_character(x) |
|
| 613 | +379 | ! |
- if (inherits(modules, "teal_modules")) {
+ do.call( |
|
| 614 | +380 | ! |
- modules$children <- lapply(modules$children, set_datanames, datanames)- |
- |
| 615 | -- |
- } else {
+ tagList, |
||
| 616 | +381 | ! |
- if (identical(modules$datanames, "all")) {
+ lapply(seq_along(x), function(.ix) {
|
|
| 617 | +382 | ! |
- modules$datanames <- datanames- |
- |
| 618 | -- |
- } else {
+ tagList( |
||
| 619 | +383 | ! |
- warning(+ tags$code(x[.ix]), |
|
| 620 | +384 | ! |
- "Not possible to modify datanames of the module ", modules$label,+ if (.ix != length(x)) {
|
|
| 621 | +385 | ! |
- ". set_datanames() can only change datanames if it was set to \"all\".",+ tags$span(ifelse(.ix == length(x) - 1, " and ", ", ")) |
|
| 622 | -! | +|||
| 386 | +
- call. = FALSE+ } |
|||
| 623 | +387 |
) |
||
| 624 | +388 |
- }+ }) |
||
| 625 | +389 |
- }+ ) |
||
| 626 | -! | +|||
| 390 | +
- modules+ } |
|||
| 627 | +391 |
- }+ |
||
| 628 | +392 |
-
+ #' Build datanames error string for error message |
||
| 629 | +393 |
- # utilities ----+ #' |
||
| 630 | +394 |
- ## subset or modify modules ----+ #' tags and tagList are overwritten in arguments allowing to create strings for |
||
| 631 | +395 |
-
+ #' logging purposes |
||
| 632 | +396 |
- #' Append a `teal_module` to `children` of a `teal_modules` object+ #' @noRd |
||
| 633 | +397 |
- #' @keywords internal+ build_datanames_error_message <- function(label = NULL, |
||
| 634 | +398 |
- #' @param modules (`teal_modules`)+ datanames, |
||
| 635 | +399 |
- #' @param module (`teal_module`) object to be appended onto the children of `modules`+ extra_datanames, |
||
| 636 | +400 |
- #' @return A `teal_modules` object with `module` appended.+ tags = list(span = shiny::tags$span, code = shiny::tags$code), |
||
| 637 | +401 |
- append_module <- function(modules, module) {
+ tagList = shiny::tagList) { # nolint: object_name.
|
||
| 638 | -8x | +|||
| 402 | +! |
- checkmate::assert_class(modules, "teal_modules")+ tags$span( |
||
| 639 | -6x | +|||
| 403 | +! |
- checkmate::assert_class(module, "teal_module")+ tags$span(ifelse(length(extra_datanames) > 1, "Datasets", "Dataset")), |
||
| 640 | -4x | +|||
| 404 | +! |
- modules$children <- c(modules$children, list(module))+ paste_datanames_character(extra_datanames, tags, tagList), |
||
| 641 | -4x | +|||
| 405 | +! |
- labels <- vapply(modules$children, function(submodule) submodule$label, character(1))+ tags$span( |
||
| 642 | -4x | +|||
| 406 | +! |
- names(modules$children) <- get_unique_labels(labels)+ paste0( |
||
| 643 | -4x | +|||
| 407 | +! |
- modules+ ifelse(length(extra_datanames) > 1, "are missing", "is missing"), |
||
| 644 | -+ | |||
| 408 | +! |
- }+ ifelse(is.null(label), ".", sprintf(" for tab '%s'.", label))
|
||
| 645 | +409 |
-
+ ) |
||
| 646 | +410 |
- #' Extract/Remove module(s) of specific class+ ), |
||
| 647 | -+ | |||
| 411 | +! |
- #'+ if (length(datanames) >= 1) {
|
||
| 648 | -+ | |||
| 412 | +! |
- #' Given a `teal_module` or a `teal_modules`, return the elements of the structure according to `class`.+ tagList( |
||
| 649 | -+ | |||
| 413 | +! |
- #'+ tags$span(ifelse(length(datanames) > 1, "Datasets", "Dataset")), |
||
| 650 | -+ | |||
| 414 | +! |
- #' @param modules (`teal_modules`)+ tags$span("available in data:"),
|
||
| 651 | -+ | |||
| 415 | +! |
- #' @param class The class name of `teal_module` to be extracted or dropped.+ tagList( |
||
| 652 | -+ | |||
| 416 | +! |
- #' @keywords internal+ tags$span( |
||
| 653 | -+ | |||
| 417 | +! |
- #' @return+ paste_datanames_character(datanames, tags, tagList), |
||
| 654 | -+ | |||
| 418 | +! |
- #' - For `extract_module`, a `teal_module` of class `class` or `teal_modules` containing modules of class `class`.+ tags$span(".", .noWS = "outside"),
+ |
+ ||
| 419 | +! | +
+ .noWS = c("outside")
|
||
| 655 | +420 |
- #' - For `drop_module`, the opposite, which is all `teal_modules` of class other than `class`.+ ) |
||
| 656 | +421 |
- #' @rdname module_management+ ) |
||
| 657 | +422 |
- extract_module <- function(modules, class) {
+ ) |
||
| 658 | -24x | +|||
| 423 | +
- if (inherits(modules, class)) {
+ } else {
|
|||
| 659 | +424 | ! |
- modules+ tags$span("No datasets are available in data.")
|
|
| 660 | -24x | +|||
| 425 | +
- } else if (inherits(modules, "teal_module")) {
+ } |
|||
| 661 | -13x | +|||
| 426 | +
- NULL+ ) |
|||
| 662 | -11x | +|||
| 427 | +
- } else if (inherits(modules, "teal_modules")) {
+ } |
|||
| 663 | -11x | +|||
| 428 | +
- Filter(function(x) length(x) > 0L, lapply(modules$children, extract_module, class))+ |
|||
| 664 | +429 |
- }+ #' Smart `rbind` |
||
| 665 | +430 |
- }+ #' |
||
| 666 | +431 |
-
+ #' Combine `data.frame` objects which have different columns |
||
| 667 | +432 |
- #' @keywords internal+ #' |
||
| 668 | +433 |
- #' @return `teal_modules`+ #' @param ... (`data.frame`) |
||
| 669 | +434 |
- #' @rdname module_management+ #' @keywords internal |
||
| 670 | +435 |
- drop_module <- function(modules, class) {
+ .smart_rbind <- function(...) {
|
||
| 671 | -! | -
- if (inherits(modules, class)) {
+ | ||
| 436 | +82x | +
+ dots <- list(...) |
||
| 672 | -! | +|||
| 437 | +82x |
- NULL+ checkmate::assert_list(dots, "data.frame", .var.name = "...") |
||
| 673 | -! | +|||
| 438 | +82x |
- } else if (inherits(modules, "teal_module")) {
+ Reduce( |
||
| 674 | -! | +|||
| 439 | +82x |
- modules+ x = dots, |
||
| 675 | -! | +|||
| 440 | +82x |
- } else if (inherits(modules, "teal_modules")) {
+ function(x, y) {
|
||
| 676 | -! | +|||
| 441 | +69x |
- do.call(+ all_columns <- union(colnames(x), colnames(y)) |
||
| 677 | -! | +|||
| 442 | +69x |
- "modules",+ x[setdiff(all_columns, colnames(x))] <- NA |
||
| 678 | -! | +|||
| 443 | +69x |
- c(Filter(function(x) length(x) > 0L, lapply(modules$children, drop_module, class)), label = modules$label)+ y[setdiff(all_columns, colnames(y))] <- NA+ |
+ ||
| 444 | +69x | +
+ rbind(x, y) |
||
| 679 | +445 |
- )+ } |
||
| 680 | +446 |
- }+ ) |
||
| 681 | +447 |
} |
| 682 | +1 |
-
+ #' Manage multiple `FilteredData` objects |
||
| 683 | +2 |
- ## read modules ----+ #' |
||
| 684 | +3 |
-
+ #' @description |
||
| 685 | +4 |
- #' Does the object make use of the `arg`+ #' Oversee filter states across the entire application. |
||
| 686 | +5 |
#' |
||
| 687 | +6 |
- #' @param modules (`teal_module` or `teal_modules`) object+ #' @section Slices global: |
||
| 688 | +7 |
- #' @param arg (`character(1)`) names of the arguments to be checked against formals of `teal` modules.+ #' The key role in maintaining the module-specific filter states is played by the `.slicesGlobal` |
||
| 689 | +8 |
- #' @return `logical` whether the object makes use of `arg`.+ #' object. It is a reference class that holds the following fields: |
||
| 690 | +9 |
- #' @rdname is_arg_used+ #' - `all_slices` (`reactiveVal`) - reactive value containing all filters registered in an app. |
||
| 691 | +10 |
- #' @keywords internal+ #' - `module_slices_api` (`reactiveValues`) - reactive field containing references to each modules' |
||
| 692 | +11 |
- is_arg_used <- function(modules, arg) {
+ #' `FilteredData` object methods. At this moment it is used only in `srv_filter_manager` to display |
||
| 693 | -486x | +|||
| 12 | +
- checkmate::assert_string(arg)+ #' the filter states in a table combining informations from `all_slices` and from |
|||
| 694 | -483x | +|||
| 13 | +
- if (inherits(modules, "teal_modules")) {
+ #' `FilteredData$get_available_teal_slices()`. |
|||
| 695 | -18x | +|||
| 14 | +
- any(unlist(lapply(modules$children, is_arg_used, arg)))+ #' |
|||
| 696 | -465x | +|||
| 15 | +
- } else if (inherits(modules, "teal_module")) {
+ #' During a session only new filters are added to `all_slices` unless [`module_snapshot_manager`] is |
|||
| 697 | -30x | +|||
| 16 | +
- is_arg_used(modules$server, arg) || is_arg_used(modules$ui, arg)+ #' used to restore previous state. Filters from `all_slices` can be activated or deactivated in a |
|||
| 698 | -435x | +|||
| 17 | +
- } else if (is.function(modules)) {
+ #' module which is linked (both ways) by `attr(, "mapping")` so that: |
|||
| 699 | -433x | +|||
| 18 | +
- isTRUE(arg %in% names(formals(modules)))+ #' - If module's filter is added or removed in its `FilteredData` object, this information is passed |
|||
| 700 | +19 |
- } else {
+ #' to `SlicesGlobal` which updates `attr(, "mapping")` accordingly. |
||
| 701 | -2x | +|||
| 20 | +
- stop("is_arg_used function not implemented for this object")
+ #' - When mapping changes in a `SlicesGlobal`, filters are set or removed from module's |
|||
| 702 | +21 |
- }+ #' `FilteredData`. |
||
| 703 | +22 |
- }+ #' |
||
| 704 | +23 |
-
+ #' @section Filter manager: |
||
| 705 | +24 |
-
+ #' Filter-manager is split into two parts: |
||
| 706 | +25 |
- #' Get module depth+ #' 1. `ui/srv_filter_manager_panel` - Called once for the whole app. This module observes changes in |
||
| 707 | +26 |
- #'+ #' the filters in `slices_global` and displays them in a table utilizing information from `mapping`: |
||
| 708 | +27 |
- #' Depth starts at 0, so a single `teal.module` has depth 0.+ #' - (`TRUE`) - filter is active in the module |
||
| 709 | +28 |
- #' Nesting it increases overall depth by 1.+ #' - (`FALSE`) - filter is inactive in the module |
||
| 710 | +29 |
- #'+ #' - (`NA`) - filter is not available in the module |
||
| 711 | +30 |
- #' @inheritParams init+ #' 2. `ui/srv_module_filter_manager` - Called once for each `teal_module`. Handling filter states |
||
| 712 | +31 |
- #' @param depth optional integer determining current depth level+ #' for of single module and keeping module `FilteredData` consistent with `slices_global`, so that |
||
| 713 | +32 |
- #'+ #' local filters are always reflected in the `slices_global` and its mapping and vice versa. |
||
| 714 | +33 |
- #' @return Depth level for given module.+ #' |
||
| 715 | +34 |
- #' @keywords internal+ #' |
||
| 716 | +35 |
- modules_depth <- function(modules, depth = 0L) {
+ #' @param id (`character(1)`) |
||
| 717 | -12x | +|||
| 36 | +
- checkmate::assert_multi_class(modules, c("teal_module", "teal_modules"))
+ #' `shiny` module instance id. |
|||
| 718 | -12x | +|||
| 37 | +
- checkmate::assert_int(depth, lower = 0)+ #' |
|||
| 719 | -11x | +|||
| 38 | +
- if (inherits(modules, "teal_modules")) {
+ #' @param slices_global (`reactiveVal`) |
|||
| 720 | -4x | +|||
| 39 | +
- max(vapply(modules$children, modules_depth, integer(1), depth = depth + 1L))+ #' containing `teal_slices`. |
|||
| 721 | +40 |
- } else {
+ #' |
||
| 722 | -7x | +|||
| 41 | +
- depth+ #' @param module_fd (`FilteredData`) |
|||
| 723 | +42 |
- }+ #' Object containing the data to be filtered in a single `teal` module. |
||
| 724 | +43 |
- }+ #' |
||
| 725 | +44 |
-
+ #' @return |
||
| 726 | +45 |
- #' Retrieve labels from `teal_modules`+ #' Module returns a `slices_global` (`reactiveVal`) containing a `teal_slices` object with mapping. |
||
| 727 | +46 |
#' |
||
| 728 | +47 |
- #' @param modules (`teal_modules`)+ #' @encoding UTF-8 |
||
| 729 | +48 |
- #' @return A `list` containing the labels of the modules. If the modules are nested,+ #' |
||
| 730 | +49 |
- #' the function returns a nested `list` of labels.+ #' @name module_filter_manager |
||
| 731 | +50 |
- #' @keywords internal+ #' @rdname module_filter_manager |
||
| 732 | +51 |
- module_labels <- function(modules) {
+ #' |
||
| 733 | -189x | +|||
| 52 | +
- if (inherits(modules, "teal_modules")) {
+ NULL |
|||
| 734 | -82x | +|||
| 53 | +
- lapply(modules$children, module_labels)+ |
|||
| 735 | +54 |
- } else {
+ #' @rdname module_filter_manager |
||
| 736 | -107x | +|||
| 55 | +
- modules$label+ ui_filter_manager_panel <- function(id) {
|
|||
| 737 | -+ | |||
| 56 | +! |
- }+ ns <- NS(id) |
||
| 738 | -+ | |||
| 57 | +! |
- }+ tags$button( |
||
| 739 | -+ | |||
| 58 | +! |
-
+ id = ns("show_filter_manager"),
|
||
| 740 | -+ | |||
| 59 | +! |
- #' Retrieve `teal_bookmarkable` attribute from `teal_modules`+ class = "btn action-button wunder_bar_button",+ |
+ ||
| 60 | +! | +
+ title = "View filter mapping",+ |
+ ||
| 61 | +! | +
+ suppressMessages(icon("fas fa-grip"))
|
||
| 741 | +62 |
- #'+ ) |
||
| 742 | +63 |
- #' @param modules (`teal_modules` or `teal_module`) object+ } |
||
| 743 | +64 |
- #' @return named list of the same structure as `modules` with `TRUE` or `FALSE` values indicating+ |
||
| 744 | +65 |
- #' whether the module is bookmarkable.+ #' @rdname module_filter_manager |
||
| 745 | +66 |
#' @keywords internal |
||
| 746 | +67 |
- modules_bookmarkable <- function(modules) {
+ srv_filter_manager_panel <- function(id, slices_global) {
|
||
| 747 | -189x | +68 | +82x |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ checkmate::assert_string(id) |
| 748 | -189x | +69 | +82x |
- if (inherits(modules, "teal_modules")) {
+ checkmate::assert_class(slices_global, ".slicesGlobal") |
| 749 | +70 | 82x |
- setNames(+ moduleServer(id, function(input, output, session) {
|
|
| 750 | +71 | 82x |
- lapply(modules$children, modules_bookmarkable),+ setBookmarkExclude(c("show_filter_manager"))
|
|
| 751 | +72 | 82x |
- vapply(modules$children, `[[`, "label", FUN.VALUE = character(1))+ observeEvent(input$show_filter_manager, {
|
|
| 752 | -+ | |||
| 73 | +! |
- )+ logger::log_debug("srv_filter_manager_panel@1 show_filter_manager button has been clicked.")
|
||
| 753 | -+ | |||
| 74 | +! |
- } else {
+ showModal( |
||
| 754 | -107x | +|||
| 75 | +! |
- attr(modules, "teal_bookmarkable", exact = TRUE)+ modalDialog( |
||
| 755 | -+ | |||
| 76 | +! |
- }+ ui_filter_manager(session$ns("filter_manager")),
|
||
| 756 | -+ | |||
| 77 | +! |
- }+ class = "filter_manager_modal", |
| 1 | -+ | |||
| 78 | +! |
- #' Validate that dataset has a minimum number of observations+ size = "l", |
||
| 2 | -+ | |||
| 79 | +! |
- #'+ footer = NULL, |
||
| 3 | -+ | |||
| 80 | +! |
- #' `r lifecycle::badge("stable")`
+ easyClose = TRUE |
||
| 4 | +81 |
- #'+ ) |
||
| 5 | +82 |
- #' This function is a wrapper for `shiny::validate`.+ ) |
||
| 6 | +83 |
- #'+ }) |
||
| 7 | -+ | |||
| 84 | +82x |
- #' @param x (`data.frame`)+ srv_filter_manager("filter_manager", slices_global = slices_global)
|
||
| 8 | +85 |
- #' @param min_nrow (`numeric(1)`) Minimum allowed number of rows in `x`.+ }) |
||
| 9 | +86 |
- #' @param complete (`logical(1)`) Flag specifying whether to check only complete cases. Defaults to `FALSE`.+ } |
||
| 10 | +87 |
- #' @param allow_inf (`logical(1)`) Flag specifying whether to allow infinite values. Defaults to `TRUE`.+ |
||
| 11 | +88 |
- #' @param msg (`character(1)`) Additional message to display alongside the default message.+ #' @rdname module_filter_manager |
||
| 12 | +89 |
- #'+ ui_filter_manager <- function(id) {
|
||
| 13 | -+ | |||
| 90 | +! |
- #' @export+ ns <- NS(id) |
||
| 14 | -+ | |||
| 91 | +! |
- #'+ actionButton(ns("filter_manager"), NULL, icon = icon("fas fa-filter"))
|
||
| 15 | -+ | |||
| 92 | +! |
- #' @examples+ tags$div( |
||
| 16 | -+ | |||
| 93 | +! |
- #' library(teal)+ class = "filter_manager_content", |
||
| 17 | -+ | |||
| 94 | +! |
- #' ui <- fluidPage(+ tableOutput(ns("slices_table"))
|
||
| 18 | +95 |
- #' sliderInput("len", "Max Length of Sepal",
+ ) |
||
| 19 | +96 |
- #' min = 4.3, max = 7.9, value = 5+ } |
||
| 20 | +97 |
- #' ),+ |
||
| 21 | +98 |
- #' plotOutput("plot")
+ #' @rdname module_filter_manager |
||
| 22 | +99 |
- #' )+ srv_filter_manager <- function(id, slices_global) {
|
||
| 23 | -+ | |||
| 100 | +82x |
- #'+ checkmate::assert_string(id) |
||
| 24 | -+ | |||
| 101 | +82x |
- #' server <- function(input, output) {
+ checkmate::assert_class(slices_global, ".slicesGlobal") |
||
| 25 | +102 |
- #' output$plot <- renderPlot({
+
|
||
| 26 | -+ | |||
| 103 | +82x |
- #' iris_df <- iris[iris$Sepal.Length <= input$len, ]+ moduleServer(id, function(input, output, session) {
|
||
| 27 | -+ | |||
| 104 | +82x |
- #' validate_has_data(+ logger::log_debug("filter_manager_srv initializing.")
|
||
| 28 | +105 |
- #' iris_df,+ |
||
| 29 | +106 |
- #' min_nrow = 10,+ # Bookmark slices global with mapping. |
||
| 30 | -+ | |||
| 107 | +82x |
- #' complete = FALSE,+ session$onBookmark(function(state) {
|
||
| 31 | -+ | |||
| 108 | +! |
- #' msg = "Please adjust Max Length of Sepal"+ logger::log_debug("filter_manager_srv@onBookmark: storing filter state")
|
||
| 32 | -+ | |||
| 109 | +! |
- #' )+ state$values$filter_state_on_bookmark <- as.list( |
||
| 33 | -+ | |||
| 110 | +! |
- #'+ slices_global$all_slices(), |
||
| 34 | -+ | |||
| 111 | +! |
- #' hist(iris_df$Sepal.Length, breaks = 5)+ recursive = TRUE |
||
| 35 | +112 |
- #' })+ ) |
||
| 36 | +113 |
- #' }+ }) |
||
| 37 | +114 |
- #' if (interactive()) {
+
|
||
| 38 | -+ | |||
| 115 | +82x |
- #' shinyApp(ui, server)+ bookmarked_slices <- restoreValue(session$ns("filter_state_on_bookmark"), NULL)
|
||
| 39 | -+ | |||
| 116 | +82x |
- #' }+ if (!is.null(bookmarked_slices)) {
|
||
| 40 | -+ | |||
| 117 | +! |
- #'+ logger::log_debug("filter_manager_srv: restoring filter state from bookmark.")
|
||
| 41 | -+ | |||
| 118 | +! |
- validate_has_data <- function(x,+ slices_global$slices_set(bookmarked_slices) |
||
| 42 | +119 |
- min_nrow = NULL,+ } |
||
| 43 | +120 |
- complete = FALSE,+ + |
+ ||
| 121 | +82x | +
+ mapping_table <- reactive({
|
||
| 44 | +122 |
- allow_inf = TRUE,+ # We want this to be reactive on slices_global$all_slices() only as get_available_teal_slices() |
||
| 45 | +123 |
- msg = NULL) {
+ # is dependent on slices_global$all_slices(). |
||
| 46 | -17x | +124 | +91x |
- checkmate::assert_string(msg, null.ok = TRUE)+ module_labels <- setdiff( |
| 47 | -15x | +125 | +91x |
- checkmate::assert_data_frame(x)+ names(attr(slices_global$all_slices(), "mapping")), |
| 48 | -15x | +126 | +91x |
- if (!is.null(min_nrow)) {
+ "Report previewer"+ |
+
| 127 | ++ |
+ ) |
||
| 49 | -15x | +128 | +91x |
- if (complete) {
+ isolate({
|
| 50 | -5x | +129 | +91x |
- complete_index <- stats::complete.cases(x)+ mm <- as.data.frame( |
| 51 | -5x | +130 | +91x |
- validate(need(+ sapply( |
| 52 | -5x | +131 | +91x |
- sum(complete_index) > 0 && nrow(x[complete_index, , drop = FALSE]) >= min_nrow,+ module_labels, |
| 53 | -5x | +132 | +91x |
- paste(c(paste("Number of complete cases is less than:", min_nrow), msg), collapse = "\n")
+ simplify = FALSE, |
| 54 | -+ | |||
| 133 | +91x |
- ))+ function(module_label) {
|
||
| 55 | -+ | |||
| 134 | +104x |
- } else {
+ available_slices <- slices_global$module_slices_api[[module_label]]$get_available_teal_slices() |
||
| 56 | -10x | +135 | +96x |
- validate(need(+ global_ids <- sapply(slices_global$all_slices(), `[[`, "id", simplify = FALSE) |
| 57 | -10x | +136 | +96x |
- nrow(x) >= min_nrow,+ module_ids <- sapply(slices_global$slices_get(module_label), `[[`, "id", simplify = FALSE) |
| 58 | -10x | +137 | +96x |
- paste(+ allowed_ids <- vapply(available_slices, `[[`, character(1L), "id") |
| 59 | -10x | +138 | +96x |
- c(paste("Minimum number of records not met: >=", min_nrow, "records required."), msg),
+ active_ids <- global_ids %in% module_ids |
| 60 | -10x | +139 | +96x |
- collapse = "\n"+ setNames(nm = global_ids, ifelse(global_ids %in% allowed_ids, active_ids, NA)) |
| 61 | +140 |
- )+ } |
||
| 62 | +141 |
- ))+ ), |
||
| 63 | -+ | |||
| 142 | +91x |
- }+ check.names = FALSE |
||
| 64 | +143 |
-
+ ) |
||
| 65 | -10x | +144 | +83x |
- if (!allow_inf) {
+ colnames(mm)[colnames(mm) == "global_filters"] <- "Global filters" |
| 66 | -6x | +|||
| 145 | +
- validate(need(+ |
|||
| 67 | -6x | +146 | +83x |
- all(vapply(x, function(col) !is.numeric(col) || !any(is.infinite(col)), logical(1))),+ mm |
| 68 | -6x | +|||
| 147 | +
- "Dataframe contains Inf values which is not allowed."+ }) |
|||
| 69 | +148 |
- ))+ }) |
||
| 70 | +149 |
- }+ |
||
| 71 | -+ | |||
| 150 | +82x |
- }+ output$slices_table <- renderTable( |
||
| 72 | -+ | |||
| 151 | +82x |
- }+ expr = {
|
||
| 73 | -+ | |||
| 152 | +91x |
-
+ logger::log_debug("filter_manager_srv@1 rendering slices_table.")
|
||
| 74 | -+ | |||
| 153 | +91x |
- #' Validate that dataset has unique rows for key variables+ mm <- mapping_table() |
||
| 75 | +154 |
- #'+ |
||
| 76 | +155 |
- #' `r lifecycle::badge("stable")`
+ # Display logical values as UTF characters. |
||
| 77 | -+ | |||
| 156 | +83x |
- #'+ mm[] <- lapply(mm, ifelse, yes = intToUtf8(9989), no = intToUtf8(10060)) |
||
| 78 | -+ | |||
| 157 | +83x |
- #' This function is a wrapper for `shiny::validate`.+ mm[] <- lapply(mm, function(x) ifelse(is.na(x), intToUtf8(128306), x)) |
||
| 79 | +158 |
- #'+ |
||
| 80 | +159 |
- #' @param x (`data.frame`)+ # Display placeholder if no filters defined. |
||
| 81 | -+ | |||
| 160 | +83x |
- #' @param key (`character`) Vector of ID variables from `x` that identify unique records.+ if (nrow(mm) == 0L) {
|
||
| 82 | -+ | |||
| 161 | +59x |
- #'+ mm <- data.frame(`Filter manager` = "No filters specified.", check.names = FALSE) |
||
| 83 | -+ | |||
| 162 | +59x |
- #' @export+ rownames(mm) <- "" |
||
| 84 | +163 |
- #'+ } |
||
| 85 | -+ | |||
| 164 | +83x |
- #' @examples+ mm |
||
| 86 | +165 |
- #' iris$id <- rep(1:50, times = 3)+ }, |
||
| 87 | -+ | |||
| 166 | +82x |
- #' ui <- fluidPage(+ rownames = TRUE |
||
| 88 | +167 |
- #' selectInput(+ ) |
||
| 89 | +168 |
- #' inputId = "species",+ |
||
| 90 | -+ | |||
| 169 | +82x |
- #' label = "Select species",+ mapping_table # for testing purpose |
||
| 91 | +170 |
- #' choices = c("setosa", "versicolor", "virginica"),
+ }) |
||
| 92 | +171 |
- #' selected = "setosa",+ } |
||
| 93 | +172 |
- #' multiple = TRUE+ |
||
| 94 | +173 |
- #' ),+ #' @rdname module_filter_manager |
||
| 95 | +174 |
- #' plotOutput("plot")
+ srv_module_filter_manager <- function(id, module_fd, slices_global) {
|
||
| 96 | -+ | |||
| 175 | +107x |
- #' )+ checkmate::assert_string(id) |
||
| 97 | -+ | |||
| 176 | +107x |
- #' server <- function(input, output) {
+ assert_reactive(module_fd) |
||
| 98 | -+ | |||
| 177 | +107x |
- #' output$plot <- renderPlot({
+ checkmate::assert_class(slices_global, ".slicesGlobal") |
||
| 99 | +178 |
- #' iris_f <- iris[iris$Species %in% input$species, ]+ |
||
| 100 | -+ | |||
| 179 | +107x |
- #' validate_one_row_per_id(iris_f, key = c("id"))
+ moduleServer(id, function(input, output, session) {
|
||
| 101 | -+ | |||
| 180 | +107x |
- #'+ logger::log_debug("srv_module_filter_manager initializing for module: { id }.")
|
||
| 102 | +181 |
- #' hist(iris_f$Sepal.Length, breaks = 5)+ # Track filter global and local states. |
||
| 103 | -+ | |||
| 182 | +107x |
- #' })+ slices_global_module <- reactive({
|
||
| 104 | -+ | |||
| 183 | +193x |
- #' }+ slices_global$slices_get(module_label = id) |
||
| 105 | +184 |
- #' if (interactive()) {
+ }) |
||
| 106 | -+ | |||
| 185 | +107x |
- #' shinyApp(ui, server)+ slices_module <- reactive(req(module_fd())$get_filter_state()) |
||
| 107 | +186 |
- #' }+ + |
+ ||
| 187 | +107x | +
+ module_fd_previous <- reactiveVal(NULL) |
||
| 108 | +188 |
- #'+ |
||
| 109 | +189 |
- validate_one_row_per_id <- function(x, key = c("USUBJID", "STUDYID")) {
+ # Set (reactively) available filters for the module. |
||
| 110 | -! | +|||
| 190 | +107x |
- validate(need(!any(duplicated(x[key])), paste("Found more than one row per id.")))
+ obs1 <- observeEvent(module_fd(), priority = 1, {
|
||
| 111 | -+ | |||
| 191 | +88x |
- }+ logger::log_debug("srv_module_filter_manager@1 setting initial slices for module: { id }.")
|
||
| 112 | +192 |
-
+ # Filters relevant for the module in module-specific app. |
||
| 113 | -+ | |||
| 193 | +88x |
- #' Validates that vector includes all expected values+ slices <- slices_global_module() |
||
| 114 | +194 |
- #'+ |
||
| 115 | +195 |
- #' `r lifecycle::badge("stable")`
+ # Clean up previous filter states and refresh cache of previous module_fd with current |
||
| 116 | -+ | |||
| 196 | +3x |
- #'+ if (!is.null(module_fd_previous())) module_fd_previous()$finalize() |
||
| 117 | -+ | |||
| 197 | +88x |
- #' This function is a wrapper for `shiny::validate`.+ module_fd_previous(module_fd()) |
||
| 118 | +198 |
- #'+ |
||
| 119 | +199 |
- #' @param x Vector of values to test.+ # Setting filter states from slices_global: |
||
| 120 | +200 |
- #' @param choices Vector to test against.+ # 1. when app initializes slices_global set to initial filters (specified by app developer) |
||
| 121 | +201 |
- #' @param msg (`character(1)`) Error message to display if some elements of `x` are not elements of `choices`.+ # 2. when data reinitializes slices_global reflects latest filter states |
||
| 122 | +202 |
- #'+ |
||
| 123 | -+ | |||
| 203 | +88x |
- #' @export+ module_fd()$set_filter_state(slices) |
||
| 124 | +204 |
- #'+ |
||
| 125 | +205 |
- #' @examples+ # irrelevant filters are discarded in FilteredData$set_available_teal_slices |
||
| 126 | +206 |
- #' ui <- fluidPage(+ # it means we don't need to subset slices_global$all_slices() from filters refering to irrelevant datasets |
||
| 127 | -+ | |||
| 207 | +88x |
- #' selectInput(+ module_fd()$set_available_teal_slices(slices_global$all_slices) |
||
| 128 | +208 |
- #' "species",+ |
||
| 129 | +209 |
- #' "Select species",+ # this needed in filter_manager_srv |
||
| 130 | -+ | |||
| 210 | +88x |
- #' choices = c("setosa", "versicolor", "virginica", "unknown species"),
+ slices_global$module_slices_api_set( |
||
| 131 | -+ | |||
| 211 | +88x |
- #' selected = "setosa",+ id, |
||
| 132 | -+ | |||
| 212 | +88x |
- #' multiple = FALSE+ list( |
||
| 133 | -+ | |||
| 213 | +88x |
- #' ),+ get_available_teal_slices = module_fd()$get_available_teal_slices(), |
||
| 134 | -+ | |||
| 214 | +88x |
- #' verbatimTextOutput("summary")
+ set_filter_state = module_fd()$set_filter_state, # for testing purpose |
||
| 135 | -+ | |||
| 215 | +88x |
- #' )+ get_filter_state = module_fd()$get_filter_state # for testing purpose |
||
| 136 | +216 |
- #'+ ) |
||
| 137 | +217 |
- #' server <- function(input, output) {
+ ) |
||
| 138 | +218 |
- #' output$summary <- renderPrint({
+ }) |
||
| 139 | +219 |
- #' validate_in(input$species, iris$Species, "Species does not exist.")+ |
||
| 140 | +220 |
- #' nrow(iris[iris$Species == input$species, ])+ # Update global state and mapping matrix when module filters change. |
||
| 141 | -+ | |||
| 221 | +107x |
- #' })+ obs2 <- observeEvent(slices_module(), priority = 0, {
|
||
| 142 | -+ | |||
| 222 | +110x |
- #' }+ this_slices <- slices_module() |
||
| 143 | -+ | |||
| 223 | +110x |
- #' if (interactive()) {
+ slices_global$slices_append(this_slices) # append new slices to the all_slices list |
||
| 144 | -+ | |||
| 224 | +110x |
- #' shinyApp(ui, server)+ mapping_elem <- setNames(nm = id, list(vapply(this_slices, `[[`, character(1L), "id"))) |
||
| 145 | -+ | |||
| 225 | +110x |
- #' }+ slices_global$slices_active(mapping_elem) |
||
| 146 | +226 |
- #'+ }) |
||
| 147 | +227 |
- validate_in <- function(x, choices, msg) {
+
|
||
| 148 | -! | +|||
| 228 | +107x |
- validate(need(length(x) > 0 && length(choices) > 0 && all(x %in% choices), msg))+ obs3 <- observeEvent(slices_global_module(), {
|
||
| 149 | -+ | |||
| 229 | +130x |
- }+ global_vs_module <- setdiff_teal_slices(slices_global_module(), slices_module()) |
||
| 150 | -+ | |||
| 230 | +130x |
-
+ module_vs_global <- setdiff_teal_slices(slices_module(), slices_global_module()) |
||
| 151 | -+ | |||
| 231 | +121x |
- #' Validates that vector has length greater than 0+ if (length(global_vs_module) || length(module_vs_global)) {
|
||
| 152 | +232 |
- #'+ # Comment: (Nota Bene) Normally new filters for a module are added through module-filter-panel, and slices |
||
| 153 | +233 |
- #' `r lifecycle::badge("stable")`
+ # global are updated automatically so slices_module -> slices_global_module are equal. |
||
| 154 | +234 |
- #'+ # this if is valid only when a change is made on the global level so the change needs to be propagated down |
||
| 155 | +235 |
- #' This function is a wrapper for `shiny::validate`.+ # to the module (for example through snapshot manager). If it happens both slices are different |
||
| 156 | -+ | |||
| 236 | +13x |
- #'+ logger::log_debug("srv_module_filter_manager@3 (N.B.) global state has changed for a module:{ id }.")
|
||
| 157 | -+ | |||
| 237 | +13x |
- #' @param x vector+ module_fd()$clear_filter_states() |
||
| 158 | -+ | |||
| 238 | +13x |
- #' @param msg message to display+ module_fd()$set_filter_state(slices_global_module()) |
||
| 159 | +239 |
- #'+ } |
||
| 160 | +240 |
- #' @export+ }) |
||
| 161 | +241 |
- #'+ |
||
| 162 | -+ | |||
| 242 | +107x |
- #' @examples+ slices_module # returned for testing purpose |
||
| 163 | +243 |
- #' data <- data.frame(+ }) |
||
| 164 | +244 |
- #' id = c(1:10, 11:20, 1:10),+ } |
||
| 165 | +245 |
- #' strata = rep(c("A", "B"), each = 15)
+
|
||
| 166 | +246 |
- #' )+ #' @importFrom shiny reactiveVal reactiveValues |
||
| 167 | +247 |
- #' ui <- fluidPage(+ methods::setOldClass("reactiveVal")
|
||
| 168 | +248 |
- #' selectInput("ref1", "Select strata1 to compare",
+ methods::setOldClass("reactivevalues")
|
||
| 169 | +249 |
- #' choices = c("A", "B", "C"), selected = "A"
+
|
||
| 170 | +250 |
- #' ),+ #' @importFrom methods new |
||
| 171 | +251 |
- #' selectInput("ref2", "Select strata2 to compare",
+ #' @rdname module_filter_manager |
||
| 172 | +252 |
- #' choices = c("A", "B", "C"), selected = "B"
+ .slicesGlobal <- methods::setRefClass(".slicesGlobal", # nolint: object_name.
|
||
| 173 | +253 |
- #' ),+ fields = list( |
||
| 174 | +254 |
- #' verbatimTextOutput("arm_summary")
+ all_slices = "reactiveVal", |
||
| 175 | +255 |
- #' )+ module_slices_api = "reactivevalues" |
||
| 176 | +256 |
- #'+ ), |
||
| 177 | +257 |
- #' server <- function(input, output) {
+ methods = list( |
||
| 178 | +258 |
- #' output$arm_summary <- renderText({
+ initialize = function(slices = teal_slices(), module_labels) {
|
||
| 179 | -+ | |||
| 259 | +82x |
- #' sample_1 <- data$id[data$strata == input$ref1]+ shiny::isolate({
|
||
| 180 | -+ | |||
| 260 | +82x |
- #' sample_2 <- data$id[data$strata == input$ref2]+ checkmate::assert_class(slices, "teal_slices") |
||
| 181 | +261 |
- #'+ # needed on init to not mix "global_filters" with module-specific-slots |
||
| 182 | -+ | |||
| 262 | +82x |
- #' validate_has_elements(sample_1, "No subjects in strata1.")+ if (isTRUE(attr(slices, "module_specific"))) {
|
||
| 183 | -+ | |||
| 263 | +11x |
- #' validate_has_elements(sample_2, "No subjects in strata2.")+ old_mapping <- attr(slices, "mapping") |
||
| 184 | -+ | |||
| 264 | +11x |
- #'+ new_mapping <- sapply(module_labels, simplify = FALSE, function(module_label) {
|
||
| 185 | -+ | |||
| 265 | +20x |
- #' paste0(+ unique(unlist(old_mapping[c(module_label, "global_filters")])) |
||
| 186 | +266 |
- #' "Number of samples in: strata1=", length(sample_1),+ }) |
||
| 187 | -+ | |||
| 267 | +11x |
- #' " comparions strata2=", length(sample_2)+ attr(slices, "mapping") <- new_mapping |
||
| 188 | +268 |
- #' )+ } |
||
| 189 | -+ | |||
| 269 | +82x |
- #' })+ .self$all_slices <<- shiny::reactiveVal(slices) |
||
| 190 | -+ | |||
| 270 | +82x |
- #' }+ .self$module_slices_api <<- shiny::reactiveValues() |
||
| 191 | -+ | |||
| 271 | +82x |
- #' if (interactive()) {
+ .self$slices_append(slices) |
||
| 192 | -+ | |||
| 272 | +82x |
- #' shinyApp(ui, server)+ .self$slices_active(attr(slices, "mapping")) |
||
| 193 | -+ | |||
| 273 | +82x |
- #' }+ invisible(.self) |
||
| 194 | +274 |
- validate_has_elements <- function(x, msg) {
+ }) |
||
| 195 | -! | +|||
| 275 | +
- validate(need(length(x) > 0, msg))+ }, |
|||
| 196 | +276 |
- }+ is_module_specific = function() {
|
||
| 197 | -+ | |||
| 277 | +283x |
-
+ isTRUE(attr(.self$all_slices(), "module_specific")) |
||
| 198 | +278 |
- #' Validates no intersection between two vectors+ }, |
||
| 199 | +279 |
- #'+ module_slices_api_set = function(module_label, functions_list) {
|
||
| 200 | -+ | |||
| 280 | +88x |
- #' `r lifecycle::badge("stable")`
+ shiny::isolate({
|
||
| 201 | -+ | |||
| 281 | +88x |
- #'+ if (!.self$is_module_specific()) {
|
||
| 202 | -+ | |||
| 282 | +72x |
- #' This function is a wrapper for `shiny::validate`.+ module_label <- "global_filters" |
||
| 203 | +283 |
- #'+ } |
||
| 204 | -+ | |||
| 284 | +88x |
- #' @param x vector+ if (!identical(.self$module_slices_api[[module_label]], functions_list)) {
|
||
| 205 | -+ | |||
| 285 | +88x |
- #' @param y vector+ .self$module_slices_api[[module_label]] <- functions_list |
||
| 206 | +286 |
- #' @param msg (`character(1)`) message to display if `x` and `y` intersect+ } |
||
| 207 | -+ | |||
| 287 | +88x |
- #'+ invisible(.self) |
||
| 208 | +288 |
- #' @export+ }) |
||
| 209 | +289 |
- #'+ }, |
||
| 210 | +290 |
- #' @examples+ slices_deactivate_all = function(module_label) {
|
||
| 211 | -+ | |||
| 291 | +! |
- #' data <- data.frame(+ shiny::isolate({
|
||
| 212 | -+ | |||
| 292 | +! |
- #' id = c(1:10, 11:20, 1:10),+ new_slices <- .self$all_slices() |
||
| 213 | -+ | |||
| 293 | +! |
- #' strata = rep(c("A", "B", "C"), each = 10)
+ old_mapping <- attr(new_slices, "mapping") |
||
| 214 | +294 |
- #' )+ |
||
| 215 | -+ | |||
| 295 | +! |
- #'+ new_mapping <- if (.self$is_module_specific()) {
|
||
| 216 | -+ | |||
| 296 | +! |
- #' ui <- fluidPage(+ new_module_mapping <- setNames(nm = module_label, list(character(0))) |
||
| 217 | -+ | |||
| 297 | +! |
- #' selectInput("ref1", "Select strata1 to compare",
+ modifyList(old_mapping, new_module_mapping) |
||
| 218 | -+ | |||
| 298 | +! |
- #' choices = c("A", "B", "C"),
+ } else if (missing(module_label)) {
|
||
| 219 | -+ | |||
| 299 | +! |
- #' selected = "A"+ lapply( |
||
| 220 | -+ | |||
| 300 | +! |
- #' ),+ attr(.self$all_slices(), "mapping"), |
||
| 221 | -+ | |||
| 301 | +! |
- #' selectInput("ref2", "Select strata2 to compare",
+ function(x) character(0) |
||
| 222 | +302 |
- #' choices = c("A", "B", "C"),
+ ) |
||
| 223 | +303 |
- #' selected = "B"+ } else {
|
||
| 224 | -+ | |||
| 304 | +! |
- #' ),+ old_mapping[[module_label]] <- character(0) |
||
| 225 | -+ | |||
| 305 | +! |
- #' verbatimTextOutput("summary")
+ old_mapping |
||
| 226 | +306 |
- #' )+ } |
||
| 227 | +307 |
- #'+ |
||
| 228 | -+ | |||
| 308 | +! |
- #' server <- function(input, output) {
+ if (!identical(new_mapping, old_mapping)) {
|
||
| 229 | -+ | |||
| 309 | +! |
- #' output$summary <- renderText({
+ logger::log_debug(".slicesGlobal@slices_deactivate_all: deactivating all slices.")
|
||
| 230 | -+ | |||
| 310 | +! |
- #' sample_1 <- data$id[data$strata == input$ref1]+ attr(new_slices, "mapping") <- new_mapping |
||
| 231 | -+ | |||
| 311 | +! |
- #' sample_2 <- data$id[data$strata == input$ref2]+ .self$all_slices(new_slices) |
||
| 232 | +312 |
- #'+ } |
||
| 233 | -+ | |||
| 313 | +! |
- #' validate_no_intersection(+ invisible(.self) |
||
| 234 | +314 |
- #' sample_1, sample_2,+ }) |
||
| 235 | +315 |
- #' "subjects within strata1 and strata2 cannot overlap"+ }, |
||
| 236 | +316 |
- #' )+ slices_active = function(mapping_elem) {
|
||
| 237 | -+ | |||
| 317 | +195x |
- #' paste0(+ shiny::isolate({
|
||
| 238 | -+ | |||
| 318 | +195x |
- #' "Number of subject in: reference treatment=", length(sample_1),+ if (.self$is_module_specific()) {
|
||
| 239 | -+ | |||
| 319 | +36x |
- #' " comparions treatment=", length(sample_2)+ new_mapping <- modifyList(attr(.self$all_slices(), "mapping"), mapping_elem) |
||
| 240 | +320 |
- #' )+ } else {
|
||
| 241 | -+ | |||
| 321 | +159x |
- #' })+ new_mapping <- setNames(nm = "global_filters", list(unique(unlist(mapping_elem)))) |
||
| 242 | +322 |
- #' }+ } |
||
| 243 | +323 |
- #' if (interactive()) {
+
|
||
| 244 | -+ | |||
| 324 | +195x |
- #' shinyApp(ui, server)+ if (!identical(new_mapping, attr(.self$all_slices(), "mapping"))) {
|
||
| 245 | -+ | |||
| 325 | +138x |
- #' }+ mapping_modules <- toString(names(new_mapping)) |
||
| 246 | -+ | |||
| 326 | +138x |
- #'+ logger::log_debug(".slicesGlobal@slices_active: changing mapping for module(s): { mapping_modules }.")
|
||
| 247 | -+ | |||
| 327 | +138x |
- validate_no_intersection <- function(x, y, msg) {
+ new_slices <- .self$all_slices() |
||
| 248 | -! | +|||
| 328 | +138x |
- validate(need(length(intersect(x, y)) == 0, msg))+ attr(new_slices, "mapping") <- new_mapping |
||
| 249 | -+ | |||
| 329 | +138x |
- }+ .self$all_slices(new_slices) |
||
| 250 | +330 |
-
+ } |
||
| 251 | +331 | |||
| 252 | -+ | |||
| 332 | +195x |
- #' Validates that dataset contains specific variable+ invisible(.self) |
||
| 253 | +333 |
- #'+ }) |
||
| 254 | +334 |
- #' `r lifecycle::badge("stable")`
+ }, |
||
| 255 | +335 |
- #'+ # - only new filters are appended to the $all_slices |
||
| 256 | +336 |
- #' This function is a wrapper for `shiny::validate`.+ # - mapping is not updated here |
||
| 257 | +337 |
- #'+ slices_append = function(slices, activate = FALSE) {
|
||
| 258 | -+ | |||
| 338 | +195x |
- #' @param data (`data.frame`)+ shiny::isolate({
|
||
| 259 | -+ | |||
| 339 | +195x |
- #' @param varname (`character(1)`) name of variable to check for in `data`+ if (!is.teal_slices(slices)) {
|
||
| 260 | -+ | |||
| 340 | +! |
- #' @param msg (`character(1)`) message to display if `data` does not include `varname`+ slices <- as.teal_slices(slices) |
||
| 261 | +341 |
- #'+ } |
||
| 262 | +342 |
- #' @export+ |
||
| 263 | +343 |
- #'+ # to make sure that we don't unnecessary trigger $all_slices <reactiveVal> |
||
| 264 | -+ | |||
| 344 | +195x |
- #' @examples+ new_slices <- setdiff_teal_slices(slices, .self$all_slices()) |
||
| 265 | -+ | |||
| 345 | +195x |
- #' data <- data.frame(+ old_mapping <- attr(.self$all_slices(), "mapping") |
||
| 266 | -+ | |||
| 346 | +195x |
- #' one = rep("a", length.out = 20),
+ if (length(new_slices)) {
|
||
| 267 | -+ | |||
| 347 | +6x |
- #' two = rep(c("a", "b"), length.out = 20)
+ new_ids <- vapply(new_slices, `[[`, character(1L), "id") |
||
| 268 | -+ | |||
| 348 | +6x |
- #' )+ logger::log_debug(".slicesGlobal@slices_append: appending new slice(s): { new_ids }.")
|
||
| 269 | -+ | |||
| 349 | +6x |
- #' ui <- fluidPage(+ slices_ids <- vapply(.self$all_slices(), `[[`, character(1L), "id") |
||
| 270 | -+ | |||
| 350 | +6x |
- #' selectInput(+ lapply(new_slices, function(slice) {
|
||
| 271 | +351 |
- #' "var",+ # In case the new state has the same id as an existing one, add a suffix |
||
| 272 | -+ | |||
| 352 | +6x |
- #' "Select variable",+ if (slice$id %in% slices_ids) {
|
||
| 273 | -+ | |||
| 353 | +1x |
- #' choices = c("one", "two", "three", "four"),
+ slice$id <- utils::tail(make.unique(c(slices_ids, slice$id), sep = "_"), 1) |
||
| 274 | +354 |
- #' selected = "one"+ } |
||
| 275 | +355 |
- #' ),+ }) |
||
| 276 | +356 |
- #' verbatimTextOutput("summary")
+
|
||
| 277 | -+ | |||
| 357 | +6x |
- #' )+ new_slices_all <- c(.self$all_slices(), new_slices) |
||
| 278 | -+ | |||
| 358 | +6x |
- #'+ attr(new_slices_all, "mapping") <- old_mapping |
||
| 279 | -+ | |||
| 359 | +6x |
- #' server <- function(input, output) {
+ .self$all_slices(new_slices_all) |
||
| 280 | +360 |
- #' output$summary <- renderText({
+ } |
||
| 281 | +361 |
- #' validate_has_variable(data, input$var)+ |
||
| 282 | -+ | |||
| 362 | +195x |
- #' paste0("Selected treatment variables: ", paste(input$var, collapse = ", "))
+ invisible(.self) |
||
| 283 | +363 |
- #' })+ }) |
||
| 284 | +364 |
- #' }+ }, |
||
| 285 | +365 |
- #' if (interactive()) {
+ slices_get = function(module_label) {
|
||
| 286 | -+ | |||
| 366 | +289x |
- #' shinyApp(ui, server)+ if (missing(module_label)) {
|
||
| 287 | -+ | |||
| 367 | +! |
- #' }+ .self$all_slices() |
||
| 288 | +368 |
- validate_has_variable <- function(data, varname, msg) {
+ } else {
|
||
| 289 | -! | +|||
| 369 | +289x |
- if (length(varname) != 0) {
+ module_ids <- unlist(attr(.self$all_slices(), "mapping")[c(module_label, "global_filters")]) |
||
| 290 | -! | +|||
| 370 | +289x |
- has_vars <- varname %in% names(data)+ Filter(+ |
+ ||
| 371 | +289x | +
+ function(slice) slice$id %in% module_ids,+ |
+ ||
| 372 | +289x | +
+ .self$all_slices() |
||
| 291 | +373 |
-
+ ) |
||
| 292 | -! | +|||
| 374 | +
- if (!all(has_vars)) {
+ } |
|||
| 293 | -! | +|||
| 375 | +
- if (missing(msg)) {
+ }, |
|||
| 294 | -! | +|||
| 376 | +
- msg <- sprintf(+ slices_set = function(slices) {
|
|||
| 295 | -! | +|||
| 377 | +7x |
- "%s does not have the required variables: %s.",+ shiny::isolate({
|
||
| 296 | -! | +|||
| 378 | +7x |
- deparse(substitute(data)),+ if (!is.teal_slices(slices)) {
|
||
| 297 | +379 | ! |
- toString(varname[!has_vars])+ slices <- as.teal_slices(slices) |
|
| 298 | +380 |
- )+ } |
||
| 299 | -+ | |||
| 381 | +7x |
- }+ .self$all_slices(slices) |
||
| 300 | -! | +|||
| 382 | +7x |
- validate(need(FALSE, msg))+ invisible(.self) |
||
| 301 | +383 |
- }+ }) |
||
| 302 | +384 |
- }+ }, |
||
| 303 | +385 |
- }+ show = function() {
|
||
| 304 | -+ | |||
| 386 | +! |
-
+ shiny::isolate(print(.self$all_slices())) |
||
| 305 | -+ | |||
| 387 | +! |
- #' Validate that variables has expected number of levels+ invisible(.self) |
||
| 306 | +388 |
- #'+ } |
||
| 307 | +389 |
- #' `r lifecycle::badge("stable")`
+ ) |
||
| 308 | +390 |
- #'+ ) |
||
| 309 | +391 |
- #' If the number of levels of `x` is less than `min_levels`+ # todo: prevent any teal_slices attribute except mapping |
| 310 | +1 |
- #' or greater than `max_levels` the validation will fail.+ # This is the main function from teal to be used by the end-users. Although it delegates |
|
| 311 | +2 |
- #' This function is a wrapper for `shiny::validate`.+ # directly to `module_teal_with_splash.R`, we keep it in a separate file because its documentation is quite large |
|
| 312 | +3 |
- #'+ # and it is very end-user oriented. It may also perform more argument checking with more informative |
|
| 313 | +4 |
- #' @param x variable name. If `x` is not a factor, the unique values+ # error messages. |
|
| 314 | +5 |
- #' are treated as levels.+ |
|
| 315 | +6 |
- #' @param min_levels cutoff for minimum number of levels of `x`+ #' Create the server and UI function for the `shiny` app |
|
| 316 | +7 |
- #' @param max_levels cutoff for maximum number of levels of `x`+ #' |
|
| 317 | +8 |
- #' @param var_name name of variable being validated for use in+ #' @description `r lifecycle::badge("stable")`
|
|
| 318 | +9 |
- #' validation message+ #' |
|
| 319 | +10 |
- #'+ #' End-users: This is the most important function for you to start a |
|
| 320 | +11 |
- #' @export+ #' `teal` app that is composed of `teal` modules. |
|
| 321 | +12 |
- #' @examples+ #' |
|
| 322 | +13 |
- #' data <- data.frame(+ #' @param data (`teal_data` or `teal_data_module`) |
|
| 323 | +14 |
- #' one = rep("a", length.out = 20),
+ #' For constructing the data object, refer to [teal_data()] and [teal_data_module()]. |
|
| 324 | +15 |
- #' two = rep(c("a", "b"), length.out = 20),
+ #' If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used. |
|
| 325 | +16 |
- #' three = rep(c("a", "b", "c"), length.out = 20),
+ #' @param modules (`list` or `teal_modules` or `teal_module`) |
|
| 326 | +17 |
- #' four = rep(c("a", "b", "c", "d"), length.out = 20),
+ #' Nested list of `teal_modules` or `teal_module` objects or a single |
|
| 327 | +18 |
- #' stringsAsFactors = TRUE+ #' `teal_modules` or `teal_module` object. These are the specific output modules which |
|
| 328 | +19 |
- #' )+ #' will be displayed in the `teal` application. See [modules()] and [module()] for |
|
| 329 | +20 |
- #' ui <- fluidPage(+ #' more details. |
|
| 330 | +21 |
- #' selectInput(+ #' @param filter (`teal_slices`) Optionally, |
|
| 331 | +22 |
- #' "var",+ #' specifies the initial filter using [teal_slices()]. |
|
| 332 | +23 |
- #' "Select variable",+ #' @param title (`shiny.tag` or `character(1)`) Optionally, |
|
| 333 | +24 |
- #' choices = c("one", "two", "three", "four"),
+ #' the browser window title. Defaults to a title "teal app" with the icon of NEST. |
|
| 334 | +25 |
- #' selected = "one"+ #' Can be created using the `build_app_title()` or |
|
| 335 | +26 |
- #' ),+ #' by passing a valid `shiny.tag` which is a head tag with title and link tag. |
|
| 336 | +27 |
- #' verbatimTextOutput("summary")
+ #' @param header (`shiny.tag` or `character(1)`) Optionally, |
|
| 337 | +28 |
- #' )+ #' the header of the app. |
|
| 338 | +29 |
- #'+ #' @param footer (`shiny.tag` or `character(1)`) Optionally, |
|
| 339 | +30 |
- #' server <- function(input, output) {
+ #' the footer of the app. |
|
| 340 | +31 |
- #' output$summary <- renderText({
+ #' @param id (`character`) Optionally, |
|
| 341 | +32 |
- #' validate_n_levels(data[[input$var]], min_levels = 2, max_levels = 15, var_name = input$var)+ #' a string specifying the `shiny` module id in cases it is used as a `shiny` module |
|
| 342 | +33 |
- #' paste0(+ #' rather than a standalone `shiny` app. This is a legacy feature. |
|
| 343 | +34 |
- #' "Levels of selected treatment variable: ",+ #' @param landing_popup (`teal_module_landing`) Optionally, |
|
| 344 | +35 |
- #' paste(levels(data[[input$var]]),+ #' a `landing_popup_module` to show up as soon as the teal app is initialized. |
|
| 345 | +36 |
- #' collapse = ", "+ #' |
|
| 346 | +37 |
- #' )+ #' @return Named list containing server and UI functions. |
|
| 347 | +38 |
- #' )+ #' |
|
| 348 | +39 |
- #' })+ #' @export |
|
| 349 | +40 |
- #' }+ #' |
|
| 350 | +41 |
- #' if (interactive()) {
+ #' @include modules.R |
|
| 351 | +42 |
- #' shinyApp(ui, server)+ #' |
|
| 352 | +43 |
- #' }+ #' @examples |
|
| 353 | +44 |
- validate_n_levels <- function(x, min_levels = 1, max_levels = 12, var_name) {
- |
- |
| 354 | -! | -
- x_levels <- if (is.factor(x)) {
- |
- |
| 355 | -! | -
- levels(x)+ #' app <- init( |
|
| 356 | +45 |
- } else {
- |
- |
| 357 | -! | -
- unique(x)+ #' data = within( |
|
| 358 | +46 |
- }+ #' teal_data(), |
|
| 359 | +47 | - - | -|
| 360 | -! | -
- if (!is.null(min_levels) && !(is.null(max_levels))) {
- |
- |
| 361 | -! | -
- validate(need(- |
- |
| 362 | -! | -
- length(x_levels) >= min_levels && length(x_levels) <= max_levels,- |
- |
| 363 | -! | -
- sprintf(- |
- |
| 364 | -! | -
- "%s variable needs minimum %s level(s) and maximum %s level(s).",- |
- |
| 365 | -! | -
- var_name, min_levels, max_levels+ #' {
|
|
| 366 | +48 |
- )+ #' new_iris <- transform(iris, id = seq_len(nrow(iris))) |
|
| 367 | +49 |
- ))- |
- |
| 368 | -! | -
- } else if (!is.null(min_levels)) {
- |
- |
| 369 | -! | -
- validate(need(- |
- |
| 370 | -! | -
- length(x_levels) >= min_levels,- |
- |
| 371 | -! | -
- sprintf("%s variable needs minimum %s levels(s)", var_name, min_levels)
+ #' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars))) |
|
| 372 | +50 |
- ))+ #' } |
|
| 373 | -! | +||
| 51 | +
- } else if (!is.null(max_levels)) {
+ #' ), |
||
| 374 | -! | +||
| 52 | +
- validate(need(+ #' modules = modules( |
||
| 375 | -! | +||
| 53 | +
- length(x_levels) <= max_levels,+ #' module( |
||
| 376 | -! | +||
| 54 | +
- sprintf("%s variable needs maximum %s level(s)", var_name, max_levels)
+ #' label = "data source", |
||
| 377 | +55 |
- ))+ #' server = function(input, output, session, data) {},
|
|
| 378 | +56 |
- }+ #' ui = function(id, ...) tags$div(p("information about data source")),
|
|
| 379 | +57 |
- }+ #' datanames = "all" |
| 1 | +58 |
- #' Filter state snapshot management+ #' ), |
||
| 2 | +59 |
- #'+ #' example_module(label = "example teal module"), |
||
| 3 | +60 |
- #' Capture and restore snapshots of the global (app) filter state.+ #' module( |
||
| 4 | +61 |
- #'+ #' "Iris Sepal.Length histogram", |
||
| 5 | +62 |
- #' This module introduces snapshots: stored descriptions of the filter state of the entire application.+ #' server = function(input, output, session, data) {
|
||
| 6 | +63 |
- #' Snapshots allow the user to save the current filter state of the application for later use in the session,+ #' output$hist <- renderPlot( |
||
| 7 | +64 |
- #' as well as to save it to file in order to share it with an app developer or other users,+ #' hist(data()[["new_iris"]]$Sepal.Length) |
||
| 8 | +65 |
- #' who in turn can upload it to their own session.+ #' ) |
||
| 9 | +66 |
- #'+ #' }, |
||
| 10 | +67 |
- #' The snapshot manager is accessed with the camera icon in the tabset bar.+ #' ui = function(id, ...) {
|
||
| 11 | +68 |
- #' At the beginning of a session it presents three icons: a camera, an upload, and an circular arrow.+ #' ns <- NS(id) |
||
| 12 | +69 |
- #' Clicking the camera captures a snapshot, clicking the upload adds a snapshot from a file+ #' plotOutput(ns("hist"))
|
||
| 13 | +70 |
- #' and applies the filter states therein, and clicking the arrow resets initial application state.+ #' }, |
||
| 14 | +71 |
- #' As snapshots are added, they will show up as rows in a table and each will have a select button and a save button.+ #' datanames = "new_iris" |
||
| 15 | +72 |
- #'+ #' ) |
||
| 16 | +73 |
- #' @section Server logic:+ #' ), |
||
| 17 | +74 |
- #' Snapshots are basically `teal_slices` objects, however, since each module is served by a separate instance+ #' filter = teal_slices( |
||
| 18 | +75 |
- #' of `FilteredData` and these objects require shared state, `teal_slice` is a `reactiveVal` so `teal_slices`+ #' teal_slice(dataname = "new_iris", varname = "Species"), |
||
| 19 | +76 |
- #' cannot be stored as is. Therefore, `teal_slices` are reversibly converted to a list of lists representation+ #' teal_slice(dataname = "new_iris", varname = "Sepal.Length"), |
||
| 20 | +77 |
- #' (attributes are maintained).+ #' teal_slice(dataname = "new_mtcars", varname = "cyl"), |
||
| 21 | +78 |
- #'+ #' exclude_varnames = list(new_iris = c("Sepal.Width", "Petal.Width")),
|
||
| 22 | +79 |
- #' Snapshots are stored in a `reactiveVal` as a named list.+ #' module_specific = TRUE, |
||
| 23 | +80 |
- #' The first snapshot is the initial state of the application and the user can add a snapshot whenever they see fit.+ #' mapping = list( |
||
| 24 | +81 |
- #'+ #' `example teal module` = "new_iris Species", |
||
| 25 | +82 |
- #' For every snapshot except the initial one, a piece of UI is generated that contains+ #' `Iris Sepal.Length histogram` = "new_iris Species", |
||
| 26 | +83 |
- #' the snapshot name, a select button to restore that snapshot, and a save button to save it to a file.+ #' global_filters = "new_mtcars cyl" |
||
| 27 | +84 |
- #' The initial snapshot is restored by a separate "reset" button.+ #' ) |
||
| 28 | +85 |
- #' It cannot be saved directly but a user is welcome to capture the initial state as a snapshot and save that.+ #' ), |
||
| 29 | +86 |
- #'+ #' title = "App title", |
||
| 30 | +87 |
- #' @section Snapshot mechanics:+ #' header = tags$h1("Sample App"),
|
||
| 31 | +88 |
- #' When a snapshot is captured, the user is prompted to name it.+ #' footer = tags$p("Sample footer")
|
||
| 32 | +89 |
- #' Names are displayed as is but since they are used to create button ids,+ #' ) |
||
| 33 | +90 |
- #' under the hood they are converted to syntactically valid strings.+ #' if (interactive()) {
|
||
| 34 | +91 |
- #' New snapshot names are validated so that their valid versions are unique.+ #' shinyApp(app$ui, app$server) |
||
| 35 | +92 |
- #' Leading and trailing white space is trimmed.+ #' } |
||
| 36 | +93 |
#' |
||
| 37 | +94 |
- #' The module can read the global state of the application from `slices_global` and `mapping_matrix`.+ init <- function(data, |
||
| 38 | +95 |
- #' The former provides a list of all existing `teal_slice`s and the latter says which slice is active in which module.+ modules, |
||
| 39 | +96 |
- #' Once a name has been accepted, `slices_global` is converted to a list of lists - a snapshot.+ filter = teal_slices(), |
||
| 40 | +97 |
- #' The snapshot contains the `mapping` attribute of the initial application state+ title = build_app_title(), |
||
| 41 | +98 |
- #' (or one that has been restored), which may not reflect the current one,+ header = tags$p(), |
||
| 42 | +99 |
- #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that,+ footer = tags$p(), |
||
| 43 | +100 |
- #' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping.+ id = character(0), |
||
| 44 | +101 |
- #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list.+ landing_popup = NULL) {
|
||
| 45 | -+ | |||
| 102 | +12x |
- #'+ logger::log_debug("init initializing teal app with: data ('{ class(data) }').")
|
||
| 46 | +103 |
- #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object.+ |
||
| 47 | +104 |
- #' Then state of all `FilteredData` objects (provided in `datasets`) is cleared+ # argument checking (independent) |
||
| 48 | +105 |
- #' and set anew according to the `mapping` attribute of the snapshot.+ ## `data` |
||
| 49 | -+ | |||
| 106 | +12x |
- #' The snapshot is then set as the current content of `slices_global`.+ if (inherits(data, "TealData")) {
|
||
| 50 | -+ | |||
| 107 | +! |
- #'+ lifecycle::deprecate_stop( |
||
| 51 | -+ | |||
| 108 | +! |
- #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring,+ when = "0.15.0", |
||
| 52 | -+ | |||
| 109 | +! |
- #' and then saved to file with [slices_store()].+ what = "init(data)", |
||
| 53 | -+ | |||
| 110 | +! |
- #'+ paste( |
||
| 54 | -+ | |||
| 111 | +! |
- #' When a snapshot is uploaded, it will first be added to storage just like a newly created one,+ "TealData is no longer supported. Use teal_data() instead.", |
||
| 55 | -+ | |||
| 112 | +! |
- #' and then used to restore app state much like a snapshot taken from storage.+ "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/988." |
||
| 56 | +113 |
- #' Upon clicking the upload icon the user will be prompted for a file to upload+ ) |
||
| 57 | +114 |
- #' and may choose to name the new snapshot. The name defaults to the name of the file (the extension is dropped)+ ) |
||
| 58 | +115 |
- #' and normal naming rules apply. Loading the file yields a `teal_slices` object,+ } |
||
| 59 | -+ | |||
| 116 | +12x |
- #' which is disassembled for storage and used directly for restoring app state.+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
|
||
| 60 | -+ | |||
| 117 | +12x |
- #'+ checkmate::assert_class(landing_popup, "teal_module_landing", null.ok = TRUE) |
||
| 61 | +118 |
- #' @section Transferring snapshots:+ |
||
| 62 | +119 |
- #' Snapshots uploaded from disk should only be used in the same application they come from,+ ## `modules` |
||
| 63 | -+ | |||
| 120 | +12x |
- #' _i.e._ an application that uses the same data and the same modules.+ checkmate::assert( |
||
| 64 | -+ | |||
| 121 | +12x |
- #' To ensure this is the case, `init` stamps `teal_slices` with an app id that is stored in the `app_id` attribute of+ .var.name = "modules", |
||
| 65 | -+ | |||
| 122 | +12x |
- #' a `teal_slices` object. When a snapshot is restored from file, its `app_id` is compared to that+ checkmate::check_multi_class(modules, c("teal_modules", "teal_module")),
|
||
| 66 | -+ | |||
| 123 | +12x |
- #' of the current app state and only if the match is the snapshot admitted to the session.+ checkmate::check_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
|
||
| 67 | +124 |
- #'+ ) |
||
| 68 | -+ | |||
| 125 | +12x |
- #' @section Bookmarks:+ if (inherits(modules, "teal_module")) {
|
||
| 69 | -+ | |||
| 126 | +1x |
- #' An `onBookmark` callback creates a snapshot of the current filter state.+ modules <- list(modules) |
||
| 70 | +127 |
- #' This is done on the app session, not the module session.+ } |
||
| 71 | -+ | |||
| 128 | +12x |
- #' (The snapshot will be retrieved by `module_teal` in order to set initial app state in a restored app.)+ if (checkmate::test_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))) {
|
||
| 72 | -+ | |||
| 129 | +6x |
- #' Then that snapshot, and the previous snapshot history are dumped into the `values.rds` file in `<bookmark_dir>`.+ modules <- do.call(teal::modules, modules) |
||
| 73 | +130 |
- #'+ } |
||
| 74 | +131 |
- #' @param id (`character(1)`) `shiny` module instance id.+ |
||
| 75 | +132 |
- #' @param slices_global (`reactiveVal`) that contains a `teal_slices` object+ ## `filter` |
||
| 76 | -+ | |||
| 133 | +12x |
- #' containing all `teal_slice`s existing in the app, both active and inactive.+ checkmate::assert_class(filter, "teal_slices") |
||
| 77 | +134 |
- #'+ |
||
| 78 | +135 |
- #' @return `list` containing the snapshot history, where each element is an unlisted `teal_slices` object.+ ## all other arguments |
||
| 79 | -+ | |||
| 136 | +11x |
- #'+ checkmate::assert( |
||
| 80 | -+ | |||
| 137 | +11x |
- #' @name module_snapshot_manager+ .var.name = "title", |
||
| 81 | -+ | |||
| 138 | +11x |
- #' @rdname module_snapshot_manager+ checkmate::check_string(title), |
||
| 82 | -+ | |||
| 139 | +11x |
- #'+ checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 83 | +140 |
- #' @author Aleksander Chlebowski+ ) |
||
| 84 | -+ | |||
| 141 | +11x |
- #' @keywords internal+ checkmate::assert( |
||
| 85 | -+ | |||
| 142 | +11x |
- NULL+ .var.name = "header", |
||
| 86 | -+ | |||
| 143 | +11x |
-
+ checkmate::check_string(header), |
||
| 87 | -+ | |||
| 144 | +11x |
- #' @rdname module_snapshot_manager+ checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 88 | +145 |
- ui_snapshot_manager_panel <- function(id) {
+ ) |
||
| 89 | -! | +|||
| 146 | +11x |
- ns <- NS(id)+ checkmate::assert( |
||
| 90 | -! | +|||
| 147 | +11x |
- tags$button(+ .var.name = "footer", |
||
| 91 | -! | +|||
| 148 | +11x |
- id = ns("show_snapshot_manager"),
+ checkmate::check_string(footer), |
||
| 92 | -! | +|||
| 149 | +11x |
- class = "btn action-button wunder_bar_button",+ checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
|
||
| 93 | -! | +|||
| 150 | +
- title = "View filter mapping",+ ) |
|||
| 94 | -! | +|||
| 151 | +11x |
- suppressMessages(icon("fas fa-camera"))
+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
||
| 95 | +152 |
- )+ |
||
| 96 | +153 |
- }+ # log+ |
+ ||
| 154 | +11x | +
+ teal.logger::log_system_info() |
||
| 97 | +155 | |||
| 98 | +156 |
- #' @rdname module_snapshot_manager+ # argument transformations |
||
| 99 | +157 |
- srv_snapshot_manager_panel <- function(id, slices_global) {
+ ## `modules` - landing module |
||
| 100 | -82x | +158 | +11x |
- moduleServer(id, function(input, output, session) {
+ landing <- extract_module(modules, "teal_module_landing") |
| 101 | -82x | +159 | +11x |
- logger::log_debug("srv_snapshot_manager_panel initializing")
+ if (length(landing) == 1L) {
|
| 102 | -82x | +|||
| 160 | +! |
- setBookmarkExclude(c("show_snapshot_manager"))
+ landing_popup <- landing[[1L]] |
||
| 103 | -82x | +|||
| 161 | +! |
- observeEvent(input$show_snapshot_manager, {
+ modules <- drop_module(modules, "teal_module_landing") |
||
| 104 | +162 | ! |
- logger::log_debug("srv_snapshot_manager_panel@1 show_snapshot_manager button has been clicked.")
+ lifecycle::deprecate_soft( |
|
| 105 | +163 | ! |
- showModal(+ when = "0.15.3", |
|
| 106 | +164 | ! |
- modalDialog(+ what = "landing_popup_module()", |
|
| 107 | +165 | ! |
- ui_snapshot_manager(session$ns("module")),
+ details = paste( |
|
| 108 | +166 | ! |
- class = "snapshot_manager_modal",+ "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ", |
|
| 109 | +167 | ! |
- size = "m",+ "instead of wrapping it into `modules()` and passing to the `modules` argument" |
|
| 110 | -! | +|||
| 168 | +
- footer = NULL,+ )+ |
+ |||
| 169 | ++ |
+ )+ |
+ ||
| 170 | +11x | +
+ } else if (length(landing) > 1L) {
|
||
| 111 | +171 | ! |
- easyClose = TRUE+ stop("Only one `landing_popup_module` can be used.")
|
|
| 112 | +172 |
- )+ } |
||
| 113 | +173 |
- )+ |
||
| 114 | +174 |
- })+ ## `filter` - set app_id attribute unless present (when restoring bookmark) |
||
| 115 | -82x | +175 | +11x |
- srv_snapshot_manager("module", slices_global = slices_global)
+ if (is.null(attr(filter, "app_id", exact = TRUE))) attr(filter, "app_id") <- create_app_id(data, modules) |
| 116 | +176 |
- })+ |
||
| 117 | +177 |
- }+ ## `filter` - convert teal.slice::teal_slices to teal::teal_slices+ |
+ ||
| 178 | +11x | +
+ filter <- as.teal_slices(as.list(filter)) |
||
| 118 | +179 | |||
| 119 | +180 |
- #' @rdname module_snapshot_manager+ # argument checking (interdependent) |
||
| 120 | +181 |
- ui_snapshot_manager <- function(id) {
+ ## `filter` - `modules` |
||
| 121 | -! | +|||
| 182 | +11x |
- ns <- NS(id)+ if (isTRUE(attr(filter, "module_specific"))) {
|
||
| 122 | +183 | ! |
- tags$div(+ module_names <- unlist(c(module_labels(modules), "global_filters")) |
|
| 123 | +184 | ! |
- class = "manager_content",+ failed_mod_names <- setdiff(names(attr(filter, "mapping")), module_names) |
|
| 124 | +185 | ! |
- tags$div(+ if (length(failed_mod_names)) {
|
|
| 125 | +186 | ! |
- class = "manager_table_row",+ stop( |
|
| 126 | +187 | ! |
- tags$span(tags$b("Snapshot manager")),
+ sprintf( |
|
| 127 | +188 | ! |
- actionLink(ns("snapshot_add"), label = NULL, icon = icon("fas fa-camera"), title = "add snapshot"),
+ "Some module names in the mapping arguments don't match module labels.\n %s not in %s", |
|
| 128 | +189 | ! |
- actionLink(ns("snapshot_load"), label = NULL, icon = icon("fas fa-upload"), title = "upload snapshot"),
+ toString(failed_mod_names), |
|
| 129 | +190 | ! |
- actionLink(ns("snapshot_reset"), label = NULL, icon = icon("fas fa-undo"), title = "reset initial state"),
+ toString(unique(module_names)) |
|
| 130 | -! | +|||
| 191 | +
- NULL+ ) |
|||
| 131 | +192 |
- ),+ ) |
||
| 132 | -! | +|||
| 193 | +
- uiOutput(ns("snapshot_list"))
+ } |
|||
| 133 | +194 |
- )+ |
||
| 134 | -+ | |||
| 195 | +! |
- }+ if (anyDuplicated(module_names)) {
|
||
| 135 | +196 |
-
+ # In teal we are able to set nested modules with duplicated label. |
||
| 136 | +197 |
- #' @rdname module_snapshot_manager+ # Because mapping argument bases on the relationship between module-label and filter-id, |
||
| 137 | +198 |
- srv_snapshot_manager <- function(id, slices_global) {
+ # it is possible that module-label in mapping might refer to multiple teal_module (identified by the same label) |
||
| 138 | -82x | +|||
| 199 | +! |
- checkmate::assert_character(id)+ stop( |
||
| 139 | -+ | |||
| 200 | +! |
-
+ sprintf( |
||
| 140 | -82x | +|||
| 201 | +! |
- moduleServer(id, function(input, output, session) {
+ "Module labels should be unique when teal_slices(mapping = TRUE). Duplicated labels:\n%s ", |
||
| 141 | -82x | +|||
| 202 | +! |
- logger::log_debug("srv_snapshot_manager initializing")
+ toString(module_names[duplicated(module_names)]) |
||
| 142 | +203 |
-
+ ) |
||
| 143 | +204 |
- # Set up bookmarking callbacks ----+ ) |
||
| 144 | +205 |
- # Register bookmark exclusions (all buttons and text fields).+ } |
||
| 145 | -82x | +|||
| 206 | +
- setBookmarkExclude(c(+ }+ |
+ |||
| 207 | ++ | + + | +||
| 208 | ++ |
+ ## `data` - `modules` |
||
| 146 | -82x | +209 | +11x |
- "snapshot_add", "snapshot_load", "snapshot_reset",+ if (inherits(data, "teal_data")) {
|
| 147 | -82x | +210 | +10x |
- "snapshot_name_accept", "snaphot_file_accept",+ if (length(data) == 0) {
|
| 148 | -82x | +211 | +1x |
- "snapshot_name", "snapshot_file"+ stop("The environment of `data` is empty.")
|
| 149 | +212 |
- ))+ } |
||
| 150 | +213 |
- # Add snapshot history to bookmark.+ |
||
| 151 | -82x | +214 | +9x |
- session$onBookmark(function(state) {
- |
-
| 152 | -! | -
- logger::log_debug("srv_snapshot_manager@onBookmark: storing snapshot and bookmark history")
- |
- ||
| 153 | -! | -
- state$values$snapshot_history <- snapshot_history() # isolate this?- |
- ||
| 154 | -- |
- })- |
- ||
| 155 | -- |
-
+ is_modules_ok <- check_modules_datanames(modules, names(data)) |
||
| 156 | -82x | +215 | +9x |
- ns <- session$ns+ if (!isTRUE(is_modules_ok) && length(unlist(extract_transformers(modules))) == 0) {
|
| 157 | -+ | |||
| 216 | +2x |
-
+ warning(is_modules_ok, call. = FALSE) |
||
| 158 | +217 |
- # Track global filter states ----- |
- ||
| 159 | -82x | -
- snapshot_history <- reactiveVal({
+ } |
||
| 160 | +218 |
- # Restore directly from bookmarked state, if applicable.+ |
||
| 161 | -82x | +219 | +9x |
- restoreValue(+ is_filter_ok <- check_filter_datanames(filter, names(data)) |
| 162 | -82x | +220 | +9x |
- ns("snapshot_history"),
+ if (!isTRUE(is_filter_ok)) {
|
| 163 | -82x | +221 | +1x |
- list("Initial application state" = shiny::isolate(as.list(slices_global$all_slices(), recursive = TRUE)))
+ warning(is_filter_ok) |
| 164 | +222 |
- )+ # we allow app to continue if applied filters are outside |
||
| 165 | +223 |
- })+ # of possible data range |
||
| 166 | +224 |
-
+ } |
||
| 167 | +225 |
- # Snapshot current application state ----+ } |
||
| 168 | +226 |
- # Name snaphsot.+ |
||
| 169 | -82x | -
- observeEvent(input$snapshot_add, {
- |
- ||
| 170 | -! | -
- logger::log_debug("srv_snapshot_manager: snapshot_add button clicked")
- |
- ||
| 171 | -! | -
- showModal(- |
- ||
| 172 | -! | +227 | +10x |
- modalDialog(+ reporter <- teal.reporter::Reporter$new()$set_id(attr(filter, "app_id")) |
| 173 | -! | +|||
| 228 | +10x |
- textInput(ns("snapshot_name"), "Name the snapshot", width = "100%", placeholder = "Meaningful, unique name"),
+ if (is_arg_used(modules, "reporter") && length(extract_module(modules, "teal_module_previewer")) == 0) {
|
||
| 174 | +229 | ! |
- footer = tagList(+ modules <- append_module( |
|
| 175 | +230 | ! |
- actionButton(ns("snapshot_name_accept"), "Accept", icon = icon("far fa-thumbs-up")),
+ modules, |
|
| 176 | +231 | ! |
- modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
+ reporter_previewer_module(server_args = list(previewer_buttons = c("download", "reset")))
|
|
| 177 | +232 |
- ),- |
- ||
| 178 | -! | -
- size = "s"+ ) |
||
| 179 | +233 |
- )+ } |
||
| 180 | +234 |
- )+ |
||
| 181 | -+ | |||
| 235 | +10x |
- })+ ns <- NS(id) |
||
| 182 | +236 |
- # Store snaphsot.+ # Note: UI must be a function to support bookmarking. |
||
| 183 | -82x | +237 | +10x |
- observeEvent(input$snapshot_name_accept, {
+ res <- list( |
| 184 | -! | +|||
| 238 | +10x |
- logger::log_debug("srv_snapshot_manager: snapshot_name_accept button clicked")
+ ui = function(request) {
|
||
| 185 | +239 | ! |
- snapshot_name <- trimws(input$snapshot_name)+ ui_teal( |
|
| 186 | +240 | ! |
- if (identical(snapshot_name, "")) {
+ id = ns("teal"),
|
|
| 187 | +241 | ! |
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ modules = modules, |
|
| 188 | +242 | ! |
- showNotification(+ title = title, |
|
| 189 | +243 | ! |
- "Please name the snapshot.",+ header = header, |
|
| 190 | +244 | ! |
- type = "message"+ footer = footer |
|
| 191 | +245 |
- )+ ) |
||
| 192 | -! | +|||
| 246 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ }, |
|||
| 193 | -! | +|||
| 247 | +10x |
- } else if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
+ server = function(input, output, session) {
|
||
| 194 | +248 | ! |
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ if (!is.null(landing_popup)) {
|
|
| 195 | +249 | ! |
- showNotification(+ do.call(landing_popup$server, c(list(id = "landing_module_shiny_id"), landing_popup$server_args)) |
|
| 196 | -! | +|||
| 250 | +
- "This name is in conflict with other snapshot names. Please choose a different one.",+ } |
|||
| 197 | +251 | ! |
- type = "message"+ srv_teal(id = ns("teal"), data = data, modules = modules, filter = deep_copy_filter(filter))
|
|
| 198 | +252 |
- )+ } |
||
| 199 | -! | +|||
| 253 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ ) |
|||
| 200 | +254 |
- } else {
+
|
||
| 201 | -! | +|||
| 255 | +10x |
- logger::log_debug("srv_snapshot_manager: snapshot name accepted, adding snapshot")
+ logger::log_debug("init teal app has been initialized.")
|
||
| 202 | -! | +|||
| 256 | +
- snapshot <- as.list(slices_global$all_slices(), recursive = TRUE)+ |
|||
| 203 | -! | +|||
| 257 | +10x |
- snapshot_update <- c(snapshot_history(), list(snapshot))+ res |
||
| 204 | -! | +|||
| 258 | +
- names(snapshot_update)[length(snapshot_update)] <- snapshot_name+ } |
|||
| 205 | -! | +
| 1 | +
- snapshot_history(snapshot_update)+ #' Filter state snapshot management |
|||
| 206 | -! | +|||
| 2 | +
- removeModal()+ #' |
|||
| 207 | +3 |
- # Reopen filter manager modal by clicking button in the main application.+ #' Capture and restore snapshots of the global (app) filter state. |
||
| 208 | -! | +|||
| 4 | +
- shinyjs::click(id = "teal-wunder_bar-show_snapshot_manager", asis = TRUE)+ #' |
|||
| 209 | +5 |
- }+ #' This module introduces snapshots: stored descriptions of the filter state of the entire application. |
||
| 210 | +6 |
- })+ #' Snapshots allow the user to save the current filter state of the application for later use in the session, |
||
| 211 | +7 |
-
+ #' as well as to save it to file in order to share it with an app developer or other users, |
||
| 212 | +8 |
- # Upload a snapshot file ----+ #' who in turn can upload it to their own session. |
||
| 213 | +9 |
- # Select file.+ #' |
||
| 214 | -82x | +|||
| 10 | +
- observeEvent(input$snapshot_load, {
+ #' The snapshot manager is accessed with the camera icon in the tabset bar. |
|||
| 215 | -! | +|||
| 11 | +
- logger::log_debug("srv_snapshot_manager: snapshot_load button clicked")
+ #' At the beginning of a session it presents three icons: a camera, an upload, and an circular arrow. |
|||
| 216 | -! | +|||
| 12 | +
- showModal(+ #' Clicking the camera captures a snapshot, clicking the upload adds a snapshot from a file |
|||
| 217 | -! | +|||
| 13 | +
- modalDialog(+ #' and applies the filter states therein, and clicking the arrow resets initial application state. |
|||
| 218 | -! | +|||
| 14 | +
- fileInput(ns("snapshot_file"), "Choose snapshot file", accept = ".json", width = "100%"),
+ #' As snapshots are added, they will show up as rows in a table and each will have a select button and a save button. |
|||
| 219 | -! | +|||
| 15 | +
- textInput(+ #' |
|||
| 220 | -! | +|||
| 16 | +
- ns("snapshot_name"),
+ #' @section Server logic: |
|||
| 221 | -! | +|||
| 17 | +
- "Name the snapshot (optional)",+ #' Snapshots are basically `teal_slices` objects, however, since each module is served by a separate instance |
|||
| 222 | -! | +|||
| 18 | +
- width = "100%",+ #' of `FilteredData` and these objects require shared state, `teal_slice` is a `reactiveVal` so `teal_slices` |
|||
| 223 | -! | +|||
| 19 | +
- placeholder = "Meaningful, unique name"+ #' cannot be stored as is. Therefore, `teal_slices` are reversibly converted to a list of lists representation |
|||
| 224 | +20 |
- ),+ #' (attributes are maintained). |
||
| 225 | -! | +|||
| 21 | +
- footer = tagList(+ #' |
|||
| 226 | -! | +|||
| 22 | +
- actionButton(ns("snaphot_file_accept"), "Accept", icon = icon("far fa-thumbs-up")),
+ #' Snapshots are stored in a `reactiveVal` as a named list. |
|||
| 227 | -! | +|||
| 23 | +
- modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
+ #' The first snapshot is the initial state of the application and the user can add a snapshot whenever they see fit. |
|||
| 228 | +24 |
- )+ #' |
||
| 229 | +25 |
- )+ #' For every snapshot except the initial one, a piece of UI is generated that contains |
||
| 230 | +26 |
- )+ #' the snapshot name, a select button to restore that snapshot, and a save button to save it to a file. |
||
| 231 | +27 |
- })+ #' The initial snapshot is restored by a separate "reset" button. |
||
| 232 | +28 |
- # Store new snapshot to list and restore filter states.+ #' It cannot be saved directly but a user is welcome to capture the initial state as a snapshot and save that. |
||
| 233 | -82x | +|||
| 29 | +
- observeEvent(input$snaphot_file_accept, {
+ #' |
|||
| 234 | -! | +|||
| 30 | +
- logger::log_debug("srv_snapshot_manager: snapshot_file_accept button clicked")
+ #' @section Snapshot mechanics: |
|||
| 235 | -! | +|||
| 31 | +
- snapshot_name <- trimws(input$snapshot_name)+ #' When a snapshot is captured, the user is prompted to name it. |
|||
| 236 | -! | +|||
| 32 | +
- if (identical(snapshot_name, "")) {
+ #' Names are displayed as is but since they are used to create button ids, |
|||
| 237 | -! | +|||
| 33 | +
- logger::log_debug("srv_snapshot_manager: no snapshot name provided, naming after file")
+ #' under the hood they are converted to syntactically valid strings. |
|||
| 238 | -! | +|||
| 34 | +
- snapshot_name <- tools::file_path_sans_ext(input$snapshot_file$name)+ #' New snapshot names are validated so that their valid versions are unique. |
|||
| 239 | +35 |
- }+ #' Leading and trailing white space is trimmed. |
||
| 240 | -! | +|||
| 36 | +
- if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
+ #' |
|||
| 241 | -! | +|||
| 37 | +
- logger::log_debug("srv_snapshot_manager: snapshot name rejected")
+ #' The module can read the global state of the application from `slices_global` and `mapping_matrix`. |
|||
| 242 | -! | +|||
| 38 | +
- showNotification(+ #' The former provides a list of all existing `teal_slice`s and the latter says which slice is active in which module. |
|||
| 243 | -! | +|||
| 39 | +
- "This name is in conflict with other snapshot names. Please choose a different one.",+ #' Once a name has been accepted, `slices_global` is converted to a list of lists - a snapshot. |
|||
| 244 | -! | +|||
| 40 | +
- type = "message"+ #' The snapshot contains the `mapping` attribute of the initial application state |
|||
| 245 | +41 |
- )+ #' (or one that has been restored), which may not reflect the current one, |
||
| 246 | -! | +|||
| 42 | +
- updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name")+ #' so `mapping_matrix` is transformed to obtain the current mapping, i.e. a list that, |
|||
| 247 | +43 |
- } else {
+ #' when passed to the `mapping` argument of [teal_slices()], would result in the current mapping. |
||
| 248 | +44 |
- # Restore snapshot and verify app compatibility.+ #' This is substituted as the snapshot's `mapping` attribute and the snapshot is added to the snapshot list. |
||
| 249 | -! | +|||
| 45 | +
- logger::log_debug("srv_snapshot_manager: snapshot name accepted, loading snapshot")
+ #' |
|||
| 250 | -! | +|||
| 46 | +
- snapshot_state <- try(slices_restore(input$snapshot_file$datapath))+ #' To restore app state, a snapshot is retrieved from storage and rebuilt into a `teal_slices` object. |
|||
| 251 | -! | +|||
| 47 | +
- if (!inherits(snapshot_state, "modules_teal_slices")) {
+ #' Then state of all `FilteredData` objects (provided in `datasets`) is cleared |
|||
| 252 | -! | +|||
| 48 | +
- logger::log_debug("srv_snapshot_manager: snapshot file corrupt")
+ #' and set anew according to the `mapping` attribute of the snapshot. |
|||
| 253 | -! | +|||
| 49 | +
- showNotification(+ #' The snapshot is then set as the current content of `slices_global`. |
|||
| 254 | -! | +|||
| 50 | +
- "File appears to be corrupt.",+ #' |
|||
| 255 | -! | +|||
| 51 | +
- type = "error"+ #' To save a snapshot, the snapshot is retrieved and reassembled just like for restoring, |
|||
| 256 | +52 |
- )+ #' and then saved to file with [slices_store()]. |
||
| 257 | -! | +|||
| 53 | +
- } else if (!identical(attr(snapshot_state, "app_id"), attr(slices_global$all_slices(), "app_id"))) {
+ #' |
|||
| 258 | -! | +|||
| 54 | +
- logger::log_debug("srv_snapshot_manager: snapshot not compatible with app")
+ #' When a snapshot is uploaded, it will first be added to storage just like a newly created one, |
|||
| 259 | -! | +|||
| 55 | +
- showNotification(+ #' and then used to restore app state much like a snapshot taken from storage. |
|||
| 260 | -! | +|||
| 56 | +
- "This snapshot file is not compatible with the app and cannot be loaded.",+ #' Upon clicking the upload icon the user will be prompted for a file to upload |
|||
| 261 | -! | +|||
| 57 | +
- type = "warning"+ #' and may choose to name the new snapshot. The name defaults to the name of the file (the extension is dropped) |
|||
| 262 | +58 |
- )+ #' and normal naming rules apply. Loading the file yields a `teal_slices` object, |
||
| 263 | +59 |
- } else {
+ #' which is disassembled for storage and used directly for restoring app state. |
||
| 264 | +60 |
- # Add to snapshot history.+ #' |
||
| 265 | -! | +|||
| 61 | +
- logger::log_debug("srv_snapshot_manager: snapshot loaded, adding to history")
+ #' @section Transferring snapshots: |
|||
| 266 | -! | +|||
| 62 | +
- snapshot <- as.list(slices_global$all_slices(), recursive = TRUE)+ #' Snapshots uploaded from disk should only be used in the same application they come from, |
|||
| 267 | -! | +|||
| 63 | +
- snapshot_update <- c(snapshot_history(), list(snapshot))+ #' _i.e._ an application that uses the same data and the same modules. |
|||
| 268 | -! | +|||
| 64 | +
- names(snapshot_update)[length(snapshot_update)] <- snapshot_name+ #' To ensure this is the case, `init` stamps `teal_slices` with an app id that is stored in the `app_id` attribute of |
|||
| 269 | -! | +|||
| 65 | +
- snapshot_history(snapshot_update)+ #' a `teal_slices` object. When a snapshot is restored from file, its `app_id` is compared to that |
|||
| 270 | +66 |
- ### Begin simplified restore procedure. ###+ #' of the current app state and only if the match is the snapshot admitted to the session. |
||
| 271 | -! | +|||
| 67 | +
- logger::log_debug("srv_snapshot_manager: restoring snapshot")
+ #' |
|||
| 272 | -! | +|||
| 68 | +
- slices_global$slices_set(snapshot_state)+ #' @section Bookmarks: |
|||
| 273 | -! | +|||
| 69 | +
- removeModal()+ #' An `onBookmark` callback creates a snapshot of the current filter state. |
|||
| 274 | +70 |
- ### End simplified restore procedure. ###+ #' This is done on the app session, not the module session. |
||
| 275 | +71 |
- }+ #' (The snapshot will be retrieved by `module_teal` in order to set initial app state in a restored app.) |
||
| 276 | +72 |
- }+ #' Then that snapshot, and the previous snapshot history are dumped into the `values.rds` file in `<bookmark_dir>`. |
||
| 277 | +73 |
- })+ #' |
||
| 278 | +74 |
- # Apply newly added snapshot.+ #' @param id (`character(1)`) `shiny` module instance id. |
||
| 279 | +75 |
-
+ #' @param slices_global (`reactiveVal`) that contains a `teal_slices` object |
||
| 280 | +76 |
- # Restore initial state ----+ #' containing all `teal_slice`s existing in the app, both active and inactive. |
||
| 281 | -82x | +|||
| 77 | +
- observeEvent(input$snapshot_reset, {
+ #' |
|||
| 282 | -2x | +|||
| 78 | +
- logger::log_debug("srv_snapshot_manager: snapshot_reset button clicked, restoring snapshot")
+ #' @return `list` containing the snapshot history, where each element is an unlisted `teal_slices` object. |
|||
| 283 | -2x | +|||
| 79 | +
- s <- "Initial application state"+ #' |
|||
| 284 | +80 |
- ### Begin restore procedure. ###+ #' @name module_snapshot_manager |
||
| 285 | -2x | +|||
| 81 | +
- snapshot <- snapshot_history()[[s]]+ #' @rdname module_snapshot_manager |
|||
| 286 | +82 |
- # todo: as.teal_slices looses module-mapping if is not global+ #' |
||
| 287 | -2x | +|||
| 83 | +
- snapshot_state <- as.teal_slices(snapshot)+ #' @author Aleksander Chlebowski |
|||
| 288 | -2x | +|||
| 84 | +
- slices_global$slices_set(snapshot_state)+ #' @keywords internal |
|||
| 289 | -2x | +|||
| 85 | +
- removeModal()+ NULL |
|||
| 290 | +86 |
- ### End restore procedure. ###+ |
||
| 291 | +87 |
- })+ #' @rdname module_snapshot_manager |
||
| 292 | +88 |
-
+ ui_snapshot_manager_panel <- function(id) {
+ |
+ ||
| 89 | +! | +
+ ns <- NS(id)+ |
+ ||
| 90 | +! | +
+ tags$button(+ |
+ ||
| 91 | +! | +
+ id = ns("show_snapshot_manager"),
+ |
+ ||
| 92 | +! | +
+ class = "btn action-button wunder_bar_button",+ |
+ ||
| 93 | +! | +
+ title = "View filter mapping",+ |
+ ||
| 94 | +! | +
+ suppressMessages(icon("fas fa-camera"))
|
||
| 293 | +95 |
- # Build snapshot table ----+ ) |
||
| 294 | +96 |
- # Create UI elements and server logic for the snapshot table.+ } |
||
| 295 | +97 |
- # Observers must be tracked to avoid duplication and excess reactivity.+ |
||
| 296 | +98 |
- # Remaining elements are tracked likewise for consistency and a slight speed margin.+ #' @rdname module_snapshot_manager |
||
| 297 | -82x | +|||
| 99 | +
- observers <- reactiveValues()+ srv_snapshot_manager_panel <- function(id, slices_global) {
|
|||
| 298 | +100 | 82x |
- handlers <- reactiveValues()+ moduleServer(id, function(input, output, session) {
|
|
| 299 | +101 | 82x |
- divs <- reactiveValues()- |
- |
| 300 | -- |
-
+ logger::log_debug("srv_snapshot_manager_panel initializing")
|
||
| 301 | +102 | 82x |
- observeEvent(snapshot_history(), {
+ setBookmarkExclude(c("show_snapshot_manager"))
|
|
| 302 | -72x | +103 | +82x |
- logger::log_debug("srv_snapshot_manager: snapshot history modified, updating snapshot list")
+ observeEvent(input$show_snapshot_manager, {
|
| 303 | -72x | +|||
| 104 | +! |
- lapply(names(snapshot_history())[-1L], function(s) {
+ logger::log_debug("srv_snapshot_manager_panel@1 show_snapshot_manager button has been clicked.")
|
||
| 304 | +105 | ! |
- id_pickme <- sprintf("pickme_%s", make.names(s))
+ showModal( |
|
| 305 | +106 | ! |
- id_saveme <- sprintf("saveme_%s", make.names(s))
+ modalDialog( |
|
| 306 | +107 | ! |
- id_rowme <- sprintf("rowme_%s", make.names(s))
+ ui_snapshot_manager(session$ns("module")),
|
|
| 307 | -+ | |||
| 108 | +! |
-
+ class = "snapshot_manager_modal", |
||
| 308 | -+ | |||
| 109 | +! |
- # Observer for restoring snapshot.+ size = "m", |
||
| 309 | +110 | ! |
- if (!is.element(id_pickme, names(observers))) {
+ footer = NULL, |
|
| 310 | +111 | ! |
- observers[[id_pickme]] <- observeEvent(input[[id_pickme]], {
+ easyClose = TRUE |
|
| 311 | +112 |
- ### Begin restore procedure. ###+ ) |
||
| 312 | -! | +|||
| 113 | +
- snapshot <- snapshot_history()[[s]]- |
- |||
| 313 | -! | -
- snapshot_state <- as.teal_slices(snapshot)+ ) |
||
| 314 | +114 |
-
+ }) |
||
| 315 | -! | +|||
| 115 | +82x |
- slices_global$slices_set(snapshot_state)+ srv_snapshot_manager("module", slices_global = slices_global)
|
||
| 316 | -! | +|||
| 116 | +
- removeModal()+ }) |
|||
| 317 | +117 |
- ### End restore procedure. ###+ } |
||
| 318 | +118 |
- })+ |
||
| 319 | +119 |
- }+ #' @rdname module_snapshot_manager |
||
| 320 | +120 |
- # Create handler for downloading snapshot.+ ui_snapshot_manager <- function(id) {
|
||
| 321 | +121 | ! |
- if (!is.element(id_saveme, names(handlers))) {
+ ns <- NS(id) |
|
| 322 | +122 | ! |
- output[[id_saveme]] <- downloadHandler(+ tags$div( |
|
| 323 | +123 | ! |
- filename = function() {
+ class = "manager_content", |
|
| 324 | +124 | ! |
- sprintf("teal_snapshot_%s_%s.json", s, Sys.Date())
+ tags$div( |
|
| 325 | -+ | |||
| 125 | +! |
- },+ class = "manager_table_row", |
||
| 326 | +126 | ! |
- content = function(file) {
+ tags$span(tags$b("Snapshot manager")),
|
|
| 327 | +127 | ! |
- snapshot <- snapshot_history()[[s]]+ actionLink(ns("snapshot_add"), label = NULL, icon = icon("fas fa-camera"), title = "add snapshot"),
|
|
| 328 | +128 | ! |
- snapshot_state <- as.teal_slices(snapshot)+ actionLink(ns("snapshot_load"), label = NULL, icon = icon("fas fa-upload"), title = "upload snapshot"),
|
|
| 329 | +129 | ! |
- slices_store(tss = snapshot_state, file = file)+ actionLink(ns("snapshot_reset"), label = NULL, icon = icon("fas fa-undo"), title = "reset initial state"),
|
|
| 330 | -+ | |||
| 130 | +! |
- }+ NULL |
||
| 331 | +131 |
- )+ ), |
||
| 332 | +132 | ! |
- handlers[[id_saveme]] <- id_saveme+ uiOutput(ns("snapshot_list"))
|
|
| 333 | +133 |
- }+ ) |
||
| 334 | +134 |
- # Create a row for the snapshot table.- |
- ||
| 335 | -! | -
- if (!is.element(id_rowme, names(divs))) {
- |
- ||
| 336 | -! | -
- divs[[id_rowme]] <- tags$div(+ } |
||
| 337 | -! | +|||
| 135 | +
- class = "manager_table_row",+ |
|||
| 338 | -! | +|||
| 136 | +
- tags$span(tags$h5(s)),+ #' @rdname module_snapshot_manager |
|||
| 339 | -! | +|||
| 137 | +
- actionLink(inputId = ns(id_pickme), label = icon("far fa-circle-check"), title = "select"),
+ srv_snapshot_manager <- function(id, slices_global) {
|
|||
| 340 | -! | +|||
| 138 | +82x |
- downloadLink(outputId = ns(id_saveme), label = icon("far fa-save"), title = "save to file")
+ checkmate::assert_character(id) |
||
| 341 | +139 |
- )+ |
||
| 342 | -+ | |||
| 140 | +82x |
- }+ moduleServer(id, function(input, output, session) {
|
||
| 343 | -+ | |||
| 141 | +82x |
- })+ logger::log_debug("srv_snapshot_manager initializing")
|
||
| 344 | +142 |
- })+ |
||
| 345 | +143 |
-
+ # Set up bookmarking callbacks ---- |
||
| 346 | +144 |
- # Create table to display list of snapshots and their actions.+ # Register bookmark exclusions (all buttons and text fields). |
||
| 347 | +145 | 82x |
- output$snapshot_list <- renderUI({
- |
- |
| 348 | -72x | -
- rows <- rev(reactiveValuesToList(divs))+ setBookmarkExclude(c( |
||
| 349 | -72x | +146 | +82x |
- if (length(rows) == 0L) {
+ "snapshot_add", "snapshot_load", "snapshot_reset", |
| 350 | -72x | +147 | +82x |
- tags$div(+ "snapshot_name_accept", "snaphot_file_accept", |
| 351 | -72x | +148 | +82x |
- class = "manager_placeholder",+ "snapshot_name", "snapshot_file" |
| 352 | -72x | +|||
| 149 | +
- "Snapshots will appear here."+ )) |
|||
| 353 | +150 |
- )+ # Add snapshot history to bookmark. |
||
| 354 | -+ | |||
| 151 | +82x |
- } else {
+ session$onBookmark(function(state) {
|
||
| 355 | +152 | ! |
- rows+ logger::log_debug("srv_snapshot_manager@onBookmark: storing snapshot and bookmark history")
|
|
| 356 | -+ | |||
| 153 | +! |
- }+ state$values$snapshot_history <- snapshot_history() # isolate this? |
||
| 357 | +154 |
}) |
||
| 358 | +155 | |||
| 359 | +156 | 82x |
- snapshot_history+ ns <- session$ns |
|
| 360 | +157 |
- })+ |
||
| 361 | +158 |
- }+ # Track global filter states ---- |
| 1 | -+ | |||
| 159 | +82x |
- #' `teal` main module+ snapshot_history <- reactiveVal({
|
||
| 2 | +160 |
- #'+ # Restore directly from bookmarked state, if applicable. |
||
| 3 | -+ | |||
| 161 | +82x |
- #' @description+ restoreValue( |
||
| 4 | -+ | |||
| 162 | +82x |
- #' `r lifecycle::badge("stable")`
+ ns("snapshot_history"),
|
||
| 5 | -+ | |||
| 163 | +82x |
- #' Module to create a `teal` app. This module can be called directly instead of [init()] and+ list("Initial application state" = shiny::isolate(as.list(slices_global$all_slices(), recursive = TRUE)))
|
||
| 6 | +164 |
- #' included in your custom application. Please note that [init()] adds `reporter_previewer_module`+ ) |
||
| 7 | +165 |
- #' automatically, which is not a case when calling `ui/srv_teal` directly.+ }) |
||
| 8 | +166 |
- #'+ |
||
| 9 | +167 |
- #' @details+ # Snapshot current application state ---- |
||
| 10 | +168 |
- #'+ # Name snaphsot. |
||
| 11 | -+ | |||
| 169 | +82x |
- #' Module is responsible for creating the main `shiny` app layout and initializing all the necessary+ observeEvent(input$snapshot_add, {
|
||
| 12 | -+ | |||
| 170 | +! |
- #' components. This module establishes reactive connection between the input `data` and every other+ logger::log_debug("srv_snapshot_manager: snapshot_add button clicked")
|
||
| 13 | -+ | |||
| 171 | +! |
- #' component in the app. Reactive change of the `data` passed as an argument, reloads the app and+ showModal( |
||
| 14 | -+ | |||
| 172 | +! |
- #' possibly keeps all input settings the same so the user can continue where one left off.+ modalDialog( |
||
| 15 | -+ | |||
| 173 | +! |
- #'+ textInput(ns("snapshot_name"), "Name the snapshot", width = "100%", placeholder = "Meaningful, unique name"),
|
||
| 16 | -+ | |||
| 174 | +! |
- #' ## data flow in `teal` application+ footer = tagList( |
||
| 17 | -+ | |||
| 175 | +! |
- #'+ actionButton(ns("snapshot_name_accept"), "Accept", icon = icon("far fa-thumbs-up")),
|
||
| 18 | -+ | |||
| 176 | +! |
- #' This module supports multiple data inputs but eventually, they are all converted to `reactive`+ modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
|
||
| 19 | +177 |
- #' returning `teal_data` in this module. On this `reactive teal_data` object several actions are+ ), |
||
| 20 | -+ | |||
| 178 | +! |
- #' performed:+ size = "s" |
||
| 21 | +179 |
- #' - data loading in [`module_init_data`]+ ) |
||
| 22 | +180 |
- #' - data filtering in [`module_filter_data`]+ ) |
||
| 23 | +181 |
- #' - data transformation in [`module_transform_data`]+ }) |
||
| 24 | +182 |
- #'+ # Store snaphsot. |
||
| 25 | -+ | |||
| 183 | +82x |
- #' ## Fallback on failure+ observeEvent(input$snapshot_name_accept, {
|
||
| 26 | -+ | |||
| 184 | +! |
- #'+ logger::log_debug("srv_snapshot_manager: snapshot_name_accept button clicked")
|
||
| 27 | -+ | |||
| 185 | +! |
- #' `teal` is designed in such way that app will never crash if the error is introduced in any+ snapshot_name <- trimws(input$snapshot_name) |
||
| 28 | -+ | |||
| 186 | +! |
- #' custom `shiny` module provided by app developer (e.g. [teal_data_module()], [teal_transform_module()]).+ if (identical(snapshot_name, "")) {
|
||
| 29 | -+ | |||
| 187 | +! |
- #' If any module returns a failing object, the app will halt the evaluation and display a warning message.+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 30 | -+ | |||
| 188 | +! |
- #' App user should always have a chance to fix the improper input and continue without restarting the session.+ showNotification( |
||
| 31 | -+ | |||
| 189 | +! |
- #'+ "Please name the snapshot.", |
||
| 32 | -+ | |||
| 190 | +! |
- #' @rdname module_teal+ type = "message" |
||
| 33 | +191 |
- #' @name module_teal+ ) |
||
| 34 | -+ | |||
| 192 | +! |
- #'+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
||
| 35 | -+ | |||
| 193 | +! |
- #' @inheritParams module_init_data+ } else if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
|
||
| 36 | -+ | |||
| 194 | +! |
- #' @inheritParams init+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 37 | -+ | |||
| 195 | +! |
- #'+ showNotification( |
||
| 38 | -- |
- #' @return `NULL` invisibly- |
- ||
| 39 | -- |
- NULL- |
- ||
| 40 | -- | - - | -||
| 41 | -- |
- #' @rdname module_teal- |
- ||
| 42 | -+ | |||
| 196 | +! |
- #' @export+ "This name is in conflict with other snapshot names. Please choose a different one.", |
||
| 43 | -+ | |||
| 197 | +! |
- ui_teal <- function(id,+ type = "message" |
||
| 44 | +198 |
- modules,+ ) |
||
| 45 | -+ | |||
| 199 | +! |
- title = build_app_title(),+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
||
| 46 | +200 |
- header = tags$p(),+ } else {
|
||
| 47 | -+ | |||
| 201 | +! |
- footer = tags$p()) {
+ logger::log_debug("srv_snapshot_manager: snapshot name accepted, adding snapshot")
|
||
| 48 | +202 | ! |
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ snapshot <- as.list(slices_global$all_slices(), recursive = TRUE) |
|
| 49 | +203 | ! |
- checkmate::assert(+ snapshot_update <- c(snapshot_history(), list(snapshot)) |
|
| 50 | +204 | ! |
- .var.name = "title",+ names(snapshot_update)[length(snapshot_update)] <- snapshot_name |
|
| 51 | +205 | ! |
- checkmate::check_string(title),+ snapshot_history(snapshot_update) |
|
| 52 | +206 | ! |
- checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
+ removeModal() |
|
| 53 | +207 |
- )+ # Reopen filter manager modal by clicking button in the main application. |
||
| 54 | +208 | ! |
- checkmate::assert(+ shinyjs::click(id = "teal-wunder_bar-show_snapshot_manager", asis = TRUE) |
|
| 55 | -! | +|||
| 209 | +
- .var.name = "header",+ } |
|||
| 56 | -! | +|||
| 210 | +
- checkmate::check_string(header),+ }) |
|||
| 57 | -! | +|||
| 211 | +
- checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
+
|
|||
| 58 | +212 |
- )+ # Upload a snapshot file ---- |
||
| 59 | -! | +|||
| 213 | +
- checkmate::assert(+ # Select file. |
|||
| 60 | -! | +|||
| 214 | +82x |
- .var.name = "footer",+ observeEvent(input$snapshot_load, {
|
||
| 61 | +215 | ! |
- checkmate::check_string(footer),+ logger::log_debug("srv_snapshot_manager: snapshot_load button clicked")
|
|
| 62 | +216 | ! |
- checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
- |
- |
| 63 | -- |
- )- |
- ||
| 64 | -- |
-
+ showModal( |
||
| 65 | +217 | ! |
- if (is.character(title)) {
+ modalDialog( |
|
| 66 | +218 | ! |
- title <- build_app_title(title)- |
- |
| 67 | -- |
- } else {
+ fileInput(ns("snapshot_file"), "Choose snapshot file", accept = ".json", width = "100%"),
|
||
| 68 | +219 | ! |
- validate_app_title_tag(title)+ textInput( |
|
| 69 | -+ | |||
| 220 | +! |
- }+ ns("snapshot_name"),
|
||
| 70 | -+ | |||
| 221 | +! |
-
+ "Name the snapshot (optional)", |
||
| 71 | +222 | ! |
- if (checkmate::test_string(header)) {
+ width = "100%", |
|
| 72 | +223 | ! |
- header <- tags$p(header)+ placeholder = "Meaningful, unique name" |
|
| 73 | +224 |
- }+ ), |
||
| 74 | -+ | |||
| 225 | +! |
-
+ footer = tagList( |
||
| 75 | +226 | ! |
- if (checkmate::test_string(footer)) {
+ actionButton(ns("snaphot_file_accept"), "Accept", icon = icon("far fa-thumbs-up")),
|
|
| 76 | +227 | ! |
- footer <- tags$p(footer)+ modalButton(label = "Cancel", icon = icon("far fa-thumbs-down"))
|
|
| 77 | +228 |
- }+ ) |
||
| 78 | +229 |
-
+ ) |
||
| 79 | -! | +|||
| 230 | +
- ns <- NS(id)+ ) |
|||
| 80 | +231 |
-
+ }) |
||
| 81 | +232 |
- # show busy icon when `shiny` session is busy computing stuff+ # Store new snapshot to list and restore filter states. |
||
| 82 | -+ | |||
| 233 | +82x |
- # based on https://stackoverflow.com/questions/17325521/r-shiny-display-loading-message-while-function-is-running/22475216#22475216 # nolint: line_length.+ observeEvent(input$snaphot_file_accept, {
|
||
| 83 | +234 | ! |
- shiny_busy_message_panel <- conditionalPanel(+ logger::log_debug("srv_snapshot_manager: snapshot_file_accept button clicked")
|
|
| 84 | +235 | ! |
- condition = "(($('html').hasClass('shiny-busy')) && (document.getElementById('shiny-notification-panel') == null))", # nolint: line_length.
+ snapshot_name <- trimws(input$snapshot_name) |
|
| 85 | +236 | ! |
- tags$div(+ if (identical(snapshot_name, "")) {
|
|
| 86 | +237 | ! |
- icon("arrows-rotate", class = "fa-spin", prefer_type = "solid"),
+ logger::log_debug("srv_snapshot_manager: no snapshot name provided, naming after file")
|
|
| 87 | +238 | ! |
- "Computing ...",+ snapshot_name <- tools::file_path_sans_ext(input$snapshot_file$name) |
|
| 88 | +239 |
- # CSS defined in `custom.css`+ } |
||
| 89 | +240 | ! |
- class = "shinybusymessage"+ if (is.element(make.names(snapshot_name), make.names(names(snapshot_history())))) {
|
|
| 90 | -+ | |||
| 241 | +! |
- )+ logger::log_debug("srv_snapshot_manager: snapshot name rejected")
|
||
| 91 | -+ | |||
| 242 | +! |
- )+ showNotification( |
||
| 92 | -+ | |||
| 243 | +! |
-
+ "This name is in conflict with other snapshot names. Please choose a different one.", |
||
| 93 | +244 | ! |
- fluidPage(+ type = "message" |
|
| 94 | -! | +|||
| 245 | +
- id = id,+ ) |
|||
| 95 | +246 | ! |
- title = title,+ updateTextInput(inputId = "snapshot_name", value = "", placeholder = "Meaningful, unique name") |
|
| 96 | -! | +|||
| 247 | +
- theme = get_teal_bs_theme(),+ } else {
|
|||
| 97 | -! | +|||
| 248 | +
- include_teal_css_js(),+ # Restore snapshot and verify app compatibility. |
|||
| 98 | +249 | ! |
- tags$header(header),+ logger::log_debug("srv_snapshot_manager: snapshot name accepted, loading snapshot")
|
|
| 99 | +250 | ! |
- tags$hr(class = "my-2"),+ snapshot_state <- try(slices_restore(input$snapshot_file$datapath)) |
|
| 100 | +251 | ! |
- shiny_busy_message_panel,+ if (!inherits(snapshot_state, "modules_teal_slices")) {
|
|
| 101 | +252 | ! |
- tags$div(+ logger::log_debug("srv_snapshot_manager: snapshot file corrupt")
|
|
| 102 | +253 | ! |
- id = ns("tabpanel_wrapper"),
+ showNotification( |
|
| 103 | +254 | ! |
- class = "teal-body",+ "File appears to be corrupt.", |
|
| 104 | +255 | ! |
- ui_teal_module(id = ns("teal_modules"), modules = modules)
+ type = "error" |
|
| 105 | +256 |
- ),+ ) |
||
| 106 | +257 | ! |
- tags$div(+ } else if (!identical(attr(snapshot_state, "app_id"), attr(slices_global$all_slices(), "app_id"))) {
|
|
| 107 | +258 | ! |
- id = ns("options_buttons"),
+ logger::log_debug("srv_snapshot_manager: snapshot not compatible with app")
|
|
| 108 | +259 | ! |
- style = "position: absolute; right: 10px;",+ showNotification( |
|
| 109 | +260 | ! |
- ui_bookmark_panel(ns("bookmark_manager"), modules),
+ "This snapshot file is not compatible with the app and cannot be loaded.", |
|
| 110 | +261 | ! |
- tags$button(+ type = "warning" |
|
| 111 | -! | +|||
| 262 | +
- class = "btn action-button filter_hamburger", # see sidebar.css for style filter_hamburger+ ) |
|||
| 112 | -! | +|||
| 263 | +
- href = "javascript:void(0)",+ } else {
|
|||
| 113 | -! | +|||
| 264 | +
- onclick = sprintf("toggleFilterPanel('%s');", ns("tabpanel_wrapper")),
+ # Add to snapshot history. |
|||
| 114 | +265 | ! |
- title = "Toggle filter panel",+ logger::log_debug("srv_snapshot_manager: snapshot loaded, adding to history")
|
|
| 115 | +266 | ! |
- icon("fas fa-bars")
+ snapshot <- as.list(slices_global$all_slices(), recursive = TRUE) |
|
| 116 | -+ | |||
| 267 | +! |
- ),+ snapshot_update <- c(snapshot_history(), list(snapshot)) |
||
| 117 | +268 | ! |
- ui_snapshot_manager_panel(ns("snapshot_manager_panel")),
+ names(snapshot_update)[length(snapshot_update)] <- snapshot_name |
|
| 118 | +269 | ! |
- ui_filter_manager_panel(ns("filter_manager_panel"))
+ snapshot_history(snapshot_update) |
|
| 119 | +270 |
- ),+ ### Begin simplified restore procedure. ### |
||
| 120 | +271 | ! |
- tags$script(+ logger::log_debug("srv_snapshot_manager: restoring snapshot")
|
|
| 121 | +272 | ! |
- HTML(+ slices_global$slices_set(snapshot_state) |
|
| 122 | +273 | ! |
- sprintf(+ removeModal() |
|
| 123 | +274 |
- "- |
- ||
| 124 | -! | -
- $(document).ready(function() {
- |
- ||
| 125 | -! | -
- $('#%s').appendTo('#%s');
+ ### End simplified restore procedure. ### |
||
| 126 | +275 |
- });+ } |
||
| 127 | +276 |
- ",- |
- ||
| 128 | -! | -
- ns("options_buttons"),
+ } |
||
| 129 | -! | +|||
| 277 | +
- ns("teal_modules-active_tab")
+ }) |
|||
| 130 | +278 |
- )+ # Apply newly added snapshot. |
||
| 131 | +279 |
- )+ |
||
| 132 | +280 |
- ),+ # Restore initial state ---- |
||
| 133 | -! | +|||
| 281 | +82x |
- tags$hr(),+ observeEvent(input$snapshot_reset, {
|
||
| 134 | -! | +|||
| 282 | +2x |
- tags$footer(+ logger::log_debug("srv_snapshot_manager: snapshot_reset button clicked, restoring snapshot")
|
||
| 135 | -! | +|||
| 283 | +2x |
- tags$div(+ s <- "Initial application state" |
||
| 136 | -! | +|||
| 284 | +
- footer,+ ### Begin restore procedure. ### |
|||
| 137 | -! | +|||
| 285 | +2x |
- teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
+ snapshot <- snapshot_history()[[s]] |
||
| 138 | -! | +|||
| 286 | +
- br(),+ # todo: as.teal_slices looses module-mapping if is not global |
|||
| 139 | -! | +|||
| 287 | +2x |
- ui_teal_lockfile(ns("lockfile")),
+ snapshot_state <- as.teal_slices(snapshot) |
||
| 140 | -! | +|||
| 288 | +2x |
- textOutput(ns("identifier"))
+ slices_global$slices_set(snapshot_state) |
||
| 141 | -+ | |||
| 289 | +2x |
- )+ removeModal() |
||
| 142 | +290 |
- )+ ### End restore procedure. ### |
||
| 143 | +291 |
- )+ }) |
||
| 144 | +292 |
- }+ |
||
| 145 | +293 |
-
+ # Build snapshot table ---- |
||
| 146 | +294 |
- #' @rdname module_teal+ # Create UI elements and server logic for the snapshot table. |
||
| 147 | +295 |
- #' @export+ # Observers must be tracked to avoid duplication and excess reactivity. |
||
| 148 | +296 |
- srv_teal <- function(id, data, modules, filter = teal_slices()) {
- |
- ||
| 149 | -84x | -
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ # Remaining elements are tracked likewise for consistency and a slight speed margin. |
||
| 150 | -84x | +297 | +82x |
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
+ observers <- reactiveValues() |
| 151 | -83x | +298 | +82x |
- checkmate::assert_class(modules, "teal_modules")+ handlers <- reactiveValues() |
| 152 | -83x | +299 | +82x |
- checkmate::assert_class(filter, "teal_slices")+ divs <- reactiveValues() |
| 153 | +300 | |||
| 154 | -83x | +301 | +82x |
- moduleServer(id, function(input, output, session) {
+ observeEvent(snapshot_history(), {
|
| 155 | -83x | +302 | +72x |
- logger::log_debug("srv_teal initializing.")
+ logger::log_debug("srv_snapshot_manager: snapshot history modified, updating snapshot list")
|
| 156 | -+ | |||
| 303 | +72x |
-
+ lapply(names(snapshot_history())[-1L], function(s) {
|
||
| 157 | -83x | +|||
| 304 | +! |
- if (getOption("teal.show_js_log", default = FALSE)) {
+ id_pickme <- sprintf("pickme_%s", make.names(s))
|
||
| 158 | +305 | ! |
- shinyjs::showLog()+ id_saveme <- sprintf("saveme_%s", make.names(s))
|
|
| 159 | -+ | |||
| 306 | +! |
- }+ id_rowme <- sprintf("rowme_%s", make.names(s))
|
||
| 160 | +307 | |||
| 161 | -83x | -
- srv_teal_lockfile("lockfile")
- |
- ||
| 162 | +308 |
-
+ # Observer for restoring snapshot. |
||
| 163 | -83x | +|||
| 309 | +! |
- output$identifier <- renderText(+ if (!is.element(id_pickme, names(observers))) {
|
||
| 164 | -83x | +|||
| 310 | +! |
- paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
+ observers[[id_pickme]] <- observeEvent(input[[id_pickme]], {
|
||
| 165 | +311 |
- )+ ### Begin restore procedure. ### |
||
| 166 | -+ | |||
| 312 | +! |
-
+ snapshot <- snapshot_history()[[s]] |
||
| 167 | -83x | +|||
| 313 | +! |
- teal.widgets::verbatim_popup_srv(+ snapshot_state <- as.teal_slices(snapshot) |
||
| 168 | -83x | +|||
| 314 | +
- "sessionInfo",+ |
|||
| 169 | -83x | +|||
| 315 | +! |
- verbatim_content = utils::capture.output(utils::sessionInfo()),+ slices_global$slices_set(snapshot_state) |
||
| 170 | -83x | +|||
| 316 | +! |
- title = "SessionInfo"+ removeModal() |
||
| 171 | +317 |
- )+ ### End restore procedure. ### |
||
| 172 | +318 |
-
+ }) |
||
| 173 | +319 |
- # `JavaScript` code+ } |
||
| 174 | -83x | +|||
| 320 | +
- run_js_files(files = "init.js")+ # Create handler for downloading snapshot. |
|||
| 175 | -+ | |||
| 321 | +! |
-
+ if (!is.element(id_saveme, names(handlers))) {
|
||
| 176 | -+ | |||
| 322 | +! |
- # set timezone in shiny app+ output[[id_saveme]] <- downloadHandler( |
||
| 177 | -+ | |||
| 323 | +! |
- # timezone is set in the early beginning so it will be available also+ filename = function() {
+ |
+ ||
| 324 | +! | +
+ sprintf("teal_snapshot_%s_%s.json", s, Sys.Date())
|
||
| 178 | +325 |
- # for `DDL` and all shiny modules+ }, |
||
| 179 | -83x | +|||
| 326 | +! |
- get_client_timezone(session$ns)+ content = function(file) {
|
||
| 180 | -83x | +|||
| 327 | +! |
- observeEvent(+ snapshot <- snapshot_history()[[s]] |
||
| 181 | -83x | +|||
| 328 | +! |
- eventExpr = input$timezone,+ snapshot_state <- as.teal_slices(snapshot) |
||
| 182 | -83x | +|||
| 329 | +! |
- once = TRUE,+ slices_store(tss = snapshot_state, file = file) |
||
| 183 | -83x | +|||
| 330 | +
- handlerExpr = {
+ } |
|||
| 184 | -! | +|||
| 331 | +
- session$userData$timezone <- input$timezone+ ) |
|||
| 185 | +332 | ! |
- logger::log_debug("srv_teal@1 Timezone set to client's timezone: { input$timezone }.")
+ handlers[[id_saveme]] <- id_saveme |
|
| 186 | +333 |
- }+ } |
||
| 187 | +334 |
- )+ # Create a row for the snapshot table. |
||
| 188 | -+ | |||
| 335 | +! |
-
+ if (!is.element(id_rowme, names(divs))) {
|
||
| 189 | -83x | +|||
| 336 | +! |
- data_pulled <- srv_init_data("data", data = data)
+ divs[[id_rowme]] <- tags$div( |
||
| 190 | -82x | +|||
| 337 | +! |
- data_validated <- srv_validate_reactive_teal_data(+ class = "manager_table_row", |
||
| 191 | -82x | +|||
| 338 | +! |
- "validate",+ tags$span(tags$h5(s)), |
||
| 192 | -82x | +|||
| 339 | +! |
- data = data_pulled,+ actionLink(inputId = ns(id_pickme), label = icon("far fa-circle-check"), title = "select"),
|
||
| 193 | -82x | +|||
| 340 | +! |
- modules = modules,+ downloadLink(outputId = ns(id_saveme), label = icon("far fa-save"), title = "save to file")
|
||
| 194 | -82x | +|||
| 341 | +
- validate_shiny_silent_error = FALSE+ ) |
|||
| 195 | +342 |
- )+ } |
||
| 196 | -82x | +|||
| 343 | +
- data_rv <- reactive({
+ }) |
|||
| 197 | -142x | +|||
| 344 | +
- req(inherits(data_validated(), "teal_data"))+ })+ |
+ |||
| 345 | ++ | + + | +||
| 346 | ++ |
+ # Create table to display list of snapshots and their actions. |
||
| 198 | -70x | +347 | +82x |
- is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data_validated())))+ output$snapshot_list <- renderUI({
|
| 199 | -70x | +348 | +72x |
- if (!isTRUE(is_filter_ok)) {
+ rows <- rev(reactiveValuesToList(divs)) |
| 200 | -2x | +349 | +72x |
- showNotification(+ if (length(rows) == 0L) {
|
| 201 | -2x | +350 | +72x |
- "Some filters were not applied because of incompatibility with data. Contact app developer.",+ tags$div( |
| 202 | -2x | +351 | +72x |
- type = "warning",+ class = "manager_placeholder", |
| 203 | -2x | +352 | +72x |
- duration = 10+ "Snapshots will appear here." |
| 204 | +353 |
) |
||
| 205 | -2x | +|||
| 354 | +
- warning(is_filter_ok)+ } else {
|
|||
| 206 | -+ | |||
| 355 | +! |
- }+ rows |
||
| 207 | -70x | +|||
| 356 | +
- .add_signature_to_data(data_validated())+ } |
|||
| 208 | +357 |
}) |
||
| 209 | +358 | |||
| 210 | +359 | 82x |
- data_load_status <- reactive({
- |
- |
| 211 | -75x | -
- if (inherits(data_pulled(), "teal_data")) {
- |
- ||
| 212 | -70x | -
- "ok"+ snapshot_history |
||
| 213 | +360 |
- # todo: should we hide warnings on top for a data?- |
- ||
| 214 | -5x | -
- } else if (inherits(data, "teal_data_module")) {
- |
- ||
| 215 | -5x | -
- "teal_data_module failed"+ }) |
||
| 216 | +361 |
- } else {
- |
- ||
| 217 | -! | -
- "external failed"+ } |
| 218 | +1 |
- }+ #' Data summary |
|
| 219 | +2 |
- })+ #' @description |
|
| 220 | +3 | - - | -|
| 221 | -82x | -
- datasets_rv <- if (!isTRUE(attr(filter, "module_specific"))) {
- |
- |
| 222 | -71x | -
- eventReactive(data_rv(), {
- |
- |
| 223 | -61x | -
- req(inherits(data_rv(), "teal_data"))- |
- |
| 224 | -61x | -
- logger::log_debug("srv_teal@1 initializing FilteredData")
- |
- |
| 225 | -61x | -
- teal_data_to_filtered_data(data_rv())+ #' Module and its utils to display the number of rows and subjects in the filtered and unfiltered data. |
|
| 226 | +4 |
- })+ #' |
|
| 227 | +5 |
- }+ #' @details Handling different data classes: |
|
| 228 | +6 | - - | -|
| 229 | -82x | -
- if (inherits(data, "teal_data_module")) {
- |
- |
| 230 | -9x | -
- setBookmarkExclude(c("teal_modules-active_tab"))
- |
- |
| 231 | -9x | -
- shiny::insertTab(- |
- |
| 232 | -9x | -
- inputId = "teal_modules-active_tab",- |
- |
| 233 | -9x | -
- position = "before",- |
- |
| 234 | -9x | -
- select = TRUE,- |
- |
| 235 | -9x | -
- tabPanel(- |
- |
| 236 | -9x | -
- title = icon("fas fa-database"),
- |
- |
| 237 | -9x | -
- value = "teal_data_module",- |
- |
| 238 | -9x | -
- tags$div(- |
- |
| 239 | -9x | -
- ui_init_data(session$ns("data")),
- |
- |
| 240 | -9x | -
- ui_validate_reactive_teal_data(session$ns("validate"))
+ #' `get_filter_overview()` is a pseudo S3 method which has variants for: |
|
| 241 | +7 |
- )+ #' - `array` (`data.frame`, `DataFrame`, `array`, `Matrix` and `SummarizedExperiment`): Method variant |
|
| 242 | +8 |
- )+ #' can be applied to any two-dimensional objects on which [ncol()] can be used. |
|
| 243 | +9 |
- )+ #' - `MultiAssayExperiment`: for which summary contains counts for `colData` and all `experiments`. |
|
| 244 | +10 | - - | -|
| 245 | -9x | -
- if (attr(data, "once")) {
- |
- |
| 246 | -9x | -
- observeEvent(data_rv(), once = TRUE, {
- |
- |
| 247 | -4x | -
- logger::log_debug("srv_teal@2 removing data tab.")
+ #' - For other data types module displays data name with warning icon and no more details. |
|
| 248 | +11 |
- # when once = TRUE we pull data once and then remove data tab+ #' |
|
| 249 | -4x | +||
| 12 | +
- removeTab("teal_modules-active_tab", target = "teal_data_module")
+ #' Module includes also "Show/Hide unsupported" button to toggle rows of the summary table |
||
| 250 | +13 |
- })+ #' containing datasets where number of observations are not calculated. |
|
| 251 | +14 |
- }+ #' |
|
| 252 | +15 |
- } else {
+ #' @param id (`character(1)`) `shiny` module instance id. |
|
| 253 | +16 |
- # when no teal_data_module then we want to display messages above tabsetPanel (because there is no data-tab)+ #' @param teal_data (`reactive` returning `teal_data`) |
|
| 254 | -73x | +||
| 17 | +
- insertUI(+ #' |
||
| 255 | -73x | +||
| 18 | +
- selector = sprintf("#%s", session$ns("tabpanel_wrapper")),
+ #' @name module_data_summary |
||
| 256 | -73x | +||
| 19 | +
- where = "beforeBegin",+ #' @rdname module_data_summary |
||
| 257 | -73x | +||
| 20 | +
- ui = tags$div(ui_validate_reactive_teal_data(session$ns("validate")), tags$br())
+ #' @keywords internal |
||
| 258 | +21 |
- )+ #' @return `NULL`. |
|
| 259 | +22 |
- }+ NULL |
|
| 260 | +23 | ||
| 261 | -82x | -
- module_labels <- unlist(module_labels(modules), use.names = FALSE)- |
- |
| 262 | -82x | -
- slices_global <- methods::new(".slicesGlobal", filter, module_labels)
- |
- |
| 263 | -82x | -
- modules_output <- srv_teal_module(- |
- |
| 264 | -82x | -
- id = "teal_modules",- |
- |
| 265 | -82x | +||
| 24 | +
- data_rv = data_rv,+ #' @rdname module_data_summary |
||
| 266 | -82x | +||
| 25 | +
- datasets = datasets_rv,+ ui_data_summary <- function(id) {
|
||
| 267 | -82x | +||
| 26 | +! |
- modules = modules,+ ns <- NS(id) |
|
| 268 | -82x | +||
| 27 | +! |
- slices_global = slices_global,+ content_id <- ns("filters_overview_contents")
|
|
| 269 | -82x | +||
| 28 | +! |
- data_load_status = data_load_status+ tags$div( |
|
| 270 | -+ | ||
| 29 | +! |
- )+ id = id, |
|
| 271 | -82x | +||
| 30 | +! |
- mapping_table <- srv_filter_manager_panel("filter_manager_panel", slices_global = slices_global)
+ class = "well", |
|
| 272 | -82x | +||
| 31 | +! |
- snapshots <- srv_snapshot_manager_panel("snapshot_manager_panel", slices_global = slices_global)
+ tags$div( |
|
| 273 | -82x | +||
| 32 | +! |
- srv_bookmark_panel("bookmark_manager", modules)
+ class = "row", |
|
| 274 | -+ | ||
| 33 | +! |
- })+ tags$div( |
|
| 275 | -+ | ||
| 34 | +! |
-
+ class = "col-sm-9", |
|
| 276 | -82x | +||
| 35 | +! |
- invisible(NULL)+ tags$label("Active Filter Summary", class = "text-primary mb-4")
|
|
| 277 | +36 |
- }+ ), |
| 1 | -+ | |||
| 37 | +! |
- # This is the main function from teal to be used by the end-users. Although it delegates+ tags$div( |
||
| 2 | -+ | |||
| 38 | +! |
- # directly to `module_teal_with_splash.R`, we keep it in a separate file because its documentation is quite large+ class = "col-sm-3", |
||
| 3 | -+ | |||
| 39 | +! |
- # and it is very end-user oriented. It may also perform more argument checking with more informative+ tags$i( |
||
| 4 | -+ | |||
| 40 | +! |
- # error messages.+ class = "remove pull-right fa fa-angle-down", |
||
| 5 | -+ | |||
| 41 | +! |
-
+ style = "cursor: pointer;", |
||
| 6 | -+ | |||
| 42 | +! |
- #' Create the server and UI function for the `shiny` app+ title = "fold/expand data summary panel", |
||
| 7 | -+ | |||
| 43 | +! |
- #'+ onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", content_id)
|
||
| 8 | +44 |
- #' @description `r lifecycle::badge("stable")`
+ ) |
||
| 9 | +45 |
- #'+ ) |
||
| 10 | +46 |
- #' End-users: This is the most important function for you to start a+ ), |
||
| 11 | -+ | |||
| 47 | +! |
- #' `teal` app that is composed of `teal` modules.+ tags$div( |
||
| 12 | -+ | |||
| 48 | +! |
- #'+ id = content_id, |
||
| 13 | -+ | |||
| 49 | +! |
- #' @param data (`teal_data` or `teal_data_module`)+ tags$div( |
||
| 14 | -+ | |||
| 50 | +! |
- #' For constructing the data object, refer to [teal_data()] and [teal_data_module()].+ class = "teal_active_summary_filter_panel", |
||
| 15 | -+ | |||
| 51 | +! |
- #' If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used.+ tableOutput(ns("table"))
|
||
| 16 | +52 |
- #' @param modules (`list` or `teal_modules` or `teal_module`)+ ) |
||
| 17 | +53 |
- #' Nested list of `teal_modules` or `teal_module` objects or a single+ ) |
||
| 18 | +54 |
- #' `teal_modules` or `teal_module` object. These are the specific output modules which+ ) |
||
| 19 | +55 |
- #' will be displayed in the `teal` application. See [modules()] and [module()] for+ } |
||
| 20 | +56 |
- #' more details.+ |
||
| 21 | +57 |
- #' @param filter (`teal_slices`) Optionally,+ #' @rdname module_data_summary |
||
| 22 | +58 |
- #' specifies the initial filter using [teal_slices()].+ srv_data_summary <- function(id, teal_data) {
|
||
| 23 | -+ | |||
| 59 | +81x |
- #' @param title (`shiny.tag` or `character(1)`) Optionally,+ assert_reactive(teal_data) |
||
| 24 | -+ | |||
| 60 | +81x |
- #' the browser window title. Defaults to a title "teal app" with the icon of NEST.+ moduleServer( |
||
| 25 | -+ | |||
| 61 | +81x |
- #' Can be created using the `build_app_title()` or+ id = id, |
||
| 26 | -+ | |||
| 62 | +81x |
- #' by passing a valid `shiny.tag` which is a head tag with title and link tag.+ function(input, output, session) {
|
||
| 27 | -+ | |||
| 63 | +81x |
- #' @param header (`shiny.tag` or `character(1)`) Optionally,+ logger::log_debug("srv_data_summary initializing")
|
||
| 28 | +64 |
- #' the header of the app.+ |
||
| 29 | -+ | |||
| 65 | +81x |
- #' @param footer (`shiny.tag` or `character(1)`) Optionally,+ summary_table <- reactive({
|
||
| 30 | -+ | |||
| 66 | +89x |
- #' the footer of the app.+ req(inherits(teal_data(), "teal_data")) |
||
| 31 | -+ | |||
| 67 | +83x |
- #' @param id (`character`) Optionally,+ if (!length(teal_data())) {
|
||
| 32 | -+ | |||
| 68 | +2x |
- #' a string specifying the `shiny` module id in cases it is used as a `shiny` module+ return(NULL) |
||
| 33 | +69 |
- #' rather than a standalone `shiny` app. This is a legacy feature.+ } |
||
| 34 | -+ | |||
| 70 | +81x |
- #' @param landing_popup (`teal_module_landing`) Optionally,+ get_filter_overview_wrapper(teal_data) |
||
| 35 | +71 |
- #' a `landing_popup_module` to show up as soon as the teal app is initialized.+ }) |
||
| 36 | +72 |
- #'+ |
||
| 37 | -+ | |||
| 73 | +81x |
- #' @return Named list containing server and UI functions.+ output$table <- renderUI({
|
||
| 38 | -+ | |||
| 74 | +89x |
- #'+ summary_table_out <- try(summary_table(), silent = TRUE) |
||
| 39 | -+ | |||
| 75 | +89x |
- #' @export+ if (inherits(summary_table_out, "try-error")) {
|
||
| 40 | +76 |
- #'+ # Ignore silent shiny error |
||
| 41 | -+ | |||
| 77 | +6x |
- #' @include modules.R+ if (!inherits(attr(summary_table_out, "condition"), "shiny.silent.error")) {
|
||
| 42 | -+ | |||
| 78 | +! |
- #'+ stop("Error occurred during data processing. See details in the main panel.")
|
||
| 43 | +79 |
- #' @examples+ } |
||
| 44 | -+ | |||
| 80 | +83x |
- #' app <- init(+ } else if (is.null(summary_table_out)) {
|
||
| 45 | -+ | |||
| 81 | +2x |
- #' data = within(+ "no datasets to show" |
||
| 46 | +82 |
- #' teal_data(),+ } else {
|
||
| 47 | -+ | |||
| 83 | +81x |
- #' {
+ is_unsupported <- apply(summary_table(), 1, function(x) all(is.na(x[-1]))) |
||
| 48 | -+ | |||
| 84 | +81x |
- #' new_iris <- transform(iris, id = seq_len(nrow(iris)))+ summary_table_out[is.na(summary_table_out)] <- "" |
||
| 49 | -+ | |||
| 85 | +81x |
- #' new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))+ body_html <- apply( |
||
| 50 | -+ | |||
| 86 | +81x |
- #' }+ summary_table_out, |
||
| 51 | -+ | |||
| 87 | +81x |
- #' ),+ 1, |
||
| 52 | -+ | |||
| 88 | +81x |
- #' modules = modules(+ function(x) {
|
||
| 53 | -+ | |||
| 89 | +154x |
- #' module(+ is_supported <- !all(x[-1] == "") |
||
| 54 | -+ | |||
| 90 | +154x |
- #' label = "data source",+ if (is_supported) {
|
||
| 55 | -+ | |||
| 91 | +147x |
- #' server = function(input, output, session, data) {},
+ tags$tr( |
||
| 56 | -+ | |||
| 92 | +147x |
- #' ui = function(id, ...) tags$div(p("information about data source")),
+ tagList( |
||
| 57 | -+ | |||
| 93 | +147x |
- #' datanames = "all"+ tags$td(x[1]), |
||
| 58 | -+ | |||
| 94 | +147x |
- #' ),+ lapply(x[-1], tags$td) |
||
| 59 | +95 |
- #' example_module(label = "example teal module"),+ ) |
||
| 60 | +96 |
- #' module(+ ) |
||
| 61 | +97 |
- #' "Iris Sepal.Length histogram",+ } |
||
| 62 | +98 |
- #' server = function(input, output, session, data) {
+ } |
||
| 63 | +99 |
- #' output$hist <- renderPlot(+ ) |
||
| 64 | +100 |
- #' hist(data()[["new_iris"]]$Sepal.Length)+ |
||
| 65 | -+ | |||
| 101 | +81x |
- #' )+ header_labels <- tools::toTitleCase(names(summary_table_out)) |
||
| 66 | -+ | |||
| 102 | +81x |
- #' },+ header_labels[header_labels == "Dataname"] <- "Data Name" |
||
| 67 | -+ | |||
| 103 | +81x |
- #' ui = function(id, ...) {
+ header_html <- tags$tr(tagList(lapply(header_labels, tags$td))) |
||
| 68 | +104 |
- #' ns <- NS(id)+ |
||
| 69 | -+ | |||
| 105 | +81x |
- #' plotOutput(ns("hist"))
+ table_html <- tags$table( |
||
| 70 | -+ | |||
| 106 | +81x |
- #' },+ class = "table custom-table", |
||
| 71 | -+ | |||
| 107 | +81x |
- #' datanames = "new_iris"+ tags$thead(header_html), |
||
| 72 | -+ | |||
| 108 | +81x |
- #' )+ tags$tbody(body_html) |
||
| 73 | +109 |
- #' ),+ ) |
||
| 74 | -+ | |||
| 110 | +81x |
- #' filter = teal_slices(+ div( |
||
| 75 | -+ | |||
| 111 | +81x |
- #' teal_slice(dataname = "new_iris", varname = "Species"),+ table_html, |
||
| 76 | -+ | |||
| 112 | +81x |
- #' teal_slice(dataname = "new_iris", varname = "Sepal.Length"),+ if (any(is_unsupported)) {
|
||
| 77 | -+ | |||
| 113 | +7x |
- #' teal_slice(dataname = "new_mtcars", varname = "cyl"),+ p( |
||
| 78 | -+ | |||
| 114 | +7x |
- #' exclude_varnames = list(new_iris = c("Sepal.Width", "Petal.Width")),
+ class = c("pull-right", "float-right", "text-secondary"),
|
||
| 79 | -+ | |||
| 115 | +7x |
- #' module_specific = TRUE,+ style = "font-size: 0.8em;", |
||
| 80 | -+ | |||
| 116 | +7x |
- #' mapping = list(+ sprintf("And %s more unfilterable object(s)", sum(is_unsupported)),
|
||
| 81 | -+ | |||
| 117 | +7x |
- #' `example teal module` = "new_iris Species",+ icon( |
||
| 82 | -+ | |||
| 118 | +7x |
- #' `Iris Sepal.Length histogram` = "new_iris Species",+ name = "far fa-circle-question", |
||
| 83 | -+ | |||
| 119 | +7x |
- #' global_filters = "new_mtcars cyl"+ title = paste( |
||
| 84 | -+ | |||
| 120 | +7x |
- #' )+ sep = "", |
||
| 85 | -+ | |||
| 121 | +7x |
- #' ),+ collapse = "\n", |
||
| 86 | -+ | |||
| 122 | +7x |
- #' title = "App title",+ shQuote(summary_table()[is_unsupported, "dataname"]), |
||
| 87 | +123 |
- #' header = tags$h1("Sample App"),
+ " (",
|
||
| 88 | -+ | |||
| 124 | +7x |
- #' footer = tags$p("Sample footer")
+ vapply( |
||
| 89 | -+ | |||
| 125 | +7x |
- #' )+ summary_table()[is_unsupported, "dataname"], |
||
| 90 | -+ | |||
| 126 | +7x |
- #' if (interactive()) {
+ function(x) class(teal_data()[[x]])[1], |
||
| 91 | -+ | |||
| 127 | +7x |
- #' shinyApp(app$ui, app$server)+ character(1L) |
||
| 92 | +128 |
- #' }+ ), |
||
| 93 | +129 |
- #'+ ")" |
||
| 94 | +130 |
- init <- function(data,+ ) |
||
| 95 | +131 |
- modules,+ ) |
||
| 96 | +132 |
- filter = teal_slices(),+ ) |
||
| 97 | +133 |
- title = build_app_title(),+ } |
||
| 98 | +134 |
- header = tags$p(),+ ) |
||
| 99 | +135 |
- footer = tags$p(),+ } |
||
| 100 | +136 |
- id = character(0),+ }) |
||
| 101 | +137 |
- landing_popup = NULL) {
+
|
||
| 102 | -12x | +138 | +81x |
- logger::log_debug("init initializing teal app with: data ('{ class(data) }').")
+ NULL |
| 103 | +139 |
-
+ } |
||
| 104 | +140 |
- # argument checking (independent)+ ) |
||
| 105 | +141 |
- ## `data`- |
- ||
| 106 | -12x | -
- if (inherits(data, "TealData")) {
- |
- ||
| 107 | -! | -
- lifecycle::deprecate_stop(- |
- ||
| 108 | -! | -
- when = "0.15.0",- |
- ||
| 109 | -! | -
- what = "init(data)",- |
- ||
| 110 | -! | -
- paste(- |
- ||
| 111 | -! | -
- "TealData is no longer supported. Use teal_data() instead.",+ } |
||
| 112 | -! | +|||
| 142 | +
- "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/988."+ |
|||
| 113 | +143 |
- )+ #' @rdname module_data_summary |
||
| 114 | +144 |
- )+ get_filter_overview_wrapper <- function(teal_data) {
|
||
| 115 | +145 |
- }+ # Sort datanames in topological order |
||
| 116 | -12x | +146 | +81x |
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module"))
+ datanames <- names(teal_data()) |
| 117 | -12x | +147 | +81x |
- checkmate::assert_class(landing_popup, "teal_module_landing", null.ok = TRUE)+ joinkeys <- teal.data::join_keys(teal_data()) |
| 118 | +148 | |||
| 119 | -- |
- ## `modules`- |
- ||
| 120 | -12x | +149 | +81x |
- checkmate::assert(+ current_data_objs <- sapply( |
| 121 | -12x | +150 | +81x |
- .var.name = "modules",+ datanames, |
| 122 | -12x | +151 | +81x |
- checkmate::check_multi_class(modules, c("teal_modules", "teal_module")),
+ function(name) teal.code::get_var(teal_data(), name), |
| 123 | -12x | +152 | +81x |
- checkmate::check_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))
+ simplify = FALSE |
| 124 | +153 |
) |
||
| 125 | -12x | +154 | +81x |
- if (inherits(modules, "teal_module")) {
+ initial_data_objs <- teal.code::get_var(teal_data(), ".raw_data")+ |
+
| 155 | ++ | + | ||
| 126 | -1x | +156 | +81x |
- modules <- list(modules)+ out <- lapply( |
| 127 | -+ | |||
| 157 | +81x |
- }+ datanames, |
||
| 128 | -12x | +158 | +81x |
- if (checkmate::test_list(modules, min.len = 1, any.missing = FALSE, types = c("teal_module", "teal_modules"))) {
+ function(dataname) {
|
| 129 | -6x | +159 | +149x |
- modules <- do.call(teal::modules, modules)+ parent <- teal.data::parent(joinkeys, dataname) |
| 130 | +160 |
- }+ # todo: what should we display for a parent dataset? |
||
| 131 | +161 |
-
+ # - Obs and Subjects |
||
| 132 | +162 |
- ## `filter`+ # - Obs only |
||
| 133 | -12x | +|||
| 163 | +
- checkmate::assert_class(filter, "teal_slices")+ # - Subjects only |
|||
| 134 | +164 |
-
+ # todo (for later): summary table should be displayed in a way that child datasets |
||
| 135 | +165 |
- ## all other arguments+ # are indented under their parent dataset to form a tree structure |
||
| 136 | -11x | +166 | +149x |
- checkmate::assert(+ subject_keys <- if (length(parent) > 0) {
|
| 137 | -11x | +167 | +7x |
- .var.name = "title",+ names(joinkeys[dataname, parent]) |
| 138 | -11x | +|||
| 168 | +
- checkmate::check_string(title),+ } else {
|
|||
| 139 | -11x | +169 | +142x |
- checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
+ joinkeys[dataname, dataname] |
| 140 | +170 |
- )+ } |
||
| 141 | -11x | +171 | +149x |
- checkmate::assert(+ get_filter_overview( |
| 142 | -11x | +172 | +149x |
- .var.name = "header",+ current_data = current_data_objs[[dataname]], |
| 143 | -11x | +173 | +149x |
- checkmate::check_string(header),+ initial_data = initial_data_objs[[dataname]], |
| 144 | -11x | +174 | +149x |
- checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
+ dataname = dataname,+ |
+
| 175 | +149x | +
+ subject_keys = subject_keys |
||
| 145 | +176 |
- )+ ) |
||
| 146 | -11x | +|||
| 177 | +
- checkmate::assert(+ } |
|||
| 147 | -11x | +|||
| 178 | +
- .var.name = "footer",+ ) |
|||
| 148 | -11x | +|||
| 179 | +
- checkmate::check_string(footer),+ |
|||
| 149 | -11x | +180 | +81x |
- checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
+ do.call(.smart_rbind, out) |
| 150 | +181 |
- )+ } |
||
| 151 | -11x | +|||
| 182 | +
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ |
|||
| 152 | +183 | |||
| 153 | +184 |
- # log+ #' @rdname module_data_summary |
||
| 154 | -11x | +|||
| 185 | +
- teal.logger::log_system_info()+ #' @param current_data (`object`) current object (after filtering and transforming). |
|||
| 155 | +186 |
-
+ #' @param initial_data (`object`) initial object. |
||
| 156 | +187 |
- # argument transformations+ #' @param dataname (`character(1)`) |
||
| 157 | +188 |
- ## `modules` - landing module+ #' @param subject_keys (`character`) names of the columns which determine a single unique subjects+ |
+ ||
| 189 | ++ |
+ get_filter_overview <- function(current_data, initial_data, dataname, subject_keys) {
|
||
| 158 | -11x | +190 | +154x |
- landing <- extract_module(modules, "teal_module_landing")+ if (inherits(current_data, c("data.frame", "DataFrame", "array", "Matrix", "SummarizedExperiment"))) {
|
| 159 | -11x | +191 | +146x |
- if (length(landing) == 1L) {
+ get_filter_overview_array(current_data, initial_data, dataname, subject_keys) |
| 160 | -! | +|||
| 192 | +8x |
- landing_popup <- landing[[1L]]+ } else if (inherits(current_data, "MultiAssayExperiment")) {
|
||
| 161 | -! | +|||
| 193 | +1x |
- modules <- drop_module(modules, "teal_module_landing")+ get_filter_overview_MultiAssayExperiment(current_data, initial_data, dataname) |
||
| 162 | -! | +|||
| 194 | +
- lifecycle::deprecate_soft(+ } else {
|
|||
| 163 | -! | +|||
| 195 | +7x |
- when = "0.15.3",+ data.frame(dataname = dataname) |
||
| 164 | -! | +|||
| 196 | +
- what = "landing_popup_module()",+ } |
|||
| 165 | -! | +|||
| 197 | +
- details = paste(+ } |
|||
| 166 | -! | +|||
| 198 | +
- "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ",+ |
|||
| 167 | -! | +|||
| 199 | +
- "instead of wrapping it into `modules()` and passing to the `modules` argument"+ #' @rdname module_data_summary |
|||
| 168 | +200 |
- )+ get_filter_overview_array <- function(current_data, |
||
| 169 | +201 | ++ |
+ initial_data,+ |
+ |
| 202 | ++ |
+ dataname,+ |
+ ||
| 203 |
- )+ subject_keys) {
+ |
+ |||
| 204 | +146x | +
+ if (length(subject_keys) == 0) {
|
||
| 170 | -11x | +205 | +133x |
- } else if (length(landing) > 1L) {
+ data.frame( |
| 171 | -! | +|||
| 206 | +133x |
- stop("Only one `landing_popup_module` can be used.")
+ dataname = dataname, |
||
| 172 | -+ | |||
| 207 | +133x |
- }+ obs = if (!is.null(initial_data)) {
|
||
| 173 | -+ | |||
| 208 | +124x |
-
+ sprintf("%s/%s", nrow(current_data), nrow(initial_data))
|
||
| 174 | +209 |
- ## `filter` - set app_id attribute unless present (when restoring bookmark)+ } else {
|
||
| 175 | -11x | +210 | +9x |
- if (is.null(attr(filter, "app_id", exact = TRUE))) attr(filter, "app_id") <- create_app_id(data, modules)+ nrow(current_data) |
| 176 | +211 |
-
+ } |
||
| 177 | +212 |
- ## `filter` - convert teal.slice::teal_slices to teal::teal_slices+ ) |
||
| 178 | -11x | +|||
| 213 | +
- filter <- as.teal_slices(as.list(filter))+ } else {
|
|||
| 179 | -+ | |||
| 214 | +13x |
-
+ data.frame( |
||
| 180 | -+ | |||
| 215 | +13x |
- # argument checking (interdependent)+ dataname = dataname, |
||
| 181 | -+ | |||
| 216 | +13x |
- ## `filter` - `modules`+ obs = if (!is.null(initial_data)) {
|
||
| 182 | -11x | +217 | +13x |
- if (isTRUE(attr(filter, "module_specific"))) {
+ sprintf("%s/%s", nrow(current_data), nrow(initial_data))
|
| 183 | -! | +|||
| 218 | +
- module_names <- unlist(c(module_labels(modules), "global_filters"))+ } else {
|
|||
| 184 | +219 | ! |
- failed_mod_names <- setdiff(names(attr(filter, "mapping")), module_names)+ nrow(current_data) |
|
| 185 | -! | +|||
| 220 | +
- if (length(failed_mod_names)) {
+ }, |
|||
| 186 | -! | +|||
| 221 | +13x |
- stop(+ subjects = if (!is.null(initial_data)) {
|
||
| 187 | -! | +|||
| 222 | +13x |
- sprintf(+ sprintf("%s/%s", nrow(unique(current_data[subject_keys])), nrow(unique(initial_data[subject_keys])))
|
||
| 188 | -! | +|||
| 223 | +
- "Some module names in the mapping arguments don't match module labels.\n %s not in %s",+ } else {
|
|||
| 189 | +224 | ! |
- toString(failed_mod_names),+ nrow(unique(current_data[subject_keys])) |
|
| 190 | -! | +|||
| 225 | +
- toString(unique(module_names))+ } |
|||
| 191 | +226 |
- )+ ) |
||
| 192 | +227 |
- )+ } |
||
| 193 | +228 |
- }+ } |
||
| 194 | +229 | |||
| 195 | -! | +|||
| 230 | +
- if (anyDuplicated(module_names)) {
+ #' @rdname module_data_summary |
|||
| 196 | +231 |
- # In teal we are able to set nested modules with duplicated label.+ get_filter_overview_MultiAssayExperiment <- function(current_data, # nolint: object_length, object_name. |
||
| 197 | +232 |
- # Because mapping argument bases on the relationship between module-label and filter-id,+ initial_data, |
||
| 198 | +233 |
- # it is possible that module-label in mapping might refer to multiple teal_module (identified by the same label)+ dataname) {
|
||
| 199 | -! | +|||
| 234 | +1x |
- stop(+ experiment_names <- names(current_data) |
||
| 200 | -! | +|||
| 235 | +1x |
- sprintf(+ mae_info <- data.frame( |
||
| 201 | -! | +|||
| 236 | +1x |
- "Module labels should be unique when teal_slices(mapping = TRUE). Duplicated labels:\n%s ",+ dataname = dataname,+ |
+ ||
| 237 | +1x | +
+ subjects = if (!is.null(initial_data)) {
|
||
| 202 | +238 | ! |
- toString(module_names[duplicated(module_names)])+ sprintf("%s/%s", nrow(current_data@colData), nrow(initial_data@colData))
|
|
| 203 | +239 |
- )+ } else {
|
||
| 204 | -+ | |||
| 240 | +1x |
- )+ nrow(current_data@colData) |
||
| 205 | +241 |
} |
||
| 206 | +242 |
- }+ ) |
||
| 207 | +243 | |||
| 208 | -- |
- ## `data` - `modules`- |
- ||
| 209 | -11x | +244 | +1x |
- if (inherits(data, "teal_data")) {
+ experiment_obs_info <- do.call("rbind", lapply(
|
| 210 | -10x | +245 | +1x |
- if (length(ls(teal.code::get_env(data))) == 0) {
+ experiment_names, |
| 211 | +246 | 1x |
- stop("The environment of `data` is empty.")
+ function(experiment_name) {
|
|
| 212 | -+ | |||
| 247 | +5x |
- }+ transform( |
||
| 213 | -+ | |||
| 248 | +5x |
-
+ get_filter_overview( |
||
| 214 | -9x | +249 | +5x |
- is_modules_ok <- check_modules_datanames(modules, ls(teal.code::get_env(data)))+ current_data[[experiment_name]], |
| 215 | -9x | +250 | +5x |
- if (!isTRUE(is_modules_ok) && length(unlist(extract_transformers(modules))) == 0) {
+ initial_data[[experiment_name]], |
| 216 | -2x | +251 | +5x |
- warning(is_modules_ok, call. = FALSE)+ dataname = experiment_name, |
| 217 | -+ | |||
| 252 | +5x |
- }+ subject_keys = join_keys() # empty join keys |
||
| 218 | +253 | - - | -||
| 219 | -9x | -
- is_filter_ok <- check_filter_datanames(filter, ls(teal.code::get_env(data)))- |
- ||
| 220 | -9x | -
- if (!isTRUE(is_filter_ok)) {
+ ), |
||
| 221 | -1x | -
- warning(is_filter_ok)- |
- ||
| 222 | -+ | 254 | +5x |
- # we allow app to continue if applied filters are outside+ dataname = paste0(" - ", experiment_name)
|
| 223 | +255 |
- # of possible data range+ ) |
||
| 224 | +256 |
} |
||
| 225 | +257 |
- }+ )) |
||
| 226 | +258 | |||
| 227 | -10x | +259 | +1x |
- reporter <- teal.reporter::Reporter$new()$set_id(attr(filter, "app_id"))+ get_experiment_keys <- function(mae, experiment) {
|
| 228 | -10x | -
- if (is_arg_used(modules, "reporter") && length(extract_module(modules, "teal_module_previewer")) == 0) {
- |
- ||
| 229 | -! | -
- modules <- append_module(- |
- ||
| 230 | -! | -
- modules,- |
- ||
| 231 | -! | +260 | +5x |
- reporter_previewer_module(server_args = list(previewer_buttons = c("download", "reset")))
+ sample_subset <- mae@sampleMap[mae@sampleMap$colname %in% colnames(experiment), ] |
| 232 | -+ | |||
| 261 | +5x |
- )+ length(unique(sample_subset$primary)) |
||
| 233 | +262 |
} |
||
| 234 | +263 | |||
| 235 | -10x | -
- ns <- NS(id)- |
- ||
| 236 | -+ | 264 | +1x |
- # Note: UI must be a function to support bookmarking.+ experiment_subjects_info <- do.call("rbind", lapply(
|
| 237 | -10x | +265 | +1x |
- res <- list(+ experiment_names, |
| 238 | -10x | +266 | +1x |
- ui = function(request) {
+ function(experiment_name) {
|
| 239 | -! | +|||
| 267 | +5x |
- ui_teal(+ data.frame( |
||
| 240 | -! | +|||
| 268 | +5x |
- id = ns("teal"),
+ subjects = if (!is.null(initial_data)) {
|
||
| 241 | +269 | ! |
- modules = modules,+ sprintf( |
|
| 242 | +270 | ! |
- title = title,+ "%s/%s", |
|
| 243 | +271 | ! |
- header = header,+ get_experiment_keys(current_data, current_data[[experiment_name]]), |
|
| 244 | +272 | ! |
- footer = footer+ get_experiment_keys(current_data, initial_data[[experiment_name]]) |
|
| 245 | +273 |
- )+ ) |
||
| 246 | +274 |
- },+ } else {
|
||
| 247 | -10x | -
- server = function(input, output, session) {
- |
- ||
| 248 | -! | -
- if (!is.null(landing_popup)) {
- |
- ||
| 249 | -! | +275 | +5x |
- do.call(landing_popup$server, c(list(id = "landing_module_shiny_id"), landing_popup$server_args))+ get_experiment_keys(current_data, current_data[[experiment_name]]) |
| 250 | +276 |
- }+ } |
||
| 251 | -! | +|||
| 277 | +
- srv_teal(id = ns("teal"), data = data, modules = modules, filter = deep_copy_filter(filter))
+ ) |
|||
| 252 | +278 |
} |
||
| 253 | +279 |
- )+ )) |
||
| 254 | +280 | |||
| 255 | -10x | -
- logger::log_debug("init teal app has been initialized.")
- |
- ||
| 256 | -+ | 281 | +1x |
-
+ experiment_info <- cbind(experiment_obs_info, experiment_subjects_info) |
| 257 | -10x | +282 | +1x |
- res+ .smart_rbind(mae_info, experiment_info) |
| 258 | +283 |
}@@ -28004,28 +27864,28 @@ teal coverage - 59.99% |
| 1 |
- #' Data summary+ #' Validate that dataset has a minimum number of observations |
||
| 2 |
- #' @description+ #' |
||
| 3 |
- #' Module and its utils to display the number of rows and subjects in the filtered and unfiltered data.+ #' `r lifecycle::badge("stable")`
|
||
| 5 |
- #' @details Handling different data classes:+ #' This function is a wrapper for `shiny::validate`. |
||
| 6 |
- #' `get_filter_overview()` is a pseudo S3 method which has variants for:+ #' |
||
| 7 |
- #' - `array` (`data.frame`, `DataFrame`, `array`, `Matrix` and `SummarizedExperiment`): Method variant+ #' @param x (`data.frame`) |
||
| 8 |
- #' can be applied to any two-dimensional objects on which [ncol()] can be used.+ #' @param min_nrow (`numeric(1)`) Minimum allowed number of rows in `x`. |
||
| 9 |
- #' - `MultiAssayExperiment`: for which summary contains counts for `colData` and all `experiments`.+ #' @param complete (`logical(1)`) Flag specifying whether to check only complete cases. Defaults to `FALSE`. |
||
| 10 |
- #' - For other data types module displays data name with warning icon and no more details.+ #' @param allow_inf (`logical(1)`) Flag specifying whether to allow infinite values. Defaults to `TRUE`. |
||
| 11 |
- #'+ #' @param msg (`character(1)`) Additional message to display alongside the default message. |
||
| 12 |
- #' Module includes also "Show/Hide unsupported" button to toggle rows of the summary table+ #' |
||
| 13 |
- #' containing datasets where number of observations are not calculated.+ #' @export |
||
| 15 |
- #' @param id (`character(1)`) `shiny` module instance id.+ #' @examples |
||
| 16 |
- #' @param teal_data (`reactive` returning `teal_data`)+ #' library(teal) |
||
| 17 |
- #'+ #' ui <- fluidPage( |
||
| 18 |
- #' @name module_data_summary+ #' sliderInput("len", "Max Length of Sepal",
|
||
| 19 |
- #' @rdname module_data_summary+ #' min = 4.3, max = 7.9, value = 5 |
||
| 20 |
- #' @keywords internal+ #' ), |
||
| 21 |
- #' @return `NULL`.+ #' plotOutput("plot")
|
||
| 22 |
- NULL+ #' ) |
||
| 23 |
-
+ #' |
||
| 24 |
- #' @rdname module_data_summary+ #' server <- function(input, output) {
|
||
| 25 |
- ui_data_summary <- function(id) {
+ #' output$plot <- renderPlot({
|
||
| 26 | -! | +
- ns <- NS(id)+ #' iris_df <- iris[iris$Sepal.Length <= input$len, ] |
|
| 27 | -! | +
- content_id <- ns("filters_overview_contents")
+ #' validate_has_data( |
|
| 28 | -! | +
- tags$div(+ #' iris_df, |
|
| 29 | -! | +
- id = id,+ #' min_nrow = 10, |
|
| 30 | -! | +
- class = "well",+ #' complete = FALSE, |
|
| 31 | -! | +
- tags$div(+ #' msg = "Please adjust Max Length of Sepal" |
|
| 32 | -! | +
- class = "row",+ #' ) |
|
| 33 | -! | +
- tags$div(+ #' |
|
| 34 | -! | +
- class = "col-sm-9",+ #' hist(iris_df$Sepal.Length, breaks = 5) |
|
| 35 | -! | +
- tags$label("Active Filter Summary", class = "text-primary mb-4")
+ #' }) |
|
| 36 |
- ),+ #' } |
||
| 37 | -! | +
- tags$div(+ #' if (interactive()) {
|
|
| 38 | -! | +
- class = "col-sm-3",+ #' shinyApp(ui, server) |
|
| 39 | -! | +
- tags$i(+ #' } |
|
| 40 | -! | +
- class = "remove pull-right fa fa-angle-down",+ #' |
|
| 41 | -! | +
- style = "cursor: pointer;",+ validate_has_data <- function(x, |
|
| 42 | -! | +
- title = "fold/expand data summary panel",+ min_nrow = NULL, |
|
| 43 | -! | +
- onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", content_id)
+ complete = FALSE, |
|
| 44 |
- )+ allow_inf = TRUE, |
||
| 45 |
- )+ msg = NULL) {
|
||
| 46 | -+ | 17x |
- ),+ checkmate::assert_string(msg, null.ok = TRUE) |
| 47 | -! | +15x |
- tags$div(+ checkmate::assert_data_frame(x) |
| 48 | -! | +15x |
- id = content_id,+ if (!is.null(min_nrow)) {
|
| 49 | -! | +15x |
- tags$div(+ if (complete) {
|
| 50 | -! | +5x |
- class = "teal_active_summary_filter_panel",+ complete_index <- stats::complete.cases(x) |
| 51 | -! | +5x |
- tableOutput(ns("table"))
+ validate(need( |
| 52 | -+ | 5x |
- )+ sum(complete_index) > 0 && nrow(x[complete_index, , drop = FALSE]) >= min_nrow, |
| 53 | -+ | 5x |
- )+ paste(c(paste("Number of complete cases is less than:", min_nrow), msg), collapse = "\n")
|
| 54 |
- )+ )) |
||
| 55 |
- }+ } else {
|
||
| 56 | -+ | 10x |
-
+ validate(need( |
| 57 | -+ | 10x |
- #' @rdname module_data_summary+ nrow(x) >= min_nrow, |
| 58 | -+ | 10x |
- srv_data_summary <- function(id, teal_data) {
+ paste( |
| 59 | -81x | +10x |
- assert_reactive(teal_data)+ c(paste("Minimum number of records not met: >=", min_nrow, "records required."), msg),
|
| 60 | -81x | +10x |
- moduleServer(+ collapse = "\n" |
| 61 | -81x | +
- id = id,+ ) |
|
| 62 | -81x | +
- function(input, output, session) {
+ )) |
|
| 63 | -81x | +
- logger::log_debug("srv_data_summary initializing")
+ } |
|
| 65 | -81x | +10x |
- summary_table <- reactive({
+ if (!allow_inf) {
|
| 66 | -89x | +6x |
- req(inherits(teal_data(), "teal_data"))+ validate(need( |
| 67 | -83x | +6x |
- if (!length(ls(teal.code::get_env(teal_data())))) {
+ all(vapply(x, function(col) !is.numeric(col) || !any(is.infinite(col)), logical(1))), |
| 68 | -2x | +6x |
- return(NULL)+ "Dataframe contains Inf values which is not allowed." |
| 69 |
- }+ )) |
||
| 70 | -81x | +
- get_filter_overview_wrapper(teal_data)+ } |
|
| 71 |
- })+ } |
||
| 72 |
-
+ } |
||
| 73 | -81x | +
- output$table <- renderUI({
+
|
|
| 74 | -89x | +
- summary_table_out <- try(summary_table(), silent = TRUE)+ #' Validate that dataset has unique rows for key variables |
|
| 75 | -89x | +
- if (inherits(summary_table_out, "try-error")) {
+ #' |
|
| 76 |
- # Ignore silent shiny error+ #' `r lifecycle::badge("stable")`
|
||
| 77 | -6x | +
- if (!inherits(attr(summary_table_out, "condition"), "shiny.silent.error")) {
+ #' |
|
| 78 | -! | +
- stop("Error occurred during data processing. See details in the main panel.")
+ #' This function is a wrapper for `shiny::validate`. |
|
| 79 |
- }+ #' |
||
| 80 | -83x | +
- } else if (is.null(summary_table_out)) {
+ #' @param x (`data.frame`) |
|
| 81 | -2x | +
- "no datasets to show"+ #' @param key (`character`) Vector of ID variables from `x` that identify unique records. |
|
| 82 |
- } else {
+ #' |
||
| 83 | -81x | +
- is_unsupported <- apply(summary_table(), 1, function(x) all(is.na(x[-1])))+ #' @export |
|
| 84 | -81x | +
- summary_table_out[is.na(summary_table_out)] <- ""+ #' |
|
| 85 | -81x | +
- body_html <- apply(+ #' @examples |
|
| 86 | -81x | +
- summary_table_out,+ #' iris$id <- rep(1:50, times = 3) |
|
| 87 | -81x | +
- 1,+ #' ui <- fluidPage( |
|
| 88 | -81x | +
- function(x) {
+ #' selectInput( |
|
| 89 | -154x | +
- is_supported <- !all(x[-1] == "")+ #' inputId = "species", |
|
| 90 | -154x | +
- if (is_supported) {
+ #' label = "Select species", |
|
| 91 | -147x | +
- tags$tr(+ #' choices = c("setosa", "versicolor", "virginica"),
|
|
| 92 | -147x | +
- tagList(+ #' selected = "setosa", |
|
| 93 | -147x | +
- tags$td(x[1]),+ #' multiple = TRUE |
|
| 94 | -147x | +
- lapply(x[-1], tags$td)+ #' ), |
|
| 95 |
- )+ #' plotOutput("plot")
|
||
| 96 |
- )+ #' ) |
||
| 97 |
- }+ #' server <- function(input, output) {
|
||
| 98 |
- }+ #' output$plot <- renderPlot({
|
||
| 99 |
- )+ #' iris_f <- iris[iris$Species %in% input$species, ] |
||
| 100 |
-
+ #' validate_one_row_per_id(iris_f, key = c("id"))
|
||
| 101 | -81x | +
- header_labels <- tools::toTitleCase(names(summary_table_out))+ #' |
|
| 102 | -81x | +
- header_labels[header_labels == "Dataname"] <- "Data Name"+ #' hist(iris_f$Sepal.Length, breaks = 5) |
|
| 103 | -81x | +
- header_html <- tags$tr(tagList(lapply(header_labels, tags$td)))+ #' }) |
|
| 104 |
-
+ #' } |
||
| 105 | -81x | +
- table_html <- tags$table(+ #' if (interactive()) {
|
|
| 106 | -81x | +
- class = "table custom-table",+ #' shinyApp(ui, server) |
|
| 107 | -81x | +
- tags$thead(header_html),+ #' } |
|
| 108 | -81x | +
- tags$tbody(body_html)+ #' |
|
| 109 |
- )+ validate_one_row_per_id <- function(x, key = c("USUBJID", "STUDYID")) {
|
||
| 110 | -81x | +! |
- div(+ validate(need(!any(duplicated(x[key])), paste("Found more than one row per id.")))
|
| 111 | -81x | +
- table_html,+ } |
|
| 112 | -81x | +
- if (any(is_unsupported)) {
+
|
|
| 113 | -7x | +
- p(+ #' Validates that vector includes all expected values |
|
| 114 | -7x | +
- class = c("pull-right", "float-right", "text-secondary"),
+ #' |
|
| 115 | -7x | +
- style = "font-size: 0.8em;",+ #' `r lifecycle::badge("stable")`
|
|
| 116 | -7x | +
- sprintf("And %s more unfilterable object(s)", sum(is_unsupported)),
+ #' |
|
| 117 | -7x | +
- icon(+ #' This function is a wrapper for `shiny::validate`. |
|
| 118 | -7x | +
- name = "far fa-circle-question",+ #' |
|
| 119 | -7x | +
- title = paste(+ #' @param x Vector of values to test. |
|
| 120 | -7x | +
- sep = "",+ #' @param choices Vector to test against. |
|
| 121 | -7x | +
- collapse = "\n",+ #' @param msg (`character(1)`) Error message to display if some elements of `x` are not elements of `choices`. |
|
| 122 | -7x | +
- shQuote(summary_table()[is_unsupported, "dataname"]),+ #' |
|
| 123 |
- " (",
+ #' @export |
||
| 124 | -7x | +
- vapply(+ #' |
|
| 125 | -7x | +
- summary_table()[is_unsupported, "dataname"],+ #' @examples |
|
| 126 | -7x | +
- function(x) class(teal_data()[[x]])[1],+ #' ui <- fluidPage( |
|
| 127 | -7x | +
- character(1L)+ #' selectInput( |
|
| 128 |
- ),+ #' "species", |
||
| 129 |
- ")"+ #' "Select species", |
||
| 130 |
- )+ #' choices = c("setosa", "versicolor", "virginica", "unknown species"),
|
||
| 131 |
- )+ #' selected = "setosa", |
||
| 132 |
- )+ #' multiple = FALSE |
||
| 133 |
- }+ #' ), |
||
| 134 |
- )+ #' verbatimTextOutput("summary")
|
||
| 135 |
- }+ #' ) |
||
| 136 |
- })+ #' |
||
| 137 |
-
+ #' server <- function(input, output) {
|
||
| 138 | -81x | +
- NULL+ #' output$summary <- renderPrint({
|
|
| 139 |
- }+ #' validate_in(input$species, iris$Species, "Species does not exist.") |
||
| 140 |
- )+ #' nrow(iris[iris$Species == input$species, ]) |
||
| 141 |
- }+ #' }) |
||
| 142 |
-
+ #' } |
||
| 143 |
- #' @rdname module_data_summary+ #' if (interactive()) {
|
||
| 144 |
- get_filter_overview_wrapper <- function(teal_data) {
+ #' shinyApp(ui, server) |
||
| 145 | -81x | +
- datanames <- teal.data::datanames(teal_data())+ #' } |
|
| 146 | -81x | +
- joinkeys <- teal.data::join_keys(teal_data())+ #' |
|
| 147 |
-
+ validate_in <- function(x, choices, msg) {
|
||
| 148 | -81x | +! |
- current_data_objs <- sapply(+ validate(need(length(x) > 0 && length(choices) > 0 && all(x %in% choices), msg)) |
| 149 | -81x | +
- datanames,+ } |
|
| 150 | -81x | +
- function(name) teal.code::get_var(teal_data(), name),+ |
|
| 151 | -81x | +
- simplify = FALSE+ #' Validates that vector has length greater than 0 |
|
| 152 |
- )+ #' |
||
| 153 | -81x | +
- initial_data_objs <- teal.code::get_var(teal_data(), ".raw_data")+ #' `r lifecycle::badge("stable")`
|
|
| 154 |
-
+ #' |
||
| 155 | -81x | +
- out <- lapply(+ #' This function is a wrapper for `shiny::validate`. |
|
| 156 | -81x | +
- datanames,+ #' |
|
| 157 | -81x | +
- function(dataname) {
+ #' @param x vector |
|
| 158 | -149x | +
- parent <- teal.data::parent(joinkeys, dataname)+ #' @param msg message to display |
|
| 159 |
- # todo: what should we display for a parent dataset?+ #' |
||
| 160 |
- # - Obs and Subjects+ #' @export |
||
| 161 |
- # - Obs only+ #' |
||
| 162 |
- # - Subjects only+ #' @examples |
||
| 163 |
- # todo (for later): summary table should be displayed in a way that child datasets+ #' data <- data.frame( |
||
| 164 |
- # are indented under their parent dataset to form a tree structure+ #' id = c(1:10, 11:20, 1:10), |
||
| 165 | -149x | +
- subject_keys <- if (length(parent) > 0) {
+ #' strata = rep(c("A", "B"), each = 15)
|
|
| 166 | -7x | +
- names(joinkeys[dataname, parent])+ #' ) |
|
| 167 |
- } else {
+ #' ui <- fluidPage( |
||
| 168 | -142x | +
- joinkeys[dataname, dataname]+ #' selectInput("ref1", "Select strata1 to compare",
|
|
| 169 |
- }+ #' choices = c("A", "B", "C"), selected = "A"
|
||
| 170 | -149x | +
- get_filter_overview(+ #' ), |
|
| 171 | -149x | +
- current_data = current_data_objs[[dataname]],+ #' selectInput("ref2", "Select strata2 to compare",
|
|
| 172 | -149x | +
- initial_data = initial_data_objs[[dataname]],+ #' choices = c("A", "B", "C"), selected = "B"
|
|
| 173 | -149x | +
- dataname = dataname,+ #' ), |
|
| 174 | -149x | +
- subject_keys = subject_keys+ #' verbatimTextOutput("arm_summary")
|
|
| 175 |
- )+ #' ) |
||
| 176 |
- }+ #' |
||
| 177 |
- )+ #' server <- function(input, output) {
|
||
| 178 |
-
+ #' output$arm_summary <- renderText({
|
||
| 179 | -81x | +
- do.call(.smart_rbind, out)+ #' sample_1 <- data$id[data$strata == input$ref1] |
|
| 180 |
- }+ #' sample_2 <- data$id[data$strata == input$ref2] |
||
| 181 |
-
+ #' |
||
| 182 |
-
+ #' validate_has_elements(sample_1, "No subjects in strata1.") |
||
| 183 |
- #' @rdname module_data_summary+ #' validate_has_elements(sample_2, "No subjects in strata2.") |
||
| 184 |
- #' @param current_data (`object`) current object (after filtering and transforming).+ #' |
||
| 185 |
- #' @param initial_data (`object`) initial object.+ #' paste0( |
||
| 186 |
- #' @param dataname (`character(1)`)+ #' "Number of samples in: strata1=", length(sample_1), |
||
| 187 |
- #' @param subject_keys (`character`) names of the columns which determine a single unique subjects+ #' " comparions strata2=", length(sample_2) |
||
| 188 |
- get_filter_overview <- function(current_data, initial_data, dataname, subject_keys) {
+ #' ) |
||
| 189 | -154x | +
- if (inherits(current_data, c("data.frame", "DataFrame", "array", "Matrix", "SummarizedExperiment"))) {
+ #' }) |
|
| 190 | -146x | +
- get_filter_overview_array(current_data, initial_data, dataname, subject_keys)+ #' } |
|
| 191 | -8x | +
- } else if (inherits(current_data, "MultiAssayExperiment")) {
+ #' if (interactive()) {
|
|
| 192 | -1x | +
- get_filter_overview_MultiAssayExperiment(current_data, initial_data, dataname)+ #' shinyApp(ui, server) |
|
| 193 |
- } else {
+ #' } |
||
| 194 | -7x | +
- data.frame(dataname = dataname)+ validate_has_elements <- function(x, msg) {
|
|
| 195 | -+ | ! |
- }+ validate(need(length(x) > 0, msg)) |
| 198 |
- #' @rdname module_data_summary+ #' Validates no intersection between two vectors |
||
| 199 |
- get_filter_overview_array <- function(current_data,+ #' |
||
| 200 |
- initial_data,+ #' `r lifecycle::badge("stable")`
|
||
| 201 |
- dataname,+ #' |
||
| 202 |
- subject_keys) {
+ #' This function is a wrapper for `shiny::validate`. |
||
| 203 | -146x | +
- if (length(subject_keys) == 0) {
+ #' |
|
| 204 | -133x | +
- data.frame(+ #' @param x vector |
|
| 205 | -133x | +
- dataname = dataname,+ #' @param y vector |
|
| 206 | -133x | +
- obs = if (!is.null(initial_data)) {
+ #' @param msg (`character(1)`) message to display if `x` and `y` intersect |
|
| 207 | -124x | +
- sprintf("%s/%s", nrow(current_data), nrow(initial_data))
+ #' |
|
| 208 |
- } else {
+ #' @export |
||
| 209 | -9x | +
- nrow(current_data)+ #' |
|
| 210 |
- }+ #' @examples |
||
| 211 |
- )+ #' data <- data.frame( |
||
| 212 |
- } else {
+ #' id = c(1:10, 11:20, 1:10), |
||
| 213 | -13x | +
- data.frame(+ #' strata = rep(c("A", "B", "C"), each = 10)
|
|
| 214 | -13x | +
- dataname = dataname,+ #' ) |
|
| 215 | -13x | +
- obs = if (!is.null(initial_data)) {
+ #' |
|
| 216 | -13x | +
- sprintf("%s/%s", nrow(current_data), nrow(initial_data))
+ #' ui <- fluidPage( |
|
| 217 |
- } else {
+ #' selectInput("ref1", "Select strata1 to compare",
|
||
| 218 | -! | +
- nrow(current_data)+ #' choices = c("A", "B", "C"),
|
|
| 219 |
- },+ #' selected = "A" |
||
| 220 | -13x | +
- subjects = if (!is.null(initial_data)) {
+ #' ), |
|
| 221 | -13x | +
- sprintf("%s/%s", nrow(unique(current_data[subject_keys])), nrow(unique(initial_data[subject_keys])))
+ #' selectInput("ref2", "Select strata2 to compare",
|
|
| 222 |
- } else {
+ #' choices = c("A", "B", "C"),
|
||
| 223 | -! | +
- nrow(unique(current_data[subject_keys]))+ #' selected = "B" |
|
| 224 |
- }+ #' ), |
||
| 225 |
- )+ #' verbatimTextOutput("summary")
|
||
| 226 |
- }+ #' ) |
||
| 227 |
- }+ #' |
||
| 228 |
-
+ #' server <- function(input, output) {
|
||
| 229 |
- #' @rdname module_data_summary+ #' output$summary <- renderText({
|
||
| 230 |
- get_filter_overview_MultiAssayExperiment <- function(current_data, # nolint: object_length, object_name.+ #' sample_1 <- data$id[data$strata == input$ref1] |
||
| 231 |
- initial_data,+ #' sample_2 <- data$id[data$strata == input$ref2] |
||
| 232 |
- dataname) {
+ #' |
||
| 233 | -1x | +
- experiment_names <- names(current_data)+ #' validate_no_intersection( |
|
| 234 | -1x | +
- mae_info <- data.frame(+ #' sample_1, sample_2, |
|
| 235 | -1x | +
- dataname = dataname,+ #' "subjects within strata1 and strata2 cannot overlap" |
|
| 236 | -1x | +
- subjects = if (!is.null(initial_data)) {
+ #' ) |
|
| 237 | -! | +
- sprintf("%s/%s", nrow(current_data@colData), nrow(initial_data@colData))
+ #' paste0( |
|
| 238 |
- } else {
+ #' "Number of subject in: reference treatment=", length(sample_1), |
||
| 239 | -1x | +
- nrow(current_data@colData)+ #' " comparions treatment=", length(sample_2) |
|
| 240 |
- }+ #' ) |
||
| 241 |
- )+ #' }) |
||
| 242 |
-
+ #' } |
||
| 243 | -1x | +
- experiment_obs_info <- do.call("rbind", lapply(
+ #' if (interactive()) {
|
|
| 244 | -1x | +
- experiment_names,+ #' shinyApp(ui, server) |
|
| 245 | -1x | +
- function(experiment_name) {
+ #' } |
|
| 246 | -5x | -
- transform(- |
- |
| 247 | -5x | -
- get_filter_overview(- |
- |
| 248 | -5x | -
- current_data[[experiment_name]],- |
- |
| 249 | -5x | -
- initial_data[[experiment_name]],- |
- |
| 250 | -5x | -
- dataname = experiment_name,- |
- |
| 251 | -5x | +
- subject_keys = join_keys() # empty join keys+ #' |
|
| 252 | +247 |
- ),- |
- |
| 253 | -5x | -
- dataname = paste0(" - ", experiment_name)
+ validate_no_intersection <- function(x, y, msg) {
|
|
| 254 | -+ | ||
| 248 | +! |
- )+ validate(need(length(intersect(x, y)) == 0, msg)) |
|
| 255 | +249 |
- }+ } |
|
| 256 | +250 |
- ))+ |
|
| 257 | +251 | ||
| 258 | -1x | -
- get_experiment_keys <- function(mae, experiment) {
- |
- |
| 259 | -5x | -
- sample_subset <- mae@sampleMap[mae@sampleMap$colname %in% colnames(experiment), ]- |
- |
| 260 | -5x | -
- length(unique(sample_subset$primary))- |
- |
| 261 | +252 |
- }+ #' Validates that dataset contains specific variable |
|
| 262 | +253 | - - | -|
| 263 | -1x | -
- experiment_subjects_info <- do.call("rbind", lapply(
- |
- |
| 264 | -1x | -
- experiment_names,- |
- |
| 265 | -1x | -
- function(experiment_name) {
- |
- |
| 266 | -5x | -
- data.frame(- |
- |
| 267 | -5x | -
- subjects = if (!is.null(initial_data)) {
- |
- |
| 268 | -! | -
- sprintf(- |
- |
| 269 | -! | -
- "%s/%s",- |
- |
| 270 | -! | -
- get_experiment_keys(current_data, current_data[[experiment_name]]),- |
- |
| 271 | -! | -
- get_experiment_keys(current_data, initial_data[[experiment_name]])+ #' |
|
| 272 | +254 |
- )+ #' `r lifecycle::badge("stable")`
|
|
| 273 | +255 |
- } else {
- |
- |
| 274 | -5x | -
- get_experiment_keys(current_data, current_data[[experiment_name]])+ #' |
|
| 275 | +256 |
- }+ #' This function is a wrapper for `shiny::validate`. |
|
| 276 | +257 |
- )+ #' |
|
| 277 | +258 |
- }+ #' @param data (`data.frame`) |
|
| 278 | +259 |
- ))+ #' @param varname (`character(1)`) name of variable to check for in `data` |
|
| 279 | +260 | - - | -|
| 280 | -1x | -
- experiment_info <- cbind(experiment_obs_info, experiment_subjects_info)- |
- |
| 281 | -1x | -
- .smart_rbind(mae_info, experiment_info)+ #' @param msg (`character(1)`) message to display if `data` does not include `varname` |
|
| 282 | +261 |
- }+ #' |
| 1 | +262 |
- #' App state management.+ #' @export |
|
| 2 | +263 |
#' |
|
| 3 | +264 |
- #' @description+ #' @examples |
|
| 4 | +265 |
- #' `r lifecycle::badge("experimental")`
+ #' data <- data.frame( |
|
| 5 | +266 |
- #'+ #' one = rep("a", length.out = 20),
|
|
| 6 | +267 |
- #' Capture and restore the global (app) input state.+ #' two = rep(c("a", "b"), length.out = 20)
|
|
| 7 | +268 |
- #'+ #' ) |
|
| 8 | +269 |
- #' @details+ #' ui <- fluidPage( |
|
| 9 | +270 |
- #' This module introduces bookmarks into `teal` apps: the `shiny` bookmarking mechanism becomes enabled+ #' selectInput( |
|
| 10 | +271 |
- #' and server-side bookmarks can be created.+ #' "var", |
|
| 11 | +272 |
- #'+ #' "Select variable", |
|
| 12 | +273 |
- #' The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar.+ #' choices = c("one", "two", "three", "four"),
|
|
| 13 | +274 |
- #' When clicked, the button creates a bookmark and opens a modal which displays the bookmark URL.+ #' selected = "one" |
|
| 14 | +275 |
- #'+ #' ), |
|
| 15 | +276 |
- #' `teal` does not guarantee that all modules (`teal_module` objects) are bookmarkable.+ #' verbatimTextOutput("summary")
|
|
| 16 | +277 |
- #' Those that are, have a `teal_bookmarkable` attribute set to `TRUE`. If any modules are not bookmarkable,+ #' ) |
|
| 17 | +278 |
- #' the bookmark manager modal displays a warning and the bookmark button displays a flag.+ #' |
|
| 18 | +279 |
- #' In order to communicate that a external module is bookmarkable, the module developer+ #' server <- function(input, output) {
|
|
| 19 | +280 |
- #' should set the `teal_bookmarkable` attribute to `TRUE`.+ #' output$summary <- renderText({
|
|
| 20 | +281 |
- #'+ #' validate_has_variable(data, input$var) |
|
| 21 | +282 |
- #' @section Server logic:+ #' paste0("Selected treatment variables: ", paste(input$var, collapse = ", "))
|
|
| 22 | +283 |
- #' A bookmark is a URL that contains the app address with a `/?_state_id_=<bookmark_dir>` suffix.+ #' }) |
|
| 23 | +284 |
- #' `<bookmark_dir>` is a directory created on the server, where the state of the application is saved.+ #' } |
|
| 24 | +285 |
- #' Accessing the bookmark URL opens a new session of the app that starts in the previously saved state.+ #' if (interactive()) {
|
|
| 25 | +286 |
- #'+ #' shinyApp(ui, server) |
|
| 26 | +287 |
- #' @section Note:+ #' } |
|
| 27 | +288 |
- #' To enable bookmarking use either:+ validate_has_variable <- function(data, varname, msg) {
|
|
| 28 | -+ | ||
| 289 | +! |
- #' - `shiny` app by using `shinyApp(..., enableBookmarking = "server")` (not supported in `shinytest2`)+ if (length(varname) != 0) {
|
|
| 29 | -+ | ||
| 290 | +! |
- #' - set `options(shiny.bookmarkStore = "server")` before running the app+ has_vars <- varname %in% names(data) |
|
| 30 | +291 |
- #'+ |
|
| 31 | -+ | ||
| 292 | +! |
- #'+ if (!all(has_vars)) {
|
|
| 32 | -+ | ||
| 293 | +! |
- #' @inheritParams init+ if (missing(msg)) {
|
|
| 33 | -+ | ||
| 294 | +! |
- #'+ msg <- sprintf( |
|
| 34 | -+ | ||
| 295 | +! |
- #' @return Invisible `NULL`.+ "%s does not have the required variables: %s.", |
|
| 35 | -+ | ||
| 296 | +! |
- #'+ deparse(substitute(data)), |
|
| 36 | -+ | ||
| 297 | +! |
- #' @aliases bookmark bookmark_manager bookmark_manager_module+ toString(varname[!has_vars]) |
|
| 37 | +298 |
- #'+ ) |
|
| 38 | +299 |
- #' @name module_bookmark_manager+ } |
|
| 39 | -+ | ||
| 300 | +! |
- #' @rdname module_bookmark_manager+ validate(need(FALSE, msg)) |
|
| 40 | +301 |
- #'+ } |
|
| 41 | +302 |
- #' @keywords internal+ } |
|
| 42 | +303 |
- #'+ } |
|
| 43 | +304 |
- NULL+ |
|
| 44 | +305 |
-
+ #' Validate that variables has expected number of levels |
|
| 45 | +306 |
- #' @rdname module_bookmark_manager+ #' |
|
| 46 | +307 |
- ui_bookmark_panel <- function(id, modules) {
+ #' `r lifecycle::badge("stable")`
|
|
| 47 | -! | +||
| 308 | +
- ns <- NS(id)+ #' |
||
| 48 | +309 |
-
+ #' If the number of levels of `x` is less than `min_levels` |
|
| 49 | -! | +||
| 310 | +
- bookmark_option <- get_bookmarking_option()+ #' or greater than `max_levels` the validation will fail. |
||
| 50 | -! | +||
| 311 | +
- is_unbookmarkable <- need_bookmarking(modules)+ #' This function is a wrapper for `shiny::validate`. |
||
| 51 | -! | +||
| 312 | +
- shinyOptions(bookmarkStore = bookmark_option)+ #' |
||
| 52 | +313 |
-
+ #' @param x variable name. If `x` is not a factor, the unique values |
|
| 53 | +314 |
- # Render bookmark warnings count+ #' are treated as levels. |
|
| 54 | -! | +||
| 315 | +
- if (!all(is_unbookmarkable) && identical(bookmark_option, "server")) {
+ #' @param min_levels cutoff for minimum number of levels of `x` |
||
| 55 | -! | +||
| 316 | +
- tags$button(+ #' @param max_levels cutoff for maximum number of levels of `x` |
||
| 56 | -! | +||
| 317 | +
- id = ns("do_bookmark"),
+ #' @param var_name name of variable being validated for use in |
||
| 57 | -! | +||
| 318 | +
- class = "btn action-button wunder_bar_button bookmark_manager_button",+ #' validation message |
||
| 58 | -! | +||
| 319 | +
- title = "Add bookmark",+ #' |
||
| 59 | -! | +||
| 320 | +
- tags$span(+ #' @export |
||
| 60 | -! | +||
| 321 | +
- suppressMessages(icon("fas fa-bookmark")),
+ #' @examples |
||
| 61 | -! | +||
| 322 | +
- if (any(is_unbookmarkable)) {
+ #' data <- data.frame( |
||
| 62 | -! | +||
| 323 | +
- tags$span(+ #' one = rep("a", length.out = 20),
|
||
| 63 | -! | +||
| 324 | +
- sum(is_unbookmarkable),+ #' two = rep(c("a", "b"), length.out = 20),
|
||
| 64 | -! | +||
| 325 | +
- class = "badge-warning badge-count text-white bg-danger"+ #' three = rep(c("a", "b", "c"), length.out = 20),
|
||
| 65 | +326 |
- )+ #' four = rep(c("a", "b", "c", "d"), length.out = 20),
|
|
| 66 | +327 |
- }+ #' stringsAsFactors = TRUE |
|
| 67 | +328 |
- )+ #' ) |
|
| 68 | +329 |
- )+ #' ui <- fluidPage( |
|
| 69 | +330 |
- }+ #' selectInput( |
|
| 70 | +331 |
- }+ #' "var", |
|
| 71 | +332 |
-
+ #' "Select variable", |
|
| 72 | +333 |
- #' @rdname module_bookmark_manager+ #' choices = c("one", "two", "three", "four"),
|
|
| 73 | +334 |
- srv_bookmark_panel <- function(id, modules) {
+ #' selected = "one" |
|
| 74 | -82x | +||
| 335 | +
- checkmate::assert_character(id)+ #' ), |
||
| 75 | -82x | +||
| 336 | +
- checkmate::assert_class(modules, "teal_modules")+ #' verbatimTextOutput("summary")
|
||
| 76 | -82x | +||
| 337 | +
- moduleServer(id, function(input, output, session) {
+ #' ) |
||
| 77 | -82x | +||
| 338 | +
- logger::log_debug("bookmark_manager_srv initializing")
+ #' |
||
| 78 | -82x | +||
| 339 | +
- ns <- session$ns+ #' server <- function(input, output) {
|
||
| 79 | -82x | +||
| 340 | +
- bookmark_option <- get_bookmarking_option()+ #' output$summary <- renderText({
|
||
| 80 | -82x | +||
| 341 | +
- is_unbookmarkable <- need_bookmarking(modules)+ #' validate_n_levels(data[[input$var]], min_levels = 2, max_levels = 15, var_name = input$var) |
||
| 81 | +342 |
-
+ #' paste0( |
|
| 82 | +343 |
- # Set up bookmarking callbacks ----+ #' "Levels of selected treatment variable: ", |
|
| 83 | +344 |
- # Register bookmark exclusions: do_bookmark button to avoid re-bookmarking+ #' paste(levels(data[[input$var]]), |
|
| 84 | -82x | +||
| 345 | +
- setBookmarkExclude(c("do_bookmark"))
+ #' collapse = ", " |
||
| 85 | +346 |
- # This bookmark can only be used on the app session.+ #' ) |
|
| 86 | -82x | +||
| 347 | +
- app_session <- .subset2(session, "parent")+ #' ) |
||
| 87 | -82x | +||
| 348 | +
- app_session$onBookmarked(function(url) {
+ #' }) |
||
| 88 | -! | +||
| 349 | +
- logger::log_debug("bookmark_manager_srv@onBookmarked: bookmark button clicked, registering bookmark")
+ #' } |
||
| 89 | -! | +||
| 350 | +
- modal_content <- if (bookmark_option != "server") {
+ #' if (interactive()) {
|
||
| 90 | -! | +||
| 351 | +
- msg <- sprintf(+ #' shinyApp(ui, server) |
||
| 91 | -! | +||
| 352 | +
- "Bookmarking has been set to \"%s\".\n%s\n%s",+ #' } |
||
| 92 | -! | +||
| 353 | +
- bookmark_option,+ validate_n_levels <- function(x, min_levels = 1, max_levels = 12, var_name) {
|
||
| 93 | +354 | ! |
- "Only server-side bookmarking is supported.",+ x_levels <- if (is.factor(x)) {
|
| 94 | +355 | ! |
- "Please contact your app developer."+ levels(x) |
| 95 | +356 |
- )- |
- |
| 96 | -! | -
- tags$div(+ } else {
|
|
| 97 | +357 | ! |
- tags$p(msg, class = "text-warning")+ unique(x) |
| 98 | +358 |
- )+ } |
|
| 99 | +359 |
- } else {
+
|
|
| 100 | +360 | ! |
- tags$div(+ if (!is.null(min_levels) && !(is.null(max_levels))) {
|
| 101 | +361 | ! |
- tags$span(+ validate(need( |
| 102 | +362 | ! |
- tags$pre(url)- |
-
| 103 | -- |
- ),+ length(x_levels) >= min_levels && length(x_levels) <= max_levels, |
|
| 104 | +363 | ! |
- if (any(is_unbookmarkable)) {
+ sprintf( |
| 105 | +364 | ! |
- bkmb_summary <- rapply2(+ "%s variable needs minimum %s level(s) and maximum %s level(s).", |
| 106 | +365 | ! |
- modules_bookmarkable(modules),+ var_name, min_levels, max_levels |
| 107 | -! | +||
| 366 | +
- function(x) {
+ ) |
||
| 108 | -! | +||
| 367 | +
- if (isTRUE(x)) {
+ )) |
||
| 109 | +368 | ! |
- "\u2705" # check mark+ } else if (!is.null(min_levels)) {
|
| 110 | +369 | ! |
- } else if (isFALSE(x)) {
+ validate(need( |
| 111 | +370 | ! |
- "\u274C" # cross mark- |
-
| 112 | -- |
- } else {
+ length(x_levels) >= min_levels, |
|
| 113 | +371 | ! |
- "\u2753" # question mark- |
-
| 114 | -- |
- }+ sprintf("%s variable needs minimum %s levels(s)", var_name, min_levels)
|
|
| 115 | +372 |
- }+ )) |
|
| 116 | -+ | ||
| 373 | +! |
- )+ } else if (!is.null(max_levels)) {
|
|
| 117 | +374 | ! |
- tags$div(+ validate(need( |
| 118 | +375 | ! |
- tags$p(+ length(x_levels) <= max_levels, |
| 119 | +376 | ! |
- icon("fas fa-exclamation-triangle"),
+ sprintf("%s variable needs maximum %s level(s)", var_name, max_levels)
|
| 120 | -! | +||
| 377 | +
- "Some modules will not be restored when using this bookmark.",+ )) |
||
| 121 | -! | +||
| 378 | +
- tags$br(),+ } |
||
| 122 | -! | +||
| 379 | +
- "Check the list below to see which modules are not bookmarkable.",+ } |
||
| 123 | -! | +
| 1 | +
- class = "text-warning"+ #' Execute and validate `teal_data_module` |
|||
| 124 | +2 |
- ),+ #' |
||
| 125 | -! | +|||
| 3 | +
- tags$pre(yaml::as.yaml(bkmb_summary))+ #' This is a low level module to handle `teal_data_module` execution and validation. |
|||
| 126 | +4 |
- )+ #' [teal_transform_module()] inherits from [teal_data_module()] so it is handled by this module too. |
||
| 127 | +5 |
- }+ #' [srv_teal()] accepts various `data` objects and eventually they are all transformed to `reactive` |
||
| 128 | +6 |
- )+ #' [teal_data()] which is a standard data class in whole `teal` framework. |
||
| 129 | +7 |
- }+ #' |
||
| 130 | +8 |
-
+ #' @section data validation: |
||
| 131 | -! | +|||
| 9 | +
- showModal(+ #' |
|||
| 132 | -! | +|||
| 10 | +
- modalDialog(+ #' Executed [teal_data_module()] is validated and output is validated for consistency. |
|||
| 133 | -! | +|||
| 11 | +
- id = ns("bookmark_modal"),
+ #' Output `data` is invalid if: |
|||
| 134 | -! | +|||
| 12 | +
- title = "Bookmarked teal app url",+ #' 1. [teal_data_module()] is invalid if server doesn't return `reactive`. **Immediately crashes an app!** |
|||
| 135 | -! | +|||
| 13 | +
- modal_content,+ #' 2. `reactive` throws a `shiny.error` - happens when module creating [teal_data()] fails. |
|||
| 136 | -! | +|||
| 14 | +
- easyClose = TRUE+ #' 3. `reactive` returns `qenv.error` - happens when [teal_data()] evaluates a failing code. |
|||
| 137 | +15 |
- )+ #' 4. `reactive` object doesn't return [teal_data()]. |
||
| 138 | +16 |
- )+ #' 5. [teal_data()] object lacks any `datanames` specified in the `modules` argument. |
||
| 139 | +17 |
- })+ #' |
||
| 140 | +18 |
-
+ #' `teal` (observers in `srv_teal`) always waits to render an app until `reactive` `teal_data` is |
||
| 141 | +19 |
- # manually trigger bookmarking because of the problems reported on windows with bookmarkButton in teal+ #' returned. If error 2-4 occurs, relevant error message is displayed to the app user. Once the issue is |
||
| 142 | -82x | +|||
| 20 | +
- observeEvent(input$do_bookmark, {
+ #' resolved, the app will continue to run. `teal` guarantees that errors in data don't crash the app |
|||
| 143 | -! | +|||
| 21 | +
- logger::log_debug("bookmark_manager_srv@1 do_bookmark module clicked.")
+ #' (except error 1). |
|||
| 144 | -! | +|||
| 22 | +
- session$doBookmark()+ #' |
|||
| 145 | +23 |
- })+ #' @param id (`character(1)`) Module id |
||
| 146 | +24 |
-
+ #' @param data (`reactive teal_data`) |
||
| 147 | -82x | +|||
| 25 | +
- invisible(NULL)+ #' @param data_module (`teal_data_module`) |
|||
| 148 | +26 |
- })+ #' @param modules (`teal_modules` or `teal_module`) For `datanames` validation purpose |
||
| 149 | +27 |
- }+ #' @param validate_shiny_silent_error (`logical`) If `TRUE`, then `shiny.silent.error` is validated and |
||
| 150 | +28 |
-
+ #' @param is_transformer_failed (`reactiveValues`) contains `logical` flags named after each transformer. |
||
| 151 | +29 |
-
+ #' Help to determine if any previous transformer failed, so that following transformers can be disabled |
||
| 152 | +30 |
- #' @rdname module_bookmark_manager+ #' and display a generic failure message. |
||
| 153 | +31 |
- get_bookmarking_option <- function() {
+ #' |
||
| 154 | -82x | +|||
| 32 | +
- bookmark_option <- getShinyOption("bookmarkStore")
+ #' @return `reactive` `teal_data` |
|||
| 155 | -82x | +|||
| 33 | +
- if (is.null(bookmark_option) && identical(getOption("shiny.bookmarkStore"), "server")) {
+ #' |
|||
| 156 | -! | +|||
| 34 | +
- bookmark_option <- getOption("shiny.bookmarkStore")
+ #' @rdname module_teal_data |
|||
| 157 | +35 |
- }+ #' @name module_teal_data |
||
| 158 | -82x | +|||
| 36 | +
- bookmark_option+ #' @keywords internal |
|||
| 159 | +37 |
- }+ NULL |
||
| 160 | +38 | |||
| 161 | +39 |
- #' @rdname module_bookmark_manager+ #' @rdname module_teal_data |
||
| 162 | +40 |
- need_bookmarking <- function(modules) {
+ ui_teal_data <- function(id, data_module = function(id) NULL) {
|
||
| 163 | -82x | +|||
| 41 | +! |
- unlist(rapply2(+ checkmate::assert_string(id) |
||
| 164 | -82x | +|||
| 42 | +! |
- modules_bookmarkable(modules),+ checkmate::assert_function(data_module, args = "id") |
||
| 165 | -82x | +|||
| 43 | +! |
- Negate(isTRUE)+ ns <- NS(id) |
||
| 166 | +44 |
- ))+ |
||
| 167 | -+ | |||
| 45 | +! |
- }+ shiny::tagList( |
||
| 168 | -+ | |||
| 46 | +! |
-
+ tags$div(id = ns("wrapper"), data_module(id = ns("data"))),
+ |
+ ||
| 47 | +! | +
+ ui_validate_reactive_teal_data(ns("validate"))
|
||
| 169 | +48 |
-
+ ) |
||
| 170 | +49 |
- # utilities ----+ } |
||
| 171 | +50 | |||
| 172 | +51 |
- #' Restore value from bookmark.+ #' @rdname module_teal_data |
||
| 173 | +52 |
- #'+ srv_teal_data <- function(id, |
||
| 174 | +53 |
- #' Get value from bookmark or return default.+ data_module = function(id) NULL, |
||
| 175 | +54 |
- #'+ modules = NULL, |
||
| 176 | +55 |
- #' Bookmarks can store not only inputs but also arbitrary values.+ validate_shiny_silent_error = TRUE, |
||
| 177 | +56 |
- #' These values are stored by `onBookmark` callbacks and restored by `onBookmarked` callbacks,+ is_transformer_failed = reactiveValues()) {
|
||
| 178 | -+ | |||
| 57 | +20x |
- #' and they are placed in the `values` environment in the `session$restoreContext` field.+ checkmate::assert_string(id) |
||
| 179 | -+ | |||
| 58 | +20x |
- #' Using `teal_data_module` makes it impossible to run the callbacks+ checkmate::assert_function(data_module, args = "id") |
||
| 180 | -+ | |||
| 59 | +20x |
- #' because the app becomes ready before modules execute and callbacks are registered.+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
|
||
| 181 | -+ | |||
| 60 | +20x |
- #' In those cases the stored values can still be recovered from the `session` object directly.+ checkmate::assert_class(is_transformer_failed, "reactivevalues") |
||
| 182 | +61 |
- #'+ |
||
| 183 | -+ | |||
| 62 | +20x |
- #' Note that variable names in the `values` environment are prefixed with module name space names,+ moduleServer(id, function(input, output, session) {
|
||
| 184 | -+ | |||
| 63 | +20x |
- #' therefore, when using this function in modules, `value` must be run through the name space function.+ logger::log_debug("srv_teal_data initializing.")
|
||
| 185 | -+ | |||
| 64 | +20x |
- #'+ is_transformer_failed[[id]] <- FALSE |
||
| 186 | -+ | |||
| 65 | +20x |
- #' @param value (`character(1)`) name of value to restore+ data_out <- data_module(id = "data") |
||
| 187 | -+ | |||
| 66 | +20x |
- #' @param default fallback value+ data_handled <- reactive(tryCatch(data_out(), error = function(e) e)) |
||
| 188 | -+ | |||
| 67 | +20x |
- #'+ observeEvent(data_handled(), {
|
||
| 189 | -+ | |||
| 68 | +22x |
- #' @return+ if (!inherits(data_handled(), "teal_data")) {
|
||
| 190 | -+ | |||
| 69 | +6x |
- #' In an application restored from a server-side bookmark,+ is_transformer_failed[[id]] <- TRUE |
||
| 191 | +70 |
- #' the variable specified by `value` from the `values` environment.+ } else {
|
||
| 192 | -+ | |||
| 71 | +16x |
- #' Otherwise `default`.+ is_transformer_failed[[id]] <- FALSE |
||
| 193 | +72 |
- #'+ } |
||
| 194 | +73 |
- #' @keywords internal+ }) |
||
| 195 | +74 |
- #'+ |
||
| 196 | -+ | |||
| 75 | +20x |
- restoreValue <- function(value, default) { # nolint: object_name.
+ is_previous_failed <- reactive({
|
||
| 197 | -164x | +76 | +20x |
- checkmate::assert_character("value")
+ idx_this <- which(names(is_transformer_failed) == id) |
| 198 | -164x | +77 | +20x |
- session_default <- shiny::getDefaultReactiveDomain()+ is_transformer_failed_list <- reactiveValuesToList(is_transformer_failed) |
| 199 | -164x | +78 | +20x |
- session_parent <- .subset2(session_default, "parent")+ idx_failures <- which(unlist(is_transformer_failed_list)) |
| 200 | -164x | +79 | +20x |
- session <- if (is.null(session_parent)) session_default else session_parent+ any(idx_failures < idx_this) |
| 201 | +80 | ++ |
+ })+ |
+ |
| 81 | ||||
| 202 | -164x | +82 | +20x |
- if (isTRUE(session$restoreContext$active) && exists(value, session$restoreContext$values, inherits = FALSE)) {
+ observeEvent(is_previous_failed(), {
+ |
+
| 83 | +20x | +
+ if (is_previous_failed()) {
|
||
| 203 | +84 | ! |
- session$restoreContext$values[[value]]+ shinyjs::disable("wrapper")
|
|
| 204 | +85 |
- } else {
+ } else {
|
||
| 205 | -164x | +86 | +20x |
- default+ shinyjs::enable("wrapper")
|
| 206 | +87 |
- }+ } |
||
| 207 | +88 |
- }+ }) |
||
| 208 | +89 | - + + | +||
| 90 | +20x | +
+ srv_validate_reactive_teal_data(+ |
+ ||
| 91 | +20x | +
+ "validate",+ |
+ ||
| 92 | +20x | +
+ data = data_handled,+ |
+ ||
| 93 | +20x | +
+ modules = modules, |
||
| 209 | -+ | |||
| 94 | +20x |
- #' Compare bookmarks.+ validate_shiny_silent_error = validate_shiny_silent_error, |
||
| 210 | -+ | |||
| 95 | +20x |
- #'+ hide_validation_error = is_previous_failed |
||
| 211 | +96 |
- #' Test if two bookmarks store identical state.+ ) |
||
| 212 | +97 |
- #'+ }) |
||
| 213 | +98 |
- #' `input` environments are compared one variable at a time and if not identical,+ } |
||
| 214 | +99 |
- #' values in both bookmarks are reported. States of `datatable`s are stripped+ |
||
| 215 | +100 |
- #' of the `time` element before comparing because the time stamp is always different.+ #' @rdname module_teal_data |
||
| 216 | +101 |
- #' The contents themselves are not printed as they are large and the contents are not informative.+ ui_validate_reactive_teal_data <- function(id) {
|
||
| 217 | -+ | |||
| 102 | +82x |
- #' Elements present in one bookmark and absent in the other are also reported.+ ns <- NS(id) |
||
| 218 | -+ | |||
| 103 | +82x |
- #' Differences are printed as messages.+ tagList( |
||
| 219 | -+ | |||
| 104 | +82x |
- #'+ div( |
||
| 220 | -+ | |||
| 105 | +82x |
- #' `values` environments are compared with `all.equal`.+ id = ns("validate_messages"),
|
||
| 221 | -+ | |||
| 106 | +82x |
- #'+ class = "teal_validated", |
||
| 222 | -+ | |||
| 107 | +82x |
- #' @section How to use:+ ui_validate_error(ns("silent_error")),
|
||
| 223 | -+ | |||
| 108 | +82x |
- #' Open an application, change relevant inputs (typically, all of them), and create a bookmark.+ ui_check_class_teal_data(ns("class_teal_data")),
|
||
| 224 | -+ | |||
| 109 | +82x |
- #' Then open that bookmark and immediately create a bookmark of that.+ ui_check_shiny_warnings(ns("shiny_warnings"))
|
||
| 225 | +110 |
- #' If restoring bookmarks occurred properly, the two bookmarks should store the same state.+ ), |
||
| 226 | -+ | |||
| 111 | +82x |
- #'+ div( |
||
| 227 | -+ | |||
| 112 | +82x |
- #'+ class = "teal_validated", |
||
| 228 | -+ | |||
| 113 | +82x |
- #' @param book1,book2 bookmark directories stored in `shiny_bookmarks/`;+ uiOutput(ns("previous_failed"))
|
||
| 229 | +114 |
- #' default to the two most recently modified directories+ ) |
||
| 230 | +115 |
- #'+ ) |
||
| 231 | +116 |
- #' @return+ } |
||
| 232 | +117 |
- #' Invisible `NULL` if bookmarks are identical or if there are no bookmarks to test.+ |
||
| 233 | +118 |
- #' `FALSE` if inconsistencies are detected.+ #' @rdname module_teal_data |
||
| 234 | +119 |
- #'+ srv_validate_reactive_teal_data <- function(id, # nolint: object_length |
||
| 235 | +120 |
- #' @keywords internal+ data, |
||
| 236 | +121 |
- #'+ modules = NULL, |
||
| 237 | +122 |
- bookmarks_identical <- function(book1, book2) {
+ validate_shiny_silent_error = FALSE, |
||
| 238 | -! | +|||
| 123 | +
- if (!dir.exists("shiny_bookmarks")) {
+ hide_validation_error = reactive(FALSE)) {
|
|||
| 239 | -! | +|||
| 124 | +183x |
- message("no bookmark directory")
+ checkmate::assert_string(id) |
||
| 240 | -! | +|||
| 125 | +183x |
- return(invisible(NULL))+ checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"), null.ok = TRUE)
|
||
| 241 | -+ | |||
| 126 | +183x |
- }+ checkmate::assert_flag(validate_shiny_silent_error) |
||
| 242 | +127 | |||
| 243 | -! | +|||
| 128 | +183x |
- ans <- TRUE+ moduleServer(id, function(input, output, session) {
|
||
| 244 | +129 | - - | -||
| 245 | -! | -
- if (missing(book1) && missing(book2)) {
- |
- ||
| 246 | -! | -
- dirs <- list.dirs("shiny_bookmarks", recursive = FALSE)
+ # there is an empty reactive cycle on `init` and `data_rv` has `shiny.silent.error` class |
||
| 247 | -! | +|||
| 130 | +183x |
- bookmarks_sorted <- basename(rev(dirs[order(file.mtime(dirs))]))+ srv_validate_error("silent_error", data, validate_shiny_silent_error)
|
||
| 248 | -! | +|||
| 131 | +183x |
- if (length(bookmarks_sorted) < 2L) {
+ srv_check_class_teal_data("class_teal_data", data)
|
||
| 249 | -! | +|||
| 132 | +183x |
- message("no bookmarks to compare")
+ srv_check_shiny_warnings("shiny_warnings", data, modules)
|
||
| 250 | -! | +|||
| 133 | +183x |
- return(invisible(NULL))+ output$previous_failed <- renderUI({
|
||
| 251 | -+ | |||
| 134 | +173x |
- }+ if (hide_validation_error()) {
|
||
| 252 | +135 | ! |
- book1 <- bookmarks_sorted[2L]+ shinyjs::hide("validate_messages")
|
|
| 253 | +136 | ! |
- book2 <- bookmarks_sorted[1L]+ tags$div("One of previous transformers failed. Please fix and continue.", class = "teal-output-warning")
|
|
| 254 | +137 |
- } else {
+ } else {
|
||
| 255 | -! | +|||
| 138 | +173x |
- if (!dir.exists(file.path("shiny_bookmarks", book1))) stop(book1, " not found")
+ shinyjs::show("validate_messages")
|
||
| 256 | -! | +|||
| 139 | +173x |
- if (!dir.exists(file.path("shiny_bookmarks", book2))) stop(book2, " not found")
+ NULL |
||
| 257 | +140 |
- }+ } |
||
| 258 | +141 | - - | -||
| 259 | -! | -
- book1_input <- readRDS(file.path("shiny_bookmarks", book1, "input.rds"))
- |
- ||
| 260 | -! | -
- book2_input <- readRDS(file.path("shiny_bookmarks", book2, "input.rds"))
+ }) |
||
| 261 | +142 | |||
| 262 | -! | -
- elements_common <- intersect(names(book1_input), names(book2_input))- |
- ||
| 263 | -! | -
- dt_states <- grepl("_state$", elements_common)
- |
- ||
| 264 | -! | -
- if (any(dt_states)) {
- |
- ||
| 265 | -! | -
- for (el in elements_common[dt_states]) {
- |
- ||
| 266 | -! | -
- book1_input[[el]][["time"]] <- NULL- |
- ||
| 267 | -! | +|||
| 143 | +183x |
- book2_input[[el]][["time"]] <- NULL+ .trigger_on_success(data) |
||
| 268 | +144 |
- }+ }) |
||
| 269 | +145 |
- }+ } |
||
| 270 | +146 | |||
| 271 | -! | -
- identicals <- mapply(identical, book1_input[elements_common], book2_input[elements_common])- |
- ||
| 272 | -! | -
- non_identicals <- names(identicals[!identicals])- |
- ||
| 273 | -! | +|||
| 147 | +
- compares <- sprintf("$ %s:\t%s --- %s", non_identicals, book1_input[non_identicals], book2_input[non_identicals])
+ #' @keywords internal |
|||
| 274 | -! | +|||
| 148 | +
- if (length(compares) != 0L) {
+ ui_validate_error <- function(id) {
|
|||
| 275 | -! | +|||
| 149 | +82x |
- message("common elements not identical: \n", paste(compares, collapse = "\n"))
+ ns <- NS(id) |
||
| 276 | -! | +|||
| 150 | +82x |
- ans <- FALSE+ uiOutput(ns("message"))
|
||
| 277 | +151 |
- }+ } |
||
| 278 | +152 | |||
| 279 | -! | -
- elements_boook1 <- setdiff(names(book1_input), names(book2_input))- |
- ||
| 280 | -! | -
- if (length(elements_boook1) != 0L) {
- |
- ||
| 281 | -! | -
- dt_states <- grepl("_state$", elements_boook1)
- |
- ||
| 282 | -! | +|||
| 153 | +
- if (any(dt_states)) {
+ #' @keywords internal |
|||
| 283 | -! | +|||
| 154 | +
- for (el in elements_boook1[dt_states]) {
+ srv_validate_error <- function(id, data, validate_shiny_silent_error) {
|
|||
| 284 | -! | +|||
| 155 | +183x |
- if (is.list(book1_input[[el]])) book1_input[[el]] <- "--- data table state ---"+ checkmate::assert_string(id) |
||
| 285 | -+ | |||
| 156 | +183x |
- }+ checkmate::assert_flag(validate_shiny_silent_error) |
||
| 286 | -+ | |||
| 157 | +183x |
- }+ moduleServer(id, function(input, output, session) {
|
||
| 287 | -! | +|||
| 158 | +183x |
- excess1 <- sprintf("$ %s:\t%s", elements_boook1, book1_input[elements_boook1])
+ output$message <- renderUI({
|
||
| 288 | -! | +|||
| 159 | +186x |
- message("elements only in book1: \n", paste(excess1, collapse = "\n"))
+ is_shiny_silent_error <- inherits(data(), "shiny.silent.error") && identical(data()$message, "") |
||
| 289 | -! | +|||
| 160 | +180x |
- ans <- FALSE+ if (inherits(data(), "qenv.error")) {
|
||
| 290 | -+ | |||
| 161 | +2x |
- }+ validate( |
||
| 291 | -+ | |||
| 162 | +2x |
-
+ need( |
||
| 292 | -! | +|||
| 163 | +2x |
- elements_boook2 <- setdiff(names(book2_input), names(book1_input))+ FALSE, |
||
| 293 | -! | +|||
| 164 | +2x |
- if (length(elements_boook2) != 0L) {
+ paste( |
||
| 294 | -! | +|||
| 165 | +2x |
- dt_states <- grepl("_state$", elements_boook1)
+ "Error when executing the `data` module:", |
||
| 295 | -! | +|||
| 166 | +2x |
- if (any(dt_states)) {
+ strip_style(paste(data()$message, collapse = "\n")), |
||
| 296 | -! | +|||
| 167 | +2x |
- for (el in elements_boook1[dt_states]) {
+ "\nCheck your inputs or contact app developer if error persists.", |
||
| 297 | -! | +|||
| 168 | +2x |
- if (is.list(book2_input[[el]])) book2_input[[el]] <- "--- data table state ---"+ collapse = "\n" |
||
| 298 | +169 |
- }+ ) |
||
| 299 | +170 |
- }+ ) |
||
| 300 | -! | +|||
| 171 | +
- excess2 <- sprintf("$ %s:\t%s", elements_boook2, book2_input[elements_boook2])
+ ) |
|||
| 301 | -! | +|||
| 172 | +178x |
- message("elements only in book2: \n", paste(excess2, collapse = "\n"))
+ } else if (inherits(data(), "error")) {
|
||
| 302 | -! | +|||
| 173 | +7x |
- ans <- FALSE+ if (is_shiny_silent_error && !validate_shiny_silent_error) {
|
||
| 303 | -+ | |||
| 174 | +1x |
- }+ return(NULL) |
||
| 304 | +175 |
-
+ } |
||
| 305 | -! | +|||
| 176 | +6x |
- book1_values <- readRDS(file.path("shiny_bookmarks", book1, "values.rds"))
+ validate( |
||
| 306 | -! | +|||
| 177 | +6x |
- book2_values <- readRDS(file.path("shiny_bookmarks", book2, "values.rds"))
+ need( |
||
| 307 | -+ | |||
| 178 | +6x |
-
+ FALSE, |
||
| 308 | -! | +|||
| 179 | +6x |
- if (!isTRUE(all.equal(book1_values, book2_values))) {
+ sprintf( |
||
| 309 | -! | +|||
| 180 | +6x |
- message("different values detected")
+ "Shiny error when executing the `data` module.\n%s\n%s", |
||
| 310 | -! | +|||
| 181 | +6x |
- message("choices for numeric filters MAY be different, see RangeFilterState$set_choices")
+ data()$message, |
||
| 311 | -! | +|||
| 182 | +6x |
- ans <- FALSE+ "Check your inputs or contact app developer if error persists." |
||
| 312 | +183 |
- }+ ) |
||
| 313 | +184 |
-
+ ) |
||
| 314 | -! | +|||
| 185 | +
- if (ans) message("perfect!")
+ ) |
|||
| 315 | -! | +|||
| 186 | +
- invisible(NULL)+ } |
|||
| 316 | +187 |
- }+ }) |
||
| 317 | +188 |
-
+ }) |
||
| 318 | +189 |
-
+ } |
||
| 319 | +190 |
- # Replacement for [base::rapply] which doesn't handle NULL values - skips the evaluation+ |
||
| 320 | +191 |
- # of the function and returns NULL for given element.+ |
||
| 321 | +192 |
- rapply2 <- function(x, f) {
+ #' @keywords internal |
||
| 322 | -189x | +|||
| 193 | +
- if (inherits(x, "list")) {
+ ui_check_class_teal_data <- function(id) {
|
|||
| 323 | +194 | 82x |
- lapply(x, rapply2, f = f)- |
- |
| 324 | -- |
- } else {
+ ns <- NS(id) |
||
| 325 | -107x | +195 | +82x |
- f(x)+ uiOutput(ns("message"))
|
| 326 | +196 |
- }+ } |
||
| 327 | +197 |
- }+ |
| 1 | +198 |
- #' Generate lockfile for application's environment reproducibility+ #' @keywords internal |
||
| 2 | +199 |
- #'+ srv_check_class_teal_data <- function(id, data) {
|
||
| 3 | -+ | |||
| 200 | +183x |
- #' @param lockfile_path (`character`) path to the lockfile.+ checkmate::assert_string(id) |
||
| 4 | -+ | |||
| 201 | +183x |
- #'+ moduleServer(id, function(input, output, session) {
|
||
| 5 | -+ | |||
| 202 | +183x |
- #' @section Different ways of creating lockfile:+ output$message <- renderUI({
|
||
| 6 | -+ | |||
| 203 | +186x |
- #' `teal` leverages [renv::snapshot()], which offers multiple methods for lockfile creation.+ validate( |
||
| 7 | -+ | |||
| 204 | +186x |
- #'+ need( |
||
| 8 | -+ | |||
| 205 | +186x |
- #' - **Working directory lockfile**: `teal`, by default, will create an `implicit` type lockfile that uses+ inherits(data(), c("teal_data", "error")),
|
||
| 9 | -+ | |||
| 206 | +186x |
- #' `renv::dependencies()` to detect all R packages in the current project's working directory.+ "Did not receive `teal_data` object. Cannot proceed further." |
||
| 10 | +207 |
- #' - **`DESCRIPTION`-based lockfile**: To generate a lockfile based on a `DESCRIPTION` file in your working+ ) |
||
| 11 | +208 |
- #' directory, set `renv::settings$snapshot.type("explicit")`. The naming convention for `type` follows
+ ) |
||
| 12 | +209 |
- #' `renv::snapshot()`. For the `"explicit"` type, refer to `renv::settings$package.dependency.fields()` for the+ }) |
||
| 13 | +210 |
- #' `DESCRIPTION` fields included in the lockfile.+ }) |
||
| 14 | +211 |
- #' - **Custom files-based lockfile**: To specify custom files as the basis for the lockfile, set+ } |
||
| 15 | +212 |
- #' `renv::settings$snapshot.type("custom")` and configure the `renv.snapshot.filter` option.
+
|
||
| 16 | +213 |
- #'+ #' @keywords internal |
||
| 17 | +214 |
- #' @section lockfile usage:+ ui_check_shiny_warnings <- function(id) {
|
||
| 18 | -+ | |||
| 215 | +82x |
- #' After creating the lockfile, you can restore the application's environment using `renv::restore()`.+ ns <- NS(id) |
||
| 19 | -+ | |||
| 216 | +82x |
- #'+ uiOutput(NS(id, "message")) |
||
| 20 | +217 |
- #' @seealso [renv::snapshot()], [renv::restore()].+ } |
||
| 21 | +218 |
- #'+ |
||
| 22 | +219 |
- #' @return `NULL`+ #' @keywords internal |
||
| 23 | +220 |
- #'+ srv_check_shiny_warnings <- function(id, data, modules) {
|
||
| 24 | -+ | |||
| 221 | +183x |
- #' @name module_teal_lockfile+ checkmate::assert_string(id) |
||
| 25 | -+ | |||
| 222 | +183x |
- #' @rdname module_teal_lockfile+ moduleServer(id, function(input, output, session) {
|
||
| 26 | -+ | |||
| 223 | +183x |
- #'+ output$message <- renderUI({
|
||
| 27 | -+ | |||
| 224 | +186x |
- #' @keywords internal+ if (inherits(data(), "teal_data")) {
|
||
| 28 | -+ | |||
| 225 | +169x |
- NULL+ is_modules_ok <- check_modules_datanames_html( |
||
| 29 | -+ | |||
| 226 | +169x |
-
+ modules = modules, datanames = names(data()) |
||
| 30 | +227 |
- #' @rdname module_teal_lockfile+ ) |
||
| 31 | -+ | |||
| 228 | +169x |
- ui_teal_lockfile <- function(id) {
+ if (!isTRUE(is_modules_ok)) {
|
||
| 32 | -! | +|||
| 229 | +15x |
- ns <- NS(id)+ tags$div(is_modules_ok, class = "teal-output-warning") |
||
| 33 | -! | +|||
| 230 | +
- shiny::tagList(+ } |
|||
| 34 | -! | +|||
| 231 | +
- tags$span("", id = ns("lockFileStatus")),
+ } |
|||
| 35 | -! | +|||
| 232 | +
- shinyjs::disabled(downloadLink(ns("lockFileLink"), "Download lockfile"))
+ }) |
|||
| 36 | +233 |
- )+ }) |
||
| 37 | +234 |
} |
||
| 38 | +235 | |||
| 39 | +236 |
- #' @rdname module_teal_lockfile+ .trigger_on_success <- function(data) {
|
||
| 40 | -+ | |||
| 237 | +183x |
- srv_teal_lockfile <- function(id) {
+ out <- reactiveVal(NULL) |
||
| 41 | -83x | +238 | +183x |
- moduleServer(id, function(input, output, session) {
+ observeEvent(data(), {
|
| 42 | -83x | +239 | +180x |
- logger::log_debug("Initialize srv_teal_lockfile.")
+ if (inherits(data(), "teal_data")) {
|
| 43 | -83x | +240 | +169x |
- enable_lockfile_download <- function() {
+ if (!identical(data(), out())) {
|
| 44 | -! | +|||
| 241 | +169x |
- shinyjs::html("lockFileStatus", "Application lockfile ready.")
+ out(data()) |
||
| 45 | -! | +|||
| 242 | +
- shinyjs::hide("lockFileStatus", anim = TRUE)
+ } |
|||
| 46 | -! | +|||
| 243 | +
- shinyjs::enable("lockFileLink")
+ } |
|||
| 47 | -! | +|||
| 244 | +
- output$lockFileLink <- shiny::downloadHandler(+ }) |
|||
| 48 | -! | +|||
| 245 | +
- filename = function() {
+
|
|||
| 49 | -! | +|||
| 246 | +183x |
- "renv.lock"+ out |
||
| 50 | +247 |
- },+ } |
||
| 51 | -! | +
| 1 | +
- content = function(file) {
+ #' Store and restore `teal_slices` object |
|||
| 52 | -! | +|||
| 2 | +
- file.copy(lockfile_path, file)+ #' |
|||
| 53 | -! | +|||
| 3 | +
- file+ #' Functions that write a `teal_slices` object to a file in the `JSON` format, |
|||
| 54 | +4 |
- },+ #' and also restore the object from disk. |
||
| 55 | -! | +|||
| 5 | +
- contentType = "application/json"+ #' |
|||
| 56 | +6 |
- )+ #' Date and date time objects are stored in the following formats: |
||
| 57 | +7 |
- }+ #' |
||
| 58 | -83x | +|||
| 8 | +
- disable_lockfile_download <- function() {
+ #' - `Date` class is converted to the `"ISO8601"` standard (`YYYY-MM-DD`). |
|||
| 59 | -! | +|||
| 9 | +
- warning("Lockfile creation failed.", call. = FALSE)
+ #' - `POSIX*t` classes are converted to character by using |
|||
| 60 | -! | +|||
| 10 | +
- shinyjs::html("lockFileStatus", "Lockfile creation failed.")
+ #' `format.POSIX*t(usetz = TRUE, tz = "UTC")` (`YYYY-MM-DD HH:MM:SS UTC`, where |
|||
| 61 | -! | +|||
| 11 | +
- shinyjs::hide("lockFileLink")
+ #' `UTC` is the `Coordinated Universal Time` timezone short-code). |
|||
| 62 | +12 |
- }+ #' |
||
| 63 | +13 |
-
+ #' This format is assumed during `slices_restore`. All `POSIX*t` objects in |
||
| 64 | -83x | +|||
| 14 | +
- shiny::onStop(function() {
+ #' `selected` or `choices` fields of `teal_slice` objects are always printed in |
|||
| 65 | -83x | +|||
| 15 | +
- if (file.exists(lockfile_path) && !shiny::isRunning()) {
+ #' `UTC` timezone as well. |
|||
| 66 | -1x | +|||
| 16 | +
- logger::log_debug("Removing lockfile after shutting down the app")
+ #' |
|||
| 67 | -1x | +|||
| 17 | +
- file.remove(lockfile_path)+ #' @param tss (`teal_slices`) object to be stored. |
|||
| 68 | +18 |
- }+ #' @param file (`character(1)`) file path where `teal_slices` object will be |
||
| 69 | +19 |
- })+ #' saved and restored. The file extension should be `".json"`. |
||
| 70 | +20 |
-
+ #' |
||
| 71 | -83x | +|||
| 21 | +
- lockfile_path <- "teal_app.lock"+ #' @return `slices_store` returns `NULL`, invisibly. |
|||
| 72 | -83x | +|||
| 22 | +
- mode <- getOption("teal.lockfile.mode", default = "")
+ #' |
|||
| 73 | +23 |
-
+ #' @seealso [teal_slices()] |
||
| 74 | -83x | +|||
| 24 | +
- if (!(mode %in% c("auto", "enabled", "disabled"))) {
+ #' |
|||
| 75 | -! | +|||
| 25 | +
- stop("'teal.lockfile.mode' option can only be one of \"auto\", \"disabled\" or \"disabled\". ")
+ #' @keywords internal |
|||
| 76 | +26 |
- }+ #' |
||
| 77 | +27 |
-
+ slices_store <- function(tss, file) {
|
||
| 78 | -83x | +28 | +9x |
- if (mode == "disabled") {
+ checkmate::assert_class(tss, "teal_slices") |
| 79 | -1x | +29 | +9x |
- logger::log_debug("'teal.lockfile.mode' option is set to 'disabled'. Hiding lockfile download button.")
+ checkmate::assert_path_for_output(file, overwrite = TRUE, extension = "json") |
| 80 | -1x | +|||
| 30 | +
- shinyjs::hide("lockFileLink")
+
|
|||
| 81 | -1x | +31 | +9x |
- return(NULL)+ cat(format(tss, trim_lines = FALSE), "\n", file = file) |
| 82 | +32 |
- }+ } |
||
| 83 | +33 | |||
| 84 | -82x | +|||
| 34 | +
- if (file.exists(lockfile_path)) {
+ #' @rdname slices_store |
|||
| 85 | -! | +|||
| 35 | +
- logger::log_debug("Lockfile has already been created for this app - skipping automatic creation.")
+ #' @return `slices_restore` returns a `teal_slices` object restored from the file. |
|||
| 86 | -! | +|||
| 36 | +
- enable_lockfile_download()+ #' @keywords internal |
|||
| 87 | -! | +|||
| 37 | +
- return(NULL)+ slices_restore <- function(file) {
|
|||
| 88 | -+ | |||
| 38 | +9x |
- }+ checkmate::assert_file_exists(file, access = "r", extension = "json") |
||
| 89 | +39 | |||
| 90 | -82x | +40 | +9x |
- if (mode == "auto" && .is_disabled_lockfile_scenario()) {
+ tss_json <- jsonlite::fromJSON(file, simplifyDataFrame = FALSE) |
| 91 | -81x | +41 | +9x |
- logger::log_debug(+ tss_json$slices <- |
| 92 | -81x | +42 | +9x |
- "Automatic lockfile creation disabled. Execution scenario satisfies teal:::.is_disabled_lockfile_scenario()."+ lapply(tss_json$slices, function(slice) {
|
| 93 | -+ | |||
| 43 | +9x |
- )+ for (field in c("selected", "choices")) {
|
||
| 94 | -81x | +44 | +18x |
- shinyjs::hide("lockFileLink")
+ if (!is.null(slice[[field]])) {
|
| 95 | -81x | +45 | +12x |
- return(NULL)+ if (length(slice[[field]]) > 0) {
|
| 96 | -+ | |||
| 46 | +9x |
- }+ date_partial_regex <- "^[0-9]{4}-[0-9]{2}-[0-9]{2}"
+ |
+ ||
| 47 | +9x | +
+ time_stamp_regex <- paste0(date_partial_regex, "\\s[0-9]{2}:[0-9]{2}:[0-9]{2}\\sUTC$")
|
||
| 97 | +48 | |||
| 98 | -1x | +49 | +9x |
- if (!.is_lockfile_deps_installed()) {
+ slice[[field]] <- |
| 99 | -! | +|||
| 50 | +9x |
- warning("Automatic lockfile creation disabled. `mirai` and `renv` packages must be installed.")
+ if (all(grepl(paste0(date_partial_regex, "$"), slice[[field]]))) {
|
||
| 100 | -! | +|||
| 51 | +3x |
- shinyjs::hide("lockFileLink")
+ as.Date(slice[[field]]) |
||
| 101 | -! | +|||
| 52 | +9x |
- return(NULL)+ } else if (all(grepl(time_stamp_regex, slice[[field]]))) {
|
||
| 102 | -+ | |||
| 53 | +3x |
- }+ as.POSIXct(slice[[field]], tz = "UTC") |
||
| 103 | +54 |
-
+ } else {
|
||
| 104 | -+ | |||
| 55 | +3x |
- # - Will be run only if the lockfile doesn't exist (see the if-s above)+ slice[[field]] |
||
| 105 | +56 |
- # - We render to the tempfile because the process might last after session is closed and we don't+ } |
||
| 106 | +57 |
- # want to make a "teal_app.renv" then. This is why we copy only during active session.- |
- ||
| 107 | -1x | -
- process <- .teal_lockfile_process_invoke(lockfile_path)+ } else {
|
||
| 108 | -1x | -
- observeEvent(process$status(), {
- |
- ||
| 109 | -! | -
- if (process$status() %in% c("initial", "running")) {
- |
- ||
| 110 | -! | -
- shinyjs::html("lockFileStatus", "Creating lockfile...")
- |
- ||
| 111 | -! | -
- } else if (process$status() == "success") {
- |
- ||
| 112 | -! | +58 | +3x |
- result <- process$result()+ slice[[field]] <- character(0) |
| 113 | -! | +|||
| 59 | +
- if (any(grepl("Lockfile written to", result$out))) {
+ } |
|||
| 114 | -! | +|||
| 60 | +
- logger::log_debug("Lockfile containing { length(result$res$Packages) } packages created.")
+ } |
|||
| 115 | -! | +|||
| 61 | +
- if (any(grepl("(WARNING|ERROR):", result$out))) {
+ } |
|||
| 116 | -! | +|||
| 62 | +9x |
- warning("Lockfile created with warning(s) or error(s):", call. = FALSE)
+ slice |
||
| 117 | -! | +|||
| 63 | +
- for (i in result$out) {
+ }) |
|||
| 118 | -! | +|||
| 64 | +
- warning(i, call. = FALSE)+ |
|||
| 119 | -+ | |||
| 65 | +9x |
- }+ tss_elements <- lapply(tss_json$slices, as.teal_slice) |
||
| 120 | +66 |
- }+ |
||
| 121 | -! | +|||
| 67 | +9x |
- enable_lockfile_download()+ do.call(teal_slices, c(tss_elements, tss_json$attributes)) |
||
| 122 | +68 |
- } else {
+ } |
||
| 123 | -! | +
| 1 | +
- disable_lockfile_download()+ #' @title `TealReportCard` |
|||
| 124 | +2 |
- }+ #' @description `r lifecycle::badge("experimental")`
|
||
| 125 | -! | +|||
| 3 | +
- } else if (process$status() == "error") {
+ #' Child class of [`ReportCard`] that is used for `teal` specific applications. |
|||
| 126 | -! | +|||
| 4 | +
- disable_lockfile_download()+ #' In addition to the parent methods, it supports rendering `teal` specific elements such as |
|||
| 127 | +5 |
- }+ #' the source code, the encodings panel content and the filter panel content as part of the |
||
| 128 | +6 |
- })+ #' meta data. |
||
| 129 | +7 |
-
+ #' @export |
||
| 130 | -1x | +|||
| 8 | +
- NULL+ #' |
|||
| 131 | +9 |
- })+ TealReportCard <- R6::R6Class( # nolint: object_name. |
||
| 132 | +10 |
- }+ classname = "TealReportCard", |
||
| 133 | +11 |
-
+ inherit = teal.reporter::ReportCard, |
||
| 134 | +12 |
- utils::globalVariables(c("opts", "sysenv", "libpaths", "wd", "lockfilepath", "run")) # needed for mirai call
+ public = list( |
||
| 135 | +13 |
- #' @rdname module_teal_lockfile+ #' @description Appends the source code to the `content` meta data of this `TealReportCard`. |
||
| 136 | +14 |
- .teal_lockfile_process_invoke <- function(lockfile_path) {
+ #' |
||
| 137 | -1x | +|||
| 15 | +
- mirai_obj <- NULL+ #' @param src (`character(1)`) code as text. |
|||
| 138 | -1x | +|||
| 16 | +
- process <- shiny::ExtendedTask$new(function() {
+ #' @param ... any `rmarkdown` `R` chunk parameter and its value. |
|||
| 139 | -1x | +|||
| 17 | +
- m <- mirai::mirai(+ #' But `eval` parameter is always set to `FALSE`. |
|||
| 140 | +18 |
- {
+ #' @return Object of class `TealReportCard`, invisibly. |
||
| 141 | -1x | +|||
| 19 | +
- options(opts)+ #' @examples |
|||
| 142 | -1x | +|||
| 20 | +
- do.call(Sys.setenv, sysenv)+ #' card <- TealReportCard$new()$append_src( |
|||
| 143 | -1x | +|||
| 21 | +
- .libPaths(libpaths)+ #' "plot(iris)" |
|||
| 144 | -1x | +|||
| 22 | +
- setwd(wd)+ #' ) |
|||
| 145 | -1x | +|||
| 23 | +
- run(lockfile_path = lockfile_path)+ #' card$get_content()[[1]]$get_content() |
|||
| 146 | +24 |
- },+ append_src = function(src, ...) {
|
||
| 147 | -1x | +25 | +4x |
- run = .renv_snapshot,+ checkmate::assert_character(src, min.len = 0, max.len = 1) |
| 148 | -1x | +26 | +4x |
- lockfile_path = lockfile_path,+ params <- list(...) |
| 149 | -1x | +27 | +4x |
- opts = options(),+ params$eval <- FALSE |
| 150 | -1x | +28 | +4x |
- libpaths = .libPaths(),+ rblock <- RcodeBlock$new(src) |
| 151 | -1x | +29 | +4x |
- sysenv = as.list(Sys.getenv()),+ rblock$set_params(params) |
| 152 | -1x | -
- wd = getwd()- |
- ||
| 153 | -+ | 30 | +4x |
- )+ self$append_content(rblock) |
| 154 | -1x | +31 | +4x |
- mirai_obj <<- m+ self$append_metadata("SRC", src)
|
| 155 | -1x | +32 | +4x |
- m+ invisible(self) |
| 156 | +33 |
- })+ }, |
||
| 157 | +34 |
-
+ #' @description Appends the filter state list to the `content` and `metadata` of this `TealReportCard`. |
||
| 158 | -1x | +|||
| 35 | +
- shiny::onStop(function() {
+ #' If the filter state list has an attribute named `formatted`, it appends it to the card otherwise it uses |
|||
| 159 | -1x | +|||
| 36 | +
- if (mirai::unresolved(mirai_obj)) {
+ #' the default `yaml::as.yaml` to format the list. |
|||
| 160 | -! | +|||
| 37 | +
- logger::log_debug("Terminating a running lockfile process...")
+ #' If the filter state list is empty, nothing is appended to the `content`. |
|||
| 161 | -! | +|||
| 38 | +
- mirai::stop_mirai(mirai_obj) # this doesn't stop running - renv will be created even if session is closed+ #' |
|||
| 162 | +39 |
- }+ #' @param fs (`teal_slices`) object returned from [teal_slices()] function. |
||
| 163 | +40 |
- })+ #' @return `self`, invisibly. |
||
| 164 | +41 |
-
+ append_fs = function(fs) {
|
||
| 165 | -1x | +42 | +5x |
- suppressWarnings({ # 'package:stats' may not be available when loading
+ checkmate::assert_class(fs, "teal_slices") |
| 166 | -1x | +43 | +4x |
- process$invoke()+ self$append_text("Filter State", "header3")
|
| 167 | -+ | |||
| 44 | +4x |
- })+ if (length(fs)) {
+ |
+ ||
| 45 | +3x | +
+ self$append_content(TealSlicesBlock$new(fs)) |
||
| 168 | +46 |
-
+ } else {
|
||
| 169 | +47 | 1x |
- logger::log_debug("Lockfile creation started based on { getwd() }.")
+ self$append_text("No filters specified.")
|
|
| 170 | +48 |
-
+ } |
||
| 171 | -1x | +49 | +4x |
- process+ invisible(self) |
| 172 | +50 |
- }+ }, |
||
| 173 | +51 |
-
+ #' @description Appends the encodings list to the `content` and `metadata` of this `TealReportCard`. |
||
| 174 | +52 |
- #' @rdname module_teal_lockfile+ #' |
||
| 175 | +53 |
- .renv_snapshot <- function(lockfile_path) {
- |
- ||
| 176 | -1x | -
- out <- utils::capture.output(- |
- ||
| 177 | -1x | -
- res <- renv::snapshot(- |
- ||
| 178 | -1x | -
- lockfile = lockfile_path,+ #' @param encodings (`list`) list of encodings selections of the `teal` app. |
||
| 179 | -1x | +|||
| 54 | +
- prompt = FALSE,+ #' @return `self`, invisibly. |
|||
| 180 | -1x | +|||
| 55 | +
- force = TRUE,+ #' @examples |
|||
| 181 | -1x | +|||
| 56 | +
- type = renv::settings$snapshot.type() # see the section "Different ways of creating lockfile" above here+ #' card <- TealReportCard$new()$append_encodings(list(variable1 = "X")) |
|||
| 182 | +57 |
- )+ #' card$get_content()[[1]]$get_content() |
||
| 183 | +58 |
- )+ #' |
||
| 184 | +59 |
-
+ append_encodings = function(encodings) {
|
||
| 185 | -1x | +60 | +4x |
- list(out = out, res = res)+ checkmate::assert_list(encodings) |
| 186 | -+ | |||
| 61 | +4x |
- }+ self$append_text("Selected Options", "header3")
|
||
| 187 | -+ | |||
| 62 | +4x |
-
+ if (requireNamespace("yaml", quietly = TRUE)) {
|
||
| 188 | -+ | |||
| 63 | +4x |
- #' @rdname module_teal_lockfile+ self$append_text(yaml::as.yaml(encodings, handlers = list( |
||
| 189 | -+ | |||
| 64 | +4x |
- .is_lockfile_deps_installed <- function() {
+ POSIXct = function(x) format(x, "%Y-%m-%d"), |
||
| 190 | -1x | +65 | +4x |
- requireNamespace("mirai", quietly = TRUE) && requireNamespace("renv", quietly = TRUE)
+ POSIXlt = function(x) format(x, "%Y-%m-%d"), |
| 191 | -+ | |||
| 66 | +4x |
- }+ Date = function(x) format(x, "%Y-%m-%d") |
||
| 192 | -+ | |||
| 67 | +4x |
-
+ )), "verbatim") |
||
| 193 | +68 |
- #' @rdname module_teal_lockfile+ } else {
|
||
| 194 | -+ | |||
| 69 | +! |
- .is_disabled_lockfile_scenario <- function() {
+ stop("yaml package is required to format the encodings list")
|
||
| 195 | -81x | +|||
| 70 | +
- identical(Sys.getenv("CALLR_IS_RUNNING"), "true") || # inside callr process
+ } |
|||
| 196 | -81x | +71 | +4x |
- identical(Sys.getenv("TESTTHAT"), "true") || # inside devtools::test
+ self$append_metadata("Encodings", encodings)
|
| 197 | -81x | +72 | +4x |
- !identical(Sys.getenv("QUARTO_PROJECT_ROOT"), "") || # inside Quarto process
+ invisible(self) |
| 198 | +73 |
- (- |
- ||
| 199 | -81x | -
- ("CheckExEnv" %in% search()) || any(c("_R_CHECK_TIMINGS_", "_R_CHECK_LICENSE_") %in% names(Sys.getenv()))
+ } |
||
| 200 | -81x | +|||
| 74 | +
- ) # inside R CMD CHECK+ ), |
|||
| 201 | +75 |
- }+ private = list( |
| 1 | +76 |
- #' An example `teal` module+ dispatch_block = function(block_class) {
|
||
| 2 | -+ | |||
| 77 | +! |
- #'+ eval(str2lang(block_class)) |
||
| 3 | +78 |
- #' `r lifecycle::badge("experimental")`
+ } |
||
| 4 | +79 |
- #'+ ) |
||
| 5 | +80 |
- #' @inheritParams teal_modules+ ) |
||
| 6 | +81 |
- #' @return A `teal` module which can be included in the `modules` argument to [init()].+ |
||
| 7 | +82 |
- #' @examples+ #' @title `TealSlicesBlock` |
||
| 8 | +83 |
- #' app <- init(+ #' @docType class |
||
| 9 | +84 |
- #' data = teal_data(IRIS = iris, MTCARS = mtcars),+ #' @description |
||
| 10 | +85 |
- #' modules = example_module()+ #' Specialized `TealSlicesBlock` block for managing filter panel content in reports. |
||
| 11 | +86 |
- #' )+ #' @keywords internal |
||
| 12 | +87 |
- #' if (interactive()) {
+ TealSlicesBlock <- R6::R6Class( # nolint: object_name_linter. |
||
| 13 | +88 |
- #' shinyApp(app$ui, app$server)+ classname = "TealSlicesBlock", |
||
| 14 | +89 |
- #' }+ inherit = teal.reporter:::TextBlock, |
||
| 15 | +90 |
- #' @export+ public = list( |
||
| 16 | +91 |
- example_module <- function(label = "example teal module", datanames = "all", transformers = list()) {
+ #' @description Returns a `TealSlicesBlock` object. |
||
| 17 | -38x | +|||
| 92 | +
- checkmate::assert_string(label)+ #' |
|||
| 18 | -38x | +|||
| 93 | +
- ans <- module(+ #' @details Returns a `TealSlicesBlock` object with no content and no parameters. |
|||
| 19 | -38x | +|||
| 94 | +
- label,+ #' |
|||
| 20 | -38x | +|||
| 95 | +
- server = function(id, data) {
+ #' @param content (`teal_slices`) object returned from [teal_slices()] function. |
|||
| 21 | -2x | +|||
| 96 | +
- checkmate::assert_class(isolate(data()), "teal_data")+ #' @param style (`character(1)`) string specifying style to apply. |
|||
| 22 | -2x | +|||
| 97 | +
- moduleServer(id, function(input, output, session) {
+ #' |
|||
| 23 | -2x | +|||
| 98 | +
- datanames_rv <- reactive(ls(teal.code::get_env((req(data())))))+ #' @return Object of class `TealSlicesBlock`, invisibly. |
|||
| 24 | -2x | +|||
| 99 | +
- observeEvent(datanames_rv(), {
+ #' |
|||
| 25 | -2x | +|||
| 100 | +
- selected <- input$dataname+ initialize = function(content = teal_slices(), style = "verbatim") {
|
|||
| 26 | -2x | -
- if (identical(selected, "")) {
- |
- ||
| 27 | -! | +101 | +9x |
- selected <- restoreInput(session$ns("dataname"), NULL)
+ self$set_content(content) |
| 28 | -2x | +102 | +8x |
- } else if (isFALSE(selected %in% datanames_rv())) {
+ self$set_style(style) |
| 29 | -! | +|||
| 103 | +8x |
- selected <- datanames_rv()[1]+ invisible(self) |
||
| 30 | +104 |
- }- |
- ||
| 31 | -2x | -
- updateSelectInput(- |
- ||
| 32 | -2x | -
- session = session,+ }, |
||
| 33 | -2x | +|||
| 105 | +
- inputId = "dataname",+ |
|||
| 34 | -2x | +|||
| 106 | +
- choices = datanames_rv(),+ #' @description Sets content of this `TealSlicesBlock`. |
|||
| 35 | -2x | +|||
| 107 | +
- selected = selected+ #' Sets content as `YAML` text which represents a list generated from `teal_slices`. |
|||
| 36 | +108 |
- )+ #' The list displays limited number of fields from `teal_slice` objects, but this list is |
||
| 37 | +109 |
- })+ #' sufficient to conclude which filters were applied. |
||
| 38 | +110 |
-
+ #' When `selected` field in `teal_slice` object is a range, then it is displayed as a "min" |
||
| 39 | -2x | +|||
| 111 | +
- output$text <- renderPrint({
+ #' |
|||
| 40 | -2x | +|||
| 112 | +
- req(input$dataname)+ #' |
|||
| 41 | -! | +|||
| 113 | +
- data()[[input$dataname]]+ #' @param content (`teal_slices`) object returned from [teal_slices()] function. |
|||
| 42 | +114 |
- })+ #' @return `self`, invisibly. |
||
| 43 | +115 |
-
+ set_content = function(content) {
|
||
| 44 | -2x | +116 | +9x |
- teal.widgets::verbatim_popup_srv(+ checkmate::assert_class(content, "teal_slices") |
| 45 | -2x | +117 | +8x |
- id = "rcode",+ if (length(content) != 0) {
|
| 46 | -2x | +118 | +6x |
- verbatim_content = reactive(teal.code::get_code(data())),+ states_list <- lapply(content, function(x) {
|
| 47 | -2x | +119 | +6x |
- title = "Example Code"+ x_list <- shiny::isolate(as.list(x)) |
| 48 | -+ | |||
| 120 | +6x |
- )+ if ( |
||
| 49 | -+ | |||
| 121 | +6x |
- })+ inherits(x_list$choices, c("integer", "numeric", "Date", "POSIXct", "POSIXlt")) &&
|
||
| 50 | -+ | |||
| 122 | +6x |
- },+ length(x_list$choices) == 2 && |
||
| 51 | -38x | +123 | +6x |
- ui = function(id) {
+ length(x_list$selected) == 2 |
| 52 | -! | +|||
| 124 | +
- ns <- NS(id)+ ) {
|
|||
| 53 | +125 | ! |
- teal.widgets::standard_layout(+ x_list$range <- paste(x_list$selected, collapse = " - ") |
|
| 54 | +126 | ! |
- output = verbatimTextOutput(ns("text")),
+ x_list["selected"] <- NULL |
|
| 55 | -! | +|||
| 127 | +
- encoding = tags$div(+ } |
|||
| 56 | -! | +|||
| 128 | +6x |
- selectInput(ns("dataname"), "Choose a dataset", choices = NULL),
+ if (!is.null(x_list$arg)) {
|
||
| 57 | +129 | ! |
- teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
- |
- |
| 58 | -- |
- )+ x_list$arg <- if (x_list$arg == "subset") "Genes" else "Samples" |
||
| 59 | +130 |
- )+ } |
||
| 60 | +131 |
- },+ |
||
| 61 | -38x | +132 | +6x |
- datanames = datanames,+ x_list <- x_list[ |
| 62 | -38x | +133 | +6x |
- transformers = transformers+ c("dataname", "varname", "experiment", "arg", "expr", "selected", "range", "keep_na", "keep_inf")
|
| 63 | +134 |
- )+ ] |
||
| 64 | -38x | +135 | +6x |
- attr(ans, "teal_bookmarkable") <- TRUE+ names(x_list) <- c( |
| 65 | -38x | +136 | +6x |
- ans+ "Dataset name", "Variable name", "Experiment", "Filtering by", "Applied expression", |
| 66 | -+ | |||
| 137 | +6x |
- }+ "Selected Values", "Selected range", "Include NA values", "Include Inf values" |
| 1 | +138 |
- #' Create a `teal` module for previewing a report+ ) |
||
| 2 | +139 |
- #'+ |
||
| 3 | -+ | |||
| 140 | +6x |
- #' @description `r lifecycle::badge("experimental")`
+ Filter(Negate(is.null), x_list) |
||
| 4 | +141 |
- #'+ }) |
||
| 5 | +142 |
- #' This function wraps [teal.reporter::reporter_previewer_ui()] and+ |
||
| 6 | -+ | |||
| 143 | +6x |
- #' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be+ if (requireNamespace("yaml", quietly = TRUE)) {
+ |
+ ||
| 144 | +6x | +
+ super$set_content(yaml::as.yaml(states_list)) |
||
| 7 | +145 |
- #' used in `teal` applications.+ } else {
+ |
+ ||
| 146 | +! | +
+ stop("yaml package is required to format the filter state list")
|
||
| 8 | +147 |
- #'+ } |
||
| 9 | +148 |
- #' If you are creating a `teal` application using [init()] then this+ }+ |
+ ||
| 149 | +8x | +
+ private$teal_slices <- content+ |
+ ||
| 150 | +8x | +
+ invisible(self) |
||
| 10 | +151 |
- #' module will be added to your application automatically if any of your `teal_modules`+ }, |
||
| 11 | +152 |
- #' support report generation.+ #' @description Create the `TealSlicesBlock` from a list. |
||
| 12 | +153 |
- #'+ #' |
||
| 13 | +154 |
- #' @inheritParams teal_modules+ #' @param x (`named list`) with two fields `text` and `style`. |
||
| 14 | +155 |
- #' @param server_args (named `list`)+ #' Use the `get_available_styles` method to get all possible styles. |
||
| 15 | +156 |
- #' Arguments passed to [teal.reporter::reporter_previewer_srv()].+ #' |
||
| 16 | +157 |
- #'+ #' @return `self`, invisibly. |
||
| 17 | +158 |
- #' @return+ #' @examples |
||
| 18 | +159 |
- #' `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer functionality.+ #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
|
||
| 19 | +160 |
- #'+ #' block <- TealSlicesBlock$new() |
||
| 20 | +161 |
- #' @export+ #' block$from_list(list(text = "sth", style = "default")) |
||
| 21 | +162 |
- #'+ #' |
||
| 22 | +163 |
- reporter_previewer_module <- function(label = "Report previewer", server_args = list()) {
+ from_list = function(x) {
|
||
| 23 | -7x | +164 | +1x |
- checkmate::assert_string(label)+ checkmate::assert_list(x) |
| 24 | -5x | +165 | +1x |
- checkmate::assert_list(server_args, names = "named")+ checkmate::assert_names(names(x), must.include = c("text", "style"))
|
| 25 | -5x | +166 | +1x |
- checkmate::assert_true(all(names(server_args) %in% names(formals(teal.reporter::reporter_previewer_srv))))+ super$set_content(x$text) |
| 26 | -+ | |||
| 167 | +1x |
-
+ super$set_style(x$style) |
||
| 27 | -3x | +168 | +1x |
- message("Initializing reporter_previewer_module")
+ invisible(self) |
| 28 | +169 |
-
+ }, |
||
| 29 | -3x | +|||
| 170 | +
- srv <- function(id, reporter, ...) {
+ #' @description Convert the `TealSlicesBlock` to a list. |
|||
| 30 | -! | +|||
| 171 | +
- teal.reporter::reporter_previewer_srv(id, reporter, ...)+ #' |
|||
| 31 | +172 |
- }+ #' @return `named list` with a text and style. |
||
| 32 | +173 |
-
+ #' @examples |
||
| 33 | -3x | +|||
| 174 | +
- ui <- function(id, ...) {
+ #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
|
|||
| 34 | -! | +|||
| 175 | +
- teal.reporter::reporter_previewer_ui(id, ...)+ #' block <- TealSlicesBlock$new() |
|||
| 35 | +176 |
- }+ #' block$to_list() |
||
| 36 | +177 |
-
+ #'+ |
+ ||
| 178 | ++ |
+ to_list = function() {
|
||
| 37 | -3x | +179 | +2x |
- module <- module(+ content <- self$get_content() |
| 38 | -3x | +180 | +2x |
- label = "temporary label",+ list( |
| 39 | -3x | +181 | +2x |
- server = srv, ui = ui,+ text = if (length(content)) content else "", |
| 40 | -3x | +182 | +2x |
- server_args = server_args, ui_args = list(), datanames = NULL+ style = self$get_style() |
| 41 | +183 |
- )+ ) |
||
| 42 | +184 |
- # Module is created with a placeholder label and the label is changed later.+ } |
||
| 43 | +185 |
- # This is to prevent another module being labeled "Report previewer".+ ), |
||
| 44 | -3x | +|||
| 186 | +
- class(module) <- c(class(module), "teal_module_previewer")+ private = list( |
|||
| 45 | -3x | +|||
| 187 | +
- module$label <- label+ style = "verbatim", |
|||
| 46 | -3x | +|||
| 188 | +
- attr(module, "teal_bookmarkable") <- TRUE+ teal_slices = NULL # teal_slices |
|||
| 47 | -3x | +|||
| 189 | +
- module+ ) |
|||
| 48 | +190 |
- }+ ) |
| 1 |
- #' Data Module for teal+ #' App state management. |
||
| 3 |
- #' This module manages the `data` argument for `srv_teal`. The `teal` framework uses [teal_data()],+ #' @description |
||
| 4 |
- #' which can be provided in various ways:+ #' `r lifecycle::badge("experimental")`
|
||
| 5 |
- #' 1. Directly as a [teal.data::teal_data()] object. This will automatically convert it into a `reactive` `teal_data`.+ #' |
||
| 6 |
- #' 2. As a `reactive` object that returns a [teal.data::teal_data()] object.+ #' Capture and restore the global (app) input state. |
||
| 9 |
- #' ## Reactive `teal_data`:+ #' This module introduces bookmarks into `teal` apps: the `shiny` bookmarking mechanism becomes enabled |
||
| 10 |
- #'+ #' and server-side bookmarks can be created. |
||
| 11 |
- #' The data in the application can be reactively updated, prompting [srv_teal()] to rebuild the+ #' |
||
| 12 |
- #' content accordingly. There are two methods for creating interactive `teal_data`:+ #' The bookmark manager presents a button with the bookmark icon and is placed in the tab-bar. |
||
| 13 |
- #' 1. Using a `reactive` object provided from outside the `teal` application. In this scenario,+ #' When clicked, the button creates a bookmark and opens a modal which displays the bookmark URL. |
||
| 14 |
- #' reactivity is controlled by an external module, and `srv_teal` responds to changes.+ #' |
||
| 15 |
- #' 2. Using [teal_data_module()], which is embedded within the `teal` application, allowing data to+ #' `teal` does not guarantee that all modules (`teal_module` objects) are bookmarkable. |
||
| 16 |
- #' be resubmitted by the user as needed.+ #' Those that are, have a `teal_bookmarkable` attribute set to `TRUE`. If any modules are not bookmarkable, |
||
| 17 |
- #'+ #' the bookmark manager modal displays a warning and the bookmark button displays a flag. |
||
| 18 |
- #' Since the server of [teal_data_module()] must return a `reactive` `teal_data` object, both+ #' In order to communicate that a external module is bookmarkable, the module developer |
||
| 19 |
- #' methods (1 and 2) produce the same reactive behavior within a `teal` application. The distinction+ #' should set the `teal_bookmarkable` attribute to `TRUE`. |
||
| 20 |
- #' lies in data control: the first method involves external control, while the second method+ #' |
||
| 21 |
- #' involves control from a custom module within the app.+ #' @section Server logic: |
||
| 22 |
- #'+ #' A bookmark is a URL that contains the app address with a `/?_state_id_=<bookmark_dir>` suffix. |
||
| 23 |
- #' For more details, see [`module_teal_data`].+ #' `<bookmark_dir>` is a directory created on the server, where the state of the application is saved. |
||
| 24 |
- #'+ #' Accessing the bookmark URL opens a new session of the app that starts in the previously saved state. |
||
| 25 |
- #' @inheritParams init+ #' |
||
| 26 |
- #'+ #' @section Note: |
||
| 27 |
- #' @param data (`teal_data`, `teal_data_module`, or `reactive` returning `teal_data`)+ #' To enable bookmarking use either: |
||
| 28 |
- #' The data which application will depend on.+ #' - `shiny` app by using `shinyApp(..., enableBookmarking = "server")` (not supported in `shinytest2`) |
||
| 29 |
- #'+ #' - set `options(shiny.bookmarkStore = "server")` before running the app |
||
| 30 |
- #' @return A `reactive` object that returns:+ #' |
||
| 31 |
- #' Output of the `data`. If `data` fails then returned error is handled (after [tryCatch()]) so that+ #' |
||
| 32 |
- #' rest of the application can respond to this respectively.+ #' @inheritParams init |
||
| 34 |
- #' @rdname module_init_data+ #' @return Invisible `NULL`. |
||
| 35 |
- #' @name module_init_data+ #' |
||
| 36 |
- #' @keywords internal+ #' @aliases bookmark bookmark_manager bookmark_manager_module |
||
| 37 |
- NULL+ #' |
||
| 38 |
-
+ #' @name module_bookmark_manager |
||
| 39 |
- #' @rdname module_init_data+ #' @rdname module_bookmark_manager |
||
| 40 |
- ui_init_data <- function(id) {
+ #' |
||
| 41 | -9x | +
- ns <- shiny::NS(id)+ #' @keywords internal |
|
| 42 | -9x | +
- shiny::div(+ #' |
|
| 43 | -9x | +
- id = ns("content"),
+ NULL |
|
| 44 | -9x | +
- style = "display: inline-block; width: 100%;",+ |
|
| 45 | -9x | +
- uiOutput(ns("data"))
+ #' @rdname module_bookmark_manager |
|
| 46 |
- )+ ui_bookmark_panel <- function(id, modules) {
|
||
| 47 | -+ | ! |
- }+ ns <- NS(id) |
| 49 | -+ | ! |
- #' @rdname module_init_data+ bookmark_option <- get_bookmarking_option() |
| 50 | -+ | ! |
- srv_init_data <- function(id, data) {
+ is_unbookmarkable <- need_bookmarking(modules) |
| 51 | -83x | +! |
- checkmate::assert_character(id, max.len = 1, any.missing = FALSE)+ shinyOptions(bookmarkStore = bookmark_option) |
| 52 | -83x | +
- checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
+
|
|
| 53 |
-
+ # Render bookmark warnings count |
||
| 54 | -83x | +! |
- moduleServer(id, function(input, output, session) {
+ if (!all(is_unbookmarkable) && identical(bookmark_option, "server")) {
|
| 55 | -83x | +! |
- logger::log_debug("srv_data initializing.")
+ tags$button( |
| 56 | -+ | ! |
- # data_rv contains teal_data object+ id = ns("do_bookmark"),
|
| 57 | -+ | ! |
- # either passed to teal::init or returned from teal_data_module+ class = "btn action-button wunder_bar_button bookmark_manager_button", |
| 58 | -83x | +! |
- data_out <- if (inherits(data, "teal_data_module")) {
+ title = "Add bookmark", |
| 59 | -10x | +! |
- output$data <- renderUI(data$ui(id = session$ns("teal_data_module")))
+ tags$span( |
| 60 | -10x | +! |
- data$server("teal_data_module")
+ suppressMessages(icon("fas fa-bookmark")),
|
| 61 | -83x | +! |
- } else if (inherits(data, "teal_data")) {
+ if (any(is_unbookmarkable)) {
|
| 62 | -43x | +! |
- reactiveVal(data)+ tags$span( |
| 63 | -83x | +! |
- } else if (test_reactive(data)) {
+ sum(is_unbookmarkable), |
| 64 | -30x | +! |
- data+ class = "badge-warning badge-count text-white bg-danger" |
| 65 |
- }+ ) |
||
| 66 |
-
+ } |
||
| 67 | -82x | +
- data_handled <- reactive({
+ ) |
|
| 68 | -75x | +
- tryCatch(data_out(), error = function(e) e)+ ) |
|
| 69 |
- })+ } |
||
| 70 |
-
+ } |
||
| 71 |
- # We want to exclude teal_data_module elements from bookmarking as they might have some secrets+ |
||
| 72 | -82x | +
- observeEvent(data_handled(), {
+ #' @rdname module_bookmark_manager |
|
| 73 | -75x | +
- if (inherits(data_handled(), "teal_data")) {
+ srv_bookmark_panel <- function(id, modules) {
|
|
| 74 | -70x | +82x |
- app_session <- .subset2(shiny::getDefaultReactiveDomain(), "parent")+ checkmate::assert_character(id) |
| 75 | -70x | +82x |
- setBookmarkExclude(+ checkmate::assert_class(modules, "teal_modules") |
| 76 | -70x | +82x |
- session$ns(+ moduleServer(id, function(input, output, session) {
|
| 77 | -70x | +82x |
- grep(+ logger::log_debug("bookmark_manager_srv initializing")
|
| 78 | -70x | +82x |
- pattern = "teal_data_module-",+ ns <- session$ns |
| 79 | -70x | +82x |
- x = names(reactiveValuesToList(input)),+ bookmark_option <- get_bookmarking_option() |
| 80 | -70x | +82x |
- value = TRUE+ is_unbookmarkable <- need_bookmarking(modules) |
| 81 |
- )+ |
||
| 82 |
- ),+ # Set up bookmarking callbacks ---- |
||
| 83 | -70x | +
- session = app_session+ # Register bookmark exclusions: do_bookmark button to avoid re-bookmarking |
|
| 84 | -+ | 82x |
- )+ setBookmarkExclude(c("do_bookmark"))
|
| 85 |
- }+ # This bookmark can only be used on the app session. |
||
| 86 | -+ | 82x |
- })+ app_session <- .subset2(session, "parent") |
| 87 | -+ | 82x |
-
+ app_session$onBookmarked(function(url) {
|
| 88 | -82x | +! |
- data_handled+ logger::log_debug("bookmark_manager_srv@onBookmarked: bookmark button clicked, registering bookmark")
|
| 89 | -+ | ! |
- })+ modal_content <- if (bookmark_option != "server") {
|
| 90 | -+ | ! |
- }+ msg <- sprintf( |
| 91 | -+ | ! |
-
+ "Bookmarking has been set to \"%s\".\n%s\n%s", |
| 92 | -+ | ! |
- #' Adds signature protection to the `datanames` in the data+ bookmark_option, |
| 93 | -+ | ! |
- #' @param data (`teal_data`)+ "Only server-side bookmarking is supported.", |
| 94 | -+ | ! |
- #' @return `teal_data` with additional code that has signature of the `datanames`+ "Please contact your app developer." |
| 95 |
- #' @keywords internal+ ) |
||
| 96 | -+ | ! |
- .add_signature_to_data <- function(data) {
+ tags$div( |
| 97 | -70x | +! |
- hashes <- .get_hashes_code(data)+ tags$p(msg, class = "text-warning") |
| 98 | -70x | +
- tdata <- do.call(+ ) |
|
| 99 | -70x | +
- teal.data::teal_data,+ } else {
|
|
| 100 | -70x | +! |
- c(+ tags$div( |
| 101 | -70x | +! |
- list(code = trimws(c(teal.code::get_code(data), hashes), which = "right")),+ tags$span( |
| 102 | -70x | +! |
- list(join_keys = teal.data::join_keys(data)),+ tags$pre(url) |
| 103 | -70x | +
- sapply(+ ), |
|
| 104 | -70x | +! |
- ls(teal.code::get_env(data)),+ if (any(is_unbookmarkable)) {
|
| 105 | -70x | +! |
- teal.code::get_var,+ bkmb_summary <- rapply2( |
| 106 | -70x | +! |
- object = data,+ modules_bookmarkable(modules), |
| 107 | -70x | +! |
- simplify = FALSE+ function(x) {
|
| 108 | -+ | ! |
- )+ if (isTRUE(x)) {
|
| 109 | -+ | ! |
- )+ "\u2705" # check mark |
| 110 | -+ | ! |
- )+ } else if (isFALSE(x)) {
|
| 111 | -+ | ! |
-
+ "\u274C" # cross mark |
| 112 | -70x | +
- tdata@verified <- data@verified+ } else {
|
|
| 113 | -70x | +! |
- tdata+ "\u2753" # question mark |
| 114 |
- }+ } |
||
| 115 |
-
+ } |
||
| 116 |
- #' Get code that tests the integrity of the reproducible data+ ) |
||
| 117 | -+ | ! |
- #'+ tags$div( |
| 118 | -+ | ! |
- #' @param data (`teal_data`) object holding the data+ tags$p( |
| 119 | -+ | ! |
- #' @param datanames (`character`) names of `datasets`+ icon("fas fa-exclamation-triangle"),
|
| 120 | -+ | ! |
- #'+ "Some modules will not be restored when using this bookmark.", |
| 121 | -+ | ! |
- #' @return A character vector with the code lines.+ tags$br(), |
| 122 | -+ | ! |
- #' @keywords internal+ "Check the list below to see which modules are not bookmarkable.", |
| 123 | -+ | ! |
- #'+ class = "text-warning" |
| 124 |
- .get_hashes_code <- function(data, datanames = ls(teal.code::get_env(data))) {
+ ), |
||
| 125 | -70x | +! |
- vapply(+ tags$pre(yaml::as.yaml(bkmb_summary)) |
| 126 | -70x | +
- datanames,+ ) |
|
| 127 | -70x | +
- function(dataname, datasets) {
+ } |
|
| 128 | -125x | +
- x <- data[[dataname]]+ ) |
|
| 129 |
-
+ } |
||
| 130 | -125x | +
- code <- if (is.function(x) && !is.primitive(x)) {
+
|
|
| 131 | -6x | +! |
- x <- deparse1(x)+ showModal( |
| 132 | -6x | +! |
- bquote(rlang::hash(deparse1(.(as.name(dataname)))))+ modalDialog( |
| 133 | -+ | ! |
- } else {
+ id = ns("bookmark_modal"),
|
| 134 | -119x | +! |
- bquote(rlang::hash(.(as.name(dataname))))+ title = "Bookmarked teal app url", |
| 135 | -+ | ! |
- }+ modal_content, |
| 136 | -125x | +! |
- sprintf(+ easyClose = TRUE |
| 137 | -125x | +
- "stopifnot(%s == %s) # @linksto %s",+ ) |
|
| 138 | -125x | +
- deparse1(code),+ ) |
|
| 139 | -125x | +
- deparse1(rlang::hash(x)),+ }) |
|
| 140 | -125x | +
- dataname+ |
|
| 141 |
- )+ # manually trigger bookmarking because of the problems reported on windows with bookmarkButton in teal |
||
| 142 | -+ | 82x |
- },+ observeEvent(input$do_bookmark, {
|
| 143 | -70x | +! |
- character(1L),+ logger::log_debug("bookmark_manager_srv@1 do_bookmark module clicked.")
|
| 144 | -70x | +! |
- USE.NAMES = TRUE+ session$doBookmark() |
| 145 |
- )+ }) |
||
| 146 |
- }+ |
| 1 | -+ | ||
| 147 | +82x |
- #' Calls all `modules`+ invisible(NULL) |
|
| 2 | +148 |
- #'+ }) |
|
| 3 | +149 |
- #' On the UI side each `teal_modules` is translated to a `tabsetPanel` and each `teal_module` is a+ } |
|
| 4 | +150 |
- #' `tabPanel`. Both, UI and server are called recursively so that each tab is a separate module and+ |
|
| 5 | +151 |
- #' reflect nested structure of `modules` argument.+ |
|
| 6 | +152 |
- #'+ #' @rdname module_bookmark_manager |
|
| 7 | +153 |
- #' @name module_teal_module+ get_bookmarking_option <- function() {
|
|
| 8 | -+ | ||
| 154 | +82x |
- #'+ bookmark_option <- getShinyOption("bookmarkStore")
|
|
| 9 | -+ | ||
| 155 | +82x |
- #' @inheritParams module_teal+ if (is.null(bookmark_option) && identical(getOption("shiny.bookmarkStore"), "server")) {
|
|
| 10 | -+ | ||
| 156 | +! |
- #'+ bookmark_option <- getOption("shiny.bookmarkStore")
|
|
| 11 | +157 |
- #' @param data_rv (`reactive` returning `teal_data`)+ } |
|
| 12 | -+ | ||
| 158 | +82x |
- #'+ bookmark_option |
|
| 13 | +159 |
- #' @param slices_global (`reactiveVal` returning `modules_teal_slices`)+ } |
|
| 14 | +160 |
- #' see [`module_filter_manager`]+ |
|
| 15 | +161 |
- #'+ #' @rdname module_bookmark_manager |
|
| 16 | +162 |
- #' @param depth (`integer(1)`)+ need_bookmarking <- function(modules) {
|
|
| 17 | -+ | ||
| 163 | +82x |
- #' number which helps to determine depth of the modules nesting.+ unlist(rapply2( |
|
| 18 | -+ | ||
| 164 | +82x |
- #'+ modules_bookmarkable(modules), |
|
| 19 | -+ | ||
| 165 | +82x |
- #' @param datasets (`reactive` returning `FilteredData` or `NULL`)+ Negate(isTRUE) |
|
| 20 | +166 |
- #' When `datasets` is passed from the parent module (`srv_teal`) then `dataset` is a singleton+ )) |
|
| 21 | +167 |
- #' which implies in filter-panel to be "global". When `NULL` then filter-panel is "module-specific".+ } |
|
| 22 | +168 |
- #'+ |
|
| 23 | +169 |
- #' @param data_load_status (`reactive` returning `character`)+ |
|
| 24 | +170 |
- #' Determines action dependent on a data loading status:+ # utilities ---- |
|
| 25 | +171 |
- #' - `"ok"` when `teal_data` is returned from the data loading.+ |
|
| 26 | +172 |
- #' - `"teal_data_module failed"` when [teal_data_module()] didn't return `teal_data`. Disables tabs buttons.+ #' Restore value from bookmark. |
|
| 27 | +173 |
- #' - `"external failed"` when a `reactive` passed to `srv_teal(data)` didn't return `teal_data`. Hides the whole tab+ #' |
|
| 28 | +174 |
- #' panel.+ #' Get value from bookmark or return default. |
|
| 29 | +175 |
#' |
|
| 30 | +176 |
- #' @return+ #' Bookmarks can store not only inputs but also arbitrary values. |
|
| 31 | +177 |
- #' output of currently active module.+ #' These values are stored by `onBookmark` callbacks and restored by `onBookmarked` callbacks, |
|
| 32 | +178 |
- #' - `srv_teal_module.teal_module` returns `reactiveVal` containing output of the called module.+ #' and they are placed in the `values` environment in the `session$restoreContext` field. |
|
| 33 | +179 |
- #' - `srv_teal_module.teal_modules` returns output of module selected by `input$active_tab`.+ #' Using `teal_data_module` makes it impossible to run the callbacks |
|
| 34 | +180 |
- #'+ #' because the app becomes ready before modules execute and callbacks are registered. |
|
| 35 | +181 |
- #' @keywords internal+ #' In those cases the stored values can still be recovered from the `session` object directly. |
|
| 36 | +182 |
- NULL+ #' |
|
| 37 | +183 |
-
+ #' Note that variable names in the `values` environment are prefixed with module name space names, |
|
| 38 | +184 |
- #' @rdname module_teal_module+ #' therefore, when using this function in modules, `value` must be run through the name space function. |
|
| 39 | +185 |
- ui_teal_module <- function(id, modules, depth = 0L) {
- |
- |
| 40 | -! | -
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module", "shiny.tag"))
- |
- |
| 41 | -! | -
- checkmate::assert_count(depth)+ #' |
|
| 42 | -! | +||
| 186 | +
- UseMethod("ui_teal_module", modules)
+ #' @param value (`character(1)`) name of value to restore |
||
| 43 | +187 |
- }+ #' @param default fallback value |
|
| 44 | +188 |
-
+ #' |
|
| 45 | +189 |
- #' @rdname module_teal_module+ #' @return |
|
| 46 | +190 |
- #' @export+ #' In an application restored from a server-side bookmark, |
|
| 47 | +191 |
- ui_teal_module.default <- function(id, modules, depth = 0L) {
+ #' the variable specified by `value` from the `values` environment. |
|
| 48 | -! | +||
| 192 | +
- stop("Modules class not supported: ", paste(class(modules), collapse = " "))
+ #' Otherwise `default`. |
||
| 49 | +193 |
- }+ #' |
|
| 50 | +194 |
-
+ #' @keywords internal |
|
| 51 | +195 |
- #' @rdname module_teal_module+ #' |
|
| 52 | +196 |
- #' @export+ restoreValue <- function(value, default) { # nolint: object_name.
|
|
| 53 | -+ | ||
| 197 | +164x |
- ui_teal_module.teal_modules <- function(id, modules, depth = 0L) {
+ checkmate::assert_character("value")
|
|
| 54 | -! | +||
| 198 | +164x |
- ns <- NS(id)+ session_default <- shiny::getDefaultReactiveDomain() |
|
| 55 | -! | +||
| 199 | +164x |
- tags$div(+ session_parent <- .subset2(session_default, "parent") |
|
| 56 | -! | +||
| 200 | +164x |
- id = ns("wrapper"),
+ session <- if (is.null(session_parent)) session_default else session_parent |
|
| 57 | -! | +||
| 201 | +
- do.call(+ |
||
| 58 | -! | +||
| 202 | +164x |
- tabsetPanel,+ if (isTRUE(session$restoreContext$active) && exists(value, session$restoreContext$values, inherits = FALSE)) {
|
|
| 59 | +203 | ! |
- c(+ session$restoreContext$values[[value]] |
| 60 | +204 |
- # by giving an id, we can reactively respond to tab changes+ } else {
|
|
| 61 | -! | +||
| 205 | +164x |
- list(+ default |
|
| 62 | -! | +||
| 206 | +
- id = ns("active_tab"),
+ } |
||
| 63 | -! | +||
| 207 | +
- type = if (modules$label == "root") "pills" else "tabs"+ } |
||
| 64 | +208 |
- ),+ |
|
| 65 | -! | +||
| 209 | +
- lapply(+ #' Compare bookmarks. |
||
| 66 | -! | +||
| 210 | +
- names(modules$children),+ #' |
||
| 67 | -! | +||
| 211 | +
- function(module_id) {
+ #' Test if two bookmarks store identical state. |
||
| 68 | -! | +||
| 212 | +
- module_label <- modules$children[[module_id]]$label+ #' |
||
| 69 | -! | +||
| 213 | +
- if (is.null(module_label)) {
+ #' `input` environments are compared one variable at a time and if not identical, |
||
| 70 | -! | +||
| 214 | +
- module_label <- icon("fas fa-database")
+ #' values in both bookmarks are reported. States of `datatable`s are stripped |
||
| 71 | +215 |
- }+ #' of the `time` element before comparing because the time stamp is always different. |
|
| 72 | -! | +||
| 216 | +
- tabPanel(+ #' The contents themselves are not printed as they are large and the contents are not informative. |
||
| 73 | -! | +||
| 217 | +
- title = module_label,+ #' Elements present in one bookmark and absent in the other are also reported. |
||
| 74 | -! | +||
| 218 | +
- value = module_id, # when clicked this tab value changes input$<tabset panel id>+ #' Differences are printed as messages. |
||
| 75 | -! | +||
| 219 | +
- ui_teal_module(+ #' |
||
| 76 | -! | +||
| 220 | +
- id = ns(module_id),+ #' `values` environments are compared with `all.equal`. |
||
| 77 | -! | +||
| 221 | +
- modules = modules$children[[module_id]],+ #' |
||
| 78 | -! | +||
| 222 | +
- depth = depth + 1L+ #' @section How to use: |
||
| 79 | +223 |
- )+ #' Open an application, change relevant inputs (typically, all of them), and create a bookmark. |
|
| 80 | +224 |
- )+ #' Then open that bookmark and immediately create a bookmark of that. |
|
| 81 | +225 |
- }+ #' If restoring bookmarks occurred properly, the two bookmarks should store the same state. |
|
| 82 | +226 |
- )+ #' |
|
| 83 | +227 |
- )+ #' |
|
| 84 | +228 |
- )+ #' @param book1,book2 bookmark directories stored in `shiny_bookmarks/`; |
|
| 85 | +229 |
- )+ #' default to the two most recently modified directories |
|
| 86 | +230 |
- }+ #' |
|
| 87 | +231 |
-
+ #' @return |
|
| 88 | +232 |
- #' @rdname module_teal_module+ #' Invisible `NULL` if bookmarks are identical or if there are no bookmarks to test. |
|
| 89 | +233 |
- #' @export+ #' `FALSE` if inconsistencies are detected. |
|
| 90 | +234 |
- ui_teal_module.teal_module <- function(id, modules, depth = 0L) {
+ #' |
|
| 91 | -! | +||
| 235 | +
- ns <- NS(id)+ #' @keywords internal |
||
| 92 | -! | +||
| 236 | +
- args <- c(list(id = ns("module")), modules$ui_args)
+ #' |
||
| 93 | +237 |
-
+ bookmarks_identical <- function(book1, book2) {
|
|
| 94 | +238 | ! |
- ui_teal <- tagList(+ if (!dir.exists("shiny_bookmarks")) {
|
| 95 | +239 | ! |
- div(+ message("no bookmark directory")
|
| 96 | +240 | ! |
- id = ns("validate_datanames"),
+ return(invisible(NULL)) |
| 97 | -! | +||
| 241 | +
- ui_validate_reactive_teal_data(ns("validate_datanames"))
+ } |
||
| 98 | +242 |
- ),+ |
|
| 99 | +243 | ! |
- shinyjs::hidden(+ ans <- TRUE |
| 100 | -! | +||
| 244 | +
- tags$div(+ |
||
| 101 | +245 | ! |
- id = ns("transformer_failure_info"),
+ if (missing(book1) && missing(book2)) {
|
| 102 | +246 | ! |
- class = "teal_validated",+ dirs <- list.dirs("shiny_bookmarks", recursive = FALSE)
|
| 103 | +247 | ! |
- div(+ bookmarks_sorted <- basename(rev(dirs[order(file.mtime(dirs))])) |
| 104 | +248 | ! |
- class = "teal-output-warning",+ if (length(bookmarks_sorted) < 2L) {
|
| 105 | +249 | ! |
- "One of transformers failed. Please fix and continue."+ message("no bookmarks to compare")
|
| 106 | -+ | ||
| 250 | +! |
- )+ return(invisible(NULL)) |
|
| 107 | +251 |
- )+ } |
|
| 108 | -+ | ||
| 252 | +! |
- ),+ book1 <- bookmarks_sorted[2L] |
|
| 109 | +253 | ! |
- tags$div(+ book2 <- bookmarks_sorted[1L]+ |
+
| 254 | ++ |
+ } else {
|
|
| 110 | +255 | ! |
- id = ns("teal_module_ui"),
+ if (!dir.exists(file.path("shiny_bookmarks", book1))) stop(book1, " not found")
|
| 111 | +256 | ! |
- do.call(modules$ui, args)+ if (!dir.exists(file.path("shiny_bookmarks", book2))) stop(book2, " not found")
|
| 112 | +257 |
- )+ } |
|
| 113 | +258 |
- )+ + |
+ |
| 259 | +! | +
+ book1_input <- readRDS(file.path("shiny_bookmarks", book1, "input.rds"))
+ |
+ |
| 260 | +! | +
+ book2_input <- readRDS(file.path("shiny_bookmarks", book2, "input.rds"))
|
|
| 114 | +261 | ||
| 115 | +262 | ! |
- div(+ elements_common <- intersect(names(book1_input), names(book2_input)) |
| 116 | +263 | ! |
- id = id,+ dt_states <- grepl("_state$", elements_common)
|
| 117 | +264 | ! |
- class = "teal_module",+ if (any(dt_states)) {
|
| 118 | +265 | ! |
- uiOutput(ns("data_reactive"), inline = TRUE),
+ for (el in elements_common[dt_states]) {
|
| 119 | +266 | ! |
- tagList(+ book1_input[[el]][["time"]] <- NULL |
| 120 | +267 | ! |
- if (depth >= 2L) tags$div(style = "mt-6"),+ book2_input[[el]][["time"]] <- NULL+ |
+
| 268 | ++ |
+ }+ |
+ |
| 269 | ++ |
+ }+ |
+ |
| 270 | ++ | + | |
| 121 | +271 | ! |
- if (!is.null(modules$datanames)) {
+ identicals <- mapply(identical, book1_input[elements_common], book2_input[elements_common]) |
| 122 | +272 | ! |
- fluidRow(+ non_identicals <- names(identicals[!identicals]) |
| 123 | +273 | ! |
- column(width = 9, ui_teal, class = "teal_primary_col"),+ compares <- sprintf("$ %s:\t%s --- %s", non_identicals, book1_input[non_identicals], book2_input[non_identicals])
|
| 124 | +274 | ! |
- column(+ if (length(compares) != 0L) {
|
| 125 | +275 | ! |
- width = 3,+ message("common elements not identical: \n", paste(compares, collapse = "\n"))
|
| 126 | +276 | ! |
- ui_data_summary(ns("data_summary")),
+ ans <- FALSE+ |
+
| 277 | ++ |
+ }+ |
+ |
| 278 | ++ | + | |
| 127 | +279 | ! |
- ui_filter_data(ns("filter_panel")),
+ elements_boook1 <- setdiff(names(book1_input), names(book2_input)) |
| 128 | +280 | ! |
- ui_transform_data(ns("data_transform"), transformers = modules$transformers, class = "well"),
+ if (length(elements_boook1) != 0L) {
|
| 129 | +281 | ! |
- class = "teal_secondary_col"+ dt_states <- grepl("_state$", elements_boook1)
|
| 130 | -+ | ||
| 282 | +! | +
+ if (any(dt_states)) {
+ |
+ |
| 283 | +! | +
+ for (el in elements_boook1[dt_states]) {
+ |
+ |
| 284 | +! |
- )+ if (is.list(book1_input[[el]])) book1_input[[el]] <- "--- data table state ---" |
|
| 131 | +285 |
- )+ } |
|
| 132 | +286 |
- } else {
+ } |
|
| 133 | +287 | ! |
- div(+ excess1 <- sprintf("$ %s:\t%s", elements_boook1, book1_input[elements_boook1])
|
| 134 | +288 | ! |
- div(+ message("elements only in book1: \n", paste(excess1, collapse = "\n"))
|
| 135 | +289 | ! |
- class = "teal_validated",+ ans <- FALSE |
| 136 | -! | +||
| 290 | +
- uiOutput(ns("data_input_error"))
+ } |
||
| 137 | +291 |
- ),+ |
|
| 138 | +292 | ! |
- ui_teal+ elements_boook2 <- setdiff(names(book2_input), names(book1_input)) |
| 139 | -+ | ||
| 293 | +! |
- )+ if (length(elements_boook2) != 0L) {
|
|
| 140 | -+ | ||
| 294 | +! |
- }+ dt_states <- grepl("_state$", elements_boook1)
|
|
| 141 | -+ | ||
| 295 | +! |
- )+ if (any(dt_states)) {
|
|
| 142 | -+ | ||
| 296 | +! |
- )+ for (el in elements_boook1[dt_states]) {
|
|
| 143 | -+ | ||
| 297 | +! |
- }+ if (is.list(book2_input[[el]])) book2_input[[el]] <- "--- data table state ---" |
|
| 144 | +298 |
-
+ } |
|
| 145 | +299 |
- #' @rdname module_teal_module+ } |
|
| 146 | -+ | ||
| 300 | +! |
- srv_teal_module <- function(id,+ excess2 <- sprintf("$ %s:\t%s", elements_boook2, book2_input[elements_boook2])
|
|
| 147 | -+ | ||
| 301 | +! |
- data_rv,+ message("elements only in book2: \n", paste(excess2, collapse = "\n"))
|
|
| 148 | -+ | ||
| 302 | +! |
- modules,+ ans <- FALSE |
|
| 149 | +303 |
- datasets = NULL,+ } |
|
| 150 | +304 |
- slices_global,+ |
|
| 151 | -+ | ||
| 305 | +! |
- reporter = teal.reporter::Reporter$new(),+ book1_values <- readRDS(file.path("shiny_bookmarks", book1, "values.rds"))
|
|
| 152 | -+ | ||
| 306 | +! |
- data_load_status = reactive("ok"),
+ book2_values <- readRDS(file.path("shiny_bookmarks", book2, "values.rds"))
|
|
| 153 | +307 |
- is_active = reactive(TRUE)) {
+
|
|
| 154 | -189x | +||
| 308 | +! |
- checkmate::assert_string(id)+ if (!isTRUE(all.equal(book1_values, book2_values))) {
|
|
| 155 | -189x | +||
| 309 | +! |
- assert_reactive(data_rv)+ message("different values detected")
|
|
| 156 | -189x | +||
| 310 | +! |
- checkmate::assert_multi_class(modules, c("teal_modules", "teal_module"))
+ message("choices for numeric filters MAY be different, see RangeFilterState$set_choices")
|
|
| 157 | -189x | +||
| 311 | +! |
- assert_reactive(datasets, null.ok = TRUE)+ ans <- FALSE |
|
| 158 | -189x | +||
| 312 | +
- checkmate::assert_class(slices_global, ".slicesGlobal")+ } |
||
| 159 | -189x | +||
| 313 | +
- checkmate::assert_class(reporter, "Reporter")+ |
||
| 160 | -189x | +||
| 314 | +! |
- assert_reactive(data_load_status)+ if (ans) message("perfect!")
|
|
| 161 | -189x | +||
| 315 | +! |
- UseMethod("srv_teal_module", modules)
+ invisible(NULL) |
|
| 162 | +316 |
} |
|
| 163 | +317 | ||
| 164 | +318 |
- #' @rdname module_teal_module+ |
|
| 165 | +319 |
- #' @export+ # Replacement for [base::rapply] which doesn't handle NULL values - skips the evaluation |
|
| 166 | +320 |
- srv_teal_module.default <- function(id,+ # of the function and returns NULL for given element. |
|
| 167 | +321 |
- data_rv,+ rapply2 <- function(x, f) {
|
|
| 168 | -+ | ||
| 322 | +189x |
- modules,+ if (inherits(x, "list")) {
|
|
| 169 | -+ | ||
| 323 | +82x |
- datasets = NULL,+ lapply(x, rapply2, f = f) |
|
| 170 | +324 |
- slices_global,+ } else {
|
|
| 171 | -+ | ||
| 325 | +107x |
- reporter = teal.reporter::Reporter$new(),+ f(x) |
|
| 172 | +326 |
- data_load_status = reactive("ok"),
+ } |
|
| 173 | +327 |
- is_active = reactive(TRUE)) {
+ } |
|
| 174 | -! | +
| 1 | +
- stop("Modules class not supported: ", paste(class(modules), collapse = " "))
+ #' An example `teal` module |
|||
| 175 | +2 |
- }+ #' |
||
| 176 | +3 |
-
+ #' `r lifecycle::badge("experimental")`
|
||
| 177 | +4 |
- #' @rdname module_teal_module+ #' |
||
| 178 | +5 |
- #' @export+ #' @inheritParams teal_modules |
||
| 179 | +6 |
- srv_teal_module.teal_modules <- function(id,+ #' @return A `teal` module which can be included in the `modules` argument to [init()]. |
||
| 180 | +7 |
- data_rv,+ #' @examples |
||
| 181 | +8 |
- modules,+ #' app <- init( |
||
| 182 | +9 |
- datasets = NULL,+ #' data = teal_data(IRIS = iris, MTCARS = mtcars), |
||
| 183 | +10 |
- slices_global,+ #' modules = example_module() |
||
| 184 | +11 |
- reporter = teal.reporter::Reporter$new(),+ #' ) |
||
| 185 | +12 |
- data_load_status = reactive("ok"),
+ #' if (interactive()) {
|
||
| 186 | +13 |
- is_active = reactive(TRUE)) {
+ #' shinyApp(app$ui, app$server) |
||
| 187 | -82x | +|||
| 14 | +
- moduleServer(id = id, module = function(input, output, session) {
+ #' } |
|||
| 188 | -82x | +|||
| 15 | +
- logger::log_debug("srv_teal_module.teal_modules initializing the module { deparse1(modules$label) }.")
+ #' @export |
|||
| 189 | +16 |
-
+ example_module <- function(label = "example teal module", datanames = "all", transformers = list()) {
|
||
| 190 | -82x | +17 | +38x |
- observeEvent(data_load_status(), {
+ checkmate::assert_string(label) |
| 191 | -75x | +18 | +38x |
- tabs_selector <- sprintf("#%s li a", session$ns("active_tab"))
+ ans <- module( |
| 192 | -75x | +19 | +38x |
- if (identical(data_load_status(), "ok")) {
+ label, |
| 193 | -70x | +20 | +38x |
- logger::log_debug("srv_teal_module@1 enabling modules tabs.")
+ server = function(id, data) {
|
| 194 | -70x | +21 | +2x |
- shinyjs::show("wrapper")
+ checkmate::assert_class(isolate(data()), "teal_data") |
| 195 | -70x | +22 | +2x |
- shinyjs::enable(selector = tabs_selector)+ moduleServer(id, function(input, output, session) {
|
| 196 | -5x | +23 | +2x |
- } else if (identical(data_load_status(), "teal_data_module failed")) {
+ datanames_rv <- reactive(names(req(data()))) |
| 197 | -5x | +24 | +2x |
- logger::log_debug("srv_teal_module@1 disabling modules tabs.")
+ observeEvent(datanames_rv(), {
|
| 198 | -5x | -
- shinyjs::disable(selector = tabs_selector)- |
- ||
| 199 | -! | +25 | +2x |
- } else if (identical(data_load_status(), "external failed")) {
+ selected <- input$dataname |
| 200 | -! | +|||
| 26 | +2x |
- logger::log_debug("srv_teal_module@1 hiding modules tabs.")
+ if (identical(selected, "")) {
|
||
| 201 | +27 | ! |
- shinyjs::hide("wrapper")
+ selected <- restoreInput(session$ns("dataname"), NULL)
|
|
| 202 | -+ | |||
| 28 | +2x |
- }+ } else if (isFALSE(selected %in% datanames_rv())) {
|
||
| 203 | -+ | |||
| 29 | +! |
- })+ selected <- datanames_rv()[1] |
||
| 204 | +30 | - - | -||
| 205 | -82x | -
- modules_output <- sapply(- |
- ||
| 206 | -82x | -
- names(modules$children),- |
- ||
| 207 | -82x | -
- function(module_id) {
- |
- ||
| 208 | -107x | -
- srv_teal_module(- |
- ||
| 209 | -107x | -
- id = module_id,- |
- ||
| 210 | -107x | -
- data_rv = data_rv,- |
- ||
| 211 | -107x | -
- modules = modules$children[[module_id]],- |
- ||
| 212 | -107x | -
- datasets = datasets,- |
- ||
| 213 | -107x | -
- slices_global = slices_global,+ } |
||
| 214 | -107x | +31 | +2x |
- reporter = reporter,+ updateSelectInput( |
| 215 | -107x | +32 | +2x |
- is_active = reactive(+ session = session, |
| 216 | -107x | +33 | +2x |
- is_active() &&+ inputId = "dataname", |
| 217 | -107x | +34 | +2x |
- input$active_tab == module_id &&+ choices = datanames_rv(), |
| 218 | -107x | +35 | +2x |
- identical(data_load_status(), "ok")+ selected = selected |
| 219 | +36 |
) |
||
| 220 | +37 |
- )+ }) |
||
| 221 | +38 |
- },+ |
||
| 222 | -82x | +39 | +2x |
- simplify = FALSE+ output$text <- renderPrint({
+ |
+
| 40 | +2x | +
+ req(input$dataname)+ |
+ ||
| 41 | +! | +
+ data()[[input$dataname]] |
||
| 223 | +42 |
- )+ }) |
||
| 224 | +43 | |||
| 225 | -82x | +44 | +2x |
- modules_output+ teal.widgets::verbatim_popup_srv( |
| 226 | -+ | |||
| 45 | +2x |
- })+ id = "rcode", |
||
| 227 | -+ | |||
| 46 | +2x |
- }+ verbatim_content = reactive(teal.code::get_code(data())), |
||
| 228 | -+ | |||
| 47 | +2x |
-
+ title = "Example Code" |
||
| 229 | +48 |
- #' @rdname module_teal_module+ ) |
||
| 230 | +49 |
- #' @export+ }) |
||
| 231 | +50 |
- srv_teal_module.teal_module <- function(id,+ }, |
||
| 232 | -+ | |||
| 51 | +38x |
- data_rv,+ ui = function(id) {
|
||
| 233 | -+ | |||
| 52 | +! |
- modules,+ ns <- NS(id) |
||
| 234 | -+ | |||
| 53 | +! |
- datasets = NULL,+ teal.widgets::standard_layout( |
||
| 235 | -+ | |||
| 54 | +! |
- slices_global,+ output = verbatimTextOutput(ns("text")),
+ |
+ ||
| 55 | +! | +
+ encoding = tags$div(+ |
+ ||
| 56 | +! | +
+ selectInput(ns("dataname"), "Choose a dataset", choices = NULL),
+ |
+ ||
| 57 | +! | +
+ teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
|
||
| 236 | +58 |
- reporter = teal.reporter::Reporter$new(),+ ) |
||
| 237 | +59 |
- data_load_status = reactive("ok"),
+ ) |
||
| 238 | +60 |
- is_active = reactive(TRUE)) {
+ }, |
||
| 239 | -107x | +61 | +38x |
- logger::log_debug("srv_teal_module.teal_module initializing the module: { deparse1(modules$label) }.")
+ datanames = datanames, |
| 240 | -107x | +62 | +38x |
- moduleServer(id = id, module = function(input, output, session) {
+ transformers = transformers+ |
+
| 63 | ++ |
+ ) |
||
| 241 | -107x | +64 | +38x |
- module_out <- reactiveVal()+ attr(ans, "teal_bookmarkable") <- TRUE+ |
+
| 65 | +38x | +
+ ans |
||
| 242 | +66 |
-
+ } |
||
| 243 | -107x | +
| 1 | +
- active_datanames <- reactive({
+ #' Filter settings for `teal` applications |
|||
| 244 | -84x | +|||
| 2 | +
- .resolve_module_datanames(data = data_rv(), modules = modules)+ #' |
|||
| 245 | +3 |
- })+ #' Specify initial filter states and filtering settings for a `teal` app. |
||
| 246 | -107x | +|||
| 4 | +
- if (is.null(datasets)) {
+ #' |
|||
| 247 | -20x | +|||
| 5 | +
- datasets <- eventReactive(data_rv(), {
+ #' Produces a `teal_slices` object. |
|||
| 248 | -16x | +|||
| 6 | +
- req(inherits(data_rv(), "teal_data"))+ #' The `teal_slice` components will specify filter states that will be active when the app starts. |
|||
| 249 | -16x | +|||
| 7 | +
- logger::log_debug("srv_teal_module@1 initializing module-specific FilteredData")
+ #' Attributes (created with the named arguments) will configure the way the app applies filters. |
|||
| 250 | -16x | +|||
| 8 | +
- teal_data_to_filtered_data(data_rv(), datanames = active_datanames())+ #' See argument descriptions for details. |
|||
| 251 | +9 |
- })+ #' |
||
| 252 | +10 |
- }+ #' @inheritParams teal.slice::teal_slices |
||
| 253 | +11 |
-
+ #' |
||
| 254 | +12 |
- # manage module filters on the module level+ #' @param module_specific (`logical(1)`) optional, |
||
| 255 | +13 |
- # important:+ #' - `FALSE` (default) when one filter panel applied to all modules. |
||
| 256 | +14 |
- # filter_manager_module_srv needs to be called before filter_panel_srv+ #' All filters will be shared by all modules. |
||
| 257 | +15 |
- # Because available_teal_slices is used in FilteredData$srv_available_slices (via srv_filter_panel)+ #' - `TRUE` when filter panel module-specific. |
||
| 258 | +16 |
- # and if it is not set, then it won't be available in the srv_filter_panel+ #' Modules can have different set of filters specified - see `mapping` argument. |
||
| 259 | -107x | +|||
| 17 | +
- srv_module_filter_manager(modules$label, module_fd = datasets, slices_global = slices_global)+ #' @param mapping `r lifecycle::badge("experimental")`
|
|||
| 260 | +18 |
-
+ #' _This is a new feature. Do kindly share your opinions on |
||
| 261 | -107x | +|||
| 19 | +
- call_once_when(is_active(), {
+ #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._ |
|||
| 262 | -81x | +|||
| 20 | +
- filtered_teal_data <- srv_filter_data(+ #' |
|||
| 263 | -81x | +|||
| 21 | +
- "filter_panel",+ #' (named `list`) specifies which filters will be active in which modules on app start. |
|||
| 264 | -81x | +|||
| 22 | +
- datasets = datasets,+ #' Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]). |
|||
| 265 | -81x | +|||
| 23 | +
- active_datanames = active_datanames,+ #' Names of the list should correspond to `teal_module` `label` set in [module()] function. |
|||
| 266 | -81x | +|||
| 24 | +
- data_rv = data_rv,+ #' - `id`s listed under `"global_filters` will be active in all modules. |
|||
| 267 | -81x | +|||
| 25 | +
- is_active = is_active+ #' - If missing, all filters will be applied to all modules. |
|||
| 268 | +26 |
- )+ #' - If empty list, all filters will be available to all modules but will start inactive. |
||
| 269 | -81x | +|||
| 27 | +
- is_transformer_failed <- reactiveValues()+ #' - If `module_specific` is `FALSE`, only `global_filters` will be active on start. |
|||
| 270 | -81x | +|||
| 28 | +
- transformed_teal_data <- srv_transform_data(+ #' @param app_id (`character(1)`) |
|||
| 271 | -81x | +|||
| 29 | +
- "data_transform",+ #' For internal use only, do not set manually. |
|||
| 272 | -81x | +|||
| 30 | +
- data = filtered_teal_data,+ #' Added by `init` so that a `teal_slices` can be matched to the app in which it was used. |
|||
| 273 | -81x | +|||
| 31 | +
- transformers = modules$transformers,+ #' Used for verifying snapshots uploaded from file. See `snapshot`. |
|||
| 274 | -81x | +|||
| 32 | +
- modules = modules,+ #' |
|||
| 275 | -81x | +|||
| 33 | +
- is_transformer_failed = is_transformer_failed+ #' @param x (`list`) of lists to convert to `teal_slices` |
|||
| 276 | +34 |
- )+ #' |
||
| 277 | -81x | +|||
| 35 | +
- any_transformer_failed <- reactive({
+ #' @return |
|||
| 278 | -81x | +|||
| 36 | +
- any(unlist(reactiveValuesToList(is_transformer_failed)))+ #' A `teal_slices` object. |
|||
| 279 | +37 |
- })+ #' |
||
| 280 | +38 |
-
+ #' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()] |
||
| 281 | -81x | +|||
| 39 | +
- observeEvent(any_transformer_failed(), {
+ #' |
|||
| 282 | -81x | +|||
| 40 | +
- if (isTRUE(any_transformer_failed())) {
+ #' @examples |
|||
| 283 | -6x | +|||
| 41 | +
- shinyjs::hide("teal_module_ui")
+ #' filter <- teal_slices( |
|||
| 284 | -6x | +|||
| 42 | +
- shinyjs::hide("validate_datanames")
+ #' teal_slice(dataname = "iris", varname = "Species", id = "species"), |
|||
| 285 | -6x | +|||
| 43 | +
- shinyjs::show("transformer_failure_info")
+ #' teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"), |
|||
| 286 | +44 |
- } else {
+ #' teal_slice( |
||
| 287 | -75x | +|||
| 45 | +
- shinyjs::show("teal_module_ui")
+ #' dataname = "iris", id = "long_petals", title = "Long petals", expr = "Petal.Length > 5" |
|||
| 288 | -75x | +|||
| 46 | +
- shinyjs::show("validate_datanames")
+ #' ), |
|||
| 289 | -75x | +|||
| 47 | +
- shinyjs::hide("transformer_failure_info")
+ #' teal_slice(dataname = "mtcars", varname = "mpg", id = "mtcars_mpg"), |
|||
| 290 | +48 |
- }+ #' mapping = list( |
||
| 291 | +49 |
- })+ #' module1 = c("species", "sepal_length"),
|
||
| 292 | +50 |
-
+ #' module2 = c("mtcars_mpg"),
|
||
| 293 | -81x | +|||
| 51 | +
- module_teal_data <- reactive({
+ #' global_filters = "long_petals" |
|||
| 294 | -89x | +|||
| 52 | +
- req(inherits(transformed_teal_data(), "teal_data"))+ #' ) |
|||
| 295 | -83x | +|||
| 53 | +
- all_teal_data <- transformed_teal_data()+ #' ) |
|||
| 296 | -83x | +|||
| 54 | +
- module_datanames <- .resolve_module_datanames(data = all_teal_data, modules = modules)+ #' |
|||
| 297 | -83x | +|||
| 55 | +
- .subset_teal_data(all_teal_data, module_datanames)+ #' app <- init( |
|||
| 298 | +56 |
- })+ #' data = teal_data(iris = iris, mtcars = mtcars), |
||
| 299 | +57 |
-
+ #' modules = list( |
||
| 300 | -81x | +|||
| 58 | +
- srv_validate_reactive_teal_data(+ #' module("module1"),
|
|||
| 301 | -81x | +|||
| 59 | +
- "validate_datanames",+ #' module("module2")
|
|||
| 302 | -81x | +|||
| 60 | +
- data = module_teal_data,+ #' ), |
|||
| 303 | -81x | +|||
| 61 | +
- modules = modules+ #' filter = filter |
|||
| 304 | +62 |
- )+ #' ) |
||
| 305 | +63 |
-
+ #' |
||
| 306 | -81x | +|||
| 64 | +
- summary_table <- srv_data_summary("data_summary", module_teal_data)
+ #' if (interactive()) {
|
|||
| 307 | +65 |
-
+ #' shinyApp(app$ui, app$server) |
||
| 308 | +66 |
- # Call modules.+ #' } |
||
| 309 | -81x | +|||
| 67 | +
- if (!inherits(modules, "teal_module_previewer")) {
+ #' |
|||
| 310 | -81x | +|||
| 68 | +
- obs_module <- call_once_when(+ #' @export |
|||
| 311 | -81x | +|||
| 69 | +
- !is.null(module_teal_data()),+ teal_slices <- function(..., |
|||
| 312 | -81x | +|||
| 70 | +
- ignoreNULL = TRUE,+ exclude_varnames = NULL, |
|||
| 313 | -81x | +|||
| 71 | +
- handlerExpr = {
+ include_varnames = NULL, |
|||
| 314 | -75x | +|||
| 72 | +
- module_out(.call_teal_module(modules, datasets, module_teal_data, reporter))+ count_type = NULL, |
|||
| 315 | +73 |
- }+ allow_add = TRUE, |
||
| 316 | +74 |
- )+ module_specific = FALSE, |
||
| 317 | +75 |
- } else {
+ mapping, |
||
| 318 | +76 |
- # Report previewer must be initiated on app start for report cards to be included in bookmarks.+ app_id = NULL) {
|
||
| 319 | -+ | |||
| 77 | +161x |
- # When previewer is delayed, cards are bookmarked only if previewer has been initiated (visited).+ shiny::isolate({
|
||
| 320 | -! | +|||
| 78 | +161x |
- module_out(.call_teal_module(modules, datasets, module_teal_data, reporter))+ checkmate::assert_flag(allow_add) |
||
| 321 | -+ | |||
| 79 | +161x |
- }+ checkmate::assert_flag(module_specific)+ |
+ ||
| 80 | +51x | +
+ if (!missing(mapping)) checkmate::assert_list(mapping, types = c("character", "NULL"), names = "named")
+ |
+ ||
| 81 | +158x | +
+ checkmate::assert_string(app_id, null.ok = TRUE) |
||
| 322 | +82 | |||
| 323 | -+ | |||
| 83 | +158x |
- # todo: (feature request) add a ReporterCard to the reporter as an output from the teal_module+ slices <- list(...) |
||
| 324 | -+ | |||
| 84 | +158x |
- # how to determine if module returns a ReporterCard so that reportPreviewer is needed?+ all_slice_id <- vapply(slices, `[[`, character(1L), "id") |
||
| 325 | +85 |
- # Should we insertUI of the ReportPreviewer then?+ |
||
| 326 | -+ | |||
| 86 | +158x |
- # What about attr(module, "reportable") - similar to attr(module, "bookmarkable")+ if (missing(mapping)) {
|
||
| 327 | -81x | +87 | +110x |
- if ("report" %in% names(module_out)) {
+ mapping <- if (length(all_slice_id)) {
+ |
+
| 88 | +26x | +
+ list(global_filters = all_slice_id) |
||
| 328 | +89 |
- # (reactively) add card to the reporter+ } else {
+ |
+ ||
| 90 | +84x | +
+ list() |
||
| 329 | +91 |
} |
||
| 330 | +92 |
- })+ } |
||
| 331 | +93 | |||
| 332 | -107x | +94 | +158x |
- module_out+ if (!module_specific) {
|
| 333 | -+ | |||
| 95 | +139x |
- })+ mapping[setdiff(names(mapping), "global_filters")] <- NULL |
||
| 334 | +96 |
- }+ } |
||
| 335 | +97 | |||
| 336 | -+ | |||
| 98 | +158x |
- # This function calls a module server function.+ failed_slice_id <- setdiff(unlist(mapping), all_slice_id) |
||
| 337 | -+ | |||
| 99 | +158x |
- .call_teal_module <- function(modules, datasets, filtered_teal_data, reporter) {
+ if (length(failed_slice_id)) {
|
||
| 338 | -+ | |||
| 100 | +1x |
- # collect arguments to run teal_module+ stop(sprintf( |
||
| 339 | -75x | +101 | +1x |
- args <- c(list(id = "module"), modules$server_args)+ "Filters in mapping don't match any available filter.\n %s not in %s", |
| 340 | -75x | +102 | +1x |
- if (is_arg_used(modules$server, "reporter")) {
+ toString(failed_slice_id), |
| 341 | +103 | 1x |
- args <- c(args, list(reporter = reporter))+ toString(all_slice_id) |
|
| 342 | +104 |
- }+ )) |
||
| 343 | +105 | - - | -||
| 344 | -75x | -
- if (is_arg_used(modules$server, "datasets")) {
+ } |
||
| 345 | -1x | +|||
| 106 | +
- args <- c(args, datasets = datasets())+ |
|||
| 346 | -1x | +107 | +157x |
- warning("datasets argument is not reactive and therefore it won't be updated when data is refreshed.")
+ tss <- teal.slice::teal_slices( |
| 347 | +108 |
- }+ ..., |
||
| 348 | -+ | |||
| 109 | +157x |
-
+ exclude_varnames = exclude_varnames, |
||
| 349 | -75x | +110 | +157x |
- if (is_arg_used(modules$server, "data")) {
+ include_varnames = include_varnames, |
| 350 | -71x | +111 | +157x |
- args <- c(args, data = list(filtered_teal_data))+ count_type = count_type, |
| 351 | -+ | |||
| 112 | +157x |
- }+ allow_add = allow_add |
||
| 352 | +113 |
-
+ ) |
||
| 353 | -75x | +114 | +157x |
- if (is_arg_used(modules$server, "filter_panel_api")) {
+ attr(tss, "mapping") <- mapping |
| 354 | -1x | +115 | +157x |
- args <- c(args, filter_panel_api = teal.slice::FilterPanelAPI$new(datasets()))+ attr(tss, "module_specific") <- module_specific |
| 355 | -+ | |||
| 116 | +157x |
- }+ attr(tss, "app_id") <- app_id |
||
| 356 | -+ | |||
| 117 | +157x |
-
+ class(tss) <- c("modules_teal_slices", class(tss))
|
||
| 357 | -75x | +118 | +157x |
- if (is_arg_used(modules$server, "id")) {
+ tss |
| 358 | -75x | +|||
| 119 | +
- do.call(modules$server, args)+ }) |
|||
| 359 | +120 |
- } else {
+ } |
||
| 360 | -! | +|||
| 121 | +
- do.call(callModule, c(args, list(module = modules$server)))+ |
|||
| 361 | +122 |
- }+ |
||
| 362 | +123 |
- }+ #' @rdname teal_slices |
||
| 363 | +124 |
-
+ #' @export |
||
| 364 | +125 |
- .resolve_module_datanames <- function(data, modules) {
+ #' @keywords internal |
||
| 365 | -167x | +|||
| 126 | +
- stopifnot("data_rv must be teal_data object." = inherits(data, "teal_data"))
+ #'+ |
+ |||
| 127 | ++ |
+ as.teal_slices <- function(x) { # nolint: object_name.
|
||
| 366 | -167x | +128 | +13x |
- if (is.null(modules$datanames) || identical(modules$datanames, "all")) {
+ checkmate::assert_list(x) |
| 367 | -135x | +129 | +13x |
- .topologically_sort_datanames(ls(teal.code::get_env(data)), teal.data::join_keys(data))+ lapply(x, checkmate::assert_list, names = "named", .var.name = "list element") |
| 368 | +130 |
- } else {
+
+ |
+ ||
| 131 | +13x | +
+ attrs <- attributes(unclass(x)) |
||
| 369 | -32x | +132 | +13x |
- intersect(+ ans <- lapply(x, function(x) if (is.teal_slice(x)) x else as.teal_slice(x)) |
| 370 | -32x | +133 | +13x |
- .include_parent_datanames(modules$datanames, teal.data::join_keys(data)),+ do.call(teal_slices, c(ans, attrs)) |
| 371 | -32x | +|||
| 134 | +
- ls(teal.code::get_env(data))+ } |
|||
| 372 | +135 |
- )+ |
||
| 373 | +136 |
- }+ |
||
| 374 | +137 |
- }+ #' @rdname teal_slices |
||
| 375 | +138 |
-
+ #' @export |
||
| 376 | +139 |
- #' Calls expression when condition is met+ #' @keywords internal |
||
| 377 | +140 |
#' |
||
| 378 | +141 |
- #' Function postpones `handlerExpr` to the moment when `eventExpr` (condition) returns `TRUE`,+ c.teal_slices <- function(...) {
|
||
| 379 | -+ | |||
| 142 | +6x |
- #' otherwise nothing happens.+ x <- list(...) |
||
| 380 | -+ | |||
| 143 | +6x |
- #' @param eventExpr A (quoted or unquoted) logical expression that represents the event;+ checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices") |
||
| 381 | +144 |
- #' this can be a simple reactive value like input$click, a call to a reactive expression+ |
||
| 382 | -+ | |||
| 145 | +6x |
- #' like dataset(), or even a complex expression inside curly braces.+ all_attributes <- lapply(x, attributes) |
||
| 383 | -+ | |||
| 146 | +6x |
- #' @param ... additional arguments passed to `observeEvent` with the exception of `eventExpr` that is not allowed.+ all_attributes <- coalesce_r(all_attributes) |
||
| 384 | -+ | |||
| 147 | +6x |
- #' @inheritParams shiny::observeEvent+ all_attributes <- all_attributes[names(all_attributes) != "class"] |
||
| 385 | +148 |
- #'+ |
||
| 386 | -+ | |||
| 149 | +6x |
- #' @return An observer.+ do.call( |
||
| 387 | -+ | |||
| 150 | +6x |
- #'+ teal_slices, |
||
| 388 | -+ | |||
| 151 | +6x |
- #' @keywords internal+ c(+ |
+ ||
| 152 | +6x | +
+ unique(unlist(x, recursive = FALSE)),+ |
+ ||
| 153 | +6x | +
+ all_attributes |
||
| 389 | +154 |
- call_once_when <- function(eventExpr, # nolint: object_name.+ ) |
||
| 390 | +155 |
- handlerExpr, # nolint: object_name.+ ) |
||
| 391 | +156 |
- event.env = parent.frame(), # nolint: object_name.+ } |
||
| 392 | +157 |
- handler.env = parent.frame(), # nolint: object_name.+ |
||
| 393 | +158 |
- ...) {
+
|
||
| 394 | -188x | +|||
| 159 | +
- event_quo <- rlang::new_quosure(substitute(eventExpr), env = event.env)+ #' Deep copy `teal_slices` |
|||
| 395 | -188x | +|||
| 160 | +
- handler_quo <- rlang::new_quosure(substitute(handlerExpr), env = handler.env)+ #' |
|||
| 396 | +161 |
-
+ #' it's important to create a new copy of `teal_slices` when |
||
| 397 | +162 |
- # When `condExpr` is TRUE, then `handlerExpr` is evaluated once.+ #' starting a new `shiny` session. Otherwise, object will be shared |
||
| 398 | -188x | +|||
| 163 | +
- activator <- reactive({
+ #' by multiple users as it is created in global environment before |
|||
| 399 | -188x | +|||
| 164 | +
- if (isTRUE(rlang::eval_tidy(event_quo))) {
+ #' `shiny` session starts. |
|||
| 400 | -156x | +|||
| 165 | +
- TRUE+ #' @param filter (`teal_slices`) |
|||
| 401 | +166 |
- }+ #' @return `teal_slices` |
||
| 402 | +167 |
- })+ #' @keywords internal |
||
| 403 | +168 |
-
+ deep_copy_filter <- function(filter) {
|
||
| 404 | -188x | +169 | +1x |
- observeEvent(+ checkmate::assert_class(filter, "teal_slices") |
| 405 | -188x | +170 | +1x |
- eventExpr = activator(),+ shiny::isolate({
|
| 406 | -188x | +171 | +1x |
- once = TRUE,+ filter_copy <- lapply(filter, function(slice) {
|
| 407 | -188x | +172 | +2x |
- handlerExpr = rlang::eval_tidy(handler_quo),+ teal.slice::as.teal_slice(as.list(slice)) |
| 408 | +173 |
- ...+ })+ |
+ ||
| 174 | +1x | +
+ attributes(filter_copy) <- attributes(filter)+ |
+ ||
| 175 | +1x | +
+ filter_copy |
||
| 409 | +176 |
- )+ }) |
||
| 410 | +177 |
}@@ -39615,14 +39293,14 @@ teal coverage - 59.99% |
| 1 |
- #' Send input validation messages to output+ #' `teal` main module |
|||
| 3 |
- #' Captures messages from `InputValidator` objects and collates them+ #' @description |
|||
| 4 |
- #' into one message passed to `validate`.+ #' `r lifecycle::badge("stable")`
|
|||
| 5 |
- #'+ #' Module to create a `teal` app. This module can be called directly instead of [init()] and |
|||
| 6 |
- #' `shiny::validate` is used to withhold rendering of an output element until+ #' included in your custom application. Please note that [init()] adds `reporter_previewer_module` |
|||
| 7 |
- #' certain conditions are met and to print a validation message in place+ #' automatically, which is not a case when calling `ui/srv_teal` directly. |
|||
| 8 |
- #' of the output element.+ #' |
|||
| 9 |
- #' `shinyvalidate::InputValidator` allows to validate input elements+ #' @details |
|||
| 10 |
- #' and to display specific messages in their respective input widgets.+ #' |
|||
| 11 |
- #' `validate_inputs` provides a hybrid solution.+ #' Module is responsible for creating the main `shiny` app layout and initializing all the necessary |
|||
| 12 |
- #' Given an `InputValidator` object, messages corresponding to inputs that fail validation+ #' components. This module establishes reactive connection between the input `data` and every other |
|||
| 13 |
- #' are extracted and placed in one validation message that is passed to a `validate`/`need` call.+ #' component in the app. Reactive change of the `data` passed as an argument, reloads the app and |
|||
| 14 |
- #' This way the input `validator` messages are repeated in the output.+ #' possibly keeps all input settings the same so the user can continue where one left off. |
|||
| 16 |
- #' The `...` argument accepts any number of `InputValidator` objects+ #' ## data flow in `teal` application |
|||
| 17 |
- #' or a nested list of such objects.+ #' |
|||
| 18 |
- #' If `validators` are passed directly, all their messages are printed together+ #' This module supports multiple data inputs but eventually, they are all converted to `reactive` |
|||
| 19 |
- #' under one (optional) header message specified by `header`. If a list is passed,+ #' returning `teal_data` in this module. On this `reactive teal_data` object several actions are |
|||
| 20 |
- #' messages are grouped by `validator`. The list's names are used as headers+ #' performed: |
|||
| 21 |
- #' for their respective message groups.+ #' - data loading in [`module_init_data`] |
|||
| 22 |
- #' If neither of the nested list elements is named, a header message is taken from `header`.+ #' - data filtering in [`module_filter_data`] |
|||
| 23 |
- #'+ #' - data transformation in [`module_transform_data`] |
|||
| 24 |
- #' @param ... either any number of `InputValidator` objects+ #' |
|||
| 25 |
- #' or an optionally named, possibly nested `list` of `InputValidator`+ #' ## Fallback on failure |
|||
| 26 |
- #' objects, see `Details`+ #' |
|||
| 27 |
- #' @param header (`character(1)`) generic validation message; set to NULL to omit+ #' `teal` is designed in such way that app will never crash if the error is introduced in any |
|||
| 28 |
- #'+ #' custom `shiny` module provided by app developer (e.g. [teal_data_module()], [teal_transform_module()]). |
|||
| 29 |
- #' @return+ #' If any module returns a failing object, the app will halt the evaluation and display a warning message. |
|||
| 30 |
- #' Returns NULL if the final validation call passes and a `shiny.silent.error` if it fails.+ #' App user should always have a chance to fix the improper input and continue without restarting the session. |
|||
| 32 |
- #' @seealso [`shinyvalidate::InputValidator`], [`shiny::validate`]+ #' @rdname module_teal |
|||
| 33 |
- #'+ #' @name module_teal |
|||
| 34 |
- #' @examplesIf require("shinyvalidate")
+ #' |
|||
| 35 |
- #' library(shiny)+ #' @inheritParams module_init_data |
|||
| 36 |
- #' library(shinyvalidate)+ #' @inheritParams init |
|||
| 38 |
- #' ui <- fluidPage(+ #' @return `NULL` invisibly |
|||
| 39 |
- #' selectInput("method", "validation method", c("sequential", "combined", "grouped")),
+ NULL |
|||
| 40 |
- #' sidebarLayout(+ |
|||
| 41 |
- #' sidebarPanel(+ #' @rdname module_teal |
|||
| 42 |
- #' selectInput("letter", "select a letter:", c(letters[1:3], LETTERS[4:6])),
+ #' @export |
|||
| 43 |
- #' selectInput("number", "select a number:", 1:6),
+ ui_teal <- function(id, |
|||
| 44 |
- #' tags$br(),+ modules, |
|||
| 45 |
- #' selectInput("color", "select a color:",
+ title = build_app_title(), |
|||
| 46 |
- #' c("black", "indianred2", "springgreen2", "cornflowerblue"),
+ header = tags$p(), |
|||
| 47 |
- #' multiple = TRUE+ footer = tags$p()) {
|
|||
| 48 | -+ | ! |
- #' ),+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
|
| 49 | -+ | ! |
- #' sliderInput("size", "select point size:",
+ checkmate::assert( |
|
| 50 | -+ | ! |
- #' min = 0.1, max = 4, value = 0.25+ .var.name = "title", |
|
| 51 | -+ | ! |
- #' )+ checkmate::check_string(title), |
|
| 52 | -+ | ! |
- #' ),+ checkmate::check_multi_class(title, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 53 |
- #' mainPanel(plotOutput("plot"))
+ ) |
|||
| 54 | -+ | ! |
- #' )+ checkmate::assert( |
|
| 55 | -+ | ! |
- #' )+ .var.name = "header", |
|
| 56 | -+ | ! |
- #'+ checkmate::check_string(header), |
|
| 57 | -+ | ! |
- #' server <- function(input, output) {
+ checkmate::check_multi_class(header, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 58 |
- #' # set up input validation+ ) |
|||
| 59 | -+ | ! |
- #' iv <- InputValidator$new()+ checkmate::assert( |
|
| 60 | -+ | ! |
- #' iv$add_rule("letter", sv_in_set(LETTERS, "choose a capital letter"))
+ .var.name = "footer", |
|
| 61 | -+ | ! |
- #' iv$add_rule("number", function(x) {
+ checkmate::check_string(footer), |
|
| 62 | -+ | ! |
- #' if (as.integer(x) %% 2L == 1L) "choose an even number"+ checkmate::check_multi_class(footer, c("shiny.tag", "shiny.tag.list", "html"))
|
|
| 63 |
- #' })+ ) |
|||
| 64 |
- #' iv$enable()+ |
|||
| 65 | -+ | ! |
- #' # more input validation+ if (is.character(title)) {
|
|
| 66 | -+ | ! |
- #' iv_par <- InputValidator$new()+ title <- build_app_title(title) |
|
| 67 |
- #' iv_par$add_rule("color", sv_required(message = "choose a color"))
+ } else {
|
|||
| 68 | -+ | ! |
- #' iv_par$add_rule("color", function(x) {
+ validate_app_title_tag(title) |
|
| 69 |
- #' if (length(x) > 1L) "choose only one color"+ } |
|||
| 70 |
- #' })+ |
|||
| 71 | -+ | ! |
- #' iv_par$add_rule(+ if (checkmate::test_string(header)) {
|
|
| 72 | -+ | ! |
- #' "size",+ header <- tags$p(header) |
|
| 73 |
- #' sv_between(+ } |
|||
| 74 |
- #' left = 0.5, right = 3,+ |
|||
| 75 | -+ | ! |
- #' message_fmt = "choose a value between {left} and {right}"
+ if (checkmate::test_string(footer)) {
|
|
| 76 | -+ | ! |
- #' )+ footer <- tags$p(footer) |
|
| 77 |
- #' )+ } |
|||
| 78 |
- #' iv_par$enable()+ |
|||
| 79 | -+ | ! |
- #'+ ns <- NS(id) |
|
| 80 |
- #' output$plot <- renderPlot({
+
|
|||
| 81 |
- #' # validate output+ # show busy icon when `shiny` session is busy computing stuff |
|||
| 82 |
- #' switch(input[["method"]],+ # based on https://stackoverflow.com/questions/17325521/r-shiny-display-loading-message-while-function-is-running/22475216#22475216 # nolint: line_length. |
|||
| 83 | -+ | ! |
- #' "sequential" = {
+ shiny_busy_message_panel <- conditionalPanel( |
|
| 84 | -+ | ! |
- #' validate_inputs(iv)+ condition = "(($('html').hasClass('shiny-busy')) && (document.getElementById('shiny-notification-panel') == null))", # nolint: line_length.
|
|
| 85 | -+ | ! |
- #' validate_inputs(iv_par, header = "Set proper graphical parameters")+ tags$div( |
|
| 86 | -+ | ! |
- #' },+ icon("arrows-rotate", class = "fa-spin", prefer_type = "solid"),
|
|
| 87 | -+ | ! |
- #' "combined" = validate_inputs(iv, iv_par),+ "Computing ...", |
|
| 88 |
- #' "grouped" = validate_inputs(list(+ # CSS defined in `custom.css` |
|||
| 89 | -+ | ! |
- #' "Some inputs require attention" = iv,+ class = "shinybusymessage" |
|
| 90 |
- #' "Set proper graphical parameters" = iv_par+ ) |
|||
| 91 |
- #' ))+ ) |
|||
| 92 |
- #' )+ |
|||
| 93 | -+ | ! |
- #'+ fluidPage( |
|
| 94 | -+ | ! |
- #' plot(faithful$eruptions ~ faithful$waiting,+ id = id, |
|
| 95 | -+ | ! |
- #' las = 1, pch = 16,+ title = title, |
|
| 96 | -+ | ! |
- #' col = input[["color"]], cex = input[["size"]]+ theme = get_teal_bs_theme(), |
|
| 97 | -+ | ! |
- #' )+ include_teal_css_js(), |
|
| 98 | -+ | ! |
- #' })+ tags$header(header), |
|
| 99 | -+ | ! |
- #' }+ tags$hr(class = "my-2"), |
|
| 100 | -+ | ! |
- #'+ shiny_busy_message_panel, |
|
| 101 | -+ | ! |
- #' if (interactive()) {
+ tags$div( |
|
| 102 | -+ | ! |
- #' shinyApp(ui, server)+ id = ns("tabpanel_wrapper"),
|
|
| 103 | -+ | ! |
- #' }+ class = "teal-body", |
|
| 104 | -+ | ! |
- #'+ ui_teal_module(id = ns("teal_modules"), modules = modules)
|
|
| 105 |
- #' @export+ ), |
|||
| 106 | -+ | ! |
- #'+ tags$div( |
|
| 107 | -+ | ! |
- validate_inputs <- function(..., header = "Some inputs require attention") {
+ id = ns("options_buttons"),
|
|
| 108 | -36x | +! |
- dots <- list(...)+ style = "position: absolute; right: 10px;", |
|
| 109 | -2x | +! |
- if (!is_validators(dots)) stop("validate_inputs accepts validators or a list thereof")
+ ui_bookmark_panel(ns("bookmark_manager"), modules),
|
|
| 110 | -+ | ! |
-
+ tags$button( |
|
| 111 | -34x | +! |
- messages <- extract_validator(dots, header)+ class = "btn action-button filter_hamburger", # see sidebar.css for style filter_hamburger |
|
| 112 | -34x | +! |
- failings <- if (!any_names(dots)) {
+ href = "javascript:void(0)", |
|
| 113 | -29x | +! |
- add_header(messages, header)+ onclick = sprintf("toggleFilterPanel('%s');", ns("tabpanel_wrapper")),
|
|
| 114 | -+ | ! |
- } else {
+ title = "Toggle filter panel", |
|
| 115 | -5x | +! |
- unlist(messages)+ icon("fas fa-bars")
|
|
| 116 |
- }+ ), |
|||
| 117 | -+ | ! |
-
+ ui_snapshot_manager_panel(ns("snapshot_manager_panel")),
|
|
| 118 | -34x | +! |
- shiny::validate(shiny::need(is.null(failings), failings))+ ui_filter_manager_panel(ns("filter_manager_panel"))
|
|
| 119 |
- }+ ), |
|||
| 120 | -+ | ! |
-
+ tags$script( |
|
| 121 | -+ | ! |
- ### internal functions+ HTML( |
|
| 122 | -+ | ! |
-
+ sprintf( |
|
| 123 |
- #' @noRd+ " |
|||
| 124 | -+ | ! |
- #' @keywords internal+ $(document).ready(function() {
|
|
| 125 | -+ | ! |
- # recursive object type test+ $('#%s').appendTo('#%s');
|
|
| 126 |
- # returns logical of length 1+ }); |
|||
| 127 |
- is_validators <- function(x) {
+ ", |
|||
| 128 | -118x | +! |
- all(if (is.list(x)) unlist(lapply(x, is_validators)) else inherits(x, "InputValidator"))+ ns("options_buttons"),
|
|
| 129 | -+ | ! |
- }+ ns("teal_modules-active_tab")
|
|
| 130 |
-
+ ) |
|||
| 131 |
- #' @noRd+ ) |
|||
| 132 |
- #' @keywords internal+ ), |
|||
| 133 | -+ | ! |
- # test if an InputValidator object is enabled+ tags$hr(), |
|
| 134 | -+ | ! |
- # returns logical of length 1+ tags$footer( |
|
| 135 | -+ | ! |
- # official method requested at https://github.com/rstudio/shinyvalidate/issues/64+ tags$div( |
|
| 136 | -+ | ! |
- validator_enabled <- function(x) {
+ footer, |
|
| 137 | -49x | +! |
- x$.__enclos_env__$private$enabled+ teal.widgets::verbatim_popup_ui(ns("sessionInfo"), "Session Info", type = "link"),
|
|
| 138 | -+ | ! |
- }+ br(), |
|
| 139 | -+ | ! |
-
+ ui_teal_lockfile(ns("lockfile")),
|
|
| 140 | -+ | ! |
- #' Recursively extract messages from validator list+ textOutput(ns("identifier"))
|
|
| 141 |
- #' @return A character vector or a list of character vectors, possibly nested and named.+ ) |
|||
| 142 |
- #' @noRd+ ) |
|||
| 143 |
- #' @keywords internal+ ) |
|||
| 144 | - |
- extract_validator <- function(iv, header) {
- |
- ||
| 145 | -113x | -
- if (inherits(iv, "InputValidator")) {
- |
- ||
| 146 | -49x | -
- add_header(gather_messages(iv), header)- |
- ||
| 147 | -- |
- } else {
- |
- ||
| 148 | -58x | -
- if (is.null(names(iv))) names(iv) <- rep("", length(iv))
- |
- ||
| 149 | -64x | -
- mapply(extract_validator, iv = iv, header = names(iv), SIMPLIFY = FALSE)- |
- ||
| 150 | -- |
- }- |
- ||
| 151 | -
} |
|||
| 152 | +145 | |||
| 153 | -- |
- #' Collate failing messages from validator.- |
- ||
| 154 | -- |
- #' @return `list`- |
- ||
| 155 | +146 |
- #' @noRd+ #' @rdname module_teal |
||
| 156 | +147 |
- #' @keywords internal+ #' @export |
||
| 157 | +148 |
- gather_messages <- function(iv) {
- |
- ||
| 158 | -49x | -
- if (validator_enabled(iv)) {
- |
- ||
| 159 | -46x | -
- status <- iv$validate()+ srv_teal <- function(id, data, modules, filter = teal_slices()) {
|
||
| 160 | -46x | +149 | +84x |
- failing_inputs <- Filter(Negate(is.null), status)+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
| 161 | -46x | -
- unique(lapply(failing_inputs, function(x) x[["message"]]))- |
- ||
| 162 | -+ | 150 | +84x |
- } else {
+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
|
| 163 | -3x | +151 | +83x |
- warning("Validator is disabled and will be omitted.")
+ checkmate::assert_class(modules, "teal_modules") |
| 164 | -3x | -
- list()- |
- ||
| 165 | -- |
- }- |
- ||
| 166 | -+ | 152 | +83x |
- }+ checkmate::assert_class(filter, "teal_slices") |
| 167 | +153 | |||
| 168 | -- |
- #' Add optional header to failing messages- |
- ||
| 169 | -- |
- #' @noRd- |
- ||
| 170 | -- |
- #' @keywords internal- |
- ||
| 171 | -- |
- add_header <- function(messages, header = "") {
- |
- ||
| 172 | -78x | -
- ans <- unlist(messages)- |
- ||
| 173 | -78x | -
- if (length(ans) != 0L && isTRUE(nchar(header) > 0L)) {
- |
- ||
| 174 | -31x | -
- ans <- c(paste0(header, "\n"), ans, "\n")- |
- ||
| 175 | -+ | 154 | +83x |
- }+ moduleServer(id, function(input, output, session) {
|
| 176 | -78x | -
- ans- |
- ||
| 177 | -- |
- }- |
- ||
| 178 | -- | - - | -||
| 179 | -+ | 155 | +83x |
- #' Recursively check if the object contains a named list+ logger::log_debug("srv_teal initializing.")
|
| 180 | +156 |
- #' @noRd+ |
||
| 181 | -+ | |||
| 157 | +83x |
- #' @keywords internal+ if (getOption("teal.show_js_log", default = FALSE)) {
|
||
| 182 | -+ | |||
| 158 | +! |
- any_names <- function(x) {
+ shinyjs::showLog() |
||
| 183 | -103x | +|||
| 159 | +
- any(+ } |
|||
| 184 | -103x | +|||
| 160 | +
- if (is.list(x)) {
+
|
|||
| 185 | -58x | +161 | +83x |
- if (!is.null(names(x)) && any(names(x) != "")) TRUE else unlist(lapply(x, any_names))+ srv_teal_lockfile("lockfile")
|
| 186 | +162 |
- } else {
+
|
||
| 187 | -40x | +163 | +83x |
- FALSE+ output$identifier <- renderText( |
| 188 | -+ | |||
| 164 | +83x |
- }+ paste0("Pid:", Sys.getpid(), " Token:", substr(session$token, 25, 32))
|
||
| 189 | +165 |
- )+ ) |
||
| 190 | +166 |
- }+ |
| 1 | -+ | ||
| 167 | +83x |
- #' Create a `tdata` object+ teal.widgets::verbatim_popup_srv( |
|
| 2 | -+ | ||
| 168 | +83x |
- #'+ "sessionInfo", |
|
| 3 | -+ | ||
| 169 | +83x |
- #' @description `r lifecycle::badge("superseded")`
+ verbatim_content = utils::capture.output(utils::sessionInfo()), |
|
| 4 | -+ | ||
| 170 | +83x |
- #'+ title = "SessionInfo" |
|
| 5 | +171 |
- #' Recent changes in `teal` cause modules to fail because modules expect a `tdata` object+ ) |
|
| 6 | +172 |
- #' to be passed to the `data` argument but instead they receive a `teal_data` object,+ |
|
| 7 | +173 |
- #' which is additionally wrapped in a reactive expression in the server functions.+ # `JavaScript` code |
|
| 8 | -+ | ||
| 174 | +83x |
- #' In order to easily adapt such modules without a proper refactor,+ run_js_files(files = "init.js") |
|
| 9 | +175 |
- #' use this function to downgrade the `data` argument.+ |
|
| 10 | +176 |
- #'+ # set timezone in shiny app |
|
| 11 | +177 |
- #' @name tdata+ # timezone is set in the early beginning so it will be available also |
|
| 12 | +178 |
- #' @param ... ignored+ # for `DDL` and all shiny modules |
|
| 13 | -+ | ||
| 179 | +83x |
- #' @return nothing+ get_client_timezone(session$ns) |
|
| 14 | -+ | ||
| 180 | +83x |
- NULL+ observeEvent( |
|
| 15 | -+ | ||
| 181 | +83x |
-
+ eventExpr = input$timezone, |
|
| 16 | -+ | ||
| 182 | +83x |
- #' @rdname tdata+ once = TRUE, |
|
| 17 | -+ | ||
| 183 | +83x |
- #' @export+ handlerExpr = {
|
|
| 18 | -+ | ||
| 184 | +! |
- new_tdata <- function(...) {
+ session$userData$timezone <- input$timezone |
|
| 19 | +185 | ! |
- .deprecate_tdata_msg()+ logger::log_debug("srv_teal@1 Timezone set to client's timezone: { input$timezone }.")
|
| 20 | +186 |
- }+ } |
|
| 21 | +187 |
-
+ ) |
|
| 22 | +188 |
- #' @rdname tdata+ |
|
| 23 | -+ | ||
| 189 | +83x |
- #' @export+ data_pulled <- srv_init_data("data", data = data)
|
|
| 24 | -+ | ||
| 190 | +82x |
- tdata2env <- function(...) {
+ data_validated <- srv_validate_reactive_teal_data( |
|
| 25 | -! | +||
| 191 | +82x |
- .deprecate_tdata_msg()+ "validate", |
|
| 26 | -+ | ||
| 192 | +82x |
- }+ data = data_pulled, |
|
| 27 | -+ | ||
| 193 | +82x |
-
+ modules = modules, |
|
| 28 | -+ | ||
| 194 | +82x |
- #' @rdname tdata+ validate_shiny_silent_error = FALSE |
|
| 29 | +195 |
- #' @export+ ) |
|
| 30 | -+ | ||
| 196 | +82x |
- get_code_tdata <- function(...) {
+ data_rv <- reactive({
|
|
| 31 | -! | +||
| 197 | +142x |
- .deprecate_tdata_msg()+ req(inherits(data_validated(), "teal_data")) |
|
| 32 | -+ | ||
| 198 | +70x |
- }+ is_filter_ok <- check_filter_datanames(filter, names(data_validated())) |
|
| 33 | -+ | ||
| 199 | +70x |
-
+ if (!isTRUE(is_filter_ok)) {
|
|
| 34 | -+ | ||
| 200 | +2x |
- #' @rdname tdata+ showNotification( |
|
| 35 | -+ | ||
| 201 | +2x |
- #' @export+ "Some filters were not applied because of incompatibility with data. Contact app developer.", |
|
| 36 | -+ | ||
| 202 | +2x |
- join_keys.tdata <- function(...) {
+ type = "warning", |
|
| 37 | -! | +||
| 203 | +2x |
- .deprecate_tdata_msg()+ duration = 10 |
|
| 38 | +204 |
- }+ ) |
|
| 39 | -+ | ||
| 205 | +2x |
-
+ warning(is_filter_ok) |
|
| 40 | +206 |
- #' @rdname tdata+ }+ |
+ |
| 207 | +70x | +
+ .add_signature_to_data(data_validated()) |
|
| 41 | +208 |
- #' @export+ }) |
|
| 42 | +209 |
- get_metadata <- function(...) {
+
|
|
| 43 | -! | +||
| 210 | +82x |
- .deprecate_tdata_msg()+ data_load_status <- reactive({
|
|
| 44 | -+ | ||
| 211 | +75x |
- }+ if (inherits(data_pulled(), "teal_data")) {
|
|
| 45 | -+ | ||
| 212 | +70x |
-
+ "ok" |
|
| 46 | +213 |
- #' @rdname tdata+ # todo: should we hide warnings on top for a data? |
|
| 47 | -+ | ||
| 214 | +5x |
- #' @export+ } else if (inherits(data, "teal_data_module")) {
+ |
+ |
| 215 | +5x | +
+ "teal_data_module failed" |
|
| 48 | +216 |
- as_tdata <- function(...) {
+ } else {
|
|
| 49 | +217 | ! |
- .deprecate_tdata_msg()+ "external failed" |
| 50 | +218 |
- }+ } |
|
| 51 | +219 |
-
+ }) |
|
| 52 | +220 | ||
| 53 | -- |
- .deprecate_tdata_msg <- function() {
- |
- |
| 54 | -! | +||
| 221 | +82x |
- lifecycle::deprecate_stop(+ datasets_rv <- if (!isTRUE(attr(filter, "module_specific"))) {
|
|
| 55 | -! | +||
| 222 | +71x |
- when = "0.16",+ eventReactive(data_rv(), {
|
|
| 56 | -! | +||
| 223 | +61x |
- what = "tdata()",+ req(inherits(data_rv(), "teal_data")) |
|
| 57 | -! | +||
| 224 | +61x |
- details = paste(+ logger::log_debug("srv_teal@1 initializing FilteredData")
|
|
| 58 | -! | +||
| 225 | +61x |
- "tdata has been removed in favour of `teal_data`.\n",+ teal_data_to_filtered_data(data_rv()) |
|
| 59 | -! | +||
| 226 | +
- "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987."+ }) |
||
| 60 | +227 |
- )+ } |
|
| 61 | +228 |
- )+ |
|
| 62 | -+ | ||
| 229 | +82x |
- }+ if (inherits(data, "teal_data_module")) {
|
| 1 | -+ | |||
| 230 | +9x |
- #' @title `TealReportCard`+ setBookmarkExclude(c("teal_modules-active_tab"))
|
||
| 2 | -+ | |||
| 231 | +9x |
- #' @description `r lifecycle::badge("experimental")`
+ shiny::insertTab( |
||
| 3 | -+ | |||
| 232 | +9x |
- #' Child class of [`ReportCard`] that is used for `teal` specific applications.+ inputId = "teal_modules-active_tab", |
||
| 4 | -+ | |||
| 233 | +9x |
- #' In addition to the parent methods, it supports rendering `teal` specific elements such as+ position = "before", |
||
| 5 | -+ | |||
| 234 | +9x |
- #' the source code, the encodings panel content and the filter panel content as part of the+ select = TRUE, |
||
| 6 | -+ | |||
| 235 | +9x |
- #' meta data.+ tabPanel( |
||
| 7 | -+ | |||
| 236 | +9x |
- #' @export+ title = icon("fas fa-database"),
|
||
| 8 | -+ | |||
| 237 | +9x |
- #'+ value = "teal_data_module", |
||
| 9 | -+ | |||
| 238 | +9x |
- TealReportCard <- R6::R6Class( # nolint: object_name.+ tags$div( |
||
| 10 | -+ | |||
| 239 | +9x |
- classname = "TealReportCard",+ ui_init_data(session$ns("data")),
|
||
| 11 | -+ | |||
| 240 | +9x |
- inherit = teal.reporter::ReportCard,+ ui_validate_reactive_teal_data(session$ns("validate"))
|
||
| 12 | +241 |
- public = list(+ ) |
||
| 13 | +242 |
- #' @description Appends the source code to the `content` meta data of this `TealReportCard`.+ ) |
||
| 14 | +243 |
- #'+ ) |
||
| 15 | +244 |
- #' @param src (`character(1)`) code as text.+ |
||
| 16 | -+ | |||
| 245 | +9x |
- #' @param ... any `rmarkdown` `R` chunk parameter and its value.+ if (attr(data, "once")) {
|
||
| 17 | -+ | |||
| 246 | +9x |
- #' But `eval` parameter is always set to `FALSE`.+ observeEvent(data_rv(), once = TRUE, {
|
||
| 18 | -+ | |||
| 247 | +4x |
- #' @return Object of class `TealReportCard`, invisibly.+ logger::log_debug("srv_teal@2 removing data tab.")
|
||
| 19 | +248 |
- #' @examples+ # when once = TRUE we pull data once and then remove data tab |
||
| 20 | -+ | |||
| 249 | +4x |
- #' card <- TealReportCard$new()$append_src(+ removeTab("teal_modules-active_tab", target = "teal_data_module")
|
||
| 21 | +250 |
- #' "plot(iris)"+ }) |
||
| 22 | +251 |
- #' )+ } |
||
| 23 | +252 |
- #' card$get_content()[[1]]$get_content()+ } else {
|
||
| 24 | +253 |
- append_src = function(src, ...) {
- |
- ||
| 25 | -4x | -
- checkmate::assert_character(src, min.len = 0, max.len = 1)- |
- ||
| 26 | -4x | -
- params <- list(...)- |
- ||
| 27 | -4x | -
- params$eval <- FALSE- |
- ||
| 28 | -4x | -
- rblock <- RcodeBlock$new(src)+ # when no teal_data_module then we want to display messages above tabsetPanel (because there is no data-tab) |
||
| 29 | -4x | +254 | +73x |
- rblock$set_params(params)+ insertUI( |
| 30 | -4x | +255 | +73x |
- self$append_content(rblock)+ selector = sprintf("#%s", session$ns("tabpanel_wrapper")),
|
| 31 | -4x | +256 | +73x |
- self$append_metadata("SRC", src)
+ where = "beforeBegin", |
| 32 | -4x | -
- invisible(self)- |
- ||
| 33 | -+ | 257 | +73x |
- },+ ui = tags$div(ui_validate_reactive_teal_data(session$ns("validate")), tags$br())
|
| 34 | +258 |
- #' @description Appends the filter state list to the `content` and `metadata` of this `TealReportCard`.+ ) |
||
| 35 | +259 |
- #' If the filter state list has an attribute named `formatted`, it appends it to the card otherwise it uses+ } |
||
| 36 | +260 |
- #' the default `yaml::as.yaml` to format the list.+ |
||
| 37 | -+ | |||
| 261 | +82x |
- #' If the filter state list is empty, nothing is appended to the `content`.+ module_labels <- unlist(module_labels(modules), use.names = FALSE) |
||
| 38 | -+ | |||
| 262 | +82x |
- #'+ slices_global <- methods::new(".slicesGlobal", filter, module_labels)
|
||
| 39 | -+ | |||
| 263 | +82x |
- #' @param fs (`teal_slices`) object returned from [teal_slices()] function.+ modules_output <- srv_teal_module( |
||
| 40 | -+ | |||
| 264 | +82x |
- #' @return `self`, invisibly.+ id = "teal_modules", |
||
| 41 | -+ | |||
| 265 | +82x |
- append_fs = function(fs) {
+ data_rv = data_rv, |
||
| 42 | -5x | +266 | +82x |
- checkmate::assert_class(fs, "teal_slices")+ datasets = datasets_rv, |
| 43 | -4x | +267 | +82x |
- self$append_text("Filter State", "header3")
+ modules = modules, |
| 44 | -4x | +268 | +82x |
- if (length(fs)) {
+ slices_global = slices_global, |
| 45 | -3x | +269 | +82x |
- self$append_content(TealSlicesBlock$new(fs))+ data_load_status = data_load_status |
| 46 | +270 |
- } else {
+ ) |
||
| 47 | -1x | +271 | +82x |
- self$append_text("No filters specified.")
+ mapping_table <- srv_filter_manager_panel("filter_manager_panel", slices_global = slices_global)
|
| 48 | -+ | |||
| 272 | +82x |
- }+ snapshots <- srv_snapshot_manager_panel("snapshot_manager_panel", slices_global = slices_global)
|
||
| 49 | -4x | +273 | +82x |
- invisible(self)+ srv_bookmark_panel("bookmark_manager", modules)
|
| 50 | +274 |
- },+ }) |
||
| 51 | +275 |
- #' @description Appends the encodings list to the `content` and `metadata` of this `TealReportCard`.+ |
||
| 52 | -+ | |||
| 276 | +82x |
- #'+ invisible(NULL) |
||
| 53 | +277 |
- #' @param encodings (`list`) list of encodings selections of the `teal` app.+ } |
| 54 | +1 |
- #' @return `self`, invisibly.+ #' Module to transform `reactive` `teal_data` |
||
| 55 | +2 |
- #' @examples+ #' |
||
| 56 | +3 |
- #' card <- TealReportCard$new()$append_encodings(list(variable1 = "X"))+ #' Module calls multiple [`module_teal_data`] in sequence so that `reactive teal_data` output |
||
| 57 | +4 |
- #' card$get_content()[[1]]$get_content()+ #' from one module is handed over to the following module's input. |
||
| 58 | +5 |
- #'+ #' |
||
| 59 | +6 |
- append_encodings = function(encodings) {
- |
- ||
| 60 | -4x | -
- checkmate::assert_list(encodings)+ #' @inheritParams module_teal_data |
||
| 61 | -4x | +|||
| 7 | +
- self$append_text("Selected Options", "header3")
+ #' @inheritParams teal_modules |
|||
| 62 | -4x | +|||
| 8 | +
- if (requireNamespace("yaml", quietly = TRUE)) {
+ #' @return `reactive` `teal_data` |
|||
| 63 | -4x | +|||
| 9 | +
- self$append_text(yaml::as.yaml(encodings, handlers = list(+ #' |
|||
| 64 | -4x | +|||
| 10 | +
- POSIXct = function(x) format(x, "%Y-%m-%d"),+ #' |
|||
| 65 | -4x | +|||
| 11 | +
- POSIXlt = function(x) format(x, "%Y-%m-%d"),+ #' @name module_transform_data |
|||
| 66 | -4x | +|||
| 12 | +
- Date = function(x) format(x, "%Y-%m-%d")+ #' @keywords internal |
|||
| 67 | -4x | +|||
| 13 | +
- )), "verbatim")+ NULL |
|||
| 68 | +14 |
- } else {
+
|
||
| 69 | -! | +|||
| 15 | +
- stop("yaml package is required to format the encodings list")
+ #' @rdname module_transform_data |
|||
| 70 | +16 |
- }+ ui_transform_data <- function(id, transformers = list(), class = "well") {
|
||
| 71 | -4x | +|||
| 17 | +! |
- self$append_metadata("Encodings", encodings)
+ checkmate::assert_string(id) |
||
| 72 | -4x | +|||
| 18 | +! |
- invisible(self)+ checkmate::assert_list(transformers, "teal_transform_module") |
||
| 73 | +19 |
- }+ |
||
| 74 | -+ | |||
| 20 | +! |
- ),+ ns <- NS(id) |
||
| 75 | -+ | |||
| 21 | +! |
- private = list(+ labels <- lapply(transformers, function(x) attr(x, "label")) |
||
| 76 | -+ | |||
| 22 | +! |
- dispatch_block = function(block_class) {
+ ids <- get_unique_labels(labels) |
||
| 77 | +23 | ! |
- eval(str2lang(block_class))+ names(transformers) <- ids |
|
| 78 | +24 |
- }+ |
||
| 79 | -+ | |||
| 25 | +! |
- )+ lapply( |
||
| 80 | -+ | |||
| 26 | +! |
- )+ names(transformers), |
||
| 81 | -+ | |||
| 27 | +! |
-
+ function(name) {
|
||
| 82 | -+ | |||
| 28 | +! |
- #' @title `TealSlicesBlock`+ data_mod <- transformers[[name]] |
||
| 83 | -+ | |||
| 29 | +! |
- #' @docType class+ wrapper_id <- ns(sprintf("wrapper_%s", name))
|
||
| 84 | -+ | |||
| 30 | +! |
- #' @description+ div( # todo: accordion? |
||
| 85 | +31 |
- #' Specialized `TealSlicesBlock` block for managing filter panel content in reports.+ # class .teal_validated changes the color of the boarder on error in ui_validate_reactive_teal_data |
||
| 86 | +32 |
- #' @keywords internal+ # For details see tealValidate.js file. |
||
| 87 | -+ | |||
| 33 | +! |
- TealSlicesBlock <- R6::R6Class( # nolint: object_name_linter.+ class = c(class, "teal_validated"), |
||
| 88 | -+ | |||
| 34 | +! |
- classname = "TealSlicesBlock",+ title = attr(data_mod, "label"), |
||
| 89 | -+ | |||
| 35 | +! |
- inherit = teal.reporter:::TextBlock,+ tags$span( |
||
| 90 | -+ | |||
| 36 | +! |
- public = list(+ class = "text-primary mb-4", |
||
| 91 | -+ | |||
| 37 | +! |
- #' @description Returns a `TealSlicesBlock` object.+ icon("fas fa-square-pen"),
|
||
| 92 | -+ | |||
| 38 | +! |
- #'+ attr(data_mod, "label") |
||
| 93 | +39 |
- #' @details Returns a `TealSlicesBlock` object with no content and no parameters.+ ), |
||
| 94 | -+ | |||
| 40 | +! |
- #'+ tags$i( |
||
| 95 | -+ | |||
| 41 | +! |
- #' @param content (`teal_slices`) object returned from [teal_slices()] function.+ class = "remove pull-right fa fa-angle-down", |
||
| 96 | -+ | |||
| 42 | +! |
- #' @param style (`character(1)`) string specifying style to apply.+ style = "cursor: pointer;", |
||
| 97 | -+ | |||
| 43 | +! |
- #'+ title = "fold/expand transform panel", |
||
| 98 | -+ | |||
| 44 | +! |
- #' @return Object of class `TealSlicesBlock`, invisibly.+ onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", wrapper_id)
|
||
| 99 | +45 |
- #'+ ), |
||
| 100 | -+ | |||
| 46 | +! |
- initialize = function(content = teal_slices(), style = "verbatim") {
+ div( |
||
| 101 | -9x | +|||
| 47 | +! |
- self$set_content(content)+ id = wrapper_id, |
||
| 102 | -8x | +|||
| 48 | +! |
- self$set_style(style)+ ui_teal_data(id = ns(name), data_module = transformers[[name]]$ui) |
||
| 103 | -8x | +|||
| 49 | +
- invisible(self)+ ) |
|||
| 104 | +50 |
- },+ ) |
||
| 105 | +51 |
-
+ } |
||
| 106 | +52 |
- #' @description Sets content of this `TealSlicesBlock`.+ ) |
||
| 107 | +53 |
- #' Sets content as `YAML` text which represents a list generated from `teal_slices`.+ } |
||
| 108 | +54 |
- #' The list displays limited number of fields from `teal_slice` objects, but this list is+ |
||
| 109 | +55 |
- #' sufficient to conclude which filters were applied.+ #' @rdname module_transform_data |
||
| 110 | +56 |
- #' When `selected` field in `teal_slice` object is a range, then it is displayed as a "min"+ srv_transform_data <- function(id, data, transformers = list(), modules, is_transformer_failed = reactiveValues()) {
|
||
| 111 | -+ | |||
| 57 | +81x |
- #'+ checkmate::assert_string(id) |
||
| 112 | -+ | |||
| 58 | +81x |
- #'+ assert_reactive(data) |
||
| 113 | -+ | |||
| 59 | +81x |
- #' @param content (`teal_slices`) object returned from [teal_slices()] function.+ checkmate::assert_list(transformers, "teal_transform_module") |
||
| 114 | -+ | |||
| 60 | +81x |
- #' @return `self`, invisibly.+ checkmate::assert_class(modules, "teal_module") |
||
| 115 | -+ | |||
| 61 | +81x |
- set_content = function(content) {
+ labels <- lapply(transformers, function(x) attr(x, "label")) |
||
| 116 | -9x | +62 | +81x |
- checkmate::assert_class(content, "teal_slices")+ ids <- get_unique_labels(labels) |
| 117 | -8x | +63 | +81x |
- if (length(content) != 0) {
+ names(transformers) <- ids |
| 118 | -6x | +64 | +81x |
- states_list <- lapply(content, function(x) {
+ moduleServer(id, function(input, output, session) {
|
| 119 | -6x | +65 | +81x |
- x_list <- shiny::isolate(as.list(x))+ logger::log_debug("srv_teal_data_modules initializing.")
|
| 120 | -6x | +66 | +81x |
- if (+ Reduce( |
| 121 | -6x | +67 | +81x |
- inherits(x_list$choices, c("integer", "numeric", "Date", "POSIXct", "POSIXlt")) &&
+ function(previous_result, name) {
|
| 122 | -6x | +68 | +20x |
- length(x_list$choices) == 2 &&+ srv_teal_data( |
| 123 | -6x | +69 | +20x |
- length(x_list$selected) == 2+ id = name, |
| 124 | -+ | |||
| 70 | +20x |
- ) {
+ data_module = function(id) transformers[[name]]$server(id, previous_result), |
||
| 125 | -! | +|||
| 71 | +20x |
- x_list$range <- paste(x_list$selected, collapse = " - ")+ modules = modules, |
||
| 126 | -! | +|||
| 72 | +20x |
- x_list["selected"] <- NULL+ is_transformer_failed = is_transformer_failed |
||
| 127 | +73 |
- }+ )+ |
+ ||
| 74 | ++ |
+ }, |
||
| 128 | -6x | +75 | +81x |
- if (!is.null(x_list$arg)) {
+ x = names(transformers), |
| 129 | -! | +|||
| 76 | +81x |
- x_list$arg <- if (x_list$arg == "subset") "Genes" else "Samples"+ init = data |
||
| 130 | +77 |
- }+ ) |
||
| 131 | +78 |
-
+ }) |
||
| 132 | -6x | +|||
| 79 | +
- x_list <- x_list[+ } |
|||
| 133 | -6x | +
| 1 | +
- c("dataname", "varname", "experiment", "arg", "expr", "selected", "range", "keep_na", "keep_inf")
+ #' Create a `tdata` object |
||
| 134 | +2 |
- ]+ #' |
|
| 135 | -6x | +||
| 3 | +
- names(x_list) <- c(+ #' @description `r lifecycle::badge("superseded")`
|
||
| 136 | -6x | +||
| 4 | +
- "Dataset name", "Variable name", "Experiment", "Filtering by", "Applied expression",+ #' |
||
| 137 | -6x | +||
| 5 | +
- "Selected Values", "Selected range", "Include NA values", "Include Inf values"+ #' Recent changes in `teal` cause modules to fail because modules expect a `tdata` object |
||
| 138 | +6 |
- )+ #' to be passed to the `data` argument but instead they receive a `teal_data` object, |
|
| 139 | +7 |
-
+ #' which is additionally wrapped in a reactive expression in the server functions. |
|
| 140 | -6x | +||
| 8 | +
- Filter(Negate(is.null), x_list)+ #' In order to easily adapt such modules without a proper refactor, |
||
| 141 | +9 |
- })+ #' use this function to downgrade the `data` argument. |
|
| 142 | +10 |
-
+ #' |
|
| 143 | -6x | +||
| 11 | +
- if (requireNamespace("yaml", quietly = TRUE)) {
+ #' @name tdata |
||
| 144 | -6x | +||
| 12 | +
- super$set_content(yaml::as.yaml(states_list))+ #' @param ... ignored |
||
| 145 | +13 |
- } else {
+ #' @return nothing |
|
| 146 | -! | +||
| 14 | +
- stop("yaml package is required to format the filter state list")
+ NULL |
||
| 147 | +15 |
- }+ |
|
| 148 | +16 |
- }+ #' @rdname tdata |
|
| 149 | -8x | +||
| 17 | +
- private$teal_slices <- content+ #' @export |
||
| 150 | -8x | +||
| 18 | +
- invisible(self)+ new_tdata <- function(...) {
+ |
+ ||
| 19 | +! | +
+ .deprecate_tdata_msg() |
|
| 151 | +20 |
- },+ } |
|
| 152 | +21 |
- #' @description Create the `TealSlicesBlock` from a list.+ |
|
| 153 | +22 |
- #'+ #' @rdname tdata |
|
| 154 | +23 |
- #' @param x (`named list`) with two fields `text` and `style`.+ #' @export |
|
| 155 | +24 |
- #' Use the `get_available_styles` method to get all possible styles.+ tdata2env <- function(...) {
+ |
+ |
| 25 | +! | +
+ .deprecate_tdata_msg() |
|
| 156 | +26 |
- #'+ } |
|
| 157 | +27 |
- #' @return `self`, invisibly.+ |
|
| 158 | +28 |
- #' @examples+ #' @rdname tdata |
|
| 159 | +29 |
- #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
+ #' @export |
|
| 160 | +30 |
- #' block <- TealSlicesBlock$new()+ get_code_tdata <- function(...) {
+ |
+ |
| 31 | +! | +
+ .deprecate_tdata_msg()+ |
+ |
| 32 | ++ |
+ } |
|
| 161 | +33 |
- #' block$from_list(list(text = "sth", style = "default"))+ |
|
| 162 | +34 |
- #'+ #' @rdname tdata |
|
| 163 | +35 |
- from_list = function(x) {
+ #' @export |
|
| 164 | -1x | +||
| 36 | +
- checkmate::assert_list(x)+ join_keys.tdata <- function(...) {
|
||
| 165 | -1x | +||
| 37 | +! |
- checkmate::assert_names(names(x), must.include = c("text", "style"))
+ .deprecate_tdata_msg() |
|
| 166 | -1x | +||
| 38 | +
- super$set_content(x$text)+ } |
||
| 167 | -1x | +||
| 39 | +
- super$set_style(x$style)+ |
||
| 168 | -1x | +||
| 40 | +
- invisible(self)+ #' @rdname tdata |
||
| 169 | +41 |
- },+ #' @export |
|
| 170 | +42 |
- #' @description Convert the `TealSlicesBlock` to a list.+ get_metadata <- function(...) {
|
|
| 171 | -+ | ||
| 43 | +! |
- #'+ .deprecate_tdata_msg() |
|
| 172 | +44 |
- #' @return `named list` with a text and style.+ } |
|
| 173 | +45 |
- #' @examples+ |
|
| 174 | +46 |
- #' TealSlicesBlock <- getFromNamespace("TealSlicesBlock", "teal")
+ #' @rdname tdata |
|
| 175 | +47 |
- #' block <- TealSlicesBlock$new()+ #' @export |
|
| 176 | +48 |
- #' block$to_list()+ as_tdata <- function(...) {
|
|
| 177 | -+ | ||
| 49 | +! |
- #'+ .deprecate_tdata_msg() |
|
| 178 | +50 |
- to_list = function() {
+ } |
|
| 179 | -2x | +||
| 51 | +
- content <- self$get_content()+ |
||
| 180 | -2x | +||
| 52 | +
- list(+ |
||
| 181 | -2x | +||
| 53 | +
- text = if (length(content)) content else "",+ .deprecate_tdata_msg <- function() {
|
||
| 182 | -2x | +||
| 54 | +! |
- style = self$get_style()+ lifecycle::deprecate_stop( |
|
| 183 | -+ | ||
| 55 | +! |
- )+ when = "0.16", |
|
| 184 | -+ | ||
| 56 | +! |
- }+ what = "tdata()", |
|
| 185 | -+ | ||
| 57 | +! |
- ),+ details = paste( |
|
| 186 | -+ | ||
| 58 | +! |
- private = list(+ "tdata has been removed in favour of `teal_data`.\n", |
|
| 187 | -+ | ||
| 59 | +! |
- style = "verbatim",+ "Please follow migration instructions https://github.com/insightsengineering/teal/discussions/987." |
|
| 188 | +60 |
- teal_slices = NULL # teal_slices+ ) |
|
| 189 | +61 |
) |
|
| 190 | +62 |
- )+ } |
| 1 |
- #' Data module for `teal` applications+ #' Send input validation messages to output |
||
| 3 |
- #' @description+ #' Captures messages from `InputValidator` objects and collates them |
||
| 4 |
- #' `r lifecycle::badge("experimental")`
+ #' into one message passed to `validate`. |
||
| 6 |
- #' Create a `teal_data_module` object and evaluate code on it with history tracking.+ #' `shiny::validate` is used to withhold rendering of an output element until |
||
| 7 |
- #'+ #' certain conditions are met and to print a validation message in place |
||
| 8 |
- #' @details+ #' of the output element. |
||
| 9 |
- #' `teal_data_module` creates a `shiny` module to interactively supply or modify data in a `teal` application.+ #' `shinyvalidate::InputValidator` allows to validate input elements |
||
| 10 |
- #' The module allows for running any code (creation _and_ some modification) after the app starts or reloads.+ #' and to display specific messages in their respective input widgets. |
||
| 11 |
- #' The body of the server function will be run in the app rather than in the global environment.+ #' `validate_inputs` provides a hybrid solution. |
||
| 12 |
- #' This means it will be run every time the app starts, so use sparingly.+ #' Given an `InputValidator` object, messages corresponding to inputs that fail validation |
||
| 13 |
- #'+ #' are extracted and placed in one validation message that is passed to a `validate`/`need` call. |
||
| 14 |
- #' Pass this module instead of a `teal_data` object in a call to [init()].+ #' This way the input `validator` messages are repeated in the output. |
||
| 15 |
- #' Note that the server function must always return a `teal_data` object wrapped in a reactive expression.+ #' |
||
| 16 |
- #'+ #' The `...` argument accepts any number of `InputValidator` objects |
||
| 17 |
- #' See vignette `vignette("data-as-shiny-module", package = "teal")` for more details.
+ #' or a nested list of such objects. |
||
| 18 |
- #'+ #' If `validators` are passed directly, all their messages are printed together |
||
| 19 |
- #' @param ui (`function(id)`)+ #' under one (optional) header message specified by `header`. If a list is passed, |
||
| 20 |
- #' `shiny` module UI function; must only take `id` argument+ #' messages are grouped by `validator`. The list's names are used as headers |
||
| 21 |
- #' @param server (`function(id)`)+ #' for their respective message groups. |
||
| 22 |
- #' `shiny` module server function; must only take `id` argument;+ #' If neither of the nested list elements is named, a header message is taken from `header`. |
||
| 23 |
- #' must return reactive expression containing `teal_data` object+ #' |
||
| 24 |
- #' @param label (`character(1)`) Label of the module.+ #' @param ... either any number of `InputValidator` objects |
||
| 25 |
- #' @param once (`logical(1)`)+ #' or an optionally named, possibly nested `list` of `InputValidator` |
||
| 26 |
- #' If `TRUE`, the data module will be shown only once and will disappear after successful data loading.+ #' objects, see `Details` |
||
| 27 |
- #' App user will no longer be able to interact with this module anymore.+ #' @param header (`character(1)`) generic validation message; set to NULL to omit |
||
| 28 |
- #' If `FALSE`, the data module can be reused multiple times.+ #' |
||
| 29 |
- #' App user will be able to interact and change the data output from the module multiple times.+ #' @return |
||
| 30 |
- #'+ #' Returns NULL if the final validation call passes and a `shiny.silent.error` if it fails. |
||
| 31 |
- #' @return+ #' |
||
| 32 |
- #' `teal_data_module` returns a list of class `teal_data_module` containing two elements, `ui` and+ #' @seealso [`shinyvalidate::InputValidator`], [`shiny::validate`] |
||
| 33 |
- #' `server` provided via arguments.+ #' |
||
| 34 |
- #'+ #' @examplesIf require("shinyvalidate")
|
||
| 35 |
- #' @examples+ #' library(shiny) |
||
| 36 |
- #' tdm <- teal_data_module(+ #' library(shinyvalidate) |
||
| 37 |
- #' ui = function(id) {
+ #' |
||
| 38 |
- #' ns <- NS(id)+ #' ui <- fluidPage( |
||
| 39 |
- #' actionButton(ns("submit"), label = "Load data")
+ #' selectInput("method", "validation method", c("sequential", "combined", "grouped")),
|
||
| 40 |
- #' },+ #' sidebarLayout( |
||
| 41 |
- #' server = function(id) {
+ #' sidebarPanel( |
||
| 42 |
- #' moduleServer(id, function(input, output, session) {
+ #' selectInput("letter", "select a letter:", c(letters[1:3], LETTERS[4:6])),
|
||
| 43 |
- #' eventReactive(input$submit, {
+ #' selectInput("number", "select a number:", 1:6),
|
||
| 44 |
- #' data <- within(+ #' tags$br(), |
||
| 45 |
- #' teal_data(),+ #' selectInput("color", "select a color:",
|
||
| 46 |
- #' {
+ #' c("black", "indianred2", "springgreen2", "cornflowerblue"),
|
||
| 47 |
- #' dataset1 <- iris+ #' multiple = TRUE |
||
| 48 |
- #' dataset2 <- mtcars+ #' ), |
||
| 49 |
- #' }+ #' sliderInput("size", "select point size:",
|
||
| 50 |
- #' )+ #' min = 0.1, max = 4, value = 0.25 |
||
| 51 |
- #' datanames(data) <- c("dataset1", "dataset2")
+ #' ) |
||
| 52 |
- #'+ #' ), |
||
| 53 |
- #' data+ #' mainPanel(plotOutput("plot"))
|
||
| 54 |
- #' })+ #' ) |
||
| 55 |
- #' })+ #' ) |
||
| 56 |
- #' }+ #' |
||
| 57 |
- #' )+ #' server <- function(input, output) {
|
||
| 58 |
- #'+ #' # set up input validation |
||
| 59 |
- #' @name teal_data_module+ #' iv <- InputValidator$new() |
||
| 60 |
- #' @seealso [`teal.data::teal_data-class`], [teal.code::qenv()]+ #' iv$add_rule("letter", sv_in_set(LETTERS, "choose a capital letter"))
|
||
| 61 |
- #'+ #' iv$add_rule("number", function(x) {
|
||
| 62 |
- #' @export+ #' if (as.integer(x) %% 2L == 1L) "choose an even number" |
||
| 63 |
- teal_data_module <- function(ui, server, label = "data module", once = TRUE) {
+ #' }) |
||
| 64 | -33x | +
- checkmate::assert_function(ui, args = "id", nargs = 1)+ #' iv$enable() |
|
| 65 | -32x | +
- checkmate::assert_function(server, args = "id", nargs = 1)+ #' # more input validation |
|
| 66 | -30x | +
- checkmate::assert_string(label)+ #' iv_par <- InputValidator$new() |
|
| 67 | -30x | +
- checkmate::assert_flag(once)+ #' iv_par$add_rule("color", sv_required(message = "choose a color"))
|
|
| 68 | -30x | +
- structure(+ #' iv_par$add_rule("color", function(x) {
|
|
| 69 | -30x | +
- list(+ #' if (length(x) > 1L) "choose only one color" |
|
| 70 | -30x | +
- ui = ui,+ #' }) |
|
| 71 | -30x | +
- server = function(id) {
+ #' iv_par$add_rule( |
|
| 72 | -23x | +
- data_out <- server(id)+ #' "size", |
|
| 73 | -22x | +
- decorate_err_msg(+ #' sv_between( |
|
| 74 | -22x | +
- assert_reactive(data_out),+ #' left = 0.5, right = 3, |
|
| 75 | -22x | +
- pre = sprintf("From: 'teal_data_module()':\nA 'teal_data_module' with \"%s\" label:", label),
+ #' message_fmt = "choose a value between {left} and {right}"
|
|
| 76 | -22x | +
- post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter.+ #' ) |
|
| 77 |
- )+ #' ) |
||
| 78 |
- }+ #' iv_par$enable() |
||
| 79 |
- ),+ #' |
||
| 80 | -30x | +
- label = label,+ #' output$plot <- renderPlot({
|
|
| 81 | -30x | +
- class = "teal_data_module",+ #' # validate output |
|
| 82 | -30x | +
- once = once+ #' switch(input[["method"]], |
|
| 83 |
- )+ #' "sequential" = {
|
||
| 84 |
- }+ #' validate_inputs(iv) |
||
| 85 |
-
+ #' validate_inputs(iv_par, header = "Set proper graphical parameters") |
||
| 86 |
- #' Data module for `teal` transformers.+ #' }, |
||
| 87 |
- #'+ #' "combined" = validate_inputs(iv, iv_par), |
||
| 88 |
- #' @description+ #' "grouped" = validate_inputs(list( |
||
| 89 |
- #' `r lifecycle::badge("experimental")`
+ #' "Some inputs require attention" = iv, |
||
| 90 |
- #'+ #' "Set proper graphical parameters" = iv_par |
||
| 91 |
- #' Create a `teal_data_module` object for custom transformation of data for pre-processing+ #' )) |
||
| 92 |
- #' before passing the data into the module.+ #' ) |
||
| 94 |
- #' @details+ #' plot(faithful$eruptions ~ faithful$waiting, |
||
| 95 |
- #' `teal_transform_module` creates a [`teal_data_module`] object to transform data in a `teal`+ #' las = 1, pch = 16, |
||
| 96 |
- #' application. This transformation happens after the data has passed through the filtering activity+ #' col = input[["color"]], cex = input[["size"]] |
||
| 97 |
- #' in teal. The transformed data is then sent to the server of the [teal_module()].+ #' ) |
||
| 98 |
- #'+ #' }) |
||
| 99 |
- #' See vignette `vignette("data-transform-as-shiny-module", package = "teal")` for more details.
+ #' } |
||
| 101 |
- #'+ #' if (interactive()) {
|
||
| 102 |
- #' @inheritParams teal_data_module+ #' shinyApp(ui, server) |
||
| 103 |
- #' @param server (`function(id, data)`)+ #' } |
||
| 104 |
- #' `shiny` module server function; that takes `id` and `data` argument,+ #' |
||
| 105 |
- #' where the `id` is the module id and `data` is the reactive `teal_data` input.+ #' @export |
||
| 106 |
- #' The server function must return reactive expression containing `teal_data` object.+ #' |
||
| 107 |
- #'+ validate_inputs <- function(..., header = "Some inputs require attention") {
|
||
| 108 | -+ | 36x |
- #' The server function definition should not use `eventReactive` as it may lead to+ dots <- list(...) |
| 109 | -+ | 2x |
- #' unexpected behavior.+ if (!is_validators(dots)) stop("validate_inputs accepts validators or a list thereof")
|
| 110 |
- #' See `vignettes("data-transform-as-shiny-module")` for more information.
+
|
||
| 111 | -+ | 34x |
- #' @param datanames (`character`)+ messages <- extract_validator(dots, header) |
| 112 | -+ | 34x |
- #' Names of the datasets that are relevant for this module to evaluate. If set to `character(0)`+ failings <- if (!any_names(dots)) {
|
| 113 | -+ | 29x |
- #' then module would receive [modules()] `datanames`.+ add_header(messages, header) |
| 114 |
- #' @examples+ } else {
|
||
| 115 | -+ | 5x |
- #' my_transformers <- list(+ unlist(messages) |
| 116 |
- #' teal_transform_module(+ } |
||
| 117 |
- #' label = "Custom transform for iris",+ |
||
| 118 | -+ | 34x |
- #' datanames = "iris",+ shiny::validate(shiny::need(is.null(failings), failings)) |
| 119 |
- #' ui = function(id) {
+ } |
||
| 120 |
- #' ns <- NS(id)+ |
||
| 121 |
- #' tags$div(+ ### internal functions |
||
| 122 |
- #' numericInput(ns("n_rows"), "Subset n rows", value = 6, min = 1, max = 150, step = 1)
+
|
||
| 123 |
- #' )+ #' @noRd |
||
| 124 |
- #' },+ #' @keywords internal |
||
| 125 |
- #' server = function(id, data) {
+ # recursive object type test |
||
| 126 |
- #' moduleServer(id, function(input, output, session) {
+ # returns logical of length 1 |
||
| 127 |
- #' reactive({
+ is_validators <- function(x) {
|
||
| 128 | -+ | 118x |
- #' within(data(),+ all(if (is.list(x)) unlist(lapply(x, is_validators)) else inherits(x, "InputValidator")) |
| 129 |
- #' {
+ } |
||
| 130 |
- #' iris <- head(iris, num_rows)+ |
||
| 131 |
- #' },+ #' @noRd |
||
| 132 |
- #' num_rows = input$n_rows+ #' @keywords internal |
||
| 133 |
- #' )+ # test if an InputValidator object is enabled |
||
| 134 |
- #' })+ # returns logical of length 1 |
||
| 135 |
- #' })+ # official method requested at https://github.com/rstudio/shinyvalidate/issues/64 |
||
| 136 |
- #' }+ validator_enabled <- function(x) {
|
||
| 137 | -+ | 49x |
- #' )+ x$.__enclos_env__$private$enabled |
| 138 |
- #' )+ } |
||
| 139 |
- #'+ |
||
| 140 |
- #' @name teal_transform_module+ #' Recursively extract messages from validator list |
||
| 141 |
- #'+ #' @return A character vector or a list of character vectors, possibly nested and named. |
||
| 142 |
- #' @export+ #' @noRd |
||
| 143 |
- teal_transform_module <- function(ui = function(id) NULL,+ #' @keywords internal |
||
| 144 |
- server = function(id, data) data,+ extract_validator <- function(iv, header) {
|
||
| 145 | -+ | 113x |
- label = "transform module",+ if (inherits(iv, "InputValidator")) {
|
| 146 | -+ | 49x |
- datanames = character(0)) {
+ add_header(gather_messages(iv), header) |
| 147 | -20x | +
- checkmate::assert_function(ui, args = "id", nargs = 1)+ } else {
|
|
| 148 | -20x | +58x |
- checkmate::assert_function(server, args = c("id", "data"), nargs = 2)
+ if (is.null(names(iv))) names(iv) <- rep("", length(iv))
|
| 149 | -20x | +64x |
- checkmate::assert_string(label)+ mapply(extract_validator, iv = iv, header = names(iv), SIMPLIFY = FALSE) |
| 150 | -20x | +
- checkmate::assert_character(datanames)+ } |
|
| 151 | -20x | +
- if (identical(datanames, "all")) {
+ } |
|
| 152 | -1x | +
- stop(+ |
|
| 153 | -1x | +
- "teal_transform_module can't have datanames property equal to 'all'. Set `datanames = character(0)` instead.",+ #' Collate failing messages from validator. |
|
| 154 | -1x | +
- call. = FALSE+ #' @return `list` |
|
| 155 |
- )+ #' @noRd |
||
| 156 |
- }+ #' @keywords internal |
||
| 157 | -19x | +
- structure(+ gather_messages <- function(iv) {
|
|
| 158 | -19x | +49x |
- list(+ if (validator_enabled(iv)) {
|
| 159 | -19x | +46x |
- ui = ui,+ status <- iv$validate() |
| 160 | -19x | +46x |
- server = function(id, data) {
+ failing_inputs <- Filter(Negate(is.null), status) |
| 161 | -20x | +46x |
- data_out <- server(id, data)+ unique(lapply(failing_inputs, function(x) x[["message"]])) |
| 162 |
-
+ } else {
|
||
| 163 | -20x | +3x |
- if (inherits(data_out, "reactive.event")) {
+ warning("Validator is disabled and will be omitted.")
|
| 164 | -+ | 3x |
- # This warning message partially detects when `eventReactive` is used in `data_module`.+ list() |
| 165 | -1x | +
- warning(+ } |
|
| 166 | -1x | +
- "teal_transform_module() ",+ } |
|
| 167 | -1x | +
- "Using eventReactive in teal_transform module server code should be avoided as it ",+ |
|
| 168 | -1x | +
- "may lead to unexpected behavior. See the vignettes for more information ",+ #' Add optional header to failing messages |
|
| 169 | -1x | +
- "(`vignette(\"data-transform-as-shiny-module\", package = \"teal\")`).",+ #' @noRd |
|
| 170 | -1x | +
- call. = FALSE+ #' @keywords internal |
|
| 171 |
- )+ add_header <- function(messages, header = "") {
|
||
| 172 | -+ | 78x |
- }+ ans <- unlist(messages) |
| 173 | -+ | 78x |
-
+ if (length(ans) != 0L && isTRUE(nchar(header) > 0L)) {
|
| 174 | -20x | +31x |
- decorate_err_msg(+ ans <- c(paste0(header, "\n"), ans, "\n") |
| 175 | -20x | +
- assert_reactive(data_out),+ } |
|
| 176 | -20x | +78x |
- pre = sprintf("From: 'teal_transform_module()':\nA 'teal_transform_module' with \"%s\" label:", label),
+ ans |
| 177 | -20x | +
- post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter.+ } |
|
| 178 |
- )+ |
||
| 179 |
- }+ #' Recursively check if the object contains a named list |
||
| 180 |
- ),+ #' @noRd |
||
| 181 | -19x | +
- label = label,+ #' @keywords internal |
|
| 182 | -19x | +
- datanames = datanames,+ any_names <- function(x) {
|
|
| 183 | -19x | +103x |
- class = c("teal_transform_module", "teal_data_module")
+ any( |
| 184 | -+ | 103x |
- )+ if (is.list(x)) {
|
| 185 | -+ | 58x |
- }+ if (!is.null(names(x)) && any(names(x) != "")) TRUE else unlist(lapply(x, any_names)) |
| 186 |
-
+ } else {
|
||
| 187 | -+ | 40x |
-
+ FALSE |
| 188 |
- #' Extract all `transformers` from `modules`.+ } |
||
| 189 |
- #'+ ) |
||
| 190 |
- #' @param modules `teal_modules` or `teal_module`+ } |
| 191 | +1 |
- #' @return A list of `teal_transform_module` nested in the same way as input `modules`.+ #' Data module for `teal` applications |
|
| 192 | +2 |
- #' @keywords internal+ #' |
|
| 193 | +3 |
- extract_transformers <- function(modules) {
+ #' @description |
|
| 194 | -6x | +||
| 4 | +
- if (inherits(modules, "teal_module")) {
+ #' `r lifecycle::badge("experimental")`
|
||
| 195 | -3x | +||
| 5 | +
- modules$transformers+ #' |
||
| 196 | -3x | +||
| 6 | +
- } else if (inherits(modules, "teal_modules")) {
+ #' Create a `teal_data_module` object and evaluate code on it with history tracking. |
||
| 197 | -3x | +||
| 7 | +
- lapply(modules$children, extract_transformers)+ #' |
||
| 198 | +8 |
- }+ #' @details |
|
| 199 | +9 |
- }+ #' `teal_data_module` creates a `shiny` module to interactively supply or modify data in a `teal` application. |
| 1 | +10 |
- .onLoad <- function(libname, pkgname) {
+ #' The module allows for running any code (creation _and_ some modification) after the app starts or reloads. |
|
| 2 | +11 |
- # adapted from https://github.com/r-lib/devtools/blob/master/R/zzz.R+ #' The body of the server function will be run in the app rather than in the global environment. |
|
| 3 | +12 |
-
+ #' This means it will be run every time the app starts, so use sparingly. |
|
| 4 | -! | +||
| 13 | +
- teal_default_options <- list(+ #' |
||
| 5 | -! | +||
| 14 | +
- teal.show_js_log = FALSE,+ #' Pass this module instead of a `teal_data` object in a call to [init()]. |
||
| 6 | -! | +||
| 15 | +
- teal.lockfile.mode = "auto",+ #' Note that the server function must always return a `teal_data` object wrapped in a reactive expression. |
||
| 7 | -! | +||
| 16 | +
- shiny.sanitize.errors = FALSE+ #' |
||
| 8 | +17 |
- )+ #' See vignette `vignette("data-as-shiny-module", package = "teal")` for more details.
|
|
| 9 | +18 |
-
+ #' |
|
| 10 | -! | +||
| 19 | +
- op <- options()+ #' @param ui (`function(id)`) |
||
| 11 | -! | +||
| 20 | +
- toset <- !(names(teal_default_options) %in% names(op))+ #' `shiny` module UI function; must only take `id` argument |
||
| 12 | -! | +||
| 21 | +
- if (any(toset)) options(teal_default_options[toset])+ #' @param server (`function(id)`) |
||
| 13 | +22 |
-
+ #' `shiny` module server function; must only take `id` argument; |
|
| 14 | +23 |
- # Set up the teal logger instance+ #' must return reactive expression containing `teal_data` object |
|
| 15 | -! | +||
| 24 | +
- teal.logger::register_logger("teal")
+ #' @param label (`character(1)`) Label of the module. |
||
| 16 | -! | +||
| 25 | +
- teal.logger::register_handlers("teal")
+ #' @param once (`logical(1)`) |
||
| 17 | +26 |
-
+ #' If `TRUE`, the data module will be shown only once and will disappear after successful data loading. |
|
| 18 | -! | +||
| 27 | +
- invisible()+ #' App user will no longer be able to interact with this module anymore. |
||
| 19 | +28 |
- }+ #' If `FALSE`, the data module can be reused multiple times. |
|
| 20 | +29 |
-
+ #' App user will be able to interact and change the data output from the module multiple times. |
|
| 21 | +30 |
- .onAttach <- function(libname, pkgname) {
+ #' |
|
| 22 | -2x | +||
| 31 | +
- packageStartupMessage(+ #' @return |
||
| 23 | -2x | +||
| 32 | +
- "\nYou are using teal version ",+ #' `teal_data_module` returns a list of class `teal_data_module` containing two elements, `ui` and |
||
| 24 | +33 |
- # `system.file` uses the `shim` of `system.file` by `teal`+ #' `server` provided via arguments. |
|
| 25 | +34 |
- # we avoid `desc` dependency here to get the version+ #' |
|
| 26 | -2x | +||
| 35 | +
- read.dcf(system.file("DESCRIPTION", package = "teal"))[, "Version"]
+ #' @examples+ |
+ ||
| 36 | ++ |
+ #' tdm <- teal_data_module(+ |
+ |
| 37 | ++ |
+ #' ui = function(id) {
+ |
+ |
| 38 | ++ |
+ #' ns <- NS(id)+ |
+ |
| 39 | ++ |
+ #' actionButton(ns("submit"), label = "Load data")
|
|
| 27 | +40 |
- )+ #' }, |
|
| 28 | +41 |
- }+ #' server = function(id) {
|
|
| 29 | +42 |
-
+ #' moduleServer(id, function(input, output, session) {
|
|
| 30 | +43 |
- # This one is here because setdiff_teal_slice should not be exported from teal.slice.+ #' eventReactive(input$submit, {
|
|
| 31 | +44 |
- setdiff_teal_slices <- getFromNamespace("setdiff_teal_slices", "teal.slice")
+ #' data <- within( |
|
| 32 | +45 |
- # This one is here because it is needed by c.teal_slices but we don't want it exported from teal.slice.+ #' teal_data(), |
|
| 33 | +46 |
- coalesce_r <- getFromNamespace("coalesce_r", "teal.slice")
+ #' {
|
|
| 34 | +47 |
- # all *Block objects are private in teal.reporter+ #' dataset1 <- iris |
|
| 35 | +48 |
- RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") # nolint: object_name.
+ #' dataset2 <- mtcars |
|
| 36 | +49 |
-
+ #' } |
|
| 37 | +50 |
- # Use non-exported function(s) from teal.code+ #' ) |
|
| 38 | +51 |
- # This one is here because lang2calls should not be exported from teal.code+ #' |
|
| 39 | +52 |
- lang2calls <- getFromNamespace("lang2calls", "teal.code")
+ #' data |
| 1 | +53 |
- #' Store and restore `teal_slices` object+ #' }) |
||
| 2 | +54 |
- #'+ #' }) |
||
| 3 | +55 |
- #' Functions that write a `teal_slices` object to a file in the `JSON` format,+ #' } |
||
| 4 | +56 |
- #' and also restore the object from disk.+ #' ) |
||
| 5 | +57 |
#' |
||
| 6 | +58 |
- #' Date and date time objects are stored in the following formats:+ #' @name teal_data_module |
||
| 7 | +59 |
- #'+ #' @seealso [`teal.data::teal_data-class`], [teal.code::qenv()] |
||
| 8 | +60 |
- #' - `Date` class is converted to the `"ISO8601"` standard (`YYYY-MM-DD`).+ #' |
||
| 9 | +61 |
- #' - `POSIX*t` classes are converted to character by using+ #' @export |
||
| 10 | +62 |
- #' `format.POSIX*t(usetz = TRUE, tz = "UTC")` (`YYYY-MM-DD HH:MM:SS UTC`, where+ teal_data_module <- function(ui, server, label = "data module", once = TRUE) {
|
||
| 11 | -+ | |||
| 63 | +33x |
- #' `UTC` is the `Coordinated Universal Time` timezone short-code).+ checkmate::assert_function(ui, args = "id", nargs = 1) |
||
| 12 | -+ | |||
| 64 | +32x |
- #'+ checkmate::assert_function(server, args = "id", nargs = 1) |
||
| 13 | -+ | |||
| 65 | +30x |
- #' This format is assumed during `slices_restore`. All `POSIX*t` objects in+ checkmate::assert_string(label) |
||
| 14 | -+ | |||
| 66 | +30x |
- #' `selected` or `choices` fields of `teal_slice` objects are always printed in+ checkmate::assert_flag(once) |
||
| 15 | -+ | |||
| 67 | +30x |
- #' `UTC` timezone as well.+ structure( |
||
| 16 | -+ | |||
| 68 | +30x |
- #'+ list( |
||
| 17 | -+ | |||
| 69 | +30x |
- #' @param tss (`teal_slices`) object to be stored.+ ui = ui, |
||
| 18 | -+ | |||
| 70 | +30x |
- #' @param file (`character(1)`) file path where `teal_slices` object will be+ server = function(id) {
|
||
| 19 | -+ | |||
| 71 | +23x |
- #' saved and restored. The file extension should be `".json"`.+ data_out <- server(id) |
||
| 20 | -+ | |||
| 72 | +22x |
- #'+ decorate_err_msg( |
||
| 21 | -+ | |||
| 73 | +22x |
- #' @return `slices_store` returns `NULL`, invisibly.+ assert_reactive(data_out), |
||
| 22 | -+ | |||
| 74 | +22x |
- #'+ pre = sprintf("From: 'teal_data_module()':\nA 'teal_data_module' with \"%s\" label:", label),
|
||
| 23 | -+ | |||
| 75 | +22x |
- #' @seealso [teal_slices()]+ post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter. |
||
| 24 | +76 |
- #'+ ) |
||
| 25 | +77 |
- #' @keywords internal+ } |
||
| 26 | +78 |
- #'+ ), |
||
| 27 | -+ | |||
| 79 | +30x |
- slices_store <- function(tss, file) {
+ label = label, |
||
| 28 | -9x | +80 | +30x |
- checkmate::assert_class(tss, "teal_slices")+ class = "teal_data_module", |
| 29 | -9x | +81 | +30x |
- checkmate::assert_path_for_output(file, overwrite = TRUE, extension = "json")+ once = once |
| 30 | +82 | ++ |
+ )+ |
+ |
| 83 | ++ |
+ }+ |
+ ||
| 84 | ||||
| 31 | -9x | +|||
| 85 | +
- cat(format(tss, trim_lines = FALSE), "\n", file = file)+ #' Data module for `teal` transformers. |
|||
| 32 | +86 |
- }+ #' |
||
| 33 | +87 |
-
+ #' @description |
||
| 34 | +88 |
- #' @rdname slices_store+ #' `r lifecycle::badge("experimental")`
|
||
| 35 | +89 |
- #' @return `slices_restore` returns a `teal_slices` object restored from the file.+ #' |
||
| 36 | +90 |
- #' @keywords internal+ #' Create a `teal_data_module` object for custom transformation of data for pre-processing |
||
| 37 | +91 |
- slices_restore <- function(file) {
+ #' before passing the data into the module. |
||
| 38 | -9x | +|||
| 92 | +
- checkmate::assert_file_exists(file, access = "r", extension = "json")+ #' |
|||
| 39 | +93 |
-
+ #' @details |
||
| 40 | -9x | +|||
| 94 | +
- tss_json <- jsonlite::fromJSON(file, simplifyDataFrame = FALSE)+ #' `teal_transform_module` creates a [`teal_data_module`] object to transform data in a `teal` |
|||
| 41 | -9x | +|||
| 95 | +
- tss_json$slices <-+ #' application. This transformation happens after the data has passed through the filtering activity |
|||
| 42 | -9x | +|||
| 96 | +
- lapply(tss_json$slices, function(slice) {
+ #' in teal. The transformed data is then sent to the server of the [teal_module()]. |
|||
| 43 | -9x | +|||
| 97 | +
- for (field in c("selected", "choices")) {
+ #' |
|||
| 44 | -18x | +|||
| 98 | +
- if (!is.null(slice[[field]])) {
+ #' See vignette `vignette("data-transform-as-shiny-module", package = "teal")` for more details.
|
|||
| 45 | -12x | +|||
| 99 | +
- if (length(slice[[field]]) > 0) {
+ #' |
|||
| 46 | -9x | +|||
| 100 | +
- date_partial_regex <- "^[0-9]{4}-[0-9]{2}-[0-9]{2}"
+ #' |
|||
| 47 | -9x | +|||
| 101 | +
- time_stamp_regex <- paste0(date_partial_regex, "\\s[0-9]{2}:[0-9]{2}:[0-9]{2}\\sUTC$")
+ #' @inheritParams teal_data_module |
|||
| 48 | +102 |
-
+ #' @param server (`function(id, data)`) |
||
| 49 | -9x | +|||
| 103 | +
- slice[[field]] <-+ #' `shiny` module server function; that takes `id` and `data` argument, |
|||
| 50 | -9x | +|||
| 104 | +
- if (all(grepl(paste0(date_partial_regex, "$"), slice[[field]]))) {
+ #' where the `id` is the module id and `data` is the reactive `teal_data` input. |
|||
| 51 | -3x | +|||
| 105 | +
- as.Date(slice[[field]])+ #' The server function must return reactive expression containing `teal_data` object. |
|||
| 52 | -9x | +|||
| 106 | +
- } else if (all(grepl(time_stamp_regex, slice[[field]]))) {
+ #' |
|||
| 53 | -3x | +|||
| 107 | +
- as.POSIXct(slice[[field]], tz = "UTC")+ #' The server function definition should not use `eventReactive` as it may lead to |
|||
| 54 | +108 |
- } else {
+ #' unexpected behavior. |
||
| 55 | -3x | +|||
| 109 | +
- slice[[field]]+ #' See `vignettes("data-transform-as-shiny-module")` for more information.
|
|||
| 56 | +110 |
- }+ #' @param datanames (`character`) |
||
| 57 | +111 |
- } else {
+ #' Names of the datasets that are relevant for this module to evaluate. If set to `character(0)` |
||
| 58 | -3x | +|||
| 112 | +
- slice[[field]] <- character(0)+ #' then module would receive [modules()] `datanames`. |
|||
| 59 | +113 |
- }+ #' @examples |
||
| 60 | +114 |
- }+ #' my_transformers <- list( |
||
| 61 | +115 |
- }+ #' teal_transform_module( |
||
| 62 | -9x | +|||
| 116 | +
- slice+ #' label = "Custom transform for iris", |
|||
| 63 | +117 |
- })+ #' datanames = "iris", |
||
| 64 | +118 |
-
+ #' ui = function(id) {
|
||
| 65 | -9x | +|||
| 119 | +
- tss_elements <- lapply(tss_json$slices, as.teal_slice)+ #' ns <- NS(id) |
|||
| 66 | +120 |
-
+ #' tags$div( |
||
| 67 | -9x | +|||
| 121 | +
- do.call(teal_slices, c(tss_elements, tss_json$attributes))+ #' numericInput(ns("n_rows"), "Subset n rows", value = 6, min = 1, max = 150, step = 1)
|
|||
| 68 | +122 |
- }+ #' ) |
| 1 | +123 |
- #' Module to transform `reactive` `teal_data`+ #' }, |
||
| 2 | +124 |
- #'+ #' server = function(id, data) {
|
||
| 3 | +125 |
- #' Module calls multiple [`module_teal_data`] in sequence so that `reactive teal_data` output+ #' moduleServer(id, function(input, output, session) {
|
||
| 4 | +126 |
- #' from one module is handed over to the following module's input.+ #' reactive({
|
||
| 5 | +127 |
- #'+ #' within(data(),+ |
+ ||
| 128 | ++ |
+ #' {
|
||
| 6 | +129 |
- #' @inheritParams module_teal_data+ #' iris <- head(iris, num_rows) |
||
| 7 | +130 |
- #' @inheritParams teal_modules+ #' }, |
||
| 8 | +131 |
- #' @return `reactive` `teal_data`+ #' num_rows = input$n_rows |
||
| 9 | +132 |
- #'+ #' ) |
||
| 10 | +133 |
- #'+ #' }) |
||
| 11 | +134 |
- #' @name module_transform_data+ #' }) |
||
| 12 | +135 |
- #' @keywords internal+ #' } |
||
| 13 | +136 |
- NULL+ #' ) |
||
| 14 | +137 |
-
+ #' ) |
||
| 15 | +138 |
- #' @rdname module_transform_data+ #' |
||
| 16 | +139 |
- ui_transform_data <- function(id, transformers = list(), class = "well") {
+ #' @name teal_transform_module |
||
| 17 | -! | +|||
| 140 | +
- checkmate::assert_string(id)+ #' |
|||
| 18 | -! | +|||
| 141 | +
- checkmate::assert_list(transformers, "teal_transform_module")+ #' @export |
|||
| 19 | +142 |
-
+ teal_transform_module <- function(ui = function(id) NULL, |
||
| 20 | -! | +|||
| 143 | +
- ns <- NS(id)+ server = function(id, data) data, |
|||
| 21 | -! | +|||
| 144 | +
- labels <- lapply(transformers, function(x) attr(x, "label"))+ label = "transform module", |
|||
| 22 | -! | +|||
| 145 | +
- ids <- get_unique_labels(labels)+ datanames = character(0)) {
|
|||
| 23 | -! | +|||
| 146 | +20x |
- names(transformers) <- ids+ checkmate::assert_function(ui, args = "id", nargs = 1) |
||
| 24 | -+ | |||
| 147 | +20x |
-
+ checkmate::assert_function(server, args = c("id", "data"), nargs = 2)
|
||
| 25 | -! | +|||
| 148 | +20x |
- lapply(+ checkmate::assert_string(label) |
||
| 26 | -! | +|||
| 149 | +20x |
- names(transformers),+ checkmate::assert_character(datanames) |
||
| 27 | -! | +|||
| 150 | +20x |
- function(name) {
+ if (identical(datanames, "all")) {
|
||
| 28 | -! | +|||
| 151 | +1x |
- data_mod <- transformers[[name]]+ stop( |
||
| 29 | -! | +|||
| 152 | +1x |
- wrapper_id <- ns(sprintf("wrapper_%s", name))
+ "teal_transform_module can't have datanames property equal to 'all'. Set `datanames = character(0)` instead.", |
||
| 30 | -! | +|||
| 153 | +1x |
- div( # todo: accordion?+ call. = FALSE |
||
| 31 | +154 |
- # class .teal_validated changes the color of the boarder on error in ui_validate_reactive_teal_data+ ) |
||
| 32 | +155 |
- # For details see tealValidate.js file.- |
- ||
| 33 | -! | -
- class = c(class, "teal_validated"),+ } |
||
| 34 | -! | +|||
| 156 | +19x |
- title = attr(data_mod, "label"),+ structure( |
||
| 35 | -! | +|||
| 157 | +19x |
- tags$span(+ list( |
||
| 36 | -! | +|||
| 158 | +19x |
- class = "text-primary mb-4",+ ui = ui, |
||
| 37 | -! | +|||
| 159 | +19x |
- icon("fas fa-square-pen"),
+ server = function(id, data) {
|
||
| 38 | -! | +|||
| 160 | +20x |
- attr(data_mod, "label")+ data_out <- server(id, data) |
||
| 39 | +161 |
- ),- |
- ||
| 40 | -! | -
- tags$i(- |
- ||
| 41 | -! | -
- class = "remove pull-right fa fa-angle-down",- |
- ||
| 42 | -! | -
- style = "cursor: pointer;",- |
- ||
| 43 | -! | -
- title = "fold/expand transform panel",+ |
||
| 44 | -! | +|||
| 162 | +20x |
- onclick = sprintf("togglePanelItems(this, '%s', 'fa-angle-right', 'fa-angle-down');", wrapper_id)
+ if (inherits(data_out, "reactive.event")) {
|
||
| 45 | +163 |
- ),+ # This warning message partially detects when `eventReactive` is used in `data_module`. |
||
| 46 | -! | +|||
| 164 | +1x |
- div(+ warning( |
||
| 47 | -! | +|||
| 165 | +1x |
- id = wrapper_id,+ "teal_transform_module() ", |
||
| 48 | -! | +|||
| 166 | +1x |
- ui_teal_data(id = ns(name), data_module = transformers[[name]]$ui)+ "Using eventReactive in teal_transform module server code should be avoided as it ", |
||
| 49 | -+ | |||
| 167 | +1x |
- )+ "may lead to unexpected behavior. See the vignettes for more information ", |
||
| 50 | -+ | |||
| 168 | +1x |
- )+ "(`vignette(\"data-transform-as-shiny-module\", package = \"teal\")`).", |
||
| 51 | -+ | |||
| 169 | +1x |
- }+ call. = FALSE |
||
| 52 | +170 |
- )+ ) |
||
| 53 | +171 |
- }+ } |
||
| 54 | +172 | |||
| 55 | -+ | |||
| 173 | +20x |
- #' @rdname module_transform_data+ decorate_err_msg( |
||
| 56 | -+ | |||
| 174 | +20x |
- srv_transform_data <- function(id, data, transformers = list(), modules, is_transformer_failed = reactiveValues()) {
+ assert_reactive(data_out), |
||
| 57 | -81x | +175 | +20x |
- checkmate::assert_string(id)+ pre = sprintf("From: 'teal_transform_module()':\nA 'teal_transform_module' with \"%s\" label:", label),
|
| 58 | -81x | +176 | +20x |
- assert_reactive(data)+ post = "Please make sure that this module returns a 'reactive` object containing 'teal_data' class of object." # nolint: line_length_linter. |
| 59 | -81x | +|||
| 177 | +
- checkmate::assert_list(transformers, "teal_transform_module")+ ) |
|||
| 60 | -81x | +|||
| 178 | +
- checkmate::assert_class(modules, "teal_module")+ } |
|||
| 61 | -81x | +|||
| 179 | +
- labels <- lapply(transformers, function(x) attr(x, "label"))+ ), |
|||
| 62 | -81x | +180 | +19x |
- ids <- get_unique_labels(labels)+ label = label, |
| 63 | -81x | +181 | +19x |
- names(transformers) <- ids+ datanames = datanames, |
| 64 | -81x | +182 | +19x |
- moduleServer(id, function(input, output, session) {
+ class = c("teal_transform_module", "teal_data_module")
|
| 65 | -81x | +|||
| 183 | +
- logger::log_debug("srv_teal_data_modules initializing.")
+ ) |
|||
| 66 | -81x | +|||
| 184 | +
- Reduce(+ } |
|||
| 67 | -81x | +|||
| 185 | +
- function(previous_result, name) {
+
|
|||
| 68 | -20x | +|||
| 186 | +
- srv_teal_data(+ |
|||
| 69 | -20x | +|||
| 187 | +
- id = name,+ #' Extract all `transformers` from `modules`. |
|||
| 70 | -20x | +|||
| 188 | +
- data_module = function(id) transformers[[name]]$server(id, previous_result),+ #' |
|||
| 71 | -20x | +|||
| 189 | +
- modules = modules,+ #' @param modules `teal_modules` or `teal_module` |
|||
| 72 | -20x | +|||
| 190 | +
- is_transformer_failed = is_transformer_failed+ #' @return A list of `teal_transform_module` nested in the same way as input `modules`. |
|||
| 73 | +191 |
- )+ #' @keywords internal |
||
| 74 | +192 |
- },+ extract_transformers <- function(modules) {
|
||
| 75 | -81x | +193 | +6x |
- x = names(transformers),+ if (inherits(modules, "teal_module")) {
|
| 76 | -81x | +194 | +3x |
- init = data+ modules$transformers |
| 77 | -+ | |||
| 195 | +3x |
- )+ } else if (inherits(modules, "teal_modules")) {
+ |
+ ||
| 196 | +3x | +
+ lapply(modules$children, extract_transformers) |
||
| 78 | +197 |
- })+ } |
||
| 79 | +198 |
}@@ -45446,14 +44965,14 @@ teal coverage - 59.99% |
| 1 |
- #' Filter settings for `teal` applications+ #' Data Module for teal |
|||
| 3 |
- #' Specify initial filter states and filtering settings for a `teal` app.+ #' This module manages the `data` argument for `srv_teal`. The `teal` framework uses [teal_data()], |
|||
| 4 |
- #'+ #' which can be provided in various ways: |
|||
| 5 |
- #' Produces a `teal_slices` object.+ #' 1. Directly as a [teal.data::teal_data()] object. This will automatically convert it into a `reactive` `teal_data`. |
|||
| 6 |
- #' The `teal_slice` components will specify filter states that will be active when the app starts.+ #' 2. As a `reactive` object that returns a [teal.data::teal_data()] object. |
|||
| 7 |
- #' Attributes (created with the named arguments) will configure the way the app applies filters.+ #' |
|||
| 8 |
- #' See argument descriptions for details.+ #' @details |
|||
| 9 |
- #'+ #' ## Reactive `teal_data`: |
|||
| 10 |
- #' @inheritParams teal.slice::teal_slices+ #' |
|||
| 11 |
- #'+ #' The data in the application can be reactively updated, prompting [srv_teal()] to rebuild the |
|||
| 12 |
- #' @param module_specific (`logical(1)`) optional,+ #' content accordingly. There are two methods for creating interactive `teal_data`: |
|||
| 13 |
- #' - `FALSE` (default) when one filter panel applied to all modules.+ #' 1. Using a `reactive` object provided from outside the `teal` application. In this scenario, |
|||
| 14 |
- #' All filters will be shared by all modules.+ #' reactivity is controlled by an external module, and `srv_teal` responds to changes. |
|||
| 15 |
- #' - `TRUE` when filter panel module-specific.+ #' 2. Using [teal_data_module()], which is embedded within the `teal` application, allowing data to |
|||
| 16 |
- #' Modules can have different set of filters specified - see `mapping` argument.+ #' be resubmitted by the user as needed. |
|||
| 17 |
- #' @param mapping `r lifecycle::badge("experimental")`
+ #' |
|||
| 18 |
- #' _This is a new feature. Do kindly share your opinions on+ #' Since the server of [teal_data_module()] must return a `reactive` `teal_data` object, both |
|||
| 19 |
- #' [`teal`'s GitHub repository](https://github.com/insightsengineering/teal/)._+ #' methods (1 and 2) produce the same reactive behavior within a `teal` application. The distinction |
|||
| 20 |
- #'+ #' lies in data control: the first method involves external control, while the second method |
|||
| 21 |
- #' (named `list`) specifies which filters will be active in which modules on app start.+ #' involves control from a custom module within the app. |
|||
| 22 |
- #' Elements should contain character vector of `teal_slice` `id`s (see [`teal.slice::teal_slice`]).+ #' |
|||
| 23 |
- #' Names of the list should correspond to `teal_module` `label` set in [module()] function.+ #' For more details, see [`module_teal_data`]. |
|||
| 24 |
- #' - `id`s listed under `"global_filters` will be active in all modules.+ #' |
|||
| 25 |
- #' - If missing, all filters will be applied to all modules.+ #' @inheritParams init |
|||
| 26 |
- #' - If empty list, all filters will be available to all modules but will start inactive.+ #' |
|||
| 27 |
- #' - If `module_specific` is `FALSE`, only `global_filters` will be active on start.+ #' @param data (`teal_data`, `teal_data_module`, or `reactive` returning `teal_data`) |
|||
| 28 |
- #' @param app_id (`character(1)`)+ #' The data which application will depend on. |
|||
| 29 |
- #' For internal use only, do not set manually.+ #' |
|||
| 30 |
- #' Added by `init` so that a `teal_slices` can be matched to the app in which it was used.+ #' @return A `reactive` object that returns: |
|||
| 31 |
- #' Used for verifying snapshots uploaded from file. See `snapshot`.+ #' Output of the `data`. If `data` fails then returned error is handled (after [tryCatch()]) so that |
|||
| 32 |
- #'+ #' rest of the application can respond to this respectively. |
|||
| 33 |
- #' @param x (`list`) of lists to convert to `teal_slices`+ #' |
|||
| 34 |
- #'+ #' @rdname module_init_data |
|||
| 35 |
- #' @return+ #' @name module_init_data |
|||
| 36 |
- #' A `teal_slices` object.+ #' @keywords internal |
|||
| 37 |
- #'+ NULL |
|||
| 38 |
- #' @seealso [`teal.slice::teal_slices`], [`teal.slice::teal_slice`], [slices_store()]+ |
|||
| 39 |
- #'+ #' @rdname module_init_data |
|||
| 40 |
- #' @examples+ ui_init_data <- function(id) {
|
|||
| 41 | -+ | 9x |
- #' filter <- teal_slices(+ ns <- shiny::NS(id) |
|
| 42 | -+ | 9x |
- #' teal_slice(dataname = "iris", varname = "Species", id = "species"),+ shiny::div( |
|
| 43 | -+ | 9x |
- #' teal_slice(dataname = "iris", varname = "Sepal.Length", id = "sepal_length"),+ id = ns("content"),
|
|
| 44 | -+ | 9x |
- #' teal_slice(+ style = "display: inline-block; width: 100%;", |
|
| 45 | -+ | 9x |
- #' dataname = "iris", id = "long_petals", title = "Long petals", expr = "Petal.Length > 5"+ uiOutput(ns("data"))
|
|
| 46 |
- #' ),+ ) |
|||
| 47 |
- #' teal_slice(dataname = "mtcars", varname = "mpg", id = "mtcars_mpg"),+ } |
|||
| 48 |
- #' mapping = list(+ |
|||
| 49 |
- #' module1 = c("species", "sepal_length"),
+ #' @rdname module_init_data |
|||
| 50 |
- #' module2 = c("mtcars_mpg"),
+ srv_init_data <- function(id, data) {
|
|||
| 51 | -+ | 83x |
- #' global_filters = "long_petals"+ checkmate::assert_character(id, max.len = 1, any.missing = FALSE) |
|
| 52 | -+ | 83x |
- #' )+ checkmate::assert_multi_class(data, c("teal_data", "teal_data_module", "reactive"))
|
|
| 53 |
- #' )+ |
|||
| 54 | -+ | 83x |
- #'+ moduleServer(id, function(input, output, session) {
|
|
| 55 | -+ | 83x |
- #' app <- init(+ logger::log_debug("srv_data initializing.")
|
|
| 56 |
- #' data = teal_data(iris = iris, mtcars = mtcars),+ # data_rv contains teal_data object |
|||
| 57 |
- #' modules = list(+ # either passed to teal::init or returned from teal_data_module |
|||
| 58 | -+ | 83x |
- #' module("module1"),
+ data_out <- if (inherits(data, "teal_data_module")) {
|
|
| 59 | -+ | 10x |
- #' module("module2")
+ output$data <- renderUI(data$ui(id = session$ns("teal_data_module")))
|
|
| 60 | -+ | 10x |
- #' ),+ data$server("teal_data_module")
|
|
| 61 | -+ | 83x |
- #' filter = filter+ } else if (inherits(data, "teal_data")) {
|
|
| 62 | -+ | 43x |
- #' )+ reactiveVal(data) |
|
| 63 | -+ | 83x |
- #'+ } else if (test_reactive(data)) {
|
|
| 64 | -+ | 30x |
- #' if (interactive()) {
+ data |
|
| 65 |
- #' shinyApp(app$ui, app$server)+ } |
|||
| 66 |
- #' }+ |
|||
| 67 | -+ | 82x |
- #'+ data_handled <- reactive({
|
|
| 68 | -+ | 75x |
- #' @export+ tryCatch(data_out(), error = function(e) e) |
|
| 69 |
- teal_slices <- function(...,+ }) |
|||
| 70 |
- exclude_varnames = NULL,+ |
|||
| 71 |
- include_varnames = NULL,+ # We want to exclude teal_data_module elements from bookmarking as they might have some secrets |
|||
| 72 | -+ | 82x |
- count_type = NULL,+ observeEvent(data_handled(), {
|
|
| 73 | -+ | 75x |
- allow_add = TRUE,+ if (inherits(data_handled(), "teal_data")) {
|
|
| 74 | -+ | 70x |
- module_specific = FALSE,+ app_session <- .subset2(shiny::getDefaultReactiveDomain(), "parent") |
|
| 75 | -+ | 70x |
- mapping,+ setBookmarkExclude( |
|
| 76 | -+ | 70x |
- app_id = NULL) {
+ session$ns( |
|
| 77 | -161x | +70x |
- shiny::isolate({
+ grep( |
|
| 78 | -161x | +70x |
- checkmate::assert_flag(allow_add)+ pattern = "teal_data_module-", |
|
| 79 | -161x | +70x |
- checkmate::assert_flag(module_specific)+ x = names(reactiveValuesToList(input)), |
|
| 80 | -51x | +70x |
- if (!missing(mapping)) checkmate::assert_list(mapping, types = c("character", "NULL"), names = "named")
+ value = TRUE |
|
| 81 | -158x | +
- checkmate::assert_string(app_id, null.ok = TRUE)+ ) |
||
| 82 |
-
+ ), |
|||
| 83 | -158x | +70x |
- slices <- list(...)+ session = app_session |
|
| 84 | -158x | +
- all_slice_id <- vapply(slices, `[[`, character(1L), "id")+ ) |
||
| 85 |
-
+ } |
|||
| 86 | -158x | +
- if (missing(mapping)) {
+ }) |
||
| 87 | -110x | +
- mapping <- if (length(all_slice_id)) {
+
|
||
| 88 | -26x | +82x |
- list(global_filters = all_slice_id)+ data_handled |
|
| 89 |
- } else {
+ }) |
|||
| 90 | -84x | +
- list()+ } |
||
| 91 |
- }+ |
|||
| 92 |
- }+ #' Adds signature protection to the `datanames` in the data |
|||
| 93 |
-
+ #' @param data (`teal_data`) |
|||
| 94 | -158x | +
- if (!module_specific) {
+ #' @return `teal_data` with additional code that has signature of the `datanames` |
||
| 95 | -139x | +
- mapping[setdiff(names(mapping), "global_filters")] <- NULL+ #' @keywords internal |
||
| 96 |
- }+ .add_signature_to_data <- function(data) {
|
|||
| 97 | -+ | 70x |
-
+ hashes <- .get_hashes_code(data) |
|
| 98 | -158x | +70x |
- failed_slice_id <- setdiff(unlist(mapping), all_slice_id)+ tdata <- do.call( |
|
| 99 | -158x | +70x |
- if (length(failed_slice_id)) {
+ teal.data::teal_data, |
|
| 100 | -1x | +70x |
- stop(sprintf(+ c( |
|
| 101 | -1x | +70x |
- "Filters in mapping don't match any available filter.\n %s not in %s",+ list(code = trimws(c(teal.code::get_code(data), hashes), which = "right")), |
|
| 102 | -1x | +70x |
- toString(failed_slice_id),+ list(join_keys = teal.data::join_keys(data)), |
|
| 103 | -1x | +70x | +
+ sapply(+ |
+ |
| 104 | +70x | +
+ names(data),+ |
+ ||
| 105 | +70x | +
+ teal.code::get_var,+ |
+ ||
| 106 | +70x | +
+ object = data,+ |
+ ||
| 107 | +70x | +
+ simplify = FALSE+ |
+ ||
| 108 | ++ |
+ )+ |
+ ||
| 109 | ++ |
+ )+ |
+ ||
| 110 | ++ |
+ )+ |
+ ||
| 111 | ++ | + + | +||
| 112 | +70x | +
+ tdata@verified <- data@verified+ |
+ ||
| 113 | +70x | +
+ tdata+ |
+ ||
| 114 | ++ |
+ }+ |
+ ||
| 115 | ++ | + + | +||
| 116 | ++ |
+ #' Get code that tests the integrity of the reproducible data+ |
+ ||
| 117 | ++ |
+ #'+ |
+ ||
| 118 | ++ |
+ #' @param data (`teal_data`) object holding the data+ |
+ ||
| 119 | ++ |
+ #' @param datanames (`character`) names of `datasets`+ |
+ ||
| 120 | ++ |
+ #'+ |
+ ||
| 121 | ++ |
+ #' @return A character vector with the code lines.+ |
+ ||
| 122 | ++ |
+ #' @keywords internal+ |
+ ||
| 123 | ++ |
+ #'+ |
+ ||
| 124 | ++ |
+ .get_hashes_code <- function(data, datanames = names(data)) {
+ |
+ ||
| 125 | +70x | +
+ vapply(+ |
+ ||
| 126 | +70x | +
+ datanames,+ |
+ ||
| 127 | +70x | +
+ function(dataname, datasets) {
+ |
+ ||
| 128 | +125x | +
+ x <- data[[dataname]]+ |
+ ||
| 129 | ++ | + + | +||
| 130 | +125x |
- toString(all_slice_id)+ code <- if (is.function(x) && !is.primitive(x)) {
|
||
| 104 | -+ | |||
| 131 | +6x |
- ))+ x <- deparse1(x) |
||
| 105 | -+ | |||
| 132 | +6x |
- }+ bquote(rlang::hash(deparse1(.(as.name(dataname))))) |
||
| 106 | +133 |
-
+ } else {
|
||
| 107 | -157x | +134 | +119x |
- tss <- teal.slice::teal_slices(+ bquote(rlang::hash(.(as.name(dataname)))) |
| 108 | +135 |
- ...,+ } |
||
| 109 | -157x | +136 | +125x |
- exclude_varnames = exclude_varnames,+ sprintf( |
| 110 | -157x | +137 | +125x |
- include_varnames = include_varnames,+ "stopifnot(%s == %s) # @linksto %s", |
| 111 | -157x | +138 | +125x |
- count_type = count_type,+ deparse1(code), |
| 112 | -157x | -
- allow_add = allow_add- |
- ||
| 113 | -+ | 139 | +125x |
- )+ deparse1(rlang::hash(x)), |
| 114 | -157x | +140 | +125x |
- attr(tss, "mapping") <- mapping+ dataname |
| 115 | -157x | +|||
| 141 | +
- attr(tss, "module_specific") <- module_specific+ ) |
|||
| 116 | -157x | +|||
| 142 | +
- attr(tss, "app_id") <- app_id+ }, |
|||
| 117 | -157x | +143 | +70x |
- class(tss) <- c("modules_teal_slices", class(tss))
+ character(1L), |
| 118 | -157x | +144 | +70x |
- tss+ USE.NAMES = TRUE |
| 119 | +145 |
- })+ ) |
||
| 120 | +146 |
} |
| 121 | +1 |
-
+ #' `teal_data` utils |
||
| 122 | +2 |
-
+ #' |
||
| 123 | +3 |
- #' @rdname teal_slices+ #' In `teal` we need to recreate the `teal_data` object due to two operations: |
||
| 124 | +4 |
- #' @export+ #' - we need to append filter-data code and objects which have been evaluated in `FilteredData` and |
||
| 125 | +5 |
- #' @keywords internal+ #' we want to avoid double-evaluation. |
||
| 126 | +6 |
- #'+ #' - we need to subset `teal_data` to `datanames` used by the module, to shorten obtainable R-code |
||
| 127 | +7 |
- as.teal_slices <- function(x) { # nolint: object_name.
+ #' |
||
| 128 | -13x | +|||
| 8 | +
- checkmate::assert_list(x)+ #' Due to above recreation of `teal_data` object can't be done simply by using public |
|||
| 129 | -13x | +|||
| 9 | +
- lapply(x, checkmate::assert_list, names = "named", .var.name = "list element")+ #' `teal.code` and `teal.data` methods. |
|||
| 130 | +10 |
-
+ #' |
||
| 131 | -13x | +|||
| 11 | +
- attrs <- attributes(unclass(x))+ #' @param data (`teal_data`) |
|||
| 132 | -13x | +|||
| 12 | +
- ans <- lapply(x, function(x) if (is.teal_slice(x)) x else as.teal_slice(x))+ #' @param code (`character`) code to append to the object's code slot. |
|||
| 133 | -13x | +|||
| 13 | +
- do.call(teal_slices, c(ans, attrs))+ #' @param objects (`list`) objects to append to object's environment. |
|||
| 134 | +14 |
- }+ #' @param datanames (`character`) names of the datasets |
||
| 135 | +15 |
-
+ #' @return modified `teal_data` |
||
| 136 | +16 |
-
+ #' @keywords internal |
||
| 137 | +17 |
- #' @rdname teal_slices+ #' @name teal_data_utilities |
||
| 138 | +18 |
- #' @export+ NULL |
||
| 139 | +19 |
- #' @keywords internal+ |
||
| 140 | +20 |
- #'+ #' @rdname teal_data_utilities |
||
| 141 | +21 |
- c.teal_slices <- function(...) {
+ .append_evaluated_code <- function(data, code) {
|
||
| 142 | -6x | +22 | +84x |
- x <- list(...)+ checkmate::assert_class(data, "teal_data") |
| 143 | -6x | +23 | +84x |
- checkmate::assert_true(all(vapply(x, is.teal_slices, logical(1L))), .var.name = "all arguments are teal_slices")+ data@code <- c(data@code, code) |
| 144 | -+ | |||
| 24 | +84x |
-
+ data@id <- c(data@id, max(data@id) + 1L + seq_along(code)) |
||
| 145 | -6x | +25 | +84x |
- all_attributes <- lapply(x, attributes)+ data@messages <- c(data@messages, rep("", length(code)))
|
| 146 | -6x | +26 | +84x |
- all_attributes <- coalesce_r(all_attributes)+ data@warnings <- c(data@warnings, rep("", length(code)))
|
| 147 | -6x | +27 | +84x |
- all_attributes <- all_attributes[names(all_attributes) != "class"]+ methods::validObject(data)+ |
+
| 28 | +84x | +
+ data |
||
| 148 | +29 | ++ |
+ }+ |
+ |
| 30 | ||||
| 149 | -6x | +|||
| 31 | +
- do.call(+ #' @rdname teal_data_utilities+ |
+ |||
| 32 | ++ |
+ .append_modified_data <- function(data, objects) {
|
||
| 150 | -6x | +33 | +84x |
- teal_slices,+ checkmate::assert_class(data, "teal_data") |
| 151 | -6x | +34 | +84x |
- c(+ checkmate::assert_class(objects, "list") |
| 152 | -6x | +35 | +84x |
- unique(unlist(x, recursive = FALSE)),+ new_env <- list2env(objects, parent = .GlobalEnv) |
| 153 | -6x | +36 | +84x |
- all_attributes+ rlang::env_coalesce(new_env, as.environment(data)) |
| 154 | -+ | |||
| 37 | +84x |
- )+ data@.xData <- new_env |
||
| 155 | -+ | |||
| 38 | +84x |
- )+ data |
||
| 156 | +39 |
} |
||
| 157 | +40 | |||
| 158 | +41 |
-
+ #' @rdname teal_data_utilities |
||
| 159 | +42 |
- #' Deep copy `teal_slices`+ .subset_teal_data <- function(data, datanames) {
|
||
| 160 | -+ | |||
| 43 | +83x |
- #'+ checkmate::assert_class(data, "teal_data") |
||
| 161 | -+ | |||
| 44 | +83x |
- #' it's important to create a new copy of `teal_slices` when+ checkmate::assert_class(datanames, "character") |
||
| 162 | -+ | |||
| 45 | +83x |
- #' starting a new `shiny` session. Otherwise, object will be shared+ datanames_corrected <- intersect(datanames, names(data)) |
||
| 163 | -+ | |||
| 46 | +83x |
- #' by multiple users as it is created in global environment before+ datanames_corrected_with_raw <- c(datanames_corrected, ".raw_data") |
||
| 164 | -+ | |||
| 47 | +83x |
- #' `shiny` session starts.+ if (!length(datanames_corrected)) {
|
||
| 165 | -+ | |||
| 48 | +2x |
- #' @param filter (`teal_slices`)+ return(teal_data()) |
||
| 166 | +49 |
- #' @return `teal_slices`+ } |
||
| 167 | +50 |
- #' @keywords internal+ |
||
| 168 | -+ | |||
| 51 | +81x |
- deep_copy_filter <- function(filter) {
+ new_data <- do.call( |
||
| 169 | -1x | +52 | +81x |
- checkmate::assert_class(filter, "teal_slices")+ teal.data::teal_data, |
| 170 | -1x | +53 | +81x |
- shiny::isolate({
+ args = c( |
| 171 | -1x | +54 | +81x |
- filter_copy <- lapply(filter, function(slice) {
+ mget(x = datanames_corrected_with_raw, envir = as.environment(data)), |
| 172 | -2x | +55 | +81x |
- teal.slice::as.teal_slice(as.list(slice))+ list( |
| 173 | -+ | |||
| 56 | +81x |
- })+ code = teal.code::get_code(data, names = datanames_corrected_with_raw), |
||
| 174 | -1x | +57 | +81x |
- attributes(filter_copy) <- attributes(filter)+ join_keys = teal.data::join_keys(data)[datanames_corrected] |
| 175 | -1x | +|||
| 58 | +
- filter_copy+ ) |
|||
| 176 | +59 |
- })+ ) |
||
| 177 | +60 | ++ |
+ )+ |
+ |
| 61 | +81x | +
+ new_data@verified <- data@verified+ |
+ ||
| 62 | +81x | +
+ new_data+ |
+ ||
| 63 |
}@@ -46691,452 +46440,479 @@ teal coverage - 59.99% |
| 1 |
- #' `teal_data` utils+ .onLoad <- function(libname, pkgname) {
|
||
| 2 |
- #'+ # adapted from https://github.com/r-lib/devtools/blob/master/R/zzz.R |
||
| 3 |
- #' In `teal` we need to recreate the `teal_data` object due to two operations:+ |
||
| 4 | -+ | ! |
- #' - we need to append filter-data code and objects which have been evaluated in `FilteredData` and+ teal_default_options <- list( |
| 5 | -+ | ! |
- #' we want to avoid double-evaluation.+ teal.show_js_log = FALSE, |
| 6 | -+ | ! |
- #' - we need to subset `teal_data` to `datanames` used by the module, to shorten obtainable R-code+ teal.lockfile.mode = "auto", |
| 7 | -+ | ! |
- #'+ shiny.sanitize.errors = FALSE |
| 8 |
- #' Due to above recreation of `teal_data` object can't be done simply by using public+ ) |
||
| 9 |
- #' `teal.code` and `teal.data` methods.+ |
||
| 10 | -+ | ! |
- #'+ op <- options() |
| 11 | -+ | ! |
- #' @param data (`teal_data`)+ toset <- !(names(teal_default_options) %in% names(op)) |
| 12 | -+ | ! |
- #' @param code (`character`) code to append to `data@code`+ if (any(toset)) options(teal_default_options[toset]) |
| 13 |
- #' @param objects (`list`) objects to append to `data@env`+ |
||
| 14 |
- #' @param datanames (`character`) names of the datasets+ # Set up the teal logger instance |
||
| 15 | -+ | ! |
- #' @return modified `teal_data`+ teal.logger::register_logger("teal")
|
| 16 | -+ | ! |
- #' @keywords internal+ teal.logger::register_handlers("teal")
|
| 17 |
- #' @name teal_data_utilities+ |
||
| 18 | -+ | ! |
- NULL+ invisible() |
| 19 |
-
+ } |
||
| 20 |
- #' @rdname teal_data_utilities+ |
||
| 21 |
- .append_evaluated_code <- function(data, code) {
+ .onAttach <- function(libname, pkgname) {
|
||
| 22 | -84x | +2x |
- checkmate::assert_class(data, "teal_data")+ packageStartupMessage( |
| 23 | -84x | +2x |
- data@code <- c(data@code, code)+ "\nYou are using teal version ", |
| 24 | -84x | +
- data@id <- c(data@id, max(data@id) + 1L + seq_along(code))+ # `system.file` uses the `shim` of `system.file` by `teal` |
|
| 25 | -84x | +
- data@messages <- c(data@messages, rep("", length(code)))
+ # we avoid `desc` dependency here to get the version |
|
| 26 | -84x | +2x |
- data@warnings <- c(data@warnings, rep("", length(code)))
+ read.dcf(system.file("DESCRIPTION", package = "teal"))[, "Version"]
|
| 27 | -84x | +
- methods::validObject(data)+ ) |
|
| 28 | -84x | +
- data+ } |
|
| 29 |
- }+ |
||
| 30 |
-
+ # This one is here because setdiff_teal_slice should not be exported from teal.slice. |
||
| 31 |
- #' @rdname teal_data_utilities+ setdiff_teal_slices <- getFromNamespace("setdiff_teal_slices", "teal.slice")
|
||
| 32 |
- .append_modified_data <- function(data, objects) {
+ # This one is here because it is needed by c.teal_slices but we don't want it exported from teal.slice. |
||
| 33 | -84x | +
- checkmate::assert_class(data, "teal_data")+ coalesce_r <- getFromNamespace("coalesce_r", "teal.slice")
|
|
| 34 | -84x | +
- checkmate::assert_class(objects, "list")+ # all *Block objects are private in teal.reporter |
|
| 35 | -84x | +
- new_env <- list2env(objects, parent = .GlobalEnv)+ RcodeBlock <- getFromNamespace("RcodeBlock", "teal.reporter") # nolint: object_name.
|
|
| 36 | -84x | +
- rlang::env_coalesce(new_env, teal.code::get_env(data))+ |
|
| 37 | -84x | +
- data@env <- new_env+ # Use non-exported function(s) from teal.code |
|
| 38 | -84x | +
- data+ # This one is here because lang2calls should not be exported from teal.code |
|
| 39 |
- }+ lang2calls <- getFromNamespace("lang2calls", "teal.code")
|
| 40 | +1 |
-
+ #' Generates library calls from current session info |
||
| 41 | +2 |
- #' @rdname teal_data_utilities+ #' |
||
| 42 | +3 |
- .subset_teal_data <- function(data, datanames) {
+ #' Function to create multiple library calls out of current session info to ensure reproducible code works. |
||
| 43 | -83x | +|||
| 4 | +
- checkmate::assert_class(data, "teal_data")+ #' |
|||
| 44 | -83x | +|||
| 5 | +
- checkmate::assert_class(datanames, "character")+ #' @return Character vector of `library(<package>)` calls. |
|||
| 45 | -83x | +|||
| 6 | ++ |
+ #' @keywords internal+ |
+ ||
| 7 | +
- datanames_corrected <- intersect(datanames, ls(teal.code::get_env(data)))+ get_rcode_libraries <- function() {
|
|||
| 46 | -83x | +8 | +1x |
- datanames_corrected_with_raw <- c(datanames_corrected, ".raw_data")+ libraries <- vapply( |
| 47 | -83x | +9 | +1x |
- if (!length(datanames_corrected)) {
+ utils::sessionInfo()$otherPkgs, |
| 48 | -2x | +10 | +1x |
- return(teal_data())+ function(x) {
|
| 49 | -+ | |||
| 11 | +15x |
- }+ paste0("library(", x$Package, ")")
|
||
| 50 | +12 |
-
+ }, |
||
| 51 | -81x | +13 | +1x |
- new_data <- do.call(+ character(1) |
| 52 | -81x | +|||
| 14 | +
- teal.data::teal_data,+ ) |
|||
| 53 | -81x | +15 | +1x |
- args = c(+ paste0(paste0(rev(libraries), sep = "\n"), collapse = "") |
| 54 | -81x | +|||
| 16 | +
- mget(x = datanames_corrected_with_raw, envir = teal.code::get_env(data)),+ } |
|||
| 55 | -81x | +|||
| 17 | +
- list(+ |
|||
| 56 | -81x | +|||
| 18 | +
- code = teal.code::get_code(data, names = datanames_corrected_with_raw),+ |
|||
| 57 | -81x | +|||
| 19 | +
- join_keys = teal.data::join_keys(data)[datanames_corrected]+ #' @noRd |
|||
| 58 | +20 |
- )+ #' @keywords internal |
||
| 59 | +21 |
- )+ get_rcode_str_install <- function() {
|
||
| 60 | -+ | |||
| 22 | +5x |
- )+ code_string <- getOption("teal.load_nest_code")
|
||
| 61 | -81x | +23 | +5x |
- new_data@verified <- data@verified+ if (is.character(code_string)) {
|
| 62 | -81x | +24 | +2x | +
+ code_string+ |
+
| 25 | +
- teal.data::datanames(new_data) <- datanames_corrected+ } else {
|
|||
| 63 | -81x | +26 | +3x |
- new_data+ "# Add any code to install/load your NEST environment here\n" |
| 64 | +27 | ++ |
+ }+ |
+ |
| 28 |
}@@ -47145,14 +46921,14 @@ teal coverage - 59.99% |
| 1 |
- #' Generates library calls from current session info+ #' Show `R` code modal |
||
| 3 |
- #' Function to create multiple library calls out of current session info to ensure reproducible code works.+ #' @description `r lifecycle::badge("deprecated")`
|
||
| 5 |
- #' @return Character vector of `library(<package>)` calls.+ #' Use the [shiny::showModal()] function to show the `R` code inside. |
||
| 6 |
- #' @keywords internal+ #' |
||
| 7 |
- get_rcode_libraries <- function() {
+ #' @param title (`character(1)`) |
||
| 8 | -1x | +
- libraries <- vapply(+ #' Title of the modal, displayed in the first comment of the `R` code. |
|
| 9 | -1x | +
- utils::sessionInfo()$otherPkgs,+ #' @param rcode (`character`) |
|
| 10 | -1x | +
- function(x) {
+ #' vector with `R` code to show inside the modal. |
|
| 11 | -15x | +
- paste0("library(", x$Package, ")")
+ #' @param session (`ShinySession`) optional |
|
| 12 |
- },+ #' `shiny` session object, defaults to [shiny::getDefaultReactiveDomain()]. |
||
| 13 | -1x | +
- character(1)+ #' |
|
| 14 |
- )+ #' @references [shiny::showModal()] |
||
| 15 | -1x | +
- paste0(paste0(rev(libraries), sep = "\n"), collapse = "")+ #' @export |
|
| 16 |
- }+ show_rcode_modal <- function(title = NULL, rcode, session = getDefaultReactiveDomain()) {
|
||
| 17 | +! | +
+ lifecycle::deprecate_soft(+ |
+ |
| 18 | +! | +
+ when = "0.16",+ |
+ |
| 19 | +! | +
+ what = "show_rcode_modal()",+ |
+ |
| 20 | +! | +
+ details = "This function will be removed in the next release."+ |
+ |
| 21 |
-
+ ) |
||
| 18 | +22 | ||
| 23 | +! | +
+ rcode <- paste(rcode, collapse = "\n")+ |
+ |
| 19 | +24 |
- #' @noRd+ + |
+ |
| 25 | +! | +
+ ns <- session$ns+ |
+ |
| 26 | +! | +
+ showModal(modalDialog(+ |
+ |
| 27 | +! | +
+ tagList(+ |
+ |
| 28 | +! | +
+ tags$div(+ |
+ |
| 29 | +! | +
+ actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
+ |
+ |
| 30 | +! | +
+ modalButton("Dismiss"),
+ |
+ |
| 31 | +! | +
+ style = "mb-4" |
|
| 20 | +32 |
- #' @keywords internal+ ),+ |
+ |
| 33 | +! | +
+ tags$div(tags$pre(id = ns("r_code"), rcode)),
|
|
| 21 | +34 |
- get_rcode_str_install <- function() {
+ ), |
|
| 22 | -5x | +||
| 35 | +! |
- code_string <- getOption("teal.load_nest_code")
+ title = title, |
|
| 23 | -5x | +||
| 36 | +! |
- if (is.character(code_string)) {
+ footer = tagList( |
|
| 24 | -2x | +||
| 37 | +! |
- code_string+ actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
+ |
+ |
| 38 | +! | +
+ modalButton("Dismiss")
|
|
| 25 | +39 |
- } else {
+ ), |
|
| 26 | -3x | +||
| 40 | +! |
- "# Add any code to install/load your NEST environment here\n"+ size = "l",+ |
+ |
| 41 | +! | +
+ easyClose = TRUE |
|
| 27 | +42 |
- }+ )) |
|
| 28 | +43 |
}@@ -48066,14 +47947,14 @@ teal coverage - 59.99% |
| 1 |
- #' UI and server modules of `teal`+ #' Create a `teal` module for previewing a report |
||
| 3 |
- #' @description `r lifecycle::badge("deprecated")`
+ #' @description `r lifecycle::badge("experimental")`
|
||
| 4 |
- #' Please use [`module_teal`] instead.+ #' |
||
| 5 |
- #'+ #' This function wraps [teal.reporter::reporter_previewer_ui()] and |
||
| 6 |
- #' @inheritParams ui_teal+ #' [teal.reporter::reporter_previewer_srv()] into a `teal_module` to be |
||
| 7 |
- #' @inheritParams srv_teal+ #' used in `teal` applications. |
||
| 9 |
- #' @return+ #' If you are creating a `teal` application using [init()] then this |
||
| 10 |
- #' Returns a `reactive` expression containing a `teal_data` object when data is loaded or `NULL` when it is not.+ #' module will be added to your application automatically if any of your `teal_modules` |
||
| 11 |
- #' @name module_teal_with_splash+ #' support report generation. |
||
| 13 |
- NULL+ #' @inheritParams teal_modules |
||
| 14 |
-
+ #' @param server_args (named `list`) |
||
| 15 |
- #' @export+ #' Arguments passed to [teal.reporter::reporter_previewer_srv()]. |
||
| 16 |
- #' @rdname module_teal_with_splash+ #' |
||
| 17 |
- ui_teal_with_splash <- function(id,+ #' @return |
||
| 18 |
- data,+ #' `teal_module` (extended with `teal_module_previewer` class) containing the `teal.reporter` previewer functionality. |
||
| 19 |
- title = build_app_title(),+ #' |
||
| 20 |
- header = tags$p(),+ #' @export |
||
| 21 |
- footer = tags$p()) {
+ #' |
||
| 22 | -! | +
- lifecycle::deprecate_soft(+ reporter_previewer_module <- function(label = "Report previewer", server_args = list()) {
|
|
| 23 | -! | +7x |
- when = "0.16",+ checkmate::assert_string(label) |
| 24 | -! | +5x |
- what = "ui_teal_with_splash()",+ checkmate::assert_list(server_args, names = "named") |
| 25 | -! | +5x |
- details = "Deprecated, please use `ui_teal` instead"+ checkmate::assert_true(all(names(server_args) %in% names(formals(teal.reporter::reporter_previewer_srv)))) |
| 26 |
- )+ |
||
| 27 | -! | +3x |
- ui_teal(id = id, title = title, header = header, footer = footer)+ message("Initializing reporter_previewer_module")
|
| 28 |
- }+ |
||
| 29 | -+ | 3x |
-
+ srv <- function(id, reporter, ...) {
|
| 30 | -+ | ! |
- #' @export+ teal.reporter::reporter_previewer_srv(id, reporter, ...) |
| 31 |
- #' @rdname module_teal_with_splash+ } |
||
| 32 |
- srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
+
|
||
| 33 | -! | +3x |
- lifecycle::deprecate_soft(+ ui <- function(id, ...) {
|
| 34 | ! |
- when = "0.16",+ teal.reporter::reporter_previewer_ui(id, ...) |
|
| 35 | -! | +
- what = "srv_teal_with_splash()",+ } |
|
| 36 | -! | +
- details = "Deprecated, please use `srv_teal` instead"+ |
|
| 37 | +3x | +
+ module <- module(+ |
+ |
| 38 | +3x | +
+ label = "temporary label",+ |
+ |
| 39 | +3x | +
+ server = srv, ui = ui,+ |
+ |
| 40 | +3x | +
+ server_args = server_args, ui_args = list(), datanames = NULL+ |
+ |
| 41 |
) |
||
| 38 | -! | +||
| 42 | +
- srv_teal(id = id, data = data, modules = modules, filter = filter)+ # Module is created with a placeholder label and the label is changed later. |
||
| 39 | +43 | ++ |
+ # This is to prevent another module being labeled "Report previewer".+ |
+
| 44 | +3x | +
+ class(module) <- c(class(module), "teal_module_previewer")+ |
+ |
| 45 | +3x | +
+ module$label <- label+ |
+ |
| 46 | +3x | +
+ attr(module, "teal_bookmarkable") <- TRUE+ |
+ |
| 47 | +3x | +
+ module+ |
+ |
| 48 |
}@@ -48694,14 +48638,14 @@ teal coverage - 59.99% |
| 1 |
- #' Show `R` code modal+ #' UI and server modules of `teal` |
||
| 4 |
- #'+ #' Please use [`module_teal`] instead. |
||
| 5 |
- #' Use the [shiny::showModal()] function to show the `R` code inside.+ #' |
||
| 6 |
- #'+ #' @inheritParams ui_teal |
||
| 7 |
- #' @param title (`character(1)`)+ #' @inheritParams srv_teal |
||
| 8 |
- #' Title of the modal, displayed in the first comment of the `R` code.+ #' |
||
| 9 |
- #' @param rcode (`character`)+ #' @return |
||
| 10 |
- #' vector with `R` code to show inside the modal.+ #' Returns a `reactive` expression containing a `teal_data` object when data is loaded or `NULL` when it is not. |
||
| 11 |
- #' @param session (`ShinySession`) optional+ #' @name module_teal_with_splash |
||
| 12 |
- #' `shiny` session object, defaults to [shiny::getDefaultReactiveDomain()].+ #' |
||
| 13 |
- #'+ NULL |
||
| 14 |
- #' @references [shiny::showModal()]+ |
||
| 16 |
- show_rcode_modal <- function(title = NULL, rcode, session = getDefaultReactiveDomain()) {
+ #' @rdname module_teal_with_splash |
||
| 17 | -! | +
- lifecycle::deprecate_soft(+ ui_teal_with_splash <- function(id, |
|
| 18 | -! | +
- when = "0.16",+ data, |
|
| 19 | -! | +
- what = "show_rcode_modal()",+ title = build_app_title(), |
|
| 20 | -! | +
- details = "This function will be removed in the next release."+ header = tags$p(), |
|
| 21 |
- )+ footer = tags$p()) {
|
||
| 22 | -+ | ! |
-
+ lifecycle::deprecate_soft( |
| 23 | ! |
- rcode <- paste(rcode, collapse = "\n")+ when = "0.16", |
|
| 24 | -+ | ! |
-
+ what = "ui_teal_with_splash()", |
| 25 | ! |
- ns <- session$ns+ details = "Deprecated, please use `ui_teal` instead" |
|
| 26 | -! | +
- showModal(modalDialog(+ ) |
|
| 27 | ! |
- tagList(+ ui_teal(id = id, title = title, header = header, footer = footer) |
|
| 28 | -! | +
- tags$div(+ } |
|
| 29 | -! | +
- actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
+
|
|
| 30 | -! | +
- modalButton("Dismiss"),
+ #' @export |
|
| 31 | -! | +
- style = "mb-4"+ #' @rdname module_teal_with_splash |
|
| 32 |
- ),+ srv_teal_with_splash <- function(id, data, modules, filter = teal_slices()) {
|
||
| 33 | ! |
- tags$div(tags$pre(id = ns("r_code"), rcode)),
+ lifecycle::deprecate_soft( |
|
| 34 | -+ | ! |
- ),+ when = "0.16", |
| 35 | ! |
- title = title,+ what = "srv_teal_with_splash()", |
|
| 36 | ! |
- footer = tagList(+ details = "Deprecated, please use `srv_teal` instead" |
|
| 37 | -! | +
- actionButton(ns("copyRCode"), "Copy to Clipboard", `data-clipboard-target` = paste0("#", ns("r_code"))),
+ ) |
|
| 38 | ! |
- modalButton("Dismiss")
+ srv_teal(id = id, data = data, modules = modules, filter = filter) |
|
| 39 | - |
- ),- |
- |
| 40 | -! | -
- size = "l",- |
- |
| 41 | -! | -
- easyClose = TRUE- |
- |
| 42 | -- |
- ))- |
- |
| 43 | -
} |